温度因子B-factor

《温度因子B-factor》由会员上传分享，免费在线阅读，更多相关内容在教育资源-天天文库。

1、温度因子B-factor的概念起源于晶体研究，主要是用来体现晶体中原子构象状态的一种模糊度，实际上反映了蛋白质分子在晶体中的构象状态，B-factor越高，模糊度越大，相应部位的构象就越不稳定或柔性越强。在晶体学数据中B-factor一般是以原子为单位给出的，通常我们将其换算成相应氨基酸残基的B-factor值，从而可以分析氨基酸残基的构象稳定性或其柔性。研究发现将蛋白质结构中B-factor值较高的氨基酸突变后部分突变体的热稳定性可以得到明显的提高。WhatisaB-factor?Thefollowingisheavil

2、ybasedon Truebloodetal.,1996 andreferencestherein.DisplacementofatomsfromtheirmeanpositioninacrystalstructurediminishesthescatteredX-rayintensity.Thedisplacementmaybetheresultoftemperature-dependentatomicvibrationsorstaticdisorderinacrystallattice.Iftheatomicdispl

3、acementsareassumedtobeharmonicandanisotropic,theattenuationofatomicscatteringfactorscanberepresentedbytheatomicanisotropicGaussianDebye-WallerfactorT(h)=exp[−8π2⟨u2h⟩sin2θλ2]T(h)=exp⁡[−8π2⟨uh2⟩sin2⁡θλ2].(1)(equation1.4.12from Truebloodetal.,1996).Here uhuh isthepr

4、ojectionoftheatomicdisplacement uu onthedirectionofdiffractionvector hh, θθ isthescatteringangleand λλ istheX-raywavelength.Theaverageintheexponentdenotesanaverageoverspaceandtime.Themean-squaredisplacementsaretermedanisotropicdisplacementparameters(ADPs)astheaver

5、agedependsonthedirectionof hh.ReferredtoaCartesianbasis,anequivalentrepresentationofeq.(1)isT(h)=exp[−2π2hTUh]T(h)=exp⁡[−2π2hTUh].(2)TheADPsdefinethesymmetricatomicmean-squaredisplacementtensorU=⎛⎝⎜U11U12U13U12U22U23U13U23U33⎞⎠⎟U=(U11U12U13U12U22U23U13U23U33).(3)A

6、nelement UijUij of UU hasdimension(length)2.Ifthedisplacementsare(assumedtobe)isotropic,theaverageineq.(1)isconstantandtheDebye-Wallerfactoronlydependsonthemagnitudeof hh:T(

7、h

8、)=exp[−8π2⟨u2⟩sin2θλ2]T(

9、h

10、)=exp⁡[−8π2⟨u2⟩sin2⁡θλ2].(4)(equation1.4.13from Truebloodetal

11、.,1996).TheB-factorisdirectlyrelatedtothemeansquareisotropicdisplacementoftheatom:B=8π2⟨u2⟩B=8π2⟨u2⟩.(5)Amacromolecularcrystalstructureistypicallyrepresentedbythreecoordinates(X,Y,Z),an occupancy parameter,anda"temperaturefactor"inthe coordinatesection ofPDBfiles(

12、Figure1).Theseparametersareestimatedduringacomputationalprocesscrystallographersrefertoas refinement.Thegoalofrefinementistoimprovetheagreementbetweenth