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For: Gunner MR, Mao J, Song Y, Kim J. Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations. Biochim Biophys Acta 2006;1757:942-68. [PMID: 16905113 PMCID: PMC2760439 DOI: 10.1016/j.bbabio.2006.06.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Revised: 06/07/2006] [Accepted: 06/13/2006] [Indexed: 11/15/2022]
Number Cited by Other Article(s)
1
Jain A, Judy E, Kishore N. Analytical Aspects of ANSA-BSA Association: A Thermodynamic and Conformational Approach. J Phys Chem B 2024;128:5344-5362. [PMID: 38773936 DOI: 10.1021/acs.jpcb.4c01751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
2
Lasham J, Djurabekova A, Zickermann V, Vonck J, Sharma V. Role of Protonation States in the Stability of Molecular Dynamics Simulations of High-Resolution Membrane Protein Structures. J Phys Chem B 2024;128:2304-2316. [PMID: 38430110 PMCID: PMC11389979 DOI: 10.1021/acs.jpcb.3c07421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
3
Mazmanian K, Chen T, Sargsyan K, Lim C. From quantum-derived principles underlying cysteine reactivity to combating the COVID-19 pandemic. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022;12:e1607. [PMID: 35600063 PMCID: PMC9111396 DOI: 10.1002/wcms.1607] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/31/2022] [Accepted: 02/13/2022] [Indexed: 12/20/2022]
4
Ali F, Shafaa MW, Amin M. Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I. BIOLOGY 2022;11:362. [PMID: 35336736 PMCID: PMC8945787 DOI: 10.3390/biology11030362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022]
5
Ovung A, Mavani A, Ghosh A, Chatterjee S, Das A, Suresh Kumar G, Ray D, Aswal VK, Bhattacharyya J. Heme Protein Binding of Sulfonamide Compounds: A Correlation Study by Spectroscopic, Calorimetric, and Computational Methods. ACS OMEGA 2022;7:4932-4944. [PMID: 35187312 PMCID: PMC8851458 DOI: 10.1021/acsomega.1c05554] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/24/2022] [Indexed: 05/16/2023]
6
Kaur D, Khaniya U, Zhang Y, Gunner MR. Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient. Front Chem 2021;9:660954. [PMID: 34211960 PMCID: PMC8239185 DOI: 10.3389/fchem.2021.660954] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022]  Open
7
Johé P, Jaenicke E, Neuweiler H, Schirmeister T, Kersten C, Hellmich UA. Structure, interdomain dynamics, and pH-dependent autoactivation of pro-rhodesain, the main lysosomal cysteine protease from African trypanosomes. J Biol Chem 2021;296:100565. [PMID: 33745969 PMCID: PMC8080524 DOI: 10.1016/j.jbc.2021.100565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/18/2021] [Accepted: 03/17/2021] [Indexed: 02/06/2023]  Open
8
Hofer F, Kraml J, Kahler U, Kamenik AS, Liedl KR. Catalytic Site pKa Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations. J Chem Inf Model 2020;60:3030-3042. [PMID: 32348143 PMCID: PMC7312390 DOI: 10.1021/acs.jcim.0c00190] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
9
Cruzeiro VWD, Feliciano GT, Roitberg AE. Exploring Coupled Redox and pH Processes with a Force-Field-Based Approach: Applications to Five Different Systems. J Am Chem Soc 2020;142:3823-3835. [PMID: 32011132 DOI: 10.1021/jacs.9b11433] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
10
Hofer F, Dietrich V, Kamenik AS, Tollinger M, Liedl KR. pH-Dependent Protonation of the Phl p 6 Pollen Allergen Studied by NMR and cpH-aMD. J Chem Theory Comput 2019;15:5716-5726. [PMID: 31476118 PMCID: PMC6994067 DOI: 10.1021/acs.jctc.9b00540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
11
A Membrane-Bound Cytochrome Enables Methanosarcina acetivorans To Conserve Energy from Extracellular Electron Transfer. mBio 2019;10:mBio.00789-19. [PMID: 31431545 PMCID: PMC6703419 DOI: 10.1128/mbio.00789-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
12
Pang S, Yang J, Zhao Y, Li Y, Wang J. Computational prediction and functional analysis of arsenic-binding proteins in human cells. QUANTITATIVE BIOLOGY 2019. [DOI: 10.1007/s40484-019-0169-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
13
Cossettini A, Selmi L, Cossettini A, Selmi L, Selmi L, Cossettini A. On the Response of Nanoelectrode Impedance Spectroscopy Measures to Plant, Animal, and Human Viruses. IEEE Trans Nanobioscience 2019;17:102-109. [PMID: 29870333 DOI: 10.1109/tnb.2018.2826919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
14
Cruzeiro VWD, Roitberg AE. Multidimensional Replica Exchange Simulations for Efficient Constant pH and Redox Potential Molecular Dynamics. J Chem Theory Comput 2019;15:871-881. [DOI: 10.1021/acs.jctc.8b00935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
15
Cruzeiro VWD, Amaral MS, Roitberg AE. Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation. J Chem Phys 2018;149:072338. [DOI: 10.1063/1.5027379] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
16
Zhang H, Wu W, Mo Y. Study of proton-coupled electron transfer (PCET) with four explicit diabatic states at the ab initio level. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
17
Gunner MR, Koder R. The design features cells use to build their transmembrane proton gradient. Phys Biol 2017;14:013001. [DOI: 10.1088/1478-3975/14/1/013001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
18
Electrogenic steps of light-driven proton transport in ESR, a retinal protein from Exiguobacterium sibiricum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016;1857:1741-1750. [DOI: 10.1016/j.bbabio.2016.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/06/2016] [Accepted: 08/11/2016] [Indexed: 02/01/2023]
19
Cornish AJ, Ginovska B, Thelen A, da Silva JCS, Soares TA, Raugei S, Dupuis M, Shaw WJ, Hegg EL. Single-Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-Hydrogenase. Biochemistry 2016;55:3165-73. [PMID: 27186945 DOI: 10.1021/acs.biochem.5b01044] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
20
Ge X, Gunner MR. Unraveling the mechanism of proton translocation in the extracellular half-channel of bacteriorhodopsin. Proteins 2016;84:639-54. [DOI: 10.1002/prot.25013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 01/24/2016] [Accepted: 02/04/2016] [Indexed: 01/06/2023]
21
Olson TL, Espiritu E, Edwardraja S, Simmons CR, Williams JC, Ghirlanda G, Allen JP. Design of dinuclear manganese cofactors for bacterial reaction centers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015;1857:539-547. [PMID: 26392146 DOI: 10.1016/j.bbabio.2015.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/14/2015] [Indexed: 12/28/2022]
22
Amin M, Vogt L, Szejgis W, Vassiliev S, Brudvig GW, Bruce D, Gunner MR. Proton-Coupled Electron Transfer During the S-State Transitions of the Oxygen-Evolving Complex of Photosystem II. J Phys Chem B 2015;119:7366-77. [PMID: 25575266 DOI: 10.1021/jp510948e] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
23
Morozova OB, Yurkovskaya AV. Modulation of the Rate of Reversible Electron Transfer in Oxidized Tryptophan and Tyrosine Containing Peptides in Acidic Aqueous Solution. J Phys Chem B 2014;119:140-9. [DOI: 10.1021/jp511068n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
24
Halorhodopsin pumps Cl- and bacteriorhodopsin pumps protons by a common mechanism that uses conserved electrostatic interactions. Proc Natl Acad Sci U S A 2014;111:16377-82. [PMID: 25362051 DOI: 10.1073/pnas.1411119111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
25
Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014;114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 584] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
26
Zizzari ZV, Smolders I, Koene JM. Alternative delivery of male accessory gland products. Front Zool 2014;11:32. [PMID: 24708537 PMCID: PMC3984499 DOI: 10.1186/1742-9994-11-32] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 04/01/2014] [Indexed: 02/04/2023]  Open
27
Dutta A, Lense S, Hou J, Engelhard MH, Roberts JAS, Shaw WJ. Minimal proton channel enables H2 oxidation and production with a water-soluble nickel-based catalyst. J Am Chem Soc 2013;135:18490-6. [PMID: 24206187 DOI: 10.1021/ja407826d] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
28
Gunner MR, Amin M, Zhu X, Lu J. Molecular mechanisms for generating transmembrane proton gradients. BIOCHIMICA ET BIOPHYSICA ACTA 2013;1827:892-913. [PMID: 23507617 PMCID: PMC3714358 DOI: 10.1016/j.bbabio.2013.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/28/2013] [Accepted: 03/01/2013] [Indexed: 01/02/2023]
29
Brzezinski P, Öjemyr LN, Ädelroth P. Intermediates generated during the reaction of reduced Rhodobacter sphaeroides cytochrome c oxidase with dioxygen. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013;1827:843-7. [DOI: 10.1016/j.bbabio.2013.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/18/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
30
Amin M, Vogt L, Vassiliev S, Rivalta I, Sultan MM, Bruce D, Brudvig GW, Batista VS, Gunner MR. Electrostatic effects on proton coupled electron transfer in oxomanganese complexes inspired by the oxygen-evolving complex of photosystem II. J Phys Chem B 2013;117:6217-26. [PMID: 23570540 DOI: 10.1021/jp403321b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
31
Paasche A, Schirmeister T, Engels B. Benchmark Study for the Cysteine-Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches. J Chem Theory Comput 2013;9:1765-77. [PMID: 26587634 DOI: 10.1021/ct301082y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
32
Renger T, Müh F. Understanding photosynthetic light-harvesting: a bottom up theoretical approach. Phys Chem Chem Phys 2013;15:3348-71. [PMID: 23361062 DOI: 10.1039/c3cp43439g] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
33
Wang L, Luan Q, Yang D, Yao X, Zhou K. Strong electron-conjugation interaction facilitates electron transfer of hemoglobin by Ce(OH)3 nanorods. RSC Adv 2013. [DOI: 10.1039/c3ra40336j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
34
Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012;112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
35
Di Russo NV, Estrin DA, Martí MA, Roitberg AE. pH-Dependent conformational changes in proteins and their effect on experimental pK(a)s: the case of Nitrophorin 4. PLoS Comput Biol 2012;8:e1002761. [PMID: 23133364 PMCID: PMC3486867 DOI: 10.1371/journal.pcbi.1002761] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 09/13/2012] [Indexed: 11/21/2022]  Open
36
Site saturation mutagenesis demonstrates a central role for cysteine 298 as proton donor to the catalytic site in CaHydA [FeFe]-hydrogenase. PLoS One 2012;7:e48400. [PMID: 23133586 PMCID: PMC3485046 DOI: 10.1371/journal.pone.0048400] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/25/2012] [Indexed: 01/24/2023]  Open
37
Trana EN, Nocek JM, Knutson AK, Hoffman BM. Evolving the [myoglobin, cytochrome b(5)] complex from dynamic toward simple docking: charging the electron transfer reactive patch. Biochemistry 2012;51:8542-53. [PMID: 23067206 DOI: 10.1021/bi301134f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
38
Lošdorfer Božič A, Siber A, Podgornik R. How simple can a model of an empty viral capsid be? Charge distributions in viral capsids. J Biol Phys 2012;38:657-71. [PMID: 24615225 PMCID: PMC3473132 DOI: 10.1007/s10867-012-9278-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 07/13/2012] [Indexed: 12/21/2022]  Open
39
Ullmann RT, Andrade SLA, Ullmann GM. Thermodynamics of transport through the ammonium transporter Amt-1 investigated with free energy calculations. J Phys Chem B 2012;116:9690-703. [PMID: 22804733 DOI: 10.1021/jp305440f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
40
Yuan S, Le Roy K, Venken T, Lammens W, Van den Ende W, De Maeyer M. pKa modulation of the acid/base catalyst within GH32 and GH68: a role in substrate/inhibitor specificity? PLoS One 2012;7:e37453. [PMID: 22662155 PMCID: PMC3360783 DOI: 10.1371/journal.pone.0037453] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 04/21/2012] [Indexed: 11/18/2022]  Open
41
Nazmutdinov RR, Bronshtein MD, Zinkicheva TT, Chi Q, Zhang J, Ulstrup J. Modeling and computations of the intramolecular electron transfer process in the two-heme protein cytochrome c(4). Phys Chem Chem Phys 2012;14:5953-65. [PMID: 22430606 DOI: 10.1039/c2cp24084j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
42
Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. J Comput Aided Mol Des 2012;26:475-87. [PMID: 22366955 DOI: 10.1007/s10822-012-9554-1] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 02/13/2012] [Indexed: 10/28/2022]
43
Ullmann RT, Ullmann GM. GMCT : a Monte Carlo simulation package for macromolecular receptors. J Comput Chem 2012;33:887-900. [PMID: 22278916 DOI: 10.1002/jcc.22919] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/21/2011] [Accepted: 12/02/2011] [Indexed: 11/08/2022]
44
Riccardi D, Zhu X, Goyal P, Yang S, Hou G, Cui Q. Toward molecular models of proton pumping: Challenges, methods and relevant applications. Sci China Chem 2011. [DOI: 10.1007/s11426-011-4458-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
45
Nielsen JE, Gunner MR, Bertrand García-Moreno E. The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins. Proteins 2011;79:3249-59. [PMID: 22002877 PMCID: PMC3375608 DOI: 10.1002/prot.23194] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 09/13/2011] [Indexed: 12/13/2022]
46
Ullmann RT, Ullmann GM. Coupling of Protonation, Reduction, and Conformational Change in azurin from Pseudomonas aeruginosa Investigated with Free Energy Measures of Cooperativity. J Phys Chem B 2011;115:10346-59. [DOI: 10.1021/jp204644h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
47
Mellor BL, Cruz Cortés E, Busath DD, Mazzeo BA. Method for Estimating the Internal Permittivity of Proteins Using Dielectric Spectroscopy. J Phys Chem B 2011;115:2205-13. [DOI: 10.1021/jp1111873] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
48
Gamiz-Hernandez AP, Kieseritzky G, Ishikita H, Knapp EW. Rubredoxin Function: Redox Behavior from Electrostatics. J Chem Theory Comput 2011;7:742-52. [DOI: 10.1021/ct100476h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. J Chem Theory Comput 2011;7:525-37. [PMID: 26596171 DOI: 10.1021/ct100578z] [Citation(s) in RCA: 2930] [Impact Index Per Article: 225.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ma L, Sundlass NK, Raines RT, Cui Q. Disruption and formation of surface salt bridges are coupled to DNA binding by the integration host factor: a computational analysis. Biochemistry 2010;50:266-75. [PMID: 21121696 DOI: 10.1021/bi101096k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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