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Lipskij A, Arbeitman C, Rojas P, Ojeda-May P, Garcia ME. Dramatic Differences between the Structural Susceptibility of the S1 Pre- and S2 Postfusion States of the SARS-CoV-2 Spike Protein to External Electric Fields Revealed by Molecular Dynamics Simulations. Viruses 2023; 15:2405. [PMID: 38140646 PMCID: PMC10748067 DOI: 10.3390/v15122405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In its prefusion state, the SARS-CoV-2 spike protein (similarly to other class I viral fusion proteins) is metastable, which is considered to be an important feature for optimizing or regulating its functions. After the binding process of its S1 subunit (S1) with ACE2, the spike protein (S) undergoes a dramatic conformational change where S1 splits from the S2 subunit, which then penetrates the membrane of the host cell, promoting the fusion of the viral and cell membranes. This results in the infection of the host cell. In a previous work, we showed-using large-scale molecular dynamics simulations-that the application of external electric fields (EFs) induces drastic changes and damage in the receptor-binding domain (RBD) of the wild-type spike protein, as well of the Alpha, Beta, and Gamma variants, leaving a structure which cannot be recognized anymore by ACE2. In this work, we first extend the study to the Delta and Omicron variants and confirm the high sensitivity and extreme vulnerability of the RBD of the prefusion state of S to moderate EF (as weak as 104 V/m), but, more importantly, we also show that, in contrast, the S2 subunit of the postfusion state of the spike protein does not suffer structural damage even if electric field intensities four orders of magnitude higher are applied. These results provide a solid scientific basis to confirm the connection between the prefusion-state metastability of the SARS-CoV-2 spike protein and its susceptibility to be damaged by EF. After the virus docks to the ACE2 receptor, the stable and robust postfusion conformation develops, which exhibits a similar resistance to EF (damage threshold higher than 108 V/m) like most globular proteins.
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Affiliation(s)
- Alexander Lipskij
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
| | - Claudia Arbeitman
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
- CONICET Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, Buenos Aires C1425FQB, Argentina
- GIBIO-Universidad Tecnológica Nacional-Facultad Regional Buenos Aires, Medrano 951, Buenos Aires C1179AAQ, Argentina
| | - Pablo Rojas
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
| | - Pedro Ojeda-May
- High Performance Computing Center North (HPC2N), Umeå University, S-90187 Umeå, Sweden;
| | - Martin E. Garcia
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
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2
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Begum S, Parvej H, Dalui R, Paul S, Maity S, Sepay N, Afzal M, Chandra Halder U. Structural modulation of insulin by hydrophobic and hydrophilic molecules. RSC Adv 2023; 13:34097-34106. [PMID: 38019994 PMCID: PMC10662218 DOI: 10.1039/d3ra06647a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
In the bloodstream, insulin interacts with various kinds of molecules, which can alter its structure and modulate its function. In this work, we have synthesized two molecules having extremely hydrophilic and hydrophobic side chains. The effects of hydrophilic and hydrophobic molecules on the binding with insulin have been investigated through a multi-spectroscopic approach. We found that hydrophilic molecules have a slightly higher binding affinity towards insulin. Insulin can bind with the hydrophilic molecules as it binds glucose. The high insulin binding affinity of a hydrophobic molecule indicates its dual nature. The hydrophobic molecule binds at the hydrophobic pocket of the insulin surface, where hydrophilic molecules interact at the polar surface of the insulin. Such binding with the hydrophobic molecule perturbs strongly the secondary structure of the insulin much more in comparison to hydrophilic molecules. Therefore, the stability of insulin decreases in the presence of hydrophobic molecules.
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Affiliation(s)
- Shahnaz Begum
- Department of Chemistry, Jadavpur University Kolkata-700032 India
| | - Hasan Parvej
- Department of Chemistry, Jadavpur University Kolkata-700032 India
| | - Ramkrishna Dalui
- Department of Chemistry, Jadavpur University Kolkata-700032 India
| | - Swarnali Paul
- Department of Chemistry, Jadavpur University Kolkata-700032 India
| | - Sanhita Maity
- Department of Chemistry, Jadavpur University Kolkata-700032 India
| | - Nayim Sepay
- Department of Chemistry, Lady Brabourne College Kolkata-700017 India
| | - Mohd Afzal
- Department of Chemistry, College of Science, King Saud University Riyadh 11451 Saudi Arabia
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3
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Tenchurin TK, Sharikov RV, Belousov SI, Streltsov DR, Malakhov SN, Yastremsky EV, Chesnokov YM, Davydova LI, Bogush VG, Chvalun SN. Effect of Recombinant Spidroins Self-Assembly on Rheological Behavior of Their Dispersions and Structure of Electrospun Nanofibrous Materials. Polymers (Basel) 2023; 15:3001. [PMID: 37514391 PMCID: PMC10384844 DOI: 10.3390/polym15143001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The effect of primary amino acid sequence in recombinant spidroins on their spatial organization is crucial for the fabrication of artificial fibers and fibrous materials. This study focuses on the rheological properties of aqueous and alcoholic solutions of recombinant analogs of natural spidroins (rS1/9 and rS2/12), as well as the structure of their films and nanofibrous materials. Non-Newtonian flow behavior of aqueous solutions of these proteins was observed at certain concentrations in contrast to their solutions in hexafluoroisopropanol. The secondary structure of recombinant spidroins was addressed by IR spectroscopy, whereas their self-organization in various solvents was studied by AFM and cryo-TEM. The influence of the solvent on the structure and properties of the films and nanofibrous materials produced by electrospinning has been established.
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Affiliation(s)
| | - Roman V Sharikov
- National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Sergei I Belousov
- National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Dmitry R Streltsov
- National Research Center "Kurchatov Institute", 123182 Moscow, Russia
- Enikolopov Institute of Synthetic Polymeric Materials, Russian Academy of Sciences, 117393 Moscow, Russia
| | - Sergey N Malakhov
- National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Evgeny V Yastremsky
- Shubnikov Institute of Crystallography, Federal Research Center Crystallography and Photonics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Yuri M Chesnokov
- National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Lyubov I Davydova
- National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Vladimir G Bogush
- National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Sergei N Chvalun
- National Research Center "Kurchatov Institute", 123182 Moscow, Russia
- Enikolopov Institute of Synthetic Polymeric Materials, Russian Academy of Sciences, 117393 Moscow, Russia
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4
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Song HK. Quo Vadis Experimental Structural Biology? Mol Cells 2023; 46:71-73. [PMID: 36859471 PMCID: PMC9982055 DOI: 10.14348/molcells.2023.2197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/02/2023] [Accepted: 01/27/2023] [Indexed: 03/03/2023] Open
Affiliation(s)
- Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul 02841, Korea
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5
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Hendeniya N, Hillery K, Chang BS. Processive Pathways to Metastability in Block Copolymer Thin Films. Polymers (Basel) 2023; 15:polym15030498. [PMID: 36771799 PMCID: PMC9920306 DOI: 10.3390/polym15030498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/19/2023] Open
Abstract
Block copolymers (BCPs) self-assemble into intricate nanostructures that enhance a multitude of advanced applications in semiconductor processing, membrane science, nanopatterned coatings, nanocomposites, and battery research. Kinetics and thermodynamics of self-assembly are crucial considerations in controlling the nanostructure of BCP thin films. The equilibrium structure is governed by a molecular architecture and the chemistry of its repeat units. An enormous library of materials has been synthesized and they naturally produce a rich equilibrium phase diagram. Non-equilibrium phases could potentially broaden the structural diversity of BCPs and relax the synthetic burden of creating new molecules. Furthermore, the reliance on synthesis could be complicated by the scalability and the materials compatibility. Non-equilibrium phases in BCPs, however, are less explored, likely due to the challenges in stabilizing the metastable structures. Over the past few decades, a variety of processing techniques were introduced that influence the phase transformation of BCPs to achieve a wide range of morphologies. Nonetheless, there is a knowledge gap on how different processive pathways can induce and control the non-equilibrium phases in BCP thin films. In this review, we focus on different solvent-induced and thermally induced processive pathways, and their potential to control the non-equilibrium phases with regards to their unique aspects and advantages. Furthermore, we elucidate the limitations of these pathways and discuss the potential avenues for future investigations.
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Fang M, Wu O, Cupp-Sutton KA, Smith K, Wu S. Elucidating Protein-Ligand Interactions in Cell Lysates Using High-Throughput Hydrogen-Deuterium Exchange Mass Spectrometry with Integrated Protein Thermal Depletion. Anal Chem 2023; 95:10.1021/acs.analchem.2c04266. [PMID: 36608260 PMCID: PMC10323047 DOI: 10.1021/acs.analchem.2c04266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) is a powerful technique for the characterization of protein-ligand interactions. Currently, there is a growing need for breakthroughs in the application of HDX-MS analysis to protein-ligand interactions in highly complex biological samples such as cell lysates. However, HDX-MS analysis in such systems suffers from extreme spectral complexity as a result of high sample complexity and limited LC separation power due to the traditional use of short LC gradients. Here, we introduced protein thermal depletion (PTD) to reduce protein complexity in E. coli cell lysate for our subzero-temperature long gradient UPLC-HDX-MS platform (PTD-HDX-MS) to facilitate high-throughput analysis of protein-ligand interactions in cell lysates. We spiked bovine carbonic anhydrase II (CaII) and its inhibitor acetazolamide (AZM) into E. coli cell lysate as a model system in our study. We demonstrated that PTD at 60 °C greatly reduces protein complexity in cell lysates, while the AZM-targeted CaII complex remains in solution due to improved thermal stability upon binding. Using both PTD to reduce sample complexity and subzero-temperature long gradient UPLC to boost LC separation power, we successfully elucidated the interaction sites between AZM and CaII in E. coli cell lysate from the high-throughput HDX-MS analysis of thousands of deuterated peptides from hundreds of proteins. Our results highlight the great promise of the PTD-HDX-MS platform for the identification of ligand targets and characterization of protein-ligand interactions in highly complex biological samples such as cell lysates.
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Affiliation(s)
- Mulin Fang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Oliver Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | | | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
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7
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Ebel H, Benecke T, Vollmer B. Stabilisation of Viral Membrane Fusion Proteins in Prefusion Conformation by Structure-Based Design for Structure Determination and Vaccine Development. Viruses 2022; 14:1816. [PMID: 36016438 PMCID: PMC9415420 DOI: 10.3390/v14081816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/08/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
The membrane surface of enveloped viruses contains dedicated proteins enabling the fusion of the viral with the host cell membrane. Working with these proteins is almost always challenging because they are membrane-embedded and naturally metastable. Fortunately, based on a range of different examples, researchers now have several possibilities to tame membrane fusion proteins, making them amenable for structure determination and immunogen generation. This review describes the structural and functional similarities of the different membrane fusion proteins and ways to exploit these features to stabilise them by targeted mutational approaches. The recent determination of two herpesvirus membrane fusion proteins in prefusion conformation holds the potential to apply similar methods to this group of viral fusogens. In addition to a better understanding of the herpesviral fusion mechanism, the structural insights gained will help to find ways to further stabilise these proteins using the methods described to obtain stable immunogens that will form the basis for the development of the next generation of vaccines and antiviral drugs.
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Affiliation(s)
- Henriette Ebel
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany
- Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
- Leibniz Institute of Virology (LIV), 20251 Hamburg, Germany
| | - Tim Benecke
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany
- Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
- Leibniz Institute of Virology (LIV), 20251 Hamburg, Germany
| | - Benjamin Vollmer
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany
- Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
- Leibniz Institute of Virology (LIV), 20251 Hamburg, Germany
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8
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A conserved asparagine residue in the inner surface of BRI1 superhelix is essential for protein native conformation. Biochem Biophys Res Commun 2022; 615:49-55. [DOI: 10.1016/j.bbrc.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/04/2022] [Indexed: 11/19/2022]
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9
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Melo EP, Konno T, Farace I, Awadelkareem MA, Skov LR, Teodoro F, Sancho TP, Paton AW, Paton JC, Fares M, Paulo PMR, Zhang X, Avezov E. Stress-induced protein disaggregation in the endoplasmic reticulum catalysed by BiP. Nat Commun 2022; 13:2501. [PMID: 35523806 PMCID: PMC9076838 DOI: 10.1038/s41467-022-30238-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 04/20/2022] [Indexed: 01/31/2023] Open
Abstract
Protein synthesis is supported by cellular machineries that ensure polypeptides fold to their native conformation, whilst eliminating misfolded, aggregation prone species. Protein aggregation underlies pathologies including neurodegeneration. Aggregates’ formation is antagonised by molecular chaperones, with cytoplasmic machinery resolving insoluble protein aggregates. However, it is unknown whether an analogous disaggregation system exists in the Endoplasmic Reticulum (ER) where ~30% of the proteome is synthesised. Here we show that the ER of a variety of mammalian cell types, including neurons, is endowed with the capability to resolve protein aggregates under stress. Utilising a purpose-developed protein aggregation probing system with a sub-organellar resolution, we observe steady-state aggregate accumulation in the ER. Pharmacological induction of ER stress does not augment aggregates, but rather stimulate their clearance within hours. We show that this dissagregation activity is catalysed by the stress-responsive ER molecular chaperone – BiP. This work reveals a hitherto unknow, non-redundant strand of the proteostasis-restorative ER stress response. Aggregation of misfolded proteins underlie dementias. Here, the authors show that stressed cells activate an innate mechanism to resolve aggregates of defective proteins in the endoplasmic reticulum, where a third of cellular proteins are produced.
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Affiliation(s)
- Eduardo Pinho Melo
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge, UK. .,CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, Faro, Portugal.
| | - Tasuku Konno
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Ilaria Farace
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Mosab Ali Awadelkareem
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Lise R Skov
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Fernando Teodoro
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Teresa P Sancho
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Adrienne W Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Matthew Fares
- Department of Chemistry, The Pennsylvania State University, University Park, State College, PA, USA
| | - Pedro M R Paulo
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, Lisboa, Portugal
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, State College, PA, USA
| | - Edward Avezov
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge, UK.
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10
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Parray ZA, Shahid M, Islam A. Insights into Fluctuations of Structure of Proteins: Significance of Intermediary States in Regulating Biological Functions. Polymers (Basel) 2022; 14:polym14081539. [PMID: 35458289 PMCID: PMC9025146 DOI: 10.3390/polym14081539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/30/2022] [Accepted: 04/05/2022] [Indexed: 02/01/2023] Open
Abstract
Proteins are indispensable to cellular communication and metabolism. The structure on which cells and tissues are developed is deciphered from proteins. To perform functions, proteins fold into a three-dimensional structural design, which is specific and fundamentally determined by their characteristic sequence of amino acids. Few of them have structural versatility, allowing them to adapt their shape to the task at hand. The intermediate states appear momentarily, while protein folds from denatured (D) ⇔ native (N), which plays significant roles in cellular functions. Prolific effort needs to be taken in characterizing these intermediate species if detected during the folding process. Protein folds into its native structure through definite pathways, which involve a limited number of transitory intermediates. Intermediates may be essential in protein folding pathways and assembly in some cases, as well as misfolding and aggregation folding pathways. These intermediate states help to understand the machinery of proper folding in proteins. In this review article, we highlight the various intermediate states observed and characterized so far under in vitro conditions. Moreover, the role and significance of intermediates in regulating the biological function of cells are discussed clearly.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
- Department of Chemistry, Indian Institute of Technology Delhi, IIT Campus, Hauz Khas, New Delhi 110016, India
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, Al Kharj 11942, Saudi Arabia;
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
- Correspondence: ; Tel.: +91-93-1281-2007
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11
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Chetri PB, Shukla R, Khan JM, Padhi AK, Tripathi T. Unraveling the structural basis of urea-induced unfolding of Fasciola gigantica cytosolic malate dehydrogenase. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Multifunctionality of prostatic acid phosphatase in prostate cancer pathogenesis. Biosci Rep 2021; 41:229977. [PMID: 34677582 PMCID: PMC8536833 DOI: 10.1042/bsr20211646] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/18/2021] [Accepted: 10/04/2021] [Indexed: 11/24/2022] Open
Abstract
The role of human prostatic acid phosphatase (PAcP, P15309|PPAP_HUMAN) in prostate cancer was investigated using a new proteomics tool termed signal sequence swapping (replacement of domains from the native cleaved amino terminal signal sequence of secretory/membrane proteins with corresponding regions of functionally distinct signal sequence subtypes). This manipulation preferentially redirects proteins to different pathways of biogenesis at the endoplasmic reticulum (ER), magnifying normally difficult to detect subsets of the protein of interest. For PAcP, this technique reveals three forms identical in amino acid sequence but profoundly different in physiological functions, subcellular location, and biochemical properties. These three forms of PAcP can also occur with the wildtype PAcP signal sequence. Clinical specimens from patients with prostate cancer demonstrate that one form, termed PLPAcP, correlates with early prostate cancer. These findings confirm the analytical power of this method, implicate PLPAcP in prostate cancer pathogenesis, and suggest novel anticancer therapeutic strategies.
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Kumar A, Ghosh DK, Ranjan A. Differential Stabilities of Mefloquine-Bound Human and Plasmodium falciparum Acyl-CoA-Binding Proteins. ACS OMEGA 2021; 6:1883-1893. [PMID: 33521428 PMCID: PMC7841788 DOI: 10.1021/acsomega.0c04582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/01/2020] [Indexed: 05/03/2023]
Abstract
Toxic effects of pharmacological drugs restrict their robust application against human diseases. Although used as a drug in the combinatorial therapy to treat malaria, the use of mefloquine is not highly recommended because of its adverse effects in humans. Mefloquine inhibits the binding of acyl-CoAs to acyl-CoA-binding proteins of Plasmodium falciparum (PfACBPs) and human (hACBP). In this study, we have used molecular dynamics simulation and other computational approaches to investigate the differences of stabilities of mefloquine-PfACBP749 and mefloquine-hACBP complexes. The stability of mefloquine in the binding cavity of PfACBP749 is less than its stability in the binding pocket of hACBP. Although the essential tyrosine residues (tyrosine-30 and tyrosine-33 of PfACBP749 and tyrosine-29 and tyrosine-32 of hACBP) mediate the initial binding of mefloquine to the proteins by π-stacking interactions, additional temporally longer interactions between mefloquine and aspartate-22 and methionine-25 of hACBP result in stronger binding of mefloquine to hACBP. The higher fluctuation of mefloquine-binding residues of PfACBP749 contributes to the instability of mefloquine in the binding cavity of the protein. On the contrary, in the mefloquine-bound state, the stability of hACBP protein is less than the stability of PfACBP749. The helix-to-coil transition of the N-terminal hydrophobic region of hACBP has a destabilizing effect upon the protein's structure. This causes the induction of aggregation properties in the hACBP in the mefloquine-bound state. Taken together, we describe the mechanistic features that affect the differential dynamic stabilities of mefloquine-bound PfACBP749 and hACBP proteins.
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Affiliation(s)
- Abhishek Kumar
- Computational
and Functional Genomics Group, Centre for
DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana 500039, India
- Graduate
Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Debasish Kumar Ghosh
- Computational
and Functional Genomics Group, Centre for
DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana 500039, India
| | - Akash Ranjan
- Computational
and Functional Genomics Group, Centre for
DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana 500039, India
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14
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Ghosh DK, Ranjan A. The metastable states of proteins. Protein Sci 2020; 29:1559-1568. [PMID: 32223005 PMCID: PMC7314396 DOI: 10.1002/pro.3859] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/26/2022]
Abstract
The intriguing process of protein folding comprises discrete steps that stabilize the protein molecules in different conformations. The metastable state of protein is represented by specific conformational characteristics, which place the protein in a local free energy minimum state of the energy landscape. The native-to-metastable structural transitions are governed by transient or long-lived thermodynamic and kinetic fluctuations of the intrinsic interactions of the protein molecules. Depiction of the structural and functional properties of metastable proteins is not only required to understand the complexity of folding patterns but also to comprehend the mechanisms of anomalous aggregation of different proteins. In this article, we review the properties of metastable proteins in context of their stability and capability of undergoing atypical aggregation in physiological conditions.
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Affiliation(s)
- Debasish Kumar Ghosh
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and DiagnosticsUppal, HyderabadTelanganaIndia
| | - Akash Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and DiagnosticsUppal, HyderabadTelanganaIndia
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