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Titolo:
Use of a database of structural alignments and phylogenetic trees in investigating the relationship between sequence and structural variability amonghomologous proteins
Autore:
Balaji, S; Srinivasan, N;
Indirizzi:
Indian Inst Sci, Mol Biophys Unit, Bangalore 560012, Karnataka, India Indian Inst Sci Bangalore Karnataka India 560012 560012, Karnataka, India
Titolo Testata:
PROTEIN ENGINEERING
fascicolo: 4, volume: 14, anno: 2001,
pagine: 219 - 226
SICI:
0269-2139(200104)14:4<219:UOADOS>2.0.ZU;2-X
Fonte:
ISI
Lingua:
ENG
Soggetto:
AMINO-ACID-SEQUENCES; SIMILAR FOLDS; CLASSIFICATION; FAMILIES; EVOLUTION; DOMAINS; SCOP; CORE;
Keywords:
comparative modelling; homologous proteins; phylogeny; structural comparison; structure-based alignments;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
45
Recensione:
Indirizzi per estratti:
Indirizzo: Srinivasan, N Indian Inst Sci, Mol Biophys Unit, Bangalore 560012, Karnataka, India Indian Inst Sci Bangalore Karnataka India 560012 aka, India
Citazione:
S. Balaji e N. Srinivasan, "Use of a database of structural alignments and phylogenetic trees in investigating the relationship between sequence and structural variability amonghomologous proteins", PROTEIN ENG, 14(4), 2001, pp. 219-226

Abstract

The database PALI (Phylogeny and ALIgnment of homologous protein structures) consists of families of protein domains of known three-dimensional (3D) structure. In a PALI family, every member has been structurally aligned with every other member (pairwise) and also simultaneous superposition (multiple) of all the members has been performed. The database also contains 3D structure-based and structure-dependent sequence similarity-based phylogenetic dendrograms for all the families. The PALI release used in the present analysis comprises 225 families derived largely from the HOMSTRAD and SCOP databases. The quality of the multiple rigid-body structural alignments in PALI was compared with that obtained from COMPARER, which encodes a procedurebased on properties and relationships. The alignments from the two procedures agreed very well and variations are seen only in the low sequence similarity cases often in the loop regions. A validation of Direct Pairwise Alignment (DPA) between two proteins is provided by comparing it with Pairwise alignment extracted from Multiple Alignment of all the members in the family (PMA). In general, DPA and PMA are found to vary rarely. The ready availability of pairwise alignments allows the analysis of variations in structural distances as a function of sequence similarities and number of topologically equivalent Ca atoms. The structural distance metric used in the analysis combines root mean square deviation (r.m.s.d.) and number of equivalences, and is shown to vary similarly to r.m.s.d. The correlation between sequence similarity and structural similarity is poor in pairs with low sequencesimilarities. A comparison of sequence and 3D structure-based phylogenies for all the families suggests that only a few families have a radical difference in the two kinds of dendrograms. The difference could occur when the sequence similarity among the homologues is low or when the structures are subjected to evolutionary pressure for the retention of function. The PALI database is expected to be useful in furthering our understanding of the relationship between sequences and structures of homologous proteins and their evolution.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 29/11/20 alle ore 03:27:03