NMR characterization of the energy landscape of SUMO-1 in the native-state ensemble

Kumar, Ashutosh ; Srivastava, Sudha ; Hosur, Ramakrishna V. (2007) NMR characterization of the energy landscape of SUMO-1 in the native-state ensemble Journal of Molecular Biology, 367 (5). pp. 1480-1493. ISSN 0022-2836

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Official URL: http://linkinghub.elsevier.com/retrieve/pii/S00222...

Related URL: http://dx.doi.org/10.1016/j.jmb.2007.01.035


Characterizing the low energy excited states in the energy landscape of a protein is one of the exciting and demanding problems in structural biology at the present time. These describe the adaptability of the protein structure to external perturbations. In this context, we used here non-linear dependence of amide proton chemical shifts on temperature to identify residues accessing alternative conformations in SUMO-1 in the native state as well as in the near-native states created by sub-denaturing concentrations of urea. The number of residues accessing alternative conformations increases and the profiles of curved temperature dependence also change with increasing urea concentration. In every case these alternative conformations lie within 2 kcal/mol from the ground state, and are separated from it by low energy barriers. The residues that access alternative conformations span the length of the protein chain but are located at particular regions on the protein structure. These include many of the loops, β2 and β5 strands, and some edges of the helices. We observed that some of the regions of the protein structure that exhibit such fluctuations coincide with the protein's binding surfaces with different substrate like GTPase effector domain (GED) of dynamin, SUMO binding motifs (SBM), E1 (activating enzyme, SAE1/SAE2) and E2 (conjugating enzyme, UBC9) enzymes of sumoylation machinery, reported earlier. We speculate that this would have significant implications for the binding of diversity of targets by SUMO-1 for the variety of functions it is involved in.

Item Type:Article
Source:Copyright of this article belongs to Elsevier Science.
Keywords:Energy Landscape; SUMO-1; Native-state Ensemble; NMR
ID Code:16629
Deposited On:15 Nov 2010 13:32
Last Modified:17 May 2016 01:21

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