Residue-specific description of non-native transient structures in the ensemble of acid-denatured structures of the all-beta protein c-src SH3

TY - JOUR

T1 - Residue-specific description of non-native transient structures in the ensemble of acid-denatured structures of the all-beta protein c-src SH3

AU - Rösner, Heike I

AU - Poulsen, Flemming Martin

PY - 2010/4/20

Y1 - 2010/4/20

N2 - Secondary chemical shift analysis has been used to characterize the unfolded state of acid-denatured c-src SH3. Even though native c-src SH3 adopts an all-β fold, we found evidence of transient helicity in regions corresponding to native loops. In particular, residues 40-46, connecting the n-src loop to the third β-strand, exhibited an apparent helicity of nearly 45%. Furthermore, the RT loop and the diverging turn appeared to adopt non-native-like helical conformations. Interestingly, none of the residues found in transient helical conformations exhibited significant ø-values [Riddle, D. S., et al. (1999) Nat. Struct. Biol. 6, 1016-1024]. This indicated that the transient helicity has no influence or only a weak influence on the actual protein folding reaction. The residual structural propensities were compared to those of other SH3 domains, revealing heterogeneity in the unfolded ensemble that clearly contrasts with the conserved character of the topology of native state and transition state ensembles typical for SH3 domains.

AB - Secondary chemical shift analysis has been used to characterize the unfolded state of acid-denatured c-src SH3. Even though native c-src SH3 adopts an all-β fold, we found evidence of transient helicity in regions corresponding to native loops. In particular, residues 40-46, connecting the n-src loop to the third β-strand, exhibited an apparent helicity of nearly 45%. Furthermore, the RT loop and the diverging turn appeared to adopt non-native-like helical conformations. Interestingly, none of the residues found in transient helical conformations exhibited significant ø-values [Riddle, D. S., et al. (1999) Nat. Struct. Biol. 6, 1016-1024]. This indicated that the transient helicity has no influence or only a weak influence on the actual protein folding reaction. The residual structural propensities were compared to those of other SH3 domains, revealing heterogeneity in the unfolded ensemble that clearly contrasts with the conserved character of the topology of native state and transition state ensembles typical for SH3 domains.

KW - Circular Dichroism

KW - Helix-Turn-Helix Motifs

KW - Hydrogen-Ion Concentration

KW - Kinetics

KW - Magnetic Resonance Spectroscopy

KW - Phosphates

KW - Protein Conformation

KW - Protein Denaturation

KW - Protein Structure, Secondary

KW - Protein-Tyrosine Kinases

KW - Spectrometry, Fluorescence

KW - Thermodynamics

KW - Urea

KW - src Homology Domains

U2 - 10.1021/bi902125j

DO - 10.1021/bi902125j

M3 - Journal article

C2 - 20218679

SN - 0006-2960

VL - 49

SP - 3246

EP - 3253

JO - Biochemistry

JF - Biochemistry

IS - 15

ER -