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Lebedenko OO, Salikov VA, Izmailov SA, Podkorytov IS, Skrynnikov NR. Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4. Biophys J 2024; 123:80-100. [PMID: 37990496 PMCID: PMC10808029 DOI: 10.1016/j.bpj.2023.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/28/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
MD simulations can provide uniquely detailed models of intrinsically disordered proteins (IDPs). However, these models need careful experimental validation. The coefficient of translational diffusion Dtr, measurable by pulsed field gradient NMR, offers a potentially useful piece of experimental information related to the compactness of the IDP's conformational ensemble. Here, we investigate, both experimentally and via the MD modeling, the translational diffusion of a 25-residue N-terminal fragment from histone H4 (N-H4). We found that the predicted values of Dtr, as obtained from mean-square displacement of the peptide in the MD simulations, are largely determined by the viscosity of the MD water (which has been reinvestigated as a part of our study). Beyond that, our analysis of the diffusion data indicates that MD simulations of N-H4 in the TIP4P-Ew water give rise to an overly compact conformational ensemble for this peptide. In contrast, TIP4P-D and OPC simulations produce the ensembles that are consistent with the experimental Dtr result. These observations are supported by the analyses of the 15N spin relaxation rates. We also tested a number of empirical methods to predict Dtr based on IDP's coordinates extracted from the MD snapshots. In particular, we show that the popular approach involving the program HYDROPRO can produce misleading results. This happens because HYDROPRO is not intended to predict the diffusion properties of highly flexible biopolymers such as IDPs. Likewise, recent empirical schemes that exploit the relationship between the small-angle x-ray scattering-informed conformational ensembles of IDPs and the respective experimental Dtr values also prove to be problematic. In this sense, the first-principle calculations of Dtr from the MD simulations, such as demonstrated in this work, should provide a useful benchmark for future efforts in this area.
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Affiliation(s)
- Olga O Lebedenko
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Vladislav A Salikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Sergei A Izmailov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Ivan S Podkorytov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia; Department of Chemistry, Purdue University, West Lafayette, Indiana.
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Kim YL, Gordon MS, Garcia A, Evans JW. Rotational and translational diffusion of liquid n-hexane: EFP-based molecular dynamics analysis. J Chem Phys 2022; 156:114503. [DOI: 10.1063/5.0079212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular Dynamics (MD) simulations based on the Effective Fragment Potential (EFP) method are utilized to provide a comprehensive assessment of diffusion in liquid n-hexane. We decompose translational diffusion into components along and orthogonal to the long axis of the molecule. Rotational diffusion is decomposed into tumbling and spinning motions about this axis. Our analysis yields four corresponding diffusion coefficients which are related to diagonal entries in the complete 6 × 6 diffusion tensor accounting for the three rotational and three translational degrees of freedom and for the potential coupling between them. However, coupling between different degrees of freedom is expected to be minimal for a natural choice of the molecular body-fixed axis, so then off-diagonal entries in the tensor are negligible. This expectation is supported by a hydrodynamic analysis of the diffusion tensor which treats the liquid surrounding the molecule being tracked as a viscous continuum. Thus, the EFP MD analysis provides a comprehensive characterization of diffusion and also reveals expected shortcomings of the hydrodynamic treatment, particularly for rotational diffusion, when applied to neat liquids.
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Affiliation(s)
- Yu Lim Kim
- Ames Laboratory – U.S. Department of Energy, Iowa State University, Ames, Iowa 50011, USA
- Department of Chemistry, Iowa State University, Ames, Iowa 50010, USA
| | - Mark S. Gordon
- Ames Laboratory – U.S. Department of Energy, Iowa State University, Ames, Iowa 50011, USA
- Department of Chemistry, Iowa State University, Ames, Iowa 50010, USA
| | - Andres Garcia
- Ames Laboratory – U.S. Department of Energy, Iowa State University, Ames, Iowa 50011, USA
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50010, USA
| | - James W. Evans
- Ames Laboratory – U.S. Department of Energy, Iowa State University, Ames, Iowa 50011, USA
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50010, USA
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Kim YL, Han Y, Evans JW, Gordon MS. Effective Fragment Potential-Based Molecular Dynamics Studies of Diffusion in Acetone and Hexane. J Phys Chem A 2021; 125:3398-3405. [PMID: 33861600 DOI: 10.1021/acs.jpca.1c01865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To facilitate more reliable descriptions of transport properties in liquids, molecular dynamics (MD) simulations are performed based on the effective fragment potential (EFP) method derived from first-principles quantum mechanics (in contrast to MD based upon empirically fitted potentials). The EFP method describes molecular interactions in terms of Coulomb, polarization/induction, dispersion, exchange-repulsion, and charge-transfer interactions. The EFP MD simulations described in this paper, performed on hexane and acetone, are able to track the mean-square displacement of molecules for sufficient time to reliably extract translational diffusion coefficients. The results reported here are in reasonable agreement with experiment.
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Affiliation(s)
- Yu Lim Kim
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa 50011, United States.,Department of Chemistry, Iowa State University, Ames, Iowa 50010, United States
| | - Yong Han
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa 50011, United States.,Department of Physics & Astronomy, Iowa State University, Ames, Iowa 50010, United States
| | - James W Evans
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa 50011, United States.,Department of Physics & Astronomy, Iowa State University, Ames, Iowa 50010, United States
| | - Mark S Gordon
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa 50011, United States.,Department of Chemistry, Iowa State University, Ames, Iowa 50010, United States
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Liu H, Cavaliere S, Jones DJ, Rozière J, Paddison SJ. Scaling Behavior of Nafion with Different Model Parameterizations in Dissipative Particle Dynamics Simulations. MACROMOL THEOR SIMUL 2018. [DOI: 10.1002/mats.201800003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hongjun Liu
- Department of Chemical and Biomolecular Engineering; University of Tennessee; Knoxville TN 37996 USA
| | - Sara Cavaliere
- Institut Charles Gerhardt de Montpellier; Agrégats; Interfaces et Matériaux pour l'Energie; UMR 5253 CNRS; Université de Montpellier; 34095 Montpellier Cedex 5 France
| | - Deborah J. Jones
- Institut Charles Gerhardt de Montpellier; Agrégats; Interfaces et Matériaux pour l'Energie; UMR 5253 CNRS; Université de Montpellier; 34095 Montpellier Cedex 5 France
| | - Jacques Rozière
- Institut Charles Gerhardt de Montpellier; Agrégats; Interfaces et Matériaux pour l'Energie; UMR 5253 CNRS; Université de Montpellier; 34095 Montpellier Cedex 5 France
| | - Stephen J. Paddison
- Department of Chemical and Biomolecular Engineering; University of Tennessee; Knoxville TN 37996 USA
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Ewen JP, Gattinoni C, Thakkar FM, Morgan N, Spikes HA, Dini D. A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants. MATERIALS 2016; 9:ma9080651. [PMID: 28773773 PMCID: PMC5509262 DOI: 10.3390/ma9080651] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/20/2016] [Accepted: 07/28/2016] [Indexed: 01/26/2023]
Abstract
For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed.
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Affiliation(s)
- James P Ewen
- Department of Mechanical Engineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK.
| | - Chiara Gattinoni
- Department of Mechanical Engineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK.
| | - Foram M Thakkar
- Shell India Markets Private Limited, 8B RMZ Centennial Building, Kundanahalli Main Road, Bangalore 560048, India.
| | - Neal Morgan
- Shell Global Solutions UK Ltd., Brabazon House, Manchester M22 0RR, UK.
| | - Hugh A Spikes
- Department of Mechanical Engineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK.
| | - Daniele Dini
- Department of Mechanical Engineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK.
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Posel Z, Rousseau B, Lísal M. Scaling behaviour of different polymer models in dissipative particle dynamics of unentangled melts. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.869803] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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