IMPLEMENTING KNOT-THEORETICAL CHARACTERIZATION METHODS TO ANALYZE THE BACKBONE STRUCTURE OF PROTEINS - APPLICATION TO CTF L7 L12 AND CARBOXYPEPTIDASE-A INHIBITOR PROTEINS

被引:16
作者
ARTECA, GA
TAPIA, O
MEZEY, PG
机构
[1] UNIV UPPSALA,DEPT PHYS CHEM,BOX 532,S-75121 UPPSALA,SWEDEN
[2] UNIV SASKATCHEWAN,DEPT CHEM,SASKATOON S7N 0W0,SASKATCHEWAN,CANADA
[3] UNIV SASKATCHEWAN,DEPT MATH,SASKATOON S7N 0W0,SASKATCHEWAN,CANADA
来源
JOURNAL OF MOLECULAR GRAPHICS | 1991年 / 9卷 / 03期
基金
加拿大自然科学与工程研究理事会;
关键词
PROTEIN STRUCTURE; FOLDING ANALYSIS; KNOT-THEORY; JONES POLYNOMIALS; CTF L7 L12 RIBOSOMAL PROTEIN; CARBOXYPEPTIDASE INHIBITOR PROTEIN;
D O I
10.1016/0263-7855(91)80002-H
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
In this work we apply a recently developed method for characterizing the shape of the tertiary structure of proteins. The approach is based on a combination of graph- and knot-theoretical characterizations of Cartesian projections of the space curve describing the protein backbone. The proposed technique reduces the essential shape features to a topologically based code formed by a sequence of knot symbols and polynomials. These polynomials are topological invariants that describe the overcrossing and knotting patterns of curves derived from the molecular space curve. These descriptors are algorithmically computed. The procedure is applied to describe the structure of the carboxy terminal fragment of the L7/L12 chloroplast ribosomal protein (CTF L7/L12) and the potato carboxypeptidase A inhibitor protein (PCI), which has a set of three disulfide bridges. In the former case, we describe the protein's shape features in terms of its alpha-helices, and a backbone simplified by considering helices without internal structure. An extension of the methodology to describe disulfide bridges is discussed and applied to PCI. Changes in the knot-theoretical characterization due to possible uncertainties in the resolution of the X-ray structure, as well as the inclusion of low-frequency motions of the backbone, are also discussed.
引用
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页码:148 / &
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