title: Multidimensional free energy surface of unfolding of HP-36: microscopic origin of ruggedness.
abstract: The protein folding funnel paradigm suggests that folding and unfolding proceed as directed diffusion in a multidimensional free energy surface where a multitude of pathways can be traversed during the protein's sojourn from initial to final state. However, finding even a single pathway, with the detail chronicling of intermediates, is an arduous task. In this work we explore the free energy surface of unfolding pathway through umbrella sampling, for a small globular α-helical protein chicken-villin headpiece (HP-36) when the melting of secondary structures is induced by adding DMSO in aqueous solution. We find that the unfolding proceeds through the initial separation or melting of aggregated hydrophobic core that comprises of three phenylalanine residues (Phe7, Phe11, and Phe18). This separation is accompanied by simultaneous melting of the second helix. Unfolding is found to be a multistage process involving crossing of three consecutive minima and two barriers at the initial stage. At a molecular level, Phe18 is observed to reorient itself towards other hydrophobic grooves to stabilize the intermediate states. We identify the configuration of the intermediates and correlate the intermediates with those obtained in our previous works. We also give an estimate of the barriers for different transition states and observe the softening of the barriers with increasing DMSO concentration. We show that higher concentration of DMSO tunes the unfolding pathway by destabilizing the third minimum and stabilizing the second one, indicating the development of a solvent modified, less rugged pathway. The prime outcome of this work is the demonstration that mixed solvents can profoundly transform the nature of the energy landscape and induce unfolding via a modified route. A successful application of Kramer's rate equation correlating the free energy simulation results shows faster rate of unfolding with increasing DMSO concentration. This work perhaps presents the first systematic theoretical study of the effect of a chemical denaturant on the microscopic free energy surface and rates of unfolding of HP-36.
authors.affiliation: Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
authors.forename: Rikhia
authors.initials: R
authors.lastname: Ghosh
authors.affiliation: Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
authors.forename: Susmita
authors.initials: S
authors.lastname: Roy
authors.affiliation: Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
authors.forename: Biman
authors.initials: B
authors.lastname: Bagchi
mesh_terms: D000818:Animals; D002645:Chickens; D004121:Dimethyl Sulfoxide / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D016900:Neurofilament Proteins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D017433:Protein Structure, Secondary; D058767:Protein Unfolding; D013816:Thermodynamics
chemical_list: D016900:Neurofilament Proteins; D010446:Peptide Fragments; C115223:villin headpiece subdomain peptide; D004121:Dimethyl Sulfoxide