1
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Lu D, Luo D, Zhang Y, Wang B. A Robust Induced Fit Docking Approach with the Combination of the Hybrid All-Atom/United-Atom/Coarse-Grained Model and Simulated Annealing. J Chem Theory Comput 2024. [PMID: 38966989 DOI: 10.1021/acs.jctc.4c00653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Molecular docking remains an indispensable tool in computational biology and structure-based drug discovery. However, the correct prediction of binding poses remains a major challenge for molecular docking, especially for target proteins where a substrate binding induces significant reorganization of the active site. Here, we introduce an Induced Fit Docking (IFD) approach named AA/UA/CG-SA-IFD, which combines a hybrid All-Atom/United-Atom/Coarse-Grained model with Simulated Annealing. In this approach, the core region is represented by the All-Atom(AA) model, while the protein environment beyond the core region and the solvent are treated with either the United-Atom (UA) or the Coarse-Grained (CG) model. By combining the Elastic Network Model (ENM) for the CG region, the hybrid model ensures a reasonable description of ligand binding and the environmental effects of the protein, facilitating highly efficient and reliable sampling of ligand binding through Simulated Annealing (SA) at a high temperature. Upon validation with two testing sets, the AA/UA/CG-SA-IFD approach demonstrates remarkable accuracy and efficiency in induced fit docking, even for challenging cases where the docked poses significantly deviate from crystal structures.
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Affiliation(s)
- Dexin Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Ding Luo
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Yuwei Zhang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
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2
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Ahyayauch H, Masserini ME, Alonso A, Goñi FM. Understanding Aβ Peptide Binding to Lipid Membranes: A Biophysical Perspective. Int J Mol Sci 2024; 25:6401. [PMID: 38928107 PMCID: PMC11203662 DOI: 10.3390/ijms25126401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Aβ peptides are known to bind neural plasma membranes in a process leading to the deposit of Aβ-enriched plaques. These extracellular structures are characteristic of Alzheimer's disease, the major cause of late-age dementia. The mechanisms of Aβ plaque formation and deposition are far from being understood. A vast number of studies in the literature describe the efforts to analyze those mechanisms using a variety of tools. The present review focuses on biophysical studies mostly carried out with model membranes or with computational tools. This review starts by describing basic physical aspects of lipid phases and commonly used model membranes (monolayers and bilayers). This is followed by a discussion of the biophysical techniques applied to these systems, mainly but not exclusively Langmuir monolayers, isothermal calorimetry, density-gradient ultracentrifugation, and molecular dynamics. The Methodological Section is followed by the core of the review, which includes a summary of important results obtained with each technique. The last section is devoted to an overall reflection and an effort to understand Aβ-bilayer binding. Concepts such as Aβ peptide membrane binding, adsorption, and insertion are defined and differentiated. The roles of membrane lipid order, nanodomain formation, and electrostatic forces in Aβ-membrane interaction are separately identified and discussed.
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Affiliation(s)
- Hasna Ahyayauch
- Departamento de Bioquímica, Instituto Biofisika (CSIC, UPV/EHU), Universidad del País Vasco, 48940 Leioa, Spain; (H.A.); (A.A.)
- Institut Supérieur des Professions Infirmières et Techniques de Santé, Rabat 60000, Morocco
- Laboratoire de Biologie et Santé, Unité Neurosciences, Neuroimmunologie et Comportement, Faculty of Sciences, Ibn Tofail University, Kénitra 14000, Morocco
| | - Massimo E. Masserini
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Alicia Alonso
- Departamento de Bioquímica, Instituto Biofisika (CSIC, UPV/EHU), Universidad del País Vasco, 48940 Leioa, Spain; (H.A.); (A.A.)
| | - Félix M. Goñi
- Departamento de Bioquímica, Instituto Biofisika (CSIC, UPV/EHU), Universidad del País Vasco, 48940 Leioa, Spain; (H.A.); (A.A.)
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3
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Pusara S, Wenzel W, Kozlowska M. Impact of DNA on interactions between core proteins of Hepatitis B virus-like particles comprising different C-terminals. Int J Biol Macromol 2024; 263:130365. [PMID: 38401590 DOI: 10.1016/j.ijbiomac.2024.130365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
Hepatitis B virus (HBV) virus-like particles (VLPs) are promising therapeutic agents derived from HBV core proteins (Cp). This study investigates the assembly dynamics of HBV VLPs, which is crucial for their potential as drug carriers or gene delivery systems. Coarse-grained molecular dynamics simulations explore the impact of C-terminal domain length (in the Cp ranging from Cp149 to wild-type Cp183) on Cp assembly and stability, particularly in the presence of DNA. Our findings reveal that the C-terminal nucleic acid binding region significantly influences Cp assembly and stability of trimers comprising Cp dimers. Shorter C-terminal domains (Cp164, Cp167) enhance stability and protein-protein interactions, while interactions between naturally occurring Cp183 are destabilized in the absence of DNA. Interestingly, DNA addition further stabilizes Cp assemblies, and this effect is influenced by the length of the nucleic acid binding region. Shorter C-terminal domains show less dependency on DNA content. This stabilization is attributed to electrostatic forces between positively charged C-terminal chains and negatively charged nucleic acids. Our study sheds light on the molecular mechanisms governing protein-protein and protein-DNA interactions in HBV VLP assembly, providing insights into Cp processability and informing the development of efficient gene therapy carriers using VLP technology.
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Affiliation(s)
- Srdjan Pusara
- Institute of Nanotechnology, Karlsruhe Institute of Technology KIT, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology KIT, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - Mariana Kozlowska
- Institute of Nanotechnology, Karlsruhe Institute of Technology KIT, Kaiserstraße 12, 76131 Karlsruhe, Germany.
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4
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Song Y, Selmani S, Freites JA, Guan Z, Tobias DJ. Multiscale Molecular Dynamics Simulations of an Active Self-Assembling Material. J Phys Chem B 2024; 128:1266-1274. [PMID: 38290526 DOI: 10.1021/acs.jpcb.3c06572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Inspired by the adaptability observed in biological materials, self-assembly processes have attracted significant interest for their potential to yield novel materials with unique properties. However, experimental methods have often fallen short in capturing the molecular details of the assembly process. In this study, we employ a multiscale molecular dynamics simulation approach, complemented by NMR quantification, to investigate the mechanism of self-assembly in a redox-fueled bioinspired system. Contrary to conventional assumptions, we have uncovered a significant role played by the monomer precursor in the assembly process, with its presence varying with concentration and the extent of conversion of the monomer to the dimer. Experimental confirmation through NMR quantification underscores the concentration-dependent incorporation of monomers into the fibrous structures. Furthermore, our simulations also shed light on the diverse intermolecular interactions, including T-shaped and parallel π stacking, as well as hydrogen bonds, in stabilizing the aggregates. Overall, the open conformation of the dimer is preferred within these aggregates. However, inside the aggregates, the distribution of conformations shifts slightly to the closed conformation compared to on the surface. These findings contribute to the growing field of bioinspired materials science by providing valuable mechanistic and structural insights to guide the design and development of self-assembling materials with biomimetic functionalities.
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Affiliation(s)
- Yuanming Song
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Center for Complex and Active Materials, University of California, Irvine, Irvine, California 92697, United States
| | - Serxho Selmani
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Center for Complex and Active Materials, University of California, Irvine, Irvine, California 92697, United States
| | - J Alfredo Freites
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Zhibin Guan
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Center for Complex and Active Materials, University of California, Irvine, Irvine, California 92697, United States
| | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Center for Complex and Active Materials, University of California, Irvine, Irvine, California 92697, United States
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5
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Garay PG, Machado MR, Verli H, Pantano S. SIRAH Late Harvest: Coarse-Grained Models for Protein Glycosylation. J Chem Theory Comput 2024; 20:963-976. [PMID: 38175797 DOI: 10.1021/acs.jctc.3c00783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Glycans constitute one of the most complex families of biological molecules. Despite their crucial role in a plethora of biological processes, they remain largely uncharacterized because of their high complexity. Their intrinsic flexibility and the vast variability associated with the many combination possibilities have hampered their experimental determination. Although theoretical methods have proven to be a valid alternative to the study of glycans, the large size associated with polysaccharides, proteoglycans, and glycolipids poses significant challenges to a fully atomistic description of biologically relevant glycoconjugates. On the other hand, the exquisite dependence on hydrogen bonds to determine glycans' structure makes the development of simplified or coarse-grained (CG) representations extremely challenging. This is particularly the case when glycan representations are expected to be compatible with CG force fields that include several molecular types. We introduce a CG representation able to simulate a wide variety of polysaccharides and common glycosylation motifs in proteins, which is fully compatible with the CG SIRAH force field. Examples of application to N-glycosylated proteins, including antibody recognition and calcium-mediated glycan-protein interactions, highlight the versatility of the enlarged set of CG molecules provided by SIRAH.
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Affiliation(s)
- Pablo G Garay
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Matias R Machado
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Hugo Verli
- Programa de Pos-Graduacao em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Goncalves, 9500, Porto Alegre 91509-900, Brazil
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
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6
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Robles A, Dinamarca-Villarroel L, Torres GE, Fierro A. Collective and Coordinated Conformational Changes Determine Agonism or Antagonism at the Human Trace Amine-Associated Receptor 1. ACS OMEGA 2023; 8:43051-43059. [PMID: 38024694 PMCID: PMC10652269 DOI: 10.1021/acsomega.3c06315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
The human trace amine-associated receptor (hTAAR1), a G protein-coupled receptor, has been postulated as a new target in the treatment of neuropsychiatric conditions. The mechanism associated with activation or inactivation by agonists or antagonists in hTAAR1 and other GPCRs has not yet been fully elucidated. In this study, we combined computational methods including homology modeling, docking, and molecular dynamic simulations to reveal novel conformational changes associated with agonist and antagonist interactions in hTAAR1. Our findings suggest a differential cascade of coordinated movements based on the presence of either an agonist or antagonist and primarily involving the second extracellular loop, transmembrane domain 5, and the third intracellular domains of hTAAR1. Our study provides an opportunity to predict the effects on new ligands with agonistic or antagonistic activity at hTAAR1 based on the reported conformational changes.
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Affiliation(s)
- Agustín
I. Robles
- Departamento
de Química Orgánica, Escuela de Química, Facultad
de Química y de Farmacia, Pontificia
Universidad Católica de Chile, Santiago 7820436, Chile
- Department
of Molecular Pharmacology & Neuroscience, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois 60611-2001, United States
| | - Luis Dinamarca-Villarroel
- Departamento
de Química Orgánica, Escuela de Química, Facultad
de Química y de Farmacia, Pontificia
Universidad Católica de Chile, Santiago 7820436, Chile
- Department
of Molecular Pharmacology & Neuroscience, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois 60611-2001, United States
| | - Gonzalo E. Torres
- Department
of Molecular Pharmacology & Neuroscience, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois 60611-2001, United States
| | - Angélica Fierro
- Departamento
de Química Orgánica, Escuela de Química, Facultad
de Química y de Farmacia, Pontificia
Universidad Católica de Chile, Santiago 7820436, Chile
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7
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Frigini EN, Porasso RD, Beke-Somfai T, López Cascales JJ, Enriz RD, Pantano S. The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations. J Chem Inf Model 2023; 63:6877-6889. [PMID: 37905818 DOI: 10.1021/acs.jcim.3c01348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Antimicrobial cationic peptides (AMPs) are excellent candidates for use as therapeutic antimicrobial agents. Among them, short peptides possessing sequences of 9-11 amino acids have some advantages over long-sequence peptides. However, one of the main limitations of short peptides is that their mechanism of action at the molecular level is not well-known. In this article, we report a model based on multiscale molecular dynamics simulations of short peptides interacting with vesicles containing palmitoyl-oleoyl-phosphatidylglycerol (POPG)/palmitoyl-oleoyl-phosphatidylethanolamine (POPE). Simulations using this approach have allowed us to understand the different behaviors of peptides with antimicrobial activity with respect to those that do not produce this effect. We found remarkable agreement with a series of experimental results directly supporting our model. Moreover, these results allow us to understand the mechanism of action at the molecular level of these short peptides. Our simulations suggest that mechanical inhomogeneities appear in the membrane, promoting membrane rupture when a threshold concentration of peptides adsorbed on the membrane is achieved. These results explain the high structural demand for these peptides to maintain a delicate balance between the affinity for the bilayer surface, a low peptide-peptide repulsion (in order to reach the threshold concentration), and an acceptable tendency to penetrate into the bilayer. This mechanism is different from those proposed for peptides with long amino acid sequences. Such information is very useful from the medicinal chemistry point of view for the design of new small antimicrobial peptides.
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Affiliation(s)
- Ezequiel N Frigini
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, San Luis 5700, Argentina
| | - Tamás Beke-Somfai
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - José Javier López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoleculas (BioMac), Area de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
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8
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Na H, Song G. Coarse-Graining Waters: Unveiling The Effective Hydrophilicity/Hydrophobicity of Individual Protein Atoms and The Roles of Waters' Hydrogens. J Chem Theory Comput 2023; 19:7307-7323. [PMID: 37782694 PMCID: PMC10601925 DOI: 10.1021/acs.jctc.3c00700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Indexed: 10/04/2023]
Abstract
There have been many coarse-graining methods developed that aim to reduce the sizes of simulated systems and their computational costs. In this work, we develop a new coarse-graining method, called coarse-graining-delta (or δ-CG in short), that reduces the degrees of freedom of the potential energy surface by coarse-graining relative locations of atoms from their unit centers. Our method extends and generalizes the methods used in the coarse-grained normal mode analysis and enables us to study the roles of the individual removed atoms in a system, which have been difficult to study in molecular dynamics simulations. By applying δ-CG to coarse-grain three-point water molecules into single-point solvent particles, we successfully identify the effective hydrophilicity and hydrophobicity of all the individual protein atom types, which collectively correlate well with the known hydrophilic, hydrophobic, and amphipathic characteristics of amino acids. Moreover, our investigation shows that water's hydrogens have two roles in interacting with protein atoms. First, water molecules adjust their poses around different amino acids and their atoms, and the statistical preferences of the hydrogen poses near the atoms determine the effective hydrophilicity and hydrophobicity of the atoms, which have not been successfully addressed before. Second, the collective dynamics of the hydrogens assist the water molecules in escaping from the potential energy wells of the hydrophilic atoms. Our method also shows that coarse-graining a system mathematically leads to breaking antisymmetry of the nonbonded interactions; as a result, two interacting coarse-grained units exert different forces on each other. Our study indicates that the accuracy of coarse-grained force fields, such as the MARTINI force field and the UNRES force field, can be improved in two ways: (i) refining their potential energy functions and coefficients by analyzing the coarse-grained potential energy surface using δ-CG, and (ii) introducing non-antisymmetric interactions.
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Affiliation(s)
- Hyuntae Na
- Department
of Computer Science, Penn State Harrisburg, Middletown, Pennsylvania 17057, United States
| | - Guang Song
- Department
of Mathematics and Computer Science, Westmont
College, Santa
Barbara, California 93108, United States
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9
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Borges-Araújo L, Patmanidis I, Singh AP, Santos LHS, Sieradzan AK, Vanni S, Czaplewski C, Pantano S, Shinoda W, Monticelli L, Liwo A, Marrink SJ, Souza PCT. Pragmatic Coarse-Graining of Proteins: Models and Applications. J Chem Theory Comput 2023; 19:7112-7135. [PMID: 37788237 DOI: 10.1021/acs.jctc.3c00733] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.
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Affiliation(s)
- Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Ilias Patmanidis
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Akhil P Singh
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Lucianna H S Santos
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Inserm, CNRS, 06560 Valbonne, France
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita, Okayama 700-8530, Japan
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
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10
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Klein F, Soñora M, Helene Santos L, Nazareno Frigini E, Ballesteros-Casallas A, Rodrigo Machado M, Pantano S. The SIRAH force field: A suite for simulations of complex biological systems at the coarse-grained and multiscale levels. J Struct Biol 2023; 215:107985. [PMID: 37331570 DOI: 10.1016/j.jsb.2023.107985] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/18/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
The different combinations of molecular dynamics simulations with coarse-grained representations have acquired considerable popularity among the scientific community. Especially in biocomputing, the significant speedup granted by simplified molecular models opened the possibility of increasing the diversity and complexity of macromolecular systems, providing realistic insights on large assemblies for more extended time windows. However, a holistic view of biological ensembles' structural and dynamic features requires a self-consistent force field, namely, a set of equations and parameters that describe the intra and intermolecular interactions among moieties of diverse chemical nature (i.e., nucleic and amino acids, lipids, solvent, ions, etc.). Nevertheless, examples of such force fields are scarce in the literature at the fully atomistic and coarse-grained levels. Moreover, the number of force fields capable of handling simultaneously different scales is restricted to a handful. Among those, the SIRAH force field, developed in our group, furnishes a set of topologies and tools that facilitate the setting up and running of molecular dynamics simulations at the coarse-grained and multiscale levels. SIRAH uses the same classical pairwise Hamiltonian function implemented in the most popular molecular dynamics software. In particular, it runs natively in AMBER and Gromacs engines, and porting it to other simulation packages is straightforward. This review describes the underlying philosophy behind the development of SIRAH over the years and across families of biological molecules, discussing current limitations and future implementations.
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Affiliation(s)
- Florencia Klein
- Laboratoire de Biochimie Théorique, UPR9080, CNRS, Paris, France
| | - Martín Soñora
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | | | - Ezequiel Nazareno Frigini
- Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (IMIBIO-SL), Universidad Nacional de San Luis - CONICET, San Luis, Argentina
| | - Andrés Ballesteros-Casallas
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay; Area Bioinformática, DETEMA, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, 11600, Uruguay
| | | | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay; Area Bioinformática, DETEMA, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, 11600, Uruguay.
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11
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Ko SK, Björkengren G, Berner C, Winter G, Harris P, Peters GHJ. Combining Molecular Dynamics Simulations and Biophysical Characterization to Investigate Protein-Specific Excipient Effects on Reteplase during Freeze Drying. Pharmaceutics 2023; 15:1854. [PMID: 37514040 PMCID: PMC10384596 DOI: 10.3390/pharmaceutics15071854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
We performed molecular dynamics simulations of Reteplase in the presence of different excipients to study the stabilizing mechanisms and to identify the role of excipients during freeze drying. To simulate the freeze-drying process, we divided the process into five distinct steps: (i) protein-excipient formulations at room temperature, (ii) the ice-growth process, (iii)-(iv) the partially solvated and fully dried formulations, and (v) the reconstitution. Furthermore, coarse-grained (CG) simulations were employed to explore the protein-aggregation process in the presence of arginine. By using a coarse-grained representation, we could observe the collective behavior and interactions between protein molecules during the aggregation process. The CG simulations revealed that the presence of arginine prevented intermolecular interactions of the catalytic domain of Reteplase, thus reducing the aggregation propensity. This suggests that arginine played a stabilizing role by interacting with protein-specific regions. From the freeze-drying simulations, we could identify several protein-specific events: (i) collapse of the domain structure, (ii) recovery of the drying-induced damages during reconstitution, and (iii) stabilization of the local aggregation-prone region via direct interactions with excipients. Complementary to the simulations, we employed nanoDSF, size-exclusion chromatography, and CD spectroscopy to investigate the effect of the freeze-drying process on the protein structure and stability.
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Affiliation(s)
- Suk Kyu Ko
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gabriella Björkengren
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Carolin Berner
- Department of Pharmacy, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Gerhard Winter
- Department of Pharmacy, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Pernille Harris
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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12
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Zhang H, Huo QY, Gao YQ. DNA Sequence-Dependent Binding of Linker Histone gH1 Regulates Nucleosome Conformations. J Phys Chem B 2022; 126:6771-6779. [PMID: 36062461 DOI: 10.1021/acs.jpcb.2c03785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sequence-dependent binding between DNA and proteins in chromatin is an essential part of gene expression. Linker histone H1 is an important protein in the regulation of chromatin compartmentalization and compaction, and its binding with the nucleosome is sensitive to the DNA sequence. Although the interactions of H1 and DNA have been widely investigated, the mechanism of nucleosome conformation changes induced by the DNA-sequence-dependent binding with gH1 (globular H1.0) remains largely unclear at the atomic level. In the present molecular dynamics simulations, both linker and dyad DNAs were mutated to investigate the conformational changes of the nucleosome induced by the sequence-dependent binding of gH1 based on the on-dyad binding mode. Our results indicate that gH1 is insensitive to the DNA sequence of the dyad DNA but presents an apparent preference to linker DNA with an AT-rich sequence. Moreover, this specific binding induces the entry/exit region of a nucleosome to a tight conformation and regulates the accessibility of core histones. Considering that the entry/exit region of the nucleosome is a crucial binding site for many functional proteins related to gene expression, the conformational change at this region could represent an important gene regulation signal.
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Affiliation(s)
- Hong Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qin Yuan Huo
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
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13
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Coarse-grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins. J Mol Model 2022; 28:201. [PMID: 35748949 DOI: 10.1007/s00894-022-05154-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 10/17/2022]
Abstract
Metal ions play important biological roles, e.g., activation or deactivation of enzymatic reactions and signal transduction. Moreover, they can stabilize protein structure, or even be actively involved in the protein folding process. Therefore, accurate treatment of the ions is crucial to model and investigate biological phenomena properly. In this work the coarse-grained UNRES (UNited RESidue) force field was extended to include the interactions between proteins and four alkali or alkaline earth metal cations of biological significance, i.e., calcium, magnesium, sodium and potassium. Additionally, chloride anions were introduced as counter-ions. Parameters were derived from all-atom simulations and incorporate water in an implicit manner. The new force field was tested on the set of the proteins and was able to reproduce the ion-binding preferences.
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14
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Kyu Ko S, Berner C, Kulakova A, Schneider M, Antes I, Winter G, Harris P, Peters GH. Investigation of the pH-dependent aggregation mechanisms of GCSF using low resolution protein characterization techniques and advanced molecular dynamics simulations. Comput Struct Biotechnol J 2022; 20:1439-1455. [PMID: 35386098 PMCID: PMC8956964 DOI: 10.1016/j.csbj.2022.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Granulocyte-colony stimulating factor (GCSF) is a widely used therapeutic protein to treat neutropenia. GCSF has an increased propensity to aggregate if the pH is increased above 5.0. Although GCSF is very well experimentally characterized, the exact pH-dependent aggregation mechanism of GCSF is still under debate. This study aimed to model the complex pH-dependent aggregation behavior of GCSF using state-of-the-art simulation techniques. The conformational stability of GCSF was investigated by performing metadynamics simulations, while the protein-protein interactions were investigated using coarse-grained (CG) simulations of multiple GCSF monomers. The CG simulations were directly compared with small-angle X-ray (SAXS) data. The metadynamics simulations demonstrated that the orientations of Trp residues in GCSF are dependent on pH. The conformational change of Trp residues is due to the loss of Trp-His interactions at the physiological pH, which in turn may increase protein flexibility. The helical structure of GCSF was not affected by the pH conditions of the simulations. Our CG simulations indicate that at pH 4.0, the colloidal stability may be more important than the conformational stability of GCSF. The electrostatic potential surface and CG simulations suggested that the basic residues are mainly responsible for colloidal stability as deprotonation of these residues causes a reduction of the highly positively charged electrostatic barrier close to the aggregation-prone long loop regions.
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15
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Patel D, Haag SL, Patel JS, Ytreberg FM, Bernards MT. Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin. J Chem Inf Model 2022; 62:1282-1293. [PMID: 35194993 DOI: 10.1021/acs.jcim.1c01104] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Serum albumin is the most abundant protein in blood plasma, and it is involved in multiple biological processes. Serum albumin has recently been adapted for improving biomaterial integration with bone tissue, and studies have shown the importance of this protein in bone repair and regeneration. However, the mechanism of action is not yet clear. In stark contrast, other studies have demonstrated that albumin blocks cell adhesion to surfaces, which is seen as a limitation to its bone healing role. These apparent contradictions suggest that the conformation of albumin facilitates its bioactivity, leading to enhanced bone repair. Serum albumin is known to play a major role in maintaining the calcium ion concentration in blood plasma. Due to the prevalence of calcium at bone repair and regeneration sites, it has been hypothesized that calcium binding to serum albumin triggers a conformational change, leading to bioactivity. In the current study, molecular modeling approaches including molecular docking, atomic molecular dynamics (MD) simulation, and coarse-grained MD simulation were used to test this hypothesis by investigating the conformational changes induced in bovine serum albumin by interaction with calcium ions. The computational results were qualitatively validated with experimental Fourier-transform infrared spectroscopy analysis. We find that free calcium ions in solution transiently bind with the three major loops in albumin, triggering a conformational change where N-terminal and C-terminal domains separate from each other in a partial unfolding process. The separation distance between these domains was found to correlate with the calcium ion concentration. The experimental data support the simulation results showing that albumin has enhanced conformational heterogeneity upon exposure to intermediate levels of calcium, without any significant secondary structure changes.
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Affiliation(s)
- Dharmeshkumar Patel
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow 83844, Idaho, United States.,Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta 30322, Georgia, United States
| | - Stephanie L Haag
- Department of Chemical and Biological Engineering, University of Idaho, Moscow 83844, Idaho, United States
| | - Jagdish Suresh Patel
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow 83844, Idaho, United States.,Department of Biological Sciences, University of Idaho, Moscow 83844, Idaho, United States
| | - F Marty Ytreberg
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow 83844, Idaho, United States.,Department of Physics, University of Idaho, Moscow 83844, Idaho, United States
| | - Matthew T Bernards
- Department of Chemical and Biological Engineering, University of Idaho, Moscow 83844, Idaho, United States
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16
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Esmaeeli R, Andal B, Perez A. Searching for Low Probability Opening Events in a DNA Sliding Clamp. Life (Basel) 2022; 12:life12020261. [PMID: 35207548 PMCID: PMC8876151 DOI: 10.3390/life12020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/27/2022] Open
Abstract
The β subunit of E. coli DNA polymererase III is a DNA sliding clamp associated with increasing the processivity of DNA synthesis. In its free form, it is a circular homodimer structure that can accomodate double-stranded DNA in a nonspecific manner. An open state of the clamp must be accessible before loading the DNA. The opening mechanism is still a matter of debate, as is the effect of bound DNA on opening/closing kinetics. We use a combination of atomistic, coarse-grained, and enhanced sampling strategies in both explicit and implicit solvents to identify opening events in the sliding clamp. Such simulations of large nucleic acid and their complexes are becoming available and are being driven by improvements in force fields and the creation of faster computers. Different models support alternative opening mechanisms, either through an in-plane or out-of-plane opening event. We further note some of the current limitations, despite advances, in modeling these highly charged systems with implicit solvent.
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17
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Co NT, Li MS, Krupa P. Computational Models for the Study of Protein Aggregation. Methods Mol Biol 2022; 2340:51-78. [PMID: 35167070 DOI: 10.1007/978-1-0716-1546-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein aggregation has been studied by many groups around the world for many years because it can be the cause of a number of neurodegenerative diseases that have no effective treatment. Obtaining the structure of related fibrils and toxic oligomers, as well as describing the pathways and main factors that govern the self-organization process, is of paramount importance, but it is also very difficult. To solve this problem, experimental and computational methods are often combined to get the most out of each method. The effectiveness of the computational approach largely depends on the construction of a reasonable molecular model. Here we discussed different versions of the four most popular all-atom force fields AMBER, CHARMM, GROMOS, and OPLS, which have been developed for folded and intrinsically disordered proteins, or both. Continuous and discrete coarse-grained models, which were mainly used to study the kinetics of aggregation, are also summarized.
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Affiliation(s)
- Nguyen Truong Co
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Pawel Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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18
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Caceres-Delpiano J, Wang LP, Essex JW. The automated optimisation of a coarse-grained force field using free energy data. Phys Chem Chem Phys 2021; 23:24842-24851. [PMID: 34723311 PMCID: PMC8579472 DOI: 10.1039/d0cp05041e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/18/2021] [Indexed: 11/21/2022]
Abstract
Atomistic models provide a detailed representation of molecular systems, but are sometimes inadequate for simulations of large systems over long timescales. Coarse-grained models enable accelerated simulations by reducing the number of degrees of freedom, at the cost of reduced accuracy. New optimisation processes to parameterise these models could improve their quality and range of applicability. We present an automated approach for the optimisation of coarse-grained force fields, by reproducing free energy data derived from atomistic molecular simulations. To illustrate the approach, we implemented hydration free energy gradients as a new target for force field optimisation in ForceBalance and applied it successfully to optimise the un-charged side-chains and the protein backbone in the SIRAH protein coarse-grain force field. The optimised parameters closely reproduced hydration free energies of atomistic models and gave improved agreement with experiment.
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Affiliation(s)
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California 95616, USA.
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Southapton, S017 1BJ, UK.
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19
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Kist R, Timmers LFSM, Caceres RA. Understanding the role of mTOR-mLst8 binding through coarse-grained simulation approaches. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1962525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Roger Kist
- Graduate Program in Health Sciences of Federal University of Health Sciences of Porto Alegre – UFCSPA, Porto Alegre City, Brazil
| | | | - Rafael Andrade Caceres
- Graduate Program in Health Sciences of Federal University of Health Sciences of Porto Alegre – UFCSPA, Porto Alegre City, Brazil
- Pharmacosciences Department of Federal University of Health Sciences of Porto Alegre – UFCSPA, Porto Alegre City, Brazil
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20
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Abstract
It is a great challenge to develop ultra-coarse-grained models in simulations of biological macromolecules. In this study, the original coarse-graining strategy proposed in our previous work [M. Li and J. Z. H. Zhang, Phys. Chem. Chem. Phys. 23, 8926 (2021)] is first extended to the ultra-coarse-graining (UCG) modeling of liquid water, with the NC increasing from 4-10 to 20-500. The UCG force field is parameterized by the top-down strategy and subsequently refined on important properties of liquid water by the trial-and-error scheme. The optimal cutoffs for non-bonded interactions in the NC = 20/100/500 UCG simulations are, respectively, determined on energy convergence. The results show that the average density at 300 K can be accurately reproduced from the well-refined UCG models while it is largely different in describing compressibility, self-diffusion coefficient, etc. The density-temperature relationships predicted by these UCG models are in good agreement with the experiment result. Besides, two polarizable states of the UCG molecules are observed after simulated systems are equilibrated. The ion-water RDFs from the ion-involved NC = 100 UCG simulation are nearly in accord with the scaled AA ones. Furthermore, the concentration of ions can influence the ratio of two polarizable states in the NC = 100 simulation. Finally, it is illustrated that the proposed UCG models can accelerate liquid water simulation by 114-135 times, compared with the TIP3P force field. The proposed UCG force field is simple, generic, and transferable, potentially providing valuable information for UCG simulations of large biomolecules.
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Affiliation(s)
- Min Li
- College of Physics, Qingdao University, Qingdao, Shandong 266071, People's Republic of China
| | - WenCai Lu
- College of Physics, Qingdao University, Qingdao, Shandong 266071, People's Republic of China
| | - John ZengHui Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, People's Republic of China
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21
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González-Puelma J, Aldridge J, Montes de Oca M, Pinto M, Uribe-Paredes R, Fernández-Goycoolea J, Alvarez-Saravia D, Álvarez H, Encina G, Weitzel T, Muñoz R, Olivera-Nappa Á, Pantano S, Navarrete MA. Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Viruses 2021; 13:883. [PMID: 34064904 PMCID: PMC8151058 DOI: 10.3390/v13050883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
The emergence of SARS-CoV-2 variants, as observed with the D614G spike protein mutant and, more recently, with B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1) lineages, represent a continuous threat and might lead to strains of higher infectivity and/or virulence. We report on the occurrence of a SARS-CoV-2 haplotype with nine mutations including D614G/T307I double-mutation of the spike. This variant expanded and completely replaced previous lineages within a short period in the subantarctic Magallanes Region, southern Chile. The rapid lineage shift was accompanied by a significant increase of cases, resulting in one of the highest incidence rates worldwide. Comparative coarse-grained molecular dynamic simulations indicated that T307I and D614G belong to a previously unrecognized dynamic domain, interfering with the mobility of the receptor binding domain of the spike. The T307I mutation showed a synergistic effect with the D614G. Continuous surveillance of new mutations and molecular analyses of such variations are important tools to understand the molecular mechanisms defining infectivity and virulence of current and future SARS-CoV-2 strains.
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Affiliation(s)
- Jorge González-Puelma
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Jacqueline Aldridge
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | - Marco Montes de Oca
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | - Mónica Pinto
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Enfermedades Infecciosas, Hospital Clínico de Magallanes, Punta Arenas 6210005, Chile
| | - Roberto Uribe-Paredes
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | | | - Diego Alvarez-Saravia
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Hermy Álvarez
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Gonzalo Encina
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, Chile;
| | - Thomas Weitzel
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, Chile;
- Instituto de Ciencias e Innovación en Medicina (ICIM), Universidad del Desarrollo, Santiago 7610658, Chile
| | - Rodrigo Muñoz
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Enfermedades Infecciosas, Hospital Clínico de Magallanes, Punta Arenas 6210005, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago 8370456, Chile;
- Facultad de Ciencias, Físicas y Matemáticas, Universidad de Chile, Santiago 8370456, Chile
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Marcelo A. Navarrete
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
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22
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Hernández-Meza JM, Mares-Sámano S, Garduño-Juárez R. Insights into the Molecular Inhibition of the Oncogenic Channel K V10.1 by Globular Toxins. J Chem Inf Model 2021; 61:2328-2340. [PMID: 33900765 DOI: 10.1021/acs.jcim.0c01353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Inhibition of the expression of the human ether-à-go-go (hEAG1 or hKV10.1) channel is associated with a dramatic reduction in the growth of several cancerous tumors. The modulation of this channel's activity is a promising target for the development of new anticancer drugs. Although some small molecules have shown inhibitory activity against KV10.1, their lack of specificity has prevented their use in humans. In vitro studies have recently identified a limited number of peptide toxins with proven specificity in their hKV10.1 channel inhibitory effect. These peptide toxins have become desirable candidates to use as lead compounds to design more potent and specific hKV10.1 inhibitors. However, the currently available studies lack the atomic resolution needed to characterize the molecular features that favor their binding to hKV10.1. In this work, we present the first attempt to locate the possible hKV10.1 binding sites of the animal peptide toxins APETx4, Aa1a, Ap1a, and k-hefutoxin 1, all of which described as hKV10.1 inhibitors. Our studies incorporated homology modeling to construct a robust three-dimensional (3D) model of hKV10.1, applied protein docking, and multiscale molecular dynamics techniques to reveal in atomic resolution the toxin-channel interactions. Our approach suggests that some peptide toxins bind in the outer vestibule surrounding the pore of hKV10.1; it also identified the channel residues Met397 and Asp398 as possible anchors that stabilize the binding of the evaluated toxins. Finally, a description of the possible mechanism for inhibition and gating is presented.
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Affiliation(s)
- Juan M Hernández-Meza
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, México
| | - Sergio Mares-Sámano
- CONACYT - Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, México
| | - Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, México
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23
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Li M, Zhang JZH. Multiscale polarizable coarse-graining water models on cluster-level electrostatic dipoles. Phys Chem Chem Phys 2021; 23:8926-8935. [PMID: 33876052 DOI: 10.1039/d1cp00338k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The development of a coarse-grained (CG) water model is increasingly important in CG studies of biological processes. In this work, we developed a generic CG force field of liquid water on cluster-level electrostatic dipoles. An exponential term is introduced in the non-bonded potential to adjust the well depth. The whole force field is parametrized on the AMOEBA simulation and then refined on the experimental density, dielectric permittivity and isothermal compressibility. The new CG water force field is suitable for the construction of multi-resolution water models and here the NC = 4/5/10 systems are taken as examples. The results show that the NC = 4/5/10 models can correctly reproduce the density and relative dielectric permittivity. The models can well predict the pressure-density/density-temperature relationships close to the all-atom or experiment results. However, the new models behave differently from other CG models in several water properties such as the air-water surface tension. Through dipole distributions, two representative polarizable configurations are captured after the NC = 4/5/10 systems are dynamically equilibrated. Besides, the NC = 4 model is coupled with the Martini Na+/Cl- models to predict ion-relevant radial distribution functions in comparison to the Martini result. Lastly, CPU tests suggest that the new CG models can enhance simulation efficiency by factors of 20-42, compared to the TIP3P force field. The newly proposed polarizable water force field is practical and transferable and can be flexibly extended to higher coarse-graining of liquid water.
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Affiliation(s)
- Min Li
- College of Physics, Qingdao University, Qingdao, Shandong 266071, P. R. China.
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24
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Barrera EE, Zonta F, Pantano S. Dissecting the role of glutamine in seeding peptide aggregation. Comput Struct Biotechnol J 2021; 19:1595-1602. [PMID: 33868596 PMCID: PMC8039506 DOI: 10.1016/j.csbj.2021.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 12/02/2022] Open
Abstract
Poly glutamine and glutamine-rich peptides play a central role in a plethora of pathological aggregation events. However, biophysical characterization of soluble oligomers -the most toxic species involved in these processes- remains elusive due to their structural heterogeneity and dynamical nature. Here, we exploit the high spatio-temporal resolution of coarse-grained simulations as a computational microscope to characterize the aggregation propensity and morphology of a series of polyglutamine and glutamine-rich peptides. Comparative analysis of ab-initio aggregation pinpointed a double role for glutamines. In the first phase, glutamines mediate seeding by pairing monomeric peptides, which serve as primers for higher-order nucleation. According to the glutamine content, these low molecular-weight oligomers may then proceed to create larger aggregates. Once within the aggregates, buried glutamines continue to play a role in their maturation by optimizing solvent-protected hydrogen bonds networks.
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Affiliation(s)
- Exequiel E. Barrera
- Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Sergio Pantano
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
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25
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Garay PG, Barrera EE, Klein F, Machado MR, Soñora M, Pantano S. The SIRAH-CoV-2 Initiative: A Coarse-Grained Simulations' Dataset of the SARS-CoV-2 Proteome. FRONTIERS IN MEDICAL TECHNOLOGY 2021; 3:644039. [PMID: 35047913 PMCID: PMC8757729 DOI: 10.3389/fmedt.2021.644039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 01/20/2021] [Indexed: 12/03/2022] Open
Affiliation(s)
| | | | | | | | | | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo, Uruguay
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26
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Jin J, Han Y, Pak AJ, Voth GA. A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model. J Chem Phys 2021; 154:044104. [PMID: 33514116 PMCID: PMC7826168 DOI: 10.1063/5.0026651] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Water is undoubtedly one of the most important molecules for a variety of chemical and physical systems, and constructing precise yet effective coarse-grained (CG) water models has been a high priority for computer simulations. To recapitulate important local correlations in the CG water model, explicit higher-order interactions are often included. However, the advantages of coarse-graining may then be offset by the larger computational cost in the model parameterization and simulation execution. To leverage both the computational efficiency of the CG simulation and the inclusion of higher-order interactions, we propose a new statistical mechanical theory that effectively projects many-body interactions onto pairwise basis sets. The many-body projection theory presented in this work shares similar physics from liquid state theory, providing an efficient approach to account for higher-order interactions within the reduced model. We apply this theory to project the widely used Stillinger-Weber three-body interaction onto a pairwise (two-body) interaction for water. Based on the projected interaction with the correct long-range behavior, we denote the new CG water model as the Bottom-Up Many-Body Projected Water (BUMPer) model, where the resultant CG interaction corresponds to a prior model, the iteratively force-matched model. Unlike other pairwise CG models, BUMPer provides high-fidelity recapitulation of pair correlation functions and three-body distributions, as well as N-body correlation functions. BUMPer extensively improves upon the existing bottom-up CG water models by extending the accuracy and applicability of such models while maintaining a reduced computational cost.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yining Han
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander J. Pak
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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Soñora M, Martínez L, Pantano S, Machado MR. Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus. J Chem Inf Model 2021; 61:408-422. [PMID: 33415985 DOI: 10.1021/acs.jcim.0c01205] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Simulating huge biomolecular complexes of million atoms at relevant biological time scales is becoming accessible to the broad scientific community. That proves to be crucial for urgent responses against emergent diseases in real time. Yet, there are still issues to sort regarding the system setup so that molecular dynamics (MD) simulations can be run in a simple and standard way. Here, we introduce an optimized pipeline for building and simulating enveloped virus-like particles (VLP). First, the membrane packing problem is tackled with new features and optimized options in PACKMOL. This allows preparing accurate membrane models of thousands of lipids in the context of a VLP within a few hours using a single CPU. Then, the assembly of the VLP system is done within the multiscale framework of the coarse-grained SIRAH force field. Finally, the equilibration protocol provides a system ready for production MD simulations within a few days on broadly accessible GPU resources. The pipeline is applied to study the Zika virus as a test case for large biomolecular systems. The VLP stabilizes at approximately 0.5 μs of MD simulation, reproducing correlations greater than 0.90 against experimental density maps from cryo-electron microscopy. Detailed structural analysis of the protein envelope also shows very good agreement in root-mean-square deviations and B-factors with the experimental data. The level of details attained shows for the first time a possible role for anionic phospholipids in stabilizing the envelope. Combining an efficient and reliable setup procedure with an accurate coarse-grained force field provides a valuable pipeline for simulating arbitrary viral systems or subcellular compartments, paving the way toward whole-cell simulations.
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Affiliation(s)
- Martín Soñora
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | - Leandro Martínez
- Institute of Chemistry and Center for Computational Engineering & Science, University of Campinas, Rua Josué de Castro s/n, Cidade Universitária "Zeferino Vaz", Barão Geraldo, 13083-861 Campinas, SP, Brazil
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | - Matías R Machado
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
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Ramis R, Ortega-Castro J, Vilanova B, Adrover M, Frau J. Cu 2+, Ca 2+, and methionine oxidation expose the hydrophobic α-synuclein NAC domain. Int J Biol Macromol 2020; 169:251-263. [PMID: 33345970 DOI: 10.1016/j.ijbiomac.2020.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/04/2020] [Accepted: 12/03/2020] [Indexed: 11/25/2022]
Abstract
α-Synuclein is an intrinsically disordered protein whose aggregation is related to Parkinson's disease and other neurodegenerative disorders. Metal cations are one of the main factors affecting the propensity of α-synuclein to aggregate, either by directly binding to it or by catalyzing the production of reactive oxygen species that oxidize it. His50, Asp121 and several additional C-terminal α-synuclein residues are binding sites for numerous metal cations, while methionine sulfoxidation occurs readily on this protein under oxidative stress conditions. Molecular dynamics simulations are an excellent tool to obtain a microscopic picture of how metal binding or methionine sulfoxidation alter the conformational preferences of α-synuclein and, hence, its aggregation propensity. In this work, we report the first coarse-grained molecular dynamics study comparing the conformational ensembles of the native protein, the protein bound to either Cu2+ or Ca2+ at its main binding sites, and the methionine-sulfoxidized protein. Our results suggest that these events alter the transient α-synuclein intramolecular contacts, inducing a greater solvent exposure of its hydrophobic, aggregation-prone NAC domain, in full agreement with a recent experimental study on Ca2+ binding. Moreover, metal-binding residues directly participate in the long-range contacts that shield this domain and regulate α-synuclein aggregation. These results provide a molecular-level rationalization of the enhanced fibrillation experimentally observed in the presence of Cu2+ or Ca2+ and the oligomerization induced by methionine sulfoxidation.
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Affiliation(s)
- Rafael Ramis
- Institut Universitari d'Investigació en Cièencies de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Joaquín Ortega-Castro
- Institut Universitari d'Investigació en Cièencies de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain.
| | - Bartolomé Vilanova
- Institut Universitari d'Investigació en Cièencies de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut Universitari d'Investigació en Cièencies de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Juan Frau
- Institut Universitari d'Investigació en Cièencies de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
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CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations. Molecules 2020; 25:molecules25245934. [PMID: 33333836 PMCID: PMC7765266 DOI: 10.3390/molecules25245934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/21/2020] [Accepted: 11/28/2020] [Indexed: 12/17/2022] Open
Abstract
Advances in coarse-grained molecular dynamics (CGMD) simulations have extended the use of computational studies on biological macromolecules and their complexes, as well as the interactions of membrane protein and lipid complexes at a reduced level of representation, allowing longer and larger molecular dynamics simulations. Here, we present a computational platform dedicated to the preparation, running, and analysis of CGMD simulations. The platform is built on a completely revisited version of our Martini coarsE gRained MembrAne proteIn Dynamics (MERMAID) web server, and it integrates this with other three dedicated services. In its current version, the platform expands the existing implementation of the Martini force field for membrane proteins to also allow the simulation of soluble proteins using the Martini and the SIRAH force fields. Moreover, it offers an automated protocol for carrying out the backmapping of the coarse-grained description of the system into an atomistic one.
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Ramis R, Ortega-Castro J, Vilanova B, Adrover M, Frau J. Unraveling the NaCl Concentration Effect on the First Stages of α-Synuclein Aggregation. Biomacromolecules 2020; 21:5200-5212. [PMID: 33140640 DOI: 10.1021/acs.biomac.0c01292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intraneuronal aggregation of the intrinsically disordered protein α-synuclein is at the core of Parkinson's disease and related neurodegenerative disorders. Several reports show that the concentration of salts in the medium heavily affects its aggregation rate and fibril morphology, but a characterization of the individual monomeric conformations underlying these effects is still lacking. In this work, we have applied our α-synuclein-optimized coarse-grained molecular dynamics approach to decipher the structural features of the protein monomer under a range of NaCl concentrations (0.0-1.0 M). The results show that key intramolecular contacts between the terminal domains are lost at intermediate concentrations (leading to extended conformations likely to fibrillate), but recovered at high concentrations (leading to compact conformations likely to evolve toward amorphous aggregates). The pattern of direct interactions of the terminal α-synuclein domains with Na+ and Cl- ions plays a key role in explaining this effect. Our results are consistent with a recent study reporting a fibrillation enhancement at moderate NaCl concentrations but an inhibition at higher concentrations. The present work will contribute to improving our understanding of the structural features of monomeric α-synuclein, determining its NaCl-induced fibrillation propensity and the molecular basis of synucleinopathies, necessary for the future development of disease-halting therapies.
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Affiliation(s)
- Rafael Ramis
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Joaquín Ortega-Castro
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Bartolomé Vilanova
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Juan Frau
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
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31
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Ahyayauch H, García-Arribas AB, Masserini ME, Pantano S, Goñi FM, Alonso A. β-Amyloid (1-42) peptide adsorbs but does not insert into ganglioside-containing phospholipid membranes in the liquid-disordered state: modelling and experimental studies. Int J Biol Macromol 2020; 164:2651-2658. [PMID: 32846182 DOI: 10.1016/j.ijbiomac.2020.08.165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/09/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022]
Abstract
β-Amyloid (Aβ) is a 39-43 residue peptide involved in the pathogenesis of Alzheimer's disease. Aβ deposits onto the cells and gives rise to the plaques that are characteristic of the disease. In an effort to understand the molecular mechanism of plaque formation, we have examined the interaction of Aβ42, considered to be the most pathogenic of the peptides, with lipid bilayers consisting of 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC) to which small amounts of GM1 ganglioside (1-5 mol%) were incorporated. POPC bilayers exist in the fluid, or liquid-disordered state at room temperature, mimicking the fluidity of cell membranes. An Aβ42 preparation consisting essentially of peptide monomers was used. A combination of molecular dynamics (MD), isothermal calorimetry and Langmuir balance measurements was applied. Our results show that Aβ binds POPC bilayers, and that binding increases (ΔG of binding decreases) with GM1, but only up to 3 mol% of the ganglioside, larger concentrations appearing to have a lower effect. MD and Langmuir balance measurements concur in showing that the peptide adsorbs onto the bilayer surface, but does not become inserted into it at surface pressures compatible with the cell membrane conditions. Thioflavin T measurements agree with MD in revealing a very low degree of peptide oligomerization/aggregation under our conditions. This is in contrast with previous studies showing peptide aggregation and insertion when interacting with membranes in the liquid-ordered state. The present contribution underlines the importance of bilayer lipid composition and properties for Aβ plaque formation.
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Affiliation(s)
- Hasna Ahyayauch
- Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Bilbao, Spain; Institut Supérieur des Professions Infirmières et Techniques de Santé, Rabat, Morocco; Neuroendocrinology Unit, Laboratory of Genetics, Neuroendocrinology and Biotechnology, Faculty of Sciences, Ibn Tofail University, Kénitra, Morocco
| | - Aritz B García-Arribas
- Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Bilbao, Spain
| | | | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Félix M Goñi
- Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Bilbao, Spain
| | - Alicia Alonso
- Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Bilbao, Spain.
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32
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Li M, Lu W, Zhang JZ. A three-point coarse-grained model of five-water cluster with permanent dipoles and quadrupoles. Phys Chem Chem Phys 2020; 22:26289-26298. [PMID: 33174895 DOI: 10.1039/d0cp04782a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As coarse-grained (CG) studies of large biomolecules increase, developments of reliable CG solvent models become particularly important. In this work, we reduce five water molecules into a three-point CG model with permanent dipole and quadrupole moments. In the CG force field, the modified Morse potential is utilized and an ideal three-water cluster is designed to derive CG-level permanent multipoles. The new CG model is parametrized on the AMOEBA polarizable force field. Various important properties of liquid water are examined to validate the new CG model. Results show that the new CG model can correctly reproduce certain important experimental properties such as density, isothermal compressibility and relative static dielectric permittivity, even better than the existing AA models. Additionally, the CPU tests reveal that the CG model can accelerate molecular dynamics simulations by a factor of 19 compared to the popular AA force field. Compared with the fix-point-charge model widely used in other CG models, the permanent-multipole-based CG model describes more rigid electrostatic attractions. This study also illustrates that the permanent multipole moments contribute a lot to the electrostatic calculations in CG simulation.
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Affiliation(s)
- Min Li
- College of Physics, Qingdao University, Qingdao, Shandong 266071, P. R. China.
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33
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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Klein F, Cáceres D, Carrasco MA, Tapia JC, Caballero J, Alzate-Morales J, Pantano S. Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field. J Chem Inf Model 2020; 60:3935-3943. [DOI: 10.1021/acs.jcim.0c00160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Florencia Klein
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Daniela Cáceres
- Escuela de Medicina, Universidad de Talca, 1 Poniente 1141, Talca 3460000, Chile
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingenierı́a, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Talca 3460000, Chile
| | - Mónica A. Carrasco
- Escuela de Medicina, Universidad de Talca, 1 Poniente 1141, Talca 3460000, Chile
| | - Juan Carlos Tapia
- Escuela de Medicina, Universidad de Talca, 1 Poniente 1141, Talca 3460000, Chile
| | - Julio Caballero
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingenierı́a, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Talca 3460000, Chile
| | - Jans Alzate-Morales
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingenierı́a, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Talca 3460000, Chile
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
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35
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Roel-Touris J, Bonvin AM. Coarse-grained (hybrid) integrative modeling of biomolecular interactions. Comput Struct Biotechnol J 2020; 18:1182-1190. [PMID: 32514329 PMCID: PMC7264466 DOI: 10.1016/j.csbj.2020.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/23/2020] [Accepted: 05/06/2020] [Indexed: 12/23/2022] Open
Abstract
The computational modeling field has vastly evolved over the past decades. The early developments of simplified protein systems represented a stepping stone towards establishing more efficient approaches to sample intricated conformational landscapes. Downscaling the level of resolution of biomolecules to coarser representations allows for studying protein structure, dynamics and interactions that are not accessible by classical atomistic approaches. The combination of different resolutions, namely hybrid modeling, has also been proved as an alternative when mixed levels of details are required. In this review, we provide an overview of coarse-grained/hybrid models focusing on their applicability in the modeling of biomolecular interactions. We give a detailed list of ready-to-use modeling software for studying biomolecular interactions allowing various levels of coarse-graining and provide examples of complexes determined by integrative coarse-grained/hybrid approaches in combination with experimental information.
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36
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Delle Site L, Praprotnik M, Bell JB, Klein R. Particle–Continuum Coupling and its Scaling Regimes: Theory and Applications. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.201900232] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Luigi Delle Site
- Freie Universität Berlin Institute of Mathematics Arnimallee 6, 14195 Berlin Germany
| | - Matej Praprotnik
- Laboratory for Molecular Modeling National Institute of Chemistry SI‐1001 Ljubljana, Slovenia & Department of Physics Faculty of Mathematics and Physics University of Ljubljana SI‐1000 Ljubljana Slovenia
| | - John B. Bell
- Lawrence Berkeley National Lab 1 Cyclotron Rd. Berkeley CA 94720 USA
| | - Rupert Klein
- Freie Universität Berlin Institute of Mathematics Arnimallee 6, 14195 Berlin Germany
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37
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Machado MR, Pantano S. Split the Charge Difference in Two! A Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations. J Chem Theory Comput 2020; 16:1367-1372. [PMID: 31999456 DOI: 10.1021/acs.jctc.9b00953] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.
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Affiliation(s)
- Matías R Machado
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP 11400, Uruguay
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP 11400, Uruguay
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38
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Garay PG, Barrera EE, Pantano S. Post-Translational Modifications at the Coarse-Grained Level with the SIRAH Force Field. J Chem Inf Model 2020; 60:964-973. [PMID: 31840995 DOI: 10.1021/acs.jcim.9b00900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Post-translational modifications (PTMs) on proteins significantly enlarge the physicochemical diversity present in biological macromolecules, altering function, localization, and interactions. Despite their critical role in regulating cellular processes, theoretical methods are not yet fully capable of coping with this diversity. These limitations are particularly more marked for coarse-grained (CG) models, in which comprehensive and self-consistent parametrizations are less frequent. Here we present a set of topologies and interaction parameters for the most common PTMs, fully compatible with the SIRAH force field. The PTMs introduced here reach the same level of structural description of the existing SIRAH force field, expanding the chemical spectrum with promising applications in dynamical protein-protein interactions in large and complex cellular environments.
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Affiliation(s)
- Pablo G Garay
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020, CP 11400 Montevideo , Uruguay
| | - Exequiel E Barrera
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020, CP 11400 Montevideo , Uruguay
| | - Sergio Pantano
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020, CP 11400 Montevideo , Uruguay.,Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Shanghai 201210 , China
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39
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Li C, Qin Z, Han W. Bottom-up derived flexible water model with dipole and quadrupole moments for coarse-grained molecular simulations. Phys Chem Chem Phys 2020; 22:27394-27412. [DOI: 10.1039/d0cp04185h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A bottom-up CG water model is developed to capture the electrostatic multipoles, structural correlation and thermodynamics of water.
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Affiliation(s)
- Chen Li
- State Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Zhongyuan Qin
- State Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Wei Han
- State Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
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Miyazaki Y, Okazaki S, Shinoda W. pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model. J Chem Theory Comput 2019; 16:782-793. [DOI: 10.1021/acs.jctc.9b00946] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yusuke Miyazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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41
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Frigini EN, Barrera EE, Pantano S, Porasso RD. Role of membrane curvature on the activation/deactivation of Carnitine Palmitoyltransferase 1A: A coarse grain molecular dynamic study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183094. [PMID: 31705849 DOI: 10.1016/j.bbamem.2019.183094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 10/25/2022]
Abstract
Carnitine Palmitoyltransferase 1A (CPT 1A) is an enzyme anchored to the outer mitochondrial membrane (OMM), where it regulates the passage of fatty acids into the mitochondria and intervenes in the process of β-oxidation of long-chain fatty acids. Although CPT 1A is inhibited by malonyl-CoA, its activity is also modulated by the curvature of OMM. This modulation depends on the behavior of the N-terminal domain (NTD), which can be adsorbed onto the OMM (nonactive CPT 1A) or interacting with the C-terminal domain (active CPT 1A). Aimed to provide mechanistic insights on the regulatory mechanism of CPT 1A, we studied the influence of the bilayer curvature on the NTD behavior through a series of coarse-grained (CG) molecular dynamics simulations using curved and planar membranes. Comparative analysis suggests that the main determinant for the activation/deactivation of the enzyme is the tilt angle orientation of the transmembrane (TM) domains. Planar membranes induce a wide variation on the tilt angle orientation of TM helices, while curved geometries promote small angles with the membrane normal. Our results identify the first TM domain as an important component of the membrane sensing mechanism.
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Affiliation(s)
- Ezequiel N Frigini
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Quimica, Bioquimica y Farmacia, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, San Luis 5700, Argentina
| | - Exequiel E Barrera
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Quimica, Bioquimica y Farmacia, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, San Luis 5700, Argentina.
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42
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Barrera EE, Machado MR, Pantano S. Fat SIRAH: Coarse-Grained Phospholipids To Explore Membrane-Protein Dynamics. J Chem Theory Comput 2019; 15:5674-5688. [PMID: 31433946 DOI: 10.1021/acs.jctc.9b00435] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The capability to handle highly heterogeneous molecular assemblies in a consistent manner is among the greatest challenges faced when deriving simulation parameters. This is particularly the case for coarse-grained (CG) simulations in which chemical functional groups are lumped into effective interaction centers for which transferability between different chemical environments is not guaranteed. Here, we introduce the parametrization of a set of CG phospholipids compatible with the latest version of the SIRAH force field for proteins. The newly introduced lipid species include different acylic chain lengths and partial unsaturation, as well as polar and acidic head groups that show a very good reproduction of structural membrane determinants, such as areas per lipid, thickness, order parameter, etc., and their dependence with temperature. Simulation of membrane proteins showed unprecedented accuracy in the unbiased description of the thickness-dependent membrane-protein orientation in systems where this information is experimentally available (namely, the SarcoEndoplasmic Reticulum Calcium-SERCA-pump and its regulator Phospholamban). The interactions that lead to this faithful reproduction can be traced down to the single amino acid-lipid interaction level and show full agreement with biochemical data present in the literature. Finally, the present parametrization is implemented in the GROMACS and AMBER simulation packages facilitating its use by a wide portion of the biocomputing community.
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Affiliation(s)
- Exequiel E Barrera
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Matías R Machado
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Sergio Pantano
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay.,Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , Shanghai 201210 , China
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43
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Machado MR, Zeida A, Darré L, Pantano S. From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field. Interface Focus 2019; 9:20180085. [PMID: 31065347 PMCID: PMC6501346 DOI: 10.1098/rsfs.2018.0085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2019] [Indexed: 12/11/2022] Open
Abstract
Modern molecular and cellular biology profits from astonishing resolution structural methods, currently even reaching the whole cell level. This is encompassed by the development of computational methods providing a deep view into the structure and dynamics of molecular processes happening at very different scales in time and space. Linking such scales is of paramount importance when aiming at far-reaching biological questions. Computational methods at the interface between classical and coarse-grained resolutions are gaining momentum with several research groups dedicating important efforts to their development and tuning. An overview of such methods is addressed herein, with special emphasis on the SIRAH force field for coarse-grained and multi-scale simulations. Moreover, we provide proof of concept calculations on the implementation of a multi-scale simulation scheme including quantum calculations on a classical fine-grained/coarse-grained representation of double-stranded DNA. This opens the possibility to include the effect of large conformational fluctuations in chromatin segments on, for instance, the reactivity of particular base pairs within the same simulation framework.
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Affiliation(s)
- Matías R. Machado
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Leonardo Darré
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
- Institut Pasteur de Montevideo, Functional Genomics Unit, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
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Zavadlav J, Marrink SJ, Praprotnik M. SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids. Interface Focus 2019; 9:20180075. [PMID: 31065343 PMCID: PMC6501350 DOI: 10.1098/rsfs.2018.0075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
In this contribution, we review recent developments and applications of a dynamic clustering algorithm SWINGER tailored for the multiscale molecular simulations of biomolecular systems. The algorithm on-the-fly redistributes solvent molecules among supramolecular clusters. In particular, we focus on its applications in combination with the adaptive resolution scheme, which concurrently couples atomistic and coarse-grained molecular representations. We showcase the versatility of our multiscale approach on a few applications to biomolecular systems coupling atomistic and supramolecular water models such as the well-established MARTINI and dissipative particle dynamics models and provide an outlook for future work.
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Affiliation(s)
- Julija Zavadlav
- Computational Science and Engineering Laboratory, ETH-Zurich, Clausiusstrasse 33, 8092 Zurich, Switzerland
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands
| | - Matej Praprotnik
- Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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45
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Gunaratne RS, Wilson DB, Flegg MB, Erban R. Multi-resolution dimer models in heat baths with short-range and long-range interactions. Interface Focus 2019; 9:20180070. [PMID: 31065341 PMCID: PMC6501348 DOI: 10.1098/rsfs.2018.0070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2019] [Indexed: 11/16/2022] Open
Abstract
This work investigates multi-resolution methodologies for simulating dimer models. The solvent particles which make up the heat bath interact with the monomers of the dimer either through direct collisions (short-range) or through harmonic springs (long-range). Two types of multi-resolution methodologies are considered in detail: (a) describing parts of the solvent far away from the dimer by a coarser approach; (b) describing each monomer of the dimer by using a model with different level of resolution. These methodologies are then used to investigate the effect of a shared heat bath versus two uncoupled heat baths, one for each monomer. Furthermore, the validity of the multi-resolution methods is discussed by comparison to dynamics of macroscopic Langevin equations.
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Affiliation(s)
- Ravinda S. Gunaratne
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
| | - Daniel B. Wilson
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
| | - Mark B. Flegg
- School of Mathematical Sciences, Monash University, 9 Rainforest walk, Clayton campus, Victoria 3168, Australia
| | - Radek Erban
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
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46
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Ramis R, Ortega-Castro J, Casasnovas R, Mariño L, Vilanova B, Adrover M, Frau J. A Coarse-Grained Molecular Dynamics Approach to the Study of the Intrinsically Disordered Protein α-Synuclein. J Chem Inf Model 2019; 59:1458-1471. [DOI: 10.1021/acs.jcim.8b00921] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rafael Ramis
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Joaquín Ortega-Castro
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Rodrigo Casasnovas
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Laura Mariño
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Bartolomé Vilanova
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Juan Frau
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
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47
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Machado MR, Barrera EE, Klein F, Sóñora M, Silva S, Pantano S. The SIRAH 2.0 Force Field: Altius, Fortius, Citius. J Chem Theory Comput 2019; 15:2719-2733. [PMID: 30810317 DOI: 10.1021/acs.jctc.9b00006] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A new version of the coarse-grained (CG) SIRAH force field for proteins has been developed. Modifications to bonded and non-bonded interactions on the existing molecular topologies significantly ameliorate the structural description and flexibility of a non-redundant set of proteins. The SIRAH 2.0 force field has also been ported to the popular simulation package AMBER, which along with the former implementation in GROMACS expands significantly the potential range of users and performance of this CG force field on CPU/GPU codes. As a non-trivial example of its application, we undertook the structural and dynamical analysis of the most abundant and conserved calcium-binding protein, calmodulin (CaM). CaM is composed of two calcium-binding motifs called EF-hands, which in the presence of calcium specifically recognize a cognate peptide by embracing it. CG simulations of CaM bound to four calcium ions in the presence or absence of a binding peptide (holo and apo forms, respectively) resulted in good and stable ion coordination. The simulation of the holo form starting from an experimental structure sampled near-native conformations, retrieving quasi-atomistic precision. Removing the binding peptide enabled the EF-hands to perform large reciprocal movements, comparable to those observed in NMR structures. On the other hand, the isolated peptide starting from the helical conformation experienced spontaneous unfolding, in agreement with previous experimental data. However, repositioning the peptide in the neighborhood of one EF-hand not only prevented the peptide from unfolding but also drove CaM to a fully bound conformation, with both EF-hands embracing the cognate peptide, resembling the experimental holo structure. Therefore, SIRAH 2.0 shows the capacity to handle a number of structurally and dynamically challenging situations, including metal ion coordination, unbiased conformational sampling, and specific protein-peptide recognition.
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Affiliation(s)
- Matías R Machado
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Exequiel E Barrera
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Florencia Klein
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Martín Sóñora
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Steffano Silva
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Sergio Pantano
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
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48
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Nieto-Draghi C, Rousseau B. Thermodynamically Consistent Force Field for Coarse-Grained Modeling of Aqueous Electrolyte Solution. J Phys Chem B 2019; 123:2424-2431. [DOI: 10.1021/acs.jpcb.8b11190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Carlos Nieto-Draghi
- IFP Energies nouvelles, 1-4 Avenue de Bois Préau, 92852 Rueil-Malmaison, France
| | - Bernard Rousseau
- Laboratoire de Chimie Physique, UMR 8000 CNRS, Université Paris-Sud, 91405 Orsay, France
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49
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Bore SL, Kolli HB, Kawakatsu T, Milano G, Cascella M. Mesoscale Electrostatics Driving Particle Dynamics in Nonhomogeneous Dielectrics. J Chem Theory Comput 2019; 15:2033-2041. [DOI: 10.1021/acs.jctc.8b01201] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Hima Bindu Kolli
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Miyagi, Japan
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan ,Yonezawa, Yamagata-ken 992-8510, Japan
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
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50
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Toomjeen P, Phanchai W, Choodet C, Chompoosor A, Thanan R, Sakonsinsiri C, Puangmali T. Designing an Aptasensor Based on Cysteamine-Capped AuNPs for 8-Oxo-dG Detection: A Molecular Dynamics Approach and Experimental Validation. J Phys Chem B 2019; 123:1129-1138. [DOI: 10.1021/acs.jpcb.8b10436] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | | | | | - Apiwat Chompoosor
- Department of Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand
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