Random Field Model Reveals Structure of the Protein Recombinational Landscape 英文参考文献.docVIP

RandomFieldModelRevealsStructureoftheProtein RecombinationalLandscape PhilipA.Romero,FrancesH.Arnold* DivisionofChemistryandChemicalEngineering,CaliforniaInstituteofTechnology,Pasadena,California,UnitedStatesofAmerica Abstract We are interested in how intragenic recombination contributes to the evolution of proteins and how this mechanism complements and enhances the diversity generated by random mutation. Experiments have revealed that proteins are highly tolerant to recombination with homologous sequences (mutation by recombination is conservative); more surprisingly,theyhavealsoshownthathomologoussequencefragmentsmakelargelyadditivecontributionstobiophysical properties such as stability. Here, we develop a random field model to describe the statistical features of the subset of protein space accessible by recombination, which we refer to as the recombinational landscape. This model shows quantitative agreement with experimental results compiled from eight libraries of proteins that were generated by recombining gene fragments from homologous proteins. The model reveals a recombinational landscape that is highly enriched in functional sequences, with properties dominated by a large-scale additive structure. It also quantifies the relative contributions of parent sequence identity, crossover locations, and protein fold to the tolerance of proteins to recombination. Intragenic recombination explores a unique subset of sequence space that promotes rapid molecular diversificationandfunctionaladaptation. Citation:RomeroPA,ArnoldFH(2012)RandomFieldModelRevealsStructureoftheProteinRecombinationalLandscape.PLoSComputBiol8(10):e1002713. doi:10.1371/journal.pcbi.1002713 Editor:PeterJosephArtymiuk,UniversityofSheffield,UnitedKingdom ReceivedJune5,2012;AcceptedAugust3,2012;PublishedOctober4,2012 Copyright: ?2012 Romero, Arnold. This isan open-access article distributed under the terms of the CreativeCommons Attribution License, which permits unrestricteduse,distribution,and