A differential geometric treatment of protein structure comparison |
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Authors: | Ding Da-Fu Qian Jiang Feng Zu-Kang |
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Institution: | (1) Laboratory of Computational Molecular Biology, Shanghai Institute of Biochemistry, Academia Sinica, 320 Yue-Yang Road, 200031 Shanghai, China |
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Abstract: | The technique of model-building a protein of known sequence but unknown tertiary structure from the structures of homologous
proteins is probably so far the most reliable means of mapping from primary to tertiary structure. A key step towards the
realization of the aim is to develop ways of aligning three-dimensional structures of homologus proteins, thereby deriving
the rules useful for protein modelling. We have developed a generalized differential-geometric representation of protein local
conformation for use in a protein comparison program which aligns protein sequences on the basis of their sequence and conformational
knowledge. Because the differetial-geometric distance measure between local conformations is independent of the coordinate
frame and remains chirality information, the comparison program is easily implemented, relatively rational and reasonably
fast. The utility of this program for aligning closely and distantly related homologous proteins is demonstrated by multiple
alignment of globins, serine proteinases and aspartic proteinase domains. Particularly, the method has reached the rational
alignment between the mammalian and microbial serine proteinases as compared with many published alignment programs. |
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