2023-Fall-Zubaer-L15-Protein.pdf

Computational Molecular Microbiology (MBIO 4700) ABDULLAH ZUBAER UNIVERSITY OF MANITOBA More programs: http://en.wikipedia.org/wiki/List_of_protein_structure_prediction_software http://mistic.leloir.org.ar/docs/ help.html#WhatIsMI Colell EA, Iserte JA, Simonetti FL, Marino-Buslje C. MISTIC2:...

Computational Molecular Microbiology (MBIO 4700) ABDULLAH ZUBAER UNIVERSITY OF MANITOBA More programs: http://en.wikipedia.org/wiki/List_of_protein_structure_prediction_software http://mistic.leloir.org.ar/docs/ help.html#WhatIsMI Colell EA, Iserte JA, Simonetti FL, Marino-Buslje C. MISTIC2: comprehensive server to study coevolution in protein families. Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W323– W328. Use: fasta version of alignment and select 1st sequence as reference 1. Load MSA (fasta) 2. Select a sequence to be the reference Optional – but would add more information Notification ON and 3. RUN job (wait for email) Slow ~ few days Cytoscape Example: rps3 Rps3 – ribosomal protein (for small subunit) Conserved – there are nuclear, mitochondrial and chloroplast versions. Bacteria/Archaea also have rps3 homologs Example - Strategy: Phyre2 – get preliminary secondary and 3D structure Save PDB file Use MISTIC to find out what residues interact with each other Use MISTIC to find “nearest neighbors” In PyMOL - annotate the model with data from MISTIC and secondary structure data from Phyre2. Mutual Information Circos MI Circo is a sequential circular representation of the MSA and the information it contains. Colored square boxes of the second circle indicate the MSA position conservation (highly conserved positions are in red, while less conserved ones are in blue). Lines connect pairs of positions with MI greater than 6.5 (Marino Buslje et al, 2009). Red edges represent the top 5% (>95 %), black ones are between 70% and 95%, and gray edges account for the remaining 70%. More information can be found here “outer ring = reference sequence (N. crassa) MSA – MISTIC - CYTOscape MSA – MISTIC - CYTOscape Logo for Position 56 Position 56 Positions based on your reference sequence! (alignments used to determine MI, cytoscape, logos etc.) Options: Logo for Position 504 MSA – MISTIC - CYTOscape 479 Logo for 479 504 CIRCOS MISTIC -annotated based on PHYRE2 56 rps3 A. Wai Blue dots and stars identify coevolving positions rps3 A. Wai https://pymol.org/2/ N terminus Phyre2 → Pymol2 -> combine info with MISTIC Free graphics program INKSPACE - https://inkscape.org/ MEGA6 ML and NJ plus bootstrap analysis mtDNA RPS3: mtDNA intron FREE Integration: rps3 can be intron encoded or freestanding or in few examples – nuclear encoded. BUT they are all homologs. Structure: similar to bacterial rps3. Nuclear encoded A. Wai (2016, 2019) ComplexContact Hong Zeng, Sheng Wang, Tianming Zhou, Feifeng Zhao, Xiufeng Li, Qing Wu, Jinbo Xu, ComplexContact: a web server for inter-protein contact prediction using deep learning, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W432– W437, https://doi.org/10.1093/nar/gky420 Alternative to MISTIC – find inter-protein contact points. http://raptorx.uchicago.edu/ComplexContact/ http://predictioncenter.org/in dex.cgi Useful link: many programs/tools http://predictioncenter.org/index.cgi?page=links Expand your “tool box” Resource: https://services.healthtech.dtu.dk/ https://services.healthtech.dtu.dk/ Example: https://services.healthtech.dtu.dk/ ConSurf Server: Phylogeny, structure and function Direct quote from webpage: “1. Introduction The ConSurf server (Glaser et al., 2003; Landau et al., 2005; Ashkenazy et al., 2010; Celniker et al., 2013; Ashkenazy et al., 2016) is a bioinformatics tool for estimating the evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous sequences. The degree to which an amino (or nucleic) acid position is evolutionarily conserved (i.e., its evolutionary rate) is strongly dependent on its structural and functional importance. Thus, conservation analysis of positions among members from the same family can often reveal the importance of each position for the protein (or nucleic acid)'s structure or function. In ConSurf, the evolutionary rate is estimated based on the evolutionary relatedness between the protein (DNA/RNA) and its homologues and considering the similarity between amino (nucleic) acids as reflected in the substitutions matrix (Pupko et al., 2002; Mayrose et al., 2004). One of the advantages of ConSurf in comparison to other methods is the accurate computation of the evolutionary rate by using either an empirical Bayesian method or a maximum likelihood (ML) method (Pupko et al., 2002).” http://consurf.tau.ac.il/overview.php Evolutionary conservation within DNA/RNA or protein sequences Identify positions that might be of functional significance. More tools https://foldxsuite.crg.eu/node/196 Effect of mutations on protein structure https://foldxsuite.crg.eu/ ProDy — Protein Dynamics and Sequence Analysis (pitt.edu) Protein dynamics study More tools Bioinformatics Toolkit (mpg.de)