Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database

Gowri, Vijayendran; Pandit, Shashi Bhushan; Karthik, P. S.; Srinivasan, Narayanaswamy; Balaji, S.

doi:10.1093/nar/gkg063

Cited by 39 publications

(37 citation statements)

References 17 publications

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“…Very recently, a substitution matrix in terms of Protein Blocks was developed based on the analysis of local structure variations in the alignments of homologous proteins from the large PALI database [372]. The number of substitutions between any two PBs was counted based on the alignment corresponding only to structurally conserved regions identified in PALI [373][374][375][376][377]. This caution was exercised, as the alignment of residues in the structurally variable regions is meaningless in the rigid body alignments.…”

Section: Hal Author Manuscript Inserm-00175058 Versionmentioning

confidence: 99%

Local Protein Structures

Offmann¹,

Tyagi²,

Brevern

2007

CBIO

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Protein structures are classically described as composed of two regular states, the α-helices and the β-strands and one non-regular and variable state, the coil. Nonetheless, this simple definition of secondary structures hides numerous limitations. In fact, the rules for secondary structure assignment are complex. Thus, numerous assignment methods based on different criteria have emerged leading to heterogeneous and diverging results. In the same way, 3 states may over-simplify the description of protein structure; 50% of all residues, i.e., the coil, are not genuinely described even when it encompass precise local protein structures.Description of local protein structures have hence focused on the elaboration of complete sets of small prototypes or "structural alphabets", able to analyze local protein structures and to approximate every part of the protein backbone. They have also been used to predict the protein backbone conformation and in ab initio / de novo methods. In this paper, we review different approaches towards the description of local structures, mainly through their description in terms of secondary structures and in terms of structural alphabets. We provide some insights into their potential applications.

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Section: Hal Author Manuscript Inserm-00175058 Versionmentioning

confidence: 99%

Local Protein Structures

Offmann¹,

Tyagi²,

Brevern

2007

CBIO

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“…A total of 108 families having 10 or more members in the PALI database Sujatha et al 2001;Gowri et al 2003) (release 2.1) were analysed. PALI database (http://pauling.mbu.iisc.ernet.in/~pali) comprises of protein structural families in which every member is structurally aligned pairwise with every other member in that family and multiple structural alignment of all members in the family is also available.…”

Section: Methodsmentioning

confidence: 99%

Comparison of sequence-based and structure-based phylogenetic trees of homologous proteins: Inferences on protein evolution

Balaji

Srinivasan

2007

J Biosci

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Several studies based on the known three-dimensional (3-D) structures of proteins show that two homologous proteins with insignificant sequence similarity could adopt a common fold and may perform same or similar biochemical functions. Hence, it is appropriate to use similarities in 3-D structure of proteins rather than the amino acid sequence similarities in modelling evolution of distantly related proteins. Here we present an assessment of using 3-D structures in modelling evolution of homologous proteins. Using a dataset of 108 protein domain families of known structures with at least 10 members per family we present a comparison of extent of structural and sequence dissimilarities among pairs of proteins which are inputs into the construction of phylogenetic trees. We find that correlation between the structure-based dissimilarity measures and the sequence-based dissimilarity measures is usually good if the sequence similarity among the homologues is about 30% or more. For protein families with low sequence similarity among the members, the correlation coefficient between the sequence-based and the structure-based dissimilarities are poor. In these cases the structure-based dendrogram clusters proteins with most similar biochemical functional properties better than the sequence-similarity based dendrogram. In multi-domain protein families and disulphide-rich protein families the correlation coefficient for the match of sequence-based and structure-based dissimilarity (SDM) measures can be poor though the sequence identity could be higher than 30%. Hence it is suggested that protein evolution is best modelled using 3-D structures if the sequence similarities (SSM) of the homologues are very low.

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“…(ii) The recent version of PALI dataset V 2.8a [48,54] consists of 1,922 domain families comprising of 231,022 alignment pairs. Structural alignments in this version are generated using MUSTANG [17].…”

Section: Benchmark Datasets Of Structural Alignmentsmentioning

confidence: 99%

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

2012

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Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string.A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition.Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods.3

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Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database

Cited by 39 publications

References 17 publications

Local Protein Structures

Local Protein Structures

Comparison of sequence-based and structure-based phylogenetic trees of homologous proteins: Inferences on protein evolution

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

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