NMR Characterization of the Energy Landscape of SUMO-1 in the Native-state Ensemble

High-Pressure NMR Spectroscopy Reveals Functional Sub-states of Ubiquitin and Ubiquitin-Like Proteins

“…Within the limited pressure range sampled, SUMO-2 does not significantly populate alternative high-energy conformations. However, alternative conformations have been observed in temperatureaxis experiments for SUMO-1, which has a 47 % sequence identity and similar topology to SUMO-2 (Kumar et al 2007). Further examinations are required to detect the occurrence of an alternatively folded state N 2 , similar to those observed for ubiquitin and NEDD8.…”

NMR Investigations on Ruggedness of Native State Energy Landscape in Folded Proteins

“…Investigations by Kumar et al (Kumar et al 2007) on SUMO-1 suggested that the alternative conformations span the length of the protein chain but are located at particular regions on the protein structure. The authors observed that several 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 and speculated that these conformational fluctuations have significant implications for the binding of diversity of targets by SUMO-1.…”

“…Similar experiments on B1 domains of streptococcal proteins G and L (Tunnicliffe et al 2005), which are structurally similar, but have different sequences and folding established that several of the residues have curved amide proton temperature and indicated approximately 4-6 local minima for each protein. Further, reports on N-terminal domain of phosphoglycerate kinase, hen eggwhite lysozyme, SUMO1 and BPTI (Baxter et al 1998;Kumar et al 2007) established that conformational heterogeneity arises from a number of independent sources such as, aromatic ring current effects, a minor conformer generated through disulphide bond isomerisation; an alternative hydrogen bond network associated with buried water molecules; alternative hydrogen bonds involving backbone amides and surface-exposed side-chain hydrogen bond acceptors; and the disruption of loops, ends of secondary structural elements and chain termini.…”

“…A large body of evidence using a diverse spectrum of biophysical methods clearly establishes that proteins are dynamic over a broad range of timescales and such dynamics play critical roles in various biological processes, such as: initial formation of encounter complexes in macromolecular association, target searching in specific protein-protein/protein-DNA recognition, conformational preferences in ligand binding, conformational transitions associated with allostery, the course of enzyme catalysis, intermediates along the protein folding pathway, and early events in self-assembly processes (Bai et al 1995;Boehr et al 2006;Clore 2011;Dunker et al 2002;Eisenmesser et al 2005;Feher and Cavanagh 1999;Fraser et al 2009;Kitahara et al 2005;Korzhnev et al 2003;Kumar et al 2007;Lambers et al 2006;Mohan et al 2006;Piana et al 2002;Popovych et al 2006;Tang et al 2008;Villali and Kern 2010). The amplitudes and the timescales of motion that characterize the dynamics of a protein under a given set of conditions can be understood in terms of an 'energy landscape' as described above.…”

NMR Characterization of the Near Native and Unfolded States of the PTB Domain of Dok1: Alternate Conformations and Residual Clusters

“…The folded conformation of a protein, largely populated under physiological solution condition, often undergoes excursion to other low-lying energy states that surrounds the free energy minimum[1], [2], [3], [4]. These alternate conformations, largely folded in nature, have been implicated in ligand binding, substrate recognition and response to the changes of environmental conditions[1], [3], [4], [5], [6]. Whereas, partially folded and unfolded states of a protein are of significance for a number of reasons.…”