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For: Song Y, Mao J, Gunner MR. Electrostatic environment of hemes in proteins: pK(a)s of hydroxyl ligands. Biochemistry 2006;45:7949-58. [PMID: 16800621 PMCID: PMC2727071 DOI: 10.1021/bi052182l] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Podgorski MN, Harbort JS, Lee JHZ, Nguyen GT, Bruning JB, Donald WA, Bernhardt PV, Harmer JR, Bell SG. An Altered Heme Environment in an Engineered Cytochrome P450 Enzyme Enables the Switch from Monooxygenase to Peroxygenase Activity. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05877] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
2
Röhrig UF, Majjigapu SR, Reynaud A, Pojer F, Dilek N, Reichenbach P, Ascencao K, Irving M, Coukos G, Vogel P, Michielin O, Zoete V. Azole-Based Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors. J Med Chem 2021;64:2205-2227. [PMID: 33557523 DOI: 10.1021/acs.jmedchem.0c01968] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
3
Cai X, Son CY, Mao J, Kaur D, Zhang Y, Khaniya U, Cui Q, Gunner MR. Identifying the proton loading site cluster in the ba3 cytochrome c oxidase that loads and traps protons. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020;1861:148239. [PMID: 32531221 DOI: 10.1016/j.bbabio.2020.148239] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/05/2020] [Accepted: 06/04/2020] [Indexed: 12/29/2022]
4
Zhang Y, Wang J, Yuan C, Liu W, Tan H, Li X, Chen G. Ruffling drives coproheme decarboxylation by facilitating PCET: a theoretical investigation of ChdC. Phys Chem Chem Phys 2020;22:16117-16124. [DOI: 10.1039/d0cp02690e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
5
Tracing the Pathways of Waters and Protons in Photosystem II and Cytochrome c Oxidase. INORGANICS 2019. [DOI: 10.3390/inorganics7020014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
6
Wu X, Clavaguera C, Lagardère L, Piquemal JP, de la Lande A. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms. J Chem Theory Comput 2018;14:2705-2720. [PMID: 29630819 DOI: 10.1021/acs.jctc.7b01128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
7
Analyzing the electrogenicity of cytochrome c oxidase. Proc Natl Acad Sci U S A 2016;113:7810-5. [PMID: 27357681 DOI: 10.1073/pnas.1608118113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
8
Lichtenstein BR, Bialas C, Cerda JF, Fry BA, Dutton PL, Moser CC. Designing Light-Activated Charge-Separating Proteins with a Naphthoquinone Amino Acid. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
9
Lichtenstein BR, Bialas C, Cerda JF, Fry BA, Dutton PL, Moser CC. Designing Light-Activated Charge-Separating Proteins with a Naphthoquinone Amino Acid. Angew Chem Int Ed Engl 2015;54:13626-9. [PMID: 26366882 DOI: 10.1002/anie.201507094] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 11/09/2022]
10
Boaz NC, Bell SR, Groves JT. Ferryl protonation in oxoiron(IV) porphyrins and its role in oxygen transfer. J Am Chem Soc 2015;137:2875-85. [PMID: 25651467 PMCID: PMC4363944 DOI: 10.1021/ja508759t] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
11
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]
12
Spectroscopic characterization of the acid-alkaline transition of a thermophilic cytochrome P450. FEBS Lett 2012. [DOI: 10.1016/j.febslet.2012.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
13
Popović DM, Stuchebrukhov AA. Coupled electron and proton transfer reactions during the O→E transition in bovine cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011;1817:506-17. [PMID: 22086149 DOI: 10.1016/j.bbabio.2011.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/27/2011] [Accepted: 10/29/2011] [Indexed: 11/30/2022]
14
Madeo J, Mihajlovic M, Lazaridis T, Gunner MR. Slow dissociation of a charged ligand: analysis of the primary quinone Q(A) site of photosynthetic bacterial reaction centers. J Am Chem Soc 2011;133:17375-85. [PMID: 21863833 PMCID: PMC3202297 DOI: 10.1021/ja205811f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Indexed: 12/14/2022]
15
Chakrabarty S, Namslauer I, Brzezinski P, Warshel A. Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011;1807:413-26. [PMID: 21232525 DOI: 10.1016/j.bbabio.2011.01.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 12/22/2010] [Accepted: 01/05/2011] [Indexed: 10/18/2022]
16
Kaila VR, Sharma V, Wikström M. The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011;1807:80-4. [DOI: 10.1016/j.bbabio.2010.08.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 08/26/2010] [Accepted: 08/31/2010] [Indexed: 10/19/2022]
17
Zhang J, Gunner MR. Multiconformation continuum electrostatics analysis of the effects of a buried Asp introduced near heme a in Rhodobacter sphaeroides cytochrome c oxidase. Biochemistry 2010;49:8043-52. [PMID: 20701325 DOI: 10.1021/bi100663u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
18
Song Y, Mao J, Gunner MR. MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling. J Comput Chem 2009;30:2231-47. [PMID: 19274707 PMCID: PMC2735604 DOI: 10.1002/jcc.21222] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
19
Zheng Z, Gunner MR. Analysis of the electrochemistry of hemes with E(m)s spanning 800 mV. Proteins 2009;75:719-34. [PMID: 19003997 DOI: 10.1002/prot.22282] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
20
Tejero J, Biswas A, Wang ZQ, Page RC, Haque MM, Hemann C, Zweier JL, Misra S, Stuehr DJ. Stabilization and characterization of a heme-oxy reaction intermediate in inducible nitric-oxide synthase. J Biol Chem 2008;283:33498-507. [PMID: 18815130 PMCID: PMC2586280 DOI: 10.1074/jbc.m806122200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 09/24/2008] [Indexed: 11/06/2022]  Open
21
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase. Proc Natl Acad Sci U S A 2008;105:7726-31. [PMID: 18509049 DOI: 10.1073/pnas.0800580105] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
22
Side-chain protonation and mobility in the sarcoplasmic reticulum Ca2+-ATPase: implications for proton countertransport and Ca2+ release. Biophys J 2007;93:3259-70. [PMID: 17938423 DOI: 10.1529/biophysj.107.109363] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
23
Andersson J, Hauser K, Karjalainen EL, Barth A. Protonation and hydrogen bonding of Ca2+ site residues in the E2P phosphoenzyme intermediate of sarcoplasmic reticulum Ca2+-ATPase studied by a combination of infrared spectroscopy and electrostatic calculations. Biophys J 2007;94:600-11. [PMID: 17890386 PMCID: PMC2157260 DOI: 10.1529/biophysj.107.114033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
24
Stojanović SD, Medaković VB, Predović G, Beljanski M, Zarić SD. XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins. J Biol Inorg Chem 2007;12:1063-71. [PMID: 17659366 DOI: 10.1007/s00775-007-0276-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 06/28/2007] [Indexed: 11/29/2022]
25
Olsson MHM, Siegbahn PEM, Blomberg MRA, Warshel A. Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives. BIOCHIMICA ET BIOPHYSICA ACTA 2007;1767:244-60. [PMID: 17350588 PMCID: PMC2025695 DOI: 10.1016/j.bbabio.2007.01.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 01/19/2007] [Accepted: 01/24/2007] [Indexed: 11/28/2022]
26
Song Y, Michonova-Alexova E, Gunner MR. Calculated proton uptake on anaerobic reduction of cytochrome C oxidase: is the reaction electroneutral? Biochemistry 2006;45:7959-75. [PMID: 16800622 PMCID: PMC2727075 DOI: 10.1021/bi052183d] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
27
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. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 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] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Revised: 06/07/2006] [Accepted: 06/13/2006] [Indexed: 11/15/2022]
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