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Ando N, Barquera B, Bartlett DH, Boyd E, Burnim AA, Byer AS, Colman D, Gillilan RE, Gruebele M, Makhatadze G, Royer CA, Shock E, Wand AJ, Watkins MB. The Molecular Basis for Life in Extreme Environments. Annu Rev Biophys 2021; 50:343-372. [PMID: 33637008 DOI: 10.1146/annurev-biophys-100120-072804] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure-function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.
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Affiliation(s)
- Nozomi Ando
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Blanca Barquera
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Eric Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Audrey A Burnim
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Amanda S Byer
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Daniel Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Richard E Gillilan
- Center for High Energy X-ray Sciences (CHEXS), Ithaca, New York 14853, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Department of Physics, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - George Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Everett Shock
- GEOPIG, School of Earth & Space Exploration, School of Molecular Sciences, Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona 85287, USA
| | - A Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77845, USA.,Department of Chemistry, Texas A&M University, College Station, Texas 77845, USA.,Department of Molecular & Cellular Medicine, Texas A&M University, College Station, Texas 77845, USA
| | - Maxwell B Watkins
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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Akiyama T, Kunishima N, Nemoto S, Kazama K, Hirose M, Sudo Y, Matsuura Y, Naitow H, Murata T. Further thermo-stabilization of thermophilic rhodopsin from Thermus thermophilus JL-18 through engineering in extramembrane regions. Proteins 2020; 89:301-310. [PMID: 33064333 PMCID: PMC7894484 DOI: 10.1002/prot.26015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/26/2020] [Accepted: 10/12/2020] [Indexed: 11/11/2022]
Abstract
It is known that a hyperthermostable protein tolerable at temperatures over 100°C can be designed from a soluble globular protein by introducing mutations. To expand the applicability of this technology to membrane proteins, here we report a further thermo-stabilization of the thermophilic rhodopsin from Thermus thermophilus JL-18 as a model membrane protein. Ten single mutations in the extramembrane regions were designed based on a computational prediction of folding free-energy differences upon mutation. Experimental characterizations using the UV-visible spectroscopy and the differential scanning calorimetry revealed that four of ten mutations were thermo-stabilizing: V79K, T114D, A115P, and A116E. The mutation-structure relationship of the TR constructs was analyzed using molecular dynamics simulations at 300 K and at 1800 K that aimed simulating structures in the native and in the random-coil states, respectively. The native-state simulation exhibited an ion-pair formation of the stabilizing V79K mutant as it was designed, and suggested a mutation-induced structural change of the most stabilizing T114D mutant. On the other hand, the random-coil-state simulation revealed a higher structural fluctuation of the destabilizing mutant S8D when compared to the wild type, suggesting that the higher entropy in the random-coil state deteriorated the thermal stability. The present thermo-stabilization design in the extramembrane regions based on the free-energy calculation and the subsequent evaluation by the molecular dynamics may be useful to improve the production of membrane proteins for structural studies.
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Affiliation(s)
- Tomoki Akiyama
- Department of Chemistry, Graduate School of Science, and Molecular Chirality Research, Chiba University, Chiba, Japan
| | - Naoki Kunishima
- RIKEN RSC-Rigaku Collaboration Center, RIKEN SPring-8 Center, Sayo-gun, Hyogo, Japan.,RIKEN SPring-8 Center, Sayo-gun, Hyogo, Japan
| | - Sayaka Nemoto
- Department of Chemistry, Graduate School of Science, and Molecular Chirality Research, Chiba University, Chiba, Japan
| | - Kazuki Kazama
- Department of Chemistry, Graduate School of Science, and Molecular Chirality Research, Chiba University, Chiba, Japan
| | - Masako Hirose
- Malvern Panalytical division of Spectris Co., Ltd, Tokyo, Japan
| | - Yuki Sudo
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | | | | | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, and Molecular Chirality Research, Chiba University, Chiba, Japan
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Abstract
To achieve the full potential of pharmacogenomics, one must accurately predict the functional outcomes that arise from amino acid substitutions in proteins. Classically, researchers have focused on understanding the consequences of individual substitutions. However, literature surveys have shown that most substitutions were created at evolutionarily conserved positions. Awareness of this bias leads to a shift in perspective, from considering the outcomes of individual substitutions to understanding the roles of individual protein positions. Conserved positions tend to act as “toggle” switches, with most substitutions abolishing function. However, nonconserved positions have been found equally capable of affecting protein function. Indeed, many nonconserved positions act like functional dimmer switches (“rheostat” positions): this is revealed when multiple substitutions are made at a single position. Each substitution has a different functional outcome; the set of substitutions spans a range of outcomes. Finally, some nonconserved positions appear neutral, capable of accommodating all amino acid types without modifying function. This paper reviews the currently-known properties of rheostat positions, with examples shown for pyruvate kinase, organic anion transporting polypeptide 1B1, the beta-lactamase inhibitory protein, and angiotensin-converting enzyme 2. Outcomes observed for rheostat positions have implications for the rational design of drug analogs and allosteric drugs. Furthermore, this new framework—comprising three types of protein positions—provides a new approach to interpreting disease and population-based databases of amino acid changes. In conclusion, although a full understanding of substitution outcomes at rheostat positions poses a challenge, utilization of this new frame of reference will further advance the application of pharmacogenomics.
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Yutani K, Matsuura Y, Joti Y. Confirmation of the formation of salt bridges in the denatured state of CutA1 protein using molecular dynamics simulations. Biophys Physicobiol 2019; 16:176-184. [PMID: 31984170 PMCID: PMC6976010 DOI: 10.2142/biophysico.16.0_176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/25/2019] [Indexed: 12/01/2022] Open
Abstract
It remains unclear how the abundant charged residues in proteins from hyperthermophiles contribute to the stabilization of proteins. Previously, based on molecular dynamics (MD) simulations, we proposed that these charged residues decrease the entropic effect by forming salt bridges in the denatured state under physiological conditions (Yutani et al., Sci. Rep. 8, 7613 (2018)). Because the quality of MD results is strongly dependent on the force fields used, in this study we performed the MD simulations using a different force field (AMBER99SB) along with the one we used before (Gromos43a1), at the same temperatures examined previously as well as at higher temperatures. In these experiments, we used the same ionic mutant (Ec0VV6) of CutA1 from Escherichia coli as in the previous study. In MD simulations at 300 K, Lys87 and Arg88 in the loop region of Ec0VV6 formed salt bridges with different favorable pairs in different force fields. Furthermore, the helical content and radius of gyration differed slightly between two force fields. However, at a higher temperature (600 K), the average numbers of salt bridges for the six substituted residues of Ec0VV6 were 0.87 per residue for Gromos43a1 and 0.88 for AMBER99SB in 400-ns MD simulation, indicating that the values were similar despite the use of different force fields. These observations suggest that the charged residues in Ec0VV6 can form a considerable number of salt bridges, even in the denatured state with drastic fluctuation at 600 K. These results corroborate our previous proposal.
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Affiliation(s)
| | | | - Yasumasa Joti
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan.,Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198 Japan
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Matsuura Y, Joti Y, Bagautdinov B, Yutani K. Evaluating the strengths of salt bridges in the CutA1 protein using molecular dynamic simulations: a comparison of different force fields. FEBS Open Bio 2019; 9:1939-1956. [PMID: 31509647 PMCID: PMC6823277 DOI: 10.1002/2211-5463.12731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/01/2019] [Accepted: 09/06/2019] [Indexed: 11/15/2022] Open
Abstract
Ion–ion interactions (salt bridges) between favorable pairs of charged residues are important for the conformational stability of proteins. Molecular dynamic (MD) simulations are useful for elucidating the interactions among charged residues fluctuating in solution. However, the quality of MD results depends strongly on the force fields used. In this study, we compared the strengths of salt bridges among force fields by performing MD simulations using the CutA1 protein (trimer) from the hyperthermophile Pyrococcus horikoshii (PhCutA1), which has an unusually large proportion of charged residues. The force fields Chemistry at HARvard Macromolecular Mechanics (Charmm)27, Assisted Model Building and Energy Refinement (Amber)99sb, Amber14sb, GROningen Molecular Simulation (Gromos)43a1, and Gromos53a6 were used in combination with two different water models, tip3p (for Charmm27, Amber99sb, and Amber14sb) and simple point charge/extended (for Amber99sb, Gromos43a1, and Gromos53a6), yielding a total of six combinations. The RMSDs of all Cα atoms of PhCutA1 were similar among force fields, except for Charmm27, during 400‐ns MD simulations at 300 K; however, the radius of gyration (Rg) was greater for Amber99sb and shorter for Gromos43a1. The average strengths of salt bridges for each positively charged residue did not differ greatly among force fields, but the strengths at specific sites within the structure depended sensitively on the force field used. In the case of the Gromos group, positively charged residues could engage in favorable interactions with many more charged residues than in the other force fields, especially in loop regions; consequently, the apparent strength at each site was lower.
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Affiliation(s)
| | - Yasumasa Joti
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan.,Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan
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