Notice: NOT-OD-09-058, NIH Announces the Availability of Recovery Act Funds for Competitive Applications SUMMARY STATEMENT """"""""Group Theoretic Methods in Protein Structure Determination"""""""" The emphasis of this supplemental application is to analyze the statistics of ensembles of conformations of flexible proteins. That is, whereas the original grant focuses on new algorithms for determining protein structures from a variety of experimental modalities, the goal of this supplemental application is to quantify the variability of conformations represented in structural data. One of the most obvious examples of this is in NMR, where ensembles of conformations are often reported rather than an individual structure. The following specific aims to be addressed in this highly focused nine-month effort add to the original three specific aims:
Specific Aim 4 : Efficient Generation of Ensemble Statistics of Flexible Loop Conformations. In this specific aim, new methods from the field of robotic manipulator kinematics based on the concept of convolution and covariance propagation on the group of rigid-body motions will be used to generate ensemble statistics of candidate loop conformations without explicitly sampling conformational space. By circumventing the exponential price associated with traditional sampling techniques, we anticipate making a qualitative difference in the way protein-loop conformations are analyzed, not just a quantitative difference in particular computations. As a concrete test case, we will apply this methodology to the structure determination of human Ube2g2.
Specific Aim 5 : Evaluation of the Biasing Effects of Loops in the Assembly of Secondary Structures. In this specific aim we will study the correlation between loop length/composition and the special geometric characteristics of the resulting secondary structure interactions. We will begin by considering the helix-helix interaction in the helix-loop-helix motif and the relationship between helix interaction parameters and the parameters defining the loop. In other words, we will examine geometric characteristics such as crossing angle and where along the helix lengths the helices contact each other that depends on loop parameters. This is a purely in- silico objective, which will involve mining data from the Protein Data Bank.
Specific Aim 6 : Characterizing the Tertiary Ensemble. We will evaluate the following hypothesis: Protein tertiary structures do not always exist as single conformations, and enumeration of members of the 'tertiary ensemble'will better match experimental data than models in which a single conformation is assumed. We will test this hypothesis by validating tertiary ensembles against NMR residual dipolar couplings. In particular, we propose to utilize Neisseria meningitidis Heme Oxygenase (nmHO) as a test case of our ability to generate tertiary ensembles which maintain, or even improve, agreement with NMR data such as RDCs. Since the original grant is currently in no-cost extension, and almost all of the funds have been spent, this competitive renewal will provide an avenue for the continued funding of PI/co-PI salaries, a postdoc, and two students for a nine-month period. This, together with the proposed budget for laboratory supplies, constitutes the proposed request.

Public Health Relevance

The emphasis of this supplemental application is to analyze the statistics of ensembles of conformations of flexible proteins. That is, whereas the original grant focuses on new algorithms for determining protein structures from a variety of experimental modalities, the goal of this supplemental application is to quantify the variability of conformations represented in structural data.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
3R01GM075310-04S1
Application #
7845819
Study Section
Special Emphasis Panel (ZRG1-BCMB-A (96))
Program Officer
Remington, Karin A
Project Start
2009-09-30
Project End
2010-09-30
Budget Start
2009-09-30
Budget End
2010-09-30
Support Year
4
Fiscal Year
2009
Total Cost
$159,567
Indirect Cost
Name
Johns Hopkins University
Department
Engineering (All Types)
Type
Schools of Engineering
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21218
Park, Wooram; Midgett, Charles R; Madden, Dean R et al. (2011) A Stochastic Kinematic Model of Class Averaging in Single-Particle Electron Microscopy. Int J Rob Res 30:730-754
Bocik, William E; Sircar, Aroop; Gray, Jeffrey J et al. (2011) Mechanism of polyubiquitin chain recognition by the human ubiquitin conjugating enzyme Ube2g2. J Biol Chem 286:3981-91
Chirikjian, Gregory S (2011) Modeling loop entropy. Methods Enzymol 487:99-132
Chirikjian, Gregory S (2011) Mathematical aspects of molecular replacement. I. Algebraic properties of motion spaces. Acta Crystallogr A 67:435-46
Chirikjian, Gregory S (2010) INFORMATION-THEORETIC INEQUALITIES ON UNIMODULAR LIE GROUPS. J Geom Mech 2:119-158
Skliros, Aris; Park, Wooram; Chirikjian, Gregory S (2010) Position and Orientation Distributions for Non-Reversal Random Walks using Space-Group Fourier Transforms. J Algebr Stat 1:27-46
Birdsey-Benson, Amanda; Gill, Avinash; Henderson, Leslie P et al. (2010) Enhanced efficacy without further cleft closure: reevaluating twist as a source of agonist efficacy in AMPA receptors. J Neurosci 30:1463-70
Park, Wooram; Madden, Dean R; Rockmore, Daniel N et al. (2010) Deblurring of Class-Averaged Images in Single-Particle Electron Microscopy. Inverse Probl 26:3500521-35005229
Chirikjian, Gregory S (2010) Group theory and biomolecular conformation: I. Mathematical and computational models. J Phys Condens Matter 22:323103
Genovese, Giulio; Leibon, Gregory; Pollak, Martin R et al. (2010) Improved IBD detection using incomplete haplotype information. BMC Genet 11:58

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