The use of solution NMR to determine MP structure is now in a rapid state of growth. Recently, this approach has been employed to solve a number of new MP structures of high biological impact, demonstrating its potential in MP structural genomics. However, there is not yet a specialized center that focuses on broad development of this important emerging area of structural biophysics. We propose a Protein Structure Initiative (PSI) Center that aims to develop an efficient solution NMR pipeline for solving MP structures. This Center consists of a team of investigators who are among the most productive in the world in solving MP structures by NMR, including James Chou, Gerhard Wagner, Charles Sanders, and Volker Dotsch. The Center also includes a synthetic core for providing the materials used in MP NMR, an NMR/computational core for developing faster methods of structure determination, and an administrative core for management and dissemination of technology. To drive technology development and to test the proposed pipeline, we have selected 10 MP targets for which the structures are not known, including membrane-embedded transporters, enzymes, and receptors. These targets are polytopic helical MPs with 3-7 transmembrane helices and with sizes from 18-43 kDa. The Center will develop technologies that will have immediate and practical impact on structure determination. They include (1) cell-free expression platforms for production of MPs and for screening for NMR-feasible MP targets;(2) new detergents, bicelles and MP refolding methods;(3) non-uniform sampled high resolution 4D NOESYs;(4) new strategies for selective isotope labeling of methyl groups for acquiring long-range NOEs;(5) novel reagent for site-directed paramagnetic tagging and universal DNA-nanotube alignment media for RDC measurements;and (6) RDC-based molecular fragment replacement and structure calculation protocols. Although the phrase "high-throughput" does not yet apply to MP in any technological context, we aim to establish a NMR tool package within the proposed funding period that has the capacity for systematic production of MP structures, while delivering the structures of the target MPs.

Public Health Relevance

MPs constitute about 50% of drug targets, but their structures for rational drug design are generally not available due to the technical challenges involved in solving MP structures. The NMR technologies proposed in this grant would constitute a robust pipeline for systematic production of MP structures. This pipeline would nicely complement the existing crystallography-based Centers in the coverage of MP structure space.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
5U54GM094608-04
Application #
8508950
Study Section
Special Emphasis Panel (ZGM1-CBB-3 (MP))
Program Officer
Wehrle, Janna P
Project Start
2010-09-15
Project End
2015-06-30
Budget Start
2013-07-01
Budget End
2014-06-30
Support Year
4
Fiscal Year
2013
Total Cost
$4,432,226
Indirect Cost
$1,356,239
Name
Harvard University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
047006379
City
Boston
State
MA
Country
United States
Zip Code
02115
Schlebach, Jonathan P; Sanders, Charles R (2015) Influence of Pathogenic Mutations on the Energetics of Translocon-Mediated Bilayer Integration of Transmembrane Helices. J Membr Biol 248:371-81
Yang, Qin; Bruschweiler, Sven; Chou, James J (2014) A self-sequestered calmodulin-like Caýýýýý sensor of mitochondrial SCaMC carrier and its implication to Caýýýýý-dependent ATP-Mg/P(i) transport. Structure 22:209-17
Roos, Christian; Kai, Lei; Haberstock, Stefan et al. (2014) High-level cell-free production of membrane proteins with nanodiscs. Methods Mol Biol 1118:109-30
OuYang, Bo; Chou, James J (2014) The minimalist architectures of viroporins and their therapeutic implications. Biochim Biophys Acta 1838:1058-67
Yang, Qin; Brüschweiler, Sven; Chou, James J (2014) Purification, crystallization and preliminary X-ray diffraction of the N-terminal calmodulin-like domain of the human mitochondrial ATP-Mg/Pi carrier SCaMC1. Acta Crystallogr F Struct Biol Commun 70:68-71
Mittendorf, Kathleen F; Kroncke, Brett M; Meiler, Jens et al. (2014) The homology model of PMP22 suggests mutations resulting in peripheral neuropathy disrupt transmembrane helix packing. Biochemistry 53:6139-41
Song, Yuanli; Mittendorf, Kathleen F; Lu, Zhenwei et al. (2014) Impact of bilayer lipid composition on the structure and topology of the transmembrane amyloid precursor C99 protein. J Am Chem Soc 136:4093-6
Elter, Shantha; Raschle, Thomas; Arens, Sabine et al. (2014) The use of amphipols for NMR structural characterization of 7-TM proteins. J Membr Biol 247:957-64
Sun, Zhen-Yu J; Cheng, Yuxing; Kim, Mikyung et al. (2014) Disruption of helix-capping residues 671 and 674 reveals a role in HIV-1 entry for a specialized hinge segment of the membrane proximal external region of gp41. J Mol Biol 426:1095-108
Song, Yuanli; Kenworthy, Anne K; Sanders, Charles R (2014) Cholesterol as a co-solvent and a ligand for membrane proteins. Protein Sci 23:1-22

Showing the most recent 10 out of 41 publications