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Maiti S, Heyden M. Model-Dependent Solvation of the K-18 Domain of the Intrinsically Disordered Protein Tau. J Phys Chem B 2023; 127:7220-7230. [PMID: 37556237 DOI: 10.1021/acs.jpcb.3c01726] [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: 08/11/2023]
Abstract
A known imbalance between intra-protein and protein-water interactions in many empirical force fields results in collapsed conformational ensembles of intrinsically disordered proteins in explicit solvent simulations that disagree with experiments. Multiple strategies have been introduced in the literature to modify protein-water interactions, which improve agreement between experiments and simulations. In this work, we combine simulations with standard and modified force fields with a spatially resolved analysis of solvation free energy contributions and compare the consequences of each strategy. We find that enhanced Lennard-Jones (LJ) interactions between protein atoms and water oxygens primarily improve the solvation of nonpolar functional groups of the protein. In contrast, modified electrostatics in the water model or strengthened LJ interactions between the protein and water hydrogens mainly affect the hydration of polar functional groups. Modified electrostatics further impact the average orientation of water molecules in the hydration shell. As a result, protein-water interactions with the first hydration layers are strengthened, while interactions with water molecules in higher hydration shells are weakened. Hence, distinct strategies to balance intra-protein and protein-water interactions in simulations have qualitatively different effects on protein solvation. These differences are not necessarily captured by comparisons to experiments that report on global parameters describing protein conformational ensembles, e.g., the radius of gyration, but will influence the tendency of a protein to form aggregates or phase-separated droplets.
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Affiliation(s)
- Sthitadhi Maiti
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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Roy UC, Bandyopadhyay P. Correlation between protein conformations and water structure and thermodynamics at high pressure: A molecular dynamics study of the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein. J Chem Phys 2023; 158:095102. [PMID: 36889972 DOI: 10.1063/5.0124837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Pressure-induced perturbation of a protein structure leading to its folding-unfolding mechanism is an important yet not fully understood phenomenon. The key point here is the role of water and its coupling with protein conformations as a function of pressure. In the current work, using extensive molecular dynamics simulation at 298 K, we systematically examine the coupling between protein conformations and water structures of pressures of 0.001, 5, 10, 15, 20 kbar, starting from (partially) unfolded structures of the protein Bovine Pancreatic Trypsin Inhibitor (BPTI). We also calculate localized thermodynamics at those pressures as a function of protein-water distance. Our findings show that both protein-specific and generic effects of pressure are operating. In particular, we found that (1) the amount of increase in water density near the protein depends on the protein structural heterogeneity; (2) the intra-protein hydrogen bond decreases with pressure, while the water-water hydrogen bond per water in the first solvation shell (FSS) increases; protein-water hydrogen bonds also found to increase with pressure, (3) with pressure hydrogen bonds of waters in the FSS getting twisted; and (4) water's tetrahedrality in the FSS decreases with pressure, but it is dependent on the local environment. Thermodynamically, at higher pressure, the structural perturbation of BPTI is due to the pressure-volume work, while the entropy decreases with the increase of pressure due to the higher translational and rotational rigidity of waters in the FSS. The local and subtle effects of pressure, found in this work, are likely to be typical of pressure-induced protein structure perturbation.
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Affiliation(s)
- Umesh C Roy
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Oliva R, Winter R. Harnessing Pressure-Axis Experiments to Explore Volume Fluctuations, Conformational Substates, and Solvation of Biomolecular Systems. J Phys Chem Lett 2022; 13:12099-12115. [PMID: 36546666 DOI: 10.1021/acs.jpclett.2c03186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Intrinsic thermodynamic fluctuations within biomolecules are crucial for their function, and flexibility is one of the strategies that evolution has developed to adapt to extreme environments. In this regard, pressure perturbation is an important tool for mechanistically exploring the causes and effects of volume fluctuations in biomolecules and biomolecular assemblies, their role in biomolecular interactions and reactions, and how they are affected by the solvent properties. High hydrostatic pressure is also a key parameter in the context of deep-sea and subsurface biology and the study of the origin and physical limits of life. We discuss the role of pressure-axis experiments in revealing intrinsic structural fluctuations as well as high-energy conformational substates of proteins and other biomolecular systems that are important for their function and provide some illustrative examples. We show that the structural and dynamic information obtained from such pressure-axis studies improves our understanding of biomolecular function, disease, biological evolution, and adaptation.
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Affiliation(s)
- Rosario Oliva
- Department of Chemistry and Chemical Biology, Physical Chemistry I, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 6, Dortmund44227, Germany
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126Naples, Italy
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Physical Chemistry I, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 6, Dortmund44227, Germany
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Waskasi MM, Lazaric A, Heyden M. Solvent-mediated forces in protein dielectrophoresis. Electrophoresis 2021; 42:2060-2069. [PMID: 34302698 DOI: 10.1002/elps.202100087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/09/2021] [Accepted: 07/15/2021] [Indexed: 12/23/2022]
Abstract
DEP is an established method to manipulate micrometer-sized particles, but standard continuum theories predict only negligible effects for nanometer-sized proteins despite contrary experimental evidence. A theoretical description of protein DEP needs to consider details on the molecular scale. Previous work toward this goal addressed the role of orientational polarization of static protein dipole moments for dielectrophoretic effects, which successfully predicts the general magnitude of dielectrophoretic forces on proteins but does not readily explain negative DEP forces observed for proteins in some experiments. However, contributions to the protein chemical potential due to protein-water interactions have not yet been considered in this context. Here, we utilize atomistic molecular dynamics simulations to evaluate polarization-induced changes in the protein solvation free energy, which result in a solvent-mediated contribution to dielectrophoretic forces. We quantify solvent-mediated dielectrophoretic forces for two proteins and a small peptide in water, which follow expectations for protein-water dipole-dipole interactions. The magnitude of solvent-mediated dielectrophoretic forces exceeds predictions of nonmolecular continuum theories, but plays a minor role for the total dielectrophoretic force for the simulated proteins due to dominant contributions from the orientational polarization of their static protein dipoles. However, we extrapolate that solvent-mediated contributions to negative protein DEP forces will become increasingly relevant for multidomain proteins, complexes and aggregates with large protein-water interfaces, as well as for high electric field frequencies, which provides a potential mechanism for corresponding experimental observations of negative protein DEP.
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Affiliation(s)
- Morteza M Waskasi
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | | | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
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5
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Sun H, Jiao R, An G, Xu H, Wang D. Influence of particle size on the aggregation behavior of nanoparticles: Role of structural hydration layer. J Environ Sci (China) 2021; 103:33-42. [PMID: 33743914 DOI: 10.1016/j.jes.2020.10.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/10/2020] [Accepted: 10/11/2020] [Indexed: 06/12/2023]
Abstract
More and more attention has been paid to the aggregation behavior of nanoparticles, but little research has been done on the effect of particle size. Therefore, this study systematically evaluated the aggregation behavior of nano-silica particles with diameter 130-480 nm at different initial particle concentration, pH, ionic strength, and ionic valence of electrolytes. The modified Smoluchowski theory failed to describe the aggregation kinetics for nano-silica particles with diameters less than 190 nm. Besides, ionic strength, cation species and pH all affected fast aggregation rate coefficients of 130 nm nanoparticles. Through incorporating structural hydration force into the modified Smoluchowski theory, it is found that the reason for all the anomalous aggregation behavior was the different structural hydration layer thickness of nanoparticles with various sizes. The thickness decreased with increasing of particle size, and remained basically unchanged for particles larger than 190 nm. Only when the distance at primary minimum was twice the thickness of structural hydration layer, the structural hydration force dominated, leading to the higher stability of nanoparticles. This study clearly clarified the unique aggregation mechanism of nanoparticles with smaller size, which provided reference for predicting transport and fate of nanoparticles and could help facilitate the evaluation of their environment risks.
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Affiliation(s)
- Hongyan Sun
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruyuan Jiao
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Guangyu An
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hui Xu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Dongsheng Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Le Vay K, Carter BM, Watkins DW, Dora Tang TY, Ting VP, Cölfen H, Rambo RP, Smith AJ, Ross Anderson JL, Perriman AW. Controlling Protein Nanocage Assembly with Hydrostatic Pressure. J Am Chem Soc 2020; 142:20640-20650. [PMID: 33252237 DOI: 10.1021/jacs.0c07285] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Controlling the assembly and disassembly of nanoscale protein cages for the capture and internalization of protein or non-proteinaceous components is fundamentally important to a diverse range of bionanotechnological applications. Here, we study the reversible, pressure-induced dissociation of a natural protein nanocage, E. coli bacterioferritin (Bfr), using synchrotron radiation small-angle X-ray scattering (SAXS) and circular dichroism (CD). We demonstrate that hydrostatic pressures of 450 MPa are sufficient to completely dissociate the Bfr 24-mer into protein dimers, and the reversibility and kinetics of the reassembly process can be controlled by selecting appropriate buffer conditions. We also demonstrate that the heme B prosthetic group present at the subunit dimer interface influences the stability and pressure lability of the cage, despite its location being discrete from the interdimer interface that is key to cage assembly. This indicates a major cage-stabilizing role for heme within this family of ferritins.
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Affiliation(s)
- Kristian Le Vay
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
- Bristol Centre for Functional Nanomaterials, HH Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K
| | - Ben M Carter
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - T-Y Dora Tang
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Valeska P Ting
- Bristol Composites Institute (ACCIS), Department of Mechanical Engineering, University of Bristol, Queen's Building, Bristol BS8 1TR, U.K
| | - Helmut Cölfen
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Robert P Rambo
- Diamond House, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Fermi Ave., Didcot OX11 0DE, U.K
| | - Andrew J Smith
- Diamond House, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Fermi Ave., Didcot OX11 0DE, U.K
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Adam W Perriman
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K
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