beta-bulge-pnas - Proc.Natl.Acad.Sd.USA...

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Unformatted text preview: Proc.Natl.Acad.Sd.USA Vol.75,No.6,pp.2574-2578,June1978 Biochemistry The v3 bulge: A common smallunitof nonrepetitiveprotein structure (Isheet/,8 barrel/secondarystructure/tightturn/strandtwist) JANES.RICHARDSONt, ELIZABETH D. GETZOFFt, AND DAVID C.RICHARDSONt t AnatomyDepartmentand * BiochemistryDepartment,DukeUniversity,Durham,NorthCarolina27710 CommunicatedbyC.B. Anfinsen,February16,1978 ABSTRACr A ft bulgeisaregionbetweentwoconsecutive a-4ype hydrogen bondswhichincludestworesidues (positions 1and2)ononestrandoppositeasingleresidue(positionx)on theotherstrand.ComparedtoregularIstructure,a,Bbulgeputs theusualalternationofside-chaindirectionoutofregisteron oneofthestrands,introducesa slightbendinthe P sheet,and locallyaccentuatestheusualright-handedstrandtwist.Almost all,bulgesarebetweenantiparallelstrands,usuallybetween anarrowratherthanawidepairofhydrogenbonds.Ninety-one examplesarelisted. Thetwocommonesttypesarethe"classic" P bulge,withposition1inapproximatelya-helicalconforma- tion,andthe"GI" Bbulge, witharequiredglycineatposition 1in approximatelyleft-handeda-helicalconformation.GI bulges almostalwaysoccurincombinationwithatypeIltight turn.Thefunctionalrolesof bulgesprobably includecom- pensatingfortheeffectsofa single-residueinsertionordeletion within P structureandprovidingthestronglocaltwistrequired toformclosed P barretstructures. One oftheoutstandingproblemsinglobularproteinstructure is thetaskofdescribingthenonrepetitive"coil"regionsthat are neitherhelicesnor(3sheets.Theonereallymajoradvance in thisregardwasidentificationofthetightturn(1),aloopin whichthe carbonyloxygenofresiduenhydrogenbondsto,or at leastiscloseto,the NH group ofresiduen + 3.Ifallfour residuesarecountedaspartofthetightturnandthehydrogen bondisnotrequired,thensuchturnsaccountforuptoathird ofproteinstructure,andtheiroccurrencecanbepredictedfrom thesequencewithamoderatedegreeofsuccess(e.g.,ref.2). Severalothernon-a,non-,8conformationshavebeendescribed, butexceptforthetransitionto 310 or allconformationatthe endsofa-helices(3), it happensthateachofthemhasbeen identifiedforonlyoneoraveryfewexamples.The yturn(4), whichoccursinthermolysin(5),isatighterturninvolvingonly threeresiduesandahighlybenthydrogenbond.Shortpieces ofpolyproline IIstructure havebeenidentifiedinpancreatic trypsin inhibitor(6)andincytochrome cssm (7). Anextended- chain"e-helix" (rather similarto polyproline) hasbeeniden- tifiedinchymotrypsin(8).Twocis-prolineshavebeendem- onstratedintheBence-JonesdimerREI,whichformadistinct subclassoftightturnswitha cis-prolineinposition 3 (9). Al- though,surely,additionalexamplesofalltheseconformations couldbefoundinotherproteinstructures,eachofthem is ap- parentlyrather rare. Thepresentpaperdescribesasmallunit ofnonrepetitivestructurewhichoccursalmostasoftenas tight turns andwhichmayalsoproveveryusefulforthedescription andunderstandingofproteinstructure....
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This note was uploaded on 05/28/2010 for the course WE BIBI010000 taught by Professor Marnikvuylsteke during the Spring '10 term at Ghent University.

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beta-bulge-pnas - Proc.Natl.Acad.Sd.USA...

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