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Hong SY, Yoon J, An YJ, Lee S, Cha HG, Pandey A, Yoo YJ, Joo JC. Statistical Analysis of the Role of Cavity Flexibility in Thermostability of Proteins. Polymers (Basel) 2024; 16:291. [PMID: 38276699 PMCID: PMC10819066 DOI: 10.3390/polym16020291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Conventional statistical investigations have primarily focused on the comparison of the simple one-dimensional characteristics of protein cavities, such as number, surface area, and volume. These studies have failed to discern the crucial distinctions in cavity properties between thermophilic and mesophilic proteins that contribute to protein thermostability. In this study, the significance of cavity properties, i.e., flexibility and location, in protein thermostability was investigated by comparing structural differences between homologous thermophilic and mesophilic proteins. Three dimensions of protein structure were categorized into three regions (core, boundary, and surface) and a comparative analysis of cavity properties using this structural index was conducted. The statistical analysis revealed that cavity flexibility is closely related to protein thermostability. The core cavities of thermophilic proteins were less flexible than those of mesophilic proteins (averaged B' factor values, -0.6484 and -0.5111), which might be less deleterious to protein thermostability. Thermophilic proteins exhibited fewer cavities in the boundary and surface regions. Notably, cavities in mesophilic proteins, across all regions, exhibited greater flexibility than those in thermophilic proteins (>95% probability). The increased flexibility of cavities in the boundary and surface regions of mesophilic proteins, as opposed to thermophilic proteins, may compromise stability. Recent protein engineering investigations involving mesophilic xylanase and protease showed results consistent with the findings of this study, suggesting that the manipulation of flexible cavities in the surface region can enhance thermostability. Consequently, our findings suggest that a rational or computational approach to the design of flexible cavities in surface or boundary regions could serve as an effective strategy to enhance the thermostability of mesophilic proteins.
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Affiliation(s)
- So Yeon Hong
- Department of Chemical and Biological Engineering, Inha Technical College, Inha-ro 100, Michuhol-gu, Incheon 22212, Republic of Korea;
| | - Jihyun Yoon
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Republic of Korea (S.L.)
| | - Young Joo An
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Republic of Korea (S.L.)
| | - Siseon Lee
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Republic of Korea (S.L.)
| | - Haeng-Geun Cha
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Republic of Korea (S.L.)
| | - Ashutosh Pandey
- Institute for Water and Wastewater Technology, Durban University of Technology, 19 Steve Biko Road, Durban 4000, South Africa;
- Department of Biotechnology, Faculty of Life Science and Technology, AKS University, Satna 485001, Madhya Pradesh, India
| | - Young Je Yoo
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea;
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Republic of Korea (S.L.)
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2
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Jaafar NR, Mahadi NM, Mackeen MM, Illias RM, Murad AMA, Abu Bakar FD. Structural and functional characterisation of a cold-active yet heat-tolerant dehydroquinase from Glaciozyma antarctica PI12. J Biotechnol 2021; 329:118-127. [PMID: 33539893 DOI: 10.1016/j.jbiotec.2021.01.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 11/25/2022]
Abstract
Dehydroquinase or 3-dehydroquinate dehydratase (DHQD) reversibly cleaves 3-dehydroquinate to form 3-dehydroshikimate. Here, we describe the functional and structural features of a cold active type II 3-dehydroquinate dehydratase from the psychrophilic yeast, Glaciozyma antarctica PI12 (GaDHQD). Functional studies showed that the enzyme was active at low temperatures (10-30 °C), but displayed maximal activity at 40 °C. Yet the enzyme was stable over a wide range of temperatures (10-70 °C) and between pH 6.0-10.0 with an optimum pH of 8.0. Interestingly, the enzyme was highly thermo-tolerant, denaturing only at approximately 84 °C. Three-dimensional structure analyses showed that the G. antarctica dehydroquinase (GaDHQD) possesses psychrophilic features in comparison with its mesophilic and thermophilic counterparts such as higher numbers of non-polar residues on the surface, lower numbers of arginine and higher numbers of glycine-residues with lower numbers of hydrophobic interactions. On the other hand, GaDHQD shares some traits (i.e. total number of hydrogen bonds, number of proline residues and overall folding) with its mesophilic and thermophilic counterparts. Combined, these features contribute synergistically towards the enzyme's ability to function at both low and high temperatures.
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Affiliation(s)
- Nardiah Rizwana Jaafar
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81210, Skudai, Johor Darul Takzim, Malaysia; Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Nor Muhammad Mahadi
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Mukram Mohamed Mackeen
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia; Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Rosli Md Illias
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81210, Skudai, Johor Darul Takzim, Malaysia
| | - Abdul Munir Abdul Murad
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Farah Diba Abu Bakar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia.
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3
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A Novel Thermostable Cytochrome P450 from Sequence-Based Metagenomics of Binh Chau Hot Spring as a Promising Catalyst for Testosterone Conversion. Catalysts 2020. [DOI: 10.3390/catal10091083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Biotechnological applications of cytochromes P450 show difficulties, such as low activity, thermal and/or solvent instability, narrow substrate specificity and redox partner dependence. In an attempt to overcome these limitations, an exploitation of novel thermophilic P450 enzymes from nature via uncultured approaches is desirable due to their great advantages that can resolve nearly all mentioned impediments. From the metagenomics library of the Binh Chau hot spring, an open reading frame (ORF) encoding a thermostable cytochrome P450—designated as P450-T3—which shared 66.6% amino acid sequence identity with CYP109C2 of Sorangium cellulosum So ce56 was selected for further identification and characterization. The ORF was synthesized artificially and heterologously expressed in Escherichia coli C43(DE3) using the pET17b system. The purified enzyme had a molecular weight of approximately 43 kDa. The melting temperature of the purified enzyme was 76.2 °C and its apparent half-life at 60 °C was 38.7 min. Redox partner screening revealed that P450-T3 was reduced well by the mammalian AdR-Adx4-108 and the yeast Arh1-Etp1 redox partners. Lauric acid, palmitic acid, embelin, retinoic acid (all-trans) and retinoic acid (13-cis) demonstrated binding to P450-T3. Interestingly, P450-T3 also bound and converted testosterone. Overall, P450-T3 might become a good candidate for biocatalytic applications on a larger scale.
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4
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Kargar F, Mortazavi M, Torkzadeh-Mahani M, Lotfi S, Shakeri S. Evaluation of Luciferase Thermal Stability by Arginine Saturation in the Flexible Loops. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190320151005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The firefly luciferase enzyme is widely used in protein engineering and diverse
areas of biotechnology, but the main problem with this enzyme is low-temperature stability. Previous
reports indicated that surface areas of thermostable proteins are rich in arginine, which increased
their thermal stability. In this study, this aspect of thermophilic proteins evaluated by mutations of surface
residues to Arg. Here, we report the construction, purification, and studying of these mutated luciferases.
Methods:
For mutagenesis, the QuikChange site-directed mutagenesis was used and the I108R,
T156R, and N177R mutant luciferases were created. In the following, the expression and purification
of wild-type and mutant luciferases were conducted and their kinetic and structural properties were analyzed.
To analyze the role of these Arg in these loops, the 3D models of these mutants’ enzymes were
constructed in the I-TASSER server and the exact situation of these mutants was studied by the
SPDBV and PyMOL software.
Results:
Overall, the optimum temperature of these mutated enzymes was not changed. However, after
30 min incubation of these mutated enzymes at 30°C, the I108R, T156R, N177R, and wild-type kept the
80%, 50%, 20%, and 20% of their original activity, respectively. It should be noted that substitution of
these residues by Arg preserved the specific activity of firefly luciferase.
Conclusion:
Based on these results, it can be concluded that T156R and N177R mutants by compacting
local protein structure, increased the thermostability of luciferase. However, insertion of positively
charged residues in these positions create the new hydrogen bonds that associated with a series of
structural changes and confirmed by intrinsic and extrinsic fluorescence spectroscopy and homology
modeling studies.
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Affiliation(s)
- Farzane Kargar
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Safa Lotfi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Shahryar Shakeri
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
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5
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Kovacic F, Mandrysch A, Poojari C, Strodel B, Jaeger KE. Structural features determining thermal adaptation of esterases. Protein Eng Des Sel 2016; 29:65-76. [PMID: 26647400 PMCID: PMC5943684 DOI: 10.1093/protein/gzv061] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 11/14/2022] Open
Abstract
The adaptation of microorganisms to extreme living temperatures requires the evolution of enzymes with a high catalytic efficiency under these conditions. Such extremophilic enzymes represent valuable tools to study the relationship between protein stability, dynamics and function. Nevertheless, the multiple effects of temperature on the structure and function of enzymes are still poorly understood at the molecular level. Our analysis of four homologous esterases isolated from bacteria living at temperatures ranging from 10°C to 70°C suggested an adaptation route for the modulation of protein thermal properties through the optimization of local flexibility at the protein surface. While the biochemical properties of the recombinant esterases are conserved, their thermal properties have evolved to resemble those of the respective bacterial habitats. Molecular dynamics simulations at temperatures around the optimal temperatures for enzyme catalysis revealed temperature-dependent flexibility of four surface-exposed loops. While the flexibility of some loops increased with raising the temperature and decreased with lowering the temperature, as expected for those loops contributing to the protein stability, other loops showed an increment of flexibility upon lowering and raising the temperature. Preserved flexibility in these regions seems to be important for proper enzyme function. The structural differences of these four loops, distant from the active site, are substantially larger than for the overall protein structure, indicating that amino acid exchanges within these loops occurred more frequently thereby allowing the bacteria to tune atomic interactions for different temperature requirements without interfering with the overall enzyme function.
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Affiliation(s)
- Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426 Juelich, Germany
| | - Agathe Mandrysch
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426 Juelich, Germany
| | - Chetan Poojari
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Juelich GmbH, D-52426 Juelich, Germany Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Birgit Strodel
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Juelich GmbH, D-52426 Juelich, Germany Institute of Theoretical and Computational Chemistry, Heinrich-Heine-University Duesseldorf, D-40225 Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426 Juelich, Germany Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Juelich GmbH, D-52426 Juelich, Germany
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6
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Abstract
Using structure and sequence based analysis we can engineer proteins to increase their thermal stability.
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Affiliation(s)
- H. Pezeshgi Modarres
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - M. R. Mofrad
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - A. Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory
- Department of Mechanical and Manufacturing Engineering
- University of Calgary
- Calgary
- Canada
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7
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Protein cold adaptation: Role of physico-chemical parameters in adaptation of proteins to low temperatures. J Theor Biol 2015; 383:130-7. [DOI: 10.1016/j.jtbi.2015.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/21/2015] [Accepted: 07/16/2015] [Indexed: 11/21/2022]
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8
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Yun HS, Park HJ, Joo JC, Yoo YJ. Thermostabilization of Bacillus subtilis lipase A by minimizing the structural deformation caused by packing enhancement. ACTA ACUST UNITED AC 2013; 40:1223-9. [DOI: 10.1007/s10295-013-1330-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 08/06/2013] [Indexed: 11/24/2022]
Abstract
Abstract
Enzyme thermostabilization is a critical research topic due to potential industrial benefits. Among the various reasons to increase enzyme thermostability, enhancement of residual packing at the core of the enzyme structure has been commonly accepted as a successful strategy. However, structural changes that occur with residual packing enhancement may decrease enzyme activity. In this study, a strategy to minimize structural deformation by calculating the overlapping packing volume of a single-point mutation followed by applying a double-point mutation was suggested. Four double mutants, A38V_K23A, A75V_T83A, G80A_N106A, and G172A_V100A, were selected for the in vitro experiment; three of the four showed enhancements in both thermostability and catalytic activity. In particular, G80A_N106A showed 2.78 times higher catalytic activity compared with wild type.
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Affiliation(s)
- Hong Seung Yun
- grid.31501.36 0000000404705905 School of Chemical and Biological Engineering Seoul National University 151-742 Seoul Korea
| | - Hyun June Park
- grid.31501.36 0000000404705905 Graduate Program of Bioengineering Seoul National University 151-742 Seoul Korea
| | - Jeong Chan Joo
- grid.31501.36 0000000404705905 School of Chemical and Biological Engineering Seoul National University 151-742 Seoul Korea
| | - Young Je Yoo
- grid.31501.36 0000000404705905 School of Chemical and Biological Engineering Seoul National University 151-742 Seoul Korea
- grid.31501.36 0000000404705905 Graduate Program of Bioengineering Seoul National University 151-742 Seoul Korea
- grid.31501.36 0000000404705905 Bio-Max Institute Seoul National University 151-742 Seoul Korea
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9
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Mallik S, Kundu S. A comparison of structural and evolutionary attributes of Escherichia coli and Thermus thermophilus small ribosomal subunits: signatures of thermal adaptation. PLoS One 2013; 8:e69898. [PMID: 23940533 PMCID: PMC3734280 DOI: 10.1371/journal.pone.0069898] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/16/2013] [Indexed: 12/04/2022] Open
Abstract
Here we compare the structural and evolutionary attributes of Thermus thermophilus and Escherichia coli small ribosomal subunits (SSU). Our results indicate that with few exceptions, thermophilic 16S ribosomal RNA (16S rRNA) is densely packed compared to that of mesophilic at most of the analogous spatial regions. In addition, we have located species-specific cavity clusters (SSCCs) in both species. E. coli SSCCs are numerous and larger compared to T. thermophilus SSCCs, which again indicates densely packed thermophilic 16S rRNA. Thermophilic ribosomal proteins (r-proteins) have longer disordered regions than their mesophilic homologs and they experience larger disorder-to-order transitions during SSU-assembly. This is reflected in the predicted higher conformational changes of thermophilic r-proteins compared to their mesophilic homologs during SSU-assembly. This high conformational change of thermophilic r-proteins may help them to associate with the 16S ribosomal RNA with high complementary interfaces, larger interface areas, and denser molecular contacts, compared to those of mesophilic. Thus, thermophilic protein-rRNA interfaces are tightly associated with 16S rRNA than their mesophilic homologs. Densely packed 16S rRNA interior and tight protein-rRNA binding of T. thermophilus (compared to those of E. coli) are likely the signatures of its thermal adaptation. We have found a linear correlation between the free energy of protein-RNA interface formation, interface size, and square of conformational changes, which is followed in both prokaryotic and eukaryotic SSU. Disorder is associated with high protein-RNA interface polarity. We have found an evolutionary tendency to maintain high polarity (thereby disorder) at protein-rRNA interfaces, than that at rest of the protein structures. However, some proteins exhibit exceptions to this general trend.
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Affiliation(s)
- Saurav Mallik
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
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10
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Pack SP, Kang TJ, Yoo YJ. Protein Thermostabilizing Factors: High Relative Occurrence of Amino Acids, Residual Properties, and Secondary Structure Type in Different Residual State. Appl Biochem Biotechnol 2013; 171:1212-26. [DOI: 10.1007/s12010-013-0195-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 03/12/2013] [Indexed: 11/29/2022]
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11
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Park HJ, Joo JC, Park K, Kim YH, Yoo YJ. Prediction of the solvent affecting site and the computational design of stable Candida antarctica lipase B in a hydrophilic organic solvent. J Biotechnol 2013. [DOI: 10.1016/j.jbiotec.2012.11.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Park ST, Min K, Choi YS, Yoo YJ. Screening of stable cutinase from Fusarium solani pisi using plasmid display system. BIOTECHNOL BIOPROC E 2012. [DOI: 10.1007/s12257-012-0022-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Compositional and Structural Features Related to Thermal Stability in the Archaea SRP19 and SRP54 Signal Recognition Particle Proteins. J Mol Evol 2011; 72:450-65. [DOI: 10.1007/s00239-011-9443-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 04/01/2011] [Indexed: 10/18/2022]
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14
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Guncheva M, Zhiryakova D. Catalytic properties and potential applications of Bacillus lipases. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2010.09.002] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Abraham T, Abraham T, Pil Pack S, Je Yoo Y. Stabilization ofBacillus subtilisLipase A by increasing the residual packing. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500193013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Baldasseroni F, Pascarella S. Subunit interfaces of oligomeric hyperthermophilic enzymes display enhanced compactness. Int J Biol Macromol 2009; 44:353-60. [DOI: 10.1016/j.ijbiomac.2009.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Revised: 12/28/2008] [Accepted: 02/02/2009] [Indexed: 10/21/2022]
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17
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Joo JC, Yoo YJ. Cavity design of Bacillus circulans xylanase to increase the thermostability using computational approach. J Biotechnol 2008. [DOI: 10.1016/j.jbiotec.2008.07.896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Jahandideh M, Barkooie SMH, Jahandideh S, Abdolmaleki P, Movahedi MM, Hoseini S, Asadabadi EB, Jouni FJ, Karami Z, Firoozabadi NH. Elucidating the protein cold-adaptation: Investigation of the parameters enhancing protein psychrophilicity. J Theor Biol 2008; 255:113-8. [PMID: 18718477 DOI: 10.1016/j.jtbi.2008.07.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2008] [Revised: 06/10/2008] [Accepted: 07/27/2008] [Indexed: 11/28/2022]
Abstract
To investigate the role of the critical parameters in adaptation of proteins to low temperatures, a comparative systematic analysis was performed. Several parameters were proposed to have contribution to cold adaptation of proteins. Among proposed parameters, total values of residual structure states, secondary structure states and oligomeric states were alike in both psychrophilic and mesophilic proteins. In addition, our results provided new quantitative information about the trends in the substitution preference of Ile, Phe, Tyr, Lys, Arg, His, Glu and Leu with most of amino acids and substitution avoidance of Gly, Thr and Ala with most of amino acids. These findings would help future efforts propose a strategy for designing psychrophilic proteins.
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Affiliation(s)
- Mina Jahandideh
- Department of Mathematics, Faculty of Science, Vali-E-Asr University, Rafsanjan, Iran
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19
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Vondrásek J, Kubar T, Jenney FE, Adams MWW, Kozísek M, Cerný J, Sklenár V, Hobza P. Dispersion interactions govern the strong thermal stability of a protein. Chemistry 2008; 13:9022-7. [PMID: 17696186 DOI: 10.1002/chem.200700428] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Rubredoxin from the hyperthermophile Pyrococcus furiosus (Pf Rd) is an extremely thermostable protein, which makes it an attractive subject of protein folding and stability studies. A fundamental question arises as to what the reason for such extreme stability is and how it can be elucidated from a complex set of interatomic interactions. We addressed this issue first theoretically through a computational analysis of the hydrophobic core of the protein and its mutants, including the interactions taking place inside the core. Here we show that a single mutation of one of phenylalanine's residues inside the protein's hydrophobic core results in a dramatic decrease in its thermal stability. The calculated unfolding Gibbs energy as well as the stabilization energy differences between a few core residues follows the same trend as the melting temperature of protein variants determined experimentally by microcalorimetry measurements. NMR spectroscopy experiments have shown that the only part of the protein affected by mutation is the reasonably rearranged hydrophobic core. It is hence concluded that stabilization energies, which are dominated by London dispersion, represent the main source of stability of this protein.
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Affiliation(s)
- Jirí Vondrásek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, Praha 6, Czech Republic.
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20
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Goldstein RA. Amino-acid interactions in psychrophiles, mesophiles, thermophiles, and hyperthermophiles: insights from the quasi-chemical approximation. Protein Sci 2007; 16:1887-95. [PMID: 17766385 PMCID: PMC2206978 DOI: 10.1110/ps.072947007] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We investigate the mechanisms used by proteins to maintain thermostability throughout a wide range of temperatures. We use the quasi-chemical approximation to estimate interaction strengths for psychrophiles, mesophiles, thermophiles, and hyperthermophiles. Our results highlight the importance of core packing in thermophilic stability. Although we observed an increase in the number of charged residues, the contribution of salt bridges appears to be relatively modest by comparison. We observed results consistent with a gradual loosening of structure in psychrophiles, including a weakening of almost all types of interactions.
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Affiliation(s)
- Richard A Goldstein
- Mathematical Biology, National Institute of Medical Research, Mill Hill, London NW7 1AA, United Kingdom.
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21
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Pechkova E, Sivozhelezov V, Nicolini C. Protein thermal stability: The role of protein structure and aqueous environment. Arch Biochem Biophys 2007; 466:40-8. [PMID: 17765863 DOI: 10.1016/j.abb.2007.07.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 07/03/2007] [Accepted: 07/13/2007] [Indexed: 10/23/2022]
Abstract
A comprehensive bioinformatic analysis was performed on all protein homologous pairs from mesophilic and thermophilic microorganisms present in the RCSB Protein Data Bank in order to yield a clue on the role of protein structure and aqueous environment. Subsequently self-assembly and LB studies were carried out at increasing temperature by nanogravimetry with thermostable thioredoxin (Trx) from Alicyclobacillus acidocaldarius (BacTrx) versus the mesophilic Escherichia coli counterpart (EcTrx). The comparison with earlier 3D atomic structure determined on the same proteins by X-ray crystallographic diffraction and nuclear magnetic resonance confirm the role inner bound water in determining protein thermostability, as suggested by the bioinformatic and nanogravimetric analysis. The above comparative characterizations in protein solution, thin film and crystal allow to draw a possible coherent explanation for the origin and the molecular mechanisms of both heat stability and radiation resistance in proteins.
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Affiliation(s)
- Eugenia Pechkova
- Nanoworld Institute, University of Genova, Corso Europa 30, 16132 Genova, Italy
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22
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Jahandideh S, Barzegari Asadabadi E, Abdolmaleki P, Jahandideh M, Hoseini S. Protein psychrophilicity: Role of residual structural properties in adaptation of proteins to low temperatures. J Theor Biol 2007; 248:721-6. [PMID: 17669434 DOI: 10.1016/j.jtbi.2007.06.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 05/26/2007] [Accepted: 06/25/2007] [Indexed: 11/20/2022]
Abstract
In order to investigate the structural distribution responsible for protein psychrophilicity, a systematic comparative analysis of 13 pairs of psychrophilic and mesophilic proteins is reported. Three kinds of residue structural states such as exposed, intermediate and buried were considered for analyzing the structural patterns of single amino acids and amino acids in different groups. The statistical test revealed that higher frequency in exposed state of Ala, higher frequency in intermediate state of His, lower frequency in buried state of Lys, lower frequency in exposed state of Gln, higher frequency in exposed state and in intermediate state of Thr, higher frequency in exposed and intermediate state of tiny and small amino acids groups could be critical factors related with protein psychrophilicity. Such structure-based differences of residual properties would help to develop a strategy for designing psychrophilic proteins.
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Affiliation(s)
- Samad Jahandideh
- Department of Biophysics, Faculty of Science, Tarbiat Modares University, P.O. Box 14115/175, Tehran, Iran
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23
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Zhou XX, Wang YB, Pan YJ, Li WF. Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins. Amino Acids 2007; 34:25-33. [PMID: 17710363 DOI: 10.1007/s00726-007-0589-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Accepted: 07/12/2007] [Indexed: 10/22/2022]
Abstract
Thermophilic proteins show substantially higher intrinsic thermal stability than their mesophilic counterparts. Amino acid composition is believed to alter the intrinsic stability of proteins. Several investigations and mutagenesis experiment have been carried out to understand the amino acid composition for the thermostability of proteins. This review presents some generalized features of amino acid composition found in thermophilic proteins, including an increase in residue hydrophobicity, a decrease in uncharged polar residues, an increase in charged residues, an increase in aromatic residues, certain amino acid coupling patterns and amino acid preferences for thermophilic proteins. The differences of amino acids composition between thermophilic and mesophilic proteins are related to some properties of amino acids. These features provide guidelines for engineering mesophilic protein to thermophilic protein.
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Affiliation(s)
- X-X Zhou
- Institute of Chemical Biology and Pharmaceutical Chemistry, Zhejiang University, Hangzhou, China
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24
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Glyakina AV, Garbuzynskiy SO, Lobanov MY, Galzitskaya OV. Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms. Bioinformatics 2007; 23:2231-8. [PMID: 17599925 DOI: 10.1093/bioinformatics/btm345] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Understanding the basis of protein stability in thermophilic organisms raises a general question: what structural properties of proteins are responsible for the higher thermostability of proteins from thermophilic organisms compared to proteins from mesophilic organisms? RESULTS A unique database of 373 structurally well-aligned protein pairs from thermophilic and mesophilic organisms is constructed. Comparison of proteins from thermophilic and mesophilic organisms has shown that the external, water-accessible residues of the first group are more closely packed than those of the second. Packing of interior parts of proteins (residues inaccessible to water molecules) is the same in both cases. The analysis of amino acid composition of external residues of proteins from thermophilic organisms revealed an increased fraction of such amino acids as Lys, Arg and Glu, and a decreased fraction of Ala, Asp, Asn, Gln, Thr, Ser and His. Our theoretical investigation of folding/unfolding behavior confirms the experimental observations that the interactions that differ in thermophilic and mesophilic proteins form only after the passing of the transition state during folding. Thus, different packing of external residues can explain differences in thermostability of proteins from thermophilic and mesophilic organisms. AVAILABILITY The database of 373 structurally well-aligned protein pairs is available at http://phys.protres.ru/resources/termo_meso_base.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anna V Glyakina
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
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25
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Saelensminde G, Halskau Ø, Helland R, Willassen NP, Jonassen I. Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins. Extremophiles 2007; 11:585-96. [PMID: 17429573 DOI: 10.1007/s00792-007-0072-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Accepted: 02/27/2007] [Indexed: 10/23/2022]
Abstract
We studied the amino acid frequency and substitution patterns between homologues of prokaryotic species adapted to temperatures in the range 0-102 degrees C, and found a significant temperature-dependent difference in frequency for many of the amino acids. This was particularly clear when we analysed the surface and core residues separately. The difference between the surface and the core is getting more pronounced in proteins adapted to warmer environments, with a more hydrophobic core, and more charged and long-chained amino acids on the surface of the proteins. We also see that mesophiles have a more similar amino acid composition to psychrophiles than to thermophiles, and that archea appears to have a slightly different pattern of substitutions than bacteria.
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Affiliation(s)
- Gisle Saelensminde
- Computational Biology Unit (CBU), BCCS, University of Bergen, Bergen, Norway.
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