1
|
Holfeld A, Schuster D, Sesterhenn F, Gillingham AK, Stalder P, Haenseler W, Barrio-Hernandez I, Ghosh D, Vowles J, Cowley SA, Nagel L, Khanppnavar B, Serdiuk T, Beltrao P, Korkhov VM, Munro S, Riek R, de Souza N, Picotti P. Systematic identification of structure-specific protein-protein interactions. Mol Syst Biol 2024:10.1038/s44320-024-00037-6. [PMID: 38702390 DOI: 10.1038/s44320-024-00037-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
The physical interactome of a protein can be altered upon perturbation, modulating cell physiology and contributing to disease. Identifying interactome differences of normal and disease states of proteins could help understand disease mechanisms, but current methods do not pinpoint structure-specific PPIs and interaction interfaces proteome-wide. We used limited proteolysis-mass spectrometry (LiP-MS) to screen for structure-specific PPIs by probing for protease susceptibility changes of proteins in cellular extracts upon treatment with specific structural states of a protein. We first demonstrated that LiP-MS detects well-characterized PPIs, including antibody-target protein interactions and interactions with membrane proteins, and that it pinpoints interfaces, including epitopes. We then applied the approach to study conformation-specific interactors of the Parkinson's disease hallmark protein alpha-synuclein (aSyn). We identified known interactors of aSyn monomer and amyloid fibrils and provide a resource of novel putative conformation-specific aSyn interactors for validation in further studies. We also used our approach on GDP- and GTP-bound forms of two Rab GTPases, showing detection of differential candidate interactors of conformationally similar proteins. This approach is applicable to screen for structure-specific interactomes of any protein, including posttranslationally modified and unmodified, or metabolite-bound and unbound protein states.
Collapse
Affiliation(s)
- Aleš Holfeld
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Dina Schuster
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Fabian Sesterhenn
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Patrick Stalder
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Walther Haenseler
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- University Research Priority Program AdaBD (Adaptive Brain Circuits in Development and Learning), University of Zurich, Zurich, Switzerland
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Jane Vowles
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sally A Cowley
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Luise Nagel
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Basavraj Khanppnavar
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Tetiana Serdiuk
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Pedro Beltrao
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Volodymyr M Korkhov
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Natalie de Souza
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
2
|
Chowdhury MR, Chatterjee C, Ghosh D, Mukherjee J, Shaw S, Basak J. Deciphering miRNA-lncRNA-mRNA interaction through experimental validation of miRNAs, lncRNAs, and miRNA targets on mRNAs in Cajanus cajan. Plant Biol (Stuttg) 2024. [PMID: 38520244 DOI: 10.1111/plb.13639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 02/14/2024] [Indexed: 03/25/2024]
Abstract
Pigeon pea (Cajanus cajan) is widely cultivated for its nutritional and medicinal value yet remains an orphan crop as productivity has not been improved because of a lack of genome and non-coding genome information. Non-coding RNAs, like miRNAs and long non-coding RNAs (lncRNAs), are involved in regulation of growth, metabolism, development, and stress response, and have a critical role in post-transcriptional gene regulation (PTGR). We attempted to elucidate the roles of miRNAs and lncRNAs in pigeon pea through experimental validation of computationally predicted miRNAs and lncRNAs and targets of miRNAs on mRNAs. We experimentally validated 20 miRNAs and 11 lncRNAs. We predicted cleavage sites of three miRNA targets: serine/threonine-protein kinase, polygalacturonase, beta-galactosidase. We identified 469 targets of 265 miRNAs and their functional annotations using computational methods. We built a miRNA-mRNA-lncRNA network model, with the miRNAs targeting both mRNAs and lncRNAs, to obtain information on the interplay of these three molecules. A confirmed interaction through experimental validation was established between miRNA, namely cca-miR1535a targeting the mRNA for beta-galactosidase, as well as the lncRNA cca-lnc-020033. Our findings increase knowledge of the non-coding genome of pigeon pea and their roles in PTGR and in improving agronomic traits of this pulse crop.
Collapse
Affiliation(s)
- M R Chowdhury
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, India
| | - C Chatterjee
- Department of Biotechnology, Visva-Bharati, Santiniketan, India
| | - D Ghosh
- Department of Biotechnology, Visva-Bharati, Santiniketan, India
| | - J Mukherjee
- Department of Computer Science and Engineering, Birla Institute of Technology, Mesra, India
| | - S Shaw
- Department of Biotechnology, Visva-Bharati, Santiniketan, India
| | - J Basak
- Department of Biotechnology, Visva-Bharati, Santiniketan, India
| |
Collapse
|
3
|
Ademuyiwa AO, Bhangu A, Chakrabortee S, Glasbey J, Kamarajah SK, Ledda V, Li E, Morton D, Nepogodiev D, Picciochi M, Simoes JFF, Lapitan MC, Cheetham M, Forkman E, El-Boghdadly E, Ghosh D, Harrison EM, Hutchinson P, Lawani I, Aguilera ML, Martin J, Meara JG, Ntirenganya F, Medina ARDL, Tabiri S. Strategies to strengthen elective surgery systems during the SARS-CoV-2 pandemic: systematic review and framework development. Br J Surg 2024; 111:znad405. [PMID: 38300731 PMCID: PMC10833142 DOI: 10.1093/bjs/znad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/12/2023] [Accepted: 10/27/2023] [Indexed: 02/03/2024]
|
4
|
Das S, Mondal S, Ghosh D. Carbon quantum dots in bioimaging and biomedicines. Front Bioeng Biotechnol 2024; 11:1333752. [PMID: 38318419 PMCID: PMC10841552 DOI: 10.3389/fbioe.2023.1333752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024] Open
Abstract
Carbon quantum dots (CQDs) are gaining a lot more attention than traditional semiconductor quantum dots owing to their intrinsic fluorescence property, chemical inertness, biocompatibility, non-toxicity, and simple and inexpensive synthetic route of preparation. These properties allow CQDs to be utilized for a broad range of applications in various fields of scientific research including biomedical sciences, particularly in bioimaging and biomedicines. CQDs are a promising choice for advanced nanomaterials research for bioimaging and biomedicines owing to their unique chemical, physical, and optical properties. CQDs doped with hetero atom, or polymer composite materials are extremely advantageous for biochemical, biological, and biomedical applications since they are easy to prepare, biocompatible, and have beneficial properties. This type of CQD is highly useful in phototherapy, gene therapy, medication delivery, and bioimaging. This review explores the applications of CQDs in bioimaging and biomedicine, highlighting recent advancements and future possibilities to increase interest in their numerous advantages for therapeutic applications.
Collapse
Affiliation(s)
- Surya Das
- Department of Chemistry, University of Kalyani, Kalyani, India
| | - Somnath Mondal
- Department of Chemistry, Pennsylvania State University, State College, PA, United States
| | - Dhiman Ghosh
- Department of Chemistry and Applied Biosciences, Zurich, Switzerland
| |
Collapse
|
5
|
Adachi I, Adamczyk K, Aggarwal L, Aihara H, Akopov N, Aloisio A, Anh Ky N, Asner DM, Atmacan H, Aushev T, Aushev V, Aversano M, Babu V, Bae H, Bahinipati S, Bambade P, Banerjee S, Barrett M, Baudot J, Bauer M, Baur A, Beaubien A, Becherer F, Becker J, Behera PK, Bennett JV, Bernlochner FU, Bertacchi V, Bertemes M, Bertholet E, Bessner M, Bettarini S, Bhuyan B, Bianchi F, Bilka T, Biswas D, Bobrov A, Bodrov D, Bolz A, Bondar A, Borah J, Bozek A, Bračko M, Branchini P, Briere RA, Browder TE, Budano A, Bussino S, Campajola M, Cao L, Casarosa G, Cecchi C, Cerasoli J, Chang MC, Chang P, Cheaib R, Cheema P, Chekelian V, Cheon BG, Chilikin K, Chirapatpimol K, Cho HE, Cho K, Choi SK, Choudhury S, Cochran J, Corona L, Cremaldi LM, Das S, Dattola F, De La Cruz-Burelo E, De La Motte SA, De Nardo G, De Nuccio M, De Pietro G, de Sangro R, Destefanis M, Dey S, Dhamija R, Di Canto A, Di Capua F, Dingfelder J, Doležal Z, Domínguez Jiménez I, Dong TV, Dorigo M, Dort K, Dossett D, Dreyer S, Dubey S, Dujany G, Ecker P, Eliachevitch M, Epifanov D, Feichtinger P, Ferber T, Ferlewicz D, Fillinger T, Finck C, Finocchiaro G, Fodor A, Forti F, Frey A, Fulsom BG, Gabrielli A, Ganiev E, Garcia-Hernandez M, Garg R, Garmash A, Gaudino G, Gaur V, Gaz A, Gellrich A, Ghevondyan G, Ghosh D, Ghumaryan H, Giakoustidis G, Giordano R, Giri A, Gobbo B, Godang R, Gogota O, Goldenzweig P, Gradl W, Granderath S, Graziani E, Greenwald D, Gruberová Z, Gu T, Guan Y, Gudkova K, Halder S, Han Y, Hara T, Hayasaka K, Hayashii H, Hazra S, Hearty C, Hedges MT, Heidelbach A, Heredia de la Cruz I, Hernández Villanueva M, Hershenhorn A, Higuchi T, Hill EC, Hoek M, Hohmann M, Horak P, Hsu CL, Iijima T, Inami K, Inguglia G, Ipsita N, Ishikawa A, Ito S, Itoh R, Iwasaki M, Jackson P, Jacobs WW, Jang EJ, Ji QP, Jia S, Jin Y, Johnson A, Junkerkalefeld H, Kaliyar AB, Kandra J, Kang KH, Karyan G, Kawasaki T, Keil F, Ketter C, Kiesling C, Kim CH, Kim DY, Kim KH, Kim YK, Kindo H, Kinoshita K, Kodyš P, Koga T, Kohani S, Kojima K, Konno T, Korobov A, Korpar S, Kovalenko E, Kowalewski R, Kraetzschmar TMG, Križan P, Krokovny P, Kuhr T, Kumar J, Kumar M, Kumara K, Kunigo T, Kuzmin A, Kwon YJ, Lacaprara S, Lai YT, Lam T, Lanceri L, Lange JS, Laurenza M, Leboucher R, Le Diberder FR, Leitl P, Levit D, Lewis PM, Li C, Li LK, Li Y, Libby J, Liu QY, Liu ZQ, Liventsev D, Longo S, Lueck T, Luo T, Lyu C, Ma Y, Maggiora M, Maharana SP, Maiti R, Maity S, Mancinelli G, Manfredi R, Manoni E, Manthei AC, Mantovano M, Marcantonio D, Marcello S, Marinas C, Martel L, Martellini C, Martini A, Martinov T, Massaccesi L, Masuda M, Matsuda T, Matvienko D, Maurya SK, McKenna JA, Mehta R, Meier F, Merola M, Metzner F, Milesi M, Miller C, Mirra M, Miyabayashi K, Mohanty GB, Molina-Gonzalez N, Mondal S, Moneta S, Moser HG, Mrvar M, Mussa R, Nakamura I, Nakazawa Y, Narimani Charan A, Naruki M, Natkaniec Z, Natochii A, Nayak L, Nazaryan G, Nisar NK, Nishida S, Ogawa S, Ono H, Oskin P, Otani F, Pakhlov P, Pakhlova G, Paladino A, Panta A, Paoloni E, Pardi S, Parham K, Park SH, Paschen B, Passeri A, Patra S, Paul S, Pedlar TK, Peruzzi I, Peschke R, Pestotnik R, Pham F, Piccolo M, Piilonen LE, Podesta-Lerma PLM, Podobnik T, Pokharel S, Praz C, Prell S, Prencipe E, Prim MT, Purwar H, Rad N, Rados P, Raeuber G, Raiz S, Reif M, Reiter S, Remnev M, Ripp-Baudot I, Rizzo G, Robertson SH, Roehrken M, Roney JM, Rostomyan A, Rout N, Russo G, Sahoo D, Sandilya S, Sangal A, Santelj L, Sato Y, Savinov V, Scavino B, Schmitt C, Schnepf M, Schwanda C, Seino Y, Selce A, Senyo K, Serrano J, Sevior ME, Sfienti C, Shan W, Sharma C, Shen CP, Shi XD, Shillington T, Shiu JG, Shtol D, Shwartz B, Sibidanov A, Simon F, Singh JB, Skorupa J, Sobie RJ, Sobotzik M, Soffer A, Sokolov A, Solovieva E, Spataro S, Spruck B, Starič M, Stavroulakis P, Stefkova S, Stottler ZS, Stroili R, Strube J, Sumihama M, Sumisawa K, Sutcliffe W, Svidras H, Takahashi M, Takizawa M, Tamponi U, Tanida K, Tenchini F, Thaller A, Tittel O, Tiwary R, Tonelli D, Torassa E, Toutounji N, Trabelsi K, Tsaklidis I, Uchida M, Ueda I, Uematsu Y, Uglov T, Unger K, Unno Y, Uno K, Uno S, Urquijo P, Ushiroda Y, Vahsen SE, van Tonder R, Varner GS, Varvell KE, Veronesi M, Vismaya VS, Vitale L, Vobbilisetti V, Volpe R, Wach B, Waheed E, Wakai M, Wallner S, Wang E, Wang MZ, Wang Z, Warburton A, Watanabe M, Watanuki S, Welsch M, Wessel C, Xu XP, Yabsley BD, Yamada S, Yan W, Yang SB, Yin JH, Yoshihara K, Yuan CZ, Zani L, Zhang Y, Zhilich V, Zhou JS, Zhou QD, Zhukova VI, Žlebčík R. Tests of Light-Lepton Universality in Angular Asymmetries of B^{0}→D^{*-}ℓν Decays. Phys Rev Lett 2023; 131:181801. [PMID: 37977641 DOI: 10.1103/physrevlett.131.181801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/29/2023] [Indexed: 11/19/2023]
Abstract
We present the first comprehensive tests of the universality of the light leptons in the angular distributions of semileptonic B^{0}-meson decays to charged spin-1 charmed mesons. We measure five angular-asymmetry observables as functions of the decay recoil that are sensitive to lepton-universality-violating contributions. We use events where one neutral B is fully reconstructed in ϒ(4S)→BB[over ¯] decays in data corresponding to 189 fb^{-1} integrated luminosity from electron-positron collisions collected with the Belle II detector. We find no significant deviation from the standard model expectations.
Collapse
|
6
|
Mikucki JA, Schuler CG, Digel I, Kowalski J, Tuttle MJ, Chua M, Davis R, Purcell AM, Ghosh D, Francke G, Feldmann M, Espe C, Heinen D, Dachwald B, Clemens J, Lyons WB, Tulaczyk S. Field-Based Planetary Protection Operations for Melt Probes: Validation of Clean Access into the Blood Falls, Antarctica, Englacial Ecosystem. Astrobiology 2023; 23:1165-1178. [PMID: 37962840 DOI: 10.1089/ast.2021.0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Subglacial environments on Earth offer important analogs to Ocean World targets in our solar system. These unique microbial ecosystems remain understudied due to the challenges of access through thick glacial ice (tens to hundreds of meters). Additionally, sub-ice collections must be conducted in a clean manner to ensure sample integrity for downstream microbiological and geochemical analyses. We describe the field-based cleaning of a melt probe that was used to collect brine samples from within a glacier conduit at Blood Falls, Antarctica, for geomicrobiological studies. We used a thermoelectric melting probe called the IceMole that was designed to be minimally invasive in that the logistical requirements in support of drilling operations were small and the probe could be cleaned, even in a remote field setting, so as to minimize potential contamination. In our study, the exterior bioburden on the IceMole was reduced to levels measured in most clean rooms, and below that of the ice surrounding our sampling target. Potential microbial contaminants were identified during the cleaning process; however, very few were detected in the final englacial sample collected with the IceMole and were present in extremely low abundances (∼0.063% of 16S rRNA gene amplicon sequences). This cleaning protocol can help minimize contamination when working in remote field locations, support microbiological sampling of terrestrial subglacial environments using melting probes, and help inform planetary protection challenges for Ocean World analog mission concepts.
Collapse
Affiliation(s)
- J A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - C G Schuler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - I Digel
- FH Aachen - Campus Jülich, Institute of Bioengineering, Julich, Nordrhein-Westfalen, Germany
| | - J Kowalski
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - M J Tuttle
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - M Chua
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - R Davis
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - A M Purcell
- Northern Arizona University, Flagstaff, Arizona, USA
| | - D Ghosh
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - G Francke
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - M Feldmann
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - C Espe
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - D Heinen
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - B Dachwald
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - J Clemens
- University of Bremen, Bremen, Germany
| | - W B Lyons
- The Ohio State University, Byrd Polar Research Center, Columbus, Ohio, USA
| | - S Tulaczyk
- University of California Santa Cruz, Santa Cruz, California, USA
| |
Collapse
|
7
|
Schutte SC, Ghosh D, Moset Zupan A, Warwar R, Dawson MR. Differential Response to Mechanical Cues in Uterine Fibroid Versus Paired Myometrial Cells. Reprod Sci 2023; 30:3305-3314. [PMID: 37253935 DOI: 10.1007/s43032-023-01267-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/08/2023] [Indexed: 06/01/2023]
Abstract
Uterine leiomyomas, or fibroids, are common, benign tumors for which hysterectomy is the only definitive treatment. The extracellular matrix of fibroids is disorganized and stiffer than the surrounding myometrial tissue. To understand how stiffness affects fibroid cells, patient-matched fibroid and myometrial cells were cultured on substrates with stiffnesses varying from 0.2 to 150 kPa. Fibroid cells grew more slowly than myometrial cells overall, and only the myometrial cells altered their growth rate in response to stiffness. In both cell types, cell proliferation decreased with inhibition of PI3K and increased with inhibition of IGF-1. The cellular area was greater for the fibroid cells. The only significant effect of stiffness on the cell area was between the 0.2 and 64 kPa substrates, and this was true for both cell types. To investigate intracellular stiffness, intracellular particle tracking microrheology was used. Fibroid cells exhibited a more than 100-fold increase in elastic modulus at a frequency of 1 Hz in response to the addition of external stress, while myometrial cells showed little change in elastic modulus. Overall, the responses of both cells followed similar trends in response to stiffness and inhibitors, although the response was attenuated in the fibroid cells. The changes that were demonstrated by the change in intracellular stiffness with response to compression suggest that other mechanical forces may provide insight into differences in the two cell types.
Collapse
Affiliation(s)
- S C Schutte
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA.
| | - D Ghosh
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - A Moset Zupan
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA
| | - R Warwar
- Department of Obstetrics and Gynecology, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - M R Dawson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.
| |
Collapse
|
8
|
Adachi I, Aggarwal L, Aihara H, Akopov N, Aloisio A, Anh Ky N, Asner DM, Atmacan H, Aushev T, Aushev V, Aversano M, Babu V, Bae H, Bahinipati S, Bambade P, Banerjee S, Barrett M, Baudot J, Bauer M, Baur A, Beaubien A, Becker J, Behera PK, Bennett JV, Bernlochner FU, Bertacchi V, Bertemes M, Bertholet E, Bessner M, Bettarini S, Bhuyan B, Bianchi F, Bilka T, Biswas D, Bodrov D, Bondar A, Bozek A, Bračko M, Branchini P, Briere RA, Browder TE, Budano A, Bussino S, Campajola M, Cao L, Casarosa G, Cecchi C, Cerasoli J, Chang MC, Chang P, Cheema P, Chekelian V, Cheon BG, Chilikin K, Chirapatpimol K, Cho HE, Cho K, Choi SK, Choudhury S, Cochran J, Corona L, Das S, Dattola F, De La Motte SA, de Marino G, De Nardo G, De Nuccio M, De Pietro G, de Sangro R, Destefanis M, Dey S, Dhamija R, Di Canto A, Di Capua F, Dingfelder J, Doležal Z, Domínguez Jiménez I, Dong TV, Dorigo M, Dort K, Dreyer S, Dubey S, Dujany G, Ecker P, Epifanov D, Feichtinger P, Ferlewicz D, Finck C, Finocchiaro G, Fodor A, Forti F, Frey A, Fulsom BG, Gabrielli A, Ganiev E, Garcia-Hernandez M, Garmash A, Gaudino G, Gaur V, Gaz A, Gellrich A, Ghevondyan G, Ghosh D, Ghumaryan H, Giakoustidis G, Giordano R, Giri A, Glazov A, Gobbo B, Godang R, Gogota O, Goldenzweig P, Gradl W, Graziani E, Greenwald D, Gruberová Z, Gu T, Guan Y, Gudkova K, Han Y, Hayasaka K, Hayashii H, Hazra S, Hearty C, Heredia de la Cruz I, Hershenhorn A, Higuchi T, Hill EC, Hoek M, Hohmann M, Hsu CL, Humair T, Iijima T, Inami K, Ipsita N, Ishikawa A, Ito S, Itoh R, Iwasaki M, Jackson P, Jacobs WW, Jaffe DE, Jang EJ, Ji QP, Jia S, Jin Y, Junkerkalefeld H, Kaliyar AB, Kandra J, Karyan G, Kawasaki T, Keil F, Ketter C, Kiesling C, Kim CH, Kim DY, Kim KH, Kim YK, Kindo H, Kinoshita K, Kodyš P, Koga T, Kohani S, Kojima K, Korobov A, Korpar S, Kowalewski R, Kraetzschmar TMG, Križan P, Krokovny P, Kuhr T, Kumar J, Kumar M, Kumar R, Kumara K, Kuzmin A, Kwon YJ, Lacaprara S, Lai YT, Lam T, Lange JS, Laurenza M, Leboucher R, Le Diberder FR, Leitl P, Levit D, Lewis PM, Li LK, Libby J, Liu QY, Liu ZQ, Liventsev D, Longo S, Lueck T, Lyu C, Ma Y, Maggiora M, Maharana SP, Maiti R, Maity S, Manfredi R, Manoni E, Mantovano M, Marcantonio D, Marcello S, Marinas C, Martellini C, Martini A, Martinov T, Massaccesi L, Masuda M, Matsuda T, Matsuoka K, Matvienko D, Maurya SK, McKenna JA, Mehta R, Meier F, Merola M, Metzner F, Milesi M, Miller C, Mirra M, Miyabayashi K, Mohanty GB, Molina-Gonzalez N, Mondal S, Moneta S, Moser HG, Mrvar M, Mussa R, Nakamura I, Nakazawa Y, Narimani Charan A, Naruki M, Natkaniec Z, Natochii A, Nayak L, Nazaryan G, Nisar NK, Nishida S, Ono H, Otani F, Oxford ER, Pakhlov P, Pakhlova G, Paladino A, Panta A, Paoloni E, Pardi S, Passeri A, Patra S, Paul S, Pedlar TK, Peruzzi I, Peschke R, Pestotnik R, Pham F, Piccolo M, Piilonen LE, Podobnik T, Pokharel S, Praz C, Prell S, Prencipe E, Prim MT, Purwar H, Rados P, Raeuber G, Raiz S, Reif M, Reiter S, Remnev M, Ripp-Baudot I, Rizzo G, Roney JM, Rostomyan A, Rout N, Russo G, Sandilya S, Sangal A, Santelj L, Sato Y, Savinov V, Scavino B, Schmitt C, Schwanda C, Schwartz AJ, Seino Y, Selce A, Senyo K, Serrano J, Sevior ME, Sfienti C, Shan W, Shi XD, Shillington T, Shiu JG, Shtol D, Sibidanov A, Simon F, Sobie RJ, Sobotzik M, Soffer A, Sokolov A, Solovieva E, Spataro S, Spruck B, Starič M, Stavroulakis P, Stottler ZS, Stroili R, Sumihama M, Svidras H, Takahashi M, Takizawa M, Tamponi U, Tanida K, Tenchini F, Tittel O, Tonelli D, Torassa E, Trabelsi K, Tsaklidis I, Unger K, Unno Y, Uno K, Uno S, Urquijo P, Ushiroda Y, Vahsen SE, van Tonder R, Varvell KE, Veronesi M, Vismaya VS, Vitale L, Volpe R, Wach B, Wallner S, Wang E, Wang MZ, Wang XL, Wang Z, Warburton A, Watanabe M, Wessel C, Won E, Xu XP, Yabsley BD, Yamada S, Yan W, Yang SB, Yoshihara K, Yuan CZ, Yusa Y, Zhang Y, Zhilich V, Zhou JS, Zhou QD, Zhukova VI, Žlebčík R. Precise Measurement of the D_{s}^{+} Lifetime at Belle II. Phys Rev Lett 2023; 131:171803. [PMID: 37955504 DOI: 10.1103/physrevlett.131.171803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/14/2023] [Indexed: 11/14/2023]
Abstract
We measure the lifetime of the D_{s}^{+} meson using a data sample of 207 fb^{-1} collected by the Belle II experiment running at the SuperKEKB asymmetric-energy e^{+}e^{-} collider. The lifetime is determined by fitting the decay-time distribution of a sample of 116×10^{3} D_{s}^{+}→ϕπ^{+} decays. Our result is τ_{D_{s}^{+}}=(499.5±1.7±0.9) fs, where the first uncertainty is statistical and the second is systematic. This result is significantly more precise than previous measurements.
Collapse
|
9
|
Ghosh D, Thomas M. Surgical care delivery in India during the COVID pandemic. J Postgrad Med 2023; 69:190-191. [PMID: 37787264 PMCID: PMC10846803 DOI: 10.4103/jpgm.jpgm_568_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/29/2023] [Accepted: 09/02/2023] [Indexed: 10/04/2023] Open
Affiliation(s)
- D Ghosh
- Department of Pediatric Surgery, NIHR Global Health Research Unit on Global Surgery, Christian Medical College and Hospital, Ludhiana, Punjab, India
| | - M Thomas
- Department of Pediatric Surgery, NIHR Global Health Research Unit on Global Surgery, Christian Medical College and Hospital, Ludhiana, Punjab, India
| |
Collapse
|
10
|
Adachi I, Adamczyk K, Aggarwal L, Ahmed H, Aihara H, Akopov N, Aloisio A, Anh Ky N, Asner DM, Atmacan H, Aushev T, Aushev V, Aversano M, Babu V, Bae H, Bahinipati S, Bambade P, Banerjee S, Bansal S, Barrett M, Baudot J, Bauer M, Baur A, Beaubien A, Becker J, Behera PK, Bennett JV, Bernieri E, Bernlochner FU, Bertacchi V, Bertemes M, Bertholet E, Bessner M, Bettarini S, Bhardwaj V, Bhuyan B, Bianchi F, Bilka T, Bilokin S, Biswas D, Bobrov A, Bodrov D, Bolz A, Borah J, Bozek A, Bračko M, Branchini P, Browder TE, Budano A, Bussino S, Campajola M, Cao L, Casarosa G, Cecchi C, Cerasoli J, Chang MC, Chang P, Cheaib R, Cheema P, Chekelian V, Chen YQ, Cheon BG, Chilikin K, Chirapatpimol K, Cho HE, Cho K, Cho SJ, Choi SK, Choudhury S, Cinabro D, Cochran J, Corona L, Cremaldi LM, Cunliffe S, Czank T, Das S, Dattola F, De La Cruz-Burelo E, De La Motte SA, de Marino G, De Nardo G, De Nuccio M, De Pietro G, de Sangro R, Destefanis M, Dey S, De Yta-Hernandez A, Dhamija R, Di Canto A, Di Capua F, Dingfelder J, Doležal Z, Domínguez Jiménez I, Dong TV, Dorigo M, Dort K, Dossett D, Dreyer S, Dubey S, Dujany G, Ecker P, Eliachevitch M, Epifanov D, Feichtinger P, Ferber T, Ferlewicz D, Fillinger T, Finck C, Finocchiaro G, Fodor A, Forti F, Frey A, Fulsom BG, Gabrielli A, Ganiev E, Garcia-Hernandez M, Garmash A, Gaudino G, Gaur V, Gaz A, Gellrich A, Ghevondyan G, Ghosh D, Ghumaryan H, Giakoustidis G, Giordano R, Giri A, Glazov A, Gobbo B, Godang R, Gogota O, Goldenzweig P, Gradl W, Grammatico T, Granderath S, Graziani E, Greenwald D, Gruberová Z, Gu T, Guan Y, Gudkova K, Guilliams J, Halder S, Han Y, Hara T, Hayasaka K, Hayashii H, Hazra S, Hearty C, Hedges MT, Heredia de la Cruz I, Hernández Villanueva M, Hershenhorn A, Higuchi T, Hill EC, Hirata H, Hoek M, Hohmann M, Hsu CL, Humair T, Iijima T, Inami K, Inguglia G, Ipsita N, Ishikawa A, Ito S, Itoh R, Iwasaki M, Jackson P, Jacobs WW, Jaffe DE, Jang EJ, Ji QP, Jia S, Jin Y, Johnson A, Joo KK, Junkerkalefeld H, Kakuno H, Kaleta M, Kalita D, Kaliyar AB, Kandra J, Kang KH, Kang S, Karl R, Karyan G, Kawasaki T, Keil F, Ketter C, Kiesling C, Kim CH, Kim DY, Kim KH, Kim YK, Kindo H, Kodyš P, Koga T, Kohani S, Kojima K, Konno T, Korobov A, Korpar S, Kovalenko E, Kowalewski R, Kraetzschmar TMG, Križan P, Krokovny P, Kuhr T, Kumar J, Kumar M, Kumar R, Kumara K, Kunigo T, Kuzmin A, Kwon YJ, Lacaprara S, Lai YT, Lam T, Lanceri L, Lange JS, Laurenza M, Lautenbach K, Leboucher R, Le Diberder FR, Leitl P, Levit D, Lewis PM, Li C, Li LK, Li YB, Libby J, Lieret K, Liu QY, Liu ZQ, Liventsev D, Longo S, Lozar A, Lueck T, Lyu C, Ma Y, Maggiora M, Maharana SP, Maiti R, Maity S, Manfredi R, Manoni E, Manthei AC, Mantovano M, Marcantonio D, Marcello S, Marinas C, Martel L, Martellini C, Martini A, Martinov T, Massaccesi L, Masuda M, Matsuda T, Matsuoka K, Matvienko D, Maurya SK, McKenna JA, Mehta R, Merola M, Metzner F, Milesi M, Miller C, Mirra M, Miyabayashi K, Miyake H, Mizuk R, Mohanty GB, Molina-Gonzalez N, Mondal S, Moneta S, Moser HG, Mrvar M, Mussa R, Nakamura I, Nakamura KR, Nakao M, Nakayama H, Nakazawa H, Nakazawa Y, Narimani Charan A, Naruki M, Narwal D, Natkaniec Z, Natochii A, Nayak L, Nayak M, Nazaryan G, Niebuhr C, Nisar NK, Nishida S, Ogawa S, Ono H, Onuki Y, Oskin P, Otani F, Pakhlov P, Pakhlova G, Paladino A, Panta A, Paoloni E, Pardi S, Parham K, Park J, Park SH, Paschen B, Passeri A, Patra S, Paul S, Pedlar TK, Peruzzi I, Peschke R, Pestotnik R, Pham F, Piccolo M, Piilonen LE, Pinna Angioni G, Podesta-Lerma PLM, Podobnik T, Pokharel S, Polat L, Praz C, Prell S, Prencipe E, Prim MT, Purwar H, Rad N, Rados P, Raeuber G, Raiz S, Ramirez Morales A, Reif M, Reiter S, Remnev M, Ripp-Baudot I, Rizzo G, Rizzuto LB, Robertson SH, Rodríguez Pérez D, Roehrken M, Roney JM, Rostomyan A, Rout N, Russo G, Sahoo D, Sanders DA, Sandilya S, Sangal A, Santelj L, Sato Y, Savinov V, Scavino B, Schnepf M, Schueler J, Schwanda C, Seino Y, Selce A, Senyo K, Serrano J, Sevior ME, Sfienti C, Shan W, Sharma C, Shen CP, Shi XD, Shillington T, Shiu JG, Shtol D, Shwartz B, Sibidanov A, Simon F, Singh JB, Skorupa J, Sobie RJ, Sobotzik M, Soffer A, Sokolov A, Solovieva E, Spataro S, Spruck B, Starič M, Stavroulakis P, Stefkova S, Stottler ZS, Stroili R, Strube J, Sue Y, Sumihama M, Sumisawa K, Sutcliffe W, Suzuki SY, Svidras H, Takahashi M, Takizawa M, Tamponi U, Tanaka S, Tanida K, Tanigawa H, Tenchini F, Thaller A, Tiwary R, Tonelli D, Torassa E, Toutounji N, Trabelsi K, Tsaklidis I, Uchida M, Ueda I, Uematsu Y, Uglov T, Unger K, Unno Y, Uno K, Uno S, Urquijo P, Ushiroda Y, Vahsen SE, van Tonder R, Varner GS, Varvell KE, Vinokurova A, Vismaya VS, Vitale L, Vobbilisetti V, Volpe R, Vossen A, Wach B, Wakai M, Wakeling HM, Wallner S, Wang E, Wang MZ, Wang XL, Wang Z, Warburton A, Watanabe M, Watanuki S, Welsch M, Wessel C, Won E, Xu XP, Yabsley BD, Yamada S, Yan W, Yang SB, Ye H, Yelton J, Yin JH, Yook YM, Yoshihara K, Yuan CZ, Yusa Y, Zani L, Zhai Y, Zhang Y, Zhilich V, Zhou JS, Zhou QD, Zhou XY, Zhukova VI, Žlebčík R. Search for a τ^{+}τ^{-} Resonance in e^{+}e^{-}→μ^{+}μ^{-}τ^{+}τ^{-} Events with the Belle II Experiment. Phys Rev Lett 2023; 131:121802. [PMID: 37802942 DOI: 10.1103/physrevlett.131.121802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/08/2023] [Indexed: 10/08/2023]
Abstract
We report the first search for a nonstandard-model resonance decaying into τ pairs in e^{+}e^{-}→μ^{+}μ^{-}τ^{+}τ^{-} events in the 3.6-10 GeV/c^{2} mass range. We use a 62.8 fb^{-1} sample of e^{+}e^{-} collisions collected at a center-of-mass energy of 10.58 GeV by the Belle II experiment at the SuperKEKB collider. The analysis probes three different models predicting a spin-1 particle coupling only to the heavier lepton families, a Higgs-like spin-0 particle that couples preferentially to charged leptons (leptophilic scalar), and an axionlike particle, respectively. We observe no evidence for a signal and set exclusion limits at 90% confidence level on the product of cross section and branching fraction into τ pairs, ranging from 0.7 to 24 fb, and on the couplings of these processes. We obtain world-leading constraints on the couplings for the leptophilic scalar model for masses above 6.5 GeV/c^{2} and for the axionlike particle model over the entire mass range.
Collapse
|
11
|
Adachi I, Adamczyk K, Aggarwal L, Ahmed H, Aihara H, Akopov N, Aloisio A, Anh Ky N, Asner DM, Atmacan H, Aushev T, Aushev V, Aversano M, Babu V, Bae H, Bahinipati S, Bambade P, Banerjee S, Barrett M, Baudot J, Bauer M, Baur A, Beaubien A, Becker J, Behera PK, Bennett JV, Bertacchi V, Bertemes M, Bertholet E, Bessner M, Bettarini S, Bhuyan B, Bianchi F, Bilka T, Biswas D, Bodrov D, Bondar A, Borah J, Bozek A, Bračko M, Branchini P, Briere RA, Browder TE, Budano A, Bussino S, Campajola M, Cao L, Casarosa G, Cecchi C, Cerasoli J, Chang P, Cheaib R, Cheema P, Chekelian V, Chen C, Cheon BG, Chilikin K, Chirapatpimol K, Cho HE, Cho K, Cho SJ, Choi SK, Choudhury S, Cochran J, Corona L, Cremaldi LM, Das S, Dattola F, De La Cruz-Burelo E, De La Motte SA, de Marino G, De Nuccio M, De Pietro G, de Sangro R, Destefanis M, De Yta-Hernandez A, Dhamija R, Di Canto A, Di Capua F, Dingfelder J, Doležal Z, Domínguez Jiménez I, Dong TV, Dorigo M, Dort K, Dreyer S, Dubey S, Dujany G, Ecker P, Eliachevitch M, Feichtinger P, Ferber T, Ferlewicz D, Fillinger T, Finck C, Finocchiaro G, Fodor A, Forti F, Fulsom BG, Gabrielli A, Ganiev E, Garcia-Hernandez M, Garg R, Garmash A, Gaudino G, Gaur V, Gaz A, Gellrich A, Ghosh D, Giakoustidis G, Giordano R, Giri A, Glazov A, Gobbo B, Godang R, Goldenzweig P, Gradl W, Grammatico T, Granderath S, Graziani E, Greenwald D, Gruberová Z, Gu T, Guan Y, Gudkova K, Halder S, Han Y, Hara K, Hara T, Hayasaka K, Hayashii H, Hazra S, Hearty C, Hedges MT, Heredia de la Cruz I, Hernández Villanueva M, Hershenhorn A, Higuchi T, Hill EC, Hoek M, Hohmann M, Hsu CL, Humair T, Iijima T, Inami K, Ipsita N, Ishikawa A, Ito S, Itoh R, Iwasaki M, Jackson P, Jacobs WW, Jang EJ, Ji QP, Jia S, Jin Y, Johnson A, Joo KK, Junkerkalefeld H, Kaleta M, Kaliyar AB, Kandra J, Kang KH, Kang S, Kar S, Karyan G, Kawasaki T, Keil F, Ketter C, Kiesling C, Kim CH, Kim DY, Kim KH, Kim YK, Kindo H, Kodyš P, Koga T, Kohani S, Kojima K, Korobov A, Korpar S, Kovalenko E, Kowalewski R, Kraetzschmar TMG, Križan P, Krokovny P, Kuhr T, Kumar J, Kumar M, Kumara K, Kunigo T, Kuzmin A, Kwon YJ, Lacaprara S, Lai YT, Lam T, Lange JS, Laurenza M, Leboucher R, Le Diberder FR, Leitl P, Levit D, Li C, Li LK, Libby J, Liu QY, Liu ZQ, Liventsev D, Longo S, Lueck T, Luo T, Lyu C, Ma Y, Maggiora M, Maharana SP, Maiti R, Maity S, Mancinelli G, Manfredi R, Manoni E, Mantovano M, Marcantonio D, Marcello S, Marinas C, Martel L, Martellini C, Martinov T, Massaccesi L, Masuda M, Matsuda T, Matsuoka K, Matvienko D, Maurya SK, McKenna JA, Mehta R, Meier F, Merola M, Metzner F, Milesi M, Miller C, Mirra M, Miyabayashi K, Mizuk R, Mohanty GB, Molina-Gonzalez N, Mondal S, Moneta S, Moser HG, Mrvar M, Mussa R, Nakamura I, Nakazawa Y, Narimani Charan A, Naruki M, Natochii A, Nayak L, Nayak M, Nazaryan G, Nisar NK, Nishida S, Ono H, Onuki Y, Oskin P, Pakhlov P, Pakhlova G, Paladino A, Paoloni E, Pardi S, Parham K, Park H, Park SH, Passeri A, Patra S, Paul S, Pedlar TK, Peschke R, Pestotnik R, Pham F, Piccolo M, Piilonen LE, Podesta-Lerma PLM, Podobnik T, Pokharel S, Praz C, Prell S, Prencipe E, Prim MT, Purwar H, Rad N, Rados P, Raeuber G, Raiz S, Reif M, Reiter S, Remnev M, Ripp-Baudot I, Rizzo G, Robertson SH, Roehrken M, Roney JM, Rostomyan A, Rout N, Russo G, Sahoo D, Sandilya S, Sangal A, Santelj L, Sato Y, Savinov V, Scavino B, Schmitt C, Schwanda C, Schwartz AJ, Seino Y, Selce A, Senyo K, Serrano J, Sevior ME, Sfienti C, Shan W, Sharma C, Shi XD, Shillington T, Shiu JG, Shtol D, Sibidanov A, Simon F, Singh JB, Skorupa J, Sobie RJ, Sobotzik M, Soffer A, Sokolov A, Solovieva E, Spataro S, Spruck B, Starič M, Stavroulakis P, Stefkova S, Stottler ZS, Stroili R, Sumihama M, Sumisawa K, Sutcliffe W, Svidras H, Takahashi M, Takizawa M, Tamponi U, Tanaka S, Tanida K, Tenchini F, Thaller A, Tittel O, Tiwary R, Tonelli D, Torassa E, Trabelsi K, Tsaklidis I, Uchida M, Ueda I, Uglov T, Unger K, Unno Y, Uno K, Uno S, Urquijo P, Ushiroda Y, Vahsen SE, van Tonder R, Varner GS, Varvell KE, Vinokurova A, Vismaya VS, Vitale L, Wach B, Wakai M, Wakeling HM, Wallner S, Wang E, Wang MZ, Wang Z, Warburton A, Watanabe M, Watanuki S, Welsch M, Wessel C, Won E, Xu XP, Yabsley BD, Yamada S, Yan W, Yang SB, Yin JH, Yoshihara K, Yuan CZ, Yusa Y, Zani L, Zhang Y, Zhilich V, Zhou QD, Zhukova VI. Measurement of CP Violation in B^{0}→K_{S}^{0}π^{0} Decays at Belle II. Phys Rev Lett 2023; 131:111803. [PMID: 37774261 DOI: 10.1103/physrevlett.131.111803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/26/2023] [Indexed: 10/01/2023]
Abstract
We report a measurement of the CP-violating parameters C and S in B^{0}→K_{S}^{0}π^{0} decays at Belle II using a sample of 387×10^{6} BB[over ¯] events recorded in e^{+}e^{-} collisions at a center-of-mass energy corresponding to the ϒ(4S) resonance. These parameters are determined by fitting the proper decay-time distribution of a sample of 415 signal events. We obtain C=-0.04_{-0.15}^{+0.14}±0.05 and S=0.75_{-0.23}^{+0.20}±0.04, where the first uncertainties are statistical and the second are systematic.
Collapse
|
12
|
Sofińska K, Batys P, Cernescu A, Ghosh D, Skirlińska-Nosek K, Barbasz J, Seweryn S, Wilkosz N, Riek R, Szymoński M, Lipiec E. Nanoscale insights into the local structural rearrangements of amyloid-β induced by bexarotene. Nanoscale 2023; 15:14606-14614. [PMID: 37614107 DOI: 10.1039/d3nr01608k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
A better understanding of the abnormal protein aggregation and the effect of anti-aggregation agents on the fibrillation pathways and the secondary structure of aggregates can determine strategies for the early treatment of dementia. Herein, we present a combination of experimental and theoretical studies providing new insights into the influence of the anti-aggregation drug bexarotene on the secondary structure of individual amyloid-β aggregates and its primary aggregation. The molecular rearrangements and the spatial distribution of β-sheets within individual aggregates were monitored at the nanoscale with infrared nanospectroscopy. We observed that bexarotene limits the parallel β-sheets formation, known to be highly abundant in fibrils at later phases of the amyloid-β aggregation composed of in-register cross-β structure. Moreover, we applied molecular dynamics to provide molecular-level insights into the investigated system. Both theoretical and experimental results revealed that bexarotene slows down the protein aggregation process via steric effects, largely prohibiting the antiparallel to parallel β-sheet rearrangement. We also found that bexarotene interacts not only via the single hydrogen bond formation with the peptide backbone but also with the amino acid side residue via a hydrophobic effect. The studied model of the drug-amyloid-β interaction contributes to a better understanding of the inhibition mechanism of the amyloid-β aggregation by the small molecule drugs. However, our nanoscale findings need to meet in vivo research requiring different analytical approaches.
Collapse
Affiliation(s)
- Kamila Sofińska
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
| | - Piotr Batys
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | | | - Dhiman Ghosh
- ETH Zürich, Laboratory of Physical Chemistry, 8093 Zürich, Switzerland
| | - Katarzyna Skirlińska-Nosek
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Krakow, Poland
| | - Jakub Barbasz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Sara Seweryn
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Krakow, Poland
| | - Natalia Wilkosz
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Reymonta 19, 30-059 Krakow, Poland
| | - Roland Riek
- ETH Zürich, Laboratory of Physical Chemistry, 8093 Zürich, Switzerland
| | - Marek Szymoński
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
| | - Ewelina Lipiec
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
| |
Collapse
|
13
|
Das S, Chakraborty K, Ghosh D, Pulimi M, Chandrasekaran N, Anand S, Rai PK, Mukherjee A. Systematic assessment of f-MWCNT transport in aqueous medium: the effect of shear and non-shear forces. Int J Environ Sci Technol 2023; 20:6291-6306. [DOI: 10.1007/s13762-022-04295-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/24/2022] [Accepted: 05/18/2022] [Indexed: 10/26/2023]
|
14
|
Gao Z, Ghosh D, Harrington HA, Restrepo JG, Taylor D. Dynamics on networks with higher-order interactions. Chaos 2023; 33:040401. [PMID: 37097941 DOI: 10.1063/5.0151265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Affiliation(s)
- Z Gao
- School of Electrical and Information Engineering, Tianjin University, Tianjin 300072, China
| | - D Ghosh
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, India
| | - H A Harrington
- Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - J G Restrepo
- Department of Applied Mathematics, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - D Taylor
- Department of Mathematics, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| |
Collapse
|
15
|
Ghosh D, Wälti MA, Riek R. An Efficient Method of Expression and Purification of Amyloid-Beta (Aβ 1-42) Peptide from E. coli. Methods Mol Biol 2023; 2551:41-51. [PMID: 36310195 DOI: 10.1007/978-1-0716-2597-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Amyloid-beta (Aβ) aggregation into soluble oligomers and fibril formation are associated with Alzheimer's disease (AD) pathogenesis. Aβ1-42 is the major form of the Aβ peptide present in neuritic plaques and shown to be neurotoxic both in vivo and in vitro. However, understanding the mechanism of its toxicity, aggregation, and other biochemical properties is limited because of its difficult production (recombinant or synthetic) and irreproducibility issues attributed to batch-to-batch preparation differences. Chemically synthetic Aβ1-42 is now well established, but it always introduces up to 5% D-isomers along with its L-isomeric form, and thus it is not fruitful for biochemical/structural studies. Here, we optimized an efficient published method for expression and purification of Aβ1-42 upon overexpression in Escherichia coli (E. coli) that provides a satisfactory yield as well as minimizes the variability between batch preparations. With the present protocol, ~7-8 mg/liter of unlabeled peptide and ~3.5-4 mg/liter for 13C,15N-labeled (double-labeled) Aβ1-42 were obtained.
Collapse
Affiliation(s)
- Dhiman Ghosh
- Laboratory for Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Roland Riek
- Laboratory for Physical Chemistry, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
16
|
Gerez JA, Prymaczok NC, Kadavath H, Ghosh D, Bütikofer M, Fleischmann Y, Güntert P, Riek R. Protein structure determination in human cells by in-cell NMR and a reporter system to optimize protein delivery or transexpression. Commun Biol 2022; 5:1322. [PMID: 36460747 PMCID: PMC9718737 DOI: 10.1038/s42003-022-04251-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Most experimental methods for structural biology proceed in vitro and therefore the contribution of the intracellular environment on protein structure and dynamics is absent. Studying proteins at atomic resolution in living mammalian cells has been elusive due to the lack of methodologies. In-cell nuclear magnetic resonance spectroscopy (in-cell NMR) is an emerging technique with the power to do so. Here, we improved current methods of in-cell NMR by the development of a reporter system that allows monitoring the delivery of exogenous proteins into mammalian cells, a process that we called here "transexpression". The reporter system was used to develop an efficient protocol for in-cell NMR which enables spectral acquisition with higher quality for both disordered and folded proteins. With this method, the 3D atomic resolution structure of the model protein GB1 in human cells was determined with a backbone root-mean-square deviation (RMSD) of 1.1 Å.
Collapse
Affiliation(s)
- Juan A Gerez
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland.
| | | | | | - Dhiman Ghosh
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | | | | | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, 192-0397, Tokyo, Japan
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland.
| |
Collapse
|
17
|
Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso ÍP, Felli IC, Da Poian AT, de Amorim GC, Fourkiotis NK, Gallo A, Ghosh D, Gomes-Neto F, Gorbatyuk O, Hao B, Kurauskas V, Lecoq L, Li Y, Mebus-Antunes NC, Mompean M, Neves-Martins TC, Ninot-Pedrosa M, Pinheiro AS, Pontoriero L, Pustovalova Y, Riek R, Robertson A, Abi Saad MJ, Treviño MA, Tsika AC, Almeida FC, Bax A, Henzler-Wildman K, Hoch JC, Jaudzems K, Laurents DV, Orts J, Pieratelli R, Spyroulias GA, Duchardt-Ferner E, Ferner J, Fuertig B, Hengesbach M, Löhr F, Qureshi N, Richter C, Saxena K, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Woehnert J, Schwalbe H. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hannes Berg
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Nadide Altincekic
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Islam Alshamleh
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Jasleen Kaur Bains
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julius Blechar
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Betül Ceylan
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Vanessa de Jesus
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Christin Fuks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Santosh L. Gande
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Bruno Hargittay
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Marie T. Hutchinson
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Robin Krishnathas
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Felicitas Kutz
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Verena Linhard
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Tobias Matzel
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nathalie Meiser
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Niesteruk
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Dennis J. Pyper
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Linda Schulte
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Sven Trucks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Kamal Azzaoui
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Marcel J J Blommers
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Yojana Gadiya
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Drug Discovery Research ScreeningPort Screening Unit GERMANY
| | - Reagon Karki
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Marcius da Silva Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institue for Medical Biochemistry BRAZIL
| | - Cristiane Dinis Anobom
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Anna Lina Bula
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Institute of Organic Synthesis LATVIA
| | - Matthias Buetikofer
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute für Physikalische Chemie GERMANY
| | - Ícaro Putinhon Caruso
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics BRAZIL
| | - Isabella Caterina Felli
- University of Florence: Universita degli Studi di Firenze Magnetic Resonance Center (CERM) ITALY
| | - Andrea T Da Poian
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics GERMANY
| | - Gisele Cardoso de Amorim
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Multidisciplinary Center for Research in Biology BRAZIL
| | - Nikolaos K Fourkiotis
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Angelo Gallo
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Dhiman Ghosh
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | | | - Oksana Gorbatyuk
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Bing Hao
- UConn Health Department of Molecular Biology and Biopyhsics UNITED STATES
| | - Vilius Kurauskas
- UW Madison: University of Wisconsin Madison Department of Biochemistry UNITED STATES
| | - Lauriane Lecoq
- Universite de Lyon Molecular Microbiology and Structural Biochemistry FRANCE
| | - Yunfeng Li
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Nathane Cunha Mebus-Antunes
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Miguel Mompean
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Thais Cristtina Neves-Martins
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Marti Ninot-Pedrosa
- Universite Lyon 1 IUT Lyon 1 Molecular Microbiology and Structural Biochemistry FRANCE
| | - Anderson S Pinheiro
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Letizia Pontoriero
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Yulia Pustovalova
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Roland Riek
- ETH Zürich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | - Angus Robertson
- NIAMDD: National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | - Marie Jose Abi Saad
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Miguel A Treviño
- CSIC: Consejo Superior de Investigaciones Cientificas "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Aikaterini C Tsika
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Fabio C.L. Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Ad Bax
- National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | | | - Jeffrey C Hoch
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Kristaps Jaudzems
- Institute of Organic Synthesis of the Latvian Academy of Sciences: Latvijas Organiskas sintezes instituts Institute for Organic Chemistry LATVIA
| | - Douglas V Laurents
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Julien Orts
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Roberta Pieratelli
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Georgios A Spyroulias
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | | | - Jan Ferner
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Boris Fuertig
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Martin Hengesbach
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Frank Löhr
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nusrat Qureshi
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Christian Richter
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Krishna Saxena
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Andreas Schlundt
- Goethe-Universitat Frankfurt am Main Department for Biosciences GERMANY
| | - Sridhar Sreeramulu
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Wacker
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julia E Weigand
- TU Darmstadt: Technische Universitat Darmstadt Department of Biology GERMANY
| | | | - Jens Woehnert
- Goethe-Universitat Frankfurt am Main Department of Biological Sciences GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie Max-von-Laue-Str. 7 60438 Frankfurt GERMANY
| |
Collapse
|
18
|
Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso ÍP, Felli IC, Da Poian AT, de Amorim GC, Fourkiotis NK, Gallo A, Ghosh D, Gomes-Neto F, Gorbatyuk O, Hao B, Kurauskas V, Lecoq L, Li Y, Mebus-Antunes NC, Mompean M, Neves-Martins TC, Ninot-Pedrosa M, Pinheiro AS, Pontoriero L, Pustovalova Y, Riek R, Robertson A, Abi Saad MJ, Treviño MA, Tsika AC, Almeida FC, Bax A, Henzler-Wildman K, Hoch JC, Jaudzems K, Laurents DV, Orts J, Pieratelli R, Spyroulias GA, Duchardt-Ferner E, Ferner J, Fuertig B, Hengesbach M, Löhr F, Qureshi N, Richter C, Saxena K, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Woehnert J, Schwalbe H. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development. Angew Chem Int Ed Engl 2022; 61:e202205858. [PMID: 36115062 PMCID: PMC9539013 DOI: 10.1002/anie.202205858] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Indexed: 11/17/2022]
Abstract
SARS‐CoV‐2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti‐virals. Within the international Covid19‐NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80% of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR‐detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure‐based drug design against the SCoV2 proteome.
Collapse
Affiliation(s)
- Hannes Berg
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Nadide Altincekic
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Islam Alshamleh
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Jasleen Kaur Bains
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julius Blechar
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Betül Ceylan
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Vanessa de Jesus
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Christin Fuks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Santosh L. Gande
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Bruno Hargittay
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Marie T. Hutchinson
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Robin Krishnathas
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Felicitas Kutz
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Verena Linhard
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Tobias Matzel
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nathalie Meiser
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Niesteruk
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Dennis J. Pyper
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Linda Schulte
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Sven Trucks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Kamal Azzaoui
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Marcel J J Blommers
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Yojana Gadiya
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Drug Discovery Research ScreeningPort Screening Unit GERMANY
| | - Reagon Karki
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Marcius da Silva Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institue for Medical Biochemistry BRAZIL
| | - Cristiane Dinis Anobom
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Anna Lina Bula
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Institute of Organic Synthesis LATVIA
| | - Matthias Buetikofer
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute für Physikalische Chemie GERMANY
| | - Ícaro Putinhon Caruso
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics BRAZIL
| | - Isabella Caterina Felli
- University of Florence: Universita degli Studi di Firenze Magnetic Resonance Center (CERM) ITALY
| | - Andrea T Da Poian
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics GERMANY
| | - Gisele Cardoso de Amorim
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Multidisciplinary Center for Research in Biology BRAZIL
| | - Nikolaos K Fourkiotis
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Angelo Gallo
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Dhiman Ghosh
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | | | - Oksana Gorbatyuk
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Bing Hao
- UConn Health Department of Molecular Biology and Biopyhsics UNITED STATES
| | - Vilius Kurauskas
- UW Madison: University of Wisconsin Madison Department of Biochemistry UNITED STATES
| | - Lauriane Lecoq
- Universite de Lyon Molecular Microbiology and Structural Biochemistry FRANCE
| | - Yunfeng Li
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Nathane Cunha Mebus-Antunes
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Miguel Mompean
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Thais Cristtina Neves-Martins
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Marti Ninot-Pedrosa
- Universite Lyon 1 IUT Lyon 1 Molecular Microbiology and Structural Biochemistry FRANCE
| | - Anderson S Pinheiro
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Letizia Pontoriero
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Yulia Pustovalova
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Roland Riek
- ETH Zürich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | - Angus Robertson
- NIAMDD: National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | - Marie Jose Abi Saad
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Miguel A Treviño
- CSIC: Consejo Superior de Investigaciones Cientificas "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Aikaterini C Tsika
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Fabio C.L. Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Ad Bax
- National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | | | - Jeffrey C Hoch
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Kristaps Jaudzems
- Institute of Organic Synthesis of the Latvian Academy of Sciences: Latvijas Organiskas sintezes instituts Institute for Organic Chemistry LATVIA
| | - Douglas V Laurents
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Julien Orts
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Roberta Pieratelli
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Georgios A Spyroulias
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | | | - Jan Ferner
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Boris Fuertig
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Martin Hengesbach
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Frank Löhr
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nusrat Qureshi
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Christian Richter
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Krishna Saxena
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Andreas Schlundt
- Goethe-Universitat Frankfurt am Main Department for Biosciences GERMANY
| | - Sridhar Sreeramulu
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Wacker
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julia E Weigand
- TU Darmstadt: Technische Universitat Darmstadt Department of Biology GERMANY
| | | | - Jens Woehnert
- Goethe-Universitat Frankfurt am Main Department of Biological Sciences GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie Max-von-Laue-Str. 7 60438 Frankfurt GERMANY
| |
Collapse
|
19
|
Abstract
The animal model deals with the species other than the human, as it can imitate the disease progression, its’ diagnosis as well as a treatment similar to human. Discovery of a drug and/or component, equipment, their toxicological studies, dose, side effects are in vivo studied for future use in humans considering its’ ethical issues. Here lies the importance of the animal model for its enormous use in biomedical research. Animal models have many facets that mimic various disease conditions in humans like systemic autoimmune diseases, rheumatoid arthritis, epilepsy, Alzheimer’s disease, cardiovascular diseases, Atherosclerosis, diabetes, etc., and many more. Besides, the model has tremendous importance in drug development, development of medical devices, tissue engineering, wound healing, and bone and cartilage regeneration studies, as a model in vascular surgeries as well as the model for vertebral disc regeneration surgery. Though, all the models have some advantages as well as challenges, but, present review has emphasized the importance of various small and large animal models in pharmaceutical drug development, transgenic animal models, models for medical device developments, studies for various human diseases, bone and cartilage regeneration model, diabetic and burn wound model as well as surgical models like vascular surgeries and surgeries for intervertebral disc degeneration considering all the ethical issues of that specific animal model. Despite, the process of using the animal model has facilitated researchers to carry out the researches that would have been impossible to accomplish in human considering the ethical prohibitions.
Collapse
Affiliation(s)
- P Mukherjee
- Department of Veterinary Clinical Complex, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, India
| | - S Roy
- Department of Veterinary Clinical Complex, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, India
| | - D Ghosh
- Department of Veterinary Surgery and Radiology, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - S K Nandi
- Department of Veterinary Surgery and Radiology, West Bengal University of Animal and Fishery Sciences, Kolkata, India.
| |
Collapse
|
20
|
Pal D, Ghosh D, Santra PK, Mahapatra GS. Mathematical Analysis of a COVID-19 Epidemic Model by Using Data Driven Epidemiological Parameters of Diseases Spread in India. Biophysics (Nagoya-shi) 2022; 67:231-244. [PMID: 35789554 DOI: 10.1101/2020.04.25.20079111] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/18/2021] [Accepted: 12/23/2021] [Indexed: 05/27/2023] Open
Abstract
This paper attempts to describe the outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (COVID-19) via an epidemic model. This virus has dissimilar effects in different countries. The number of new active coronavirus cases is increasing gradually across the globe. India is now in the second stage of COVID-19 spreading, it will be an epidemic very quickly if proper protection is not undertaken based on the database of the transmission of the disease. This paper is using the current data of COVID-19 for the mathematical modeling and its dynamical analysis. We bring in a new representation to appraise and manage the outbreak of infectious disease COVID-19 through SEQIR pandemic model, which is based on the supposition that the infected but undetected by testing individuals are send to quarantine during the incubation period. During the incubation period if any individual be infected by COVID-19, then that confirmed infected individuals are isolated and the necessary treatments are arranged so that they cannot taint the other residents in the community. Dynamics of the SEQIR model is presented by basic reproduction number R 0 and the comprehensive stability analysis. Numerical results are depicted through apt graphical appearances using the data of five states and India.
Collapse
Affiliation(s)
- D Pal
- Chandrahati Dilip Kumar High School, 712504 Chandrahati, West Bengal India
| | - D Ghosh
- Department of Mathematics, National Institute of Technology Puducherry, 609609 Karaikal, India
| | - P K Santra
- Maulana Abul Kalam Azad University of Technology, 700064 Kolkata, India
| | - G S Mahapatra
- Department of Mathematics, National Institute of Technology Puducherry, 609609 Karaikal, India
| |
Collapse
|
21
|
Pal D, Ghosh D, Santra PK, Mahapatra GS. Mathematical Analysis of a COVID-19 Epidemic Model by Using Data Driven Epidemiological Parameters of Diseases Spread in India. Biophysics (Nagoya-shi) 2022; 67:231-244. [PMID: 35789554 PMCID: PMC9244063 DOI: 10.1134/s0006350922020154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/18/2021] [Accepted: 12/23/2021] [Indexed: 11/29/2022] Open
Abstract
This paper attempts to describe the outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (COVID-19) via an epidemic model. This virus has dissimilar effects in different countries. The number of new active coronavirus cases is increasing gradually across the globe. India is now in the second stage of COVID-19 spreading, it will be an epidemic very quickly if proper protection is not undertaken based on the database of the transmission of the disease. This paper is using the current data of COVID-19 for the mathematical modeling and its dynamical analysis. We bring in a new representation to appraise and manage the outbreak of infectious disease COVID-19 through SEQIR pandemic model, which is based on the supposition that the infected but undetected by testing individuals are send to quarantine during the incubation period. During the incubation period if any individual be infected by COVID-19, then that confirmed infected individuals are isolated and the necessary treatments are arranged so that they cannot taint the other residents in the community. Dynamics of the SEQIR model is presented by basic reproduction number R 0 and the comprehensive stability analysis. Numerical results are depicted through apt graphical appearances using the data of five states and India.
Collapse
Affiliation(s)
- D Pal
- Chandrahati Dilip Kumar High School, 712504 Chandrahati, West Bengal India
| | - D Ghosh
- Department of Mathematics, National Institute of Technology Puducherry, 609609 Karaikal, India
| | - P K Santra
- Maulana Abul Kalam Azad University of Technology, 700064 Kolkata, India
| | - G S Mahapatra
- Department of Mathematics, National Institute of Technology Puducherry, 609609 Karaikal, India
| |
Collapse
|
22
|
Kumar RP, Basu S, Santra P, Ghosh D, Mahapatra G. Optimal control design incorporating vaccination and treatment on six compartment pandemic dynamical system. Results in Control and Optimization 2022. [PMCID: PMC8969442 DOI: 10.1016/j.rico.2022.100115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this paper, a mathematical model of the COVID-19 pandemic with lockdown that provides a more accurate representation of the infection rate has been analyzed. In this model, the total population is divided into six compartments: the susceptible class, lockdown class, exposed class, asymptomatic infected class, symptomatic infected class, and recovered class. The basic reproduction number (R0) is calculated using the next-generation matrix method and presented graphically based on different progression rates and effective contact rates of infective individuals. The COVID-19 epidemic model exhibits the disease-free equilibrium and endemic equilibrium. The local and global stability analysis has been done at the disease-free and endemic equilibrium based on R0. The stability analysis of the model shows that the disease-free equilibrium is both locally and globally stable when R0<1, and the endemic equilibrium is locally and globally stable when R0>1 under some conditions. A control strategy including vaccination and treatment has been studied on this pandemic model with an objective functional to minimize. Finally, numerical simulation of the COVID-19 outbreak in India is carried out using MATLAB, highlighting the usefulness of the COVID-19 pandemic model and its mathematical analysis.
Collapse
|
23
|
Roongta R, Sircar G, Ghosh P, Sit H, Ghosh D. AB0399 COMPARISON OF RITUXIMAB VERSUS LEFLUNOMIDE IN COMBINATION WITH METHOTREXATE IN PATIENTS WITH ACTIVE RHEUMATOID ARTHRITIS DESPITE METHOTREXATE TREATMENT- AN OPEN LABEL, RANDOMISED CONTROLLED TRIAL. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.1913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundActive rheumatoid arthritis (RA) despite methotrexate monotherapy is seen in about 43% of patients1. The current American College of Rheumatology (ACR) guidelines recommend adding a biologic or targeted synthetic Disease Modifying Anti-rheumatic Drug (DMARD) to methotrexate (MTX) therapy in such cases. The European Alliance of Associations for Rheumatology (EULAR) guidelines recommend combination DMARDs but the most commonly used combination is that of MTX with sulphasalazine and hydroxychloroquine. In a resource limited country like ours, it is not always possible to give a biological or a targeted synthetic DMARD, and a more cost effective method needs to be implemented. Often, leflunomide (LEF) is added in such cases and is effective.ObjectivesWe aimed to study if LEF with MTX combination is non inferior to rituximab (RTX) and MTX combination in patients with active RA despite MTX.MethodsThis open label, randomised controlled trial, carried out on patients with moderate to high disease activity despite MTX therapy for atleast 3 months (Clinical Trials Registry- India - REF/2021/04/042755) was conducted in a tertiary care centre in India. Patients were randomised to receive either LEF (10-20mg/day) or RTX (2 doses of 1gm, 2 weeks apart) along with background MTX (10-25mg/week) and followed up at 12, 18 and 24 weeks. The primary outcome ACR20 response at 24 weeks and secondary outcomes were ACR50 and 70 responses at 24 weeks.ResultsThere were 21 patients in each arm. At baseline, all patients in both groups had seropositive RA and had high disease activity according to Disease Activity Score (DAS)28 scores. The ACR20 response at 24 weeks was achieved by 14 (66.6%) and 16 (76.19%) patients respectively in the LEF and RTX arms. The ACR50 response was achieved by 11 (52.38%) patients in both groups and ACR70 response by 4 (19%) and 7 (33.3%) in the LEF and RTX arms respectively (Figure 1). The mean dose of LEF at week 24 was 17.6 mg/day. Improvement of various parameters at week 24 as compared to the baseline values were similar in both groups (Table 1). No major adverse events were noted. Two patients receiving RTX had a mild infusion reaction. Elevation in liver enzymes (<3 times the upper limit of normal) were noted in 4 patients in the LEF arm which normalised subsequently. No patient required drug withdrawal.Table 1.Responses in both groups at week 24 (p= Not significant for all)Leflunomide, n=21Rituximab, n=21Mean ±SD reduction in SJC-4.57 ± 3.4-5.43 ± 4.6Mean ±SD reduction in TJC-6.2 ± 3.9-7.1 ± 6.1Mean ±SD reduction in PhGA-3.42 ± 1.8-4.04 ± 2.5Mean ±SD reduction in PGA-3.05 ± 1.8-3.42 ± 2.4Mean ±SD reduction in pain VAS-33.57 ± 23.2-38.57 ± 24.4Mean ±SD reduction in DAS28-ESR-1.95 ± 1.2-2.08 ± 1.4Mean ±SD reduction in DAS28-CRP-1.81 ± 1.2-2.07 ± 1.4Mean ±SD reduction in HAQ-DI-0.65 ± 0.5-0.82 ± 0.6EULAR good response (%)1 (4.76%)1 (4.76%)EULAR moderate response (%)15 (71.43%)14 (66.6%)EULAR non-responders (%)5 (23.81%)6 (28.57%)CRP, C- Reactive Protein; DAS, Disease Activity Score; ESR, Erythrocyte Sedimentation Rate; HAQ-DI, Healthy Assessment Questionnaire-Disability Index; PGA, Patient’s global assessment of disease activity; PhGA, Physician’s global assessment of disease activity; SJC, Swollen Joint Count; TJC, Tender Joint Count; VAS, Visual analogue scale.Figure 1.Number of patients achieving ACR20, 50 and 70 responses at week 24ConclusionIn our study, LEF was comparable to RTX for achievement of ACR20/50/70 responses at 24 weeks. LEF can be considered as an add-on option to MTX instead of more expensive biologic agents in MTX refractory RA. Larger studies are needed to confirm this hypothesis.References[1]Sergeant JC, Hyrich KL, Anderson J, et al. Prediction of primary non-response to methotrexate therapy using demographic, clinical and psychosocial variables: results from the UK Rheumatoid Arthritis Medication Study (RAMS). Arthritis Res Ther. 2018;20(1):147. Published 2018 Jul 13.Disclosure of InterestsNone declared
Collapse
|
24
|
Ghosh D, Santra PK, Mahapatra GS, Elsonbaty A, Elsadany AA. A discrete-time epidemic model for the analysis of transmission of COVID19 based upon data of epidemiological parameters. Eur Phys J Spec Top 2022; 231:3461-3470. [PMID: 35313624 PMCID: PMC8924950 DOI: 10.1140/epjs/s11734-022-00537-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/05/2022] [Indexed: 05/31/2023]
Abstract
The forecasting of the nature and dynamics of emerging coronavirus (COVID-19) pandemic has gained a great concern for health care organizations and governments. The efforts aim to to suppress the rapid and global spread of its tentacles and also control the infection with the limited available resources. The aim of this work is to employ real data set to propose and analyze a compartmental discrete time COVID-19 pandemic model with non-linear incidence and hence predict and control its outbreak through dynamical research. The Basic Reproduction Number ( R 0 ) is calculated analytically to study the disease-free steady state ( R 0 < 1 ), and also the permanency case ( R 0 > 1 ) of the disease. Numerical results show that the transmission rates α > 0 and β > 0 are quite effective in reducing the COVID-19 infections in India or any country. The fitting and predictive capability of the proposed discrete-time system are presented for relishing the effect of disease through stability analysis using real data sets.
Collapse
Affiliation(s)
- D. Ghosh
- Department of Mathematics, National Institute of Technology Puducherry, Karaikal, 609609 India
| | - P. K. Santra
- Maulana Abul Kalam Azad University of Technology, Kolkata, 700064 India
| | - G. S. Mahapatra
- Department of Mathematics, National Institute of Technology Puducherry, Karaikal, 609609 India
| | - Amr Elsonbaty
- Department of Mathematics, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942 Saudi Arabia
- Department of Engineering Mathematics and Physics, Faculty of Engineering, Mansoura University, Mansoura, 35516 Egypt
| | - A. A. Elsadany
- Department of Mathematics, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942 Saudi Arabia
- Department of Basic Science, Faculty of Computers and Informatics, Suez Canal University, Ismailia, 41522 Egypt
| |
Collapse
|
25
|
Sawner AS, Ray S, Yadav P, Mukherjee S, Panigrahi R, Poudyal M, Patel K, Ghosh D, Kummerant E, Kumar A, Riek R, Maji SK. Modulating α-Synuclein Liquid-Liquid Phase Separation. Biochemistry 2021; 60:3676-3696. [PMID: 34431665 DOI: 10.1021/acs.biochem.1c00434] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Liquid-liquid phase separation (LLPS) is a crucial phenomenon for the formation of functional membraneless organelles. However, LLPS is also responsible for protein aggregation in various neurodegenerative diseases such as amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease (PD). Recently, several reports, including ours, have shown that α-synuclein (α-Syn) undergoes LLPS and a subsequent liquid-to-solid phase transition, which leads to amyloid fibril formation. However, how the environmental (and experimental) parameters modulate the α-Syn LLPS remains elusive. Here, we show that in vitro α-Syn LLPS is strongly dependent on the presence of salts, which allows charge neutralization at both terminal segments of protein and therefore promotes hydrophobic interactions supportive for LLPS. Using various purification methods and experimental conditions, we showed, depending upon conditions, α-Syn undergoes either spontaneous (instantaneous) or delayed LLPS. Furthermore, we delineate that the kinetics of liquid droplet formation (i.e., the critical concentration and critical time) is relative and can be modulated by the salt/counterion concentration, pH, presence of surface, PD-associated multivalent cations, and N-terminal acetylation, which are all known to regulate α-Syn aggregation in vitro. Together, our observations suggest that α-Syn LLPS and subsequent liquid-to-solid phase transition could be pathological, which can be triggered only under disease-associated conditions (high critical concentration and/or conditions promoting α-Syn self-assembly). This study will significantly improve our understanding of the molecular mechanisms of α-Syn LLPS and the liquid-to-solid transition.
Collapse
Affiliation(s)
- Ajay Singh Sawner
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Soumik Ray
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Preeti Yadav
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Semanti Mukherjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Rajlaxmi Panigrahi
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Dhiman Ghosh
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Eric Kummerant
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Roland Riek
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| |
Collapse
|
26
|
Das S, Rashid MM, Khan SI, Sarker AC, Ghosh D, Mahbub H. Surgical Outcome of CSF Drainage in Paediatric Obstructive Hydrocephalus. Mymensingh Med J 2021; 30:1146-1153. [PMID: 34605489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hydrocephalus (HCP) is occurred when there is inequality in the formation and absorption of CSF to such a level which causes accumulation of fluid and causing raised intracranial pressure. Hydrocephalus is the most frequent neurosurgical problem encountered in the paediatric age group. CSF diversion surgically is needed as treatment for certain condition. Endoscopic third ventriculostomy (ETV) and Ventriculo-peritoneal shunt (VPS) are most widely used CSF diversion procedure. Therefore, this study was conducted for comparing the surgical outcome of ETV and VP shunt in obstructive hydrocephalus. This is a prospective experimental study conducted in the Department of Neurosurgery, Dhaka Medical College and Hospital (DMCH) and Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh from January 2017 to December 2019. Paediatric patients of both sex and 6 months to 18 years of age with obstructive hydrocephalus undergone endoscopic third ventriculostomy (ETV) or ventriculo-peritoneal shunt (VP shunt) were included after fulfilling inclusion and exclusion criteria. The patients divided into two groups (Group A and Group B). The Group A included 30 patients who treated by Endoscopic third ventriculostomy and the Group B include 30 patients, who was treated by Ventriculo-peritoneal shunt. Surgical outcome was analyzed in two procedures separately. In Group A (ETV group) symptomatic improvement, GCS score improves earlier and post-operative complications relatively less than Group B (VP shunt group). But in VP shunt group 3 months follow up reveals- improvement of papilledema, Occipital frontal circumference (OFC) regression and fontanelle size improvement was more than that of ETV group. This study concluded with suggesting that Endoscopic third ventriculostomy (ETV) is technologically superior surgical technique than VP shunt. Though ETV showed relatively more immediate procedural failure and intraventricular hemorrhage but long-term outcome is better and also associated with lower incidence of infection and re-operation in comparison to VP shunt.
Collapse
Affiliation(s)
- S Das
- Dr Sukriti Das, Associate Professor, Department of Neurosurgery, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh; E-mail:
| | | | | | | | | | | |
Collapse
|
27
|
Hall MJR, Martín‐Vega D, Clark B, Ghosh D, Rogers M, Pigoli D, Veriegh FBD, Tetteh‐Kumah A, Osei‐Atweneboana MY, Cheke RA. Micro-CT imaging of Onchocerca infection of Simulium damnosum s.l. blackflies and comparison of the peritrophic membrane thickness of forest and savannah flies. Med Vet Entomol 2021; 35:231-238. [PMID: 33480060 PMCID: PMC8451916 DOI: 10.1111/mve.12509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/27/2020] [Accepted: 12/28/2020] [Indexed: 05/08/2023]
Abstract
Onchocerciasis is a neglected tropical disease (NTD) caused by Onchocerca Diesing 1841 (Spirurida: Onchocercidae) nematodes transmitted by blackflies. It is associated with poverty and imposes a significant health, welfare and economic burden on many tropical countries. Current methods to visualize infections within the vectors rely on invasive methods. However, using micro-computed tomography techniques, without interference from physical tissue manipulation, we visualized in three dimensions for the first time an L1 larva of an Onchocerca species within the thoracic musculature of a blackfly, Simulium damnosum s.l. Theobald 1903 (Diptera: Simuliidae), naturally infected in Ghana. The possibility that thicker peritrophic membranes in savannah flies could account for their lower parasite loads was not supported, but there were limits to our analysis. While there were no statistically significant differences between the mean thicknesses of the peritrophic membranes, in the anterior, dorsal and ventral regions, of forest and savannah blackflies killed 34-48 min after a blood-meal, the thickness of the peritrophic membrane in the posterior region could not be measured. Micro-computed tomography has the potential to provide novel information on many other parasite/vector systems and impactful images for public engagement in health education.
Collapse
Affiliation(s)
- M. J. R. Hall
- Departments of Life Sciences and Core Research LaboratoriesNatural History MuseumLondonUK
| | - D. Martín‐Vega
- Departments of Life Sciences and Core Research LaboratoriesNatural History MuseumLondonUK
- Departamento de Ciencias de la Vida (Unidad Docente de Zoología)Universidad de AlcaláAlcalá de Henares (Madrid)Spain
| | - B. Clark
- Departments of Life Sciences and Core Research LaboratoriesNatural History MuseumLondonUK
| | - D. Ghosh
- Nutrition and Clinical Services DivisionInternational Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b)DhakaBangladesh
| | - M. Rogers
- Department of Disease ControlLondon School of Hygiene and Tropical MedicineLondonUK
| | - D. Pigoli
- Department of MathematicsKing's College LondonLondonUK
| | - F. B. D. Veriegh
- Council for Scientific and Industrial ResearchWater Research InstituteAccraGhana
| | - A. Tetteh‐Kumah
- Council for Scientific and Industrial ResearchWater Research InstituteAccraGhana
| | | | - R. A. Cheke
- Agriculture, Health and Environment Department, Natural Resources InstituteUniversity of GreenwichMedway CampusChatham MaritimeKentUK
| |
Collapse
|
28
|
Altincekic N, Korn SM, Qureshi NS, Dujardin M, Ninot-Pedrosa M, Abele R, Abi Saad MJ, Alfano C, Almeida FCL, Alshamleh I, de Amorim GC, Anderson TK, Anobom CD, Anorma C, Bains JK, Bax A, Blackledge M, Blechar J, Böckmann A, Brigandat L, Bula A, Bütikofer M, Camacho-Zarco AR, Carlomagno T, Caruso IP, Ceylan B, Chaikuad A, Chu F, Cole L, Crosby MG, de Jesus V, Dhamotharan K, Felli IC, Ferner J, Fleischmann Y, Fogeron ML, Fourkiotis NK, Fuks C, Fürtig B, Gallo A, Gande SL, Gerez JA, Ghosh D, Gomes-Neto F, Gorbatyuk O, Guseva S, Hacker C, Häfner S, Hao B, Hargittay B, Henzler-Wildman K, Hoch JC, Hohmann KF, Hutchison MT, Jaudzems K, Jović K, Kaderli J, Kalniņš G, Kaņepe I, Kirchdoerfer RN, Kirkpatrick J, Knapp S, Krishnathas R, Kutz F, zur Lage S, Lambertz R, Lang A, Laurents D, Lecoq L, Linhard V, Löhr F, Malki A, Bessa LM, Martin RW, Matzel T, Maurin D, McNutt SW, Mebus-Antunes NC, Meier BH, Meiser N, Mompeán M, Monaca E, Montserret R, Mariño Perez L, Moser C, Muhle-Goll C, Neves-Martins TC, Ni X, Norton-Baker B, Pierattelli R, Pontoriero L, Pustovalova Y, Ohlenschläger O, Orts J, Da Poian AT, Pyper DJ, Richter C, Riek R, Rienstra CM, Robertson A, Pinheiro AS, Sabbatella R, Salvi N, Saxena K, Schulte L, Schiavina M, Schwalbe H, Silber M, Almeida MDS, Sprague-Piercy MA, Spyroulias GA, Sreeramulu S, Tants JN, Tārs K, Torres F, Töws S, Treviño MÁ, Trucks S, Tsika AC, Varga K, Wang Y, Weber ME, Weigand JE, Wiedemann C, Wirmer-Bartoschek J, Wirtz Martin MA, Zehnder J, Hengesbach M, Schlundt A. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications. Front Mol Biosci 2021; 8:653148. [PMID: 34041264 PMCID: PMC8141814 DOI: 10.3389/fmolb.2021.653148] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/04/2021] [Indexed: 01/18/2023] Open
Abstract
The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
Collapse
Affiliation(s)
- Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sophie Marianne Korn
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Dujardin
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Martí Ninot-Pedrosa
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Rupert Abele
- Institute for Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Jose Abi Saad
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Caterina Alfano
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Fabio C. L. Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Islam Alshamleh
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisele Cardoso de Amorim
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil
| | - Thomas K. Anderson
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cristiane D. Anobom
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chelsea Anorma
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Adriaan Bax
- LCP, NIDDK, NIH, Bethesda, MD, United States
| | | | - Julius Blechar
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Louis Brigandat
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Anna Bula
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Matthias Bütikofer
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Teresa Carlomagno
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Icaro Putinhon Caruso
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Marquise G. Crosby
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Karthikeyan Dhamotharan
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Isabella C. Felli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yanick Fleischmann
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Christin Fuks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Angelo Gallo
- Department of Pharmacy, University of Patras, Patras, Greece
| | - Santosh L. Gande
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Juan Atilio Gerez
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Dhiman Ghosh
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Francisco Gomes-Neto
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Oksana Gorbatyuk
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | | | - Sabine Häfner
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Bing Hao
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Bruno Hargittay
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - K. Henzler-Wildman
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie T. Hutchison
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Katarina Jović
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Janina Kaderli
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Iveta Kaņepe
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Robert N. Kirchdoerfer
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - John Kirkpatrick
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Robin Krishnathas
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Felicitas Kutz
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susanne zur Lage
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Roderick Lambertz
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andras Lang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Douglas Laurents
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Verena Linhard
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank Löhr
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anas Malki
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Tobias Matzel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Damien Maurin
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Seth W. McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Nathane Cunha Mebus-Antunes
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Beat H. Meier
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Nathalie Meiser
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Mompeán
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Elisa Monaca
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Celine Moser
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | - Thais Cristtina Neves-Martins
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Xiamonin Ni
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Brenna Norton-Baker
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Roberta Pierattelli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Letizia Pontoriero
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Yulia Pustovalova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | - Julien Orts
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Andrea T. Da Poian
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dennis J. Pyper
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Roland Riek
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Chad M. Rienstra
- Department of Biochemistry and National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anderson S. Pinheiro
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Nicola Salvi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Linda Schulte
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marco Schiavina
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mara Silber
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcius da Silva Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marc A. Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | | | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jan-Niklas Tants
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Felix Torres
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Sabrina Töws
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Á. Treviño
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Krisztina Varga
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Ying Wang
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Marco E. Weber
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Julia E. Weigand
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Christoph Wiedemann
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria Alexandra Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johannes Zehnder
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andreas Schlundt
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| |
Collapse
|
29
|
Strotz D, Orts J, Kadavath H, Friedmann M, Ghosh D, Olsson S, Chi CN, Güntert P, Vögeli B, Riek R. Protein Allostery at Atomic Resolution. Angew Chem Int Ed Engl 2020; 59:22132-22139. [PMID: 32797659 PMCID: PMC9202374 DOI: 10.1002/anie.202008734] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/23/2020] [Indexed: 08/15/2023]
Abstract
Protein allostery is a phenomenon involving the long range coupling between two distal sites in a protein. In order to elucidate allostery at atomic resoluion on the ligand-binding WW domain of the enzyme Pin1, multistate structures were calculated from exact nuclear Overhauser effect (eNOE). In its free form, the protein undergoes a microsecond exchange between two states, one of which is predisposed to interact with its parent catalytic domain. In presence of the positive allosteric ligand, the equilibrium between the two states is shifted towards domain-domain interaction, suggesting a population shift model. In contrast, the allostery-suppressing ligand decouples the side-chain arrangement at the inter-domain interface thereby reducing the inter-domain interaction. As such, this mechanism is an example of dynamic allostery. The presented distinct modes of action highlight the power of the interplay between dynamics and function in the biological activity of proteins.
Collapse
Affiliation(s)
- Dean Strotz
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Julien Orts
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Harindranath Kadavath
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Michael Friedmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Simon Olsson
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Celestine N. Chi
- Department of Medical Biochemistry and Microbiology, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden
| | - Peter Güntert
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, J.W. Goethe-Universität, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, 12801 East 17 Avenue, Aurora, CO 80045, USA
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| |
Collapse
|
30
|
Strotz D, Orts J, Kadavath H, Friedmann M, Ghosh D, Olsson S, Chi CN, Pokharna A, Güntert P, Vögeli B, Riek R. Protein Allostery at Atomic Resolution. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dean Strotz
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| | - Julien Orts
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| | - Harindranath Kadavath
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| | - Michael Friedmann
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| | - Simon Olsson
- Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 6 14195 Berlin Germany
| | - Celestine N. Chi
- Department of Medical Biochemistry and Microbiology Uppsala Biomedical Center Uppsala University 751 23 Uppsala Sweden
| | - Aditya Pokharna
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| | - Peter Güntert
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies J.W. Goethe-Universität Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
- Graduate School of Science Tokyo Metropolitan University, Hachioji Tokyo 192-0397 Japan
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics University of Colorado at Denver 12801 East 17th Avenue Aurora CO 80045 USA
| | - Roland Riek
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| |
Collapse
|
31
|
Abstract
Fermentation is one of the safest and most economical means of producing foods
acceptable to human beings. It improves the nutritional quality of foods by increasing the
bioavailability and thus, renders the food safe palatable and easily acceptable to mankind.
The present study showed the effects of fermentation on the nutritional quality and safety
of fermented foods with respect to nutrient composition and digestibility measures.
Sauerkraut and fermented mixed vegetable were selected for study and the effects of
fermentation on nutrient were observed. Digestibility, shelf-life and biochemical aspects
were also studied. Level of all principle nutrients was significantly increased. In course of
fermentation, total sugar and reducing sugar in the brine increased slowly to 3% and 2%,
respectively up to 8th day and then decreased in sauerkraut fermentation. The maximum
total acidity (1.98-2.22%) was observed on 15th day in fermented mixed vegetables. The
pH of the shredded cabbage was 6.9 and decreased to around 4 after 15 days and then
remained constant.
Collapse
|
32
|
Singh PK, Chen ZL, Ghosh D, Strickland S, Norris EH. Increased plasma bradykinin level is associated with cognitive impairment in Alzheimer's patients. Neurobiol Dis 2020; 139:104833. [PMID: 32173555 PMCID: PMC7175647 DOI: 10.1016/j.nbd.2020.104833] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/28/2020] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by the presence of proteinaceous brain deposits, brain atrophy, vascular dysfunction, and chronic inflammation. Along with cerebral inflammation, peripheral inflammation is also evident in many AD patients. Bradykinin, a proinflammatory plasma peptide, is also linked to AD pathology. For example, bradykinin infusion into the hippocampus causes learning and memory deficits in rats, and blockade of the bradykinin receptor lessens cognitive impairment in AD mouse models. Even though it has been hypothesized that plasma bradykinin could contribute to inflammation in AD, the level of plasma bradykinin and its association with beta-amyloid (Aβ) pathology in AD patients had not been explored. Here, we assessed plasma bradykinin levels in AD patients and age-matched non-demented (ND) control individuals. We found significantly elevated plasma bradykinin levels in AD patients compared to ND subjects. Additionally, changes in plasma bradykinin levels were more profound in many AD patients with severe cognitive impairment, suggesting that peripheral bradykinin could play a role in dementia most likely via inflammation. Bradykinin levels in the cerebrospinal fluid (CSF) were reduced in AD patients and exhibited an inverse correlation with the CSF Aβ40/Aβ42 ratio. We also report that bradykinin interacts with the fibrillar form of Aβ and co-localizes with Aβ plaques in the post-mortem human AD brain. These findings connect the peripheral inflammatory pathway to cerebral abnormalities and identify a novel mechanism of inflammatory pathology in AD.
Collapse
Affiliation(s)
- Pradeep K Singh
- Patricia and John Rosenwald Laboratory of Neurobiology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Zu-Lin Chen
- Patricia and John Rosenwald Laboratory of Neurobiology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry, ETH Zürich, WolfgangPauli-Str. 10, 8093 Zürich, Switzerland
| | - Sidney Strickland
- Patricia and John Rosenwald Laboratory of Neurobiology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Erin H Norris
- Patricia and John Rosenwald Laboratory of Neurobiology and Genetics, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
33
|
Torres F, Ghosh D, Strotz D, Chi CN, Davis B, Orts J. Protein-fragment complex structures derived by NMR molecular replacement. RSC Med Chem 2020; 11:591-596. [PMID: 33479661 PMCID: PMC7649837 DOI: 10.1039/d0md00068j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/23/2020] [Indexed: 01/16/2023] Open
Abstract
Recently we have established an NMR molecular replacement method, which is capable of solving the structure of the interaction site of protein-ligand complexes in a fully automated manner. While the method was successfully applied for ligands with strong and weak binding affinities, including small molecules and peptides, its applicability on ligand fragments remains to be shown. Structures of fragment-protein complexes are more challenging for the method since fragments contain only few protons. Here we show a successful application of the NMR molecular replacement method in solving structures of complexes between three derivatives of a ligand fragment and the protein receptor PIN1. We anticipate that this approach will find a broad application in fragment-based lead discovery.
Collapse
Affiliation(s)
- Felix Torres
- Laboratory of Physical Chemistry , ETH , Swiss Federal Institute of Technology , HCI F217, Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland .
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry , ETH , Swiss Federal Institute of Technology , HCI F217, Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland .
| | - Dean Strotz
- Laboratory of Physical Chemistry , ETH , Swiss Federal Institute of Technology , HCI F217, Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland .
| | - Celestine N Chi
- Laboratory of Physical Chemistry , ETH , Swiss Federal Institute of Technology , HCI F217, Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland .
| | - Ben Davis
- Vernalis , Granta Park , Cambridge , UK
| | - Julien Orts
- Laboratory of Physical Chemistry , ETH , Swiss Federal Institute of Technology , HCI F217, Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland .
| |
Collapse
|
34
|
Sacco A, Chen R, Ghosh D, Worden F, Wong D, Adkins D, Swiecicki P, Chai-Ho W, Pittman E, Messer K, Gold K, Daniels G, Sutton B, Natsuhara A, Cohen E. An open-label, non-randomized, multi-arm, phase II trial evaluating pembrolizumab combined with cetuximab in patients (pts) with recurrent/metastatic (R/M) head and neck squamous cell carcinoma (HNSCC): updated results of cohort 1 analysis. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2019.11.376] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
35
|
Majumdar P, Banerjee B, Ghosh D. Antibacterial activity and pharmacological effect of some mixed-ligand tris-chelates of copper(II) containing neutral N,N-donors and kinetics study of the novel synthetic route for the complexes. B CHEM SOC ETHIOPIA 2019. [DOI: 10.4314/bcse.v33i3.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
36
|
Orts J, Aulikki Wälti M, Ghosh D, Campioni S, Saupe SJ, Riek R. Rational Structure-Based Design of Fluorescent Probes for Amyloid Folds. Chembiochem 2019; 20:1161-1166. [PMID: 30548150 DOI: 10.1002/cbic.201800664] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 11/09/2022]
Abstract
Amyloid fibrils are pathological hallmarks of various human diseases, including Parkinson's, Alzheimer's, amyotrophic lateral sclerosis (ALS or motor neurone disease), and prion diseases. Treatment of the amyloid diseases are hindered, among other factors, by timely detection and therefore, early detection of the amyloid fibrils would be beneficial for treatment against these disorders. Here, a small molecular fluorescent probe is reported that selectively recognize the fibrillar form of amyloid beta(1-42), α-synuclein, and HET-s(218-289) protein over their monomeric conformation. The rational design of the reporters relies on the well-known cross-β-sheet repetition motif, the key structural feature of amyloids.
Collapse
Affiliation(s)
- Julien Orts
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Marielle Aulikki Wälti
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Silvia Campioni
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland.,Present address: Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600, Dübendorf, Switzerland
| | - Sven J Saupe
- Institut de Biochimie et Génétique Cellulaires, UMR 5095, Université de Bordeaux, 1, rue Camille Saint Saëns, 33077, Bordeaux, France
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| |
Collapse
|
37
|
Yelamanchi SD, Tyagi A, Mohanty V, Dutta P, Korbonits M, Chavan S, Advani J, Madugundu AK, Dey G, Datta KK, Rajyalakshmi M, Sahasrabuddhe NA, Chaturvedi A, Kumar A, Das AA, Ghosh D, Jogdand GM, Nair HH, Saini K, Panchal M, Sarvaiya MA, Mohanraj SS, Sengupta N, Saxena P, Subramani PA, Kumar P, Akkali R, Reshma SV, Santhosh RS, Rastogi S, Kumar S, Ghosh SK, Irlapati VK, Srinivasan A, Radotra BD, Mathur PP, Wong GW, Satishchandra P, Chatterjee A, Gowda H, Bhansali A, Pandey A, Shankar SK, Mahadevan A, Prasad TSK. Proteomic Analysis of the Human Anterior Pituitary Gland. OMICS 2019; 22:759-769. [PMID: 30571610 DOI: 10.1089/omi.2018.0160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The pituitary function is regulated by a complex system involving the hypothalamus and biological networks within the pituitary. Although the hormones secreted from the pituitary have been well studied, comprehensive analyses of the pituitary proteome are limited. Pituitary proteomics is a field of postgenomic research that is crucial to understand human health and pituitary diseases. In this context, we report here a systematic proteomic profiling of human anterior pituitary gland (adenohypophysis) using high-resolution Fourier transform mass spectrometry. A total of 2164 proteins were identified in this study, of which 105 proteins were identified for the first time compared with high-throughput proteomic-based studies from human pituitary glands. In addition, we identified 480 proteins with secretory potential and 187 N-terminally acetylated proteins. These are the first region-specific data that could serve as a vital resource for further investigations on the physiological role of the human anterior pituitary glands and the proteins secreted by them. We anticipate that the identification of previously unknown proteins in the present study will accelerate biomedical research to decipher their role in functioning of the human anterior pituitary gland and associated human diseases.
Collapse
Affiliation(s)
| | - Ankur Tyagi
- 2 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Varshasnata Mohanty
- 2 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Pinaki Dutta
- 3 Department of Endocrinology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Márta Korbonits
- 4 Department of Endocrinology, Barts and the London School of Medicine, Queen Mary University of London, London, United Kingdom
| | - Sandip Chavan
- 1 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Jayshree Advani
- 1 Institute of Bioinformatics, International Technology Park, Bangalore, India.,5 Manipal Academy of Higher Education, Manipal, India
| | - Anil K Madugundu
- 1 Institute of Bioinformatics, International Technology Park, Bangalore, India.,5 Manipal Academy of Higher Education, Manipal, India.,6 Center for Molecular Medicine, National Institute of Mental Health & Neurosciences, Bangalore, India.,7 Department of Laboratory Medicine and Pathology and Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Gourav Dey
- 1 Institute of Bioinformatics, International Technology Park, Bangalore, India.,5 Manipal Academy of Higher Education, Manipal, India
| | - Keshava K Datta
- 1 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - M Rajyalakshmi
- 8 Department of Biotechnology, BMS College of Engineering, Bangalore, India
| | | | - Abhishek Chaturvedi
- 9 Department of Biochemistry, Melaka Manipal Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Amit Kumar
- 10 Institute of Life Sciences, Nalco Square, Bhubaneswar, India
| | - Apabrita Ayan Das
- 11 Cell Biology and Physiology Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Dhiman Ghosh
- 12 Protein Engineering and Neurobiology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, India
| | | | - Haritha H Nair
- 13 Division of Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Keshav Saini
- 14 Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| | - Manoj Panchal
- 15 Department of Life Science, Central University of South Bihar, Gaya, India
| | | | - Soundappan S Mohanraj
- 17 Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Nabonita Sengupta
- 18 Neuroinflammation Laboratory, National Brain Research Centre, Manesar, India
| | - Priti Saxena
- 14 Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| | | | - Pradeep Kumar
- 20 Department of Biotechnology, VBS Purvanchal University, Jaunpur, India
| | - Rakhil Akkali
- 21 Department of Biotechnology, Indian Institute of Technology, Madras, India
| | | | | | - Sangita Rastogi
- 24 Microbiology Laboratory, National Institute of Pathology, New Delhi, India
| | - Sudarshan Kumar
- 25 Proteomics and Structural Biology Laboratory, Animal Biotechnology Center, National Dairy Research Institute, Karnal, India
| | - Susanta Kumar Ghosh
- 19 Department of Molecular Parasitology, National Institute of Malaria Research, Bangalore, India
| | | | - Anand Srinivasan
- 27 Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bishan Das Radotra
- 28 Department of Histopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Premendu P Mathur
- 29 Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - G William Wong
- 30 Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Aditi Chatterjee
- 1 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Harsha Gowda
- 1 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Anil Bhansali
- 3 Department of Endocrinology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Akhilesh Pandey
- 1 Institute of Bioinformatics, International Technology Park, Bangalore, India.,5 Manipal Academy of Higher Education, Manipal, India.,6 Center for Molecular Medicine, National Institute of Mental Health & Neurosciences, Bangalore, India.,7 Department of Laboratory Medicine and Pathology and Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,32 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,33 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland.,34 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,35 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Susarla K Shankar
- 36 Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India.,37 Human Brain Tissue Repository, National Institute of Mental Health and Neuro Sciences, Neurobiology Research Centre, Bangalore, India
| | - Anita Mahadevan
- 36 Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India.,37 Human Brain Tissue Repository, National Institute of Mental Health and Neuro Sciences, Neurobiology Research Centre, Bangalore, India
| | - T S Keshava Prasad
- 1 Institute of Bioinformatics, International Technology Park, Bangalore, India.,2 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| |
Collapse
|
38
|
Ghosh D, Roy AK, Murmu N, Mandal S, Roy A. Risk Categorization with Different Grades of Cervical Pre-Neoplastic Lesions - High Risk HPV Associations and Expression of p53 and RARβ. Asian Pac J Cancer Prev 2019; 20:549-555. [PMID: 30803219 PMCID: PMC6897033 DOI: 10.31557/apjcp.2019.20.2.549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Objective: To identify high risk HPV associations by evaluating linked p16 overexpression and also the expression of p53 and RARβ together with histopathology for risk categorization of cervical pre-neoplastic lesions. Materials and Methods: Immunohistochemical staining was performed on 100 cases of cervical pre- neoplastic lesions for expression of biomarkers like p16, p53 and RARβ for comparison with haematoxylin/eosin (HE) findings. All the experimentally generated data were statistically analyzed. Results: In this study 70% cases showed overexpression of p16INK4A increasing progressively from CIN I to CIN II but reduced in CIN III (p <0.01). p53 oncoprotein expression was seen in 51% cases, again with increments from CIN I to CIN II with slight reduction in CIN III (p<0.01). Some 24% cases showed negative immunoreactivity for the putative tumor suppressor gene RARβ (p>0.05). Conclusion: Our study provides support for the idea that p16 can be used to identify associations with HPV , as well as having potential along with p53 and RARβ for categorizing cervical pre-neoplastic cases having a higher risk of neoplastic conversion. Thus it may be concluded that accurate risk categorization can be achieved with the help of genetic markers as well as histopathology.
Collapse
Affiliation(s)
- D Ghosh
- Department of Pathology and Cancer Screening, Chittaranjan National Cancer Institute, Kolkata, India.
| | | | | | | | | |
Collapse
|
39
|
Jeon FHK, Varghese J, Griffin M, Butler PE, Ghosh D, Mosahebi A. Systematic review of methodologies used to assess mastectomy flap viability. BJS Open 2018; 2:175-184. [PMID: 30079386 PMCID: PMC6069344 DOI: 10.1002/bjs5.61] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 02/22/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Accurate prediction of mastectomy skin flap viability is vital as necrosis causes significant morbidity, potentially compromising results and delaying oncological management. Traditionally assessed by clinical judgement, a more objective evaluation can be provided using intraoperative imaging modalities. This systematic review aimed to compare all intraoperative techniques for assessment of mastectomy flap viability. METHODS A systematic literature review was performed using MEDLINE and Embase databases. Primary outcomes reported included specificity, sensitivity and predictive values of each test, and mean rates of mastectomy flap necrosis and reoperation. Secondary outcomes included cost analysis. RESULTS Some 18 studies were included. Designs were prospective cohort study (8), retrospective case series (4), prospective case series (3), retrospective case-control study (1), prospective pilot trial (1) and cost analysis study (1). The studies compared indocyanine green angiography (ICGA) (16 studies) and fluorescein dye angiography (FA) (3 studies) with clinical judgement. Sensitivity and specificity were highest for ICGA (5 studies) ranging from 38 to 100 and 68 to 91 per cent respectively. Both methods overpredicted necrosis. Mean rates of flap necrosis and reoperation decreased with ICGA (7·9 and 5·5 per cent respectively) and FA (3 and 0 per cent) compared with clinical judgement (19·4 and 12·9 per cent). Two studies were designed to define numerical parameters corresponding to perfusion using intraoperative techniques. Two studies performed a cost analysis for ICGA; one claimed a cost benefit and the other advocated its use in high-risk patients only. CONCLUSION ICGA and FA are potentially useful tools for mastectomy flap assessment. However, the predictive accuracy is subject to the specific settings and model of equipment used. Current recommendations support their use in high-risk patients.
Collapse
Affiliation(s)
- F. H. K. Jeon
- Division of Surgery and Interventional ScienceUniversity College LondonLondonUK
| | - J. Varghese
- Division of Surgery and Interventional ScienceUniversity College LondonLondonUK
- Department of Plastic Surgery, Royal Free HospitalUniversity College LondonLondonUK
| | - M. Griffin
- Division of Surgery and Interventional ScienceUniversity College LondonLondonUK
- Department of Plastic Surgery, Royal Free HospitalUniversity College LondonLondonUK
| | - P. E. Butler
- Division of Surgery and Interventional ScienceUniversity College LondonLondonUK
- Department of Plastic Surgery, Royal Free HospitalUniversity College LondonLondonUK
| | - D. Ghosh
- Division of Surgery and Interventional ScienceUniversity College LondonLondonUK
- Department of Breast Surgery, Royal Free HospitalUniversity College LondonLondonUK
| | - A. Mosahebi
- Division of Surgery and Interventional ScienceUniversity College LondonLondonUK
- Department of Plastic Surgery, Royal Free HospitalUniversity College LondonLondonUK
| |
Collapse
|
40
|
Mohite GM, Navalkar A, Kumar R, Mehra S, Das S, Gadhe LG, Ghosh D, Alias B, Chandrawanshi V, Ramakrishnan A, Mehra S, Maji SK. The Familial α-Synuclein A53E Mutation Enhances Cell Death in Response to Environmental Toxins Due to a Larger Population of Oligomers. Biochemistry 2018; 57:5014-5028. [DOI: 10.1021/acs.biochem.8b00321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ganesh M. Mohite
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Subhadeep Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India 400076
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Laxmikant G. Gadhe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Dhiman Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Basil Alias
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Vikas Chandrawanshi
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Aishwarya Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Sarika Mehra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Samir K. Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| |
Collapse
|
41
|
Kirti S, Patel K, Das S, Shrimali P, Samanta S, Kumar R, Chatterjee D, Ghosh D, Kumar A, Tayalia P, Maji SK. Amyloid Fibrils with Positive Charge Enhance Retroviral Transduction in Mammalian Cells. ACS Biomater Sci Eng 2018; 5:126-138. [DOI: 10.1021/acsbiomaterials.8b00248] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
42
|
Mehra S, Ghosh D, Kumar R, Mondal M, Gadhe LG, Das S, Anoop A, Jha NN, Jacob RS, Chatterjee D, Ray S, Singh N, Kumar A, Maji SK. Glycosaminoglycans have variable effects on α-synuclein aggregation and differentially affect the activities of the resulting amyloid fibrils. J Biol Chem 2018; 293:12975-12991. [PMID: 29959225 DOI: 10.1074/jbc.ra118.004267] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/22/2018] [Indexed: 01/06/2023] Open
Abstract
Parkinson's disease is mainly a sporadic disorder in which both environmental and cellular factors play a major role in the initiation of this disease. Glycosaminoglycans (GAG) are integral components of the extracellular matrix and are known to influence amyloid aggregation of several proteins, including α-synuclein (α-Syn). However, the mechanism by which different GAGs and related biological polymers influence protein aggregation and the structure and intercellular spread of these aggregates remains elusive. In this study, we used three different GAGs and related charged polymers to establish their role in α-Syn aggregation and associated biological activities of these aggregates. Heparin, a representative GAG, affected α-Syn aggregation in a concentration-dependent manner, whereas biphasic α-Syn aggregation kinetics was observed in the presence of chondroitin sulfate B. Of note, as indicated by 2D NMR analysis, different GAGs uniquely modulated α-Syn aggregation because of the diversity of their interactions with soluble α-Syn. Moreover, subtle differences in the GAG backbone structure and charge density significantly altered the properties of the resulting amyloid fibrils. Each GAG/polymer facilitated the formation of morphologically and structurally distinct α-Syn amyloids, which not only displayed variable levels of cytotoxicity but also exhibited an altered ability to internalize into cells. Our study supports the role of GAGs as key modulators in α-Syn amyloid formation, and their distinct activities may regulate amyloidogenesis depending on the type of GAG being up- or down-regulated in vivo.
Collapse
Affiliation(s)
- Surabhi Mehra
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| | - Dhiman Ghosh
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| | - Rakesh Kumar
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| | - Mrityunjoy Mondal
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| | - Laxmikant G Gadhe
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| | - Subhadeep Das
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and.,the IITB-Monash Research Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arunagiri Anoop
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| | - Narendra N Jha
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| | - Reeba S Jacob
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| | - Debdeep Chatterjee
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| | - Soumik Ray
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| | - Nitu Singh
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| | - Ashutosh Kumar
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| | - Samir K Maji
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India and
| |
Collapse
|
43
|
Ghosh D, Clay C, Bernstein JA. The utility of monitoring trimellitic anhydride (TMA)-specific IgG to predict IgE-mediated sensitization in an immunosurveillance program. Allergy 2018; 73:1075-1083. [PMID: 29117440 DOI: 10.1111/all.13348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2017] [Indexed: 01/27/2023]
Abstract
BACKGROUND Workplace exposure to trimellitic anhydride (TMA) can elicit TMA-specific IgE (sIgE), which may lead to occupational asthma (OA). An occupational immunosurveillance program (OISP) has been implemented to monitor TMA exposure and immunologic outcomes. The purpose of this study was to determine whether TMA-specific IgG (sIgG) responses can discriminate between TMA-exposed workers with and without sIgE responses. METHODS Serum TMA-specific antibody (IgG, IgG4, and IgE) levels were estimated longitudinally (years 2006 to 2014) in TMA-exposed workers recruited in low, medium, and high exposure areas. sIgG and sIgE titers plotted against exposure duration were compared between workers with (a) sIgG only and (b) with sIgG who developed sIgE. RESULTS Among 92 TMA-exposed workers continuously monitored for sIgG and sIgE, 38 developed sIgG; 11 developed a sIgE response 342.38 ± 186.03 days posthire and were removed from exposure. The average detection time of sIgG in removed workers (159 ± 92 days) was significantly shorter than for actively exposed workers with only sIgG (346 ± 187 days). Workers with earlier sIgG responses of higher titer (mean value 42.25 μg/mL) compared to delayed responders with lower sIgG titers (mean value 14.79 μg/mL) more frequently developed sIgE responses. Hierarchical clustering showed the initial magnitude and exposure time required for detectable sIgG production discriminated between workers with only sIgG from workers who subsequently produced sIgE. CONCLUSIONS This study demonstrates the utility of longitudinally monitoring TMA-specific antibodies in an OISP as exposed workers with early sIgG responses and of higher magnitude are more likely to develop TMA sIgE sensitization.
Collapse
Affiliation(s)
- D. Ghosh
- Division of Immunology/Allergy Section; Department of Internal Medicine; University of Cincinnati College of Medicine; Cincinnati OH USA
| | - C. Clay
- Division of Immunology/Allergy Section; Department of Internal Medicine; University of Cincinnati College of Medicine; Cincinnati OH USA
| | - J. A. Bernstein
- Division of Immunology/Allergy Section; Department of Internal Medicine; University of Cincinnati College of Medicine; Cincinnati OH USA
| |
Collapse
|
44
|
Bhattacharya D, Ghosh D, Bhattacharya S, Sarkar S, Karmakar P, Koley H, Gachhui R. Antibacterial activity of polyphenolic fraction of Kombucha against Vibrio cholerae: targeting cell membrane. Lett Appl Microbiol 2018; 66:145-152. [PMID: 29193174 DOI: 10.1111/lam.12829] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/22/2017] [Accepted: 11/23/2017] [Indexed: 11/28/2022]
Abstract
The present study was undertaken to determine the mechanism of antibacterial activity of a polyphenolic fraction, composed of mainly catechin and isorhamnetin, previously isolated from Kombucha, a 14-day fermented beverage of sugared black tea, against the enteropathogen Vibrio cholerae N16961. Bacterial growth was found to be seriously impaired by the polyphenolic fraction in a dose-dependent manner. Scanning Electron Microscopy demonstrated morphological alterations in bacterial cells when exposed to the polyphenolic fraction in a concentration-dependent manner. Permeabilization assays confirmed that the fraction disrupted bacterial membrane integrity in both time- and dose-dependent manners, which were proportional to the production of intracellular reactive oxygen species (ROS). Furthermore, each of the polyphenols catechin and isorhamnetin showed the ability to permeate bacterial cell membranes by generating oxidative stress, thereby suggesting their role in the antibacterial potential of Kombucha. Thus, the basic mechanism of antibacterial activity of the Kombucha polyphenolic fraction against V. cholerae involved bacterial membrane permeabilization and morphological changes, which might be due to the generation of intracellular ROS. To the best of our knowledge, this is the first report on the investigation of antibacterial mechanism of Kombucha, which is mostly attributed to its polyphenolic content. SIGNIFICANCE AND IMPACT OF THE STUDY The emergence of multidrug-resistant Vibrio cholerae strains has hindered an efficient anti-Vibrio therapy. This study has demonstrated the membrane damage-mediated antibacterial mechanism of Kombucha, a popular fermented beverage of sugared tea, which is mostly attributed to its polyphenolic content. This study also implies the exploitation of Kombucha as a potential new source of bioactive polyphenols against V. cholerae.
Collapse
Affiliation(s)
- D Bhattacharya
- Department of Life Science & Biotechnology, Jadavpur University, Kolkata, India
| | - D Ghosh
- Department of Life Science & Biotechnology, Jadavpur University, Kolkata, India
| | - S Bhattacharya
- Department of Life Science & Biotechnology, Jadavpur University, Kolkata, India
| | - S Sarkar
- Department of Life Science & Biotechnology, Jadavpur University, Kolkata, India
| | - P Karmakar
- Department of Life Science & Biotechnology, Jadavpur University, Kolkata, India
| | - H Koley
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases (NICED), Beliaghata, Kolkata, India
| | - R Gachhui
- Department of Life Science & Biotechnology, Jadavpur University, Kolkata, India
| |
Collapse
|
45
|
Ghosh D, Biswas JK. Impact of Jute Retting on Physicochemical Profile of Chhariganga Oxbow Lake in Nadia District, West Bengal, India. ACTA ACUST UNITED AC 2018. [DOI: 10.26832/24566632.2018.030104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
46
|
Jha NN, Ranganathan S, Kumar R, Mehra S, Panigrahi R, Navalkar A, Ghosh D, Kumar A, Padinhateeri R, Maji SK. Complexation of NAC-Derived Peptide Ligands with the C-Terminus of α-Synuclein Accelerates Its Aggregation. Biochemistry 2018; 57:791-804. [DOI: 10.1021/acs.biochem.7b01090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Narendra Nath Jha
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | | | - Rakesh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Rajlaxmi Panigrahi
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Dhiman Ghosh
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | | | - Samir K. Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| |
Collapse
|
47
|
Jha NN, Kumar R, Panigrahi R, Navalkar A, Ghosh D, Sahay S, Mondal M, Kumar A, Maji SK. Comparison of α-Synuclein Fibril Inhibition by Four Different Amyloid Inhibitors. ACS Chem Neurosci 2017; 8:2722-2733. [PMID: 28872299 DOI: 10.1021/acschemneuro.7b00261] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aggregation of α-synuclein (α-Syn) into toxic oligomers and fibrils leads to Parkinson's disease (PD) pathogenesis. Molecules that can inhibit the fibrillization and oligomerization of α-Syn have potential therapeutic value. Here, we studied four selective amyloid inhibitors: dopamine (Dopa), amphotericin-B (Amph), epigallocatechingallate (EGCG), and quinacrinedihydrochloride (Quin) for their effect on oligomerization, fibrillization, and preformed fibrils of α-Syn. The aggregation kinetics of α-Syn using ThT fluorescence and conformational transition by circular dichroism (CD) in the presence and absence of these four compounds suggest that, except Quin, the remaining three molecules inhibit α-Syn aggregation in a concentration dependent manner. Consistent with the aggregation kinetics data, the morphological study of aggregates formed in the presence of these compounds showed corresponding decrease in fibrillar size. The analysis of cell viability using MTT assay showed reduction in toxicity of α-Syn aggregates formed in the presence of these compounds, which also correlates with reduction of exposed hydrophobic surface as studied by ANS binding. Additionally, these inhibitors, except Quin, demonstrated reduction in size as well as the toxicity of oligomeric/fibrillar aggregates of α-Syn. The residue specific interaction to low molecular weight (LMW) species of α-Syn by 2D NMR study revealed that, the region and extent of binding are different for all these molecules. Furthermore, fibril-binding data using SPR suggested that there is no direct relationship between the binding affinity and fibril inhibition by these compounds. The present study suggests that sequence based interaction of small molecules with soluble α-Syn might dictate their inhibition or modulation capacity, which might be helpful in designing modulators of α-Syn aggregation.
Collapse
Affiliation(s)
- Narendra Nath Jha
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Rajlaxmi Panigrahi
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Dhiman Ghosh
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Shruti Sahay
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Mritunjoy Mondal
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Samir. K. Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| |
Collapse
|
48
|
Sahay S, Ghosh D, Singh PK, Maji SK. Alteration of Structure and Aggregation of α-Synuclein by Familial Parkinson's Disease Associated Mutations. Curr Protein Pept Sci 2017; 18:656-676. [PMID: 26972727 DOI: 10.2174/1389203717666160314151706] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/10/2016] [Indexed: 11/22/2022]
Abstract
α-Synuclein (α-Syn) aggregation is directly associated with Parkinson's disease (PD) pathogenesis. In vitro aggregation and in vivo animal model studies of α-Syn recapitulate many features of the disease pathogenesis. Six familial PD associated mutations of α-Syn have been discovered; many of which are associated with early onset PD. Three of PD associated mutations have been shown to accelerate the α-Syn aggregation, whereas other three are shown to delay the aggregation kinetics. The membrane binding studies also suggest that few of these PD mutants strongly bind to synthetic membrane vesicles, while others are shown to have attenuated membrane binding ability. Furthermore, the PD mutations do not drastically alter the toxicity of α-Syn oligomers/fibrils. Although according to recent suggestions that early formed oligomers are the most potent toxic species responsible for PD, only p.A30P mutant is shown to form faster oligomers and delayed conversion from oligomers to fibrils. Therefore, it is difficult to establish a unifying mechanism of how familial PD associated mutations affect the α-Syn structure, aggregation and function for their disease association. It is possible that each PD associated mutation alters α-Syn biology in a unique way, which might be responsible for disease pathogenesis. In this review, we discuss the structure function of α- Syn and how these are altered due to the PD associated mutations and their relationship to disease pathogenesis.
Collapse
Affiliation(s)
- Shruti Sahay
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Dhiman Ghosh
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Pardeep K Singh
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India
| |
Collapse
|
49
|
Ghosh S, Salot S, Sengupta S, Navalkar A, Ghosh D, Jacob R, Das S, Kumar R, Jha NN, Sahay S, Mehra S, Mohite GM, Ghosh SK, Kombrabail M, Krishnamoorthy G, Chaudhari P, Maji SK. p53 amyloid formation leading to its loss of function: implications in cancer pathogenesis. Cell Death Differ 2017; 24. [PMID: 28644435 PMCID: PMC5596421 DOI: 10.1038/cdd.2017.105] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The transcriptional regulator p53 has an essential role in tumor suppression. Almost 50% of human cancers are associated with the loss of p53 functions, where p53 often accumulates in the nucleus as well as in cytoplasm. Although it has been previously suggested that amyloid formation could be a cause of p53 loss-of-function in subset of tumors, the characterization of these amyloids and its structure-function relationship is not yet established. In the current study, we provide several evidences for the presence of p53 amyloid formation (in human and animal cancer tissues); along with its isolation from human cancer tissues and the biophysical characterization of these tissue-derived fibrils. Using amyloid seed of p53 fragment (P8, p53(250-257)), we show that p53 amyloid formation in cells not only leads to its functional inactivation but also transforms it into an oncoprotein. The in vitro studies further show that cancer-associated mutation destabilizes the fold of p53 core domain and also accelerates the aggregation and amyloid formation by this protein. Furthermore, we also show evidence of prion-like cell-to-cell transmission of different p53 amyloid species including full-length p53, which is induced by internalized P8 fibrils. The present study suggests that p53 amyloid formation could be one of the possible cause of p53 loss of function and therefore, inhibiting p53 amyloidogenesis could restore p53 tumor suppressor functions.
Collapse
Affiliation(s)
- Saikat Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shimul Salot
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shinjinee Sengupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Dhiman Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Reeba Jacob
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Subhadeep Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Mumbai, India
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Narendra Nath Jha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shruti Sahay
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ganesh M Mohite
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Santanu K Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Mamata Kombrabail
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Guruswamy Krishnamoorthy
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
- Department of Biotechnology, Anna University, Chennai, India
| | - Pradip Chaudhari
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India. Tel: +91 22 25767774; Fax: +91 2225767760, E-mail:
| |
Collapse
|
50
|
Tomita M, Olewnik A, Ghosh D, Ahrens L, Clark E, Grzebinski K, Haering C. NOVEL ACCURATE APPROACH TOWARD PREDCTING FRAIL OLDER ADULTS’ FALLS WITHIN THREE MONTHS. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.3324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- M.R. Tomita
- Rehabilitation Science, University at Buffalo, Buffalo, New York,
| | - A. Olewnik
- Mechanical Engineering, University at Buffalo, Buffalo, New York
| | - D. Ghosh
- Mechanical Engineering, University at Buffalo, Buffalo, New York
| | - L. Ahrens
- Rehabilitation Science, University at Buffalo, Buffalo, New York,
| | - E. Clark
- Rehabilitation Science, University at Buffalo, Buffalo, New York,
| | - K. Grzebinski
- Rehabilitation Science, University at Buffalo, Buffalo, New York,
| | - C. Haering
- Rehabilitation Science, University at Buffalo, Buffalo, New York,
| |
Collapse
|