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lecture1 (1) - Bioinformatics 2 Molecular Modeling Lecture...

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Bioinformatics 2: Molecular Modeling Lecture 1: Intro to amino acid structure, peptides, and proteins
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Administrative stuff Set office hours Read syllabus Install MOE, starting now. Install Rasmol. Course website: http://www.bioinfo.rpi.edu/bystrc/courses/ biol4550/biol4550.html
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MOE 3
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Two underlying principles 1. Evolution -- proteins sequences are selected for function . 2. Energy -- biochemical systems seek the lowest free energy state . Keep these two principles in the back of your mind at all times. One on the left side, one on the right side. Encourage them to talk to each other.
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What a protein looks like...from Bioinformatics 1 point of view. MSAIQASWPSGTECIAKYNFHGTAEQDLPFC KGDVLTIVAVTKDPNWYKAKNKVGREGIIPA NYVQKREGV In theory this is all the information you need to make a 3D protein. Maximum information compression. Add water, add physical forces, add time (1 sec will do) and you will get a unique (within reason) 3D structure.
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the backbone atoms O C C N O C C N N O C C N R 1 H H H H H H R 3 R 2 Backbone atom names are “N, “C-alpha” and “C” (or N,CA,C). Oxygen “O” is also considered a backbone atom, though strictly speaking it is a one-atom sidechain. All atoms in all amino acids have conventional names. Address them by name or they will not answer. partial double “peptide” bond
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the sidechains There are 20 natural amino acids [OK, 21. Seleno-cysteine is also a “natural” amino acid.] These chemical nature of these 20 sidechains account for the folding and function of proteins. Memorize the sidechains ! Yes, all 20. (ok, 21)
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9 Walczak, R; Westhof E, Carbon P, Krol A (1996). "A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs". RNA 2: 367–379. Selenocysteine The presence of a selenocysteine insertion sequence, SECIS , signals the cell to translate UGA Stop codons with a special, modified tRNA. Initially charged with serine, Ser- tRNA(Sec) is then converted to Sec- tRNA(Sec) by selenocysteine synthase. Selenocysteine is not formed if no selenium (Se) is present, leading to translation stop. SECIS is located within the coding sequence (bacteria) or in the 3’-UTR (eukaryotes, archea). (3-letter code Sec , one-letter code U )
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Venn diagram 10 BLOSUM substitution matrix Compare and contrast ....
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Free AA vs polypeptides Free amino acid O C C N R H H O C C N R H HO H H O O C C N R H H H H + Zwitterionic form, pH7 Polymer repeating unit (“ residue ”)
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Why is it called a “residue”?
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