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Škerlová J, Brynda J, Šobotník J, Zákopčaník M, Novák P, Bourguignon T, Sillam-Dussès D, Řezáčová P. Crystal structure of blue laccase BP76, a unique termite suicidal defense weapon. Structure 2024; 32:1581-1585.e5. [PMID: 39151418 DOI: 10.1016/j.str.2024.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/21/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Aging workers of the termite Neocapritermes taracua can defend their colony by sacrificing themselves by body rupture, mixing the externally stored blue laccase BP76 with hydroquinones to produce a sticky liquid rich in toxic benzoquinones. Here, we describe the crystal structure of BP76 isolated from N. taracua in its native form. The structure reveals several stabilization strategies, including compact folding, glycosylation, and flexible loops with disulfide bridges and tight dimer interface. The remarkable stability of BP76 maintains its catalytic activity in solid state during the lifespan of N. taracua workers, providing old workers with an efficient defensive weapon to protect their colony.
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Affiliation(s)
- Jana Škerlová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, 165 00 Prague, Czech Republic; Institute of Entomology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Marek Zákopčaník
- Institute of Microbiology, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Petr Novák
- Institute of Microbiology, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology, UR 4443, Université Sorbonne Paris Nord, 93430 Villetaneuse, France
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
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2
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Yamaguchi S, Sunagawa N, Samejima M, Igarashi K. Thermotolerance Mechanism of Fungal GH6 Cellobiohydrolase. Part I. Characterization of Thermotolerant Mutant from the Basidiomycete Phanerochaete chrysosporium. J Appl Glycosci (1999) 2024; 71:55-62. [PMID: 38863951 PMCID: PMC11163330 DOI: 10.5458/jag.jag.jag-2023_0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/14/2024] [Indexed: 06/13/2024] Open
Abstract
Cellobiohydrolase (CBH), belonging to glycoside hydrolase family 6 (GH6), plays an essential role in cellulose saccharification, but its low thermotolerance presents a challenge in improving the reaction efficiency. Based on a report that chimeric CBH II (GH6) engineered to remove non-disulfide-bonded free Cys shows increased thermotolerance, we previously mutated the two free Cys residues to Ser in GH6 CBH from the basidiomycete Phanerochaete chrysosporium (PcCel6A) and obtained a thermotolerant double mutant, C240S/C393S (Yamaguchi et al., J. Appl. Glycosci. 2020; 67: 79-86). Here, characterization of the double mutant revealed that its activity towards both amorphous and crystalline cellulose was higher than that of the wild-type enzyme at elevated temperature, suggesting that the catalytic domain is the major contributor to the increased thermotolerance. To investigate the role of each free Cys residue, we prepared both single mutants, C240S and C393S, of the catalytic domain of PcCel6A and examined their residual activity at high temperature and the temperature-dependent changes of folding by means of circular dichroism measurements and thermal shift assay. The results indicate that the C393S mutation is the main contributor to both the increased thermotolerance of C240S/C393S and the increased activity of the catalytic domain at high temperature.
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Affiliation(s)
- Sora Yamaguchi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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3
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Benrezkallah D. Molecular dynamics simulations at high temperatures of the Aeropyrum pernix L7Ae thermostable protein: Insight into the unfolding pathway. J Mol Graph Model 2024; 127:108700. [PMID: 38183846 DOI: 10.1016/j.jmgm.2023.108700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024]
Abstract
Most life forms on earth live at temperatures below 50 °C. Within these organisms are proteins that form the three-dimensional structures essential to their biological activity and function. However, some thermophilic life forms can resist higher temperatures and have corresponding adaptations to preserve protein function at these high temperatures. Among the structural factors responsible for this resistance of thermophilic proteins to high temperatures is the presence of additional hydrogen bonds in the thermophilic proteins, which means that the structure of the protein is more resistant to unfolding. Similarly, thermostable proteins are rich in structure-stabilizing salt bridges and/or disulfide bridges. In this context, we perform multiple replica molecular dynamics simulations at different temperatures on the Aeropyrum pernix (L7Ae) protein (from the crenarchaeal species A. pernix), known for its high melting temperature, and this in the aim to elucidate the structural factors responsible for its high thermostability. The results reveal that between the most sensitive regions of the protein to the increase of temperature are the loops L1, and L5, which surround the hydrophobic core region of the protein, besides the loop L9, and the C-terminal α5 region. This latter is the longer alpha helix of the protein secondary structure motifs and it is the first to be denaturated at 450 K, while the rest of the protein secondary structure motifs at this temperature were intact. The mechanism of unfolding that follows this protein at 550 K is similar to other thermophile proteins found in literature, with the opening of the loops that surround the hydrophobic core of the protein. So, the latter is completely exposed to the solvent, and partially denatured. The total denaturation process of the protein takes an average time of 40 ns to be achieved. Our investigation also shows that all the calculated salt bridges, with distances less than or equal to 6 A°, are on the periphery part of the protein, exposed to the solvent. However, the hydrophobic core of the protein is not involved in the formation of salt bridges, but rather with formation of some important hydrogen bondings that still persist even at 450 K. So, optimizing hydrogen bonding, near or within the core region, at high temperatures is a strategy that follows this thermostable protein to protect its hydrophobic core from denaturation, and ensure the thermal stability of the protein.
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Affiliation(s)
- Djamila Benrezkallah
- Department of Basic Teachings in Sciences and Technologies (EBST), Faculty of Technology, Djillali Liabes University, Ben M'Hidi BP 89, Sidi Bel Abbes 22000, Algeria; LCPM Laboratory, Chemistry Department, Faculty of Exact and Applied Sciences, University Oran 1 Ahmed Ben Bella, El Mnaouer BP 1524, Oran 31000, Algeria.
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4
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Pant R, Kumar R, Sharma S, Karuppasamy R, Veerappapillai S. Exploring the potential of Halalkalibacterium halodurans laccase for endosulfan and chlorophacinone degradation: insights from molecular docking and molecular dynamics simulations. J Biomol Struct Dyn 2023:1-15. [PMID: 37990551 DOI: 10.1080/07391102.2023.2283165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023]
Abstract
Pesticides are widely used in agriculture but at the same time, a majority of them are known to cause serious harm to health and the environment. In the recent past, laccases have been reported as key enzymes having the ability to degrade pollutants by converting them into less toxic forms. In this investigation, laccase from polyextremophilic bacterium Halalkalibacterium halodurans C-125 was analyzed for its structural, physicochemical, and functional characterization using in silico approaches. The 3D model of the said enzyme is unknown; therefore, the model was generated by template-independent modeling using ROBETTA, I-TASSER, and Alphafold server. The best-generated model from Alphafold with a confidence of 0.95 was validated from ERRAT and Verify 3D scores of 89.95 and 91.80%, respectively. The Ramachandran plot generated using the PROCHECK server further predicted the accuracy of the model with 93.7% and 5.9% of residues present in most favored and additional allowed regions of the plot respectively. The active sites, ion binding sites, and subcellular localization of laccase were also predicted. The generated model was docked with 121 pollutants (pesticides, insecticides, herbicides, fungicides, and rodenticides) for its degradation potential towards these pollutants. Two ligands chlorophacinone (based on the highest binding energy) and endosulfan (based on agricultural uses) were selected for molecular dynamic simulation studies. Endosulfan as a pesticide is banned but in some countries governments allow its use for special purposes which need serious consideration on developing bioremediation approaches for endosulfan degradation. MD simulation studies revealed that both chlorophacinone and endosulfan form hydrogen bonds and hydrophobic bonds with the active site of laccase and chlorophacinone-laccase complex were more stable in comparison to endosulfan. The present investigation provides insight into the structural features of laccase and its potential for the degradation of pesticides which can be further validated by experimental data.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajat Pant
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Ravi Kumar
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
- Department of Biological Sciences and Engineering, Netaji Subhas Institute of Technology (University of Delhi), New Delhi, India
| | - Shilpa Sharma
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Shanthi Veerappapillai
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Borhani S, Arab SS. Investigation of thermal stability characteristic in family A DNA polymerase - A theoretical study. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 182:15-25. [PMID: 37187447 DOI: 10.1016/j.pbiomolbio.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/17/2023]
Abstract
DNA polymerases create complementary DNA strands in living cells and are crucial to genome transmission and maintenance. These enzymes possess similar human right-handed folds which contain thumb, fingers, and palm subdomains and contribute to polymerization activities. These enzymes are classified into seven evolutionary families, A, B, C, D, X, Y, and RT, based on amino acid sequence analysis and biochemical characteristics. Family A DNA polymerases exist in an extended range of organisms including mesophilic, thermophilic, and hyper-thermophilic bacteria, participate in DNA replication and repair, and have a broad application in molecular biology and biotechnology. In this study, we attempted to detect factors that play a role in the thermostability properties of this family member despite their remarkable similarities in structure and function. For this purpose, similarities and differences in amino acid sequences, structure, and dynamics of these enzymes have been inspected. Our results demonstrated that thermophilic and hyper-thermophilic enzymes have more charged, aromatic, and polar residues than mesophilic ones and consequently show further electrostatic and cation-pi interactions. In addition, in thermophilic enzymes, aliphatic residues tend to position in buried states more than mesophilic enzymes. These residues within their aliphatic parts increase hydrophobic core packing and therefore enhance the thermostability of these enzymes. Furthermore, a decrease in thermophilic cavities volumes assists in the protein compactness enhancement. Moreover, molecular dynamic simulation results revealed that increasing temperature impacts mesophilic enzymes further than thermophilic ones that reflect on polar and aliphatic residues surface area and hydrogen bonds changes.
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Affiliation(s)
- Seddigheh Borhani
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Shahriar Arab
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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6
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Pathirage R, Favrot L, Petit C, Yamsek M, Singh S, Mallareddy JR, Rana S, Natarajan A, Ronning DR. Mycobacterium tuberculosis CitA activity is modulated by cysteine oxidation and pyruvate binding. RSC Med Chem 2023; 14:921-933. [PMID: 37252106 PMCID: PMC10211323 DOI: 10.1039/d3md00058c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/05/2023] [Indexed: 11/12/2023] Open
Abstract
As an adaptation for survival during infection, Mycobacterium tuberculosis becomes dormant, reducing its metabolism and growth. Two types of citrate synthases have been identified in Mycobacterium tuberculosis, GltA2 and CitA. Previous work shows that overexpression of CitA, the secondary citrate synthase, stimulates the growth of Mycobacterium tuberculosis under hypoxic conditions without showing accumulation of triacylglycerols and makes mycobacteria more sensitive to antibiotics, suggesting that CitA may play a role as a metabolic switch during infection and may be an interesting TB drug target. To assess the druggability and possible mechanisms of targeting CitA with small-molecule compounds, the CitA crystal structure was solved to 2.1 Å by X-ray crystallography. The solved structure shows that CitA lacks an NADH binding site that would afford allosteric regulation, which is atypical of most citrate synthases. However, a pyruvate molecule is observed within the analogous domain, suggesting pyruvate may instead be the allosteric regulator for CitA. The R149 and R153 residues forming the charged portion of the pyruvate binding pocket were mutated to glutamate and methionine, respectively, to assess the effect of mutations on activity. Protein thermal shift assay shows thermal stabilization of CitA in the presence of pyruvate compared to the two CitA variants designed to decrease pyruvate affinity. Solved crystal structures of both variants show no significant structural changes. However, the catalytic efficiency of the R153M variant increases by 2.6-fold. Additionally, we show that covalent modification of C143 of CitA by Ebselen completely arrests enzyme activity. Similar inhibition is observed using two spirocyclic Michael acceptor containing compounds, which inhibit CitA with ICapp50 values of 6.6 and 10.9 μM. A crystal structure of CitA modified by Ebselen was solved, but significant structural changes were lacking. Considering that covalent modification of C143 inactivates CitA and the proximity of C143 to the pyruvate binding site, this suggests that structural and/or chemical changes in this sub-domain are responsible for regulating CitA enzymatic activity.
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Affiliation(s)
- Rasangi Pathirage
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center Omaha NE 68198 USA
| | - Lorenza Favrot
- Department of Chemistry and Biochemistry, University of Toledo Toledo OH 43606 USA
| | - Cecile Petit
- Department of Chemistry and Biochemistry, University of Toledo Toledo OH 43606 USA
| | - Melvin Yamsek
- Department of Chemistry and Biochemistry, University of Toledo Toledo OH 43606 USA
| | - Sarbjit Singh
- Eppley Institute for Cancer Research, University of Nebraska Medical Center Omaha NE 68198 USA
| | | | - Sandeep Rana
- Eppley Institute for Cancer Research, University of Nebraska Medical Center Omaha NE 68198 USA
| | - Amarnath Natarajan
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center Omaha NE 68198 USA
- Eppley Institute for Cancer Research, University of Nebraska Medical Center Omaha NE 68198 USA
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center Omaha NE 68198 USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center Omaha NE USA
| | - Donald R Ronning
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center Omaha NE 68198 USA
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7
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A Statistical Analysis of the Sequence and Structure of Thermophilic and Non-Thermophilic Proteins. Int J Mol Sci 2022; 23:ijms231710116. [PMID: 36077513 PMCID: PMC9456548 DOI: 10.3390/ijms231710116] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Thermophilic proteins have various practical applications in theoretical research and in industry. In recent years, the demand for thermophilic proteins on an industrial scale has been increasing; therefore, the engineering of thermophilic proteins has become a hot direction in the field of protein engineering. However, the exact mechanism of thermostability of proteins is not yet known, for engineering thermophilic proteins knowing the basis of thermostability is necessary. In order to understand the basis of the thermostability in proteins, we have made a statistical analysis of the sequences, secondary structures, hydrogen bonds, salt bridges, DHA (Donor-Hydrogen-Accepter) angles, and bond lengths of ten pairs of thermophilic proteins and their non-thermophilic orthologous. Our findings suggest that polar amino acids contribute to thermostability in proteins by forming hydrogen bonds and salt bridges which provide resistance against protein denaturation. Short bond length and a wider DHA angle provide greater bond stability in thermophilic proteins. Moreover, the increased frequency of aromatic amino acids in thermophilic proteins contributes to thermal stability by forming more aromatic interactions. Additionally, the coil, helix, and loop in the secondary structure also contribute to thermostability.
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8
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Nezhad NG, Rahman RNZRA, Normi YM, Oslan SN, Shariff FM, Leow TC. Thermostability engineering of industrial enzymes through structure modification. Appl Microbiol Biotechnol 2022; 106:4845-4866. [PMID: 35804158 DOI: 10.1007/s00253-022-12067-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/25/2022] [Accepted: 07/02/2022] [Indexed: 01/14/2023]
Abstract
Thermostability is an essential requirement of enzymes in the industrial processes to catalyze the reactions at high temperatures; thus, enzyme engineering through directed evolution, semi-rational design and rational design are commonly employed to construct desired thermostable mutants. Several strategies are implemented to fulfill enzymes' thermostability demand including decreasing the entropy of the unfolded state through substitutions Gly → Xxx or Xxx → Pro, hydrogen bond, salt bridge, introducing two different simultaneous interactions through single mutant, hydrophobic interaction, filling the hydrophobic cavity core, decreasing surface hydrophobicity, truncating loop, aromatic-aromatic interaction and introducing positively charged residues to enzyme surface. In the current review, horizons about compatibility between secondary structures and substitutions at preferable structural positions to generate the most desirable thermostability in industrial enzymes are broadened. KEY POINTS: • Protein engineering is a powerful tool for generating thermostable industrial enzymes. • Directed evolution and rational design are practical approaches in enzyme engineering. • Substitutions in preferable structural positions can increase thermostability.
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Affiliation(s)
- Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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9
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Some Clues about Enzymes from Psychrophilic Microorganisms. Microorganisms 2022; 10:microorganisms10061161. [PMID: 35744679 PMCID: PMC9227589 DOI: 10.3390/microorganisms10061161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/29/2022] [Accepted: 06/03/2022] [Indexed: 02/04/2023] Open
Abstract
Enzymes purified from psychrophilic microorganisms prove to be efficient catalysts at low temperatures and possess a great potential for biotechnological applications. The low-temperature catalytic activity has to come from specific structural fluctuations involving the active site region, however, the relationship between protein conformational stability and enzymatic activity is subtle. We provide a survey of the thermodynamic stability of globular proteins and their rationalization grounded in a theoretical approach devised by one of us. Furthermore, we provide a link between marginal conformational stability and protein flexibility grounded in the harmonic approximation of the vibrational degrees of freedom, emphasizing the occurrence of long-wavelength and excited vibrations in all globular proteins. Finally, we offer a close view of three enzymes: chloride-dependent α-amylase, citrate synthase, and β-galactosidase.
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10
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Mahfooz S, Shankar G, Narayan J, Singh P, Akhter Y. Simple sequence repeat insertion induced stability and potential 'gain of function' in the proteins of extremophilic bacteria. Extremophiles 2022; 26:17. [PMID: 35511349 DOI: 10.1007/s00792-022-01265-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/11/2022] [Indexed: 11/26/2022]
Abstract
Here, we analysed the genomic evolution in extremophilic bacteria using long simple sequence repeats (SSRs). Frequencies of occurrence, relative abundance (RA) and relative density (RD) of long SSRs were analysed in the genomes of extremophilic bacteria. Thermus aquaticus had the most RA and RD of long SSRs in its coding sequences (110.6 and 1408.3), followed by Rhodoferax antarcticus (77.0 and 1187.4). A positive correlation was observed between G + C content and the RA-RD of long SSRs. Geobacillus kaustophilus, Geobacillus thermoleovorans, Halothermothrix orenii, R. antarcticus, and T. aquaticus preferred trinucleotide repeats within their genomes, whereas others preferred a higher number of tetranucleotide repeats. Gene enrichment showed the presence of these long SSRs in metabolic enzyme encoding genes related to stress tolerance. To analyse the functional implications of SSR insertions, three-dimensional protein structure modelling of SSR containing diguanylate cyclase (DGC) gene encoding protein was carried out. Removal of SSR sequence led to an inappropriate folding and instability of the modelled protein structure.
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Affiliation(s)
- Sahil Mahfooz
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Gauri Shankar
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Jitendra Narayan
- CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi, 110025, India
| | - Pallavi Singh
- Department of Biotechnology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Uttar Pradesh, 226031, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India.
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11
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Tal L, Palayam M, Ron M, Young A, Britt A, Shabek N. A conformational switch in the SCF-D3/MAX2 ubiquitin ligase facilitates strigolactone signalling. NATURE PLANTS 2022; 8:561-573. [PMID: 35484202 DOI: 10.1038/s41477-022-01145-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/28/2022] [Indexed: 05/22/2023]
Abstract
Strigolactones (SLs) are a class of plant hormones that regulate numerous processes of growth and development. SL perception and signal activation involves interaction between F-box E3 ubiquitin ligase D3/MAX2 and DWARF14 (D14) α/β-hydrolase in a SL-dependent manner and targeting of D53/SMXL6/7/8 transcriptional repressors (SMXLs) for proteasome-mediated degradation. D3/MAX2 has been shown to exist in multiple conformational states in which the C-terminal helix (CTH) undergoes a closed-to-open dynamics and regulates D14 binding and SL perception. Despite the multiple modes of D3-D14 interactions found in vitro, the residues that regulate the conformational switch of D3/MAX2 CTH in targeting D53/SMXLs and the subsequent effect on SL signalling remain unclear. Here we elucidate the functional dynamics of ASK1-D3/MAX2 in SL signalling by leveraging conformational switch mutants in vitro and in plants. We report the crystal structure of a dislodged CTH of the ASK1-D3 mutant and demonstrate that disruptions in CTH plasticity via either CRISPR-Cas9 genome editing or expression of point mutation mutants result in impairment of SL signalling. We show that the conformational switch in ASK1-D3/MAX2 CTH directly regulates ubiquitin-mediated protein degradation. A dislodged conformation involved in D53/SMXLs SL-dependent recruitment and ubiquitination and an engaged conformation are required for the release of polyubiquitinated D53/SMXLs and subsequently D14 for proteasomal degradation. Finally, we uncovered an organic acid metabolite that can directly trigger the D3/MAX2 CTH conformational switch. Our findings unravel a new regulatory function of a SKP1-CUL1-F-box ubiquitin ligase in plant signalling.
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Affiliation(s)
- Lior Tal
- Department of Plant Biology, College of Biological Sciences, University of California - Davis, Davis, CA, USA
| | - Malathy Palayam
- Department of Plant Biology, College of Biological Sciences, University of California - Davis, Davis, CA, USA
| | - Mily Ron
- Department of Plant Biology, College of Biological Sciences, University of California - Davis, Davis, CA, USA
| | - Aleczander Young
- Department of Plant Biology, College of Biological Sciences, University of California - Davis, Davis, CA, USA
| | - Anne Britt
- Department of Plant Biology, College of Biological Sciences, University of California - Davis, Davis, CA, USA
| | - Nitzan Shabek
- Department of Plant Biology, College of Biological Sciences, University of California - Davis, Davis, CA, USA.
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12
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Elgrail MM, Chen E, Shaffer MG, Srinivasa V, Griffith MP, Mustapha MM, Shields RK, Van Tyne D, Culyba MJ. Convergent Evolution of Antibiotic Tolerance in Patients with Persistent Methicillin-Resistant Staphylococcus aureus Bacteremia. Infect Immun 2022; 90:e0000122. [PMID: 35285704 PMCID: PMC9022596 DOI: 10.1128/iai.00001-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/12/2022] [Indexed: 02/06/2023] Open
Abstract
Severe infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are often complicated by persistent bacteremia (PB) despite active antibiotic therapy. Antibiotic resistance rarely contributes to MRSA-PB, suggesting an important role for antibiotic tolerance pathways. To identify bacterial factors associated with PB, we sequenced the whole genomes of 206 MRSA isolates derived from 20 patients with PB and looked for genetic signatures of adaptive within-host evolution. We found that genes involved in the tricarboxylic acid cycle (citZ and odhA) and stringent response (rel) bore repeated, independent, protein-altering mutations across multiple infections, indicative of convergent evolution. Both pathways have been linked previously to antibiotic tolerance. Mutations in citZ were identified most frequently, and further study showed they caused antibiotic tolerance through the loss of citrate synthase activity. Isolates harboring mutant alleles (citZ, odhA, and rel) were sampled at a low frequency from each patient but were detected in 10 (50%) of the patients. These results suggest that subpopulations of antibiotic-tolerant mutants emerge commonly during MRSA-PB. Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of hospital-acquired infection. In severe cases, bacteria invade the bloodstream and cause bacteremia, a condition associated with high mortality. We analyzed the genomes of serial MRSA isolates derived from patients with bacteremia that persisted through active antibiotic therapy and found a frequent evolution of pathways leading to antibiotic tolerance. Antibiotic tolerance is distinct from antibiotic resistance, and the role of tolerance in clinical failure of antibiotic therapy is defined poorly. Our results show genetic evidence that perturbation of specific metabolic pathways plays an important role in the ability of MRSA to evade antibiotics during severe infection.
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Affiliation(s)
- Mitra M. Elgrail
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Edwin Chen
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marla G. Shaffer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Vatsala Srinivasa
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marissa P. Griffith
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mustapha M. Mustapha
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ryan K. Shields
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daria Van Tyne
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Matthew J. Culyba
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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13
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Van Wyk JC, Sewell BT, Danson MJ, Tsekoa TL, Sayed MF, Cowan DA. Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase. Curr Res Struct Biol 2022; 4:256-270. [PMID: 36106339 PMCID: PMC9465369 DOI: 10.1016/j.crstbi.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/27/2022] [Accepted: 07/19/2022] [Indexed: 11/20/2022] Open
Abstract
Nitrile hydratases (NHases) are important biocatalysts for the enzymatic conversion of nitriles to industrially-important amides such as acrylamide and nicotinamide. Although thermostability in this enzyme class is generally low, there is not sufficient understanding of its basis for rational enzyme design. The gene expressing the Co-type NHase from the moderate thermophile, Geobacillus pallidus RAPc8 (NRRL B-59396), was subjected to random mutagenesis. Four mutants were selected that were 3 to 15-fold more thermostable than the wild-type NHase, resulting in a 3.4–7.6 kJ/mol increase in the activation energy of thermal inactivation at 63 °C. High resolution X-ray crystal structures (1.15–1.80 Å) were obtained of the wild-type and four mutant enzymes. Mutant 9E, with a resolution of 1.15 Å, is the highest resolution crystal structure obtained for a nitrile hydratase to date. Structural comparisons between the wild-type and mutant enzymes illustrated the importance of salt bridges and hydrogen bonds in enhancing NHase thermostability. These additional interactions variously improved thermostability by increased intra- and inter-subunit interactions, preventing cooperative unfolding of α-helices and stabilising loop regions. Some hydrogen bonds were mediated via a water molecule, specifically highlighting the significance of structured water molecules in protein thermostability. Although knowledge of the mutant structures makes it possible to rationalize their behaviour, it would have been challenging to predict in advance that these mutants would be stabilising. Random mutagenesis yields a 15-fold increase in nitrile hydratase thermostability. Salt bridges and hydrogen bonds improves nitrile hydratase thermostability. Water-mediated hydrogen bonds improves protein thermostability.
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14
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Zhang H, Zhai W, Lin L, Wang P, Xu X, Wei W, Wei D. In Silico Rational Design and Protein Engineering of Disulfide Bridges of an α‐Amylase from
Geobacillus
sp. to Improve Thermostability. STARCH-STARKE 2021. [DOI: 10.1002/star.202000274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Heng Zhang
- State Key Laboratory of Bioreactor Engineering Newworld Institute of Biotechnology East China University of Science and Technology Shanghai 200237 P. R. China
| | - Wenxin Zhai
- State Key Laboratory of Bioreactor Engineering Newworld Institute of Biotechnology East China University of Science and Technology Shanghai 200237 P. R. China
| | - Lin Lin
- Shanghai University of Medicine and Health Sciences Shanghai 200093 P. R. China
- Research Laboratory for Functional Nanomaterial National Engineering Research Center for Nanotechnology Shanghai 200241 P. R. China
| | - Ping Wang
- Weigao Shanghai R&D Center Shanghai 201203 P. R. China
| | - Xiangyang Xu
- Zaozhuang jie nuo enzyme co. ltd Zaozhuang 277100 P. R. China
| | - Wei Wei
- State Key Laboratory of Bioreactor Engineering Newworld Institute of Biotechnology East China University of Science and Technology Shanghai 200237 P. R. China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering Newworld Institute of Biotechnology East China University of Science and Technology Shanghai 200237 P. R. China
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15
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Yin S, Friedrich S, Hrupins V, Cox RJ. In vitro studies of maleidride-forming enzymes. RSC Adv 2021; 11:14922-14931. [PMID: 35424071 PMCID: PMC8697804 DOI: 10.1039/d1ra02118d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/15/2021] [Indexed: 11/21/2022] Open
Abstract
In vitro assays of enzymes involved in the biosynthesis of maleidrides from polyketides in fungi were performed. The results show that the enzymes are closely related to primary metabolism enzymes of the citric acid cycle in terms of stereochemical preferences, but with an expanded substrate selectivity. A key citrate synthase can react both saturated and unsaturated acyl CoA substrates to give solely anti substituted citrates. This undergoes anti-dehydration to afford an unsaturated precursor which is cyclised in vitro by ketosteroid-isomerase-like enzymes to give byssochlamic acid.
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Affiliation(s)
- Sen Yin
- OCI, BMWZ, Leibniz University of Hannover Schneiderberg 38 30167 Hannover Germany
| | - Steffen Friedrich
- OCI, BMWZ, Leibniz University of Hannover Schneiderberg 38 30167 Hannover Germany
| | - Vjaceslavs Hrupins
- OCI, BMWZ, Leibniz University of Hannover Schneiderberg 38 30167 Hannover Germany
| | - Russell J Cox
- OCI, BMWZ, Leibniz University of Hannover Schneiderberg 38 30167 Hannover Germany
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16
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Evolution of Protein Structure and Stability in Global Warming. Int J Mol Sci 2020; 21:ijms21249662. [PMID: 33352933 PMCID: PMC7767258 DOI: 10.3390/ijms21249662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
This review focuses on the molecular signatures of protein structures in relation to evolution and survival in global warming. It is based on the premise that the power of evolutionary selection may lead to thermotolerant organisms that will repopulate the planet and continue life in general, but perhaps with different kinds of flora and fauna. Our focus is on molecular mechanisms, whereby known examples of thermoresistance and their physicochemical characteristics were noted. A comparison of interactions of diverse residues in proteins from thermophilic and mesophilic organisms, as well as reverse genetic studies, revealed a set of imprecise molecular signatures that pointed to major roles of hydrophobicity, solvent accessibility, disulfide bonds, hydrogen bonds, ionic and π-electron interactions, and an overall condensed packing of the higher-order structure, especially in the hydrophobic regions. Regardless of mutations, specialized protein chaperones may play a cardinal role. In evolutionary terms, thermoresistance to global warming will likely occur in stepwise mutational changes, conforming to the molecular signatures, such that each "intermediate" fits a temporary niche through punctuated equilibrium, while maintaining protein functionality. Finally, the population response of different species to global warming may vary substantially, and, as such, some may evolve while others will undergo catastrophic mass extinction.
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17
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Pang WC, Ramli ANM, Hamid AAA. Comparative modelling studies of fruit bromelain using molecular dynamics simulation. J Mol Model 2020; 26:142. [PMID: 32417971 DOI: 10.1007/s00894-020-04398-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/28/2020] [Indexed: 12/25/2022]
Abstract
Fruit bromelain is a cysteine protease accumulated in pineapple fruits. This proteolytic enzyme has received high demand for industrial and therapeutic applications. In this study, fruit bromelain sequences QIM61759, QIM61760 and QIM61761 were retrieved from the National Center for Biotechnology Information (NCBI) Genbank Database. The tertiary structure of fruit bromelain QIM61759, QIM61760 and QIM61761 was generated by using MODELLER. The result revealed that the local stereochemical quality of the generated models was improved by using multiple templates during modelling process. Moreover, by comparing with the available papain model, structural analysis provides an insight on how pro-peptide functions as a scaffold in fruit bromelain folding and contributing to inactivation of mature protein. The structural analysis also disclosed the similarities and differences between these models. Lastly, thermal stability of fruit bromelain was studied. Molecular dynamics simulation of fruit bromelain structures at several selected temperatures demonstrated how fruit bromelain responds to elevation of temperature.
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Affiliation(s)
- Wei Cheng Pang
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Aizi Nor Mazila Ramli
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia. .,Bio Aromatic Research Centre of Excellence, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia.,Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
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18
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Collier AM, Nemtsova Y, Kuber N, Banach-Petrosky W, Modak A, Sleat DE, Nanda V, Lobel P. Lysosomal protein thermal stability does not correlate with cellular half-life: global observations and a case study of tripeptidyl-peptidase 1. Biochem J 2020; 477:727-745. [PMID: 31957806 PMCID: PMC8442665 DOI: 10.1042/bcj20190874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/16/2022]
Abstract
Late-infantile neuronal ceroid lipofuscinosis (LINCL) is a neurodegenerative lysosomal storage disorder caused by mutations in the gene encoding the protease tripeptidyl-peptidase 1 (TPP1). Progression of LINCL can be slowed or halted by enzyme replacement therapy, where recombinant human TPP1 is administered to patients. In this study, we utilized protein engineering techniques to increase the stability of recombinant TPP1 with the rationale that this may lengthen its lysosomal half-life, potentially increasing the potency of the therapeutic protein. Utilizing multiple structure-based methods that have been shown to increase the stability of other proteins, we have generated and evaluated over 70 TPP1 variants. The most effective mutation, R465G, increased the melting temperature of TPP1 from 55.6°C to 64.4°C and increased its enzymatic half-life at 60°C from 5.4 min to 21.9 min. However, the intracellular half-life of R465G and all other variants tested in cultured LINCL patient-derived lymphoblasts was similar to that of WT TPP1. These results provide structure/function insights into TPP1 and indicate that improving in vitro thermal stability alone is insufficient to generate TPP1 variants with improved physiological stability. This conclusion is supported by a proteome-wide analysis that indicates that lysosomal proteins have higher melting temperatures but also higher turnover rates than proteins of other organelles. These results have implications for similar efforts where protein engineering approaches, which are frequently evaluated in vitro, may be considered for improving the physiological properties of proteins, particularly those that function in the lysosomal environment.
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Affiliation(s)
- Aaron M. Collier
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - Yuliya Nemtsova
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - Narendra Kuber
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | | | - Anurag Modak
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - David E. Sleat
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
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19
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Ge YD, Jiang LL, Hou SL, Su FZ, Wang P, Zhang G. Heteroexpression and biochemical characterization of thermostable citrate synthase from the cyanobacteria Anabaena sp. PCC7120. Protein Expr Purif 2019; 168:105565. [PMID: 31887428 DOI: 10.1016/j.pep.2019.105565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/26/2019] [Accepted: 12/26/2019] [Indexed: 11/25/2022]
Abstract
The present study recombinantly expressed a citrate synthase from cyanobacteria Anabaena sp. PCC7120 (AnCS) in Escherichia coli and characterized its enzymatic activity. The molecular mass of native AnCS was 88,533.1 Da containing two 44,162.7 Da subunits. Recombinant AnCS revealed the highest activity at pH 9.0 and 25 °C. AnCS displayed high thermal stability with a half-life time (t1/2) of approximately 6.5 h at 60 °C, which was more thermostable than most CS from general organisms, but less than those from hyperthermophilic bacteria. The Km values of oxaloacetate and acetyl-CoA were 138.50 and 18.15 μM respectively, suggesting a higher affinity to acetyl-CoA than oxaloacetate. Our inhibition assays showed that AnCS activity was not severely affected by most metal ions, but was strongly inhibited by Cu2+ and Zn2+. Treatments with ATP, ADP, AMP, NADH, and DTT depressed the AnCS activity. Overall, our results provide information on the enzymatic properties of AnCS, which contributes to the basic knowledge on CS selection for industrial utilizations.
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Affiliation(s)
- Ya-Dong Ge
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Lu-Lu Jiang
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Shao-Lin Hou
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Feng-Zhi Su
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Peng Wang
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Gen Zhang
- Shenzhen GenProMetab Biotechnology Company Limited, Shenzhen, 518000, China.
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20
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Ge YD, Hou SL, Jiang LL, Su FZ, Wang P. Expression and characterization of a thermostable citrate synthase from Microcystis aeruginosa PCC7806. FEMS Microbiol Lett 2019; 366:5637861. [PMID: 31755935 DOI: 10.1093/femsle/fnz236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/21/2019] [Indexed: 12/13/2022] Open
Abstract
Citrate synthase (CS) is an important enzyme in energy conversion and material circulation, participating in many important biochemical processes. In the present study, CS from Microcystis aeruginosa PCC7806 (MaCS) was cloned and expressed in Escherichia coli Rosetta (DE3). The recombinant MaCS was purified and its enzymological properties were characterized. The results showed that MaCS formed dimers in native status. The optimum temperature and pH of MaCS was 30°C and 8.2, respectively. MaCS displayed relative high thermal stability. Treatment at 50°C for 20 min only decreased 11.30% activity of MaCS and the half-life of MaCS was approximately 35 min at 55°C. The kcat and Km of acetyl-CoA and oxaloacetic acid were 17.133 s-1 (kcat) and 11.62 μM (Km), 24.502 s-1 and 103.00 μM, respectively. MaCS activity was not drastically inhibited by monovalent ions and NADH but depressed by divalent ions and some small molecular compounds, especially Mg2+, Zn2+, Co2+ and DTT. Overall, these data contributed to further understanding of energy metabolism in cyanobacteria and also provided basic information for industrial application of CS.
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Affiliation(s)
- Ya-Dong Ge
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Shao-Lin Hou
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Lu-Lu Jiang
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Feng-Zhi Su
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Peng Wang
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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21
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Kumar R, Goomber S, Kaur J. Engineering lipases for temperature adaptation: Structure function correlation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140261. [PMID: 31401312 DOI: 10.1016/j.bbapap.2019.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 01/13/2023]
Abstract
Bacillus lipases are industrially attractive enzymes due to their broad substrate specificity and optimum alkaline pH. However, narrow temperature range of action and low thermostability restrain their optimal use and thus, necessitate attention. Several laboratories are engaged in protein engineering of Bacillus lipases to generate variants with improved attributes for decades using techniques such as directed evolution or rational design. This review summarizes the effect of mutations on the conformational changes through in silico modeling and their manifestation with respect to various biochemical parameters. Various studies have been put together to develop a perspective on the molecular basis of biocatalysis of lipases holding industrial importance.
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Affiliation(s)
- Rakesh Kumar
- Department of Biotechnology, Panjab University, Chandigarh 160014, India; Department of Microbiology and Cell Biology, Indian Institute Of Science, Bangalore, Karnataka 560012, India
| | - Shelly Goomber
- Department of Biotechnology, Panjab University, Chandigarh 160014, India; National Institute of Malaria Research, Dwarka, New Delhi, Delhi 110077, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh 160014, India.
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22
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Banach M, Wiśniowski Z, Ptak M, Roterman I. Aggregation-promoting conditions necessary to create the complexes by acylphosphatase from the hyperthermophile Sulfolobus solfataricus. BIO-ALGORITHMS AND MED-SYSTEMS 2019. [DOI: 10.1515/bams-2019-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The structural transition from the globular to the amyloid form of proteins requires aggregation-promoting conditions. The protein example of this category is acylphosphatase from the hyperthermophile Sulfolobus solfataricus. This protein represents a structure with a well-defined hydrophobic core. This is why the complexation (including oligomerization) of this protein is of low probability. The chain fragment participating in aggregation in comparison to the status with respect to the fuzzy oil drop model is discussed in this paper.
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23
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Xia Q, Ding Y. Thermostability of Lipase A and Dynamic Communication Based on Residue Interaction Network. Protein Pept Lett 2019; 26:702-716. [PMID: 31215367 DOI: 10.2174/0929866526666190617091812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/10/2019] [Accepted: 04/25/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Dynamic communication caused by mutation affects protein stability. The main objective of this study is to explore how mutations affect communication and to provide further insight into the relationship between heat resistance and signal propagation of Bacillus subtilis lipase (Lip A). METHODS The relationship between dynamic communication and Lip A thermostability is studied by long-time MD simulation and residue interaction network. The Dijkstra algorithm is used to get the shortest path of each residue pair. Subsequently, time-series frequent paths and spatio-temporal frequent paths are mined through an Apriori-like algorithm. RESULTS Time-series frequent paths show that the communication between residue pairs, both in wild-type lipase (WTL) and mutant 6B, becomes chaotic with an increase in temperature; however, more residues in 6B can maintain stable communication at high temperature, which may be associated with the structural rigidity. Furthermore, spatio-temporal frequent paths reflect the interactions among secondary structures. For WTL at 300K, β7, αC, αB, the longest loop, αA and αF contact frequently. The 310-helix between β3 and αA is penetrated by spatio-temporal frequent paths. At 400K, only αC can be frequently transmitted. For 6B, when at 300K, αA and αF are in more tight contact by spatio-temporal frequent paths though I157M and N166Y. Moreover, the rigidity of the active site His156 and the C-terminal of Lip A are increased, as reflected by the spatio-temporal frequent paths. At 400K, αA and αF, 310-helix between β3 and αA, the longest loop, and the loop where the active site Asp133 is located can still maintain stable communication. CONCLUSION From the perspective of residue dynamic communication, it is obviously found that mutations cause changes in interactions between secondary structures and enhance the rigidity of the structure, contributing to the thermal stability and functional activity of 6B.
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Affiliation(s)
- Qian Xia
- Laboratory of Media Design and Software Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yanrui Ding
- Laboratory of Media Design and Software Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.,Key Laboratory of Industrial Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
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24
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An allosteric mechanism for potent inhibition of human ATP-citrate lyase. Nature 2019; 568:566-570. [PMID: 30944472 DOI: 10.1038/s41586-019-1094-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/08/2019] [Indexed: 11/08/2022]
Abstract
ATP-citrate lyase (ACLY) is a central metabolic enzyme and catalyses the ATP-dependent conversion of citrate and coenzyme A (CoA) to oxaloacetate and acetyl-CoA1-5. The acetyl-CoA product is crucial for the metabolism of fatty acids6,7, the biosynthesis of cholesterol8, and the acetylation and prenylation of proteins9,10. There has been considerable interest in ACLY as a target for anti-cancer drugs, because many cancer cells depend on its activity for proliferation2,5,11. ACLY is also a target against dyslipidaemia and hepatic steatosis, with a compound currently in phase 3 clinical trials4,5. Many inhibitors of ACLY have been reported, but most of them have weak activity5. Here we report the development of a series of low nanomolar, small-molecule inhibitors of human ACLY. We have also determined the structure of the full-length human ACLY homo-tetramer in complex with one of these inhibitors (NDI-091143) by cryo-electron microscopy, which reveals an unexpected mechanism of inhibition. The compound is located in an allosteric, mostly hydrophobic cavity next to the citrate-binding site, and requires extensive conformational changes in the enzyme that indirectly disrupt citrate binding. The observed binding mode is supported by and explains the structure-activity relationships of these compounds. This allosteric site greatly enhances the 'druggability' of ACLY and represents an attractive target for the development of new ACLY inhibitors.
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25
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Verschueren KHG, Blanchet C, Felix J, Dansercoer A, De Vos D, Bloch Y, Van Beeumen J, Svergun D, Gutsche I, Savvides SN, Verstraete K. Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle. Nature 2019; 568:571-575. [DOI: 10.1038/s41586-019-1095-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 03/08/2019] [Indexed: 01/28/2023]
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26
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Kumar S, Dangi AK, Shukla P, Baishya D, Khare SK. Thermozymes: Adaptive strategies and tools for their biotechnological applications. BIORESOURCE TECHNOLOGY 2019; 278:372-382. [PMID: 30709766 DOI: 10.1016/j.biortech.2019.01.088] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 05/10/2023]
Abstract
In today's scenario of global climate change, there is a colossal demand for sustainable industrial processes and enzymes from thermophiles. Plausibly, thermozymes are an important toolkit, as they are known to be polyextremophilic in nature. Small genome size and diverse molecular conformational modifications have been implicated in devising adaptive strategies. Besides, the utilization of chemical technology and gene editing attributions according to mechanical necessities are the additional key factor for efficacious bioprocess development. Microbial thermozymes have been extensively used in waste management, biofuel, food, paper, detergent, medicinal and pharmaceutical industries. To understand the strength of enzymes at higher temperatures different models utilize X-ray structures of thermostable proteins, machine learning calculations, neural networks, but unified adaptive measures are yet to be totally comprehended. The present review provides a recent updates on thermozymes and various interdisciplinary applications including the aspects of thermophiles bioengineering utilizing synthetic biology and gene editing tools.
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Affiliation(s)
- Sumit Kumar
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Arun K Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Debabrat Baishya
- Department of Bioengineering and Technology, Institute of Science and Technology, Gauhati University, Guwahati 781014, Assam, India
| | - Sunil K Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India.
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Lee SH, Son HF, Kim KJ. Structural insights into the inhibition properties of archaeon citrate synthase from Metallosphaera sedula. PLoS One 2019; 14:e0212807. [PMID: 30794680 PMCID: PMC6386500 DOI: 10.1371/journal.pone.0212807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/08/2019] [Indexed: 11/19/2022] Open
Abstract
Metallosphaera sedula is a thermoacidophilic archaeon and has an incomplete TCA/glyoxylate cycle that is used for production of biosynthetic precursors of essential metabolites. Citrate synthase from M. sedula (MsCS) is an enzyme involved in the first step of the incomplete TCA/glyoxylate cycle by converting oxaloacetate and acetyl-CoA into citrate and coenzyme A. To elucidate the inhibition properties of MsCS, we determined its crystal structure at 1.7 Å resolution. Like other Type-I CS, MsCS functions as a dimer and each monomer consists of two distinct domains, a large domain and a small domain. The oxaloacetate binding site locates at the cleft between the two domains, and the active site was more closed upon binding of the oxaloacetate substrate than binding of the citrate product. Interestingly, the inhibition kinetic analysis showed that, unlike other Type-I CSs, MsCS is non-competitively inhibited by NADH. Finally, amino acids and structural comparison of MsCS with other Type-II CSs, which were reported to be non-competitively inhibited by NADH, revealed that MsCS has quite unique NADH binding mode for non-competitive inhibition.
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Affiliation(s)
- Seul Hoo Lee
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, Republic of Korea
| | - Hyeoncheol Francis Son
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, Republic of Korea
- * E-mail:
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28
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Lee SH, Kim KJ. Crystal structure and biochemical properties of msed_0281, the citrate synthase from Metallosphaera sedula. Biochem Biophys Res Commun 2019; 509:722-727. [PMID: 30611567 DOI: 10.1016/j.bbrc.2018.12.172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 12/27/2018] [Indexed: 11/25/2022]
Abstract
Metallosphaera sedula is a thermoacidophilic archaeon that has carbon fixation ability using the 3-hydroxypropionate/4-hydroxybutyrate(3-HP/4-HB) cycle, and has an incomplete TCA cycle to produce necessary biosynthetic precursors. The citrate synthase from M. sedula (MsCS) is an enzyme involved in the first step of the incomplete TCA cycle, catalyzing the conversion of oxaloacetate and acetyl-CoA into citrate and coenzyme A. To investigate the molecular mechanism of MsCS, we determined its crystal structure at 1.8 Å resolution. As other known CSs, MsCS functions as a dimer, and each monomer consists of two domains, a large domain and a small domain. We also determined the structure of the complex with acetyl-CoA and revealed the acetyl-CoA binding mode of MsCS. Structural comparison of MsCS with another CS in complex with oxaloacetate enabled us to predict the oxaloacetate binding site. Moreover, we performed inhibitory kinetic analyses of MsCS, and showed that the protein is inhibited by citrate and ATP by competitive and non-competitive inhibition modes, respectively, but not by NADH. Based on these results, we suggest that MsCS belongs to the type-I CS with structural and biochemical properties similar to those of CSs involved in the conventional TCA cycle.
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Affiliation(s)
- Seul Hoo Lee
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.
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29
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Matsumoto A, Uehara Y, Shimizu Y, Ueda T, Uchiumi T, Ito K. High-resolution crystal structure of peptidyl-tRNA hydrolase fromThermus thermophilus. Proteins 2018; 87:226-235. [DOI: 10.1002/prot.25643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/11/2018] [Accepted: 11/29/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Ami Matsumoto
- Faculty of Science, Department of Biology; Niigata University; Niigata Japan
| | - Yuji Uehara
- Faculty of Science, Department of Biology; Niigata University; Niigata Japan
| | - Yoshihiro Shimizu
- Department of Medical Genome Sciences; Graduate School of Frontier Sciences, The University of Tokyo; Chiba Japan
- Laboratory for Cell-Free Protein Synthesis; RIKEN Center for Biosystems Dynamics Research; Osaka Japan
| | - Takuya Ueda
- Department of Medical Genome Sciences; Graduate School of Frontier Sciences, The University of Tokyo; Chiba Japan
| | - Toshio Uchiumi
- Faculty of Science, Department of Biology; Niigata University; Niigata Japan
| | - Kosuke Ito
- Faculty of Science, Department of Biology; Niigata University; Niigata Japan
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30
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Pcal_0970: an extremely thermostable l-asparaginase from Pyrobaculum calidifontis with no detectable glutaminase activity. Folia Microbiol (Praha) 2018; 64:313-320. [DOI: 10.1007/s12223-018-0656-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
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31
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Chakravorty D, Patra S. RankProt: A multi criteria-ranking platform to attain protein thermostabilizing mutations and its in vitro applications - Attribute based prediction method on the principles of Analytical Hierarchical Process. PLoS One 2018; 13:e0203036. [PMID: 30286107 PMCID: PMC6171822 DOI: 10.1371/journal.pone.0203036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/14/2018] [Indexed: 01/15/2023] Open
Abstract
Attaining recombinant thermostable proteins is still a challenge for protein engineering. The complexity is the length of time and enormous efforts required to achieve the desired results. Present work proposes a novel and economic strategy of attaining protein thermostability by predicting site-specific mutations at the shortest possible time. The success of the approach can be attributed to Analytical Hierarchical Process and the outcome was a rationalized thermostable mutation(s) prediction tool- RankProt. Briefly the method involved ranking of 17 biophysical protein features as class predictors, derived from 127 pairs of thermostable and mesostable proteins. Among the 17 predictors, ionic interactions and main-chain to main-chain hydrogen bonds were the highest ranked features with eigen value of 0.091. The success of the tool was judged by multi-fold in silico validation tests and it achieved the prediction accuracy of 91% with AUC 0.927. Further, in vitro validation was carried out by predicting thermostabilizing mutations for mesostable Bacillus subtilis lipase and performing the predicted mutations by multi-site directed mutagenesis. The rationalized method was successful to render the lipase thermostable with optimum temperature stability and Tm increase by 20°C and 7°C respectively. Conclusively it can be said that it was the minimum number of mutations in comparison to the number of mutations incorporated to render Bacillus subtilis lipase thermostable, by directed evolution techniques. The present work shows that protein stabilizing mutations can be rationally designed by balancing the biophysical pleiotropy of proteins, in accordance to the selection pressure.
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Affiliation(s)
- Debamitra Chakravorty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- * E-mail:
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32
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Hayes K, Noor M, Djeghader A, Armshaw P, Pembroke T, Tofail S, Soulimane T. The quaternary structure of Thermus thermophilus aldehyde dehydrogenase is stabilized by an evolutionary distinct C-terminal arm extension. Sci Rep 2018; 8:13327. [PMID: 30190503 PMCID: PMC6127216 DOI: 10.1038/s41598-018-31724-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/22/2018] [Indexed: 12/04/2022] Open
Abstract
Aldehyde dehydrogenases (ALDH) form a superfamily of dimeric or tetrameric enzymes that catalyze the oxidation of a broad range of aldehydes into their corresponding carboxylic acids with the concomitant reduction of the cofactor NAD(P) into NAD(P)H. Despite their varied polypeptide chain length and oligomerisation states, ALDHs possess a conserved architecture of three domains: the catalytic domain, NAD(P)+ binding domain, and the oligomerization domain. Here, we describe the structure and function of the ALDH from Thermus thermophilus (ALDHTt) which exhibits non-canonical features of both dimeric and tetrameric ALDH and a previously uncharacterized C-terminal arm extension forming novel interactions with the N-terminus in the quaternary structure. This unusual tail also interacts closely with the substrate entry tunnel in each monomer providing further mechanistic detail for the recent discovery of tail-mediated activity regulation in ALDH. However, due to the novel distal extension of the tail of ALDHTt and stabilizing termini-interactions, the current model of tail-mediated substrate access is not apparent in ALDHTt. The discovery of such a long tail in a deeply and early branching phylum such as Deinococcus-Thermus indicates that ALDHTt may be an ancestral or primordial metabolic model of study. This structure provides invaluable evidence of how metabolic regulation has evolved and provides a link to early enzyme regulatory adaptations.
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Affiliation(s)
- Kevin Hayes
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Mohamed Noor
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Ahmed Djeghader
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Patricia Armshaw
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Tony Pembroke
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Syed Tofail
- Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland.,Physics Department, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Tewfik Soulimane
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland. .,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland.
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33
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Guo J, Coker AR, Wood SP, Cooper JB, Keegan RM, Ahmad N, Muhammad MA, Rashid N, Akhtar M. Structure and function of the type III pullulan hydrolase from Thermococcus kodakarensis. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:305-314. [PMID: 29652257 DOI: 10.1107/s2059798318001754] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 01/29/2018] [Indexed: 11/10/2022]
Abstract
Pullulan-hydrolysing enzymes, more commonly known as debranching enzymes for starch and other polysaccharides, are of great interest and have been widely used in the starch-saccharification industry. Type III pullulan hydrolase from Thermococcus kodakarensis (TK-PUL) possesses both pullulanase and α-amylase activities. Until now, only two enzymes in this class, which are capable of hydrolysing both α-1,4- and α-1,6-glycosidic bonds in pullulan to produce a mixture of maltose, panose and maltotriose, have been described. TK-PUL shows highest activity in the temperature range 95-100°C and has a pH optimum in the range 3.5-4.2. Its unique ability to hydrolyse maltotriose into maltose and glucose has not been reported for other homologous enzymes. The crystal structure of TK-PUL has been determined at a resolution of 2.8 Å and represents the first analysis of a type III pullulan hydrolyse. The structure reveals that the last part of the N-terminal domain and the C-terminal domain are significantly different from homologous structures. In addition, the loop regions at the active-site end of the central catalytic domain are quite different. The enzyme has a well defined calcium-binding site and possesses a rare vicinal disulfide bridge. The thermostability of TK-PUL and its homologues may be attributable to several factors, including the increased content of salt bridges, helical segments, Pro, Arg and Tyr residues and the decreased content of serine.
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Affiliation(s)
- Jingxu Guo
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Alun R Coker
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Steve P Wood
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Jonathan B Cooper
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Ronan M Keegan
- CCP4, Research Complex at Harwell and Science and Technology Facilities Council, Rutherford Appleton Laboratories, Harwell Oxford, Didcot OX11 0FA, England
| | - Nasir Ahmad
- Institute of Agricultural Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Majida Atta Muhammad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Muhummad Akhtar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
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34
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Gao H, Li C, Bandikari R, Liu Z, Hu N, Yong Q. A novel cold-adapted esterase from Enterobacter cloacae: Characterization and improvement of its activity and thermostability via the site of Tyr193Cys. Microb Cell Fact 2018; 17:45. [PMID: 29554914 PMCID: PMC5858142 DOI: 10.1186/s12934-018-0885-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 02/26/2018] [Indexed: 11/10/2022] Open
Abstract
Background In industries lipolytic reactions occur in insensitive conditions such as high temperature thus novel stout esterases with unique properties are attracts to the industrial application. Protein engineering is the tool to obtain desirable characters of enzymes. A novel esterase gene was isolated from South China Sea and subjected to a random mutagenesis and site directed mutagenesis for higher activity and thermo-stability compared to wild type. Results A novel esterase showed the highest hydrolytic activity against p-nitrophenyl acetate (pNPA, C2) and the optimal activity at 40 °C and pH 8.5. It was a cold-adapted enzyme and retained approximately 40% of its maximum activity at 0 °C. A mutant, with higher activity and thermo-stability was obtained by random mutagenesis. Kinetic analysis indicated that the mutant Val29Ala/Tyr193Cys shown 43.5% decrease in Km, 2.6-fold increase in Kcat, and 4.7-fold increase in Kcat/Km relative to the wild type. Single mutants V29A and Y193C were constructed and their kinetic parameters were measured. The results showed that the values of Km, Kcat, and Kcat/Km of V29A were similar to those of the wild type while Y193C showed 52.7% decrease in Km, 2.7-fold increase in Kcat, and 5.6-fold increase in Kcat/Km compared with the wild type. The 3-D structure and docking analysis revealed that the replacement of Tyr by Cys could enlarge the binding pocket. Moreover Y193C also showed a better thermo-stability for the reason its higher hydrophobicity and retained 67% relative activity after incubation for 3 h at 50 °C. Conclusions The superior quality of modified esterase suggested it has great potential application in extreme conditions and the mutational work recommended that important information for the study of esterase structure and function. Electronic supplementary material The online version of this article (10.1186/s12934-018-0885-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haofeng Gao
- College of Light Industry Science and Engineering, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210018, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211800, China
| | - Chanjuan Li
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ramesh Bandikari
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ziduo Liu
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nan Hu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211800, China.
| | - Qiang Yong
- College of Light Industry Science and Engineering, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210018, China.
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35
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Hendriks A, van Lier J, de Kreuk M. Growth media in anaerobic fermentative processes: The underestimated potential of thermophilic fermentation and anaerobic digestion. Biotechnol Adv 2018; 36:1-13. [DOI: 10.1016/j.biotechadv.2017.08.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/08/2017] [Accepted: 08/30/2017] [Indexed: 11/24/2022]
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36
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Bibi T, Ali M, Rashid N, Muhammad MA, Akhtar M. Enhancement of gene expression in Escherichia coli and characterization of highly stable ATP-dependent glucokinase from Pyrobaculum calidifontis. Extremophiles 2017; 22:247-257. [DOI: 10.1007/s00792-017-0993-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/08/2017] [Indexed: 11/30/2022]
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37
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Anand S, Sharma C. Glycine-rich loop encompassing active site at interface of hexameric M. tuberculosis Eis protein contributes to its structural stability and activity. Int J Biol Macromol 2017; 109:124-135. [PMID: 29247728 DOI: 10.1016/j.ijbiomac.2017.12.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/23/2022]
Abstract
RvEis is a crucial thermostable hexameric aminoglycoside acetyltransferase of Mycobacterium tuberculosis, overexpression of which confers Kanamycin resistance in clinical strains. The thermostability associated with hexameric RvEis is important for the enhanced intracellular survival of mycobacteria. However, the structural determinants responsible for its thermal stability remain unexplored. In this study, we have assessed the role of glycines of conserved glycine-rich motif (G123GIYG127) present at the oligomeric interface in the hydrophobic core of RvEis in sustenance of its structural stability, oligomerization and functional activity. Substitution of glycines to alanine (G123A/G127A) result in significant decrease in melting temperature (Tm), reduction in the oligomerization with concomitant increase in the monomeric form and higher susceptibility towards the denaturants like GdmCl and urea relative to wild type. G123A/G127A mutant displayed lower catalytic efficiency (kcat/Km) and is completely inactive at 60 °C. ANS binding assay and the complete dissociation of hexameric complex into monomers at lower concentration of urea in G123A/G127A relative to wtRvEis suggests that altered hydrophobic environment could be the reason for its instability. In sum, these results demonstrate the role of G123GIYG127 motif in structural stability and activity of RvEis.
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Affiliation(s)
- Shashi Anand
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Charu Sharma
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India.
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38
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Sindhu R, Binod P, Madhavan A, Beevi US, Mathew AK, Abraham A, Pandey A, Kumar V. Molecular improvements in microbial α-amylases for enhanced stability and catalytic efficiency. BIORESOURCE TECHNOLOGY 2017; 245:1740-1748. [PMID: 28478894 DOI: 10.1016/j.biortech.2017.04.098] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
α-Amylases is one of the most important industrial enzyme which contributes to 25% of the industrial enzyme market. Though it is produced by plant, animals and microbial source, those from microbial source seems to have potential applications due to their stability and economic viability. However a large number of α-amylases from different sources have been detailed in the literature, only few numbers of them could withstand the harsh industrial conditions. Thermo-stability, pH tolerance, calcium independency and oxidant stability and starch hydrolyzing efficiency are the crucial qualities for α-amylase in starch based industries. Microbes can be genetically modified and fine tuning can be done for the production of enzymes with desired characteristics for specific applications. This review focuses on the native and recombinant α-amylases from microorganisms, their heterologous production and the recent molecular strategies which help to improve the properties of this industrial enzyme.
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Affiliation(s)
- Raveendran Sindhu
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India.
| | - Parameswaran Binod
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Aravind Madhavan
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India
| | - Ummalyma Sabeela Beevi
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Institute of Bioresources and Sustainable Development, Takyelpat, Imphal 795 001, India
| | - Anil Kuruvilla Mathew
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Amith Abraham
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Ashok Pandey
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Center of Innovative and Applied Bioprocessing, Sector 81, Mohali, Punjab, India
| | - Vinod Kumar
- Center of Innovative and Applied Bioprocessing, Sector 81, Mohali, Punjab, India
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39
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Aziz I, Rashid N, Ashraf R, Siddiqui MA, Imanaka T, Akhtar M. Pcal_0632, a phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Pyrobaculum calidifontis. Extremophiles 2017; 22:121-129. [DOI: 10.1007/s00792-017-0982-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/20/2017] [Indexed: 11/25/2022]
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40
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Shah MA, Mishra S, Chaudhuri TK. Marginal stability drives irreversible unfolding of large multi-domain family 3 glycosylhydrolases from thermo-tolerant yeast. Int J Biol Macromol 2017; 108:1322-1330. [PMID: 29141194 DOI: 10.1016/j.ijbiomac.2017.11.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/01/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
Abstract
Protein folding is an extremely complex and fast, yet perfectly defined process, involving interplay of many intra and inter-molecular forces. In vitro, these molecular interactions are reversible for many proteins e.g., smaller and monomeric, organized into single domains. However, refolding of larger multi-domain/multimeric proteins is much more complicated, proceeds in a hierarchal way and is often irreversible. In a comparative study on two large, multi-domain and multimeric isozymes, β-glucosidase I (BGLI) and β-glucosidase II (BGLII) from Pichia etchellsii, we studied spontaneous and assisted refolding under three denaturing conditions viz. GdnHCl, alkaline pH and heat. During refolding, higher refolding yields were obtained for BGLII in case of pH induced unfolding (13.89%±0.25) than BGLI (6%±0.85) while for GdnHCl induced unfolding, refolding was marginal (BGLI=5%±0.5; BGLII=6%±0.69). Thermal unfolding was irreversible while assisted refolding also showed little structural gain for both proteins. When the apparent free energies of unfolding (ΔGUapp) were calculated from GdnHCl unfolding data, their values were strikingly found to be lower (BGLI ΔGUapp=3.02kcal/mol; BGLII ΔGUapp=2.99kcal/mol) than reported for globular (ΔGU=5-15kcal/mol)/multimeric proteins (ΔGU=23-29kcal/mol) indicating marginal stability results in low refolding.
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Affiliation(s)
- Mohammad Asif Shah
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Saroj Mishra
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Tapan Kumar Chaudhuri
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India; Ksuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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41
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Guo J, Coker AR, Wood SP, Cooper JB, Chohan SM, Rashid N, Akhtar M. Structure and function of the thermostableL-asparaginase fromThermococcus kodakarensis. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:889-895. [DOI: 10.1107/s2059798317014711] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 10/11/2017] [Indexed: 11/10/2022]
Abstract
L-Asparaginases catalyse the hydrolysis of asparagine to aspartic acid and ammonia. In addition, L-asparaginase is involved in the biosynthesis of amino acids such as lysine, methionine and threonine. These enzymes have been used as chemotherapeutic agents for the treatment of acute lymphoblastic leukaemia and other haematopoietic malignancies since the tumour cells cannot synthesize sufficient L-asparagine and are thus killed by deprivation of this amino acid. L-Asparaginases are also used in the food industry and have potential in the development of biosensors, for example for asparagine levels in leukaemia. The thermostable type I L-asparaginase fromThermococcus kodakarensis(TkA) is composed of 328 amino acids and forms homodimers in solution, with the highest catalytic activity being observed at pH 9.5 and 85°C. It has aKmvalue of 5.5 mMfor L-asparagine, with no glutaminase activity being observed. The crystal structure of TkA has been determined at 2.18 Å resolution, confirming the presence of two α/β domains connected by a short linker region. The N-terminal domain contains a highly flexible β-hairpin which adopts `open' and `closed' conformations in different subunits of the solved TkA structure. In previously solved L-asparaginase structures this β-hairpin was only visible when in the `closed' conformation, whilst it is characterized with good electron density in all of the subunits of the TkA structure. A phosphate anion resides at the active site, which is formed by residues from both of the neighbouring monomers in the dimer. The high thermostability of TkA is attributed to the high arginine and salt-bridge content when compared with related mesophilic enzymes.
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Jegousse C, Yang Y, Zhan J, Wang J, Zhou Y. Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA. PLoS One 2017; 12:e0184722. [PMID: 28910383 PMCID: PMC5598986 DOI: 10.1371/journal.pone.0184722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/29/2017] [Indexed: 12/02/2022] Open
Abstract
Temperature adaptation of bacterial RNAs is a subject of both fundamental and practical interest because it will allow a better understanding of molecular mechanism of RNA folding with potential industrial application of functional thermophilic or psychrophilic RNAs. Here, we performed a comprehensive study of rRNA, tRNA, and mRNA of more than 200 bacterial species with optimal growth temperatures (OGT) ranging from 4°C to 95°C. We investigated temperature adaptation at primary, secondary and tertiary structure levels. We showed that unlike mRNA, tRNA and rRNA were optimized for their structures at compositional levels with significant tertiary structural features even for their corresponding randomly permutated sequences. tRNA and rRNA are more exposed to solvent but remain structured for hyperthermophiles with nearly OGT-independent fluctuation of solvent accessible surface area within a single RNA chain. mRNA in hyperthermophiles is essentially the same as random sequences without tertiary structures although many mRNA in mesophiles and psychrophiles have well-defined tertiary structures based on their low overall solvent exposure with clear separation of deeply buried from partly exposed bases as in tRNA and rRNA. These results provide new insight into temperature adaptation of different RNAs.
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MESH Headings
- Bacteria/genetics
- Databases, Genetic
- Models, Molecular
- Nucleic Acid Conformation
- RNA Folding/drug effects
- RNA, Bacterial/chemistry
- RNA, Bacterial/drug effects
- RNA, Messenger/chemistry
- RNA, Messenger/drug effects
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/drug effects
- RNA, Transfer/chemistry
- RNA, Transfer/drug effects
- Solvents/pharmacology
- Temperature
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Affiliation(s)
- Clara Jegousse
- UFR Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière, Nantes, France
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Yuedong Yang
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Jian Zhan
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- * E-mail:
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43
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Jing X, Evangelista Falcon W, Baudry J, Serpersu EH. Thermophilic Enzyme or Mesophilic Enzyme with Enhanced Thermostability: Can We Draw a Line? J Phys Chem B 2017; 121:7086-7094. [DOI: 10.1021/acs.jpcb.7b04519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Wilfredo Evangelista Falcon
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Jerome Baudry
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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Kandhari N, Sinha S. Complex network analysis of thermostable mutants of Bacillus subtilis Lipase A. APPLIED NETWORK SCIENCE 2017; 2:18. [PMID: 30443573 PMCID: PMC6214246 DOI: 10.1007/s41109-017-0039-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/01/2017] [Indexed: 06/09/2023]
Abstract
Three-dimensional structures of proteins that regulate their functions can be modelled using complex network based approaches for understanding the structure-function relationship. The six mutants of the protein Lipase A from Bacillus subtilis, harbouring 2 to 12 mutations, retain their function at higher temperatures with negligible variation in their overall three-dimensional crystallographic structures. This enhanced thermostability of the mutants questions the structure-function paradigm. In this paper, a coarse-grained complex network approach is used to elucidate the structural basis of enhanced thermostability in the mutant proteins, by uncovering small but significant local changes distributed throughout the structure, rendering stability to the mutants at higher temperatures. Community structure analysis of the six mutant protein networks uncovers the specific reorganisations among the nodes/residues that occur, in absence of overall structural variations, which induce enhanced rigidity underlying the increased thermostability. This study offers a novel and significant application of complex network analysis that proposes to be useful in the understanding and designing of thermostable proteins.
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Affiliation(s)
- Nitika Kandhari
- Centre for Protein Science Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Punjab 140306 India
| | - Somdatta Sinha
- Centre for Protein Science Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Punjab 140306 India
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45
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46
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Garg DK, Kundu B. Hyperthermophilic l -asparaginase bypasses monomeric intermediates during folding to retain cooperativity and avoid amyloid assembly. Arch Biochem Biophys 2017; 622:36-46. [DOI: 10.1016/j.abb.2017.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 10/19/2022]
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47
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Liu Y, Wu X, Hou W, Li P, Sha W, Tian Y. Structure and function of seed storage proteins in faba bean (Vicia faba L.). 3 Biotech 2017; 7:74. [PMID: 28452019 DOI: 10.1007/s13205-017-0691-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/10/2017] [Indexed: 02/07/2023] Open
Abstract
The protein subunit is the most important basic unit of protein, and its study can unravel the structure and function of seed storage proteins in faba bean. In this study, we identified six specific protein subunits in Faba bean (cv. Qinghai 13) combining liquid chromatography (LC), liquid chromatography-electronic spray ionization mass (LC-ESI-MS/MS) and bio-information technology. The results suggested a diversity of seed storage proteins in faba bean, and a total of 16 proteins (four GroEL molecular chaperones and 12 plant-specific proteins) were identified from 97-, 96-, 64-, 47-, 42-, and 38-kD-specific protein subunits in faba bean based on the peptide sequence. We also analyzed the composition and abundance of the amino acids, the physicochemical characteristics, secondary structure, three-dimensional structure, transmembrane domain, and possible subcellular localization of these identified proteins in faba bean seed, and finally predicted function and structure. The three-dimensional structures were generated based on homologous modeling, and the protein function was analyzed based on the annotation from the non-redundant protein database (NR database, NCBI) and function analysis of optimal modeling. The objective of this study was to identify the seed storage proteins in faba bean and confirm the structure and function of these proteins. Our results can be useful for the study of protein nutrition and achieve breeding goals for optimal protein quality in faba bean.
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Affiliation(s)
- Yujiao Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai Academy of Agricultural and Forestry Science, Xining, Qinghai, 810016, People's Republic of China.
| | - Xuexia Wu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai Academy of Agricultural and Forestry Science, Xining, Qinghai, 810016, People's Republic of China
| | - Wanwei Hou
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai Academy of Agricultural and Forestry Science, Xining, Qinghai, 810016, People's Republic of China
| | - Ping Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai Academy of Agricultural and Forestry Science, Xining, Qinghai, 810016, People's Republic of China
| | - Weichao Sha
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai Academy of Agricultural and Forestry Science, Xining, Qinghai, 810016, People's Republic of China
| | - Yingying Tian
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai Academy of Agricultural and Forestry Science, Xining, Qinghai, 810016, People's Republic of China
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48
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Aziz I, Rashid N, Ashraf R, Bashir Q, Imanaka T, Akhtar M. Pcal_0111, a highly thermostable bifunctional fructose-1,6-bisphosphate aldolase/phosphatase from Pyrobaculum calidifontis. Extremophiles 2017; 21:513-521. [PMID: 28299451 DOI: 10.1007/s00792-017-0921-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/27/2017] [Indexed: 01/30/2023]
Abstract
Pyrobaculum calidifontis genome harbors an open reading frame Pcal_0111 annotated as fructose bisphosphate aldolase. Although the gene is annotated as fructose bisphosphate aldolase, it exhibits a high homology with previously reported fructose-1,6-bisphosphate aldolase/phosphatase from Thermoproteus neutrophilus. To examine the biochemical properties of Pcal_0111, we have cloned and expressed the gene in Escherichia coli. Purified recombinant Pcal_0111 catalyzed both phosphatase and aldolase reactions with specific activity values of 4 U and 1.3 U, respectively. These values are highest among the fructose 1,6-bisphosphatases/aldolases characterized from archaea. The enzyme activity increased linearly with the increase in temperature until 100 °C. Recombinant Pcal_0111 is highly stable with a half-life of 120 min at 100 °C. There was no significant change in the circular dichroism spectra of the protein up to 90 °C. The enzyme activity was not affected by AMP but strongly inhibited by ATP with an IC50 value of 0.75 mM and mildly by ADP. High thermostability and inhibition by ATP make Pcal_0111 a unique fructose 1,6-bisphosphatase/aldolase.
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Affiliation(s)
- Iram Aziz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.
| | - Raza Ashraf
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Qamar Bashir
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Tadayuki Imanaka
- The Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Muhammad Akhtar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.,School of Biological Sciences, University of Southampton, Southampton, SO16 7PX, UK
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49
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Hang Y, Ran S, Wang X, Jiao J, Wang S, Liu Z. Mutational analysis and stability characterization of a novel esterase of lipolytic enzyme family VI from Shewanella sp. Int J Biol Macromol 2016; 93:655-664. [PMID: 27632949 DOI: 10.1016/j.ijbiomac.2016.09.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/19/2016] [Accepted: 09/11/2016] [Indexed: 11/17/2022]
Abstract
Esterases are widely used in different industries. Here, a novel esterase, Esth, with low identity with previously reported esterases, was identified and characterized. The results showed that Esth was a cold-adapted esterase and retained 50% of its maximum activity at 0°C. Besides, Esth showed great activity and stability in high concentrations of NaCl. When treated with some organic solvents, detergents and metal ions, Esth showed high activity as well. The kcat/Km value of Esth was 29.5s-1mM-1, suggesting that it has higher catalytic efficiency than all the previously reported esterases from the same family, lipolytic enzyme family VI. The structural modeling showed that changing Ala129 into Gly would form a new hydrogen bond between ser125 and Gly129 and make theα-helix longer, which might influence on the thermostability of enzymes (Kumar, 2000). To confirm this, the mutant EsthA129G was obtained by site-directed mutagenesis. The result indicated that EsthA129G retained over 70% of the activity versus 12% for Esth after incubation at 55°C for 120min, showed a nearly six fold increase when compared with wild type. Overall, Esth shows a potential application prospect in extreme conditions and the mutation research can provide some structural information about thermostable enzymes.
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Affiliation(s)
- Yian Hang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shi Ran
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiangyu Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jingwen Jiao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shunyao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ziduo Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
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50
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Crystal Structures of Two Isozymes of Citrate Synthase from Sulfolobus tokodaii Strain 7. Biochem Res Int 2016; 2016:7560919. [PMID: 27656296 PMCID: PMC5021468 DOI: 10.1155/2016/7560919] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/17/2016] [Indexed: 11/17/2022] Open
Abstract
Thermoacidophilic archaeon Sulfolobus tokodaii strain 7 has two citrate synthase genes (ST1805-CS and ST0587-CS) in the genome with 45% sequence identity. Because they exhibit similar optimal temperatures of catalytic activity and thermal inactivation profiles, we performed structural comparisons between these isozymes to elucidate adaptation mechanisms to high temperatures in thermophilic CSs. The crystal structures of ST1805-CS and ST0587-CS were determined at 2.0 Å and 2.7 Å resolutions, respectively. Structural comparison reveals that both of them are dimeric enzymes composed of two identical subunits, and these dimeric structures are quite similar to those of citrate synthases from archaea and eubacteria. ST0587-CS has, however, 55 ion pairs within whole dimer structure, while having only 36 in ST1805-CS. Although the number and distributions of ion pairs are distinct from each other, intersubunit ion pairs between two domains of each isozyme are identical especially in interterminal region. Because the location and number of ion pairs are in a trend with other CSs from thermophilic microorganisms, the factors responsible for thermal adaptation of ST-CS isozymes are characterized by ion pairs in interterminal region.
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