Secondary structure specific entropy change of a partially unfolded protein molecule.
The conformational disorder of a protein in its partially unfolded molten globule (MG) form leads to an overall gain in the configurational entropy of the protein molecule. However, considering the differential degree of unfolding of different secondary structural segments of the protein, the entropy gained by them may be nonuniform. In this work, our attempt has been to explore whether any correlation exists between the degree of unfolding of different segments of a protein and their entropy gains. For that, we have carried out atomistic molecular dynamics simulations of the folded native and a partially unfolded structures of the protein villin headpiece subdomain or HP-36 in aqueous medium. It is found that among the three alpha-helical segments of the protein, the central alpha-helix (helix-2) underwent unfolding during the transition with a consequent entropy gain significantly higher than that of the other two helical segments. The calculations further revealed that the differential entropy gain by the segments of a protein can be used as an effective measure to identify the unfolded segments of the protein and hence to explore the folding pathways.
Sinha
Sudipta Kumar
SK
Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur -721302, India.
Chakraborty
Sudip
S
Bandyopadhyay
Sanjoy
S
D019277:Entropy; D008840:Microfilament Proteins / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D016900:Neurofilament Proteins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary
D008840:Microfilament Proteins; D016900:Neurofilament Proteins; D010446:Peptide Fragments; C026615:villin; C115223:villin headpiece subdomain peptide