A less-biased analysis of metalloproteins reveals novel zinc coordination geometries

Proteins: Structure, Function and Bioinformatics

Volumn 83, Issue 8, 2015, Pages 1470-1487

  Yao, Sen ^a,b   Flight, Robert M ^c,d   Rouchka, Eric C ^a,b   Moseley, Hunter N B ^c,d  

^a UNIVERSITY OF LOUISVILLE   (United States)

^b University of Louisville   (United States)

^c UNIVERSITY OF KENTUCKY   (United States)

^d UNIVERSITY OF KENTUCKY   (United States)

Author keywords

3D structure; Bidentation; Carboxylate shift; Compressed angle; Structural bioinformatics; Structure function relationship

Indexed keywords

AMINO ACID; LIGAND; METALLOPROTEIN; UNCLASSIFIED DRUG; ZINC; ZINC METALLOPROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; GEOMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; STRUCTURAL BIOINFORMATICS; STRUCTURE ACTIVITY RELATION; BIOLOGY; CHEMISTRY; METABOLISM; PROCEDURES;

ALGORITHMS; COMPUTATIONAL BIOLOGY; METALLOPROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; ZINC;

EID: 84937721833     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24834     Document Type: Article

References (43)

1. Keilin D, Mann T. Carbonic anhydrase. Nature 1939;144:442-443.
2. Tan D, Zhou M, Kiledjian M, Tong L. The ROQ domain of Roquin recognizes mRNA constitutive-decay element and double-stranded RNA. Nat Struct Mol Biol 2014;21:679-685.
3. Miller J, McLachlan AD, Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J 1985;4:1609-1614.
4. Elrod-Erickson M, Benson TE, Pabo CO. High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. Structure 1998;6:451-464.
5. Carrigan CN, Poulter CD. Zinc is an essential cofactor for type I isopentenyl diphosphate:dimethylallyl diphosphate isomerase. J Am Chem Soc 2003;125:9008-9009.
6. Rowlett RS. Structure catalytic mechanism of beta-carbonic anhydrases. Subcell Biochem 2014;75:53-76.
7. Bellomo E, Massarotti A, Hogstrand C, Maret W. Zinc ions modulate protein tyrosine phosphatase 1B activity. Metallomics 2014;6:1229-1239.
8. Jiang LJ, Vasak M, Vallee BL, Maret W. Zinc transfer potentials of the alpha- and beta-clusters of metallothionein are affected by domain interactions in the whole molecule. Proc Natl Acad Sci USA 2000;97:2503-2508.
9. Takeda A. Zinc homeostasis and functions of zinc in the brain. Biometals 2001;14:343-351.
10. Rink L, Haase H. Zinc homeostasis and immunity. Trends Immunol 2007;28:1-4.
11. Fukada T, Yamasaki S, Nishida K, Murakami M, Hirano T. Zinc homeostasis and signaling in health and diseases: zinc signaling. J Biol Inorg Chem 2011;16:1123-1134.
12. Milne A, Landing W, Bizimis M, Morton P. Determination of Mn, Fe, Co, Ni, Cu, Zn, Cd and Pb in seawater using high resolution magnetic sector inductively coupled mass spectrometry (HR-ICP-MS). Anal Chim Acta 2010;665:200-207.
13. Wang C, Li B, Ao J. Separation and identification of zinc-chelating peptides from sesame protein hydrolysate using IMAC-Zn(2)(+) and LC-MS/MS. Food Chem 2012;134:1231-1238.
14. Andreini C, Bertini I, Rosato A. Metalloproteomes: a bioinformatic approach. Acc Chem Res 2009;42:1471-1479.
15. Andreini C, Bertini I, Rosato A. A hint to search for metalloproteins in gene banks. Bioinformatics 2004;20:1373-1380.
16. Maret W. Zinc biochemistry: from a single zinc enzyme to a key element of life. Adv Nutr 2013;4:82-91.
17. Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics 2009;25:2088-2089.
18. Andreini C, Cavallaro G, Lorenzini S. FindGeo: a tool for determining metal coordination geometry. Bioinformatics 2012;28:1658-1660.
19. Berman H, Henrick K, Nakamura H. Announcing the worldwide Protein Data Bank. Nat Struct Biol 2003;10:980.
20. Castagnetto JM, Hennessy SW, Roberts VA, Getzoff ED, Tainer JA, Pique ME. MDB: the Metalloprotein Database and Browser at The Scripps Research Institute. Nucleic Acids Res 2002;30:379-382.
21. Harding MM, Hsin KY. Mespeus-a database of metal interactions with proteins. Methods Mol Biol 2014;1091:333-342.
22. Andreini C, Cavallaro G, Lorenzini S, Rosato A. MetalPDB: a database of metal sites in biological macromolecular structures. Nucleic Acids Res 2013;41(Database issue):D312-D319.
23. Andreini C, Bertini I. A bioinformatics view of zinc enzymes. J Inorg Biochem 2012;111:150-156.
24. Zastrow ML, Pecoraro VL. Designing hydrolytic zinc metalloenzymes. Biochemistry 2014;53:957-978.
25. Alberts IL, Nadassy K, Wodak SJ. Analysis of zinc binding sites in protein crystal structures. Protein Sci 1998;7:1700-1716.
26. Patel K, Kumar A, Durani S. Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures. Biochim Biophys Acta 2007;1774:1247-1253.
27. Liu Z, Wang Y, Zhou C, Xue Y, Zhao W, Liu H. Computationally characterizing and comprehensive analysis of zinc-binding sites in proteins. Biochim Biophys Acta 2014;1844:171-180.
28. Breiman L. Random forests. Mach Learn 2001;45:5-32.
29. Breiman L. Manual-setting up, using, and understanding random forests V4. 0. 2003. Available at: https://www.stat.berkeley.edu/~breiman/Using_random_forests_v4.0.pdf
30. Hartigan JA, Wong MA. Algorithm AS 136: a k-means clustering algorithm. Appl Stat 1979; 28:100-108.
31. Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G. InterProScan 5: genome-scale protein function classification. Bioinformatics 2014;30:1236-1240.
32. Murtagh F, Legendre P. Ward's hierarchical agglomerative clustering method: which algorithms implement Ward's criterion? J Classif 2014;31:274-295.
33. Murtagh F. Multidimensional clustering algorithms. Compstat lectures, Vol. 4. Vienna: Physika Verlag; 1985.
34. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012;40:D109-D114.
35. Harding MM. Small revisions to predicted distances around metal sites in proteins. Acta Crystallogr D Biol Crystallogr 2006;62:678-682.
36. Tamames B, Sousa SF, Tamames J, Fernandes PA, Ramos MJ. Analysis of zinc-ligand bond lengths in metalloproteins: trends and patterns. Proteins 2007;69:466-475.
37. Harding MM, Nowicki MW, Walkinshaw MD. Metals in protein structures: a review of their principal features. Crystallogr Rev 2010;16:247-302.
38. Onoa B, Moreno V. Nickel (II) and copper (II)-l-cysteine, l-methionine, l-tryptophan-nucleotide ternary complexes. Transit Metal Chem 1998;23:485-490.
39. Roe RR, Pang Y-P. Zinc's exclusive tetrahedral coordination governed by its electronic structure. J Mol Model 1999;5:134-140.
40. McCall KA, Huang C, Fierke CA. Function and mechanism of zinc metalloenzymes. J Nutr 2000;130:1437S-1446S.
41. Sousa SF, Fernandes PA, Ramos MJ. The carboxylate shift in zinc enzymes: a computational study. J Am Chem Soc 2007;129:1378-1385.
42. Huang YJ, Montelione GT. Structural biology: proteins flex to function. Nature 2005;438:36-37.
43. Hofer TS, Randolf BR, Rode BM. Molecular dynamics simulation methods including quantum effects. In: Canuto S, editor. Solvation effects on molecules and biomolecules. Challenges and advances in computational chemistry and physics. The Netherlands: Springer; 2008. pp 247-278.