1
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Kimijima J, Inagawa A, Miyagawa A, Nasuno E, Uehara N. Probing the interaction between biomolecules under sub-zero temperature conditions by electrophoresis in ice grain boundaries. Anal Chim Acta 2024; 1311:342713. [PMID: 38816152 DOI: 10.1016/j.aca.2024.342713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Psychrophiles can survive under cryogenic conditions because of various biomolecules. These molecules interact with cells, ice crystals, and lipid bilayers to enhance their functionality. Previous studies typically measured these interactions by thawing frozen samples and conducting biological assays at room temperature; however, studying these interactions under cryogenic conditions is crucial. This is because these biomolecules can function at lower temperatures. Therefore, a platform for measuring chemical interactions under sub-zero temperature conditions must be established. RESULTS The chemical interactions between biomolecules under sub-zero temperature conditions were evaluated within ice grain boundaries with a channel-like structure, which circumvents the need for thawing. An aqueous solution of sucrose was frozen within a microfluidic channel, facilitating the formation of freeze-concentrated solutions (FCSs) that functioned as size-tunable electrophoretic fields. Avidin proteins or single-stranded DNA (ssDNA) were introduced into the FCS in advance. Probe micro/nanospheres whose surfaces were modified with molecules complementary to the target analytes were introduced into the FCS. If the targets have functionalities under sub-zero temperature conditions, they interact with complementary molecules. The chemical interactions between the target molecules and nanospheres led to the aggregation of the particles. The size tunability of the diameter of the FCS channels enabled the recognition of aggregation levels, which is indicative of interaction reactivity. The avidin-biotin interaction and ssDNA hybridization served as models for chemical interactions, demonstrating interactivity under sub-zero temperature conditions. The results presented herein suggest the potential for in situ measurement of biochemical assays in the frozen state, elucidating the functionality of bio-related macromolecules at or slightly below 0 °C. SIGNIFICANCE This is the first methodology to evaluate chemical interactions under sub-zero temperature conditions without employing the freeze-and-thaw process. This method has the advantage of revealing the chemical interactions only at low temperatures. Therefore, it can be used to screen and evaluate the functionality of cryo-related biomolecules, including cold-shock and antifreeze proteins.
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Affiliation(s)
- Junya Kimijima
- School of Engineering, Utsunomiya University, 7-1-2, Yoto, Utsunomiya, Tochigi, 321-8585, Japan
| | - Arinori Inagawa
- School of Engineering, Utsunomiya University, 7-1-2, Yoto, Utsunomiya, Tochigi, 321-8585, Japan.
| | - Akihisa Miyagawa
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8571, Japan
| | - Eri Nasuno
- School of Engineering, Utsunomiya University, 7-1-2, Yoto, Utsunomiya, Tochigi, 321-8585, Japan
| | - Nobuo Uehara
- School of Engineering, Utsunomiya University, 7-1-2, Yoto, Utsunomiya, Tochigi, 321-8585, Japan
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2
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Choudhary P, Bhatt S, Chatterjee S. From freezing to functioning: cellular strategies of cold-adapted bacteria for surviving in extreme environments. Arch Microbiol 2024; 206:329. [PMID: 38940837 DOI: 10.1007/s00203-024-04058-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 06/29/2024]
Abstract
The ability of cold-adapted bacteria to survive in extreme cold and diverse temperatures is due to their unique attributes like cell membrane stability, up-regulation of peptidoglycan biosynthesis, increased production of extracellular polymeric substances, and expansion of membrane pigment. Various cold-adapted proteins, including ice-nucleating proteins (INPs), antifreeze proteins (AFPs), cold shock proteins (Csps), and cold-acclimated proteins (CAPs), help the bacteria to survive in these environments. To sustain cells from extreme cold conditions and maintain stability in temperature fluctuations, survival strategies at the molecular level and their mechanism play significant roles in adaptations in cryospheric conditions. Furthermore, cold shock domains present in the multifunctional cold shock proteins play crucial roles in their adaptation strategies. The considerable contribution of lipopeptides, osmolytes, and membrane pigments plays an integral part in their survival in extreme environments. This review summarizes the evolutionary history of cold-adapted bacteria and their molecular and cellular adaptation strategies to thrive in harsh cold environments. It also discusses the importance of carotenoids produced, lipid composition, cryoprotectants, proteins, and chaperones related to this adaptation. Furthermore, the functions and mechanisms of adaptations within the cell are discussed briefly. One can utilize and explore their potential in various biotechnology applications and their evolutionary journey by knowing the inherent mechanism of their molecular and cellular adaptation to cold climatic conditions. This review will help all branches of the life science community understand the basic microbiology of psychrophiles and their hidden prospect in life science research.
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Affiliation(s)
- Priyanka Choudhary
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Academic Block-Shahpur, Kangra, Himachal Pradesh, 176206, India
| | - Sunidhi Bhatt
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Academic Block-Shahpur, Kangra, Himachal Pradesh, 176206, India
| | - Subhankar Chatterjee
- Bioremediation and Metabolomics Research Group, Dept. of Ecology & Environmental Sciences, School of Life Sciences, Pondicherry University, R.V. Nagar, Kalapet, Puducherry, 605014, India.
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3
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Avagyan S, Makhatadze GI. Effects of Hydrostatic Pressure on the Thermodynamics of CspB-Bs Interactions with the ssDNA Template. Biochemistry 2021; 60:3086-3097. [PMID: 34613715 DOI: 10.1021/acs.biochem.1c00561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the thermodynamic mechanisms of adaptation of biomacromolecules to high hydrostatic pressure can help shed light on how piezophilic organisms can survive at pressures reaching over 1000 atmospheres. Interaction of proteins with nucleic acids is one of the central processes that allow information flow encoded in the sequence of DNA. Here, we report the results of a study on the interaction of cold shock protein B from Bacillus subtilis (CspB-Bs) with heptadeoxythymine template (pDT7) as a function of temperature and hydrostatic pressure. Experimental data collected at different CspB-Bs:pDT7 ratios were analyzed using a thermodynamic linkage model that accounts for both protein unfolding and CspB-Bs:pDT7 binding. The global fit to the model provided estimates of the stability of CspB-Bs, ΔGProto, the volume change upon CspB-Bs unfolding, ΔVProt, the association constant for CspB-Bs:pDT7 complex, Kao, and the volume changes upon pDT7 single-stranded DNA (ssDNA) template binding, ΔVBind. The protein, CspB-Bs, unfolds with an increase in hydrostatic pressure (ΔVProt < 0). Surprisingly, our study showed that ΔVBind < 0, which means that the binding of CspB-Bs to ssDNA is stabilized by an increase in hydrostatic pressure. Thus, CspB-Bs binding to pDT7 represents a case of linked equilibrium in which folding and binding react differently upon an increase in hydrostatic pressure: protein folding/unfolding equilibrium favors the unfolded state, while protein-ligand binding equilibrium favors the bound state. These opposing effects set a "maximum attainable" pressure tolerance to the protein-ssDNA complex under given conditions.
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Affiliation(s)
- Samvel Avagyan
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - George I Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department on Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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4
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Basu S, Chakravarty D, Bhattacharyya D, Saha P, Patra HK. Plausible blockers of Spike RBD in SARS-CoV2-molecular design and underlying interaction dynamics from high-level structural descriptors. J Mol Model 2021; 27:191. [PMID: 34057647 PMCID: PMC8165686 DOI: 10.1007/s00894-021-04779-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/26/2021] [Indexed: 12/24/2022]
Abstract
Abstract COVID-19 is characterized by an unprecedented abrupt increase in the viral transmission rate (SARS-CoV-2) relative to its pandemic evolutionary ancestor, SARS-CoV (2003). The complex molecular cascade of events related to the viral pathogenicity is triggered by the Spike protein upon interacting with the ACE2 receptor on human lung cells through its receptor binding domain (RBDSpike). One potential therapeutic strategy to combat COVID-19 could thus be limiting the infection by blocking this key interaction. In this current study, we adopt a protein design approach to predict and propose non-virulent structural mimics of the RBDSpike which can potentially serve as its competitive inhibitors in binding to ACE2. The RBDSpike is an independently foldable protein domain, resilient to conformational changes upon mutations and therefore an attractive target for strategic re-design. Interestingly, in spite of displaying an optimal shape fit between their interacting surfaces (attributed to a consequently high mutual affinity), the RBDSpike–ACE2 interaction appears to have a quasi-stable character due to a poor electrostatic match at their interface. Structural analyses of homologous protein complexes reveal that the ACE2 binding site of RBDSpike has an unusually high degree of solvent-exposed hydrophobic residues, attributed to key evolutionary changes, making it inherently “reaction-prone.” The designed mimics aimed to block the viral entry by occupying the available binding sites on ACE2, are tested to have signatures of stable high-affinity binding with ACE2 (cross-validated by appropriate free energy estimates), overriding the native quasi-stable feature. The results show the apt of directly adapting natural examples in rational protein design, wherein, homology-based threading coupled with strategic “hydrophobic ↔ polar” mutations serve as a potential breakthrough. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00894-021-04779-0.
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Affiliation(s)
- Sankar Basu
- Department of Microbiology, Asutosh College (affiliated to University of Calcutta), Kolkata, 700026, West Bengal, India.
| | - Devlina Chakravarty
- Department of Chemistry, University of Rutgers-Camden, Camden, 08102, NJ, USA
| | - Dhananjay Bhattacharyya
- Computational Science Division, Saha Institute of Nuclear Physics, Kolkata, 700064, West Bengal, India
| | - Pampa Saha
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Hirak K Patra
- Department of Surgical Biotechnology, Division of Surgery and Interventional Science, University College London, London, NW3 2PF, UK
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5
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Cao JR, Fan FF, Lv CJ, Wang HP, Li Y, Hu S, Zhao WR, Chen HB, Huang J, Mei LH. Improving the Thermostability and Activity of Transaminase From Aspergillus terreus by Charge-Charge Interaction. Front Chem 2021; 9:664156. [PMID: 33937200 PMCID: PMC8081293 DOI: 10.3389/fchem.2021.664156] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/23/2021] [Indexed: 11/13/2022] Open
Abstract
Transaminases that promote the amination of ketones into amines are an emerging class of biocatalysts for preparing a series of drugs and their intermediates. One of the main limitations of (R)-selective amine transaminase from Aspergillus terreus (At-ATA) is its weak thermostability, with a half-life (t 1/2) of only 6.9 min at 40°C. To improve its thermostability, four important residue sites (E133, D224, E253, and E262) located on the surface of At-ATA were identified using the enzyme thermal stability system (ETSS). Subsequently, 13 mutants (E133A, E133H, E133K, E133R, E133Q, D224A, D224H, D224K, D224R, E253A, E253H, E253K, and E262A) were constructed by site-directed mutagenesis according to the principle of turning the residues into opposite charged ones. Among them, three substitutions, E133Q, D224K, and E253A, displayed higher thermal stability than the wild-type enzyme. Molecular dynamics simulations indicated that these three mutations limited the random vibration amplitude in the two α-helix regions of 130-135 and 148-158, thereby increasing the rigidity of the protein. Compared to the wild-type, the best mutant, D224K, showed improved thermostability with a 4.23-fold increase in t 1/2 at 40°C, and 6.08°C increase in T 50 10 . Exploring the three-dimensional structure of D224K at the atomic level, three strong hydrogen bonds were added to form a special "claw structure" of the α-helix 8, and the residues located at 151-156 also stabilized the α-helix 9 by interacting with each other alternately.
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Affiliation(s)
- Jia-Ren Cao
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Fang-Fang Fan
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Chang-Jiang Lv
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Hong-Peng Wang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Ye Li
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Sheng Hu
- School of Biotechnology and Chemical Engineering, NingboTech University, Ningbo, China
| | - Wei-Rui Zhao
- School of Biotechnology and Chemical Engineering, NingboTech University, Ningbo, China
| | - Hai-Bin Chen
- Enzymaster (Ningbo) Bio-Engineering Co., Ltd., Ningbo, China
| | - Jun Huang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Le-He Mei
- School of Biotechnology and Chemical Engineering, NingboTech University, Ningbo, China.,Jinhua Advanced Research Institute, Jinhua, China.,Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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6
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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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7
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Heinemann U, Roske Y. Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding. Cancers (Basel) 2021; 13:cancers13020190. [PMID: 33430354 PMCID: PMC7825780 DOI: 10.3390/cancers13020190] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Proteins are composed of compact domains, often of known three-dimensional structure, and natively unstructured polypeptide regions. The abundant cold-shock domain is among the set of canonical nucleic acid-binding domains and conserved from bacteria to man. Proteins containing cold-shock domains serve a large variety of biological functions, which are mostly linked to DNA or RNA binding. These functions include the regulation of transcription, RNA splicing, translation, stability and sequestration. Cold-shock domains have a simple architecture with a conserved surface ideally suited to bind single-stranded nucleic acids. Because the binding is mostly by non-specific molecular interactions which do not involve the sugar-phosphate backbone, cold-shock domains are not strictly sequence-specific and do not discriminate reliably between DNA and RNA. Many, but not all functions of cold shock-domain proteins in health and disease can be understood based of the physical and structural properties of their cold-shock domains. Abstract The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains’ ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration.
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8
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de Oliveira VM, Caetano DLZ, da Silva FB, Mouro PR, de Oliveira AB, de Carvalho SJ, Leite VBP. pH and Charged Mutations Modulate Cold Shock Protein Folding and Stability: A Constant pH Monte Carlo Study. J Chem Theory Comput 2020; 16:765-772. [PMID: 31756296 DOI: 10.1021/acs.jctc.9b00894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The folding and stability of proteins is a fundamental problem in several research fields. In the present paper, we have used different computational approaches to study the effects caused by changes in pH and for charged mutations in cold shock proteins from Bacillus subtilis (Bs-CspB). First, we have investigated the contribution of each ionizable residue for these proteins to their thermal stability using the TKSA-MC, a Web server for rational mutation via optimizing the protein charge interactions. Based on these results, we have proposed a new mutation in an already optimized Bs-CspB variant. We have evaluated the effects of this new mutation in the folding energy landscape using structure-based models in Monte Carlo simulation at constant pH, SBM-CpHMC. Our results using this approach have indicated that the charge rearrangements already in the unfolded state are critical to the thermal stability of Bs-CspB. Furthermore, the conjunction of these simplified methods was able not only to predict stabilizing mutations in different pHs but also to provide essential information about their effects in each stage of protein folding.
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Affiliation(s)
- Vinícius M de Oliveira
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, LNBio/CNPEM , Campinas , São Paulo , 13083-970 , Brazil
| | - Daniel L Z Caetano
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Fernando B da Silva
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Paulo R Mouro
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Antonio B de Oliveira
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Sidney J de Carvalho
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Vitor B P Leite
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil.,Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States
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9
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Contessoto VG, de Oliveira VM, Fernandes BR, Slade GG, Leite VBP. TKSA-MC: A web server for rational mutation through the optimization of protein charge interactions. Proteins 2018; 86:1184-1188. [PMID: 30218467 DOI: 10.1002/prot.25599] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/24/2018] [Accepted: 08/31/2018] [Indexed: 11/06/2022]
Abstract
The TKSAMC is a web server which calculates protein charge-charge interactions via the Tanford-Kirkwood Surface Accessibility model with the Monte Carlo method for sampling different protein protonation states. The optimization of charge-charge interactions via directed mutations has successfully enhanced the thermal stability of different proteins and could be a key to protein engineering improvement. The server presents the electrostatic free energy contribution of each polar-charged residue to the protein native state stability. Specific residues are suggested to be mutated for improving thermal stability. The choice of a residue is based on its fraction of side chain exposed to solvent and its positive free energy contribution, which tends to destabilize the protein native state. Any residue energy contribution can be shown as a function of pH condition. The web server is freely available at UNESP (São Paulo State University - DF/IBILCE): http://tksamc.df.ibilce.unesp.br and also on GitHub https://github.com/contessoto/tksamc.
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Affiliation(s)
- Vinícius G Contessoto
- Brazilian Bioethanol Science and Technology Laboratory - CTBE, Campinas, São Paulo, Brazil.,Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Vinícius M de Oliveira
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Bruno R Fernandes
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Gabriel G Slade
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil.,Theoretical Biophysics Laboratory, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro - UFTM, Uberaba, Minas Gerais, Brazil
| | - Vitor B P Leite
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil
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10
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Carlsson ACC, Scholfield MR, Rowe RK, Ford MC, Alexander AT, Mehl RA, Ho PS. Increasing Enzyme Stability and Activity through Hydrogen Bond-Enhanced Halogen Bonds. Biochemistry 2018; 57:4135-4147. [PMID: 29921126 PMCID: PMC6052408 DOI: 10.1021/acs.biochem.8b00603] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
The construction of more stable proteins
is important in biomolecular
engineering, particularly in the design of biologics-based therapeutics.
We show here that replacing the tyrosine at position 18 (Y18) of T4
lysozyme with the unnatural amino acid m-chlorotyrosine
(mClY) increases both the thermal stability
(increasing the melting temperature by ∼1 °C and the melting
enthalpy by 3 kcal/mol) and the enzymatic activity at elevated temperatures
(15% higher than that of the parent enzyme at 40 °C) of this
classic enzyme. The chlorine of mClY forms
a halogen bond (XB) to the carbonyl oxygen of the peptide bond at
glycine 28 (G28) in a tight loop near the active site. In this case,
the XB potential of the typically weak XB donor Cl is shown from quantum
chemical calculations to be significantly enhanced by polarization
via an intramolecular hydrogen bond (HB) from the adjacent hydroxyl
substituent of the tyrosyl side chain, resulting in a distinctive
synergistic HB-enhanced XB (or HeX-B for short) interaction. The larger
halogens (bromine and iodine) are not well accommodated within this
same loop and, consequently, do not exhibit the effects on protein
stability or function associated with the HeX-B interaction. Thus,
we have for the first time demonstrated that an XB can be engineered
to stabilize and increase the activity of an enzyme, with the increased
stabilizing potential of the HeX-B further extending the application
of halogenated amino acids in the design of more stable protein therapeutics.
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Affiliation(s)
- Anna-Carin C Carlsson
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Matthew R Scholfield
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Rhianon K Rowe
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Melissa Coates Ford
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Austin T Alexander
- Department of Biochemistry & Biophysics , Oregon State University , Corvallis , Oregon 97333 , United States
| | - Ryan A Mehl
- Department of Biochemistry & Biophysics , Oregon State University , Corvallis , Oregon 97333 , United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
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11
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Martins de Oliveira V, Godoi Contessoto VD, Bruno da Silva F, Zago Caetano DL, Jurado de Carvalho S, Pereira Leite VB. Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models. Biophys J 2018; 114:65-75. [PMID: 29320697 PMCID: PMC5984902 DOI: 10.1016/j.bpj.2017.11.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/20/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022] Open
Abstract
The importance of charge-charge interactions in the thermal stability of proteins is widely known. pH and ionic strength play a crucial role in these electrostatic interactions, as well as in the arrangement of ionizable residues in each protein-folding stage. In this study, two coarse-grained models were used to evaluate the effect of pH and salt concentration on the thermal stability of a protein G variant (1PGB-QDD), which was chosen due to the quantity of experimental data exploring these effects on its stability. One of these coarse-grained models, the TKSA, calculates the electrostatic free energy of the protein in the native state via the Tanford-Kirkwood approach for each residue. The other one, CpHMD-SBM, uses a Coulomb screening potential in addition to the structure-based model Cα. Both models simulate the system in constant pH. The comparison between the experimental stability analysis and the computational results obtained by these simple models showed a good agreement. Through the TKSA method, the role of each charged residue in the protein's thermal stability was inferred. Using CpHMD-SBM, it was possible to evaluate salt and pH effects throughout the folding process. Finally, the computational pKa values were calculated by both methods and presented a good level of agreement with the experiments. This study provides, to our knowledge, new information and a comprehensive description of the electrostatic contribution to protein G stability.
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Affiliation(s)
- Vinícius Martins de Oliveira
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Vinícius de Godoi Contessoto
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil; Brazilian Bioethanol Science and Technology Laboratory- (CTBE), Campinas, Brazil
| | - Fernando Bruno da Silva
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Daniel Lucas Zago Caetano
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Sidney Jurado de Carvalho
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Vitor Barbanti Pereira Leite
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil.
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12
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Caruso IP, Panwalkar V, Coronado MA, Dingley AJ, Cornélio ML, Willbold D, Arni RK, Eberle RJ. Structure and interaction of Corynebacterium pseudotuberculosis cold shock protein A with Y-box single-stranded DNA fragment. FEBS J 2017; 285:372-390. [PMID: 29197185 DOI: 10.1111/febs.14350] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/07/2017] [Accepted: 11/29/2017] [Indexed: 11/28/2022]
Abstract
Cold shock proteins (Csps) function to preserve cell viability at low temperatures by binding to nucleic acids and consequently control gene expression. The mesophilic bacterium Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis in animals, and infection in livestock is a considerable economic burden worldwide. In this report, the structure of cold shock protein A from Cp (Cp-CspA) and biochemical analysis of its temperature-dependent interaction with a Y-box ssDNA motif is presented. The Cp-CspA structure contains five β-strands making up a β-barrel fold with 11 hydrophobic core residues and two salt bridges that confers it with a melting temperature of ~ 54 °C that is similar to mesophilic Bs-CspB. Chemical shift perturbations analysis revealed that residues in the nucleic acid-binding motifs (RNP 1 and 2) and loop 3 are involved in binding to the Y-box fragment either by direct interaction or by conformational rearrangements remote from the binding region. Fluorescence quenching experiments of Cp-CspA showed that the dissociation constants for Y-box ssDNA binding is nanomolar and the binding affinity decreased as the temperature increased, indicating that the interaction is enthalpically driven and the hydrogen bonds and van der Waals forces are important contributions for complex stabilization. The Y31 of Cp-CspA is a particular occurrence among Csps from mesophilic bacteria that provide a possible explanation for the higher binding affinity to ssDNA than that observed for Bs-CspB. Anisotropy measurements indicated that the reduction in molecular mobility of Cp-CspA upon Y-box binding is characterized by a cooperative process. DATABASE Resonance assignment and structural data are available in the Biological Magnetic Resonance Data Bank and Protein Data Bank under accession number 26802 and 5O6F, respectively.
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Affiliation(s)
- Icaro P Caruso
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Vineet Panwalkar
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Monika A Coronado
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Andrew J Dingley
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Marinônio L Cornélio
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Dieter Willbold
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Raghuvir K Arni
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Raphael J Eberle
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
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13
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Makhatadze GI. Linking computation and experiments to study the role of charge-charge interactions in protein folding and stability. Phys Biol 2017; 14:013002. [PMID: 28169222 DOI: 10.1088/1478-3975/14/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past two decades there has been an increase in appreciation for the role of surface charge-charge interactions in protein folding and stability. The perception shifted from the belief that charge-charge interactions are not important for protein folding and stability to the near quantitative understanding of how these interactions shape the folding energy landscape. This led to the ability of computational approaches to rationally redesign surface charge-charge interactions to modulate thermodynamic properties of proteins. Here we summarize our progress in understanding the role of charge-charge interactions for protein stability using examples drawn from my own laboratory and touch upon unanswered questions.
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Affiliation(s)
- George I Makhatadze
- Center for Biotechnology and Interdisciplinary Studies, and Department of Biological Sciences, Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180 USA
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14
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Gopi S, Singh A, Suresh S, Paul S, Ranu S, Naganathan AN. Toward a quantitative description of microscopic pathway heterogeneity in protein folding. Phys Chem Chem Phys 2017; 19:20891-20903. [DOI: 10.1039/c7cp03011h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimentally consistent statistical modeling of protein folding thermodynamics reveals unprecedented complexity with numerous parallel folding routes in five different proteins.
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Affiliation(s)
- Soundhararajan Gopi
- Department of Biotechnology
- Bhupat & Jyoti Mehta School of Biosciences
- Indian Institute of Technology Madras
- Chennai 600036
- India
| | - Animesh Singh
- Department of Computer Science and Engineering
- Indian Institute of Technology Madras
- Chennai 600036
- India
| | | | - Suvadip Paul
- Department of Computer Science and Engineering
- Indian Institute of Technology Madras
- Chennai 600036
- India
| | - Sayan Ranu
- Department of Computer Science and Engineering
- Indian Institute of Technology Madras
- Chennai 600036
- India
| | - Athi N. Naganathan
- Department of Biotechnology
- Bhupat & Jyoti Mehta School of Biosciences
- Indian Institute of Technology Madras
- Chennai 600036
- India
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15
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Batra J, Tjong H, Zhou HX. Electrostatic effects on the folding stability of FKBP12. Protein Eng Des Sel 2016; 29:301-308. [PMID: 27381026 PMCID: PMC4955870 DOI: 10.1093/protein/gzw014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 03/28/2016] [Accepted: 04/15/2016] [Indexed: 01/17/2023] Open
Abstract
The roles of electrostatic interactions in protein folding stability have been a matter of debate, largely due to the complexity in the theoretical treatment of these interactions. We have developed computational methods for calculating electrostatic effects on protein folding stability. To rigorously test and further refine these methods, here we carried out experimental studies into electrostatic effects on the folding stability of the human 12-kD FK506 binding protein (FKBP12). This protein has a close homologue, FKBP12.6, with amino acid substitutions in only 18 of their 107 residues. Of the 18 substitutions, 8 involve charged residues. Upon mutating FKBP12 residues at these 8 positions individually into the counterparts in FKBP12.6, the unfolding free energy (ΔGu) of FKBP12 changed by -0.3 to 0.7 kcal/mol. Accumulating stabilizing substitutions resulted in a mutant with a 0.9 kcal/mol increase in stability. Additional charge mutations were grafted from a thermophilic homologue, MtFKBP17, which aligns to FKBP12 with 31% sequence identity over 89 positions. Eleven such charge mutations were studied, with ΔΔGu varying from -2.9 to 0.1 kcal/mol. The predicted electrostatic effects by our computational methods with refinements herein had a root-mean-square deviation of 0.9 kcal/mol from the experimental ΔΔGu values on 16 single mutations of FKBP12. The difference in ΔΔGu between mutations grafted from FKBP12.6 and those from MtFKBP17 suggests that more distant homologues are less able to provide guidance for enhancing folding stability.
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Affiliation(s)
- Jyotica Batra
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Present address: Department of Chemistry and Physics, Bellarmine University, 2001 Newburg Road, Louisville, KY40205, USA
| | - Harianto Tjong
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Present address: Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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16
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Su JG, Han XM, Zhao SX, Hou YX, Li XY, Qi LS, Wang JH. Impacts of the charged residues mutation S48E/N62H on the thermostability and unfolding behavior of cold shock protein: insights from molecular dynamics simulation with Gō model. J Mol Model 2016; 22:91. [DOI: 10.1007/s00894-016-2958-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/07/2016] [Indexed: 10/22/2022]
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17
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Estrada J, Echenique P, Sancho J. Predicting stabilizing mutations in proteins using Poisson-Boltzmann based models: study of unfolded state ensemble models and development of a successful binary classifier based on residue interaction energies. Phys Chem Chem Phys 2015; 17:31044-54. [PMID: 26530878 DOI: 10.1039/c5cp04348d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In many cases the stability of a protein has to be increased to permit its biotechnological use. Rational methods of protein stabilization based on optimizing electrostatic interactions have provided some fine successful predictions. However, the precise calculation of stabilization energies remains challenging, one reason being that the electrostatic effects on the unfolded state are often neglected. We have explored here the feasibility of incorporating Poisson-Boltzmann model electrostatic calculations performed on representations of the unfolded state as large ensembles of geometrically optimized conformations calculated using the ProtSA server. Using a data set of 80 electrostatic mutations experimentally tested in two-state proteins, the predictive performance of several such models has been compared to that of a simple one that considers an unfolded structure of non-interacting residues. The unfolded ensemble models, while showing correlation between the predicted stabilization values and the experimental ones, are worse than the simple model, suggesting that the ensembles do not capture well the energetics of the unfolded state. A more attainable goal is classifying potential mutations as either stabilizing or non-stabilizing, rather than accurately calculating their stabilization energies. To implement a fast classification method that can assist in selecting stabilizing mutations, we have used a much simpler electrostatic model based only on the native structure and have determined its precision using different stabilizing energy thresholds. The binary classifier developed finds 7 true stabilizing mutants out of every 10 proposed candidates and can be used as a robust tool to propose stabilizing mutations.
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Affiliation(s)
- Jorge Estrada
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain. and Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC), Mariano Esquillor s/n, Edificio I+D, 50018, Zaragoza, Spain
| | - Pablo Echenique
- Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC), Mariano Esquillor s/n, Edificio I+D, 50018, Zaragoza, Spain and Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006, Madrid, Spain
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain. and Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC), Mariano Esquillor s/n, Edificio I+D, 50018, Zaragoza, Spain
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18
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Petrauskas V, Maximowitsch E, Matulis D. Thermodynamics of Ion Pair Formations Between Charged Poly(Amino Acid)s. J Phys Chem B 2015; 119:12164-71. [PMID: 26317887 DOI: 10.1021/acs.jpcb.5b05767] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Electrostatic interactions between the positively and negatively charged amino acids in proteins play an important role in macromolecular stability, binding, and recognition. Numerous amino acids in proteins are ionizable and may exist in negatively (e.g., Glu, Asp, Cys, Tyr) or positively (e.g., Arg, Lys, His, Orn) charged form dependent on pH and their pKas. In this work, isothermal titration calorimetry was used to determine the average standard values of thermodynamic parameters (the Gibbs free energy, enthalpy, entropy, and the heat capacity) of interaction between the positively charged amino acid homopolymers (polyarginine, polylysine, and polyornithine) and the negatively charged homopolymers (polyaspartic and polyglutamic acids). These values are of potential use in the computational models of interacting proteins and other biological macromolecules. The study showed that oppositely charged poly(amino acid)s bound each other with the stoichiometry of one positive to one negative charge. Arginine bound to the negatively charged amino acids with exothermic enthalpy and higher affinity than lysine. This result also suggests that positive charges in proteins should not be considered entirely equivalent if carried by lysine or arginine. The difference in binding energy of arginine and lysine association with the negatively charged amino acids was attributed to the enthalpy of the second ionic hydrogen bond formation between the guanidine and carboxylic groups. Despite the favorable enthalpic contribution, all such ion pair formation reactions were largely entropy-driven. Consistent with previously observed ionic interactions, the positive heat capacity was always observed during the amino acid ion pair formation.
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Affiliation(s)
- Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University , V. A. Graičiu̅no 8, LT-02241 Vilnius, Lithuania
| | - Eglė Maximowitsch
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University , V. A. Graičiu̅no 8, LT-02241 Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University , V. A. Graičiu̅no 8, LT-02241 Vilnius, Lithuania
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19
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Modulation of folding energy landscape by charge-charge interactions: linking experiments with computational modeling. Proc Natl Acad Sci U S A 2015; 112:E259-66. [PMID: 25564663 DOI: 10.1073/pnas.1410424112] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The kinetics of folding-unfolding of a structurally diverse set of four proteins optimized for thermodynamic stability by rational redesign of surface charge-charge interactions is characterized experimentally. The folding rates are faster for designed variants compared with their wild-type proteins, whereas the unfolding rates are largely unaffected. A simple structure-based computational model, which incorporates the Debye-Hückel formalism for the electrostatics, was used and found to qualitatively recapitulate the experimental results. Analysis of the energy landscapes of the designed versus wild-type proteins indicates the differences in refolding rates may be correlated with the degree of frustration of their respective energy landscapes. Our simulations indicate that naturally occurring wild-type proteins have frustrated folding landscapes due to the surface electrostatics. Optimization of the surface electrostatics seems to remove some of that frustration, leading to enhanced formation of native-like contacts in the transition-state ensembles (TSE) and providing a less frustrated energy landscape between the unfolded and TS ensembles. Macroscopically, this results in faster folding rates. Furthermore, analyses of pairwise distances and radii of gyration suggest that the less frustrated energy landscapes for optimized variants are a result of more compact unfolded and TS ensembles. These findings from our modeling demonstrates that this simple model may be used to: (i) gain a detailed understanding of charge-charge interactions and their effects on modulating the energy landscape of protein folding and (ii) qualitatively predict the kinetic behavior of protein surface electrostatic interactions.
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20
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Jin B, Jeong KW, Kim Y. Structure and flexibility of the thermophilic cold-shock protein of Thermus aquaticus. Biochem Biophys Res Commun 2014; 451:402-7. [PMID: 25101648 DOI: 10.1016/j.bbrc.2014.07.127] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 07/28/2014] [Indexed: 11/15/2022]
Abstract
The thermophilic bacterium Thermus aquaticus is a well-known source of Taq polymerase. Here, we studied the structure and dynamics of the T. aquaticus cold-shock protein (Ta-Csp) to better understand its thermostability using NMR spectroscopy. We found that Ta-Csp has a five-stranded β-barrel structure with five salt bridges which are important for more rigid structure and a higher melting temperature (76 °C) of Ta-Csp compared to mesophilic and psychrophilic Csps. Microsecond to millisecond time scale exchange processes occur only at the β1-β2 surface region of the nucleic acid binding site with an average conformational exchange rate constant of 674 s(-1). The results imply that thermophilic Ta-Csp has a more rigid structure and may not need high structural flexibility to accommodate nucleic acids upon cold shock compared to its mesophile and psychrophile counterparts.
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Affiliation(s)
- Bonghwan Jin
- Department of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul 143-701, South Korea
| | - Ki-Woong Jeong
- Department of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul 143-701, South Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul 143-701, South Korea.
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21
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Ruggiero A, Dattelbaum JD, Staiano M, Berisio R, D'Auria S, Vitagliano L. A loose domain swapping organization confers a remarkable stability to the dimeric structure of the arginine binding protein from Thermotoga maritima. PLoS One 2014; 9:e96560. [PMID: 24832102 PMCID: PMC4022495 DOI: 10.1371/journal.pone.0096560] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/09/2014] [Indexed: 01/08/2023] Open
Abstract
The arginine binding protein from Thermatoga maritima (TmArgBP), a substrate binding protein (SBP) involved in the ABC system of solute transport, presents a number of remarkable properties. These include an extraordinary stability to temperature and chemical denaturants and the tendency to form multimeric structures, an uncommon feature among SBPs involved in solute transport. Here we report a biophysical and structural characterization of the TmArgBP dimer. Our data indicate that the dimer of the protein is endowed with a remarkable stability since its full dissociation requires high temperature as well as SDS and urea at high concentrations. In order to elucidate the atomic level structural properties of this intriguing protein, we determined the crystallographic structures of the apo and the arginine-bound forms of TmArgBP using MAD and SAD methods, respectively. The comparison of the liganded and unliganded models demonstrates that TmArgBP tertiary structure undergoes a very large structural re-organization upon arginine binding. This transition follows the Venus Fly-trap mechanism, although the entity of the re-organization observed in TmArgBP is larger than that observed in homologous proteins. Intriguingly, TmArgBP dimerizes through the swapping of the C-terminal helix. This dimer is stabilized exclusively by the interactions established by the swapping helix. Therefore, the TmArgBP dimer combines a high level of stability and conformational freedom. The structure of the TmArgBP dimer represents an uncommon example of large tertiary structure variations amplified at quaternary structure level by domain swapping. Although the biological relevance of the dimer needs further assessments, molecular modelling suggests that the two TmArgBP subunits may simultaneously interact with two distinct ABC transporters. Moreover, the present protein structures provide some clues about the determinants of the extraordinary stability of the biomolecule. The availability of an accurate 3D model represents a powerful tool for the design of new TmArgBP suited for biotechnological applications.
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Affiliation(s)
| | - Jonathan D Dattelbaum
- Department of Chemistry, University of Richmond, Richmond, Virginia, United States of America
| | - Maria Staiano
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Napoli, Italy
| | - Sabato D'Auria
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy
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22
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Liu CC, LiCata VJ. The stability ofTaqDNA polymerase results from a reduced entropic folding penalty; identification of other thermophilic proteins with similar folding thermodynamics. Proteins 2013; 82:785-93. [DOI: 10.1002/prot.24458] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/26/2013] [Accepted: 10/10/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Chin-Chi Liu
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana 70803
| | - Vince J. LiCata
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana 70803
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23
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Zhang L, Tang X, Cui D, Yao Z, Gao B, Jiang S, Yin B, Yuan YA, Wei D. A method to rationally increase protein stability based on the charge-charge interaction, with application to lipase LipK107. Protein Sci 2013; 23:110-6. [PMID: 24353171 DOI: 10.1002/pro.2388] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/14/2013] [Accepted: 10/21/2013] [Indexed: 11/10/2022]
Abstract
We report a suite of enzyme redesign protocol based on the surface charge-charge interaction calculation, which is potentially applied to improve the stability of an enzyme without compromising its catalytic activity. Together with the experimental validation, we have released a suite of enzyme redesign algorithm Enzyme Thermal Stability System, written based on our model, for open access to meet the needs in wet labs. Lipk107, a lipase of a versatile industrial use, was chosen to test our software. Our calculation determined that four residues, D113, D149, D213, and D253, located on the surface of LipK107 were critical to the stability of the enzyme. The model was validated with mutagenesis at these four residues followed by stability and activity tests. LipK107 mutants D113A and D149K were more resistant to thermal inactivation with ∼10°C higher half-inactivation temperature than wild-type LipK107. Moreover, mutant D149K exhibited significant retention in residual activity under constant heat, showing a 14-fold increase in the half-inactivation time at 50°C. Activity tests showed that these mutants retained the equal or higher specific activity, among which noteworthy was the mutant D253A with as much as 20% higher activity. We suggest that our protocol could be used as a general guideline to redesign protein enzymes with increased stabilities and enhanced activities.
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Affiliation(s)
- Lujia Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing University of Technology, Nanjing, Jiangsu 211800, People's Republic of China
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24
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Lee J, Jeong KW, Jin B, Ryu KS, Kim EH, Ahn JH, Kim Y. Structural and dynamic features of cold-shock proteins of Listeria monocytogenes, a psychrophilic bacterium. Biochemistry 2013; 52:2492-504. [PMID: 23506337 DOI: 10.1021/bi301641b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cold-shock proteins (Csps), proteins expressed when the ambient temperature drops below the growth-supporting temperature, bind to single-stranded nucleic acids and act as RNA chaperones to regulate translation. Listeria monocytogenes is a psychrophilic food-borne pathogen that is problematic for the food industry. Structures of Csps from psychrophilic bacteria have not yet been studied. Despite dramatic differences in the thermostability of Csps of various thermophilic microorganisms, these proteins share a high degree of primary sequence homology and a high degree of three-dimensional structural similarity. Here, we investigated the structural and dynamic features as well as the thermostability of L. monocytogenes CspA (Lm-CspA). Lm-CspA has a five-stranded β-barrel structure with hydrophobic core packing and two salt bridges. When heptathymidine (dT(7)) binds, values for the heteronuclear nuclear Overhauser effect and order parameters of residues in surface loop regions near nucleic acid binding sites increase dramatically. Moreover, Carr-Purcell-Meiboom-Gill experiments showed that slow motions observed for the nucleic acid binding residues K7, W8, F15, F27, and R56 disappeared in Lm-CspA-dT(7). Lm-CspA is less thermostable than mesophilic and thermophilic Csps, with a lower melting temperature (40 °C). The structural flexibility that accompanies longer surface loops and less hydrophobic core packing and a number of salt bridges and unfavorable electrostatic repulsion are likely key factors in the low thermostability of Lm-CspA. This implies that the large conformational flexibility of psychrophilic Lm-CspA, which more easily accommodates nucleic acids at low temperature, is required for RNA chaperone function under cold-shock conditions and for the cold adaptation of L. monocytogenes.
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Affiliation(s)
- Juho Lee
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, South Korea
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25
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Sokalingam S, Madan B, Raghunathan G, Lee SG. In silico study on the effect of surface lysines and arginines on the electrostatic interactions and protein stability. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0516-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Chin IS, Murad AMA, Mahadi NM, Nathan S, Bakar FDA. Thermal stability engineering of Glomerella cingulata cutinase. Protein Eng Des Sel 2013; 26:369-75. [DOI: 10.1093/protein/gzt007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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27
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Tripathi S, Makhatadze GI, Garcia AE. Backtracking due to residual structure in the unfolded state changes the folding of the third fibronectin type III domain from tenascin-C. J Phys Chem B 2013; 117:800-10. [PMID: 23268597 DOI: 10.1021/jp310046k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual structure in the unfolded state of a protein may play a crucial role in folding and stability. In the present study, using an all (heavy)-atom structure based model and replica exchange molecular dynamics simulations, we explored the folding landscape of the third fibronectin type III domain from tenascin-C (TNfn3). Specifically, both the wild type (WT) and a variant with two additional amino acids, Gly-Leu (GL), at the C-terminus (WT(+GL)) were studied. We found that, although both domains of TNfn3 are topologically frustrated, the early formation of the native contacts from the C-terminal end of WT(+GL) causes more "backtracking" than in the WT. As a result, the WT exhibits a two-state folding behavior with a broad transition-state ensemble, whereas the WT(+GL) folds through a metastable intermediate state. Furthermore, our study confirmed that the core of both proteins is conformationally heterogeneous and noncompact, and folds late mainly due to backtracking of the part of the core. Finally, in agreement with the previous experimental studies, our results clearly demonstrated distinct thermodynamic behavior of the two proteins with WT(+GL) being more stable.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
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28
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Naganathan AN. Predictions from an Ising-like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics. J Chem Theory Comput 2012; 8:4646-56. [PMID: 26605620 DOI: 10.1021/ct300676w] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Charged residues on the surface of a protein are known hot-spots for post-translational modification, protein/ligand-binding, and tuning conformational stabilities. Recent experimental evidence points to the fact that surface electrostatics can also modulate thermodynamic barriers and hence folding mechanisms. To probe for this behavior across different proteins, we develop a novel version of the Wako-Saitô-Muñoz-Eaton (WSME) model in which we include an electrostatic potential term in the energy function while simplifying the treatment of solvation free energy. Both of the energy terms are obtained by quantitatively fitting the model to differential scanning calorimetry (DSC) experiments that carry critical information on the protein partition function. We characterize four sets of structural/functional homologues (HEWL/BLA, CspB, engrailed, α-spectrin) either by fitting the experimental data of a single domain in the homologous set and predicting the conformational behavior of the rest with the same set of parameters or by performing semiblind predictions. The model with the added electrostatic term is able to successfully reproduce the order of thermodynamic stabilities and relaxation rates of most of the homologues. In parallel, we predict diverse conformational features including a wide range of thermodynamic barriers (∼9-40 kJ/mol), broad native ensembles in helical proteins, structured unfolded states and intermediates, rugged folding landscapes, and further provide an independent protein-specific estimate of the folding speed limit at 298 K (1/(7-300 μs)). Our results are evidence that protein surface electrostatics can be tailored to not only engineer stabilities but also folding mechanisms and the ruggedness of the underlying landscape.
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Affiliation(s)
- Athi N Naganathan
- Department of Biotechnology, Indian Institute of Technology Madras , Chennai-600036, India
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29
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Sokalingam S, Raghunathan G, Soundrarajan N, Lee SG. A study on the effect of surface lysine to arginine mutagenesis on protein stability and structure using green fluorescent protein. PLoS One 2012; 7:e40410. [PMID: 22792305 PMCID: PMC3392243 DOI: 10.1371/journal.pone.0040410] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/06/2012] [Indexed: 11/17/2022] Open
Abstract
Two positively charged basic amino acids, arginine and lysine, are mostly exposed to protein surface, and play important roles in protein stability by forming electrostatic interactions. In particular, the guanidinium group of arginine allows interactions in three possible directions, which enables arginine to form a larger number of electrostatic interactions compared to lysine. The higher pKa of the basic residue in arginine may also generate more stable ionic interactions than lysine. This paper reports an investigation whether the advantageous properties of arginine over lysine can be utilized to enhance protein stability. A variant of green fluorescent protein (GFP) was created by mutating the maximum possible number of lysine residues on the surface to arginines while retaining the activity. When the stability of the variant was examined under a range of denaturing conditions, the variant was relatively more stable compared to control GFP in the presence of chemical denaturants such as urea, alkaline pH and ionic detergents, but the thermal stability of the protein was not changed. The modeled structure of the variant indicated putative new salt bridges and hydrogen bond interactions that help improve the rigidity of the protein against different chemical denaturants. Structural analyses of the electrostatic interactions also confirmed that the geometric properties of the guanidinium group in arginine had such effects. On the other hand, the altered electrostatic interactions induced by the mutagenesis of surface lysines to arginines adversely affected protein folding, which decreased the productivity of the functional form of the variant. These results suggest that the surface lysine mutagenesis to arginines can be considered one of the parameters in protein stability engineering.
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Affiliation(s)
- Sriram Sokalingam
- Department of Chemical Engineering, Pusan National University, Busan, South Korea
| | - Govindan Raghunathan
- Department of Chemical Engineering, Pusan National University, Busan, South Korea
| | | | - Sun-Gu Lee
- Department of Chemical Engineering, Pusan National University, Busan, South Korea
- * E-mail:
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30
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Schmid FX. Lessons about Protein Stability from in vitro Selections. Chembiochem 2011; 12:1501-7. [DOI: 10.1002/cbic.201100018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Indexed: 11/07/2022]
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31
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D’Auria G, Esposito C, Falcigno L, Calvanese L, Iaccarino E, Ruggiero A, Pedone C, Pedone E, Berisio R. Dynamical properties of cold shock protein A from Mycobacterium tuberculosis. Biochem Biophys Res Commun 2010; 402:693-8. [DOI: 10.1016/j.bbrc.2010.10.086] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 10/20/2010] [Indexed: 10/18/2022]
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32
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Fu H, Grimsley G, Scholtz JM, Pace CN. Increasing protein stability: importance of DeltaC(p) and the denatured state. Protein Sci 2010; 19:1044-52. [PMID: 20340133 DOI: 10.1002/pro.381] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Increasing the conformational stability of proteins is an important goal for both basic research and industrial applications. In vitro selection has been used successfully to increase protein stability, but more often site-directed mutagenesis is used to optimize the various forces that contribute to protein stability. In previous studies, we showed that improving electrostatic interactions on the protein surface and improving the beta-turn sequences were good general strategies for increasing protein stability, and used them to increase the stability of RNase Sa. By incorporating seven of these mutations in RNase Sa, we increased the stability by 5.3 kcal/mol. Adding one more mutation, D79F, gave a total increase in stability of 7.7 kcal/mol, and a melting temperature 28 degrees C higher than the wild-type enzyme. Surprisingly, the D79F mutation lowers the change in heat capacity for folding, DeltaC(p), by 0.6 kcal/mol/K. This suggests that this mutation stabilizes structure in the denatured state ensemble. We made other mutants that give some insight into the structure present in the denatured state. Finally, the thermodynamics of folding of these stabilized variants of RNase Sa are compared with those observed for proteins from thermophiles.
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Affiliation(s)
- Hailong Fu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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33
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MOTONO C, GROMIHA MM. Dynamic and Structural Analysis of Hyperthermophilic Cold Shock Protein Stability. KOBUNSHI RONBUNSHU 2010. [DOI: 10.1295/koron.67.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chie MOTONO
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
| | - M. Michael GROMIHA
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
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34
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Recombinant Expression, Isotope Labeling, and Purification of Cold shock Protein from Colwellia psychrerythraea for NMR Study. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.11.2647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Basu S, Sen S. Turning a Mesophilic Protein into a Thermophilic One: A Computational Approach Based on 3D Structural Features. J Chem Inf Model 2009; 49:1741-50. [DOI: 10.1021/ci900183m] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Sohini Basu
- Molecular Modeling Section, Biolab, Chembiotek, TCG Lifesciences Ltd., Bengal Intelligent Park, Tower-B 2nd Floor, Block-EP & GP, Sector-V, Salt Lake Electronic Complex, Calcutta-700091, India
| | - Srikanta Sen
- Molecular Modeling Section, Biolab, Chembiotek, TCG Lifesciences Ltd., Bengal Intelligent Park, Tower-B 2nd Floor, Block-EP & GP, Sector-V, Salt Lake Electronic Complex, Calcutta-700091, India
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36
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Rational stabilization of enzymes by computational redesign of surface charge-charge interactions. Proc Natl Acad Sci U S A 2009; 106:2601-6. [PMID: 19196981 DOI: 10.1073/pnas.0808220106] [Citation(s) in RCA: 177] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here, we report the application of a computational approach that allows the rational design of enzymes with enhanced thermostability while retaining full enzymatic activity. The approach is based on the optimization of the energy of charge-charge interactions on the protein surface. We experimentally tested the validity of the approach on 2 human enzymes, acylphosphatase (AcPh) and Cdc42 GTPase, that differ in size (98 vs. 198-aa residues, respectively) and tertiary structure. We show that the designed proteins are significantly more stable than the corresponding WT proteins. The increase in stability is not accompanied by significant changes in structure, oligomerization state, or, most importantly, activity of the designed AcPh or Cdc42. This success of the design methodology suggests that it can be universally applied to other enzymes, on its own or in combination with the other strategies based on redesign of the interactions in the protein core.
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37
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Schweiker KL, Makhatadze GI. Protein stabilization by the rational design of surface charge-charge interactions. Methods Mol Biol 2009; 490:261-83. [PMID: 19157087 DOI: 10.1007/978-1-59745-367-7_11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The design of proteins with increased stability has many important applications in biotechnology. In recent years, strategies involving directed evolution, sequence-based design, or computational design have proven successful for generating stabilized proteins. A brief overview of the various methods that have been used to increase protein stability is presented, followed by a detailed example of how the rational design of surface charge-charge interactions has provided a robust method for protein stabilization.
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Affiliation(s)
- Katrina L Schweiker
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
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38
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Schweiker KL, Makhatadze GI. A computational approach for the rational design of stable proteins and enzymes: optimization of surface charge-charge interactions. Methods Enzymol 2009; 454:175-211. [PMID: 19216927 DOI: 10.1016/s0076-6879(08)03807-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The design of stable proteins and enzymes is not only of particular biotechnological importance, but also addresses some important fundamental questions. While there are a number of different options available for designing or engineering stable proteins, the field of computational design provides fast and universal methods for stabilizing proteins of interest. One of the successful computational design strategies focuses on stabilizing proteins through the optimization of charge-charge interactions on the protein surface. By optimizing surface interactions, it is possible to alleviate some of the challenges that accompany efforts to redesign the protein core. The rational design of surface charge-charge interactions also allows one to optimize only the interactions that are distant from binding sites or active sites, making it possible to increase stability without adversely affecting activity. The optimization of surface charge-charge interactions is discussed in detail along with the experimental evidence to demonstrate that this is a robust and universal approach to designing proteins with enhanced stability.
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Affiliation(s)
- Katrina L Schweiker
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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39
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Ruggiero A, Masullo M, Ruocco MR, Grimaldi P, Lanzotti MA, Arcari P, Zagari A, Vitagliano L. Structure and stability of a thioredoxin reductase from Sulfolobus solfataricus: a thermostable protein with two functions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:554-62. [PMID: 19110078 DOI: 10.1016/j.bbapap.2008.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Revised: 11/13/2008] [Accepted: 11/14/2008] [Indexed: 10/21/2022]
Abstract
Recent investigations have demonstrated that disulfide bridges may play a crucial role in the stabilization of proteins in hyperthermophilic organisms. A major role in the process of disulfide formation is played by ubiquitous proteins belonging to the thioredoxin superfamily, which includes thioredoxins (Trx), thioredoxin reductases (TrxR), and disulfide oxidases/isomerases (PDO/PDI). Here we report a characterization of the structure and stability of the TrxR (SsTrxRB3) isolated from the archaeon Sulfolobus solfataricus. This protein is particularly interesting since it is able to process different substrates (Trxs and PDO) and it is endowed with an additional NADH oxidase activity. The crystal structure of the wild-type enzyme, of its complex with NADP and of the C147A mutant provides interesting clues on the enzyme function. In contrast to what is observed for class II TrxRs, in the structure of the oxidized enzyme, the FAD binding site is occupied by a partially disordered NAD molecule. In the active site of the C147A mutant, which exhibits a marginal NADH oxidase activity, the FAD is canonically bound to the enzyme. Molecular modeling indicates that a FAD molecule can be accommodated in the site of the reduced SsTrxRB3. Depending on the oxidation state, SsTrxRB3 can bind a different cofactor in its active site. This peculiar feature has been related to its dual activity. Denaturation experiments followed by circular dichroism indicate that electrostatic interactions play an important role in the stabilization of this thermostable protein. The analysis of the enzyme 3D-structure has also provided insights into the bases of SsTrxRB3 stability.
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Affiliation(s)
- Alessia Ruggiero
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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40
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Changing the Determinants of Protein Stability from Covalent to Non-Covalent Interactions by In Vitro Evolution: A Structural and Energetic Analysis. J Mol Biol 2008; 381:1040-54. [DOI: 10.1016/j.jmb.2008.06.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 06/11/2008] [Indexed: 11/16/2022]
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41
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Motono C, Gromiha MM, Kumar S. Thermodynamic and kinetic determinants ofThermotoga maritimacold shock protein stability: A structural and dynamic analysis. Proteins 2008; 71:655-69. [DOI: 10.1002/prot.21729] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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42
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Koga Y, Katsumi R, You DJ, Matsumura H, Takano K, Kanaya S. Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form. FEBS J 2008; 275:2632-43. [DOI: 10.1111/j.1742-4658.2008.06410.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Sawano M, Yamamoto H, Ogasahara K, Kidokoro SI, Katoh S, Ohnuma T, Katoh E, Yokoyama S, Yutani K. Thermodynamic basis for the stabilities of three CutA1s from Pyrococcus horikoshii,Thermus thermophilus, and Oryza sativa, with unusually high denaturation temperatures. Biochemistry 2007; 47:721-30. [PMID: 18154307 DOI: 10.1021/bi701761m] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to elucidate the stabilization mechanism of CutA1 from Pyrococcus horikoshii (PhCutA1) with a denaturation temperature of nearly 150 degrees C, GuHCl denaturation and heat denaturation were examined at neutral and acidic pHs. As a comparison, CutA1 proteins from Thermus thermophilus (TtCutA1) and Oryza sativa (OsCutA1) were also examined, which have lower optimum growth temperatures of 75 and 28 degrees C, respectively, than that (98 degrees C) of P. horikoshii. GuHCl-induced unfolding and refolding curves of the three proteins showed hysteresis effects due to an unusually slow unfolding rate. The midpoints of refolding for PhCutA1, TtCutA1 and OsCutA1 were 5.7 M, 3.3 M, and 2.3 M GuHCl, respectively, at pH 8.0 and 37 degrees C. DSC experiments with TtCutA1 and OsCutA1 showed that the denaturation temperatures were remarkably high, 112.8 and 97.3 degrees C, respectively, at pH 7.0 and that the good heat reversibility was amenable to thermodynamic analyses. At acidic pH, TtCutA1 showed higher stability to both heat and denaturant than PhCutA1. Combined with the data for DSC and denaturant denaturation, the unfolding Gibbs energy of PhCutA1 could be depicted as a function of temperature. It was experimentally revealed that (1) the unusually high stability of PhCutA1 basically originates from a common trimer structure of the three proteins, (2) the stability of PhCutA1 is superior to those of the other two CutA1s over all temperatures above 0 degrees C at neutral pH, due to the decrease in both enthalpy and entropy, and (3) ion pairs of PhCutA1 contribute to the unusually high stability at neutral pH.
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Affiliation(s)
- Masahide Sawano
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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44
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Schweiker KL, Zarrine-Afsar A, Davidson AR, Makhatadze GI. Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions. Protein Sci 2007; 16:2694-702. [PMID: 18029422 PMCID: PMC2222822 DOI: 10.1110/ps.073091607] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2007] [Revised: 08/29/2007] [Accepted: 08/29/2007] [Indexed: 10/22/2022]
Abstract
Computational design of surface charge-charge interactions has been demonstrated to be an effective way to increase both the thermostability and the stability of proteins. To test the robustness of this approach for proteins with predominantly beta-sheet secondary structure, the chicken isoform of the Fyn SH3 domain was used as a model system. Computational analysis of the optimal distribution of surface charges showed that the increase in favorable energy per substitution begins to level off at five substitutions; hence, the designed Fyn sequence contained four charge reversals at existing charged positions and one introduction of a new charge. Three additional variants were also constructed to explore stepwise contributions of these substitutions to Fyn stability. The thermodynamic stabilities of the variants were experimentally characterized using differential scanning calorimetry and far-UV circular dichroism spectroscopy and are in very good agreement with theoretical predictions from the model. The designed sequence was found to have increased the melting temperature, DeltaT (m) = 12.3 +/- 0.2 degrees C, and stability, DeltaDeltaG(25 degrees C) = 7.1 +/- 2.2 kJ/mol, relative to the wild-type protein. The experimental data suggest that a significant increase in stability can be achieved through a very small number of amino acid substitutions. Consistent with a number of recent studies, the presented results clearly argue for a seminal role of surface charge-charge interactions in determining protein stability and suggest that the optimization of surface interactions can be an attractive strategy to complement algorithms optimizing interactions in the protein core to further enhance protein stability.
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Affiliation(s)
- Katrina L Schweiker
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
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45
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Wen X, Patel KM, Russell BS, Bren KL. Effects of heme pocket structure and mobility on cytochrome c stability. Biochemistry 2007; 46:2537-44. [PMID: 17279778 DOI: 10.1021/bi602380v] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Unfolding thermodynamics of a thermophilic cytochrome c552 from Hydrogenobacter thermophilus (Ht cyt c552) and its mesophilic homologue from Pseudomonas aeruginosa (Pa cyt c551) as well as two heme pocket point mutants (Ht-Q64N and Pa-N64Q) are characterized by determination of protein stability curves (plots of unfolding free energy, DeltaG, vs T). These proteins show revealing differences in heme pocket hydrogen bonding and mobility. It previously has been shown that Asn64 in Pa cyt c551 and in Ht-Q64N interacts with the heme axial Met to fix it in a single conformation [Wen, X., and Bren, K. L. (2005) Biochemistry 44, 5225-5233]. In Ht cyt c552 and Pa-N64Q, Gln64 does not interact with the axial Met; in these variants the axial Met samples more than one conformation [Wen, X., and Bren, K. L. (2005) Inorg. Chem. 44, 8587-8593]. Here it is demonstrated that, relative to wild type, Pa-N64Q displays enhanced stability with an increase in unfolding free energy (DeltaDeltaG) of 7.1 kJ/mol and an increase in denaturation temperature (DeltaTm) of 8 degrees C. Correspondingly, Ht-Q64N is less stable than Ht cyt c552, with a DeltaDeltaG of -10 kJ/mol and a DeltaTm of -10 degrees C. Analysis of unfolding thermodynamics indicates that the net changes in stability resulting from the position 64 mutations are primarily attributable to entropic factors. For Pa-N64Q (Ht-Q64N) it is proposed that the favorable release (unfavorable burial) of residue 64 is the dominant factor impacting stability. The mobility of the axial Met also is proposed to contribute. These results provide a specific illustration of how amino acid side chain mobility and burial or release contribute to protein stability.
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Affiliation(s)
- Xin Wen
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
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46
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Gribenko AV, Makhatadze GI. Role of the Charge–Charge Interactions in Defining Stability and Halophilicity of the CspB Proteins. J Mol Biol 2007; 366:842-56. [PMID: 17188709 DOI: 10.1016/j.jmb.2006.11.061] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Revised: 10/20/2006] [Accepted: 11/17/2006] [Indexed: 11/28/2022]
Abstract
Charge-charge interactions on the surface of native proteins are important for protein stability and can be computationally redesigned in a rational way to modulate protein stability. Such computational effort led to an engineered protein, CspB-TB that has the same core as the mesophilic cold shock protein CspB-Bs from Bacillus subtilis, but optimized distribution of charge-charge interactions on the surface. The CspB-TB protein shows an increase in the transition temperature by 20 degrees C relative to the unfolding temperature of CspB-Bs. The CspB-TB and CspB-Bs protein pair offers a unique opportunity to further explore the energetics of charge-charge interactions as the substitutions at the same sequence positions are done in largely similar structural but different electrostatic environments. In particular we addressed two questions. What is the contribution of charge-charge interactions in the unfolded state to the protein stability and how amino acid substitutions modulate the effect of increase in ionic strength on protein stability (i.e. protein halophilicity). To this end, we experimentally measured the stabilities of over 100 variants of CspB-TB and CspB-Bs proteins with substitutions at charged residues. We also performed computational modeling of these protein variants. Analysis of the experimental and computational data allowed us to conclude that the charge-charge interactions in the unfolded state of two model proteins CspB-Bs and CspB-TB are not very significant and computational models that are based only on the native state structure can adequately, i.e. qualitatively (stabilizing versus destabilizing) and semi-quantitatively (relative rank order), predict the effects of surface charge neutralization or reversal on protein stability. We also show that the effect of ionic strength on protein stability (protein halophilicity) appears to be mainly due to the screening of the long-range charge-charge interactions.
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Affiliation(s)
- Alexey V Gribenko
- Department of Biochemistry and Molecular Biology, Penn State University, College of Medicine, Hershey, PA 17033, USA
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47
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Abstract
PHEPS (pH-dependent Protein Electrostatics Server) is a web service for fast prediction and experiment planning support, as well as for correlation and analysis of experimentally obtained results, reflecting charge-dependent phenomena in globular proteins. Its implementation is based on long-term experience (PHEI package) and the need to explain measured physicochemical characteristics at the level of protein atomic structure. The approach is semi-empirical and based on a mean field scheme for description and evaluation of global and local pH-dependent electrostatic properties: protein proton binding; ionic sites proton population; free energy electrostatic term; ionic groups proton affinities (pKa,i) and their Coulomb interaction with whole charge multipole; electrostatic potential of whole molecule at fixed pH and pH-dependent local electrostatic potentials at user-defined set of points. The speed of calculation is based on fast determination of distance-dependent pair charge-charge interactions as empirical three exponential function that covers charge–charge, charge–dipole and dipole–dipole contributions. After atomic coordinates input, all standard parameters are used as defaults to facilitate non-experienced users. Special attention was given to interactive addition of non-polypeptide charges, extra ionizable groups with intrinsic pKas or fixed ions. The output information is given as plain-text, readable by ‘RasMol’, ‘Origin’ and the like. The PHEPS server is accessible at .
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Affiliation(s)
| | - Boris P. Atanasov
- To whom correspondence should be addressed. Tel: +359-2 960 6123; Fax: +359-2 870 0225;
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Tanaka T, Sawano M, Ogasahara K, Sakaguchi Y, Bagautdinov B, Katoh E, Kuroishi C, Shinkai A, Yokoyama S, Yutani K. Hyper-thermostability of CutA1 protein, with a denaturation temperature of nearly 150 °C. FEBS Lett 2006; 580:4224-30. [PMID: 16831434 DOI: 10.1016/j.febslet.2006.06.084] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 06/06/2006] [Accepted: 06/27/2006] [Indexed: 10/24/2022]
Abstract
We found that the CutA1 protein, from Pyrococcus horikoshii (PhCutA1), has an extremely high denaturation temperature (T(d)) of nearly 150 degrees C, which exceeds the highest record determined by DSC by about 30 degrees C. To elucidate the mechanism of the ultra-high stability of PhCutA1, we analyzed the crystal structures of CutA1 proteins from three different sources, P. horikoshii, Thermus thermophilus, and Escherichia coli, with different growth temperatures (98, 75, and 37 degrees C). This analysis revealed that the remarkably increased number of ion pairs in the monomeric structure contributes to the stabilization of the trimeric structure and plays an important role in enhancing the T(d), up to 150 degrees C, for PhCutA1.
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Affiliation(s)
- Tomoyuki Tanaka
- RIKEN SPring-8 Center, Harima Institute, Kouto, Sayo, Hyogo 679-5148, Japan
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Guo Z, Xu LN, Zhou LX. The Mechanism of TC230′s Thermostability: A Molecular Dynamics Simulation Study. J Biomol Struct Dyn 2006; 23:603-12. [PMID: 16615806 DOI: 10.1080/07391102.2006.10507085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The quasielastic neutron scattering index beta and the modulus of a protein's quasi-electric dipole moment were utilized to quantitate the thermostability of wildtype TC23O and its mutants. Charged residues Arg314, Glu246, Glu291, and some prolines near the C-terminus of the sequence (Pro228, Pro296, and Pro308) were identified to be critical for the thermostability of wildtype TC23O according to these two criteria. By analyzing the molecular conformation changes during the simulation, it was demonstrated how the mutant P228S was destabilized by disrupting two salt-bridges Asp116OD1-Lys215N and Glu210OE1-Lys217N at an adjacent beta-turn. The destabilization of P296S also shown to be intimate correlated with the break down of ion pair Lys188N-Glu291OE1. The sensitivity of its electrostatic network to the local structure is an important feature. It reveals that the 'proline effect' and electrostatic interactions together influences the thermostability of TC23O a lot.
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Affiliation(s)
- Zhi Guo
- Surface Physics National Key Laboratory, Department of Physics, Fudan University, Shanghai 200433, China.
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Gribenko AV, Keiffer TR, Makhatadze GI. Amino acid substitutions affecting protein dynamics in eglin C do not affect heat capacity change upon unfolding. Proteins 2006; 64:295-300. [PMID: 16705642 DOI: 10.1002/prot.20974] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The heat capacity change upon unfolding (deltaC(p)) is a thermodynamic parameter that defines the temperature dependence of the thermodynamic stability of proteins; however, physical basis of the heat capacity change is not completely understood. Although empirical surface area-based calculations can predict heat capacity changes reasonably well, accumulating evidence suggests that changes in hydration of those surfaces is not the only parameter contributing to the observed heat capacity changes upon unfolding. Because packing density in the protein interior is similar to that observed in organic crystals, we hypothesized that changes in protein dynamics resulting in increased rigidity of the protein structure might contribute to the observed heat capacity change upon unfolding. Using differential scanning calorimetry we characterized the thermodynamic behavior of a serine protease inhibitor eglin C and two eglin C variants with altered native state dynamics, as determined by NMR. We found no evidence of changes in deltaC(p) in either of the variants, suggesting that changes in rigidity do not contribute to the heat capacity change upon unfolding in this model system.
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Affiliation(s)
- Alexey V Gribenko
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, USA
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