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Jon JS, Ri WK, Sin KR, Son YC, Pak JS, Kim SJ, Choe CB, Jang MC. Derivation of limiting ion mobility equation based on the application of solvation effect-incorporated Poisson-Boltzmann equation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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2
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Rosário-Ferreira N, Marques-Pereira C, Gouveia RP, Mourão J, Moreira IS. Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View. Methods Mol Biol 2021; 2315:3-28. [PMID: 34302667 DOI: 10.1007/978-1-0716-1468-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Membrane proteins (MPs) encompass a large family of proteins with distinct cellular functions, and although representing over 50% of existing pharmaceutical drug targets, their structural and functional information is still very scarce. Over the last years, in silico analysis and algorithm development were essential to characterize MPs and overcome some limitations of experimental approaches. The optimization and improvement of these methods remain an ongoing process, with key advances in MPs' structure, folding, and interface prediction being continuously tackled. Herein, we discuss the latest trends in computational methods toward a deeper understanding of the atomistic and mechanistic details of MPs.
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Affiliation(s)
- Nícia Rosário-Ferreira
- Coimbra Chemistry Center, Department of Chemistry, University of Coimbra, Coimbra, Portugal.,Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Catarina Marques-Pereira
- Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Raquel P Gouveia
- Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Joana Mourão
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Irina S Moreira
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
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3
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Shock CJ, Stevens MJ, Frischknecht AL, Nakamura I. Solvation Energy of Ions in a Stockmayer Fluid. J Phys Chem B 2020; 124:4598-4604. [PMID: 32368916 DOI: 10.1021/acs.jpcb.0c00769] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We calculate the solvation energy of monovalent and divalent ions in various liquids with coarse-grained molecular dynamics simulations. Our theory treats the solvent as a Stockmayer fluid, which accounts for the intrinsic dipole moment of molecules and the rotational dynamics of the dipoles. Despite the simplicity of the model, we obtain qualitative agreement between the simulations and experimental data for the free energy and enthalpy of ion solvation, which indicates that the primary contribution to the solvation energy arises mainly from the first and possibly second solvation shells near the ions. Our results suggest that a Stockmayer fluid can serve as a reference model that enables direct comparison between theory and experiment and may be invoked to scale up electrostatic interactions from the atomic to the molecular length scale.
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Affiliation(s)
- Cameron J Shock
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Amalie L Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Issei Nakamura
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
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4
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Howell SC, Qiu X, Curtis JE. Monte Carlo simulation algorithm for B-DNA. J Comput Chem 2018; 37:2553-63. [PMID: 27671358 DOI: 10.1002/jcc.24474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/12/2016] [Accepted: 07/23/2016] [Indexed: 01/12/2023]
Abstract
Understanding the structure-function relationship of biomolecules containing DNA has motivated experiments aimed at determining molecular structure using methods such as small-angle X-ray and neutron scattering (SAXS and SANS). SAXS and SANS are useful for determining macromolecular shape in solution, a process which benefits by using atomistic models that reproduce the scattering data. The variety of algorithms available for creating and modifying model DNA structures lack the ability to rapidly modify all-atom models to generate structure ensembles. This article describes a Monte Carlo algorithm for simulating DNA, not with the goal of predicting an equilibrium structure, but rather to generate an ensemble of plausible structures which can be filtered using experimental results to identify a sub-ensemble of conformations that reproduce the solution scattering of DNA macromolecules. The algorithm generates an ensemble of atomic structures through an iterative cycle in which B-DNA is represented using a wormlike bead-rod model, new configurations are generated by sampling bend and twist moves, then atomic detail is recovered by back mapping from the final coarse-grained configuration. Using this algorithm on commodity computing hardware, one can rapidly generate an ensemble of atomic level models, each model representing a physically realistic configuration that could be further studied using molecular dynamics. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Steven C Howell
- Neutron Condensed Matter Science Group, NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899-8562
| | - Xiangyun Qiu
- Department of Physics, The George Washington University, Washington, District of Columbia, 20052
| | - Joseph E Curtis
- Neutron Condensed Matter Science Group, NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899-8562.
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5
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Wang C, Ren P, Luo R. Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling. J Phys Chem B 2017; 121:11169-11179. [PMID: 29164898 DOI: 10.1021/acs.jpcb.7b09616] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solvent-mediated electrostatic interactions were well recognized to be important in the structure and function of molecular systems. Ionic interaction is an important component in electrostatic interactions, especially in highly charged molecules, such as nucleic acids. Here, we focus on the quality of the widely used Poisson-Boltzmann surface area (PBSA) continuum models in modeling ionic interactions by comparing with both explicit solvent simulations and the experiment. In this work, the molality-dependent chemical potentials for sodium chloride (NaCl) electrolyte were first simulated in the SPC/E explicit solvent. Our high-quality simulation agrees well with both the previous study and the experiment. Given the free-energy simulations in SPC/E as the benchmark, we used the same sets of snapshots collected in the SPC/E solvent model for PBSA free-energy calculations in the hope to achieve the maximum consistency between the two solvent models. Our comparative analysis shows that the molality-dependent chemical potentials of NaCl were reproduced well with both linear PB and nonlinear PB methods, although nonlinear PB agrees better with SPC/E and the experiment. Our free-energy simulations also show that the presence of salt increases the hydrophobic effect in a nonlinear fashion, in qualitative agreement with previous theoretical studies of Onsager and Samaras. However, the lack of molality-dependency in the nonelectrostatics continuum models dramatically reduces the overall quality of PBSA methods in modeling salt-dependent energetics. These analyses point to further improvements needed for more robust modeling of solvent-mediated interactions by the continuum solvation frameworks.
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Affiliation(s)
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas , Austin, Texas 78712, United States
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6
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Lake PT, McCullagh M. Implicit Solvation Using the Superposition Approximation (IS-SPA): An Implicit Treatment of the Nonpolar Component to Solvation for Simulating Molecular Aggregation. J Chem Theory Comput 2017; 13:5911-5924. [PMID: 29120632 DOI: 10.1021/acs.jctc.7b00698] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonpolar solute-solvent interactions are the driving force for aggregation in important chemical and biological phenomena including protein folding, peptide self-assembly, and oil-water emulsion formation. Currently, the most accurate and computationally efficient description of these processes requires an explicit treatment of all solvent and solute atoms. Previous computationally feasible implicit solvent models, such as solute surface area approaches, are unsuccessful at capturing aggregation features including both structural and energetic trends while more theoretically rigorous approaches, such as Reference Interaction Site Model (RISM), are accurate but extremely computationally demanding. Our approach, denoted Implicit Solvation using the Superposition Approximation (IS-SPA), builds on previous theory utilizing the Kirkwood superposition approximation to approximate the mean force of the solvent from solute parameters. We introduce and verify a parabolic first solvation shell truncation of atomic solvation, fitting water distributions around a molecule, and a Monte Carlo integration of the mean solvent force. These extensions allow this method to be implemented as an efficient nonpolar implicit solvent model for molecular simulation. The approximations in IS-SPA are first explored and justified for the homodimerization of an array of different sized Lennard-Jones spheres. The accuracy and transferability of the approach are demonstrated by its ability to capture the position and relative energies of the desolvation barrier and free energy minimum of alkane homodimers. The model is then shown to reproduce the phase separation and solubility of cyclohexane and water. These promising results, coupled with 2 orders of magnitude speed-up for dilute systems as compared to explicit solvent simulations, demonstrate that IS-SPA is an appealing approach to boost the time- and length-scale of molecular aggregation simulations.
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Affiliation(s)
- Peter T Lake
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523, United States
| | - Martin McCullagh
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523, United States
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7
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Bu B, Tong X, Li D, Hu Y, He W, Zhao C, Hu R, Li X, Shao Y, Liu C, Zhao Q, Ji B, Diao J. N-Terminal Acetylation Preserves α-Synuclein from Oligomerization by Blocking Intermolecular Hydrogen Bonds. ACS Chem Neurosci 2017; 8:2145-2151. [PMID: 28741930 DOI: 10.1021/acschemneuro.7b00250] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The abnormal aggregation of α-synuclein (α-Syn) is closely associated with Parkinson's disease. Different post-translational modifications of α-Syn have been identified and contribute distinctly in α-Syn aggregation and cytotoxicity. Recently, α-Syn was reported to be N-terminally acetylated in cells, yet the functional implication of this modification, especially in α-Syn oligomerization, remains unclear. By using a solid-state nanopore system, we found that N-terminal acetylation can significantly decrease α-Syn oligomerization. Replica-exchange molecular dynamics simulations further revealed that addition of an acetyl group at the N-terminus disrupts intermolecular hydrogen bonds, which slows down the initial α-Syn oligomerization. Our finding highlights the essential role of N-terminal acetylation of α-Syn in preserving its native conformation against pathological aggregation.
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Affiliation(s)
- Bing Bu
- Biomechanics
and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing 100081, China
| | - Xin Tong
- State
Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory,
School of Physics, Peking University, Beijing 100871, China
| | - Dechang Li
- Biomechanics
and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing 100081, China
| | - Yachong Hu
- Department
of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States
- Key
Laboratory of Biomedical Information Engineering of the Ministry of
Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Wangxiao He
- Key
Laboratory of Biomedical Information Engineering of the Ministry of
Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Chunyu Zhao
- Interdisciplinary
Research Center on Biology and Chemistry, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Rui Hu
- State
Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory,
School of Physics, Peking University, Beijing 100871, China
| | - Xiaoqing Li
- State
Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory,
School of Physics, Peking University, Beijing 100871, China
| | - Yongping Shao
- Key
Laboratory of Biomedical Information Engineering of the Ministry of
Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Cong Liu
- Interdisciplinary
Research Center on Biology and Chemistry, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qing Zhao
- State
Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory,
School of Physics, Peking University, Beijing 100871, China
| | - Baohua Ji
- Biomechanics
and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing 100081, China
| | - Jiajie Diao
- Department
of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States
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8
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Abstract
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.
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Affiliation(s)
- Taejin Kim
- Department of Chemistry, New York University, 10th Floor Silver Center, 100 Washington Square East, New York, NY, 10003, USA
| | - Wojciech K Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Bruce A Shapiro
- RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
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9
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Coarse-grained modeling of RNA 3D structure. Methods 2016; 103:138-56. [PMID: 27125734 DOI: 10.1016/j.ymeth.2016.04.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/21/2022] Open
Abstract
Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.
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10
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Henke PS, Mak CH. An implicit divalent counterion force field for RNA molecular dynamics. J Chem Phys 2016; 144:105104. [DOI: 10.1063/1.4943387] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Paul S. Henke
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Chi H. Mak
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
- Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089, USA
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11
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Zachmann M, Mathias G, Antes I. Parameterization of the Hamiltonian Dielectric Solvent (HADES) Reaction-Field Method for the Solvation Free Energies of Amino Acid Side-Chain Analogs. Chemphyschem 2015; 16:1739-49. [PMID: 25820235 DOI: 10.1002/cphc.201402861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/02/2015] [Indexed: 11/10/2022]
Abstract
Optimization of the Hamiltonian dielectric solvent (HADES) method for biomolecular simulations in a dielectric continuum is presented with the goal of calculating accurate absolute solvation free energies while retaining the model's accuracy in predicting conformational free-energy differences. The solvation free energies of neutral and polar amino acid side-chain analogs calculated by using HADES, which may optionally include nonpolar contributions, were optimized against experimental data to reach a chemical accuracy of about 0.5 kcal mol(-1). The new parameters were evaluated for charged side-chain analogs. The HADES results were compared with explicit-solvent, generalized Born, Poisson-Boltzmann, and QM-based methods. The potentials of mean force (PMFs) between pairs of side-chain analogs obtained by using HADES and explicit-solvent simulations were used to evaluate the effects of the improved parameters optimized for solvation free energies on intermolecular potentials.
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Affiliation(s)
- Martin Zachmann
- Theoretical Chemical Biology and Protein Modelling Group, Technische Universiät München (Germany)
| | - Gerald Mathias
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians Universität München (Germany).
| | - Iris Antes
- Theoretical Chemical Biology and Protein Modelling Group, Technische Universiät München (Germany).
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12
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Tuszynski JA, Winter P, White D, Tseng CY, Sahu KK, Gentile F, Spasevska I, Omar SI, Nayebi N, Churchill CD, Klobukowski M, El-Magd RMA. Mathematical and computational modeling in biology at multiple scales. Theor Biol Med Model 2014; 11:52. [PMID: 25542608 PMCID: PMC4396153 DOI: 10.1186/1742-4682-11-52] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 11/25/2014] [Indexed: 01/08/2023] Open
Abstract
A variety of topics are reviewed in the area of mathematical and computational modeling in biology, covering the range of scales from populations of organisms to electrons in atoms. The use of maximum entropy as an inference tool in the fields of biology and drug discovery is discussed. Mathematical and computational methods and models in the areas of epidemiology, cell physiology and cancer are surveyed. The technique of molecular dynamics is covered, with special attention to force fields for protein simulations and methods for the calculation of solvation free energies. The utility of quantum mechanical methods in biophysical and biochemical modeling is explored. The field of computational enzymology is examined.
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Affiliation(s)
- Jack A Tuszynski
- Department of Physics and Department of Oncology, University of Alberta, Edmonton, Canada.
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13
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Freed KF. Perturbative many-body expansion for electrostatic energy and field for system of polarizable charged spherical ions in a dielectric medium. J Chem Phys 2014; 141:034115. [DOI: 10.1063/1.4890077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Kleinjung J, Fraternali F. Design and application of implicit solvent models in biomolecular simulations. Curr Opin Struct Biol 2014; 25:126-34. [PMID: 24841242 PMCID: PMC4045398 DOI: 10.1016/j.sbi.2014.04.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/07/2014] [Accepted: 04/09/2014] [Indexed: 11/23/2022]
Abstract
Implicit solvent replaces explicit water by a potential of mean force. Popular models are SASA, VOL and Generalized Born. Implicit solvent is used in MD, protein modelling, folding, design, prediction and drug screening. Large-scale simulations allow for parametrisation via force matching. Application to nucleic acids and membranes is challenging.
We review implicit solvent models and their parametrisation by introducing the concepts and recent devlopments of the most popular models with a focus on parametrisation via force matching. An overview of recent applications of the solvation energy term in protein dynamics, modelling, design and prediction is given to illustrate the usability and versatility of implicit solvation in reproducing the physical behaviour of biomolecular systems. Limitations of implicit modes are discussed through the example of more challenging systems like nucleic acids and membranes.
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Affiliation(s)
- Jens Kleinjung
- Division of Mathematical Biology, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London SE1 1UL, United Kingdom.
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