Understanding protein folding is a central life process and is essential for many of the primary quests of structural biology including structure prediction, protein design, mapping evolutionary pathways, learning how mutations cause disease, drug design, and relating structure to function. Consequently, there has been an enormous effort over the years to understand how proteins fold. Essentially all of the effort has been directed to water soluble proteins, however, leaving us largely in the dark about membrane proteins. The gap in our knowledge has occurred, not because membrane proteins are inherently less important, but because they are technically challenging to study. We have been working to understand how membrane protein structures are defined by their amino acid sequence and their complex environment. In prior grant periods we have made membrane protein folding increasingly accessible to detailed examination and have been able to experimentally probe fundamental aspects of membrane protein structure including hydrogen bond strengths, helix kinks and packing efficiency. We propose to continue our examination of key structural features of membrane proteins and to continue developing techniques to advance this still fledgling field.
The specific aims are:
Aim I. How are kinks induced in transmembrane helices? A hallmark of transmembrane helices is the large fraction of kinks. Thus, an important question in membrane protein folding is how kinks are generated. We will use double mutant cycle analysis to identify residues that collaborate in kink formation.
Aim II. How are new strongly polar side chains accommodated in membrane protein tertiary structure? Strongly polar side chains play prominent structural and functional roles in membrane proteins. Thus, the evolutionary process must encounter and tolerate new polar substitutions. Yet mutations to or from polar side chains are the most common disease-causing changes, so there are clearly dangers that must be understood. We therefore propose discover the structural consequences of introducing single Asn residues at different points in the bacteriorhodopsin structure.
Aim III. Develop a steric trapping to study the unfolding of membrane proteins under native conditions. The folding of large helical membrane proteins must currently be done in detergents. We will develop a new method for controlling the folding equilibrium within natural bilayers or bilayer-like environments. This development will be a major advance in the field because it will finally allow us to study how the protein and the membrane environment collaborate to fold membrane proteins.

Public Health Relevance

The genome is manifest in part by the protein molecules it encodes. These proteins are often designed to fold up into a unique structure that is essential for its biological role. Disease can occur if the folding process is disrupted by mutation or other physiological processes. We are working to understand how the large class of proteins that float in cell membranes manage to assemble so that we can learn how to intervene in folding diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM063919-11
Application #
8245056
Study Section
Special Emphasis Panel (ZRG1-BCMB-B (02))
Program Officer
Chin, Jean
Project Start
2001-08-01
Project End
2014-03-31
Budget Start
2012-04-01
Budget End
2013-03-31
Support Year
11
Fiscal Year
2012
Total Cost
$290,174
Indirect Cost
$90,194
Name
University of California Los Angeles
Department
Genetics
Type
Schools of Medicine
DUNS #
092530369
City
Los Angeles
State
CA
Country
United States
Zip Code
90095
Lu, Peilong; Min, Duyoung; DiMaio, Frank et al. (2018) Accurate computational design of multipass transmembrane proteins. Science 359:1042-1046
Jefferson, Robert E; Min, Duyoung; Corin, Karolina et al. (2018) Applications of Single-Molecule Methods to Membrane Protein Folding Studies. J Mol Biol 430:424-437
Min, Duyoung; Jefferson, Robert E; Qi, Yifei et al. (2018) Unfolding of a ClC chloride transporter retains memory of its evolutionary history. Nat Chem Biol 14:489-496
Woodall, Nicholas B; Hadley, Sarah; Yin, Ying et al. (2017) Complete topology inversion can be part of normal membrane protein biogenesis. Protein Sci 26:824-833
Cao, Zheng; Hutchison, James M; Sanders, Charles R et al. (2017) Backbone Hydrogen Bond Strengths Can Vary Widely in Transmembrane Helices. J Am Chem Soc 139:10742-10749
Cheng, Xi; Kim, Jin-Kyoung; Kim, Yangmee et al. (2016) Molecular dynamics simulation strategies for protein-micelle complexes. Biochim Biophys Acta 1858:1566-72
Nam, Hyun-Jun; Kim, Inhae; Bowie, James U et al. (2015) Metazoans evolved by taking domains from soluble proteins to expand intercellular communication network. Sci Rep 5:9576
Woodall, Nicholas B; Yin, Ying; Bowie, James U (2015) Dual-topology insertion of a dual-topology membrane protein. Nat Commun 6:8099
Min, Duyoung; Jefferson, Robert E; Bowie, James U et al. (2015) Mapping the energy landscape for second-stage folding of a single membrane protein. Nat Chem Biol 11:981-7
Cao, Zheng; Bowie, James U (2014) An energetic scale for equilibrium H/D fractionation factors illuminates hydrogen bond free energies in proteins. Protein Sci 23:566-75

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