title: Equilibrium unfolding of DLC8 monomer by urea and guanidine hydrochloride: Distinctive global and residue level features.
abstract: We present circular dichroism (CD), steady state fluorescence and multidimensional NMR investigations on the equilibrium unfolding of monomeric dynein light chain protein (DLC8) by urea and guanidine hydrochloride (GdnHCl). Quantitative analysis of the CD and fluorescence denaturation curves reveals that urea unfolding is a two-state process, whereas guanidine unfolding is more complex. NMR investigations in the native state and in the near native states created by low denaturant concentrations enabled residue level characterization of the early structural and dynamic perturbations by the two denaturants. Firstly, (15)N transverse relaxation rates in the native state indicate that the regions around N10, Q27, the loop between beta2 and beta4 strands, and K87 at the C-terminal are potential unfolding initiation sites in the protein. Amide and (15)N chemical shift perturbations indicate different accessibilities of the residues along the chain and help identify locations of the early perturbations by the two denaturants. Guanidine and urea are seen to interact at several sites some of which are different in the two cases. Notable among the common interaction site is that around K87 which is in close proximity to W54 on the protein structure, but the interaction modes of the two denaturants are different. The secondary chemical shifts indicate that the structural perturbation by 1M urea is small, compared to that by guanidine which is more encompassing over the length of the chain. The probable (phi, psi) changes at the individual residues have been calculated using the TALOS algorithm. It appears that the helices in the protein are significantly perturbed by guanidine. Further, comparison of the spectral density functions of the native and the two near native states in the two denaturants implicate greater loosening of the structure by guanidine as compared to that by urea, even though the structures are still in the native state ensemble. These differences in the early perturbations of the native state structure and dynamics by the two denaturants might direct the protein along different pathways, as the unfolding progresses on further increasing the denaturant concentration.
authors.affiliation: Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, Maharashtra, India.
authors.forename: Amarnath
authors.initials: A
authors.lastname: Chatterjee
authors.forename: P M
authors.initials: PM
authors.lastname: Krishna Mohan
authors.forename: Arati
authors.initials: A
authors.lastname: Prabhu
authors.forename: Anindya
authors.initials: A
authors.lastname: Ghosh-Roy
authors.forename: Ramakrishna V
authors.initials: RV
authors.lastname: Hosur
mesh_terms: D002352:Carrier Proteins / Q000737:chemistry*; D002942:Circular Dichroism; D029721:Drosophila Proteins / Q000737:chemistry*; D004398:Dyneins; D019791:Guanidine / Q000494:pharmacology*; D008279:Magnetic Resonance Imaging; D011487:Protein Conformation; D011489:Protein Denaturation; D011994:Recombinant Proteins; D014508:Urea / Q000494:pharmacology*
chemical_list: D002352:Carrier Proteins; D029721:Drosophila Proteins; D011994:Recombinant Proteins; D014508:Urea; D004398:Dyneins; D019791:Guanidine