Conserved structural and dynamics features in the denatured states of drosophila SUMO, human SUMO and ubiquitin proteins: Implications to sequence‐folding paradigm

Abstract

We have characterized here the structural and dynamics properties of urea-denatured state of dSmt3 by multidimensional NMR at 27 degrees C and pH 5.6. The various results suggest that hydrophobic clusters as well as different native and non-native secondary structural elements are transiently formed. The backbone in the regions Gln26-Lys31 and Gly47-Gln60 shows conformationally restricted motions. The AABUF profile of the sequence reflected that this region has the highest tendency to undergo hydrophobic clustering and may thus assist the formation of transient structures. The secondary chemical shifts and coupling constants indicated that this region has strong tendency to occupy the broad beta-domain of (phi,psi) space. A number of NMR parameters indicated that the region Asp58-Gln60 (corresponding to beta3-beta4 turn in the folded state) has residual turn-like structure. The present structural and dynamics results on urea-denatured dSmt3 have been compared with the previously published results on denatured states of similar fold proteins e.g. human SUMO-1 (55% homologous), ubiquitin (13.8% homologous) and GB1. Although the sequence homology is rather poor between them, the residual structure in all cases seems to be largely native type. The implications of these to sequence-folding paradigm and initial folding processes have been discussed.

NMR elucidation of monomer–dimer transition and conformational heterogeneity in histone‐like DNA binding protein of Helicobacter pylori

“…The T 1 and T 2 data sets were recorded with 1,024 (t 2 ) and 200 (t 1 ) complex data points, respectively, along the 1 H (SW = 12 ppm, offset = 4.66 ppm) and 15 N (SW = 34 ppm, offset = 114.7 ppm) dimensions. Each t1 data point was collected using 48 scans and a recycle delay of 2.0 s. For T 1 measurements, the relaxation delays used were 10, 50, 90, 150, 250, 350, 550, 770, and 990 ms; whereas residue‐wise T 2 parameters were measured using CPMG delays of (interpulse delay = 2τxC P = 900 μs) 0.0, 18.56, 37.12, 55.68, 74.24, and 92.8 ms. All the acquired 2D spectra were processed using Bruker software program Topspin (v3.5) and analyzed using Mathematica Notebooks from Leo Spyracopaulose Group . Most of the peaks were well resolved for intensity measurements, whereas overlapping peaks were not considered for the relaxation analysis.…”

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

“…As evident from a number of studies long-range interactions are largely absent in the unfolded states of proteins at a high concentration of denaturant [26] , [32] , [82] , [83] , [84] . Short-range or local interactions and intrinsic sequence propensity of the polypeptide chain appear to be the major determinant for the deviations from random-coil behavior in unfolded proteins.…”

Take home lessons from studies of related proteins

“…The alternate sequence retains significant helical structure in the denatured state, which leads to the all-α helical bundle. Residual structure in the denatured state has also recently been shown to be important for the folding of the ribonuclease domains [77 • ] and the SUMO proteins [78]. …”