Structure of Proteins

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Structure of Proteins
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Quick review

• DNA -gt RNA -gt 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

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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

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• 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

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• Hydrophobicity
• Containing no polar side chains
• Interact less favorably with water
• Mainly found in the proteins interior

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• Aromicity
• If the protein has an aromatic side chain
• Have a tendency to be stacked rather than
  participate in hydrogen bonds

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• 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

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• Special
• Cycteines
• Can form a disulfide bridge a Sulfur to sulfur
  linkage, responsible for the structure of tough
  proteins such as hair and keratin

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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

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• Acidic
• Asp,Glu
• Basic
• His,Arg,Lys
• Conformation ally important
• Gly,Pro

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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

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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

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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

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Looking at protein structures

• Installing NCBIs free viewer Cn3D
• NCBI viewer
• www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

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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

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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