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Evolution of Protein Structure and Stability in Global Warming. Int J Mol Sci 2020; 21:ijms21249662. [PMID: 33352933 PMCID: PMC7767258 DOI: 10.3390/ijms21249662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
This review focuses on the molecular signatures of protein structures in relation to evolution and survival in global warming. It is based on the premise that the power of evolutionary selection may lead to thermotolerant organisms that will repopulate the planet and continue life in general, but perhaps with different kinds of flora and fauna. Our focus is on molecular mechanisms, whereby known examples of thermoresistance and their physicochemical characteristics were noted. A comparison of interactions of diverse residues in proteins from thermophilic and mesophilic organisms, as well as reverse genetic studies, revealed a set of imprecise molecular signatures that pointed to major roles of hydrophobicity, solvent accessibility, disulfide bonds, hydrogen bonds, ionic and π-electron interactions, and an overall condensed packing of the higher-order structure, especially in the hydrophobic regions. Regardless of mutations, specialized protein chaperones may play a cardinal role. In evolutionary terms, thermoresistance to global warming will likely occur in stepwise mutational changes, conforming to the molecular signatures, such that each "intermediate" fits a temporary niche through punctuated equilibrium, while maintaining protein functionality. Finally, the population response of different species to global warming may vary substantially, and, as such, some may evolve while others will undergo catastrophic mass extinction.
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Sinha D, Chakraborty T, Sinha D, Poddar A, Chattopadhyaya R, Sau S. Understanding the structure, stability, and anti-sigma factor-binding thermodynamics of an anti-anti-sigma factor from Staphylococcus aureus. J Biomol Struct Dyn 2020; 39:6539-6552. [PMID: 32755297 DOI: 10.1080/07391102.2020.1801511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | | | - Debasmita Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Asim Poddar
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | | | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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Seal S, Polley S, Sau S. A staphylococcal cyclophilin carries a single domain and unfolds via the formation of an intermediate that preserves cyclosporin A binding activity. PLoS One 2019; 14:e0210771. [PMID: 30925148 PMCID: PMC6440624 DOI: 10.1371/journal.pone.0210771] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 03/18/2019] [Indexed: 12/22/2022] Open
Abstract
Cyclophilin (Cyp), a peptidyl-prolyl cis-trans isomerase (PPIase), acts as a virulence factor in many bacteria including Staphylococcus aureus. The enzymatic activity of Cyp is inhibited by cyclosporin A (CsA), an immunosuppressive drug. To precisely determine the unfolding mechanism and the domain structure of Cyp, we have investigated a chimeric S. aureus Cyp (rCyp) using various probes. Our limited proteolysis and the consequent analysis of the proteolytic fragments indicate that rCyp is composed of one domain with a short flexible tail at the C-terminal end. We also show that the urea-induced unfolding of both rCyp and rCyp-CsA is completely reversible and proceeds via the synthesis of at least one stable intermediate. Both the secondary structure and the tertiary structure of each intermediate appears very similar to those of the corresponding native protein. Conversely, the hydrophobic surface areas of the intermediates are comparatively less. Further analyses reveal no loss of CsA binding activity in rCyp intermediate. The thermodynamic stability of rCyp was also significantly increased in the presence of CsA, recommending that this protein could be employed to screen new CsA derivatives in the future.
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Affiliation(s)
- Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Soumitra Polley
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
- * E-mail:
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Sinha D, Mondal R, Mahapa A, Sau K, Chattopadhyaya R, Sau S. A staphylococcal anti-sigma factor possesses a single-domain, carries different denaturant-sensitive regions and unfolds via two intermediates. PLoS One 2018; 13:e0195416. [PMID: 29621342 PMCID: PMC5886543 DOI: 10.1371/journal.pone.0195416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/21/2018] [Indexed: 11/26/2022] Open
Abstract
RsbW, an anti-sigma factor possessing kinase activity, is expressed by many Gram-positive bacteria including Staphylococcus aureus. To obtain clues about the domain structure and the folding-unfolding mechanism of RsbW, we have elaborately studied rRsbW, a recombinant S. aureus RsbW. Sequence analysis of the protein fragments, generated by the limited proteolysis of rRsbW, has proposed it to be a single-domain protein. The unfolding of rRsbW in the presence of GdnCl or urea was completely reversible in nature and occurred through the formation of at least two intermediates. The structure, shape, and the surface hydrophobicity of no intermediate completely matches with those of other intermediates or the native rRsbW. Interestingly, one of the intermediates, formed in the presence of less GdnCl concentrations, has a molten globule-like structure. Conversely, all of the intermediates, like native rRsbW, exist as dimers in aqueous solution. The putative molten globule and the urea-generated intermediates also have retained some kinase activity. Additionally, the putative ATP binding site/catalytic site of rRsbW shows higher denaturant sensitivity than the tentative dimerization region of this enzyme.
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Affiliation(s)
- Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Rajkrishna Mondal
- Department of Biotechnology, Nagaland University, Dimapur, Nagaland, India
| | - Avisek Mahapa
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | | | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
- * E-mail:
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Polley S, Seal S, Mahapa A, Jana B, Biswas A, Mandal S, Sinha D, Sau K, Sau S. Identification and characterization of a cyclosporin binding cyclophilin from Staphylococcus aureus Newman. Bioinformation 2017; 13:78-85. [PMID: 28584448 PMCID: PMC5450249 DOI: 10.6026/97320630013078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/04/2017] [Indexed: 01/24/2023] Open
Abstract
Cyclophilins, a class of peptidyl-prolyl cis-trans isomerase (PPIase) enzymes, are inhibited by cyclosporin A (CsA), an
immunosuppressive drug. Staphylococcus aureus Newman, a pathogenic bacterium, carries a gene for encoding a putative cyclophilin
(SaCyp). SaCyp shows significant homology with other cyclophilins at the sequence level. A three-dimensional model structure of
SaCyp harbors a binding site for CsA. To verify whether SaCyp possesses both the PPIase activity and the CsA binding ability, we
have purified and investigated a recombinant SaCyp (rCyp) using various in vitro tools. Our RNase T1 refolding assay indicates that
rCyp has a substantial extent of PPIase activity. rCyp that exists as a monomer in the aqueous solution is truly a cyclophilin as its
catalytic activity specifically shows sensitivity to CsA. rCyp appears to bind CsA with a reasonably high affinity. Additional
investigations reveal that binding of CsA to rCyp alters its structure and shape to some extent. Both rCyp and rCyp-CsA are unfolded
via the formation of at least one intermediate in the presence of guanidine hydrochloride. Unfolding study also indicates that there is
substantial extent of thermodynamic stabilization of rCyp in the presence of CsA as well. The data suggest that rCyp may be exploited
to screen the new antimicrobial agents in the future.
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Affiliation(s)
- Soumitra Polley
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Avisek Mahapa
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Biswanath Jana
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Anindya Biswas
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Sukhendu Mandal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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Polley S, Chakravarty D, Chakrabarti G, Sau S. Determining the roles of a conserved tyrosine residue in a Mip-like peptidyl-prolyl cis–trans isomerase. Int J Biol Macromol 2016; 87:273-80. [DOI: 10.1016/j.ijbiomac.2016.02.070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 02/25/2016] [Accepted: 02/27/2016] [Indexed: 11/16/2022]
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Mahapa A, Mandal S, Biswas A, Jana B, Polley S, Sau S, Sau K. Chemical and thermal unfolding of a global staphylococcal virulence regulator with a flexible C-terminal end. PLoS One 2015; 10:e0122168. [PMID: 25822635 PMCID: PMC4379015 DOI: 10.1371/journal.pone.0122168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/07/2015] [Indexed: 11/19/2022] Open
Abstract
SarA, a Staphylococcus aureus-specific dimeric protein, modulates the expression of numerous proteins including various virulence factors. Interestingly, S. aureus synthesizes multiple SarA paralogs seemingly for optimizing the expression of its virulence factors. To understand the domain structure/flexibility and the folding/unfolding mechanism of the SarA protein family, we have studied a recombinant SarA (designated rSarA) using various in vitro probes. Limited proteolysis of rSarA and the subsequent analysis of the resulting protein fragments suggested it to be a single-domain protein with a long, flexible C-terminal end. rSarA was unfolded by different mechanisms in the presence of different chemical and physical denaturants. While urea-induced unfolding of rSarA occurred successively via the formation of a dimeric and a monomeric intermediate, GdnCl-induced unfolding of this protein proceeded through the production of two dimeric intermediates. The surface hydrophobicity and the structures of the intermediates were not identical and also differed significantly from those of native rSarA. Of the intermediates, the GdnCl-generated intermediates not only possessed a molten globule-like structure but also exhibited resistance to dissociation during their unfolding. Compared to the native rSarA, the intermediate that was originated at lower GdnCl concentration carried a compact shape, whereas, other intermediates owned a swelled shape. The chemical-induced unfolding, unlike thermal unfolding of rSarA, was completely reversible in nature.
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Affiliation(s)
- Avisek Mahapa
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Sukhendu Mandal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Anindya Biswas
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Biswanath Jana
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Soumitra Polley
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
- * E-mail: (SS); (KS)
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
- * E-mail: (SS); (KS)
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