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1.
Summary A structure-based scoring matrix MDPRE was derived from amino acid spatial preferences in protein structures. Sequence alignment
and evolutionary studies by using MDPRE matrix gave similar results as those from ordinary sequence and structure alignments.
It is interesting that a matrix derived from structure data solely could give comparable alignment results, strongly indicating
the intimate connection between protein sequences and structures. The branch order and length from this approach were close
to those obtained by a structure comparison method. Thus, by applying this structure-based matrix, the trees obtained should
reflect evolutionary characteristics of protein structure. This approach takes advantage over a direct structure comparison
in that (1) only a sequence and MDPRE matrix are needed, making it simple and widely applicable (especially in the absence
of 3-dimensional protein structure data); (2) an established algorithm for sequence alignment and tree building could be employed,
providing opportunities for direct comparison between matrices from different methodologies. One of the most striking features
of this method is its capability to detect protein structure homologies when the sequence identities are low. This was well
reflected in the given examples of the alignment of dinucleotidebinding domains. 相似文献
2.
Bujnicki JM 《Journal of molecular evolution》2000,50(1):39-44
To date all attempts to derive a phyletic relationship among restriction endonucleases (ENases) from multiple sequence alignments
have been limited by extreme divergence of these enzymes. Based on the approach of Johnson et al. (1990), I report for the
first time the evolutionary tree of the ENase-like protein superfamily inferred from quantitative comparison of atomic coordinates
of structurally characterized enzymes. The results presented are in harmony with previous comparisons obtained by crystallographic
analyses. It is shown that λ-exonuclease initially diverged from the common ancestor and then two ``endonucleolytic' families
branched out, separating ``blunt end cutters' from ``5′ four-base overhang cutters.' These data may contribute to a better
understanding of ENases and encourage the use of structure-based methods for inference of phylogenetic relationship among
extremely divergent proteins. In addition, the comparison of three-dimensional structures of ENase-like domains provides a
platform for further clustering analyses of sequence similarities among different branches of this large protein family, rational
choice of homology modeling templates, and targets for protein engineering.
Received: 14 June 1999 / Accepted: 11 August 1999 相似文献