A Stevedores Protein Knot 英文参考文献.docVIP

AStevedore’sProteinKnot DanielBo¨linger1.,JoannaI.Su?kowska2.,Hsiao-PingHsu1,LeonidA.Mirny3,MehranKardar4,Jose′ N. Onuchic2,PeterVirnau1* 1Department of Physics, Johannes Gutenberg-Universita¨t Mainz, Mainz, Germany, 2CTBP, University of California San Diego, San Diego, California, United States of America, 3Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, United States of America, 4Department of Physics, Massachusetts InstituteofTechnology,Cambridge,Massachusetts,UnitedStatesofAmerica Abstract Proteinknots,mostlyregardedasintriguingoddities,aregraduallybeingrecognizedassignificantstructuralmotifs.Seven distinctlyknottedfoldshavealreadybeenidentified.Itisbyandlargeunclearhowtheseexceptionalstructuresactually fold, and only recently, experiments and simulations have begun to shed some light on this issue. In checking the new proteinstructuressubmittedtotheProteinDataBank,weencounteredthemostcomplexandthesmallestknotstodate:A recentlyuncovereda-haloaciddehalogenasestructurecontainsaknotwithsixcrossings,aso-calledStevedoreknot,ina projectionontoaplane.Thesmallestproteinknotispresentinanasyetunclassifiedproteinfragmentthatconsistsofonly 92aminoacids.ThetopologicalcomplexityoftheStevedoreknotpresentsapuzzleastohowitcouldpossiblyfold.To unravel this enigma, we performed folding simulations with a structure-based coarse-grained model and uncovered a possiblemechanismbywhichtheknotformsinasingleloopflip. Citation: Bo¨linger D, Su?kowska JI, Hsu H-P, Mirny LA, Kardar M, et al. (2010) A Stevedore’s Protein Knot. PLoS Comput Biol 6(4): e1000731. doi:10.1371/ journal.pcbi.1000731 Editor:WilliamTaylor,NationalInstituteforMedicalResearch,UnitedKingdom ReceivedJune18,2009;AcceptedMarch2,2010;PublishedApril1,2010 Copyright: ? 2010 Bo¨linger et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalaut