101
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Liao C, de Molliens MP, Schneebeli ST, Brewer M, Song G, Chatenet D, Braas KM, May V, Li J. Targeting the PAC1 Receptor for Neurological and Metabolic Disorders. Curr Top Med Chem 2019; 19:1399-1417. [PMID: 31284862 PMCID: PMC6761004 DOI: 10.2174/1568026619666190709092647] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/23/2018] [Accepted: 12/26/2018] [Indexed: 12/16/2022]
Abstract
The pituitary adenylate cyclase-activating polypeptide (PACAP)-selective PAC1 receptor (PAC1R, ADCYAP1R1) is a member of the vasoactive intestinal peptide (VIP)/secretin/glucagon family of G protein-coupled receptors (GPCRs). PAC1R has been shown to play crucial roles in the central and peripheral nervous systems. The activation of PAC1R initiates diverse downstream signal transduction pathways, including adenylyl cyclase, phospholipase C, MEK/ERK, and Akt pathways that regulate a number of physiological systems to maintain functional homeostasis. Accordingly, at times of tissue injury or insult, PACAP/PAC1R activation of these pathways can be trophic to blunt or delay apoptotic events and enhance cell survival. Enhancing PAC1R signaling under these conditions has the potential to mitigate cellular damages associated with cerebrovascular trauma (including stroke), neurodegeneration (such as Parkinson's and Alzheimer's disease), or peripheral organ insults. Conversely, maladaptive PACAP/PAC1R signaling has been implicated in a number of disorders, including stressrelated psychopathologies (i.e., depression, posttraumatic stress disorder, and related abnormalities), chronic pain and migraine, and metabolic diseases; abrogating PAC1R signaling under these pathological conditions represent opportunities for therapeutic intervention. Given the diverse PAC1R-mediated biological activities, the receptor has emerged as a relevant pharmaceutical target. In this review, we first describe the current knowledge regarding the molecular structure, dynamics, and function of PAC1R. Then, we discuss the roles of PACAP and PAC1R in the activation of a variety of signaling cascades related to the physiology and diseases of the nervous system. Lastly, we examine current drug design and development of peptides and small molecules targeting PAC1R based on a number of structure- activity relationship studies and key pharmacophore elements. At present, the rational design of PAC1R-selective peptide or small-molecule therapeutics is largely hindered by the lack of structural information regarding PAC1R activation mechanisms, the PACAP-PAC1R interface, and the core segments involved in receptor activation. Understanding the molecular basis governing the PACAP interactions with its different cognate receptors will undoubtedly provide a basis for the development and/or refinement of receptor-selective therapeutics.
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Affiliation(s)
- Chenyi Liao
- Department of Chemistry, University of Vermont, Burlington, VT 05405, United States
| | | | - Severin T Schneebeli
- Department of Chemistry, University of Vermont, Burlington, VT 05405, United States
| | - Matthias Brewer
- Department of Chemistry, University of Vermont, Burlington, VT 05405, United States
| | - Gaojie Song
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - David Chatenet
- INRS - Institut Armand-Frappier, 531 boul. des Prairies, Laval, QC H7V 1B7, Canada
| | - Karen M Braas
- Department of Neurological Sciences, University of Vermont, Larner College of Medicine, 149 Beaumont Avenue, Burlington, VT 05405, United States
| | - Victor May
- Department of Neurological Sciences, University of Vermont, Larner College of Medicine, 149 Beaumont Avenue, Burlington, VT 05405, United States
| | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, VT 05405, United States
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102
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Li Y, Wang M, Gao N, Li D, Lin J. The effect of dimerization on the activation and conformational dynamics of adenosine A 1 receptor. Phys Chem Chem Phys 2019; 21:22763-22773. [PMID: 31595279 DOI: 10.1039/c9cp04060a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adenosine A1 receptor (A1R) is one of four adenosine receptors in humans, which are involved in the function of the cardiovascular, respiratory and central nervous systems. Experimental results indicate that A1R can form a homodimer and that the protomer-protomer interaction in the A1R dimer is related to certain pharmacological characteristics of A1R activation. In this work, we performed docking, metadynamics simulation, conventional molecular dynamics simulations, Gaussian-accelerated molecular dynamics simulations, potential of mean force calculations, dynamic cross-correlation motions analysis and community network analysis to study the binding mode of 5'-N-ethylcarboxamidoadenosine (NECA) to A1R and the effect of dimerization on the activation of A1R. Our results show that NECA binds to A1R in a similar mode to adenosine in the A1R crystal structure and NECA in the A2AR crystal structure. The A1R homodimer can be activated by one or two agonists with NECA occupying its orthosteric pockets in one (which we call the NECA-A1R system) or both protomers (which we call the dNECA-A1R system). In the NECA-A1R system, activation is predicated in the protomer without NECA bound. In the dNECA-A1R system, only one protomer achieves the active state. These findings suggest an asymmetrical activation mechanism of the homodimer and a negative cooperativity between the two protomers. We envision that our results may further facilitate the drug development of A1R.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China.
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103
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Reconstruction of apo A2A receptor activation pathways reveal ligand-competent intermediates and state-dependent cholesterol hotspots. Sci Rep 2019; 9:14199. [PMID: 31578448 PMCID: PMC6775061 DOI: 10.1038/s41598-019-50752-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/27/2019] [Indexed: 02/07/2023] Open
Abstract
G-protein coupled receptors (GPCRs) play a pivotal role in transmitting signals at the cellular level. Structural insights can be exploited to support GPCR structure-based drug discovery endeavours. Despite advances in GPCR crystallography, active state structures are scarce. Molecular dynamics (MD) simulations have been used to explore the conformational landscape of GPCRs. Efforts have been made to retrieve active state conformations starting from inactive structures, however to date this has not been possible without using an energy bias. Here, we reconstruct the activation pathways of the apo adenosine receptor (A2A), starting from an inactive conformation, by applying adaptive sampling MD combined with a goal-oriented scoring function. The reconstructed pathways reconcile well with experiments and help deepen our understanding of A2A regulatory mechanisms. Exploration of the apo conformational landscape of A2A reveals the existence of ligand-competent states, active intermediates and state-dependent cholesterol hotspots of relevance for drug discovery. To the best of our knowledge this is the first time an activation process has been elucidated for a GPCR starting from an inactive structure only, using a non-biased MD approach, opening avenues for the study of ligand binding to elusive yet pharmacologically relevant GPCR states.
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104
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Zou Y, Ewalt J, Ng HL. Recent Insights from Molecular Dynamics Simulations for G Protein-Coupled Receptor Drug Discovery. Int J Mol Sci 2019; 20:E4237. [PMID: 31470676 PMCID: PMC6747122 DOI: 10.3390/ijms20174237] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are critical drug targets. GPCRs convey signals from the extracellular to the intracellular environment through G proteins. Some ligands that bind to GPCRs activate different downstream signaling pathways. G protein activation, or -arrestin biased signaling, involves ligands binding to receptors and stabilizing conformations that trigger a specific pathway. -arrestin biased signaling has become a hot target for structure-based drug discovery. However, challenges include that there are few crystal structures available in the Protein Data Bank and that GPCRs are highly dynamic. Hence, molecular dynamics (MD) simulations are especially valuable for obtaining detailed mechanistic information, including identification of allosteric sites and understanding modulators' interactions with receptors and ligands. Here, we highlight recent MD simulation studies and enhanced sampling methods used to study biased G protein-coupled receptor signaling and their conformational dynamics as well as applications to drug discovery.
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Affiliation(s)
- Ye Zou
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - John Ewalt
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Ho-Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA.
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105
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Abstract
Most current molecular dynamics simulation and analysis methods rely on the idea that the molecular system can be represented by a single global state (e.g., a Markov state in a Markov state model [MSM]). In this approach, molecules can be extensively sampled and analyzed when they only possess a few metastable states, such as small- to medium-sized proteins. However, this approach breaks down in frustrated systems and in large protein assemblies, where the number of global metastable states may grow exponentially with the system size. To address this problem, we here introduce dynamic graphical models (DGMs) that describe molecules as assemblies of coupled subsystems, akin to how spins interact in the Ising model. The change of each subsystem state is only governed by the states of itself and its neighbors. DGMs require fewer parameters than MSMs or other global state models; in particular, we do not need to observe all global system configurations to characterize them. Therefore, DGMs can predict previously unobserved molecular configurations. As a proof of concept, we demonstrate that DGMs can faithfully describe molecular thermodynamics and kinetics and predict previously unobserved metastable states for Ising models and protein simulations.
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Affiliation(s)
- Simon Olsson
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany;
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany;
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
- Department of Chemistry, Rice University, Houston, TX 77005
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106
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Da LT, Shi Y, Ning G, Yu J. Dynamics of the excised base release in thymine DNA glycosylase during DNA repair process. Nucleic Acids Res 2019; 46:568-581. [PMID: 29253232 PMCID: PMC5778594 DOI: 10.1093/nar/gkx1261] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/06/2017] [Indexed: 01/09/2023] Open
Abstract
Thymine DNA glycosylase (TDG) initiates base excision repair by cleaving the N-glycosidic bond between the sugar and target base. After catalysis, the release of excised base is a requisite step to terminate the catalytic cycle and liberate the TDG for the following enzymatic reactions. However, an atomistic-level understanding of the dynamics of the product release process in TDG remains unknown. Here, by employing molecular dynamics simulations combined with the Markov State Model, we reveal the dynamics of the thymine release after the excision at microseconds timescale and all-atom resolution. We identify several key metastable states of the thymine and its dominant releasing pathway. Notably, after replacing the TDG residue Gly142 with tyrosine, the thymine release is delayed compared to the wild-type (wt) TDG, as supported by our potential of mean force (PMF) calculations. These findings warrant further experimental tests to potentially trap the excised base in the active site of TDG after the catalysis, which had been unsuccessful by previous attempts. Finally, we extended our studies to other TDG products, including the uracil, 5hmU, 5fC and 5caC bases in order to compare the product release for different targeting bases in the TDG–DNA complex.
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Affiliation(s)
- Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yi Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Guodong Ning
- Technical Center of Erlianhot Entry-exit Inspection and Quarantine Bureau, 1266 Qianjin North Road, Erlianhot, Inner Mongolia, China
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing 100193, China
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107
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Selvam B, Yu YC, Chen LQ, Shukla D. Molecular Basis of the Glucose Transport Mechanism in Plants. ACS CENTRAL SCIENCE 2019; 5:1085-1096. [PMID: 31263768 PMCID: PMC6598156 DOI: 10.1021/acscentsci.9b00252] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Indexed: 05/04/2023]
Abstract
The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane (SWEET, Sugars Will Eventually Be Exported Transporter). However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in the OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as for the glucose transport mechanism. SWEETs undergo a structural transition to outward-facing (OF), occluded (OC), and inward-facing (IF) and strongly support an alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly the same for OF, OC, and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and acts as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass-like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.
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Affiliation(s)
- Balaji Selvam
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ya-Chi Yu
- Department
of Plant Biology, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Li-Qing Chen
- Department
of Plant Biology, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Diwakar Shukla
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department
of Plant Biology, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- NIH
Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- E-mail:
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108
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Syed Haneef SA, Ranganathan S. Structural bioinformatics analysis of variants on GPCR function. Curr Opin Struct Biol 2019; 55:161-177. [PMID: 31174013 DOI: 10.1016/j.sbi.2019.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 10/26/2022]
Abstract
G protein-coupled receptors (GPCRs) are key membrane-embedded receptor proteins, with critical roles in cellular signal transduction. In the era of precision medicine, understanding the role of natural variants on GPCR function is critical, especially from a pharmacogenomics viewpoint. Studies involved in mapping variants to GPCR structures are briefly reviewed here. The endocannabinoid system involving the central nervous system (CNS), the human cannabinoid receptor 1 (CB1), is an important drug target and its variability has implications for disease susceptibility and altered drug and pain response. We have carried out a computational study to map deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) to CB1. CB1 mutations were computationally evaluated from neutral to deleterious, and the top twelve deleterious mutations, with structural information, were found to be either close to the ligand binding region or the G-protein binding site. We have mapped these to the active and inactive CB1 X-ray crystallographic structures to correlate variants with available phenotypic information. We have also carried out molecular dynamics simulations to functionally characterize four selected mutants.
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Affiliation(s)
- Syed Askar Syed Haneef
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia.
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109
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Lamim Ribeiro JM, Filizola M. Allostery in G protein-coupled receptors investigated by molecular dynamics simulations. Curr Opin Struct Biol 2019; 55:121-128. [PMID: 31096158 DOI: 10.1016/j.sbi.2019.03.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/07/2019] [Accepted: 03/11/2019] [Indexed: 01/14/2023]
Abstract
G-protein-coupled receptors (GPCRs) are allosteric signaling machines that trigger distinct functional responses depending on the particular conformational state they adopt upon binding. This so-called GPCR functional selectivity is prompted by ligands of different efficacy binding at orthosteric or allosteric sites on the receptor, as well as by interactions with intracellular protein partners or other receptor types. Molecular dynamics (MD) simulations can provide important mechanistic, thermodynamic, and kinetic insights into these interactions at a level of molecular detail that is necessary to rightly inform modern drug discovery. Here, we review the most recent MD contributions to understanding GPCR allostery, with an emphasis on their strengths and limitations.
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Affiliation(s)
- João Marcelo Lamim Ribeiro
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, NY, 10029, USA
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, NY, 10029, USA.
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110
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Cong X, Chéron JB, Golebiowski J, Antonczak S, Fiorucci S. Allosteric Modulation Mechanism of the mGluR 5 Transmembrane Domain. J Chem Inf Model 2019; 59:2871-2878. [PMID: 31025859 DOI: 10.1021/acs.jcim.9b00045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Positive allosteric modulators (PAMs) of metabotropic glutamate receptor type 5 (mGluR5), a prototypical class C G protein-coupled receptor (GPCR), have shown therapeutic potential for various neurological disorders. Understanding the allosteric activation mechanism is essential for the rational design of mGluR5 PAMs. We studied the actions of positive and negative allosteric modulators within the transmembrane domain of mGluR5, using enhance-sampling all-atom molecular dynamics simulations. We found dual binding modes of the PAM, associated with distinct shapes of the allosteric pocket. The negative allosteric modulators, in contrast, showed only one binding mode. The simulations revealed the mechanism by which the PAM activated the receptor, in the absence of the orthosteric agonist (the so-called allosteric agonism). The mechanism relied on dynamic communications between amino-acid motifs that are highly conserved across class C GPCRs. The findings may guide structure-based design and virtual screening of allosteric modulators for mGluR5 as well as for other class C GPCRs.
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Affiliation(s)
- Xiaojing Cong
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , Nice 06108 , France
| | - Jean-Baptiste Chéron
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , Nice 06108 , France
| | - Jérôme Golebiowski
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , Nice 06108 , France.,Department of Brain and Cognitive Sciences , Daegu Gyeongbuk Institute of Science and Technology , Daegu 711-873 , South Korea
| | - Serge Antonczak
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , Nice 06108 , France
| | - Sébastien Fiorucci
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , Nice 06108 , France
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111
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Yuan S, Dahoun T, Brugarolas M, Pick H, Filipek S, Vogel H. Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds. Commun Biol 2019; 2:141. [PMID: 31044166 PMCID: PMC6478719 DOI: 10.1038/s42003-019-0384-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 03/11/2019] [Indexed: 12/17/2022] Open
Abstract
The mammalian olfactory system uses hundreds of specialized G-protein-coupled olfactory receptors (ORs) to discriminate a nearly unlimited number of odorants. Cognate agonists of most ORs have not yet been identified and potential non-olfactory processes mediated by ORs are unknown. Here, we used molecular modeling, fingerprint interaction analysis and molecular dynamics simulations to show that the binding pocket of the prototypical olfactory receptor Olfr73 is smaller, but more flexible, than binding pockets of typical non-olfactory G-protein-coupled receptors. We extended our modeling to virtual screening of a library of 1.6 million compounds against Olfr73. Our screen predicted 25 Olfr73 agonists beyond traditional odorants, of which 17 compounds, some with therapeutic potential, were validated in cell-based assays. Our modeling suggests a molecular basis for reduced interaction contacts between an odorant and its OR and thus the typical low potency of OR-activating compounds. These results provide a proof-of-principle for identifying novel therapeutic OR agonists.
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Affiliation(s)
- Shuguang Yuan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Laboratory of Biomodelling, Faculty of Chemistry & Biological and Chemical Research Centre, Uni-versity of Warsaw, 02-093 Warsaw, Poland
| | - Thamani Dahoun
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Marc Brugarolas
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Horst Pick
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Slawomir Filipek
- Laboratory of Biomodelling, Faculty of Chemistry & Biological and Chemical Research Centre, Uni-versity of Warsaw, 02-093 Warsaw, Poland
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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112
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Xia J, Flynn W, Gallicchio E, Uplinger K, Armstrong JD, Forli S, Olson AJ, Levy RM. Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. J Chem Inf Model 2019; 59:1382-1397. [PMID: 30758197 PMCID: PMC6496938 DOI: 10.1021/acs.jcim.8b00817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To perform massive-scale replica exchange molecular dynamics (REMD) simulations for calculating binding free energies of protein-ligand complexes, we implemented the asynchronous replica exchange (AsyncRE) framework of the binding energy distribution analysis method (BEDAM) in implicit solvent on the IBM World Community Grid (WCG) and optimized the simulation parameters to reduce the overhead and improve the prediction power of the WCG AsyncRE simulations. We also performed the first massive-scale binding free energy calculations using the WCG distributed computing grid and 301 ligands from the SAMPL4 challenge for large-scale binding free energy predictions of HIV-1 integrase complexes. In total there are ∼10000 simulated complexes, ∼1 million replicas, and ∼2000 μs of aggregated MD simulations. Running AsyncRE MD simulations on the WCG requires accepting a trade-off between the number of replicas that can be run (breadth) and the number of full RE cycles that can be completed per replica (depth). As compared with synchronous Replica Exchange (SyncRE) running on tightly coupled clusters like XSEDE, on the WCG many more replicas can be launched simultaneously on heterogeneous distributed hardware, but each full RE cycle requires more overhead. We compared the WCG results with that from AutoDock and more advanced RE simulations including the use of flattening potentials to accelerate sampling of selected degrees of freedom of ligands and/or receptors related to slow dynamics due to high energy barriers. We propose a suitable strategy of RE simulations to refine high throughput docking results which can be matched to corresponding computing resources: from HPC clusters, to small or medium-size distributed campus grids, and finally to massive-scale computing networks including millions of CPUs like the resources available on the WCG.
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Affiliation(s)
- Junchao Xia
- Center for Biophysics and Computational Biology and Department of Physics , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - William Flynn
- Center for Biophysics and Computational Biology and Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Emilio Gallicchio
- Department of Chemistry , CUNY Brooklyn College , Brooklyn , New York 11210 , United States
| | - Keith Uplinger
- IBM WCG Team, 1177 South Belt Line Road , Coppell , Texas 75019 , United States
| | - Jonathan D Armstrong
- IBM WCG Team, 11400 Burnet Road , 0453B129, Austin , Texas 78758 , United States
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037-1000 , United States
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037-1000 , United States
| | - Ronald M Levy
- Center for Biophysics and Computational Biology and Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
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113
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Pinamonti G, Paul F, Noé F, Rodriguez A, Bussi G. The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models. J Chem Phys 2019; 150:154123. [DOI: 10.1063/1.5083227] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Giovanni Pinamonti
- Department for Mathematics and Computer Science, Freie Universität, Berlin, Germany
| | - Fabian Paul
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, The University of Chicago, Chicago, Illinois 60637, USA
| | - Frank Noé
- Department for Mathematics and Computer Science, Freie Universität, Berlin, Germany
| | - Alex Rodriguez
- ICTP, International Centre for Theoretical Physics, Trieste, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste, Italy
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114
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Zhao LH, Ma S, Sutkeviciute I, Shen DD, Zhou XE, de Waal PW, Li CY, Kang Y, Clark LJ, Jean-Alphonse FG, White AD, Yang D, Dai A, Cai X, Chen J, Li C, Jiang Y, Watanabe T, Gardella TJ, Melcher K, Wang MW, Vilardaga JP, Xu HE, Zhang Y. Structure and dynamics of the active human parathyroid hormone receptor-1. Science 2019; 364:148-153. [PMID: 30975883 PMCID: PMC6929210 DOI: 10.1126/science.aav7942] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/08/2019] [Indexed: 12/23/2022]
Abstract
The parathyroid hormone receptor-1 (PTH1R) is a class B G protein-coupled receptor central to calcium homeostasis and a therapeutic target for osteoporosis and hypoparathyroidism. Here we report the cryo-electron microscopy structure of human PTH1R bound to a long-acting PTH analog and the stimulatory G protein. The bound peptide adopts an extended helix with its amino terminus inserted deeply into the receptor transmembrane domain (TMD), which leads to partial unwinding of the carboxyl terminus of transmembrane helix 6 and induces a sharp kink at the middle of this helix to allow the receptor to couple with G protein. In contrast to a single TMD structure state, the extracellular domain adopts multiple conformations. These results provide insights into the structural basis and dynamics of PTH binding and receptor activation.
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Affiliation(s)
- Li-Hua Zhao
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shanshan Ma
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ieva Sutkeviciute
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Dan-Dan Shen
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - X Edward Zhou
- Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Parker W de Waal
- Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Chen-Yao Li
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyong Kang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lisa J Clark
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Graduate Program in Molecular Biophysics and Structural Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Frederic G Jean-Alphonse
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Alex D White
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Graduate Program in Molecular Pharmacology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Dehua Yang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Antao Dai
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaoqing Cai
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jian Chen
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Cong Li
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tomoyuki Watanabe
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Thomas J Gardella
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Ming-Wei Wang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jean-Pierre Vilardaga
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - H Eric Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
- Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Yan Zhang
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China.
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115
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Pramanik D, Smith Z, Kells A, Tiwary P. Can One Trust Kinetic and Thermodynamic Observables from Biased Metadynamics Simulations?: Detailed Quantitative Benchmarks on Millimolar Drug Fragment Dissociation. J Phys Chem B 2019; 123:3672-3678. [DOI: 10.1021/acs.jpcb.9b01813] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Debabrata Pramanik
- Department of Chemistry and Biochemistry and Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Zachary Smith
- Biophysics Program and Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Adam Kells
- Department of Chemistry, King’s College London, SE1 1DB, London, U.K
| | - Pratyush Tiwary
- Department of Chemistry and Biochemistry and Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
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116
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Current status of multiscale simulations on GPCRs. Curr Opin Struct Biol 2019; 55:93-103. [DOI: 10.1016/j.sbi.2019.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/19/2019] [Accepted: 02/27/2019] [Indexed: 01/14/2023]
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117
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Zhu L, Sheong FK, Cao S, Liu S, Unarta IC, Huang X. TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules. J Chem Phys 2019; 150:124105. [DOI: 10.1063/1.5082633] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Lizhe Zhu
- Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong 518172, China
| | - Fu Kit Sheong
- Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Siqin Cao
- Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Song Liu
- Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Ilona C. Unarta
- Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuhui Huang
- Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Bioengineering Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- HKUST-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China
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118
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Peeking at G-protein-coupled receptors through the molecular dynamics keyhole. Future Med Chem 2019; 11:599-615. [DOI: 10.4155/fmc-2018-0393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Molecular dynamics is a state of the art computational tool for the investigation of biophysics phenomenon at a molecular scale, as it enables the modeling of dynamic processes, such as conformational motions, molecular solvation and ligand binding. The recent advances in structural biology have led to a bloom in published G-protein-coupled receptor structures, representing a solid and valuable resource for molecular dynamics studies. During the last decade, indeed, a plethora of physiological and pharmacological facets of this membrane protein superfamily have been addressed by means of molecular dynamics simulations, including the activation mechanism, allosterism and, very recently, biased signaling. Here, we try to recapitulate some of the main contributions that molecular dynamics has recently produced in the field.
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119
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Hruska E, Abella JR, Nüske F, Kavraki LE, Clementi C. Quantitative comparison of adaptive sampling methods for protein dynamics. J Chem Phys 2019; 149:244119. [PMID: 30599712 DOI: 10.1063/1.5053582] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Adaptive sampling methods, often used in combination with Markov state models, are becoming increasingly popular for speeding up rare events in simulation such as molecular dynamics (MD) without biasing the system dynamics. Several adaptive sampling strategies have been proposed, but it is not clear which methods perform better for different physical systems. In this work, we present a systematic evaluation of selected adaptive sampling strategies on a wide selection of fast folding proteins. The adaptive sampling strategies were emulated using models constructed on already existing MD trajectories. We provide theoretical limits for the sampling speed-up and compare the performance of different strategies with and without using some a priori knowledge of the system. The results show that for different goals, different adaptive sampling strategies are optimal. In order to sample slow dynamical processes such as protein folding without a priori knowledge of the system, a strategy based on the identification of a set of metastable regions is consistently the most efficient, while a strategy based on the identification of microstates performs better if the goal is to explore newer regions of the conformational space. Interestingly, the maximum speed-up achievable for the adaptive sampling of slow processes increases for proteins with longer folding times, encouraging the application of these methods for the characterization of slower processes, beyond the fast-folding proteins considered here.
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Affiliation(s)
- Eugen Hruska
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Jayvee R Abella
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Feliks Nüske
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Cecilia Clementi
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
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120
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Abstract
Biomolecular simulations rely heavily on the availability of suitable compute infrastructure for data-driven tasks like modeling, sampling, and analysis. These resources are typically available on a per-lab and per-facility basis, or through dedicated national supercomputing centers. In recent years, cloud computing has emerged as an alternative by offering an abundance of on-demand, specialist-maintained resources that enable efficiency and increased turnaround through rapid scaling.Scientific computations that take the shape of parallel workloads using large datasets are commonplace, making them ideal candidates for distributed computing in the cloud. Recent developments have greatly simplified the task for the experimenter to configure the cloud for use and job submission. This chapter will show how to use Google's Cloud Platform for biomolecular simulations by example of the molecular dynamics package GROningen MAchine for Chemical Simulations (GROMACS). The instructions readily transfer to a large variety of other tasks, allowing the reader to use the cloud for their specific purposes.Importantly, by using Docker containers, a popular light-weight virtualization solution, and cloud storage, key issues in scientific research are addressed: reproducibility of results, record keeping, and the possibility for other researchers to obtain copies and directly build upon previous work for further experimentation and hypothesis testing.
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121
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122
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Zhou Y, Liu Z, Zhang J, Dou T, Chen J, Ge G, Zhu S, Wang F. Prediction of ligand modulation patterns on membrane receptors via lysine reactivity profiling. Chem Commun (Camb) 2019; 55:4311-4314. [DOI: 10.1039/c9cc00520j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A mass spectrometry-based lysine reactivity profiling strategy for the prediction of the ligand modulation patterns on neuronal membrane receptors.
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Affiliation(s)
- Ye Zhou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Jinbao Zhang
- Institute of Neuroscience
- CAS Center for Excellence in Brain Science and Intelligence Technology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai
| | - Tongyi Dou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Jin Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Guangbo Ge
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Shujia Zhu
- Institute of Neuroscience
- CAS Center for Excellence in Brain Science and Intelligence Technology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
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123
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Zhang X, Yuan Y, Wang L, Guo Y, Li M, Li C, Pu X. Use multiscale simulation to explore the effects of the homodimerizations between different conformation states on the activation and allosteric pathway for the μ-opioid receptor. Phys Chem Chem Phys 2018; 20:13485-13496. [PMID: 29726867 DOI: 10.1039/c8cp02016g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recently, oligomers of G-protein coupled receptors (GPCRs) have been an important topic in the GPCR fields. However, knowledge about their structures and activation mechanisms is very limited due to the absence of crystal structures reported. In this work, we used multiscale simulations to study the effects of homodimerization between different conformation states on their activation, dynamic behaviors, and allosteric communication pathways for μ-OR. The results indicated that the dimerization of one inactive monomer with either one inactive monomer or one active one could enhance its constitutive activation. However, the conformation state of the other protomer (e.g., active or inactive) can influence the activated extent. The dimerization between the two inactive protomers leads to a negative cooperativity for their activation, which should contribute to the asymmetric activation of GPCR dimers observed in some experiments. On the other hand, for the active monomer, its dimerization with one inactive receptor could alleviate its deactivation, whereby negative and positive cooperativities can be observed between the two subunits of the dimer, depending on the different regions. Observations from protein structure network (PSN) analysis indicated that the dimerization of one inactive monomer with one active one would cause a significant drop in the number of main pathways from the ligand binding pocket to the G-protein coupled region for the inactive protomer, while the impact is minor for the active protomer. But, for the active monomer or the inactive one, its dimerization with one inactive monomer would significantly change the types of residues participating in the pathway with the highest frequency.
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Affiliation(s)
- Xi Zhang
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu 610041, P. R. China
| | - Longrong Wang
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Chuan Li
- College of Computer Science, Sichuan University, Chengdu, Sichuan 610064, P. R. China.
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
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124
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Cong X, Golebiowski J. Allosteric Na +-binding site modulates CXCR4 activation. Phys Chem Chem Phys 2018; 20:24915-24920. [PMID: 30238101 DOI: 10.1039/c8cp04134b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
G protein-coupled receptors (GPCRs) control most cellular communications with the environment and are the largest protein family of drug targets. As strictly regulated molecular machines, profound comprehension of their activation mechanism is expected to significantly facilitate structure-based drug design. This study provides atomistic-level description of the activation dynamics of the C-X-C chemokine receptor type 4 (CXCR4), a class A GPCR and important drug target. Using molecular dynamics and enhanced sampling, we demonstrate how mutations and protonation of conserved residues trigger activation through microswitches at the receptor core, while sodium ion - a known allosteric modulator - inhibits it. The findings point to a conserved mechanism of activation and the allosteric modulation by sodium in the chemokine receptor family. From the technical aspect, the enhanced sampling protocol effectively samples receptor conformational changes toward activation, and differentiates three variants of the receptor by their basal activity. This work provides structural basis and a powerful in silico tool for CXCR4 agonist design.
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Affiliation(s)
- Xiaojing Cong
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, 06108 Nice, France.
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125
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Menzer WM, Li C, Sun W, Xie B, Minh DDL. Simple Entropy Terms for End-Point Binding Free Energy Calculations. J Chem Theory Comput 2018; 14:6035-6049. [PMID: 30296084 DOI: 10.1021/acs.jctc.8b00418] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We introduce a number of computationally inexpensive modifications to the MM/PBSA and MM/GBSA estimators for binding free energies, which are based on average receptor-ligand interaction energies in simulations of a noncovalent complex, to improve the treatment of entropy: second- and higher-order terms in a cumulant expansion and a confining potential on ligand external degrees of freedom. We also consider a filter for snapshots where ligands have drifted from the initial binding pose. The variations were tested on six sets of systems for which binding modes and free energies have previously been experimentally determined. For some data sets, none of the tested estimators led to results significantly correlated with measured free energies. In data sets with nontrivial correlation, a ligand RMSD cutoff of 3 Å and a second-order truncation of the cumulant expansion was found to be comparable or better than the average interaction energy by several statistical metrics.
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126
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Mittal S, Shukla D. Maximizing Kinetic Information Gain of Markov State Models for Optimal Design of Spectroscopy Experiments. J Phys Chem B 2018; 122:10793-10805. [DOI: 10.1021/acs.jpcb.8b07076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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127
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Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. Overview of the SAMPL6 host-guest binding affinity prediction challenge. J Comput Aided Mol Des 2018; 32:937-963. [PMID: 30415285 PMCID: PMC6301044 DOI: 10.1007/s10822-018-0170-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/07/2018] [Indexed: 10/27/2022]
Abstract
Accurately predicting the binding affinities of small organic molecules to biological macromolecules can greatly accelerate drug discovery by reducing the number of compounds that must be synthesized to realize desired potency and selectivity goals. Unfortunately, the process of assessing the accuracy of current computational approaches to affinity prediction against binding data to biological macromolecules is frustrated by several challenges, such as slow conformational dynamics, multiple titratable groups, and the lack of high-quality blinded datasets. Over the last several SAMPL blind challenge exercises, host-guest systems have emerged as a practical and effective way to circumvent these challenges in assessing the predictive performance of current-generation quantitative modeling tools, while still providing systems capable of possessing tight binding affinities. Here, we present an overview of the SAMPL6 host-guest binding affinity prediction challenge, which featured three supramolecular hosts: octa-acid (OA), the closely related tetra-endo-methyl-octa-acid (TEMOA), and cucurbit[8]uril (CB8), along with 21 small organic guest molecules. A total of 119 entries were received from ten participating groups employing a variety of methods that spanned from electronic structure and movable type calculations in implicit solvent to alchemical and potential of mean force strategies using empirical force fields with explicit solvent models. While empirical models tended to obtain better performance than first-principle methods, it was not possible to identify a single approach that consistently provided superior results across all host-guest systems and statistical metrics. Moreover, the accuracy of the methodologies generally displayed a substantial dependence on the system considered, emphasizing the need for host diversity in blind evaluations. Several entries exploited previous experimental measurements of similar host-guest systems in an effort to improve their physical-based predictions via some manner of rudimentary machine learning; while this strategy succeeded in reducing systematic errors, it did not correspond to an improvement in statistical correlation. Comparison to previous rounds of the host-guest binding free energy challenge highlights an overall improvement in the correlation obtained by the affinity predictions for OA and TEMOA systems, but a surprising lack of improvement regarding root mean square error over the past several challenge rounds. The data suggests that further refinement of force field parameters, as well as improved treatment of chemical effects (e.g., buffer salt conditions, protonation states), may be required to further enhance predictive accuracy.
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Affiliation(s)
- Andrea Rizzi
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA
| | - Steven Murkli
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - John N McNeill
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Wei Yao
- Department of Chemistry, Tulane University, Louisiana, LA, 70118, USA
| | - Matthew Sullivan
- Department of Chemistry, Tulane University, Louisiana, LA, 70118, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Michael W Chiu
- Qualcomm Institute, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Bruce C Gibb
- Department of Chemistry, Tulane University, Louisiana, LA, 70118, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, California, 92697, USA.
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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128
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Selvam B, Mittal S, Shukla D. Free Energy Landscape of the Complete Transport Cycle in a Key Bacterial Transporter. ACS CENTRAL SCIENCE 2018; 4:1146-1154. [PMID: 30276247 PMCID: PMC6161048 DOI: 10.1021/acscentsci.8b00330] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Indexed: 05/21/2023]
Abstract
PepTSo is a proton-coupled bacterial symporter, from the major facilitator superfamily (MFS), which transports di-/tripeptide molecules. The recently obtained crystal structure of PepTSo provides an unprecedented opportunity to gain an understanding of functional insights of the substrate transport mechanism. Binding of the proton and peptide molecule induces conformational changes into occluded (OC) and outward-facing (OF) states, which we are able to characterize using molecular dynamics (MD) simulations. The structural knowledge of the OC and OF state is important to fully understand the major energy barrier associated with the transport cycle. In order to gain functional insight into the interstate dynamics, we performed extensive all atom MD simulations. The Markov state model was constructed to identify the free energy barriers between the states, and kinetic information on intermediate pathways was obtained using the transition pathway theory (TPT). TPT shows that the OF state is obtained by the movement of TM1 and TM7 at the extracellular side approximately 12-16 Å away from each other, and the inward movement of TM4 and TM10 at the intracellular halves to 3-4 Å characterizes the OC state. Helix distance distributions obtained from MD simulations were compared with experimental double electron-electron resonance spectroscopy and were found to be in excellent agreement with previous studies. We also predicted the optimal positions for placement of methane thiosulfonate spin label probes to capture the slowest protein dynamics. Our finding sheds light on the conformational cycle of this key membrane transporter and the functional relationships between the multiple intermediate states.
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Affiliation(s)
- Balaji Selvam
- Department of Chemical and Biomolecular Engineering, Center for Biophysics and Quantitative
Biology, and Department
of Plant Biology, University of Illinois
at Urbana-Champaign, Urbana, Illinois, United States
| | - Shriyaa Mittal
- Department of Chemical and Biomolecular Engineering, Center for Biophysics and Quantitative
Biology, and Department
of Plant Biology, University of Illinois
at Urbana-Champaign, Urbana, Illinois, United States
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, Center for Biophysics and Quantitative
Biology, and Department
of Plant Biology, University of Illinois
at Urbana-Champaign, Urbana, Illinois, United States
- E-mail:
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129
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Abstract
G-protein-coupled receptors (GPCRs) are a large group of membrane-bound receptor proteins that are involved in a plethora of diverse processes (e.g., vision, hormone response). In mammals, and particularly in humans, GPCRs are involved in many signal transduction pathways and, as such, are heavily studied for their immense pharmaceutical potential. Indeed, a large fraction of drugs target various GPCRs, and drug-development is often aimed at GPCRs. Therefore, understanding the activation of GPCRs is a challenge of major importance both from fundamental and practical considerations. And yet, despite the remarkable progress in structural understanding, we still do not have a translation of the structural information to an energy-based picture. Here we use coarse-grained (CG) modeling to chart the free-energy landscape of the activation process of the β-2 adrenergic receptor (β2AR) as a representative GPCR. The landscape provides the needed tool for analyzing the processes that lead to activation of the receptor upon binding of the ligand (adrenaline) while limiting constitutive activation. Our results pave the way to better understand the biological mechanisms of action of the β2AR and GPCRs, from a physical chemistry point of view rather than simply by observing the receptor's behavior physiologically.
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130
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Papadourakis M, Bosisio S, Michel J. Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge. J Comput Aided Mol Des 2018; 32:1047-1058. [PMID: 30159717 DOI: 10.1007/s10822-018-0154-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 08/24/2018] [Indexed: 10/28/2022]
Abstract
In the context of the SAMPL6 challenges, series of blinded predictions of standard binding free energies were made with the SOMD software for a dataset of 27 host-guest systems featuring two octa-acids hosts (OA and TEMOA) and a cucurbituril ring (CB8) host. Three different models were used, ModelA computes the free energy of binding based on a double annihilation technique; ModelB additionally takes into account long-range dispersion and standard state corrections; ModelC additionally introduces an empirical correction term derived from a regression analysis of SAMPL5 predictions previously made with SOMD. The performance of each model was evaluated with two different setups; buffer explicitly matches the ionic strength from the binding assays, whereas no-buffer merely neutralizes the host-guest net charge with counter-ions. ModelC/no-buffer shows the lowest mean-unsigned error for the overall dataset (MUE 1.29 < 1.39 < 1.50 kcal mol-1, 95% CI), while explicit modelling of the buffer improves significantly results for the CB8 host only. Correlation with experimental data ranges from excellent for the host TEMOA (R2 0.91 < 0.94 < 0.96), to poor for CB8 (R2 0.04 < 0.12 < 0.23). Further investigations indicate a pronounced dependence of the binding free energies on the modelled ionic strength, and variable reproducibility of the binding free energies between different simulation packages.
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Affiliation(s)
- Michail Papadourakis
- EaStCHEM School of Chemistry, Joseph Black Building, King's Buildings, Edinburgh, EH9 3FJ, UK
| | - Stefano Bosisio
- EaStCHEM School of Chemistry, Joseph Black Building, King's Buildings, Edinburgh, EH9 3FJ, UK
| | - Julien Michel
- EaStCHEM School of Chemistry, Joseph Black Building, King's Buildings, Edinburgh, EH9 3FJ, UK.
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131
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Shamsi Z, Cheng KJ, Shukla D. Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes. J Phys Chem B 2018; 122:8386-8395. [DOI: 10.1021/acs.jpcb.8b06521] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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132
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Cong X, Fiorucci S, Golebiowski J. Activation Dynamics of the Neurotensin G Protein-Coupled Receptor 1. J Chem Theory Comput 2018; 14:4467-4473. [PMID: 29965755 DOI: 10.1021/acs.jctc.8b00216] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A replica-exchange protocol remarkably enhances the sampling of the activation dynamics of the neurotensin receptor type 1, a G protein-coupled receptor (GPCR) and important drug target. Our work highlights the dynamic communication between conformational changes of the agonist and the G protein-binding site, via contraction-oscillation of the orthosteric pocket. It also gives insights into the mechanism by which certain mutations diminish or stimulate activation. The replica-exchange protocol effectively enhances barrier crossing where standard brute-force molecular dynamics simulations fail. It is readily applicable to other GPCRs and represents a promising approach for virtual ligand screening, using the typical features of receptor activation as a benchmark.
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Affiliation(s)
- Xiaojing Cong
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , 06108 Nice , France
| | - Sébastien Fiorucci
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , 06108 Nice , France
| | - Jérôme Golebiowski
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , 06108 Nice , France.,Department of Brain and Cognitive Sciences , Daegu Gyeongbuk Institute of Science and Technology , Daegu , 711-873 , South Korea
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133
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Keri D, Barth P. Reprogramming G protein coupled receptor structure and function. Curr Opin Struct Biol 2018; 51:187-194. [PMID: 30055347 DOI: 10.1016/j.sbi.2018.07.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 07/18/2018] [Indexed: 12/22/2022]
Abstract
The prominence of G protein-coupled receptors (GPCRs) in human physiology and disease has resulted in their intense study in various fields of research ranging from neuroscience to structural biology. With over 800 members in the human genome and their involvement in a myriad of diseases, GPCRs are the single largest family of drug targets, and an ever-present interest exists in further drug discovery and structural characterization efforts. However, low GPCR expression and stability outside the natural lipid environments have challenged these efforts. In vivo functional studies of GPCR signaling are complicated not only by the need for specific spatiotemporal activation, but also by downstream effector promiscuity. In this review, we summarize the present and emerging GPCR engineering methods that have been employed to overcome the challenges involved in receptor characterization, and to better understand the functional role of these receptors.
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Affiliation(s)
- D Keri
- Swiss Federal Institute of Technology (EPFL), Interfaculty Institute of Bioengineering, 1015 Lausanne, Switzerland
| | - P Barth
- Swiss Federal Institute of Technology (EPFL), Interfaculty Institute of Bioengineering, 1015 Lausanne, Switzerland; Ludwig Institute for Cancer Research Lausanne Branch, 1066 Lausanne, Switzerland; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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134
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Delarue M, Koehl P. Combined approaches from physics, statistics, and computer science for ab initio protein structure prediction: ex unitate vires (unity is strength)? F1000Res 2018; 7. [PMID: 30079234 PMCID: PMC6058471 DOI: 10.12688/f1000research.14870.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/19/2018] [Indexed: 11/20/2022] Open
Abstract
Connecting the dots among the amino acid sequence of a protein, its structure, and its function remains a central theme in molecular biology, as it would have many applications in the treatment of illnesses related to misfolding or protein instability. As a result of high-throughput sequencing methods, biologists currently live in a protein sequence-rich world. However, our knowledge of protein structure based on experimental data remains comparatively limited. As a consequence, protein structure prediction has established itself as a very active field of research to fill in this gap. This field, once thought to be reserved for theoretical biophysicists, is constantly reinventing itself, borrowing ideas informed by an ever-increasing assembly of scientific domains, from biology, chemistry, (statistical) physics, mathematics, computer science, statistics, bioinformatics, and more recently data sciences. We review the recent progress arising from this integration of knowledge, from the development of specific computer architecture to allow for longer timescales in physics-based simulations of protein folding to the recent advances in predicting contacts in proteins based on detection of coevolution using very large data sets of aligned protein sequences.
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Affiliation(s)
- Marc Delarue
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, and UMR 3528 du CNRS, Paris, France
| | - Patrice Koehl
- Department of Computer Science, Genome Center, University of California, Davis, Davis, California, USA
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135
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Yuan X, Xu Y. Recent Trends and Applications of Molecular Modeling in GPCR⁻Ligand Recognition and Structure-Based Drug Design. Int J Mol Sci 2018; 19:ijms19072105. [PMID: 30036949 PMCID: PMC6073596 DOI: 10.3390/ijms19072105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled receptors represent the largest family of human membrane proteins and are modulated by a variety of drugs and endogenous ligands. Molecular modeling techniques, especially enhanced sampling methods, have provided significant insight into the mechanism of GPCR–ligand recognition. Notably, the crucial role of the membrane in the ligand-receptor association process has earned much attention. Additionally, docking, together with more accurate free energy calculation methods, is playing an important role in the design of novel compounds targeting GPCRs. Here, we summarize the recent progress in the computational studies focusing on the above issues. In the future, with continuous improvement in both computational hardware and algorithms, molecular modeling would serve as an indispensable tool in a wider scope of the research concerning GPCR–ligand recognition as well as drug design targeting GPCRs.
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Affiliation(s)
- Xiaojing Yuan
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
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136
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Sultan MM, Kiss G, Pande VS. Towards simple kinetic models of functional dynamics for a kinase subfamily. Nat Chem 2018; 10:903-909. [PMID: 29988151 DOI: 10.1038/s41557-018-0077-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 05/08/2018] [Indexed: 11/09/2022]
Abstract
Kinases are ubiquitous enzymes involved in the regulation of critical cellular pathways. However, in silico modelling of the conformational ensembles of these enzymes is difficult due to inherent limitations and the cost of computational approaches. Recent algorithmic advances combined with homology modelling and parallel simulations have enabled researchers to address this computational sampling bottleneck. Here, we present the results of molecular dynamics studies for seven Src family kinase (SFK) members: Fyn, Lyn, Lck, Hck, Fgr, Yes and Blk. We present a sequence invariant extension to Markov state models, which allows us to quantitatively compare the structural ensembles of the seven kinases. Our findings indicate that in the absence of their regulatory partners, SFK members have similar in silico dynamics with active state populations ranging from 4 to 40% and activation timescales in the hundreds of microseconds. Furthermore, we observe several potentially druggable intermediate states, including a pocket next to the adenosine triphosphate binding site that could potentially be targeted via a small-molecule inhibitor.
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Affiliation(s)
| | - Gert Kiss
- Department of Chemistry, Stanford University, Stanford, CA, USA.,Center for Molecular Analysis and Design, Stanford University, Stanford, CA, USA.,Revolution Medicines, Redwood City, CA, USA
| | - Vijay S Pande
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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137
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Wehmeyer C, Noé F. Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics. J Chem Phys 2018; 148:241703. [PMID: 29960344 DOI: 10.1063/1.5011399] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Inspired by the success of deep learning techniques in the physical and chemical sciences, we apply a modification of an autoencoder type deep neural network to the task of dimension reduction of molecular dynamics data. We can show that our time-lagged autoencoder reliably finds low-dimensional embeddings for high-dimensional feature spaces which capture the slow dynamics of the underlying stochastic processes-beyond the capabilities of linear dimension reduction techniques.
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Affiliation(s)
- Christoph Wehmeyer
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
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138
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Sinitskiy AV, Pande VS. Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors. Biophys J 2018; 115:841-852. [PMID: 30029773 DOI: 10.1016/j.bpj.2018.06.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 01/07/2023] Open
Abstract
N-methyl-D-aspartate receptors (NMDARs)-i.e., transmembrane proteins expressed in neurons-play a central role in the molecular mechanisms of learning and memory formation. It is unclear how the known atomic structures of NMDARs determined by x-ray crystallography and electron cryomicroscopy (18 published Protein Data Bank entries) relate to the functional states of NMDARs inferred from electrophysiological recordings (multiple closed, open, preopen, etc. states). We address this problem by using molecular dynamics simulations at atomic resolution, a method successfully applied in the past to much smaller biomolecules. Our simulations predict that several conformations of NMDARs with experimentally determined geometries, including four "nonactive" electron cryomicroscopy structures, rapidly interconvert on submicrosecond timescales and therefore may correspond to the same functional state of the receptor (specifically, one of the closed states). This conclusion is not trivial because these conformational transitions involve changes in certain interatomic distances as large as tens of Å. The simulations also predict differences in the conformational dynamics of the apo and holo (i.e., agonist and coagonist bound) forms of the receptor on the microsecond timescale. To our knowledge, five new conformations of NMDARs, with geometries joining various features from different known experimental structures, are also predicted by the model. The main limitation of this work stems from its limited sampling (30 μs of aggregate length of molecular dynamics trajectories). Though this level significantly exceeds the sampling in previous simulations of parts of NMDARs, it is still much lower than the sampling recently achieved for smaller biomolecules (up to a few milliseconds), thus precluding, in particular, the observation of transitions between different functional states of NMDARs. Despite this limitation, such computational predictions may guide further experimental studies on the structure, dynamics, and function of NMDARs, for example by suggesting optimal locations of spectroscopic probes. Overall, atomic resolution simulations provide, to our knowledge, a novel perspective on the structure and dynamics of NMDARs, complementing information obtained by experimental methods.
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Affiliation(s)
- Anton V Sinitskiy
- Department of Bioengineering, Stanford University, Stanford, California.
| | - Vijay S Pande
- Department of Bioengineering, Stanford University, Stanford, California.
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139
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Dibak M, Del Razo MJ, De Sancho D, Schütte C, Noé F. MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations. J Chem Phys 2018; 148:214107. [PMID: 29884049 DOI: 10.1063/1.5020294] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long time-scale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large length scales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time and length scales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step toward MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B ⇌ C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported.
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Affiliation(s)
- Manuel Dibak
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Mauricio J Del Razo
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - David De Sancho
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Christof Schütte
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
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140
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Sadeghi M, Weikl TR, Noé F. Particle-based membrane model for mesoscopic simulation of cellular dynamics. J Chem Phys 2018; 148:044901. [PMID: 29390800 DOI: 10.1063/1.5009107] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on interacting and reacting particles, each representing a coarse patch of a lipid monolayer. Particle interactions include nearest-neighbor bond-stretching and angle-bending and are parameterized so as to reproduce the local membrane mechanics given by the Helfrich energy density over a range of relevant curvatures. In-plane fluidity is implemented with Monte Carlo bond-flipping moves. The physical accuracy of the model is verified by five tests: (i) Power spectrum analysis of equilibrium thermal undulations is used to verify that the particle-based representation correctly captures the dynamics predicted by the continuum model of fluid membranes. (ii) It is verified that the input bending stiffness, against which the potential parameters are optimized, is accurately recovered. (iii) Isothermal area compressibility modulus of the membrane is calculated and is shown to be tunable to reproduce available values for different lipid bilayers, independent of the bending rigidity. (iv) Simulation of two-dimensional shear flow under a gravity force is employed to measure the effective in-plane viscosity of the membrane model and show the possibility of modeling membranes with specified viscosities. (v) Interaction of the bilayer membrane with a spherical nanoparticle is modeled as a test case for large membrane deformations and budding involved in cellular processes such as endocytosis. The results are shown to coincide well with the predicted behavior of continuum models, and the membrane model successfully mimics the expected budding behavior. We expect our model to be of high practical usability for ultra coarse-grained molecular dynamics or particle-based reaction-diffusion simulations of biological systems.
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Affiliation(s)
- Mohsen Sadeghi
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Thomas R Weikl
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
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141
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O’Connor M, Deeks HM, Dawn E, Metatla O, Roudaut A, Sutton M, Thomas LM, Glowacki BR, Sage R, Tew P, Wonnacott M, Bates P, Mulholland AJ, Glowacki DR. Sampling molecular conformations and dynamics in a multiuser virtual reality framework. SCIENCE ADVANCES 2018; 4:eaat2731. [PMID: 29963636 PMCID: PMC6025904 DOI: 10.1126/sciadv.aat2731] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/18/2018] [Indexed: 05/28/2023]
Abstract
We describe a framework for interactive molecular dynamics in a multiuser virtual reality (VR) environment, combining rigorous cloud-mounted atomistic physics simulations with commodity VR hardware, which we have made accessible to readers (see isci.itch.io/nsb-imd). It allows users to visualize and sample, with atomic-level precision, the structures and dynamics of complex molecular structures "on the fly" and to interact with other users in the same virtual environment. A series of controlled studies, in which participants were tasked with a range of molecular manipulation goals (threading methane through a nanotube, changing helical screw sense, and tying a protein knot), quantitatively demonstrate that users within the interactive VR environment can complete sophisticated molecular modeling tasks more quickly than they can using conventional interfaces, especially for molecular pathways and structural transitions whose conformational choreographies are intrinsically three-dimensional. This framework should accelerate progress in nanoscale molecular engineering areas including conformational mapping, drug development, synthetic biology, and catalyst design. More broadly, our findings highlight the potential of VR in scientific domains where three-dimensional dynamics matter, spanning research and education.
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Affiliation(s)
- Michael O’Connor
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
| | - Helen M. Deeks
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
| | - Edward Dawn
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Oussama Metatla
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
| | - Anne Roudaut
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
| | - Matthew Sutton
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
| | - Lisa May Thomas
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
- Department of Theatre, University of Bristol, Cantock’s Close, Bristol BS8 1UP, UK
| | - Becca Rose Glowacki
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
- School of Art and Design, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Rebecca Sage
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, UK
| | - Philip Tew
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, UK
| | - Mark Wonnacott
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, UK
| | - Phil Bates
- Oracle Cloud Development Centre, Tower Wharf, Cheese Lane, Bristol BS2 2JJ, UK
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - David R. Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
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142
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Kang Y, Kuybeda O, de Waal PW, Mukherjee S, Van Eps N, Dutka P, Zhou XE, Bartesaghi A, Erramilli S, Morizumi T, Gu X, Yin Y, Liu P, Jiang Y, Meng X, Zhao G, Melcher K, Ernst OP, Kossiakoff AA, Subramaniam S, Xu HE. Cryo-EM structure of human rhodopsin bound to an inhibitory G protein. Nature 2018; 558:553-558. [PMID: 29899450 PMCID: PMC8054211 DOI: 10.1038/s41586-018-0215-y] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/02/2018] [Indexed: 11/08/2022]
Abstract
G-protein-coupled receptors comprise the largest family of mammalian transmembrane receptors. They mediate numerous cellular pathways by coupling with downstream signalling transducers, including the hetrotrimeric G proteins Gs (stimulatory) and Gi (inhibitory) and several arrestin proteins. The structural mechanisms that define how G-protein-coupled receptors selectively couple to a specific type of G protein or arrestin remain unknown. Here, using cryo-electron microscopy, we show that the major interactions between activated rhodopsin and Gi are mediated by the C-terminal helix of the Gi α-subunit, which is wedged into the cytoplasmic cavity of the transmembrane helix bundle and directly contacts the amino terminus of helix 8 of rhodopsin. Structural comparisons of inactive, Gi-bound and arrestin-bound forms of rhodopsin with inactive and Gs-bound forms of the β2-adrenergic receptor provide a foundation to understand the unique structural signatures that are associated with the recognition of Gs, Gi and arrestin by activated G-protein-coupled receptors.
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MESH Headings
- Arrestin/chemistry
- Arrestin/metabolism
- Binding Sites
- Cryoelectron Microscopy
- GTP-Binding Protein alpha Subunits, Gi-Go/chemistry
- GTP-Binding Protein alpha Subunits, Gi-Go/metabolism
- GTP-Binding Protein alpha Subunits, Gi-Go/ultrastructure
- GTP-Binding Protein alpha Subunits, Gs/chemistry
- GTP-Binding Protein alpha Subunits, Gs/metabolism
- Humans
- Models, Molecular
- Receptors, Adrenergic, beta-2/chemistry
- Receptors, Adrenergic, beta-2/metabolism
- Rhodopsin/chemistry
- Rhodopsin/metabolism
- Rhodopsin/ultrastructure
- Signal Transduction
- Substrate Specificity
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Affiliation(s)
- Yanyong Kang
- Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Oleg Kuybeda
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Parker W de Waal
- Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Przemyslaw Dutka
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - X Edward Zhou
- Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Alberto Bartesaghi
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Satchal Erramilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Xin Gu
- Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Yanting Yin
- Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Ping Liu
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yi Jiang
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xing Meng
- David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Gongpu Zhao
- David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
| | - Sriram Subramaniam
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
| | - H Eric Xu
- Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA.
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
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143
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Examining a Thermodynamic Order Parameter of Protein Folding. Sci Rep 2018; 8:7148. [PMID: 29740018 PMCID: PMC5940758 DOI: 10.1038/s41598-018-25406-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/18/2018] [Indexed: 01/26/2023] Open
Abstract
Dimensionality reduction with a suitable choice of order parameters or reaction coordinates is commonly used for analyzing high-dimensional time-series data generated by atomistic biomolecular simulations. So far, geometric order parameters, such as the root mean square deviation, fraction of native amino acid contacts, and collective coordinates that best characterize rare or large conformational transitions, have been prevailing in protein folding studies. Here, we show that the solvent-averaged effective energy, which is a thermodynamic quantity but unambiguously defined for individual protein conformations, serves as a good order parameter of protein folding. This is illustrated through the application to the folding-unfolding simulation trajectory of villin headpiece subdomain. We rationalize the suitability of the effective energy as an order parameter by the funneledness of the underlying protein free energy landscape. We also demonstrate that an improved conformational space discretization is achieved by incorporating the effective energy. The most distinctive feature of this thermodynamic order parameter is that it works in pointing to near-native folded structures even when the knowledge of the native structure is lacking, and the use of the effective energy will also find applications in combination with methods of protein structure prediction.
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144
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Meng Y, Gao C, Clawson D, Atwell S, Russell M, Vieth M, Roux B. Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models. J Chem Theory Comput 2018; 14:2721-2732. [PMID: 29474075 PMCID: PMC6317529 DOI: 10.1021/acs.jctc.7b01170] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding protein conformational variability remains a challenge in drug discovery. The issue arises in protein kinases, whose multiple conformational states can affect the binding of small-molecule inhibitors. To overcome this challenge, we propose a comprehensive computational framework based on Markov state models (MSMs). Our framework integrates the information from explicit-solvent molecular dynamics simulations to accurately rank-order the accessible conformational variants of a target protein. We tested the methodology using Abl kinase with a reference and blind-test set. Only half of the Abl conformational variants discovered by our approach are present in the disclosed X-ray structures. The approach successfully identified a protein conformational state not previously observed in public structures but evident in a retrospective analysis of Lilly in-house structures: the X-ray structure of Abl with WHI-P154. Using a MSM-derived model, the free energy landscape and kinetic profile of Abl was analyzed in detail highlighting opportunities for targeting the unique metastable states.
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Affiliation(s)
- Yilin Meng
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Cen Gao
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - David Clawson
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Shane Atwell
- Applied Molecular Evolution, Eli Lilly and Company, Lilly Biotechnology Center, 10290 Campus Point Drive, San Diego, CA, 92121, USA
| | - Marijane Russell
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Biotechnology Center, 10290 Campus Point Drive, San Diego, CA, 92121, USA
| | - Michal Vieth
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Biotechnology Center, 10290 Campus Point Drive, San Diego, CA, 92121, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
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145
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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146
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Amaro RE, Mulholland AJ. Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures. Nat Rev Chem 2018; 2:0148. [PMID: 30949587 PMCID: PMC6445369 DOI: 10.1038/s41570-018-0148] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Drug action is inherently multiscale: it connects molecular interactions to emergent properties at cellular and larger scales. Simulation techniques at each of these different scales are already central to drug design and development, but methods capable of connecting across these scales will extend understanding of complex mechanisms and the ability to predict biological effects. Improved algorithms, ever-more-powerful computing architectures and the accelerating growth of rich datasets are driving advances in multiscale modeling methods capable of bridging chemical and biological complexity from the atom to the cell. Particularly exciting is the development of highly detailed, structure-based, physical simulations of biochemical systems, which are now able to access experimentally relevant timescales for large systems and, at the same time, achieve unprecedented accuracy. In this Perspective, we discuss how emerging data-rich, physics-based multiscale approaches are of the cusp of realizing long-promised impact in the discovery, design and development of novel therapeutics. We highlight emerging methods and applications in this growing field, and outline how different scales can be combined in practical modelling and simulation strategies.
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Affiliation(s)
- Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0304
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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147
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Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. Ensemble Docking in Drug Discovery. Biophys J 2018; 114:2271-2278. [PMID: 29606412 DOI: 10.1016/j.bpj.2018.02.038] [Citation(s) in RCA: 263] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/13/2018] [Accepted: 02/20/2018] [Indexed: 12/11/2022] Open
Abstract
Ensemble docking corresponds to the generation of an "ensemble" of drug target conformations in computational structure-based drug discovery, often obtained by using molecular dynamics simulation, that is used in docking candidate ligands. This approach is now well established in the field of early-stage drug discovery. This review gives a historical account of the development of ensemble docking and discusses some pertinent methodological advances in conformational sampling.
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Affiliation(s)
- Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Jerome Baudry
- University of Alabama at Huntsville, Huntsville, Alabama
| | - John Chodera
- University of California, Berkeley, Berkeley, California
| | - Özlem Demir
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Yinglong Miao
- Department of Computational Biology and Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
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148
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Abstract
Background Much of the structure-based mechanistic understandings of the function of SLC6A neurotransmitter transporters emerged from the study of their bacterial LeuT-fold homologs. It has become evident, however, that structural differences such as the long N- and C-termini of the eukaryotic neurotransmitter transporters are involved in an expanded set of functional properties to the eukaryotic transporters. These functional properties are not shared by the bacterial homologs, which lack the structural elements that appeared later in evolution. However, mechanistic insights into some of the measured functional properties of the eukaryotic transporters that have been suggested to involve these structural elements are sparse or merely descriptive. Results To learn how the structural elements added in evolution enable mechanisms of the eukaryotic transporters in ways not shared with their bacterial LeuT-like homologs, we focused on the human dopamine transporter (hDAT) as a prototype. We present the results of a study employing large-scale molecular dynamics simulations and comparative Markov state model analysis of experimentally determined properties of the wild-type and mutant hDAT constructs. These offer a quantitative outline of mechanisms in which a rich spectrum of interactions of the hDAT N-terminus and C-terminus contribute to the regulation of transporter function (e.g., by phosphorylation) and/or to entirely new phenotypes (e.g., reverse uptake (efflux)) that were added in evolution. Conclusions The findings are consistent with the proposal that the size of eukaryotic neurotransmitter transporter termini increased during evolution to enable more functions (e.g., efflux) not shared with the bacterial homologs. The mechanistic explanations for the experimental findings about the modulation of function in DAT, the serotonin transporter, and other eukaryotic transporters reveal separate roles for the distal and proximal segments of the much larger N-terminus in eukaryotic transporters compared to the bacterial ones. The involvement of the proximal and distal segments — such as the role of the proximal segment in sustaining transport in phosphatidylinositol 4,5-bisphosphate-depleted membranes and of the distal segment in modulating efflux — may represent an evolutionary adaptation required for the function of eukaryotic transporters expressed in various cell types of the same organism that differ in the lipid composition and protein complement of their membrane environment. Electronic supplementary material The online version of this article (10.1186/s12915-018-0495-6) contains supplementary material, which is available to authorized users.
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149
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Mittal S, Shukla D. Recruiting machine learning methods for molecular simulations of proteins. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1448976] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Shriyaa Mittal
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Urbana, IL, USA
| | - Diwakar Shukla
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign , Urbana, IL, USA
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150
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Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor. Proc Natl Acad Sci U S A 2018; 115:3036-3041. [PMID: 29507218 DOI: 10.1073/pnas.1800756115] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Protein-protein binding is key in cellular signaling processes. Molecular dynamics (MD) simulations of protein-protein binding, however, are challenging due to limited timescales. In particular, binding of the medically important G-protein-coupled receptors (GPCRs) with intracellular signaling proteins has not been simulated with MD to date. Here, we report a successful simulation of the binding of a G-protein mimetic nanobody to the M2 muscarinic GPCR using the robust Gaussian accelerated MD (GaMD) method. Through long-timescale GaMD simulations over 4,500 ns, the nanobody was observed to bind the receptor intracellular G-protein-coupling site, with a minimum rmsd of 2.48 Å in the nanobody core domain compared with the X-ray structure. Binding of the nanobody allosterically closed the orthosteric ligand-binding pocket, being consistent with the recent experimental finding. In the absence of nanobody binding, the receptor orthosteric pocket sampled open and fully open conformations. The GaMD simulations revealed two low-energy intermediate states during nanobody binding to the M2 receptor. The flexible receptor intracellular loops contribute remarkable electrostatic, polar, and hydrophobic residue interactions in recognition and binding of the nanobody. These simulations provided important insights into the mechanism of GPCR-nanobody binding and demonstrated the applicability of GaMD in modeling dynamic protein-protein interactions.
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