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For: Speranskiy K, Kurnikova M. Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: a case study of a glutamate molecule in water solution and in a protein-bound form. J Chem Phys 2007;121:1516-24. [PMID: 15260697 PMCID: PMC4492463 DOI: 10.1063/1.1752887] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Vibrational spectroscopy of imidazolium-based ionic liquids: A combined MD/DFT study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111282] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
2
Sakipov S, Sobolevsky AI, Kurnikova MG. Ion Permeation Mechanism in Epithelial Calcium Channel TRVP6. Sci Rep 2018;8:5715. [PMID: 29632318 PMCID: PMC5890290 DOI: 10.1038/s41598-018-23972-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/20/2018] [Indexed: 12/14/2022]  Open
3
Yelshanskaya MV, Mesbahi-Vasey S, Kurnikova MG, Sobolevsky AI. Role of the Ion Channel Extracellular Collar in AMPA Receptor Gating. Sci Rep 2017;7:1050. [PMID: 28432359 PMCID: PMC5430913 DOI: 10.1038/s41598-017-01146-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/21/2017] [Indexed: 11/09/2022]  Open
4
Offenbacher AR, Polander BC, Barry BA. An intrinsically disordered photosystem II subunit, PsbO, provides a structural template and a sensor of the hydrogen-bonding network in photosynthetic water oxidation. J Biol Chem 2013;288:29056-68. [PMID: 23940038 DOI: 10.1074/jbc.m113.487561] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
5
Floris FM, Filippi C, Amovilli C. A density functional and quantum Monte Carlo study of glutamic acid in vacuo and in a dielectric continuum medium. J Chem Phys 2013;137:075102. [PMID: 22920143 DOI: 10.1063/1.4746390] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
6
Pirc G, Stare J, Mavri J. Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate. J Chem Phys 2010;132:224506. [PMID: 20550407 DOI: 10.1063/1.3429251] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
7
Waegele MM, Gai F. Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water. J Phys Chem Lett 2010;1:781-786. [PMID: 20436926 PMCID: PMC2860969 DOI: 10.1021/jz900429z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
8
Pang J, Scrutton NS, Visser SPD, Sutcliffe MJ. Assignment of the Vibrational Spectra of Enzyme-Bound Tryptophan Tryptophyl Quinones Using a Combined QM/MM Approach. J Phys Chem A 2009;114:1212-7. [DOI: 10.1021/jp910161k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
9
Lindquist BA, Haws RT, Corcelli SA. Optimized Quantum Mechanics/Molecular Mechanics Strategies for Nitrile Vibrational Probes: Acetonitrile and para-Tolunitrile in Water and Tetrahydrofuran. J Phys Chem B 2008;112:13991-4001. [DOI: 10.1021/jp804900u] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
10
Mamonova T, Yonkunas MJ, Kurnikova MG. Energetics of the cleft closing transition and the role of electrostatic interactions in conformational rearrangements of the glutamate receptor ligand binding domain. Biochemistry 2008;47:11077-85. [PMID: 18823129 DOI: 10.1021/bi801367d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
11
Leenders EJM, Bolhuis PG, Meijer EJ. Microscopic Picture of the Aqueous Solvation of Glutamic Acid. J Chem Theory Comput 2008;4:898-907. [DOI: 10.1021/ct700344f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
12
Li S, Schmidt JR, Corcelli SA, Lawrence CP, Skinner JL. Approaches for the calculation of vibrational frequencies in liquids: comparison to benchmarks for azide/water clusters. J Chem Phys 2007;124:204110. [PMID: 16774322 DOI: 10.1063/1.2200690] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
13
FT-Raman and QM/MM study of the interaction between histamine and DNA. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2005.11.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
14
Mamonova T, Hespenheide B, Straub R, Thorpe MF, Kurnikova M. Protein flexibility using constraints from molecular dynamics simulations. Phys Biol 2005;2:S137-47. [PMID: 16280619 DOI: 10.1088/1478-3975/2/4/s08] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
15
Speranskiy K, Kurnikova M. On the Binding Determinants of the Glutamate Agonist with the Glutamate Receptor Ligand Binding Domain. Biochemistry 2005;44:11508-17. [PMID: 16114887 DOI: 10.1021/bi050547w] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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