Protein Planes Bob Fraser CSCBC 2007 Overview Motivation Points to examine
Results Further work C trace problem Given: only approximate positions of the C atoms of a protein Aim: Construct the entire backbone of the
protein This is an open problem! C trace problem Why do it? Some PDB files contain only C atoms. Refinement of X-ray or NMR skeletons.
More importantly, many predictive approaches are incremental, and begin by producing the C trace. C trace problem Possible solutions: De novo, CHARMM fields (Correa 90)
Fragment matching (Levitt 92) Maximize hydrogen bonding (Scheraga et al. 93) Idealized covalent geometry Used by Engh & Huber (91) for X-ray crystallography refinement Supplemented by including additional information (Payne 93, Blundell 03)
All methods achieve <1 rmsd, ~0.5 rmsd is good. Perhaps including more information about the plane could further improve results. Idealized covalent geometry
The task Survey the structures in the PDB, and determine how close the known structures adhere to these values. Next look at the relationship between the planes and secondary structures Is this information useful?
If so, could it be used in refinement? Length of plane (C C distance) The so-called bond distance when given a C trace. If all bond angles and lengths are fixed, this distance should also be constant.
Lets check this distance in the PDB, and determine the average, standard deviation, maximum and minimum values found. cis vs. trans
Secondary Structure Angle between helix axis and plane It is assumed that the planar regions for amino acids in a helix are parallel to the axis of the helix. Lets put this to the test!
How do we measure the axis of helix? It is a subjective measure Well use the method of Walther et al. (96), it provides a local helix axis Plane-axis angle Now we have a peptide plane and the
helix axis, so we can find the angle between them easily. This same method could be applied to beta strands and 3-10 helices. We should expect that some pattern should arise since beta strands are have regular patterns, particularly when in beta
sheets. Data Analysis Use the entire PDB database as a source Compare the results obtained to the expected values for the plane lengths and alpha helices
Determine whether a preferential orientation exists for beta strands and 3-10 helices Plane length trans and cis cases need to be distinguished
because they are different inherently Plane length is composed of 5 elements of idealized covalent geometry -helix 3-10 Helix
-strand Results Future Work Develop algorithm for using secondary
structure to solve trace problem. Test it on proteins with perfect C traces to verify the accuracy of reconstruction. Test on randomized C traces. Integrate this information with refinement Thanks!
Selected References M.A. DePristo, P.I.W. de Bakker, R.P. Shetty, and T.L. Blundell. Discrete restraint-based protein modeling and the C -trace problem. Protein Science, 12:2032-2046, 2003. A. Liwo, M.R. Pincus, R.J. Wawak, S. Rackovsky, and H.A. Scheraga. Calculation of protein backbone geometry from alphacarbon coordinates based on peptide-group dipole alignment. Protein Sci., 2(10):1697-1714, 1993.
G.A. Petsko and D. Ringe. Protein Structure and Function. New Science Press Ltd, London, 2004. D. Walther, F. Eisenhaber, and P. Argos. Principles of helix-helix packing in proteins: the helical lattice superimposition model. J.Mol.Biol., 255: 536-553, 1996. Walther axis calculation
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