NUS CS 5247 David Hsu Protein Motion. NUS CS 5247 David Hsu2 What is a protein?  Primary level - a sequence of alphabets (amino acid molecules)  Amino.

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NUS CS 5247 David Hsu Protein Motion

NUS CS 5247 David Hsu2 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…

NUS CS 5247 David Hsu3 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

NUS CS 5247 David Hsu4 Protein conformational changes

NUS CS 5247 David Hsu5 The relationship between structure & function  Exist to realize protein functionality  Analysis critical to biological understanding Lactate Dehydrogenase in different conformations (red and yellow)

NUS CS 5247 David Hsu6 Two Approaches  Data driven With lots of data, the problem becomes that of finding out the salient motion from data.  Model driven Assume a simple model of protein motion and fit it against a small amount of data. We then need to validate the model.

NUS CS 5247 David Hsu7 Principal Components X y

NUS CS 5247 David Hsu8 Singular Value Decomposition = AUΣVTVT DOF samples xx = x x

NUS CS 5247 David Hsu9 Principal Components  Patterns in data  New orthogonal vectors that maximize variance  Compact representation of original data  With / without loss X y