This application is in response to PA-09-164 for NIH Exploratory/Developmental Research Grants. The overall goal of the project is to develop new computational methods for NMR structural analysis of integral membrane proteins within their native, functional environment of the phospholipid bilayer membrane. These protein/lipid macromolecular complexes are challenging for the conventional methods of structural biology but can be characterized using solid-state NMR spectroscopy of oriented samples. The development of computational methods is an essential aspect of this approach. The information contained in the spectra from oriented samples is unique in its ability to provide direct images of protein structures, and very different from that of NMR spectra obtained from isotropic samples. Thus, it requires a different approach for data analysis.
The Specific Aims of this project are designed to take advantage of recent developments in bioinformatics, numerical methods, and molecular dynamics for simulated annealing methods. The computational methods will be developed, tested and implemented for a large body of NMR data obtained in the laboratories of the two investigators on this project, Marassi (Burnham) and Opella (UCSD), for both a-helical and ?-barrel integral membrane proteins in membranes. These investigators will work closely with computer scientists with complementary expertise in biomolecular structure calculation, and bioinformatics and structure prediction.
The Aims will be to combine the oriented sample NMR computational methods with the capabilities of the XPLOR- NIH and ROSETTA programs.

Public Health Relevance

This research will develop and implement new computational tools for calculating the three-dimensional structures of membrane proteins from experimental NMR data. Membrane proteins are the principal class of drug receptors and this research will accelerate the discovery of drugs for many diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Exploratory/Developmental Grants (R21)
Project #
5R21GM094727-02
Application #
8136905
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Wehrle, Janna P
Project Start
2010-09-30
Project End
2012-08-31
Budget Start
2011-09-01
Budget End
2012-08-31
Support Year
2
Fiscal Year
2011
Total Cost
$218,345
Indirect Cost
Name
Sanford-Burnham Medical Research Institute
Department
Type
DUNS #
020520466
City
La Jolla
State
CA
Country
United States
Zip Code
92037
Tian, Ye; Schwieters, Charles D; Opella, Stanley J et al. (2014) A practical implicit solvent potential for NMR structure calculation. J Magn Reson 243:54-64
Cheng, Xi; Jo, Sunhwan; Marassi, Francesca M et al. (2013) NMR-based simulation studies of Pf1 coat protein in explicit membranes. Biophys J 105:691-8
Yao, Yong; Ding, Yi; Tian, Ye et al. (2013) Membrane protein structure determination: back to the membrane. Methods Mol Biol 1063:145-58
Ding, Yi; Yao, Yong; Marassi, Francesca M (2013) Membrane protein structure determination in membrana. Acc Chem Res 46:2182-90
Cook, Gabriel A; Dawson, Lindsay A; Tian, Ye et al. (2013) Three-dimensional structure and interaction studies of hepatitis C virus p7 in 1,2-dihexanoyl-sn-glycero-3-phosphocholine by solution nuclear magnetic resonance. Biochemistry 52:5295-303
Wang, Yan; Park, Sang Ho; Tian, Ye et al. (2013) Impact of histidine residues on the transmembrane helices of viroporins. Mol Membr Biol 30:360-9
Tian, Ye; Schwieters, Charles D; Opella, Stanley J et al. (2012) AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra. J Magn Reson 214:42-50
Das, Bibhuti B; Nothnagel, Henry J; Lu, George J et al. (2012) Structure determination of a membrane protein in proteoliposomes. J Am Chem Soc 134:2047-56
Park, Sang Ho; Das, Bibhuti B; Casagrande, Fabio et al. (2012) Structure of the chemokine receptor CXCR1 in phospholipid bilayers. Nature 491:779-83
Tian, Ye; Opella, Stanley J; Marassi, Francesca M (2012) Improved chemical shift prediction by Rosetta conformational sampling. J Biomol NMR 54:237-43

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