GAMMA: a new docking program utilizing an advanced evolution system algorithm as an engine

S. Ness, T. Hart, R. Read
1996 Acta Crystallographica Section A Foundations of Crystallography  
Characteristics of sequentially identical short peptides in a protein 3-dimensional representative data set and their relationship with protein folding were studied. Sequentially identical short peptides have the same intrinsic properties. They are ideal candidates for studying how short peptides conformation are influenced by their surrounding structural environment. We have carried out an exhaustive search on sequentially identical pep tides in a protein structure representative set generated
more » ... from the Brookhaven Protein Data Bank. The relationships among their sequence. secondary structure, protein fold class and short peptide structure adaptability in protein were analyzed. Six examples were found in the same protein fold class but having totally different structures. The proteins they are in have sequence identity less than 50%. This result implies that the conformation of some short peptides are influenced by more detailed structural environment than protein fold class, so that protein fold class dependent secondary structure prediction algorithm will still encounter the structural plasticity dilemma. From the sequence and structure analysis, we found that although some of the sequentially identical peptide pairs take different structures, most of the sequentially identical sequence peptide pairs have similar structure. A positive correlation was found between the accuracy of secondary structure prediction and the structure conservation of common sequence short peptides. The common sequence peptide pairs which preserve their structure in unrelated protein and different local structural environment have been proposed to be in the folding nucleation site or folding initiation site. One of them bas found expelimental evidence. The results of this study give helpful clues to protein secondary structure prediction and folding study. PS03.05.09 THE CUPREDOXIN FOLD: DEFll'!ITION AND ANALYSIS OF THE COMMON CORE STRUCTURE. The cupredoxin fold is found in a fQmily of copper containing proteins that include single domain electTon transfer proteins and multi-domain multi-subunit enzymes that caL"1lyze a vmiety of redox reactions including cytochrome c oxidase, nitlite reducto"1se and the blue oxidase family. A method of multiple coordinate superposition was used to compme the three-dimensional Stll.Ictures of members of this fmnily. Equivalent residues were identified by semching for a minimum of four consecutive residues with a r.m.s. deviation fi·om the average coordinates under a defined cut off. TI1e conectness of the alignment was validated by examining main chain hydrogen bonding pattems. A total of 53 alpha cm·bons (r.m.s. of 1.3 A) were identified as being equivalent in 23 cupredoxin domains using a cut off of 2.5 A. The core SUl.Ictme contains both beta-su·m1ds and loop regions. None of the helices present in these stll.Ictmes m·e conserved. A u·ee was constll.Icted based on positional similmity of the core residue alpha cmbons. TI1is u·ee shows that domains of the multi-domain enzymes m·e more closely related bet\veen enzymes than domains within a single enzyme. Suq:nisingly, these relationships m·e independent of the metal content and function of these domains and suggests that domain duplication m1d differentiation occuned before fi.mctional specialization. The structure based tl-ee agrees well with previously published phylogenetic u·ees. TI1e sequence identity of the equivalent residues between all 23 domains is l9.5'7c. Despite tilis low sequence identity the resulting sequence alig1m1ent does conL1in recognizable pattems which may be of use in identifying other members of the Stll.Jctural family including proteins that do not cont<lin copper. PS03.05.10 GAMMA: A NEW DOCKING PROGRAM UTILIZING AN ADVANCED EVOLUTION SYSTEM ALGORITHM AS AN ENGINE.
doi:10.1107/s0108767396095499 fatcat:fv4cprjhfrdllohn3wg36acqca