Protein Planes - University of Manitoba

Protein Planes - University of Manitoba

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

Recently Viewed Presentations

  • MRSA module - Educational Testing Service

    MRSA module - Educational Testing Service

    It requires grappling with a wide variety of complex texts, considering who wrote a particular text, what the author's perspective, biases and purposes may be, the intended audience, the historical context in which the author is situated, , etc., first...
  • Working Within the Requirements of ASME B31.9 NEIL

    Working Within the Requirements of ASME B31.9 NEIL

    Fusion-Weld (FAILURE) 6in O.D. Seam-Welded Tube. 8in NPS Seamless Pipe. Back Plate. Soap bubble test found leak. Project Approach. Operations, Installation, MachShop, Meng, RadCon, QA, & Facilities met to determine whether repair would be made now or later and discuss...
  • Opakování z minulého cvičení

    Opakování z minulého cvičení

    Physics of stars Syllabus week topics-----Statistics of stars, spectroscopy, HR diagram.
  • PD Lecture 1999 - University of Pittsburgh

    PD Lecture 1999 - University of Pittsburgh

    Dalen Fuchs' nodule - histiocytes, prolif epithelial cells like cannon balls seen in all inflamm uveitis including TB, characteristic of SO Benign acquired melanosis Unilateral flat pigmentation of conj and periph cornea - completely flat pigmentation rarely is malignant Stains...

    How do I get paid? First you need a Social Insurance Number (SIN) Domestic Students provide a photocopy of your SIN to me before September 9th. International Students - Go to Service Canada to obtain a SIN.
  • Mutal Funds -

    Mutal Funds -

    Determine the fund's objective, asset class, and investment style. Identify funds that meet your criteria for performance, size, fees, management, etc. Step 4: Evaluate the Funds. How do you evaluate funds (some advice from a fund manager in a previous...
  • Stewardship of the Gift of Time

    Stewardship of the Gift of Time

    Time Robbers. What Robs Our Time? Thirty leaders identified their biggest time robbers. The most frequently mentioned were: Procrastination. "The greatest time wasted is the time getting started," observed Dawson Trotman, the founder and first president of The Navigators.
  • Digital transformation: Why and what? Jeff Murray Chief

    Digital transformation: Why and what? Jeff Murray Chief

    But innovation is often thought to be using the latest technology, the latest model of smart phone, a new fad - remember cloud computing, or service oriented architectures, enterprise architecture before that or the rise of b2b - all fashionable...