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1、TheorChemAcc(2006)116:297306DOI10.1007/s00214-005-0070-4REGULARARTICLEXavierDauraMoleculardynamicssimulationofpeptidefoldingReceived:20April2005/Accepted:28September2005/Publishedonline:21December2005©Springer-Verlag2005AbstractThesimulationofpeptidefoldingwit
2、hatomicres-anysize,itsthermodynamicsandkineticsaretypicallydiffer-olutionhasevolvedremarkablyduringthelast7years,i.e.,entforoligopeptidesformingsecondarystructureelements,fromabsoluteskepticismonthecapabilityofclassicalpolypeptides(over20residues)withsomedegre
3、eoftertiarymoleculardynamics(MD)methodologytoreproducecom-structureandproteins(over50residues)withasubstantialplexbiologicalphenomenasuchasthefoldingofevensimplesolvent-excludedvolume(hydrophobiccore).Thiscanbeoligopeptides(615residues)totheseeminglyrealisticr
4、ep-broadlyexplainedwithreferencetothedifferentdimensi-resentationofthethermodynamicsandkineticsoffoldingofonalitiesofthefreeenthalpyhypersurfacesofthesethreearapidlyincreasingnumberofpolypeptides(over20resi-classesofpolymersofaminoacids.dues).Fourfactorspermit
5、tedthisrapidprogress:thebreak-Historically,researchonpeptideandproteinstructure,throughofasecondgenerationofforcefields,arapidandwhetherbyexperimentalorcomputationalmeans,hasfocusedsteadyincreaseof(commodity)computerperformance,aonthefoldedstateonly.Thisisbecau
6、seanarrayofmethodsmovefromlocalcomputationalresourcestolargedistrib-existsforthedetailedinvestigationofthefoldedstateofautedclustersand,lastbutnotlessimportant,adecisionofpeptideorprotein,andbecausethefoldedstateiscommonlyparticulargroupstospendalargecomputati
7、onaleffortonthefunctionallyactiveone.Thereare,however,twoscenariosprojectsthatmostothergroupstrustedunrealizableattheinwhichafullcharacterizationoftheunfoldedstatebecomestime.Thepresentaccountgoesoversomeaspectsofpeptideasessentialasthedeterminationofthefolded
8、conformation.foldinganditssimulationwithMDtechniqueswhilesweep-Thefirstisinthestudyofthephysical,chemical,orbio-ingthroughthesimulationlandmarksofthelast7yearsandlogicalpropertiesof
