computational biochemistry and biophysics - oren m. becker

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1、ISBN:0-8247-0455-XThisbookisprintedonacid-freepaper.HeadquartersMarcelDekker,Inc.270MadisonAvenue,NewYork,NY10016tel:212-696-9000;fax:212-685-4540EasternHemisphereDistributionMarcelDekkerAGHutgasse4,Postfach812,CH-4001Basel,Switzerlandtel:41-61-261-8482;fax:41-61-261-8896WorldWideWebhttp://www.dek

2、ker.comThepublisheroffersdiscountsonthisbookwhenorderedinbulkquantities.Formoreinformation,writetoSpecialSales/ProfessionalMarketingattheheadquartersaddressabove.Copyright2001byMarcelDekker,Inc.AllRightsReserved.Neitherthisbooknoranypartmaybereproducedortransmittedinanyformorbyanymeans,electronic

3、ormechanical,includingphotocopying,microfilming,andrecording,orbyanyinforma-tionstorageandretrievalsystem,withoutpermissioninwritingfromthepublisher.Currentprinting(lastdigit):10987654321PRINTEDINTHEUNITEDSTATESOFAMERICAForewordThelong-rangegoalofmolecularapproachestobiologyistodescribelivingsystem

4、sintermsofchemistryandphysics.Overthelast70yearsgreatprogresshasbeenmadeinapplyingthequantummechanicalequationsrepresentingtheunderlyingphysicallawstochemicalproblemsinvolvingthestructuresandreactionsofsmallmolecules.ThisworkwasrecognizedintheawardingoftheNobelPrizeinChemistrytoWalterKohnandJohnPo

5、plein1998.Computationalstudiesofmesoscopicsystemsofbiologicalinteresthavebeenattemptedonlymorerecently.Classicalmechanicsisadequatefordescribingmostofthepropertiesofthesesystems,andthemoleculardynamicssimulationmethodisthemostimportanttheoreticalapproachusedinsuchstudies.Thefirstmoleculardynamicssi

6、mulationofaprotein,thebovinepancreatictrypsininhibitor(BPTI),waspublishedmorethan20yearsago[1].Althoughthesimulationwas‘‘crude’’bypresentstandards,itwasimportantbecauseitintroducedanimportantconceptualchangeinourviewofbiomolecules.Theclassicviewofbiopolymers,likeproteinsandnucleicacids,hadbeenstat

7、icincharacter.Theremarkabledetailevidentintheproteincrystalstructuresavailableatthattimeledtoanimageof‘‘rigid’’biomoleculeswitheveryatomfixedinplace[2].ThemoleculardynamicssimulationofBPTIwasinstrumentalinchanging