Automated sequence-specific NMR assignment of homologous proteins using the program GARANT
Automated sequence-specific NMR assignment of homologous proteins using the program GARANT
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DOI：
10.1007/bf00202037
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发表时间：
1996-05-01
影响因子：
2.7
通讯作者：
Wuthrich, K
中科院分区：
文献类型：
--
作者：
Bartels, C;Billeter, M;Wuthrich, K
用于蛋白质的自动序列特异性NMR分配的程序GARANT（用于共振分配的通用算法）基于从氨基酸序列预测的峰到多维光谱中观察到的峰的映射[C. Bartels，P. Guntert，M. Billeter和K. Wuthrich（1996）J. Comput.化学成分：投稿出版]。在本文中，我们证明了潜在的GARANT分配同源蛋白质时，无论是三维结构或化学位移的亲本蛋白质是已知的。在这些应用中，GARANT利用补充信息，或者以源自三维结构的原子间距离的形式，以便将反映三级结构的核Overhauser效应添加到预期峰的列表中，或者以母体蛋白质的化学位移的形式，以便获得对预期峰的位置的更好估计。该程序用三种不同的蛋白质来说明：（i）Tendamistat的突变形式（74个残基），使用同源2D H-1 NMR光谱和野生型蛋白质的三维结构或化学位移;（ii）突变的Antp（C39 S，W56 S）同源结构域（68个残基），使用同源2D H-1 NMR光谱和Antp（C39 S）同源结构域的三维结构;和（iii）游离亲环素A（165个残基），使用杂原子3D NMR光谱和亲环素A-环孢菌素A复合物的三维结构。在这三个系统中，几乎完全的多肽骨架共振的分配和超过80%的氨基酸侧链共振的分配，而无需人工干预。
The program GARANT (General Algorithm for Resonance Assignment) for automated sequence-specific NMR assignment of proteins is based on the mapping of peaks predicted from the amino acid sequence onto the peaks observed in multidimensional spectra [C. Bartels, P. Guntert, M. Billeter and K. Wuthrich (1996) J. Comput. Chem., manuscript submitted for publication]. In this paper we demonstrate the potential of GARANT for the assignment of homologous proteins when either the three-dimensional structure or the chemical shifts of the parent protein are known. In these applications, GARANT utilizes supplementary information either in the form of interatomic distances derived from the three-dimensional structure, in order to add nuclear Overhauser effects reflecting the tertiary structure to the list of expected peaks, or in the form of the chemical shifts of the parent protein, in order to obtain a better estimate of the positions of the expected peaks. The procedure is illustrated with three different proteins: (i) a mutant form of Tendamistat (74 residues), using homonuclear 2D H-1 NMR spectra and either the three-dimensional structure or the chemical shifts of the wild-type protein; (ii) the mutant Antp(C39S, W56S) homeodomain (68 residues), using homonuclear 2D H-1 NMR spectra and the three-dimensional structure of the Antp(C39S) homeodomain; and (iii) free cyclophilin A (165 residues), using heteronuclear 3D NMR spectra and the three-dimensional structure of a cyclophilin A-cyclosporin A complex. In these three systems nearly complete assignment of the polypeptide backbone resonances and assignment of over 80% of the amino acid side-chain resonances was obtained without manual intervention.