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  • 利用蛋白质序列的预测方法

  • 点击:    作者:   来源: 日期:2007-07-04    本站论坛

 

三级结构

结构预测大概是基于蛋白质序列数据的预测方法中最复杂和技术上最困难的。从序列充分和准确地预测蛋白质结构的重要性扎根于这样的认识:既然序列可以决定构象,那么多个序列就可能决定同一个构象。根据结构比序列更加保守,以及蛋白质骨架motif数量有限的想法(Chothia和Lesk,1986;Chothia,1992)说明,没必要仅仅从传统的基于序列比对的方法去寻找蛋白之间的相似性。序列与结构的关系问题的根源在于“蛋白质折叠过程”的问题,这是近来一些综述的讨论的焦点(Bryant和Altschul,1995;Eisenhaber等,1995;Lemer等,1995)。

当前最健壮的结构预测方法是同源建模,或称“threading”方法(Bryant和Lawrence,1993;Fetrow和Bryant,1993;Jones和Thornton,1996)。这种方法将未知结构的蛋白质序列“穿过”由X光晶体衍射或NMR核磁共振得到的已知结构靶蛋白的结构坐标。对于序列-结构的每次定位,算出残基间相互作用力和疏水作用大小。这些热力学计算的目的是找出未知结构序列在目标结构上的能量最优和构象最稳固的比对位置。这样的程序要作密集的计算,要求计算机硬件至少是一台强大的UNIX工作站,以及要有特定计算机语言的知识。

虽然threading这样的技术很强大,但是它对硬件和专门知识的要求可能仍是大多生物学家应用的障碍。为了降低应用的障碍,一些易于使用的程序被开发出来为大多生物学家提供了比较蛋白建模的良好初步近似。(许多商业蛋白结构分析工具,如WHAT-IF和LOOK都提供了更深入功能,但这里只限于讨论基于Web的免费软件)。

一个序列结构自动比较程序SWISS-MODEL(Peitsch,1996)是一个两步过程。“First Approach”模式,先用来决定序列能否被建模:当序列提交到程序,SWISS-MODEL将其与晶体图像数据库(ExPdb)比较,只有当ExPdb中存在与序列充分相似的同源序列时才被接受建模。如果这一步在ExPdb中找到了一个或多个合适的同源物,则会建立一个原子模型,并将结果由电子邮件返回。这些结果能再提交给SWISS-MODEL的“Optimize”模式,利用其它知识如生物化学信息,来修正提出的结构模型。

第二种方法是将结构与结构相对比,与第七章中讨论的向量比对搜索工具(VAST)原理类似。DALI算法在两个蛋白之间寻找相似的接触模式,并进行优化后返回最佳的结构比对方案(Holm和Sander,1993)。这种方法允许任意长度的空隙,并允许比对片段间互相交替连接,这样就帮助了在整体上不相似的不同蛋白之间寻找相似的特定结构域。DALI的Web界面能对PDB中已有的两组坐标进行分析,也可由用户提交一组PDB格式的坐标。其中,若两个目标蛋白都在PDB库中,则可以在一个“全对全”的PDB比较数据库FSSP蛋白折叠类家族结构比对库(Holm和Sander,1994)中找到已经算好的结构近邻。

最后一种方法是对前面的PHD二级结构预测方法的补充。TOPITS方法(Rost,1995)中,PDB库里的蛋白质三维结构被翻译成二级结构的一维“字符串”,构成搜索的数据库。然后,查询序列的二级结构和溶液可及性通过PHD方法被确定,结果也存成一维字符串。查询和目标字符串再以动态规划方法进行比对,并以此作出结构预测。返回的结果是分级列表,给出查询序列与目标结构的最优比对,以及对预测准确性概率的评估(Z score)。

这里讨论的三种方法都是相当基本的方法,因此它们能较快返回结果并可以使用Web类界面。但它们在检测结构间弱相似性中所表现出的水平令人信服。“threading”方法的最终潜力可以通过最近的Aslomar会议来说明,许多工作小组应邀参与了一个“结构预测竞赛”(Lemer等,1995)。这个为前面提到的更复杂技术开设的实验场表明,虽然蛋白质折叠问题还远未得到解决,大量蛋白质折叠类还是能得到可靠的辨识。尽管不同方法在竞赛中各有所长,竞赛主持人还是建议采用“一致相似方法”的结构,就象前面二级结构预测中给出例子的方法一样。这些发展成果所处时代时机十分令人振奋,紧随着人类基因组计划的同时发展,为研究者在辨识出假定基因产物后能预测结构与功能的关系提供了强有力的工具。

 

第11章中涉及内容的因特网资源

PREDICTION OF PHYSICAL PROPERTIES

Compute pI/MW

http://expasy.hcuge.ch/ch2d/pi.tool.thml

PeptideMass

http://expasy.hcuge.ch/sprot/peptide-mass.html

TGREASE

ftp://ftp.vrgnia.edu/pub/fasta/

SAPS

http://ulrec2.unil.ch/software/SAPS_form.html

PREDICTION OF PROTEIN IDENTITY BASED ON COMPOSITION

AACompIdent

http://expasy.hcuge.ch/ch2d/aacompi.html

AACompSim

http://expasy.hcuge.ch/ch2d/aacsim.html

PROPSEARCH

http://www.embl-heidelerg.de/prs.html

PREDICTION OF SECONDARY STRUCTURE AND FOLDING CLASS

nnpredict

http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html

PredictProtein

http://www.embl-heidelerg.de/predictprotein/

SOPMA

http://www.ibcp.fr/predict.html

SSPRED

http://www.embl-heidelberg.de/sspred/sspred_info.html

PREDICTION OF SPECIALIZED STRUCTURES OR FEATURES

COILS

http://ulrec3.unil.ch/software/COILS_form.html

MacStrip

http://www.wi.mit.edu/matsudaira/macstripe.html

SignalP

http://www.cbs.dtu.dk/services/SignalP/

TMAP

http://ww.embl-heidelberg.de/tmap/tmap_sin.html

TMpred

http://ulrec3.unil.ch/software/TMPRED_form.htm

STRUCTURE PREDICTION

Bryant-Lawrence

ftp://ncbi.nlm.nih.gov/pub/pkb

DALI

http://www.embl-heidelberg.de/dali/dali.html

FSSP

http://www.embl-heidelberg.de/dali/fssp/fssp.html

SWISS-MODEL

http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html

TOPITS

http://www.embl-heidelberg.de/predictprotein/phd_help.html

 

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