Phyletic relationships of protein structures based on spatial preference of residues
- 38 Downloads
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.
Key wordsStructure-based scoring matrix MDPRE Phyletic relationship of protein structure Spatial preference factor Sequence alignment Protein homology detect Globins Immunoglobulins Cytochromes c Serine proteinases Dinucleotide-binding domains
Unable to display preview. Download preview PDF.
- Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model for evolutionary change. In: Dayhoff MO (ed) Atlas of protein sequence and structure, vol 5, suppl 3. National Biomedical Research Foundation, Washington D.C., pp 345–358Google Scholar
- Doolittle RF (1989) Redundancies in protein sequences. In Fasman GD (ed) Prediction of protein structure and the principles of protein conformation. Plenum, New York and London, p 600Google Scholar
- Fitch WM, Margoliash E (1967) Construction of phyletic trees. Science 15:279–284Google Scholar
- NBRF PIR 23.0: National Biomedical Research Foundation. Georgetown University Medical Center, 1900 Reservior Road, N.W., Washington, D.C. 20007, USAGoogle Scholar
- Taylor WR, Orengo CA (1989) A holistic approach to protein structure alignment. Prot Eng 2:505–519Google Scholar