Identification of Semaphorin 5A Interacting Protein by Applying Apriori Knowledge and Peptide Complementarity Related to Protein Evolution and Structure

Anguraj Sadanandam, Michelle L. Varney, Rakesh K Singh

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

In the post-genomic era, various computational methods that predict protein-protein interactions at the genome level are available; however, each method has its own advantages and disadvantages, resulting in false predictions. Here we developed a unique integrated approach to identify interacting partner(s) of Semaphorin 5A (SEMA5A), beginning with seven proteins sharing similar ligand interacting residues as putative binding partners. The methods include Dwyer and Root-Bernstein/Dillon theories of protein evolution, hydropathic complementarity of protein structure, pattern of protein functions among molecules, information on domain-domain interactions, co-expression of genes and protein evolution. Among the set of seven proteins selected as putative SEMA5A interacting partners, we found the functions of Plexin B3 and Neuropilin-2 to be associated with SEMA5A. We modeled the semaphorin domain structure of Plexin B3 and found that it shares similarity with SEMA5A. Moreover, a virtual expression database search and RT-PCR analysis showed co-expression of SEMA5A and Plexin B3 and these proteins were found to have co-evolved. In addition, we confirmed the interaction of SEMA5A with Plexin B3 in co-immunoprecipitation studies. Overall, these studies demonstrate that an integrated method of prediction can be used at the genome level for discovering many unknown protein binding partners with known ligand binding domains.

Original languageEnglish (US)
Pages (from-to)163-174
Number of pages12
JournalGenomics, Proteomics and Bioinformatics
Volume6
Issue number3-4
DOIs
StatePublished - Dec 1 2008

Fingerprint

Semaphorins
Complementarity
Peptides
Proteins
Protein
Genes
Genome
Neuropilin-2
Ligands
Prediction
Protein-protein Interaction
Protein Structure
Knowledge
Interaction
Computational Methods
Genomics
Sharing
Computational methods
Immunoprecipitation
Protein Binding

Keywords

  • domain-domain interaction
  • plexin
  • protein interaction prediction
  • semaphorin

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Biochemistry
  • Computational Mathematics

Cite this

Identification of Semaphorin 5A Interacting Protein by Applying Apriori Knowledge and Peptide Complementarity Related to Protein Evolution and Structure. / Sadanandam, Anguraj; Varney, Michelle L.; Singh, Rakesh K.

In: Genomics, Proteomics and Bioinformatics, Vol. 6, No. 3-4, 01.12.2008, p. 163-174.

Research output: Contribution to journalArticle

@article{d266a21198a44272b831e74b8ff70b55,
title = "Identification of Semaphorin 5A Interacting Protein by Applying Apriori Knowledge and Peptide Complementarity Related to Protein Evolution and Structure",
abstract = "In the post-genomic era, various computational methods that predict protein-protein interactions at the genome level are available; however, each method has its own advantages and disadvantages, resulting in false predictions. Here we developed a unique integrated approach to identify interacting partner(s) of Semaphorin 5A (SEMA5A), beginning with seven proteins sharing similar ligand interacting residues as putative binding partners. The methods include Dwyer and Root-Bernstein/Dillon theories of protein evolution, hydropathic complementarity of protein structure, pattern of protein functions among molecules, information on domain-domain interactions, co-expression of genes and protein evolution. Among the set of seven proteins selected as putative SEMA5A interacting partners, we found the functions of Plexin B3 and Neuropilin-2 to be associated with SEMA5A. We modeled the semaphorin domain structure of Plexin B3 and found that it shares similarity with SEMA5A. Moreover, a virtual expression database search and RT-PCR analysis showed co-expression of SEMA5A and Plexin B3 and these proteins were found to have co-evolved. In addition, we confirmed the interaction of SEMA5A with Plexin B3 in co-immunoprecipitation studies. Overall, these studies demonstrate that an integrated method of prediction can be used at the genome level for discovering many unknown protein binding partners with known ligand binding domains.",
keywords = "domain-domain interaction, plexin, protein interaction prediction, semaphorin",
author = "Anguraj Sadanandam and Varney, {Michelle L.} and Singh, {Rakesh K}",
year = "2008",
month = "12",
day = "1",
doi = "10.1016/S1672-0229(09)60004-8",
language = "English (US)",
volume = "6",
pages = "163--174",
journal = "Genomics Proteomics Bioinformatics",
issn = "1672-0229",
publisher = "Beijing Genomics Institute",
number = "3-4",

}

TY - JOUR

T1 - Identification of Semaphorin 5A Interacting Protein by Applying Apriori Knowledge and Peptide Complementarity Related to Protein Evolution and Structure

AU - Sadanandam, Anguraj

AU - Varney, Michelle L.

AU - Singh, Rakesh K

PY - 2008/12/1

Y1 - 2008/12/1

N2 - In the post-genomic era, various computational methods that predict protein-protein interactions at the genome level are available; however, each method has its own advantages and disadvantages, resulting in false predictions. Here we developed a unique integrated approach to identify interacting partner(s) of Semaphorin 5A (SEMA5A), beginning with seven proteins sharing similar ligand interacting residues as putative binding partners. The methods include Dwyer and Root-Bernstein/Dillon theories of protein evolution, hydropathic complementarity of protein structure, pattern of protein functions among molecules, information on domain-domain interactions, co-expression of genes and protein evolution. Among the set of seven proteins selected as putative SEMA5A interacting partners, we found the functions of Plexin B3 and Neuropilin-2 to be associated with SEMA5A. We modeled the semaphorin domain structure of Plexin B3 and found that it shares similarity with SEMA5A. Moreover, a virtual expression database search and RT-PCR analysis showed co-expression of SEMA5A and Plexin B3 and these proteins were found to have co-evolved. In addition, we confirmed the interaction of SEMA5A with Plexin B3 in co-immunoprecipitation studies. Overall, these studies demonstrate that an integrated method of prediction can be used at the genome level for discovering many unknown protein binding partners with known ligand binding domains.

AB - In the post-genomic era, various computational methods that predict protein-protein interactions at the genome level are available; however, each method has its own advantages and disadvantages, resulting in false predictions. Here we developed a unique integrated approach to identify interacting partner(s) of Semaphorin 5A (SEMA5A), beginning with seven proteins sharing similar ligand interacting residues as putative binding partners. The methods include Dwyer and Root-Bernstein/Dillon theories of protein evolution, hydropathic complementarity of protein structure, pattern of protein functions among molecules, information on domain-domain interactions, co-expression of genes and protein evolution. Among the set of seven proteins selected as putative SEMA5A interacting partners, we found the functions of Plexin B3 and Neuropilin-2 to be associated with SEMA5A. We modeled the semaphorin domain structure of Plexin B3 and found that it shares similarity with SEMA5A. Moreover, a virtual expression database search and RT-PCR analysis showed co-expression of SEMA5A and Plexin B3 and these proteins were found to have co-evolved. In addition, we confirmed the interaction of SEMA5A with Plexin B3 in co-immunoprecipitation studies. Overall, these studies demonstrate that an integrated method of prediction can be used at the genome level for discovering many unknown protein binding partners with known ligand binding domains.

KW - domain-domain interaction

KW - plexin

KW - protein interaction prediction

KW - semaphorin

UR - http://www.scopus.com/inward/record.url?scp=62949084182&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=62949084182&partnerID=8YFLogxK

U2 - 10.1016/S1672-0229(09)60004-8

DO - 10.1016/S1672-0229(09)60004-8

M3 - Article

VL - 6

SP - 163

EP - 174

JO - Genomics Proteomics Bioinformatics

JF - Genomics Proteomics Bioinformatics

SN - 1672-0229

IS - 3-4

ER -