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Tellez LA, Blancas-Mejia LM, Carrillo-Nava E, Mendoza-Hernández G, Cisneros DA, Fernández-Velasco DA. Thermal Unfolding of Triosephosphate Isomerase from Entamoeba histolytica: Dimer Dissociation Leads to Extensive Unfolding. Biochemistry 2008; 47:11665-73. [DOI: 10.1021/bi801360k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luis A. Tellez
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - Luis M. Blancas-Mejia
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - Ernesto Carrillo-Nava
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - Guillermo Mendoza-Hernández
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - David A. Cisneros
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - D. Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
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Olivares-Illana V, Rodríguez-Romero A, Becker I, Berzunza M, García J, Pérez-Montfort R, Cabrera N, López-Calahorra F, de Gómez-Puyou MT, Gómez-Puyou A. Perturbation of the dimer interface of triosephosphate isomerase and its effect on Trypanosoma cruzi. PLoS Negl Trop Dis 2007; 1:e1. [PMID: 17989778 PMCID: PMC2041813 DOI: 10.1371/journal.pntd.0000001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 06/07/2007] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Chagas disease affects around 18 million people in the American continent. Unfortunately, there is no satisfactory treatment for the disease. The drugs currently used are not specific and exert serious toxic effects. Thus, there is an urgent need for drugs that are effective. Looking for molecules to eliminate the parasite, we have targeted a central enzyme of the glycolytic pathway: triosephosphate isomerase (TIM). The homodimeric enzyme is catalytically active only as a dimer. Because there are significant differences in the interface of the enzymes from the parasite and humans, we searched for small molecules that specifically disrupt contact between the two subunits of the enzyme from Trypanosoma cruzi but not those of TIM from Homo sapiens (HTIM), and tested if they kill the parasite. METHODOLOGY/PRINCIPAL FINDINGS Dithiodianiline (DTDA) at nanomolar concentrations completely inactivates recombinant TIM of T. cruzi (TcTIM). It also inactivated HTIM, but at concentrations around 400 times higher. DTDA was also tested on four TcTIM mutants with each of its four cysteines replaced with either valine or alanine. The sensitivity of the mutants to DTDA was markedly similar to that of the wild type. The crystal structure of the TcTIM soaked in DTDA at 2.15 A resolution, and the data on the mutants showed that inactivation resulted from alterations of the dimer interface. DTDA also prevented the growth of Escherichia coli cells transformed with TcTIM, had no effect on normal E. coli, and also killed T. cruzi epimastigotes in culture. CONCLUSIONS/SIGNIFICANCE By targeting on the dimer interface of oligomeric enzymes from parasites, it is possible to discover small molecules that selectively thwart the life of the parasite. Also, the conformational changes that DTDA induces in the dimer interface of the trypanosomal enzyme are unique and identify a region of the interface that could be targeted for drug discovery.
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Affiliation(s)
- Vanesa Olivares-Illana
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Ingeborg Becker
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miriam Berzunza
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juventino García
- Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ruy Pérez-Montfort
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Nallely Cabrera
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | - Armando Gómez-Puyou
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Gabdoulline RR, Stein M, Wade RC. qPIPSA: relating enzymatic kinetic parameters and interaction fields. BMC Bioinformatics 2007; 8:373. [PMID: 17919319 PMCID: PMC2174957 DOI: 10.1186/1471-2105-8-373] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 10/05/2007] [Indexed: 11/29/2022] Open
Abstract
Background The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computational methods to estimate these parameters are needed. It is possible to use the three-dimensional structure of an enzyme to perform simulations of a reaction and derive kinetic parameters. However, this is computationally demanding and requires detailed knowledge of the enzyme mechanism. We have therefore sought to develop a general, simple and computationally efficient procedure to relate protein structural information to enzymatic kinetic parameters that allows consistency between the kinetic and structural information to be checked and estimation of kinetic constants for structurally and mechanistically similar enzymes. Results We describe qPIPSA: quantitative Protein Interaction Property Similarity Analysis. In this analysis, molecular interaction fields, for example, electrostatic potentials, are computed from the enzyme structures. Differences in molecular interaction fields between enzymes are then related to the ratios of their kinetic parameters. This procedure can be used to estimate unknown kinetic parameters when enzyme structural information is available and kinetic parameters have been measured for related enzymes or were obtained under different conditions. The detailed interaction of the enzyme with substrate or cofactors is not modeled and is assumed to be similar for all the proteins compared. The protein structure modeling protocol employed ensures that differences between models reflect genuine differences between the protein sequences, rather than random fluctuations in protein structure. Conclusion Provided that the experimental conditions and the protein structural models refer to the same protein state or conformation, correlations between interaction fields and kinetic parameters can be established for sets of related enzymes. Outliers may arise due to variation in the importance of different contributions to the kinetic parameters, such as protein stability and conformational changes. The qPIPSA approach can assist in the validation as well as estimation of kinetic parameters, and provide insights into enzyme mechanism.
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Affiliation(s)
- Razif R Gabdoulline
- Molecular and Cellular Modeling Group, EML Research gGmbH, Schloss Wolfsbrunnenweg 33, Heidelberg, 69118, Germany.
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Leisola M, Turunen O. Protein engineering: opportunities and challenges. Appl Microbiol Biotechnol 2007; 75:1225-32. [PMID: 17404726 DOI: 10.1007/s00253-007-0964-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Revised: 03/20/2007] [Accepted: 03/21/2007] [Indexed: 11/26/2022]
Abstract
The extraordinary properties of natural proteins demonstrate that life-like protein engineering is both achievable and valuable. Rapid progress and impressive results have been made towards this goal using rational design and random techniques or a combination of both. However, we still do not have a general theory on how to specify a structure that is suited to a target function nor can we specify a sequence that folds to a target structure. There is also overreliance on the Darwinian blind search to obtain practical results. In the long run, random methods cannot replace insight in constructing life-like proteins. For the near future, however, in enzyme development, we need to rely on a combination of both.
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Affiliation(s)
- Matti Leisola
- Laboratory of Bioprocess Engineering, Helsinki University of Technology, P.O. Box 6100, 02015 HUT, Espoo, Finland.
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Reyes-Vivas H, Diaz A, Peon J, Mendoza-Hernandez G, Hernandez-Alcantara G, De la Mora-De la Mora I, Enriquez-Flores S, Dominguez-Ramirez L, Lopez-Velazquez G. Disulfide bridges in the mesophilic triosephosphate isomerase from Giardia lamblia are related to oligomerization and activity. J Mol Biol 2006; 365:752-63. [PMID: 17095008 DOI: 10.1016/j.jmb.2006.10.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 10/12/2006] [Accepted: 10/17/2006] [Indexed: 11/25/2022]
Abstract
Triosephosphate isomerase from the mesophile Giardia lamblia (GlTIM) is the only known TIM with natural disulfide bridges. We previously found that oxidized and reduced thiol states of GlTIM are involved in the interconversion between native dimers and higher oligomeric species, and in the regulation of enzymatic activity. Here, we found that trophozoites and cysts have different oligomeric species of GlTIM and complexes of GlTIM with other proteins. Our data indicate that the internal milieu of G. lamblia is favorable for the formation of disulfide bonds. Enzyme mutants of the three most solvent exposed Cys of GlTIM (C202A, C222A, and C228A) were prepared to ascertain their contribution to oligomerization and activity. The data show that the establishment of a disulfide bridge between two C202 of two dimeric GlTIMs accounts for multimerization. In addition, we found that the establishment of an intramonomeric disulfide bond between C222 and C228 abolishes catalysis. Multimerization and inactivation are both reversed by reducing conditions. The 3D structure of the C202A GlTIM was solved at 2.1 A resolution, showing that the environment of the C202 is prone to hydrophobic interactions. Molecular dynamics of an in silico model of GlTIM when the intramonomeric disulfide bond is formed, showed that S216 is displaced 4.6 A from its original position, causing loss of hydrogen bonds with residues of the active-site loop. This suggests that this change perturb the conformational state that aligns the catalytic center with the substrate, inducing enzyme inactivation.
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Affiliation(s)
- Horacio Reyes-Vivas
- Laboratorio de Bioquimica Genetica, Instituto Nacional de Pediatria, 04530 Mexico, D.F
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Sterner R, Höcker B. Catalytic Versatility, Stability, and Evolution of the (βα)8-Barrel Enzyme Fold. Chem Rev 2005; 105:4038-55. [PMID: 16277370 DOI: 10.1021/cr030191z] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Reinhard Sterner
- Institut für Biophysik und physikalische Biochemie, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany.
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58
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Eijsink VGH, Gåseidnes S, Borchert TV, van den Burg B. Directed evolution of enzyme stability. ACTA ACUST UNITED AC 2005; 22:21-30. [PMID: 15857780 DOI: 10.1016/j.bioeng.2004.12.003] [Citation(s) in RCA: 303] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2004] [Revised: 11/29/2004] [Accepted: 12/02/2004] [Indexed: 11/16/2022]
Abstract
Modern enzyme development relies to an increasing extent on strategies based on diversity generation followed by screening for variants with optimised properties. In principle, these directed evolution strategies might be used for optimising any enzyme property, which can be screened for in an economically feasible way, even if the molecular basis of that property is not known. Stability is an interesting property of enzymes because (1) it is of great industrial importance, (2) it is relatively easy to screen for, and (3) the molecular basis of stability relates closely to contemporary issues in protein science such as the protein folding problem and protein folding diseases. Thus, engineering enzyme stability is of both commercial and scientific interest. Here, we review how directed evolution has contributed to the development of stable enzymes and to new insight into the principles of protein stability. Several recent examples are described. These examples show that directed evolution is an effective strategy to obtain stable enzymes, especially when used in combination with rational or semi-rational engineering strategies. With respect to the principles of protein stability, some important lessons to learn from recent efforts in directed evolution are (1) that there are many structural ways to stabilize a protein, which are not always easy to rationalize, (2) that proteins may very well be stabilized by optimizing their surfaces, and (3) that high thermal stability may be obtained without forfeiture of catalytic performance at low temperatures.
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Affiliation(s)
- Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Agricultural University of Norway, P.O. Box 5003, N-1432 As, Norway
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59
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Saugar I, Luque D, Oña A, Rodríguez JF, Carrascosa JL, Trus BL, Castón JR. Structural Polymorphism of the Major Capsid Protein of a Double-Stranded RNA Virus: An Amphipathic α Helix as a Molecular Switch. Structure 2005; 13:1007-17. [PMID: 16004873 DOI: 10.1016/j.str.2005.04.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 04/05/2005] [Accepted: 04/05/2005] [Indexed: 11/26/2022]
Abstract
The infectious bursal disease virus T=13 viral particle is composed of two major proteins, VP2 and VP3. Here, we show that the molecular basis of the conformational flexibility of the major capsid protein precursor, pVP2, is an amphipatic alpha helix formed by the sequence GFKDIIRAIR. VP2 containing this alpha helix is able to assemble into the T=13 capsid only when expressed as a chimeric protein with an N-terminal His tag. An amphiphilic alpha helix, which acts as a conformational switch, is thus responsible for the inherent structural polymorphism of VP2. The His tag mimics the VP3 C-terminal region closely and acts as a molecular triggering factor. Using cryo-electron microscopy difference imaging, both polypeptide elements were detected on the capsid inner surface. We propose that electrostatic interactions between these two morphogenic elements are transmitted to VP2 to acquire the competent conformations for capsid assembly.
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Affiliation(s)
- Irene Saugar
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Höcker B. Directed evolution of (βα)8-barrel enzymes. ACTA ACUST UNITED AC 2005; 22:31-8. [PMID: 15857781 DOI: 10.1016/j.bioeng.2004.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2004] [Revised: 09/23/2004] [Accepted: 09/24/2004] [Indexed: 10/25/2022]
Abstract
Natural molecular evolution supplies us with manifold examples of protein engineering. The imitation of these natural processes in the design of new enzymes has led to surprising and insightful results. Well-suited for design by evolutionary methods are enzymes with the common and versatile (betaalpha)(8)-barrel fold. Studies of enzyme stability, folding and design as well as the evolution of (betaalpha)(8)-barrel enzymes are discussed.
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Affiliation(s)
- Birte Höcker
- Duke University Medical Center, Department of Biochemistry, Box 3711, Durham, NC 27710, USA.
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Eijsink VGH, Bjørk A, Gåseidnes S, Sirevåg R, Synstad B, van den Burg B, Vriend G. Rational engineering of enzyme stability. J Biotechnol 2004; 113:105-20. [PMID: 15380651 DOI: 10.1016/j.jbiotec.2004.03.026] [Citation(s) in RCA: 326] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2003] [Revised: 02/16/2004] [Accepted: 03/04/2004] [Indexed: 11/19/2022]
Abstract
During the past 15 years there has been a continuous flow of reports describing proteins stabilized by the introduction of mutations. These reports span a period from pioneering rational design work on small enzymes such as T4 lysozyme and barnase to protein design, and directed evolution. Concomitantly, the purification and characterization of naturally occurring hyperstable proteins has added to our understanding of protein stability. Along the way, many strategies for rational protein stabilization have been proposed, some of which (e.g. entropic stabilization by introduction of prolines or disulfide bridges) have reasonable success rates. On the other hand, comparative studies and efforts in directed evolution have revealed that there are many mutational strategies that lead to high stability, some of which are not easy to define and rationalize. Recent developments in the field include increasing awareness of the importance of the protein surface for stability, as well as the notion that normally a very limited number of mutations can yield a large increase in stability. Another development concerns the notion that there is a fundamental difference between the "laboratory stability" of small pure proteins that unfold reversibly and completely at high temperatures and "industrial stability", which is usually governed by partial unfolding processes followed by some kind of irreversible inactivation process (e.g. aggregation). Provided that one has sufficient knowledge of the mechanism of thermal inactivation, successful and efficient rational stabilization of enzymes can be achieved.
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Affiliation(s)
- Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Agricultural University of Norway, PO Box 5040, N-1432 As.
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Bjørk A, Dalhus B, Mantzilas D, Sirevåg R, Eijsink VGH. Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface. J Mol Biol 2004; 341:1215-26. [PMID: 15321717 DOI: 10.1016/j.jmb.2004.06.079] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2004] [Revised: 06/06/2004] [Accepted: 06/22/2004] [Indexed: 10/26/2022]
Abstract
The stability of tetrameric malate dehydrogenase from the green phototrophic bacterium Chloroflexus aurantiacus (CaMDH) is at least in part determined by electrostatic interactions at the dimer-dimer interface. Since previous studies had indicated that the thermal stability of CaMDH becomes lower with increasing pH, attempts were made to increase the stability by removal of (excess) negative charge at the dimer-dimer interface. Mutation of Glu165 to Gln or Lys yielded a dramatic increase in thermal stability at pH 7.5 (+23.6 -- + 23.9 degrees C increase in apparent t(m)) and a more moderate increase at pH 4.4 (+4.6 -- + 5.4 degrees C). The drastically increased stability at neutral pH was achieved without forfeiture of catalytic performance at low temperatures. The crystal structures of the two mutants showed only minor structural changes close to the mutated residues, and indicated that the observed stability effects are solely due to subtle changes in the complex network of electrostatic interactions in the dimer-dimer interface. Both mutations reduced the concentration dependency of thermal stability, suggesting that the oligomeric structure had been reinforced. Interestingly, the two mutations had similar effects on stability, despite the charge difference between the introduced side-chains. Together with the loss of concentration dependency, this may indicate that both E165Q and E165K stabilize CaMDH to such an extent that disruption of the inter-dimer electrostatic network around residue 165 no longer limits kinetic thermal stability.
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Affiliation(s)
- Alexandra Bjørk
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, N-0316 Oslo, Norway.
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63
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Xiang T, Liu Q, Deacon AM, Koshy M, Kriksunov IA, Lei XG, Hao Q, Thiel DJ. Crystal structure of a heat-resilient phytase from Aspergillus fumigatus, carrying a phosphorylated histidine. J Mol Biol 2004; 339:437-45. [PMID: 15136045 DOI: 10.1016/j.jmb.2004.03.057] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2004] [Revised: 03/09/2004] [Accepted: 03/09/2004] [Indexed: 11/16/2022]
Abstract
In order to understand the structural basis for the high thermostability of phytase from Aspergillus fumigatus, its crystal structure was determined at 1.5 A resolution. The overall fold resembles the structure of other phytase enzymes. Aspergillus niger phytase shares 66% sequence identity, however, it is much less heat-resistant. A superimposition of these two structures reveals some significant differences. In particular, substitutions with polar residues appear to remove repulsive ion pair interactions and instead form hydrogen bond interactions, which stabilize the enzyme; the formation of a C-terminal helical capping, induced by arginine residue substitutions also appears to be critical for the enzyme's ability to refold to its active form after denaturation at high temperature. The heat-resilient property of A.fumigatus phytase could be due to the improved stability of regions that are critical for the refolding of the protein; and a heat-resistant A.niger phytase may be achieved by mutating certain critical residues with the equivalent residues in A.fumigatus phytase. Six predicted N-glycosylation sites were observed to be glycosylated from the experimental electron density. Furthermore, the enzyme's catalytic residue His59 was found to be partly phosphorylated and thus showed a reaction intermediate, providing structural insight, which may help understand the catalytic mechanism of the acid phosphatase family. The trap of this catalytic intermediate confirms the two-step catalytic mechanism of the acid histidine phosphatase family.
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Affiliation(s)
- Tao Xiang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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64
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Bjørk A, Dalhus B, Mantzilas D, Eijsink VGH, Sirevåg R. Stabilization of a Tetrameric Malate Dehydrogenase by Introduction of a Disulfide Bridge at the Dimer–Dimer Interface. J Mol Biol 2003; 334:811-21. [PMID: 14636605 DOI: 10.1016/j.jmb.2003.10.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Malate dehydrogenase (MDH) from the moderately thermophilic bacterium Chloroflexus aurantiacus (CaMDH) is a tetrameric enzyme, while MDHs from mesophilic organisms usually are dimers. To investigate the potential contribution of the extra dimer-dimer interface in CaMDH with respect to thermal stability, we have engineered an intersubunit disulfide bridge designed to strengthen dimer-dimer interactions. The resulting mutant (T187C, containing two 187-187 disulfide bridges in the tetramer) showed a 200-fold increase in half-life at 75 degrees C and an increase of 15 deg. C in apparent melting temperature compared to the wild-type. The crystal structure of the mutant (solved at 1.75 A resolution) was essentially identical with that of the wild-type, with the exception of the added inter-dimer disulfide bridge and the loss of an aromatic intra-dimer contact. Remarkably, the mutant and the wild-type had similar temperature optima and activities at their temperature optima, thus providing a clear case of uncoupling of thermal stability and thermoactivity. The results show that tetramerization may contribute to MDH stability to an extent that depends strongly on the number of stabilizing interactions in the dimer-dimer interface.
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Affiliation(s)
- Alexandra Bjørk
- Department of Biology, University of Oslo, PO Box 1031 Blindern, N-0316 Oslo, Norway.
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65
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Aparicio R, Ferreira ST, Polikarpov I. Closed Conformation of the Active Site Loop of Rabbit Muscle Triosephosphate Isomerase in the Absence of Substrate: Evidence of Conformational Heterogeneity. J Mol Biol 2003; 334:1023-41. [PMID: 14643664 DOI: 10.1016/j.jmb.2003.10.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The active site loop of triosephosphate isomerase (TIM) exhibits a hinged-lid motion, alternating between the two well defined "open" and "closed" conformations. Until now the closed conformation had only been observed in protein complexes with substrate analogues. Here, we present the first rabbit muscle apo TIM structure, refined to 1.5A resolution, in which the active site loop is either in the open or in the closed conformation in different subunits of the enzyme. In the closed conformation described here, the lid loop residues participate in stabilizing hydrogen bonds characteristic of holo TIM structures, whereas chemical interactions observed in the open loop conformation are similar to those found in the apo structures of TIM. In the closed conformation, a number of water molecules are observed at the projected ligand atom positions that are hydrogen bonded to the active site residues. Additives used during crystallization (DMSO and Tris molecules and magnesium atoms) were modeled in the electron density maps. However, no specific binding of these molecules is observed at, or close to, the active site and the lid loop. To further investigate this unusual closed conformation of the apo enzyme, two more rabbit muscle TIM structures, one in the same and another in a different crystal form, were determined. These structures present the open lid conformation only, indicating that the closed conformation cannot be explained by crystal contact effects. To rationalize why the active site loop is closed in the absence of ligand in one of the subunits, extensive comparison with previously solved TIM structures was carried out, supported by the bulk of available experimental information about enzyme kinetics and reaction mechanism of TIM. The observation of both open and closed lid conformations in TIM crystals might be related to a persistent conformational heterogeneity of this protein in solution.
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Affiliation(s)
- Ricardo Aparicio
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador SãoCarlense, 400, São Carlos, SP 13560-970, Brazil
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66
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Gåseidnes S, Synstad B, Nielsen JE, Eijsink VG. Rational engineering of the stability and the catalytic performance of enzymes. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1381-1177(02)00136-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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67
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Rodríguez-Romero A, Hernández-Santoyo A, del Pozo Yauner L, Kornhauser A, Fernández-Velasco DA. Structure and inactivation of triosephosphate isomerase from Entamoeba histolytica. J Mol Biol 2002; 322:669-75. [PMID: 12270704 DOI: 10.1016/s0022-2836(02)00809-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Triosephosphate isomerase (TIM) has been proposed as a target for drug design. TIMs from several parasites have a cysteine residue at the dimer interface, whose derivatization with thiol-specific reagents induces enzyme inactivation and aggregation. TIMs lacking this residue, such as human TIM, are less affected. TIM from Entamoeba histolytica (EhTIM) has the interface cysteine residue and presents more than ten insertions when compared with the enzyme from other pathogens. To gain further insight into the role that interface residues play in the stability and reactivity of these enzymes, we determined the high-resolution structure and characterized the effect of methylmethane thiosulfonate (MMTS) on the activity and conformational properties of EhTIM. The structure of this enzyme was determined at 1.5A resolution using molecular replacement, observing that the dimer is not symmetric. EhTIM is completely inactivated by MMTS, and dissociated into stable monomers that possess considerable secondary structure. Structural and spectroscopic analysis of EhTIM and comparison with TIMs from other pathogens reveal that conformational rearrangements of the interface after dissociation, as well as intramonomeric contacts formed by the inserted residues, may contribute to the unusual stability of the derivatized EhTIM monomer.
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Affiliation(s)
- Adela Rodríguez-Romero
- Laboratorio Universitario de Estructura de Proteínas and Departamento de Bioquímica, Instituto de Química, Universidad Nacional Autónoma de México, DF, Mexico.
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68
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Abstract
There are many ways to select mutations that increase the stability of proteins, including rational design, functional screening of randomly generated mutant libraries, and comparison of naturally occurring homologous proteins. The protein engineer's toolbox is expanding and the number of successful examples of engineered protein stability is increasing. Still, the selection of thermostable mutations is not a standard process. Selection is complicated by lack of knowledge of the process that leads to thermal inactivation and by the fact that proteins employ a large variety of structural tricks to achieve stability.
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69
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Brinda KV, Kannan N, Vishveshwara S. Analysis of homodimeric protein interfaces by graph-spectral methods. Protein Eng Des Sel 2002; 15:265-77. [PMID: 11983927 DOI: 10.1093/protein/15.4.265] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The quaternary structures impart structural and functional credibility to proteins. In a multi-subunit protein, it is important to understand the factors that drive the association or dissociation of the subunits. It is a well known fact that both hydrophobic and charged interactions contribute to the stability of the protein interface. The interface residues are also known to be highly conserved. Though they are buried in the oligomer, these residues are either exposed or partially exposed in the monomer. It is felt that a systematic and objective method of identifying interface clusters and their analysis can significantly contribute to the identification of a residue or a collection of residues important for oligomerization. Recently, we have applied the techniques of graph-spectral methods to a variety of problems related to protein structure and folding. A major advantage of this methodology is that the problem is viewed from a global protein topology point of view rather than localized regions of the protein structure. In the present investigation, we have applied the methods of graph-spectral analysis to identify side chain clusters at the interface and the centers of these clusters in a set of homodimeric proteins. These clusters are analyzed in terms of properties such as amino acid composition, accessibility to solvent and conservation of residues. Interesting results such as participation of charged and aromatic residues like arginine, glutamic acid, histidine, phenylalanine and tyrosine, consistent with earlier investigations, have emerged from these analyses. Important additional information is that the residues involved are a part of a cluster(s) and that they are sequentially distant residues which have come closer to each other in the three-dimensional structure of the protein. These residues can easily be detected using our graph-spectral algorithm. This method has also been used to identify important residues ('hot spots') in dimerization and also to detect dimerization sites on the monomer. The residues predicted using the present algorithm have correlated well with the experiments indicating the efficacy of this method in predicting residues involved in dimer stability.
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Affiliation(s)
- K V Brinda
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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70
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Chánez-Cárdenas ME, Fernández-Velasco DA, Vázquez-Contreras E, Coria R, Saab-Rincón G, Pérez-Montfort R. Unfolding of triosephosphate isomerase from Trypanosoma brucei: identification of intermediates and insight into the denaturation pathway using tryptophan mutants. Arch Biochem Biophys 2002; 399:117-29. [PMID: 11888197 DOI: 10.1006/abbi.2001.2749] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The unfolding of triosephosphate isomerase (TIM) from Trypanosoma brucei (TbTIM) induced by guanidine hydrochloride (GdnHCl) was characterized. In contrast to other TIMs, where unfolding is a two or three state process, TbTIM showed two intermediates. The solvent exposure of different regions of the protein in the unfolding process was characterized spectroscopically with mutant proteins in which tryptophans (W) were changed to phenlylalanines (F). The midpoints of the transitions measured by circular dichroism, intrinsic fluorescence, and catalytic activity, as well as the increase in 1-aniline 8-naphthalene sulfonate fluorescence, show that the native state was destabilized in the W12F and W12F/W193F mutants, relative to the wild-type enzyme. Using the hydrodynamic profile for the unfolding of a monomeric TbTIM mutant (RMM0-1TIM) measured by size-exclusion chromatography as a standard, we determined the association state of these intermediates: D*, a partially expanded dimer, and M*, a partially expanded monomeric intermediate. High-molecular-weight aggregates were also detected. At concentrations over 2.0 M GdnHCl, the hydrodynamic properties of TbTIM and RMM0-1TIM are the same, suggesting that the dimeric intermediate dissociates and the unfolding proceeds through the denaturation of an expanded monomeric intermediate. The analysis of the denaturation process of the TbTIM mutants suggests a sequence for the gradual exposure of W residues: initially the expansion of the native dimer to form D* affects the environments of W12 and W159. The dissociation of D* to M* and further unfolding of M* to U induces the exposure of W170. The role of protein concentration in the formation of intermediates and aggregates is discussed considering the irreversibility of this unfolding process.
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Affiliation(s)
- María Elena Chánez-Cárdenas
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
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71
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Affiliation(s)
- A Gershenson
- Division of Chemistry & Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125, USA
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72
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Angrand I, Serrano L, Lacroix E. Computer-assisted re-design of spectrin SH3 residue clusters. BIOMOLECULAR ENGINEERING 2001; 18:125-34. [PMID: 11566604 DOI: 10.1016/s1389-0344(01)00093-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We have developed a protein design computer program, called Perla, which performs searches in sequence space to uncover optimal amino acid sequences for desired protein three-dimensional structures. Optimal sequences are localised at the minima of a sequence-structure energy landscape defined using a complex scoring function (an all-atom molecular mechanics force field plus statistical terms including entropy and solvation) measured with respect to a reference state simulating a denatured protein. Sequence choices eventually optimise side chain packing, secondary structure propensities, and hydrogen bonding and electrostatics interactions. Perla was used to re-design clusters of residues of the SH3 domain of alpha-spectrin. Several mutant proteins were produced and characterised. Some of our designed proteins have significantly higher stabilities (stability enhancements about 0.25, 0.70 and 1.0 kcal mol(-1)) than the wild-type protein. These successful protein re-designs, and similar examples found in the literature, establish the quality of the structure-based computational approach to protein design.
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Affiliation(s)
- I Angrand
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117, Heidelberg, Germany
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73
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Kursula I, Partanen S, Lambeir AM, Antonov DM, Augustyns K, Wierenga RK. Structural determinants for ligand binding and catalysis of triosephosphate isomerase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:5189-96. [PMID: 11589711 DOI: 10.1046/j.0014-2956.2001.02452.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The crystal structure of leishmania triosephosphate isomerase (TIM) complexed with 2-(N-formyl-N-hydroxy)-aminoethyl phosphonate (IPP) highlights the importance of Asn11 for binding and catalysis. IPP is an analogue of the substrate D-glyceraldehyde-3-phosphate, and it is observed to bind with its aldehyde oxygen in an oxyanion hole formed by ND2 of Asn11 and NE2 of His95. Comparison of the mode of binding of IPP and the transition state analogue phosphoglycolohydroxamate (PGH) suggests that the Glu167 side chain, as well as the triose part of the substrate, adopt different conformations as the catalysed reaction proceeds. Comparison of the TIM-IPP and the TIM-PGH structures with other liganded and unliganded structures also highlights the conformational flexibility of the ligand and the active site, as well as the conserved mode of ligand binding.
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Affiliation(s)
- I Kursula
- Biocenter Oulu and Department of Biochemistry, University of Oulu, FIN-90014, Oulu, Finland
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74
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Yasugi M, Suzuki T, Yamagishi A, Oshima T. Analysis of the effect of accumulation of amino acid replacements on activity of 3-isopropylmalate dehydrogenase from Thermus thermophilus. PROTEIN ENGINEERING 2001; 14:601-7. [PMID: 11579229 DOI: 10.1093/protein/14.8.601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
A newly selected cold-adapted mutant 3-isopropylmalate dehydrogenase (IPMDH) from a random mutant library was a double mutant containing the mutations I11V and S92F that were found in cold-adapted mutant IPMDHs previously isolated. To elucidate the effect of each mutation on enzymatic activity, I11V and six multiple mutant IPMDHs were constructed and analyzed. All of the multiple mutant IPMDHs were found to be improved in catalytic activity at moderate temperatures by increasing the k(cat) with a simultaneous increase of K(m) for the coenzyme NAD(+). k(cat) was improved by a decrease in the activation enthalpy, DeltaH( not equal). The multiple mutants did not show large reduction in thermal stability, and one of them showed enhanced thermal stability. Mutation from I11 to V was revealed to have a stabilizing effect. Mutants showed increased thermal stability when the mutation I11V was combined. This indicates that it is possible to construct mutants with enhanced thermal stability by combining stabilizing mutation. No additivity was observed for the thermodynamic properties of catalytic reaction in the multiple mutant IPMDHs, implying that the structural changes induced by the mutations were interacting with each other. This indicates that careful and detailed tuning is required for enhancing activity in contrast to thermal stability.
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Affiliation(s)
- M Yasugi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Horinouchi 1432-1, Hachioji, Tokyo 192-0392, Japan
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75
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Höcker B, Jürgens C, Wilmanns M, Sterner R. Stability, catalytic versatility and evolution of the (beta alpha)(8)-barrel fold. Curr Opin Biotechnol 2001; 12:376-81. [PMID: 11551466 DOI: 10.1016/s0958-1669(00)00230-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The (beta alpha)(8)-barrel is a versatile single-domain protein fold that is adopted by a large number of enzymes. The (beta alpha)(8)-barrel fold has been used as a model to elucidate the structural basis of protein thermostability and in studies to interconvert catalytic activities or substrate specificities by rational design or directed evolution. Recently, the (beta alpha)(4)-half-barrel was identified as a possible structural subdomain.
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Affiliation(s)
- B Höcker
- Universität zu Köln, Institut für Biochemie, Otto-Fischer-Strasse 12-14, D-50674 Köln, Germany
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76
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Schramm A, Kohlhoff M, Hensel R. Triose-phosphate isomerase from Pyrococcus woesei and Methanothermus fervidus. Methods Enzymol 2001; 331:62-77. [PMID: 11265484 DOI: 10.1016/s0076-6879(01)31047-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- A Schramm
- Universität Essen, Essen 45117, Germany
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77
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Wintrode PL, Arnold FH. Temperature adaptation of enzymes: lessons from laboratory evolution. ADVANCES IN PROTEIN CHEMISTRY 2001; 55:161-225. [PMID: 11050934 DOI: 10.1016/s0065-3233(01)55004-4] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- P L Wintrode
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena 91125, USA
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78
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Irún MP, Garcia-Mira MM, Sanchez-Ruiz JM, Sancho J. Native hydrogen bonds in a molten globule: the apoflavodoxin thermal intermediate. J Mol Biol 2001; 306:877-88. [PMID: 11243795 DOI: 10.1006/jmbi.2001.4436] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure and energetics of protein-folding intermediates are poorly understood. We have identified, in the thermal unfolding of the apoflavodoxin from Anabaena PCC 7119, an equilibrium intermediate with spectroscopic properties of a molten globule and substantial enthalpy and heat capacity of unfolding. The structure of the intermediate is probed by mutagenesis (and phi analysis) of polar residues involved in surface-exposed hydrogen bonds connecting secondary-structure elements in the native protein. All hydrogen bonds analysed are formed in the molten globule intermediate, either with native strength or debilitated. This suggests the overall intermediate's topology and surface tertiary interactions are close to native, and indicates that hydrogen bonding may contribute significantly to shape the conformation and energetics of folding intermediates.
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Affiliation(s)
- M P Irún
- Departamento de Bioquímica y Biología Molecular y Celular Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, 50009, Spain
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79
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Irún MP, Maldonado S, Sancho J. Stabilization of apoflavodoxin by replacing hydrogen-bonded charged Asp or Glu residues by the neutral isosteric Asn or Gln. PROTEIN ENGINEERING 2001; 14:173-81. [PMID: 11342714 DOI: 10.1093/protein/14.3.173] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Knowledge of protein stability principles provides a means to increase protein stability in a rational way. Here we explore the feasibility of stabilizing proteins by replacing solvent-exposed hydrogen-bonded charged Asp or Glu residues by the neutral isosteric Asn or GLN: The rationale behind this is a previous observation that, in some cases, neutral hydrogen bonds may be more stable that charged ones. We identified, in the apoflavodoxin from Anabaena PCC 7119, three surface-exposed aspartate or glutamate residues involved in hydrogen bonding with a single partner and we mutated them to asparagine or glutamine, respectively. The effect of the mutations on apoflavodoxin stability was measured by both urea and temperature denaturation. We observed that the three mutant proteins are more stable than wild-type (on average 0.43 kcal/mol from urea denaturation and 2.8 degrees C from a two-state analysis of fluorescence thermal unfolding data). At high ionic strength, where potential electrostatic repulsions in the acidic apoflavodoxin should be masked, the three mutants are similarly more stable (on average 0.46 kcal/mol). To rule out further that the stabilization observed is due to removal of electrostatic repulsions in apoflavodoxin upon mutation, we analysed three control mutants and showed that, when the charged residue mutated to a neutral one is not hydrogen bonded, there is no general stabilizing effect. Replacing hydrogen-bonded charged Asp or Glu residues by Asn or Gln, respectively, could be a straightforward strategy to increase protein stability.
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Affiliation(s)
- M P Irún
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain
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80
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Arnold FH, Wintrode PL, Miyazaki K, Gershenson A. How enzymes adapt: lessons from directed evolution. Trends Biochem Sci 2001; 26:100-6. [PMID: 11166567 DOI: 10.1016/s0968-0004(00)01755-2] [Citation(s) in RCA: 243] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Enzymes that are adapted to widely different temperature niches are being used to investigate the molecular basis of protein stability and enzyme function. However, natural evolution is complex: random noise, historical accidents and ignorance of the selection pressures at work during adaptation all cloud comparative studies. Here, we review how adaptation in the laboratory by directed evolution can complement studies of natural enzymes in the effort to understand stability and function. Laboratory evolution experiments can attempt to mimic natural evolution and identify different adaptive mechanisms. However, laboratory evolution might make its biggest contribution in explorations of nonnatural functions, by allowing us to distinguish the properties nutured by evolution from those dictated by the laws of physical chemistry.
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Affiliation(s)
- F H Arnold
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125, USA.
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81
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Verlinde CL, Hannaert V, Blonski C, Willson M, Périé JJ, Fothergill-Gilmore LA, Opperdoes FR, Gelb MH, Hol WG, Michels PA. Glycolysis as a target for the design of new anti-trypanosome drugs. Drug Resist Updat 2001; 4:50-65. [PMID: 11512153 DOI: 10.1054/drup.2000.0177] [Citation(s) in RCA: 170] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Glycolysis is perceived as a promising target for new drugs against parasitic trypanosomatid protozoa because this pathway plays an essential role in their ATP supply. Trypanosomatid glycolysis is unique in that it is compartmentalized, and many of its enzymes display unique structural and kinetic features. Structure- and catalytic mechanism-based approaches are applied to design compounds that inhibit the glycolytic enzymes of the parasites without affecting the corresponding proteins of the human host. For some trypanosomatid enzymes, potent and selective inhibitors have already been developed that affect only the growth of cultured trypanosomatids, and not mammalian cells.
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Affiliation(s)
- C L Verlinde
- Department of Biological Structure, Biomolecular Structure Center, University of Washington, Seattle, USA
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82
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Kajander T, Kahn PC, Passila SH, Cohen DC, Lehtiö L, Adolfsen W, Warwicker J, Schell U, Goldman A. Buried charged surface in proteins. Structure 2000; 8:1203-14. [PMID: 11080642 DOI: 10.1016/s0969-2126(00)00520-7] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
BACKGROUND The traditional picture of charged amino acids in globular proteins is that they are almost exclusively on the outside exposed to the solvent. Buried charges, when they do occur, are assumed to play an essential role in catalysis and ligand binding, or in stabilizing structure as, for instance, helix caps. RESULTS By analyzing the amount and distribution of buried charged surface and charges in proteins over a broad range of protein sizes, we show that buried charge is much more common than is generally believed. We also show that the amount of buried charge rises with protein size in a manner which differs from other types of surfaces, especially aromatic and polar uncharged surfaces. In large proteins such as hemocyanin, 35% of all charges are greater than 75% buried. Furthermore, at all sizes few charged groups are fully exposed. As an experimental test, we show that replacement of the buried D178 of muconate lactonizing enzyme by N stabilizes the enzyme by 4.2 degrees C without any change in crystallographic structure. In addition, free energy calculations of stability support the experimental results. CONCLUSIONS Nature may use charge burial to reduce protein stability; not all buried charges are fully stabilized by a prearranged protein environment. Consistent with this view, thermophilic proteins often have less buried charge. Modifying the amount of buried charge at carefully chosen sites may thus provide a general route for changing the thermophilicity or psychrophilicity of proteins.
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Affiliation(s)
- T Kajander
- Centre for Biotechnology, University of Turku, Turku, Finland
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83
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Lambeir AM, Backmann J, Ruiz-Sanz J, Filimonov V, Nielsen JE, Kursula I, Norledge BV, Wierenga RK. The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:2516-24. [PMID: 10785370 DOI: 10.1046/j.1432-1327.2000.01254.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The amino acid sequence of Leishmania mexicana triose phosphate isomerase is unique in having at position 65 a glutamic acid instead of a glutamine. The stability properties of LmTIM and the E65Q mutant were investigated by pH and guanidinium chloride-induced unfolding. The crystal structure of E65Q was determined. Three important observations were made: (a) there are no structural rearrangements as the result of the substitution; (b) the mutant is more stable than the wild-type; and (c) the stability of the wild-type enzyme shows strong pH dependence, which can be attributed to the ionization of Glu65. Burying of the Glu65 side chain in the uncharged environment of the dimer interface results in a shift in pKa of more than 3 units. The pH-dependent decrease in overall stability is due to weakening of the monomer-monomer interactions (in the dimer). The E65Q substitution causes an increase in stability as the result of the formation of an additional hydrogen bond in each subunit (DeltaDeltaG degrees of 2 kcal.mol-1 per monomer) and the elimination of a charged group in the dimer interface (DeltaDeltaG degrees of at least 9 kcal.mol-1 per dimer). The computated shift in pKa and the stability of the dimer calculated from the charge distribution in the protein structure agree closely with the experimental results. The guanidinium chloride dependence of the unfolding constant was smaller than expected from studies involving monomeric model proteins. No intermediates could be identified in the unfolding equilibrium by combining fluorescence and CD measurements. Study of a stable monomeric triose phosphate isomerase variant confirmed that the phenomenon persists in the monomer.
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Affiliation(s)
- A M Lambeir
- Laboratory for Medical Biochemistry, University of Antwerp (UIA), Wilrijk, Belgium.
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84
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Lehmann M, Kostrewa D, Wyss M, Brugger R, D'Arcy A, Pasamontes L, van Loon AP. From DNA sequence to improved functionality: using protein sequence comparisons to rapidly design a thermostable consensus phytase. PROTEIN ENGINEERING 2000; 13:49-57. [PMID: 10679530 DOI: 10.1093/protein/13.1.49] [Citation(s) in RCA: 157] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Naturally-occurring phytases having the required level of thermostability for application in animal feeding have not been found in nature thus far. We decided to de novo construct consensus phytases using primary protein sequence comparisons. A consensus enzyme based on 13 fungal phytase sequences had normal catalytic properties, but showed an unexpected 15-22 degrees C increase in unfolding temperature compared with each of its parents. As a first step towards understanding the molecular basis of increased heat resistance, the crystal structure of consensus phytase was determined and compared with that of Aspergillus niger phytase. Aspergillus niger phytase unfolds at much lower temperatures. In most cases, consensus residues were indeed expected, based on comparisons of both three-dimensional structures, to contribute more to phytase stabilization than non-consensus amino acids. For some consensus amino acids, predicted by structural comparisons to destabilize the protein, mutational analysis was performed. Interestingly, these consensus residues in fact increased the unfolding temperature of the consensus phytase. In summary, for fungal phytases apparently an unexpected direct link between protein sequence conservation and protein stability exists.
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Affiliation(s)
- M Lehmann
- F.Hoffmann-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland.
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85
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86
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Maes D, Zeelen JP, Thanki N, Beaucamp N, Alvarez M, Thi MHD, Backmann J, Martial JA, Wyns L, Jaenicke R, Wierenga RK. The crystal structure of triosephosphate isomerase (TIM) fromThermotoga maritima: A comparative thermostability structural analysis of ten different TIM structures. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(19991115)37:3<441::aid-prot11>3.0.co;2-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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87
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Alvarez M, Wouters J, Maes D, Mainfroid V, Rentier-Delrue F, Wyns L, Depiereux E, Martial JA. Lys13 plays a crucial role in the functional adaptation of the thermophilic triose-phosphate isomerase from Bacillus stearothermophilus to high temperatures. J Biol Chem 1999; 274:19181-7. [PMID: 10383424 DOI: 10.1074/jbc.274.27.19181] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The thermophilic triose-phosphate isomerases (TIMs) of Bacillus stearothermophilus (bTIM) and Thermotoga maritima (tTIM) have been found to possess a His12-Lys13 pair instead of the Asn12-Gly13 pair normally present in mesophilic TIMs. His12 in bTIM was proposed to prevent deamidation at high temperature, while the precise role of Lys13 is unknown. To investigate the role of the His12 and Lys13 pair in the enzyme's thermoadaptation, we reintroduced the "mesophilic residues" Asn and Gly into both thermophilic TIMs. Neither double mutant displayed diminished structural stability, but the bTIM double mutant showed drastically reduced catalytic activity. No similar behavior was observed with the tTIM double mutant, suggesting that the presence of the His12 and Lys13 cannot be systematically correlated to thermoadaptation in TIMs. We determined the crystal structure of the bTIM double mutant complexed with 2-phosphoglycolate to 2.4-A resolution. A molecular dynamics simulation showed that upon substitution of Lys13 to Gly an increase of the flexibility of loop 1 is observed, causing an incorrect orientation of the catalytic Lys10. This suggests that Lys13 in bTIM plays a crucial role in the functional adaptation of this enzyme to high temperature. Analysis of bTIM single mutants supports this assumption.
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Affiliation(s)
- M Alvarez
- Laboratoire de Biologie Moléculaire et de Génie Génétique, Université de Liège, B6, Sart Tilman, B4000 Liège, Belgium
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88
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Paper Alert. Structure 1999. [DOI: 10.1016/s0969-2126(99)80093-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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