Protein Interactions and Interfaces
EMSL Project ID
19837
Abstract
All proteins interact with other molecules: ligands, metals, membranes, surfaces or other proteins. Such interactions are intrinsic to protein function. We propose to leverage our successful program in Structural Genomics (Northeast Structural Genomics Consortium, NESGC), which has used EMSL NMR instrumentation extensively in the last 6 years, to address protein interactions and interfaces. We will examine three types of interfaces using high resolution liquid state NMR spectroscopy: protein-ligand intefaces, protein-metal interfaces in metalloproteins, and protein-protein interfaces in homo- and hetero-dimeric proteins. We have previously demonstrated our ability to derive atomic-resolution structural information about such interfaces within the context of our Structural Genomics project. We propose to expand our efforts in this direction. Proteins from organisms important in the environment will be selected when possible; for example the NESGC has among the many genomes from which targets are selected the metal reducing bacterium Shewanella oneidensis, and the versatile phototrophic bacterium Rhodopsuedomonas palustris, both of which are of interest to DOE.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2006-08-08
End Date
2009-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Aramini JM, P Rossi, JR Cort, LC Ma, R Xiao, T Acton, and G Montelione. 2010. "Solution NMR structure of the plasmid-encoded fimbriae regulatory protein PefI from Salmonella enterica serovar Typhimurium." Proteins. Structure, Function, and Bioinformatics 79(1):335-339. doi:10.1002/prot.22869
Bertonati C, M Punta, M Fischer, G Yachdav, F Forouhar, W Zhou, AP Kuzin, J Seetharaman, M Abashidze, TA Ramelot, MA Kennedy, JR Cort, A Belachew, JF Hunt, L Tong, G Montelione, and B Rost. 2009. "Structural genomics reveals EVE as a new ASCH/PUA-related domain." Proteins. Structure, Function, and Bioinformatics 75(3):760-773.
Cort JR, TA Ramelot, D Murray, T Acton, LC Ma, R Xiao, G Montelione, and MA Kennedy. 2008. "Structure of an Acetyl-CoA Binding Protein from Staphylococcus aureus Representing a Novel Subfamily of GCN5-related N-Acetyltransferase-like Proteins." Journal of Structural and Functional Genomics 9(1-4):7-20. doi:10.1007/s10969-008-9041-z
Cort JR, U Selan, A Schulte, F Grimm, MA Kennedy, and C Dahl. 2008. "Allochromatium vinosum DsrC: Solution-State NMR Structure, Redox Properties and Interaction with DsrEFH, a Protein Essential for Purple Sulfur Bacterial Sulfur Oxidation ." Journal of Molecular Biology 382:692-707. doi:10.1016/j.jmb.2008.07.022
Everett JK, R Tejero, SB Murthy, T Acton, JM Aramini, M Baran, J Benach, JR Cort, A Eletsky, F Forouhar, R Guan, AP Kuzin, HW Lee, G Liu, R Mani, B Mao, JL Mills, AF Montelione, K Pederson, R Powers, TA Ramelot, PM Rossi, J Seetharaman, D Snyder, GVT Swapna, SM Vorobiev, Y Wu, R Xiao, Y Yang, CH Arrowsmith, JF Hunt, MA Kennedy, JH Prestegard, T Szyperski, L Tong, and G Montelione. 2016. "A Community Resource of Experimental Data for NMR / X-ray Crystal Structure Pairs." Protein Science 25(1):30-45. doi:10.1002/pro.2774
Grimm F, JR Cort, and C Dahl. 2010. "DsrR, a Novel IscA-like Protein Lacking Iron- and Fe-S-Binding Functions, Involved in the Regulation of Sulfur Oxidation in Allochromatium Vinosum." Journal of Bacteriology 192(6):1652-1661. doi:10.1128/JB.01269-09
Ramelot TA, S Raman, AP Kuzin, R Xiao, LC Ma, T Acton, JF Hunt, G Montelione, D Baker, and MA Kennedy. 2009. "Improving NMR Protein Structure Quality by Rosetta Refinement: A Molecular Replacement Study." Proteins. Structure, Function, and Bioinformatics 75(1):147-167. doi:10.1002/prot.22229
Snyder DA, JM Aramini, B Yu, Y Huang, R Xiao, JR Cort, R Shastry, LC Ma, J Liu, B Rost, T Acton, MA Kennedy, and G Montelione. 2012. "Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus." Proteins. Structure, Function, and Bioinformatics 80(7):1901-1906.
Solution structure of ribosomoal protein S28E from Methanobacterium thermoautotrophicum Protein Sci. 2003 12: 2831-2837 Access the most recent version at doi:10.1110/ps.03358203
Wu B, A Yee, Y Huang, TA Ramelot, JR Cort, A Semesi, JW Jung, W Lee, MA Kennedy, G Montelione, and CH Arrowsmith. 2008. "The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: a structural homolog of the FF domain." Protein Science 17(3):583-588.
Wu B, JA Lukin, A Yee, A Lemak, A Semesi, TA Ramelot, MA Kennedy, and CH Arrowsmith. 2008. "Solution Structure of Ribosomal Protein L40E, a Unique C4 Zinc Finger Protein Encoded by Archaeon Sulfolobus Solfataricus." Protein Science 17:589-596. doi:10.1110/ps.073273008
Yang Y, TA Ramelot, RM McCarrick, S Ni, EA Feldmann, JR Cort, H Wang, EA Foote, C Ciccosanti, M Jiang, H Janjua, T Acton, R Xiao, JK Everett, G Montelione, and MA Kennedy. 2010. "Combining NMR, PRE, and EPR Methods For Homo-dimer Protein Structure Determination." Journal of the American Chemical Society 132(34):11910-11913.
Yin C, JM Aramini, LC Ma, JR Cort, GVT Swapna, RM Krug, and G Montelione. 2011. "Backbone and Ile-?1, Leu, Val Methyl 1H, 13C and 15N NMR chemical shift assignments for human interferon-stimulated gene 15 protein." Biomolecular NMR Assignments 5(2):215-219. doi:10.1007/s12104-011-9303-8