1
|
Deng J, Cui Q. Electronic Polarization Leads to a Drier Dewetted State for Hydrophobic Gating in the Big Potassium Channel. J Phys Chem Lett 2024; 15:7436-7441. [PMID: 39008088 DOI: 10.1021/acs.jpclett.4c01359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
In the hydrophobic gating mechanism proposed for some ion channels, ion permeation is not blocked by the physical dimension of the channel pore but by its dewetted state which constitutes the energetic bottleneck. A major source of uncertainty in the mechanism is that the dewetted state was not observed in experiments and only probed in simulations using nonpolarizable force fields, which do not accurately represent the properties of confined water. Here we analyze hydration of the central cavity in the pore-gate domain of the Big Potassium channel using molecular dynamics and grand canonical Monte Carlo simulations with enhanced sampling techniques. Including polarization leads to a much drier dewetted state and a higher barrier for the transition to the wet state, suggesting more effective hydrophobic gating. The simulations also identify two backbone carbonyls at the bottom of the selectivity filter as good candidates for characterizing the dewetted state using infrared spectroscopies.
Collapse
Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
| |
Collapse
|
2
|
Yamamoto E, Joo K, Lee J, Sansom MSP, Yasui M. Molecular mechanism of anion permeation through aquaporin 6. Biophys J 2024:S0006-3495(24)00410-7. [PMID: 38894539 DOI: 10.1016/j.bpj.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/07/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024] Open
Abstract
Aquaporins (AQPs) are recognized as transmembrane water channels that facilitate selective water permeation through their monomeric pores. Among the AQP family, AQP6 has an intriguing characteristic as an anion channel, which is allosterically controlled by pH conditions and is eliminated by a single amino acid mutation. However, the molecular mechanism of anion permeation through AQP6 remains unclear. Using molecular dynamics simulations in the presence of a transmembrane voltage utilizing an ion concentration gradient, we show that chloride ions permeate through the pore corresponding to the central axis of the AQP6 homotetramer. Under low pH conditions, a subtle opening of the hydrophobic selectivity filter (SF), located near the extracellular part of the central pore, becomes wetted and enables anion permeation. Our simulations also indicate that a single mutation (N63G) in human AQP6, located at the central pore, significantly reduces anion conduction, consistent with experimental data. Moreover, we demonstrate that the pH-sensing mechanism in which the protonation of H184 and H189 under low pH conditions allosterically triggers the gating of the SF region. These results suggest a unique pH-dependent allosteric anion permeation mechanism in AQP6 and could clarify the role of the central pore in some of the AQP tetramers.
Collapse
Affiliation(s)
- Eiji Yamamoto
- Department of System Design Engineering, Keio University, Yokohama, Kanagawa, Japan.
| | - Keehyoung Joo
- Center for Advanced Computation, Korea Institute for Advanced Study, Seoul, Korea
| | - Jooyoung Lee
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Masato Yasui
- Department of Pharmacology, Keio University School of Medicine, Tokyo, Japan
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Deng J, Cui Q. Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields. J Chem Theory Comput 2024; 20:1897-1911. [PMID: 38417108 DOI: 10.1021/acs.jctc.4c00013] [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: 03/01/2024]
Abstract
Prediction of the hydration levels of protein cavities and active sites is important to both mechanistic analysis and ligand design. Due to the unique microscopic environment of these buried water molecules, a polarizable model is expected to be crucial for an accurate treatment of protein internal hydration in simulations. Here we adapt a nonequilibrium candidate Monte Carlo approach for conducting grand canonical Monte Carlo simulations with the Drude polarizable force field. The GPU implementation enables the efficient sampling of internal cavity hydration levels in biomolecular systems. We also develop an enhanced sampling approach referred to as B-walking, which satisfies detailed balance and readily combines with grand canonical integration to efficiently calculate quantitative binding free energies of water to protein cavities. Applications of these developments are illustrated in a solvent box and the polar ligand binding site in trypsin. Our simulation results show that including electronic polarization leads to a modest but clear improvement in the description of water position and occupancy compared to the crystal structure. The B-walking approach enhances the range of water sampling in different chemical potential windows and thus improves the accuracy of water binding free energy calculations.
Collapse
Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
| |
Collapse
|
5
|
Ryan M, Gao L, Valiyaveetil FI, Kananenka AA, Zanni MT. Water inside the Selectivity Filter of a K + Ion Channel: Structural Heterogeneity, Picosecond Dynamics, and Hydrogen Bonding. J Am Chem Soc 2024; 146:1543-1553. [PMID: 38181505 PMCID: PMC10797622 DOI: 10.1021/jacs.3c11513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/08/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024]
Abstract
Water inside biological ion channels regulates the key properties of these proteins, such as selectivity, ion conductance, and gating. In this article, we measure the picosecond spectral diffusion of amide I vibrations of an isotope-labeled KcsA potassium channel using two-dimensional infrared (2D IR) spectroscopy. By combining waiting time (100-2000 fs) 2D IR measurements of the KcsA channel including 13C18O isotope-labeled Val76 and Gly77 residues with molecular dynamics simulations, we elucidated the site-specific dynamics of water and K+ ions inside the selectivity filter of KcsA. We observe inhomogeneous 2D line shapes with extremely slow spectral diffusion. Our simulations quantitatively reproduce the experiments and show that water is the only component with any appreciable dynamics, whereas K+ ions and the protein are essentially static on a picosecond timescale. By analyzing simulated and experimental vibrational frequencies, we find that water in the selectivity filter can be oriented to form hydrogen bonds with adjacent or nonadjacent carbonyl groups with the reorientation timescales being three times slower and comparable to that of water molecules in liquid, respectively. Water molecules can reside in the cavity sufficiently far from carbonyls and behave essentially like "free" gas-phase-like water with fast reorientation times. Remarkably, no interconversion between these configurations was observed on a picosecond timescale. These dynamics are in stark contrast with liquid water, which remains highly dynamic even in the presence of ions at high concentrations.
Collapse
Affiliation(s)
- Matthew
J. Ryan
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lujia Gao
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Francis I. Valiyaveetil
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Alexei A. Kananenka
- Department
of Physics and Astronomy, University of
Delaware, Newark, Delaware 19716, United States
| | - Martin T. Zanni
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
6
|
Sharma K, Panwar U, Madhavi M, Joshi I, Chopra I, Soni L, Khan A, Bhrdwaj A, Parihar AS, Mohan VP, Prajapati L, Sharma R, Agrawal S, Hussain T, Nayarisseri A, Singh SK. Unveiling the ESR1 Conformational Stability and Screening Potent Inhibitors for Breast Cancer Treatment. Med Chem 2024; 20:352-368. [PMID: 37929724 DOI: 10.2174/0115734064256978231024062937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND The current study recognizes the significance of estrogen receptor alpha (ERα) as a member of the nuclear receptor protein family, which holds a central role in the pathophysiology of breast cancer. ERα serves as a valuable prognostic marker, with its established relevance in predicting disease outcomes and treatment responses. METHODS In this study, computational methods are utilized to search for suitable drug-like compounds that demonstrate analogous ligand binding kinetics to ERα. RESULTS Docking-based simulation screened out the top 5 compounds - ZINC13377936, NCI35753, ZINC35465238, ZINC14726791, and NCI663569 against the targeted protein. Further, their dynamics studies reveal that the compounds ZINC13377936 and NCI35753 exhibit the highest binding stability and affinity. CONCLUSION Anticipating the competitive inhibition of ERα protein expression in breast cancer, we envision that both ZINC13377936 and NCI35753 compounds hold substantial promise as potential therapeutic agents. These candidates warrant thorough consideration for rigorous In vitro and In vivo evaluations within the context of clinical trials. The findings from this current investigation carry significant implications for the advancement of future diagnostic and therapeutic approaches for breast cancer.
Collapse
Affiliation(s)
- Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, 91, Sector A, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
- Computer Aided Drug Designing and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Umesh Panwar
- Computer Aided Drug Designing and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Maddala Madhavi
- Department of Zoology, Osmania University, Hyderabad - 500007, Telangana State, India
| | - Isha Joshi
- In silico Research Laboratory, Eminent Biosciences, 91, Sector A, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ishita Chopra
- In silico Research Laboratory, Eminent Biosciences, 91, Sector A, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
- School of Medicine and Health Sciences, The George Washington University, Ross Hall, 2300 Eye Street, NW Washington, D.C. - 20037, USA
| | - Lovely Soni
- In silico Research Laboratory, Eminent Biosciences, 91, Sector A, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Arshiya Khan
- In silico Research Laboratory, Eminent Biosciences, 91, Sector A, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Anushka Bhrdwaj
- In silico Research Laboratory, Eminent Biosciences, 91, Sector A, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Abhyuday Singh Parihar
- In silico Research Laboratory, Eminent Biosciences, 91, Sector A, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Vineeth Pazharathu Mohan
- In silico Research Laboratory, Eminent Biosciences, 91, Sector A, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
- Department of Biosciences, School of Science and Technology, Nottingham Trent University Clifton Campus, Nottingham, NG11 8NS, United Kingdom
| | - Leena Prajapati
- In silico Research Laboratory, Eminent Biosciences, 91, Sector A, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Rashmi Sharma
- In silico Research Laboratory, Eminent Biosciences, 91, Sector A, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Shweta Agrawal
- In silico Research Laboratory, Eminent Biosciences, 91, Sector A, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, 91, Sector A, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
- Computer Aided Drug Designing and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd., Indore - 452010, Madhya Pradesh, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| |
Collapse
|
7
|
Davolio AJ, J. Jankowski W, Várnai C, Irwin BWJ, Payne MC, Chau PL. Efficiently Differentiating Agonists and Competitive Antagonists for Weak Allosteric Protein-Ligand Interactions with Linear Response Theory. ACS OMEGA 2023; 8:44537-44544. [PMID: 38046342 PMCID: PMC10688131 DOI: 10.1021/acsomega.3c03503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/05/2023] [Indexed: 12/05/2023]
Abstract
What makes an agonist and a competitive antagonist? In this work, we aim to answer this question by performing parallel tempering Monte Carlo simulations on the serotonin type 3A (5-HT3A) receptor. We use linear response theory to predict conformational changes in the 5-HT3A receptor active site after weak perturbations are applied to its allosteric binding sites. A covariance tensor is built from conformational sampling of its apo state, and a harmonic approximation allows us to substitute the calculation of ligand-induced forces with the binding site's displacement vector. Remarkably, our study demonstrates the feasibility of effectively discerning between agonists and competitive antagonists for multiple ligands, requiring computationally expensive calculations only once per protein.
Collapse
Affiliation(s)
- Anthony J. Davolio
- Theory
of Condensed Matter Group, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Wojciech J. Jankowski
- Theory
of Condensed Matter Group, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Csilla Várnai
- Centre
for Computational Biology, University of
Birmingham, Birmingham B15 2TT, U.K.
- Institute
of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, U.K.
| | - Benedict W. J. Irwin
- Theory
of Condensed Matter Group, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Michael C. Payne
- Theory
of Condensed Matter Group, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Pak-Lee Chau
- Bioinformatique
Structurale, Institut Pasteur, CNRS URA
3528, CB3I CNRS USR 3756, 75724 Paris, France
| |
Collapse
|
8
|
Phan LX, Owji AP, Yang T, Crain J, Sansom MSP, Tucker SJ. Electronic Polarizability Tunes the Function of the Human Bestrophin 1 Cl - Channel. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567055. [PMID: 38014257 PMCID: PMC10680768 DOI: 10.1101/2023.11.14.567055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Mechanisms of anion permeation within ion channels and nanopores remain poorly understood. Recent cryo-electron microscopy structures of the human bestrophin 1 chloride channel (hBest1) provide an opportunity to evaluate ion interactions predicted by molecular dynamics (MD) simulations against experimental observations. We implement the fully polarizable forcefield AMOEBA in MD simulations of open and partially-open states of the hBest1. The AMOEBA forcefield models multipole moments up to the quadrupole; therefore, it captures induced dipole and anion- π interactions. By including polarization we demonstrate the key role that aromatic residues play in ion permeation and the functional advantages of pore asymmetry within the highly conserved hydrophobic neck of the pore. We establish that these only arise when electronic polarization is included in the molecular models. We also show that Cl - permeation in this region can be achieved through hydrophobic solvation concomitant with partial ion dehydration, which is compensated for by the formation of contacts with the edge of the phenylalanine ring. Furthermore, we demonstrate how polarizable simulations can help determine the identity of ion-like densities within high-resolution cryo-EM structures. Crucially, neglecting polarization in simulation of these systems results in the localization of Cl - at positions that do not correspond with their experimentally resolved location. Overall, our results demonstrate the importance of including electronic polarization in realistic and physically accurate models of biological systems. Statement of Significance Ion channels are nanoscale protein pores that enable the selective passage of charged ions across cell membranes. Understanding the underlying mechanisms for selective anion permeation through such pores remains a challenge. To simulate their behavior efficiently in silico , fixed charge models are typically employed. However, this approach is insufficient for the study of anions. Here, we use simulations with explicit treatment of electrostatics to investigate the interactions of chloride ions in the human bestrophin 1 channel. We find that electronic polarization tunes the state of the channel and affects the interactions of chloride ions thereby revealing a mechanism for permeation. Furthermore, these simulations can be used to resolve experimental ambiguity in ion-like densities from cryo-EM structures.
Collapse
|
9
|
Huang J, Chen J. Hydrophobic gating in bundle-crossing ion channels: a case study of TRPV4. Commun Biol 2023; 6:1094. [PMID: 37891195 PMCID: PMC10611814 DOI: 10.1038/s42003-023-05471-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Transmembrane ion channels frequently regulate ion permeation by forming bundle crossing of the pore-lining helices when deactivated. The resulting physical constriction is believed to serve as the de facto gate that imposes the major free energy barrier to ion permeation. Intriguingly, many ion channels also contain highly hydrophobic inner pores enclosed by bundle crossing, which can undergo spontaneous dewetting and give rise to a "vapor barrier" to block ion flow even in the absence of physical constriction. Using atomistic simulations, we show that hydrophobic gating and bundle-crossing mechanisms co-exist and complement one and another in the human TRPV4 channel. In particular, a single hydrophilic mutation in the lower pore can increase pore hydration and reduce the ion permeation free energy barrier by about half without affecting the bundle crossing. We believe that hydrophobic gating may play a key role in other bundle-crossing ion channels with hydrophobic inner pores.
Collapse
Affiliation(s)
- Jian Huang
- Department of Chemistry University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Jianhan Chen
- Department of Chemistry University of Massachusetts Amherst, Amherst, MA, 01003, USA.
| |
Collapse
|
10
|
Seiferth D, Tucker SJ, Biggin PC. Limitations of non-polarizable force fields in describing anion binding poses in non-polar synthetic hosts. Phys Chem Chem Phys 2023. [PMID: 37365974 DOI: 10.1039/d3cp00479a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Transmembrane anion transport by synthetic ionophores has received increasing interest not only because of its relevance for understanding endogenous anion transport, but also because of potential implications for therapeutic routes in disease states where chloride transport is impaired. Computational studies can shed light on the binding recognition process and can deepen our mechanistic understanding of them. However, the ability of molecular mechanics methods to properly capture solvation and binding properties of anions is known to be challenging. Consequently, polarizable models have been suggested to improve the accuracy of such calculations. In this study, we calculate binding free energies for different anions to the synthetic ionophore, biotin[6]uril hexamethyl ester in acetonitrile and to biotin[6]uril hexaacid in water by employing non-polarizable and polarizable force fields. Anion binding shows strong solvent dependency consistent with experimental studies. In water, the binding strengths are iodide > bromide > chloride, and reversed in acetonitrile. These trends are well captured by both classes of force fields. However, the free energy profiles obtained from potential of mean force calculations and preferred binding positions of anions depend on the treatment of electrostatics. Results from simulations using the AMOEBA force-field, which recapitulate the observed binding positions, suggest strong effects from multipoles dominate with a smaller contribution from polarization. The oxidation status of the macrocycle was also found to influence anion recognition in water. Overall, these results have implications for the understanding of anion host interactions not just in synthetic ionophores, but also in narrow cavities of biological ion channels.
Collapse
Affiliation(s)
- David Seiferth
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| |
Collapse
|
11
|
Phan LX, Chamorro VC, Martinez-Seara H, Crain J, Sansom MSP, Tucker SJ. Influence of electronic polarization on the binding of anions to a chloride-pumping rhodopsin. Biophys J 2023; 122:1548-1556. [PMID: 36945777 PMCID: PMC10147828 DOI: 10.1016/j.bpj.2023.03.026] [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: 01/03/2023] [Revised: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023] Open
Abstract
The functional properties of some biological ion channels and membrane transport proteins are proposed to exploit anion-hydrophobic interactions. Here, we investigate a chloride-pumping rhodopsin as an example of a membrane protein known to contain a defined anion binding site composed predominantly of hydrophobic residues. Using molecular dynamics simulations, we explore Cl- binding to this hydrophobic site and compare the dynamics arising when electronic polarization is neglected (CHARMM36 [c36] fixed-charge force field), included implicitly (via the prosECCo force field), or included explicitly (through the polarizable force field, AMOEBA). Free energy landscapes of Cl- moving out of the binding site and into bulk solution demonstrate that the inclusion of polarization results in stronger ion binding and a second metastable binding site in chloride-pumping rhodopsin. Simulations focused on this hydrophobic binding site also indicate longer binding durations and closer ion proximity when polarization is included. Furthermore, simulations reveal that Cl- within this binding site interacts with an adjacent loop to facilitate rebinding events that are not observed when polarization is neglected. These results demonstrate how the inclusion of polarization can influence the behavior of anions within protein binding sites and can yield results comparable with more accurate and computationally demanding methods.
Collapse
Affiliation(s)
- Linda X Phan
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK; Department of Biochemistry, University of Oxford, Oxford, UK
| | - Victor Cruces Chamorro
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, Czech Republic
| | - Jason Crain
- Department of Biochemistry, University of Oxford, Oxford, UK; IBM Research Europe, Hartree Centre, Daresbury, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| |
Collapse
|
12
|
Schackert F, Biedermann J, Abdolvand S, Minniberger S, Song C, Plested AJR, Carloni P, Sun H. Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel. J Chem Inf Model 2023; 63:1293-1300. [PMID: 36758214 PMCID: PMC9976283 DOI: 10.1021/acs.jcim.2c01494] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are neurotransmitter-activated cation channels ubiquitously expressed in vertebrate brains. The regulation of calcium flux through the channel pore by RNA-editing is linked to synaptic plasticity while excessive calcium influx poses a risk for neurodegeneration. Unfortunately, the molecular mechanisms underlying this key process are mostly unknown. Here, we investigated calcium conduction in calcium-permeable AMPAR using Molecular Dynamics (MD) simulations with recently introduced multisite force-field parameters for Ca2+. Our calculations are consistent with experiment and explain the distinct calcium permeability in different RNA-edited forms of GluA2. For one of the identified metal binding sites, multiscale Quantum Mechanics/Molecular Mechanics (QM/MM) simulations further validated the results from MD and revealed small but reproducible charge transfer between the metal ion and its first solvation shell. In addition, the ion occupancy derived from MD simulations independently reproduced the Ca2+ binding profile in an X-ray structure of an NaK channel mimicking the AMPAR selectivity filter. This integrated study comprising X-ray crystallography, multisite MD, and multiscale QM/MM simulations provides unprecedented insights into Ca2+ permeation mechanisms in AMPARs, and paves the way for studying other biological processes in which Ca2+ plays a pivotal role.
Collapse
Affiliation(s)
- Florian
Karl Schackert
- Computational
Biomedicine (IAS-5/INM-9), Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany,Department
of Physics, RWTH Aachen University, 52062 Aachen, Germany
| | - Johann Biedermann
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Saeid Abdolvand
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Sonja Minniberger
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Chen Song
- Center
for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China,Peking-Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Andrew J. R. Plested
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Paolo Carloni
- Computational
Biomedicine (IAS-5/INM-9), Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany,Department
of Physics, RWTH Aachen University, 52062 Aachen, Germany,
| | - Han Sun
- Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany,Institute
of Chemistry, TU Berlin, Straße des 17 Juni 135, 10623 Berlin, Germany,
| |
Collapse
|
13
|
Vuorte M, Kuitunen S, Van Tassel PR, Sammalkorpi M. Equilibrium state model for surfactants in oils: Colloidal assembly and adsorption. J Colloid Interface Sci 2023; 630:783-794. [DOI: 10.1016/j.jcis.2022.09.153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/11/2022]
|
14
|
Wilson MA, Pohorille A. Structure and Computational Electrophysiology of Ac-LS3, a Synthetic Ion Channel. J Phys Chem B 2022; 126:8985-8999. [PMID: 36306164 DOI: 10.1021/acs.jpcb.2c05965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Computer simulations are reported on Ac-LS3, a synthetic ion channel, containing 21 residues with a Leu-Ser-Ser-Leu-Leu-Ser-Leu heptad repeat, which forms ions channels upon application of voltage. A hexameric, coiled-coil bundle initially positioned perpendicular to the membrane settled into a stable, tilted structure after 1.5 μs, most likely to improve contacts between the non-polar exterior of the channel and the hydrophobic core of the membrane. Once tilted, the bundle remained in this state during subsequent simulations of nearly 10 μs at voltages ranging from 200 to -100 mV. In contrast, attempts to identify a stable pentameric structure failed, thus supporting the hypothesis that the channel is a hexamer. Results at 100 mV were used to reconstruct the free energy profiles for K+ and Cl- in the channel. This was done by way of several methods in which results of molecular dynamics (MD) simulations were combined with the electrodiffusion model. Two of them developed recently do not require knowledge of the diffusivity. Instead, they utilize one-sided density profiles and committor probabilities. The consistency between different methods is very good, supporting the utility of the newly developed methods for reconstructing free energies of ions in channels. The flux of K+, which accounts for most of the current through the channel, calculated directly from MD matches well the total measured current. However, the current of Cl- is somewhat overestimated, possibly due to a slightly unbalanced force field involving chloride. The current-voltage dependence was also reconstructed by way of a recently developed, efficient method that requires simulations only at a single voltage, yielding good agreement with the experiment. Taken together, the results demonstrate that computational electrophysiology has become a reliable tool for studying how channels mediate ion transport through membranes.
Collapse
Affiliation(s)
- Michael A Wilson
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California94035, United States.,SETI Institute, 189 Bernardo Avenue, Suite 200, Mountain View, California94043, United States
| | - Andrew Pohorille
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California94033, United States.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California94132, United States
| |
Collapse
|
15
|
Seiferth D, Biggin PC, Tucker SJ. When is a hydrophobic gate not a hydrophobic gate? J Gen Physiol 2022; 154:213612. [PMID: 36287215 PMCID: PMC9614698 DOI: 10.1085/jgp.202213210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The flux of ions through a channel is most commonly regulated by changes that result in steric occlusion of its pore. However, ion permeation can also be prevented by formation of a desolvation barrier created by hydrophobic residues that line the pore. As a result of relatively minor structural changes, confined hydrophobic regions in channels may undergo transitions between wet and dry states to gate the pore closed without physical constriction of the permeation pathway. This concept is referred to as hydrophobic gating, and many examples of this process have been demonstrated. However, the term is also now being used in a much broader context that often deviates from its original meaning. In this Viewpoint, we explore the formal definition of a hydrophobic gate, discuss examples of this process compared with other gating mechanisms that simply exploit hydrophobic residues and/or lipids in steric closure of the pore, and describe the best practice for identification of a hydrophobic gate.
Collapse
Affiliation(s)
- David Seiferth
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.,Department of Biochemistry, University of Oxford, Oxford, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| |
Collapse
|
16
|
Walker-Gibbons R, Kubincová A, Hünenberger PH, Krishnan M. The Role of Surface Chemistry in the Orientational Behavior of Water at an Interface. J Phys Chem B 2022; 126:4697-4710. [PMID: 35726865 PMCID: PMC9251758 DOI: 10.1021/acs.jpcb.2c01752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Molecular dynamics
studies have demonstrated that molecular water
at an interface, with either a gas or a solid, displays anisotropic
orientational behavior in contrast to its bulk counterpart. This effect
has been recently implicated in the like-charge attraction problem
for colloidal particles in solution. Here, negatively charged particles
in solution display a long-ranged attraction where continuum electrostatic
theory predicts monotonically repulsive interactions, particularly
in solutions with monovalent salt ions at low ionic strength. Anisotropic
orientational behavior of solvent molecules at an interface gives
rise to an excess interfacial electrical potential which we suggest
generates an additional solvation contribution to the total free energy
that is traditionally overlooked in continuum descriptions of interparticle
interactions in solution. In the present investigation we perform
molecular dynamics simulation based calculations of the interfacial
potential using realistic surface models representing various chemistries
as well as different solvents. Similar to previous work that focused
on simple model surfaces constructed by using oxygen atoms, we find
that solvents at more realistic model surfaces exhibit substantial
anisotropic orientational behavior. We explore the dependence of the
interfacial solvation potential on surface properties such as surface
group chemistry and group density at silica and carboxylated polystyrene
interfaces. For water, we note surprisingly good agreement between
results obtained for a simple O-atom wall and more complex surface
models, suggesting a general qualitative consistency of the interfacial
solvation effect for surfaces in contact with water. In contrast,
for an aprotic solvent such as DMSO, surface chemistry appears to
exert a stronger influence on the sign and magnitude of the interfacial
solvation potential. The study carries broad implications for molecular-scale
interactions and may find relevance in explaining a range of phenomena
in soft-matter physics and cell biology.
Collapse
Affiliation(s)
- Rowan Walker-Gibbons
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Alžbeta Kubincová
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Madhavi Krishnan
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| |
Collapse
|
17
|
Oh S, Marinelli F, Zhou W, Lee J, Choi HJ, Kim M, Faraldo-Gómez JD, Hite RK. Differential ion dehydration energetics explains selectivity in the non-canonical lysosomal K + channel TMEM175. eLife 2022; 11:75122. [PMID: 35608336 PMCID: PMC9129878 DOI: 10.7554/elife.75122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/01/2022] [Indexed: 12/31/2022] Open
Abstract
Structures of the human lysosomal K+ channel transmembrane protein 175 (TMEM175) in open and closed states revealed a novel architecture lacking the canonical K+ selectivity filter motif present in previously known K+ channel structures. A hydrophobic constriction composed of four isoleucine residues was resolved in the pore and proposed to serve as the gate in the closed state, and to confer ion selectivity in the open state. Here, we achieve higher-resolution structures of the open and closed states and employ molecular dynamics simulations to analyze the conducting properties of the putative open state, demonstrating that it is permeable to K+ and, to a lesser degree, also Na+. Both cations must dehydrate significantly to penetrate the narrow hydrophobic constriction, but ion flow is assisted by a favorable electrostatic field generated by the protein that spans the length of the pore. The balance of these opposing energetic factors explains why permeation is feasible, and why TMEM175 is selective for K+ over Na+, despite the absence of the canonical selectivity filter. Accordingly, mutagenesis experiments reveal an exquisite sensitivity of the channel to perturbations that mitigate the constriction. Together, these data reveal a novel mechanism for selective permeation of ions by TMEM175 that is unlike that of other K+ channels.
Collapse
Affiliation(s)
- SeCheol Oh
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Wenchang Zhou
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jooyeon Lee
- Department of Chemistry, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Ho Jeong Choi
- Department of Chemistry, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Min Kim
- Department of Chemistry, Chungbuk National University, Cheongju-si, Republic of Korea
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| |
Collapse
|
18
|
Phan LX, Lynch CI, Crain J, Sansom MS, Tucker SJ. Influence of effective polarization on ion and water interactions within a biomimetic nanopore. Biophys J 2022; 121:2014-2026. [DOI: 10.1016/j.bpj.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/25/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
|
19
|
Yadav M, Abdalla M, Madhavi M, Chopra I, Bhrdwaj A, Soni L, Shaheen U, Prajapati L, Sharma M, Sikarwar MS, Albogami S, Hussain T, Nayarisseri A, Singh SK. Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation and Pharmacokinetic modelling of Cyclooxygenase-2 (COX-2) inhibitor for the clinical treatment of Colorectal Cancer. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2068799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Manasi Yadav
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, PR People’s Republic of China
| | - Maddala Madhavi
- Department of Zoology, Osmania University, Hyderabad, Telangana State, India
| | - Ishita Chopra
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India
| | - Anushka Bhrdwaj
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Lovely Soni
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Uzma Shaheen
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Leena Prajapati
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Megha Sharma
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | | | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Tajamul Hussain
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| |
Collapse
|
20
|
Deng J, Cui Q. Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants. J Am Chem Soc 2022; 144:4594-4610. [PMID: 35239338 PMCID: PMC9616648 DOI: 10.1021/jacs.2c00312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Buried charged residues play important roles in the modulation of protein stabilities and conformational dynamics and make crucial contributions to protein functions. Considering the generally nonpolar nature of protein interior, a key question concerns the contribution of electronic polarization to the stabilization and properties of buried charges. We answer this question by conducting free energy simulations using the latest polarizable CHARMM force field based on Drude oscillators for a series of Staphylococcal nuclease mutants that involve a buried Glu-Lys pair in different titration states and orientations. While a nonpolarizable model suggests that the ionized form of the buried Glu-Lys pair is more than 40 kcal/mol less stable than the charge-neutral form, the two titration states are comparable in stability when electronic polarization is included explicitly, a result better reconcilable with available experimental data. Analysis of free energy components suggests that additional stabilization of the ionized Glu-Lys pair has contributions from both the enhanced salt-bridge strength and stronger interaction between the ion-pair and surrounding protein residues and penetrated water. Despite the stronger direct interaction between Glu and Lys, the ion-pair exhibits considerably larger and faster structural fluctuations when polarization is included, due to compensation of interactions in the cavity. Collectively, observations from this work provide compelling evidence that electronic polarization is essential to the stability, hydration, dynamics, and therefore function of buried charges in proteins. Therefore, our study advocates for the explicit consideration of electronic polarization for mechanistic and engineering studies that implicate buried charged residues, such as enzymes and ion transporters.
Collapse
Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
| |
Collapse
|
21
|
Choudhury K, Kasimova MA, McComas S, Howard RJ, Delemotte L. An open state of a voltage-gated sodium channel involving a π-helix and conserved pore-facing asparagine. Biophys J 2022; 121:11-22. [PMID: 34890580 PMCID: PMC8758419 DOI: 10.1016/j.bpj.2021.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/26/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
Voltage-gated sodium (Nav) channels play critical roles in propagating action potentials and otherwise manipulating ionic gradients in excitable cells. These channels open in response to membrane depolarization, selectively permeating sodium ions until rapidly inactivating. Structural characterization of the gating cycle in this channel family has proved challenging, particularly due to the transient nature of the open state. A structure from the bacterium Magnetococcus marinus Nav (NavMs) was initially proposed to be open, based on its pore diameter and voltage-sensor conformation. However, the functional annotation of this model, and the structural details of the open state, remain disputed. In this work, we used molecular modeling and simulations to test possible open-state models of NavMs. The full-length experimental structure, termed here the α-model, was consistently dehydrated at the activation gate, indicating an inability to conduct ions. Based on a spontaneous transition observed in extended simulations, and sequence/structure comparison to other Nav channels, we built an alternative π-model featuring a helix transition and the rotation of a conserved asparagine residue into the activation gate. Pore hydration, ion permeation, and state-dependent drug binding in this model were consistent with an open functional state. This work thus offers both a functional annotation of the full-length NavMs structure and a detailed model for a stable Nav open state, with potential conservation in diverse ion-channel families.
Collapse
Affiliation(s)
- Koushik Choudhury
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Marina A. Kasimova
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Sarah McComas
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rebecca J. Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden,Corresponding author
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Vuorte M, Kuitunen S, Sammalkorpi M. Physisorption of bio oil nitrogen compounds onto montmorillonite. Phys Chem Chem Phys 2021; 23:21840-21851. [PMID: 34554171 DOI: 10.1039/d1cp01880a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We assess computationally the adsorption of a series of nitrogen containing heterocycles and fatty acid amides from bio-oil on a model clay surface, Na-montmorillonite. The adsorption energies and conformations predicted by atomistic detail molecular dynamics (MD) simulations are compared against density functional theory (DFT) based molecular electrostatic potentials (MEP) and Hirshfeld, AIM, Merz-Singh-Kollman, and ChelpG charges. MD predicts systematically adsorption via cation bridging with adsorption strength of the heterocycles following purine > pyridine > imidazole > pyrrole > indole > quinoline. The fatty acid amides adsorption strength follows the steric availability and bulkiness of the head group. A comparison against the DFT calculations shows that MEP predicts adsorption geometries and the MD simulations reproduce the conformations for single adsorption site species. However, the DFT derived charge distibutions show that MD force-fields with non-polarizable fixed partial charge representations parametrized for aqueous environments cannot be used in apolar solvent environments without careful accuracy considerations. The overall trends in adsorption energies are reproduced by the Charmm GenFF employed in the MD simulations but the adsorption energies are systematically overestimated in this apolar solvent environment. The work has significance both for revealing nitrogen compound adsorption trends in technologically relevant bio oil environments but also as a methodological assessment revealing the limits of state of the art biomolecular force-fields and simulation protocols in apolar bioenvironments.
Collapse
Affiliation(s)
- Maisa Vuorte
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
| | - Susanna Kuitunen
- Neste Engineering Solutions Oy, P.O. Box 310, FI-06101 Porvoo, Finland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland. .,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| |
Collapse
|
24
|
Conductance selectivity of Na + across the K + channel via Na + trapped in a tortuous trajectory. Proc Natl Acad Sci U S A 2021; 118:2017168118. [PMID: 33741736 DOI: 10.1073/pnas.2017168118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ion selectivity of the potassium channel is crucial for regulating electrical activity in living cells; however, the mechanism underlying the potassium channel selectivity that favors large K+ over small Na+ remains unclear. Generally, Na+ is not completely excluded from permeation through potassium channels. Herein, the distinct nature of Na+ conduction through the prototypical KcsA potassium channel was examined. Single-channel current recordings revealed that, at a high Na+ concentration (200 mM), the channel was blocked by Na+, and this blocking was relieved at high membrane potentials, suggesting the passage of Na+ across the channel. At a 2,000 mM Na+ concentration, single-channel Na+ conductance was measured as one-eightieth of the K+ conductance, indicating that the selectivity filter allows substantial conduit of Na+ Molecular dynamics simulations revealed unprecedented atomic trajectories of Na+ permeation. In the selectivity filter having a series of carbonyl oxygen rings, a smaller Na+ was distributed off-center in eight carbonyl oxygen-coordinated sites as well as on-center in four carbonyl oxygen-coordinated sites. This amphipathic nature of Na+ coordination yielded a continuous but tortuous path along the filter. Trapping of Na+ in many deep free energy wells in the filter caused slow elution. Conversely, K+ is conducted via a straight path, and as the number of occupied K+ ions increased to three, the concerted conduction was accelerated dramatically, generating the conductance selectivity ratio of up to 80. The selectivity filter allows accommodation of different ion species, but the ion coordination and interactions between ions render contrast conduction rates, constituting the potassium channel conductance selectivity.
Collapse
|
25
|
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.![]()
Collapse
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
| |
Collapse
|
26
|
Wilson MA, Pohorille A. Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations. ENTROPY 2021; 23:e23050571. [PMID: 34066581 PMCID: PMC8148522 DOI: 10.3390/e23050571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022]
Abstract
We use stochastic simulations to investigate the performance of two recently developed methods for calculating the free energy profiles of ion channels and their electrophysiological properties, such as current–voltage dependence and reversal potential, from molecular dynamics simulations at a single applied voltage. These methods require neither knowledge of the diffusivity nor simulations at multiple voltages, which greatly reduces the computational effort required to probe the electrophysiological properties of ion channels. They can be used to determine the free energy profiles from either forward or backward one-sided properties of ions in the channel, such as ion fluxes, density profiles, committor probabilities, or from their two-sided combination. By generating large sets of stochastic trajectories, which are individually designed to mimic the molecular dynamics crossing statistics of models of channels of trichotoxin, p7 from hepatitis C and a bacterial homolog of the pentameric ligand-gated ion channel, GLIC, we find that the free energy profiles obtained from stochastic simulations corresponding to molecular dynamics simulations of even a modest length are burdened with statistical errors of only 0.3 kcal/mol. Even with many crossing events, applying two-sided formulas substantially reduces statistical errors compared to one-sided formulas. With a properly chosen reference voltage, the current–voltage curves can be reproduced with good accuracy from simulations at a single voltage in a range extending for over 200 mV. If possible, the reference voltages should be chosen not simply to drive a large current in one direction, but to observe crossing events in both directions.
Collapse
Affiliation(s)
- Michael A. Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA;
- SETI Institute, 189 Bernardo Ave, Suite 200, Mountain View, CA 94043, USA
| | - Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA;
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94132, USA
- Correspondence: ; Tel.: +1-650-604-5759
| |
Collapse
|
27
|
Calvelo M, Lynch CI, Granja JR, Sansom MSP, Garcia-Fandiño R. Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide Nanotubes. ACS NANO 2021; 15:7053-7064. [PMID: 33739081 PMCID: PMC8485350 DOI: 10.1021/acsnano.1c00155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/15/2021] [Indexed: 05/23/2023]
Abstract
Self-assembling cyclic peptide nanotubes can form nanopores when they are inserted in lipid bilayers, acting as ion and/or water permeable channels. In order to improve the versatility of these systems, it is possible to specifically design cyclic peptides with a combination of natural and non-natural amino acids, enabling the control of the nature of the inner cavity of the channels. Here, the behavior of two types of self-assembling peptide motifs, alternating α-amino acids with γ- or δ-aminocycloalkanecarboxylic acids, is studied via molecular dynamics (MD) simulations. The behavior of water molecules in nanopores is expected to affect the properties of these channels and therefore merits detailed examination. A number of water models commonly used in MD simulations have been validated by how well they reproduce bulk water properties. However, it is less clear how these water models behave in the nanoconfined condition inside a channel. The behavior of four different water models-TIP3P, TIP4P, TIP4P/2005, and OPC-are evaluated in MD simulations of self-assembled cyclic peptide nanotubes of distinct composition and diameter. The dynamic behavior of the water molecules and ions in these designed artificial channels depends subtly on the water model used. TIP3P water molecules move faster than those of TIP4P, TIP4P/2005, and OPC. This demeanor is clearly observed in the filling of the nanotube, in water diffusion within the pore, and in the number and stability of hydrogen bonds of the peptides with water. It was also shown that the water model influences the simulated ion flux through the nanotubes, with TIP3P producing the greatest ion flux. Additionally, the two more recent models, TIP4P/2005 and OPC, which are known to reproduce the experimental self-diffusion coefficient of bulk water quite well, exhibit very similar results under the nanoconfined conditions studied here. Because none of these models have been parametrized specifically for waters confined in peptide nanotubes, this study provides a point of reference for further validation.
Collapse
Affiliation(s)
- Martin Calvelo
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Charlotte I. Lynch
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Juan R. Granja
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Rebeca Garcia-Fandiño
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| |
Collapse
|
28
|
Rao S, Klesse G, Lynch CI, Tucker SJ, Sansom MSP. Molecular Simulations of Hydrophobic Gating of Pentameric Ligand Gated Ion Channels: Insights into Water and Ions. J Phys Chem B 2021; 125:981-994. [PMID: 33439645 PMCID: PMC7869105 DOI: 10.1021/acs.jpcb.0c09285] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/13/2020] [Indexed: 12/30/2022]
Abstract
Ion channels are proteins which form gated nanopores in biological membranes. Many channels exhibit hydrophobic gating, whereby functional closure of a pore occurs by local dewetting. The pentameric ligand gated ion channels (pLGICs) provide a biologically important example of hydrophobic gating. Molecular simulation studies comparing additive vs polarizable models indicate predictions of hydrophobic gating are robust to the model employed. However, polarizable models suggest favorable interactions of hydrophobic pore-lining regions with chloride ions, of relevance to both synthetic carriers and channel proteins. Electrowetting of a closed pLGIC hydrophobic gate requires too high a voltage to occur physiologically but may inform designs for switchable nanopores. Global analysis of ∼200 channels yields a simple heuristic for structure-based prediction of (closed) hydrophobic gates. Simulation-based analysis is shown to provide an aid to interpretation of functional states of new channel structures. These studies indicate the importance of understanding the behavior of water and ions within the nanoconfined environment presented by ion channels.
Collapse
Affiliation(s)
- Shanlin Rao
- Department
of Biochemistry, University of Oxford, Oxford, U.K.
| | - Gianni Klesse
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford, U.K.
| | | | - Stephen J. Tucker
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford, U.K.
| | | |
Collapse
|
29
|
Cholesterol content in the membrane promotes key lipid-protein interactions in a pentameric serotonin-gated ion channel. Biointerphases 2021; 15:061018. [PMID: 33397116 DOI: 10.1116/6.0000561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs), embedded in the lipid membranes of nerve cells, mediate fast synaptic transmission and are major pharmaceutical targets. Because of their complexity and the limited knowledge of their structure, their working mechanisms have still to be fully unraveled at the molecular level. Over the past few years, evidence that the lipid membrane may modulate the function of membrane proteins, including pLGICs, has emerged. Here, we investigate, by means of molecular dynamics simulations, the behavior of the lipid membrane at the interface with the 5-HT3A receptor (5-HT3AR), a representative pLGIC which is the target of nausea-suppressant drugs, in a nonconductive state. Three lipid compositions are studied, spanning different concentrations of the phospholipids, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, and of cholesterol, hence a range of viscosities. A variety of lipid interactions and persistent binding events to different parts of the receptor are revealed in the investigated models, providing snapshots of the dynamical environment at the membrane-receptor interface. Some of these events result in lipid intercalation within the transmembrane domain, and others reach out to protein key sections for signal transmission and receptor activation, such as the Cys-loop and the M2-M3 loop. In particular, phospholipids, with their long hydrophobic tails, play an important role in these interactions, potentially providing a bridge between these two structures. A higher cholesterol content appears to promote lipid persistent binding to the receptor.
Collapse
|
30
|
Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
Collapse
Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| |
Collapse
|
31
|
Cottone G, Chiodo L, Maragliano L. Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor. J Chem Inf Model 2020; 60:5045-5056. [PMID: 32803965 PMCID: PMC8011927 DOI: 10.1021/acs.jcim.0c00549] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Molecular
studies of human pentameric ligand-gated ion channels
(LGICs) expressed in neurons and at neuromuscular junctions are of
utmost importance in the development of therapeutic strategies for
neurological disorders. We focus here on the nicotinic acetylcholine
receptor nAChR-α7, a homopentameric channel widely expressed
in the human brain, with a proven role in a wide spectrum of disorders
including schizophrenia and Alzheimer’s disease. By exploiting
an all-atom structural model of the full (transmembrane and extracellular)
protein in the open, agonist-bound conformation we recently developed,
we evaluate the free energy and the mean first passage time of single-ion
permeation using molecular dynamics simulations and the milestoning
method with Voronoi tessellation. The results for the wild-type channel
provide the first available mapping of the potential of mean force
in the full-length α7 nAChR, reveal its expected cationic nature,
and are in good agreement with simulation data for other channels
of the LGIC family and with experimental data on nAChRs. We then investigate
the role of a specific mutation directly related to ion selectivity
in LGICs, the E-1′ → A-1′ substitution at the
cytoplasmatic selectivity filter. We find that the mutation strongly
affects sodium and chloride permeation in opposite directions, leading
to a complete inversion of selectivity, at variance with the limited
experimental results available that classify this mutant as cationic.
We thus provide structural determinants for the observed cationic-to-anionic
inversion, revealing a key role of the protonation state of residue
rings far from the mutation, in the proximity of the hydrophobic channel
gate.
Collapse
Affiliation(s)
- Grazia Cottone
- Department of Physics and Chemistry-Emilio Segrè, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Letizia Chiodo
- Department of Engineering, Campus Bio-Medico University of Rome, Via Á. del Portillo 21, 00128 Rome, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, 16132 Genova, Italy
| |
Collapse
|
32
|
Klesse G, Tucker SJ, Sansom MSP. Electric Field Induced Wetting of a Hydrophobic Gate in a Model Nanopore Based on the 5-HT 3 Receptor Channel. ACS NANO 2020; 14:10480-10491. [PMID: 32673478 PMCID: PMC7450702 DOI: 10.1021/acsnano.0c04387] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/16/2020] [Indexed: 05/14/2023]
Abstract
In this study we examined the influence of a transmembrane voltage on the hydrophobic gating of nanopores using molecular dynamics simulations. We observed electric field induced wetting of a hydrophobic gate in a biologically inspired model nanopore based on the 5-HT3 receptor in its closed state, with a field of at least ∼100 mV nm-1 (corresponding to a supra-physiological potential difference of ∼0.85 V across the membrane) required to hydrate the pore. We also found an unequal distribution of charged residues can generate an electric field intrinsic to the nanopore which, depending on its orientation, can alter the effect of the external field, thus making the wetting response asymmetric. This wetting response could be described by a simple model based on water surface tension, the volumetric energy contribution of the electric field, and the influence of charged amino acids lining the pore. Finally, the electric field response was used to determine time constants characterizing the phase transitions of water confined within the nanopore, revealing liquid-vapor oscillations on a time scale of ∼5 ns. This time scale was largely independent of the water model employed and was similar for different sized pores representative of the open and closed states of the pore. Furthermore, our finding that the threshold voltage required for hydrating a hydrophobic gate depends on the orientation of the electric field provides an attractive perspective for the design of rectifying artificial nanopores.
Collapse
Affiliation(s)
- Gianni Klesse
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford OX1 3PU, United Kingdom
| | - Stephen J. Tucker
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford OX1 3PU, United Kingdom
- OXION
Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| |
Collapse
|
33
|
Dämgen MA, Zaki AM, Biggin PC. Comment on "On the Functional Annotation of Open-Channel Structures in the Glycine Receptor". Structure 2020; 28:601-603. [PMID: 32492412 DOI: 10.1016/j.str.2020.04.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/30/2020] [Accepted: 04/28/2020] [Indexed: 12/26/2022]
Abstract
Recently, we reported the simulation of a stable open state of the glycine receptor. Central to the stability of the simulations was the behavior of the highly conserved leucine residues at the 9' gate, which were found to rotate into adjacent pockets, thus providing a structural rationale for decades of biochemical observations. In contrast, a previously reported model from Cerdan et al. (2018) resembled a more collapsed state. However, in support of their model, they draw attention to the agreement between calculated and experimental conductance measurements and argue that our model tends to overestimate ion flow. Here, we argue that there are many pitfalls with this approach and that the apparent agreement most likely reflects a fortuitous cancellation of errors. The computed values are highly sensitive to very small changes in model parameters. It is also likely that polarization effects will be very significant, and these have not yet been considered.
Collapse
Affiliation(s)
- Marc A Dämgen
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Afroditi Maria Zaki
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
| |
Collapse
|