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Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
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Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
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2
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Moqadam M, Tubiana T, Moutoussamy EE, Reuter N. Membrane models for molecular simulations of peripheral membrane proteins. ADVANCES IN PHYSICS: X 2021. [DOI: 10.1080/23746149.2021.1932589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Mahmoud Moqadam
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Thibault Tubiana
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Emmanuel E. Moutoussamy
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
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Loschwitz J, Olubiyi OO, Hub JS, Strodel B, Poojari CS. Computer simulations of protein-membrane systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:273-403. [PMID: 32145948 PMCID: PMC7109768 DOI: 10.1016/bs.pmbts.2020.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The interactions between proteins and membranes play critical roles in signal transduction, cell motility, and transport, and they are involved in many types of diseases. Molecular dynamics (MD) simulations have greatly contributed to our understanding of protein-membrane interactions, promoted by a dramatic development of MD-related software, increasingly accurate force fields, and available computer power. In this chapter, we present available methods for studying protein-membrane systems with MD simulations, including an overview about the various all-atom and coarse-grained force fields for lipids, and useful software for membrane simulation setup and analysis. A large set of case studies is discussed.
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Affiliation(s)
- Jennifer Loschwitz
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Olujide O Olubiyi
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Birgit Strodel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Chetan S Poojari
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany.
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4
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Leonard AN, Wang E, Monje-Galvan V, Klauda JB. Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chem Rev 2019; 119:6227-6269. [DOI: 10.1021/acs.chemrev.8b00384] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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5
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Klauda JB. Perspective: Computational modeling of accurate cellular membranes with molecular resolution. J Chem Phys 2018; 149:220901. [DOI: 10.1063/1.5055007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, USA
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6
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Zhao Y, Chen H, Yin L, Cheng X, Zhang W, Zhu X. Chirality induction of achiral polydialkylfluorenes by chiral solvation: odd–even and side chain length dependence. Polym Chem 2018. [DOI: 10.1039/c8py00114f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An “odd–even” effect for the chiral β-phase of polydialkylfluorene/limonene aggregates was first observed, depending on the odd–even alkyl side chain length.
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Affiliation(s)
- Yin Zhao
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Hailing Chen
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Lu Yin
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Xiaoxiao Cheng
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Wei Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Xiulin Zhu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- College of Chemistry
- Chemical Engineering and Materials Science
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7
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Kirschner KN, Heiden W, Reith D. Relative electronic and free energies of octane's unique conformations. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1262076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Karl N. Kirschner
- Department of Computer Science, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
- Institute of Visual Computing, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Wolfgang Heiden
- Department of Computer Science, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
- Institute of Visual Computing, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Dirk Reith
- Institute of Visual Computing, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
- Department of Electrical Engineering, Mechanical Engineering and Technical Journalism, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
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8
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Mayne CG, Arcario MJ, Mahinthichaichan P, Baylon JL, Vermaas JV, Navidpour L, Wen PC, Thangapandian S, Tajkhorshid E. The cellular membrane as a mediator for small molecule interaction with membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:2290-2304. [PMID: 27163493 PMCID: PMC4983535 DOI: 10.1016/j.bbamem.2016.04.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 01/05/2023]
Abstract
The cellular membrane constitutes the first element that encounters a wide variety of molecular species to which a cell might be exposed. Hosting a large number of structurally and functionally diverse proteins associated with this key metabolic compartment, the membrane not only directly controls the traffic of various molecules in and out of the cell, it also participates in such diverse and important processes as signal transduction and chemical processing of incoming molecular species. In this article, we present a number of cases where details of interaction of small molecular species such as drugs with the membrane, which are often experimentally inaccessible, have been studied using advanced molecular simulation techniques. We have selected systems in which partitioning of the small molecule with the membrane constitutes a key step for its final biological function, often binding to and interacting with a protein associated with the membrane. These examples demonstrate that membrane partitioning is not only important for the overall distribution of drugs and other small molecules into different compartments of the body, it may also play a key role in determining the efficiency and the mode of interaction of the drug with its target protein. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Christopher G Mayne
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Mark J Arcario
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; College of Medicine, University of Illinois at Urbana-Champaign, United States.
| | - Paween Mahinthichaichan
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States.
| | - Javier L Baylon
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Josh V Vermaas
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Latifeh Navidpour
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Po-Chao Wen
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Sundarapandian Thangapandian
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States.
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; College of Medicine, University of Illinois at Urbana-Champaign, United States.
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9
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Tavares A, Toldo JM, Vilela GD, Gonçalves PFB, Bechtold IH, Kitney SP, Kelly SM, Merlo AA. Implications of flexible spacer rotational processes on the liquid crystal behavior of 4,5-dihydroisoxazole benzoate dimers. NEW J CHEM 2016. [DOI: 10.1039/c5nj02199e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Liquid crystals behavior of the 5a–d and 9a–d was dictated by rotational aspects of the flexible spacer.
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10
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Pérez-Fuentes L, Drummond C, Faraudo J, Bastos-González D. Anions make the difference: insights from the interaction of big cations and anions with poly(N-isopropylacrylamide) chains and microgels. SOFT MATTER 2015; 11:5077-5086. [PMID: 26027700 DOI: 10.1039/c5sm00750j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Minute concentrations of big hydrophobic ions have the ability to induce substantial effects in soft matter systems, including novel phases in lipid layers, giant charge inversion in colloids and nanostructuration in polymer surfaces in contact with water. The effects are so strong that the term "soft matter disruptors" was coined to describe their deep impact on interfaces, which goes far beyond that found by using the classical ions considered in lyotropic (Hofmeister) sequences. In these effects, solvation thermodynamics plays a fundamental role. Interestingly, it is possible to obtain big hydrophobic cations and anions with an almost identical size and structure (e.g. Ph4B(-), Ph4As(+)), which only differ in their central atom. Here we employ different techniques (Molecular Dynamics (MD) simulations, electrophoretic mobility and Atomic Force Microscopy (AFM)) to demonstrate the dramatic differences in the interaction of Ph4B(-) and Ph4As(+) with poly(N-isopropylacrylamide) (PNIPAM), a thermoresponsive polymer with expanded (well hydrated) and collapsed (poorly hydrated) states. Although both ions interact strongly with neutral PNIPAM chains and cationic or anionic PNIPAM microgels in the collapsed states, the effects of Ph4B(-) on PNIPAM are always substantially stronger than the effects of Ph4As(+). MD simulations predict that ion-PNIPAM free energy of interaction is four times larger for Ph4B(-) than for Ph4As(+). Electrokinetic and AFM experiments show that, acting as counter-ions, both ions are able to invert the charge of anionic or cationic PNIPAM microgels at minute concentrations, but the charge inversion due to Ph4B(-) is much larger than that obtained with Ph4As(+). Therefore, even for big ions of identical size, shape and valence, the affinity of anions and cations for interfaces is intrinsically different.
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Affiliation(s)
- Leonor Pérez-Fuentes
- Biocolloid and Fluid Physics Group, Department of Applied Physics, University of Granada, Av. Fuentenueva S/N, E-18071 Granada, Spain.
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11
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Liakos DG, Neese F. Domain Based Pair Natural Orbital Coupled Cluster Studies on Linear and Folded Alkane Chains. J Chem Theory Comput 2015; 11:2137-43. [DOI: 10.1021/acs.jctc.5b00265] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dimitrios G. Liakos
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 32-34, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 32-34, 45470 Mülheim an der Ruhr, Germany
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12
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Boyd NJ, Wilson MR. Optimization of the GAFF force field to describe liquid crystal molecules: the path to a dramatic improvement in transition temperature predictions. Phys Chem Chem Phys 2015; 17:24851-65. [DOI: 10.1039/c5cp03702f] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Systematic optimization of the General Amber Force Field (GAFF) for mesogenic fragments leads to a dramatic improvement in the modelling of liquid crystal clearing points.
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13
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Lee S, Tran A, Allsopp M, Lim JB, Hénin J, Klauda JB. CHARMM36 united atom chain model for lipids and surfactants. J Phys Chem B 2014; 118:547-56. [PMID: 24341749 DOI: 10.1021/jp410344g] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular simulations of lipids and surfactants require accurate parameters to reproduce and predict experimental properties. Previously, a united atom (UA) chain model was developed for the CHARMM27/27r lipids (Hénin, J., et al. J. Phys. Chem. B. 2008, 112, 7008-7015) but suffers from the flaw that bilayer simulations using the model require an imposed surface area ensemble, which limits its use to pure bilayer systems. A UA-chain model has been developed based on the CHARMM36 (C36) all-atom lipid parameters, termed C36-UA, and agreed well with bulk, lipid membrane, and micelle formation of a surfactant. Molecular dynamics (MD) simulations of alkanes (heptane and pentadecane) were used to test the validity of C36-UA on density, heat of vaporization, and liquid self-diffusion constants. Then, simulations using C36-UA resulted in accurate properties (surface area per lipid, X-ray and neutron form factors, and chain order parameters) of various saturated- and unsaturated-chain bilayers. When mixed with the all-atom cholesterol model and tested with a series of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)/cholesterol mixtures, the C36-UA model performed well. Simulations of self-assembly of a surfactant (dodecylphosphocholine, DPC) using C36-UA suggest an aggregation number of 53 ± 11 DPC molecules at 0.45 M of DPC, which agrees well with experimental estimates. Therefore, the C36-UA force field offers a useful alternative to the all-atom C36 lipid force field by requiring less computational cost while still maintaining the same level of accuracy, which may prove useful for large systems with proteins.
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Affiliation(s)
- Sarah Lee
- Department of Chemical and Biomolecular Engineering, University of Maryland , College Park, Maryland 20742, United States
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14
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Martin JML. What Can We Learn about Dispersion from the Conformer Surface of n-Pentane? J Phys Chem A 2013; 117:3118-32. [DOI: 10.1021/jp401429u] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jan M. L. Martin
- Department
of Chemistry and Center for Advanced Scientific
Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76201, United States
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15
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Recent Progress in Density Functional Methodology for Biomolecular Modeling. STRUCTURE AND BONDING 2013. [DOI: 10.1007/978-3-642-32750-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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16
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Klauda JB, Monje V, Kim T, Im W. Improving the CHARMM force field for polyunsaturated fatty acid chains. J Phys Chem B 2012; 116:9424-31. [PMID: 22697583 DOI: 10.1021/jp304056p] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
CHARMM36 (C36) is the most up-to-date pairwise additive all-atom lipid force field and is able to accurately represent bilayer properties of saturated and monounsaturated lipid molecules in the natural constant particle, pressure, and temperature (NPT) ensemble. However, molecular dynamics (MD) simulations on 1-stearoyl-2-docosahexaenoyl-sn-glycerco-3-phosphocholine (SDPC) bilayers of the polyunsaturated fatty acid (PUFA) chains result in inaccuracies of the surface area per lipid (SA), deuterium order parameters (S(CD)), and X-ray form factors. Therefore, in this study, high-level quantum mechanical calculations are used to improve the dihedral potential of neighboring double bonds, and the corresponding force field is referred to as C36p. The SA for SDPC at 303 K increases from 63.2 ± 0.2 (C36) to 70.8 ± 0.2 (C36p) Å(2) and agrees favorably with X-ray diffraction results at 297 K. The resulting S(CD) are in excellent agreement with experimental values of both the sn-1 and sn-2 chains. Calculated NMR (13)C relaxation times and X-ray form factors from MD simulations of SDPC bilayers also agree with experiments. MD simulations of 1,2-diarachidonyl-phosphatidylcholine (DAPC) bilayers are used to further validate our force field parameters on a lipid with both chains containing PUFAs. As expected, the thickness of DAPC bilayers is reduced, and the SA is increased compared to the SDPC bilayers. This update in the PUFA force field should allow for accurate MD simulations of PUFA-containing bilayers in the NPT ensemble.
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Affiliation(s)
- Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA.
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17
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Fujiki M, Jalilah AJ, Suzuki N, Taguchi M, Zhang W, Abdellatif MM, Nomura K. Chiral optofluidics: gigantic circularly polarized light enhancement of all-trans-poly(9,9-di-n-octylfluorene-2,7-vinylene) during mirror-symmetry-breaking aggregation by optically tuning fluidic media. RSC Adv 2012. [DOI: 10.1039/c2ra20430d] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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18
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Yu T, Zheng J, Truhlar DG. Statistical thermodynamics of the isomerization reaction between n-heptane and isoheptane. Phys Chem Chem Phys 2012; 14:482-94. [DOI: 10.1039/c1cp22578b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Shintani M, Matsuo Y, Sakuraba S, Matubayasi N. Interaction of naphthalene derivatives with lipids in membranes studied by the 1H-nuclear Overhauser effect and molecular dynamics simulation. Phys Chem Chem Phys 2012; 14:14049-60. [DOI: 10.1039/c2cp41984j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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20
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Jo S, Im W. Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables. Biophys J 2011; 100:2913-21. [PMID: 21689524 DOI: 10.1016/j.bpj.2011.05.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2011] [Revised: 04/25/2011] [Accepted: 05/04/2011] [Indexed: 01/16/2023] Open
Abstract
As the major component of membrane proteins, transmembrane helices embedded in anisotropic bilayer environments adopt preferential orientations that are characteristic or related to their functional states. Recent developments in solid-state nuclear magnetic resonance (SSNMR) spectroscopy have made it possible to measure NMR observables that can be used to determine such orientations in a native bilayer environment. A quasistatic single conformer model is frequently used to interpret the SSNMR observables, but important motional information can be missing or misinterpreted in the model. In this work, we have investigated the orientation of the single-pass transmembrane domain of viral protein "u" (VpuTM) from HIV-1 by determining an ensemble of structures using multiple conformer models based on the SSNMR ensemble dynamics technique. The resulting structure ensemble shows significantly larger orientational fluctuations while the ensemble-averaged orientation is compatible with the orientation based on the quasistatic model. This observation is further corroborated by comparison with the VpuTM orientation from comparative molecular dynamics simulations in explicit bilayer membranes. SSNMR ensemble dynamics not only reveals the importance of transmembrane helix dynamics in interpretation of SSNMR observables, but also provides a means to simultaneously extract both transmembrane helix orientation and dynamics information from the SSNMR measurements.
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Affiliation(s)
- Sunhwan Jo
- Department of Molecular Biosciences, Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, USA
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21
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Wang Y, Markwick PRL, de Oliveira CAF, McCammon JA. Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics. J Chem Theory Comput 2011; 7:3199-3207. [PMID: 22003320 PMCID: PMC3191728 DOI: 10.1021/ct200430c] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Indexed: 11/28/2022]
Abstract
Accelerated molecular dynamics (aMD) is an enhanced sampling technique that expedites conformational space sampling by reducing the barriers separating various low-energy states of a system. Here, we present the first application of the aMD method on lipid membranes. Altogether, ∼1.5 μs simulations were performed on three systems: a pure POPC bilayer, a pure DMPC bilayer, and a mixed POPC:DMPC bilayer. Overall, the aMD simulations are found to produce significant speedup in trans–gauche isomerization and lipid lateral diffusion versus those in conventional MD (cMD) simulations. Further comparison of a 70-ns aMD run and a 300-ns cMD run of the mixed POPC:DMPC bilayer shows that the two simulations yield similar lipid mixing behaviors, with aMD generating a 2–3-fold speedup compared to cMD. Our results demonstrate that the aMD method is an efficient approach for the study of bilayer structural and dynamic properties. On the basis of simulations of the three bilayer systems, we also discuss the impact of aMD parameters on various lipid properties, which can be used as a guideline for future aMD simulations of membrane systems.
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Affiliation(s)
- Yi Wang
- Center for Theoretical Biological Physics, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California, San Diego , La Jolla, California 92093, United States
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Shintani M, Yoshida K, Sakuraba S, Nakahara M, Matubayasi N. NMR-NOE and MD simulation study on phospholipid membranes: dependence on membrane diameter and multiple time scale dynamics. J Phys Chem B 2011; 115:9106-15. [PMID: 21728286 DOI: 10.1021/jp204051f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Motional correlation times between the hydrophilic and hydrophobic terminal groups in lipid membranes are studied over a wide range of curvatures using the solution-state (1)H NMR-nuclear Overhauser effect (NOE) and molecular dynamics (MD) simulation. To enable (1)H NMR-NOE measurements for large vesicles, the transient NOE method is combined with the spin-echo method, and is successfully applied to a micelle of 1-palmitoyl-lysophosphatidylcholine (PaLPC) with diameter of 5 nm and to vesicles of dipalmitoylphosphatidylcholine (DPPC) with diameters ranging from 30 to 800 nm. It is found that the NOE intensity increases with the diameter up to ∼100 nm, and the model membrane is considered planar on the molecular level beyond ∼100 nm. While the NOE between the hydrophilic terminal and hydrophobic terminal methyl groups is absent for the micelle, its intensity is comparable to that for the neighboring group for vesicles with larger diameters. The origin of NOE signals between distant sites is analyzed by MD simulations of PaLPC micelles and DPPC planar bilayers. The slow relaxation is shown to yield an observable NOE signal even for the hydrophilic and hydrophobic terminal sites. Since the information on distance and dynamics cannot be separated in the experimental NOE alone, the correlation time in large vesicles is determined by combining the experimental NOE intensity and MD-based distance distribution. For large vesicles, the correlation time is found to vary by 2 orders of magnitude over the proton sites. This study shows that NOE provides dynamic information on large vesicles when combined with MD, which provides structural information.
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Affiliation(s)
- Megumi Shintani
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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23
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Song KC, Livanec PW, Klauda JB, Kuczera K, Dunn RC, Im W. Orientation of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations. J Phys Chem B 2011; 115:6157-65. [PMID: 21513278 DOI: 10.1021/jp109629v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule fluorescence measurements have been used to characterize membrane properties, and recently showed a linear evolution of the fluorescent lipid analogue BODIPY-PC toward small tilt angles in Langmuir-Blodgett monolayers as the lateral surface pressure is increased. In this work, we have performed comparative molecular dynamics (MD) simulations of BODIPY-PC in DPPC (dipalmitoylphosphatidylcholine) monolayers and bilayers at three surface pressures (3, 10, and 40 mN/m) to explore (1) the microscopic correspondence between monolayer and bilayer structures, (2) the fluorophore's position within the membrane, and (3) the microscopic driving forces governing the fluorophore's tilting. The MD simulations reveal very close agreement between the monolayer and bilayer systems in terms of the fluorophore's orientation and lipid chain order, suggesting that monolayer experiments can be used to approximate bilayer systems. The simulations capture the trend of reduced tilt angle of the fluorophore with increasing surface pressure, as seen in the experimental results, and provide detailed insights into fluorophore location and orientation, not obtainable in the experiments. The simulations also reveal that the enthalpic contribution is dominant at 40 mN/m, resulting in smaller tilt angles of the fluorophore, and the entropy contribution is dominant at lower pressures, resulting in larger tilt angles.
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Affiliation(s)
- Kevin C Song
- Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, USA
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24
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Woodcock HL, Miller BT, Hodoscek M, Okur A, Larkin JD, Ponder JW, Brooks BR. MSCALE: A General Utility for Multiscale Modeling. J Chem Theory Comput 2011; 7:1208-1219. [PMID: 21691425 DOI: 10.1021/ct100738h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The combination of theoretical models of macromolecules that exist at different spatial and temporal scales has become increasingly important for addressing complex biochemical problems. This work describes the extension of concurrent multiscale approaches, introduces a general framework for carrying out calculations, and describes its implementation into the CHARMM macromolecular modeling package. This functionality, termed MSCALE, generalizes both the additive and subtractive multiscale scheme (e.g. QM/MM ONIOM-type), and extends its support to classical force fields, coarse grained modeling (e.g. ENM, GNM, etc.), and a mixture of them all. The MSCALE scheme is completely parallelized with each subsystem running as an independent, but connected calculation. One of the most attractive features of MSCALE is the relative ease of implementation using the standard MPI communication protocol. This allows external access to the framework and facilitates the combination of functionality previously isolated in separate programs. This new facility is fully integrated with free energy perturbation methods, Hessian based methods, and the use of periodicity and symmetry, which allows the calculation of accurate pressures. We demonstrate the utility of this new technique with four examples; (1) subtractive QM/MM and QM/QM calculations; (2) multi-force field alchemical free energy perturbation; (3) integration with the SANDER module of AMBER and the TINKER package to gain access to potentials not available in CHARMM; and (4) mixed resolution (i.e. coarse grain / all-atom) normal mode analysis. The potential of this new tool is clearly established and in conclusion an interesting mathematical problem is highlighted and future improvements are proposed.
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Affiliation(s)
- H Lee Woodcock
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE205, Tampa, FL 33620-5250
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25
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Tarallo O, Schiavone MM, Petraccone V. Structural characterization of the δ-clathrate forms of syndiotactic polystyrene with n-alkanes. POLYMER 2011. [DOI: 10.1016/j.polymer.2011.01.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Jo S, Rui H, Lim JB, Klauda JB, Im W. Cholesterol Flip-Flop: Insights from Free Energy Simulation Studies. J Phys Chem B 2010; 114:13342-8. [DOI: 10.1021/jp108166k] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sunhwan Jo
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, United States, and Department of Chemical and Biomolecular Engineering, The University of Maryland, College Park, Maryland 20742, United States
| | - Huan Rui
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, United States, and Department of Chemical and Biomolecular Engineering, The University of Maryland, College Park, Maryland 20742, United States
| | - Joseph B. Lim
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, United States, and Department of Chemical and Biomolecular Engineering, The University of Maryland, College Park, Maryland 20742, United States
| | - Jeffery B. Klauda
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, United States, and Department of Chemical and Biomolecular Engineering, The University of Maryland, College Park, Maryland 20742, United States
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, United States, and Department of Chemical and Biomolecular Engineering, The University of Maryland, College Park, Maryland 20742, United States
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27
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Pendse PY, Brooks BR, Klauda JB. Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation. J Mol Biol 2010; 404:506-21. [PMID: 20875429 DOI: 10.1016/j.jmb.2010.09.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 08/24/2010] [Accepted: 09/17/2010] [Indexed: 10/19/2022]
Abstract
Based on the crystal structure of lactose permease (LacY) open to the cytoplasm, a hybrid molecular simulation approach with self-guided Langevin dynamics is used to describe conformational changes that lead to a periplasmic-open state. This hybrid approach consists of implicit (IM) and explicit (EX) membrane simulations and requires self-guided Langevin dynamics to enhance protein motions during the IM simulations. The pore radius of the lumen increases by 3.5 Å on the periplasmic side and decreases by 2.5 Å on the cytoplasmic side (relative to the crystal structure), suggesting a lumen that is fully open to the periplasm to allow for extracellular sugar transport and closed to the cytoplasm. Based on our simulations, the mechanism that triggers this conformational change to the periplasmic-open state is the protonation of Glu269 and binding of the disaccharide. Then, helix packing is destabilized by breaking of several side chains involved in hydrogen bonding (Asn245, Ser41, Glu374, Lys42, and Gln242). For the periplasmic-open conformations obtained from our simulations, helix-helix distances agree well with experimental measurements using double electron-electron resonance, fluorescence resonance energy transfer, and varying sized cross-linkers. The periplasmic-open conformations are also in compliance with various substrate accessibility/reactivity measurements that indicate an opening of the protein lumen on the periplasmic side on sugar binding. The comparison with these measurements suggests a possible incomplete closure of the cytoplasmic half in our simulations. However, the closure is sufficient to prevent the disaccharide from transporting to the cytoplasm, which is in accordance with the well-established alternating access model. Ser53, Gln60, and Phe354 are determined to be important in sugar transport during the periplasmic-open stage of the sugar transport cycle and the sugar is found to undergo an orientational change in order to escape the protein lumen.
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Affiliation(s)
- Pushkar Y Pendse
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
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28
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Janosi L, Gorfe AA. Simulating POPC and POPC/POPG Bilayers: Conserved Packing and Altered Surface Reactivity. J Chem Theory Comput 2010; 6:3267-73. [DOI: 10.1021/ct100381g] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Lorant Janosi
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 4.108, Houston, Texas 77030
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 4.108, Houston, Texas 77030
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29
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Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD, Pastor RW. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B 2010. [PMID: 20496934 DOI: 10.1021/jp101759q.update] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains. Motivated by the current CHARMM lipid FF (C27 and C27r) systematically yielding values of the surface area per lipid that are smaller than experimental estimates and gel-like structures of bilayers well above the gel transition temperature, selected torsional, Lennard-Jones and partial atomic charge parameters were modified by targeting both quantum mechanical (QM) and experimental data. QM calculations ranging from high-level ab initio calculations on small molecules to semiempirical QM studies on a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer in combination with experimental thermodynamic data were used as target data for parameter optimization. These changes were tested with simulations of pure bilayers at high hydration of the following six lipids: DPPC, 1,2-dimyristoyl-sn-phosphatidylcholine (DMPC), 1,2-dilauroyl-sn-phosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-sn-phosphatidylcholine (POPC), 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-phosphatidylethanolamine (POPE); simulations of a low hydration DOPC bilayer were also performed. Agreement with experimental surface area is on average within 2%, and the density profiles agree well with neutron and X-ray diffraction experiments. NMR deuterium order parameters (S(CD)) are well predicted with the new FF, including proper splitting of the S(CD) for the aliphatic carbon adjacent to the carbonyl for DPPC, POPE, and POPC bilayers. The area compressibility modulus and frequency dependence of (13)C NMR relaxation rates of DPPC and the water distribution of low hydration DOPC bilayers also agree well with experiment. Accordingly, the presented lipid FF, referred to as C36, allows for molecular dynamics simulations to be run in the tensionless ensemble (NPT), and is anticipated to be of utility for simulations of pure lipid systems as well as heterogeneous systems including membrane proteins.
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Affiliation(s)
- Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
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30
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Klauda JB, Venable RM, Freites JA, O’Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD, Pastor RW. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B 2010; 114:7830-43. [PMID: 20496934 PMCID: PMC2922408 DOI: 10.1021/jp101759q] [Citation(s) in RCA: 3131] [Impact Index Per Article: 223.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains. Motivated by the current CHARMM lipid FF (C27 and C27r) systematically yielding values of the surface area per lipid that are smaller than experimental estimates and gel-like structures of bilayers well above the gel transition temperature, selected torsional, Lennard-Jones and partial atomic charge parameters were modified by targeting both quantum mechanical (QM) and experimental data. QM calculations ranging from high-level ab initio calculations on small molecules to semiempirical QM studies on a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer in combination with experimental thermodynamic data were used as target data for parameter optimization. These changes were tested with simulations of pure bilayers at high hydration of the following six lipids: DPPC, 1,2-dimyristoyl-sn-phosphatidylcholine (DMPC), 1,2-dilauroyl-sn-phosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-sn-phosphatidylcholine (POPC), 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-phosphatidylethanolamine (POPE); simulations of a low hydration DOPC bilayer were also performed. Agreement with experimental surface area is on average within 2%, and the density profiles agree well with neutron and X-ray diffraction experiments. NMR deuterium order parameters (S(CD)) are well predicted with the new FF, including proper splitting of the S(CD) for the aliphatic carbon adjacent to the carbonyl for DPPC, POPE, and POPC bilayers. The area compressibility modulus and frequency dependence of (13)C NMR relaxation rates of DPPC and the water distribution of low hydration DOPC bilayers also agree well with experiment. Accordingly, the presented lipid FF, referred to as C36, allows for molecular dynamics simulations to be run in the tensionless ensemble (NPT), and is anticipated to be of utility for simulations of pure lipid systems as well as heterogeneous systems including membrane proteins.
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Affiliation(s)
- Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742
| | - Richard M. Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - J. Alfredo Freites
- Department of Chemistry, University of California, Irvine, CA 92697-2025
| | - Joseph W. O’Connor
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742
| | - Douglas J. Tobias
- Department of Chemistry, University of California, Irvine, CA 92697-2025
| | - Carlos Mondragon-Ramirez
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Igor Vorobyov
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Richard W. Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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31
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Oliveira RG, Schneck E, Quinn BE, Konovalov OV, Brandenburg K, Gutsmann T, Gill T, Hanna CB, Pink DA, Tanaka M. Crucial roles of charged saccharide moieties in survival of gram negative bacteria against protamine revealed by combination of grazing incidence x-ray structural characterizations and Monte Carlo simulations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:041901. [PMID: 20481747 DOI: 10.1103/physreve.81.041901] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 12/09/2009] [Indexed: 05/29/2023]
Abstract
Grazing incidence x-ray scattering techniques and Monte Carlo (MC) simulations are combined to reveal the influence of molecular structure (genetic mutation) and divalent cations on the survival of gram negative bacteria against cationic peptides such as protamine. The former yields detailed structures of bacterial lipopolysaccharide (LPS) membranes with minimized radiation damages, while the minimal computer model based on the linearized Poisson-Boltzmann theory allows for the simulation of conformational changes of macromolecules (LPSs and peptides) that occur in the time scale of ms. The complementary combination of the structural characterizations and MC simulation demonstrates that the condensations of divalent ions (Ca2+ or Mg2+) in the negatively charged core saccharides are crucial for bacterial survival.
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Affiliation(s)
- Rafael G Oliveira
- Biophysics Laboratory E22, Technical University Munich, D85748 Garching, Germany
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32
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Pink DA, Hanna CB, Sandt C, MacDonald AJ, MacEachern R, Corkery R, Rousseau D. Modeling the solid-liquid phase transition in saturated triglycerides. J Chem Phys 2010; 132:054502. [DOI: 10.1063/1.3276108] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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33
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Jo S, Lim JB, Klauda JB, Im W. CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J 2009; 97:50-8. [PMID: 19580743 DOI: 10.1016/j.bpj.2009.04.013] [Citation(s) in RCA: 1139] [Impact Index Per Article: 75.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 03/29/2009] [Accepted: 04/02/2009] [Indexed: 11/25/2022] Open
Abstract
The CHARMM-GUI Membrane Builder (http://www.charmm-gui.org/input/membrane), an intuitive, straightforward, web-based graphical user interface, was expanded to automate the building process of heterogeneous lipid bilayers, with or without a protein and with support for up to 32 different lipid types. The efficacy of these new features was tested by building and simulating lipid bilayers that resemble yeast membranes, composed of cholesterol, dipalmitoylphosphatidylcholine, dioleoylphosphatidylcholine, palmitoyloleoylphosphatidylethanolamine, palmitoyloleoylphosphatidylamine, and palmitoyloleoylphosphatidylserine. Four membranes with varying concentrations of cholesterol and phospholipids were simulated, for a total of 170 ns at 303.15 K. Unsaturated phospholipid chain concentration had the largest influence on membrane properties, such as average lipid surface area, density profiles, deuterium order parameters, and cholesterol tilt angle. Simulations with a high concentration of unsaturated chains (73%, membrane(unsat)) resulted in a significant increase in lipid surface area and a decrease in deuterium order parameters, compared with membranes with a high concentration of saturated chains (60-63%, membrane(sat)). The average tilt angle of cholesterol with respect to bilayer normal was largest, and the distribution was significantly broader for membrane(unsat). Moreover, short-lived cholesterol orientations parallel to the membrane surface existed only for membrane(unsat). The membrane(sat) simulations were in a liquid-ordered state, and agree with similar experimental cholesterol-containing membranes.
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Affiliation(s)
- Sunhwan Jo
- Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas, Lawrence, Kansas 66047, USA
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34
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Babarao R, Tong YH, Jiang J. Molecular insight into adsorption and diffusion of alkane isomer mixtures in metal-organic frameworks. J Phys Chem B 2009; 113:9129-36. [PMID: 19534507 DOI: 10.1021/jp902253p] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adsorption and diffusion of alkane isomer mixtures (C(4) and C(5)) are investigated in catenated and noncatenated metal-organic frameworks (IRMOF-13, IRMOF-14, PCN-6, and PCN-6') using molecular simulations. Competitive adsorption between isomers is observed, particularly at high pressures, at which a linear isomer shows a larger extent of adsorption due to configurational entropy. An inflection is found in the isotherm as a consequence of sequential adsorption in multiple favorable sites. Compared with the noncatenated counterparts, IRMOF-13 and PCN-6 have a greater loading at low pressures because of the constricted pores and stronger affinity with adsorbate. However, the reverse is true at high pressures due to the smaller pore volume. Catenated MOFs exhibit larger adsorption selectivity for alkane mixtures than the noncatenated counterparts. Adsorption selectivity in the four MOFs is comparable to that in carbon nanotube and silicalite, though adsorption capacity is lower in the latter. It is found that diffusivity of alkane in MOFs decreases with the degree of branching because a slender isomer diffuses faster. With the presence of constricted pores, diffusivity in catenated MOFs is smaller than that in noncatenated counterparts. In IRMOF-14 and IRMOF-13 diffusivity decreases monotonically, while it initially increases and then decreases in PCN-6'. The diffusion selectivity in catenated IRMOF-13 and PCN-6 is larger than that in noncatenated IRMOF-14 and PCN-6'. This work provides insightful microscopic mechanisms for the adsorption and diffusion of alkane isomers in MOFs and reveals that both adsorption and diffusion selectivities can be enhanced by catenation.
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Affiliation(s)
- Ravichandar Babarao
- Department of Chemical & Biomolecular Engineering, National University of Singapore, 117576 Singapore
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35
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Experimental study of a diffusion-controlled reaction involving a chain molecule with terminal reactive sites. RESEARCH ON CHEMICAL INTERMEDIATES 2009. [DOI: 10.1007/s11164-009-0055-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Hénin J, Shinoda W, Klein ML. United-atom acyl chains for CHARMM phospholipids. J Phys Chem B 2008; 112:7008-15. [PMID: 18481889 DOI: 10.1021/jp800687p] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In all-atom simulations of lipid membranes, explicit hydrogen atoms contained in the hydrocarbon region are described by a large number of degrees of freedom, although they convey only limited physical information. We propose an implicit-hydrogen model for saturated and monounsaturated acyl chains, aimed at complementing the all-atom CHARMM27 model for phospholipid headgroups. Torsional potentials and nonbonded parameters were fitted to reproduce experimental data and free energy surfaces of all-atom model systems. Comparative simulations of fluid-phase POPC bilayers were performed using the all-hydrogen force field and the present model. The hybrid model accelerates a typical bilayer simulation by about 50% while sacrificing a minimal amount of detail with respect to the fully atomistic description. In addition, the united-atom description is energetically compatible with all-atom CHARMM models, making it suitable for simulations of complex membrane systems.
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Affiliation(s)
- Jérôme Hénin
- Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA 19104-6323, USA.
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37
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Klauda JB, Venable RM, MacKerell AD, Pastor RW. Chapter 1 Considerations for Lipid Force Field Development. CURRENT TOPICS IN MEMBRANES 2008. [DOI: 10.1016/s1063-5823(08)00001-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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38
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Klauda JB, Brooks BR. CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes. J Chem Theory Comput 2007; 4:107-15. [DOI: 10.1021/ct700191v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jeffery B. Klauda
- Laboratory of Computation Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Bernard R. Brooks
- Laboratory of Computation Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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39
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Knippenberg S, Huang YR, Hajgató B, François JP, Deng JK, Deleuze MS. Probing molecular conformations in momentum space: The case of n-pentane. J Chem Phys 2007; 127:174306. [DOI: 10.1063/1.2772848] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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40
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Klauda JB, Wu X, Pastor RW, Brooks BR. Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method. J Phys Chem B 2007; 111:4393-400. [PMID: 17425357 PMCID: PMC6413507 DOI: 10.1021/jp068767m] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics (MD) simulations of heptane/vapor, hexadecane/vapor, water/vapor, hexadecane/water, and dipalmitoylphosphatidylcholine (DPPC) bilayers and monolayers are analyzed to determine the accuracy of treating long-range interactions in interfaces with the isotropic periodic sum (IPS) method. The method and cutoff (rc) dependences of surface tensions, density profiles, water dipole orientation, and electrostatic potential profiles are used as metrics. The water/vapor, heptane/vapor, and hexadecane/vapor interfaces are accurately and efficiently calculated with 2D IPS (rc=10 A). It is demonstrated that 3D IPS is not practical for any of the interfacial systems studied. However, the hybrid method PME/IPS [Particle Mesh Ewald for electrostatics and 3D IPS for Lennard-Jones (LJ) interactions] provides an efficient way to include both types of long-range forces in simulations of large liquid/vacuum and all liquid/liquid interfaces, including lipid monolayers and bilayers. A previously published pressure-based long-range LJ correction yields results similar to those of PME/IPS for liquid/liquid interfaces. The contributions to surface tension of LJ terms arising from interactions beyond 10 A range from 13 dyn/cm for the hexadecane/vapor interface to approximately 3 dyn/cm for hexadecane/water and DPPC bilayers and monolayers. Surface tensions of alkane/vapor, hexadecane/water, and DPPC monolayers based on the CHARMM lipid force fields agree very well with experiment, whereas surface tensions of the TIP3P and TIP4P-Ew water models underestimate experiment by 16 and 11 dyn/cm, respectively. Dipole potential drops (DeltaPsi) are less sensitive to long-range LJ interactions than surface tensions. However, DeltaPsi for the DPPC bilayer (845+/-3 mV proceeding from water to lipid) and water (547+/-2 mV for TIP4P-Ew and 521+/-3 mV for TIP3P) overestimate experiment by factors of 3 and 5, respectively, and represent expected deficiencies in nonpolarizable force fields.
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Affiliation(s)
- Jeffery B Klauda
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Borovkov VI, Gritsan NP, Bagryanskii VA, Molin YN. Degenerate electron exchange reaction involving n-nonane radical cation in solution. DOKLADY PHYSICAL CHEMISTRY 2007. [DOI: 10.1134/s0012501607030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Klauda JB, Brooks BR. Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure. J Mol Biol 2007; 367:1523-34. [PMID: 17320103 PMCID: PMC1995404 DOI: 10.1016/j.jmb.2007.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 01/29/2007] [Accepted: 01/30/2007] [Indexed: 11/21/2022]
Abstract
Lactose permease in Escherichia coli (LacY) transports both anomeric states of disaccharides but has greater affinity for alpha-sugars. Molecular dynamics (MD) simulations are used to probe the protein-sugar interactions, binding structures, and global protein motions in response to sugar binding by investigating LacY (the experimental mutant and wild-type) embedded in a fully hydrated lipid bilayer. A total of 12 MD simulations of 20-25 ns each with beta(alpha)-d-galactopyranosyl-(1,1)-beta-d-galactopyranoside (betabeta-(Galp)(2)) and alphabeta-(Galp)(2) result in binding conformational families that depend on the anomeric state of the sugar. Both sugars strongly interact with Glu126 and alphabeta-(Galp)(2) has a greater affinity to this residue. Binding conformations are also seen that involve protein residues not observed in the crystal structure, as well as those involved in the proton translocation (Phe118, Asn119, Asn240, His322, Glu325, and Tyr350). Common to nearly all protein-sugar structures, water acts as a hydrogen bond bridge between the disaccharide and protein. The average binding energy is more attractive for alphabeta-(Galp)(2) than betabeta-(Galp)(2), i.e. -10.7(+/-0.7) and -3.1(+/-1.0) kcal/mol, respectively. Of the 12 helices in LacY, helix-IV is the least stable with betabeta-(Galp)(2) binding resulting in larger distortion than alphabeta-(Galp)(2).
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Affiliation(s)
- Jeffery B Klauda
- Laboratory of Computational Biology, National Institutes of Health, Bldg 50, 50 South Drive, Bethesda, MD 20892, USA.
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Feller SE. Molecular dynamics simulations as a complement to nuclear magnetic resonance and X-ray diffraction measurements. Methods Mol Biol 2007; 400:89-102. [PMID: 17951729 DOI: 10.1007/978-1-59745-519-0_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Advances in the field of atomic-level membrane simulations are being driven by continued growth in computing power, improvements in the available potential energy functions for lipids, and new algorithms that implement advanced sampling techniques. These developments are allowing simulations to assess time- and length scales wherein meaningful comparisons with experimental measurements on macroscopic systems can be made. Such comparisons provide stringent tests of the simulation methodologies and force fields, and thus, advance the simulation field by pointing out shortcomings of the models. Extensive testing against available experimental data suggests that for many properties modern simulations have achieved a level of accuracy that provides substantial predictive power and can aid in the interpretation of experimental data. This combination of closely coupled laboratory experiments and molecular dynamics simulations holds great promise for the understanding of membrane systems. In the following, the molecular dynamics method is described with particular attention to those aspects critical for simulating membrane systems and to the calculation of experimental observables from the simulation trajectory.
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Affiliation(s)
- Scott E Feller
- Department of Chemistry, Wabash College, Crawfordsville, IN, USA
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