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Attri P, Han J, Choi S, Choi EH, Bogaerts A, Lee W. CAP modifies the structure of a model protein from thermophilic bacteria: mechanisms of CAP-mediated inactivation. Sci Rep 2018; 8:10218. [PMID: 29977069 PMCID: PMC6033864 DOI: 10.1038/s41598-018-28600-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/19/2018] [Indexed: 12/14/2022] Open
Abstract
Cold atmospheric plasma (CAP) has great potential for sterilization in the food industry, by deactivation of thermophilic bacteria, but the underlying mechanisms are largely unknown. Therefore, we investigate here whether CAP is able to denature/modify protein from thermophilic bacteria. We focus on MTH1880 (MTH) from Methanobacterium thermoautotrophicum as model protein, which we treated with dielectric barrier discharge (DBD) plasma operating in air for 10, 15 and 20 mins. We analysed the structural changes of MTH using circular dichroism, fluorescence and NMR spectroscopy, as well as the thermal and chemical denaturation, upon CAP treatment. Additionally, we performed molecular dynamics (MD) simulations to determine the stability, flexibility and solvent accessible surface area (SASA) of both the native and oxidised protein.
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Affiliation(s)
- Pankaj Attri
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
| | - Jeongmin Han
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 134 Shinchon-Dong, Seodaemoon-Gu, Seoul, 120-749, Korea
| | - Sooho Choi
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 134 Shinchon-Dong, Seodaemoon-Gu, Seoul, 120-749, Korea
| | - Eun Ha Choi
- Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 01897, Korea
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium.
| | - Weontae Lee
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 134 Shinchon-Dong, Seodaemoon-Gu, Seoul, 120-749, Korea.
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Kim H, Kim S, Jung Y, Han J, Yun JH, Chang I, Lee W. Probing the Folding-Unfolding Transition of a Thermophilic Protein, MTH1880. PLoS One 2016; 11:e0145853. [PMID: 26766214 PMCID: PMC4713090 DOI: 10.1371/journal.pone.0145853] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
The folding mechanism of typical proteins has been studied widely, while our understanding of the origin of the high stability of thermophilic proteins is still elusive. Of particular interest is how an atypical thermophilic protein with a novel fold maintains its structure and stability under extreme conditions. Folding-unfolding transitions of MTH1880, a thermophilic protein from Methanobacterium thermoautotrophicum, induced by heat, urea, and GdnHCl, were investigated using spectroscopic techniques including circular dichorism, fluorescence, NMR combined with molecular dynamics (MD) simulations. Our results suggest that MTH1880 undergoes a two-state N to D transition and it is extremely stable against temperature and denaturants. The reversibility of refolding was confirmed by spectroscopic methods and size exclusion chromatography. We found that the hyper-stability of the thermophilic MTH1880 protein originates from an extensive network of both electrostatic and hydrophobic interactions coordinated by the central β-sheet. Spectroscopic measurements, in combination with computational simulations, have helped to clarify the thermodynamic and structural basis for hyper-stability of the novel thermophilic protein MTH1880.
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Affiliation(s)
- Heeyoun Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Sangyeol Kim
- Department of Physics, Pusan National University, Busan, 609–735, Korea
- Center for Proteome Biophysics, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 711–873, Korea
| | - Youngjin Jung
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Jeongmin Han
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Ji-Hye Yun
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Iksoo Chang
- Center for Proteome Biophysics, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 711–873, Korea
- Department of Brain and Cognitive Sciences, DGIST, Daegu, 711–873, Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
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Kim HY, Ryu SY, Yun JH, Kim SM, Chang IS, Lee WT. Biochemical and NMR Characterization of MTH1880 Mutant Proteins for Folding-Unfolding Studies. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.12.3521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Jenney FE, Adams MWW. The impact of extremophiles on structural genomics (and vice versa). Extremophiles 2007; 12:39-50. [PMID: 17563834 DOI: 10.1007/s00792-007-0087-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 04/19/2007] [Indexed: 11/24/2022]
Abstract
The advent of the complete genome sequences of various organisms in the mid-1990s raised the issue of how one could determine the function of hypothetical proteins. While insight might be obtained from a 3D structure, the chances of being able to predict such a structure is limited for the deduced amino acid sequence of any uncharacterized gene. A template for modeling is required, but there was only a low probability of finding a protein closely-related in sequence with an available structure. Thus, in the late 1990s, an international effort known as structural genomics (SG) was initiated, its primary goal to "fill sequence-structure space" by determining the 3D structures of representatives of all known protein families. This was to be achieved mainly by X-ray crystallography and it was estimated that at least 5,000 new structures would be required. While the proteins (genes) for SG have subsequently been derived from hundreds of different organisms, extremophiles and particularly thermophiles have been specifically targeted due to the increased stability and ease of handling of their proteins, relative to those from mesophiles. This review summarizes the significant impact that extremophiles and proteins derived from them have had on SG projects worldwide. To what extent SG has influenced the field of extremophile research is also discussed.
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Affiliation(s)
- Francis E Jenney
- Department of Biochemistry and Molecular Biology, University of Georgia, Davison Life Sciences Complex, Green Street, Athens, GA 30602-7229, USA
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