Protein Motion

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Protein Motion
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What is a protein?

• Primary level - a sequence of alphabets (amino
  acid molecules)
• Amino acids are organic (carbon-based) molecules
• Chemically bond with each other through peptide
  bonds

YEPKGEVSWQ
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What is a protein?

• Protein backbone defines the overall shape
• Bond angles, lengths relatively constant
• Major degrees of freedom are dihedral angles
• Side chain motions are local and minor

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Protein conformational changes
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The relationship between structure function

• Exist to realize protein functionality
• Analysis critical to biological understanding

Lactate Dehydrogenase in different conformations
(red and yellow)
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Two Approaches

• Data drivenWith lots of data, the problem
  becomes that of finding out the salient motion
  from data.
• Model drivenAssume a simple model of protein
  motion and fit it against a small amount of data.
  We then need to validate the model.

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Principal Components
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Singular Value Decomposition
samples

DOF
x
x

x
A
U
S
VT
x
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Principal Components

• Patterns in data
• New orthogonal vectors that maximize variance
• Compact representation of original data
• With / without loss

y
X