title: Ab initio coordination chemistry for nickel chelation motifs.
abstract: Chelation therapy is one of the most appreciated methods in the treatment of metal induced disease predisposition. Coordination chemistry provides a way to understand metal association in biological structures. In this work we have implemented coordination chemistry to study nickel coordination due to its high impact in industrial usage and thereby health consequences. This paper reports the analysis of nickel coordination from a large dataset of nickel bound structures and sequences. Coordination patterns predicted from the structures are reported in terms of donors, chelate length, coordination number, chelate geometry, structural fold and architecture. The analysis revealed histidine as the most favored residue in nickel coordination. The most common chelates identified were histidine based namely HHH, HDH, HEH and HH spaced at specific intervals. Though a maximum coordination number of 8 was observed, the presence of a single protein donor was noted to be mandatory in nickel coordination. The coordination pattern did not reveal any specific fold, nevertheless we report preferable residue spacing for specific structural architecture. In contrast, the analysis of nickel binding proteins from bacterial and archeal species revealed no common coordination patterns. Nickel binding sequence motifs were noted to be organism specific and protein class specific. As a result we identified about 13 signatures derived from 13 classes of nickel binding proteins. The specifications on nickel coordination presented in this paper will prove beneficial for developing better chelation strategies.
authors.affiliation: Bioinformatics Division, SBST, VIT University, Vellore, 632 014, India.
authors.forename: R Jesu Jaya
authors.initials: RJ
authors.lastname: Sudan
authors.affiliation: Bioinformatics Division, SBST, VIT University, Vellore, 632 014, India.
authors.forename: J Lesitha Jeeva
authors.initials: JL
authors.lastname: Kumari
authors.affiliation: Bioinformatics Division, SBST, VIT University, Vellore, 632 014, India.
authors.forename: C
authors.initials: C
authors.lastname: Sudandiradoss
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D002614:Chelating Agents / Q000737:chemistry; D006639:Histidine / Q000737:chemistry; D008667:Metalloproteins / Q000737:chemistry* / Q000378:metabolism; D008969:Molecular Sequence Data; D009532:Nickel / Q000737:chemistry*
chemical_list: D002614:Chelating Agents; D008667:Metalloproteins; D006639:Histidine; D009532:Nickel