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1、免疫学信息网 http:/*,Protein-DNA Interactions,Equilibria and free energiesEstimate binding site occupancyForces driving protein-DNA interactionsLambda repressorMethods to study protein-DNA interactions,免疫学信息网 http:/*,A,A,A,A,D,D,H,1,免疫学信息网 http:/*,A,A,D,M,Major,A-T,A,A,D,M,T-A,Minor,A-T,T-A,A,A,A,A,A,A,D,
2、H,G-C,C-G,G-C,C-G,Major,H,D,A,A,A,A,D,A,A,D,Minor,The 4 Major Groove Patterns Are Distinct,2,免疫学信息网 http:/*,A,A,A,A,D,D,H,1,Hyrdophobic Groups on Bases,免疫学信息网 http:/*,3,Helix-Turn-Helix Motif,34 A,免疫学信息网 http:/*,3,4,1,2,5,N-term,3,4,免疫学信息网 http:/*,免疫学信息网 http:/*,6,免疫学信息网 http:/*,Gln33 Networks with
3、Gln44,Ser,G=4.5 kcal,Leu,G=6.2 kcal,7,免疫学信息网 http:/*,Conclusion,DNA binding specificity from major groove interactionsMutation in one AA affects neighbors-Protein-DNA interfaces contain an intricate Network of hydrogen bonds,免疫学信息网 http:/*,B DNA,434 Complex,9,4 bases dontcontact proteinBut very Impo
4、rtant!,免疫学信息网 http:/*,Filter Binding,vacuum,%Bound,Protein nM,0 20 40 60 80 100,100,50,Kd=20 nM,10,免疫学信息网 http:/*,Immunoprecipitaiton,%Bound,Protein nM,0 20 40 60 80 100,100,50,Kd=20 nM,10,A,Sepharose,免疫学信息网 http:/*,Gel-Shift,%Shifted,Protein nM,0 20 40 60 80 100,100,50,Kd=20 nM,Protein,11,免疫学信息网 ht
5、tp:/*,DNAse IFootprinting,%Protected,Protein nM,0 20 40 60 80 100,100,50,Kd=20 nM,Protein,+DNAse I,12,免疫学信息网 http:/*,Cooperative DNA binding By the repressor,13,免疫学信息网 http:/*,Interference Footprinting,DNA+MMS,+Saturating Protein,Gel Shift,14,免疫学信息网 http:/*,Electron Microscopy,15,免疫学信息网 http:/*,YFP,
6、Tilt,+Roll,Tilt,-Roll,19,Tilt,Roll,免疫学信息网 http:/*,Interaction of TBP(TATA Binding Protein)With DNA,Major Groove,Minor Groove,17,免疫学信息网 http:/*,Protein-Induced DNA Bending From Positive Roll,18,5,3,免疫学信息网 http:/*,Pyrimidine-Purine Steps Have Little Base Stacking,19A(Lecture 1),免疫学信息网 http:/*,For advanced reading:Nucleic Acids:Structures,Properties,and FunctionsV.A.BloomfieldD.M.CrothersI.Tinoco,免疫学信息网 http:/*,8,Gln,G=5.2 kcal,Lys,G=4.1 kcal,
