Building an Invisible Puzzle: Predicting Protein Structure and Function from Sequence Matthew Perella January 31, 2013

Proteins Abundance 20 Amino Acids Role in nearly all cellular processes Enzymes, hormones, signaling, immune system, muscle fibers, transporters 1 1.Nelson, D. L.; Cox, M. M., Priciples of Biochemistry. 5 ed.; W.H. Freeman and Company: New York, Image obtained from: primary protein structure | protein-pdb.com. structure/. Levels of Protein Structure 2

Understanding Structure and Function Proteomics Characterize structures – Whole-genome sequencing (<1%) – Experimentally X-Ray Crystallography NMR Spectroscopy – Computational Prediction Bioinformatics

Research Wine Spoilage Brettanomyces bruxellensis Vinylphenol Reductase 3 – Vinylphenols – Ethylphenols How?? Vinylphenol Reductase Sequence MPLMTISDSVKDSLTKSEVVPTVIHDKSFLPKGFLTIQYDSGKEV ALGNNIRPADSKNLPRIDFTLNLPSDASSTFNISKDDRFTLIVTD PDAPTRNDEKWSEYLHYLAVDVQLNTFNAENASSNDQLSTAD LKGRTLYPYIGPGPPPKTGKHRYVFLLYKQTPGVTPEAPKDRPN WGTGIRGAGAAEYAEKYKLTPYAVNFFYAQNDQQ 3 3. Tchobanov, I.; Gal, L.; Guilloux-Benatier, M. l.; Remiz, F.; Nardi, T.; Guzzo, J.; Serpaggi, V.; Alexandre, H., Partial vinylphenol reductase purification and characterization from Brettanomyces bruxellensis - Powered by Google Docs. European Federation of Microbiological Studies 2008.

Sequence Databases Protein Data Bank (PDB) – As of Wednesday, January 30th. There are 81,306 characterized structures in the PDB database 4 UniProtKB/Swiss-Prot – 538,849 reviewed sequences 29,266,939 unreviewed sequences 5 – Only 77,110 have experimentally solved structures 4. RCSB PDB - Holdings Report UniProtKB/Swiss-Prot Available at:

Classification Schemes 1.Gene Ontology (GO) 2.Secondary Structure 3.Structural Motifs 4.Family  CATH & SCOP  PROSITE  InterPro  Pfam Sandhya, S. R.; Jayaram, B., Proteins: Sequence to Structure and Function – Current Status. Current protein and peptide science 2010, (11), 498 – 514.

Resources Similar Sequence Searching Multiple Sequence Alignments Prediction – Secondary Structure – 3-D Model Viewing and Editing Software Watson, J. D.; Laskowski, R. A.; Thornton, J. M., Predicting protein function from sequence and structural data. Current Opinion in Structural Biology 2005, 15 (3),

Resource Name 1. Similarity Search (Sequence Alignments) 2. Predictions3. Viewer BLASTα COBALTα Jpredαα Phyre 2ααα SWISS-Modelαα MPI Bioinformatics Tookitαα PsiPredα ClustalWα DNASTAR Lasergene 9 Core Suite Softwareααα CLC Protein Workbench softwareααα Cnc3d viewer (Java)αα Pymol Molecular Graphics System (Java)α UCSF Chimera Molecular Visualization Software v. 1.6 (Python) αα Table 1: Bioinformatics Resource Function Analysis

Methods of Prediction 1.Pattern Recognition pattern recognition techniques are used to find sequences with high similarity in order to infer related structures and functions. 2.Ab Initio prediction method used to create 3-D model to determine structural and functional information using only the sequence Lee, D.; Redfern, O.; Orengo, C., Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 2007, 8 (12),

Sequence Similarity Searches BLAST PSI-BLAST Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25: PubMedPubMed

Multiple Alignment MUSCLE CLUSTALW COBALT RC, E., MUSCLE multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2012, 32 (5), Papadopoulos JS and Agarwala R (2007) COBALT: constraint-based alignment tool for multiple protein sequences, Bioinformatics 23: PubMed.PubMed

Template Secondary Structure Annotation

Secondary Structure Prediction

Secondary Structure Annotation

3-D Model Prediction with Template PHYRE-2 – PSI-BLAST – Psi-pred and Diso-pred – Hidden Markov Model (HMM) – HMM alignment – 3-D models from known structures – Maximizing Thermodynamic Stability Modelling insertions and deletions with loop library Modelling of AA side chains using a rotamer library to minimize steric interferences Kelley, L. A. S. M., Protein structure prediction on the web: a case study using the Phyre server. Nature Protocols 2009, 4,

Phyre2 Model Alignment Results Kelley, L. A. S. M., Protein structure prediction on the web: a case study using the Phyre server. Nature Protocols 2009, 4,

3-D Model Prediction

Superimposed Structural alignment Alignment of α-helices and β-sheets Motif conservation Infer similar function from homologues Kelley, L. A. S. M., Protein structure prediction on the web: a case study using the Phyre server. Nature Protocols 2009, 4,

Prediction Analysis QMEAN and SWISS- MODEL used to assess

Models Superimposed on Template

Resources 1. BLAST References COBALT:Multiple Alignment Tool primary protein structure | protein-pdb.com RCSB PDB - Holdings Report Kelley, L. A. S. M., Protein structure prediction on the web: a case study using the Phyre server. Nature Protocols 2009, 4, Lambert, C. L. N., De Bolle X, Depiereux E., ESyPred3D submitting form Lee, D.; Redfern, O.; Orengo, C., Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 2007, 8 (12), Linding, R. e. a., Protein disorder prediction: Implications for structural proteomics. EMBL - Biocomputing unit: Nelson, D. L.; Cox, M. M., Priciples of Biochemistry. 5 ed.; W.H. Freeman and Company: New York, RC, E., MUSCLE multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2012, 32 (5), Sandhya, S. R.; Jayaram, B., Proteins: Sequence to Structure and Function – Current Status. Current protein and peptide science 2010, (11), 498 – Shenoy, S. R.; Jayaram, B., Proteins: sequence to structure and function--current status. Curr Protein Pept Sci 2010, 11 (7), Tchobanov, I.; Gal, L.; Guilloux-Benatier, M. l.; Remiz, F.; Nardi, T.; Guzzo, J.; Serpaggi, V.; Alexandre, H., Partial vinylphenol reductase purification and characterization from Brettanomyces bruxellensis - Powered by Google Docs. European Federation of Microbiological Studies Watson, J. D.; Laskowski, R. A.; Thornton, J. M., Predicting protein function from sequence and structural data. Current Opinion in Structural Biology 2005, 15 (3),