• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4840639)   Today's Articles (10971)
For: Fukuyama K, Okada T, Kakuta Y, Takahashi Y. Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms: systematic distortion of [4Fe-4S] cluster in the protein. J Mol Biol 2002;315:1155-66. [PMID: 11827483 DOI: 10.1006/jmbi.2001.5292] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Number Cited by Other Article(s)
1
Min J, Ali F, Brooks BR, Bruce BD, Amin M. Predicting Iron-Sulfur Cluster Redox Potentials: A Simple Model Derived from Protein Structures. ACS OMEGA 2025;10:15790-15798. [PMID: 40291006 PMCID: PMC12019745 DOI: 10.1021/acsomega.5c01976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2025] [Revised: 04/02/2025] [Accepted: 04/04/2025] [Indexed: 04/30/2025]
2
Landry L, Li P. Parameterization of a Fluctuating Charge Model for Complexes Containing 3d Transition Metals. J Phys Chem B 2024;128:10329-10338. [PMID: 39395013 DOI: 10.1021/acs.jpcb.4c03219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2024]
3
Syed K. Ferredoxins: Functions, Evolution, Potential Applications, and Challenges of Subtype Classification. Curr Issues Mol Biol 2024;46:9659-9673. [PMID: 39329926 PMCID: PMC11430716 DOI: 10.3390/cimb46090574] [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: 08/03/2024] [Revised: 08/27/2024] [Accepted: 08/31/2024] [Indexed: 09/28/2024]  Open
4
Jafari S, Ryde U, Irani M. Two local minima for structures of [4Fe-4S] clusters obtained with density functional theory methods. Sci Rep 2023;13:10832. [PMID: 37402767 PMCID: PMC10319735 DOI: 10.1038/s41598-023-37755-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023]  Open
5
Kanda T, Saito K, Ishikita H. Mechanism of Mixed-Valence Fe2.5+···Fe2.5+ Formation in Fe4S4 Clusters in the Ferredoxin Binding Motif. J Phys Chem B 2022;126:3059-3066. [PMID: 35435680 PMCID: PMC9059760 DOI: 10.1021/acs.jpcb.2c01320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
6
Jafari S, Tavares Santos YA, Bergmann J, Irani M, Ryde U. Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins. Inorg Chem 2022;61:5991-6007. [PMID: 35403427 PMCID: PMC9044450 DOI: 10.1021/acs.inorgchem.1c03422] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
7
Theoretical Study on Redox Potential Control of Iron-Sulfur Cluster by Hydrogen Bonds: A Possibility of Redox Potential Programming. Molecules 2021;26:molecules26206129. [PMID: 34684710 PMCID: PMC8538827 DOI: 10.3390/molecules26206129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/02/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022]  Open
8
Kanda T, Saito K, Ishikita H. Electron Acceptor-Donor Iron Sites in the Iron-Sulfur Cluster of Photosynthetic Electron-Transfer Pathways. J Phys Chem Lett 2021;12:7431-7438. [PMID: 34338530 DOI: 10.1021/acs.jpclett.1c01896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
9
Li B, Steindel P, Haddad N, Elliott SJ. Maximizing (Electro)catalytic CO2 Reduction with a Ferredoxin-Based Reduction Potential Gradient. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
10
Miyagawa K, Shoji M, Isobe H, Yamanaka S, Kawakami T, Okumura M, Yamaguchi K. Theory of chemical bonds in metalloenzymes XXIV electronic and spin structures of FeMoco and Fe-S clusters by classical and quantum computing. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1760388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
11
Miyagawa K, Shoji M, Isobe H, Yamanaka S, Kawakami T, Okumura M, Yamaguchi K. UNO(ULO) active space for multireference calculations on classical and quantum computers. Revisit to the iron-sulfur complexes. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
12
Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
13
The competition between chemistry and biology in assembling iron-sulfur derivatives. Molecular structures and electrochemistry. Part IV. {[Fe3S4](SγCys)3} proteins. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.09.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
14
Trasviña-Arenas CH, Lopez-Castillo LM, Sanchez-Sandoval E, Brieba LG. Dispensability of the [4Fe-4S] cluster in novel homologues of adenine glycosylase MutY. FEBS J 2016;283:521-40. [PMID: 26613369 DOI: 10.1111/febs.13608] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 11/15/2015] [Accepted: 11/24/2015] [Indexed: 01/31/2023]
15
Blachly PG, Sandala GM, Giammona D, Liu T, Bashford D, McCammon JA, Noodleman L. Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition. J Chem Theory Comput 2014;10:3871-3884. [PMID: 25221444 PMCID: PMC4159220 DOI: 10.1021/ct5005214] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Indexed: 12/31/2022]
16
Tobi D. Normal Mode Dynamics Comparison of Proteins. Isr J Chem 2014. [DOI: 10.1002/ijch.201300142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
17
Sobolev OV. Detection of alternative conformations:Shift_plotandAC_predictionprograms. J Appl Crystallogr 2013. [DOI: 10.1107/s0021889812052065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
18
Mitra D, George SJ, Guo Y, Kamali S, Keable S, Peters JW, Pelmenschikov V, Case DA, Cramer SP. Characterization of [4Fe-4S] cluster vibrations and structure in nitrogenase Fe protein at three oxidation levels via combined NRVS, EXAFS, and DFT analyses. J Am Chem Soc 2013;135:2530-43. [PMID: 23282058 DOI: 10.1021/ja307027n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
19
Mitra D, Pelmenschikov V, Guo Y, Case DA, Wang H, Dong W, Tan ML, Ichiye T, Jenney FE, Adams MWW, Yoda Y, Zhao J, Cramer SP. Dynamics of the [4Fe-4S] cluster in Pyrococcus furiosus D14C ferredoxin via nuclear resonance vibrational and resonance Raman spectroscopies, force field simulations, and density functional theory calculations. Biochemistry 2011;50:5220-35. [PMID: 21500788 DOI: 10.1021/bi200046p] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
20
Crystal structures of the all-cysteinyl-coordinated D14C variant of Pyrococcus furiosus ferredoxin: [4Fe–4S] ↔ [3Fe–4S] cluster conversion. J Biol Inorg Chem 2011;16:763-75. [DOI: 10.1007/s00775-011-0778-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 03/25/2011] [Indexed: 10/18/2022]
21
Niu S, Ichiye T. Insight into environmental effects on bonding and redox properties of [4Fe-4S] clusters in proteins. J Am Chem Soc 2009;131:5724-5. [PMID: 19341280 DOI: 10.1021/ja900406j] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
22
Groysman S, Holm RH. Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites. Biochemistry 2009;48:2310-20. [PMID: 19206188 PMCID: PMC2765533 DOI: 10.1021/bi900044e] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
23
Insight into the protein and solvent contributions to the reduction potentials of [4Fe-4S]2+/+ clusters: crystal structures of the Allochromatium vinosum ferredoxin variants C57A and V13G and the homologous Escherichia coli ferredoxin. J Biol Inorg Chem 2009;14:783-99. [PMID: 19290553 DOI: 10.1007/s00775-009-0492-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 02/26/2009] [Indexed: 10/21/2022]
24
Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM. Structural analysis of metal sites in proteins: non-heme iron sites as a case study. J Mol Biol 2009;388:356-80. [PMID: 19265704 DOI: 10.1016/j.jmb.2009.02.052] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 02/19/2009] [Accepted: 02/19/2009] [Indexed: 11/24/2022]
25
Karcher A, Schele A, Hopfner KP. X-ray structure of the complete ABC enzyme ABCE1 from Pyrococcus abyssi. J Biol Chem 2007;283:7962-71. [PMID: 18160405 DOI: 10.1074/jbc.m707347200] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
26
Antonkine ML, Maes EM, Czernuszewicz RS, Breitenstein C, Bill E, Falzone CJ, Balasubramanian R, Lubner C, Bryant DA, Golbeck JH. Chemical rescue of a site-modified ligand to a [4Fe–4S] cluster in PsaC, a bacterial-like dicluster ferredoxin bound to Photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007;1767:712-24. [PMID: 17434441 DOI: 10.1016/j.bbabio.2007.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Revised: 01/21/2007] [Accepted: 02/02/2007] [Indexed: 10/23/2022]
27
Villa A, Fan H, Wassenaar T, Mark AE. How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field? J Phys Chem B 2007;111:6015-25. [PMID: 17489626 DOI: 10.1021/jp068580v] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
28
Giastas P, Pinotsis N, Efthymiou G, Wilmanns M, Kyritsis P, Moulis JM, Mavridis IM. The structure of the 2[4Fe-4S] ferredoxin from Pseudomonas aeruginosa at 1.32-A resolution: comparison with other high-resolution structures of ferredoxins and contributing structural features to reduction potential values. J Biol Inorg Chem 2006;11:445-58. [PMID: 16596388 DOI: 10.1007/s00775-006-0094-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 02/09/2006] [Indexed: 10/24/2022]
29
Xiao Y, Koutmos M, Case DA, Coucouvanis D, Wang H, Cramer SP. Dynamics of an [Fe4S4(SPh)4]2- cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using 36S substitution, DFT calculations, and empirical force fields. Dalton Trans 2006:2192-201. [PMID: 16673033 DOI: 10.1039/b513331a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
30
Shirakawa T, Takahashi Y, Wada K, Hirota J, Takao T, Ohmori D, Fukuyama K. Identification of variant molecules of Bacillus thermoproteolyticus ferredoxin: crystal structure reveals bound coenzyme A and an unexpected [3Fe-4S] cluster associated with a canonical [4Fe-4S] ligand motif. Biochemistry 2005;44:12402-10. [PMID: 16156653 DOI: 10.1021/bi0508441] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
31
Walters MA, Roche CL, Rheingold AL, Kassel SW. N-H···S Hydrogen Bonds in a Ferredoxin Model. Inorg Chem 2005;44:3777-9. [PMID: 15907101 DOI: 10.1021/ic048208z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
32
Dey A, Glaser T, Couture MMJ, Eltis LD, Holm RH, Hedman B, Hodgson KO, Solomon EI. Ligand K-Edge X-ray Absorption Spectroscopy of [Fe4S4]1+,2+,3+ Clusters:  Changes in Bonding and Electronic Relaxation upon Redox. J Am Chem Soc 2004;126:8320-8. [PMID: 15225075 DOI: 10.1021/ja0484956] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
33
Venkateswara Rao P, Holm RH. Synthetic Analogues of the Active Sites of Iron−Sulfur Proteins. Chem Rev 2004;104:527-59. [PMID: 14871134 DOI: 10.1021/cr020615+] [Citation(s) in RCA: 430] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
34
Dauter Z. Protein structures at atomic resolution. Methods Enzymol 2004;368:288-337. [PMID: 14674280 DOI: 10.1016/s0076-6879(03)68016-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
35
Fan H, Mark AE. Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study. Proteins 2003;53:111-20. [PMID: 12945054 DOI: 10.1002/prot.10496] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
36
Fee JA, Castagnetto JM, Case DA, Noodleman L, Stout CD, Torres RA. The circumsphere as a tool to assess distortion in [4Fe-4S] atom clusters. J Biol Inorg Chem 2003;8:519-526. [PMID: 12632271 DOI: 10.1007/s00775-003-0445-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2002] [Accepted: 01/23/2003] [Indexed: 11/25/2022]
PrevPage 1 of 1 1Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA