1
|
Hait S, Basu S, Kundu S. Charge reversal mutations in mesophilic-thermophilic orthologous protein pairs and their role in enhancing coulombic interaction energy. J Biomol Struct Dyn 2023; 41:1745-1752. [PMID: 34996344 DOI: 10.1080/07391102.2021.2024258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proteins from thermophilic organisms are a matter of immense interest for decades because of its application in fields like de-novo protein design, thermostable variants of biocatalysts etc. Previous studies have found several sequence and structural adaptations related to thermal stability, while charge reversal study remains ignored. Here we address whether charge reversal mutations naturally occur in mesophilic-thermophilic/hyperthermophilic orthologous proteins. Do they contribute to thermal stability? Our systematic study on 1550 mesophilic-thermophilic/hyperthermophilic orthologous protein pairs with remarkable structural and topological similarity, shows gain in coulombic interaction energy in thermophilic/hyperthermophilic proteins at short range associated with partially exposed and buried charge reversal mutations, which may enhance thermostability. Our findings call forth its application in future protein engineering studies. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sudipto Basu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| |
Collapse
|
2
|
Ó'Fágáin C. Protein Stability: Enhancement and Measurement. Methods Mol Biol 2023; 2699:369-419. [PMID: 37647007 DOI: 10.1007/978-1-0716-3362-5_18] [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] [Indexed: 09/01/2023]
Abstract
This chapter defines protein stability, emphasizes its importance, and surveys the field of protein stabilization, with summary reference to a selection of 2014-2021 publications. One can enhance stability, particularly by protein engineering strategies but also by chemical modification and by other means. General protocols are set out on how to measure a given protein's (i) kinetic thermal stability and (ii) oxidative stability and (iii) how to undertake chemical modification of a protein in solution.
Collapse
Affiliation(s)
- Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Dublin, Ireland.
| |
Collapse
|
3
|
Iannuzzelli J, Bacik JP, Moore EJ, Shen Z, Irving EM, Vargas DA, Khare SD, Ando N, Fasan R. Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization. Biochemistry 2022; 61:1041-1054. [PMID: 35612958 PMCID: PMC9178789 DOI: 10.1021/acs.biochem.2c00033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/04/2022] [Indexed: 11/30/2022]
Abstract
Enhancing the thermostability of enzymes without impacting their catalytic function represents an important yet challenging goal in protein engineering and biocatalysis. We recently introduced a novel method for enzyme thermostabilization that relies on the computationally guided installation of genetically encoded thioether "staples" into a protein via cysteine alkylation with the noncanonical amino acid O-2-bromoethyl tyrosine (O2beY). Here, we demonstrate the functionality of an expanded set of electrophilic amino acids featuring chloroacetamido, acrylamido, and vinylsulfonamido side-chain groups for protein stapling using this strategy. Using a myoglobin-based cyclopropanase as a model enzyme, our studies show that covalent stapling with p-chloroacetamido-phenylalanine (pCaaF) provides higher stapling efficiency and enhanced stability (thermodynamic and kinetic) compared to the other stapled variants and the parent protein. Interestingly, molecular simulations of conformational flexibility of the cross-links show that the pCaaF staple allows fewer energetically feasible conformers than the other staples, and this property may be a broader indicator of stability enhancement. Using this strategy, pCaaF-stapled variants with significantly enhanced stability against thermal denaturation (ΔTm' = +27 °C) and temperature-induced heme loss (ΔT50 = +30 °C) were obtained while maintaining high levels of catalytic activity and stereoselectivity. Crystallographic analyses of singly and doubly stapled variants provide key insights into the structural basis for stabilization, which includes both direct interactions of the staples with protein residues and indirect interactions through adjacent residues involved in heme binding. This work expands the toolbox of protein stapling strategies available for protein stabilization.
Collapse
Affiliation(s)
- Jacob
A. Iannuzzelli
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - John-Paul Bacik
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Eric J. Moore
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Zhuofan Shen
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Ellen M. Irving
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - David A. Vargas
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Sagar D. Khare
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Nozomi Ando
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Rudi Fasan
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| |
Collapse
|
4
|
Bhatt P, Gangola S, Bhandari G, Zhang W, Maithani D, Mishra S, Chen S. New insights into the degradation of synthetic pollutants in contaminated environments. CHEMOSPHERE 2021; 268:128827. [PMID: 33162154 DOI: 10.1016/j.chemosphere.2020.128827] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/18/2020] [Accepted: 10/28/2020] [Indexed: 05/11/2023]
Abstract
The environment is contaminated by synthetic contaminants owing to their extensive applications globally. Hence, the removal of synthetic pollutants (SPs) from the environment has received widespread attention. Different remediation technologies have been investigated for their abilities to eliminate SPs from the ecosystem; these include photocatalysis, sonochemical techniques, nanoremediation, and bioremediation. SPs, which can be organic or inorganic, can be degraded by microbial metabolism at contaminated sites. Owing to their diverse metabolisms, microbes can adapt to a wide variety of environments. Several microbial strains have been reported for their bioremediation potential concerning synthetic chemical compounds. The selection of potential strains for large-scale removal of organic pollutants is an important research priority. Additionally, novel microbial consortia have been found to be capable of efficient degradation owing to their combined and co-metabolic activities. Microbial engineering is one of the most prominent and promising techniques for providing new opportunities to develop proficient microorganisms for various biological processes; here, we have targeted the SP-degrading mechanisms of microorganisms. This review provides an in-depth discussion of microbial engineering techniques that are used to enhance the removal of both organic and inorganic pollutants from different contaminated environments and under different conditions. The degradation of these pollutants is investigated using abiotic and biotic approaches; interestingly, biotic approaches based on microbial methods are preferable owing to their high potential for pollutant removal and cost-effectiveness.
Collapse
Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal Campus, 263136, Uttarakhand, India
| | - Geeta Bhandari
- Department of Biotechnology, Sardar Bhagwan Singh University, Dehradun, 248161, Uttarakhand, India
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Damini Maithani
- Department of Microbiology, G.B Pant University of Agriculture and Technology, Pantnagar, U.S Nagar, Uttarakhand, India
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
5
|
Wullich SC, Wijma HJ, Janssen DB, Fetzner S. Stabilizing AqdC, a Pseudomonas Quinolone Signal-Cleaving Dioxygenase from Mycobacteria, by FRESCO-Based Protein Engineering. Chembiochem 2021; 22:733-742. [PMID: 33058333 PMCID: PMC7894191 DOI: 10.1002/cbic.202000641] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/13/2020] [Indexed: 12/11/2022]
Abstract
The mycobacterial PQS dioxygenase AqdC, a cofactor-less protein with an α/β-hydrolase fold, inactivates the virulence-associated quorum-sensing signal molecule 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS) produced by the opportunistic pathogen Pseudomonas aeruginosa and is therefore a potential anti-virulence tool. We have used computational library design to predict stabilizing amino acid replacements in AqdC. While 57 out of 91 tested single substitutions throughout the protein led to stabilization, as judged by increases in T app m of >2 °C, they all impaired catalytic activity. Combining substitutions, the proteins AqdC-G40K-A134L-G220D-Y238W and AqdC-G40K-G220D-Y238W showed extended half-lives and the best trade-off between stability and activity, with increases in T app m of 11.8 and 6.1 °C and relative activities of 22 and 72 %, respectively, compared to AqdC. Molecular dynamics simulations and principal component analysis suggested that stabilized proteins are less flexible than AqdC, and the loss of catalytic activity likely correlates with an inability to effectively open the entrance to the active site.
Collapse
Affiliation(s)
- Sandra C. Wullich
- Institut für Molekulare Mikrobiologie und BiotechnologieWWU MünsterCorrensstraße 348149 MünsterGermany
| | - Hein J. Wijma
- Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningen (TheNetherlands
| | - Dick B. Janssen
- Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningen (TheNetherlands
| | - Susanne Fetzner
- Institut für Molekulare Mikrobiologie und BiotechnologieWWU MünsterCorrensstraße 348149 MünsterGermany
| |
Collapse
|
6
|
Risso VA, Romero-Rivera A, Gutierrez-Rus LI, Ortega-Muñoz M, Santoyo-Gonzalez F, Gavira JA, Sanchez-Ruiz JM, Kamerlin SCL. Enhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening. Chem Sci 2020; 11:6134-6148. [PMID: 32832059 PMCID: PMC7407621 DOI: 10.1039/d0sc01935f] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 05/18/2020] [Indexed: 01/02/2023] Open
Abstract
Directed evolution has revolutionized protein engineering. Still, enzyme optimization by random library screening remains sluggish, in large part due to futile probing of mutations that are catalytically neutral and/or impair stability and folding. FuncLib is a novel approach which uses phylogenetic analysis and Rosetta design to rank enzyme variants with multiple mutations, on the basis of predicted stability. Here, we use it to target the active site region of a minimalist-designed, de novo Kemp eliminase. The similarity between the Michaelis complex and transition state for the enzymatic reaction makes this system particularly challenging to optimize. Yet, experimental screening of a small number of active-site variants at the top of the predicted stability ranking leads to catalytic efficiencies and turnover numbers (∼2 × 104 M-1 s-1 and ∼102 s-1) for this anthropogenic reaction that compare favorably to those of modern natural enzymes. This result illustrates the promise of FuncLib as a powerful tool with which to speed up directed evolution, even on scaffolds that were not originally evolved for those functions, by guiding screening to regions of the sequence space that encode stable and catalytically diverse enzymes. Empirical valence bond calculations reproduce the experimental activation energies for the optimized eliminases to within ∼2 kcal mol-1 and indicate that the enhanced activity is linked to better geometric preorganization of the active site. This raises the possibility of further enhancing the stability-guidance of FuncLib by computational predictions of catalytic activity, as a generalized approach for computational enzyme design.
Collapse
Affiliation(s)
- Valeria A Risso
- Departamento de Química Física, Facultad de Ciencias , Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente (UEQ) , Universidad de Granada , 18071 Granada , Spain .
| | - Adrian Romero-Rivera
- Science for Life Laboratory , Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden .
| | - Luis I Gutierrez-Rus
- Departamento de Química Física, Facultad de Ciencias , Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente (UEQ) , Universidad de Granada , 18071 Granada , Spain .
| | - Mariano Ortega-Muñoz
- Departamento de Química Orgánica , Facultad de Ciencias , Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente (UEQ) , Universidad de Granada , 18071 Granada , Spain
| | - Francisco Santoyo-Gonzalez
- Departamento de Química Orgánica , Facultad de Ciencias , Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente (UEQ) , Universidad de Granada , 18071 Granada , Spain
| | - Jose A Gavira
- Laboratorio de Estudios Cristalográficos , Instituto Andaluz de Ciencias de la Tierra , CSIC, Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente (UEQ) , University of Granada , Avenida de las Palmeras 4 , 18100 Armilla , Granada , Spain
| | - Jose M Sanchez-Ruiz
- Departamento de Química Física, Facultad de Ciencias , Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente (UEQ) , Universidad de Granada , 18071 Granada , Spain .
| | - Shina C L Kamerlin
- Science for Life Laboratory , Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden .
| |
Collapse
|
7
|
Maenpuen S, Pongsupasa V, Pensook W, Anuwan P, Kraivisitkul N, Pinthong C, Phonbuppha J, Luanloet T, Wijma HJ, Fraaije MW, Lawan N, Chaiyen P, Wongnate T. Creating Flavin Reductase Variants with Thermostable and Solvent-Tolerant Properties by Rational-Design Engineering. Chembiochem 2020; 21:1481-1491. [PMID: 31886941 DOI: 10.1002/cbic.201900737] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 02/06/2023]
Abstract
We have employed computational approaches-FireProt and FRESCO-to predict thermostable variants of the reductase component (C1 ) of (4-hydroxyphenyl)acetate 3-hydroxylase. With the additional aid of experimental results, two C1 variants, A166L and A58P, were identified as thermotolerant enzymes, with thermostability improvements of 2.6-5.6 °C and increased catalytic efficiency of 2- to 3.5-fold. After heat treatment at 45 °C, both of the thermostable C1 variants remain active and generate reduced flavin mononucleotide (FMNH- ) for reactions catalyzed by bacterial luciferase and by the monooxygenase C2 more efficiently than the wild type (WT). In addition to thermotolerance, the A166L and A58P variants also exhibited solvent tolerance. Molecular dynamics (MD) simulations (6 ns) at 300-500 K indicated that mutation of A166 to L and of A58 to P resulted in structural changes with increased stabilization of hydrophobic interactions, and thus in improved thermostability. Our findings demonstrated that improvements in the thermostability of C1 enzyme can lead to broad-spectrum uses of C1 as a redox biocatalyst for future industrial applications.
Collapse
Affiliation(s)
- Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, 169 Long-Hard Bangsaen Road, Chonburi, 20131, Thailand
| | - Vinutsada Pongsupasa
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Wiranee Pensook
- Department of Biochemistry, Faculty of Science, Burapha University, 169 Long-Hard Bangsaen Road, Chonburi, 20131, Thailand
| | - Piyanuch Anuwan
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
| | | | - Chatchadaporn Pinthong
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, 114 Sukhumvit 23 Road, Bangkok, 10110, Thailand
| | - Jittima Phonbuppha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Thikumporn Luanloet
- Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Hein J Wijma
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huaykaew Road, Suthep, Chiang Mai, 50200, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand.,Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
| |
Collapse
|
8
|
Atkins DL, Berrocal JA, Mason AF, Voets IK. Tandem catalysis in multicomponent solvent-free biofluids. NANOSCALE 2019; 11:19797-19805. [PMID: 31621738 DOI: 10.1039/c9nr06045f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Enzymes are widely employed to reduce the environmental impact of chemical industries as biocatalysts improve productivity and offer high selectively under mild reaction conditions in a diverse range of chemical transformations. The poor stability of biomacromolecules under reaction conditions is often a critical bottleneck to their application. Protein engineering or immobilization onto solid substrates may remedy this limitation but, unfortunately, this is often at the expense of catalytic potency or substrate specificity. In this work, we show that the combinatorial approach of chemical modification and supramolecular nanoencapsulation can endow mechanistically diverse enzymes with apparent extremophilic behavior. A protein-polymer surfactant core-shell architecture facilitates construction of increasingly complex biofluids from individual biosynthetic components, each of which retain biological activity at hydration levels almost two orders of magnitude below solvation. The herein constructed multifunctional biofluids operate in tandem up to 150 °C and in the total absence of solvent under apparent diffusional mass-transport limitation. The biosynthetic promotion of extremophilic traits for enzymes with diverse catalytic motions and chemical functions highlights the extraordinary capacity for a viscous surfactant milieu to replace both hydration and bulk waters.
Collapse
Affiliation(s)
- Dylan Luke Atkins
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands. and Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands and Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - José Augusto Berrocal
- Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands and Laboratory of Macromolecular and Organic Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Alexander Francesco Mason
- Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands and Laboratory of Bio-Organic Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Ilja Karina Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands. and Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| |
Collapse
|
9
|
Liu Z, Zheng W, Ye W, Wang C, Gao Y, Cui W, Zhou Z. Characterization of cysteine sulfinic acid decarboxylase from Tribolium castaneum and its application in the production of β-alanine. Appl Microbiol Biotechnol 2019; 103:9443-9453. [PMID: 31696283 DOI: 10.1007/s00253-019-10139-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/05/2019] [Accepted: 09/12/2019] [Indexed: 12/20/2022]
Abstract
β-alanine is a precursor for the production of pharmaceuticals and food additives that is produced by chemical methods in industry. As concerns about the environment and energy are increasing, biocatalysis using L-aspartate-α-decarboxylase (ADC) to convert L-aspartate to β-alanine has great potential. Many studies have focused on the catalytic activity of ADC, but these researches were limited to the prokaryotic enzymes. In this study, the gene encoding cysteine sulfinic acid decarboxylase from Tribolium castaneum (TcCSADC) was synthesized and overexpressed in Escherichia coli, and the enzyme was purified and characterized for the first time. It could use L-aspartate as its substrate, and the specific activity was 4.83 μmol/min/mg, which was much higher than that of ADCs from prokaryotes. A homology modeling assay indicated that TcCSADC had a dimer structure. Based on the evolutionary information from thermophilic bacteria, twenty-three variants were constructed to attempt to improve its abilities that transform L-aspartate to β-alanine. One mutant, G369A, was screened that had improved thermal stability. An analysis of the suitability of the catalytic process showed that the up to 162 g/L β-alanine could be produced using cells expressing the recombinant G369A variant, which is the highest yield to date. The CSADC from T. castaneum has important value for studies of the mechanism of ADCs and CSADCs from eukaryotes, and the engineered strain containing the G369A variant has great potential for the industrial production of β-alanine.
Collapse
Affiliation(s)
- Zhongmei Liu
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| | - Wenhui Zheng
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Wenqi Ye
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Chao Wang
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yu Gao
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| |
Collapse
|
10
|
One-Pot Biosynthesis of l-Aspartate from Maleate via an Engineered Strain Containing a Dual-Enzyme System. Appl Environ Microbiol 2019; 85:AEM.01327-19. [PMID: 31324629 DOI: 10.1128/aem.01327-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/15/2019] [Indexed: 11/20/2022] Open
Abstract
l-Aspartate has been widely used in medicine and the food and chemical industries. In this study, Serratia marcescens maleate cis-trans isomerase (MaiA) and Escherichia coli aspartase (AspA) were coupled and coexpressed in an engineered E. coli strain in which the byproduct metabolic pathway was inactivated. The engineered E. coli strain containing the dual-enzyme system (pMA) was employed to bioproduce l-aspartate from maleate with a conversion of 98%. We optimized the activity ratio of double enzymes through ribosome binding site (RBS) regulation and molecular modification of MaiA, resulting in an engineered strain: pMA-RBS4-G27A/G171A. The conversion of l-aspartate biotransformed from maleate using the pMA-RBS4-G27A/G171A strain was almost 100%. It required 40 min to complete the whole-cell catalysis, without the intermediate product and byproduct, compared to 120 min before optimization. The induction timing and the amount of inducer in a 5-liter fermentor were optimized for scale-up of the production of l-aspartate. The amount of produced l-aspartate using the cells obtained by fermentation reached 419.8 g/liter (3.15 M), and the conversion was 98.4%. Our study demonstrated an environmentally responsible and efficient method to bioproduce l-aspartate from maleate and provided an available pathway for the industrial production of l-aspartate. This work should greatly improve the economic benefits of l-aspartate, which can now be simply produced from maleate by the engineered strain constructed based on dual-enzyme coupling.IMPORTANCE l-Aspartate is currently produced from fumarate by biological methods, and fumarate is synthesized from maleate by chemical methods in industry. We established a biosynthesis method to produce l-aspartate from maleate that is environmentally responsible, convenient, and efficient. Compared to conventional l-aspartate production, no separation and purification of intermediate products is required, which could greatly improve production efficiency and reduce costs. As environmental issues are attracting increasing attention, conventional chemical methods gradually will be replaced by biological methods. Our results lay an important foundation for the industrialization of l-aspartate biosynthesis from maleate.
Collapse
|
11
|
Gong XM, Qin Z, Li FL, Zeng BB, Zheng GW, Xu JH. Development of an Engineered Ketoreductase with Simultaneously Improved Thermostability and Activity for Making a Bulky Atorvastatin Precursor. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03382] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xu-Min Gong
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Zhen Qin
- State Key Laboratory of Bioreactor Engineering and R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
| | - Fu-Long Li
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Bu-Bing Zeng
- Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai 200237, China
| | - Gao-Wei Zheng
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| |
Collapse
|
12
|
Rational design-based engineering of a thermostable phytase by site-directed mutagenesis. Mol Biol Rep 2018; 45:2053-2061. [DOI: 10.1007/s11033-018-4362-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/05/2018] [Indexed: 12/19/2022]
|
13
|
Liao ML, Zhang S, Zhang GY, Chu YM, Somero GN, Dong YW. Heat-resistant cytosolic malate dehydrogenases (cMDHs) of thermophilic intertidal snails (genus Echinolittorina): protein underpinnings of tolerance to body temperatures reaching 55°C. ACTA ACUST UNITED AC 2018; 220:2066-2075. [PMID: 28566358 DOI: 10.1242/jeb.156935] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/20/2017] [Indexed: 01/07/2023]
Abstract
Snails of the genus Echinolittorina are among the most heat-tolerant animals; they experience average body temperatures near 41-44°C in summer and withstand temperatures up to at least 55°C. Here, we demonstrate that heat stability of function (indexed by the Michaelis-Menten constant of the cofactor NADH, KMNADH) and structure (indexed by rate of denaturation) of cytosolic malate dehydrogenases (cMDHs) of two congeners (E. malaccana and E. radiata) exceeds values previously found for orthologs of this protein from less thermophilic species. The ortholog of E. malaccana is more heat stable than that of E. radiata, in keeping with the congeners' thermal environments. Only two inter-congener differences in amino acid sequence in these 332 residue proteins were identified. In both cases (positions 48 and 114), a glycine in the E. malaccana ortholog is replaced by a serine in the E. radiata protein. To explore the relationship between structure and function and to characterize how amino acid substitutions alter stability of different regions of the enzyme, we used molecular dynamics simulation methods. These computational methods allow determination of thermal effects on fine-scale movements of protein components, for example, by estimating the root mean square deviation in atom position over time and the root mean square fluctuation for individual residues. The minor changes in amino acid sequence favor temperature-adaptive change in flexibility of regions in and around the active sites. Interspecific differences in effects of temperature on fine-scale protein movements are consistent with the differences in thermal effects on binding and rates of heat denaturation.
Collapse
Affiliation(s)
- Ming-Ling Liao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen 361102, China
| | - Shu Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen 361102, China
| | - Guang-Ya Zhang
- Department of Biotechnology and Engineering, Huaqiao University, Xiamen 361021, China
| | - Yun-Meng Chu
- Department of Biotechnology and Engineering, Huaqiao University, Xiamen 361021, China
| | - George N Somero
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA 93940, USA
| | - Yun-Wei Dong
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China .,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen 361102, China
| |
Collapse
|
14
|
Abstract
The dynamic native, functional folded forms of proteins are unstable mainly because they readily unfold into flexible unstructured forms.
Collapse
Affiliation(s)
- Romas Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics
- University of Minnesota
- St Paul
- USA
| |
Collapse
|
15
|
Abstract
One of the greatest sources of metabolic and enzymatic diversity are microorganisms. In recent years, emerging recombinant DNA and genomic techniques have facilitated the development of new efficient expression systems, modification of biosynthetic pathways leading to new metabolites by metabolic engineering, and enhancement of catalytic properties of enzymes by directed evolution. Complete sequencing of industrially important microbial genomes is taking place very rapidly, and there are already hundreds of genomes sequenced. Functional genomics and proteomics are major tools used in the search for new molecules and development of higher-producing strains.
Collapse
Affiliation(s)
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CDMX, México
| |
Collapse
|
16
|
Abstract
Thermostabilization represents a critical and often obligatory step toward enhancing the robustness of enzymes for organic synthesis and other applications. While directed evolution methods have provided valuable tools for this purpose, these protocols are laborious and time-consuming and typically require the accumulation of several mutations, potentially at the expense of catalytic function. Here, we report a minimally invasive strategy for enzyme stabilization that relies on the installation of genetically encoded, nonreducible covalent staples in a target protein scaffold using computational design. This methodology enables the rapid development of myoglobin-based cyclopropanation biocatalysts featuring dramatically enhanced thermostability (ΔTm = +18.0 °C and ΔT50 = +16.0 °C) as well as increased stability against chemical denaturation [ΔCm (GndHCl) = 0.53 M], without altering their catalytic efficiency and stereoselectivity properties. In addition, the stabilized variants offer superior performance and selectivity compared with the parent enzyme in the presence of a high concentration of organic cosolvents, enabling the more efficient cyclopropanation of a water-insoluble substrate. This work introduces and validates an approach for protein stabilization which should be applicable to a variety of other proteins and enzymes.
Collapse
|
17
|
Amadei A, Del Galdo S, D'Abramo M. Density discriminates between thermophilic and mesophilic proteins. J Biomol Struct Dyn 2017; 36:3265-3273. [PMID: 28952426 DOI: 10.1080/07391102.2017.1385537] [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] [Indexed: 12/17/2022]
Abstract
Despite an intense interest and a remarkable number of studies on the subject, the relationships between thermostability and (primary, secondary and tertiary) structure of proteins are still not fully understood. Here, comparing the protein density - defined by the ratio between the residue number and protein excluded volume - for a set of thermophilic/mesophilic pairs, we provide evidence that this property is connected to the optimal growth temperature. In particular, our results indicate that thermophilic proteins have - in general - a lower density with respect to the mesophilic counterparts, being such a correlation more pronounced for optimal growth temperature differences greater than 40°C. The effect of the protein thermostability changes on the molecular shape is also presented.
Collapse
Affiliation(s)
- Andrea Amadei
- a Department of Chemical Science and Technology , University of Roma Tor Vergata , via della Ricerca Scientifica, 00133 , Roma , Italy
| | - Sara Del Galdo
- a Department of Chemical Science and Technology , University of Roma Tor Vergata , via della Ricerca Scientifica, 00133 , Roma , Italy
| | - Marco D'Abramo
- b Department of Chemistry , Sapienza University of Rome , P.le A. Moro, 5, 00185 , Rome , Italy
| |
Collapse
|
18
|
Abstract
For many years, industrial enzymes have played an important role in the benefit of our society due to their many useful properties and a wide range of applications. They are key elements in the progress of many industries including foods, beverages, pharmaceuticals, diagnostics, therapy, personal care, animal feed, detergents, pulp and paper, textiles, leather, chemicals and biofuels. During recent decades, microbial enzymes have replaced many plant and animal enzymes. This is because microbial enzymes are widely available and produced economically in short fermentations and inexpensive media. Screening is
simple, and strain improvement for increased production has been very successful. The advances in recombinant DNA technology have had a major effect on production levels of enzymes and represent a way to overproduce industrially important microbial, plant and animal enzymes. It has been calculated that 50-60% of the world enzyme market is supplied with recombinant enzymes. Molecular methods, including genomics and
metagenomics, are being used for the discovery of new enzymes from microbes. Also, directed evolution has allowed the design of enzyme specificities and better performance.
Collapse
Affiliation(s)
- Arnold L. Demain
- Research Institute for Scientists Emeriti (RISE), Drew University, Madison, New Jersey 07940, USA
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas. Universidad Nacional Autónoma de México
| |
Collapse
|
19
|
Arabnejad H, Dal Lago M, Jekel PA, Floor RJ, Thunnissen AMWH, Terwisscha van Scheltinga AC, Wijma HJ, Janssen DB. A robust cosolvent-compatible halohydrin dehalogenase by computational library design. Protein Eng Des Sel 2017; 30:173-187. [PMID: 27999093 DOI: 10.1093/protein/gzw068] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/02/2016] [Indexed: 01/05/2023] Open
Abstract
To improve the applicability of halohydrin dehalogenase as a catalyst for reactions in the presence of organic cosolvents, we explored a computational library design strategy (Framework for Rapid Enzyme Stabilization by Computational libraries) that involves discovery and in silico evaluation of stabilizing mutations. Energy calculations, disulfide bond predictions and molecular dynamics simulations identified 218 point mutations and 35 disulfide bonds with predicted stabilizing effects. Experiments confirmed 29 stabilizing point mutations, most of which were located in two distinct regions, whereas introduction of disulfide bonds was not effective. Combining the best mutations resulted in a 12-fold mutant (HheC-H12) with a 28°C higher apparent melting temperature and a remarkable increase in resistance to cosolvents. This variant also showed a higher optimum temperature for catalysis while activity at low temperature was preserved. Mutant H12 was used as a template for the introduction of mutations that enhance enantioselectivity or activity. Crystal structures showed that the structural changes in the H12 mutant mostly agreed with the computational predictions and that the enhanced stability was mainly due to mutations that redistributed surface charges and improved interactions between subunits, the latter including better interactions of water molecules at the subunit interfaces.
Collapse
Affiliation(s)
- Hesam Arabnejad
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marco Dal Lago
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Peter A Jekel
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Robert J Floor
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W H Thunnissen
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anke C Terwisscha van Scheltinga
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Hein J Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
20
|
Silva SB, Pinheiro MP, Fuzo CA, Silva SR, Ferreira TL, Lourenzoni MR, Nonato MC, Vieira DS, Ward RJ. The role of local residue environmental changes in thermostable mutants of the GH11 xylanase from Bacillus subtilis. Int J Biol Macromol 2017; 97:574-584. [DOI: 10.1016/j.ijbiomac.2017.01.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 12/24/2022]
|
21
|
Abstract
This article defines protein stability, emphasizes its importance and surveys the field of protein stabilization, with summary reference to a selection of 2009-2015 publications. One can enhance stability by, in particular, protein engineering strategies and by chemical modification (including conjugation) in solution. General protocols are set out on how to measure a given protein's (1) kinetic thermal stability, and (2) oxidative stability, and (3) how to undertake chemical modification of a protein in solution.
Collapse
Affiliation(s)
- Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
- National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland.
| |
Collapse
|
22
|
Engineering de novo disulfide bond in bacterial α-type carbonic anhydrase for thermostable carbon sequestration. Sci Rep 2016; 6:29322. [PMID: 27385052 PMCID: PMC4935852 DOI: 10.1038/srep29322] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/16/2016] [Indexed: 11/29/2022] Open
Abstract
Exploiting carbonic anhydrase (CA), an enzyme that rapidly catalyzes carbon dioxide hydration, is an attractive biomimetic route for carbon sequestration due to its environmental compatibility and potential economic viability. However, the industrial applications of CA are strongly hampered by the unstable nature of enzymes. In this work, we introduced in silico designed, de novo disulfide bond in a bacterial α-type CA to enhance thermostability. Three variants were selected and expressed in Escherichia coli with an additional disulfide bridge. One of the variants showed great enhancement in terms of both kinetic and thermodynamic stabilities. This improvement could be attributed to the loss of conformational entropy of the unfolded state, showing increased rigidity. The variant showed an upward-shifted optimal temperature and appeared to be thermoactivated, which compensated for the lowered activity at 25 °C. Collectively, the variant constructed by the rapid and effective de novo disulfide engineering can be used as an efficient biocatalyst for carbon sequestration under high temperature conditions.
Collapse
|
23
|
Huang F, Shen L, Wang J, Qu A, Yang H, Zhang Z, An Y, Shi L. Effect of the Surface Charge of Artificial Chaperones on the Refolding of Thermally Denatured Lysozymes. ACS APPLIED MATERIALS & INTERFACES 2016; 8:3669-3678. [PMID: 26570996 DOI: 10.1021/acsami.5b08843] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Artificial chaperones are of great interest in fighting protein misfolding and aggregation for the protection of protein bioactivity. A comprehensive understanding of the interaction between artificial chaperones and proteins is critical for the effective utilization of these materials in biomedicine. In this work, we fabricated three kinds of artificial chaperones with different surface charges based on mixed-shell polymeric micelles (MSPMs), and investigated their protective effect for lysozymes under thermal stress. It was found that MSPMs with different surface charges showed distinct chaperone-like behavior, and the neutral MSPM with PEG shell and PMEO2MA hydrophobic domain at high temperature is superior to the negatively and positively charged one, because of the excessive electrostatic interactions between the protein and charged MSPMs. The results may benefit to optimize this kind of artificial chaperone with enhanced properties and expand their application in the future.
Collapse
Affiliation(s)
- Fan Huang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Liangliang Shen
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Jianzu Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Aoting Qu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Huiru Yang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Zhenkun Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Yingli An
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| | - Linqi Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Nankai University , Tianjin 300071, China
| |
Collapse
|
24
|
Abstract
Using structure and sequence based analysis we can engineer proteins to increase their thermal stability.
Collapse
Affiliation(s)
- H. Pezeshgi Modarres
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - M. R. Mofrad
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - A. Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory
- Department of Mechanical and Manufacturing Engineering
- University of Calgary
- Calgary
- Canada
| |
Collapse
|
25
|
Thumarat U, Kawabata T, Nakajima M, Nakajima H, Sugiyama A, Yazaki K, Tada T, Waku T, Tanaka N, Kawai F. Comparison of genetic structures and biochemical properties of tandem cutinase-type polyesterases from Thermobifida alba AHK119. J Biosci Bioeng 2015; 120:491-7. [DOI: 10.1016/j.jbiosc.2015.03.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 03/03/2015] [Accepted: 03/05/2015] [Indexed: 11/29/2022]
|
26
|
Rational Substitution of Surface Acidic Residues for Enhancing the Thermostability of Thermolysin. Appl Biochem Biotechnol 2015; 178:725-38. [DOI: 10.1007/s12010-015-1905-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/21/2015] [Indexed: 11/26/2022]
|
27
|
Inverse relationship between chitobiase and transglycosylation activities of chitinase-D from Serratia proteamaculans revealed by mutational and biophysical analyses. Sci Rep 2015; 5:15657. [PMID: 26493546 PMCID: PMC4616163 DOI: 10.1038/srep15657] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
Serratia proteamaculans chitinase-D (SpChiD) has a unique combination of hydrolytic and transglycosylation (TG) activities. The TG activity of SpChiD can be used for large-scale production of chito-oligosaccharides (CHOS). The multiple activities (hydrolytic and/or chitobiase activities and TG) of SpChiD appear to be strongly influenced by the substrate-binding cleft. Here, we report the unique property of SpChiD substrate-binding cleft, wherein, the residues Tyr28, Val35 and Thr36 control chitobiase activity and the residues Trp160 and Trp290 are crucial for TG activity. Mutants with reduced (V35G and T36G/F) or no (SpChiDΔ30–42 and Y28A) chitobiase activity produced higher amounts of the quantifiable even-chain TG product with degree of polymerization (DP)-6, indicating that the chitobiase and TG activities are inversely related. In addition to its unprecedented catalytic properties, unlike other chitinases, the single modular SpChiD showed dual unfolding transitions. Ligand-induced thermal stability studies with the catalytically inactive mutant of SpChiD (E153A) showed that the transition temperature increased upon binding of CHOS with DP2–6. Isothermal titration calorimetry experiments revealed the exceptionally high binding affinities for E153A to CHOS with DP2–6. These observations strongly support that the architecture of SpChiD substrate-binding cleft adopted to control chitobiase and TG activities, in addition to usual chitinase-mediated hydrolysis.
Collapse
|
28
|
Panja AS, Bandopadhyay B, Maiti S. Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges. PLoS One 2015; 10:e0131495. [PMID: 26177372 PMCID: PMC4503463 DOI: 10.1371/journal.pone.0131495] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/01/2015] [Indexed: 01/08/2023] Open
Abstract
Introduction Protein thermostability is an important field for its evolutionary perspective of mesophilic versus thermophilic relationship and for its industrial/ therapeutic applications. Methods Presently, a total 400 (200 thermophilic and 200 mesophilic homologue) proteins were studied utilizing several software/databases to evaluate their amino acid preferences. Randomly selected 50 homologous proteins with available PDB-structure of each group were explored for the understanding of the protein charges, isoelectric-points, hydrophilicity, hydrophobicity, tyrosine phosphorylation and salt-bridge occurrences. These 100 proteins were further probed to generate Ramachandran plot/data for the gross secondary structure prediction in and comparison between the thermophilic and mesophilic proteins. Results Present results strongly suggest that nonpolar smaller volume amino acids Ala (χ2 = 238.54, p<0.001) and Gly (χ2 = 73.35, p<0.001) are highly and Val moderately (χ2 = 144.43, p<0.001) occurring in the 85% of thermophilic proteins. Phospho-regulated Tyr and redox-sensitive Cys are also moderately distributed (χ2~20.0, p<0.01) in a larger number of thermophilic proteins. A consistent lower distribution of thermophilicity and discretely higher distribution of hydrophobicity is noticed in a large number of thermophilic versus their mesophilic protein homolog. The mean differences of isoelectric points and charges are found to be significantly less (7.11 vs. 6.39, p<0.05 and 1 vs. -0.6, p<0.01, respectively) in thermophilic proteins compared to their mesophilic counterpart. The possible sites for Tyr phosphorylation are noticed to be 25% higher (p<0.05) in thermophilic proteins. The 60% thermophiles are found with higher number of salt bridges in this study. The average percentage of salt-bridge of thermophiles is found to be higher by 20% than their mesophilic homologue. The GLU-HIS and GLU-LYS salt-bridge dyads are calculated to be significantly higher (p<0.05 and p<0.001, respectively) in thermophilic and GLU-ARG is higher in the mesophilic proteins. The Ramachandran plot/ data suggest a higher abundance of the helix, left-handed helix, sheet, nonplanar peptide and lower occurrence of cis peptide, loop/ turn and outlier in thermophiles. Pearson’s correlation result suggests that the isoelectric points of mesophilic and thermophilic proteins are positively correlated (r = 0.93 and 0.84, respectively; p<0.001) to their corresponding charges. And their hydrophilicity is negatively associated with the corresponding hydrophobicity (r = -0.493, p<0.001 and r = -0.324, p<0.05) suggesting their reciprocal evolvement. Conclusions Present results for the first time with this large amount of datasets and multiple contributing factors suggest the greater occurrence of hydrophobicity, salt-bridges and smaller volume nonpolar residues (Gly, Ala and Val) and lesser occurrence of bulky polar residues in the thermophilic proteins. A more stoichiometric relationship amongst these factors minimized the hindrance due to side chain burial and increased compactness and secondary structural stability in thermophilic proteins.
Collapse
Affiliation(s)
- Anindya Sundar Panja
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, 721102, West Bengal, India
| | - Bidyut Bandopadhyay
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, 721102, West Bengal, India
| | - Smarajit Maiti
- Post Graduate Department of Biochemistry and Biotechnology, Cell and Molecular Therapeutics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, 721102, West Bengal, India
- * E-mail:
| |
Collapse
|
29
|
Improving the Thermostability and Activity of a Thermophilic Subtilase by Incorporating Structural Elements of Its Psychrophilic Counterpart. Appl Environ Microbiol 2015; 81:6302-13. [PMID: 26150464 DOI: 10.1128/aem.01478-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/29/2015] [Indexed: 11/20/2022] Open
Abstract
The incorporation of the structural elements of thermostable enzymes into their less stable counterparts is generally used to improve enzyme thermostability. However, the process of engineering enzymes with both high thermostability and high activity remains an important challenge. Here, we report that the thermostability and activity of a thermophilic subtilase were simultaneously improved by incorporating structural elements of a psychrophilic subtilase. There were 64 variable regions/residues (VRs) in the alignment of the thermophilic WF146 protease, mesophilic sphericase, and psychrophilic S41. The WF146 protease was subjected to systematic mutagenesis, in which each of its VRs was replaced with those from S41 and sphericase. After successive rounds of combination and screening, we constructed the variant PBL5X with eight amino acid residues from S41. The half-life of PBL5X at 85°C (57.1 min) was approximately 9-fold longer than that of the wild-type (WT) WF146 protease (6.3 min). The substitutions also led to an increase in the apparent thermal denaturation midpoint temperature (Tm) of the enzyme by 5.5°C, as determined by differential scanning calorimetry. Compared to the WT, PBL5X exhibited high caseinolytic activity (25 to 95°C) and high values of Km and kcat (25 to 80°C). Our study may provide a rational basis for developing highly stable and active enzymes, which are highly desired in industrial applications.
Collapse
|
30
|
Floor RJ, Wijma HJ, Colpa DI, Ramos-Silva A, Jekel PA, Szymański W, Feringa BL, Marrink SJ, Janssen DB. Computational library design for increasing haloalkane dehalogenase stability. Chembiochem 2014; 15:1660-72. [PMID: 24976371 DOI: 10.1002/cbic.201402128] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 11/05/2022]
Abstract
We explored the use of a computational design framework for the stabilization of the haloalkane dehalogenase LinB. Energy calculations, disulfide bond design, molecular dynamics simulations, and rational inspection of mutant structures predicted many stabilizing mutations. Screening of these in small mutant libraries led to the discovery of seventeen point mutations and one disulfide bond that enhanced thermostability. Mutations located in or contacting flexible regions of the protein had a larger stabilizing effect than mutations outside such regions. The combined introduction of twelve stabilizing mutations resulted in a LinB mutant with a 23 °C increase in apparent melting temperature (Tm,app , 72.5 °C) and an over 200-fold longer half-life at 60 °C. The most stable LinB variants also displayed increased compatibility with co-solvents, thus allowing substrate conversion and kinetic resolution at much higher concentrations than with the wild-type enzyme.
Collapse
Affiliation(s)
- Robert J Floor
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Characterization of an extensin-modifying metalloprotease: N-terminal processing and substrate cleavage pattern of Pectobacterium carotovorum Prt1. Appl Microbiol Biotechnol 2014; 98:10077-89. [DOI: 10.1007/s00253-014-5877-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/27/2014] [Accepted: 05/29/2014] [Indexed: 11/26/2022]
|
32
|
Enhancement of Thermal Stabilization of Formaldehyde Dehydrogenase fromPseudomonas putidaby Directed Evolution. Biosci Biotechnol Biochem 2014; 74:1462-5. [DOI: 10.1271/bbb.100026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
33
|
Goldstein RA. Population size dependence of fitness effect distribution and substitution rate probed by biophysical model of protein thermostability. Genome Biol Evol 2014; 5:1584-93. [PMID: 23884461 PMCID: PMC3787666 DOI: 10.1093/gbe/evt110] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The predicted effect of effective population size on the distribution of fitness effects and substitution rate is critically dependent on the relationship between sequence and fitness. This highlights the importance of using models that are informed by the molecular biology, biochemistry, and biophysics of the evolving systems. We describe a computational model based on fundamental aspects of biophysics, the requirement for (most) proteins to be thermodynamically stable. Using this model, we find that differences in population size have minimal impact on the distribution of population-scaled fitness effects, as well as on the rate of molecular evolution. This is because larger populations result in selection for more stable proteins that are less affected by mutations. This reduction in the magnitude of the fitness effects almost exactly cancels the greater selective pressure resulting from the larger population size. Conversely, changes in the population size in either direction cause transient increases in the substitution rate. As differences in population size often correspond to changes in population size, this makes comparisons of substitution rates in different lineages difficult to interpret.
Collapse
Affiliation(s)
- Richard A Goldstein
- Division of Infection and Immunity, University College London, United Kingdom
| |
Collapse
|
34
|
van Beek HL, Wijma HJ, Fromont L, Janssen DB, Fraaije MW. Stabilization of cyclohexanone monooxygenase by a computationally designed disulfide bond spanning only one residue. FEBS Open Bio 2014; 4:168-74. [PMID: 24649397 PMCID: PMC3953729 DOI: 10.1016/j.fob.2014.01.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 01/29/2014] [Accepted: 01/29/2014] [Indexed: 11/28/2022] Open
Abstract
Cyclohexanone monooxygenase was stabilized by an in silico designed disulfide bond. Stabilizing disulfide bonds were successfully designed based on a model structure. The half-life at 30 °C was increased 12-fold for the mutant enzyme. The apparent melting point was increased by 6 °C for the mutant enzyme. The most stabilizing disulfide bond spans only one residue.
Enzyme stability is an important parameter in biocatalytic applications, and there is a strong need for efficient methods to generate robust enzymes. We investigated whether stabilizing disulfide bonds can be computationally designed based on a model structure. In our approach, unlike in previous disulfide engineering studies, short bonds spanning only a few residues were included. We used cyclohexanone monooxygenase (CHMO), a Baeyer–Villiger monooxygenase (BVMO) from Acinetobacter sp. NCIMB9871 as the target enzyme. This enzyme has been the prototype BVMO for many biocatalytic studies even though it is notoriously labile. After creating a small library of mutant enzymes with introduced cysteine pairs and subsequent screening for improved thermostability, three stabilizing disulfide bonds were identified. The introduced disulfide bonds are all within 12 Å of each other, suggesting this particular region is critical for unfolding. This study shows that stabilizing disulfide bonds do not have to span many residues, as the most stabilizing disulfide bond, L323C–A325C, spans only one residue while it stabilizes the enzyme, as shown by a 6 °C increase in its apparent melting temperature.
Collapse
Affiliation(s)
- Hugo L van Beek
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hein J Wijma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Lucie Fromont
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dick B Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marco W Fraaije
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
35
|
Adrio JL, Demain AL. Microbial enzymes: tools for biotechnological processes. Biomolecules 2014; 4:117-39. [PMID: 24970208 PMCID: PMC4030981 DOI: 10.3390/biom4010117] [Citation(s) in RCA: 292] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/02/2014] [Accepted: 01/02/2014] [Indexed: 11/29/2022] Open
Abstract
Microbial enzymes are of great importance in the development of industrial bioprocesses. Current applications are focused on many different markets including pulp and paper, leather, detergents and textiles, pharmaceuticals, chemical, food and beverages, biofuels, animal feed and personal care, among others. Today there is a need for new, improved or/and more versatile enzymes in order to develop more novel, sustainable and economically competitive production processes. Microbial diversity and modern molecular techniques, such as metagenomics and genomics, are being used to discover new microbial enzymes whose catalytic properties can be improved/modified by different strategies based on rational, semi-rational and random directed evolution. Most industrial enzymes are recombinant forms produced in bacteria and fungi.
Collapse
Affiliation(s)
- Jose L Adrio
- Neol Biosolutions SA, BIC Granada, Granada 18016, Spain.
| | - Arnold L Demain
- Research Institute for Scientists Emeriti (R.I.S.E.), Drew University, Madison, NJ 07940, USA.
| |
Collapse
|
36
|
Bosshart A, Panke S, Bechtold M. Systematic Optimization of Interface Interactions Increases the Thermostability of a Multimeric Enzyme. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304141] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
37
|
Bosshart A, Panke S, Bechtold M. Systematic optimization of interface interactions increases the thermostability of a multimeric enzyme. Angew Chem Int Ed Engl 2013; 52:9673-6. [PMID: 23893529 DOI: 10.1002/anie.201304141] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Andreas Bosshart
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | | | | |
Collapse
|
38
|
Aerts D, Verhaeghe T, Joosten HJ, Vriend G, Soetaert W, Desmet T. Consensus engineering of sucrose phosphorylase: The outcome reflects the sequence input. Biotechnol Bioeng 2013; 110:2563-72. [DOI: 10.1002/bit.24940] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/30/2013] [Accepted: 04/08/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Dirk Aerts
- Department of Biochemical and Microbial Technology; Centre for Industrial Biotechnology and Biocatalysis; Ghent University; Coupure Links 653; B-9000; Ghent; Belgium
| | - Tom Verhaeghe
- Department of Biochemical and Microbial Technology; Centre for Industrial Biotechnology and Biocatalysis; Ghent University; Coupure Links 653; B-9000; Ghent; Belgium
| | - Henk-Jan Joosten
- Bio-Prodict; Castellastraat 116; Nijmegen; 6512; EZ; The Netherlands
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics; Radboud University Nijmegen Medical Centre; PO Box 9101; Nijmegen; 6500; HB; The Netherlands
| | - Wim Soetaert
- Department of Biochemical and Microbial Technology; Centre for Industrial Biotechnology and Biocatalysis; Ghent University; Coupure Links 653; B-9000; Ghent; Belgium
| | - Tom Desmet
- Department of Biochemical and Microbial Technology; Centre for Industrial Biotechnology and Biocatalysis; Ghent University; Coupure Links 653; B-9000; Ghent; Belgium
| |
Collapse
|
39
|
Detection and Characterisation of Mutations Responsible for Allele-Specific Protein Thermostabilities at the Mn-Superoxide Dismutase Gene in the Deep-Sea Hydrothermal Vent Polychaete Alvinella pompejana. J Mol Evol 2013; 76:295-310. [DOI: 10.1007/s00239-013-9559-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 03/27/2013] [Indexed: 12/19/2022]
|
40
|
Krüger DM, Rathi PC, Pfleger C, Gohlke H. CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function. Nucleic Acids Res 2013; 41:W340-8. [PMID: 23609541 PMCID: PMC3692064 DOI: 10.1093/nar/gkt292] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein’s (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement.
Collapse
Affiliation(s)
- Dennis M Krüger
- Computational Pharmaceutical Chemistry Group, Department of Mathematics and Natural Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | | | | | | |
Collapse
|
41
|
Liu X, Liu Y, Zhang Z, Huang F, Tao Q, Ma R, An Y, Shi L. Temperature-Responsive Mixed-Shell Polymeric Micelles for the Refolding of Thermally Denatured Proteins. Chemistry 2013; 19:7437-42. [DOI: 10.1002/chem.201300634] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Indexed: 11/08/2022]
|
42
|
Singh RK, Tiwari MK, Singh R, Lee JK. From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes. Int J Mol Sci 2013; 14:1232-77. [PMID: 23306150 PMCID: PMC3565319 DOI: 10.3390/ijms14011232] [Citation(s) in RCA: 268] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/14/2012] [Accepted: 12/24/2012] [Indexed: 11/16/2022] Open
Abstract
Enzymes found in nature have been exploited in industry due to their inherent catalytic properties in complex chemical processes under mild experimental and environmental conditions. The desired industrial goal is often difficult to achieve using the native form of the enzyme. Recent developments in protein engineering have revolutionized the development of commercially available enzymes into better industrial catalysts. Protein engineering aims at modifying the sequence of a protein, and hence its structure, to create enzymes with improved functional properties such as stability, specific activity, inhibition by reaction products, and selectivity towards non-natural substrates. Soluble enzymes are often immobilized onto solid insoluble supports to be reused in continuous processes and to facilitate the economical recovery of the enzyme after the reaction without any significant loss to its biochemical properties. Immobilization confers considerable stability towards temperature variations and organic solvents. Multipoint and multisubunit covalent attachments of enzymes on appropriately functionalized supports via linkers provide rigidity to the immobilized enzyme structure, ultimately resulting in improved enzyme stability. Protein engineering and immobilization techniques are sequential and compatible approaches for the improvement of enzyme properties. The present review highlights and summarizes various studies that have aimed to improve the biochemical properties of industrially significant enzymes.
Collapse
Affiliation(s)
- Raushan Kumar Singh
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 143-701, Korea.
| | | | | | | |
Collapse
|
43
|
|
44
|
Gupta SK, Rai AK, Kanwar SS, Sharma TR. Comparative analysis of zinc finger proteins involved in plant disease resistance. PLoS One 2012; 7:e42578. [PMID: 22916136 PMCID: PMC3419713 DOI: 10.1371/journal.pone.0042578] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 07/10/2012] [Indexed: 11/19/2022] Open
Abstract
A meta-analysis was performed to understand the role of zinc finger domains in proteins of resistance (R) genes cloned from different crops. We analyzed protein sequences of seventy R genes of various crops in which twenty six proteins were found to have zinc finger domains along with nucleotide binding sites - leucine rice repeats (NBS-LRR) domains. We identified thirty four zinc finger domains in the R proteins of nine crops and were grouped into 19 types of zinc fingers. The size of individual zinc finger domain within the R genes varied from 11 to 84 amino acids, whereas the size of proteins containing these domains varied from 263 to 1305 amino acids. The biophysical analysis revealed that molecular weight of Pi54 zinc finger was lowest whereas the highest one was found in rice Pib zinc finger named as Transposes Transcription Factor (TTF). The instability (R(2) =0.95) and the aliphatic (R(2) =0.94) indices profile of zinc finger domains follows the polynomial distribution pattern. The pairwise identity analysis showed that the Lin11, Isl-1 & Mec-3 (LIM) zinc finger domain of rice blast resistance protein pi21 have 12.3% similarity with the nuclear transcription factor, X-box binding-like 1 (NFX) type zinc finger domain of Pi54 protein. For the first time, we reported that Pi54 (Pi-k(h)-Tetep), a rice blast resistance (R) protein have a small zinc finger domain of NFX type located on the C-terminal in between NBS and LRR domains of the R-protein. Compositional analysis depicted by the helical wheel diagram revealed the presence of a hydrophobic region within this domain which might help in exposing the LRR region for a possible R-Avr interaction. This domain is unique among all other cloned plant disease resistance genes and might play an important role in broad-spectrum nature of rice blast resistance gene Pi54.
Collapse
Affiliation(s)
- Santosh Kumar Gupta
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India
- Department of Biotechnology, Himachal Pradesh University, Summer-Hill, Shimla, India
| | - Amit Kumar Rai
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India
- Department of Biotechnology, Himachal Pradesh University, Summer-Hill, Shimla, India
| | - Shamsher Singh Kanwar
- Department of Biotechnology, Himachal Pradesh University, Summer-Hill, Shimla, India
| | - Tilak R. Sharma
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
45
|
Farrell D, Webb H, Johnston MA, Poulsen TA, O’Meara F, Christensen LLH, Beier L, Borchert TV, Nielsen JE. Toward Fast Determination of Protein Stability Maps: Experimental and Theoretical Analysis of Mutants of a Nocardiopsis prasina Serine Protease. Biochemistry 2012; 51:5339-47. [DOI: 10.1021/bi201926f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Damien Farrell
- School of Biomolecular and Biomedical
Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Helen Webb
- School of Biomolecular and Biomedical
Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Protein Optimization, Novozymes A/S, Brudelysvej 26, 2880 Bagsværd,
Denmark
| | - Michael A. Johnston
- School of Biomolecular and Biomedical
Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Thomas A. Poulsen
- Protein Optimization, Novozymes A/S, Brudelysvej 26, 2880 Bagsværd,
Denmark
| | - Fergal O’Meara
- School of Biomolecular and Biomedical
Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Lars Beier
- Protein Optimization, Novozymes A/S, Brudelysvej 26, 2880 Bagsværd,
Denmark
| | - Torben V. Borchert
- Protein Optimization, Novozymes A/S, Brudelysvej 26, 2880 Bagsværd,
Denmark
| | - Jens Erik Nielsen
- School of Biomolecular and Biomedical
Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
46
|
The proline rich homeodomain protein PRH/Hhex forms stable oligomers that are highly resistant to denaturation. PLoS One 2012; 7:e35984. [PMID: 22540015 PMCID: PMC3335068 DOI: 10.1371/journal.pone.0035984] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 03/29/2012] [Indexed: 11/19/2022] Open
Abstract
Background Many transcription factors control gene expression by binding to specific DNA sequences at or near the genes that they regulate. However, some transcription factors play more global roles in the control of gene expression by altering the architecture of sections of chromatin or even the whole genome. The ability to form oligomeric protein assemblies allows many of these proteins to manipulate extensive segments of DNA or chromatin via the formation of structures such as DNA loops or protein-DNA fibres. Principal Findings Here we show that the proline rich homeodomain protein PRH/Hhex forms predominantly octameric and/or hexadecameric species in solution as well as larger assemblies. We show that these assemblies are highly stable resisting denaturation by temperature and chemical denaturants. Conclusion These data indicate that PRH is functionally and structurally related to the Lrp/AsnC family of proteins, a group of proteins that are known to act globally to control gene expression in bacteria and archaea.
Collapse
|
47
|
Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant. PLoS One 2012; 7:e35188. [PMID: 22514720 PMCID: PMC3325981 DOI: 10.1371/journal.pone.0035188] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 03/09/2012] [Indexed: 11/19/2022] Open
Abstract
Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.
Collapse
|
48
|
Ye X, Zhang C, Zhang YHP. Engineering a large protein by combined rational and random approaches: stabilizing the Clostridium thermocellum cellobiose phosphorylase. MOLECULAR BIOSYSTEMS 2012; 8:1815-23. [DOI: 10.1039/c2mb05492b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
49
|
Bornscheuer U, Kazlauskas RJ. Survey of protein engineering strategies. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2011; Chapter 26:26.7.1-26.7.14. [PMID: 22045562 DOI: 10.1002/0471140864.ps2607s66] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein engineering is altering the structure of a protein to improve or change its properties. This unit summarizes concepts for protein engineering using rational design, directed evolution, and combinations of them. Different strategies are presented for identifying the best mutagenesis method, how to identify desired variants by screening or selection, and examples for successful applications are given. This should enable researchers to choose the most promising tools to solve their protein engineering challenges.
Collapse
Affiliation(s)
- Uwe Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Greifswald, Germany
| | - Romas J Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics and the Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota
| |
Collapse
|
50
|
Paës G, Berrin JG, Beaugrand J. GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol Adv 2011; 30:564-92. [PMID: 22067746 DOI: 10.1016/j.biotechadv.2011.10.003] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 01/02/2023]
Abstract
For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.
Collapse
Affiliation(s)
- Gabriel Paës
- INRA, UMR614 FARE, 2 esplanade Roland-Garros, F-51686 Reims, France.
| | | | | |
Collapse
|