Local structural preferences and dynamics restrictions in the urea-denatured state of SUMO-1: NMR characterization.
We have investigated by multidimensional NMR the structural and dynamic characteristics of the urea-denatured state of activated SUMO-1, a 97-residue protein belonging to the growing family of ubiquitin-like proteins involved in post-translational modifications. Complete backbone amide and 15N resonance assignments were obtained in the denatured state by using HNN and HN(C)N experiments. These enabled other proton assignments from TOCSY-HSQC spectra. Secondary Halpha chemical shifts and 1H-1H NOE indicate that the protein chain in the denatured state has structural preferences in the broad beta-domain for many residues. Several of these are seen to populate the (phi,psi) space belonging to polyproline II structure. Although there is no evidence for any persistent structures, many contiguous stretches of three or more residues exhibit structural propensities suggesting possibilities of short-range transient structure formation. The hetero-nuclear 1H-15N NOEs are extremely weak for most residues, except for a few at the C-terminal, and the 15N relaxation rates show sequence-wise variation. Some of the regions of slow motions coincide with those of structural preferences and these are interspersed by highly flexible residues. The implications of these observations for the early folding events starting from the urea-denatured state of activated SUMO-1 have been discussed.
Kumar
Ashutosh
A
Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India.
Srivastava
Sudha
S
Mishra
Ram Kumar
RK
Mittal
Rohit
R
Hosur
Ramakrishna V
RV
D000577:Amides / Q000737:chemistry; D000595:Amino Acid Sequence; D002942:Circular Dichroism; D005998:Glycine / Q000737:chemistry; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007930:Leucine / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D011499:Protein Processing, Post-Translational; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011522:Protons; D025842:SUMO-1 Protein / Q000737:chemistry* / Q000378:metabolism; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors; D014508:Urea / Q000737:chemistry / Q000494:pharmacology*
D000577:Amides; D011522:Protons; D025842:SUMO-1 Protein; D014508:Urea; D007930:Leucine; D005998:Glycine