Wiggle-predicting functionally flexible regions from primary sequence.
The Wiggle series are support vector machine-based predictors that identify regions of functional flexibility using only protein sequence information. Functionally flexible regions are defined as regions that can adopt different conformational states and are assumed to be necessary for bioactivity. Many advances have been made in understanding the relationship between protein sequence and structure. This work contributes to those efforts by making strides to understand the relationship between protein sequence and flexibility. A coarse-grained protein dynamic modeling approach was used to generate the dataset required for support vector machine training. We define our regions of interest based on the participation of residues in correlated large-scale fluctuations. Even with this structure-based approach to computationally define regions of functional flexibility, predictors successfully extract sequence-flexibility relationships that have been experimentally confirmed to be functionally important. Thus, a sequence-based tool to identify flexible regions important for protein function has been created. The ability to identify functional flexibility using a sequence based approach complements structure-based definitions and will be especially useful for the large majority of proteins with unknown structures. The methodology offers promise to identify structural genomics targets amenable to crystallization and the possibility to engineer more flexible or rigid regions within proteins to modify their bioactivity.
Gu
Jenny
J
Department of Pharmacology and Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA. jgu@sdsc.edu
Gribskov
Michael
M
Bourne
Philip E
PE
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008390:Markov Chains; D008954:Models, Biological; D015233:Models, Statistical; D008969:Molecular Sequence Data; D016011:Normal Distribution; D011506:Proteins / Q000737:chemistry; D040901:Proteomics / Q000379:methods; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D012984:Software
D011506:Proteins