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PALI: a database of alignments and phylogeny of homologous protein structures

PALI: a database of alignments and phylogeny of homologous protein structures Vol. 17 no. 4 2001 BIOINFORMATICS APPLICATIONS NOTE Pages 375–376 PALI: a database of alignments and phylogeny of homologous protein structures S. Sujatha, S. Balaji and N. Srinivasan Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India Received on August 11, 2000; revised on November 13, 2000; accepted on November 20, 2000 ABSTRACT ily, every member in a family is structurally aligned, us- Summary: PALI is a database of structure-based se- ing the program STAMP (version 4.2) (Russell and Bar- quence alignments and phylogenetic relationships derived ton, 1992), with every other member in the family (pair- on the basis of three-dimensional structures of homolo- wise alignment). The dissimilarity in the homologous pro- gous proteins. This database enables grouping of pairs tein structures has been quantified by a structural distance of homologous protein structures on the basis of their metric defined by Johnson et al. (1990). Manual interven- sequence identity calculated from the structure-based tion was necessary to check the quality of the alignments. alignment and PALI also enables association of a new Some of the alignments, especially those involving dis- sequence to a family and automatic generation of a den- tantly related proteins, were refined manually. The rigid- drogram combining the query sequence and homologous body alignments of homologous structures, performed us- protein structures. ing STAMP (Russell and Barton, 1992) and presented in Availability: PALI can be accessed on the web at: http: PALI, are found to be highly similar to the alignments //pauling.mbu.iisc.ernet.in/∼pali made by COMPARER (Sali and Blundell, 1990) which Contact: ns@mbu.iisc.ernet.in uses multistructural features and relationships. Sequence similarity-based and structural similarity- based dendrograms have been generated for each family INTRODUCTION using PHYLIP package (Felsenstein, 1995). A compari- Variation in the amino acid sequences of evolutionarily son of these two kinds of dendrograms suggests that only related proteins is restrained by retention of the fold for a small number of families the dendrograms differ and function (e.g. Chothia and Lesk, 1986; Murzin et (Balaji and Srinivasan, 2001). al., 1995). This feature is exploited in the comparative A variety of features of PALI, especially the availability modelling wherein a three-dimensional model of a protein of pairwise alignments as well as sequence and structural is generated on the basis of related proteins of known similarity-based dendrograms, may be viewed as com- structure (Srinivasan et al., 1996; Sanchez and Sali, 1997). plementary to the other homologous protein structural One could learn about variations in structural features databases such as HOMSTRAD (Mizuguchi et al., 1998). as a function of sequence similarity within homologous proteins (e.g. Flores et al., 1993) and such knowledge WEB ACCESS TO PALI could be used in improved modelling. In order to aid The following features are integrated into the web inter- performing such analyses we have set-up a database face of PALI. of Phylogeny and ALIgnment of homologous protein structures (PALI). (1) The alignments and two types of dendrograms can be accessed family-wise. A search facility is also CONSTRUCTION OF PALI available to identify the family of interest. The current release (1.2) of PALI consists of 604 families (2) Pre-calculated structure-based and sequence-based of homologous proteins involving over 2700 protein do- dendrograms for all the families are available as mains of known structure (Balaji et al., 2001). The dataset PostScript files. has been largely derived by consulting the SCOP database (3) A search tool is available to identify pairs of proteins (release 1.50) (Murzin et al., 1995). The structure of PALI, characterised by a given range of sequence identity and access details are summarised in Figure 1. Apart from or structural similarity. the multiple structural alignment of members in a fam- (4) PSI BLAST (Altschul et al., 1997) is integrated To whom correspondence should be addressed. with PALI to help associating a new sequence to c Oxford University Press 2001 375 S.Sujatha et al. Query sequence Select pairs with Further PALI families specific range of analysis PALI orphans seq. identity PSI_BLAST Browsing & searching Family assignment with alignments Specific family PHYLIP Dendrogram with Structurebased Phylogenetic query seq. and comparison of representation homologous strs. homologues Multiple Pairwise structural alignment alignment Based on seq. Based on strl. similarity similarity Alignment display Details of seq. & s trl. similarity Superposed coordinate set Fig. 1. An overview of the organisation and access to PALI. Chothia,C. and Lesk,A.M. (1986) The relation between the diver- one of the existing families. More than 600 single gence of sequence and structure in proteins. EMBO J., 5, 823– member families (‘orphans’) are also included in PSI BLAST search. Felsenstein,J. (1995) PHYLIP (Phylogeny Inference Package). Ver- sion 3.57c. Department of Genetics, University of Washington, (5) A dendrogram generating tool is also available that Seattle, USA. can automatically incorporate a query sequence Flores,T.P., Orengo,C.A., Moss,D.S and Thornton,J.M. (1993) on to the phylogenetic relationship of an existing Comparison of conformational characteristics in structurally homologous protein family. A combination of similar protein pairs. Protein Sci., 2, 1811–1826. PSI BLAST and PHYLIP is used for this purpose. Johnson,M.S,, Sutcliffe,M.J. and Blundell,T.L. (1990) Molecular anatomy: phyletic relationships derived from three-dimensional ACKNOWLEDGEMENTS structures of proteins. J. Mol. Evol., 1,43–59. Mizuguchi,K., Deane,C.M., Blundell,T.L. and Overington,J.P. We thank Mr Sai Chetan Kumar for his help in updat- (1998) HOMSTRAD: a database of protein structure alignments ing the PALI database. S.Sujatha and S.Balaji thank the for homologous families. Protein Sci., 7, 2469–2471. Wellcome Trust, UK and CSIR, India for financial sup- Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) port. This work is supported by a Senior Fellowship grant SCOP: a structural classification of proteins database for the to N.Srinivasan from the Wellcome Trust, UK. investigation of sequences and structures. J. Mol. Biol., 247, 536– REFERENCES Russell,R.B. and Barton,G.J. (1992) Multiple protein sequence alignment from tertiary structure comparison: assignment of Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhanng,Z., global and residue confidence levels. Proteins, 2, 309–323. Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI- BLAST: a new generation of protein database search programs. Sali,A. and Blundell,T.L. (1990) Definition of general topological Nucleic Acids Res., 25, 3389–3402. equivalence in protein structures. A procedure involving compar- ison of properties and relationships through simulated annealing Balaji,S. and Srinivasan,N. (2001) Use of a database of structural and dynamic programming. J. Mol. Biol., 212, 403–428. alignments and phylogenetic trees in investigating the relation- Sanchez,R. and Sali,A. (1997) Advances in comparative protein- ship between sequence and structural variability among homolo- structure modelling. Curr. Opin. Struct. Biol., 7, 206–214. gous proteins. Protein Eng., in press. Srinivasan,N., Guruprasad,K. and Blundell,T.L. (1996) In Stern- Balaji,S., Sujatha,S., Sai Chetan Kumar,S. and Srinivasan,N. (2001) berg,M.J.E. (ed.), Protein Structure Prediction—A Practical Ap- PALI—a database of phylogeny and alignment of homologous proach. Oxford University Press, Oxford, pp. 111–140. protein structures. Nucleic Acids Res., 29,61–65. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bioinformatics Oxford University Press

PALI: a database of alignments and phylogeny of homologous protein structures

Sujatha, S.; Balaji, S.; Srinivasan, N.
Bioinformatics , Volume 17 (4): 2 – Apr 1, 2001
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Oxford University Press
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© Oxford University Press 2001
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1367-4803
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1460-2059
DOI
10.1093/bioinformatics/17.4.375
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Abstract

Vol. 17 no. 4 2001 BIOINFORMATICS APPLICATIONS NOTE Pages 375–376 PALI: a database of alignments and phylogeny of homologous protein structures S. Sujatha, S. Balaji and N. Srinivasan Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India Received on August 11, 2000; revised on November 13, 2000; accepted on November 20, 2000 ABSTRACT ily, every member in a family is structurally aligned, us- Summary: PALI is a database of structure-based se- ing the program STAMP (version 4.2) (Russell and Bar- quence alignments and phylogenetic relationships derived ton, 1992), with every other member in the family (pair- on the basis of three-dimensional structures of homolo- wise alignment). The dissimilarity in the homologous pro- gous proteins. This database enables grouping of pairs tein structures has been quantified by a structural distance of homologous protein structures on the basis of their metric defined by Johnson et al. (1990). Manual interven- sequence identity calculated from the structure-based tion was necessary to check the quality of the alignments. alignment and PALI also enables association of a new Some of the alignments, especially those involving dis- sequence to a family and automatic generation of a den- tantly related proteins, were refined manually. The rigid- drogram combining the query sequence and homologous body alignments of homologous structures, performed us- protein structures. ing STAMP (Russell and Barton, 1992) and presented in Availability: PALI can be accessed on the web at: http: PALI, are found to be highly similar to the alignments //pauling.mbu.iisc.ernet.in/∼pali made by COMPARER (Sali and Blundell, 1990) which Contact: ns@mbu.iisc.ernet.in uses multistructural features and relationships. Sequence similarity-based and structural similarity- based dendrograms have been generated for each family INTRODUCTION using PHYLIP package (Felsenstein, 1995). A compari- Variation in the amino acid sequences of evolutionarily son of these two kinds of dendrograms suggests that only related proteins is restrained by retention of the fold for a small number of families the dendrograms differ and function (e.g. Chothia and Lesk, 1986; Murzin et (Balaji and Srinivasan, 2001). al., 1995). This feature is exploited in the comparative A variety of features of PALI, especially the availability modelling wherein a three-dimensional model of a protein of pairwise alignments as well as sequence and structural is generated on the basis of related proteins of known similarity-based dendrograms, may be viewed as com- structure (Srinivasan et al., 1996; Sanchez and Sali, 1997). plementary to the other homologous protein structural One could learn about variations in structural features databases such as HOMSTRAD (Mizuguchi et al., 1998). as a function of sequence similarity within homologous proteins (e.g. Flores et al., 1993) and such knowledge WEB ACCESS TO PALI could be used in improved modelling. In order to aid The following features are integrated into the web inter- performing such analyses we have set-up a database face of PALI. of Phylogeny and ALIgnment of homologous protein structures (PALI). (1) The alignments and two types of dendrograms can be accessed family-wise. A search facility is also CONSTRUCTION OF PALI available to identify the family of interest. The current release (1.2) of PALI consists of 604 families (2) Pre-calculated structure-based and sequence-based of homologous proteins involving over 2700 protein do- dendrograms for all the families are available as mains of known structure (Balaji et al., 2001). The dataset PostScript files. has been largely derived by consulting the SCOP database (3) A search tool is available to identify pairs of proteins (release 1.50) (Murzin et al., 1995). The structure of PALI, characterised by a given range of sequence identity and access details are summarised in Figure 1. Apart from or structural similarity. the multiple structural alignment of members in a fam- (4) PSI BLAST (Altschul et al., 1997) is integrated To whom correspondence should be addressed. with PALI to help associating a new sequence to c Oxford University Press 2001 375 S.Sujatha et al. Query sequence Select pairs with Further PALI families specific range of analysis PALI orphans seq. identity PSI_BLAST Browsing & searching Family assignment with alignments Specific family PHYLIP Dendrogram with Structurebased Phylogenetic query seq. and comparison of representation homologous strs. homologues Multiple Pairwise structural alignment alignment Based on seq. Based on strl. similarity similarity Alignment display Details of seq. & s trl. similarity Superposed coordinate set Fig. 1. An overview of the organisation and access to PALI. Chothia,C. and Lesk,A.M. (1986) The relation between the diver- one of the existing families. More than 600 single gence of sequence and structure in proteins. EMBO J., 5, 823– member families (‘orphans’) are also included in PSI BLAST search. Felsenstein,J. (1995) PHYLIP (Phylogeny Inference Package). Ver- sion 3.57c. Department of Genetics, University of Washington, (5) A dendrogram generating tool is also available that Seattle, USA. can automatically incorporate a query sequence Flores,T.P., Orengo,C.A., Moss,D.S and Thornton,J.M. (1993) on to the phylogenetic relationship of an existing Comparison of conformational characteristics in structurally homologous protein family. A combination of similar protein pairs. Protein Sci., 2, 1811–1826. PSI BLAST and PHYLIP is used for this purpose. Johnson,M.S,, Sutcliffe,M.J. and Blundell,T.L. (1990) Molecular anatomy: phyletic relationships derived from three-dimensional ACKNOWLEDGEMENTS structures of proteins. J. Mol. Evol., 1,43–59. Mizuguchi,K., Deane,C.M., Blundell,T.L. and Overington,J.P. We thank Mr Sai Chetan Kumar for his help in updat- (1998) HOMSTRAD: a database of protein structure alignments ing the PALI database. S.Sujatha and S.Balaji thank the for homologous families. Protein Sci., 7, 2469–2471. Wellcome Trust, UK and CSIR, India for financial sup- Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) port. This work is supported by a Senior Fellowship grant SCOP: a structural classification of proteins database for the to N.Srinivasan from the Wellcome Trust, UK. investigation of sequences and structures. J. Mol. Biol., 247, 536– REFERENCES Russell,R.B. and Barton,G.J. (1992) Multiple protein sequence alignment from tertiary structure comparison: assignment of Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhanng,Z., global and residue confidence levels. Proteins, 2, 309–323. Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI- BLAST: a new generation of protein database search programs. Sali,A. and Blundell,T.L. (1990) Definition of general topological Nucleic Acids Res., 25, 3389–3402. equivalence in protein structures. A procedure involving compar- ison of properties and relationships through simulated annealing Balaji,S. and Srinivasan,N. (2001) Use of a database of structural and dynamic programming. J. Mol. Biol., 212, 403–428. alignments and phylogenetic trees in investigating the relation- Sanchez,R. and Sali,A. (1997) Advances in comparative protein- ship between sequence and structural variability among homolo- structure modelling. Curr. Opin. Struct. Biol., 7, 206–214. gous proteins. Protein Eng., in press. Srinivasan,N., Guruprasad,K. and Blundell,T.L. (1996) In Stern- Balaji,S., Sujatha,S., Sai Chetan Kumar,S. and Srinivasan,N. (2001) berg,M.J.E. (ed.), Protein Structure Prediction—A Practical Ap- PALI—a database of phylogeny and alignment of homologous proach. Oxford University Press, Oxford, pp. 111–140. protein structures. Nucleic Acids Res., 29,61–65.

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Bioinformatics – Oxford University Press

Published: Apr 1, 2001

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