As membrane proteins exit the translocon, they complete the folding process in the membrane. Thus, it is important to determine how their sequences define their final structures and stabilities. This is generally approached by studying natural proteins. De novo protein design provides an alternative means to test and refine our understanding of membrane protein structure and function. By designing membrane proteins we can critically test and ultimately refine our understanding of recognition, folding and function.
I Aim 1) we will define motifs that contribute largely to membrane protein folding and stability. We then determine the extent to which these motifs drive folding by designing peptides that idealize the sequence motifs. The association of peptides in phospholipid bilayers will be evaluated to determine the free energy of interaction, and how it changes upon changing residues thought to be key to the interaction.
Aim 2) addresses the question of sequence-specific recognition in membranes. A variety of methods exist for the design or selection of antibodies and other reagents that recognize the water-soluble regions of proteins. However, companion methods for targeting Transmembrane (TM) regions are not generally available. Therefore, we developed a method for the computational design of peptides that targets TM helices in a sequence-specific manner. Now, we will use this computational procedure in conjunction with a bacterial screen of heterodimerization to better define the rules that govern the tight and specific association of helices. We will focus on the design of peptides that bind several biologically important systems including: EGF receptors (Collaboration with Natalia Jura), amyloid precursor protein (S. Prusiner), and the thrombopoietin receptor (Wei Tong).
Aim 3) focuses on membrane metalloprotein assembly and metal ion transport. In the previous period, we designed model proteins that bind metal ion cofactors, including diiron and di-manganese centers in effort to determine how a protein matrix tunes the chemical properties of these cofactors to obtain diverse catalytic activities. Starting with proteins that bound metal ions but were catalytically inert we introduced substantial catalytic activities by varying the site's solvent accessibility, ligand identity, ligation geometry, and introducing substrate-binding sites.
In Aim 3 A, we now examine how immersion of the cofactor within a membrane will affect activity.
In Aim 3 B, we elaborate our design of TM metalloproteins to engineer channels that mediate passive transport down a concentration gradient as well as metal transporters that allow active transport against a concentration gradient. In preliminary results we have designed TM Zn(II) transporters that drive simultaneous proton export and Zn(II) import into liposomes. Here we characterize the conduction, structures, and dynamics (using solution and solids NMR and X-ray crystallography) of these designed transporters to determine the minimal features required for efficient facilitated transport of ions through TM helical bundles.

Public Health Relevance

Membrane proteins comprise approximately a third of the proteins expressed in our genomes, but our understanding of their structure and function lags considerably behind that of water-soluble proteins. Our lab uses de novo protein design to test the principles of membrane protein structure and function - if we understand membrane proteins we should be able to design them from scratch. We use this approach to probe the mechanisms by which membrane proteins achieve their three-dimensional structures, probe the means by which they pump antibiotics and anticancer drugs out of cells, and design peptides that recognize the membrane spanning regions of proteins in an antibody-like manner.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM054616-20
Application #
8761883
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Chin, Jean
Project Start
1996-08-01
Project End
2018-06-30
Budget Start
2014-09-01
Budget End
2015-06-30
Support Year
20
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
City
San Francisco
State
CA
Country
United States
Zip Code
94143
Fong, Karen P; Zhu, Hua; Span, Lisa M et al. (2016) Directly Activating the Integrin αIIbβ3 Initiates Outside-In Signaling by Causing αIIbβ3 Clustering. J Biol Chem 291:11706-16
Mustata, Gina-Mirela; Kim, Yong Ho; Zhang, Jian et al. (2016) Graphene Symmetry Amplified by Designed Peptide Self-Assembly. Biophys J 110:2507-16
Ulas, Gözde; Lemmin, Thomas; Wu, Yibing et al. (2016) Designed metalloprotein stabilizes a semiquinone radical. Nat Chem 8:354-9
To, Tsz-Leung; Medzihradszky, Katalin F; Burlingame, Alma L et al. (2016) Photoactivatable protein labeling by singlet oxygen mediated reactions. Bioorg Med Chem Lett 26:3359-63
Kim, Kook-Han; Ko, Dong-Kyun; Kim, Yong-Tae et al. (2016) Protein-directed self-assembly of a fullerene crystal. Nat Commun 7:11429
Snyder, Rae Ana; Butch, Susan E; Reig, Amanda J et al. (2015) Molecular-Level Insight into the Differential Oxidase and Oxygenase Reactivities of de Novo Due Ferri Proteins. J Am Chem Soc 137:9302-14
Snyder, Rae Ana; Betzu, Justine; Butch, Susan E et al. (2015) Systematic Perturbations of Binuclear Non-heme Iron Sites: Structure and Dioxygen Reactivity of de Novo Due Ferri Proteins. Biochemistry 54:4637-51
Bhate, Manasi P; Molnar, Kathleen S; Goulian, Mark et al. (2015) Signal transduction in histidine kinases: insights from new structures. Structure 23:981-94
Yu, Dan; Baird, Michelle A; Allen, John R et al. (2015) A naturally monomeric infrared fluorescent protein for protein labeling in vivo. Nat Methods 12:763-5
Zhang, Shao-Qing; Kulp, Daniel W; Schramm, Chaim A et al. (2015) The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions. Structure 23:527-41

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