CMSC423 Bioinformatic Algorithms Databases and Tools What you missed Protein folding Protein folding Note mis folded proteins may cause disease e g Creutzfeld Jakob a k a mad cow Drugs e g antibiotics often inhibit protein function knowing structure can help design drugs Folding home lend your computer s unused cycles to help fold proteins like SETI home do you believe in evolution or aliens Protein structure primary structure sequence http www tulane edu biochem med second htm Secondary structure motifs helix sheet turn http alpha2 bmc uu se kenth bioinfo structure secondary 01 html Tertiary structure 3D shape http www umass edu microbio rasmol sayle1 htm Folded shape lowest free energy Energy components electrostatic 1 D2 n2 terms van der Waals n2 terms hydrogen bonding n terms bending n terms solvent water salt terms exclusion principle no two atoms share same volume Energy minimzation small perturbations computation hill climbing simulated annealing etc Molecular dynamics How do we know the truth X ray crystallography crystallize protein shine X rays examine diffraction patterns http www cryst bbk ac uk BBS whatis cryst an html Nuclear Magnetic Resonance NMR no crystallization necessary magnetic field vibrates hydrogen atoms Nobel prize Kurt Wuethrich http www cryst bbk ac uk PPS2 projects schirra html 2dnmr htm Simpler problems Secondary structure prediction Side chain conformation assuming fixed backbone Protein docking how do proteins interact Database searches protein threading Simpler energy functions Folding on a lattice theoretical approximation Critical Assessment of Fully Automated Structure Prediction competition on proteins with unpublished 3D structure Proteomics Proteomics Large scale analysis of proteins protein protein interactions e g yeast 2 hybrid 2D gels mass vs isoelectric point Mass spectrometry Protein microarrays etc Proteomics Why proteomics Are DNA RNA microarrays not sufficient RNA abundance is not necessarily related to protein abundance Many proteins are modified post translation addition of additional molecules phosphate sugars etc creation of complexes hemoglobin is actually 4 molecules Mass spectrometry Technique for measuring the mass to charge ratio of ions Basic idea shoot ions into a magnetic field deflection depends on mass Output of a mass spectrometer ions sorted by mass for each mass bucket number of ions with that specific mass Mass spectrometry http www cem msu edu reusch VirtualText Spectrpy MassSpec masspec1 htm Tandem Mass Spectrometry First mass spectrometer focuses on a specific protein Second mass spectrometer breaks the protein into smaller chunks Problem given the chunks what was the original protein Peptide sequencing Peptide a chunk of a protein usually obtained by enzymatic cleavage of the protein using trypsin Problem Given an MS spectrum weights of fragments what was the sequence of the peptide Or find the peptide of mass m that best matches the experimental data Biological networks Biological networks Genes proteins do not exist in isolation Interactions between genes or proteins can be represented as graphs Examples metabolic pathways regulatory networks protein protein interactions e g yeast 2 hybrid genetic interactions synthetic lethality Metagenomics Why do we care Bacteria are everywhere in the environment They are not all evil Bacteria can be quite useful Bio energy Bio remediation Drug development antibiotics anti cancer Human microbiome Human 1 order of magnitude more bacterial cells than human cells critical to infant development immune system GI tract provide essential nutrients vitamin K B12 essential amino acids help digest complex molecules starches plant material imbalances in normal bacterial populations correlate with disease IBD colon cancer Human microbiome project nihroadmap nih gov hmp Some challenges on real data 25000 ZZZ UNKNOWN Verrucomicrobiae Spirochaetes Gammaproteobacteria Fusobacteria Flavobacteria Erysipelotrichi Epsilonproteobacteria Deltaproteobacteria Clostridia Betaproteobacteria Bacteroidetes Bacilli Alphaproteobacteria Actinobacteria 20000 15000 10000 5000 0 2508P1D24 2508P3D24 2510P1D24 2510P2D24 2504P2D24 2503P3D24 2508P1D13 2508P3D13 2510P1D13 2510P2D13 2504P1D24 2503P2D24 P1 P2 P3 P4 Spatial genomics Voxelation Brown V M et al High throughput imaging of brain gene expression Genome Res 2002 12 2 p 244 54 http www ncbi nlm nih gov entrez query fcgi cmd Retrieve db PubMed dopt Citatio Brown V M et al Multiplex three dimensional brain gene expression mapping in a mouse model of Parkinson s disease Genome Res 2002 12 6 p 868 84 http www ncbi nlm nih gov entrez query fcgi cmd Retrieve db PubMed dopt Citatio Gene expression information in a spatial context Combines microarray analysis with computer graphics Figure 2 Voxelation scheme Vanessa M Brown et al Genome Res 2002 12 868 884 Mouse brain cut up into voxels Run a separate microarray experiment on each voxel Figure 4 Spatial gene expression patterns for the subset of correlated genes Vanessa M Brown et al Genome Res 2002 12 868 884 Figure 7 SVD delineates anatomical regions of the brain Vanessa M Brown et al Genome Res 2002 12 868 884 Figure 5 Putative regulatory elements shared between groups of correlated and anticorrelated genes Vanessa M Brown et al Genome Res 2002 12 868 884
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