title: Denatured states of yeast cytochrome c induced by heat and guanidinium chloride are structurally and thermodynamically different.
abstract: A sequence alignment of mammalian cytochromes c with yeast iso-1-cytochrome c (y-cyt-c) shows that the yeast protein contains five extra N-terminal residues. We have been interested in understanding the question: What is the role of these five extra N-terminal residues in folding and stability of the protein? To answer this question we have prepared five deletants of y-cyt-c by sequentially removing these extra residues. During our studies on the wild type (WT) protein and its deletants, we observed that the amount of secondary structure in the guanidinium chloride (GdmCl)-induced denatured (D) state of each protein is different from that of the heat-induced denatured (H) state. This finding is confirmed by the observation of an additional cooperative transition curve of optical properties between H and D states on the addition of different concentrations of GdmCl to the already heat denatured WT y-cyt-c and its deletants at pH 6.0 and 68°C. For each protein, analysis of transition curves representing processes, native (N) state ↔ D state, N state ↔ H state, and H state ↔ D state, was done to obtain Gibbs free energy changes associated with all the three processes. This analysis showed that, for each protein, thermodynamic cycle accommodates Gibbs free energies associated with transitions between N and D states, N and H states, and H and D states, the characteristics required for a thermodynamic function. All these experimental observations have been supported by our molecular dynamics simulation studies.
authors.affiliation: a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi 110025 , India.
authors.forename: Sobia
authors.initials: S
authors.lastname: Zaidi
authors.affiliation: a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi 110025 , India.
authors.forename: Md Anzarul
authors.initials: MA
authors.lastname: Haque
authors.affiliation: a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi 110025 , India.|c Department of Biotechnology , School of Life Sciences, Central University of Kashmir (CUK) , Sonwar Campus, Srinagar 190004 , India.
authors.forename: Shah
authors.initials: S
authors.lastname: Ubaid-Ullah
authors.affiliation: a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi 110025 , India.
authors.forename: Amresh
authors.initials: A
authors.lastname: Prakash
authors.affiliation: a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi 110025 , India.
authors.forename: Md Imtaiyaz
authors.initials: MI
authors.lastname: Hassan
authors.affiliation: a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi 110025 , India.
authors.forename: Asimul
authors.initials: A
authors.lastname: Islam
authors.affiliation: b Immunochemistry Lab , National Institute of Immunology , Aruna Asaf Ali Marg, New Delhi 110067 , India.
authors.forename: Janendra K
authors.initials: JK
authors.lastname: Batra
authors.affiliation: a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi 110025 , India.
authors.forename: Faizan
authors.initials: F
authors.lastname: Ahmad
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D003001:Cloning, Molecular; D045304:Cytochromes c / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D005822:Genetic Vectors / Q000737:chemistry / Q000378:metabolism; D019791:Guanidine / Q000737:chemistry; D006358:Hot Temperature; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011489:Protein Denaturation; D017510:Protein Folding; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017384:Sequence Deletion; D013816:Thermodynamics
chemical_list: C014059:CYC1 protein, S cerevisiae; D011994:Recombinant Proteins; D029701:Saccharomyces cerevisiae Proteins; D045304:Cytochromes c; D019791:Guanidine
keywords: MD simulation; denaturation; protein folding; protein stability; residual structure; yeast iso-1-cytochrome c