1
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Zheng W, Liu X. Modeling and Simulation of the NMDA Receptor at Coarse-Grained and Atomistic Levels. Methods Mol Biol 2024; 2799:269-280. [PMID: 38727913 DOI: 10.1007/978-1-0716-3830-9_15] [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] [Indexed: 06/01/2024]
Abstract
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. While high-resolution structures were solved for an allosterically inhibited form of functional NMDA receptor, other key functional states (particularly the active open-channel state) have not yet been resolved at atomic resolutions. To decrypt the molecular mechanism of the NMDA receptor activation, structural modeling and simulation are instrumental in providing detailed information about the dynamics and energetics of the receptor in various functional states. In this chapter, we describe coarse-grained modeling of the NMDA receptor using an elastic network model and related modeling/analysis tools (e.g., normal mode analysis, flexibility and hotspot analysis, cryo-EM flexible fitting, and transition pathway modeling) based on available structures. Additionally, we show how to build an atomistic model of the active-state receptor with targeted molecular dynamics (MD) simulation and explore its energetics and dynamics with conventional MD simulation. Taken together, these modeling and simulation can offer rich structural and dynamic information which will guide experimental studies of the activation of this key receptor.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, State University of New York at Buffalo, Buffalo, NY, USA.
| | - Xing Liu
- Department of Physics, State University of New York at Buffalo, Buffalo, NY, USA
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2
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Greene D, Barton M, Luchko T, Shiferaw Y. Molecular Dynamics Simulations of the Cardiac Ryanodine Receptor Type 2 (RyR2) Gating Mechanism. J Phys Chem B 2022; 126:9790-9809. [PMID: 36384028 PMCID: PMC9720719 DOI: 10.1021/acs.jpcb.2c03031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mutations in the cardiac ryanodine receptor type 2 (RyR2) have been linked to fatal cardiac arrhythmias such as catecholaminergic polymorphic ventricular tachycardia (CPVT). While many CPVT mutations are associated with an increase in Ca2+ leak from the sarcoplasmic reticulum, the mechanistic details of RyR2 channel gating are not well understood, and this poses a barrier in the development of new pharmacological treatments. To address this, we explore the gating mechanism of the RyR2 using molecular dynamics (MD) simulations. We test the effect of changing the conformation of certain structural elements by constructing chimera RyR2 structures that are derived from the currently available closed and open cryo-electron microscopy (cryo-EM) structures, and we then use MD simulations to relax the system. Our key finding is that the position of the S4-S5 linker (S4S5L) on a single subunit can determine whether the channel as a whole is open or closed. Our analysis reveals that the position of the S4S5L is regulated by interactions with the U-motif on the same subunit and with the S6 helix on an adjacent subunit. We find that, in general, channel gating is crucially dependent on high percent occupancy interactions between adjacent subunits. We compare our interaction analysis to 49 CPVT1 mutations in the literature and find that 73% appear near a high percent occupancy interaction between adjacent subunits. This suggests that disruption of cooperative, high percent occupancy interactions between adjacent subunits is a primary cause of channel leak and CPVT in mutant RyR2 channels.
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3
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Chirasani VR, Popov KI, Meissner G, Dokholyan NV. Mapping co-regulatory interactions among ligand-binding sites in ryanodine receptor 1. Proteins 2022; 90:385-394. [PMID: 34455637 PMCID: PMC8738105 DOI: 10.1002/prot.26228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/05/2021] [Accepted: 08/25/2021] [Indexed: 02/03/2023]
Abstract
Ryanodine receptor 1 (RyR1) is an intracellular calcium ion (Ca2+ ) release channel required for skeletal muscle contraction. Although cryo-electron microscopy identified binding sites of three coactivators Ca2+ , ATP, and caffeine (CFF), the mechanism of co-regulation and synergy of these activators is unknown. Here, we report allosteric connections among the three ligand-binding sites and pore region in (i) Ca2+ bound-closed, (ii) ATP/CFF bound-closed, (iii) Ca2+ /ATP/CFF bound-closed, and (iv) Ca2+ /ATP/CFF bound-open RyR1 states. We identified two dominant networks of interactions that mediate communication between the Ca2+ -binding site and pore region in Ca2+ bound-closed state, which partially overlapped with the pore communications in ATP/CFF bound-closed RyR1 state. In Ca2+ /ATP/CFF bound-closed and -open RyR1 states, co-regulatory interactions were analogous to communications in the Ca2+ bound-closed and ATP/CFF bound-closed states. Both ATP- and CFF-binding sites mediate communication between the Ca2+ -binding site and the pore region in Ca2+ /ATP/CFF bound-open RyR1 structure. We conclude that Ca2+ , ATP, and CFF propagate their effects to the pore region through a network of overlapping interactions that mediate allosteric control and molecular synergy in channel regulation.
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Affiliation(s)
- Venkat R Chirasani
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA.,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Konstantin I Popov
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Gerhard Meissner
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA
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4
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Zheng W. Predicting cryptic ligand binding sites based on normal modes guided conformational sampling. Proteins 2021; 89:416-426. [PMID: 33244830 DOI: 10.1002/prot.26027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/26/2020] [Accepted: 11/21/2020] [Indexed: 12/22/2022]
Abstract
To greatly expand the druggable genome, fast and accurate predictions of cryptic sites for small molecules binding in target proteins are in high demand. In this study, we have developed a fast and simple conformational sampling scheme guided by normal modes solved from the coarse-grained elastic models followed by atomistic backbone refinement and side-chain repacking. Despite the observations of complex and diverse conformational changes associated with ligand binding, we found that simply sampling along each of the lowest 30 modes is near optimal for adequately restructuring cryptic sites so they can be detected by existing pocket finding programs like fpocket and concavity. We further trained machine-learning protocols to optimize the combination of the sampling-enhanced pocket scores with other dynamic and conservation scores, which only slightly improved the performance. As assessed based on a training set of 84 known cryptic sites and a test set of 14 proteins, our method achieved high accuracy of prediction (with area under the receiver operating characteristic curve >0.8) comparable to the CryptoSite server. Compared with CryptoSite and other methods based on extensive molecular dynamics simulation, our method is much faster (1-2 hours for an average-size protein) and simpler (using only pocket scores), so it is suitable for high-throughput processing of large datasets of protein structures at the genome scale.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, University at Buffalo, Buffalo, New York, USA
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5
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Zheng W, Wen H. Predicting lipid and ligand binding sites in TRPV1 channel by molecular dynamics simulation and machine learning. Proteins 2021; 89:966-977. [PMID: 33739482 DOI: 10.1002/prot.26075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/25/2021] [Accepted: 03/15/2021] [Indexed: 11/06/2022]
Abstract
As a key cellular sensor, the TRPV1 channel undergoes a gating transition from a closed state to an open state in response to many physical and chemical stimuli. This transition is regulated by small-molecule ligands including lipids and various agonists/antagonists, but the underlying molecular mechanisms remain obscure. Thanks to recent revolution in cryo-electron microscopy, a growing list of new structures of TRPV1 and other TRPV channels have been solved in complex with various ligands including lipids. Toward elucidating how ligand binding correlates with TRPV1 gating, we have performed extensive molecular dynamics simulations (with cumulative time of 20 μs), starting from high-resolution structures of TRPV1 in both the closed and open states. By comparing between the open and closed state ensembles, we have identified state-dependent binding sites for small-molecule ligands in general and lipids in particular. We further use machine learning to predict top ligand-binding sites as important features to classify the closed vs open states. The predicted binding sites are thoroughly validated by matching homologous sites in all structures of TRPV channels bound to lipids and other ligands, and with previous functional/mutational studies of ligand binding in TRPV1. Taken together, this study has integrated rich structural, dynamic, and functional data to inform future design of small-molecular drugs targeting TRPV1.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, State University of New York at Buffalo, Buffalo, New York, USA
| | - Han Wen
- Department of Physics, State University of New York at Buffalo, Buffalo, New York, USA
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6
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Aizpurua JM, Miranda JI, Irastorza A, Torres E, Eceiza M, Sagartzazu-Aizpurua M, Ferrón P, Aldanondo G, Lasa-Fernández H, Marco-Moreno P, Dadie N, López de Munain A, Vallejo-Illarramendi A. Discovery of a novel family of FKBP12 "reshapers" and their use as calcium modulators in skeletal muscle under nitro-oxidative stress. Eur J Med Chem 2021; 213:113160. [PMID: 33493827 DOI: 10.1016/j.ejmech.2021.113160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/23/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022]
Abstract
The hypothesis of rescuing FKBP12/RyR1 interaction and intracellular calcium homeostasis through molecular "reshaping" of FKBP12 was investigated. To this end, novel 4-arylthioalkyl-1-carboxyalkyl-1,2,3-triazoles were designed and synthesized, and their efficacy was tested in human myotubes. A library of 17 compounds (10a-n) designed to dock the FKBP12/RyR1 hot-spot interface contact residues, was readily prepared from free α-amino acids and arylthioalkynes using CuAAC "click" protocols amenable to one-pot transformations in high overall yields and total configurational integrity. To model nitro-oxidative stress, human myotubes were treated with the peroxynitrite donor SIN1, and evidence was found that some triazoles 10 were able to normalize calcium levels, as well as FKBP12/RyR1 interaction. For example, compound 10 b at 150 nM rescued 46% of FKBP12/RyR1 interaction and up to 70% of resting cytosolic calcium levels in human myotubes under nitro-oxidative stress. All compounds 10 analyzed showed target engagement to FKBP12 and low levels of cytotoxicity in vitro. Compounds 10b, 10c, 10h, and 10iR were identified as potential therapeutic candidates to protect myotubes in muscle disorders with underlying nitro-oxidative stress, FKBP12/RyR1 dysfunction and calcium dysregulation.
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Affiliation(s)
- Jesus M Aizpurua
- Joxe Mari Korta R&D Center, Departamento de Química Orgánica-I, Universidad Del País Vasco UPV/EHU, Avda. Tolosa-72, 20018, San Sebastián, Spain.
| | - José I Miranda
- Joxe Mari Korta R&D Center, Departamento de Química Orgánica-I, Universidad Del País Vasco UPV/EHU, Avda. Tolosa-72, 20018, San Sebastián, Spain
| | - Aitziber Irastorza
- Joxe Mari Korta R&D Center, Departamento de Química Orgánica-I, Universidad Del País Vasco UPV/EHU, Avda. Tolosa-72, 20018, San Sebastián, Spain
| | - Endika Torres
- Joxe Mari Korta R&D Center, Departamento de Química Orgánica-I, Universidad Del País Vasco UPV/EHU, Avda. Tolosa-72, 20018, San Sebastián, Spain
| | - Maite Eceiza
- Joxe Mari Korta R&D Center, Departamento de Química Orgánica-I, Universidad Del País Vasco UPV/EHU, Avda. Tolosa-72, 20018, San Sebastián, Spain
| | - Maialen Sagartzazu-Aizpurua
- Joxe Mari Korta R&D Center, Departamento de Química Orgánica-I, Universidad Del País Vasco UPV/EHU, Avda. Tolosa-72, 20018, San Sebastián, Spain
| | - Pablo Ferrón
- Miramoon Pharma S.L., Avda Tolosa-72, 20018, San Sebastián, Spain
| | - Garazi Aldanondo
- Instituto de Investigación Sanitaria Biodonostia, Grupo de Enfermedades Neuromusculares, Paseo Dr Begiristain s/n, 20014, San Sebastián, Spain; CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain
| | - Haizpea Lasa-Fernández
- Instituto de Investigación Sanitaria Biodonostia, Grupo de Enfermedades Neuromusculares, Paseo Dr Begiristain s/n, 20014, San Sebastián, Spain; CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain; Grupo de Neurosciencias, Departamentos de Pediatría y Neurociencias, Universidad Del País Vasco UPV/EHU, Hospital Donostia, Paseo Dr Begiristain S/n, 20014, San Sebastián, Spain
| | - Pablo Marco-Moreno
- Instituto de Investigación Sanitaria Biodonostia, Grupo de Enfermedades Neuromusculares, Paseo Dr Begiristain s/n, 20014, San Sebastián, Spain; CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain
| | - Naroa Dadie
- Grupo de Neurosciencias, Departamentos de Pediatría y Neurociencias, Universidad Del País Vasco UPV/EHU, Hospital Donostia, Paseo Dr Begiristain S/n, 20014, San Sebastián, Spain
| | - Adolfo López de Munain
- Instituto de Investigación Sanitaria Biodonostia, Grupo de Enfermedades Neuromusculares, Paseo Dr Begiristain s/n, 20014, San Sebastián, Spain; CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain; Grupo de Neurosciencias, Departamentos de Pediatría y Neurociencias, Universidad Del País Vasco UPV/EHU, Hospital Donostia, Paseo Dr Begiristain S/n, 20014, San Sebastián, Spain
| | - Ainara Vallejo-Illarramendi
- Instituto de Investigación Sanitaria Biodonostia, Grupo de Enfermedades Neuromusculares, Paseo Dr Begiristain s/n, 20014, San Sebastián, Spain; CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain; Grupo de Neurosciencias, Departamentos de Pediatría y Neurociencias, Universidad Del País Vasco UPV/EHU, Hospital Donostia, Paseo Dr Begiristain S/n, 20014, San Sebastián, Spain.
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7
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Dashti A, Mashayekhi G, Shekhar M, Ben Hail D, Salah S, Schwander P, des Georges A, Singharoy A, Frank J, Ourmazd A. Retrieving functional pathways of biomolecules from single-particle snapshots. Nat Commun 2020; 11:4734. [PMID: 32948759 PMCID: PMC7501871 DOI: 10.1038/s41467-020-18403-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/17/2020] [Indexed: 11/18/2022] Open
Abstract
A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.
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Affiliation(s)
- Ali Dashti
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Ghoncheh Mashayekhi
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Mrinal Shekhar
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL, 61801, USA
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA
| | - Danya Ben Hail
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, 10031, USA
| | - Salah Salah
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, 10031, USA
- Department of Chemistry & Biochemistry, City College of New York, New York, NY, 10031, USA
- Ph.D. Programs in Physics, Chemistry & Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, 10031, USA.
- Department of Chemistry & Biochemistry, City College of New York, New York, NY, 10031, USA.
- Ph.D. Programs in Physics, Chemistry & Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Abhishek Singharoy
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA.
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, 2-221 Black Building, 650 West 168th Street, New York, NY, 10032, USA.
- Department of Biological Sciences, Columbia University, 600 Fairchild Center, New York, NY, 10027, USA.
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA.
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8
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Bauerová-Hlinková V, Hajdúchová D, Bauer JA. Structure and Function of the Human Ryanodine Receptors and Their Association with Myopathies-Present State, Challenges, and Perspectives. Molecules 2020; 25:molecules25184040. [PMID: 32899693 PMCID: PMC7570887 DOI: 10.3390/molecules25184040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/28/2020] [Accepted: 08/30/2020] [Indexed: 01/28/2023] Open
Abstract
Cardiac arrhythmias are serious, life-threatening diseases associated with the dysregulation of Ca2+ influx into the cytoplasm of cardiomyocytes. This dysregulation often arises from dysfunction of ryanodine receptor 2 (RyR2), the principal Ca2+ release channel. Dysfunction of RyR1, the skeletal muscle isoform, also results in less severe, but also potentially life-threatening syndromes. The RYR2 and RYR1 genes have been found to harbor three main mutation “hot spots”, where mutations change the channel structure, its interdomain interface properties, its interactions with its binding partners, or its dynamics. In all cases, the result is a defective release of Ca2+ ions from the sarcoplasmic reticulum into the myocyte cytoplasm. Here, we provide an overview of the most frequent diseases resulting from mutations to RyR1 and RyR2, briefly review some of the recent experimental structural work on these two molecules, detail some of the computational work describing their dynamics, and summarize the known changes to the structure and function of these receptors with particular emphasis on their N-terminal, central, and channel domains.
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9
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Zheng W, Wen H. Investigating dual Ca 2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation. Proteins 2020; 88:1528-1539. [PMID: 32557910 DOI: 10.1002/prot.25971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 05/26/2020] [Accepted: 06/14/2020] [Indexed: 11/09/2022]
Abstract
The ryanodine receptors (RyR) are essential to calcium signaling in striated muscles. A deep understanding of the complex Ca2+ -activation/inhibition mechanism of RyRs requires detailed structural and dynamic information for RyRs in different functional states (eg, with Ca2+ bound to activating or inhibitory sites). Recently, high-resolution structures of the RyR isoform 1 (RyR1) were solved by cryo-electron microscopy, revealing the location of a Ca2+ binding site for activation. Toward elucidating the Ca2+ -modulation mechanism of RyR1, we performed extensive molecular dynamics simulation of the core RyR1 structure in the presence and absence of activating and solvent Ca2+ (total simulation time is >5 μs). In the presence of solvent Ca2+ , Ca2+ binding to the activating site enhanced dynamics of RyR1 with higher inter-subunit flexibility, asymmetric inter-subunit motions, outward domain motions and partial pore dilation, which may prime RyR1 for subsequent channel opening. In contrast, the solvent Ca2+ alone reduced dynamics of RyR1 and led to inward domain motions and pore contraction, which may cause inhibition. Combining our simulation with the map of disease mutation sites in RyR1, we constructed a wiring diagram of key domains coupled via specific hydrogen bonds involving the mutation sites, some of which were modulated by Ca2+ binding. The structural and dynamic information gained from this study will inform future mutational and functional studies of RyR1 activation and inhibition by Ca2+ .
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, University at Buffalo, Buffalo, New York, USA
| | - Han Wen
- Department of Physics, University at Buffalo, Buffalo, New York, USA
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10
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Bauer JA, Pavlović J, Bauerová-Hlinková V. Normal Mode Analysis as a Routine Part of a Structural Investigation. Molecules 2019; 24:E3293. [PMID: 31510014 PMCID: PMC6767145 DOI: 10.3390/molecules24183293] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Normal mode analysis (NMA) is a technique that can be used to describe the flexible states accessible to a protein about an equilibrium position. These states have been shown repeatedly to have functional significance. NMA is probably the least computationally expensive method for studying the dynamics of macromolecules, and advances in computer technology and algorithms for calculating normal modes over the last 20 years have made it nearly trivial for all but the largest systems. Despite this, it is still uncommon for NMA to be used as a component of the analysis of a structural study. In this review, we will describe NMA, outline its advantages and limitations, explain what can and cannot be learned from it, and address some criticisms and concerns that have been voiced about it. We will then review the most commonly used techniques for reducing the computational cost of this method and identify the web services making use of these methods. We will illustrate several of their possible uses with recent examples from the literature. We conclude by recommending that NMA become one of the standard tools employed in any structural study.
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Affiliation(s)
- Jacob A Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia.
| | - Jelena Pavlović
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Vladena Bauerová-Hlinková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
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11
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Zheng W, Sachs F. Investigating the structural dynamics of the PIEZO1 channel activation and inactivation by coarse-grained modeling. Proteins 2017; 85:2198-2208. [PMID: 28905417 DOI: 10.1002/prot.25384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/22/2017] [Accepted: 09/10/2017] [Indexed: 01/07/2023]
Abstract
The PIEZO channels, a family of mechanosensitive channels in vertebrates, feature a fast activation by mechanical stimuli (eg, membrane tension) followed by a slower inactivation. Although a medium-resolution structure of the trimeric form of PIEZO1 was solved by cryo-electron microscopy (cryo-EM), key structural changes responsible for the channel activation and inactivation are still unknown. Toward decrypting the structural mechanism of the PIEZO1 activation and inactivation, we performed systematic coarse-grained modeling using an elastic network model and related modeling/analysis tools (ie, normal mode analysis, flexibility and hotspot analysis, correlation analysis, and cryo-EM-based hybrid modeling and flexible fitting). We identified four key motional modes that may drive the tension-induced activation and inactivation, with fast and slow relaxation time, respectively. These modes allosterically couple the lateral and vertical motions of the peripheral domains to the opening and closing of the intra-cellular vestibule, enabling external mechanical forces to trigger, and regulate the activation/inactivation transitions. We also calculated domain-specific flexibility profiles, and predicted hotspot residues at key domain-domain interfaces and hinges. Our results offer unprecedented structural and dynamic information, which is consistent with the literature on mutational and functional studies of the PIEZO channels, and will guide future studies of this important family of mechanosensitive channels.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, State University of New York at Buffalo, Buffalo, New York
| | - Frederick Sachs
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York
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12
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Zheng W, Wen H, Iacobucci GJ, Popescu GK. Probing the Structural Dynamics of the NMDA Receptor Activation by Coarse-Grained Modeling. Biophys J 2017. [PMID: 28636915 DOI: 10.1016/j.bpj.2017.04.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. High-resolution structures have been solved for an allosterically inhibited and agonist-bound form of a functional NMDA receptor; however, other key functional states (particularly the active open-channel state) were only resolved at moderate resolutions by cryo-electron microscopy (cryo-EM). To decrypt the mechanism of the NMDA receptor activation, structural modeling is essential to provide presently missing information about structural dynamics. We performed systematic coarse-grained modeling using an elastic network model and related modeling/analysis tools (e.g., normal mode analysis, flexibility and hotspot analysis, cryo-EM flexible fitting, and transition pathway modeling) based on an active-state cryo-EM map. We observed extensive conformational changes that allosterically couple the extracellular regulatory and agonist-binding domains to the pore-forming trans-membrane domain (TMD), and validated these, to our knowledge, new observations against known mutational and functional studies. Our results predict two key modes of collective motions featuring shearing/twisting of the extracellular domains relative to the TMD, reveal subunit-specific flexibility profiles, and identify functional hotspot residues at key domain-domain interfaces. Finally, by examining the conformational transition pathway between the allosterically inhibited form and the active form, we predict a discrete sequence of domain motions, which propagate from the extracellular domains to the TMD. In summary, our results offer rich structural and dynamic information, which is consistent with the literature on structure-function relationships in NMDA receptors, and will guide in-depth studies on the activation dynamics of this important neurotransmitter receptor.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, State University of New York at Buffalo, Buffalo, New York.
| | - Han Wen
- Department of Physics, State University of New York at Buffalo, Buffalo, New York
| | - Gary J Iacobucci
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, New York
| | - Gabriela K Popescu
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, New York
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Zheng W, Liu Z. Investigating the inter-subunit/subdomain interactions and motions relevant to disease mutations in the N-terminal domain of ryanodine receptors by molecular dynamics simulation. Proteins 2017; 85:1633-1644. [PMID: 28508509 DOI: 10.1002/prot.25318] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/28/2017] [Accepted: 05/08/2017] [Indexed: 11/12/2022]
Abstract
The ryanodine receptors (RyR) are essential to calcium signaling in striated muscles, and numerous disease mutations have been identified in two RyR isoforms, RyR1 in skeletal muscle and RyR2 in cardiac muscle. A deep understanding of the activation/regulation mechanisms of RyRs has been hampered by the shortage of high-resolution structures and dynamic information for this giant tetrameric complex in different functional states. Toward elucidating the molecular mechanisms of disease mutations in RyRs, we performed molecular dynamics simulation of the N-terminal domain (NTD) which is not only the best-resolved structural component of RyRs, but also a hotspot of disease mutations. First, we simulated the tetrameric NTD of wild-type RyR1 and three disease mutants (K155E, R157Q, and R164Q) that perturb the inter-subunit interfaces. Our simulations identified a dynamic network of salt bridges involving charged residues at the inter-subunit/subdomain interfaces and disease-mutation sites. By perturbing this key network, the above three mutations result in greater flexibility with the highest inter-subunit opening probability for R157Q. Next, we simulated the monomeric NTD of RyR2 in the presence or absence of a central Cl- anion which is known to stabilize the interfaces between the three NTD subdomains (A, B, and C). We found that the loss of Cl- restructures the salt-bridge network near the Cl- -binding site, leading to rotations of subdomain A/B relative to subdomain C and enhanced mobility between the subdomains. This finding supports a mechanism for disease mutations in the NTD of RyR2 via perturbation of the Cl- binding. The rich structural and dynamic information gained from this study will guide future mutational and functional studies of the NTD of RyRs. Proteins 2017; 85:1633-1644. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, University at Buffalo, Buffalo, New York, 14260
| | - Zheng Liu
- Department of Cardiology, Shanghai Tenth People's Hospital and Pan-Vascular Research Institute, Heart, Lung, and Blood Center, Tongji University School of Medicine, Shanghai, China
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Zheng W. Probing the structural dynamics of the SNARE recycling machine based on coarse-grained modeling. Proteins 2016; 84:1055-66. [PMID: 27090373 DOI: 10.1002/prot.25052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/04/2016] [Accepted: 04/13/2016] [Indexed: 01/05/2023]
Abstract
Membrane fusion in eukaryotes is driven by the formation of a four-helix bundle by three SNARE proteins. To recycle the SNARE proteins, they must be disassembled by the ATPase NSF and four SNAP proteins which together form a 20S supercomplex. Recently, the first high-resolution structures of the NSF (in both ATP and ADP state) and 20S (in four distinct states termed I, II, IIIa, and IIIb) were solved by cryo-electron microscopy (cryo-EM), which have paved the way for structure-driven studies of the SNARE recycling mechanism. To probe the structural dynamics of SNARE disassembly at amino-acid level of details, a systematic coarse-grained modeling based on an elastic network model and related analyses were performed. Our normal mode analysis of NSF, SNARE, and 20S predicted key modes of collective motions that partially account for the observed structural changes, and illuminated how the SNARE complex can be effectively destabilized by untwisting and bending motions of the SNARE complex driven by the amino-terminal domains of NSF in state II. Our flexibility analysis identified regions with high/low flexibility that coincide with key functional sites (such as the NSF-SNAPs-SNARE binding sites). A subset of hotspot residues that control the above collective motions, which will make promising targets for future mutagenesis studies were also identified. Finally, the conformational changes in 20S as induced by the transition of NSF from ATP to ADP state were modeled, and a concerted untwisting motion of SNARE/SNAPs and a sideway flip of two amino-terminal domains were observed. In sum, the findings have offered new structural and dynamic details relevant to the SNARE disassembly mechanism, and will guide future functional studies of the SNARE recycling machinery. Proteins 2016; 84:1055-1066. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, State University of New York, Buffalo, New York, 14260
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Yuchi Z, Van Petegem F. Ryanodine receptors under the magnifying lens: Insights and limitations of cryo-electron microscopy and X-ray crystallography studies. Cell Calcium 2016; 59:209-27. [DOI: 10.1016/j.ceca.2016.04.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/08/2016] [Accepted: 04/09/2016] [Indexed: 10/21/2022]
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