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For: Andreini C, Cavallaro G, Lorenzini S, Rosato A. MetalPDB: a database of metal sites in biological macromolecular structures. Nucleic Acids Res 2012;41:D312-9. [PMID: 23155064 PMCID: PMC3531106 DOI: 10.1093/nar/gks1063] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
Number Cited by Other Article(s)
1
Zahra I, DeVine L, Cole R, Malik HA, Wu J, Wen J, Hedfi A, Liaqat A, Ijaz R, Ramzan U, Shakoori AR, Shakoori FR, Betenbaugh MJ. Insights into the differential proteome landscape of a newly isolated Paramecium multimicronucleatum in response to cadmium stress. J Proteomics 2024;300:105178. [PMID: 38636824 DOI: 10.1016/j.jprot.2024.105178] [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] [Received: 02/29/2024] [Revised: 04/01/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
2
Bazayeva M, Andreini C, Rosato A. A database overview of metal-coordination distances in metalloproteins. Acta Crystallogr D Struct Biol 2024;80:362-376. [PMID: 38682667 PMCID: PMC11066882 DOI: 10.1107/s2059798324003152] [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: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 05/01/2024]  Open
3
Sgueglia G, Vrettas MD, Chino M, De Simone A, Lombardi A. MetalHawk: Enhanced Classification of Metal Coordination Geometries by Artificial Neural Networks. J Chem Inf Model 2024;64:2356-2367. [PMID: 37956388 PMCID: PMC11005052 DOI: 10.1021/acs.jcim.3c00873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
4
Edholm F, Nandy A, Reinhardt CR, Kastner DW, Kulik HJ. Protein3D: Enabling analysis and extraction of metal-containing sites from the Protein Data Bank with molSimplify. J Comput Chem 2024;45:352-361. [PMID: 37873926 DOI: 10.1002/jcc.27242] [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: 08/09/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
5
Kim M, Le MT, Fan L, Campbell C, Sen S, Capdevila DA, Stemmler TL, Giedroc DP. Characterization of the Zinc Uptake Repressor (Zur) from Acinetobacter baumannii. Biochemistry 2024;63:660-670. [PMID: 38385972 PMCID: PMC11019503 DOI: 10.1021/acs.biochem.3c00679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
6
Luther P, Boyle AL. Differences in heavy metal binding to cysteine-containing coiled-coil peptides. J Pept Sci 2024;30:e3549. [PMID: 37828738 DOI: 10.1002/psc.3549] [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] [Received: 06/14/2023] [Revised: 09/21/2023] [Accepted: 09/24/2023] [Indexed: 10/14/2023]
7
Jafari M, Li Z, Song LF, Sagresti L, Brancato G, Merz KM. Thermodynamics of Metal-Acetate Interactions. J Phys Chem B 2024;128:684-697. [PMID: 38226860 DOI: 10.1021/acs.jpcb.3c06567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
8
Orzel B, Pelucelli A, Ostrowska M, Potocki S, Kozlowski H, Peana M, Gumienna-Kontecka E. Fe(II), Mn(II), and Zn(II) Binding to the C-Terminal Region of FeoB Protein: An Insight into the Coordination Chemistry and Specificity of the Escherichia coli Fe(II) Transporter. Inorg Chem 2023;62:18607-18624. [PMID: 37910812 PMCID: PMC10647171 DOI: 10.1021/acs.inorgchem.3c02910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 11/03/2023]
9
Laveglia V, Bazayeva M, Andreini C, Rosato A. Hunting down zinc(II)-binding sites in proteins with distance matrices. Bioinformatics 2023;39:btad653. [PMID: 37878807 PMCID: PMC10630175 DOI: 10.1093/bioinformatics/btad653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023]  Open
10
Wu H, Chen B, Wu Y, Gao J, Li X, Tong P, Wu Y, Meng X, Chen H. New Perspectives on Food Matrix Modulation of Food Allergies: Immunomodulation and Component Interactions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023;71:13181-13196. [PMID: 37646334 DOI: 10.1021/acs.jafc.3c03192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
11
Khare E, Grewal DS, Buehler MJ. Bond clusters control rupture force limit in shear loaded histidine-Ni2+ metal-coordinated proteins. NANOSCALE 2023;15:8578-8588. [PMID: 37092811 DOI: 10.1039/d3nr01287e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
12
Li J, He X, Gao S, Liang Y, Qi Z, Xi Q, Zuo Y, Xing Y. The Metal-binding Protein Atlas (MbPA): an integrated database for curating metalloproteins in all aspects. J Mol Biol 2023:168117. [PMID: 37086947 DOI: 10.1016/j.jmb.2023.168117] [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: 10/29/2022] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/24/2023]
13
Palomino-Vizcaino G, Schuth N, Domínguez-Calva JA, Rodríguez-Meza O, Martínez-Jurado E, Serebryany E, King JA, Kroll T, Costas M, Quintanar L. Copper Reductase Activity and Free Radical Chemistry by Cataract-Associated Human Lens γ-Crystallins. J Am Chem Soc 2023;145:6781-6797. [PMID: 36918380 DOI: 10.1021/jacs.2c13397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
14
A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data. Int J Mol Sci 2023;24:ijms24065440. [PMID: 36982515 PMCID: PMC10055966 DOI: 10.3390/ijms24065440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023]  Open
15
Oostrom M, Akers S, Garrett N, Hanson E, Shaw W, Laureanti JA. Classifying metal-binding sites with neural networks. Protein Sci 2023;32:e4591. [PMID: 36775934 PMCID: PMC9951193 DOI: 10.1002/pro.4591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/14/2023]
16
Bazayeva M, Laveglia V, Andreini C, Rosato A. Metal-induced structural variability of mononuclear metal-binding sites from a database perspective. J Inorg Biochem 2023;238:112025. [PMID: 36270040 DOI: 10.1016/j.jinorgbio.2022.112025] [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: 08/03/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 11/21/2022]
17
Integrated approach to elucidate metal-implant related adverse outcome pathways. Regul Toxicol Pharmacol 2022;136:105277. [DOI: 10.1016/j.yrtph.2022.105277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/29/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022]
18
Rapid diagnosis of malaria by chemometric peak-free LIBS of trace biometals in blood. Sci Rep 2022;12:20196. [PMID: 36424398 PMCID: PMC9691717 DOI: 10.1038/s41598-022-22990-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 10/21/2022] [Indexed: 11/26/2022]  Open
19
Choi TS, Tezcan FA. Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior. J Am Chem Soc 2022;144:18090-18100. [PMID: 36154053 PMCID: PMC9949983 DOI: 10.1021/jacs.2c08050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
20
Relations between Structure and Zn(II) Binding Affinity Shed Light on the Mechanisms of Rad50 Hook Domain Functioning and Its Phosphorylation. Int J Mol Sci 2022;23:ijms231911140. [PMID: 36232441 PMCID: PMC9569753 DOI: 10.3390/ijms231911140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022]  Open
21
Andreini C, Arnesano F, Rosato A. The zinc proteome of SARS-CoV-2. Metallomics 2022;14:mfac047. [PMID: 35767875 PMCID: PMC9314716 DOI: 10.1093/mtomcs/mfac047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/09/2022] [Indexed: 12/11/2022]
22
Andreini C, Rosato A. Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications. Int J Mol Sci 2022;23:ijms23147684. [PMID: 35887033 PMCID: PMC9323969 DOI: 10.3390/ijms23147684] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023]  Open
23
Laveglia V, Giachetti A, Sala D, Andreini C, Rosato A. Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network. J Chem Inf Model 2022;62:2951-2960. [PMID: 35679182 PMCID: PMC9241070 DOI: 10.1021/acs.jcim.2c00522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
24
Guan X, Tan C, Li W, Wang W, Thirumalai D. Role of water-bridged interactions in metal ion coupled protein allostery. PLoS Comput Biol 2022;18:e1010195. [PMID: 35653400 PMCID: PMC9197054 DOI: 10.1371/journal.pcbi.1010195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/14/2022] [Accepted: 05/10/2022] [Indexed: 11/18/2022]  Open
25
Aptekmann AA, Buongiorno J, Giovannelli D, Glamoclija M, Ferreiro DU, Bromberg Y. mebipred: identifying metal binding potential in protein sequence. Bioinformatics 2022;38:3532-3540. [PMID: 35639953 PMCID: PMC9272798 DOI: 10.1093/bioinformatics/btac358] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/27/2022] [Accepted: 05/22/2022] [Indexed: 11/23/2022]  Open
26
A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level. BIOMED RESEARCH INTERNATIONAL 2022;2022:8965712. [PMID: 35402609 PMCID: PMC8989566 DOI: 10.1155/2022/8965712] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/04/2022] [Indexed: 12/29/2022]
27
Lénon M, Arias-Cartín R, Barras F. The Fe-S proteome of Escherichia coli: prediction, function and fate. Metallomics 2022;14:6555457. [PMID: 35349713 DOI: 10.1093/mtomcs/mfac022] [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: 02/01/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022]
28
Dagar S, Sarkar S, Rajamani S. Porphyrin in prebiotic catalysis: Ascertaining a route for the emergence of early metalloporphyrins. Chembiochem 2022;23:e202200013. [PMID: 35233914 DOI: 10.1002/cbic.202200013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/15/2022] [Indexed: 11/09/2022]
29
Li G, Dai QQ, Li GB. MeCOM: A Method for Comparing Three-Dimensional Metalloenzyme Active Sites. J Chem Inf Model 2022;62:730-739. [PMID: 35044164 DOI: 10.1021/acs.jcim.1c01335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
30
Roversi P, Tronrud DE. Ten things I `hate' about refinement. Acta Crystallogr D Struct Biol 2021;77:1497-1515. [PMID: 34866607 PMCID: PMC8647177 DOI: 10.1107/s2059798321011700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/04/2021] [Indexed: 12/05/2022]  Open
31
Petrosino M, Stellato F, Chiaraluce R, Consalvi V, La Penna G, Pasquo A, Proux O, Rossi G, Morante S. Zn-Induced Interactions Between SARS-CoV-2 orf7a and BST2/Tetherin. ChemistryOpen 2021;10:1133-1141. [PMID: 34791819 PMCID: PMC8600262 DOI: 10.1002/open.202100217] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/27/2021] [Indexed: 12/19/2022]  Open
32
Zhang H, Chen P, Ma H, Woińska M, Liu D, Cooper DR, Peng G, Peng Y, Deng L, Minor W, Zheng H. virusMED: an atlas of hotspots of viral proteins. IUCRJ 2021;8:S2052252521009076. [PMID: 34614039 PMCID: PMC8479994 DOI: 10.1107/s2052252521009076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
33
Koebke KJ, Tebo AG, Manickas EC, Deb A, Penner-Hahn JE, Pecoraro VL. Nitrite reductase activity within an antiparallel de novo scaffold. J Biol Inorg Chem 2021;26:855-862. [PMID: 34487215 DOI: 10.1007/s00775-021-01889-1] [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: 05/18/2021] [Accepted: 07/26/2021] [Indexed: 12/28/2022]
34
Reed CJ, Hutinet G, de Crécy-Lagard V. Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase. Biomolecules 2021;11:1282. [PMID: 34572495 PMCID: PMC8469502 DOI: 10.3390/biom11091282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022]  Open
35
Kuznetsova A, Masrati G, Vigonsky E, Livnat-Levanon N, Rose J, Grupper M, Baloum A, Yang JG, Rees DC, Ben-Tal N, Lewinson O. Titratable transmembrane residues and a hydrophobic plug are essential for manganese import via the Bacillus anthracis ABC transporter MntBC-A. J Biol Chem 2021;297:101087. [PMID: 34416234 PMCID: PMC8487065 DOI: 10.1016/j.jbc.2021.101087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 11/07/2022]  Open
36
Honorato RV, Koukos PI, Jiménez-García B, Tsaregorodtsev A, Verlato M, Giachetti A, Rosato A, Bonvin AMJJ. Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem. Front Mol Biosci 2021;8:729513. [PMID: 34395534 PMCID: PMC8356364 DOI: 10.3389/fmolb.2021.729513] [Citation(s) in RCA: 271] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/13/2021] [Indexed: 12/05/2022]  Open
37
Dai Q, Yan Y, Ning X, Li G, Yu J, Deng J, Yang L, Li GB. AncPhore: A versatile tool for anchor pharmacophore steered drug discovery with applications in discovery of new inhibitors targeting metallo-β-lactamases and indoleamine/tryptophan 2,3-dioxygenases. Acta Pharm Sin B 2021;11:1931-1946. [PMID: 34386329 PMCID: PMC8343198 DOI: 10.1016/j.apsb.2021.01.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/25/2020] [Accepted: 01/13/2021] [Indexed: 11/26/2022]  Open
38
Wu Z, Johnston KE, Arnold FH, Yang KK. Protein sequence design with deep generative models. Curr Opin Chem Biol 2021;65:18-27. [PMID: 34051682 DOI: 10.1016/j.cbpa.2021.04.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 12/20/2022]
39
Shafiee RT, Snow JT, Hester S, Zhang Q, Rickaby REM. Proteomic response of the marine ammonia-oxidising archaeon Nitrosopumilus maritimus to iron limitation reveals strategies to compensate for nutrient scarcity. Environ Microbiol 2021;24:835-849. [PMID: 33876540 DOI: 10.1111/1462-2920.15491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/25/2021] [Indexed: 11/26/2022]
40
Vrancken JPM, Noguchi H, Zhang KYJ, Tame JRH, Voet ARD. The symmetric designer protein Pizza as a scaffold for metal coordination. Proteins 2021;89:945-951. [PMID: 33713051 DOI: 10.1002/prot.26072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 12/14/2020] [Accepted: 03/04/2021] [Indexed: 01/17/2023]
41
Tran JB, Krężel A. InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information. J Proteome Res 2021;20:1889-1901. [PMID: 33502860 PMCID: PMC8023803 DOI: 10.1021/acs.jproteome.0c00906] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
42
Sánchez-Aparicio JE, Tiessler-Sala L, Velasco-Carneros L, Roldán-Martín L, Sciortino G, Maréchal JD. BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization. J Chem Inf Model 2020;61:311-323. [PMID: 33337144 DOI: 10.1021/acs.jcim.0c00827] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Park S, Doherty EE, Xie Y, Padyana AK, Fang F, Zhang Y, Karki A, Lebrilla CB, Siegel JB, Beal PA. High-throughput mutagenesis reveals unique structural features of human ADAR1. Nat Commun 2020;11:5130. [PMID: 33046702 PMCID: PMC7550611 DOI: 10.1038/s41467-020-18862-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 09/11/2020] [Indexed: 01/06/2023]  Open
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Kondo HX, Kanematsu Y, Masumoto G, Takano Y. PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins. Database (Oxford) 2020;2023:baaa066. [PMID: 33002111 PMCID: PMC10755257 DOI: 10.1093/database/baaa066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/09/2020] [Accepted: 07/24/2020] [Indexed: 11/14/2022]
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Sauser L, Shoshan MS. Harnessing Peptides against lead pollution and poisoning: Achievements and prospects. J Inorg Biochem 2020;212:111251. [PMID: 32920433 DOI: 10.1016/j.jinorgbio.2020.111251] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/16/2020] [Accepted: 08/30/2020] [Indexed: 11/24/2022]
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Mih N, Monk JM, Fang X, Catoiu E, Heckmann D, Yang L, Palsson BO. Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. BMC Bioinformatics 2020;21:162. [PMID: 32349661 PMCID: PMC7191737 DOI: 10.1186/s12859-020-3505-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/17/2020] [Indexed: 12/16/2022]  Open
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SrnR from Streptomyces griseus is a nickel-binding transcriptional activator. J Biol Inorg Chem 2019;25:187-198. [PMID: 31853648 DOI: 10.1007/s00775-019-01751-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/25/2019] [Indexed: 01/24/2023]
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Predicting cracks in metalloproteins. NAT MACH INTELL 2019. [DOI: 10.1038/s42256-019-0128-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Xu Q, Fan J, Yan H, Ahmad S, Zhao Z, Yin C, Liu X, Liu Y, Zhang H. Structural basis of microcystinase activity for biodegrading microcystin-LR. CHEMOSPHERE 2019;236:124281. [PMID: 31310980 DOI: 10.1016/j.chemosphere.2019.07.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 06/20/2019] [Accepted: 07/02/2019] [Indexed: 06/10/2023]
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Matthews MM, McArthur JB, Li Y, Yu H, Chen X, Fisher AJ. Catalytic Cycle of Neisseria meningitidis CMP-Sialic Acid Synthetase Illustrated by High-Resolution Protein Crystallography. Biochemistry 2019;59:3157-3168. [PMID: 31583886 DOI: 10.1021/acs.biochem.9b00517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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