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Skvarnavičius G, Toleikis Z, Matulis D, Petrauskas V. Denaturant- or ligand-induced change in protein volume by pressure shift assay. Phys Chem Chem Phys 2022; 24:17279-17288. [DOI: 10.1039/d2cp01046a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A complete thermodynamic description of protein-ligand binding includes parameters related to pressure and temperature. The changes in protein volume and compressibility upon binding a ligand are pressure-related parameters that are...
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Xu Y, Huang J. Validating the CHARMM36m protein force field with LJ-PME reveals altered hydrogen bonding dynamics under elevated pressures. Commun Chem 2021; 4:99. [PMID: 36697521 PMCID: PMC9814493 DOI: 10.1038/s42004-021-00537-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/08/2021] [Indexed: 01/28/2023] Open
Abstract
The pressure-temperature phase diagram is important to our understanding of the physics of biomolecules. Compared to studies on temperature effects, studies of the pressure dependence of protein dynamic are rather limited. Molecular dynamics (MD) simulations with fine-tuned force fields (FFs) offer a powerful tool to explore the influence of thermodynamic conditions on proteins. Here we evaluate the transferability of the CHARMM36m (C36m) protein force field at varied pressures compared with NMR data using ubiquitin as a model protein. The pressure dependences of J couplings for hydrogen bonds and order parameters for internal motion are in good agreement with experiment. We demonstrate that the C36m FF combined with the Lennard-Jones particle-mesh Ewald (LJ-PME) method is suitable for simulations in a wide range of temperature and pressure. As the ubiquitin remains stable up to 2500 bar, we identify the mobility and stability of different hydrogen bonds in response to pressure. Based on those results, C36m is expected to be applied to more proteins in the future to further investigate protein dynamics under elevated pressures.
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Affiliation(s)
- You Xu
- grid.494629.40000 0004 8008 9315Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Jing Huang
- grid.494629.40000 0004 8008 9315Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
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Skvarnavičius G, Toleikis Z, Michailovienė V, Roumestand C, Matulis D, Petrauskas V. Protein-Ligand Binding Volume Determined from a Single 2D NMR Spectrum with Increasing Pressure. J Phys Chem B 2021; 125:5823-5831. [PMID: 34032445 PMCID: PMC8279561 DOI: 10.1021/acs.jpcb.1c02917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Proteins
undergo changes in their partial volumes in numerous biological
processes such as enzymatic catalysis, unfolding–refolding,
and ligand binding. The change in the protein volume upon ligand binding—a
parameter termed the protein–ligand binding volume—can
be extensively studied by high-pressure NMR spectroscopy. In this
study, we developed a method to determine the protein–ligand
binding volume from a single two-dimensional (2D) 1H–15N heteronuclear single quantum coherence (HSQC) spectrum
at different pressures, if the exchange between ligand-free and ligand-bound
states of a protein is slow in the NMR time-scale. This approach required
a significantly lower amount of protein and NMR time to determine
the protein–ligand binding volume of two carbonic anhydrase
isozymes upon binding their ligands. The proposed method can be used
in other protein–ligand systems and expand the knowledge about
protein volume changes upon small-molecule binding.
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Affiliation(s)
- Gediminas Skvarnavičius
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Zigmantas Toleikis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania.,Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Vilma Michailovienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Christian Roumestand
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université s de Montpellier, 34000 Montpellier, France
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
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Brosey CA, Tainer JA. Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology. Curr Opin Struct Biol 2019; 58:197-213. [PMID: 31204190 PMCID: PMC6778498 DOI: 10.1016/j.sbi.2019.04.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 11/27/2022]
Abstract
Small-angle X-ray scattering (SAXS) has emerged as an enabling
integrative technique for comprehensive analyses of macromolecular structures
and interactions in solution. Over the past two decades, SAXS has become a
mainstay of the structural biologist’s toolbox, supplying multiplexed
measurements of molecular shape and dynamics that unveil biological function.
Here, we discuss evolving SAXS theory, methods, and applications that extend the
field of small-angle scattering beyond simple shape characterization. SAXS,
coupled with size-exclusion chromatography (SEC-SAXS) and time-resolved
(TR-SAXS) methods, is now providing high-resolution insight into macromolecular
flexibility and ensembles, delineating biophysical landscapes, and facilitating
high-throughput library screening to assess macromolecular properties and to
create opportunities for drug discovery. Looking forward, we consider SAXS in
the integrative era of hybrid structural biology methods, its potential for
illuminating cellular supramolecular and mesoscale structures, and its capacity
to complement high-throughput bioinformatics sequencing data. As advances in the
field continue, we look forward to proliferating uses of SAXS based upon its
abilities to robustly produce mechanistic insights for biology and medicine.
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Affiliation(s)
- Chris A Brosey
- Molecular and Cellular Oncology and Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - John A Tainer
- Molecular and Cellular Oncology and Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Levin A, Cinar S, Paulus M, Nase J, Winter R, Czeslik C. Analyzing protein-ligand and protein-interface interactions using high pressure. Biophys Chem 2019; 252:106194. [PMID: 31177023 DOI: 10.1016/j.bpc.2019.106194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 01/06/2023]
Abstract
All protein function is based on interactions with the environment. Proteins can bind molecules for their transport, their catalytic conversion, or for signal transduction. They can bind to each other, and they adsorb at interfaces, such as lipid membranes or material surfaces. An experimental characterization is needed to understand the underlying mechanisms, but also to make use of proteins in biotechnology or biomedicine. When protein interactions are studied under high pressure, volume changes are revealed that directly describe spatial contributions to these interactions. Moreover, the strength of protein interactions with ligands or interfaces can be tuned in a smooth way by pressure modulation, which can be utilized in the design of drugs and bio-responsive interfaces. In this short review, selected studies of protein-ligand and protein-interface interactions are presented that were carried out under high pressure. Furthermore, a perspective on bio-responsive interfaces is given where protein-ligand binding is applied to create functional interfacial structures.
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Affiliation(s)
- Artem Levin
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Süleyman Cinar
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Michael Paulus
- Technische Universität Dortmund, Fakultät Physik/Delta, D-44221 Dortmund, Germany
| | - Julia Nase
- Technische Universität Dortmund, Fakultät Physik/Delta, D-44221 Dortmund, Germany
| | - Roland Winter
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Claus Czeslik
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany.
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Levin A, Czeslik C. Interaction of calmodulin with poly(acrylic acid) brushes: Effects of high pressure, pH-value and ligand binding. Colloids Surf B Biointerfaces 2018; 171:478-484. [DOI: 10.1016/j.colsurfb.2018.07.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022]
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Cinar S, Czeslik C. Inhibitor and peptide binding to calmodulin characterized by high pressure Fourier transform infrared spectroscopy and Förster resonance energy transfer. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:617-623. [DOI: 10.1016/j.bbapap.2018.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/09/2018] [Accepted: 03/15/2018] [Indexed: 10/17/2022]
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