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Antila HS, Dixit S, Kav B, Madsen JJ, Miettinen MS, Ollila OHS. Evaluating Polarizable Biomembrane Simulations against Experiments. J Chem Theory Comput 2024; 20:4325-4337. [PMID: 38718349 PMCID: PMC11137822 DOI: 10.1021/acs.jctc.3c01333] [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: 12/06/2023] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 05/29/2024]
Abstract
Owing to the increase of available computational capabilities and the potential for providing a more accurate description, polarizable molecular dynamics force fields are gaining popularity in modeling biomolecular systems. It is, however, crucial to evaluate how much precision is truly gained with increasing cost and complexity of the simulation. Here, we leverage the NMRlipids open collaboration and Databank to assess the performance of available polarizable lipid models─the CHARMM-Drude and the AMOEBA-based parameters─against high-fidelity experimental data and compare them to the top-performing nonpolarizable models. While some improvement in the description of ion binding to membranes is observed in the most recent CHARMM-Drude parameters, and the conformational dynamics of AMOEBA-based parameters are excellent, the best nonpolarizable models tend to outperform their polarizable counterparts for each property we explored. The identified shortcomings range from inaccuracies in describing the conformational space of lipids to excessively slow conformational dynamics. Our results provide valuable insights for the further refinement of polarizable lipid force fields and for selecting the best simulation parameters for specific applications.
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Affiliation(s)
- Hanne S. Antila
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
- Department
of Biomedicine, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
| | - Sneha Dixit
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
| | - Batuhan Kav
- Institute
of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jïulich 52428, Germany
| | - Jesper J. Madsen
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Center
for Global Health and Infectious Diseases Research, Global and Planetary
Health, College of Public Health, University
of South Florida, Tampa, Florida 33612, United States of America
| | - Markus S. Miettinen
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
- Department
of Chemistry, University of Bergen, Bergen 5007, Norway
| | - O. H. Samuli Ollila
- VTT Technical
Research Centre of Finland, Espoo 02044, Finland
- Institute
of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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Lynch CI, Klesse G, Rao S, Tucker SJ, Sansom MSP. Water Nanoconfined in a Hydrophobic Pore: Molecular Dynamics Simulations of Transmembrane Protein 175 and the Influence of Water Models. ACS NANO 2021; 15:19098-19108. [PMID: 34784172 PMCID: PMC7612143 DOI: 10.1021/acsnano.1c06443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Water molecules within biological ion channels are in a nanoconfined environment and therefore exhibit behaviors which differ from that of bulk water. Here, we investigate the phenomenon of hydrophobic gating, the process by which a nanopore may spontaneously dewet to form a "vapor lock" if the pore is sufficiently hydrophobic and/or narrow. This occurs without steric occlusion of the pore. Using molecular dynamics simulations with both rigid fixed-charge and polarizable (AMOEBA) force fields, we investigate this wetting/dewetting behavior in the transmembrane protein 175 ion channel. We examine how a range of rigid fixed-charge and polarizable water models affect wetting/dewetting in both the wild-type structure and in mutants chosen to cover a range of nanopore radii and pore-lining hydrophobicities. Crucially, we find that the rigid fixed-charge water models lead to similar wetting/dewetting behaviors, but that the polarizable water model resulted in an increased wettability of the hydrophobic gating region of the pore. This has significant implications for molecular simulations of nanoconfined water, as it implies that polarizability may need to be included if we are to gain detailed mechanistic insights into wetting/dewetting processes. These findings are of importance for the design of functionalized biomimetic nanopores (e.g., sensing or desalination) as well as for furthering our understanding of the mechanistic processes underlying biological ion channel function.
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Affiliation(s)
- Charlotte I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK, OX1 3QU
| | - Gianni Klesse
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, UK, OX1 3PU
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK, OX1 3QU
| | - Stephen J. Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, UK, OX1 3PU
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK, OX1 3QU
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3
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Multiscale simulations of large complexes in conjunction with cryo-EM analysis. Curr Opin Struct Biol 2021; 72:27-32. [PMID: 34399155 DOI: 10.1016/j.sbi.2021.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/21/2022]
Abstract
The cellular environment is highly crowded with most proteins and RNA/DNA forming homomeric and heteromeric complexes. Essential questions regarding how these complexes switch between functional, rest, and abnormal states with regulators or modifications remain challenging and complicated. Here, we review the recent progress integrating cryoelectron microscopy and multiscale molecular modeling to understand the dynamics and function-related mechanism in protein-RNA/DNA complexes, protein-protein complexes/assemblies, and membrane protein complexes. One future direction of multiscale simulations will be to interpret the large complex multibody regulation in assembly-induced function enhancement in conjunction with advanced atomic resolution structural-biology techniques and specialized computing architectures.
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4
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Jing Z, Rackers JA, Pratt LR, Liu C, Rempe SB, Ren P. Thermodynamics of ion binding and occupancy in potassium channels. Chem Sci 2021; 12:8920-8930. [PMID: 34257893 PMCID: PMC8246295 DOI: 10.1039/d1sc01887f] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Potassium channels modulate various cellular functions through efficient and selective conduction of K+ ions. The mechanism of ion conduction in potassium channels has recently emerged as a topic of debate. Crystal structures of potassium channels show four K+ ions bound to adjacent binding sites in the selectivity filter, while chemical intuition and molecular modeling suggest that the direct ion contacts are unstable. Molecular dynamics (MD) simulations have been instrumental in the study of conduction and gating mechanisms of ion channels. Based on MD simulations, two hypotheses have been proposed, in which the four-ion configuration is an artifact due to either averaged structures or low temperature in crystallographic experiments. The two hypotheses have been supported or challenged by different experiments. Here, MD simulations with polarizable force fields validated by ab initio calculations were used to investigate the ion binding thermodynamics. Contrary to previous beliefs, the four-ion configuration was predicted to be thermodynamically stable after accounting for the complex electrostatic interactions and dielectric screening. Polarization plays a critical role in the thermodynamic stabilities. As a result, the ion conduction likely operates through a simple single-vacancy and water-free mechanism. The simulations explained crystal structures, ion binding experiments and recent controversial mutagenesis experiments. This work provides a clear view of the mechanism underlying the efficient ion conduction and demonstrates the importance of polarization in ion channel simulations. Polarization shapes the energy landscape of ion conduction in potassium channels.![]()
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Joshua A Rackers
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University New Orleans Louisiana 70118 USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Susan B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
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Duboué-Dijon E, Javanainen M, Delcroix P, Jungwirth P, Martinez-Seara H. A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization. J Chem Phys 2021; 153:050901. [PMID: 32770904 DOI: 10.1063/5.0017775] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular simulations can elucidate atomistic-level mechanisms of key biological processes, which are often hardly accessible to experiment. However, the results of the simulations can only be as trustworthy as the underlying simulation model. In many of these processes, interactions between charged moieties play a critical role. Current empirical force fields tend to overestimate such interactions, often in a dramatic way, when polyvalent ions are involved. The source of this shortcoming is the missing electronic polarization in these models. Given the importance of such biomolecular systems, there is great interest in fixing this deficiency in a computationally inexpensive way without employing explicitly polarizable force fields. Here, we review the electronic continuum correction approach, which accounts for electronic polarization in a mean-field way, focusing on its charge scaling variant. We show that by pragmatically scaling only the charged molecular groups, we qualitatively improve the charge-charge interactions without extra computational costs and benefit from decades of force field development on biomolecular force fields.
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Affiliation(s)
- E Duboué-Dijon
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - M Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - P Delcroix
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - P Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - H Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
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Klesse G, Rao S, Tucker SJ, Sansom MS. Induced Polarization in Molecular Dynamics Simulations of the 5-HT 3 Receptor Channel. J Am Chem Soc 2020; 142:9415-9427. [PMID: 32336093 PMCID: PMC7243253 DOI: 10.1021/jacs.0c02394] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Indexed: 12/30/2022]
Abstract
Ion channel proteins form water-filled nanoscale pores within lipid bilayers, and their properties are dependent on the complex behavior of water in a nanoconfined environment. Using a simplified model of the pore of the 5-HT3 receptor (5HT3R) which restrains the backbone structure to that of the parent channel protein from which it is derived, we compare additive with polarizable models in describing the behavior of water in nanopores. Molecular dynamics simulations were performed with four conformations of the channel: two closed state structures, an intermediate state, and an open state, each embedded in a phosphatidylcholine bilayer. Water density profiles revealed that for all water models, the closed and intermediate states exhibited strong dewetting within the central hydrophobic gate region of the pore. However, the open state conformation exhibited varying degrees of hydration, ranging from partial wetting for the TIP4P/2005 water model to complete wetting for the polarizable AMOEBA14 model. Water dipole moments calculated using polarizable force fields also revealed that water molecules remaining within dewetted sections of the pore resemble gas phase water. Free energy profiles for Na+ and for Cl- ions within the open state pore revealed more rugged energy landscapes using polarizable force fields, and the hydration number profiles of these ions were also sensitive to induced polarization resulting in a substantive reduction of the number of waters within the first hydration shell of Cl- while it permeates the pore. These results demonstrate that induced polarization can influence the complex behavior of water and ions within nanoscale pores and provides important new insights into their chemical properties.
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Affiliation(s)
- Gianni Klesse
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.
- Clarendon
Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, U.K.
| | - Shanlin Rao
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.
| | - Stephen J. Tucker
- Clarendon
Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, U.K.
- OXION
Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PT, U.K.
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.
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Intramembrane ionic protein-lipid interaction regulates integrin structure and function. PLoS Biol 2018; 16:e2006525. [PMID: 30427828 PMCID: PMC6261646 DOI: 10.1371/journal.pbio.2006525] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 11/28/2018] [Accepted: 10/29/2018] [Indexed: 11/24/2022] Open
Abstract
Protein transmembrane domains (TMDs) are generally hydrophobic, but our bioinformatics analysis shows that many TMDs contain basic residues at terminal regions. Physiological functions of these membrane-snorkeling basic residues are largely unclear. Here, we show that a membrane-snorkeling Lys residue in integrin αLβ2 (also known as lymphocyte function-associated antigen 1 [LFA-1]) regulates transmembrane heterodimer formation and integrin adhesion through ionic interplay with acidic phospholipids and calcium ions (Ca2+) in T cells. The amino group of the conserved Lys ionically interacts with the phosphate group of acidic phospholipids to stabilize αLβ2 transmembrane association, thus keeping the integrin at low-affinity conformation. Intracellular Ca2+ uses its charge to directly disrupt this ionic interaction, leading to the transmembrane separation and the subsequent extracellular domain extension to increase adhesion activity. This Ca2+-mediated regulation is independent on the canonical Ca2+ signaling or integrin inside-out signaling. Our work therefore showcases the importance of intramembrane ionic protein–lipid interaction and provides a new mechanism of integrin activation. Integrin αLβ2 is the major integrin in T cells and plays a vital role in regulating T-cell activation, adhesion, and migration. The transmembrane association of αL and β2 is crucial for maintaining the integrin at low-affinity conformation. Here, we find that the conserved basic residue (K702) in the transmembrane domain of β2 contributes to transmembrane association through ternary ionic interaction with acidic phospholipid and αL cytoplasmic residue. Upon T-cell activation, influxed calcium ions (Ca2+) can directly disrupt the ionic K702–lipid interaction through its positive charges, which leads to transmembrane separation and subsequent extracellular domain extension to switch αLβ2 to high-affinity conformation. This Ca2+-mediated regulation is through the modulation of the ionic Lys–lipid interaction but not through the canonical Ca2+ signaling or integrin inside-out signaling. Our study thus reports a new regulatory mechanism of integrin activation and showcases the importance of intramembrane ionic protein–lipid interaction. This finding might have general relevance, as bioinformatics analysis shows the presence of membrane-snorkeling basic residue is a common feature of transmembrane proteins.
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