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Structure of Proteins Quick review • • • • DNA -> RNA -> AA Many AA = peptide Lots of AA = protein 3 nucleotides specify a AA – Nucleotide sequence is 3 X longer than protein sequence. • If you know the nucleotide sequence you can determine the protein sequence • If you know the protein sequence you cannot completely define the nucleotide sequence that it came from. • Sequence != function or structure Amino acids • Characteristics of amino acids that help to determine structure. – 1.Charge +/• Asp/Glu have typically one negative charge • Lsy/Arg have typically one positive charge • These charges attract each other form an ion pair or salt bridge • There is also the net charge of the protein • Polarity the ability to participate in hydrogen bonding – No electrons are exchanged as in charge effect but electrons are shared creating an attraction – Some amino acids can participate in multiple reactions acting as both donors and acceptors • Hydrophobicity – Containing no polar side chains – Interact less favorably with water – Mainly found in the proteins interior Aromicity If the protein has an aromatic side chain Have a tendency to be stacked rather than participate in hydrogen bonds Size Unusually small or large amino acids Prolyne The most rigid of the amino acids because of the covalent linkage between the side chain and the main chain nitrogen Glycine Lacks much of a side chain frequently found where the protein makes a sharp bend Special Cycteines Can form a disulfide bridge a Sulfur to sulfur linkage, responsible for the structure of tough proteins such as hair and keratin Classes of amino acids • Non-polar/alaphatic - usually found on the interior of a protein – Ala Val Leu Ile • Hydrophobic/aromatic - usually found on the interior of a protein – Tyr Trp, mostly non polar Phe non-polar • Neutral/polar – Ser, Thr, Cys, Met,Asn,Gln • Acidic – Asp,Glu • Basic – His,Arg,Lys • Conformation ally important – Gly,Pro Letter codes for amino acids • There are twenty amino acids – Each one has both a three letter code as well as a single letter code. Some frequent substitutions also have a single letter code. • It is useful to know these Basic structure of a protein How proteins are formed from amino acids peptide bonds – Two ends of the amino acid the amino terminal end and the carboxy terminal end. Abbreviated N and C Same idea with the peptide Types of structure • Alpha helix - one type of helical structure. Has allowed conformational angles and favorable hydrogen bonding between the amino acids • B sheets - anti parallel the most common configuration – 2-15 strands are common • Subunits Looking at protein structures • Installing NCBI’s free viewer Cn3D • NCBI viewer • www.ncbi.nlm.nih.gov/ Structure/CN3D/cn3d.s html Finding motifs • • • • • Blocks Interpro ProDom Others All have similar strategies look though databases of conserved elements from other proteins that have been shown to be important and try and find those elements in your sequence. • www.blocks.fhcrc.org Prep for the bioperl section go to bio.perl.org •get the bioperl-0.7.1.tar.gz file tar -xzvf bioperl-0.7.1.tar.gz rm bioperl-0.7.1.tar.gz cd bioperl-0.7.1/ perl Makefile.PL PREFIX=/home/guest/Perl_Modules make make test make install Go to www.ncbi.nlm.nih.gov/BLAST follow the links to the blast db get swissprot.Z gunzip swissprot formatdb -i swissprot