title: Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches.
abstract: We present the application of a method for protein structure prediction to aid the determination of structure-function relationships by experiment. The structure prediction method was rigourously tested by making blind predictions at the third meeting on the Critical Assessment of Protein Structure methods (CASP3). The method is a combined hierarchical approach involving exhaustive enumeration of all possible folds of a small protein sequence on a tetrahedral lattice. A set of filters, primarily in the form of discriminatory functions, are applied to these conformations. As the filters are applied, greater detail is added to the models resulting in a handful of all-atom "final" conformations. Encouraged by the results at CASP3, we used our approach to help solve a practical biological problem: the prediction of the structure and function of the 67-residue C-terminal zinc-finger region of the DNA polymerase alpha-associated zinc-finger (PAZ) protein. We discuss how the prediction points to a novel function relative to the sequence homologs, in conjunction with evidence from experiment, and how the predicted structure is guiding further experimental studies. This work represents a move from the theoretical realm to actual application of structure prediction methods for gaining unique insight to guide experimental biologists.
authors.affiliation: Department of Structural Biology, Stanford University School of Medicine, CA 94305, USA. ram@csb.stanford.edu
authors.forename: R
authors.initials: R
authors.lastname: Samudrala
authors.forename: Y
authors.initials: Y
authors.lastname: Xia
authors.forename: M
authors.initials: M
authors.lastname: Levitt
authors.forename: N J
authors.initials: NJ
authors.lastname: Cotton
authors.forename: E S
authors.initials: ES
authors.lastname: Huang
authors.forename: R
authors.initials: R
authors.lastname: Davis
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D004256:DNA Polymerase I / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D012984:Software; D016335:Zinc Fingers
chemical_list: D004256:DNA Polymerase I