PDB : 1ZTB Ligand : ZINC
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1 PDB : 1ZTB Ligand : ZINC
2 Pantothenate biosynthesis Enzymes with invariant peptides : Pantothenate kinase (CoaA), Pantothenate Synthetase (PanC) Methyltransferase (PanB)
3 Pathway3 Pathway2 E4 X X E3 Intermediate X E2 Pathway1- step1 E1 X Pathway1- step2
4 Visualizing protein-protein interactions to identify hub proteins Cytoscape: an open source platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data
5
6 Important hub proteins SecA1 PanC GroEL2 Are these good targets?
7 SecA1 - SecA Protein Translocation ATPase KEGG Pathway - Protein export
8 Docking of ligands against SecA1 Decoy molecule Rank fenofibrate Methyl Dihydrogen_phosphate 3129 Guanosine_5_monophosphate ADP Total library size used for docking > 2 million
9 PDB : 1NKT Ligand : ZINC Green Surface: VDEVDSILIDEARTPLIISGPAD Magenta Surface: GVHIVTVNDYLAKRD
10 PDB : 1NKT Ligand : ZINC Green Surface: VDEVDSILIDEARTPLIISGPAD Magenta Surface: GVHIVTVNDYLAKRD
11 Pepcluster: to identify invariant peptide regions (and annotate proteins) PepCluster is a tool for rapid detection and identification of invariant peptide signatures of high functional importance PepCluster is derived from a initial peptide library of CoPS vers 2.0 containing peptides Consists of 5620 invariant peptide signatures offers a highly useful tool for assigning function to unannotated proteins based on signature sequences. While assigning function to the unknown protein, provides detailed information on the sequence of signature peptide, its position and the functional category to which it belongs
12 PepCluster: Clustering Methodology CoPS Database Peptide Clustering Analysis (ver2) CoPS Database Peptides Peptides Cutoff 6 Manual Function Analysis CLUSTERING Homogenous Non-Homogenous Isolates Cutoff 7 RE-CLUSTERING Manual Function Analysis Homogenous Non-Homogenous Isolates Homogenous Cutoff 8 Non-Homogenous RE-CLUSTERING Manual Function Analysis Isolates Manually Analyzed REPEATS Removed Homogenous Cutoff 5 ISOLATE Peptides RE-CLUSTERING Manual Function Analysis Non-Homogenous Isolates CONSENSUS of each cluster derived by MSA (T-Coffee) ISOLATE peptide signatures CONSENSUS peptide signatures 2681 ISOLATE peptide signatures 2939 PepCluster contains a final set of 5620 signature peptides
13 Database Architecture PepID specifies the Primary Key for all signatures
14 Pepcluster Webserver
15 Search Utility and Output Display
16 Functional annotations using PepCluster: Control set: Organisms from original set of 52 bacterial genomes in CoPSv2 M. tuberculosis E. coli H. influenzae Frequency Percentage Frequency Percentage Frequency Percentage Total Unique Peptides Mapped of total of total of total Total Unique Proteins of total of total of total Total Matches Total Functional Mismatches of mapped of mapped of mapped Proteome size Number of Hypotheticals Annotated
17 Signature Matched Examples of hypotheticals annotated Mtb Protein Mtb H37Rv Annotation IPVIAAGGI Rv0021c Rv0021c: 322 aa CONSERVED PGTGKTTI Rv0282 Rv0282: 631 aa - CONSERVED ASASIAQVH Rv0647c Rv0647c: 488 aa - CONSERVED stgphlhfev Rv0950c Rv0950c: 332 aa - CONSERVED IKVDREERPD Rv1084 Rv1084: 673 aa - CONSERVED vphfekmlydna Rv1084 Rv1084: 673 aa - CONSERVED nvynlvtkra Rv1461 Rv1461: 846 aa -CONSERVED RYTTIQNW Rv1461 Rv1461: 846 aa - CONSERVED GVGTGRFA Rv2003c Rv2003c: 285 aa - CONSERVED RIAVNDEL Rv2165c Rv2165c: 396 aa - CONSERVED GPPGSGKTT Rv2559c Rv2559c: 452 aa - CONSERVED HYPOTHETICAL ALA, LEU, VAL RICH PROTEIN Proposed function by Matched Signature, SIMILAR TO 2- NITROPROPANE DIOXYGENASE ATPase, AAA family UBIQUINONE BIOSYNTHESIS PROTEIN AARF, PUTATIVE cell wall-binding protein Protein containing domain related to cellulase catalitic domain and thioredoxin domain Protein containing domain related to cellulase catalitic domain and thioredoxin domain putative iron-regulated ABC transporter iron-regulated ABC-type transporter SAM-dependent methyltransferase methyltransferase REPLICATION FACTOR C SUBUNIT
18 Acknowledgements Prof. SK Brahmachari Dr. Aparna Basu GN Ramachandran Computing facility Funding Resources CSIR, India DST-RFBR for Workshop Students Amit Katiyar Bharati Dutta Suchir Vikram Kumar Nitin Singh
19 Спасибо!
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