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A computer algorithm, CLIX, capable of searching a crystallographic data-base of small molecules for candidates which have both steric and chemical likelihood of binding a protein of known three-dimensional structure is presented. The algorithm is a significant advance over previous strategies which consider solely steric or chemical requirements for binding. The algorithm is shown to be capable of predicting the correct binding geometry of sialic acid to a mutant influenza-virus hemagglutinin and of proposing a number of potential new ligands to this protein. 相似文献
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Classification of doubly wound nucleotide binding topologies using automated loop searches
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Mark B. Swindells 《Protein science : a publication of the Protein Society》1993,2(12):2146-2153
A classification is presented of doubly wound α/β nucleotide binding topologies, whose binding sites are located in the cleft formed by a topological switch point. In particular, the switch point loop nearest the N-terminus is used to identify specific structural classes of binding protein. This yields seven structurally distinct loop conformations, which are subsequently used as motifs for scanning the Protein Data Bank. The searches, which are effective at identifying functional relationships within a large database of structures, reveal a remarkable and previously unnoticed similarity between the coenzyme binding sites of flavodoxin and tryptophan synthetase, even though there is no sequence or topological similarity between them. 相似文献
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Joël Chopineau Stéphane Robert Laurence Fenart Roméo Cecchelli Bernard Lagoutte Stéphanie Paitier Marie-Pierre Dehouck Dominique Domurado 《Letters in Peptide Science》1997,4(4-6):313-321
Acylated proteins play a crucial role in cellphysiology because of their increased interaction withmembranes. Their isolation is difficult as aconsequence of their low cellular concentration andtheir chemical preparation is problematic due tosolubility problems. Through the use of reversedmicelles, we produced tens of milligrams of acylatedribonucleases A, chosen as a model, purified them bysemi-preparative high performance liquidchromatography (HPLC) and characterized them by analyticalHPLC, capillary electrophoresis, mass spectrometry, peptide mapping, Edman degradation and enzyme activity. We nextscrutinized the interaction with an in vitro blood–brainbarrier model and demonstrated that palmitoylated andstearoylated ribonucleases A are transported from onecompartment to the other across the cellular monolayer,in contrast to the native enzyme. 相似文献
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A computer program (BBReader) was developed which performs an inverse search in theBioMagResBank database. Given (cross) peak positions of a protein, the program searchesfor atoms with matching chemical shifts and suggests possible assignments for user-specifiedhomo- and heteronuclear one- to three-dimensional COSY- and NOESY-type experiments.It can handle 1H, 13C and 15N spectra. Distance information from PDB files can be utilizedfor filtering possible NOESY cross peak assignments. 相似文献
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Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? 总被引:7,自引:6,他引:1
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J. Skolnick L. Jaroszewski A. Kolinski A. Godzik 《Protein science : a publication of the Protein Society》1997,6(3):676-688
Many existing derivations of knowledge-based statistical pair potentials invoke the quasichemical approximation to estimate the expected side-chain contact frequency if there were no amino acid pair-specific interactions. At first glance, the quasichemical approximation that treats the residues in a protein as being disconnected and expresses the side-chain contact probability as being proportional to the product of the mole fractions of the pair of residues would appear to be rather severe. To investigate the validity of this approximation, we introduce two new reference states in which no specific pair interactions between amino acids are allowed, but in which the connectivity of the protein chain is retained. The first estimates the expected number of side-chain contracts by treating the protein as a Gaussian random coil polymer. The second, more realistic reference state includes the effects of chain connectivity, secondary structure, and chain compactness by estimating the expected side-chain contrast probability by placing the sequence of interest in each member of a library of structures of comparable compactness to the native conformation. The side-chain contact maps are not allowed to readjust to the sequence of interest, i.e., the side chains cannot repack. This situation would hold rigorously if all amino acids were the same size. Both reference states effectively permit the factorization of the side-chain contact probability into sequence-dependent and structure-dependent terms. Then, because the sequence distribution of amino acids in proteins is random, the quasichemical approximation to each of these reference states is shown to be excellent. Thus, the range of validity of the quasichemical approximation is determined by the magnitude of the side-chain repacking term, which is, at present, unknown. Finally, the performance of these two sets of pair interaction potentials as well as side-chain contact fraction-based interaction scales is assessed by inverse folding tests both without and with allowing for gaps. 相似文献
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王槐春 《生物化学与生物物理进展》1995,22(4):317-322
交互网络(Internet)的发展为联网的计算机用户之间进行信息交流提供了有效途径.就分子生物学家而言,他们不仅可以利用电子邮件系统发送和接收信息,而且更重要的是能够存取大量的分子生物学数据库和软件.利用Internet可以开展多种序列分析作业,包括序列数据库的类似性检索、基因编码区鉴定和蛋白质二级结构分析等.一个数据库,例如GenBank,可以通过多种方式来存取:a.电子邮件文件服务器,b.文件传送协议(FTP),c.Gopher,WAIS或WWW等服务器-客户机(Server-Client)系统.专为分子生物学家设计的BIOSCI电子公告牌为研究人员开展学术讨论、寻求别人帮助和与数据库人员交流提供了极大的方便. 相似文献
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