1
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Stroet M, Setz M, Lee T, Malde AK, van den Bergen G, Sykacek P, Oostenbrink C, Mark AE. On the Validation of Protein Force Fields Based on Structural Criteria. J Phys Chem B 2024; 128:4602-4620. [PMID: 38711373 PMCID: PMC11103706 DOI: 10.1021/acs.jpcb.3c08469] [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: 12/29/2023] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024]
Abstract
Molecular dynamics simulations depend critically on the quality of the force field used to describe the interatomic interactions and the extent to which it has been validated for use in a specific application. Using a curated test set of 52 high-resolution structures, 39 derived from X-ray diffraction and 13 solved using NMR, we consider the extent to which different parameter sets of the GROMOS protein force field can be distinguished based on comparing a range of structural criteria, including the number of backbone hydrogen bonds, the number of native hydrogen bonds, polar and nonpolar solvent-accessible surface area, radius of gyration, the prevalence of secondary structure elements, J-coupling constants, nuclear Overhauser effect (NOE) intensities, positional root-mean-square deviations (RMSD), and the distribution of backbone ϕ and ψ dihedral angles. It is shown that while statistically significant differences between the average values of individual metrics could be detected, these were in general small. Furthermore, improvements in agreement in one metric were often offset by loss of agreement in another. The work establishes a framework and test set against which protein force fields can be validated. It also highlights the danger of inferring the relative quality of a given force field based on a small range of structural properties or small number of proteins.
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Affiliation(s)
- Martin Stroet
- The
University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Martina Setz
- Institute
for Molecular Modeling and Simulation, Department of Material Science
and Process Engineering, University of Natural
Resources and Life Sciences, Vienna Muthgasse 18, 1190 Vienna, Austria
| | - Thomas Lee
- The
University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Alpeshkumar K. Malde
- Institute
for Glycomics and School of Environment and Science, Griffith University, Gold Coast, Queensland 4222, Australia
| | | | - Peter Sykacek
- Institute
of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences,
Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute
for Molecular Modeling and Simulation, Department of Material Science
and Process Engineering, University of Natural
Resources and Life Sciences, Vienna Muthgasse 18, 1190 Vienna, Austria
- Christian
Doppler Laboratory for Molecular Informatics in the Biosciences, University of Natural Resources and Life Sciences,
Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Alan E. Mark
- The
University of Queensland, St. Lucia, Queensland 4072, Australia
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2
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Vo A, Murphy M, Phan P, Stone T, Prabhu R. Molecular Dynamics Simulation of Membrane Systems in the context of Traumatic Brain Injury. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2023. [DOI: 10.1016/j.cobme.2023.100453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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3
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Stroet M, Sanderson S, Sanzogni AV, Nada S, Lee T, Caron B, Mark AE, Burn PL. PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies. J Chem Inf Model 2023; 63:2-8. [PMID: 36539938 DOI: 10.1021/acs.jcim.2c01334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The performance of organic optoelectronic devices, such as organic light-emitting diodes (OLEDs) and organic solar cells (OSCs), is intrinsically related to the molecular-scale morphology of the thin films from which they are composed. However, the experimental characterization of morphology at the molecular level is challenging due to the often amorphous or at best semicrystalline nature of these films. Classical molecular modeling techniques, such as molecular dynamics (MD) simulation, are increasingly used to understand the relationship between morphology and the properties of thin-film devices. PyThinFilm (github.com/ATB-UQ/PyThinFilm) is an open-source Python package which allows fully automated MD simulations of thin film growth to be performed using vacuum and/or solution deposition processes. PyThinFilm utilizes the GROMACS simulation package in combination with interaction parameters from the Automated Topology Builder (atb.uq.edu.au). Here, PyThinFilm is described along with an overview of applications in which PyThinFilm has been used to study the thin films of organic semiconductor materials typically used in OLEDs and OSCs.
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Affiliation(s)
- Martin Stroet
- Centre for Organic Photonics & Electronics, The University of Queensland, St Lucia Campus, Brisbane, Queensland4072, Australia.,Molecular Dynamics Group, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland4072, Australia
| | - Stephen Sanderson
- The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia Campus, Brisbane, Queensland4072, Australia.,College of Science and Engineering, James Cook University, Townsville, Queensland4811, Australia
| | - Audrey V Sanzogni
- Centre for Organic Photonics & Electronics, The University of Queensland, St Lucia Campus, Brisbane, Queensland4072, Australia.,Molecular Dynamics Group, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland4072, Australia
| | - Sharif Nada
- Molecular Dynamics Group, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland4072, Australia
| | - Thomas Lee
- Centre for Organic Photonics & Electronics, The University of Queensland, St Lucia Campus, Brisbane, Queensland4072, Australia.,Molecular Dynamics Group, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland4072, Australia
| | - Bertrand Caron
- Molecular Dynamics Group, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland4072, Australia
| | - Alan E Mark
- Molecular Dynamics Group, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland4072, Australia
| | - Paul L Burn
- Centre for Organic Photonics & Electronics, The University of Queensland, St Lucia Campus, Brisbane, Queensland4072, Australia
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4
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Pechlaner M, Oostenbrink C, van Gunsteren WF. On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. J Comput Chem 2021; 42:1263-1282. [PMID: 33951201 PMCID: PMC8252490 DOI: 10.1002/jcc.26541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 01/06/2023]
Abstract
Computer simulation of proteins in aqueous solution at the atomic level of resolution is still limited in time span and system size due to limited computing power available and thus employs a variety of time-saving techniques that trade some accuracy against computational effort. Examples of such time-saving techniques are the application of constraints to particular degrees of freedom or the use of a multiple-time-step (MTS) algorithm distinguishing between particular forces when integrating Newton's equations of motion. The application of two types of MTS algorithms to bond-stretching forces versus the remaining forces in molecular dynamics (MD) simulations of a protein in aqueous solution or of liquid water is investigated and the results in terms of total energy conservation and the influence on various other properties are compared to those of MD simulations of the same systems using bond-length, and for water bond-angle, constraints. At comparable computational effort, the use of bond-length constraints in proteins leads to better energy conservation and less distorted properties than the two MTS algorithms investigated.
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Affiliation(s)
- Maria Pechlaner
- Laboratory of Physical ChemistrySwiss Federal Institute of TechnologyZurichSwitzerland
| | - Chris Oostenbrink
- Institute of Molecular Modelling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
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5
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van Gunsteren WF, Daura X, Fuchs PFJ, Hansen N, Horta BAC, Hünenberger PH, Mark AE, Pechlaner M, Riniker S, Oostenbrink C. On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues. Chemphyschem 2020; 22:264-282. [PMID: 33377305 DOI: 10.1002/cphc.202000968] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Indexed: 12/14/2022]
Abstract
Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.
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Affiliation(s)
- Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autonoma de Barcelona (UAB), 08193, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
| | - Patrick F J Fuchs
- Sorbonne Université, Ecole Normale Supérieure, PSL Research University, CNRS, Laboratoire des Biomolécules (LBM), F-75005, Paris, France.,Université de Paris, UFR Sciences du Vivant, F-75013, Paris, France
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569, Stuttgart, Germany
| | - Bruno A C Horta
- Instituto de Química, Universidade Federal de Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Philippe H Hünenberger
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Maria Pechlaner
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Chris Oostenbrink
- Institute of Molecular Modelling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
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6
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Diem M, Oostenbrink C. The effect of different cutoff schemes in molecular simulations of proteins. J Comput Chem 2020; 41:2740-2749. [PMID: 33026106 PMCID: PMC7756334 DOI: 10.1002/jcc.26426] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/06/2020] [Accepted: 09/09/2020] [Indexed: 01/02/2023]
Abstract
Molecular simulations of nanoscale systems invariably involve assumptions and approximations to describe the electrostatic interactions, which are long-ranged in nature. One approach is the use of cutoff schemes with a reaction-field contribution to account for the medium outside the cutoff scheme. Recent reports show that macroscopic properties may depend on the exact choice of cutoff schemes in modern day simulations. In this work, a systematic analysis of the effects of different cutoff schemes was performed using a set of 52 proteins. We find no statistically significant differences between using a twin-range or a single-range cutoff scheme. Applying the cutoff based on charge groups or based on atomic positions, does lead to significant differences, which is traced to the cutoff noise for energies and forces. While group-based cutoff schemes show increased cutoff noise in the potential energy, applying an atomistic cutoff leads to artificial structure in the solvent at the cutoff distance. Carefully setting the temperature control, or using an atomistic cutoff for the solute and a group-based cutoff for the solvent significantly reduces the effects of the cutoff noise, without introducing structure in the solvent. This study aims to deepen the understanding of the implications different cutoffs have on molecular dynamics simulations.
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Affiliation(s)
- Matthias Diem
- Institute for Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
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7
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Barfoot S, Poger D, Mark AE. Understanding the Activated Form of a Class-I Fusion Protein: Modeling the Interaction of the Ebola Virus Glycoprotein 2 with a Lipid Bilayer. Biochemistry 2020; 59:4051-4058. [PMID: 32960042 DOI: 10.1021/acs.biochem.0c00527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The fusion of the viral and target cell membranes is a key step in the life cycle of all enveloped viruses. Here, a range of structural data is used to generate an evidence-based model of the active conformation of an archetypical type-I fusion protein, the Ebola glycoprotein 2 (GP2). The stability of the trimeric complex is demonstrated using molecular dynamics and validated by simulating the interaction of the complex with a lipid bilayer. In this model, the fusion peptides project away from the central helix bundle parallel to the target membrane. This maximizes contact with the host membrane, enhances lateral stability, and would explain why, when activated, viral fusion proteins are trimeric.
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Affiliation(s)
- Shelley Barfoot
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - David Poger
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Alan E Mark
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
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8
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Diem M, Oostenbrink C. The Effect of Using a Twin-Range Cutoff Scheme for Nonbonded Interactions: Implications for Force-Field Parametrization? J Chem Theory Comput 2020; 16:5985-5990. [PMID: 32813524 PMCID: PMC7558304 DOI: 10.1021/acs.jctc.0c00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 02/01/2023]
Abstract
Recently, concerns have been voiced regarding the validity of the GROMOS force fields, being parametrized using a twin-range cutoff scheme, in which longer ranged nonbonded forces and energies are updated less frequently than shorter ranged ones. Here we demonstrate that the influence of such a scheme on the thermodynamic, structural, and dynamic properties used in the parametrization of the GROMOS force fields is minor. We find root-mean-square differences of maximally 0.5 kJ/mol for the solvation free energy and heat of vaporization and of maximally 0.4% for the density. Slightly larger differences are observed when switching from a group-based to an atom-based cutoff scheme. In cases where the twin-range cutoff scheme does result in minor differences compared to a single-range cutoff these are well within the deviation from the experimentally measured values.
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Affiliation(s)
- Matthias Diem
- Institute for Molecular Modeling
and Simulation, University of Natural Resources
and Life Sciences, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling
and Simulation, University of Natural Resources
and Life Sciences, 1190 Vienna, Austria
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9
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Lee T, Sanzogni AV, Burn PL, Mark AE. Evolution and Morphology of Thin Films Formed by Solvent Evaporation: An Organic Semiconductor Case Study. ACS APPLIED MATERIALS & INTERFACES 2020; 12:40548-40557. [PMID: 32844643 DOI: 10.1021/acsami.0c08454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The crucial role played by the solution-vapor interface in determining the growth and morphology of an organic semiconductor thin film formed by solvent evaporation has been examined in atomic detail. Specifically, how the loss of individual solvent molecules from the surface of the solution induces solute assembly has been studied using molecular dynamics simulations. The system consisted of bis(2-phenylpyridine) (acetylacetonate)iridium(III) [Ir(ppy)2(acac)] and 4,4'-bis(N-carbazolyl)-1,1'-biphenyl (CBP) in chloroform at 310 K. The simulations clearly indicate that (a) the system does not undergo uniform phase separation (spinodal decomposition), (b) solute aggregation initiates at the solution-vapor interface, (c) the distribution of solvent in the film is nonhomogeneous, (d) this nonhomogeneous distribution can induce preferential alignment of host molecules, and (e) a portion of the solvent likely remains trapped within the film. The work not only demonstrates the ability to directly model evaporation in atomic detail on the relevant length scales but also shows that atomistic simulations have the potential to shed new light on morphological properties of a wide range of organic semiconductor devices manufactured using solution-processing methods.
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Affiliation(s)
- Thomas Lee
- School of Chemistry & Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, Australia
- Centre for Organic Photonics & Electronics, The University of Queensland, St. Lucia Campus, Brisbane 4072, Australia
| | - Audrey V Sanzogni
- School of Chemistry & Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, Australia
- Centre for Organic Photonics & Electronics, The University of Queensland, St. Lucia Campus, Brisbane 4072, Australia
| | - Paul L Burn
- School of Chemistry & Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, Australia
- Centre for Organic Photonics & Electronics, The University of Queensland, St. Lucia Campus, Brisbane 4072, Australia
| | - Alan E Mark
- School of Chemistry & Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, Australia
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10
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Goossens K, Neves RP, Fernandes PA, De Winter H. A Computational and Modeling Study of the Reaction Mechanism of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes. J Chem Inf Model 2020; 60:5513-5528. [PMID: 32786224 DOI: 10.1021/acs.jcim.0c00377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Bacterial glycosyltransferases of the GT51 family are key enzymes in bacterial cell wall synthesis. Inhibiting cell wall synthesis is a very effective approach for development of antibiotics, as this can lead to either bacteriostatic or bactericidal effects. Even though the existence of this family has been known for over 50 years, only one potent inhibitor exists, which is an analog of the lipid IV product and derived from a natural product. Drug development focused on bacterial transglycosylase has been hampered due to little being know about its structure and reaction mechanism. In this study, Staphylococcus aureus monoglycosyltransferase was investigated at an atomistic level using computational methods. Classical molecular dynamics simulations were used to reveal information about the large-scale dynamics of the enzyme-substrate complex and the importance of magnesium in structure and function of the protein, while mixed mode quantum mechanics/molecular mechanics calculations unveiled a novel hypothesis for the reaction mechanism. From these results, we present a new model for the binding mode of lipid II and the reaction mechanism of the GT51 glycosyltransferases. A metal-bound hydroxide catalyzed reaction mechanism yields an estimated free energy barrier of 16.1 ± 1.0 kcal/mol, which is in line with experimental values. The importance of divalent cations is also further discussed. These findings could significantly aid targeted drug design, particularly the efficient development of transition state analogues as potential inhibitors for the GT51 glycosyltransferases.
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Affiliation(s)
- Kenneth Goossens
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Rui Pp Neves
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Hans De Winter
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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11
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Majid MF, Mohd Zaid HF, Kait CF, Jumbri K, Yuan LC, Rajasuriyan S. Futuristic advance and perspective of deep eutectic solvent for extractive desulfurization of fuel oil: A review. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112870] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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12
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F. Garrido P, Calvelo M, Garcia-Fandiño R, Piñeiro Á. Rings, Hexagons, Hetals, and Dipolar Moment Sink-Sources: The Fanciful Behavior of Water around Cyclodextrin Complexes. Biomolecules 2020; 10:E431. [PMID: 32164358 PMCID: PMC7175221 DOI: 10.3390/biom10030431] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/24/2020] [Accepted: 03/04/2020] [Indexed: 01/08/2023] Open
Abstract
The basket-like geometry of cyclodextrins (CDs), with a cavity able to host hydrophobic groups, makes these molecules well suited for a large number of fundamental and industrial applications. Most of the established CD-based applications rely on trial and error studies, often ignoring key information at the atomic level that could be employed to design new products and to optimize their use. Computational simulations are well suited to fill this gap, especially in the case of CD systems due to their low number of degrees of freedom compared with typical macromolecular systems. Thus, the design and validation of solid and efficient methods to simulate and analyze CD-based systems is key to contribute to this field. The behavior of supramolecular complexes critically depends on the media where they are embedded, so the detailed characterization of the solvent is required to fully understand these systems. In the present work, we use the inclusion complex formed by two α-CDs and one sodium dodecyl sulfate molecule to test eight different parameterizations of the GROMOS and AMBER force fields, including several methods aimed to increase the conformational sampling in computational molecular dynamics simulation trajectories. The system proved to be extremely sensitive to the employed force field, as well as to the presence of a water/air interface. In agreement with previous experiments and in contrast to the results obtained with AMBER, the analysis of the simulations using GROMOS showed a quick adsorption of the complex to the interface as well as an extremely exotic behavior of the water molecules surrounding the structure both in the bulk aqueous solution and at the water surface. The chirality of the CD molecule seems to play an important role in this behavior. All together, these results are expected to be useful to better understand the behavior of CD-based supramolecular complexes such as adsorption or aggregation driving forces, as well as to introduce new methods able to speed up general MD simulations.
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Affiliation(s)
- Pablo F. Garrido
- Departamento de Física de Aplicada, Facultade de Física, Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain;
| | - Martín Calvelo
- Departamento de Química Orgánica, Center for Research in Biological Chemistry and Molecular Materials, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain;
| | - Rebeca Garcia-Fandiño
- Departamento de Química Orgánica, Center for Research in Biological Chemistry and Molecular Materials, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain;
| | - Ángel Piñeiro
- Departamento de Física de Aplicada, Facultade de Física, Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain;
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13
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Deplazes E, Sarrami F, Poger D. Effect of H3O+ on the Structure and Dynamics of Water at the Interface with Phospholipid Bilayers. J Phys Chem B 2020; 124:1361-1373. [DOI: 10.1021/acs.jpcb.9b10169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
- School of Pharmacy and Biomedical Sciences, Curtin Institute for Computation, Curtin University, Perth, Western Australia 6845, Australia
| | - Farzaneh Sarrami
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - David Poger
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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14
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Abstract
Molecular dynamics simulations allow the conformational motion of a molecule such as a protein to be followed over time at atomic-level detail. Several choices need to be made prior to running a simulation, including the software, which molecules to include in the simulation, and the force field used to describe their behavior. Guidance on making these choices and other important aspects of running MD simulations is outlined here.
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Affiliation(s)
- Thomas A Collier
- Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Thomas J Piggot
- Chemical, Biological and Radiological Sciences, Defence Science and Technology Laboratory, Wiltshire, UK
- School of Chemistry, University of Southampton, Southampton, UK
| | - Jane R Allison
- Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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15
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Kubincová A, Riniker S, Hünenberger PH. Reaction-field electrostatics in molecular dynamics simulations: development of a conservative scheme compatible with an atomic cutoff. Phys Chem Chem Phys 2020; 22:26419-26437. [DOI: 10.1039/d0cp03835k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Shifting and switching schemes are developed to enable strict energy conservation in molecular dynamics simulations relying on reaction-field electrostatic (as well as Lennard-Jones) interactions with an atom-based cutoff truncation.
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Affiliation(s)
| | - Sereina Riniker
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
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16
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Hossein A, Deserno M. Spontaneous Curvature, Differential Stress, and Bending Modulus of Asymmetric Lipid Membranes. Biophys J 2019; 118:624-642. [PMID: 31954503 DOI: 10.1016/j.bpj.2019.11.3398] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 12/24/2022] Open
Abstract
Lipid bilayers can exhibit asymmetric states, in which the physical characteristics of one leaflet differ from those of the other. This most visibly manifests in a different lipid composition, but it can also involve opposing lateral stresses in each leaflet that combine to an overall vanishing membrane tension. Here, we use theoretical modeling and coarse-grained simulation to explore the interplay between a compositional asymmetry and a nonvanishing differential stress. Minimizing the total elastic energy leads to a preferred spontaneous curvature that balances torques due to both bending moments and differential stress, with sometimes unexpected consequences. For instance, asymmetric flat bilayers, whose specific areas in each leaflet are matched to those of corresponding tensionless symmetric flat membranes, still exhibit a residual differential stress because the conditions of vanishing area strain and vanishing bending moment differ. We also measure the curvature rigidity of asymmetric bilayers and find that a sufficiently strong differential stress, but not compositional asymmetry alone, can increase the bending modulus. The likely cause is a stiffening of the compressed leaflet, which appears to be related to its gel transition but not identical with it. We finally show that the impact of cholesterol on differential stress depends on the relative strength of elastic and thermodynamic driving forces: if cholesterol solvates equally well in both leaflets, it will redistribute to cancel both leaflet tensions almost completely, but if its partitioning free energy prefers one leaflet over the other, the resulting distribution bias may even create differential stress. Because cells keep most of their lipid bilayers in an asymmetric nonequilibrium steady state, our findings suggest that biomembranes are elastically more complex than previously thought: besides a spontaneous curvature, they might also exhibit significant differential stress, which could strongly affect their curvature energetics.
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Affiliation(s)
- Amirali Hossein
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania.
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17
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Zgorski A, Pastor RW, Lyman E. Surface Shear Viscosity and Interleaflet Friction from Nonequilibrium Simulations of Lipid Bilayers. J Chem Theory Comput 2019; 15:6471-6481. [PMID: 31476126 DOI: 10.1021/acs.jctc.9b00683] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonequilibrium simulation protocols based on shear deformations are applied to determine the surface viscosity and interleaflet friction of lipid bilayers. At high shear rates, a non-Newtonian shear thinning regime is observed, but lower shear rates yield a Newtonian plateau and results that are consistent with equilibrium measurements based on fluctuation-dissipation theorems. Application to all-atom bilayers modeled with the CHARMM36 parameter set yields values for the surface viscosity that are consistent with microscopic measurements based on membrane protein diffusion but are approximately 10 times lower than more macroscopic experimental measurements. The interleaflet friction is about 10 times lower than experimental measurements. Trends across different lipids, temperatures, and ternary liquid-disordered phase mixtures produce results that are consistent with experimental diffusion constants. Application of the protocol to the liquid-ordered phase fails to yield a Newtonian plateau, suggesting more complex rheology.
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Affiliation(s)
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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18
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Marzuoli I, Margreitter C, Fraternali F. Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description. J Chem Theory Comput 2019; 15:5175-5193. [PMID: 31433640 PMCID: PMC7377650 DOI: 10.1021/acs.jctc.9b00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Membranes
are a crucial component of both bacterial and mammalian
cells, being involved in signaling, transport, and compartmentalization.
This versatility requires a variety of lipid species to tailor the
membrane’s behavior as needed, increasing the complexity of
the system. Molecular dynamics simulations have been successfully
applied to study model membranes and their interactions with proteins,
elucidating some crucial mechanisms at the atomistic detail and thus
complementing experimental techniques. An accurate description of
the functional interplay of the diverse membrane components crucially
depends on the selected parameters that define the adopted force field.
A coherent parameterization for lipids and proteins is therefore needed.
In this work, we propose and validate new lipid head group parameters
for the GROMOS 54A8 force field, making use of recently published
parametrizations for key chemical moieties present in lipids. We make
use additionally of a new canonical set of partial charges for lipids,
chosen to be consistent with the parameterization of soluble molecules
such as proteins. We test the derived parameters on five phosphocholine
model bilayers, composed of lipid patches four times larger than the
ones used in previous studies, and run 500 ns long simulations of
each system. Reproduction of experimental data like area per lipid
and deuterium order parameters is good and comparable with previous
parameterizations, as well as the description of liquid crystal to
gel-phase transition. On the other hand, the orientational behavior
of the head groups is more realistic for this new parameter set, and
this can be crucial in the description of interactions with other
polar molecules. For that reason, we tested the interaction of the
antimicrobial peptide lactoferricin with two model membranes showing
that the new parameters lead to a weaker peptide–membrane binding
and give a more realistic outcome in comparing binding to antimicrobial
versus mammal membranes.
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Affiliation(s)
- Irene Marzuoli
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Christian Margreitter
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
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19
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Abstract
Triclosan and chloroxylenol are broad-spectrum biocides used extensively in healthcare and consumer products. They have been suggested to perturb the structure of bacterial membranes, but studies so far have not considered that most bacterial membranes contain large amounts of branched-chain lipids. Here, molecular dynamics simulation is used to examine the effect of the two biocides on membranes consisting of lipids with methyl-branched chains, cyclopropanated chains, and nonbranched chains. It is shown that triclosan and chloroxylenol induced a phase transition in membranes from a liquid-crystalline to a liquid-ordered phase irrespective of the presence and nature of branching groups. At high concentration, chloroxylenol promoted chain interdigitation. Our results suggest that triclosan and chloroxylenol decrease the degree of fluidity of membranes and that this effect is more pronounced in bacterial membranes. As a result, their biocidal activity could be associated with a change in the function of membrane proteins.
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Affiliation(s)
- David Poger
- School of Chemistry & Molecular Biosciences , The University of Queensland , Brisbane QLD 4072 , Australia
| | - Alan E Mark
- School of Chemistry & Molecular Biosciences , The University of Queensland , Brisbane QLD 4072 , Australia
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20
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 422] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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21
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Structural and barrier properties of the skin ceramide lipid bilayer: a molecular dynamics simulation study. J Mol Model 2019; 25:140. [PMID: 31041534 DOI: 10.1007/s00894-019-4008-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/29/2019] [Indexed: 10/26/2022]
Abstract
Skin provides excellent protection against the harsh external environment and foreign substances. The lipid matrix of the stratum corneum, which contains various kinds of ceramides, plays a major role in the barrier function of the skin. Here we report a study of the effects of ceramide type on the structural and transport properties of ceramide bilayers using molecular dynamics (MD) simulations. Specifically, the effects of headgroup chemistry (number and positions of hydroxyl groups) and tail structure (unsaturation of the sphingoid moiety) on the structural and transport properties of various ceramide bilayers at 310 K were analyzed. Theoretical results for structural properties such as area per lipid, bilayer thickness, lateral arrangement, order parameter, and hydrogen bonding are reported here and compared with corresponding experimental data. Our study revealed that the presence of a double bond disrupts the bilayer packing, which leads to a low area compressibility modulus, a large area per lipid, and low bilayer thickness. Furthermore, the effect of structural changes on water permeation was studied using steered MD simulations. Water permeation was found to be influenced by headgroup polarity, chain packing, and the ability of the water to hydrogen bond with the ceramides. The molecular-level information obtained from the current study should aid the design of mixed bilayer systems with desired properties and provide the basis for the development of higher order coarse-grained models.
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22
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Gonçalves YMH, Senac C, Fuchs PFJ, Hünenberger PH, Horta BAC. Influence of the Treatment of Nonbonded Interactions on the Thermodynamic and Transport Properties of Pure Liquids Calculated Using the 2016H66 Force Field. J Chem Theory Comput 2019; 15:1806-1826. [DOI: 10.1021/acs.jctc.8b00425] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Yan M. H. Gonçalves
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Caroline Senac
- Sorbonne
Université,
CNRS, INSERM, Laboratoire d’Imagerie Biomédicale (LIB), F-75006 Paris, France
| | - Patrick F. J. Fuchs
- Sorbonne Université,
École normale supérieure, PSL University, CNRS, Laboratoire
des biomolécules, LBM, 75005 Paris, France
- Université
Paris Diderot, 75013 Paris, France
| | | | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
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23
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Arvayo-Zatarain JA, Favela-Rosales F, Contreras-Aburto C, Urrutia-Bañuelos E, Maldonado A. Molecular dynamics simulation study of the effect of halothane on mixed DPPC/DPPE phospholipid membranes. J Mol Model 2018; 25:4. [PMID: 30554281 DOI: 10.1007/s00894-018-3890-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 12/03/2018] [Indexed: 11/26/2022]
Abstract
We report results of a molecular dynamics simulation study of the effect of one general anesthetic, halothane, on some properties of mixed DPPC/DPPE phospholipid membranes. This is a suitable model for the study of simple, two-phospholipid membrane systems. From the simulation runs, we determined several membrane properties for five different molecular proportions of DPPC/DPPE. The effect of halothane on the studied membrane properties (area per lipid molecule, density of membrane, order parameter, etc.) was rather small. The distribution of halothane is not uniform through the bilayer thickness. Instead, there is a maximum of anesthetic concentration around 1.2 nm from the center of the membrane. The anesthetic molecule is located close to the phospholipid headgroups. The position of the halothane density maximum depends slightly on the DPPC/DPPE molar proportion. Snapshots taken over the plane of the membrane, as well as calculated two-dimensional radial distribution functions show that the anesthetic has no preference for either phospholipid (DPPC or DPPE). Our results indicate that this anesthetic molecule has only small effects on DPPC/DPPE mixed membranes. In addition, halothane displays no preferential location around DPPC or DPPE. This is probably due to the hydrophobic nature of halothane and to the fact that the chosen phospholipids have the same hydrophobic tails.
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Affiliation(s)
| | - Fernando Favela-Rosales
- Departamento de Investigación, Instituto Tecnológico Superior Zacatecas Occidente, Ave. Tecnológico 2000, 99102, Sombrerete, Zacatecas, Mexico
| | - Claudio Contreras-Aburto
- Facultad de Ciencias en Física y Matemáticas, Universidad Autónoma de Chiapas, Carretera Emiliano Zapata km 8, 29050, Tuxtla Gutiérrez, Chiapas, Mexico
| | - Efrain Urrutia-Bañuelos
- Departamento de Investigación en Física, Universidad de Sonora, Rosales y Luis Encinas s/n, 83000, Hermosillo, Sonora, Mexico
| | - Amir Maldonado
- Departamento de Física, Universidad de Sonora, Rosales y Luis Encinas s/n, 83000, Hermosillo, Sonora, Mexico.
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24
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Sidler D, Lehner M, Frasch S, Cristófol-Clough M, Riniker S. Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations. F1000Res 2018; 7:1745. [PMID: 30997032 PMCID: PMC6441880 DOI: 10.12688/f1000research.16715.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/24/2018] [Indexed: 10/07/2023] Open
Abstract
Background: Molecular dynamics (MD) simulations have become an important tool to provide insight into molecular processes involving biomolecules such as proteins, DNA, carbohydrates and membranes. As these processes cover a wide range of time scales, multiple time-step integration methods are often employed to increase the speed of MD simulations. For example, in the twin-range (TR) scheme, the nonbonded forces within the long-range cutoff are split into a short-range contribution updated every time step (inner time step) and a less frequently updated mid-range contribution (outer time step). The presence of different time steps can, however, cause numerical artefacts. Methods: The effects of multiple time-step algorithms at interfaces between polar and apolar media are investigated with MD simulations. Such interfaces occur with biological membranes or proteins in solution. Results: In this work, it is shown that the TR splitting of the nonbonded forces leads to artificial density increases at interfaces. The presence of the observed artefacts was found to be independent of the interface shape and the thermostatting method used. It is further shown that integration with an impulse-wise reversible reference system propagation algorithm (RESPA) only shifts the occurrence of density artefacts towards larger outer time steps. Using a single-range (SR) treatment of the nonbonded interactions, on the other hand, resolves the density issue for pairlist-update periods of up to 40 fs. Conclusion: A SR scheme avoids numerical artefacts and offers an interesting alternative to TR RESPA with respect to performance optimization.
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Affiliation(s)
- Dominik Sidler
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland
| | - Marc Lehner
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland
| | - Simon Frasch
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland
| | | | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland
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25
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Sidler D, Lehner M, Frasch S, Cristófol-Clough M, Riniker S. Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations. F1000Res 2018; 7:1745. [PMID: 30997032 PMCID: PMC6441880 DOI: 10.12688/f1000research.16715.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/04/2019] [Indexed: 11/20/2022] Open
Abstract
Background: Molecular dynamics (MD) simulations have become an important tool to provide insight into molecular processes involving biomolecules such as proteins, DNA, carbohydrates and membranes. As these processes cover a wide range of time scales, multiple time-step integration methods are often employed to increase the speed of MD simulations. For example, in the twin-range (TR) scheme, the nonbonded forces within the long-range cutoff are split into a short-range contribution updated every time step (inner time step) and a less frequently updated mid-range contribution (outer time step). The presence of different time steps can, however, cause numerical artefacts. Methods: The effects of multiple time-step algorithms at interfaces between polar and apolar media are investigated with MD simulations. Such interfaces occur with biological membranes or proteins in solution. Results: In this work, it is shown that the TR splitting of the nonbonded forces leads to artificial density increases at interfaces for weak coupling and Nosé-Hoover (chain) thermostats. It is further shown that integration with an impulse-wise reversible reference system propagation algorithm (RESPA) only shifts the occurrence of density artefacts towards larger outer time steps. Using a single-range (SR) treatment of the nonbonded interactions or a stochastic dynamics thermostat, on the other hand, resolves the density issue for pairlist-update periods of up to 40 fs. Conclusion: TR schemes are not advisable to use in combination with weak coupling or Nosé-Hoover (chain) thermostats due to the occurrence of significant numerical artifacts at interfaces.
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Affiliation(s)
- Dominik Sidler
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland
| | - Marc Lehner
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland
| | - Simon Frasch
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland
| | | | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland
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26
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Sidler D, Lehner M, Frasch S, Cristófol-Clough M, Riniker S. Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations. F1000Res 2018; 7:1745. [PMID: 30997032 PMCID: PMC6441880 DOI: 10.12688/f1000research.16715.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2019] [Indexed: 10/07/2023] Open
Abstract
Background: Molecular dynamics (MD) simulations have become an important tool to provide insight into molecular processes involving biomolecules such as proteins, DNA, carbohydrates and membranes. As these processes cover a wide range of time scales, multiple time-step integration methods are often employed to increase the speed of MD simulations. For example, in the twin-range (TR) scheme, the nonbonded forces within the long-range cutoff are split into a short-range contribution updated every time step (inner time step) and a less frequently updated mid-range contribution (outer time step). The presence of different time steps can, however, cause numerical artefacts. Methods: The effects of multiple time-step algorithms at interfaces between polar and apolar media are investigated with MD simulations. Such interfaces occur with biological membranes or proteins in solution. Results: In this work, it is shown that the TR splitting of the nonbonded forces leads to artificial density increases at interfaces for weak coupling and Nosé-Hoover (chain) thermostats. It is further shown that integration with an impulse-wise reversible reference system propagation algorithm (RESPA) only shifts the occurrence of density artefacts towards larger outer time steps. Using a single-range (SR) treatment of the nonbonded interactions or a stochastic dynamics thermostat, on the other hand, resolves the density issue for pairlist-update periods of up to 40 fs. Conclusion: TR schemes are not advisable to use in combination with weak coupling or Nosé-Hoover (chain) thermostats due to the occurrence of significant numerical artifacts at interfaces.
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Affiliation(s)
- Dominik Sidler
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland
| | - Marc Lehner
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland
| | - Simon Frasch
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland
| | | | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, 8093, Switzerland
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27
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Silva TFD, Vila-Viçosa D, Reis PBPS, Victor BL, Diem M, Oostenbrink C, Machuqueiro M. The Impact of Using Single Atomistic Long-Range Cutoff Schemes with the GROMOS 54A7 Force Field. J Chem Theory Comput 2018; 14:5823-5833. [DOI: 10.1021/acs.jctc.8b00758] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Tomás F. D. Silva
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Pedro B. P. S. Reis
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Bruno L. Victor
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Matthias Diem
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
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28
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Fasano M, Crisafulli A, Cardellini A, Bergamasco L, Chiavazzo E, Asinari P. Thermally triggered nanorocket from double-walled carbon nanotube in water. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1535180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Matteo Fasano
- Department of Energy, Politecnico di Torino, Torino, Italy
| | | | | | | | | | - Pietro Asinari
- Department of Energy, Politecnico di Torino, Torino, Italy
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29
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Allolio C, Haluts A, Harries D. A local instantaneous surface method for extracting membrane elastic moduli from simulation: Comparison with other strategies. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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30
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Parra-Cruz R, Jäger CM, Lau PL, Gomes RL, Pordea A. Rational Design of Thermostable Carbonic Anhydrase Mutants Using Molecular Dynamics Simulations. J Phys Chem B 2018; 122:8526-8536. [PMID: 30114369 DOI: 10.1021/acs.jpcb.8b05926] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The stability of enzymes is critical for their application in industrial processes, which generally require different conditions from the natural enzyme environment. Both rational and random protein engineering approaches have been used to increase stability, with the latter requiring extensive experimental effort for the screening of variants. Moreover, some general rules addressing the molecular origin of protein thermostability have been established. Herein, we demonstrate the use of molecular dynamics simulations to gain molecular level understanding of protein thermostability and to engineer stabilizing mutations. Carbonic anhydrase (CA) is an enzyme with a high potential for biotechnological carbon capture applications, provided it can be engineered to withstand the high temperature process environments, inevitable in most gas treatment units. In this study, we used molecular dynamics simulations at 343, 353, and 363 K to study the relationship between structure flexibility and thermostability in bacterial α-CAs and applied this knowledge to the design of mutants with increased stability. The most thermostable α-CA known, TaCA from Thermovibrio ammonificans, had the most rigid structure during molecular dynamics simulations, but also showed regions with high flexibility. The most flexible amino acids in these regions were identified from root mean square fluctuation (RMSF) studies, and stabilizing point mutations were predicted based on their capacity to improve the calculated free energy of unfolding. Disulfide bonds were also designed at sites with suitable geometries and selected based on their location at flexible sites, assessed by B-factor calculation. Molecular dynamics simulations allowed the identification of five mutants with lower RMSF of the overall structure at 400 K, compared to wild-type TaCA. Comparison of free-energy landscapes between wild-type TaCA and the most promising mutants, Pro165Cys-Gln170Cys and Asn140Gly, showed an increased conformational stability of the mutants at 400 K.
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Affiliation(s)
- Ricardo Parra-Cruz
- Department of Chemical and Environmental Engineering , University of Nottingham Malaysia Campus , Semenyih 43500 , Malaysia
| | - Christof M Jäger
- Faculty of Engineering , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Phei Li Lau
- Department of Chemical and Environmental Engineering , University of Nottingham Malaysia Campus , Semenyih 43500 , Malaysia
| | - Rachel L Gomes
- Faculty of Engineering , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Anca Pordea
- Faculty of Engineering , University of Nottingham , Nottingham NG7 2RD , U.K
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31
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Hinsen K. Verifiability in computer-aided research: the role of digital scientific notations at the human-computer interface. PeerJ Comput Sci 2018; 4:e158. [PMID: 33816811 PMCID: PMC7924627 DOI: 10.7717/peerj-cs.158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/21/2018] [Indexed: 06/12/2023]
Abstract
Most of today's scientific research relies on computers and software for processing scientific information. Examples of such computer-aided research are the analysis of experimental data or the simulation of phenomena based on theoretical models. With the rapid increase of computational power, scientific software has integrated more and more complex scientific knowledge in a black-box fashion. As a consequence, its users do not know, and do not even have a chance of finding out, which assumptions and approximations their computations are based on. This black-box nature of scientific software has made the verification of much computer-aided research close to impossible. The present work starts with an analysis of this situation from the point of view of human-computer interaction in scientific research. It identifies the key role of digital scientific notations at the human-computer interface, reviews the most popular ones in use today, and describes a proof-of-concept implementation of Leibniz, a language designed as a verifiable digital scientific notation for models formulated as mathematical equations.
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Affiliation(s)
- Konrad Hinsen
- Centre de Biophysique Moléculaire (UPR4301), CNRS, Orléans, France
- Division Expériences, Synchrotron SOLEIL, Saint Aubin, France
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32
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Jung J, Kobayashi C, Sugita Y. Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation. J Chem Phys 2018; 148:164109. [DOI: 10.1063/1.5008438] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jaewoon Jung
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 640-0047, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 640-0047, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 640-0047, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Domański J, Sansom MSP, Stansfeld PJ, Best RB. Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association. J Chem Theory Comput 2018; 14:1706-1715. [PMID: 29424543 PMCID: PMC5852462 DOI: 10.1021/acs.jctc.7b00983] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Indexed: 01/21/2023]
Abstract
Atomistic simulations have recently been shown to be sufficiently accurate to reversibly fold globular proteins and have provided insights into folding mechanisms. Gaining similar understanding from simulations of membrane protein folding and association would be of great medical interest. All-atom simulations of the folding and assembly of transmembrane protein domains are much more challenging, not least due to very slow diffusion within the lipid bilayer membrane. Here, we focus on a simple and well-characterized prototype of membrane protein folding and assembly, namely the dimerization of glycophorin A, a homodimer of single transmembrane helices. We have determined the free energy landscape for association of the dimer using the CHARMM36 force field. We find that the native structure is a metastable state, but not stable as expected from experimental estimates of the dissociation constant and numerous experimental structures obtained under a variety of conditions. We explore two straightforward approaches to address this problem and demonstrate that they result in stable dimers with dissociation constants consistent with experimental data.
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Affiliation(s)
- Jan Domański
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Phillip J. Stansfeld
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Robert B. Best
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
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Hayatshahi HS, Henriksen NM, Cheatham TE. Consensus Conformations of Dinucleoside Monophosphates Described with Well-Converged Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:1456-1470. [PMID: 29323894 DOI: 10.1021/acs.jctc.7b00581] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dinucleoside monophosphates (DNMPs) have been described using various experimental approaches as flexible molecules which generate ensembles populating at least a small set of different conformations in solution. However, due to limitations of each approach in its ability to delineate the ensemble of conformations, an accurate and quantitative description of certain conformational features has not been performed for all DNMPs. Here, we apply a temperature replica-exchange molecular dynamics approach to fully and quickly converge conformational distributions of all RNA DNMPs immersed in the TIP3P water model using the AMBER ff14 force field. For a selection of DNMPs, the conformational ensembles were also generated when immersed in the OPC water model using alternative AMBER and CHARMM force fields. The OPC water model and other force field choices did not introduce new conformational classes but shifted the populations among existing conformations. Except for pyrimidine-pyrimidine dinucleosides, all other DNMPs populated four major conformations (which are defined in the main text and labeled A-form, Ladder, Inverted, and Sheared), in addition to an Extended form. Pyrimidine-pyrimidines did not generate the Sheared conformation. Distinguishing features and stabilizing factors of each conformation were identified and assessed based on the known experimental interpretations. The configuration of the glycosidic bond and the nonbonding interactions of hydrogen bond acceptors with the 2'-hydroxyl group were found to play determining roles in stabilizing particular conformations which could serve as a guide for potential force field modifications to improve the accuracy. Additionally, we computed stacking free energies based on the DNMP conformational distributions and found significant discrepancies with a previous study. Our investigation determined that the AMBER force field was incorrectly implemented in the previous study. In the future, this simulation approach can be used to quickly analyze the effects of new force field modifications in shifting the conformational populations of DNMPs, and can can be further applied to foresee such effects in larger RNA motifs including tetranucleotides and tetraloops.
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Affiliation(s)
- Hamed S Hayatshahi
- Department of Medicinal Chemistry, College of Pharmacy, L. S. Skaggs Pharmacy Research Institute , University of Utah , Salt Lake City , Utah 84112-5820 , United States
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California at San Diego , 9500 Gilman Drive , MC 0736, La Jolla , California 92093 , United States
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, L. S. Skaggs Pharmacy Research Institute , University of Utah , Salt Lake City , Utah 84112-5820 , United States
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Gebhardt J, Kleist C, Jakobtorweihen S, Hansen N. Validation and Comparison of Force Fields for Native Cyclodextrins in Aqueous Solution. J Phys Chem B 2018; 122:1608-1626. [PMID: 29287148 DOI: 10.1021/acs.jpcb.7b11808] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular dynamics simulations of native α-, β-, and γ-cyclodextrin in aqueous solution have been conducted with the goal to investigate the performance of the CHARMM36 force field, the AMBER-compatible q4md-CD force field, and five variants of the GROMOS force field. The properties analyzed are structural parameters derived from X-ray diffraction and NMR experiments as well as hydrogen bonds and hydration patterns, including hydration free enthalpies. Recent revisions of the torsional-angle parameters for carbohydrate systems within the GROMOS family of force fields lead to a significant improvement of the agreement between simulated and experimental NMR data. Therefore, we recommend using the variant 53A6GLYC instead of 53A6 and 56A6CARBO_R or 2016H66 instead of 56A6CARBO to simulate cyclodextrins in solution. The CHARMM36 and q4md-CD force fields show a similar performance as the three recommended GROMOS parameter sets. A significant difference is the more flexible nature of the cyclodextrins modeled with the CHARMM36 and q4md-CD force fields compared to the three recommended GROMOS parameter sets.
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Affiliation(s)
- Julia Gebhardt
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart , D-70569 Stuttgart, Germany
| | - Catharina Kleist
- Institute of Thermal Separation Processes, Hamburg University of Technology , D-21073 Hamburg, Germany
| | - Sven Jakobtorweihen
- Institute of Thermal Separation Processes, Hamburg University of Technology , D-21073 Hamburg, Germany
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart , D-70569 Stuttgart, Germany
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Deplazes E, Poger D, Cornell B, Cranfield CG. The effect of hydronium ions on the structure of phospholipid membranes. Phys Chem Chem Phys 2018; 20:357-366. [DOI: 10.1039/c7cp06776c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This work studies the mechanisms by which hydronium ions modulate the structure of phospholipid bilayers.
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Affiliation(s)
- Evelyne Deplazes
- School of Biomedical Sciences
- Curtin Health Innovation Research Institute and Curtin Institute for Computation
- Curtin University
- Perth
- Australia
| | - David Poger
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
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