Characterization of the protein unfolding processes induced by urea and temperature.
Correct folding is critical for the biological activities of proteins. As a contribution to a better understanding of the protein (un)folding problem, we studied the effect of temperature and of urea on peptostreptococcal Protein L destructuration. We performed standard molecular dynamics simulations at 300 K, 350 K, 400 K, and 480 K, both in 10 M urea and in water. Protein L followed at least two alternative unfolding pathways. Urea caused the loss of secondary structure acting preferentially on the beta-sheets, while leaving the alpha-helices almost intact; on the contrary, high temperature preserved the beta-sheets and led to a complete loss of the alpha-helices. These data suggest that urea and high temperature act through different unfolding mechanisms, and protein secondary motives reveal a differential sensitivity to various denaturant treatments. As further validation of our results, replica-exchange molecular dynamics simulations of the temperature-induced unfolding process in the presence of urea were performed. This set of simulations allowed us to compute the thermodynamical parameters of the process and confirmed that, in the configurational space of Protein L unfolding, both of the above pathways are accessible, although to a different relative extent.
Rocco
Alessandro Guerini
AG
Gruppo di Studio per la Proteomica e la Struttura delle Proteine, Dipartimento di Scienze Farmacologiche, Università degli Studi di Milano, Milano, Italy.
Mollica
Luca
L
Ricchiuto
Piero
P
Baptista
António M
AM
Gianazza
Elisabetta
E
Eberini
Ivano
I
D020816:Amino Acid Motifs; D001426:Bacterial Proteins / Q000737:chemistry; D001703:Biophysics / Q000379:methods; D003198:Computer Simulation; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008968:Molecular Conformation; D010462:Peptostreptococcus / Q000378:metabolism; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry; D013696:Temperature; D014508:Urea / Q000737:chemistry*
D001426:Bacterial Proteins; C055047:Ig L-binding protein, Peptostreptococcus; D012997:Solvents; D014508:Urea