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Weng JB, Liao CY, Li Y, Zhang DL, Li GH, Wang AH. Effect of protein dimerization on ion conductivity of gramicidin a channel studied using polarizable force field. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2103046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Jun-ben Weng
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chen-yi Liao
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Ding-lin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guo-hui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - An-hui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024, China
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2
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Barrera EE, Machado MR, Pantano S. Fat SIRAH: Coarse-Grained Phospholipids To Explore Membrane-Protein Dynamics. J Chem Theory Comput 2019; 15:5674-5688. [PMID: 31433946 DOI: 10.1021/acs.jctc.9b00435] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The capability to handle highly heterogeneous molecular assemblies in a consistent manner is among the greatest challenges faced when deriving simulation parameters. This is particularly the case for coarse-grained (CG) simulations in which chemical functional groups are lumped into effective interaction centers for which transferability between different chemical environments is not guaranteed. Here, we introduce the parametrization of a set of CG phospholipids compatible with the latest version of the SIRAH force field for proteins. The newly introduced lipid species include different acylic chain lengths and partial unsaturation, as well as polar and acidic head groups that show a very good reproduction of structural membrane determinants, such as areas per lipid, thickness, order parameter, etc., and their dependence with temperature. Simulation of membrane proteins showed unprecedented accuracy in the unbiased description of the thickness-dependent membrane-protein orientation in systems where this information is experimentally available (namely, the SarcoEndoplasmic Reticulum Calcium-SERCA-pump and its regulator Phospholamban). The interactions that lead to this faithful reproduction can be traced down to the single amino acid-lipid interaction level and show full agreement with biochemical data present in the literature. Finally, the present parametrization is implemented in the GROMACS and AMBER simulation packages facilitating its use by a wide portion of the biocomputing community.
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Affiliation(s)
- Exequiel E Barrera
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Matías R Machado
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Sergio Pantano
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay.,Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , Shanghai 201210 , China
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3
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Na S, Steinbrecher T, Koslowski T. Thermodynamic integration network approach to ion transport through protein channels: Perspectives and limits. J Comput Chem 2018; 39:2539-2550. [DOI: 10.1002/jcc.25615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/27/2018] [Accepted: 09/03/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Sehee Na
- Fakultät für Chemie und Pharmazie, Institut für Physikalische ChemieUniversität Freiburg Albertstraße 23a, 79104, Freiburg im Breisgau Germany
| | | | - Thorsten Koslowski
- Fakultät für Chemie und Pharmazie, Institut für Physikalische ChemieUniversität Freiburg Albertstraße 23a, 79104, Freiburg im Breisgau Germany
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4
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A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids. Molecules 2017; 23:molecules23010077. [PMID: 29301229 PMCID: PMC6017617 DOI: 10.3390/molecules23010077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/26/2017] [Accepted: 12/28/2017] [Indexed: 11/18/2022] Open
Abstract
In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and following the same framework as Atomic Multipole Optimized Energetics for BiomoleculAr (AMOEBA) simulation, the present effort expands the force field to new anionic lipid models, in which the new lipids contain DMPG and POPS. The parameters are compatible with the AMOEBA force field, which includes water, ions, proteins, etc. The charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments, which are derived from the ab initio gas phase calculations. Many-body polarization including the inter- and intramolecular polarization is modeled in a consistent manner with distributed atomic polarizabilities. Molecular dynamics simulations of the two aqueous DMPG and POPS membrane bilayer systems, consisting of 72 lipids with water molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, electrostatic potential difference between the center of the bilayer and water are all calculated, and compared with limited experimental data.
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Chu H, Cao L, Peng X, Li G. Polarizable force field development for lipids and their efficient applications in membrane proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1312] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics, Chinese Academy of Science; Dalian China
| | - Liaoran Cao
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics, Chinese Academy of Science; Dalian China
| | - Xiangda Peng
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics, Chinese Academy of Science; Dalian China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics, Chinese Academy of Science; Dalian China
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6
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Peng X, Zhang Y, Chu H, Li Y, Zhang D, Cao L, Li G. Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections. J Chem Theory Comput 2016; 12:2973-82. [DOI: 10.1021/acs.jctc.6b00128] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xiangda Peng
- Laboratory
of Molecular Modeling and
Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- Chinese
Academy of Science, University of Chinese Academy Sciences, Beijing 100049, P. R. China
| | - Yuebin Zhang
- Laboratory
of Molecular Modeling and
Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Huiying Chu
- Laboratory
of Molecular Modeling and
Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yan Li
- Laboratory
of Molecular Modeling and
Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Dinglin Zhang
- Laboratory
of Molecular Modeling and
Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Liaoran Cao
- Laboratory
of Molecular Modeling and
Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Guohui Li
- Laboratory
of Molecular Modeling and
Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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Sychev SV, Sukhanov SV, Telezhinskaya IN, Ovchinnikova TV. Effective lipid-detergent system for study of membrane active peptides in fluid liposomes. J Pept Sci 2016; 22:98-105. [PMID: 26751806 DOI: 10.1002/psc.2845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/16/2015] [Accepted: 11/20/2015] [Indexed: 11/12/2022]
Abstract
The structure of peptide antibiotic gramicidin A (gA) was studied in phosphatidylcholin liposomes modified by nonionic detergent Triton X-100. First, the detergent : lipid ratio at which the saturation of lipid membrane by Triton X-100 occurs (Re (sat)), was determined by light scattering. Measurements of steady-state fluorescence anisotropy of 1,6-diphenyl-1,3,5-hexatriene at sublytic concentrations of detergent showed that after saturation of the membrane by Triton X-100 microviscosity of lipid bilayer is reduced by 20%. The equilibrium conformational state of gA in phosphatidylcholine liposomes at Re (sat) was studied by CD spectroscopy. It was found that the conformational state of this channel-forming peptide changed crucially when Triton X-100 induced transition to more fluid membranes. The gA single-channel measurements were made with Triton X-100 containing bilayers. Tentative assignment of the channel type and gA structures was made by correlation of CD data with conductance histograms. Lipid-detergent system with variable viscosity developed in this work can be used to study the structure and folding of other membrane-active peptides.
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Affiliation(s)
- Sergei V Sychev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, str, Moscow, Russia
| | - Stanislav V Sukhanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, str, Moscow, Russia
| | - Irina N Telezhinskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, str, Moscow, Russia
| | - Tatiana V Ovchinnikova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, str, Moscow, Russia
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Hu K, Jiang Y, Xie Y, Liu H, Liu R, Zhao Z, Lai R, Yang L. Small-Anion Selective Transmembrane "Holes" Induced by an Antimicrobial Peptide Too Short to Span Membranes. J Phys Chem B 2015; 119:8553-60. [PMID: 26126210 DOI: 10.1021/acs.jpcb.5b03133] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Whereas many membrane-destabilization modes have been suggested for membrane-spanning antimicrobial peptides (AMPs), few are available for those too short to span membrane thickness. Here we show that ORB-1, a 15-residue disulfide-bridged AMP that is only ∼20 Å long even when fully stretched like a hairpin, may act by inducing small anion-selective transmembrane "holes" of negative mean curvature. In model membranes of Gram-negative bacteria, ORB-1 induces chloride transmembrane transport and formation of transmembrane channels of negative mean curvature, whereas the inactive analogue, ORB-N, does not, suggesting a correlation between antibacterial activity and ability to induce transmembrane channels. Given that ORB-N is the C-terminus amidated form of ORB-1, our results further suggest that formation of membrane-spanning dimers may be required to initiate the observed channel induction. Moreover, ORB-1 renders model bacterial membranes permeable to anions with effective hydration diameters of <1 nm (e.g., Cl(-) and NO3(-)), but not cations of similar sizes (e.g., H3O(+)), indicative of anion-selective transmembrane channels with an effective inner diameter of ≤1 nm. In addition, negative-intrinsic-curvature (NIC) lipids such as phosphoethanolamine (PE) may facilitate the membrane-destabilization process of ORB-1. Our findings may expand current understandings on how AMPs destabilize membranes and facilitate the pharmaceutical development of ORB-1.
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Affiliation(s)
| | | | | | | | - Rui Liu
- ‡Biotoxin Units of Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | | | - Ren Lai
- ‡Biotoxin Units of Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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Wassenaar TA, Pluhackova K, Moussatova A, Sengupta D, Marrink SJ, Tieleman DP, Böckmann RA. High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach. J Chem Theory Comput 2015; 11:2278-91. [PMID: 26574426 DOI: 10.1021/ct5010092] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interactions between membrane proteins are of great biological significance and are consequently an important target for pharmacological intervention. Unfortunately, it is still difficult to obtain detailed views on such interactions, both experimentally, where the environment hampers atomic resolution investigation, and computationally, where the time and length scales are problematic. Coarse grain simulations have alleviated the later issue, but the slow movement through the bilayer, coupled to the long life times of nonoptimal dimers, still stands in the way of characterizing binding distributions. In this work, we present DAFT, a Docking Assay For Transmembrane components, developed to identify preferred binding orientations. The method builds on a program developed recently for generating custom membranes, called insane (INSert membrANE). The key feature of DAFT is the setup of starting structures, for which optimal periodic boundary conditions are devised. The purpose of DAFT is to perform a large number of simulations with different components, starting from unbiased noninteracting initial states, such that the simulations evolve collectively, in a manner reflecting the underlying energy landscape of interaction. The implementation and characteristic features of DAFT are explained, and the efficacy and relaxation properties of the method are explored for oligomerization of glycophorin A dimers, polyleucine dimers and trimers, MS1 trimers, and rhodopsin dimers. The results suggest that, for simple helices, such as GpA and polyleucine, in POPC/DOPC membranes series of 500 simulations of 500 ns each allow characterization of the helix dimer orientations and allow comparing associating and nonassociating components. However, the results also demonstrate that short simulations may suffer significantly from nonconvergence of the ensemble and that using too few simulations may obscure or distort features of the interaction distribution. For trimers, simulation times exceeding several microseconds appear needed, due to the increased complexity. Similarly, characterization of larger proteins, such as rhodopsin, takes longer time scales due to the slower diffusion and the increased complexity of binding interfaces. DAFT and its auxiliary programs have been made available from http://cgmartini.nl/ , together with a working example.
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Affiliation(s)
- Tsjerk A Wassenaar
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrasse 5, 91058 Erlangen, Germany
| | - Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrasse 5, 91058 Erlangen, Germany
| | - Anastassiia Moussatova
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary , 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Durba Sengupta
- National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D Peter Tieleman
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary , 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrasse 5, 91058 Erlangen, Germany
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Sychev SV, Ivanov VT. Large scale conformational transitions in β
-structural motif of gramicidin A: kinetic analysis based on CD and FT-IR data. J Pept Sci 2014; 20:657-67. [DOI: 10.1002/psc.2643] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/21/2014] [Accepted: 03/28/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Sergei V. Sychev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; 16/10 Miklukho-Maklaya Str. Moscow 117997 Russia
| | - Vadim T. Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; 16/10 Miklukho-Maklaya Str. Moscow 117997 Russia
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Sychev SV, Barsukov LI, Ivanov VT. Conformation of gramicidin A in Triton X-100 micelles from CD and FTIR data: a clean example of antiparallel double β5.6 helix formation. J Pept Sci 2013; 19:452-8. [DOI: 10.1002/psc.2519] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 04/09/2013] [Accepted: 04/19/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Sergei V. Sychev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; 16/10 Miklukho-Maklaya str. Moscow 117997 Russia
| | - Leonid I. Barsukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; 16/10 Miklukho-Maklaya str. Moscow 117997 Russia
| | - Vadim T. Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; 16/10 Miklukho-Maklaya str. Moscow 117997 Russia
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Rokitskaya TI, Sorochkina AI, Kovalchuk SI, Egorova NS, Kotova EA, Sychev SV, Antonenko YN. The pH-dependent induction of lipid membrane ionic permeability by N-terminally lysine-substituted analogs of gramicidin A. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:129-38. [DOI: 10.1007/s00249-011-0764-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 09/30/2011] [Accepted: 10/11/2011] [Indexed: 11/29/2022]
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