101
|
|
102
|
Waldhauer MC, Schmitz SN, Ahlmann-Eltze C, Gleixner JG, Schmelas CC, Huhn AG, Bunne C, Büscher M, Horn M, Klughammer N, Kreft J, Schäfer E, Bayer PA, Krämer SG, Neugebauer J, Wehler P, Mayer MP, Eils R, Di Ventura B. Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation. MOLECULAR BIOSYSTEMS 2015; 11:3231-43. [DOI: 10.1039/c5mb00341e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While using a serine (S) as linker for circularization increases the thermostability, a longer linker (RGKCWE) leads to reduced aggregation after heat shock at elevated temperatures.
Collapse
|
103
|
Suplatov D, Voevodin V, Švedas V. Robust enzyme design: bioinformatic tools for improved protein stability. Biotechnol J 2014; 10:344-55. [PMID: 25524647 DOI: 10.1002/biot.201400150] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/30/2014] [Accepted: 11/04/2014] [Indexed: 01/22/2023]
Abstract
The ability of proteins and enzymes to maintain a functionally active conformation under adverse environmental conditions is an important feature of biocatalysts, vaccines, and biopharmaceutical proteins. From an evolutionary perspective, robust stability of proteins improves their biological fitness and allows for further optimization. Viewed from an industrial perspective, enzyme stability is crucial for the practical application of enzymes under the required reaction conditions. In this review, we analyze bioinformatic-driven strategies that are used to predict structural changes that can be applied to wild type proteins in order to produce more stable variants. The most commonly employed techniques can be classified into stochastic approaches, empirical or systematic rational design strategies, and design of chimeric proteins. We conclude that bioinformatic analysis can be efficiently used to study large protein superfamilies systematically as well as to predict particular structural changes which increase enzyme stability. Evolution has created a diversity of protein properties that are encoded in genomic sequences and structural data. Bioinformatics has the power to uncover this evolutionary code and provide a reproducible selection of hotspots - key residues to be mutated in order to produce more stable and functionally diverse proteins and enzymes. Further development of systematic bioinformatic procedures is needed to organize and analyze sequences and structures of proteins within large superfamilies and to link them to function, as well as to provide knowledge-based predictions for experimental evaluation.
Collapse
Affiliation(s)
- Dmitry Suplatov
- Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | | | | |
Collapse
|
104
|
Improvement of the stability and activity of the BPO-A1 haloperoxidase from Streptomyces aureofaciens by directed evolution. J Biotechnol 2014; 192 Pt A:248-54. [DOI: 10.1016/j.jbiotec.2014.10.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/16/2014] [Accepted: 10/23/2014] [Indexed: 11/19/2022]
|
105
|
Gong Y, Xu GC, Zheng GW, Li CX, Xu JH. A thermostable variant of Bacillus subtilis esterase: Characterization and application for resolving dl-menthyl acetate. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
106
|
Srivastava A, Sinha S. Thermostability of in vitro evolved Bacillus subtilis lipase A: a network and dynamics perspective. PLoS One 2014; 9:e102856. [PMID: 25122499 PMCID: PMC4133394 DOI: 10.1371/journal.pone.0102856] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 06/24/2014] [Indexed: 11/23/2022] Open
Abstract
Proteins in thermophilic organisms remain stable and function optimally at high temperatures. Owing to their important applicability in many industrial processes, such thermostable proteins have been studied extensively, and several structural factors attributed to their enhanced stability. How these factors render the emergent property of thermostability to proteins, even in situations where no significant changes occur in their three-dimensional structures in comparison to their mesophilic counter-parts, has remained an intriguing question. In this study we treat Lipase A from Bacillus subtilis and its six thermostable mutants in a unified manner and address the problem with a combined complex network-based analysis and molecular dynamic studies to find commonality in their properties. The Protein Contact Networks (PCN) of the wild-type and six mutant Lipase A structures developed at a mesoscopic scale were analyzed at global network and local node (residue) level using network parameters and community structure analysis. The comparative PCN analysis of all proteins pointed towards important role of specific residues in the enhanced thermostability. Network analysis results were corroborated with finer-scale molecular dynamics simulations at both room and high temperatures. Our results show that this combined approach at two scales can uncover small but important changes in the local conformations that add up to stabilize the protein structure in thermostable mutants, even when overall conformation differences among them are negligible. Our analysis not only supports the experimentally determined stabilizing factors, but also unveils the important role of contacts, distributed throughout the protein, that lead to thermostability. We propose that this combined mesoscopic-network and fine-grained molecular dynamics approach is a convenient and useful scheme not only to study allosteric changes leading to protein stability in the face of negligible over-all conformational changes due to mutations, but also in other molecular networks where change in function does not accompany significant change in the network structure.
Collapse
Affiliation(s)
| | - Somdatta Sinha
- Indian Institute of Science Education and Research Mohali, S. A. S. Nagar, Manauli, India
- * E-mail:
| |
Collapse
|
107
|
Moon S, Bannen RM, Rutkoski TJ, Phillips GN, Bae E. Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases. Proteins 2014; 82:2631-42. [PMID: 24931334 DOI: 10.1002/prot.24627] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/09/2014] [Accepted: 06/09/2014] [Indexed: 11/08/2022]
Abstract
Local structural entropy (LSE) is a descriptor for the extent of conformational heterogeneity in short protein sequences that is computed from structural information derived from the Protein Data Bank. Reducing the LSE of a protein sequence by introducing amino acid mutations can result in fewer conformational states and thus a more stable structure, indicating that LSE optimization can be used as a protein stabilization method. Here, we describe a series of LSE optimization experiments designed to stabilize mesophilic and thermophilic adenylate kinases (AKs) and report crystal structures of LSE-optimized AK variants. In the mesophilic AK, thermal stabilization by LSE reduction was effective but limited. Structural analyses of the LSE-optimized mesophilic AK variants revealed a strong correlation between LSE and the apolar buried surface area. Additional mutations designed to introduce noncovalent interactions between distant regions of the polypeptide resulted in further stabilization. Unexpectedly, optimizing the LSE of the thermophilic AK resulted in a decrease in thermal stability. This destabilization was reduced when charged residues were excluded from the possible substitutions during LSE optimization. These observations suggest that stabilization by LSE reduction may result from the optimization of local hydrophobic contacts. The limitations of this process are likely due to ignorance of other interactions that bridge distant regions in a given amino acid sequence. Our results illustrate the effectiveness and limitations of LSE optimization as a protein stabilization strategy and highlight the importance and complementarity of local conformational stability and global interactions in protein thermal stability.
Collapse
Affiliation(s)
- Sojin Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, Korea
| | | | | | | | | |
Collapse
|
108
|
Mitrovic A, Flicker K, Steinkellner G, Gruber K, Reisinger C, Schirrmacher G, Camattari A, Glieder A. Thermostability improvement of endoglucanase Cel7B from Hypocrea pseudokoningii. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
109
|
Diem MD, Hyun L, Yi F, Hippensteel R, Kuhar E, Lowenstein C, Swift EJ, O'Neil KT, Jacobs SA. Selection of high-affinity Centyrin FN3 domains from a simple library diversified at a combination of strand and loop positions. Protein Eng Des Sel 2014; 27:419-29. [PMID: 24786107 DOI: 10.1093/protein/gzu016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Alternative scaffold molecules represent a class of proteins important to the study of protein design and mechanisms of protein-protein interactions, as well as for the development of therapeutic proteins. Here, we describe the generation of a library built upon the framework of a consensus FN3 domain sequence resulting in binding proteins we call Centyrins. This new library employs diversified positions within the C-strand, CD-loop, F-strand and FG-loop of the FN3 domain. CIS display was used to select high-affinity Centyrin variants against three targets; c-MET, murine IL-17A and rat TNFα and scanning mutagenesis studies were used to define the positions of the library most important for target binding. Contributions from both the strand and loop positions were noted, although the pattern was different for each molecule. In addition, an affinity maturation scheme is described that resulted in a significant improvement in the affinity of one selected Centyrin variant. Together, this work provides important data contributing to our understanding of potential FN3 binding interfaces and a new tool for generating high-affinity scaffold molecules.
Collapse
Affiliation(s)
- Michael D Diem
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Linus Hyun
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Fang Yi
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Randi Hippensteel
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Elise Kuhar
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Cassandra Lowenstein
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Edward J Swift
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Karyn T O'Neil
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Steven A Jacobs
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| |
Collapse
|
110
|
Costanzo JA, O'Brien CJ, Tiller K, Tamargo E, Robinson AS, Roberts CJ, Fernandez EJ. Conformational stability as a design target to control protein aggregation. Protein Eng Des Sel 2014; 27:157-67. [DOI: 10.1093/protein/gzu008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
111
|
Reich S, Kress N, Nestl BM, Hauer B. Variations in the stability of NCR ene reductase by rational enzyme loop modulation. J Struct Biol 2014; 185:228-33. [DOI: 10.1016/j.jsb.2013.04.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/15/2013] [Accepted: 04/09/2013] [Indexed: 10/26/2022]
|
112
|
Wijma HJ, Floor RJ, Jekel PA, Baker D, Marrink SJ, Janssen DB. Computationally designed libraries for rapid enzyme stabilization. Protein Eng Des Sel 2014; 27:49-58. [PMID: 24402331 PMCID: PMC3893934 DOI: 10.1093/protein/gzt061] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 11/28/2013] [Accepted: 11/30/2013] [Indexed: 11/24/2022] Open
Abstract
The ability to engineer enzymes and other proteins to any desired stability would have wide-ranging applications. Here, we demonstrate that computational design of a library with chemically diverse stabilizing mutations allows the engineering of drastically stabilized and fully functional variants of the mesostable enzyme limonene epoxide hydrolase. First, point mutations were selected if they significantly improved the predicted free energy of protein folding. Disulfide bonds were designed using sampling of backbone conformational space, which tripled the number of experimentally stabilizing disulfide bridges. Next, orthogonal in silico screening steps were used to remove chemically unreasonable mutations and mutations that are predicted to increase protein flexibility. The resulting library of 64 variants was experimentally screened, which revealed 21 (pairs of) stabilizing mutations located both in relatively rigid and in flexible areas of the enzyme. Finally, combining 10-12 of these confirmed mutations resulted in multi-site mutants with an increase in apparent melting temperature from 50 to 85°C, enhanced catalytic activity, preserved regioselectivity and a >250-fold longer half-life. The developed Framework for Rapid Enzyme Stabilization by Computational libraries (FRESCO) requires far less screening than conventional directed evolution.
Collapse
Affiliation(s)
- Hein J. Wijma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Robert J. Floor
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Peter A. Jekel
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
| | - Siewert J. Marrink
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Department of Biophysical Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Dick B. Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
113
|
Wang ZB, Chen X, Wang W, Cheng KD, Kong JQ. Transcriptome-wide identification and characterization of Ornithogalum saundersiae phenylalanine ammonia lyase gene family. RSC Adv 2014. [DOI: 10.1039/c4ra03385j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Transcriptome-wide identification and characterization ofOrnithogalum saundersiaephenylalanine ammonia lyase gene family.
Collapse
Affiliation(s)
- Zhi-Biao Wang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College (State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products)
- Beijing, China
| | - Xi Chen
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College (State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products)
- Beijing, China
| | - Wei Wang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College (State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products)
- Beijing, China
| | - Ke-Di Cheng
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College (State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products)
- Beijing, China
| | - Jian-Qiang Kong
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College (State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products)
- Beijing, China
| |
Collapse
|
114
|
Engineering protein thermostability using a generic activity-independent biophysical screen inside the cell. Nat Commun 2013; 4:2901. [DOI: 10.1038/ncomms3901] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 11/08/2013] [Indexed: 11/08/2022] Open
|
115
|
Yu H, Huang H. Engineering proteins for thermostability through rigidifying flexible sites. Biotechnol Adv 2013; 32:308-15. [PMID: 24211474 DOI: 10.1016/j.biotechadv.2013.10.012] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 09/04/2013] [Accepted: 10/29/2013] [Indexed: 01/06/2023]
Abstract
Engineering proteins for thermostability is an exciting and challenging field since it is critical for broadening the industrial use of recombinant proteins. Thermostability of proteins arises from the simultaneous effect of several forces such as hydrophobic interactions, disulfide bonds, salt bridges and hydrogen bonds. All of these interactions lead to decreased flexibility of polypeptide chain. Structural studies of mesophilic and thermophilic proteins showed that the latter need more rigid structures to compensate for increased thermal fluctuations. Hence flexibility can be an indicator to pinpoint weak spots for enhancing thermostability of enzymes. A strategy has been proven effective in enhancing proteins' thermostability with two steps: predict flexible sites of proteins firstly and then rigidify these sites. We refer to this approach as rigidify flexible sites (RFS) and give an overview of such a method through summarizing the methods to predict flexibility of a protein, the methods to rigidify residues with high flexibility and successful cases regarding enhancing thermostability of proteins using RFS.
Collapse
Affiliation(s)
- Haoran Yu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
| |
Collapse
|
116
|
Cunha ES, Hatem CL, Barrick D. Insertion of endocellulase catalytic domains into thermostable consensus ankyrin scaffolds: effects on stability and cellulolytic activity. Appl Environ Microbiol 2013; 79:6684-96. [PMID: 23974146 PMCID: PMC3811507 DOI: 10.1128/aem.02121-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/21/2013] [Indexed: 11/20/2022] Open
Abstract
Degradation of cellulose for biofuels production holds promise in solving important environmental and economic problems. However, the low activities (and thus high enzyme-to-substrate ratios needed) of hydrolytic cellulase enzymes, which convert cellulose into simple sugars, remain a major barrier. As a potential strategy to stabilize cellulases and enhance their activities, we have embedded cellulases of extremophiles into hyperstable α-helical consensus ankyrin domain scaffolds. We found the catalytic domains CelA (CA, GH8; Clostridium thermocellum) and Cel12A (C12A, GH12; Thermotoga maritima) to be stable in the context of the ankyrin scaffold and to be active against both soluble and insoluble substrates. The ankyrin repeats in each fusion are folded, although it appears that for the C12A catalytic domain (CD; where the N and C termini are distant in the crystal structure), the two flanking ankyrin domains are independent, whereas for CA (where termini are close), the flanking ankyrin domains stabilize each other. Although the activity of CA is unchanged in the context of the ankyrin scaffold, the activity of C12A is increased between 2- and 6-fold (for regenerated amorphous cellulose and carboxymethyl cellulose substrates) at high temperatures. For C12A, activity increases with the number of flanking ankyrin repeats. These results showed ankyrin arrays to be a promising scaffold for constructing designer cellulosomes, preserving or enhancing enzymatic activity and retaining thermostability. This modular architecture will make it possible to arrange multiple cellulase domains at a precise spacing within a single polypeptide, allowing us to search for spacings that may optimize reactivity toward the repetitive cellulose lattice.
Collapse
Affiliation(s)
- Eva S. Cunha
- Institute for Multiscale Modeling of Biological Interactions, Johns Hopkins University, Baltimore, Maryland, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Christine L. Hatem
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Doug Barrick
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| |
Collapse
|
117
|
Daudé D, Topham CM, Remaud-Siméon M, André I. Probing impact of active site residue mutations on stability and activity of Neisseria polysaccharea amylosucrase. Protein Sci 2013; 22:1754-65. [PMID: 24115119 DOI: 10.1002/pro.2375] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/10/2013] [Indexed: 11/06/2022]
Abstract
The amylosucrase from Neisseria polysaccharea is a transglucosidase from the GH13 family of glycoside-hydrolases that naturally catalyzes the synthesis of α-glucans from the widely available donor sucrose. Interestingly, natural molecular evolution has modeled a dense hydrogen bond network at subsite -1 responsible for the specific recognition of sucrose and conversely, it has loosened interactions at the subsite +1 creating a highly promiscuous subsite +1. The residues forming these subsites are considered to be likely involved in the activity as well as the overall stability of the enzyme. To assess their role, a structure-based approach was followed to reshape the subsite -1. A strategy based on stability change predictions, using the FoldX algorithm, was considered to identify the best candidates for site-directed mutagenesis and guide the construction of a small targeted library. A miniaturized purification protocol was developed and both mutant stability and substrate promiscuity were explored. A range of 8 °C between extreme melting temperature values was observed and some variants were able to synthesize series of oligosaccharides with distributions differing from that of the parental enzyme. The crucial role of subsite -1 was thus highlighted and the biocatalysts generated can now be considered as starting points for further engineering purposes.
Collapse
Affiliation(s)
- David Daudé
- Université de Toulouse; INSA, UPS,INP, LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France; CNRS, UMR5504, F-31400, Toulouse, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France
| | | | | | | |
Collapse
|
118
|
Directed evolution of a soluble human IL-17A receptor for the inhibition of psoriasis plaque formation in a mouse model. ACTA ACUST UNITED AC 2013; 20:202-11. [PMID: 23438749 DOI: 10.1016/j.chembiol.2012.11.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/13/2012] [Accepted: 11/21/2012] [Indexed: 11/22/2022]
Abstract
Interleukin-17 (IL-17) is a T-cell-derived cytokine that promotes inflammatory pathology in autoimmune diseases. Blocking IL-17A interactions with its endogenous IL-17 receptor (IL-17RA) can constitute an important target for therapeutic intervention. Here, we utilized a directed evolution approach to generate soluble IL-17RA mutants that exhibit increased IL-17A binding affinity and thermostability, relative to the wild-type. Human fibroblast cell-based assay and in vivo analysis in mice indicated that two improved IL-17RA mutants efficiently inhibit the secretion of IL-17A-induced proinflammatory cytokines. Analysis of one of these mutants in a psoriasis mouse model showed its efficacy in promoting the recovery of psoriasis plaques. This mutant can be used as a promising drug candidate for the treatment of psoriasis and may be a therapeutic agent for various other autoimmune diseases.
Collapse
|
119
|
Stabilized homoserine o-succinyltransferases (MetA) or L-methionine partially recovers the growth defect in Escherichia coli lacking ATP-dependent proteases or the DnaK chaperone. BMC Microbiol 2013; 13:179. [PMID: 23898868 PMCID: PMC3735405 DOI: 10.1186/1471-2180-13-179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 07/24/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The growth of Escherichia coli at elevated temperatures is limited due to the inherent instability of homoserine o-succinyltransferase, MetA, which is the first enzyme in the methionine biosynthesis pathway. MetA is also unstable under other stressful conditions, such as weak organic acids and oxidative stress. The MetA protein unfolds, even at 25°C, forms considerable aggregates at 37°C and completely aggregates at 44°C. RESULTS We extended the MetA mutation studies using a consensus concept based on statistics and sequence database analysis to predict the point mutations resulting in increased MetA stability. In this study, four single amino acid substitutions (Q96K, I124L, I229Y and F247Y) in MetA designed according to the consensus concept and using the I-mutant2.0 modeling tool conferred accelerated growth on the E. coli strain WE at 44°C. MetA mutants that enabled E. coli growth at higher temperatures did not display increased melting temperatures (Tm) or enhanced catalytic activity but did show improved in vivo stability at mild (37°C) and elevated (44°C) temperatures. Notably, we observed that the stabilized MetA mutants partially recovered the growth defects of E. coli mutants in which ATP-dependent proteases or the DnaK chaperone was deleted. These results suggest that the impaired growth of these E. coli mutants primarily reflect the inherent instability of MetA and, thus, the methionine supply. As further evidence, the addition of methionine recovered most of the growth defects in mutants lacking either ATP-dependent proteases or the DnaK chaperone. CONCLUSIONS A collection of stable single-residue mutated MetA enzymes were constructed and investigated as background for engineering the stabilized mutants. In summary, the mutations in a single gene, metA, reframe the window of growth temperature in both normal and mutant E. coli strains.
Collapse
|
120
|
Overman RC, Green I, Truman CM, Read JA, Embrey KJ, McAlister MSB, Attwood TK. Stability and solubility engineering of the EphB4 tyrosine kinase catalytic domain using a rationally designed synthetic library. Protein Eng Des Sel 2013; 26:695-704. [DOI: 10.1093/protein/gzt032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
121
|
Arpino JAJ, Hancock EJ, Anderson J, Barahona M, Stan GBV, Papachristodoulou A, Polizzi K. Tuning the dials of Synthetic Biology. MICROBIOLOGY-SGM 2013; 159:1236-1253. [PMID: 23704788 PMCID: PMC3749727 DOI: 10.1099/mic.0.067975-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Synthetic Biology is the ‘Engineering of Biology’ – it aims to use a forward-engineering design cycle based on specifications, modelling, analysis, experimental implementation, testing and validation to modify natural or design new, synthetic biology systems so that they behave in a predictable fashion. Motivated by the need for truly plug-and-play synthetic biological components, we present a comprehensive review of ways in which the various parts of a biological system can be modified systematically. In particular, we review the list of ‘dials’ that are available to the designer and discuss how they can be modelled, tuned and implemented. The dials are categorized according to whether they operate at the global, transcriptional, translational or post-translational level and the resolution that they operate at. We end this review with a discussion on the relative advantages and disadvantages of some dials over others.
Collapse
Affiliation(s)
- James A J Arpino
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.,Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.,Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Edward J Hancock
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - James Anderson
- St John's College, St Giles, Oxford OX1 3JP, UK.,Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Guy-Bart V Stan
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.,Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | | | - Karen Polizzi
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.,Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| |
Collapse
|
122
|
Sugahara M, Takehira M, Yutani K. Effect of heavy atoms on the thermal stability of α-amylase from Aspergillus oryzae. PLoS One 2013; 8:e57432. [PMID: 23451229 PMCID: PMC3581456 DOI: 10.1371/journal.pone.0057432] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 01/22/2013] [Indexed: 11/18/2022] Open
Abstract
Currently, there are no versatile and established methods for improving stability of proteins. In an entirely different approach from conventional techniques such as mutagenesis, we attempted to enhance enzyme stability of α-amylase from Aspergillus oryzae using a heavy-atom derivatization technique. We evaluated changes in stability using differential scanning calorimetry (DSC). Candidate heavy atoms were identified using the Heavy-Atom Database System HATODAS, a Web-based tool designed to assist in heavy-atom derivatization of proteins for X-ray crystallography. The denaturation temperature of α-amylase derivatized with gadolinium (Gd) or samarium (Sm) ions increased by 6.2 or 5.7°C, respectively, compared to that of the native protein (60.6°C). The binding of six Gd ions was confirmed by X-ray crystallography of the enzyme at 1.5 Å resolution. DSC and dynamic light-scattering data revealed a correlation between stability and the aggregation state upon addition of Gd ions. These results show that HATODAS search is an effective tool for selecting heavy atoms for stabilization of this protein.
Collapse
|
123
|
Yi ZL, Zhang SB, Pei XQ, Wu ZL. Design of mutants for enhanced thermostability of β-glycosidase BglY from Thermus thermophilus. BIORESOURCE TECHNOLOGY 2013; 129:629-33. [PMID: 23317553 DOI: 10.1016/j.biortech.2012.12.098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 05/07/2023]
Abstract
Three design strategies, based on rational and semi-rational approaches, were employed to investigate the functional impact of thermostability-related amino acid substitutions in the β-glycosidase BglY from Thermus thermophilus. Five beneficial mutations were identified, of which 1 mutation was located in the active cavity of the enzyme and contributed to the released substrate inhibition. Combining all 5 beneficial substitutions resulted in the mutant HF5 with a 4.7-fold increase in half-life, with thermal inactivation at 93 °C, and complete lack of substrate inhibition toward the substrate p-nitrophenyl-β-D-glucopyranoside at lower reaction temperatures. The results of this study provide valuable information on amino acid substitutions related to thermostability and substrate inhibition of BglY.
Collapse
Affiliation(s)
- Zhuo-Lin Yi
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | | | | | | |
Collapse
|
124
|
Sankaranarayanan K, Sreedhar B, Nair B, Dhathathreyan A. Microviscosity-Induced Conformational Transition in β-Lactoglobulin in the Presence of an Ionic Liquid. J Phys Chem B 2013; 117:1234-40. [DOI: 10.1021/jp310198f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - B. Sreedhar
- Inorganic and Physical Chemistry
Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 607, India
| | - B.U. Nair
- Chemical Laboratory, CSIR-CLRI, Adyar, Chennai 600020, India
| | | |
Collapse
|
125
|
|
126
|
Meridor D, Gedanken A. Preparation of enzyme nanoparticles and studying the catalytic activity of the immobilized nanoparticles on polyethylene films. ULTRASONICS SONOCHEMISTRY 2013; 20:425-431. [PMID: 22800814 DOI: 10.1016/j.ultsonch.2012.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Revised: 06/13/2012] [Accepted: 06/13/2012] [Indexed: 06/01/2023]
Abstract
Using high-intensity ultrasound, in situ generated α-amylase nanoparticles (NPs) were immobilized on polyethylene (PE) films. The α-amylase NP-coated PE films have been characterized by E-SEM, FTIR, DLS, XPS and RBS. The PE was reacted with HNO(3) and NPs of the α-amylase were also deposited on the activated PE. The PE impregnated with α-amylase (4 μg per 1mg PE) was used for hydrolyzing soluble potato starch to maltose. The immobilization improved the catalytic activity of α-amylase at all the reaction conditions studied. The kinetic parameters, K(m) (5 and 4 g L(-1) for the regular and activated PE, respectively) and V(max) (5 × 10(-7) mol ml(-1) min(-1), almost the same numbers were obtained for the regular and activated PEs) for the immobilized amylase were found to slightly favor the respective values obtained for the free enzyme (K(m) = 6.6 g L(-1), V(max) = 3.7 × 10(-7) mol ml(-1) min(-1)). The enzyme remained bound to PE even after soaking the PE in a starch solution for 72 h and was still found to be weakly active.
Collapse
Affiliation(s)
- David Meridor
- Department of Chemistry and Kanbar Laboratory for Nanomaterials, Center for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | |
Collapse
|
127
|
Fomin ES, Alemasov NA. A study of the thermal stability of mutant barnase protein variants with MOLKERN software. ACTA ACUST UNITED AC 2012. [DOI: 10.1134/s2079059712060068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
128
|
Steiner K, Schwab H. Recent advances in rational approaches for enzyme engineering. Comput Struct Biotechnol J 2012; 2:e201209010. [PMID: 24688651 PMCID: PMC3962183 DOI: 10.5936/csbj.201209010] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/16/2012] [Accepted: 10/18/2012] [Indexed: 11/29/2022] Open
Abstract
Enzymes are an attractive alternative in the asymmetric syntheses of chiral building blocks. To meet the requirements of industrial biotechnology and to introduce new functionalities, the enzymes need to be optimized by protein engineering. This article specifically reviews rational approaches for enzyme engineering and de novo enzyme design involving structure-based approaches developed in recent years for improvement of the enzymes’ performance, broadened substrate range, and creation of novel functionalities to obtain products with high added value for industrial applications.
Collapse
Affiliation(s)
- Kerstin Steiner
- ACIB GmbH, (Austrian Centre of Industrial Biotechnology), c/o TU Graz, 8010 Graz, Austria
| | - Helmut Schwab
- ACIB GmbH, (Austrian Centre of Industrial Biotechnology), c/o TU Graz, 8010 Graz, Austria ; Institute of Molecular Biotechnology, TU Graz, 8010 Graz, Austria
| |
Collapse
|
129
|
Rayalu S, Yadav R, Wanjari S, Prabhu C, Mushnoori SC, Labhsetwar N, Satyanarayanan T, Kotwal S, Wate SR, Hong SG, Kim J. Nanobiocatalysts for Carbon Capture, Sequestration and Valorisation. Top Catal 2012. [DOI: 10.1007/s11244-012-9896-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
130
|
Buchanan A, Ferraro F, Rust S, Sridharan S, Franks R, Dean G, McCourt M, Jermutus L, Minter R. Improved drug-like properties of therapeutic proteins by directed evolution. Protein Eng Des Sel 2012; 25:631-8. [PMID: 22942395 PMCID: PMC3449403 DOI: 10.1093/protein/gzs054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 05/25/2012] [Accepted: 08/06/2012] [Indexed: 11/13/2022] Open
Abstract
Many natural human proteins have functional properties that make them useful as therapeutic drugs. However, not all these proteins are compatible with large-scale manufacturing processes or sufficiently stable to be stored for long periods prior to use. In this study, we focus on small four-helix bundle proteins and employ ribosome display in conjunction with three parallel selection pressures to favour the isolation of variant proteins with improved expression, solubility and stability. This in vitro evolution strategy was applied to two human proteins with known drug development issues, granulocyte colony-stimulating factor (G-CSF) and erythropoietin (EPO). In the case of G-CSF, the soluble expression levels in Escherichia coli were improved 1000-fold, while for EPO the level of aggregation in an accelerated shelf-life study was reduced from over 80% to undetectable levels. These results exemplify the general utility of our in vitro evolution strategy for improving the drug-like properties of therapeutic proteins.
Collapse
|
131
|
Liu M, Wang S, Sun T, Su J, Zhang Y, Yue J, Sun Z. Insight into the structure, dynamics and the unfolding property of amylosucrases: implications of rational engineering on thermostability. PLoS One 2012; 7:e40441. [PMID: 22792323 PMCID: PMC3391273 DOI: 10.1371/journal.pone.0040441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 06/07/2012] [Indexed: 11/19/2022] Open
Abstract
Amylosucrase (AS) is a kind of glucosyltransferases (E.C. 2.4.1.4) belonging to the Glycoside Hydrolase (GH) Family 13. In the presence of an activator polymer, in vitro, AS is able to catalyze the synthesis of an amylose-like polysaccharide composed of only α-1,4-linkages using sucrose as the only energy source. Unlike AS, other enzymes responsible for the synthesis of such amylose-like polymers require the addition of expensive nucleotide-activated sugars. These properties make AS an interesting enzyme for industrial applications. In this work, the structures and topology of the two AS were thoroughly investigated for the sake of explaining the reason why Deinococcus geothermalis amylosucrase (DgAS) is more stable than Neisseria polysaccharea amylosucrase (NpAS). Based on our results, there are two main factors that contribute to the superior thermostability of DgAS. On the one hand, DgAS holds some good structural features that may make positive contributions to the thermostability. On the other hand, the contacts among residues of DgAS are thought to be topologically more compact than those of NpAS. Furthermore, the dynamics and unfolding properties of the two AS were also explored by the gauss network model (GNM) and the anisotropic network model (ANM). According to the results of GNM and ANM, we have found that the two AS could exhibit a shear-like motion, which is probably associated with their functions. What is more, with the discovery of the unfolding pathway of the two AS, we can focus on the weak regions, and hence designing more appropriate mutations for the sake of thermostability engineering. Taking the results on structure, dynamics and unfolding properties of the two AS into consideration, we have predicted some novel mutants whose thermostability is possibly elevated, and hopefully these discoveries can be used as guides for our future work on rational design.
Collapse
Affiliation(s)
- Ming Liu
- Beijing Institute of Biotechnology, Beijing, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Genor Biopharma Co., Ltd, Shanghai, China
| | - Shuang Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Tingguang Sun
- Department of Biological and Chemical Engineering, Guangxi University of Technology, Liuzhou, China
| | - Jiguo Su
- College of Science, Yanshan University, Qinhuangdao, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- * E-mail: (ZS) (YZ); (JY) (JY); (YZ) (ZS)
| | - Junjie Yue
- Beijing Institute of Biotechnology, Beijing, China
- * E-mail: (ZS) (YZ); (JY) (JY); (YZ) (ZS)
| | - Zhiwei Sun
- Beijing Institute of Biotechnology, Beijing, China
- * E-mail: (ZS) (YZ); (JY) (JY); (YZ) (ZS)
| |
Collapse
|
132
|
Rathi PC, Radestock S, Gohlke H. Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio. J Biotechnol 2012; 159:135-44. [PMID: 22326626 DOI: 10.1016/j.jbiotec.2012.01.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 01/16/2012] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
Abstract
We apply Constraint Network Analysis (CNA) to investigate the relationship between structural rigidity and thermostability of five citrate synthase (CS) structures over a temperature range from 37 °C to 100 °C. For the first time, we introduce an ensemble-based variant of CNA and model the temperature-dependence of hydrophobic interactions in the constraint network. A very good correlation between the predicted thermostabilities of CS and optimal growth temperatures of their source organisms (R²=0.88, p=0.017) is obtained, which validates that CNA is able to quantitatively discriminate between less and more thermostable proteins even within a series of orthologs. Structural weak spots on a less thermostable CS, predicted by CNA to be in the top 5% with respect to the frequency of occurrence over an ensemble, have a higher mutation ratio in a more thermostable CS than other sequence positions. Furthermore, highly ranked weak spots that are also highly conserved with respect to the amino acid type found at that sequence position are nevertheless found to be mutated in the more stable CS. As for mechanisms at an atomic level that lead to a reinforcement of weak spots in more stable CS, we observe that the thermophilic CS achieve a higher thermostability by better hydrogen bonding networks whereas hyperthermophilic CS incorporate more hydrophobic contacts to reach the same goal. Overall, these findings suggest that CNA can be applied as a pre-filter in data-driven protein engineering to focus on residues that are highly likely to improve thermostability upon mutation.
Collapse
Affiliation(s)
- Prakash C Rathi
- Department of Mathematics and Natural Sciences, Heinrich Heine-University, Düsseldorf, Germany
| | | | | |
Collapse
|
133
|
Jacobs SA, Diem MD, Luo J, Teplyakov A, Obmolova G, Malia T, Gilliland GL, O'Neil KT. Design of novel FN3 domains with high stability by a consensus sequence approach. Protein Eng Des Sel 2012; 25:107-17. [PMID: 22240293 DOI: 10.1093/protein/gzr064] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The use of consensus design to produce stable proteins has been applied to numerous structures and classes of proteins. Here, we describe the engineering of novel FN3 domains from two different proteins, namely human fibronectin and human tenascin-C, as potential alternative scaffold biotherapeutics. The resulting FN3 domains were found to be robustly expressed in Escherichia coli, soluble and highly stable, with melting temperatures of 89 and 78°C, respectively. X-ray crystallography was used to confirm that the consensus approach led to a structure consistent with the FN3 design despite having only low-sequence identity to natural FN3 domains. The ability of the Tenascin consensus domain to withstand mutations in the loop regions connecting the β-strands was investigated using alanine scanning mutagenesis demonstrating the potential for randomization in these regions. Finally, rational design was used to produce point mutations that significantly increase the stability of one of the consensus domains. Together our data suggest that consensus FN3 domains have potential utility as alternative scaffold therapeutics.
Collapse
Affiliation(s)
- Steven A Jacobs
- Janssen Research & Development, L.L.C., Radnor, PA 19087, USA.
| | | | | | | | | | | | | | | |
Collapse
|
134
|
Ye X, Zhang C, Zhang YHP. Engineering a large protein by combined rational and random approaches: stabilizing the Clostridium thermocellum cellobiose phosphorylase. MOLECULAR BIOSYSTEMS 2012; 8:1815-23. [DOI: 10.1039/c2mb05492b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
135
|
Hong YH, Lee DW, Pyun YR, Lee SH. Creation of metal-independent hyperthermophilic L-arabinose isomerase by homologous recombination. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:12939-12947. [PMID: 22103589 DOI: 10.1021/jf203897a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Hyperthermophilic L-arabinose isomerases (AIs) are useful in the commercial production of D-tagatose as a low-calorie bulk sweetener. Their catalysis and thermostability are highly dependent on metals, which is a major drawback in food applications. To study the role of metal ions in the thermostability and catalysis of hyperthermophilic AI, four enzyme chimeras were generated by PCR-based hybridization to replace the variable N- and C-terminal regions of hyperthermophilic Thermotoga maritima AI (TMAI) and thermophilic Geobacillus stearothermophilus AI (GSAI) with those of the homologous mesophilic Bacillus halodurans AI (BHAI). Unlike Mn(2+)-dependent TMAI, the GSAI- and TMAI-based hybrids with the 72 C-terminal residues of BHAI were not metal-dependent for catalytic activity. By contrast, the catalytic activities of the TMAI- and GSAI-based hybrids containing the N-terminus (residues 1-89) of BHAI were significantly enhanced by metals, but their thermostabilities were poor even in the presence of Mn(2+), indicating that the effects of metals on catalysis and thermostability involve different structural regions. Moreover, in contrast to the C-terminal truncate (Δ20 residues) of GSAI, the N-terminal truncate (Δ7 residues) exhibited no activity due to loss of its native structure. The data thus strongly suggest that the metal dependence of the catalysis and thermostability of hyperthermophilic AIs evolved separately to optimize their activity and thermostability at elevated temperatures. This may provide effective target regions for engineering, thereby meeting industrial demands for the production of d-tagatose.
Collapse
Affiliation(s)
- Young-Ho Hong
- CJ Foods R & D, CJ Cheiljedang Corporation, Seoul 100-749, Korea
| | | | | | | |
Collapse
|
136
|
Amar D, Berger I, Amara N, Tafa G, Meijler MM, Aharoni A. The transition of human estrogen sulfotransferase from generalist to specialist using directed enzyme evolution. J Mol Biol 2011; 416:21-32. [PMID: 22197379 DOI: 10.1016/j.jmb.2011.12.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 12/04/2011] [Accepted: 12/06/2011] [Indexed: 11/29/2022]
Abstract
Broad specificity is believed to be a property of primordial enzymes that diverged during natural protein evolution to produce highly specific and efficient enzymes. Human estrogen sulfotransferase (SULT1E1) is a broad-specificity enzyme that detoxifies a variety of chemicals, including estrogens, by the transfer of sulfate. To study the molecular basis for the broad specificity of this enzyme and to investigate the process of SULT1E1 specialization, we have adopted a directed enzyme evolution approach. Using two iterative rounds of evolution, we generated SULT1E1 mutants with increased thermostability and narrower specificity from the broadly specific wild-type enzyme. To identify mutants with enhanced specificity, we developed an unbiased screening assay to assess sulfate transfer to three different acceptors in parallel. Such an assay enabled the isolation of SULT1E1 mutants with enhanced or wild-type activity toward an estrogen acceptor and significantly reduced activity for phenol or coumarin type of acceptors, leading to up to 3 orders of magnitude increase in specificity. We found that mutations conferring novel specificity are located in the vicinity of the active site and thus may play a direct role in reshaping the acceptor-binding site. Finally, such mutations resulted in reduced SULT1E1 thermostability, revealing a trade-off between SULT1E1 thermostability and acquisition of novel function.
Collapse
Affiliation(s)
- Dotan Amar
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | | | | | | | | |
Collapse
|
137
|
Majors BS, Chiang GG, Pederson NE, Betenbaugh MJ. Directed evolution of mammalian anti-apoptosis proteins by somatic hypermutation. Protein Eng Des Sel 2011; 25:27-38. [PMID: 22160868 DOI: 10.1093/protein/gzr052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recently, researchers have created novel fluorescent proteins by harnessing the somatic hypermutation ability of B cells. In this study, we examined if this approach could be used to evolve a non-fluorescent protein, namely the anti-apoptosis protein Bcl-x(L), using the Ramos B-cell line. After demonstrating that Ramos cells were capable of mutating a heterologous bcl-x(L) transgene, the cells were exposed to multiple rounds of the chemical apoptosis inducer staurosporine followed by rounds of recovery in fresh medium. The engineered B cells expressing Bcl-x(L) exhibited progressively lower increases in apoptosis activation as measured by caspase-3 activity after successive rounds of selective pressure with staurosporine treatment. Within the B-cell genome, a number of mutated bcl-x(L) transgene variants were identified after three rounds of evolution, including a mutation of Bcl-x(L) Asp29 to either Asn or His, in 8 out of 23 evaluated constructs that represented at least five distinct Ramos subpopulations. Subsequently, Chinese hamster ovary (CHO) cells engineered to overexpress the Bcl-x(L) Asp29Asn variant showed enhanced apoptosis resistance against an orthogonal apoptosis insult, Sindbis virus infection, when compared with cells expressing the wild-type Bcl-x(L) protein. These findings provide, to our knowledge, the first demonstration of evolution of a recombinant mammalian protein in a mammalian expression system.
Collapse
Affiliation(s)
- Brian S Majors
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, 3400 North Charles Street, 221 Maryland Hall, Baltimore, MD 21218-2694, USA
| | | | | | | |
Collapse
|
138
|
Hall M, Rubin J, Behrens SH, Bommarius AS. The cellulose-binding domain of cellobiohydrolase Cel7A from Trichoderma reesei is also a thermostabilizing domain. J Biotechnol 2011; 155:370-6. [DOI: 10.1016/j.jbiotec.2011.07.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 06/04/2011] [Accepted: 07/12/2011] [Indexed: 11/30/2022]
|
139
|
Baker PJ, Chan YM, Hertel M, Montclare JK. Characterization and identification of the protein partners of Fn3 domain in FnTm2. Protein Expr Purif 2011; 81:42-48. [PMID: 21907285 DOI: 10.1016/j.pep.2011.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 08/18/2011] [Accepted: 08/22/2011] [Indexed: 10/17/2022]
Abstract
Recently, a novel transmembrane protein was found to be up-regulated in the auditory learning pathway of birds and mammals. The protein, FnTm2, was predicted to have an extracellular fibronectin III (Fn3) domain and a single transmembrane domain. By contrast to other studied Fn3 domains the extracellular domain of FnTm2 bears several cysteine residues, which are predicted to form disulfide bonds. The Fn3 domain of the FnTm2 protein was expressed in DH5-α Escherichia coli (E. coli) cells, purified and characterized by circular dichroism (CD). In order to identify binding partners to Fn3, the isolated protein was incubated with bird brain lysate for a pull down treatment. Of the proteins recognized, myelin basic protein (MBP) was identified as a bona fide partner; it was further characterized for binding to Fn3 in vitro via fluorescence spectroscopy and confirmed via isothermal calorimetry (ITC).
Collapse
Affiliation(s)
- Peter James Baker
- Department of Chemical and Biological Sciences, Polytechnic Institute of NYU, 6 Metrotech Center, Brooklyn, NY 11201, United States
| | - Yan Mei Chan
- Department of Chemical and Biological Sciences, Polytechnic Institute of NYU, 6 Metrotech Center, Brooklyn, NY 11201, United States
| | - Moritz Hertel
- Laboratory of Animal Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Jin Kim Montclare
- Department of Chemical and Biological Sciences, Polytechnic Institute of NYU, 6 Metrotech Center, Brooklyn, NY 11201, United States; Department of Biochemistry, SUNY Downstate Medical Center, Brooklyn, NY 11203, United States.
| |
Collapse
|
140
|
Cerdobbel A, De Winter K, Aerts D, Kuipers R, Joosten HJ, Soetaert W, Desmet T. Increasing the thermostability of sucrose phosphorylase by a combination of sequence- and structure-based mutagenesis. Protein Eng Des Sel 2011; 24:829-34. [DOI: 10.1093/protein/gzr042] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
141
|
Strategy and success for the directed evolution of enzymes. Curr Opin Struct Biol 2011; 21:473-80. [DOI: 10.1016/j.sbi.2011.05.003] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 05/25/2011] [Indexed: 11/20/2022]
|
142
|
Alcolombri U, Elias M, Tawfik DS. Directed Evolution of Sulfotransferases and Paraoxonases by Ancestral Libraries. J Mol Biol 2011; 411:837-53. [DOI: 10.1016/j.jmb.2011.06.037] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 06/14/2011] [Accepted: 06/20/2011] [Indexed: 12/30/2022]
|
143
|
Recent progress in protein drug design and discovery with a focus on novel approaches to the development of anti-cocaine medications. Future Med Chem 2011; 1:515-28. [PMID: 20161378 DOI: 10.4155/fmc.09.20] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cocaine is highly addictive and no anti-cocaine medication is currently available. Accelerating cocaine metabolism, producing biologically inactive metabolites, is recognized as an ideal anti-cocaine medication strategy, especially for the treatment of acute cocaine toxicity. However, currently known wild-type enzymes have either too low a catalytic efficiency against the abused cocaine, in other words (-)-cocaine, or the in vivo half-life is too short. Novel computational strategies and design approaches have been developed recently to design and discover thermostable or high-activity mutants of enzymes based on detailed structures and catalytic/inactivation mechanisms. The structure- and mechanism-based computational design efforts have led to the discovery of high-activity mutants of butyrylcholinesterase and thermostable mutants of cocaine esterase as promising anti-cocaine therapeutics. The structure- and mechanism-based computational strategies and design approaches may be used to design high-activity and/or thermostable mutants of many other proteins that have clear therapeutic potentials and to design completely new therapeutic enzymes.
Collapse
|
144
|
Huang X, Gao D, Zhan CG. Computational design of a thermostable mutant of cocaine esterase via molecular dynamics simulations. Org Biomol Chem 2011; 9:4138-43. [PMID: 21373712 PMCID: PMC4365906 DOI: 10.1039/c0ob00972e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cocaine esterase (CocE) has been known as the most efficient native enzyme for metabolizing naturally occurring cocaine. A major obstacle to the clinical application of CocE is the thermoinstability of native CocE with a half-life of only ∼11 min at physiological temperature (37 °C). It is highly desirable to develop a thermostable mutant of CocE for therapeutic treatment of cocaine overdose and addiction. To establish a structure-thermostability relationship, we carried out molecular dynamics (MD) simulations at 400 K on wild-type CocE and previously known thermostable mutants, demonstrating that the thermostability of the active form of the enzyme correlates with the fluctuation (characterized as the root-mean square deviation and root-mean square fluctuation of atomic positions) of the catalytic residues (Y44, S117, Y118, H287, and D259) in the simulated enzyme. In light of the structure-thermostability correlation, further computational modelling including MD simulations at 400 K predicted that the active site structure of the L169K mutant should be more thermostable. The prediction has been confirmed by wet experimental tests showing that the active form of the L169K mutant had a half-life of 570 min at 37 °C, which is significantly longer than those of the wild-type and previously known thermostable mutants. The encouraging outcome suggests that the high-temperature MD simulations and the structure-thermostability relationship may be considered as a valuable tool for the computational design of thermostable mutants of an enzyme.
Collapse
Affiliation(s)
- Xiaoqin Huang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
| | - Daquan Gao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
| |
Collapse
|
145
|
Ackerman SH, Gatti DL. The contribution of coevolving residues to the stability of KDO8P synthase. PLoS One 2011; 6:e17459. [PMID: 21408011 PMCID: PMC3052366 DOI: 10.1371/journal.pone.0017459] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 02/03/2011] [Indexed: 12/03/2022] Open
Abstract
Background The evolutionary tree of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase (KDO8PS), a bacterial enzyme that catalyzes a key step in the biosynthesis of bacterial endotoxin, is evenly divided between metal and non-metal forms, both having similar structures, but diverging in various degrees in amino acid sequence. Mutagenesis, crystallographic and computational studies have established that only a few residues determine whether or not KDO8PS requires a metal for function. The remaining divergence in the amino acid sequence of KDO8PSs is apparently unrelated to the underlying catalytic mechanism. Methodology/Principal Findings The multiple alignment of all known KDO8PS sequences reveals that several residue pairs coevolved, an indication of their possible linkage to a structural constraint. In this study we investigated by computational means the contribution of coevolving residues to the stability of KDO8PS. We found that about 1/4 of all strongly coevolving pairs probably originated from cycles of mutation (decreasing stability) and suppression (restoring it), while the remaining pairs are best explained by a succession of neutral or nearly neutral covarions. Conclusions/Significance Both sequence conservation and coevolution are involved in the preservation of the core structure of KDO8PS, but the contribution of coevolving residues is, in proportion, smaller. This is because small stability gains or losses associated with selection of certain residues in some regions of the stability landscape of KDO8PS are easily offset by a large number of possible changes in other regions. While this effect increases the tolerance of KDO8PS to deleterious mutations, it also decreases the probability that specific pairs of residues could have a strong contribution to the thermodynamic stability of the protein.
Collapse
Affiliation(s)
- Sharon H. Ackerman
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Domenico L. Gatti
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- * E-mail:
| |
Collapse
|
146
|
Varnay I, Truffault V, Djuranovic S, Ursinus A, Coles M, Kessler H. Optimized measurement temperature gives access to the solution structure of a 49 kDa homohexameric β-propeller. J Am Chem Soc 2011; 132:15692-8. [PMID: 20961124 DOI: 10.1021/ja1064608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ph1500 is a homohexameric, two-domain protein of unknown function from the hyperthermophilic archaeon Pyrococcus horikoshii. The C-terminal hexamerization domain (Ph1500C) is of particular interest, as it lacks sequence homology to proteins of known structure. However, it resisted crystallization for X-ray analysis, and proteins of this size (49 kDa) present a considerable challenge to NMR structure determination in solution. We solved the high-resolution structure of Ph1500C, exploiting the hyperthermophilic nature of the protein to minimize unfavorable relaxation properties by high-temperature measurement. Thus, the side chain assignment (97%) and structure determination became possible at full proton density. To our knowledge, Ph1500C is the largest protein for which this has been achieved. To minimize detrimental fast water exchange of amide protons at increased temperature, we employed a strategy where the temperature was optimized separately for backbone and side chain experiments.
Collapse
Affiliation(s)
- Ilka Varnay
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | | | | | | | | | | |
Collapse
|
147
|
Zhang ZG, Yi ZL, Pei XQ, Wu ZL. Improving the thermostability of Geobacillus stearothermophilus xylanase XT6 by directed evolution and site-directed mutagenesis. BIORESOURCE TECHNOLOGY 2010; 101:9272-9278. [PMID: 20691586 DOI: 10.1016/j.biortech.2010.07.060] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 07/13/2010] [Accepted: 07/14/2010] [Indexed: 05/29/2023]
Abstract
Protein engineering of the thermostable xylanase XT6 from Geobacillus stearothermophilus was performed to obtain enzymes with improved thermal tolerance. Mutants producing such enzymes were obtained after several rounds of directed evolution using error-prone PCR and sequence family shuffling, in combination with a consensus-based semi-rational approach. The most thermostable mutant enzyme contained 13 amino acid substitutions and its half-life of inactivation was 52-fold of that of the wild-type. Its reaction temperature for maximum activity increased from 77 degrees C to 87 degrees C, and catalytic efficiency (k(cat)/K(m)) increased by 90%. The mutant is of potential interest for industrial applications.
Collapse
Affiliation(s)
- Zhi-Gang Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China
| | | | | | | |
Collapse
|
148
|
Jochens H, Aerts D, Bornscheuer UT. Thermostabilization of an esterase by alignment-guided focussed directed evolution. Protein Eng Des Sel 2010; 23:903-9. [DOI: 10.1093/protein/gzq071] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
149
|
Fernandes P. Enzymes in food processing: a condensed overview on strategies for better biocatalysts. Enzyme Res 2010; 2010:862537. [PMID: 21048872 PMCID: PMC2963163 DOI: 10.4061/2010/862537] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 09/01/2010] [Indexed: 11/20/2022] Open
Abstract
Food and feed is possibly the area where processing anchored in biological agents has the deepest roots. Despite this, process improvement or design and implementation of novel approaches has been consistently performed, and more so in recent years, where significant advances in enzyme engineering and biocatalyst design have fastened the pace of such developments. This paper aims to provide an updated and succinct overview on the applications of enzymes in the food sector, and of progresses made, namely, within the scope of tapping for more efficient biocatalysts, through screening, structural modification, and immobilization of enzymes. Targeted improvements aim at enzymes with enhanced thermal and operational stability, improved specific activity, modification of pH-activity profiles, and increased product specificity, among others. This has been mostly achieved through protein engineering and enzyme immobilization, along with improvements in screening. The latter has been considerably improved due to the implementation of high-throughput techniques, and due to developments in protein expression and microbial cell culture. Expanding screening to relatively unexplored environments (marine, temperature extreme environments) has also contributed to the identification and development of more efficient biocatalysts. Technological aspects are considered, but economic aspects are also briefly addressed.
Collapse
Affiliation(s)
- Pedro Fernandes
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Avenue Rovisco Pais, 1049-001 Lisboa, Portugal
| |
Collapse
|
150
|
|