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.
Binding Sites ; genetics ; Cell Line, Tumor ; Cluster Analysis ; Computational Biology ; methods ; Databases, Protein ; Gene Expression Profiling ; Humans ; Hydrophobic and Hydrophilic Interactions ; Immunoprecipitation ; Membrane Proteins ; chemistry ; genetics ; metabolism ; Models, Molecular ; Nerve Tissue Proteins ; chemistry ; genetics ; metabolism ; Neural Cell Adhesion Molecules ; chemistry ; genetics ; metabolism ; Protein Binding ; Protein Interaction Mapping ; methods ; Protein Structure, Tertiary ; Reverse Transcriptase Polymerase Chain Reaction

Pseudomonas fluorescens 1-94 induced systemic resistance in chickpea against Fusarium wilt of chickpea caused by Fusarium oxysporum f. sp. ciceri by the synthesis and accumulation of phenolic compounds, phenylalanine ammonia lyase(PAL) and pathogenesis related(PR) proteins(chitinase, beta-1,3-glucanase and peroxidase). Time-course accumulation of these enzymes in chickpea plants inoculated with P. fluorescens was significantly(LSD, P=0.05) higher than control. Maximum activities of PR-proteins were recorded at 3 days after inoculation in all induced plants; thereafter, the activity decreased progressively. Five PR peroxidases detected in induced chickpea plants. Molecular mass of these purified peroxidases was 20, 29, 43, 66 and 97 kDa. Purified peroxidases showed antifungal activity against plant pathogenic fungi.
Ammonia ; Cicer* ; Fungi ; Fusarium* ; Peroxidases ; Phenol ; Phenylalanine ; Plants ; Pseudomonas fluorescens ; Pseudomonas*

Adenocarcinoma ; complications ; Female ; Hernia ; etiology ; Humans ; Lung Diseases ; etiology ; Lung Neoplasms ; complications ; Middle Aged