51
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Leng F, Xu C, Xia XY, Pan XM. Establishing knowledge on the sequence arrangement pattern of nucleated protein folding. PLoS One 2017; 12:e0173583. [PMID: 28273143 PMCID: PMC5342263 DOI: 10.1371/journal.pone.0173583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 02/22/2017] [Indexed: 11/21/2022] Open
Abstract
The heat-tolerance mechanisms of (hyper)thermophilic proteins provide a unique opportunity to investigate the unsolved protein folding problem. In an attempt to determine whether the interval between residues in sequence might play a role in determining thermostability, we constructed a sequence interval-dependent value function to calculate the residue pair frequency. Additionally, we identified a new sequence arrangement pattern, where like-charged residues tend to be adjacently assembled, while unlike-charged residues are distributed over longer intervals, using statistical analysis of a large sequence database. This finding indicated that increasing the intervals between unlike-charged residues can increase protein thermostability, with the arrangement patterns of these charged residues serving as thermodynamically favorable nucleation points for protein folding. Additionally, we identified that the residue pairs K-E, R-E, L-V and V-V involving long sequence intervals play important roles involving increased protein thermostability. This work demonstrated a novel approach for considering sequence intervals as keys to understanding protein folding. Our findings of novel relationships between residue arrangement and protein thermostability can be used in industry and academia to aid the design of thermostable proteins.
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Affiliation(s)
- Fei Leng
- Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chao Xu
- Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xia-Yu Xia
- Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xian-Ming Pan
- Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail:
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52
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Bharatiy S, Hazra M, Paul M, Mohapatra S, Samantaray D, Dubey R, Sanyal S, Datta S, Hazra S. In Silico Designing of an Industrially Sustainable Carbonic Anhydrase Using Molecular Dynamics Simulation. ACS OMEGA 2016; 1:1081-1103. [PMID: 30023502 PMCID: PMC6044688 DOI: 10.1021/acsomega.6b00041] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/15/2016] [Indexed: 06/08/2023]
Abstract
Carbonic anhydrase (CA) is a family of metalloenzymes that has the potential to sequestrate carbon dioxide (CO2) from the environment and reduce pollution. The goal of this study is to apply protein engineering to develop a modified CA enzyme that has both higher stability and activity and hence could be used for industrial purposes. In the current study, we have developed an in silico method to understand the molecular basis behind the stability of CA. We have performed comparative molecular dynamics simulation of two homologous α-CA, one of thermophilic origin (Sulfurihydrogenibium sp.) and its mesophilic counterpart (Neisseria gonorrhoeae), for 100 ns each at 300, 350, 400, and 500 K. Comparing the trajectories of two proteins using different stability-determining factors, we have designed a highly thermostable version of mesophilic α-CA by introducing three mutations (S44R, S139E, and K168R). The designed mutant α-CA maintains conformational stability at high temperatures. This study shows the potential to develop industrially stable variants of enzymes while maintaining high activity.
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Affiliation(s)
- Sachin
Kumar Bharatiy
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Mousumi Hazra
- Department
of Botany and Microbiology, Gurukula Kangri
University, Haridwar 249404, Uttarakhand, India
| | - Manish Paul
- Department
of Microbiology, Orissa University of Agriculture
and Technology, Bhubaneswar 751003, Odisha, India
| | - Swati Mohapatra
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Deviprasad Samantaray
- Department
of Microbiology, Orissa University of Agriculture
and Technology, Bhubaneswar 751003, Odisha, India
| | - Ramesh
Chandra Dubey
- Department
of Botany and Microbiology, Gurukula Kangri
University, Haridwar 249404, Uttarakhand, India
| | - Shourjya Sanyal
- Complex
and Adaptive System Laboratory, School of Physics, University College Dublin, Dublin 4, Ireland
| | - Saurav Datta
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Saugata Hazra
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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53
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Physical and molecular bases of protein thermal stability and cold adaptation. Curr Opin Struct Biol 2016; 42:117-128. [PMID: 28040640 DOI: 10.1016/j.sbi.2016.12.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/15/2016] [Accepted: 12/11/2016] [Indexed: 11/20/2022]
Abstract
The molecular bases of thermal and cold stability and adaptation, which allow proteins to remain folded and functional in the temperature ranges in which their host organisms live and grow, are still only partially elucidated. Indeed, both experimental and computational studies fail to yield a fully precise and global physical picture, essentially because all effects are context-dependent and thus quite intricate to unravel. We present a snapshot of the current state of knowledge of this highly complex and challenging issue, whose resolution would enable large-scale rational protein design.
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54
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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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55
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Sobhani-Damavandifar Z, Hosseinkhani S, Sajedi RH. Proposed ionic bond between Arg300 and Glu270 and Glu271 are not involved in inactivation of a mutant firefly luciferase (LRR). Enzyme Microb Technol 2016; 86:17-24. [PMID: 26992788 DOI: 10.1016/j.enzmictec.2016.01.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/18/2016] [Accepted: 01/21/2016] [Indexed: 10/22/2022]
Abstract
The weakness of firefly luciferase is its rapid inactivation. Many studies have been done to develop thermostable luciferases. One of these modifications was LRR mutant in which the Leu300 was substituted with Arg in the E(354)RR(356)Lampyris turkestanicus luciferase as template. LRR was more thermostable than the wild type but with only 0.02% activity. In this study, site-directed mutagenesis was used to change the proposed ionic bond between the Arg and two neighboring residues (Glu270 and Glu271), to understand if the induced interactions were responsible for inactivation in LRR. Our results showed that substitution of Glu270 and 271 with Ala removed the interactions but the activity of enzyme did not return. The E270A mutant was more active than LRR but the E271A and E270A/E271A mutants were inactive. Fluorescence and CD measurements showed that these mutations were accompanied by conformational changes. Extrinsic fluorescence measurement and obtained quenching data by KI and acrylamide also confirmed that the mutants were less compact than the LRR enzyme. In conclusion, in LRR, the interactions between Arg300 and Glu270 and Glu271 were not responsible for the enzyme inactivation and it is proposed that the enzyme inactivation is due to conformational changes of LRR mutant of firefly luciferase.
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Affiliation(s)
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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56
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Kovacic F, Mandrysch A, Poojari C, Strodel B, Jaeger KE. Structural features determining thermal adaptation of esterases. Protein Eng Des Sel 2016; 29:65-76. [PMID: 26647400 PMCID: PMC5943684 DOI: 10.1093/protein/gzv061] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 11/14/2022] Open
Abstract
The adaptation of microorganisms to extreme living temperatures requires the evolution of enzymes with a high catalytic efficiency under these conditions. Such extremophilic enzymes represent valuable tools to study the relationship between protein stability, dynamics and function. Nevertheless, the multiple effects of temperature on the structure and function of enzymes are still poorly understood at the molecular level. Our analysis of four homologous esterases isolated from bacteria living at temperatures ranging from 10°C to 70°C suggested an adaptation route for the modulation of protein thermal properties through the optimization of local flexibility at the protein surface. While the biochemical properties of the recombinant esterases are conserved, their thermal properties have evolved to resemble those of the respective bacterial habitats. Molecular dynamics simulations at temperatures around the optimal temperatures for enzyme catalysis revealed temperature-dependent flexibility of four surface-exposed loops. While the flexibility of some loops increased with raising the temperature and decreased with lowering the temperature, as expected for those loops contributing to the protein stability, other loops showed an increment of flexibility upon lowering and raising the temperature. Preserved flexibility in these regions seems to be important for proper enzyme function. The structural differences of these four loops, distant from the active site, are substantially larger than for the overall protein structure, indicating that amino acid exchanges within these loops occurred more frequently thereby allowing the bacteria to tune atomic interactions for different temperature requirements without interfering with the overall enzyme function.
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Affiliation(s)
- Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426 Juelich, Germany
| | - Agathe Mandrysch
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426 Juelich, Germany
| | - Chetan Poojari
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Juelich GmbH, D-52426 Juelich, Germany Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Birgit Strodel
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Juelich GmbH, D-52426 Juelich, Germany Institute of Theoretical and Computational Chemistry, Heinrich-Heine-University Duesseldorf, D-40225 Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426 Juelich, Germany Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Juelich GmbH, D-52426 Juelich, Germany
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57
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Chakraborty D, Taly A, Sterpone F. Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins. J Phys Chem B 2015; 119:12760-70. [PMID: 26335353 DOI: 10.1021/acs.jpcb.5b05791] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a systematic computational investigation of the internal hydration of a set of homologous proteins of different stability content and molecular complexities. The goal of the study is to verify whether structural water can be part of the molecular mechanisms ensuring enhanced stability in thermophilic enzymes. Our free-energy calculations show that internal hydration in the thermophilic variants is generally more favorable, and that the cumulated effect of wetting multiple sites results in a meaningful contribution to stability. Moreover, thanks to a more effective capability to retain internal water, some thermophilic proteins benefit by a systematic gain from internal wetting up to their optimal working temperature. Our work supports the idea that internal wetting can be viewed as an alternative molecular variable to be tuned for increasing protein stability.
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Affiliation(s)
- Debashree Chakraborty
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Antoine Taly
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité , 13 rue Pierre et Marie Curie, 75005 Paris, France
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58
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Xie NZ, Du QS, Li JX, Huang RB. Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design. PLoS One 2015; 10:e0137113. [PMID: 26339784 PMCID: PMC4560430 DOI: 10.1371/journal.pone.0137113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/12/2015] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions. METHODS Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations. RESULTS The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions. CONCLUSION (1) The salt bridge interactions between acidic amino acids (Glu- and Asp-) and alkaline amino acids (Arg+, Lys+ and His+) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg+, Lys+ and His+) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.
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Affiliation(s)
- Neng-Zhong Xie
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
| | - Qi-Shi Du
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Gordon Life Science Institute, 53 South Cottage Road, Belmont, MA, 02478, United States of America
| | - Jian-Xiu Li
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
| | - Ri-Bo Huang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
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59
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Rahaman O, Kalimeri M, Melchionna S, Hénin J, Sterpone F. Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains. J Phys Chem B 2014; 119:8939-49. [PMID: 25317828 DOI: 10.1021/jp507571u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this work, we address the question of whether the enhanced stability of thermophilic proteins has a direct connection with internal hydration. Our model systems are two homologous G domains of different stability: the mesophilic G domain of the elongation factor thermal unstable protein from E. coli and the hyperthermophilic G domain of the EF-1α protein from S. solfataricus. Using molecular dynamics simulation at the microsecond time scale, we show that both proteins host water molecules in internal cavities and that these molecules exchange with the external solution in the nanosecond time scale. The hydration free energy of these sites evaluated via extensive calculations is found to be favorable for both systems, with the hyperthermophilic protein offering a slightly more favorable environment to host water molecules. We estimate that, under ambient conditions, the free energy gain due to internal hydration is about 1.3 kcal/mol in favor of the hyperthermophilic variant. However, we also find that, at the high working temperature of the hyperthermophile, the cavities are rather dehydrated, meaning that under extreme conditions other molecular factors secure the stability of the protein. Interestingly, we detect a clear correlation between the hydration of internal cavities and the protein conformational landscape. The emerging picture is that internal hydration is an effective observable to probe the conformational landscape of proteins. In the specific context of our investigation, the analysis confirms that the hyperthermophilic G domain is characterized by multiple states and it has a more flexible structure than its mesophilic homologue.
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Affiliation(s)
- Obaidur Rahaman
- †Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Maria Kalimeri
- †Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Simone Melchionna
- ‡CNR-IPCF, Consiglio Nazionale delle Ricerche, Physics Dept., Univ. La Sapienza, P.le A. Moro 2, 00185, Rome, Italy
| | - Jérôme Hénin
- †Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
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60
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Srivastava A, Sinha S. Thermostability of in vitro evolved Bacillus subtilis lipase A: a network and dynamics perspective. PLoS One 2014; 9:e102856. [PMID: 25122499 PMCID: PMC4133394 DOI: 10.1371/journal.pone.0102856] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 06/24/2014] [Indexed: 11/23/2022] Open
Abstract
Proteins in thermophilic organisms remain stable and function optimally at high temperatures. Owing to their important applicability in many industrial processes, such thermostable proteins have been studied extensively, and several structural factors attributed to their enhanced stability. How these factors render the emergent property of thermostability to proteins, even in situations where no significant changes occur in their three-dimensional structures in comparison to their mesophilic counter-parts, has remained an intriguing question. In this study we treat Lipase A from Bacillus subtilis and its six thermostable mutants in a unified manner and address the problem with a combined complex network-based analysis and molecular dynamic studies to find commonality in their properties. The Protein Contact Networks (PCN) of the wild-type and six mutant Lipase A structures developed at a mesoscopic scale were analyzed at global network and local node (residue) level using network parameters and community structure analysis. The comparative PCN analysis of all proteins pointed towards important role of specific residues in the enhanced thermostability. Network analysis results were corroborated with finer-scale molecular dynamics simulations at both room and high temperatures. Our results show that this combined approach at two scales can uncover small but important changes in the local conformations that add up to stabilize the protein structure in thermostable mutants, even when overall conformation differences among them are negligible. Our analysis not only supports the experimentally determined stabilizing factors, but also unveils the important role of contacts, distributed throughout the protein, that lead to thermostability. We propose that this combined mesoscopic-network and fine-grained molecular dynamics approach is a convenient and useful scheme not only to study allosteric changes leading to protein stability in the face of negligible over-all conformational changes due to mutations, but also in other molecular networks where change in function does not accompany significant change in the network structure.
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Affiliation(s)
| | - Somdatta Sinha
- Indian Institute of Science Education and Research Mohali, S. A. S. Nagar, Manauli, India
- * E-mail:
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61
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Zhang J, Wang F, Zhang Y. Molecular dynamics studies on the NMR structures of rabbit prion protein wild type and mutants: surface electrostatic charge distributions. J Biomol Struct Dyn 2014; 33:1326-35. [PMID: 25105226 DOI: 10.1080/07391102.2014.947325] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species such as sheep and goats, cattle, deer and elk, and humans. But for rabbits, studies have shown that they have a low susceptibility to be infected by prion diseases. This paper does molecular dynamics (MD) studies of rabbit NMR structures (of the wild type and its two mutants of two surface residues), in order to understand the specific mechanism of rabbit prion proteins (RaPrP(C)). Protein surface electrostatic charge distributions are specially focused to analyze the MD trajectories. This paper can conclude that surface electrostatic charge distributions indeed contribute to the structural stability of wild-type RaPrP(C); this may be useful for the medicinal treatment of prion diseases.
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Affiliation(s)
- Jiapu Zhang
- a Molecular Model Discovery Laboratory, Department of Chemistry & Biotechnology, Faculty of Science, Engineering & Technology , Swinburne University of Technology , Hawthorn , Victoria 3122 , Australia
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62
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Greenbaum BD, Kumar P, Libchaber A. Using first passage statistics to extract environmentally dependent amino acid correlations. PLoS One 2014; 9:e101665. [PMID: 25000191 PMCID: PMC4084998 DOI: 10.1371/journal.pone.0101665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 06/06/2014] [Indexed: 11/19/2022] Open
Abstract
In this work, we study the first passage statistics of amino acid primary sequences, that is the probability of observing an amino acid for the first time at a certain number of residues away from a fixed amino acid. By using this rich mathematical framework, we are able to capture the background distribution for an organism, and infer lengths at which the first passage has a probability that differs from what is expected. While many features of an organism's genome are due to natural selection, others are related to amino acid chemistry and the environment in which an organism lives, constraining the randomness of genomes upon which selection can further act. We therefore use this approach to infer amino acid correlations, and then study how these correlations vary across a wide range of organisms under a wide range of optimal growth temperatures. We find a nearly universal exponential background distribution, consistent with the idea that most amino acids are globally uncorrelated from other amino acids in genomes. When we are able to extract significant correlations, these correlations are reliably dependent on optimal growth temperature, across phylogenetic boundaries. Some of the correlations we extract, such as the enhanced probability of finding, for the first time, a cysteine three residues away from a cysteine or glutamic acid two residues away from an arginine, likely relate to thermal stability. However, other correlations, likely appearing on alpha helical surfaces, have a less clear physiochemical interpretation and may relate to thermal stability or unusual metabolic properties of organisms that live in a high temperature environment.
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Affiliation(s)
- Benjamin D. Greenbaum
- Departments of Medicine, Division of Hematology and Medical Oncology, and Pathology, and the Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America
- * E-mail:
| | - Pradeep Kumar
- Center for Studies in Physics and Biology, The Rockefeller University, New York, New York, United States of America
- Department of Physics, University of Arkansas at Little Rock, Little Rock, Arkansas, United States of America
| | - Albert Libchaber
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America
- Center for Studies in Physics and Biology, The Rockefeller University, New York, New York, United States of America
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63
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Shen T, Guo Z, Ji C. Structure of a His170Tyr mutant of thermostable pNPPase from Geobacillus stearothermophilus. Acta Crystallogr F Struct Biol Commun 2014; 70:697-702. [PMID: 24915075 PMCID: PMC4051519 DOI: 10.1107/s2053230x14007341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 04/02/2014] [Indexed: 11/10/2022] Open
Abstract
Using directed evolution based on random mutagenesis and heat-treated selection, a thermostable His170Tyr mutant of Geobacillus stearothermophilus thermostable p-nitrophenylphosphatase (TpNPPase) was obtained. The temperature at which the His170Tyr mutant lost 50% of its activity (T1/2) was found to be 4.40 K higher than that of wild-type TpNPPase, and the melting temperature of the His170Tyr mutant increased by 2.39 K. The crystal structure of the His170Tyr mutant was then determined at 2.0 Å resolution in the presence of a sodium ion and a sulfate ion in the active site. The cap domain of chain B shows a half-closed conformation. The hydrophobic side chain of the mutated residue, the hydroxyphenyl group, forms a hydrophobic contact with the methyl group of Ala166. This hydrophobic interaction was found using the Protein Interactions Calculator (PIC) web server with an interaction distance of 4.6 Å, and might be a key factor in the thermostabilization of the His170Tyr mutant. This study potentially offers a molecular basis for both investigation of the catalytic mechanism and thermostable protein engineering.
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Affiliation(s)
- Tiantian Shen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, People’s Republic of China
| | - Zheng Guo
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, People’s Republic of China
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, People’s Republic of China
- Shanghai Engineering Research Center Of Industrial Microorganisms, Shanghai, People’s Republic of China
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64
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Three-dimensional structure of an alkaline xylanase Xyn11A-LC from alkalophilic Bacillus sp. SN5 and improvement of its thermal performance by introducing arginines substitutions. Biotechnol Lett 2014; 36:1495-501. [PMID: 24682788 DOI: 10.1007/s10529-014-1512-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
Abstract
The alkaline xylanase Xyn11A-LC from the alkalophilic Bacillus sp. SN5 was expressed in E. coli, purified and crystallized. The crystal structure was determined at a resolution of 1.49 Å. Xyn11A-LC has the β-jelly roll structure typical of family 11 xylanases. To improve its thermostability and thermophilicity, a mutant SB3 was constructed by introducing three arginines on the different sides of the protein surface. SB3 increased the optimum temperature by 5 °C. The wild type and SB3 had the half-lives of 22 and 68 min at 65 °C at pH 8.0 (Tris/HCl buffer), respectively. CD spectroscopy revealed that the melting temperature (T m) of the wild type and SB3 were 55.3 and 66.9 °C, respectively. These results showed that the introduction of arginines enhance the thermophilicity and thermostability of Xyn11A-LC.
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65
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Gupta PSS, Mondal S, Mondal B, Islam RNU, Banerjee S, Bandyopadhyay AK. SBION: A Program for Analyses of Salt-Bridges from Multiple Structure Files. Bioinformation 2014; 10:164-6. [PMID: 24748757 PMCID: PMC3974244 DOI: 10.6026/97320630010164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 02/24/2014] [Accepted: 02/25/2014] [Indexed: 11/30/2022] Open
Abstract
Salt-bridge and network salt-bridge are specific electrostatic interactions that contribute to the overall stability of proteins. In
hierarchical protein folding model, these interactions play crucial role in nucleation process. The advent and growth of protein
structure database and its availability in public domain made an urgent need for context dependent rapid analysis of salt-bridges.
While these analyses on single protein is cumbersome and time-consuming, batch analyses need efficient software for rapid
topological scan of a large number of protein for extracting details on (i) fraction of salt-bridge residues (acidic and basic). (ii) Chain
specific intra-molecular salt-bridges, (iii) inter-molecular salt-bridges (protein-protein interactions) in all possible binary
combinations (iv) network salt-bridges and (v) secondary structure distribution of salt-bridge residues. To the best of our
knowledge, such efficient software is not available in public domain. At this juncture, we have developed a program i.e. SBION
which can perform all the above mentioned computations for any number of protein with any number of chain at any given
distance of ion-pair. It is highly efficient, fast, error-free and user friendly. Finally we would say that our SBION indeed possesses
potential for applications in the field of structural and comparative bioinformatics studies.
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Affiliation(s)
- Parth Sarthi Sen Gupta
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Sudipta Mondal
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Buddhadev Mondal
- Department of Zoology, Burdwan Raj College, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Rifat Nawaz Ul Islam
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Shyamashree Banerjee
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Amal K Bandyopadhyay
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
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66
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Wang D, Lu M, Wang X, Jiao Y, Fang Y, Liu Z, Wang S. Improving stability of a novel dextran-degrading enzyme from marine Arthrobacter oxydans KQ11. Carbohydr Polym 2014; 103:294-9. [DOI: 10.1016/j.carbpol.2013.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/10/2013] [Accepted: 12/09/2013] [Indexed: 11/27/2022]
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67
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Kovács K, Bánóczi G, Varga A, Szabó I, Holczinger A, Hornyánszky G, Zagyva I, Paizs C, Vértessy BG, Poppe L. Expression and properties of the highly alkalophilic phenylalanine ammonia-lyase of thermophilic Rubrobacter xylanophilus. PLoS One 2014; 9:e85943. [PMID: 24475062 PMCID: PMC3903478 DOI: 10.1371/journal.pone.0085943] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 12/04/2013] [Indexed: 11/18/2022] Open
Abstract
The sequence of a phenylalanine ammonia-lyase (PAL; EC: 4.3.1.24) of the thermophilic and radiotolerant bacterium Rubrobacter xylanophilus (RxPAL) was identified by screening the genomes of bacteria for members of the phenylalanine ammonia-lyase family. A synthetic gene encoding the RxPAL protein was cloned and overexpressed in Escherichia coli TOP 10 in a soluble form with an N-terminal His6-tag and the recombinant RxPAL protein was purified by Ni-NTA affinity chromatography. The activity assay of RxPAL with l-phenylalanine at various pH values exhibited a local maximum at pH 8.5 and a global maximum at pH 11.5. Circular dichroism (CD) studies showed that RxPAL is associated with an extensive α-helical character (far UV CD) and two distinctive near-UV CD peaks. These structural characteristics were well preserved up to pH 11.0. The extremely high pH optimum of RxPAL can be rationalized by a three-dimensional homology model indicating possible disulfide bridges, extensive salt-bridge formation and an excess of negative electrostatic potential on the surface. Due to these properties, RxPAL may be a candidate as biocatalyst in synthetic biotransformations leading to unnatural l- or d-amino acids or as therapeutic enzyme in treatment of phenylketonuria or leukemia.
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Affiliation(s)
- Klaudia Kovács
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences of Hungarian Academy of Sciences, Budapest, Hungary
| | - Gergely Bánóczi
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Andrea Varga
- Biocatalysis Research Group, Babeş-Bolyai University of Cluj-Napoca, Cluj-Napoca, Romania
| | - Izabella Szabó
- Biocatalysis Research Group, Babeş-Bolyai University of Cluj-Napoca, Cluj-Napoca, Romania
| | - András Holczinger
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary
| | - Gábor Hornyánszky
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Imre Zagyva
- Institute of Enzymology, Research Centre for Natural Sciences of Hungarian Academy of Sciences, Budapest, Hungary
| | - Csaba Paizs
- Biocatalysis Research Group, Babeş-Bolyai University of Cluj-Napoca, Cluj-Napoca, Romania
| | - Beáta G. Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences of Hungarian Academy of Sciences, Budapest, Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary
| | - László Poppe
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
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68
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The conserved lid tryptophan, W211, potentiates thermostability and thermoactivity in bacterial thermoalkalophilic lipases. PLoS One 2013; 8:e85186. [PMID: 24391996 PMCID: PMC3877348 DOI: 10.1371/journal.pone.0085186] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 12/02/2013] [Indexed: 01/13/2023] Open
Abstract
We hypothesize that aggregation of thermoalkalophilic lipases could be a thermostability mechanism. The conserved tryptophans (W211, W234) in the lid are of particular interest owing to their previous involvements in aggregation and thermostability mechanisms in many other proteins. The thermoalkalophilic lipase from Bacillus thermocatenulatus (BTL2) and its mutants (W211A, W234A) were expressed and purified to homogeneity. We found that, when aggregated, BTL2 is more thermostable than its non-aggregating form, showing that aggregation potentiates thermostability in the thermoalkalophilic lipase. Among the two lid mutants, the W211A lowered aggregation tendency drastically and resulted in a much less thermostable variant of BTL2, which indicated that W211 stabilizes the intermolecular interactions in BTL2 aggregates. Further thermoactivity and CD spectroscopy analyses showed that W211A also led to a strong decrease in the optimal and the melting temperature of BTL2, implying stabilization by W211 also to the intramolecular interactions. The other lid mutant W234A had no effects on these properties. Finally, we analyzed the molecular basis of these experimental findings in-silico using the dimer (PDB ID: 1KU0) and the monomer (PDB ID: 2W22) lipase structures. The computational analyses confirmed that W211 stabilized the intermolecular interactions in the dimer lipase and it is critical to the stability of the monomer lipase. Explicitly W211 confers stability to the dimer and the monomer lipase through distinct aromatic interactions with Y273-Y282 and H87-P232 respectively. The insights revealed by this work shed light not only on the mechanism of thermostability and its relation to aggregation but also on the particular role of the conserved lid tryptophan in the thermoalkalophilic lipases.
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69
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Protein adaptations in archaeal extremophiles. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:373275. [PMID: 24151449 PMCID: PMC3787623 DOI: 10.1155/2013/373275] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/26/2013] [Accepted: 08/14/2013] [Indexed: 12/25/2022]
Abstract
Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live. Rather than having one basic set of adaptations that works for all environments, Archaea have evolved separate protein features that are customized for each environment. We categorized the Archaea into three general groups to describe what is known about their protein adaptations: thermophilic, psychrophilic, and halophilic. Thermophilic proteins tend to have a prominent hydrophobic core and increased electrostatic interactions to maintain activity at high temperatures. Psychrophilic proteins have a reduced hydrophobic core and a less charged protein surface to maintain flexibility and activity under cold temperatures. Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and peptide insertions, which compensates for the extreme ionic conditions. While acidophiles, alkaliphiles, and piezophiles are their own class of Archaea, their protein adaptations toward pH and pressure are less discernible. By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins for industrial, environmental, and biotechnological applications where function in extreme conditions is required for activity.
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70
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Engineering and kinetic stabilization of the therapeutic enzyme Anabeana variabilis phenylalanine ammonia lyase. Appl Biochem Biotechnol 2013; 171:1805-18. [PMID: 23999738 DOI: 10.1007/s12010-013-0450-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/15/2013] [Indexed: 10/26/2022]
Abstract
Anabeana variabilis phenylalanine ammonia lyase has just recently been discovered and introduced in clinical trials of phenylketonuria enzyme replacement therapy for its outstanding kinetic properties. In the present study, kinetic stabilization of this therapeutically important enzyme has been explored by introduction of a disulfide bond into the structure. Site-directed mutagenesis was performed with quick-change PCR method. Recombinant wild-type and mutated enzymes were expressed in Escherichia coli, and his-tagged proteins were affinity purified. Formation of disulfide bond was confirmed by Ellman's method, and then chemical unfolding, kinetic behavior, and thermal inactivation of mutated enzyme were compared with the wild type. Based on our results, the Q292C mutation resulted in a significant improvement in kinetic stability and resistance against chemical unfolding of the enzyme while kinetic parameters and pH profile of enzyme activity were remained unaffected. The results of the present study provided an insight towards designing phenylalanine ammonia lyases with higher stability.
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71
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A multi-factors rational design strategy for enhancing the thermostability of Escherichia coli AppA phytase. ACTA ACUST UNITED AC 2013; 40:457-64. [DOI: 10.1007/s10295-013-1260-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 03/04/2013] [Indexed: 10/27/2022]
Abstract
Abstract
Despite recent advances in our understanding of the importance of protein surface properties for protein thermostability,there are seldom studies on multi-factors rational design strategy, so a more scientific, simple and effective rational strategy is urgent for protein engineering. Here, we first attempted to use a three-factors rational design strategy combining three common structural features, protein flexibility, protein surface, and salt bridges. Escherichia coli AppA phytase was used as a model enzyme to improve its thermostability. Moreover, the structure and enzyme features of the thermostable mutants designed by our strategy were analyzed roundly. For the single mutants, two (Q206E and Y311K), in five exhibited thermostable property with a higher success rate of prediction (40 %). For the multiple mutants, the themostable sites were combined with another site, I427L, we obtained by directed evolution, Q206E/I427L, Y311K/I427L, and Q206E/Y311K/I427L, all exhibited thermostable property. The Y311K/I427L doubled thermostability (61.7 %, and was compared to 30.97 % after being heated at 80 °C for 10 min) and catalytic efficiency (4.46 was compared to 2.37) improved more than the wild-type AppA phytase almost without hampering catalytic activity. These multi-factors of rational design strategy can be applied practically as a thermostabilization strategy instead of the conventional single-factor approach.
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72
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Stability mechanisms of a thermophilic laccase probed by molecular dynamics. PLoS One 2013; 8:e61985. [PMID: 23658618 PMCID: PMC3639223 DOI: 10.1371/journal.pone.0061985] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 03/15/2013] [Indexed: 11/25/2022] Open
Abstract
Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching Topt (∼350 K) from 300 K, this change correlated with a beginning “unzipping” of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F− (but not Cl−) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F− intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes.
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73
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Rahaman O, Melchionna S, Laage D, Sterpone F. The effect of protein composition on hydration dynamics. Phys Chem Chem Phys 2013; 15:3570-6. [PMID: 23381660 DOI: 10.1039/c3cp44582h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Water dynamics at the surface of two homologous proteins with different thermal resistances is found to be unaffected by the different underlying amino-acid compositions, and when proteins are folded it responds similarly to temperature variations. Upon unfolding the water dynamics slowdown with respect to bulk decreases by a factor of two. Our findings are explained by the dominant topological perturbation induced by the protein on the water hydrogen bond dynamics.
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Affiliation(s)
- O Rahaman
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
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74
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Tseng TS, Cheng CS, Hsu STD, Shih MF, He PL, Lyu PC. Residue-specific annotation of disorder-to-order transition and cathepsin inhibition of a propeptide-like crammer from D. melanogaster. PLoS One 2013; 8:e54187. [PMID: 23349821 PMCID: PMC3551606 DOI: 10.1371/journal.pone.0054187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/07/2012] [Indexed: 11/19/2022] Open
Abstract
Drosophila melanogaster crammer is a novel cathepsin inhibitor involved in long-term memory formation. A molten globule-to-ordered structure transition is required for cathepsin inhibition. This study reports the use of alanine scanning to probe the critical residues in the two hydrophobic cores and the salt bridges of crammer in the context of disorder-to-order transition and cathepsin inhibition. Alanine substitution of the aromatic residues W9, Y12, F16, Y20, Y32, and W53 within the hydrophobic cores, and charged residues E8, R28, R29, and E67 in the salt bridges considerably decrease the ability of crammer to inhibit Drosophila cathepsin B (CTSB). Far-UV circular dichroism (CD), intrinsic fluorescence, and nuclear magnetic resonance (NMR) spectroscopies show that removing most of the aromatic and charged side-chains substantially reduces thermostability, alters pH-dependent helix formation, and disrupts the molten globule-to-ordered structure transition. Molecular modeling indicates that W53 in the hydrophobic Core 2 is essential for the interaction between crammer and the prosegment binding loop (PBL) of CTSB; the salt bridge between R28 and E67 is critical for the appropriate alignment of the α-helix 4 toward the CTSB active cleft. The results of this study show detailed residue-specific dissection of folding transition and functional contributions of the hydrophobic cores and salt bridges in crammer, which have hitherto not been characterized for cathepsin inhibition by propeptide-like cysteine protease inhibitors. Because of the involvements of cathepsin inhibitors in neurodegenerative diseases, these structural insights can serve as a template for further development of therapeutic inhibitors against human cathepsins.
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Affiliation(s)
- Tien-Sheng Tseng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chao-Sheng Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Min-Fang Shih
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Pei-Lin He
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung, Taiwan
- * E-mail:
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75
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Fei B, Xu H, Zhang F, Li X, Ma S, Cao Y, Xie J, Qiao D, Cao Y. Relationship between Escherichia coli AppA phytase's thermostability and salt bridges. J Biosci Bioeng 2013; 115:623-7. [PMID: 23333035 DOI: 10.1016/j.jbiosc.2012.12.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/28/2012] [Accepted: 12/08/2012] [Indexed: 11/28/2022]
Abstract
In order to study on the relationship between Escherichia coli AppA phytase's thermostability and salt bridges, and indicate an effective technical route of which factor to think about and where to modify at AppA for enhancing its thermostability, a salt bridge subtraction mutant E31Q and a salt bridge addition mutant Q307D were constructed by site-directed mutagenesis. The residual activities of the wild-type AppA phytase, E31Q and Q307D were 31.42%, 17.46%, and 40.57%, respectively, after being heated at 80°C for 10 min. The salt bridge subtraction mutant E31Q showed 13.96% thermostability decreasement, and the salt bridge addition mutant Q307D showed 9.15% thermostability enhancement than the wild-type both without the pH and temperature optimum changed. It proved salt bridges play a key role in E. coli AppA phytase's thermostability and the α/β-domain of AppA may be sensitive to heat. Salt bridges and the α/β-domain of AppA should have high priority to think about to enhance AppA's thermostability for commercial application. Besides, molecular dynamics simulation was used for salt bridges analysis.
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Affiliation(s)
- Baojin Fei
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu 610064, Sichuan, PR China
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76
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McCully ME, Beck DAC, Daggett V. Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain. Protein Eng Des Sel 2012; 26:35-45. [PMID: 23012442 DOI: 10.1093/protein/gzs063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A thermostabilized variant (UVF) of the engrailed homeodomain (EnHD) was previously engineered by Mayo and co-workers. The melting temperature of the non-natural, designed protein is 50°C higher than the natural wild-type protein (>99 vs. 52°C), and the two proteins share 22% sequence identity. We have performed extensive (1 μs) all-atom, explicit solvent molecular dynamics simulations of the wild-type and engineered proteins to investigate their structural and dynamic properties at room temperature and at 100°C. Our simulations are in good agreement with nuclear magnetic resonance data available for the two proteins [nuclear Overhauser effect crosspeaks (NOEs), J-coupling constants and order parameters for EnHD; and NOEs for UVF], showing that we reproduce the backbone dynamics and side chain packing in the native state of both proteins. UVF was more dynamic at room temperature than EnHD, with respect to both its backbone and side chain motion. When the temperature was raised, the thermostable protein maintained this mobility while retaining its native conformation. EnHD, on the other hand, was unable to maintain its more rigid native structure at higher temperature and began to unfold. Heightened protein dynamics leading to promiscuous and dynamically interchangeable amino acid contacts makes UVF more tolerant to increasing temperature, providing a molecular explanation for heightened thermostability of this protein.
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Affiliation(s)
- Michelle E McCully
- Biomolecular Structure and Design Program, University of Washington, Seattle, WA 98195-5013, USA
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77
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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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78
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Yang Y, Yu Y, Cheng J, Liu Y, Liu DS, Wang J, Zhu MX, Wang R, Xu TL. Highly conserved salt bridge stabilizes rigid signal patch at extracellular loop critical for surface expression of acid-sensing ion channels. J Biol Chem 2012; 287:14443-55. [PMID: 22399291 DOI: 10.1074/jbc.m111.334250] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acid-sensing ion channels (ASICs) are non-selective cation channels activated by extracellular acidosis associated with many physiological and pathological conditions. A detailed understanding of the mechanisms that govern cell surface expression of ASICs, therefore, is critical for better understanding of the cell signaling under acidosis conditions. In this study, we examined the role of a highly conserved salt bridge residing at the extracellular loop of rat ASIC3 (Asp(107)-Arg(153)) and human ASIC1a (Asp(107)-Arg(160)) channels. Comprehensive mutagenesis and electrophysiological recordings revealed that the salt bridge is essential for functional expression of ASICs in a pH sensing-independent manner. Surface biotinylation and immunolabeling of an extracellular epitope indicated that mutations, including even minor alterations, at the salt bridge impaired cell surface expression of ASICs. Molecular dynamics simulations, normal mode analysis, and further mutagenesis studies suggested a high stability and structural constrain of the salt bridge, which serves to separate an adjacent structurally rigid signal patch, important for surface expression, from a flexible gating domain. Thus, we provide the first evidence of structural requirement that involves a stabilizing salt bridge and an exposed rigid signal patch at the destined extracellular loop for normal surface expression of ASICs. These findings will allow evaluation of new strategies aimed at preventing excessive excitability and neuronal injury associated with tissue acidosis and ASIC activation.
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Affiliation(s)
- Yang Yang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
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79
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Electrostatic contribution of surface charge residues to the stability of a thermophilic protein: benchmarking experimental and predicted pKa values. PLoS One 2012; 7:e30296. [PMID: 22279578 PMCID: PMC3261180 DOI: 10.1371/journal.pone.0030296] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 12/13/2011] [Indexed: 11/20/2022] Open
Abstract
Optimization of the surface charges is a promising strategy for increasing thermostability of proteins. Electrostatic contribution of ionizable groups to the protein stability can be estimated from the differences between the pKa values in the folded and unfolded states of a protein. Using this pKa-shift approach, we experimentally measured the electrostatic contribution of all aspartate and glutamate residues to the stability of a thermophilic ribosomal protein L30e from Thermococcus celer. The pKa values in the unfolded state were found to be similar to model compound pKas. The pKa values in both the folded and unfolded states obtained at 298 and 333 K were similar, suggesting that electrostatic contribution of ionizable groups to the protein stability were insensitive to temperature changes. The experimental pKa values for the L30e protein in the folded state were used as a benchmark to test the robustness of pKa prediction by various computational methods such as H++, MCCE, MEAD, pKD, PropKa, and UHBD. Although the predicted pKa values were affected by crystal contacts that may alter the side-chain conformation of surface charged residues, most computational methods performed well, with correlation coefficients between experimental and calculated pKa values ranging from 0.49 to 0.91 (p<0.01). The changes in protein stability derived from the experimental pKa-shift approach correlate well (r = 0.81) with those obtained from stability measurements of charge-to-alanine substituted variants of the L30e protein. Our results demonstrate that the knowledge of the pKa values in the folded state provides sufficient rationale for the redesign of protein surface charges leading to improved protein stability.
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Thangakani AM, Kumar S, Velmurugan D, Gromiha MSM. How do thermophilic proteins resist aggregation? Proteins 2012; 80:1003-15. [DOI: 10.1002/prot.24002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 11/18/2011] [Accepted: 11/21/2011] [Indexed: 11/08/2022]
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Lee KM, Yu CWH, Chiu TYH, Sze KH, Shaw PC, Wong KB. Solution structure of the dimerization domain of the eukaryotic stalk P1/P2 complex reveals the structural organization of eukaryotic stalk complex. Nucleic Acids Res 2011; 40:3172-82. [PMID: 22135285 PMCID: PMC3326305 DOI: 10.1093/nar/gkr1143] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The lateral ribosomal stalk is responsible for the kingdom-specific binding of translation factors and activation of GTP hydrolysis during protein synthesis. The eukaryotic stalk is composed of three acidic ribosomal proteins P0, P1 and P2. P0 binds two copies of P1/P2 hetero-dimers to form a pentameric P-complex. The structure of the eukaryotic stalk is currently not known. To provide a better understanding on the structural organization of eukaryotic stalk, we have determined the solution structure of the N-terminal dimerization domain (NTD) of P1/P2 hetero-dimer. Helix-1, -2 and -4 from each of the NTD-P1 and NTD-P2 form the dimeric interface that buries 2200 A2 of solvent accessible surface area. In contrast to the symmetric P2 homo-dimer, P1/P2 hetero-dimer is asymmetric. Three conserved hydrophobic residues on the surface of NTD-P1 are replaced by charged residues in NTD-P2. Moreover, NTD-P1 has an extra turn in helix-1, which forms extensive intermolecular interactions with helix-1 and -4 of NTD-P2. Truncation of this extra turn of P1 abolished the formation of P1/P2 hetero-dimer. Systematic truncation studies suggest that P0 contains two spine-helices that each binds one copy of P1/P2 hetero-dimer. Modeling studies suggest that a large hydrophobic cavity, which can accommodate the loop between the spine-helices of P0, can be found on NTD-P1 but not on NTD-P2 when the helix-4 adopts an ‘open’ conformation. Based on the asymmetric properties of NTD-P1/NTD-P2, a structural model of the eukaryotic P-complex with P2/P1:P1/P2 topology is proposed.
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Affiliation(s)
- Ka-Ming Lee
- School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Hong Kong, China
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