Integral membrane proteins account for ~30% of a proteome and play critical roles in metabolic, regulatory and intercellular processes. Human MPs are the targets for ~40% of all therapeutic drugs, but the number of MP structures is less than 0.5% of the number of soluble protein structures. The proposed Center brings together 11 Investigators at five US institutions to focus cooperatively on the overarching aim of determining integral MP structures of high biomedical impact.
The Specific Aims balance multiple priorities.
Aims 1 -3 are extensive, seeking to obtain structures by providing many targets from (1) E. coli, (2) extremophiles, and (3) human. The broad target base is triaged by dynamic bioinformatics screening to direct focus on the most tractable set by the end of year 1.
Aims 4 and 5 are intensive, targeting families of highest biomedical relevance and impact for which structures have generally not yet been obtained;
Aim 4 concerns specific prokaryotic MPs;
Aim 5 involves the most challenging eukaryotic MPs, including human therapeutic targets and components of the nuclear pore complex.
Aim 6 leverages MP structures by comparative modeling developed specifically for MPs. Ten core capabilities implement the methods that support the aims and cover every aspect of structure determination, including target selection, cloning, expression, purification, crystallization, structure determination by X-ray crystallography, NMR spectroscopy or electron microscopy, and modeling. The cores provide multi-point entry to High-Throughput-Enabled Structural Biology Partnerships. Expression cores cover prokaryotic and eukaryotic (including HEKs) in vivo systems, one using green fluorescent protein detection of expression, and an E. coli based cell-free in vitro system optimized for MP expression. The protein purification core, aided by several characterization methods, provides pure homogeneous and stable proteins free of excess detergent. The electron microscopy core provides further characterization and 2D crystallization. Structure determination methods include X-ray diffraction and NMR spectroscopy, where cell-free expression has been harnessed to a combinatorial labeling strategy for rapid determination of backbone structures. The X-ray crystallography core provides robotic crystal trials and diffraction at the Advanced Light Source beam line 8.3.1, one of the world's most productive protein crystallography facilities. Overall, the combined expertise of principal investigators provides a unique environment to achieve the proposed aims.

Public Health Relevance

Integral Membrane Proteins account for ~30% of a proteome and play critical roles in metabolic, regulatory and intercellular processes. Human MPs are the targets for ~40% of all therapeutic drugs, but the number of MP structures is less than 0.5% of the number of soluble protein structures. The proposed Center brings together 11 Investigators at five US institutions to focus cooperatively on the overarching aim of determining integral MP structures of high biomedical impact.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
5U54GM094625-05
Application #
8693620
Study Section
Special Emphasis Panel (ZGM1-CBB-3 (MP))
Program Officer
Preusch, Peter
Project Start
2010-09-30
Project End
2015-06-30
Budget Start
2014-07-01
Budget End
2015-06-30
Support Year
5
Fiscal Year
2014
Total Cost
$1,447,621
Indirect Cost
$510,649
Name
University of California San Francisco
Department
Biochemistry
Type
Schools of Medicine
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94143
Metcalf, Brian; Chuang, Chihyuan; Dufu, Kobina et al. (2017) Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin. ACS Med Chem Lett 8:321-326
Webb, Benjamin; Sali, Andrej (2017) Protein Structure Modeling with MODELLER. Methods Mol Biol 1654:39-54
Dang, Bobo; Wu, Haifan; Mulligan, Vikram Khipple et al. (2017) De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures. Proc Natl Acad Sci U S A 114:10852-10857
Li, Zhe; Partridge, James; Silva-Garcia, Abel et al. (2017) Structure-Guided Design of Novel, Potent, and Selective Macrocyclic Plasma Kallikrein Inhibitors. ACS Med Chem Lett 8:185-190
Martin-Garcia, Jose M; Conrad, Chelsie E; Coe, Jesse et al. (2016) Serial femtosecond crystallography: A revolution in structural biology. Arch Biochem Biophys 602:32-47
Arrigoni, Cristina; Rohaim, Ahmed; Shaya, David et al. (2016) Unfolding of a Temperature-Sensitive Domain Controls Voltage-Gated Channel Activation. Cell 164:922-36
Kessans, Sarah A; Linhart, Mark D; Meador, Lydia R et al. (2016) Immunological Characterization of Plant-Based HIV-1 Gag/Dgp41 Virus-Like Particles. PLoS One 11:e0151842
Schumacher, Maria A; Lee, Jeehyun; Zeng, Wenjie (2016) Molecular insights into DNA binding and anchoring by the Bacillus subtilis sporulation kinetochore-like RacA protein. Nucleic Acids Res 44:5438-49
Poncet-Montange, Guillaume; Zhan, Yanai; Bardenhagen, Jennifer P et al. (2015) Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2. Biochem J 466:337-46
Rosenberg, Oren S; Dovala, Dustin; Li, Xueming et al. (2015) Substrates Control Multimerization and Activation of the Multi-Domain ATPase Motor of Type VII Secretion. Cell 161:501-512

Showing the most recent 10 out of 54 publications