The general perspective of this project is that an understanding of the motifs and chemical principles that govern helix-helix interactions in membrane proteins will serve as a basis for understanding and predicting structure, oligomerization, and function. Given the genomic abundance of sequences that appear to encode helical membrane proteins and the paucity of detailed high resolution structures, our alternative approach should prove valuable in providing working models for structures as well as in guiding thoughts concerning functional states. The key is to develop connections between structural and thermodynamic descriptions of helix-helix interactions. Additionally, motifs may be identified that allow simple approaches using straightforward sequence analysis. Progress during the first two years of the program has resulted in a number of promising directions, which we plan to exploit during the next grant period. An important development that serves as a cornerstone for our plan is the emergence of two genetic screens for helix interaction in E. coli membranes. These will be exploited to search the E. coli genome for naturally occurring interactions and to screen random libraries to obtain global views for interacting sequences. A second platform for our future studies is provided by the determination of the glycophorin A transmembrane helix dimer structure. Using the structure, we are testing ideas concerning the energy terms important in the interaction by redesigning the interface and studying structural and energetic properties of different designs. Additionally, we are exploring the use of natural motifs, such as the leucine zipper, to design interacting transmembrane helices. Computational chemistry and genomic database studies will be used to refine chemical ideas and document the occurrence of specific interactions in naturally occurring membrane proteins. The properties of helix interaction interfaces appear encouraging with regard to new avenues for drug discovery.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
2P01GM054160-04
Application #
2902272
Study Section
Special Emphasis Panel (ZRG1-BBCA (01))
Project Start
1996-05-01
Project End
2004-06-30
Budget Start
1999-07-01
Budget End
2000-06-30
Support Year
4
Fiscal Year
1999
Total Cost
Indirect Cost
Name
Yale University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
082359691
City
New Haven
State
CT
Country
United States
Zip Code
06520
Alexandrov, Vadim; Lehnert, Ursula; Echols, Nathaniel et al. (2005) Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool. Protein Sci 14:633-43
Freeman-Cook, Lisa L; Edwards, Anne P B; Dixon, Ann M et al. (2005) Specific locations of hydrophilic amino acids in constructed transmembrane ligands of the platelet-derived growth factor beta receptor. J Mol Biol 345:907-21
Balasubramanian, Suganthi; Xia, Yu; Freinkman, Elizaveta et al. (2005) Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms. Nucleic Acids Res 33:1710-21
Lehnert, Ursula; Xia, Yu; Royce, Thomas E et al. (2004) Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions. Q Rev Biophys 37:121-46
Freeman-Cook, Lisa L; Dixon, Ann M; Frank, Jennifer B et al. (2004) Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor. J Mol Biol 338:907-20
Schneider, Dirk; Engelman, Donald M (2003) GALLEX, a measurement of heterologous association of transmembrane helices in a biological membrane. J Biol Chem 278:3105-11
Zhang, Zhaolei; Gerstein, Mark (2003) The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse. Gene 312:61-72
Lin, J; Qian, J; Greenbaum, D et al. (2002) GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucleic Acids Res 30:4574-82
Jansen, R; Gerstein, M (2000) Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins. Nucleic Acids Res 28:1481-8
MacKenzie, K R; Prestegard, J H; Engelman, D M (1997) A transmembrane helix dimer: structure and implications. Science 276:131-3