1
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Du G, Wang Y, Zhang Y, Yu H, Liu S, Ma X, Cao H, Wei X, Wen B, Li Z, Fan S, Zhou H, Xin F. Structural insights into the oligomeric effects on catalytic activity of a decameric feruloyl esterase and its application in ferulic acid production. Int J Biol Macromol 2023; 253:126540. [PMID: 37634773 DOI: 10.1016/j.ijbiomac.2023.126540] [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: 05/04/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
Oligomeric feruloyl esterase (FAE) has great application prospect in industry due to its potentially high stability and fine-tuned activity. However, the relationship between catalytic capability and oligomeric structure remains undetermined. Here we identified and characterized a novel, cold-adapted FAE (BtFae) derived from Bacteroides thetaiotaomicron. Structural studies unraveled that BtFae adopts a barrel-like decameric architecture unique in esterase families. By disrupting the interface, the monomeric variant exhibited significantly reduced catalytic activity and stability toward methyl ferulate, potentially due to its impact on the flexibility of the catalytic triad. Additionally, our results also showed that the monomerization of BtFae severely decreased the ferulic acid release from de-starched wheat bran and insoluble wheat arabinoxylan by 75 % and 80 %, respectively. Collectively, this study revealed novel connections between oligomerization and FAE catalytic function, which will benefit for further protein engineering of FAEs at the quaternary structure level for improved industrial applications.
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Affiliation(s)
- Guoming Du
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yulu Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Institute of Food Science Technology Nutrition and Health (Cangzhou), Chinese Academy of Agricultural Sciences, Cangzhou 061001, China
| | - Yuebin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Haiyan Yu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shujun Liu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Institute of Food Science Technology Nutrition and Health (Cangzhou), Chinese Academy of Agricultural Sciences, Cangzhou 061001, China
| | - Xiaochen Ma
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hao Cao
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Wei
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Boting Wen
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Institute of Food Science Technology Nutrition and Health (Cangzhou), Chinese Academy of Agricultural Sciences, Cangzhou 061001, China
| | - Zhen Li
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Institute of Food Science Technology Nutrition and Health (Cangzhou), Chinese Academy of Agricultural Sciences, Cangzhou 061001, China
| | - Shilong Fan
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Institute of Food Science Technology Nutrition and Health (Cangzhou), Chinese Academy of Agricultural Sciences, Cangzhou 061001, China.
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2
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Bana J, Warwar J, Bayer EA, Livnah O. Self-assembly of a dimeric avidin into unique higher-order oligomers. FEBS J 2023. [PMID: 36853192 DOI: 10.1111/febs.16764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/01/2023]
Abstract
The dimeric avidin family has been expanded in recent years to include many new members. All of them lack the intermonomeric Trp that plays a critical role in biotin-binding. Nevertheless, these new members of the avidins maintain the high affinity towards biotin. Additionally, all of the dimeric avidins share a very unique property: namely, the cylindrical oligomerization in the crystal structure. The newest member described here, agroavidin from the agrobacterium, Rhizobium sp. AAP43, shares their important structural features. However, the affinity of agroavidin towards biotin is lower than all other members of the avidin family, due to the presence of phenylalanine instead of a conserved tyrosine in the biotin-binding site. Mutating this phenylalanine into tyrosine regenerated the high affinity, which emphasizes the importance of this particular tyrosine residue. Another unique feature that distinguishes agroavidin from the other dimeric avidins is that it does not produce oligomers in its crystal structure. In order to understand the factors that promote oligomerization in dimeric avidins, we exchanged the C-terminal region of agroavidin with that of hoefavidin that produced octamers. This exchange resulted in a decamer rather than an octamer. This unusual outcome demonstrates the impact of the C-terminal region on the ability to produce oligomers. The decameric assembly of agroavidin expands the avidin-biotin toolbox even further and could well pave the path into new biotin-based technologies. Moreover, uncovering the factors that induce dimeric avidins into oligomeric assemblies may aid in better understanding the general molecular determinants that promote oligomerization.
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Affiliation(s)
- Juana Bana
- Department of Biological Chemistry, The Wolfson Centre for Applied Structural Biology, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel
| | - Jessica Warwar
- Department of Biological Chemistry, The Wolfson Centre for Applied Structural Biology, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Oded Livnah
- Department of Biological Chemistry, The Wolfson Centre for Applied Structural Biology, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel
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3
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Mu Y, Ju X, Fu J, Meng F, Yan L, Li L. Surface charge engineering of β-glucosidase using rational design improves catalytic capacity and ionic liquid tolerance. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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4
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Hu S, Yan J, Yang G, Ma C, Yin J. Self-Assembled Polymeric Materials: Design, Morphology, and Functional-Oriented Applications. Macromol Rapid Commun 2021; 43:e2100791. [PMID: 34967061 DOI: 10.1002/marc.202100791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/15/2021] [Indexed: 11/10/2022]
Abstract
This Review focuses on the current research advances of the synthesis of various amphiphilic block copolymers (ABCs), such as conventional ABCs and newly-presented polyprodrug amphiphiles (PPAs), and the development of corresponding self-assemblies in selective solvents driven by the intermolecular interactions, like noncovalent hydrophobic interactions, π-π interactions, and hydrogen bonds, between ABCs or preformed small polymeric nanoparticles. The design of these assemblies is systematically introduced, and the diverse examples concerning the unique assembly structures along with the fast development of their exclusive properties and various applications in different fields were discussed. Possible perspectives on the existential challenges and glorious future were elucidated finally. We hope this review will provide a convenient way for readers to motivate more evolutional innovative concepts and methods to design next generation of novel polymeric nanoassemblies, and fill the gap between material design and practical applications. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shoukui Hu
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering Hefei, Anhui, 230009, P. R. China
| | - Jinhao Yan
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering Hefei, Anhui, 230009, P. R. China
| | - Guangwei Yang
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering Hefei, Anhui, 230009, P. R. China
| | - Chao Ma
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering Hefei, Anhui, 230009, P. R. China
| | - Jun Yin
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology and Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering Hefei, Anhui, 230009, P. R. China
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5
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Abstract
For evaluating the deepest evolutionary relationships among proteins, sequence similarity is too low for application of sequence-based homology search or phylogenetic methods. In such cases, comparison of protein structures, which are often better conserved than sequences, may provide an alternative means of uncovering deep evolutionary signal. Although major protein structure databases such as SCOP and CATH hierarchically group protein structures, they do not describe the specific evolutionary relationships within a hierarchical level. Structural phylogenies have the potential to fill this gap. However, it is difficult to assess evolutionary relationships derived from structural phylogenies without some means of assessing confidence in such trees. We therefore address two shortcomings in the application of structural data to deep phylogeny. First, we examine whether phylogenies derived from pairwise structural comparisons are sensitive to differences in protein length and shape. We find that structural phylogenetics is best employed where structures have very similar lengths, and that shape fluctuations generated during molecular dynamics simulations impact pairwise comparisons, but not so drastically as to eliminate evolutionary signal. Second, we address the absence of statistical support for structural phylogeny. We present a method for assessing confidence in a structural phylogeny using shape fluctuations generated via molecular dynamics or Monte Carlo simulations of proteins. Our approach will aid the evolutionary reconstruction of relationships across structurally defined protein superfamilies. With the Protein Data Bank now containing in excess of 158,000 entries (December 2019), we predict that structural phylogenetics will become a useful tool for ordering the protein universe.
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Affiliation(s)
- Ashar J Malik
- Centre for Theoretical Chemistry and Physics, School of Natural and Computational Sciences, Massey University Auckland, Auckland, New Zealand.,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Anthony M Poole
- Bioinformatics Institute, School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Digital Life Institute, University of Auckland, Auckland, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Jane R Allison
- Bioinformatics Institute, School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Digital Life Institute, University of Auckland, Auckland, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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6
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Otsuka FAM, Chagas RS, Almeida VM, Marana SR. Homodimerization of a glycoside hydrolase family GH1 β-glucosidase suggests distinct activity of enzyme different states. Protein Sci 2020; 29:1879-1889. [PMID: 32597558 DOI: 10.1002/pro.3908] [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: 05/12/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 11/06/2022]
Abstract
In this work, we investigated how activity and oligomeric state are related in a purified GH1 β-glucosidase from Spodoptera frugiperda (Sfβgly). Gel filtration chromatography coupled to a multiple angle light scattering detector allowed separation of the homodimer and monomer states and determination of the dimer dissociation constant (KD ), which was in the micromolar range. Enzyme kinetic parameters showed that the dimer is on average 2.5-fold more active. Later, we evaluated the kinetics of homodimerization, scanning the changes in the Sfβgly intrinsic fluorescence over time when the dimer dissociates into the monomer after a large dilution. We described how the rate constant of monomerization (koff ) is affected by temperature, revealing the enthalpic and entropic contributions to the process. We also evaluated how the rate constant (kobs ) by which equilibrium is reached after dimer dilution behaves when varying the initial Sfβgly concentration. These data indicated that Sfβgly dimerizes through the conformational selection mechanism, in which the monomer undergoes a conformational exchange and then binds to a similar monomer, forming a more active homodimer. Finally, we noted that conformational selection reports and experiments usually rely on a ligand whose concentration is in excess, but for homodimerization, this approach does not hold. Hence, since our approach overcomes this limitation, this study not only is a new contribution to the comprehension of GH1 β-glucosidases, but it can also help to elucidate protein interaction pathways.
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Affiliation(s)
- Felipe A M Otsuka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Rafael S Chagas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Vitor M Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Sandro R Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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7
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Lu Y, Lin J, Wang L, Zhang L, Cai C. Self-Assembly of Copolymer Micelles: Higher-Level Assembly for Constructing Hierarchical Structure. Chem Rev 2020; 120:4111-4140. [DOI: 10.1021/acs.chemrev.9b00774] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yingqing Lu
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaping Lin
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Liquan Wang
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Liangshun Zhang
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chunhua Cai
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
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8
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Bundela R, Keown J, Watkin S, Pearce FG. Structure of a hyperthermostable dimeric archaeal Rubisco from Hyperthermus butylicus. Acta Crystallogr D Struct Biol 2019; 75:536-544. [DOI: 10.1107/s2059798319006466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/07/2019] [Indexed: 11/11/2022] Open
Abstract
The crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from the hyperthermophilic archaeonHyperthermus butylicusis presented at 1.8 Å resolution. Previous structures of archaeal Rubisco have been found to assemble into decamers, and this oligomerization was thought to be required for a highly thermally stable enzyme. In the current study,H. butylicusRubisco is shown to exist as a dimer in solution, yet has a thermal denaturation midpoint of 114°C, suggesting that high thermal stability can be achieved without an increased oligomeric state. This increased thermal stability appears to be due to an increased number of electrostatic interactions within the monomeric subunit. As such,H. butylicusRubisco presents a well characterized system in which to investigate the role of assembly and thermal stability in enzyme function.
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9
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Álvarez-Cao ME, González R, Pernas MA, Rúa ML. Contribution of the Oligomeric State to the Thermostability of Isoenzyme 3 from Candida rugosa. Microorganisms 2018; 6:E108. [PMID: 30347699 PMCID: PMC6313406 DOI: 10.3390/microorganisms6040108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 01/06/2023] Open
Abstract
Thermophilic proteins have evolved different strategies to maintain structure and function at high temperatures; they have large, hydrophobic cores, and feature increased electrostatic interactions, with disulfide bonds, salt-bridging, and surface charges. Oligomerization is also recognized as a mechanism for protein stabilization to confer a thermophilic adaptation. Mesophilic proteins are less thermostable than their thermophilic homologs, but oligomerization plays an important role in biological processes on a wide variety of mesophilic enzymes, including thermostabilization. The mesophilic yeast Candida rugosa contains a complex family of highly related lipase isoenzymes. Lip3 has been purified and characterized in two oligomeric states, monomer (mLip3) and dimer (dLip3), and crystallized in a dimeric conformation, providing a perfect model for studying the effects of homodimerization on mesophilic enzymes. We studied kinetics and stability at different pHs and temperatures, using the response surface methodology to compare both forms. At the kinetic level, homodimerization expanded Lip3 specificity (serving as a better catalyst on soluble substrates). Indeed, dimerization increased its thermostability by more than 15 °C (maximum temperature for dLip3 was out of the experimental range; >50 °C), and increased the pH stability by nearly one pH unit, demonstrating that oligomerization is a viable strategy for the stabilization of mesophilic enzymes.
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Affiliation(s)
- María-Efigenia Álvarez-Cao
- Department of Food and Analytical Chemistry, Sciences Faculty of Ourense, University of Vigo, As Lagoas s/n, 32004 Ourense, Spain.
| | - Roberto González
- Department of Food and Analytical Chemistry, Sciences Faculty of Ourense, University of Vigo, As Lagoas s/n, 32004 Ourense, Spain.
| | - María A Pernas
- Department of Food and Analytical Chemistry, Sciences Faculty of Ourense, University of Vigo, As Lagoas s/n, 32004 Ourense, Spain.
| | - María Luisa Rúa
- Department of Food and Analytical Chemistry, Sciences Faculty of Ourense, University of Vigo, As Lagoas s/n, 32004 Ourense, Spain.
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10
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Singh MK, Shivakumaraswamy S, Gummadi SN, Manoj N. Role of an N-terminal extension in stability and catalytic activity of a hyperthermostable α/β hydrolase fold esterase. Protein Eng Des Sel 2017; 30:559-570. [PMID: 28967962 DOI: 10.1093/protein/gzx049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/25/2017] [Indexed: 12/15/2022] Open
Abstract
The carbohydrate esterase family 7 (CE7) enzymes catalyze the deacetylation of acetyl esters of a broad range of alcohols and is unique in its activity towards cephalosporin C. The CE7 fold contains a conserved N-terminal extension that distinguishes it from the canonical α/β hydrolase fold. The hexameric quaternary structure indicates that the N-terminus may affect activity and specificity by controlling access of substrates to the buried active sites via an entrance tunnel. In this context, we characterized the catalytic parameters, conformation and thermal stability of two truncation variants lacking four and ten residues of the N-terminal region of the hyperthermostable Thermotoga maritima CE7 acetyl esterase (TmAcE). The truncations did not affect the secondary structure or the fold but modulated the oligomerization dynamics. A modest increase was observed in substrate specificity for acetylated xylose compared with acetylated glucose. A drastic reduction of ~30-40°C in the optimum temperature for activity of the variants indicated lower thermal stability. The loss of hyperthermostability appears to be an indirect effect associated with an increase in the conformational flexibility of an otherwise rigid neighboring loop containing a catalytic triad residue. The results suggest that the N-terminal extension was evolutionarily selected to preserve the stability of the enzyme.
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Affiliation(s)
- Mrityunjay K Singh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras, Chennai 600036, India
| | - Santosh Shivakumaraswamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras, Chennai 600036, India
| | - Sathyanarayana N Gummadi
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras, Chennai 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras, Chennai 600036, India
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11
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Jiao W, Blackmore NJ, Nazmi AR, Parker EJ. Quaternary structure is an essential component that contributes to the sophisticated allosteric regulation mechanism in a key enzyme from Mycobacterium tuberculosis. PLoS One 2017; 12:e0180052. [PMID: 28665948 PMCID: PMC5493349 DOI: 10.1371/journal.pone.0180052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/08/2017] [Indexed: 01/26/2023] Open
Abstract
The first enzyme of the shikimate pathway, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS), adopts a range of distinct allosteric regulation mechanisms in different organisms, related to different quaternary assemblies. DAH7PS from Mycobacterium tuberculosis (MtuDAH7PS) is a homotetramer, with the allosteric sites in close proximity to the interfaces. Here we examine the importance of the quaternary structure on catalysis and regulation, by amino acid substitution targeting the tetramer interface of MtuDAH7PS. Using only single amino acid substitutions either in, or remote from the interface, two dimeric variants of MtuDAH7PS (MtuDAH7PSF227D and MtuDAH7PSG232P) were successfully generated. Both dimeric variants maintained activity due to the distance between the sites of amino acid substitution and the active sites, but attenuated catalytic efficiency was observed. Both dimeric variants showed significantly disrupted allosteric regulation with greatly impaired binding affinity for one of the allosteric ligands. Molecular dynamics simulations revealed changes in protein dynamics and average conformations in the dimeric variant caused by amino acid substitution remote to the tetramer interface (MtuDAH7PSG232P), which are consistent with the observed reduction in catalytic efficiency and loss of allosteric response.
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Affiliation(s)
- Wanting Jiao
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Nicola J. Blackmore
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Ali Reza Nazmi
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Emily J. Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
- * E-mail:
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12
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Olivares-Illana V, Riveros-Rosas H, Cabrera N, Tuena de Gómez-Puyou M, Pérez-Montfort R, Costas M, Gómez-Puyou A. A guide to the effects of a large portion of the residues of triosephosphate isomerase on catalysis, stability, druggability, and human disease. Proteins 2017; 85:1190-1211. [PMID: 28378917 DOI: 10.1002/prot.25299] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 03/14/2017] [Accepted: 03/27/2017] [Indexed: 12/11/2022]
Abstract
Triosephosphate isomerase (TIM) is a ubiquitous enzyme, which appeared early in evolution. TIM is responsible for obtaining net ATP from glycolysis and producing an extra pyruvate molecule for each glucose molecule, under aerobic and anaerobic conditions. It is placed in a metabolic crossroad that allows a quick balance of the triose phosphate aldolase produced by glycolysis, and is also linked to lipid metabolism through the alternation of glycerol-3-phosphate and the pentose cycle. TIM is one of the most studied enzymes with more than 199 structures deposited in the PDB. The interest for this enzyme stems from the fact that it is involved in glycolysis, but also in aging, human diseases and metabolism. TIM has been a target in the search for chemical compounds against infectious diseases and is a model to study catalytic features. Until February 2017, 62% of all residues of the protein have been studied by mutagenesis and/or using other approaches. Here, we present a detailed and comprehensive recompilation of the reported effects on TIM catalysis, stability, druggability and human disease produced by each of the amino acids studied, contributing to a better understanding of the properties of this fundamental protein. The information reviewed here shows that the role of the noncatalytic residues depend on their molecular context, the delicate balance between the short and long-range interactions in concerted action determining the properties of the protein. Each protein should be regarded as a unique entity that has evolved to be functional in the organism to which it belongs. Proteins 2017; 85:1190-1211. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Vanesa Olivares-Illana
- Laboratorio de Interacciones Biomoleculares y Cáncer. Instituto de Física, Universidad Autónoma de San Luis Potosí, SLP, 78290, México
| | - Hector Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Marietta Tuena de Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Armando Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
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13
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Grant Pearce F, Hudson AO, Loomes K, Dobson RCJ. Dihydrodipicolinate Synthase: Structure, Dynamics, Function, and Evolution. Subcell Biochem 2017; 83:271-289. [PMID: 28271480 DOI: 10.1007/978-3-319-46503-6_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Enzymes are usually comprised of multiple subunits and more often than not they are made up of identical subunits. In this review we examine lysine biosynthesis and focus on the enzyme dihydrodipicolinate synthase in terms of its structure, function and the evolution of its varied number of subunits (quaternary structure). Dihydrodipicolinate synthase is the first committed step in the biosynthesis of lysine, which occurs naturally in plants, bacteria, archaea and fungi, but is not synthesized in mammals. In bacteria, there have been four separate pathways identified from tetrahydrodipicolinate to meso-diaminopimelate, which is the immediate precursor to lysine. Dihydrodipicolinate synthases from many bacterial and plant species have been structurally characterised and the results show considerable variability with respect to their quaternary structure, hinting at their evolution. The oligomeric state of the enzyme plays a key role, both in catalysis and in the allosteric regulation of the enzyme by lysine. While most bacteria and plants have tetrameric enzymes, where the structure of the dimeric building blocks is conserved, the arrangement of the dimers differs. We also review a key development in the field, namely the discovery of a human dihydrodipicolinate synthase-like enzyme, now known as 4-hydroxy-2-oxoglutarate aldolase . This discovery complicates the rationale underpinning drug development against bacterial dihydrodipicolinate synthases, since genetic errors in 4-hydroxy-2-oxoglutarate aldolase cause the disease Primary Hyperoxaluria Type 3 and therefore compounds that are geared towards the inhibition of bacterial dihydrodipicolinate synthase may be toxic to mammalian cells.
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Affiliation(s)
- F Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8041, New Zealand
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Kerry Loomes
- School of Biological Sciences & Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8041, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3010, Australia.
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14
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Fraser NJ, Liu JW, Mabbitt PD, Correy GJ, Coppin CW, Lethier M, Perugini MA, Murphy JM, Oakeshott JG, Weik M, Jackson CJ. Evolution of Protein Quaternary Structure in Response to Selective Pressure for Increased Thermostability. J Mol Biol 2016; 428:2359-2371. [DOI: 10.1016/j.jmb.2016.03.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/07/2016] [Accepted: 03/16/2016] [Indexed: 10/22/2022]
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15
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An extended loop in CE7 carbohydrate esterase family is dispensable for oligomerization but required for activity and thermostability. J Struct Biol 2016; 194:434-45. [DOI: 10.1016/j.jsb.2016.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/07/2016] [Accepted: 04/13/2016] [Indexed: 11/20/2022]
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16
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Nazmi AR, Schofield LR, Dobson RC, Jameson GB, Parker EJ. Destabilization of the Homotetrameric Assembly of 3-Deoxy-d-Arabino-Heptulosonate-7-Phosphate Synthase from the Hyperthermophile Pyrococcus furiosus Enhances Enzymatic Activity. J Mol Biol 2014; 426:656-73. [DOI: 10.1016/j.jmb.2013.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/05/2013] [Accepted: 11/06/2013] [Indexed: 12/30/2022]
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17
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Lansky S, Alalouf O, Solomon HV, Alhassid A, Govada L, Chayen NE, Belrhali H, Shoham Y, Shoham G. A unique octameric structure of Axe2, an intracellular acetyl-xylooligosaccharide esterase from Geobacillus stearothermophilus. ACTA ACUST UNITED AC 2014; 70:261-78. [PMID: 24531461 DOI: 10.1107/s139900471302840x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 10/15/2013] [Indexed: 08/26/2023]
Abstract
Geobacillus stearothermophilus T6 is a thermophilic, Gram-positive soil bacterium that possesses an extensive and highly regulated hemicellulolytic system, allowing the bacterium to efficiently degrade high-molecular-weight polysaccharides such as xylan, arabinan and galactan. As part of the xylan-degradation system, the bacterium uses a number of side-chain-cleaving enzymes, one of which is Axe2, a 219-amino-acid intracellular serine acetylxylan esterase that removes acetyl side groups from xylooligosaccharides. Bioinformatic analyses suggest that Axe2 belongs to the lipase GDSL family and represents a new family of carbohydrate esterases. In the current study, the detailed three-dimensional structure of Axe2 is reported, as determined by X-ray crystallography. The structure of the selenomethionine derivative Axe2-Se was initially determined by single-wavelength anomalous diffraction techniques at 1.70 Å resolution and was used for the structure determination of wild-type Axe2 (Axe2-WT) and the catalytic mutant Axe2-S15A at 1.85 and 1.90 Å resolution, respectively. These structures demonstrate that the three-dimensional structure of the Axe2 monomer generally corresponds to the SGNH hydrolase fold, consisting of five central parallel β-sheets flanked by two layers of helices (eight α-helices and five 310-helices). The catalytic triad residues, Ser15, His194 and Asp191, are lined up along a substrate channel situated on the concave surface of the monomer. Interestingly, the Axe2 monomers are assembled as a `doughnut-shaped' homo-octamer, presenting a unique quaternary structure built of two staggered tetrameric rings. The eight active sites are organized in four closely situated pairs, which face the relatively wide internal cavity. The biological relevance of this octameric structure is supported by independent results obtained from gel-filtration, TEM and SAXS experiments. These data and their comparison to the structural data of related hydrolases are used for a more general discussion focusing on the structure-function relationships of enzymes of this category.
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Affiliation(s)
- Shifra Lansky
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Onit Alalouf
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Hodaya Vered Solomon
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Anat Alhassid
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Lata Govada
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, England
| | - Naomi E Chayen
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, England
| | - Hassan Belrhali
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Gil Shoham
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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18
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Nishi H, Hashimoto K, Madej T, Panchenko AR. Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:3-24. [PMID: 23663963 PMCID: PMC3786560 DOI: 10.1016/b978-0-12-386931-9.00001-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Protein homooligomers afford several important benefits for the cell; they mediate and regulate gene expression, activity of many enzymes, ion channels, receptors, and cell-cell adhesion processes. The evolutionary and physical mechanisms of oligomer formation are very diverse and are not well understood. Certain homooligomeric states may be conserved within protein subfamilies and between different subfamilies, therefore providing the specificity to particular substrates while minimizing interactions with unwanted partners. In addition, transitions between different oligomeric states may regulate protein activity and support the switch between different pathways. In this chapter, we summarize the biological importance of homooligomeric assemblies, physicochemical properties of their interfaces, experimental methods for their identification, their evolution, and role in human diseases.
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Affiliation(s)
- Hafumi Nishi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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19
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The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture. Biochem Soc Trans 2012; 40:475-91. [PMID: 22616857 DOI: 10.1042/bst20120056] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
All proteins require physical interactions with other proteins in order to perform their functions. Most of them oligomerize into homomers, and a vast majority of these homomers interact with other proteins, at least part of the time, forming transient or obligate heteromers. In the present paper, we review the structural, biophysical and evolutionary aspects of these protein interactions. We discuss how protein function and stability benefit from oligomerization, as well as evolutionary pathways by which oligomers emerge, mostly from the perspective of homomers. Finally, we emphasize the specificities of heteromeric complexes and their structure and evolution. We also discuss two analytical approaches increasingly being used to study protein structures as well as their interactions. First, we review the use of the biological networks and graph theory for analysis of protein interactions and structure. Secondly, we discuss recent advances in techniques for detecting correlated mutations, with the emphasis on their role in identifying pathways of allosteric communication.
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20
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Reboul CF, Porebski BT, Griffin MDW, Dobson RCJ, Perugini MA, Gerrard JA, Buckle AM. Structural and dynamic requirements for optimal activity of the essential bacterial enzyme dihydrodipicolinate synthase. PLoS Comput Biol 2012; 8:e1002537. [PMID: 22685390 PMCID: PMC3369909 DOI: 10.1371/journal.pcbi.1002537] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 04/16/2012] [Indexed: 11/18/2022] Open
Abstract
Dihydrodipicolinate synthase (DHDPS) is an essential enzyme involved in the lysine biosynthesis pathway. DHDPS from E. coli is a homotetramer consisting of a 'dimer of dimers', with the catalytic residues found at the tight-dimer interface. Crystallographic and biophysical evidence suggest that the dimers associate to stabilise the active site configuration, and mutation of a central dimer-dimer interface residue destabilises the tetramer, thus increasing the flexibility and reducing catalytic efficiency and substrate specificity. This has led to the hypothesis that the tetramer evolved to optimise the dynamics within the tight-dimer. In order to gain insights into DHDPS flexibility and its relationship to quaternary structure and function, we performed comparative Molecular Dynamics simulation studies of native tetrameric and dimeric forms of DHDPS from E. coli and also the native dimeric form from methicillin-resistant Staphylococcus aureus (MRSA). These reveal a striking contrast between the dynamics of tetrameric and dimeric forms. Whereas the E. coli DHDPS tetramer is relatively rigid, both the E. coli and MRSA DHDPS dimers display high flexibility, resulting in monomer reorientation within the dimer and increased flexibility at the tight-dimer interface. The mutant E. coli DHDPS dimer exhibits disorder within its active site with deformation of critical catalytic residues and removal of key hydrogen bonds that render it inactive, whereas the similarly flexible MRSA DHDPS dimer maintains its catalytic geometry and is thus fully functional. Our data support the hypothesis that in both bacterial species optimal activity is achieved by fine tuning protein dynamics in different ways: E. coli DHDPS buttresses together two dimers, whereas MRSA dampens the motion using an extended tight-dimer interface.
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Affiliation(s)
- C. F. Reboul
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, Australia
| | - B. T. Porebski
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - M. D. W. Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - R. C. J. Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- Biomolecular Interaction Centre, and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - M. A. Perugini
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - J. A. Gerrard
- Biomolecular Interaction Centre, and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - A. M. Buckle
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- * E-mail:
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21
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Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning APJ, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 2012; 21:769-85. [PMID: 22528593 PMCID: PMC3403413 DOI: 10.1002/pro.2071] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 12/20/2022]
Abstract
Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction.
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Affiliation(s)
- David A Liberles
- Department of Molecular Biology, University of WyomingLaramie, Wyoming 82071
| | - Sarah A Teichmann
- MRC Laboratory of Molecular BiologyHills Road, Cambridge CB2 0QH, United Kingdom
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of PittsburghPittsburgh, Pennsylvania 15213
| | - Ugo Bastolla
- Bioinformatics Unit. Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autonoma de Madrid28049 Cantoblanco Madrid, Spain
| | - Jesse Bloom
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattle, Washington 98109
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, University of MuensterGermany
| | - Lucy J Colwell
- MRC Laboratory of Molecular BiologyHills Road, Cambridge CB2 0QH, United Kingdom
| | - A P Jason de Koning
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of ColoradoAurora, Colorado
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel HillNorth Carolina 27599
| | - Julian Echave
- Escuela de Ciencia y Tecnología, Universidad Nacional de San MartínMartín de Irigoyen 3100, 1650 San Martín, Buenos Aires, Argentina
| | - Arne Elofsson
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm Bioinformatics Center, Science for Life Laboratory, Swedish E-science Research Center, Stockholm University106 91 Stockholm, Sweden
| | - Dietlind L Gerloff
- Biomolecular Engineering Department, University of CaliforniaSanta Cruz, California 95064
| | - Richard A Goldstein
- Division of Mathematical Biology, National Institute for Medical Research (MRC)Mill Hill, London NW7 1AA, United Kingdom
| | - Johan A Grahnen
- Department of Molecular Biology, University of WyomingLaramie, Wyoming 82071
| | - Mark T Holder
- Department of Ecology and Evolutionary Biology, University of KansasLawrence, Kansas 66045
| | - Clemens Lakner
- Bioinformatics Research Center, North Carolina State UniversityRaleigh, North Carolina 27695
| | - Nicholas Lartillot
- Département de Biochimie, Faculté de Médecine, Université de MontréalMontréal, QC H3T1J4, Canada
| | - Simon C Lovell
- Faculty of Life Sciences, University of ManchesterManchester M13 9PT, United Kingdom
| | - Gavin Naylor
- Department of Biology, College of CharlestonCharleston, South Carolina 29424
| | - Tina Perica
- MRC Laboratory of Molecular BiologyHills Road, Cambridge CB2 0QH, United Kingdom
| | - David D Pollock
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of ColoradoAurora, Colorado
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel Aviv, Israel
| | - Lynne Regan
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven 06511
| | - Andrew Roger
- Department of Biochemistry and Molecular Biology, Dalhousie UniversityHalifax, NS, Canada
| | - Nimrod Rubinstein
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel Aviv, Israel
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridge, Massachusetts 02138
| | - Kimmen Sjölander
- Department of Bioengineering, University of CaliforniaBerkeley, Berkeley, California 94720
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School77 Avenue Louis Pasteur, Boston, Massachusetts 02115
| | - Ashley I Teufel
- Department of Molecular Biology, University of WyomingLaramie, Wyoming 82071
| | - Jeffrey L Thorne
- Bioinformatics Research Center, North Carolina State UniversityRaleigh, North Carolina 27695
| | - Joseph W Thornton
- Howard Hughes Medical Institute and Institute for Ecology and Evolution, University of OregonEugene, Oregon 97403
- Department of Human Genetics, University of ChicagoChicago, Illinois 60637
- Department of Ecology and Evolution, University of ChicagoChicago, Illinois 60637
| | - Daniel M Weinreich
- Department of Ecology and Evolutionary Biology, and Center for Computational Molecular Biology, Brown UniversityProvidence, Rhode Island 02912
| | - Simon Whelan
- Faculty of Life Sciences, University of ManchesterManchester M13 9PT, United Kingdom
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22
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Pearce FG, Dobson RCJ, Jameson GB, Perugini MA, Gerrard JA. Characterization of monomeric dihydrodipicolinate synthase variant reveals the importance of substrate binding in optimizing oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1900-9. [PMID: 21803176 DOI: 10.1016/j.bbapap.2011.07.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 07/14/2011] [Accepted: 07/15/2011] [Indexed: 01/15/2023]
Abstract
To gain insights into the role of quaternary structure in the TIM-barrel family of enzymes, we introduced mutations to the DHDPS enzyme of Thermotoga maritima, which we have previously shown to be a stable tetramer in solution. These mutations were aimed at reducing the number of salt bridges at one of the two tetramerization interface of the enzyme, which contains many more interactions than the well characterized equivalent interface of the mesophilic Escherichia coli DHDPS enzyme. The resulting variants had altered quaternary structure, as shown by analytical ultracentrifugation, gel filtration liquid chromatography, and small angle X-ray scattering, and X-ray crystallographic studies confirmed that one variant existed as an independent monomer, but with few changes to the secondary and tertiary structure. Reduction of higher order assembly resulted in a loss of thermal stability, as measured by a variety of methods, and impaired catalytic function. Binding of pyruvate increased the oligomeric status of the variants, with a concomitant increase in thermal stability, suggesting a role for substrate binding in optimizing stable, higher order structures. The results of this work show that the salt bridges located at the tetramerization interface of DHDPS play a significant role in maintaining higher order structures, and demonstrate the importance of quaternary structure in determining protein stability and in the optimization of enzyme catalysis.
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Affiliation(s)
- F Grant Pearce
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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23
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Evans G, Schuldt L, Griffin MDW, Devenish SRA, Grant Pearce F, Perugini MA, Dobson RCJ, Jameson GB, Weiss MS, Gerrard JA. A tetrameric structure is not essential for activity in dihydrodipicolinate synthase (DHDPS) from Mycobacterium tuberculosis. Arch Biochem Biophys 2011; 512:154-9. [PMID: 21672512 DOI: 10.1016/j.abb.2011.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 05/19/2011] [Accepted: 05/20/2011] [Indexed: 11/19/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) is a validated antibiotic target for which a new approach to inhibitor design has been proposed: disrupting native tetramer formation by targeting the dimer-dimer interface. In this study, rational design afforded a variant of Mycobacterium tuberculosis, Mtb-DHDPS-A204R, with disrupted quaternary structure. X-ray crystallography (at a resolution of 2.1Å) revealed a dimeric protein with an identical fold and active-site structure to the tetrameric wild-type enzyme. Analytical ultracentrifugation confirmed the dimeric structure in solution, yet the dimeric mutant has similar activity to the wild-type enzyme. Although the affinity for both substrates was somewhat decreased, the high catalytic competency of the enzyme was surprising in the light of previous results showing that dimeric variants of the Escherichia coli and Bacillus anthracis DHDPS enzymes have dramatically reduced activity compared to their wild-type tetrameric counterparts. These results suggest that Mtb-DHDPS-A204R is similar to the natively dimeric enzyme from Staphylococcus aureus, and highlight our incomplete understanding of the role played by oligomerisation in relating protein structure and function.
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Affiliation(s)
- Genevieve Evans
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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24
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Hashimoto K, Nishi H, Bryant S, Panchenko AR. Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization. Phys Biol 2011; 8:035007. [PMID: 21572178 DOI: 10.1088/1478-3975/8/3/035007] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Many soluble and membrane proteins form homooligomeric complexes in a cell which are responsible for the diversity and specificity of many pathways, may mediate and regulate gene expression, activity of enzymes, ion channels, receptors, and cell adhesion processes. The evolutionary and physical mechanisms of oligomerization are very diverse and its general principles have not yet been formulated. Homooligomeric states may be conserved within certain protein subfamilies and might be important in providing specificity to certain substrates while minimizing interactions with other unwanted partners. Moreover, recent studies have led to a greater awareness that transitions between different oligomeric states may regulate protein activity and provide the switch between different pathways. In this paper we summarize the biological importance of homooligomeric assemblies, physico-chemical properties of their interfaces, experimental and computational methods for their identification and prediction. We particularly focus on homooligomer evolution and describe the mechanisms to develop new specificities through the formation of different homooligomeric complexes. Finally, we discuss the possible role of oligomeric transitions in the regulation of protein activity and compile a set of experimental examples with such regulatory mechanisms.
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Affiliation(s)
- Kosuke Hashimoto
- National Center for Biotechnology Information, National Library of Medicine, National Institutes ofHealth, Bethesda, MD 20894, USA
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25
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Disruption of quaternary structure in Escherichia coli dihydrodipicolinate synthase (DHDPS) generates a functional monomer that is no longer inhibited by lysine. Arch Biochem Biophys 2010; 503:202-6. [PMID: 20709017 DOI: 10.1016/j.abb.2010.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 08/07/2010] [Accepted: 08/10/2010] [Indexed: 11/22/2022]
Abstract
Escherichia coli dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52), a natively homotetrameric enzyme was converted to a monomeric species through the introduction of destabilising interactions at two different subunit interfaces allowing exploration of the roles of the quaternary structure in affecting catalytic competency. The double mutant DHDPS-L197D/Y107W displays gel filtration characteristics consistent with a single non-interacting monomeric species, which was confirmed by sedimentary velocity experiments. This monomer was shown to be catalytically active, but with reduced catalytic efficiency (k(cat)=9.8±0.5s(-1)), displaying 8% of the specific activity of the wild-type enzyme. The Michaelis constants for the substrates pyruvate and for (S)-aspartate semialdehyde increased by an order of magnitude, indicating that quaternary structure plays a significant role in substrate specificity. This monomeric species exhibited an enhanced propensity for aggregation and inactivation, indicating that whilst the oligomerization is not an intrinsic criterion for catalysis, higher oligomeric forms may benefit from both increased catalytic efficiency and diminished aggregation propensity. Furthermore, allosteric inhibition by (S)-lysine was abolished for DHDPS-L197D/Y107W, confirming the importance of the dimeric unit as the minimal functional assembly for efficient (S)-lysine binding.
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26
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Devenish SR, Gerrard JA. The quaternary structure of Escherichia coli N-acetylneuraminate lyase is essential for functional expression. Biochem Biophys Res Commun 2009; 388:107-11. [DOI: 10.1016/j.bbrc.2009.07.128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 07/24/2009] [Indexed: 12/19/2022]
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27
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Characterisation of dihydrodipicolinate synthase (DHDPS) from Bacillus anthracis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1510-6. [DOI: 10.1016/j.bbapap.2009.06.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 06/05/2009] [Accepted: 06/25/2009] [Indexed: 11/20/2022]
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28
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Devenish SRA, Huisman FHA, Parker EJ, Hadfield AT, Gerrard JA. Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1168-74. [PMID: 19236959 DOI: 10.1016/j.bbapap.2009.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2008] [Revised: 01/22/2009] [Accepted: 02/05/2009] [Indexed: 11/16/2022]
Abstract
Neisseria meningitidis is an obligate commensal bacterium of humans, and also an important human pathogen. To facilitate future drug studies, we report here the biochemical and structural characterisation of a key enzyme in (S)-lysine biosynthesis, dihydrodipicolinate synthase (DHDPS), from N. meningitidis (NmeDHDPS). X-ray crystallography revealed only minor structural differences between NmeDHDPS and the enzyme from E. coli at the active and allosteric effector sites. The catalytic capabilities of NmeDHDPS are similar to those of the enzyme from E. coli, but intriguingly NmeDHDPS is subject to substrate inhibition by high concentrations of the second substrate, (S)-aspartate semialdehyde, and is also significantly more sensitive to feedback inhibition by (S)-lysine. This heightened sensitivity to inhibition at both active and allosteric sites suggests that it may be possible to target DHDPS from N. meningitidis for antibiotic development.
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Affiliation(s)
- Sean R A Devenish
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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