1
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Wan Y, Guo S, Zhen W, Xu L, Chen X, Liu F, Shen Y, Liu S, Hu L, Wang X, Ye F, Wang Q, Wen H, Yang F. Structural basis of adenine nucleotides regulation and neurodegenerative pathology in ClC-3 exchanger. Nat Commun 2024; 15:6654. [PMID: 39107281 PMCID: PMC11303396 DOI: 10.1038/s41467-024-50975-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
The ClC-3 chloride/proton exchanger is both physiologically and pathologically critical, as it is potentiated by ATP to detect metabolic energy level and point mutations in ClC-3 lead to severe neurodegenerative diseases in human. However, why this exchanger is differentially modulated by ATP, ADP or AMP and how mutations caused gain-of-function remains largely unknow. Here we determine the high-resolution structures of dimeric wildtype ClC-3 in the apo state and in complex with ATP, ADP and AMP, and the disease-causing I607T mutant in the apo and ATP-bounded state by cryo-electron microscopy. In combination with patch-clamp recordings and molecular dynamic simulations, we reveal how the adenine nucleotides binds to ClC-3 and changes in ion occupancy between apo and ATP-bounded state. We further observe I607T mutation induced conformational changes and augments in current. Therefore, our study not only lays the structural basis of adenine nucleotides regulation in ClC-3, but also clearly indicates the target region for drug discovery against ClC-3 mediated neurodegenerative diseases.
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Affiliation(s)
- Yangzhuoqun Wan
- Department of Biophysics and Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
| | - Shuangshuang Guo
- Department of Biophysics and Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
| | - Wenxuan Zhen
- Department of Biophysics and Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
| | - Lizhen Xu
- Department of Biophysics and Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
| | - Xiaoying Chen
- Department of Biophysics and Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
| | - Fangyue Liu
- Department of Neurobiology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Shen
- Department of Neurobiology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuangshuang Liu
- Core Facilities, Zhejiang University School of Medicine, Hangzhou, China
| | - Lidan Hu
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | | | | | | | - Han Wen
- DP Technology, Beijing, China.
- Institute for Advanced Algorithms Research, Shanghai, China.
- State Key Laboratory of Medical Proteomics, Shanghai, China.
- AI for Science Institute, Beijing, China.
- National Key Laboratory of Lead Druggability Research, Beijing, China.
| | - Fan Yang
- Department of Biophysics and Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China.
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2
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Kaiser S, Yue Z, Peng Y, Nguyen TD, Chen S, Teng D, Voth GA. Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package. J Phys Chem B 2024; 128:4959-4974. [PMID: 38742764 PMCID: PMC11129700 DOI: 10.1021/acs.jpcb.4c01987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system's bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.
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Affiliation(s)
- Scott Kaiser
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Zhi Yue
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Yuxing Peng
- NVIDIA
Corporation, Santa
Clara, California 95051, United States
| | - Trung Dac Nguyen
- Research
Computing Center, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sijia Chen
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Da Teng
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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3
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Liu J, Wang Y, Gao B, Zhang K, Li H, Ren J, Huo F, Zhao B, Zhang L, Zhang S, He H. Ionic Liquid Gating Induces Anomalous Permeation through Membrane Channel Proteins. J Am Chem Soc 2024; 146:13588-13597. [PMID: 38695646 DOI: 10.1021/jacs.4c03506] [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: 05/16/2024]
Abstract
Membrane channel proteins (MCPs) play key roles in matter transport through cell membranes and act as major targets for vaccines and drugs. For emerging ionic liquid (IL) drugs, a rational understanding of how ILs affect the structure and transport function of MCP is crucial to their design. In this work, GPU-accelerated microsecond-long molecular dynamics simulations were employed to investigate the modulating mechanism of ILs on MCP. Interestingly, ILs prefer to insert into the lipid bilayer and channel of aquaporin-2 (AQP2) but adsorb on the entrance of voltage-gated sodium channels (Nav). Molecular trajectory and free energy analysis reflect that ILs have a minimal impact on the structure of MCPs but significantly influence MCP functions. It demonstrates that ILs can decrease the overall energy barrier for water through AQP2 by 1.88 kcal/mol, whereas that for Na+ through Nav is increased by 1.70 kcal/mol. Consequently, the permeation rates of water and Na+ can be enhanced and reduced by at least 1 order of magnitude, respectively. Furthermore, an abnormal IL gating mechanism was proposed by combining the hydrophobic nature of MCP and confined water/ion coordination effects. More importantly, we performed experiments to confirm the influence of ILs on AQP2 in human cells and found that treatment with ILs significantly accelerated the changes in cell volume in response to altered external osmotic pressure. Overall, these quantitative results will not only deepen the understanding of IL-cell interactions but may also shed light on the rational design of drugs and disease diagnosis.
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Affiliation(s)
- Ju Liu
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanlei Wang
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Longzihu New Energy Laboratory, Zhengzhou Institute of Emerging Industrial Technology, Henan University, Zhengzhou 450000, China
| | - Bo Gao
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing 100875, China
| | - Kun Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Hui Li
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing 100875, China
| | - Jing Ren
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Feng Huo
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Longzihu New Energy Laboratory, Zhengzhou Institute of Emerging Industrial Technology, Henan University, Zhengzhou 450000, China
| | - Baofeng Zhao
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Suojiang Zhang
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Longzihu New Energy Laboratory, Zhengzhou Institute of Emerging Industrial Technology, Henan University, Zhengzhou 450000, China
| | - Hongyan He
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Longzihu New Energy Laboratory, Zhengzhou Institute of Emerging Industrial Technology, Henan University, Zhengzhou 450000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Selvam B, Chiang N, Shukla D. Energetics of substrate transport in proton-dependent oligopeptide transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592129. [PMID: 38746282 PMCID: PMC11092630 DOI: 10.1101/2024.05.01.592129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The PepT So transporter mediates the transport of peptides across biological membranes. Despite advancements in structural biology, including cryogenic electron microscopy structures resolving PepT So in different states, the molecular basis of peptide recognition and transport by PepT So is not fully elucidated. In this study, we employed molecular dynamics simulations, Markov State Models (MSMs), and Transition Path Theory (TPT) to investigate the transport mechanism of an alanine-alanine peptide (Ala-Ala) through the PepT So transporter. Our simulations revealed conformational changes and key intermediate states involved in peptide translocation. We observed that the presence of the Ala-Ala peptide substrate lowers the free energy barriers associated with transition to the inward-facing state. Furthermore, we elucidated the proton transport model and analyzed the pharmacophore features of intermediate states, providing insights for rational drug design. These findings highlight the significance of substrate binding in modulating the conformational dynamics of PepT So and identify critical residues that facilitate transport.
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5
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Drew D, Boudker O. Ion and lipid orchestration of secondary active transport. Nature 2024; 626:963-974. [PMID: 38418916 DOI: 10.1038/s41586-024-07062-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024]
Abstract
Transporting small molecules across cell membranes is an essential process in cell physiology. Many structurally diverse, secondary active transporters harness transmembrane electrochemical gradients of ions to power the uptake or efflux of nutrients, signalling molecules, drugs and other ions across cell membranes. Transporters reside in lipid bilayers on the interface between two aqueous compartments, where they are energized and regulated by symported, antiported and allosteric ions on both sides of the membrane and the membrane bilayer itself. Here we outline the mechanisms by which transporters couple ion and solute fluxes and discuss how structural and mechanistic variations enable them to meet specific physiological needs and adapt to environmental conditions. We then consider how general bilayer properties and specific lipid binding modulate transporter activity. Together, ion gradients and lipid properties ensure the effective transport, regulation and distribution of small molecules across cell membranes.
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Affiliation(s)
- David Drew
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, Weill Cornell Medicine, New York, NY, USA.
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6
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Di Pino S, Donkor ED, Sánchez VM, Rodriguez A, Cassone G, Scherlis D, Hassanali A. ZundEig: The Structure of the Proton in Liquid Water from Unsupervised Learning. J Phys Chem B 2023; 127:9822-9832. [PMID: 37930954 DOI: 10.1021/acs.jpcb.3c06078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The structure of the excess proton in liquid water has been the subject of lively debate on both experimental and theoretical fronts for the last century. Fluctuations of the proton are typically interpreted in terms of limiting states referred to as the Eigen and Zundel species. Here, we put these ideas under the microscope, taking advantage of recent advances in unsupervised learning that use local atomic descriptors to characterize environments of acidic water combined with advanced clustering techniques. Our agnostic approach leads to the observation of only one charged cluster and two neutral ones. We demonstrate that the charged cluster involving the excess proton is best seen as an ionic topological defect in water's hydrogen bond network, forming a single local minimum on the global free-energy landscape. This charged defect is a highly fluxional moiety, where the idealized Eigen and Zundel species are neither limiting configurations nor distinct thermodynamic states. Instead, the ionic defect enhances the presence of neutral water defects through strong interactions with the network. We dub the combination of the charged and neutral defect clusters as ZundEig, demonstrating that the fluctuations between these local environments provide a general framework for rationalizing more descriptive notions of the proton in the existing literature.
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Affiliation(s)
- Solana Di Pino
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Edward Danquah Donkor
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Veronica M Sánchez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Alex Rodriguez
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- Dipartimento di Matematica e Geoscienze, Universitá degli Studi di Trieste, via Alfonso Valerio 12/1, 34127 Trieste, Italy
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council (CNR-IPCF), Viale Stagno d'Alcontres 37, 98158 Messina, Italy
| | - Damian Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Ali Hassanali
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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7
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Kratochvil HT, Watkins LC, Mravic M, Thomaston JL, Nicoludis JM, Somberg NH, Liu L, Hong M, Voth GA, DeGrado WF. Transient water wires mediate selective proton transport in designed channel proteins. Nat Chem 2023; 15:1012-1021. [PMID: 37308712 PMCID: PMC10475958 DOI: 10.1038/s41557-023-01210-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 04/19/2023] [Indexed: 06/14/2023]
Abstract
Selective proton transport through proteins is essential for forming and using proton gradients in cells. Protons are conducted along hydrogen-bonded 'wires' of water molecules and polar side chains, which, somewhat surprisingly, are often interrupted by dry apolar stretches in the conduction pathways, inferred from static protein structures. Here we hypothesize that protons are conducted through such dry spots by forming transient water wires, often highly correlated with the presence of the excess protons in the water wire. To test this hypothesis, we performed molecular dynamics simulations to design transmembrane channels with stable water pockets interspersed by apolar segments capable of forming flickering water wires. The minimalist designed channels conduct protons at rates similar to viral proton channels, and they are at least 106-fold more selective for H+ over Na+. These studies inform the mechanisms of biological proton conduction and the principles for engineering proton-conductive materials.
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Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA.
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Laura C Watkins
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, IL, USA
- Kemper Insurance, Chicago, IL, USA
| | - Marco Mravic
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
- Department of Integrative Structural and Computational Biology Scripps Research Institute, La Jolla, CA, USA
| | - Jessica L Thomaston
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
| | - John M Nicoludis
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
- Genentech, San Francisco, CA, USA
| | - Noah H Somberg
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, IL, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA.
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8
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Grigorenko BL, Polyakov IV, Khrenova MG, Giudetti G, Faraji S, Krylov AI, Nemukhin AV. Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms. J Am Chem Soc 2023; 145:13204-13214. [PMID: 37294056 DOI: 10.1021/jacs.3c02229] [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: 06/10/2023]
Abstract
We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have shown experimentally the ability to inhibit MPro. Two other compounds, X77A and X77C, were designed computationally in this work. They were derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro. We modified the X77 structure by introducing warheads capable of reacting with the catalytic cysteine residue in the MPro active site. The reaction mechanisms of the four molecules with MPro were investigated by quantum mechanics/molecular mechanics (QM/MM) simulations. The results show that all four compounds form covalent adducts with the catalytic cysteine Cys 145 of MPro. From the chemical perspective, the reactions of these four molecules with MPro follow three distinct mechanisms. The reactions are initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro. In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand is accompanied by the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SNAr mechanism. The reaction of MPro with nirmatrelvir (which has a reactive nitrile group) leads to the formation of a covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site. Our results contribute to the ongoing search for efficient inhibitors of the SARS-CoV-2 enzymes.
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Affiliation(s)
- Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia
| | - Goran Giudetti
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
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9
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Yue Z, Li C, Voth GA. The role of conformational change and key glutamic acid residues in the ClC-ec1 antiporter. Biophys J 2023; 122:1068-1085. [PMID: 36698313 PMCID: PMC10111279 DOI: 10.1016/j.bpj.2023.01.025] [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: 10/24/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
The triple glutamine (Q) mutant (QQQ) structure of a Cl-/H+ antiporter from Escherichia coli (ClC-ec1) displaying a novel backbone arrangement has been used to challenge the long-held notion that Cl-/H+ antiporters do not operate through large conformational motions. The QQQ mutant substitutes the glutamine residue for an external glutamate E148, an internal glutamate E203, and a third glutamate E113 that hydrogen-bonds with E203. However, it is unknown if QQQ represents a physiologically relevant state, as well as how the protonation of the wild-type glutamates relates to the global dynamics. We herein apply continuous constant-pH molecular dynamics to investigate the H+-coupled dynamics of ClC-ec1. Although any large-scale conformational rearrangement upon acidification would be due to the accumulation of excess charge within the protein, protonation of the glutamates significantly impacts mainly the local structure and dynamics. Despite the fact that the extracellular pore enlarges at acidic pHs, an occluded ClC-ec1 within the active pH range of 3.5-7.5 requires a protonated E148 to facilitate extracellular Cl- release. E203 is also involved in the intracellular H+ transfer as an H+ acceptor. The water wire connection of E148 with the intracellular solution is regulated by the charge states of the E113/E203 dyad with coupled proton titration. However, the dynamics extracted from our simulations are not QQQ-like, indicating that the QQQ mutant does not represent the behavior of the wild-type ClC-ec1. These findings reinforce the necessity of having a protonatable residue at the E203 position in ClC-ec1 and suggest that a higher level of complexity exists for the intracellular H+ transfer in Cl-/H+ antiporters.
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Affiliation(s)
- Zhi Yue
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Chenghan Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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10
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Grigorenko B, Domratcheva T, Nemukhin A. QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase. Molecules 2023; 28:molecules28052405. [PMID: 36903648 PMCID: PMC10005588 DOI: 10.3390/molecules28052405] [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: 01/27/2023] [Revised: 02/21/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Oxygenase activity of the flavin-dependent enzyme RutA is commonly associated with the formation of flavin-oxygen adducts in the enzyme active site. We report the results of quantum mechanics/molecular mechanics (QM/MM) modeling of possible reaction pathways initiated by various triplet state complexes of the molecular oxygen with the reduced flavin mononucleotide (FMN) formed in the protein cavities. According to the calculation results, these triplet-state flavin-oxygen complexes can be located at both re-side and si-side of the isoalloxazine ring of flavin. In both cases, the dioxygen moiety is activated by electron transfer from FMN, stimulating the attack of the arising reactive oxygen species at the C4a, N5, C6, and C8 positions in the isoalloxazine ring after the switch to the singlet state potential energy surface. The reaction pathways lead to the C(4a)-peroxide, N(5)-oxide, or C(6)-hydroperoxide covalent adducts or directly to the oxidized flavin, depending on the initial position of the oxygen molecule in the protein cavities.
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Affiliation(s)
- Bella Grigorenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Tatiana Domratcheva
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
- Correspondence:
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11
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Hao H, Adams EM, Funke S, Schwaab G, Havenith M, Head-Gordon T. Highly Altered State of Proton Transport in Acid Pools in Charged Reverse Micelles. J Am Chem Soc 2023; 145:1826-1834. [PMID: 36633459 PMCID: PMC9881006 DOI: 10.1021/jacs.2c11331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Indexed: 01/13/2023]
Abstract
Transport mechanisms of solvated protons of 1 M HCl acid pools, confined within reverse micelles (RMs) containing the negatively charged surfactant sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) or the positively charged cetyltrimethylammonium bromide (CTABr), are analyzed with reactive force field simulations to interpret dynamical signatures from TeraHertz absorption and dielectric relaxation spectroscopy. We find that the forward proton hopping events for NaAOT are further suppressed compared to a nonionic RM, while the Grotthuss mechanism ceases altogether for CTABr. We attribute the sluggish proton dynamics for both charged RMs as due to headgroup and counterion charges that expel hydronium and chloride ions from the interface and into the bulk interior, thereby increasing the pH of the acid pools relative to the nonionic RM. For charged NaAOT and CTABr RMs, the localization of hydronium near a counterion or conjugate base reduces the Eigen and Zundel configurations that enable forward hopping. Thus, localized oscillatory hopping dominates, an effect that is most extreme for CTABr in which the proton residence time increases dramatically such that even oscillatory hopping is slow.
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Affiliation(s)
- Hongxia Hao
- Kenneth
S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California94720, United States
| | - Ellen M. Adams
- Cluster
of Excellence Physics of Life, Technische
Universität Dresden, 01307Dresden, Germany
- Helmholtz-Zentrum
Dresden-Rossendorf, Institute of Resource
Ecology, 01328Dresden, Germany
| | - Sarah Funke
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801Bochum, Germany
| | - Gerhard Schwaab
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801Bochum, Germany
| | - Martina Havenith
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801Bochum, Germany
| | - Teresa Head-Gordon
- Kenneth
S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California94720, United States
- Department
of Bioengineering, Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California94720, United States
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12
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Liu Y, Li C, Voth GA. Generalized Transition State Theory Treatment of Water-Assisted Proton Transport Processes in Proteins. J Phys Chem B 2022; 126:10452-10459. [PMID: 36459423 PMCID: PMC9762399 DOI: 10.1021/acs.jpcb.2c06703] [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: 09/20/2022] [Revised: 11/15/2022] [Indexed: 12/03/2022]
Abstract
Transition state theory (TST) is widely employed for estimating the transition rate of a reaction when combined with free energy sampling techniques. A derivation of the transition theory rate expression for a general n-dimensional case is presented in this work which specifically focuses on water-assisted proton transfer/transport reactions, especially for protein systems. Our work evaluates the TST prefactor calculated at the transition state dividing surface compared to one sampled, as an approximation, in the reactant state in four case studies of water-assisted proton transport inside membrane proteins and highlights the significant impact of the prefactor position dependence in proton transport processes.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois60637, United States
| | - Chenghan Li
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois60637, United States
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois60637, United States
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13
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Zuchniarz J, Liu Y, Li C, Voth GA. Accurate p Ka Calculations in Proteins with Reactive Molecular Dynamics Provide Physical Insight Into the Electrostatic Origins of Their Values. J Phys Chem B 2022; 126:7321-7330. [PMID: 36106487 PMCID: PMC9528908 DOI: 10.1021/acs.jpcb.2c04899] [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: 07/11/2022] [Revised: 08/28/2022] [Indexed: 11/29/2022]
Abstract
Classical molecular dynamics simulations are a versatile tool in the study of biomolecular systems, but they usually rely on a fixed bonding topology, precluding the explicit simulation of chemical reactivity. Certain modifications can permit the modeling of reactions. One such method, multiscale reactive molecular dynamics, makes use of a linear combination approach to describe condensed-phase free energy surfaces of reactive processes of biological interest. Before these simulations can be performed, models of the reactive moieties must first be parametrized using electronic structure data. A recent study demonstrated that gas-phase electronic structure data can be used to derive parameters for glutamate and lysine which reproduce experimental pKa values in both bulk water and the staphylococcal nuclease protein with remarkable accuracy and transferability between the water and protein environments. In this work, we first present a new model for aspartate derived in similar fashion and demonstrate that it too produces accurate pKa values in both bulk and protein contexts. We also describe a modification to the prior methodology, involving refitting some of the classical force field parameters to density functional theory calculations, which improves the transferability of the existing glutamate model. Finally and most importantly, this reactive molecular dynamics approach, based on rigorous statistical mechanics, allows one to specifically analyze the fundamental physical causes for the marked pKa shift of both aspartate and glutamate between bulk water and protein and also to demonstrate that local steric and electrostatic effects largely explain the observed differences.
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Affiliation(s)
- Joshua Zuchniarz
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois 60637, United States
| | - Yu Liu
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois 60637, United States
| | - Chenghan Li
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois 60637, United States
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14
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Nordquist EB, Schultz SA, Chen J. Using Metadynamics To Explore the Free Energy of Dewetting in Biologically Relevant Nanopores. J Phys Chem B 2022; 126:6428-6437. [PMID: 35998613 PMCID: PMC9932947 DOI: 10.1021/acs.jpcb.2c04157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Water confined within hydrophobic spaces can undergo cooperative dewetting transitions due to slight changes in water density and pressure that push water toward the vapor phase. Many transmembrane protein ion channels contain nanoscale hydrophobic pores that could undergo dewetting transitions, sometimes blocking the flow of ions without physical blockages. Standard molecular dynamics simulations have been extensively applied to study the behavior of water in nanoscale pores, but the large free energy barriers of dewetting often prevent direct sampling of both wet and dry states and quantitative studies of the hydration thermodynamics of biologically relevant pores. Here, we describe a metadynamics protocol that uses the number of waters within the pore as the collective variable to drive many reversible transitions between relevant hydration states and calculate well-converged free energy profiles of pore hydration. By creating model nanopore systems and changing their radius and morphology and including various cosolvents, we quantify how these pore properties and cosolvents affect the dewetting transition. The results reveal that the dewetting free energy of nanoscale pores is determined by two key thermodynamic parameters, namely, the effective surface tension coefficients of water-air and water-pore interfaces. Importantly, while the effect of salt can be fully captured in the water activity dependence, amphipathic cosolvents such as alcohols modify both dry and wet states of the pore and dramatically shift the wet-dry equilibrium. The metadynamics approach could be applied to studies of dewetting transitions within nanoscale pores of proteins and provide new insights into why different pore properties evolved in biological systems.
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Affiliation(s)
- Erik B. Nordquist
- Department of Chemistry, University of Massachusetts, Amherst Massachusetts, USA 01003
| | - Samantha A. Schultz
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst Massachusetts, USA 01003
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst Massachusetts, USA 01003
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst Massachusetts, USA 01003
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15
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Proton Coupling and the Multiscale Kinetic Mechanism of a Peptide Transporter. Biophys J 2022; 121:2266-2278. [PMID: 35614850 DOI: 10.1016/j.bpj.2022.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 11/02/2022] Open
Abstract
Proton coupled peptide transporters (POTs) are crucial for the uptake of di- and tri-peptides as well as drug and pro-drug molecules in prokaryotes and eukaryotic cells. We illustrate from multiscale modeling how transmembrane proton flux couples within a POT protein to drive essential steps of the full functional cycle: 1) protonation of a glutamate on transmembrane helix (TM) 7 opens the extracellular gate, allowing ligand entry; 2) inward proton flow induces the cytosolic release of ligand by varying the protonation state of a second conserved glutamate on TM10; 3) proton movement between TM7 and TM10 is thermodynamically driven and kinetically permissible via water proton shuttling without the participation of ligand. Our results, for the first time, give direct computational confirmation for the alternating access model of POTs, and point to a quantitative multiscale kinetic picture of the functioning protein mechanism.
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16
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Konermann L, Kim S. Grotthuss Molecular Dynamics Simulations for Modeling Proton Hopping in Electrosprayed Water Droplets. J Chem Theory Comput 2022; 18:3781-3794. [PMID: 35544700 DOI: 10.1021/acs.jctc.2c00001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Excess protons in water exhibit unique transport properties because they can rapidly hop along H-bonded water wires. Considerable progress has been made in unraveling this Grotthuss diffusion mechanism using quantum mechanical-based computational techniques. Unfortunately, high computational cost tends to restrict those techniques to small systems and short times. Molecular dynamics (MD) simulations can be applied to much larger systems and longer time windows. However, standard MD methods do not permit the dissociation/formation of covalent bonds, such that Grotthuss diffusion cannot be captured. Here, we bridge this gap by combining atomistic MD simulations (using Gromacs and TIP4P/2005 water) with proton hopping. Excess protons are modeled as hydronium ions that undergo H3O+ + H2O → H2O + H3O+ transitions. In accordance with ab initio MD data, these Grotthuss hopping events are executed in "bursts" with quasi-instantaneous hopping across one or more waters. The bursts are separated by regular MD periods during which H3O+ ions undergo Brownian diffusion. The resulting proton diffusion coefficient agrees with the literature value. We apply this Grotthuss MD technique to highly charged water droplets that are in a size regime encountered during electrospray ionization (5 nm radius, ∼17,000 H2O). The droplets undergo rapid solvent evaporation and occasional H3O+ ejection, keeping them at ca. 81% of the Rayleigh limit. The simulated behavior is consistent with phase Doppler anemometry data. The Grotthuss MD technique developed here should be useful for modeling the behavior of various proton-containing systems that are too large for high-level computational approaches. In particular, we envision future applications related to electrospray processes, where earlier simulations used metal cations while in reality excess protons dominate.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Scott Kim
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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17
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Ion permeation, selectivity, and electronic polarization in fluoride channels. Biophys J 2022; 121:1336-1347. [PMID: 35151630 PMCID: PMC9034187 DOI: 10.1016/j.bpj.2022.02.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 12/16/2022] Open
Abstract
Fluoride channels (Flucs) export toxic F- from the cytoplasm. Crystallography and mutagenesis have identified several conserved residues crucial for fluoride transport, but the permeation mechanism at the molecular level has remained elusive. Herein, we have applied constant-pH molecular dynamics and free-energy-sampling methods to investigate fluoride permeation through a Fluc protein from Escherichia coli. We find that fluoride is facile to permeate in its charged form, i.e., F-, by traversing through a non-bonded network. The extraordinary F- selectivity is gained by the hydrogen-bonding capability of the central binding site and the Coulombic filter at the channel entrance. The F- permeation rate calculated using an electronically polarizable force field is significantly more accurate compared with the experimental value than that calculated using a more standard additive force field, suggesting an essential role for electronic polarization in the F--Fluc interactions.
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