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Lebek T, Malaguti M, Boezio GL, Zoupi L, Briscoe J, Elfick A, Lowell S. PUFFFIN: an ultra-bright, customisable, single-plasmid system for labelling cell neighbourhoods. EMBO J 2024; 43:4110-4135. [PMID: 38997504 PMCID: PMC11405414 DOI: 10.1038/s44318-024-00154-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 07/14/2024] Open
Abstract
Cell communication coordinates developmental processes, maintains homeostasis, and contributes to disease. Therefore, understanding the relationship between cells in a shared environment is crucial. Here we introduce Positive Ultra-bright Fluorescent Fusion For Identifying Neighbours (PUFFFIN), a cell neighbour-labelling system based upon secretion and uptake of positively supercharged fluorescent protein s36GFP. We fused s36GFP to mNeonGreen or to a HaloTag, facilitating ultra-bright, sensitive, colour-of-choice labelling. Secretor cells transfer PUFFFIN to neighbours while retaining nuclear mCherry, making identification, isolation, and investigation of live neighbours straightforward. PUFFFIN can be delivered to cells, tissues, or embryos on a customisable single-plasmid construct composed of interchangeable components with the option to incorporate any transgene. This versatility enables the manipulation of cell properties, while simultaneously labelling surrounding cells, in cell culture or in vivo. We use PUFFFIN to ask whether pluripotent cells adjust the pace of differentiation to synchronise with their neighbours during exit from naïve pluripotency. PUFFFIN offers a simple, sensitive, customisable approach to profile non-cell-autonomous responses to natural or induced changes in cell identity or behaviour.
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Affiliation(s)
- Tamina Lebek
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Mattias Malaguti
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH16 4UU, UK
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3FF, UK
| | | | - Lida Zoupi
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
- Simons Initiative for the Developing Brain, The University of Edinburgh, Edinburgh, EH8 9XD, UK
| | | | - Alistair Elfick
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, EH8 3DW, UK
- UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Sally Lowell
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH16 4UU, UK.
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2
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Hristova SH, Zhivkov AM. Intermolecular Electrostatic Interactions in Cytochrome c Protein Monolayer on Montmorillonite Alumosilicate Surface: A Positive Cooperative Effect. Int J Mol Sci 2024; 25:6834. [PMID: 38999945 PMCID: PMC11241403 DOI: 10.3390/ijms25136834] [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: 05/07/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024] Open
Abstract
Montmorillonite (MM) crystal nanoplates acquire anticancer properties when coated with the mitochondrial protein cytochrome c (cytC) due to the cancer cells' capability to phagocytize cytC-MM colloid particles. The introduced exogenous cytC initiates apoptosis: an irreversible cascade of biochemical reactions leading to cell death. In the present research, we investigate the organization of the cytC layer on the MM surface by employing physicochemical and computer methods-microelectrophoresis, static, and electric light scattering-to study cytC adsorption on the MM surface, and protein electrostatics and docking to calculate the local electric potential and Gibbs free energy of interacting protein globules. The found protein concentration dependence of the adsorbed cytC quantity is nonlinear, manifesting a positive cooperative effect that emerges when the adsorbed cytC globules occupy more than one-third of the MM surface. Computer analysis reveals that the cooperative effect is caused by the formation of protein associates in which the cytC globules are oriented with oppositely charged surfaces. The formation of dimers and trimers is accompanied by a strong reduction in the electrostatic component of the Gibbs free energy of protein association, while the van der Waals component plays a secondary role.
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Affiliation(s)
- Svetlana H Hristova
- Department of Medical Physics and Biophysics, Medical Faculty, Medical University-Sofia, Zdrave Str. 2, 1431 Sofia, Bulgaria
| | - Alexandar M Zhivkov
- Scientific Research Center, "St. Kliment Ohridski" Sofia University, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria
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3
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Barati F, Hosseini F, Vafaee R, Sabouri Z, Ghadam P, Arab SS, Shadfar N, Piroozmand F. In silico approaches to investigate enzyme immobilization: a comprehensive systematic review. Phys Chem Chem Phys 2024; 26:5744-5761. [PMID: 38294035 DOI: 10.1039/d3cp03989g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Enzymes are popular catalysts with many applications, especially in industry. Biocatalyst usage on a large scale is facing some limitations, such as low operational stability, low recyclability, and high enzyme cost. Enzyme immobilization is a beneficial strategy to solve these problems. Bioinformatics tools can often correctly predict immobilization outcomes, resulting in a cost-effective experimental phase with the least time consumed. This study provides an overview of in silico methods predicting immobilization processes via a comprehensive systematic review of published articles till 11 December 2022. It also mentions the strengths and weaknesses of the processes and explains the computational analyses in each method that are required for immobilization assessment. In this regard, Web of Science and Scopus databases were screened to gain relevant publications. After screening the gathered documents (n = 3873), 60 articles were selected for the review. The selected papers have applied in silico procedures including only molecular dynamics (MD) simulations (n = 20), parallel tempering Monte Carlo (PTMC) and MD simulations (n = 3), MD and docking (n = 1), density functional theory (DFT) and MD (n = 1), only docking (n = 11), metal ion binding site prediction (MIB) server and docking (n = 2), docking and DFT (n = 1), docking and analysis of enzyme surfaces (n = 1), only DFT (n = 1), only MIB server (n = 2), analysis of an enzyme structure and surface (n = 12), rational design of immobilized derivatives (RDID) software (n = 3), and dissipative particle dynamics (DPD; n = 2). In most included studies (n = 51), enzyme immobilization was investigated experimentally in addition to in silico evaluation.
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Affiliation(s)
- Farzaneh Barati
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Fakhrisadat Hosseini
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Rayeheh Vafaee
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zahra Sabouri
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Parinaz Ghadam
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Najmeh Shadfar
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Firoozeh Piroozmand
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
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4
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Hristova SH, Zhivkov AM. Three-Dimensional Structural Stability and Local Electrostatic Potential at Point Mutations in Spike Protein of SARS-CoV-2 Coronavirus. Int J Mol Sci 2024; 25:2174. [PMID: 38396850 PMCID: PMC10889838 DOI: 10.3390/ijms25042174] [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: 01/17/2024] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
The contagiousness of SARS-CoV-2 β-coronavirus is determined by the virus-receptor electrostatic association of its positively charged spike (S) protein with the negatively charged angiotensin converting enzyme-2 (ACE2 receptor) of the epithelial cells. If some mutations occur, the electrostatic potential on the surface of the receptor-binding domain (RBD) could be altered, and the S-ACE2 association could become stronger or weaker. The aim of the current research is to investigate whether point mutations can noticeably alter the electrostatic potential on the RBD and the 3D stability of the S1-subunit of the S-protein. For this purpose, 15 mutants with different hydrophilicity and electric charge (positive, negative, or uncharged) of the substituted and substituting amino acid residues, located on the RBD at the S1-ACE2 interface, are selected, and the 3D structure of the S1-subunit is reconstructed on the base of the crystallographic structure of the S-protein of the wild-type strain and the amino acid sequence of the unfolded polypeptide chain of the mutants. Then, the Gibbs free energy of folding, isoelectric point, and pH-dependent surface electrostatic potential of the S1-subunit are computed using programs for protein electrostatics. The results show alterations in the local electrostatic potential in the vicinity of the mutant amino acid residue, which can influence the S-ACE2 association. This approach allows prediction of the relative infectivity, transmissibility, and contagiousness (at equal social immune status) of new SARS-CoV-2 mutants by reconstruction of the 3D structure of the S1-subunit and calculation of the surface electrostatic potential.
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Affiliation(s)
- Svetlana H. Hristova
- Department of Medical Physics and Biophysics, Medical Faculty, Medical University—Sofia, Zdrave Street 2, 1431 Sofia, Bulgaria;
| | - Alexandar M. Zhivkov
- Scientific Research Center, “St. Kliment Ohridski” Sofia University, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria
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5
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Willard D, Arellano JJ, Underdahl M, Lee TM, Ramaswamy AS, Fumes G, Kliman A, Wong EY, Owens CP. Mutational Analysis of the Nitrogenase Carbon Monoxide Protective Protein CowN Reveals That a Conserved C-Terminal Glutamic Acid Residue Is Necessary for Its Activity. Biochemistry 2024; 63:152-158. [PMID: 38091601 PMCID: PMC10765410 DOI: 10.1021/acs.biochem.3c00421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
Nitrogenase is the only enzyme that catalyzes the reduction of nitrogen gas into ammonia. Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Many nitrogen fixing bacteria protect nitrogenase from CO inhibition using the protective protein CowN. This work demonstrates that a conserved glutamic acid residue near the C-terminus of Gluconacetobacter diazotrophicus CowN is necessary for its function. Mutation of the glutamic acid residue abolishes both CowN's protection against CO inhibition and the ability of CowN to bind to nitrogenase. In contrast, a conserved C-terminal cysteine residue is not important for CO protection by CowN. Overall, this work uncovers structural features in CowN that are required for its function and provides new insights into its nitrogenase binding and CO protection mechanism.
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Affiliation(s)
- Dustin
L. Willard
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Joshuah J. Arellano
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Mitch Underdahl
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Terrence M. Lee
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Avinash S. Ramaswamy
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Gabriella Fumes
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Agatha Kliman
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Emily Y. Wong
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Cedric P. Owens
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
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6
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Hristova SH, Zhivkov AM. Omicron Coronavirus: pH-Dependent Electrostatic Potential and Energy of Association of Spike Protein to ACE2 Receptor. Viruses 2023; 15:1752. [PMID: 37632094 PMCID: PMC10460073 DOI: 10.3390/v15081752] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The association of the S-protein of the SARS-CoV-2 beta coronavirus to ACE2 receptors of the human epithelial cells determines its contagiousness and pathogenicity. We computed the pH-dependent electric potential on the surface of the interacting globular proteins and pH-dependent Gibbs free energy at the association of the wild-type strain and the omicron variant. The calculated isoelectric points of the ACE2 receptor (pI 5.4) and the S-protein in trimeric form (pI 7.3, wild type), (pI 7.8, omicron variant), experimentally verified by isoelectric focusing, show that at pH 6-7, the S1-ACE2 association is conditioned by electrostatic attraction of the oppositely charged receptor and viral protein. The comparison of the local electrostatic potentials of the omicron variant and the wild-type strain shows that the point mutations alter the electrostatic potential in a relatively small area on the surface of the receptor-binding domain (RBD) of the S1 subunit. The appearance of seven charge-changing point mutations in RBD (equivalent to three additional positive charges) leads to a stronger S1-ACE2 association at pH 5.5 (typical for the respiratory tract) and a weaker one at pH 7.4 (characteristic of the blood plasma); this reveals the reason for the higher contagiousness but lower pathogenicity of the omicron variant in comparison to the wild-type strain.
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Affiliation(s)
- Svetlana H. Hristova
- Department of Medical Physics and Biophysics, Medical Faculty, Medical University—Sofia, Zdrave Str. 2, 1431 Sofia, Bulgaria;
| | - Alexandar M. Zhivkov
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 11, 1113 Sofia, Bulgaria
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Qazi S, Khanna K, Raza K. Dihydroquercetin (DHQ) has the potential to promote apoptosis in ovarian cancer cells: An in silico and in vitro study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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Bibi N, Farid A, Gul S, Ali J, Amin F, Kalthiya U, Hupp T. Drug repositioning against COVID-19: a first line treatment. J Biomol Struct Dyn 2022; 40:12812-12826. [PMID: 34519259 PMCID: PMC8442756 DOI: 10.1080/07391102.2021.1977698] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
COVID-19 disease caused by the SARS-CoV-2 virus has shaken our health and wealth foundations. Although COVID-19 vaccines will become available allowing for attenuation of disease progression rates, distribution of vaccines can create other challenges and delays. Hence repurposed drugs against SARS-CoV-2 can be an attractive parallel strategy that can be integrated into routine clinical practice even in poorly-resourced countries. The present study was designed using knowledge of viral pathogenesis and pharmacodynamics of broad-spectrum antiviral agents (BSAAs). We carried out the virtual screening of BSAAs against the SARS-CoV-2 spike glycoprotein, RNA dependent RNA polymerase (RdRp), the main protease (Mpro) and the helicase enzyme of SARS-CoV-2. Imatinib (a tyrosine kinase inhibitor), Suramin (an anti-parasitic), Glycyrrhizin (an anti-inflammatory) and Bromocriptine (a dopamine agonist) showed higher binding affinity to multiple targets. Further through molecular dynamics simulation, critical conformational changes in the target protein molecules were revealed upon drug binding which illustrates the favorable binding conformations of antiviral drugs against SARS-CoV-2 target proteins. The resulting drugs from the present study in combination and in cocktails from the arsenal of existing drugs could reduce the translational distance and could offer substantial clinical benefit to decrease the burden of COVID-19 illness. This also creates a roadmap for subsequent viral diseases that emerge.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nousheen Bibi
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan,CONTACT Nousheen Bibi ; Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Ayesha Farid
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Sana Gul
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Johar Ali
- Center for Genomics Sciences RMI, Peshawar, Pakistan
| | - Farhat Amin
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Umesh Kalthiya
- International Center for Cancer Vaccine Science, Gdańsk, Poland
| | - Ted Hupp
- International Center for Cancer Vaccine Science, Gdańsk, Poland,Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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9
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Spontaneous and Electrically Induced Anisotropy of Composite Agarose Gels. Gels 2022; 8:gels8110753. [DOI: 10.3390/gels8110753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/22/2022] Open
Abstract
Agarose gels containing and not bacteriorhodopsin purple membranes (incorporated before gelling) manifest spontaneous optical anisotropy. The dependencies of the anisotropy on the agarose concentration and time have been studied. The rise in the anisotropy is explained by the predominant orientation of the agarose fibers during the gelling and subsequent deformation of the gel net. In the electric field, additional optical anisotropy rises, which is caused by the orientation of the membranes. A procedure has been developed to separate electrically induced and spontaneous anisotropy in composite gels. The isoelectric points and surface electric potential of bacteriorhodopsin trimer and purple membranes are calculated by the method of protein electrostatics to explain their electric asymmetry, which leads to perpendicular orientation in the direct electric field and longitudinal in the kilohertz sinusoidal field. The results allow for an increase in the separation capability of composite gels of electrophoresis for macromolecules with different sizes by applying an appropriate electric field to modulate the effective pore size.
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Qazi S, Jit BP, Das A, Karthikeyan M, Saxena A, Ray M, Singh AR, Raza K, Jayaram B, Sharma A. BESFA: bioinformatics based evolutionary, structural & functional analysis of prostrate, Placenta, Ovary, Testis, and Embryo (POTE) paralogs. Heliyon 2022; 8:e10476. [PMID: 36132183 PMCID: PMC9483601 DOI: 10.1016/j.heliyon.2022.e10476] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/25/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022] Open
Abstract
The POTE family comprises 14 paralogues and is primarily expressed in Prostrate, Placenta, Ovary, Testis, Embryo (POTE), and cancerous cells. The prospective function of the POTE protein family under physiological conditions is less understood. We systematically analyzed their cellular localization and molecular docking analysis to elucidate POTE proteins' structure, function, and Adaptive Divergence. Our results suggest that group three POTE paralogs (POTEE, POTEF, POTEI, POTEJ, and POTEKP (a pseudogene)) exhibits significant variation among other members could be because of their Adaptive Divergence. Furthermore, our molecular docking studies on POTE protein revealed the highest binding affinity with NCI-approved anticancer compounds. Additionally, POTEE, POTEF, POTEI, and POTEJ were subject to an explicit molecular dynamic simulation for 50ns. MM-GBSA and other essential electrostatics were calculated that showcased that only POTEE and POTEF have absolute binding affinities with minimum energy exploitation. Thus, this study’s outcomes are expected to drive cancer research to successful utilization of POTE genes family as a new biomarker, which could pave the way for the discovery of new therapies.
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Affiliation(s)
- Sahar Qazi
- Department of Biochemistry, All India Institute of Medical Sciences, Delhi 110029, India
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - Bimal Prasad Jit
- Department of Biochemistry, All India Institute of Medical Sciences, Delhi 110029, India
| | - Abhishek Das
- Department of Biochemistry, All India Institute of Medical Sciences, Delhi 110029, India
| | - Muthukumarasamy Karthikeyan
- National Chemical Laboratory, Council of Scientific and Industrial Research (NCL-CSIR), Pune, Maharashtra, India
| | - Amit Saxena
- Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - M.D. Ray
- Dr. B.R.A Institute-Rotary Cancer Hospital, All India Institute of Medical Sciences, Delhi 110029, India
| | - Angel Rajan Singh
- Dr. B.R.A Institute-Rotary Cancer Hospital, All India Institute of Medical Sciences, Delhi 110029, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - B. Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Delhi, India
| | - Ashok Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Delhi 110029, India
- Corresponding author.
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11
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Moharana M, Pattanayak SK, Khan F. Computational efforts to identify natural occurring compounds from phyllanthus niruri that target hepatitis B viral infections: DFT, docking and dynamics simulation study. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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12
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Hou J, Bhat AM, Ahmad S, Raza K, Qazi S. In silico Analysis of ACE2 Receptor to Find Potential Herbal Drugs in COVID-19 Associated Neurological Dysfunctions. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221118549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
COVID-19 mainly causes the collapse of the pulmonary system thereby causing a dearth of oxygen in the human body. Patients infected with this viral disease have been reported to experience various signs and symptoms associated with brain dysfunction, from the feeling of vagueness to loss of smell and taste to severe strokes. These neurological problems have been reported by younger COVID-19 infected patients mainly in their thirties and forties. Various researchers from around the globe have discerned numerous other brain dysfunctions, such as headache, dizziness, numbness, major depressive disorder, anosmia, encephalitis, febrile seizures, and Guillain-Barre syndrome. The involvement of the CNS by this viral infection has been predicted to be for a longer period of time, even if the patient recovers from COVID-19. The neuronal cell damage caused by COVID-19 is a potent factor responsible for cognitive, behavioral, and psychological problems among its sufferers. The hypoxic conditions can also trigger the formation of beta-amyloid plaques and tau-tangles and thus the virus can even induce Alzheimer’s in patients in the near future. The virus affects the brain directly, thereby causing encephalitis. This pandemic has also been shown to have a negative psychological toll on people. This research aims to highlight the brain dysfunction associated with the ACE2 receptor that is known to be a crucial player in the COVID-19 pandemic using genetic networking approaches. Furthermore, we have identified herbal drug candidates that bind to the ACE2 receptor in order to identify potential treatments for the neurological manifestations of COVID-19.
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Affiliation(s)
- Juan Hou
- Songjiang Hospital Affiliated to Shanghai Jiaotong, University School of Medicine (Preparatory Stage), Shanghai, China
| | - Adil Manzoor Bhat
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Shaban Ahmad
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Sahar Qazi
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
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13
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Badonyi M, Marsh JA. Large protein complex interfaces have evolved to promote cotranslational assembly. eLife 2022; 11:79602. [PMID: 35899946 PMCID: PMC9365393 DOI: 10.7554/elife.79602] [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: 04/20/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Assembly pathways of protein complexes should be precise and efficient to minimise misfolding and unwanted interactions with other proteins in the cell. One way to achieve this efficiency is by seeding assembly pathways during translation via the cotranslational assembly of subunits. While recent evidence suggests that such cotranslational assembly is widespread, little is known about the properties of protein complexes associated with the phenomenon. Here, using a combination of proteome-specific protein complex structures and publicly available ribosome profiling data, we show that cotranslational assembly is particularly common between subunits that form large intermolecular interfaces. To test whether large interfaces have evolved to promote cotranslational assembly, as opposed to cotranslational assembly being a non-adaptive consequence of large interfaces, we compared the sizes of first and last translated interfaces of heteromeric subunits in bacterial, yeast, and human complexes. When considering all together, we observe the N-terminal interface to be larger than the C-terminal interface 54% of the time, increasing to 64% when we exclude subunits with only small interfaces, which are unlikely to cotranslationally assemble. This strongly suggests that large interfaces have evolved as a means to maximise the chance of successful cotranslational subunit binding.
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Affiliation(s)
- Mihaly Badonyi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
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14
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Fusto A, Cassandrini D, Fiorillo C, Codemo V, Astrea G, D’Amico A, Maggi L, Magri F, Pane M, Tasca G, Sabbatini D, Bello L, Battini R, Bernasconi P, Fattori F, Bertini ES, Comi G, Messina S, Mongini T, Moroni I, Panicucci C, Berardinelli A, Donati A, Nigro V, Pini A, Giannotta M, Dosi C, Ricci E, Mercuri E, Minervini G, Tosatto S, Santorelli F, Bruno C, Pegoraro E. Expanding the clinical-pathological and genetic spectrum of RYR1-related congenital myopathies with cores and minicores: an Italian population study. Acta Neuropathol Commun 2022; 10:54. [PMID: 35428369 PMCID: PMC9013059 DOI: 10.1186/s40478-022-01357-0] [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: 02/03/2022] [Accepted: 03/25/2022] [Indexed: 11/10/2022] Open
Abstract
Mutations in the RYR1 gene, encoding ryanodine receptor 1 (RyR1), are a well-known cause of Central Core Disease (CCD) and Multi-minicore Disease (MmD). We screened a cohort of 153 patients carrying an histopathological diagnosis of core myopathy (cores and minicores) for RYR1 mutation. At least one RYR1 mutation was identified in 69 of them and these patients were further studied. Clinical and histopathological features were collected. Clinical phenotype was highly heterogeneous ranging from asymptomatic or paucisymptomatic hyperCKemia to severe muscle weakness and skeletal deformity with loss of ambulation. Sixty-eight RYR1 mutations, generally missense, were identified, of which 16 were novel. The combined analysis of the clinical presentation, disease progression and the structural bioinformatic analyses of RYR1 allowed to associate some phenotypes to mutations in specific domains. In addition, this study highlighted the structural bioinformatics potential in the prediction of the pathogenicity of RYR1 mutations. Further improvement in the comprehension of genotype-phenotype relationship of core myopathies can be expected in the next future: the actual lack of the human RyR1 crystal structure paired with the presence of large intrinsically disordered regions in RyR1, and the frequent presence of more than one RYR1 mutation in core myopathy patients, require designing novel investigation strategies to completely address RyR1 mutation effect.
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15
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OUP accepted manuscript. Hum Mol Genet 2022; 31:2236-2261. [DOI: 10.1093/hmg/ddac029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 11/12/2022] Open
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16
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Qazi S, Raza K. In silico approach to understand epigenetics of POTEE in ovarian cancer. J Integr Bioinform 2021; 18:jib-2021-0028. [PMID: 34788504 PMCID: PMC8709732 DOI: 10.1515/jib-2021-0028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/04/2021] [Indexed: 12/20/2022] Open
Abstract
Ovarian cancer is the third leading cause of cancer-related deaths in India. Epigenetics mechanisms seemingly plays an important role in ovarian cancer. This paper highlights the crucial epigenetic changes that occur in POTEE that get hypomethylated in ovarian cancer. We utilized the POTEE paralog mRNA sequence to identify major motifs and also performed its enrichment analysis. We identified 6 motifs of varying lengths, out of which only three motifs, including CTTCCAGCAGATGTGGATCA, GGAACTGCC, and CGCCACATGCAGGC were most likely to be present in the nucleotide sequence of POTEE. By enrichment and occurrences identification analyses, we rectified the best match motif as CTTCCAGCAGATGT. Since there is no experimentally verified structure of POTEE paralog, thus, we predicted the POTEE structure using an automated workflow for template-based modeling using the power of a deep neural network. Additionally, to validate our predicted model we used AlphaFold predicted POTEE structure and observed that the residual stretch starting from 237-958 had a very high confidence per residue. Furthermore, POTEE predicted model stability was evaluated using replica exchange molecular dynamic simulation for 50 ns. Our network-based epigenetic analysis discerns only 10 highly significant, direct, and physical associators of POTEE. Our finding aims to provide new insights about the POTEE paralog.
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Affiliation(s)
- Sahar Qazi
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
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17
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A P, G M, M T, L B, N F. Characterisation and functional role of a novel C1qDC protein from a colonial ascidian. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 122:104077. [PMID: 33905781 DOI: 10.1016/j.dci.2021.104077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
As an invertebrate, the compound ascidian Botryllus schlosseri faces nonself only with innate immunity. In this species, we already identified the key components of the lectin and alternative complement activation pathways. In the present work, by mining the transcriptome, we identified a single transcript codifying for a protein, member of the C1q-domain-containing protein family, with a signal peptide followed by two globular C1q (gC1q) domains. It shares a similar domain organisation with C1q/TNF-related proteins 4, the only vertebrate protein family with two gC1q domains. Our gC1q domain-containing protein, called BsC1qDC, is actively transcribed by immunocytes. The transcription is modulated during the Botryllus blastogenetic cycle and is upregulated following the injection of Bacillus clausii cells in the circulation. Furthermore, the injection of bsc1qdc iRNA in the vasculature results in decreased transcription of the gene and a significant impairment of phagocytosis and degranulation, suggesting the involvement of this molecule in immune responses.
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Affiliation(s)
- Peronato A
- Department of Biology, University of Padova, Italy
| | - Minervini G
- Department of Biomedical Sciences, University of Padova, Italy
| | - Tabarelli M
- PhD School in Agricultural Science and Biotechnology, University of Udine, Italy
| | - Ballarin L
- Department of Biology, University of Padova, Italy.
| | - Franchi N
- Department of Biology, University of Padova, Italy
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18
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Sequeiros-Borja CE, Surpeta B, Brezovsky J. Recent advances in user-friendly computational tools to engineer protein function. Brief Bioinform 2021; 22:bbaa150. [PMID: 32743637 PMCID: PMC8138880 DOI: 10.1093/bib/bbaa150] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/03/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. Many tools and methods are developed and upgraded each year to satisfy the increasing demands and challenges of protein engineering. To help protein engineers and bioinformaticians navigate this emerging wave of dedicated software, we have critically evaluated recent additions to the toolbox regarding their application for semi-rational and rational protein engineering. These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, protein-protein and protein-nucleic acid interactions, and electrostatic potential. We also discuss notable progress to target elusive protein dynamics and associated properties like ligand-transport processes and allosteric communication. Finally, we discuss several challenges these tools face and provide our perspectives on the further development of readily applicable methods to guide protein engineering efforts.
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Affiliation(s)
- Carlos Eduardo Sequeiros-Borja
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University and the International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Bartłomiej Surpeta
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University and the International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University and the International Institute of Molecular and Cell Biology in Warsaw
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19
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Phytochemicals from Ayurvedic plants as potential medicaments for ovarian cancer: an in silico analysis. J Mol Model 2021; 27:114. [PMID: 33765217 DOI: 10.1007/s00894-021-04736-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
Ovarian cancer is one of the highly prominent gynecological malignancies after breast cancer. Although myriad literature is available, there is no specific biomarker available for the personalized treatment strategy. The unavailability of effective drug therapy for ovarian cancer calls for an urgent push in its development from the multidisciplinary scientific community. Indian Ayurvedic medicine pharmacology is widely appreciated and accepted for its immense healthcare benefits. Bioinformatics and cheminformatics approaches can be effectively used to screen phytochemicals present in the Indian Ayurvedic plants against ovarian cancer target receptors. Recent studies discern that POTE, a cancer-testis antigen (CTA) family, plays a crucial role in the proliferation and progression of cancers including ovarian cancer. Specifically, POTEE paralog has been observed to be hypermethylated in ovarian cancer. This study undertakes an in silico analysis of Indian Ayurvedic plants for their anticancer efficacy against ovarian cancer proliferation target receptor POTEE. Structures of 100 phytochemicals from 11 Ayurvedic plants were screened with ADME criteria, and qualified phytochemicals were subjected to molecular docking and interaction analysis. Only 6 phytochemicals having a high affinity to the target receptor (POTEE) were then subjected to an all-atom replica exchange molecular dynamics simulation for 50 ns. Binding affinities of 6 phytochemicals cedeodarin, deodarin, hematoxylin, matairesinol, quercetin, and taxifolin with POTEE were -8.1, -7.7, -7.7, -7.9, -8.0, and - 7.7 kcal/mol, respectively, and their RMSD were recorded as zero. This study concludes that phytochemicals present in Indian Ayurvedic plants namely Cedrus deodara and Asparagus racemosus possess inhibitory effects against ovarian cancer proliferation receptor POTEE.
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20
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Orrego AH, Andrés-Sanz D, Velasco-Lozano S, Sanchez-Costa M, Berenguer J, Guisan JM, Rocha-Martin J, López-Gallego F. Self-sufficient asymmetric reduction of β-ketoesters catalysed by a novel and robust thermophilic alcohol dehydrogenase co-immobilised with NADH. Catal Sci Technol 2021; 11:3217-3230. [PMID: 34094502 PMCID: PMC8111925 DOI: 10.1039/d1cy00268f] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 02/25/2021] [Indexed: 12/04/2022]
Abstract
β-Hydroxyesters are essential building blocks utilised by the pharmaceutical and food industries in the synthesis of functional products. Beyond the conventional production methods based on chemical catalysis or whole-cell synthesis, the asymmetric reduction of β-ketoesters with cell-free enzymes is gaining relevance. To this end, a novel thermophilic (S)-3-hydroxybutyryl-CoA dehydrogenase from Thermus thermophilus HB27 (Tt27-HBDH) has been expressed, purified and biochemically characterised, determining its substrate specificity towards β-ketoesters and its dependence on NADH as a cofactor. The immobilization of Tt27-HBDH on agarose macroporous beads and its subsequent coating with polyethyleneimine has been found the best strategy to increase the stability and workability of the heterogeneous biocatalyst. Furthermore, we have embedded NADH in the cationic layer attached to the porous surface of the carrier. Since Tt27-HBDH catalyses cofactor recycling through 2-propanol oxidation, we achieve a self-sufficient heterogeneous biocatalyst where NADH is available for the immobilised enzymes but its lixiviation to the reaction bulk is avoided. Taking advantage of the autofluorescence of NADH, we demonstrate the activity of the enzyme towards the immobilised cofactor through single-particle analysis. Finally, we tested the operational stability in the asymmetric reduction of β-ketoesters in batch, succeeding in the reuse of both the enzyme and the co-immobilised cofactor up to 10 reaction cycles.
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Affiliation(s)
- Alejandro H Orrego
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP), CSIC Campus UAM, Cantoblanco 28049 Madrid Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, Center for Molecular Biology Severo-Ochoa (UAM-CSIC) Nicolás Cabrera 1 28049 Madrid Spain
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 182 Donostia San Sebastián Spain
| | - Daniel Andrés-Sanz
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 182 Donostia San Sebastián Spain
| | - Susana Velasco-Lozano
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 182 Donostia San Sebastián Spain
| | - Mercedes Sanchez-Costa
- Department of Molecular Biology, Universidad Autónoma de Madrid, Center for Molecular Biology Severo-Ochoa (UAM-CSIC) Nicolás Cabrera 1 28049 Madrid Spain
| | - José Berenguer
- Department of Molecular Biology, Universidad Autónoma de Madrid, Center for Molecular Biology Severo-Ochoa (UAM-CSIC) Nicolás Cabrera 1 28049 Madrid Spain
| | - José M Guisan
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP), CSIC Campus UAM, Cantoblanco 28049 Madrid Spain
| | - Javier Rocha-Martin
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP), CSIC Campus UAM, Cantoblanco 28049 Madrid Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 182 Donostia San Sebastián Spain
- IKERBASQUE, Basque Foundation for Science María Díaz de Haro 3 48013 Bilbao Spain
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21
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Medina MS, Bretzing KO, Aviles RA, Chong KM, Espinoza A, Garcia CNG, Katz BB, Kharwa RN, Hernandez A, Lee JL, Lee TM, Lo Verde C, Strul MW, Wong EY, Owens CP. CowN sustains nitrogenase turnover in the presence of the inhibitor carbon monoxide. J Biol Chem 2021; 296:100501. [PMID: 33667548 PMCID: PMC8047169 DOI: 10.1016/j.jbc.2021.100501] [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: 05/31/2020] [Revised: 01/28/2021] [Accepted: 03/01/2021] [Indexed: 11/28/2022] Open
Abstract
Nitrogenase is the only enzyme capable of catalyzing nitrogen fixation, the reduction of dinitrogen gas (N2) to ammonia (NH3). Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Nitrogen-fixing bacteria rely on the protein CowN to grow in the presence of CO. However, the mechanism by which CowN operates is unknown. Here, we present the biochemical characterization of CowN and examine how CowN protects nitrogenase from CO. We determine that CowN interacts directly with nitrogenase and that CowN protection observes hyperbolic kinetics with respect to CowN concentration. At a CO concentration of 0.001 atm, CowN restores nearly full nitrogenase activity. Our results further indicate that CowN's protection mechanism involves decreasing the binding affinity of CO to nitrogenase's active site approximately tenfold without interrupting substrate turnover. Taken together, our work suggests CowN is an important auxiliary protein in nitrogen fixation that engenders CO tolerance to nitrogenase.
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Affiliation(s)
- Michael S Medina
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Kevin O Bretzing
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Richard A Aviles
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Kiersten M Chong
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Alejandro Espinoza
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Chloe Nicole G Garcia
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Benjamin B Katz
- Department of Chemistry, University of California, Irvine, Irvine, California, USA
| | - Ruchita N Kharwa
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Andrea Hernandez
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Justin L Lee
- Department of Chemistry, University of California, Irvine, Irvine, California, USA
| | - Terrence M Lee
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Christine Lo Verde
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Max W Strul
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Emily Y Wong
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Cedric P Owens
- Schmid College of Science and Technology, Chapman University, Orange, California, USA.
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22
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Lino PR, Leandro J, Amaro M, Gonçalves LMD, Leandro P, Almeida AJ. In Silico and In Vitro Tailoring of a Chitosan Nanoformulation of a Human Metabolic Enzyme. Pharmaceutics 2021; 13:pharmaceutics13030329. [PMID: 33806405 PMCID: PMC8000282 DOI: 10.3390/pharmaceutics13030329] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/23/2021] [Accepted: 02/27/2021] [Indexed: 01/10/2023] Open
Abstract
Enzyme nanoencapsulation holds an enormous potential to develop new therapeutic approaches to a large set of human pathologies including cancer, infectious diseases and inherited metabolic disorders. However, enzyme formulation has been limited by the need to maintain the catalytic function, which is governed by protein conformation. Herein we report the rational design of a delivery system based on chitosan for effective encapsulation of a functionally and structurally complex human metabolic enzyme through ionic gelation with tripolyphosphate. The rationale was to use a mild methodology to entrap the multimeric multidomain 200 kDa human phenylalanine hydroxylase (hPAH) in a polyol-like matrix that would allow an efficient maintenance of protein structure and function, avoiding formulation stress conditions. Through an in silico and in vitro based development, the particulate system was optimized with modulation of nanomaterials protonation status, polymer, counterion and protein ratios, taking into account particle size, polydispersity index, surface charge, particle yield production, protein free energy of folding, electrostatic surface potential, charge, encapsulation efficiency, loading capacity and transmission electron microscopy morphology. Evaluation of the thermal stability, substrate binding profile, relative enzymatic activity, and substrate activation ratio of the encapsulated hPAH suggests that the formulation procedure does not affect protein stability, allowing an effective maintenance of hPAH biological function. Hence, this study provides an important framework for an enzyme formulation process.
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23
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Lai Z, Zhou C, Ma X, Xue Y, Ma Y. Enzymatic characterization of a novel thermostable and alkaline tolerant GH10 xylanase and activity improvement by multiple rational mutagenesis strategies. Int J Biol Macromol 2020; 170:164-177. [PMID: 33352153 DOI: 10.1016/j.ijbiomac.2020.12.137] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 11/15/2022]
Abstract
Thermo-alkaline xylanases are widely applied in paper pulping industry. In this study, a novel thermostable and alkaline tolerant GH10 xylanase (Xyn30Y5) gene from alkaliphilic Bacillus sp. 30Y5 was cloned and the surface-layer homology (SLH) domains truncated enzyme (Xyn30Y5-SLH) was expressed in Escherichia coli. The purified Xyn30Y5-SLH was most active at 70 °C and pH 7.0 and showed the highest specific activity of 349.4 U mg-1. It retained more than 90% activity between pH 6.0 to 9.5 and was stable at pH 6.0-10.0. To improve the activity, 47 mutants were designed based on eight rational strategies and 21 mutants showed higher activity. By combinatorial mutagenesis, the best mutant 3B demonstrated specific activity of 1016.8 U mg-1 with a doubled catalytic efficiency (kcat/Km) and RA601/2h value, accompanied by optimal pH shift to 8.0. The molecular dynamics simulation analysis indicated that the increase of flexibility of α5 helix and loop7 located near to the catalytic residues is likely responsible for its activity improvement. And the decrease of flexibility of the most unstable regions is vital for the thermostablity improvement. This work provided not only a novel thermostable and alkaline tolerant xylanase with industrial application potential but also an effective mutagenesis strategy for xylanase activity improvement.
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Affiliation(s)
- Zhihua Lai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Cheng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiaochen Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Engineering Laboratory for Industrial Enzymes, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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24
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Jayaraman M, Ramadas K. An integrated computational investigation to unveil the structural impacts of mutation on the InhA structural gene of Mycobacterium tuberculosis. J Mol Graph Model 2020; 101:107768. [DOI: 10.1016/j.jmgm.2020.107768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 10/23/2022]
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25
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Chatterjee S, Salimi A, Lee JY. Insights into amyotrophic lateral sclerosis linked Pro525Arg mutation in the fused in sarcoma protein through in silico analysis and molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:5963-5976. [DOI: 10.1080/07391102.2020.1794967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
| | - Abbas Salimi
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
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26
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Ultrasmall silica nanoparticles directly ligate the T cell receptor complex. Proc Natl Acad Sci U S A 2019; 117:285-291. [PMID: 31871161 DOI: 10.1073/pnas.1911360117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The impact of ultrasmall nanoparticles (<10-nm diameter) on the immune system is poorly understood. Recently, ultrasmall silica nanoparticles (USSN), which have gained increasing attention for therapeutic applications, were shown to stimulate T lymphocytes directly and at relatively low-exposure doses. Delineating underlying mechanisms and associated cell signaling will hasten therapeutic translation and is reported herein. Using competitive binding assays and molecular modeling, we established that the T cell receptor (TCR):CD3 complex is required for USSN-induced T cell activation, and that direct receptor complex-particle interactions are permitted both sterically and electrostatically. Activation is not limited to αβ TCR-bearing T cells since those with γδ TCR showed similar responses, implying that USSN mediate their effect by binding to extracellular domains of the flanking CD3 regions of the TCR complex. We confirmed that USSN initiated the signaling pathway immediately downstream of the TCR with rapid phosphorylation of both ζ-chain-associated protein 70 and linker for activation of T cells protein. However, T cell proliferation or IL-2 secretion were only triggered by USSN when costimulatory anti-CD28 or phorbate esters were present, demonstrating that the specific impact of USSN is in initiation of the primary, nuclear factor of activated T cells-pathway signaling from the TCR complex. Hence, we have established that USSN are partial agonists for the TCR complex because of induction of the primary T cell activation signal. Their ability to bind the TCR complex rapidly, and then to dissolve into benign orthosilicic acid, makes them an appealing option for therapies targeted at transient TCR:CD3 receptor binding.
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27
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Jha A, Kumar V, Haque S, Ayasolla K, Saha S, Lan X, Malhotra A, Saleem MA, Skorecki K, Singhal PC. Alterations in plasma membrane ion channel structures stimulate NLRP3 inflammasome activation in APOL1 risk milieu. FEBS J 2019; 287:2000-2022. [PMID: 31714001 DOI: 10.1111/febs.15133] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/23/2019] [Accepted: 11/09/2019] [Indexed: 12/01/2022]
Abstract
We evaluated alterations in the structural configurations of channels and activation of nucleotide-binding domain, leucine-rich-containing family, pyrin domain-containing-3 (NLRP3) inflammasome formation in apolipoprotein L1 (APOL1) risk and nonrisk milieus. APOL1G1- and APOL1G2-expressing podocytes (PD) displayed enhanced K+ efflux, induction of pyroptosis, and escalated transcription of interleukin (IL)-1β and IL-18. APOL1G1- and APOL1G2-expressing PD promoted the transcription as well as translation of proteins involved in the formation of inflammasomes. Since glyburide (a specific inhibitor of K+ efflux channels) inhibited the transcription of NLRP3, IL-1β, and IL-18, the role of K+ efflux in the activation of inflammasomes in APOL1 risk milieu was implicated. To evaluate the role of structural alterations in K+ channels in plasma membranes, bioinformatics studies, including molecular dynamic simulation, were carried out. Superimposition of bioinformatics reconstructions of APOL1G0, G1, and G2 showed several aligned regions. The analysis of pore-lining residues revealed that Ser342 and Tyr389 are involved in APOL1G0 pore formation and the altered conformations resulting from the Ser342Gly and Ile384Met mutation in the case of APOLG1 and deletion of the Tyr389 residue in the case of APOL1G2 are expected to alter pore characteristics, including K+ ion selectivity. Analysis of multiple membrane (lipid bilayer) models of interaction with the peripheral protein, integral membrane protein, and multimer protein revealed that for an APOL1 multimer model, APOL1G0 is not energetically favorable while the APOL1G1 and APOL1G2 moieties favor the insertion of multiple ion channels into the lipid bilayer. We conclude that altered pore configurations carry the potential to facilitate K+ ion transport in APOL1 risk milieu.
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Affiliation(s)
- Alok Jha
- Institute of Molecular Medicine, Feinstein Institute for Medical Research, Zucker School of Medicine at Hofstra-North Well, Manhasset, NY, USA
| | - Vinod Kumar
- Institute of Molecular Medicine, Feinstein Institute for Medical Research, Zucker School of Medicine at Hofstra-North Well, Manhasset, NY, USA
| | - Shabirul Haque
- Institute of Molecular Medicine, Feinstein Institute for Medical Research, Zucker School of Medicine at Hofstra-North Well, Manhasset, NY, USA
| | - Kamesh Ayasolla
- Institute of Molecular Medicine, Feinstein Institute for Medical Research, Zucker School of Medicine at Hofstra-North Well, Manhasset, NY, USA
| | - Shourav Saha
- Institute of Molecular Medicine, Feinstein Institute for Medical Research, Zucker School of Medicine at Hofstra-North Well, Manhasset, NY, USA
| | - Xiqian Lan
- Institute of Molecular Medicine, Feinstein Institute for Medical Research, Zucker School of Medicine at Hofstra-North Well, Manhasset, NY, USA
| | - Ashwani Malhotra
- Institute of Molecular Medicine, Feinstein Institute for Medical Research, Zucker School of Medicine at Hofstra-North Well, Manhasset, NY, USA
| | | | - Karl Skorecki
- Technion - Israel Institute of Technology, Rambam Health Care Campus, Haifa, Israel
| | - Pravin C Singhal
- Institute of Molecular Medicine, Feinstein Institute for Medical Research, Zucker School of Medicine at Hofstra-North Well, Manhasset, NY, USA
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Cuesta R, Yuste-Calvo C, Gil-Cartón D, Sánchez F, Ponz F, Valle M. Structure of Turnip mosaic virus and its viral-like particles. Sci Rep 2019; 9:15396. [PMID: 31659175 PMCID: PMC6817885 DOI: 10.1038/s41598-019-51823-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/07/2019] [Indexed: 01/05/2023] Open
Abstract
Turnip mosaic virus (TuMV), a potyvirus, is a flexible filamentous plant virus that displays a helical arrangement of coat protein copies (CPs) bound to the ssRNA genome. TuMV is a bona fide representative of the Potyvirus genus, one of most abundant groups of plant viruses, which displays a very wide host range. We have studied by cryoEM the structure of TuMV virions and its viral-like particles (VLPs) to explore the role of the interactions between proteins and RNA in the assembly of the virions. The results show that the CP-RNA interaction is needed for the correct orientation of the CP N-terminal arm, a region that plays as a molecular staple between CP subunits in the fully assembled virion.
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Affiliation(s)
- Rebeca Cuesta
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Carmen Yuste-Calvo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CBGP, UPM-INIA), Campus Montegancedo, 28223, Madrid, Spain
| | - David Gil-Cartón
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Flora Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CBGP, UPM-INIA), Campus Montegancedo, 28223, Madrid, Spain
| | - Fernando Ponz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CBGP, UPM-INIA), Campus Montegancedo, 28223, Madrid, Spain
| | - Mikel Valle
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, Bizkaia Technology Park, 48160, Derio, Spain.
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Analysis of mutations leading to para-aminosalicylic acid resistance in Mycobacterium tuberculosis. Sci Rep 2019; 9:13617. [PMID: 31541138 PMCID: PMC6754364 DOI: 10.1038/s41598-019-48940-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022] Open
Abstract
Thymidylate synthase A (ThyA) is the key enzyme involved in the folate pathway in Mycobacterium tuberculosis. Mutation of key residues of ThyA enzyme which are involved in interaction with substrate 2′-deoxyuridine-5′-monophosphate (dUMP), cofactor 5,10-methylenetetrahydrofolate (MTHF), and catalytic site have caused para-aminosalicylic acid (PAS) resistance in TB patients. Focusing on R127L, L143P, C146R, L172P, A182P, and V261G mutations, including wild-type, we performed long molecular dynamics (MD) simulations in explicit solvent to investigate the molecular principles underlying PAS resistance due to missense mutations. We found that these mutations lead to (i) extensive changes in the dUMP and MTHF binding sites, (ii) weak interaction of ThyA enzyme with dUMP and MTHF by inducing conformational changes in the structure, (iii) loss of the hydrogen bond and other atomic interactions and (iv) enhanced movement of protein atoms indicated by principal component analysis (PCA). In this study, MD simulations framework has provided considerable insight into mutation induced conformational changes in the ThyA enzyme of Mycobacterium.
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Agaricus bisporus mannose binding protein is not an agglutinating protein. Biochem Biophys Res Commun 2019; 519:773-776. [PMID: 31547987 DOI: 10.1016/j.bbrc.2019.09.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 09/17/2019] [Indexed: 11/21/2022]
Abstract
Agaricus bisporus mannose binding protein (Abmb) demonstrates permeability to epithelial monolayer barrier of the intestine, resistance to gastrointestinal tract conditions and to proteolysis therefore it holds potential as a drug carrier for oral route administration. Abmb also display antiproliferative activity to breast cancer cells and stimulation of immune system thus could potentially be also developed for therapeutic purpose. It is not immunogenic or toxic thereby safe for use. In this paper we further provide evidence that Abmb also lacks of agglutinating activity despite sharing high structural homology to lectins. Abmb is thereby the only mannose specific binding protein that is not member of lectin family. This evidence provides further support on the use of Abmb as pharmaceutical or medicinal agent. Its molecular globularity that may contribute to its lack of agglutination capacity was also evaluated.
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Hristova SH, Zhivkov AM. Isoelectric point of free and adsorbed cytochrome c determined by various methods. Colloids Surf B Biointerfaces 2019; 174:87-94. [DOI: 10.1016/j.colsurfb.2018.10.080] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/18/2018] [Accepted: 10/31/2018] [Indexed: 01/09/2023]
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Le DHT, Méndez-López E, Wang C, Commandeur U, Aranda MA, Steinmetz NF. Biodistribution of Filamentous Plant Virus Nanoparticles: Pepino Mosaic Virus versus Potato Virus X. Biomacromolecules 2019; 20:469-477. [PMID: 30516960 PMCID: PMC6485256 DOI: 10.1021/acs.biomac.8b01365] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nanoparticles with high aspect ratios have favorable attributes for drug delivery and bioimaging applications based on their enhanced tissue penetration and tumor homing properties. Here, we investigated a novel filamentous viral nanoparticle (VNP) based on the Pepino mosaic virus (PepMV), a relative of the established platform Potato virus X (PVX). We studied the chemical reactivity of PepMV, produced fluorescent versions of PepMV and PVX, and then evaluated their biodistribution in mouse tumor models. We found that PepMV can be conjugated to various small chemical modifiers including fluorescent probes via the amine groups of surface-exposed lysine residues, yielding VNPs carrying payloads of up to 1600 modifiers per particle. Although PepMV and PVX share similarities in particle size and shape, PepMV achieved enhanced tumor homing and less nonspecific tissue distribution compared to PVX in mouse models of triple negative breast cancer and ovarian cancer. In conclusion, PepMV provides a novel tool for nanomedical research but more research is needed to fully exploit the potential of plant VNPs for health applications.
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Affiliation(s)
- Duc H. T. Le
- Department of Biomedical Engineering, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Eduardo Méndez-López
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - Chao Wang
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Department of Biomedical Engineering, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Ulrich Commandeur
- Department of Molecular Biology, RWTH-Aachen University, Aachen 52064, Germany
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - Nicole F. Steinmetz
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- Department of Radiology, University of California, San Diego, La Jolla, California 92093, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Department of Biomedical Engineering, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
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Contessoto VG, de Oliveira VM, Fernandes BR, Slade GG, Leite VBP. TKSA-MC: A web server for rational mutation through the optimization of protein charge interactions. Proteins 2018; 86:1184-1188. [PMID: 30218467 DOI: 10.1002/prot.25599] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/24/2018] [Accepted: 08/31/2018] [Indexed: 11/06/2022]
Abstract
The TKSAMC is a web server which calculates protein charge-charge interactions via the Tanford-Kirkwood Surface Accessibility model with the Monte Carlo method for sampling different protein protonation states. The optimization of charge-charge interactions via directed mutations has successfully enhanced the thermal stability of different proteins and could be a key to protein engineering improvement. The server presents the electrostatic free energy contribution of each polar-charged residue to the protein native state stability. Specific residues are suggested to be mutated for improving thermal stability. The choice of a residue is based on its fraction of side chain exposed to solvent and its positive free energy contribution, which tends to destabilize the protein native state. Any residue energy contribution can be shown as a function of pH condition. The web server is freely available at UNESP (São Paulo State University - DF/IBILCE): http://tksamc.df.ibilce.unesp.br and also on GitHub https://github.com/contessoto/tksamc.
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Affiliation(s)
- Vinícius G Contessoto
- Brazilian Bioethanol Science and Technology Laboratory - CTBE, Campinas, São Paulo, Brazil.,Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Vinícius M de Oliveira
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Bruno R Fernandes
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Gabriel G Slade
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil.,Theoretical Biophysics Laboratory, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro - UFTM, Uberaba, Minas Gerais, Brazil
| | - Vitor B P Leite
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil
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Semplicini C, Bertolin C, Bello L, Pantic B, Guidolin F, Vianello S, Catapano F, Colombo I, Moggio M, Gavassini BF, Cenacchi G, Papa V, Previtero M, Calore C, Sorarù G, Minervini G, Tosatto SCE, Stramare R, Pegoraro E. The clinical spectrum of CASQ1-related myopathy. Neurology 2018; 91:e1629-e1641. [PMID: 30258016 DOI: 10.1212/wnl.0000000000006387] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/17/2018] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVE To identify and characterize patients with calsequestrin 1 (CASQ1)-related myopathy. METHODS Patients selected according to histopathologic features underwent CASQ1 genetic screening. CASQ1-mutated patients were clinically evaluated and underwent muscle MRI. Vacuole morphology and vacuolated fiber type were characterized. RESULTS Twenty-two CASQ1-mutated patients (12 families) were identified, 21 sharing the previously described founder mutation (p.Asp244Gly) and 1 with the p.Gly103Asp mutation. Patients usually presented in the sixth decade with exercise intolerance and myalgias and later developed mild to moderate, slowly progressive proximal weakness with quadriceps atrophy and scapular winging. Muscle MRI (n = 11) showed a recurrent fibrofatty substitution pattern. Three patients presented subclinical cardiac abnormalities. Muscle histopathology in patients with p.Asp244Gly showed vacuoles in type II fibers appearing empty in hematoxylin-eosin, Gomori, and nicotinamide adenine dinucleotide (NADH) tetrazolium reductase stains but strongly positive for sarcoplasmic reticulum proteins. The muscle histopathology of p.Gly103Asp mutation was different, showing also NADH-positive accumulation consistent with tubular aggregates. CONCLUSIONS We report the clinical and molecular details of the largest cohort of CASQ1-mutated patients. A possible heart involvement is presented, further expanding the phenotype of the disease. One mutation is common due to a founder effect, but other mutations are possible. Because of a paucity of symptoms, it is likely that CASQ1 mutations may remain undiagnosed if a muscle biopsy is not performed.
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Affiliation(s)
- Claudio Semplicini
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Cinzia Bertolin
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Luca Bello
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Boris Pantic
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Francesca Guidolin
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Sara Vianello
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Francesco Catapano
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Irene Colombo
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Maurizio Moggio
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Bruno F Gavassini
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Giovanna Cenacchi
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Valentina Papa
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Marco Previtero
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Chiara Calore
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Gianni Sorarù
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Giovanni Minervini
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Silvio C E Tosatto
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Roberto Stramare
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy
| | - Elena Pegoraro
- From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy.
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Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7480749. [PMID: 29967786 PMCID: PMC6008865 DOI: 10.1155/2018/7480749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/06/2018] [Indexed: 12/15/2022]
Abstract
Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR), i.e., the double mutant F87M/L110M (MT-TTR) and the triple mutant F87M/L110M/S117E (3M-TTR), in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets) appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.
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Alonso‐de Castro S, Cortajarena AL, López‐Gallego F, Salassa L. Bioorthogonal Catalytic Activation of Platinum and Ruthenium Anticancer Complexes by FAD and Flavoproteins. Angew Chem Int Ed Engl 2018; 57:3143-3147. [PMID: 29359850 PMCID: PMC5887934 DOI: 10.1002/anie.201800288] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 12/28/2022]
Abstract
Recent advances in bioorthogonal catalysis promise to deliver new chemical tools for performing chemoselective transformations in complex biological environments. Herein, we report how FAD (flavin adenine dinucleotide), FMN (flavin mononucleotide), and four flavoproteins act as unconventional photocatalysts capable of converting PtIV and RuII complexes into potentially toxic PtII or RuII -OH2 species. In the presence of electron donors and low doses of visible light, the flavoproteins mini singlet oxygen generator (miniSOG) and NADH oxidase (NOX) catalytically activate PtIV prodrugs with bioorthogonal selectivity. In the presence of NADH, NOX catalyzes PtIV activation in the dark as well, indicating for the first time that flavoenzymes may contribute to initiating the activity of PtIV chemotherapeutic agents.
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Affiliation(s)
| | - Aitziber L. Cortajarena
- CIC biomaGUNEPaseo de Miramón 182Donostia20014Spain
- Ikerbasque, Basque Foundation for ScienceBilbao48011Spain
| | | | - Luca Salassa
- Donostia International Physics CenterPaseo Manuel de Lardizabal 4Donostia20018Spain
- Ikerbasque, Basque Foundation for ScienceBilbao48011Spain
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37
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Scheps KG, Hasenahuer MA, Parisi G, Targovnik HM, García E, Veber ES, Crisp R, Elena G, Varela V, Fornasari MS. Two novel unstable hemoglobin variants due to in-frame deletions of key amino acids in the β-globin chain. Eur J Haematol 2018; 100:529-535. [DOI: 10.1111/ejh.13029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Karen G. Scheps
- Facultad de Farmacia y Bioquímica; Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética; Universidad de Buenos Aires; Ciudad Autónoma de Buenos Aires Argentina
- Instituto de Inmunología; Genética y Metabolismo (INIGEM); CONICET-Universidad de Buenos Aires; Ciudad Autónoma de Buenos Aires Argentina
| | - Marcia Anahí Hasenahuer
- Departamento de Ciencia y Tecnología; Universidad Nacional de Quilmes; Bernal, Buenos Aires Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología; Universidad Nacional de Quilmes; Bernal, Buenos Aires Argentina
| | - Héctor M. Targovnik
- Facultad de Farmacia y Bioquímica; Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética; Universidad de Buenos Aires; Ciudad Autónoma de Buenos Aires Argentina
- Instituto de Inmunología; Genética y Metabolismo (INIGEM); CONICET-Universidad de Buenos Aires; Ciudad Autónoma de Buenos Aires Argentina
| | - Eliana García
- Sección Hematología y Oncología; Servicio de Pediatría; Hospital Nacional A. Posadas; El Palomar Buenos Aires Argentina
| | - Ernesto Samuel Veber
- Servicio de Hemato-Oncología Pediátrica; Hospital General de Niños “Dr. Pedro de Elizalde”; Ciudad Autónoma de Buenos Aires Argentina
| | - Renée Crisp
- Sección Hematología y Oncología; Servicio de Pediatría; Hospital Nacional A. Posadas; El Palomar Buenos Aires Argentina
| | - Graciela Elena
- Servicio de Hemato-Oncología Pediátrica; Hospital General de Niños “Dr. Pedro de Elizalde”; Ciudad Autónoma de Buenos Aires Argentina
| | - Viviana Varela
- Facultad de Farmacia y Bioquímica; Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética; Universidad de Buenos Aires; Ciudad Autónoma de Buenos Aires Argentina
- Instituto de Inmunología; Genética y Metabolismo (INIGEM); CONICET-Universidad de Buenos Aires; Ciudad Autónoma de Buenos Aires Argentina
| | - María Silvina Fornasari
- Departamento de Ciencia y Tecnología; Universidad Nacional de Quilmes; Bernal, Buenos Aires Argentina
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Alonso-de Castro S, Cortajarena AL, López-Gallego F, Salassa L. Bioorthogonal Catalytic Activation of Platinum and Ruthenium Anticancer Complexes by FAD and Flavoproteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800288] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Aitziber L. Cortajarena
- CIC biomaGUNE; Paseo de Miramón 182 Donostia 20014 Spain
- Ikerbasque, Basque Foundation for Science; Bilbao 48011 Spain
| | - Fernando López-Gallego
- CIC biomaGUNE; Paseo de Miramón 182 Donostia 20014 Spain
- ARAID Foundation; Zaragoza Spain
| | - Luca Salassa
- Donostia International Physics Center; Paseo Manuel de Lardizabal 4 Donostia 20018 Spain
- Ikerbasque, Basque Foundation for Science; Bilbao 48011 Spain
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Capuano A, Fogolari F, Bucciotti F, Spessotto P, Nicolosi PA, Mucignat MT, Cervi M, Esposito G, Colombatti A, Doliana R. The α4β1/EMILIN1 interaction discloses a novel and unique integrin-ligand type of engagement. Matrix Biol 2017; 66:50-66. [PMID: 29037761 DOI: 10.1016/j.matbio.2017.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/06/2017] [Accepted: 10/07/2017] [Indexed: 10/18/2022]
Abstract
EMILIN1, a homo-trimeric adhesive ECM glycoprotein, interacts with the α4β1 integrin through its gC1q domain. Uniquely among the C1q family members, the EMILIN1 gC1q presents only nine-stranded β-sandwich fold and the missing strand is substituted by a disordered 19-residue long segment spanning from Y927 to G945 at the apex of the gC1q domain. This unstructured loop exposes to the solvent the acidic residue E933, which plays a key role in the α4β1 integrin mediated interaction. Here, we experimentally determined that the three E933 residues (one from each monomer) are all required for ligand binding. By docking the NMR structure of the gC1q to a virtual α4β1 crystal structure based on the known structures of α4β7 and α5β1 integrins we built a model of α4β1-gC1q complex where three E933 residues are smoothly forced to coordinate the Mg2+ ion at the βI MIDAS site of the integrin. By bringing the three E933 close in space, the trimeric supramolecular organization of gC1q allows the formation of a proper 3D geometry and suggests a quaternary-structure-dependent mode of interaction. Furthermore, we experimentally identified R904 as a synergistic residue for cell adhesion. Accordingly, the model showed that this residue is able to form potential stabilizing intra-chain salt bridges with residues E928 and E930. This mode of interaction likely accounts for a more stable and durable α4β1-gC1q interaction in comparison with the prototypic CS1 ligand. To our knowledge, this is the first report describing the simultaneous involvement of all the three acidic residues of a trimeric ligand in the formation of a dimeric complex with the integrin βI domain.
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Affiliation(s)
- Alessandra Capuano
- Department of Translational Research, Molecular Oncology Unit, CRO Aviano, National Cancer Institute, Via Franco Gallini 2, 33081 Aviano, PN, Italy
| | - Federico Fogolari
- Department of Computer Science, Mathematics and Physics, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Francesco Bucciotti
- Department of Translational Research, Molecular Oncology Unit, CRO Aviano, National Cancer Institute, Via Franco Gallini 2, 33081 Aviano, PN, Italy
| | - Paola Spessotto
- Department of Translational Research, Molecular Oncology Unit, CRO Aviano, National Cancer Institute, Via Franco Gallini 2, 33081 Aviano, PN, Italy
| | - Pier Andrea Nicolosi
- Department of Translational Research, Molecular Oncology Unit, CRO Aviano, National Cancer Institute, Via Franco Gallini 2, 33081 Aviano, PN, Italy
| | - Maria Teresa Mucignat
- Department of Translational Research, Molecular Oncology Unit, CRO Aviano, National Cancer Institute, Via Franco Gallini 2, 33081 Aviano, PN, Italy
| | - Marta Cervi
- Department of Translational Research, Molecular Oncology Unit, CRO Aviano, National Cancer Institute, Via Franco Gallini 2, 33081 Aviano, PN, Italy
| | - Gennaro Esposito
- Department of Computer Science, Mathematics and Physics, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy; Math&Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Alfonso Colombatti
- Department of Translational Research, Molecular Oncology Unit, CRO Aviano, National Cancer Institute, Via Franco Gallini 2, 33081 Aviano, PN, Italy.
| | - Roberto Doliana
- Department of Translational Research, Molecular Oncology Unit, CRO Aviano, National Cancer Institute, Via Franco Gallini 2, 33081 Aviano, PN, Italy.
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Zamora M, Méndez-López E, Agirrezabala X, Cuesta R, Lavín JL, Sánchez-Pina MA, Aranda MA, Valle M. Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses. SCIENCE ADVANCES 2017; 3:eaao2182. [PMID: 28948231 PMCID: PMC5606705 DOI: 10.1126/sciadv.aao2182] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/18/2017] [Indexed: 05/16/2023]
Abstract
Potyviruses constitute the second largest genus of plant viruses and cause important economic losses in a large variety of crops; however, the atomic structure of their particles remains unknown. Infective potyvirus virions are long flexuous filaments where coat protein (CP) subunits assemble in helical mode bound to a monopartite positive-sense single-stranded RNA [(+)ssRNA] genome. We present the cryo-electron microscopy (cryoEM) structure of the potyvirus watermelon mosaic virus at a resolution of 4.0 Å. The atomic model shows a conserved fold for the CPs of flexible filamentous plant viruses, including a universally conserved RNA binding pocket, which is a potential target for antiviral compounds. This conserved fold of the CP is widely distributed in eukaryotic viruses and is also shared by nucleoproteins of enveloped viruses with segmented (-)ssRNA (negative-sense ssRNA) genomes, including influenza viruses.
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Affiliation(s)
- Miguel Zamora
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - Eduardo Méndez-López
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Espinardo, 30100 Murcia, Spain
| | - Xabier Agirrezabala
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - Rebeca Cuesta
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - José L. Lavín
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - M. Amelia Sánchez-Pina
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Espinardo, 30100 Murcia, Spain
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Espinardo, 30100 Murcia, Spain
| | - Mikel Valle
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
- Corresponding author.
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41
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Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family. Sci Rep 2017; 7:6829. [PMID: 28754924 PMCID: PMC5533708 DOI: 10.1038/s41598-017-05748-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 06/02/2017] [Indexed: 12/21/2022] Open
Abstract
The emergence of genes implicated across multiple comorbid neurologic disorders allows to identify shared underlying molecular pathways. Recently, investigation of patients with diverse neurologic disorders found TANC1 and TANC2 as possible candidate disease genes. While the TANC proteins have been reported as postsynaptic scaffolds influencing synaptic spines and excitatory synapse strength, their molecular functions remain unknown. Here, we conducted a comprehensive in silico analysis of the TANC protein family to characterize their molecular role and understand possible neurobiological consequences of their disruption. The known Ankyrin and tetratricopeptide repeat (TPR) domains have been modeled. The newly predicted N-terminal ATPase domain may function as a regulated molecular switch for downstream signaling. Several putative conserved protein binding motifs allowed to extend the TANC interaction network. Interestingly, we highlighted connections with different signaling pathways converging to modulate neuronal activity. Beyond a known role for TANC family members in the glutamate receptor pathway, they seem linked to planar cell polarity signaling, Hippo pathway, and cilium assembly. This suggests an important role in neuron projection, extension and differentiation.
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42
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Srivastava G, Tripathi S, Kumar A, Sharma A. Molecular investigation of active binding site of isoniazid (INH) and insight into resistance mechanism of S315T-MtKatG in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2017; 105:18-27. [DOI: 10.1016/j.tube.2017.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 12/19/2022]
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43
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da Silva ES, Gómez-Vallejo V, Llop J, López-Gallego F. Structural, kinetic and operational characterization of an immobilized l -aminoacid dehydrogenase. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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44
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Giorgio V, Burchell V, Schiavone M, Bassot C, Minervini G, Petronilli V, Argenton F, Forte M, Tosatto S, Lippe G, Bernardi P. Ca 2+ binding to F-ATP synthase β subunit triggers the mitochondrial permeability transition. EMBO Rep 2017; 18:1065-1076. [PMID: 28507163 DOI: 10.15252/embr.201643354] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 04/02/2017] [Accepted: 04/05/2017] [Indexed: 01/28/2023] Open
Abstract
F-ATP synthases convert the electrochemical energy of the H+ gradient into the chemical energy of ATP with remarkable efficiency. Mitochondrial F-ATP synthases can also undergo a Ca2+-dependent transformation to form channels with properties matching those of the permeability transition pore (PTP), a key player in cell death. The Ca2+ binding site and the mechanism(s) through which Ca2+ can transform the energy-conserving enzyme into a dissipative structure promoting cell death remain unknown. Through in vitro, in vivo and in silico studies we (i) pinpoint the "Ca2+-trigger site" of the PTP to the catalytic site of the F-ATP synthase β subunit and (ii) define a conformational change that propagates from the catalytic site through OSCP and the lateral stalk to the inner membrane. T163S mutants of the β subunit, which show a selective decrease in Ca2+-ATP hydrolysis, confer resistance to Ca2+-induced, PTP-dependent death in cells and developing zebrafish embryos. These findings are a major advance in the molecular definition of the transition of F-ATP synthase to a channel and of its role in cell death.
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Affiliation(s)
- Valentina Giorgio
- Department of Biomedical Sciences, University of Padova, Padova, Italy .,Consiglio Nazionale delle Ricerche Neuroscience Institute, Padova, Italy
| | - Victoria Burchell
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Marco Schiavone
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Claudio Bassot
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | - Valeria Petronilli
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Consiglio Nazionale delle Ricerche Neuroscience Institute, Padova, Italy
| | | | - Michael Forte
- Vollum Institute, Oregon Health and Sciences University, Portland, OR, USA
| | - Silvio Tosatto
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Consiglio Nazionale delle Ricerche Neuroscience Institute, Padova, Italy
| | - Giovanna Lippe
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Paolo Bernardi
- Department of Biomedical Sciences, University of Padova, Padova, Italy .,Consiglio Nazionale delle Ricerche Neuroscience Institute, Padova, Italy
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Minervini G, Lopreiato R, Bortolotto R, Falconieri A, Sartori G, Tosatto SCE. Novel interactions of the von Hippel-Lindau (pVHL) tumor suppressor with the CDKN1 family of cell cycle inhibitors. Sci Rep 2017; 7:46562. [PMID: 28425505 PMCID: PMC5397843 DOI: 10.1038/srep46562] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/17/2017] [Indexed: 12/20/2022] Open
Abstract
Germline inactivation of the von Hippel-Lindau (VHL) tumor suppressor predisposes patients to develop different highly vascularized cancers. pVHL targets the hypoxia-inducible transcription factor (HIF-1α) for degradation, modulating the activation of various genes involved in hypoxia response. Hypoxia plays a relevant role in regulating cell cycle progression, inducing growth arrest in cells exposed to prolonged oxygen deprivation. However, the exact molecular details driving this transition are far from understood. Here, we present novel interactions between pVHL and the cyclin-dependent kinase inhibitor family CDKN1 (p21, p27 and p57). Bioinformatics analysis, yeast two-hybrid screening and co-immunoprecipitation assays were used to predict, dissect and validate the interactions. We found that the CDKN1 proteins share a conserved region mimicking the HIF-1α motif responsible for pVHL binding. Intriguingly, a p27 site-specific mutation associated to cancer is shown to modulate this novel interaction. Our findings suggest a new connection between the pathways regulating hypoxia and cell cycle progression.
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Affiliation(s)
- Giovanni Minervini
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padova, Italy
| | - Raffaele Lopreiato
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padova, Italy
| | - Raissa Bortolotto
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padova, Italy
| | - Antonella Falconieri
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padova, Italy
| | - Geppo Sartori
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padova, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padova, Italy.,CNR Institute of Neuroscience, Padova, Viale G. Colombo 3, 35121, Padova, Italy
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46
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Escobar S, Velasco-Lozano S, Lu CH, Lin YF, Mesa M, Bernal C, López-Gallego F. Understanding the functional properties of bio-inorganic nanoflowers as biocatalysts by deciphering the metal-binding sites of enzymes. J Mater Chem B 2017; 5:4478-4486. [PMID: 32263975 DOI: 10.1039/c6tb03295h] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biomineralisation of metal phosphates is a promising approach to develop more efficient nanobiocatalysts; however, the interactions between the protein and the inorganic mineral are poorly understood. Elucidating which protein regions most likely participate in the mineral formation will guide the fabrication of more efficient biocatalysts based on metal-phosphate nanoflowers. We have biomineralised the lipase from Thermomyces lanuginosus using three calcium, zinc and copper phosphates to fabricate different types of bio-inorganic nanoflowers. To better understand how the biomineralisation process affects the enzyme properties, we have computationally predicted the protein regions with a higher propensity for binding Ca2+, Cu2+ and Zn2+. These binding sites can be considered as presumable nucleation points where the biomineralisation process starts and explain why different metals can form bio-inorganic nanoflowers of the same enzyme with different functional properties. The formation of calcium, copper and zinc phosphates in the presence of this lipase gives rise to nanoflowers with different morphologies and different enzymatic properties such as activity, stability, hyperactivation and activity-pH profile; these functional differences are supported by structural studies based on fluorescence spectroscopy and can be explained by the different locations of the predicted nucleation sites for the different metals. Among the three metals used herein, the mineralisation of this lipase with zinc-phosphate enables the fabrication of bio-inorganic nanoflowers 34 times more stable than the soluble enzyme. These bio-inorganic nanoflowers were reused for 8 reaction cycles achieving 100% yield in the hydrolysis of p-nitrophenol butyrate but losing more than 50% of their initial activity after 6 operational cycles. Finally, this heterogeneous biocatalyst was more active and enantioselective than the soluble enzyme (ee = 79%(R)) towards the kinetic resolution of rac-1-phenylethyl acetate yielding the R enantiomer with ee = 84%.
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Affiliation(s)
- Sindy Escobar
- Grupo Ciencia de los Materiales, Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia - UdeA, Calle 70 No. 52-21, Medellín, Colombia
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Dazzo E, Leonardi E, Belluzzi E, Malacrida S, Vitiello L, Greggio E, Tosatto SCE, Nobile C. Secretion-Positive LGI1 Mutations Linked to Lateral Temporal Epilepsy Impair Binding to ADAM22 and ADAM23 Receptors. PLoS Genet 2016; 12:e1006376. [PMID: 27760137 PMCID: PMC5070869 DOI: 10.1371/journal.pgen.1006376] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/20/2016] [Indexed: 01/17/2023] Open
Abstract
Autosomal dominant lateral temporal epilepsy (ADTLE) is a focal epilepsy syndrome caused by mutations in the LGI1 gene, which encodes a secreted protein. Most ADLTE-causing mutations inhibit LGI1 protein secretion, and only a few secretion-positive missense mutations have been reported. Here we describe the effects of four disease-causing nonsynonymous LGI1 mutations, T380A, R407C, S473L, and R474Q, on protein secretion and extracellular interactions. Expression of LGI1 mutant proteins in cultured cells shows that these mutations do not inhibit protein secretion. This finding likely results from the lack of effects of these mutations on LGI1 protein folding, as suggested by 3D protein modelling. In addition, immunofluorescence and co-immunoprecipitation experiments reveal that all four mutations significantly impair interaction of LGI1 with the ADAM22 and ADAM23 receptors on the cell surface. These results support the existence of a second mechanism, alternative to inhibition of protein secretion, by which ADLTE-causing LGI1 mutations exert their loss-of-function effect extracellularly, and suggest that interactions of LGI1 with both ADAM22 and ADAM23 play an important role in the molecular mechanisms leading to ADLTE. Temporal lobe epilepsy is the most common form of focal epilepsy. It is frequently associated with structural brain abnormalities, but genetic forms caused by mutations in major genes have also been described. Autosomal dominant lateral temporal epilepsy (ADLTE) is a familial condition characterized by focal seizures with prominent auditory symptoms. ADLTE-causing mutations are found in the LGI1 gene in about 30% of affected families. LGI1 encodes a protein, LGI1, that is secreted by neurons. Most LGI1 mutations suppress protein secretion, thereby preventing protein function in the extracellular environment. In this paper, we examine the effects of four LGI1 mutations and show that they do not inhibit secretion of the LGI1 protein but impair its interaction with the neuronal receptors ADAM22 and ADAM23. In agreement with these findings, a three- dimensional model of the protein predicts that these mutations have no impact on LGI1 structure but instead may affect amino acids that are critical for interactions with ADAM receptors. Our results provide novel evidence for an extracellular mechanism through which mutant LGI1 proteins cause ADLTE and strengthen the importance of LGI1-ADAM22/23 protein complex in the mechanisms underlying ADLTE.
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Affiliation(s)
- Emanuela Dazzo
- CNR-Neuroscience Institute, Section of Padua, Padova, Italy
| | - Emanuela Leonardi
- Department of Woman and Child’s Health, University of Padua, Padova, Italy
| | - Elisa Belluzzi
- Department of Biology, University of Padua, Padova, Italy
| | - Sandro Malacrida
- Department of Biomedical Sciences, University of Padua, Padova, Italy
| | | | - Elisa Greggio
- Department of Biology, University of Padua, Padova, Italy
| | - Silvio C. E. Tosatto
- CNR-Neuroscience Institute, Section of Padua, Padova, Italy
- Department of Biomedical Sciences, University of Padua, Padova, Italy
| | - Carlo Nobile
- CNR-Neuroscience Institute, Section of Padua, Padova, Italy
- Department of Biomedical Sciences, University of Padua, Padova, Italy
- * E-mail:
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Mapping pathogenic mutations suggests an innovative structural model for the pendrin (SLC26A4) transmembrane domain. Biochimie 2016; 132:109-120. [PMID: 27771369 DOI: 10.1016/j.biochi.2016.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/03/2016] [Indexed: 12/16/2022]
Abstract
Human pendrin (SLC26A4) is an anion transporter mostly expressed in the inner ear, thyroid and kidney. SLC26A4 gene mutations are associated with a broad phenotypic spectrum, including Pendred Syndrome and non-syndromic hearing loss with enlarged vestibular aqueduct (ns-EVA). No experimental structure of pendrin is currently available, making phenotype-genotype correlations difficult as predictions of transmembrane (TM) segments vary in number. Here, we propose a novel three-dimensional (3D) pendrin transmembrane domain model based on the SLC26Dg transporter. The resulting 14 TM topology was found to include two non-canonical transmembrane segments crucial for pendrin activity. Mutation mapping of 147 clinically validated pathological mutations shows that most affect two previously undescribed TM regions.
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VHLdb: A database of von Hippel-Lindau protein interactors and mutations. Sci Rep 2016; 6:31128. [PMID: 27511743 PMCID: PMC4980628 DOI: 10.1038/srep31128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 07/08/2016] [Indexed: 01/15/2023] Open
Abstract
Mutations in von Hippel-Lindau tumor suppressor protein (pVHL) predispose to develop
tumors affecting specific target organs, such as the retina, epididymis, adrenal
glands, pancreas and kidneys. Currently, more than 400 pVHL interacting
proteins are either described in the literature or predicted in public databases.
This data is scattered among several different sources, slowing down the
comprehension of pVHL’s biological role. Here we present VHLdb, a novel
database collecting available interaction and mutation data on pVHL to provide novel
integrated annotations. In VHLdb, pVHL interactors are organized according to two
annotation levels, manual and automatic. Mutation data are easily accessible and a
novel visualization tool has been implemented. A user-friendly feedback function to
improve database content through community-driven curation is also provided. VHLdb
presently contains 478 interactors, of which 117 have been manually curated, and
1,074 mutations. This makes it the largest available database for pVHL-related
information. VHLdb is available from URL: http://vhldb.bio.unipd.it/.
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50
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Pham P, Afif SA, Shimoda M, Maeda K, Sakaguchi N, Pedersen LC, Goodman MF. Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification. DNA Repair (Amst) 2016; 43:48-56. [PMID: 27258794 DOI: 10.1016/j.dnarep.2016.05.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 05/10/2016] [Indexed: 12/18/2022]
Abstract
Activation-induced deoxycytidine deaminase (AID) initiates somatic hypermutation (SHM) and class-switch recombination (CSR) by deaminating C→U during transcription of Ig-variable (V) and Ig-switch (S) region DNA, which is essential to produce high-affinity antibodies. Here we report the crystal structure of a soluble human AID variant at 2.8Å resolution that favors targeting WRC motifs (W=A/T, R=A/G) in vitro, and executes Ig V SHM in Ramos B-cells. A specificity loop extending away from the active site to accommodate two purine bases next to C, differs significantly in sequence, length, and conformation from APOBEC proteins Apo3A and Apo3G, which strongly favor pyrimidines at -1 and -2 positions. Individual amino acid contributions to specificity and processivity were measured in relation to a proposed ssDNA binding cleft. This study provides a structural basis for residue contributions to DNA scanning properties unique to AID, and for disease mutations in human HIGM-2 syndrome.
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Affiliation(s)
- Phuong Pham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States
| | - Samir A Afif
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States
| | - Mayuko Shimoda
- Department of Immunology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan; Laboratory of Host Defence, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan; World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan
| | - Kazuhiko Maeda
- Laboratory of Host Defence, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan; World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan
| | - Nobuo Sakaguchi
- World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan; Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, United States
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, United States.
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