The general objective of the proposed research is to combine a new computational approach with complementary NMR methods for characterizing binding of small ligands to proteins. This will address a wide need for defining interactions of proteins with natural ligands, such as peptides, non-peptidic biomolecules, or with non-natural ligands, including drug leads or other chemicals. While this Component 2 is on interactions of small ligands with proteins, this approach can readily be applied to protein-protein or protein-nucleic acid interactions. This connects this research to Components 1 and 4. Thus, both aspects address the problem of characterizing weak but specific iinteractions of proteins with small molecules and other macromolecules in situations where experimental constraints are sparse. We proposeto develop an approach that will build on the recently developed TreeDock algorithm and will combine it with information from NMR spectroscopy on small-molecule inhibitors of protein-protein interactions obtained from high-throughput library screening. To define structures of weak protein-inhibitor complexes, TreeDock can search the docking space very fast by eliminating up front all configurations in which the components to be docked have no contact or penetrate each other. This is achieved with kd search trees. The algorithm uses complete enumeration of the search space at high resolution and can handle ligand mobility by querying a database of docked rigid subgroups. TreeDock can be ideally interfaced with sparse data from NMR experiments. We propose NMR methods that can provide few specific protein-ligand contacts even under difficult experimental conditions, such as intermediate exchange or poor solubility. The combination of the computational and experimental NMR methods will also be capable of dealing with structural changes of receptor proteins upon ligand binding. The research will be pursued four Specific Aims: 1: Development of a flexible docking algorithm (TreeDock II) that is capable of screening compound libraries efficiently, docking peptides and DNA/RNA to proteins. 2: Development of a compiler (parser, classifier) of chemical compound libraries. 3. Experimental methods for measuring NOEs in the intermediate exchange regime and defining anchors for TreeDock - Application to inhibitors of Bcl-2 type proteins. 4. Define complexes of small-molecule inhibitors with translation initiation factors 4E and 4A.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
5P01GM047467-20
Application #
8260524
Study Section
Special Emphasis Panel (ZRG1)
Project Start
Project End
2013-04-30
Budget Start
2011-05-01
Budget End
2013-04-30
Support Year
20
Fiscal Year
2011
Total Cost
$193,628
Indirect Cost
Name
Harvard University
Department
Type
DUNS #
047006379
City
Boston
State
MA
Country
United States
Zip Code
02115
Brazin, Kristine N; Mallis, Robert J; Boeszoermenyi, Andras et al. (2018) The T Cell Antigen Receptor ? Transmembrane Domain Coordinates Triggering through Regulation of Bilayer Immersion and CD3 Subunit Associations. Immunity 49:829-841.e6
Chhabra, Sandeep; Fischer, Patrick; Takeuchi, Koh et al. (2018) 15N detection harnesses the slow relaxation property of nitrogen: Delivering enhanced resolution for intrinsically disordered proteins. Proc Natl Acad Sci U S A 115:E1710-E1719
Zhao, Zhao; Zhang, Meng; Hogle, James M et al. (2018) DNA-Corralled Nanodiscs for the Structural and Functional Characterization of Membrane Proteins and Viral Entry. J Am Chem Soc 140:10639-10643
Hagn, Franz; Nasr, Mahmoud L; Wagner, Gerhard (2018) Assembly of phospholipid nanodiscs of controlled size for structural studies of membrane proteins by NMR. Nat Protoc 13:79-98
Nasr, Mahmoud L; Wagner, Gerhard (2018) Covalently circularized nanodiscs; challenges and applications. Curr Opin Struct Biol 51:129-134
Coote, Paul W; Robson, Scott A; Dubey, Abhinav et al. (2018) Optimal control theory enables homonuclear decoupling without Bloch-Siegert shifts in NMR spectroscopy. Nat Commun 9:3014
Ziarek, Joshua J; Baptista, Diego; Wagner, Gerhard (2018) Recent developments in solution nuclear magnetic resonance (NMR)-based molecular biology. J Mol Med (Berl) 96:1-8
Näär, Anders M (2018) miR-33: A Metabolic Conundrum. Trends Endocrinol Metab 29:667-668
Obayashi, Eiji; Luna, Rafael E; Nagata, Takashi et al. (2017) Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5. Cell Rep 18:2651-2663
Hyberts, Sven G; Robson, Scott A; Wagner, Gerhard (2017) Interpolating and extrapolating with hmsIST: seeking a tmax for optimal sensitivity, resolution and frequency accuracy. J Biomol NMR 68:139-154

Showing the most recent 10 out of 245 publications