1
|
Ahmad A, Rahamtullah, Mishra R. Structural and functional adaptation in extremophilic microbial α-amylases. Biophys Rev 2022; 14:499-515. [PMID: 35528036 PMCID: PMC9043155 DOI: 10.1007/s12551-022-00931-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/12/2022] [Indexed: 01/26/2023] Open
Abstract
Maintaining stable native conformation of a protein under a given ecological condition is the prerequisite for survival of organisms. Extremophilic bacteria and archaea have evolved to adapt under extreme conditions of temperature, pH, salt, and pressure. Molecular adaptations of proteins under these conditions are essential for their survival. These organisms have the capability to maintain stable, native conformations of proteins under extreme conditions. The enzymes produced by the extremophiles are also known as extremozyme, which are used in several industries. Stability and functionality of extremozymes under varying temperature, pH, and solvent conditions are the most desirable requirement of industry. α-Amylase is one of the most important enzymes used in food, pharmaceutical, textile, and detergent industries. This enzyme is produced by diverse microorganisms including various extremophiles. Therefore, understanding its stability is important from fundamental as well as an applied point of view. Each class of extremophiles has a distinctive set of dominant non-covalent interactions which are important for their stability. Static information obtained by comparative analysis of amino acid sequence and atomic resolution structure provides information on the prevalence of particular amino acids or a group of non-covalent interactions. Protein folding studies give the information about thermodynamic and kinetic stability in order to understand dynamic aspect of molecular adaptations. In this review, we have summarized information on amino acid sequence, structure, stability, and adaptability of α-amylases from different classes of extremophiles.
Collapse
Affiliation(s)
- Aziz Ahmad
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| | - Rahamtullah
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| | - Rajesh Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| |
Collapse
|
2
|
Jeong WJ, Yu J, Song WJ. Proteins as diverse, efficient, and evolvable scaffolds for artificial metalloenzymes. Chem Commun (Camb) 2020; 56:9586-9599. [DOI: 10.1039/d0cc03137b] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have extracted and categorized the desirable properties of proteins that are adapted as the scaffolds for artificial metalloenzymes.
Collapse
Affiliation(s)
- Woo Jae Jeong
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Jaeseung Yu
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Woon Ju Song
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| |
Collapse
|
3
|
Linde M, Heyn K, Merkl R, Sterner R, Babinger P. Hexamerization of Geranylgeranylglyceryl Phosphate Synthase Ensures Structural Integrity and Catalytic Activity at High Temperatures. Biochemistry 2018; 57:2335-2348. [DOI: 10.1021/acs.biochem.7b01284] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Mona Linde
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Kristina Heyn
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| |
Collapse
|
4
|
Stavros P, Malecki PH, Theodoridou M, Rypniewski W, Vorgias CE, Nounesis G. The stability of the TIM-barrel domain of a psychrophilic chitinase. Biochem Biophys Rep 2015; 3:108-116. [PMID: 29124173 PMCID: PMC5668695 DOI: 10.1016/j.bbrep.2015.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/24/2015] [Accepted: 07/28/2015] [Indexed: 11/22/2022] Open
Abstract
Chitinase 60 from the psychrophilic bacterium Moritella marina (MmChi60) is a four-domain protein whose structure revealed flexible hinge regions between the domains, yielding conformations in solution that range from fully extended to compact. The catalytic domain is a shallow-grooved TIM-barrel. Heat-induced denaturation experiments of the wild-type and mutants resulting from the deletions of the two-Ig-like domains and the chitin binding domain reveal calorimetric profiles that are consistent with non-collaborative thermal unfolding of the individual domains, a property that must be associated to the “hinge-regions”. The calorimetric measurements of the (β/α)8 catalytic domain reveal that the thermal unfolding is a slow-relaxation transition exhibiting a stable, partially structured intermediate state. Circular dichroism provides evidence that the intermediate exhibits features of a molten globule i.e., loss of tertiary structure while maintaining the secondary structural elements of the native. GdnHCl-induced denaturation studies of the TIM-barrel demonstrate an extraordinarily high resistance to the denaturant. Slow-relaxation kinetics characterize the unfolding with equilibration times exceeding six days, a property that is for the first time observed for a psychrophilic TIM barrel. On the other hand, the thermodynamic stability is ΔG=6.75±1.3 kcal/mol, considerably lower than for structural-insertions-containing barrels. The mutant E153Q used for the crystallographic studies of MmChi60 complexes with NAG ligands has a much lower stability than the wild-type. We use heat-induced and chemical denaturation to study MmChi60. The impact of “hinge” regions upon the DSC calorimetric profiles is explored. CD is used to characterize the thermal unfolding intermediate of the catalytic domain. The thermodynamic stability of the TIM-barrel is measured via chemical denaturation. High-resistance to denaturants is evidenced for the psychrophilic (β/α)8 domain.
Collapse
Affiliation(s)
- Philemon Stavros
- Biomolecular Physics Laboratory, INRASTES, National Centre for Scientific Research “Demokritos”, 153 10 Aghia Paraskevi, Greece
- Physics Department, National and Kapodistrian University of Athens, 157 01 Zografou, Greece
| | - Piotr H. Malecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Maria Theodoridou
- Biomolecular Physics Laboratory, INRASTES, National Centre for Scientific Research “Demokritos”, 153 10 Aghia Paraskevi, Greece
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Constantinos E. Vorgias
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 157 01 Zografou, Greece
| | - George Nounesis
- Biomolecular Physics Laboratory, INRASTES, National Centre for Scientific Research “Demokritos”, 153 10 Aghia Paraskevi, Greece
- Corresponding author.
| |
Collapse
|
5
|
Zhang J, Shi H, Xu L, Zhu X, Li X. Site-Directed Mutagenesis of a Hyperthermophilic Endoglucanase Cel12B from Thermotoga maritima Based on Rational Design. PLoS One 2015. [PMID: 26218520 PMCID: PMC4517919 DOI: 10.1371/journal.pone.0133824] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
To meet the demand for the application of high activity and thermostable cellulases in the production of new-generation bioethanol from nongrain-cellulose sources, a hyperthermostable β-1,4-endoglucase Cel12B from Thermotoga maritima was selected for further modification by gene site-directed mutagenesis method in the present study, based on homology modeling and rational design. As a result, two recombinant enzymes showed significant improvement in enzyme activity by 77% and 87%, respectively, higher than the parental enzyme TmCel12B. Furthermore, the two mutants could retain 80% and 90.5% of their initial activity after incubation at 80°C for 8 h, while only 45% for 5 h to TmCel12B. The Km and Vmax of the two recombinant enzymes were 1.97±0.05 mM, 4.23±0.15 μmol·mg(-1)·min(-1) of TmCel12B-E225H-K207G-D37V, and 2.97±0.12 mM, 3.15±0.21 μmol·mg(-1)·min(-1) of TmCel12B-E225H-K207G, respectively, when using CMC-Na as the substrate. The roles of the mutation sites were also analyzed and evaluated in terms of electron density, hydrophobicity of the modeled protein structures. The recombinant enzymes may be used in the hydrolysis of cellulose at higher temperature in the future. It was concluded that the gene mutagenesis approach of a certain active residues may effectively improve the performance of cellulases for the industrial applications and contribute to the study the thermostable mechanism of thermophilic enzymes.
Collapse
Affiliation(s)
- Jinfeng Zhang
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
| | - Hao Shi
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
| | - Linyu Xu
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
| | - Xiaoyan Zhu
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, Jiangsu 223300, P. R. China
| | - Xiangqian Li
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- * E-mail:
| |
Collapse
|
6
|
Reisinger B, Sperl J, Holinski A, Schmid V, Rajendran C, Carstensen L, Schlee S, Blanquart S, Merkl R, Sterner R. Evidence for the Existence of Elaborate Enzyme Complexes in the Paleoarchean Era. J Am Chem Soc 2013; 136:122-9. [DOI: 10.1021/ja4115677] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Bernd Reisinger
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Josef Sperl
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Alexandra Holinski
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Veronika Schmid
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Chitra Rajendran
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Linn Carstensen
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Sandra Schlee
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Samuel Blanquart
- Equipe
Bonsai,
Institut National de Recherche en Informatique et en Automatique, INRIA Lille Nord Europe, 40 avenue Halley, 59650 Villeneuve d’Ascq, France
| | - Rainer Merkl
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Reinhard Sterner
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| |
Collapse
|
7
|
Yang H, Srivastava P, Zhang C, Lewis JC. A general method for artificial metalloenzyme formation through strain-promoted azide-alkyne cycloaddition. Chembiochem 2013; 15:223-7. [PMID: 24376040 DOI: 10.1002/cbic.201300661] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Indexed: 12/29/2022]
Abstract
Strain-promoted azide-alkyne cycloaddition (SPAAC) can be used to generate artificial metalloenzymes (ArMs) from scaffold proteins containing a p-azido-L-phenylalanine (Az) residue and catalytically active bicyclononyne-substituted metal complexes. The high efficiency of this reaction allows rapid ArM formation when using Az residues within the scaffold protein in the presence of cysteine residues or various reactive components of cellular lysate. In general, cofactor-based ArM formation allows the use of any desired metal complex to build unique inorganic protein materials. SPAAC covalent linkage further decouples the native function of the scaffold from the installation process because it is not affected by native amino acid residues; as long as an Az residue can be incorporated, an ArM can be generated. We have demonstrated the scope of this method with respect to both the scaffold and cofactor components and established that the dirhodium ArMs generated can catalyze the decomposition of diazo compounds and both Si-H and olefin insertion reactions involving these carbene precursors.
Collapse
Affiliation(s)
- Hao Yang
- Department of Chemistry, University of Chicago, 5735 S. Ellis Ave., Chicago, IL 60637 (USA)
| | | | | | | |
Collapse
|
8
|
Gangadhara BN, Laine JM, Kathuria SV, Massi F, Matthews CR. Clusters of branched aliphatic side chains serve as cores of stability in the native state of the HisF TIM barrel protein. J Mol Biol 2013; 425:1065-81. [PMID: 23333740 DOI: 10.1016/j.jmb.2013.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 01/01/2013] [Accepted: 01/03/2013] [Indexed: 01/31/2023]
Abstract
Imidazole-3-glycerol phosphate synthase is a heterodimeric allosteric enzyme that catalyzes consecutive reactions in imidazole biosynthesis through its HisF and HisH subunits. The unusually slow unfolding reaction of the isolated HisF TIM barrel domain from the thermophilic bacteria, Thermotoga maritima, enabled an NMR-based site-specific analysis of the main-chain hydrogen bonds that stabilize its native conformation. Very strong protection against exchange with solvent deuterium in the native state was found in a subset of buried positions in α-helices and pervasively in the underlying β-strands associated with a pair of large clusters of isoleucine, leucine and valine (ILV) side chains located in the α7(βα)8(βα)1-2 and α2(βα)3-6β7 segments of the (βα)8 barrel. The most densely packed region of the large cluster, α3(βα)4-6β7, correlates closely with the core of stability previously observed in computational, protein engineering and NMR dynamics studies, demonstrating a key role for this cluster in determining the thermodynamic and structural properties of the native state of HisF. When considered with the results of previous studies where ILV clusters were found to stabilize the hydrogen-bonded networks in folding intermediates for other TIM barrel proteins, it appears that clusters of branched aliphatic side chains can serve as cores of stability across the entire folding reaction coordinate of one of the most common motifs in biology.
Collapse
Affiliation(s)
- Basavanapura N Gangadhara
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | | | | | | | | |
Collapse
|
9
|
Carstensen L, Sperl JM, Bocola M, List F, Schmid FX, Sterner R. Conservation of the Folding Mechanism between Designed Primordial (βα)8-Barrel Proteins and Their Modern Descendant. J Am Chem Soc 2012; 134:12786-91. [DOI: 10.1021/ja304951v] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Linn Carstensen
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Josef M. Sperl
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Marco Bocola
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Felix List
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Franz X. Schmid
- Laboratorium für Biochemie
und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Reinhard Sterner
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| |
Collapse
|