CMSC423 Bioinformatic Algorithms Databases and Tools Lecture 21 Protein folding Proteomics Mass spectrometry 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 hate water like water can t decide http web mit edu esgbio www lm proteins aa aminoacids html Not all bends equally likely Ramachandran plot 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theoretical approximation Critical Assessment of Fully Automated Structure Prediction competition on proteins with unpublished 3D structure Proteomics Large scale analysis of proteins protein protein interactions e g yeast 2 hybrid 2D gels mass vs isoelectric point Mass spectrometry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 MS Algorithms Database search build database of all possible peptides better all peptides observed in known proteins match experimental spectrum to the database closest hit is our peptide Assembly de novo sequencing start with a spectrum identify masses that likely represent the same fragment build graph spectral graph that represents adjacency of fragments nodes fragments or ion types edges edge v w indicates fragments v and w differ by exactly 1 amino acid path through this graph represents a peptide sequence Some Mass Differences between Peaks Correspond to Amino Acids u q s e s e e c e u q e n n q u e n c c e e s e
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