1
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Nin-Hill A, Mueller NPF, Molteni C, Rovira C, Alfonso-Prieto M. Photopharmacology of Ion Channels through the Light of the Computational Microscope. Int J Mol Sci 2021; 22:12072. [PMID: 34769504 PMCID: PMC8584574 DOI: 10.3390/ijms222112072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
The optical control and investigation of neuronal activity can be achieved and carried out with photoswitchable ligands. Such compounds are designed in a modular fashion, combining a known ligand of the target protein and a photochromic group, as well as an additional electrophilic group for tethered ligands. Such a design strategy can be optimized by including structural data. In addition to experimental structures, computational methods (such as homology modeling, molecular docking, molecular dynamics and enhanced sampling techniques) can provide structural insights to guide photoswitch design and to understand the observed light-regulated effects. This review discusses the application of such structure-based computational methods to photoswitchable ligands targeting voltage- and ligand-gated ion channels. Structural mapping may help identify residues near the ligand binding pocket amenable for mutagenesis and covalent attachment. Modeling of the target protein in a complex with the photoswitchable ligand can shed light on the different activities of the two photoswitch isomers and the effect of site-directed mutations on photoswitch binding, as well as ion channel subtype selectivity. The examples presented here show how the integration of computational modeling with experimental data can greatly facilitate photoswitchable ligand design and optimization. Recent advances in structural biology, both experimental and computational, are expected to further strengthen this rational photopharmacology approach.
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Affiliation(s)
- Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain; (A.N.-H.); (C.R.)
| | - Nicolas Pierre Friedrich Mueller
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany;
- Faculty of Mathematics and Natural Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Carla Molteni
- Physics Department, King’s College London, London WC2R 2LS, UK;
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain; (A.N.-H.); (C.R.)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany;
- Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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2
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Maschio MC, Fregoni J, Molteni C, Corni S. Proline isomerization effects in the amyloidogenic protein β2-microglobulin. Phys Chem Chem Phys 2021; 23:356-367. [DOI: 10.1039/d0cp04780e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protein β2-microglobulin can aggregate in insoluble amyloid fibrils. By relying on extensive sampling simulations, we study the Pro32 isomerization as a possible triggering factor leading to structural modifications in β2-m.
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Affiliation(s)
| | - Jacopo Fregoni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
| | - Carla Molteni
- Department of Physics
- King's College London
- Strand
- London WC2R 2LS
- UK
| | - Stefano Corni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
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3
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Sora V, Kumar M, Maiani E, Lambrughi M, Tiberti M, Papaleo E. Structure and Dynamics in the ATG8 Family From Experimental to Computational Techniques. Front Cell Dev Biol 2020; 8:420. [PMID: 32587856 PMCID: PMC7297954 DOI: 10.3389/fcell.2020.00420] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/06/2020] [Indexed: 12/31/2022] Open
Abstract
Autophagy is a conserved and essential intracellular mechanism for the removal of damaged components. Since autophagy deregulation is linked to different kinds of pathologies, it is fundamental to gain knowledge on the fine molecular and structural details related to the core proteins of the autophagy machinery. Among these, the family of human ATG8 proteins plays a central role in recruiting other proteins to the different membrane structures involved in the autophagic pathway. Several experimental structures are available for the members of the ATG8 family alone or in complex with their different biological partners, including disordered regions of proteins containing a short linear motif called LC3 interacting motif. Recently, the first structural details of the interaction of ATG8 proteins with biological membranes came into light. The availability of structural data for human ATG8 proteins has been paving the way for studies on their structure-function-dynamic relationship using biomolecular simulations. Experimental and computational structural biology can help to address several outstanding questions on the mechanism of human ATG8 proteins, including their specificity toward different interactors, their association with membranes, the heterogeneity of their conformational ensemble, and their regulation by post-translational modifications. We here summarize the main results collected so far and discuss the future perspectives within the field and the knowledge gaps. Our review can serve as a roadmap for future structural and dynamics studies of the ATG8 family members in health and disease.
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Affiliation(s)
- Valentina Sora
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Mukesh Kumar
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Emiliano Maiani
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Tiberti
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
- Translational Disease System Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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4
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Bradshaw RT, Dziedzic J, Skylaris CK, Essex JW. The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields? J Chem Inf Model 2020; 60:3131-3144. [DOI: 10.1021/acs.jcim.0c00217] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Richard T. Bradshaw
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
| | - Jonathan W. Essex
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
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5
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Crnjar A, Comitani F, Melis C, Molteni C. Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution. Interface Focus 2019; 9:20180067. [PMID: 31065340 PMCID: PMC6501341 DOI: 10.1098/rsfs.2018.0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 12/21/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are an important class of widely expressed membrane neuroreceptors, which play a crucial role in fast synaptic communications and are involved in several neurological conditions. They are activated by the binding of neurotransmitters, which trigger the transmission of an electrical signal via facilitated ion flux. They can also be activated, inhibited or modulated by a number of drugs. Mutagenesis electrophysiology experiments, with natural or unnatural amino acids, have provided a large body of functional data that, together with emerging structural information from X-ray spectroscopy and cryo-electron microscopy, are helping unravel the complex working mechanisms of these neuroreceptors. Computer simulations are complementing these mutagenesis experiments, with insights at various levels of accuracy and resolution. Here, we review how a selection of computational tools, including first principles methods, classical molecular dynamics and enhanced sampling techniques, are contributing to construct a picture of how pLGICs function and can be pharmacologically targeted to treat the disorders they are responsible for.
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Affiliation(s)
- Alessandro Crnjar
- King’s College London, Department of Physics, Strand, London WC2R 2LS, UK
| | - Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Claudio Melis
- Universitá degli Studi di Cagliari, Complesso Universitario di Monserrato, Dipartimento di Fisica, S.P. Monserrato-Sestu Km 0,700, Monserrato (CA) 09042, Italy
| | - Carla Molteni
- King’s College London, Department of Physics, Strand, London WC2R 2LS, UK
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6
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Crnjar A, Comitani F, Hester W, Molteni C. Trans- Cis Proline Switches in a Pentameric Ligand-Gated Ion Channel: How They Are Affected by and How They Affect the Biomolecular Environment. J Phys Chem Lett 2019; 10:694-700. [PMID: 30668119 DOI: 10.1021/acs.jpclett.8b03431] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pentameric ligand-gated ion channels (pLGICs) are important neuroreceptors, embedded in neuronal membranes, that mediate fast synaptic transmission. The molecular details of their working mechanisms have still to be fully unravelled due to their complexity and limited structural information available. Here we focus on a potential molecular switch in a prototypical pLGIC, the serotonin-activated 5-HT3 receptor, consisting of the trans- cis isomerization of a proline at the interface between the extracellular and transmembrane domain. Mutagenesis electrophysiology experiments previously showed that if such isomerization could not take place, the channel would not open, but the hypothetical role of this mechanism as key to channel gating is still debated. We investigate this switch within the receptor with molecular dynamics and enhanced sampling simulations. We analyze how the isomerization free energy landscape is affected by the receptor environment in comparison to simplified models. Moreover, we reveal how the isomerization, in turn, affects the structural and electrostatic properties of the receptor at the extracellular-transmembrane domain interface, e.g., by tuning the ion selectivity filter.
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Affiliation(s)
- Alessandro Crnjar
- Physics Department , King's College London , Strand, London WC2R 2LS , United Kingdom
| | - Federico Comitani
- Physics Department , King's College London , Strand, London WC2R 2LS , United Kingdom
- Chemistry Department , University College London , Gower Street , London WC1E 6BT , United Kingdom
| | - William Hester
- Physics Department , King's College London , Strand, London WC2R 2LS , United Kingdom
| | - Carla Molteni
- Physics Department , King's College London , Strand, London WC2R 2LS , United Kingdom
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7
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Slough DP, Yu H, McHugh SM, Lin YS. Toward accurately modeling N-methylated cyclic peptides. Phys Chem Chem Phys 2018; 19:5377-5388. [PMID: 28155950 DOI: 10.1039/c6cp07700e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cyclic peptides have unique properties and can target protein surfaces specifically and potently. N-Methylation provides a promising way to further optimize the pharmacokinetic and structural profiles of cyclic peptides. The capability to accurately model structures adopted by N-methylated cyclic peptides would facilitate rational design of this interesting and useful class of molecules. We apply molecular dynamics simulations with advanced enhanced sampling methods to efficiently characterize the structural ensembles of N-methylated cyclic peptides, while simultaneously evaluating the overall performance of several simulation force fields. We find that one of the residue-specific force fields, RSFF2, is able to recapitulate experimental structures of the N-methylated cyclic peptide benchmarks tested here when the correct amide isomers are used as initial configurations and enforced during the simulations. Thus, using our simulation approach, it is possible to accurately and efficiently predict the structures of N-methylated cyclic peptides if sufficient information is available to determine the correct amide cis/trans configuration. Moreover, our results suggest that, upon further optimization of RSFF2 to more reliably predict cis/trans isomers, molecular dynamics simulations will be able to de novo predict N-methylated cyclic peptides in the near future, strongly motivating such continued optimization.
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Affiliation(s)
- Diana P Slough
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA.
| | - Hongtao Yu
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA.
| | - Sean M McHugh
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA.
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA.
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8
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Liu Y, Liu Y, Chan-Park MB, Mu Y. Binding Modes of Teixobactin to Lipid II: Molecular Dynamics Study. Sci Rep 2017; 7:17197. [PMID: 29222455 PMCID: PMC5722933 DOI: 10.1038/s41598-017-17606-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/28/2017] [Indexed: 11/09/2022] Open
Abstract
Teixobactin (TXB) is a newly discovered antibiotic targeting the bacterial cell wall precursor Lipid II (LII). In the present work, four binding modes of TXB on LII were identified by a contact-map based clustering method. The highly flexible binary complex ensemble was generated by parallel tempering metadynamics simulation in a well-tempered ensemble (PTMetaD-WTE). In agreement with experimental findings, the pyrophosphate group and the attached first sugar subunit of LII are found to be the minimal motif for stable TXB binding. Three of the four binding modes involve the ring structure of TXB and have relatively higher binding affinities, indicating the importance of the ring motif of TXB in LII recognition. TXB-LII complexes with a ratio of 2:1 are also predicted with configurations such that the ring motif of two TXB molecules bound to the pyrophosphate-MurNAc moiety and the glutamic acid residue of one LII, respectively. Our findings disclose that the ring motif of TXB is critical to LII binding and novel antibiotics can be designed based on its mimetics.
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Affiliation(s)
- Yang Liu
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Yaxin Liu
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Mary B Chan-Park
- School of Chemical and Biomedical Engineering, Nanyang Technological University (NTU), 62 Nanyang Drive, Singapore, 637459, Singapore.,Centre for Antimicrobial Bioengineering, NTU, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore.
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9
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Saeedi M, Lyubartsev AP, Jalili S. Anesthetics mechanism on a DMPC lipid membrane model: Insights from molecular dynamics simulations. Biophys Chem 2017; 226:1-13. [DOI: 10.1016/j.bpc.2017.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/23/2017] [Accepted: 03/25/2017] [Indexed: 12/20/2022]
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10
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Comitani F, Rossi K, Ceriotti M, Sanz ME, Molteni C. Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution. J Chem Phys 2017; 146:145102. [DOI: 10.1063/1.4979519] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Federico Comitani
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Kevin Rossi
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - M. Eugenia Sanz
- Department of Chemistry, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Carla Molteni
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
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11
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Vöhringer-Martinez E, Dörner C. Conformational Substrate Selection Contributes to the Enzymatic Catalytic Reaction Mechanism of Pin1. J Phys Chem B 2016; 120:12444-12453. [DOI: 10.1021/acs.jpcb.6b09187] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Esteban Vöhringer-Martinez
- Departamento de Físico-Química,
Facultad de Ciencias Químicas, Universidad de Concepción, 4030000 Concepción, Chile
| | - Ciro Dörner
- Departamento de Físico-Química,
Facultad de Ciencias Químicas, Universidad de Concepción, 4030000 Concepción, Chile
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12
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Comitani F, Limongelli V, Molteni C. The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations. J Chem Theory Comput 2016; 12:3398-406. [PMID: 27228114 DOI: 10.1021/acs.jctc.6b00303] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop superfamily are important neuroreceptors that mediate fast synaptic transmission. They are activated by the binding of a neurotransmitter, but the details of this process are still not fully understood. As a prototypical pLGIC, here we choose the insect resistance to dieldrin (RDL) receptor involved in resistance to insecticides and investigate the binding of the neurotransmitter GABA to its extracellular domain at the atomistic level. We achieve this by means of μ-sec funnel-metadynamics simulations, which efficiently enhance the sampling of bound and unbound states by using a funnel-shaped restraining potential to limit the exploration in the solvent. We reveal the sequence of events in the binding process from the capture of GABA from the solvent to its pinning between the charged residues Arg111 and Glu204 in the binding pocket. We characterize the associated free energy landscapes in the wild-type RDL receptor and in two mutant forms, where the key residues Arg111 and Glu204 are mutated to Ala. Experimentally these mutations produce nonfunctional channels, which is reflected in the reduced ligand binding affinities due to the loss of essential interactions. We also analyze the dynamical behavior of the crucial loop C, whose opening allows the access of GABA to the binding site and closure locks the ligand into the protein. The RDL receptor shares structural and functional features with other pLGICs; hence, our work outlines a valuable protocol to study the binding of ligands to pLGICs beyond conventional docking and molecular dynamics techniques.
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Affiliation(s)
- Federico Comitani
- Department of Physics, King's College London , Strand, London WC2R 2LS, United Kingdom
| | - Vittorio Limongelli
- Universitá della Svizzera Italiana (USI) , Faculty of Informatics, Institute of Computational Science - Center for Computational Medicine in Cardiology, via G. Buffi 13, CH-6900 Lugano, Switzerland.,Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, I-80131 Naples, Italy
| | - Carla Molteni
- Department of Physics, King's College London , Strand, London WC2R 2LS, United Kingdom
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13
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Deriu MA, Grasso G, Tuszynski JA, Gallo D, Morbiducci U, Danani A. Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates. PLoS Comput Biol 2016; 12:e1004699. [PMID: 26745628 PMCID: PMC4706304 DOI: 10.1371/journal.pcbi.1004699] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 12/09/2015] [Indexed: 01/03/2023] Open
Abstract
The Josephin Domain (JD), i.e. the N-terminal domain of Ataxin 3 (At3) protein, is an interesting example of competition between physiological function and aggregation risk. In fact, the fibrillogenesis of Ataxin 3, responsible for the spinocerebbellar ataxia 3, is strictly related to the JD thermodynamic stability. Whereas recent NMR studies have demonstrated that different JD conformations exist, the likelihood of JD achievable conformational states in solution is still an open issue. Marked differences in the available NMR models are located in the hairpin region, supporting the idea that JD has a flexible hairpin in dynamic equilibrium between open and closed states. In this work we have carried out an investigation on the JD conformational arrangement by means of both classical molecular dynamics (MD) and Metadynamics employing essential coordinates as collective variables. We provide a representation of the free energy landscape characterizing the transition pathway from a JD open-like structure to a closed-like conformation. Findings of our in silico study strongly point to the closed-like conformation as the most likely for a Josephin Domain in water.
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Affiliation(s)
- Marco A. Deriu
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Manno, Switzerland
- * E-mail:
| | - Gianvito Grasso
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Manno, Switzerland
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Diego Gallo
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Andrea Danani
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Manno, Switzerland
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14
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Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations. Biochem Soc Trans 2016; 43:151-6. [PMID: 25849909 DOI: 10.1042/bst20140259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pentameric ligand-gated ion channels (pLGICs) are important biomolecules that mediate fast synaptic transmission. Their malfunctions are linked to serious neuronal disorders and they are major pharmaceutical targets; in invertebrates, they are involved in insecticide resistance. The complexity of pLGICs and the limited crystallographic information available prevent a detailed understanding of how they function. State-of-the-art computational techniques are therefore crucial to build an accurate picture at the atomic level of the mechanisms which drive the activation of pLGICs, complementing the available experimental data. We have used a series of simulation methods, including homology modelling, ligand-protein docking, density functional theory, molecular dynamics and metadynamics, a powerful scheme for accelerating rare events, with the guidance of mutagenesis electrophysiology experiments, to explore ligand-binding mechanisms, the effects of mutations and the potential role of a proline molecular switch for the gating of the ion channels. Results for the insect RDL receptor, the GABAC receptor, the 5-HT3 receptor and the nicotinic acetylcholine receptor will be reviewed.
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15
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Papaleo E, Sutto L, Gervasio FL, Lindorff-Larsen K. Conformational Changes and Free Energies in a Proline Isomerase. J Chem Theory Comput 2015; 10:4169-74. [PMID: 26588555 DOI: 10.1021/ct500536r] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proteins are dynamic molecules and their ability to adopt alternative conformations is central to their biological function. The structural and biophysical properties of transiently and sparsely populated states are, however, difficult to study and an atomic-level description of those states is challenging. We have used enhanced-sampling all-atom, explicit-solvent molecular simulations, guided by structural information from X-ray crystallography and NMR, to describe quantitatively the transition between the major and a minor state of Cyclophilin A, thus providing new insight into how dynamics can affect enzyme function. We calculate the conformational free energy between the two states, and comparison with experiments demonstrates a surprisingly high accuracy for both the wild type protein and a mutant that traps the protein in its alternative conformation. Our results demonstrate how the combination of state-of-the-art force fields and enhanced sampling methods can provide a detailed and quantitative description of the conformational changes in proteins such as those observed in Cyclophilin A.
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Affiliation(s)
- Elena Papaleo
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen , Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | | | | | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen , Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
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16
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Ladani ST, Souffrant MG, Barman A, Hamelberg D. Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl cis-trans isomerases. Biochim Biophys Acta Gen Subj 2015; 1850:1994-2004. [PMID: 25585011 DOI: 10.1016/j.bbagen.2014.12.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/23/2014] [Accepted: 12/29/2014] [Indexed: 01/16/2023]
Abstract
BACKGROUND Peptidyl prolyl cis-trans isomerization of the protein backbone is involved in the regulation of many biological processes. Cis-trans isomerization is notoriously slow and is catalyzed by a family of cis-trans peptidyl prolyl isomerases (PPIases) that have been implicated in many diseases. A general consensus on how these enzymes speed up prolyl isomerization has not been reached after decades of both experimental and computational studies. SCOPE OF REVIEW Computational studies carried out to understand the catalytic mechanism of the prototypical FK506 binding protein 12, Cyclophilin A and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) are reviewed. A summary and an evaluation of the implications of the proposed mechanisms from computational studies are presented. MAJOR CONCLUSIONS The analysis of computational studies and evaluation of the proposed mechanisms provide a general consensus and a better understanding of PPIase catalysis. The speedup of the rate of peptidyl-prolyl isomerization by PPIases can be best described by a catalytic mechanism in which the substrate in transition state configuration is stabilized. The enzymes preferentially bind the transition state configuration of the substrate relative to the cis conformation, which in most cases is bound better than the trans conformation of the substrate. Stabilization of the transition state configuration of the substrate leads to a lower free energy barrier and a faster rate of isomerization when compared to the uncatalyzed isomerization reaction. GENERAL SIGNIFICANCE Fully understanding the catalytic mechanism of PPIases has broad implications for drug design, elucidation of the molecular basis of many diseases, protein engineering, and enzyme catalysis in general. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Safieh Tork Ladani
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA
| | - Michael G Souffrant
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA
| | - Arghya Barman
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA
| | - Donald Hamelberg
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA.
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17
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Di Martino GP, Masetti M, Cavalli A, Recanatini M. Mechanistic insights into Pin1 peptidyl-prolyl cis-trans isomerization from umbrella sampling simulations. Proteins 2014; 82:2943-56. [PMID: 25066180 DOI: 10.1002/prot.24650] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 06/25/2014] [Accepted: 07/15/2014] [Indexed: 12/22/2022]
Abstract
The peptidyl-proyl isomerase Pin1 plays a key role in the regulation of phospho(p)-Ser/Thr-Pro proteins, acting as a molecular timer of the cell cycle. After recognition of these motifs, Pin1 catalyzes the rapid cis-trans isomerization of proline amide bonds of substrates, contributing to maintain the equilibrium between the two conformations. Although a great interest has arisen on this enzyme, its catalytic mechanism has long been debated. Here, the cis-trans isomerization of a model peptide system was investigated by means of umbrella sampling simulations in the Pin1-bound and unbound states. We obtained free energy barriers consistent with experimental data, and identified several enzymatic features directly linked to the acceleration of the prolyl bond isomerization. In particular, an enhanced autocatalysis, the stabilization of perturbed ground state conformations, and the substrate binding in a procatalytic conformation were found as main contributions to explain the lowering of the isomerization free energy barrier.
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Affiliation(s)
- Giovanni Paolo Di Martino
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Università di Bologna, Via Belmeloro 6, 40126, Bologna, Italy
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18
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Bian Y, Zhang J, Wang J, Wang W. On the accuracy of metadynamics and its variations in a protein folding process. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.931680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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19
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Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism. Proc Natl Acad Sci U S A 2014; 111:10203-8. [PMID: 24982184 DOI: 10.1073/pnas.1404220111] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Proline isomerization is a ubiquitous process that plays a key role in the folding of proteins and in the regulation of their functions. Different families of enzymes, known as "peptidyl-prolyl isomerases" (PPIases), catalyze this reaction, which involves the interconversion between the cis and trans isomers of the N-terminal amide bond of the amino acid proline. However, complete descriptions of the mechanisms by which these enzymes function have remained elusive. We show here that cyclophilin A, one of the most common PPIases, provides a catalytic environment that acts on the substrate through an electrostatic handle mechanism. In this mechanism, the electrostatic field in the catalytic site turns the electric dipole associated with the carbonyl group of the amino acid preceding the proline in the substrate, thus causing the rotation of the peptide bond between the two residues. We identified this mechanism using a combination of NMR measurements, molecular dynamics simulations, and density functional theory calculations to simultaneously determine the cis-bound and trans-bound conformations of cyclophilin A and its substrate as the enzymatic reaction takes place. We anticipate that this approach will be helpful in elucidating whether the electrostatic handle mechanism that we describe here is common to other PPIases and, more generally, in characterizing other enzymatic processes.
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20
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Abstract
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The Crk adaptor proteins play a central
role as a molecular timer
for the formation of protein complexes including various growth and
differentiation factors. The loss of regulation of Crk results in
many kinds of cancers. A self-regulatory mechanism for Crk was recently
proposed, which involves domain–domain rearrangement. It is
initiated by a cis–trans isomerization of a specific proline
residue (Pro238 in chicken Crk II) and can be accelerated by Cyclophilin
A. To understand how the proline switch controls the autoinhibition
at the molecular level, we performed large-scale molecular dynamics
and metadynamics simulations in the context of short peptides and
multidomain constructs of chicken Crk II. We found that the equilibrium
and kinetic properties of the macrostates are regulated not only by
the local environments of specified prolines but also by the global
organization of multiple domains. We observe the two macrostates (cis
closed/autoinhibited and trans open/uninhibited) consistent with NMR
experiments and predict barriers. We also propose an intermediate
state, the trans closed state, which interestingly was reported to
be a prevalent state in human Crk II. The existence of this macrostate
suggests that the rate of switching off the autoinhibition by Cyp
A may be limited by the relaxation rate of this intermediate state.
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Affiliation(s)
- Junchao Xia
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey , 610 Taylor Road, Piscataway, New Jersey 08854, United States
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21
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Marinelli F. Following easy slope paths on a free energy landscape: the case study of the Trp-cage folding mechanism. Biophys J 2014; 105:1236-47. [PMID: 24010667 DOI: 10.1016/j.bpj.2013.07.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 07/11/2013] [Accepted: 07/25/2013] [Indexed: 11/25/2022] Open
Abstract
In this work a new method for the automatic exploration and calculation of multidimensional free energy landscapes is proposed. Inspired by metadynamics, it uses several collective variables that are relevant for the investigated process and a bias potential that discourages the sampling of already visited configurations. The latter potential allows escaping a local free energy minimum following the direction of slow motions. This is different from metadynamics in which there is no specific direction of the biasing force and the computational effort increases significantly with the number of collective variables. The method is tested on the Ace-Ala3-Nme peptide, and then it is applied to investigate the Trp-cage folding mechanism. For this protein, within a few hundreds of nanoseconds, a broad range of conformations is explored, including nearly native ones, initiating the simulation from a completely unfolded conformation. Finally, several folding/unfolding trajectories give a systematic description of the Trp-cage folding pathways, leading to a unified view for the folding mechanisms of this protein. The proposed mechanism is consistent with NMR chemical shift data at increasing temperature and recent experimental observations pointing to a pivotal role of secondary structure elements in directing the folding process toward the native state.
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Affiliation(s)
- Fabrizio Marinelli
- Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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22
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Ramanathan A, Savol A, Burger V, Chennubhotla CS, Agarwal PK. Protein conformational populations and functionally relevant substates. Acc Chem Res 2014; 47:149-56. [PMID: 23988159 DOI: 10.1021/ar400084s] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in the nearby area of its conformational landscape, while motions on slower time scales give it access to conformations in distal areas of the landscape. Emerging evidence indicates that protein landscapes contain conformational substates with dynamic and structural features that support the designated function of the protein. Nuclear magnetic resonance (NMR) experiments provide information about conformational ensembles of proteins. X-ray crystallography allows researchers to identify the most populated states along the landscape, and computational simulations give atom-level information about the conformational substates of different proteins. This ability to characterize and obtain quantitative information about the conformational substates and the populations of proteins within them is allowing researchers to better understand the relationship between protein structure and dynamics and the mechanisms of protein function. In this Account, we discuss recent developments and challenges in the characterization of functionally relevant conformational populations and substates of proteins. In some enzymes, the sampling of functionally relevant conformational substates is connected to promoting the overall mechanism of catalysis. For example, the conformational landscape of the enzyme dihydrofolate reductase has multiple substates, which facilitate the binding and the release of the cofactor and substrate and catalyze the hydride transfer. For the enzyme cyclophilin A, computational simulations reveal that the long time scale conformational fluctuations enable the enzyme to access conformational substates that allow it to attain the transition state, therefore promoting the reaction mechanism. In the long term, this emerging view of proteins with conformational substates has broad implications for improving our understanding of enzymes, enzyme engineering, and better drug design. Researchers have already used photoactivation to modulate protein conformations as a strategy to develop a hypercatalytic enzyme. In addition, the alteration of the conformational substates through binding of ligands at locations other than the active site provides the basis for the design of new medicines through allosteric modulation.
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Affiliation(s)
- Arvind Ramanathan
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Andrej Savol
- Joint Carnegie Mellon University−University of Pittsburgh Ph.D Program in Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Virginia Burger
- Joint Carnegie Mellon University−University of Pittsburgh Ph.D Program in Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chakra S. Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pratul K. Agarwal
- Annavitas Biosciences, 2519 Caspian Drive, Knoxville, Tennessee 37932, United States
- Computational Biology Institute, and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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23
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Comitani F, Cohen N, Ashby J, Botten D, Lummis SCR, Molteni C. Insights into the binding of GABA to the insect RDL receptor from atomistic simulations: a comparison of models. J Comput Aided Mol Des 2014; 28:35-48. [PMID: 24442887 PMCID: PMC3927061 DOI: 10.1007/s10822-013-9704-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 12/26/2013] [Indexed: 01/19/2023]
Abstract
The resistance to dieldrin (RDL) receptor is an insect pentameric ligand-gated ion channel (pLGIC). It is activated by the neurotransmitter γ-aminobutyric acid (GABA) binding to its extracellular domain; hence elucidating the atomistic details of this interaction is important for understanding how the RDL receptor functions. As no high resolution structures are currently available, we built homology models of the extracellular domain of the RDL receptor using different templates, including the widely used acetylcholine binding protein and two pLGICs, the Erwinia Chrysanthemi ligand-gated ion channel (ELIC) and the more recently resolved GluCl. We then docked GABA into the selected three dimensional structures, which we used as starting points for classical molecular dynamics simulations. This allowed us to analyze in detail the behavior of GABA in the binding sites, including the hydrogen bond and cation-π interaction networks it formed, the conformers it visited and the possible role of water molecules in mediating the interactions; we also estimated the binding free energies. The models were all stable and showed common features, including interactions consistent with experimental data and similar to other pLGICs; differences could be attributed to the quality of the models, which increases with increasing sequence identity, and the use of a pLGIC template. We supplemented the molecular dynamics information with metadynamics, a rare event method, by exploring the free energy landscape of GABA binding to the RDL receptor. Overall, we show that the GluCl template provided the best models. GABA forming direct salt-bridges with Arg211 and Glu204, and cation-π interactions with an aromatic cage including Tyr109, Phe206 and Tyr254, represents a favorable binding arrangement, and the interaction with Glu204 can also be mediated by a water molecule.
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Affiliation(s)
- Federico Comitani
- Physics Department, King's College London, Strand, London, WC2R 2LS, UK
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24
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Sartori A, Dell'Amico L, Battistini L, Curti C, Rivara S, Pala D, Kerry PS, Pelosi G, Casiraghi G, Rassu G, Zanardi F. Synthesis, structure and inhibitory activity of a stereoisomer of oseltamivir carboxylate. Org Biomol Chem 2014; 12:1561-9. [DOI: 10.1039/c3ob42069h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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25
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. ENTROPY 2013. [DOI: 10.3390/e16010163] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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26
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Procacci P, Bizzarri M, Marsili S. Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange Simulations. J Chem Theory Comput 2013; 10:439-50. [DOI: 10.1021/ct400809n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Piero Procacci
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Marco Bizzarri
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Simone Marsili
- Centro Nacional de Investigaciones Oncologicas, Calle de Melchor Fernández Almagro, 3, E-28029 Madrid, Spain
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27
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Marinelli F, Sorrenti A, Corvaglia V, Leone V, Mancini G. Molecular Description of the Propagation of Chirality from Molecules to Complex Systems: Different Mechanisms Controlled by Hydrophobic Interactions. Chemistry 2012; 18:14680-8. [DOI: 10.1002/chem.201202342] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Indexed: 11/12/2022]
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28
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Ladani ST, Hamelberg D. Entropic and Surprisingly Small Intramolecular Polarization Effects in the Mechanism of Cyclophilin A. J Phys Chem B 2012; 116:10771-8. [DOI: 10.1021/jp305917c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Safieh Tork Ladani
- Department of Chemistry and Center
for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Donald Hamelberg
- Department of Chemistry and Center
for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
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29
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Keyes LR, Bego MG, Soland M, St Jeor S. Cyclophilin A is required for efficient human cytomegalovirus DNA replication and reactivation. J Gen Virol 2012; 93:722-732. [PMID: 22238232 DOI: 10.1099/vir.0.037309-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a large DNA virus belonging to the subfamily Betaherpesvirinae. Haematopoietic cells of the myeloid lineage have been shown to harbour latent HCMV. However, following terminal differentiation of these cells, virus is reactivated, and in an immunocompromised host acute infection can occur. It is currently unknown which viral and cellular factors are involved in regulating the switch between lytic and latent infections. Cyclophilin A (CyPA) is a cellular protein that acts as a major factor in virus replication and/or virion maturation for a number of different viruses, including human immunodeficiency virus, hepatitis C virus, murine cytomegalovirus, influenza A virus and vaccinia virus. This study investigated the role of CyPA during HCMV infection. CyPA expression was silenced in human foreskin fibroblast (HF) and THP-1 cells using small interfering RNA (siRNA) technology, or the cells were treated with cyclosporin A (CsA) to inhibit CyPA activity. Silencing CyPA in HF cells with siRNA resulted in an overall reduction in virus production characterized by delayed expression of immediate-early (IE) proteins, decreased viral DNA loads and reduced titres. Furthermore, silencing of CyPA in THP-1 cells pre- and post-differentiation prevented IE protein expression and virus reactivation from a non-productive state. Interestingly, it was observed that treatment of THP-1 cells with CsA prevented the cells from establishing a fully latent infection. In summary, these results demonstrate that CyPA expression is an important factor in HCMV IE protein expression and virus production in lytically infected HF cells, and is a major component in virus reactivation from infected THP-1 cells.
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Affiliation(s)
- Lisa R Keyes
- Department of Microbiology and Immunology and Graduate Program in Cell and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Mariana G Bego
- Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada.,Department of Microbiology and Immunology and Graduate Program in Cell and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Melisa Soland
- Department of Microbiology and Immunology and Graduate Program in Cell and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Stephen St Jeor
- Department of Microbiology and Immunology and Graduate Program in Cell and Molecular Biology, University of Nevada, Reno, NV 89557, USA
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30
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In Silico Strategies Toward Enzyme Function and Dynamics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012. [DOI: 10.1016/b978-0-12-398312-1.00009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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31
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Barducci A, Bonomi M, Parrinello M. Metadynamics. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.31] [Citation(s) in RCA: 712] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alessandro Barducci
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Lugano, Switzerland
| | - Massimiliano Bonomi
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Lugano, Switzerland
| | - Michele Parrinello
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Lugano, Switzerland
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32
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Biarnés X, Bongarzone S, Vargiu AV, Carloni P, Ruggerone P. Molecular motions in drug design: the coming age of the metadynamics method. J Comput Aided Mol Des 2011; 25:395-402. [PMID: 21327922 DOI: 10.1007/s10822-011-9415-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Accepted: 01/28/2011] [Indexed: 01/25/2023]
Abstract
Metadynamics is emerging as a useful free energy method in physics, chemistry and biology. Recently, it has been applied also to investigate ligand binding to biomolecules of pharmacological interest. Here, after introducing the basic idea of the method, we review applications to challenging targets for pharmaceutical intervention. We show that this methodology, especially when combined with a variety of other computational approaches such as molecular docking and/or molecular dynamics simulation, may be useful to predict structure and energetics of ligand/target complexes even when the targets lack a deep binding cavity, such as DNA and proteins undergoing fibrillation in neurodegenerative diseases. Furthermore, the method allows investigating the routes of molecular recognition and the associated binding energy profiles, providing a molecular interpretation to experimental data.
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Affiliation(s)
- Xevi Biarnés
- International School for Advanced Studies, Trieste, Italy
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33
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Davis TL, Walker JR, Campagna-Slater V, Finerty PJ, Paramanathan R, Bernstein G, MacKenzie F, Tempel W, Ouyang H, Lee WH, Eisenmesser EZ, Dhe-Paganon S. Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases. PLoS Biol 2010; 8:e1000439. [PMID: 20676357 PMCID: PMC2911226 DOI: 10.1371/journal.pbio.1000439] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 06/16/2010] [Indexed: 11/29/2022] Open
Abstract
Peptidyl-prolyl isomerases catalyze the conversion between cis and trans isomers of proline. The cyclophilin family of peptidyl-prolyl isomerases is well known for being the target of the immunosuppressive drug cyclosporin, used to combat organ transplant rejection. There is great interest in both the substrate specificity of these enzymes and the design of isoform-selective ligands for them. However, the dearth of available data for individual family members inhibits attempts to design drug specificity; additionally, in order to define physiological functions for the cyclophilins, definitive isoform characterization is required. In the current study, enzymatic activity was assayed for 15 of the 17 human cyclophilin isomerase domains, and binding to the cyclosporin scaffold was tested. In order to rationalize the observed isoform diversity, the high-resolution crystallographic structures of seven cyclophilin domains were determined. These models, combined with seven previously solved cyclophilin isoforms, provide the basis for a family-wide structure:function analysis. Detailed structural analysis of the human cyclophilin isomerase explains why cyclophilin activity against short peptides is correlated with an ability to ligate cyclosporin and why certain isoforms are not competent for either activity. In addition, we find that regions of the isomerase domain outside the proline-binding surface impart isoform specificity for both in vivo substrates and drug design. We hypothesize that there is a well-defined molecular surface corresponding to the substrate-binding S2 position that is a site of diversity in the cyclophilin family. Computational simulations of substrate binding in this region support our observations. Our data indicate that unique isoform determinants exist that may be exploited for development of selective ligands and suggest that the currently available small-molecule and peptide-based ligands for this class of enzyme are insufficient for isoform specificity.
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Affiliation(s)
- Tara L. Davis
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - John R. Walker
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Patrick J. Finerty
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Ragika Paramanathan
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Galina Bernstein
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Farrell MacKenzie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Hui Ouyang
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Wen Hwa Lee
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- University of Oxford, Headington, United Kingdom
| | - Elan Z. Eisenmesser
- Department of Biochemistry & Molecular Genetics, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Sirano Dhe-Paganon
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
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34
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Cossio P, Marinelli F, Laio A, Pietrucci F. Optimizing the Performance of Bias-Exchange Metadynamics: Folding a 48-Residue LysM Domain Using a Coarse-Grained Model. J Phys Chem B 2010; 114:3259-65. [DOI: 10.1021/jp907464b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pilar Cossio
- SISSA- Scuola Internazionale Superiore di Studi Avanzati, and CNR-INFM DEMOCRITOS National Simulation Center, via Beirut 2−4, I-34014 Trieste, Italy
| | - Fabrizio Marinelli
- SISSA- Scuola Internazionale Superiore di Studi Avanzati, and CNR-INFM DEMOCRITOS National Simulation Center, via Beirut 2−4, I-34014 Trieste, Italy
| | - Alessandro Laio
- SISSA- Scuola Internazionale Superiore di Studi Avanzati, and CNR-INFM DEMOCRITOS National Simulation Center, via Beirut 2−4, I-34014 Trieste, Italy
| | - Fabio Pietrucci
- SISSA- Scuola Internazionale Superiore di Studi Avanzati, and CNR-INFM DEMOCRITOS National Simulation Center, via Beirut 2−4, I-34014 Trieste, Italy
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35
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Modelling of β-d-glucopyranose ring distortion in different force fields: a metadynamics study. Carbohydr Res 2010; 345:530-7. [DOI: 10.1016/j.carres.2009.12.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 12/02/2009] [Accepted: 12/11/2009] [Indexed: 12/16/2022]
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36
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Pietrucci F, Marinelli F, Carloni P, Laio A. Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations. J Am Chem Soc 2009; 131:11811-8. [PMID: 19645490 DOI: 10.1021/ja903045y] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding mechanism of a peptide substrate (Thr-Ile-Met-Met-Gln-Arg, cleavage site p2-NC of the viral polyprotein) to wild-type HIV-1 protease has been investigated by 1.6 micros biased all-atom molecular dynamics simulations in explicit water. The configuration space has been explored biasing seven reaction coordinates by the bias-exchange metadynamics technique. The structure of the Michaelis complex is obtained starting from the substrate outside the enzyme within a backbone rmsd of 0.9 A. The calculated free energy of binding is -6 kcal/mol, and the kinetic constants for association and dissociation are 1.3 x 10(6) M(-1) s(-1) and 57 s(-1), respectively, consistent with experiments. In the main binding pathway, the flaps of the protease do not open sizably. The substrate slides inside the enzyme cavity from the tight lateral channel. This may contrast with the natural polyprotein substrate which is expected to bind by opening the flaps. Thus, mutations might influence differently the binding kinetics of peptidomimetic ligands and of the natural substrate.
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Affiliation(s)
- Fabio Pietrucci
- International School for Advanced Studies (SISSA-ISAS), via Beirut 2-4, I-34014 Trieste, Italy
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37
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Melis C, Bussi G, Lummis SCR, Molteni C. Trans-cis switching mechanisms in proline analogues and their relevance for the gating of the 5-HT3 receptor. J Phys Chem B 2009; 113:12148-53. [PMID: 19663504 PMCID: PMC2733763 DOI: 10.1021/jp9046962] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Indexed: 12/17/2022]
Abstract
Trans-cis isomerization of a proline peptide bond is a potential mechanism to open the channel of the 5-HT(3) receptor. Here, we have used the metadynamics method to theoretically explore such a mechanism. We have determined the free energy surfaces in aqueous solution of a series of dipeptides of proline analogues and evaluated the free energy difference between the cis and trans isomers. These theoretical results were then compared with data from mutagenesis experiments, in which the response of the 5-HT(3) receptor was measured when the proline at the apex of the M2-M3 transmembrane domain loop was mutated. The strong correlation between the experimental and the theoretical data supports the existence of a trans-cis proline switch for opening the 5-HT(3) receptor ion channel.
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Affiliation(s)
| | | | | | - Carla Molteni
- Corresponding author. Phone: +44 20 78482170. Fax: +44 20 7848 2420. E-mail:
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Kranjc A, Bongarzone S, Rossetti G, Biarnés X, Cavalli A, Bolognesi ML, Roberti M, Legname G, Carloni P. Docking Ligands on Protein Surfaces: The Case Study of Prion Protein. J Chem Theory Comput 2009; 5:2565-73. [PMID: 26616631 DOI: 10.1021/ct900257t] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular docking of ligands targeting proteins undergoing fibrillization in neurodegenerative diseases is difficult because of the lack of deep binding sites. Here we extend standard docking methods with free energy simulations in explicit solvent to address this issue in the context of the prion protein surface. We focus on a specific ligand (2-pyrrolidin-1-yl-N-[4-[4-(2-pyrrolidin-1-yl-acetylamino)-benzyl]-phenyl]-acetamide), which binds to the structured part of the protein as shown by NMR (Kuwata, K. et al. Proc Natl Acad Sci U.S.A. 2007, 104, 11921-11926). The calculated free energy of dissociation (7.8 ± 0.9 kcal/mol) is in good agreement with the value derived by the experimental dissociation constant (Kd = 3.9 μM, corresponding to ΔG(0) = -7.5 kcal/mol). Several binding poses are predicted, including the one reported previously. Our prediction is fully consistent with the presence of multiple binding sites, emerging from NMR measurements. Our molecular simulation-based approach emerges, therefore, as a useful tool to predict poses and affinities of ligand binding to protein surfaces.
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Affiliation(s)
- Agata Kranjc
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Salvatore Bongarzone
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Giulia Rossetti
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Xevi Biarnés
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Andrea Cavalli
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Maria Laura Bolognesi
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Marinella Roberti
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Giuseppe Legname
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Paolo Carloni
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
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Marinelli F, Pietrucci F, Laio A, Piana S. A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations. PLoS Comput Biol 2009; 5:e1000452. [PMID: 19662155 PMCID: PMC2711228 DOI: 10.1371/journal.pcbi.1000452] [Citation(s) in RCA: 211] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 06/29/2009] [Indexed: 11/18/2022] Open
Abstract
Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.
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Affiliation(s)
- Fabrizio Marinelli
- International School for Advanced Studies (SISSA-ISAS) and DEMOCRITOS, Trieste, Italy
- Italian Institute of Technology (IIT), Trieste, Italy
| | - Fabio Pietrucci
- International School for Advanced Studies (SISSA-ISAS) and DEMOCRITOS, Trieste, Italy
| | - Alessandro Laio
- International School for Advanced Studies (SISSA-ISAS) and DEMOCRITOS, Trieste, Italy
| | - Stefano Piana
- Nanochemistry Research Institute, Curtin University of Technology, Perth, Western Australia, Australia
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