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For: Javanainen M, Martinez-Seara H, Vattulainen I. Excessive aggregation of membrane proteins in the Martini model. PLoS One 2017;12:e0187936. [PMID: 29131844 DOI: 10.1371/journal.pone.0187936] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/27/2017] [Indexed: 11/19/2022]  Open
Number Cited by Other Article(s)
51
Co NT, Li MS, Krupa P. Computational Models for the Study of Protein Aggregation. Methods Mol Biol 2022;2340:51-78. [PMID: 35167070 DOI: 10.1007/978-1-0716-1546-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
52
Borges-Araújo L, Souza PCT, Fernandes F, Melo MN. Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse-Grain Force Field. J Chem Theory Comput 2021;18:357-373. [PMID: 34962393 DOI: 10.1021/acs.jctc.1c00615] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
53
Song W, Duncan AL, Sansom MSP. Modulation of adenosine A2a receptor oligomerization by receptor activation and PIP2 interactions. Structure 2021;29:1312-1325.e3. [PMID: 34270937 PMCID: PMC8581623 DOI: 10.1016/j.str.2021.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/28/2021] [Accepted: 06/25/2021] [Indexed: 11/23/2022]
54
Sadeghi M, Noé F. Thermodynamics and Kinetics of Aggregation of Flexible Peripheral Membrane Proteins. J Phys Chem Lett 2021;12:10497-10504. [PMID: 34677984 DOI: 10.1021/acs.jpclett.1c02954] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
55
Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021;14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022]  Open
56
Pandey PR, Różycki B, Lipowsky R, Weikl TR. Structural variability and concerted motions of the T cell receptor - CD3 complex. eLife 2021;10:e67195. [PMID: 34490842 PMCID: PMC8504971 DOI: 10.7554/elife.67195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 09/06/2021] [Indexed: 11/28/2022]  Open
57
Cholesterol plays a decisive role in tetraspanin assemblies during bilayer deformations. Biosystems 2021;209:104505. [PMID: 34403719 DOI: 10.1016/j.biosystems.2021.104505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/30/2021] [Accepted: 08/07/2021] [Indexed: 11/22/2022]
58
Sahoo AR, Buck M. Structural and Functional Insights into the Transmembrane Domain Association of Eph Receptors. Int J Mol Sci 2021;22:ijms22168593. [PMID: 34445298 PMCID: PMC8395321 DOI: 10.3390/ijms22168593] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/04/2022]  Open
59
Chakraborty S, Wagh K, Gnanakaran S, López CA. Development of Martini 2.2 parameters for N-glycans: a case study of the HIV-1 Env glycoprotein dynamics. Glycobiology 2021;31:787-799. [PMID: 33755116 PMCID: PMC8351497 DOI: 10.1093/glycob/cwab017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/15/2021] [Accepted: 03/01/2021] [Indexed: 12/18/2022]  Open
60
Molza AE, Gao P, Jakpou J, Nicolas J, Tsapis N, Ha-Duong T. Simulations of the Upper Critical Solution Temperature Behavior of Poly(ornithine-co-citrulline)s Using MARTINI-Based Coarse-Grained Force Fields. J Chem Theory Comput 2021;17:4499-4511. [PMID: 34101464 DOI: 10.1021/acs.jctc.1c00140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
61
Holdbrook DA, Marzinek JK, Boncel S, Boags A, Tan YS, Huber RG, Verma CS, Bond PJ. The nanotube express: Delivering a stapled peptide to the cell surface. J Colloid Interface Sci 2021;604:670-679. [PMID: 34280765 DOI: 10.1016/j.jcis.2021.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/23/2021] [Accepted: 07/04/2021] [Indexed: 10/20/2022]
62
Larsen AH, Sansom MSP. Binding of Ca2+-independent C2 domains to lipid membranes: A multi-scale molecular dynamics study. Structure 2021;29:1200-1213.e2. [PMID: 34081910 PMCID: PMC8507603 DOI: 10.1016/j.str.2021.05.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/26/2021] [Accepted: 05/14/2021] [Indexed: 01/17/2023]
63
Kjølbye LR, De Maria L, Wassenaar TA, Abdizadeh H, Marrink SJ, Ferkinghoff-Borg J, Schiøtt B. General Protocol for Constructing Molecular Models of Nanodiscs. J Chem Inf Model 2021;61:2869-2883. [PMID: 34048229 DOI: 10.1021/acs.jcim.1c00157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
64
Lamprakis C, Andreadelis I, Manchester J, Velez-Vega C, Duca JS, Cournia Z. Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments. J Chem Theory Comput 2021;17:3088-3102. [PMID: 33913726 DOI: 10.1021/acs.jctc.0c00507] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
65
Bartoš L, Kabelka I, Vácha R. Enhanced translocation of amphiphilic peptides across membranes by transmembrane proteins. Biophys J 2021;120:2296-2305. [PMID: 33864790 PMCID: PMC8390799 DOI: 10.1016/j.bpj.2021.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/11/2021] [Accepted: 04/08/2021] [Indexed: 11/12/2022]  Open
66
Majumder A, Straub JE. Addressing the Excessive Aggregation of Membrane Proteins in the MARTINI Model. J Chem Theory Comput 2021;17:2513-2521. [PMID: 33720709 DOI: 10.1021/acs.jctc.0c01253] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
67
Souza PCT, Alessandri R, Barnoud J, Thallmair S, Faustino I, Grünewald F, Patmanidis I, Abdizadeh H, Bruininks BMH, Wassenaar TA, Kroon PC, Melcr J, Nieto V, Corradi V, Khan HM, Domański J, Javanainen M, Martinez-Seara H, Reuter N, Best RB, Vattulainen I, Monticelli L, Periole X, Tieleman DP, de Vries AH, Marrink SJ. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nat Methods 2021;18:382-388. [PMID: 33782607 DOI: 10.1038/s41592-021-01098-3] [Citation(s) in RCA: 489] [Impact Index Per Article: 163.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/22/2021] [Indexed: 01/31/2023]
68
Kociurzynski R, Makshakova ON, Knecht V, Römer W. Multiscale Molecular Dynamics Studies Reveal Different Modes of Receptor Clustering by Gb3-Binding Lectins. J Chem Theory Comput 2021;17:2488-2501. [PMID: 33794087 DOI: 10.1021/acs.jctc.0c01145] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
69
Souza PCT, Limongelli V, Wu S, Marrink SJ, Monticelli L. Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Front Mol Biosci 2021;8:657222. [PMID: 33855050 PMCID: PMC8039319 DOI: 10.3389/fmolb.2021.657222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/05/2021] [Indexed: 01/12/2023]  Open
70
Casalini T. Not only in silico drug discovery: Molecular modeling towards in silico drug delivery formulations. J Control Release 2021;332:390-417. [PMID: 33675875 DOI: 10.1016/j.jconrel.2021.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/18/2022]
71
Mahmood MI, Poma AB, Okazaki KI. Optimizing Gō-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane. Front Mol Biosci 2021;8:619381. [PMID: 33693028 PMCID: PMC7937874 DOI: 10.3389/fmolb.2021.619381] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/14/2021] [Indexed: 12/31/2022]  Open
72
Wan M, Song J, Yang Y, Gao L, Fang W. Development of coarse-grained force field for alcohols: an efficient meta-multilinear interpolation parameterization algorithm. Phys Chem Chem Phys 2021;23:1956-1966. [PMID: 33464253 DOI: 10.1039/d0cp05503d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
73
Jarin Z, Newhouse J, Voth GA. Coarse-Grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding of the Origins of a MARTINI Hangover. J Chem Theory Comput 2021;17:1170-1180. [PMID: 33475352 PMCID: PMC7876797 DOI: 10.1021/acs.jctc.0c00638] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
74
Sica MP, Smulski CR. Coarse Grained Molecular Dynamic Simulations for the Study of TNF Receptor Family Members' Transmembrane Organization. Front Cell Dev Biol 2021;8:577278. [PMID: 33553138 PMCID: PMC7859260 DOI: 10.3389/fcell.2020.577278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/21/2020] [Indexed: 11/21/2022]  Open
75
Benayad Z, von Bülow S, Stelzl LS, Hummer G. Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model. J Chem Theory Comput 2021;17:525-537. [PMID: 33307683 PMCID: PMC7872324 DOI: 10.1021/acs.jctc.0c01064] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Indexed: 01/02/2023]
76
Caparotta M, Tomes CN, Mayorga LS, Masone D. The Synaptotagmin-1 C2B Domain Is a Key Regulator in the Stabilization of the Fusion Pore. J Chem Theory Comput 2020;16:7840-7851. [DOI: 10.1021/acs.jctc.0c00734] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
77
Mcl-1 and Bok transmembrane domains: Unexpected players in the modulation of apoptosis. Proc Natl Acad Sci U S A 2020;117:27980-27988. [PMID: 33093207 DOI: 10.1073/pnas.2008885117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
78
Ludwig J, Maibaum L. Effect of alcohol on the phase separation in model membranes. Chem Phys Lipids 2020;233:104986. [PMID: 33080278 DOI: 10.1016/j.chemphyslip.2020.104986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/20/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022]
79
Jussupow A, Messias AC, Stehle R, Geerlof A, Solbak SMØ, Paissoni C, Bach A, Sattler M, Camilloni C. The dynamics of linear polyubiquitin. SCIENCE ADVANCES 2020;6:6/42/eabc3786. [PMID: 33055165 PMCID: PMC7556843 DOI: 10.1126/sciadv.abc3786] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/25/2020] [Indexed: 05/17/2023]
80
Jayaraman K, Das AK, Luethi D, Szöllősi D, Schütz GJ, Reith MEA, Sitte HH, Stockner T. SLC6 transporter oligomerization. J Neurochem 2020;157:919-929. [PMID: 32767560 PMCID: PMC8247324 DOI: 10.1111/jnc.15145] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/18/2022]
81
Shivgan AT, Marzinek JK, Huber RG, Krah A, Henchman RH, Matsudaira P, Verma CS, Bond PJ. Extending the Martini Coarse-Grained Force Field to N-Glycans. J Chem Inf Model 2020;60:3864-3883. [PMID: 32702979 DOI: 10.1021/acs.jcim.0c00495] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
82
Rao R, Diharce J, Dugué B, Ostuni MA, Cadet F, Etchebest C. Versatile Dimerisation Process of Translocator Protein (TSPO) Revealed by an Extensive Sampling Based on a Coarse-Grained Dynamics Study. J Chem Inf Model 2020;60:3944-3957. [DOI: 10.1021/acs.jcim.0c00246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
83
Vaiwala R, Sharma P, Puranik M, Ayappa KG. Developing a Coarse-Grained Model for Bacterial Cell Walls: Evaluating Mechanical Properties and Free Energy Barriers. J Chem Theory Comput 2020;16:5369-5384. [DOI: 10.1021/acs.jctc.0c00539] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
84
Menon S, Sengupta N, Das P. Nanoscale Interplay of Membrane Composition and Amyloid Self-Assembly. J Phys Chem B 2020;124:5837-5846. [DOI: 10.1021/acs.jpcb.0c03796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
85
Löwe M, Kalacheva M, Boersma AJ, Kedrov A. The more the merrier: effects of macromolecular crowding on the structure and dynamics of biological membranes. FEBS J 2020;287:5039-5067. [DOI: 10.1111/febs.15429] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
86
Banerjee P, Lipowsky R, Santer M. Coarse-Grained Molecular Model for the Glycosylphosphatidylinositol Anchor with and without Protein. J Chem Theory Comput 2020;16:3889-3903. [PMID: 32392421 PMCID: PMC7303967 DOI: 10.1021/acs.jctc.0c00056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Indexed: 01/17/2023]
87
CX3CL1 homo-oligomerization drives cell-to-cell adherence. Sci Rep 2020;10:9069. [PMID: 32494000 PMCID: PMC7271195 DOI: 10.1038/s41598-020-65988-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/04/2020] [Indexed: 12/23/2022]  Open
88
Cholesterol-mediated oligomerization pathways of serotonin G-coupled receptor 5-HT2C. Int J Biol Macromol 2020;160:1090-1100. [PMID: 32485258 DOI: 10.1016/j.ijbiomac.2020.05.231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/23/2020] [Accepted: 05/26/2020] [Indexed: 12/22/2022]
89
Javanainen M, Ollila OHS, Martinez-Seara H. Rotational Diffusion of Membrane Proteins in Crowded Membranes. J Phys Chem B 2020;124:2994-3001. [PMID: 32188248 DOI: 10.1021/acs.jpcb.0c00884] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
90
Membrane mediated toppling mechanism of the folate energy coupling factor transporter. Nat Commun 2020;11:1763. [PMID: 32273501 PMCID: PMC7145868 DOI: 10.1038/s41467-020-15554-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/13/2020] [Indexed: 01/12/2023]  Open
91
Larsen AH, Wang Y, Bottaro S, Grudinin S, Arleth L, Lindorff-Larsen K. Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution. PLoS Comput Biol 2020;16:e1007870. [PMID: 32339173 PMCID: PMC7205321 DOI: 10.1371/journal.pcbi.1007870] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/07/2020] [Accepted: 04/13/2020] [Indexed: 11/18/2022]  Open
92
Gahbauer S, Böckmann RA. Comprehensive Characterization of Lipid-Guided G Protein-Coupled Receptor Dimerization. J Phys Chem B 2020;124:2823-2834. [DOI: 10.1021/acs.jpcb.0c00062] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
93
Hwang H, Hazel A, Lian P, Smith JC, Gumbart JC, Parks JM. A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. J Comput Chem 2020;41:528-537. [PMID: 31721253 PMCID: PMC7263448 DOI: 10.1002/jcc.26098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/17/2019] [Accepted: 10/14/2019] [Indexed: 12/28/2022]
94
Orioli S, Larsen AH, Bottaro S, Lindorff-Larsen K. How to learn from inconsistencies: Integrating molecular simulations with experimental data. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020;170:123-176. [PMID: 32145944 DOI: 10.1016/bs.pmbts.2019.12.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
95
Caparotta M, Bustos DM, Masone D. Order–disorder skewness in alpha-synuclein: a key mechanism to recognize membrane curvature. Phys Chem Chem Phys 2020;22:5255-5263. [DOI: 10.1039/c9cp04951g] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
96
Wäschenbach L, Gertzen CGW, Keitel V, Gohlke H. Dimerization energetics of the G-protein coupled bile acid receptor TGR5 from all-atom simulations. J Comput Chem 2019;41:874-884. [PMID: 31880348 DOI: 10.1002/jcc.26135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 12/20/2022]
97
Zhou W, Fiorin G, Anselmi C, Karimi-Varzaneh HA, Poblete H, Forrest LR, Faraldo-Gómez JD. Large-scale state-dependent membrane remodeling by a transporter protein. eLife 2019;8:50576. [PMID: 31855177 PMCID: PMC6957315 DOI: 10.7554/elife.50576] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/17/2019] [Indexed: 12/22/2022]  Open
98
Su Z, Wu Y. Computational simulations of TNF receptor oligomerization on plasma membrane. Proteins 2019;88:698-709. [PMID: 31710744 DOI: 10.1002/prot.25854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/30/2019] [Accepted: 11/05/2019] [Indexed: 12/21/2022]
99
Fu L, Wan M, Zhang S, Gao L, Fang W. Polymyxin B Loosens Lipopolysaccharide Bilayer but Stiffens Phospholipid Bilayer. Biophys J 2019;118:138-150. [PMID: 31812355 DOI: 10.1016/j.bpj.2019.11.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/31/2019] [Accepted: 11/08/2019] [Indexed: 12/17/2022]  Open
100
Fagerberg E, Lenton S, Skepö M. Evaluating Models of Varying Complexity of Crowded Intrinsically Disordered Protein Solutions Against SAXS. J Chem Theory Comput 2019;15:6968-6983. [DOI: 10.1021/acs.jctc.9b00723] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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