1
|
Antila HS, M. Ferreira T, Ollila OHS, Miettinen MS. Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics. J Chem Inf Model 2021; 61:938-949. [PMID: 33496579 PMCID: PMC7903423 DOI: 10.1021/acs.jcim.0c01299] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Indexed: 01/08/2023]
Abstract
Molecular dynamics (MD) simulations are widely used to monitor time-resolved motions of biomacromolecules, although it often remains unknown how closely the conformational dynamics correspond to those occurring in real life. Here, we used a large set of open-access MD trajectories of phosphatidylcholine (PC) lipid bilayers to benchmark the conformational dynamics in several contemporary MD models (force fields) against nuclear magnetic resonance (NMR) data available in the literature: effective correlation times and spin-lattice relaxation rates. We found none of the tested MD models to fully reproduce the conformational dynamics. That said, the dynamics in CHARMM36 and Slipids are more realistic than in the Amber Lipid14, OPLS-based MacRog, and GROMOS-based Berger force fields, whose sampling of the glycerol backbone conformations is too slow. The performance of CHARMM36 persists when cholesterol is added to the bilayer, and when the hydration level is reduced. However, for conformational dynamics of the PC headgroup, both with and without cholesterol, Slipids provides the most realistic description because CHARMM36 overestimates the relative weight of ∼1 ns processes in the headgroup dynamics. We stress that not a single new simulation was run for the present work. This demonstrates the worth of open-access MD trajectory databanks for the indispensable step of any serious MD study: benchmarking the available force fields. We believe this proof of principle will inspire other novel applications of MD trajectory databanks and thus aid in developing biomolecular MD simulations into a true computational microscope-not only for lipid membranes but for all biomacromolecular systems.
Collapse
Affiliation(s)
- Hanne S. Antila
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Tiago M. Ferreira
- NMR
Group−Institute for Physics, Martin-Luther
University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | | | - Markus S. Miettinen
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| |
Collapse
|
2
|
Combining NMR Spectroscopy and Molecular Dynamics Simulation to Investigate the Structure and Dynamics of Membrane-Associated Proteins. SPRINGER SERIES IN BIOPHYSICS 2017. [DOI: 10.1007/978-3-319-66601-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
3
|
Buslaev P, Gordeliy V, Grudinin S, Gushchin I. Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations. J Chem Theory Comput 2016; 12:1019-28. [PMID: 26765212 DOI: 10.1021/acs.jctc.5b01106] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations of lipid bilayers are ubiquitous nowadays. Usually, either global properties of the bilayer or some particular characteristics of each lipid molecule are evaluated in such simulations, but the structural properties of the molecules as a whole are rarely studied. Here, we show how a comprehensive quantitative description of conformational space and dynamics of a single lipid molecule can be achieved via the principal component analysis (PCA). We illustrate the approach by analyzing and comparing simulations of DOPC bilayers obtained using eight different force fields: all-atom generalized AMBER, CHARMM27, CHARMM36, Lipid14, and Slipids and united-atom Berger, GROMOS43A1-S3, and GROMOS54A7. Similarly to proteins, most of the structural variance of a lipid molecule can be described by only a few principal components. These major components are similar in different simulations, although there are notable distinctions between the older and newer force fields and between the all-atom and united-atom force fields. The DOPC molecules in the simulations generally equilibrate on the time scales of tens to hundreds of nanoseconds. The equilibration is the slowest in the GAFF simulation and the fastest in the Slipids simulation. Somewhat unexpectedly, the equilibration in the united-atom force fields is generally slower than in the all-atom force fields. Overall, there is a clear separation between the more variable previous generation force fields and significantly more similar new generation force fields (CHARMM36, Lipid14, Slipids). We expect that the presented approaches will be useful for quantitative analysis of conformations and dynamics of individual lipid molecules in other simulations of lipid bilayers.
Collapse
Affiliation(s)
- Pavel Buslaev
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS , F-38000 Grenoble, France.,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich , 52425 Jülich, Germany
| | - Sergei Grudinin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.,Université Grenoble Alpes, LJK, F-38000 Grenoble, France.,CNRS, LJK, F-38000 Grenoble, France.,Inria, F-38000 Grenoble, France
| | - Ivan Gushchin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich , 52425 Jülich, Germany
| |
Collapse
|
4
|
Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2512-2528. [PMID: 26809025 DOI: 10.1016/j.bbamem.2016.01.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/15/2016] [Accepted: 01/19/2016] [Indexed: 01/18/2023]
Abstract
Accurate details on the sampled atomistic resolution structures of lipid bilayers can be experimentally obtained by measuring C-H bond order parameters, spin relaxation rates and scattering form factors. These parameters can be also directly calculated from the classical atomistic resolution molecular dynamics simulations (MD) and compared to the experimentally achieved results. This comparison measures the simulation model quality with respect to 'reality'. If agreement is sufficient, the simulation model gives an atomistic structural interpretation of the acquired experimental data. Significant advance of MD models is made by jointly interpreting different experiments using the same structural model. Here we focus on phosphatidylcholine lipid bilayers, which out of all model membranes have been studied mostly by experiments and simulations, leading to the largest available dataset. From the applied comparisons we conclude that the acyl chain region structure and rotational dynamics are generally well described in simulation models. Also changes with temperature, dehydration and cholesterol concentration are qualitatively correctly reproduced. However, the quality of the underlying atomistic resolution structural changes is uncertain. Even worse, when focusing on the lipid bilayer properties at the interfacial region, e.g. glycerol backbone and choline structures, and cation binding, many simulation models produce an inaccurate description of experimental data. Thus extreme care must be applied when simulations are applied to understand phenomena where the interfacial region plays a significant role. This work is done by the NMRlipids Open Collaboration project running at https://nmrlipids.blogspot.fi and https://github.com/NMRLipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
Collapse
|
5
|
Lyubartsev AP, Rabinovich AL. Force Field Development for Lipid Membrane Simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2483-2497. [PMID: 26766518 DOI: 10.1016/j.bbamem.2015.12.033] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 02/04/2023]
Abstract
With the rapid development of computer power and wide availability of modelling software computer simulations of realistic models of lipid membranes, including their interactions with various molecular species, polypeptides and membrane proteins have become feasible for many research groups. The crucial issue of the reliability of such simulations is the quality of the force field, and many efforts, especially in the latest several years, have been devoted to parametrization and optimization of the force fields for biomembrane modelling. In this review, we give account of the recent development in this area, covering different classes of force fields, principles of the force field parametrization, comparison of the force fields, and their experimental validation. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
Collapse
Affiliation(s)
- Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, SE 106 91, Stockholm, Sweden.
| | - Alexander L Rabinovich
- Institute of Biology, Karelian Research Center, Russian Academy of Sciences, Pushkinskaya 11, Petrozavodsk, 185910, Russian Federation.
| |
Collapse
|
6
|
Botan A, Favela-Rosales F, Fuchs PFJ, Javanainen M, Kanduč M, Kulig W, Lamberg A, Loison C, Lyubartsev A, Miettinen MS, Monticelli L, Määttä J, Ollila OHS, Retegan M, Róg T, Santuz H, Tynkkynen J. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions. J Phys Chem B 2015; 119:15075-88. [PMID: 26509669 PMCID: PMC4677354 DOI: 10.1021/acs.jpcb.5b04878] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 10/19/2015] [Indexed: 11/28/2022]
Abstract
Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files ( https://zenodo.org/collection/user-nmrlipids ) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.
Collapse
Affiliation(s)
- Alexandru Botan
- Institut
Lumière Matière, UMR5306 Université
Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France
| | - Fernando Favela-Rosales
- Departamento
de Física, Centro de Investigación
y de Estudios Avanzados del IPN, Apartado, Postal 14-740, Mexico City, 07000 México
D.F., México
| | - Patrick F. J. Fuchs
- Institut
Jacques Monod, UMR 7592 CNRS, Université Paris
Diderot, Sorbonne, Paris Cité, F-75205 Paris, France
| | - Matti Javanainen
- Department
of Physics, Tampere University of Technology, Tampere, 33101 Finland
| | - Matej Kanduč
- Fachbereich
Physik, Freie Universität Berlin, Berlin, 14195 Germany
| | - Waldemar Kulig
- Department
of Physics, Tampere University of Technology, Tampere, 33101 Finland
| | - Antti Lamberg
- Department
of Chemical Engineering, Kyoto University, 615-8510 Kyoto, Japan
| | - Claire Loison
- Institut
Lumière Matière, UMR5306 Université
Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France
| | - Alexander Lyubartsev
- Division
of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, S-106 91 Stockholm, Sweden
| | | | - Luca Monticelli
- Institut
de Biologie et Chimie des Protéines (IBCP), CNRS UMR 5086, Lyon 69 367, France
| | - Jukka Määttä
- Department of Chemistry, Aalto University, 00076 Aalto, Finland
| | - O. H. Samuli Ollila
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Marius Retegan
- Max Planck Institute
for Chemical Energy Conversion, Stiftstr. 34-38, 45470 Mülheim an der Ruhr, Germany
| | - Tomasz Róg
- Department
of Physics, Tampere University of Technology, Tampere, 33101 Finland
| | - Hubert Santuz
- INSERM, UMR_S 1134, DSIMB, Paris 75739, France
- Université
Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France
- Institut
National de la Transfusion Sanguine (INTS), Paris 75739, France
- Laboratoire d’Excellence GR-Ex, Paris 75015, France
| | - Joona Tynkkynen
- Department
of Physics, Tampere University of Technology, Tampere, 33101 Finland
| |
Collapse
|
7
|
Ferreira TM, Ollila OHS, Pigliapochi R, Dabkowska AP, Topgaard D. Model-free estimation of the effective correlation time for C-H bond reorientation in amphiphilic bilayers: (1)H-(13)C solid-state NMR and MD simulations. J Chem Phys 2015; 142:044905. [PMID: 25638007 DOI: 10.1063/1.4906274] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics (MD) simulations give atomically detailed information on structure and dynamics in amphiphilic bilayer systems on timescales up to about 1 μs. The reorientational dynamics of the C-H bonds is conventionally verified by measurements of (13)C or (2)H nuclear magnetic resonance (NMR) longitudinal relaxation rates R1, which are more sensitive to motional processes with correlation times close to the inverse Larmor frequency, typically around 1-10 ns on standard NMR instrumentation, and are thus less sensitive to the 10-1000 ns timescale motion that can be observed in the MD simulations. We propose an experimental procedure for atomically resolved model-free estimation of the C-H bond effective reorientational correlation time τe, which includes contributions from the entire range of all-atom MD timescales and that can be calculated directly from the MD trajectories. The approach is based on measurements of (13)C R1 and R1ρ relaxation rates, as well as (1)H-(13)C dipolar couplings, and is applicable to anisotropic liquid crystalline lipid or surfactant systems using a conventional solid-state NMR spectrometer and samples with natural isotopic composition. The procedure is demonstrated on a fully hydrated lamellar phase of 1-palmitoyl-2-oleoyl-phosphatidylcholine, yielding values of τe from 0.1 ns for the methyl groups in the choline moiety and at the end of the acyl chains to 3 ns for the g1 methylene group of the glycerol backbone. MD simulations performed with a widely used united-atom force-field reproduce the τe-profile of the major part of the acyl chains but underestimate the dynamics of the glycerol backbone and adjacent molecular segments. The measurement of experimental τe-profiles can be used to study subtle effects on C-H bond reorientational motions in anisotropic liquid crystals, as well as to validate the C-H bond reorientation dynamics predicted in MD simulations of amphiphilic bilayers such as lipid membranes.
Collapse
Affiliation(s)
- Tiago Mendes Ferreira
- Department Chemie, Universität Paderborn, Warburger Straße 100, 33098 Paderborn, Germany
| | - O H Samuli Ollila
- Physical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | | | | | - Daniel Topgaard
- Physical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
8
|
Rabinovich AL, Lyubartsev AP. Computer simulation of lipid membranes: Methodology and achievements. POLYMER SCIENCE SERIES C 2013. [DOI: 10.1134/s1811238213070060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
9
|
Abstract
One of the many aspects of membrane biophysics dealt with in this Faraday Discussion regards the material moduli that describe energies at a supramolecular level. This introductory lecture first critically reviews differences in reported numerical values of the bending modulus K(C), which is a central property for the biologically important flexibility of membranes. It is speculated that there may be a reason that the shape analysis method tends to give larger values of K(C) than the micromechanical manipulation method or the more recent X-ray method that agree very well with each other. Another theme of membrane biophysics is the use of simulations to provide exquisite detail of structures and processes. This lecture critically reviews the application of atomic level simulations to the quantitative structure of simple single component lipid bilayers and diagnostics are introduced to evaluate simulations. Another theme of this Faraday Discussion was lateral heterogeneity in biomembranes with many different lipids. Coarse grained simulations and analytical theories promise to synergistically enhance experimental studies when their interaction parameters are tuned to agree with experimental data, such as the slopes of experimental tie lines in ternary phase diagrams. Finally, attention is called to contributions that add relevant biological molecules to bilayers and to contributions that study the exciting shape changes and different non-bilayer structures with different lipids.
Collapse
Affiliation(s)
- John F Nagle
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| |
Collapse
|