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Rusevich L, García Sakai V, Franzetti B, Johnson M, Natali F, Pellegrini E, Peters J, Pieper J, Weik M, Zaccai G. Perspectives in biological physics: the nDDB project for a neutron Dynamics Data Bank for biological macromolecules. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:80. [PMID: 23884625 DOI: 10.1140/epje/i2013-13080-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 02/13/2013] [Accepted: 02/19/2013] [Indexed: 06/02/2023]
Abstract
Neutron spectroscopy provides experimental data on time-dependent trajectories, which can be directly compared to molecular dynamics simulations. Its importance in helping us to understand biological macromolecules at a molecular level is demonstrated by the results of a literature survey over the last two to three decades. Around 300 articles in refereed journals relate to neutron scattering studies of biological macromolecular dynamics, and the results of the survey are presented here. The scope of the publications ranges from the general physics of protein and solvent dynamics, to the biologically relevant dynamics-function relationships in live cells. As a result of the survey we are currently setting up a neutron Dynamics Data Bank (nDDB) with the aim to make the neutron data on biological systems widely available. This will benefit, in particular, the MD simulation community to validate and improve their force fields. The aim of the database is to expose and give easy access to a body of experimental data to the scientific community. The database will be populated with as much of the existing data as possible. In the future it will give value, as part of a bigger whole, to high throughput data, as well as more detailed studies. A range and volume of experimental data will be of interest in determining how quantitatively MD simulations can reproduce trends across a range of systems and to what extent such trends may depend on sample preparation and data reduction and analysis methods. In this context, we strongly encourage researchers in the field to deposit their data in the nDDB.
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Affiliation(s)
- Leonid Rusevich
- ILL, 6, rue Jules Horowitz, BP 156, F-38042 Grenoble Cedex 9, France
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52
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Detection and Characterisation of Mutations Responsible for Allele-Specific Protein Thermostabilities at the Mn-Superoxide Dismutase Gene in the Deep-Sea Hydrothermal Vent Polychaete Alvinella pompejana. J Mol Evol 2013; 76:295-310. [DOI: 10.1007/s00239-013-9559-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 03/27/2013] [Indexed: 12/19/2022]
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53
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Psychrophily and catalysis. BIOLOGY 2013; 2:719-41. [PMID: 24832805 PMCID: PMC3960892 DOI: 10.3390/biology2020719] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/18/2013] [Accepted: 03/18/2013] [Indexed: 11/24/2022]
Abstract
Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. Since the discovery that these ecosystems, contrary to what was initially expected, sustain a rather high density and broad diversity of living organisms, increasing efforts have been dedicated to the understanding of the molecular mechanisms involved in their successful adaptation to apparently unfavorable physical conditions. The first question that comes to mind is: How do these organisms compensate for the exponential decrease of reaction rate when temperature is lowered? As most of the chemical reactions that occur in living organisms are catalyzed by enzymes, the kinetic and thermodynamic properties of cold-adapted enzymes have been investigated. Presently, many crystallographic structures of these enzymes have been elucidated and allowed for a rather clear view of their adaptation to cold. They are characterized by a high specific activity at low and moderate temperatures and a rather low thermal stability, which induces a high flexibility that prevents the freezing effect of low temperatures on structure dynamics. These enzymes also display a low activation enthalpy that renders them less dependent on temperature fluctuations. This is accompanied by a larger negative value of the activation entropy, thus giving evidence of a more disordered ground state. Appropriate folding kinetics is apparently secured through a large expression of trigger factors and peptidyl–prolyl cis/trans-isomerases.
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Nikinmaa M, McCairns RJS, Nikinmaa MW, Vuori KA, Kanerva M, Leinonen T, Primmer CR, Merilä J, Leder EH. Transcription and redox enzyme activities: comparison of equilibrium and disequilibrium levels in the three-spined stickleback. Proc Biol Sci 2013; 280:20122974. [PMID: 23363636 PMCID: PMC3574399 DOI: 10.1098/rspb.2012.2974] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/10/2013] [Indexed: 11/12/2022] Open
Abstract
Evolutionary and acclimatory responses require functional variability, but in contrast with mRNA and protein abundance data, most physiological measurements cannot be obtained in a high-throughput manner. Consequently, one must either rely on high-throughput transcriptomic or proteomic data with only predicted functional information, or accept the limitation that most physiological measurements can give fewer data than those provided by transcriptomics or proteomics. We evaluated how transcriptional and redox enzyme activity data agreed with regard to population differentiation (i.e. a system in steady state in which any time lag between transcription, translation and post-translational effects would be irrelevant) and in response to an acute 6°C increase in temperature (i.e. a disequilibrium state wherein translation could not have caught up with transcription) in the three-spined stickleback (Gasterosteus aculeatus). Transcriptional and enzyme activity data corresponded well with regard to population differentiation, but less so with regard to acute temperature increase. The data thus suggest that transcriptional and functional measurements can lead to similar conclusions when a biological system is in a steady state. The responses to acute changes must, as has been demonstrated earlier, be based on changes in cellular conditions or properties of existing proteins without significant de novo synthesis of new gene products.
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Affiliation(s)
- M Nikinmaa
- Department of Biology, University of Turku, 20014, Finland.
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55
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Jun C, Sa YS, Gu SA, Joo JC, Kim S, Kim KJ, Kim YH. Discovery and characterization of a thermostable d-lactate dehydrogenase from Lactobacillus jensenii through genome mining. Process Biochem 2013. [DOI: 10.1016/j.procbio.2012.11.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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56
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Feller G. Psychrophilic enzymes: from folding to function and biotechnology. SCIENTIFICA 2013; 2013:512840. [PMID: 24278781 PMCID: PMC3820357 DOI: 10.1155/2013/512840] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/06/2012] [Indexed: 05/10/2023]
Abstract
Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry, University of Liège, B6a, 4000 Liège, Belgium
- *Georges Feller:
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57
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Cazaméa-Catalan D, Magnanou E, Helland R, Vanegas G, Besseau L, Boeuf G, Paulin CH, Jørgensen EH, Falcón J. Functional diversity of Teleost arylalkylamineN-acetyltransferase-2: is thetimezymeevolution driven by habitat temperature? Mol Ecol 2012; 21:5027-41. [DOI: 10.1111/j.1365-294x.2012.05725.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 06/21/2012] [Accepted: 06/28/2012] [Indexed: 01/19/2023]
Affiliation(s)
| | | | - R. Helland
- Norstruct; Department of Chemistry; Faculty of Science and Technology; University of Tromsø; N-9037; Tromsø; Norway
| | - G. Vanegas
- Cátedra de Fisiología Normal; Escuela de Medicina “José María Vargas”; Facultad de Medicina; Universidad Central de Venezuela; Caracas; Venezuela
| | | | | | | | - E. H. Jørgensen
- Department of Arctic and Marine Biology; Faculty of Biosciences; Fisheries and Economy; University of Tromsø; N-9037; Tromsø; Norway
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58
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Optimization to low temperature activity in psychrophilic enzymes. Int J Mol Sci 2012; 13:11643-11665. [PMID: 23109875 PMCID: PMC3472767 DOI: 10.3390/ijms130911643] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 09/07/2012] [Accepted: 09/10/2012] [Indexed: 01/20/2023] Open
Abstract
Psychrophiles, i.e., organisms thriving permanently at near-zero temperatures, synthesize cold-active enzymes to sustain their cell cycle. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. Considering the subtle structural adjustments required for low temperature activity, directed evolution appears to be the most suitable methodology to engineer cold activity in biological catalysts.
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59
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Tattersall GJ, Sinclair BJ, Withers PC, Fields PA, Seebacher F, Cooper CE, Maloney SK. Coping with Thermal Challenges: Physiological Adaptations to Environmental Temperatures. Compr Physiol 2012; 2:2151-202. [DOI: 10.1002/cphy.c110055] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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60
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Adeniyi T, Tijani A, Adekomi D, Abayomi T. A comparative study of the lateral geniculate body of rat (Rattus norvegicus), bat (Eidolon helvum) and pangolin (Manis tricuspis). Glob J Health Sci 2012; 4:118-25. [PMID: 22980348 PMCID: PMC4776952 DOI: 10.5539/gjhs.v4n4p118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 05/27/2012] [Indexed: 11/12/2022] Open
Abstract
In this study, the lateral geniculate bodies (LGB) of rats, bats and pangolins were compared using histological and quantitative histochemical parameters to observe possible modifications that enable these mammals to cope with their habitation particularly with respect to their diet. The study was conducted using ten adult Wistar rats, ten fruit bats and eight pangolins comprising of both sexes. After being sacrificed by cervical dislocation, their skulls were opened using bone forceps to expose the brains. The lateral geniculate bodies were excised from each brain tissue, homogenized and homogenate studied spectrophotometrically for the activities of lactate dehydrogenase (LDH), glucose-6-phosphate dehydrogenase (G-6-PDH), acid phosphatase (ACP), alkaline phosphatase (ALP) and acetylcholinesterase (AChE). The LGB tissue samples meant for histological studies were fixed in 10% formol calcium and processed for paraffin wax embedding. Serial sections of 3?m thickness were stained with Hematoxylin and Eosin (H & E) and Cresyl fast violet (CFV) stains. The stained tissues were studied under the light microscope. Application of one-way ANOVA statistical method showed that there were significant differences (p<0.05) in the activities of LDH, G-6-PDH, ACP, ALP and AChE of the LGB of the three mammals as revealed in the quantitative histochemistry of these enzymes and markers. Histological observations revealed no observable differences in the relative distribution of neurons and their supporting glial cells within the LGB of the three mammalian species. The comparison of the differences observed in the histological and the quantitative histochemical activities in these mammalian species revealed a variation in the visual perception and their individual peculiarities in relation to their mode and pattern of living.
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Affiliation(s)
- Temidayo Adeniyi
- Department of Anatomy, College of Health Sciences, Osun State University, Osogbo, Osun State. temidayo.adeniyi@
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61
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Cipolla A, Delbrassine F, Da Lage JL, Feller G. Temperature adaptations in psychrophilic, mesophilic and thermophilic chloride-dependent alpha-amylases. Biochimie 2012; 94:1943-50. [PMID: 22634328 DOI: 10.1016/j.biochi.2012.05.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/12/2012] [Indexed: 11/15/2022]
Abstract
The functional and structural adaptations to temperature have been addressed in homologous chloride-dependent α-amylases from a psychrophilic Antarctic bacterium, the ectothermic fruit fly, the homeothermic pig and from a thermophilic actinomycete. This series covers nearly all temperatures encountered by living organisms. We report a striking continuum in the functional properties of these enzymes coupled to their structural stability and related to the thermal regime of the source organism. In particular, thermal stability recorded by intrinsic fluorescence, circular dichroism and differential scanning calorimetry appears to be a compromise between the requirement for a stable native state and the proper structural dynamics to sustain the function at the environmental/physiological temperatures. The thermodependence of activity, the kinetic parameters, the activations parameters and fluorescence quenching support these activity-stability relationships in the investigated α-amylases.
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Affiliation(s)
- Alexandre Cipolla
- Laboratory of Biochemistry, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium
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62
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Aleksandrov A, Field M. A hybrid elastic band string algorithm for studies of enzymatic reactions. Phys Chem Chem Phys 2012; 14:12544-53. [PMID: 22576234 DOI: 10.1039/c2cp40918f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A common challenge in theoretical biophysics is the identification of a minimum energy path (MEP) for the rearrangement of a group of atoms from one stable configuration to another. The structure with maximum energy along the MEP approximates the transition state for the process and the energy profile itself permits estimation of the transition rates. In this work we describe a computationally efficient algorithm for the identification of minimum energy paths in complicated biosystems. The algorithm is a hybrid of the nudged elastic band (NEB) and string methods. It has been implemented in the pDynamo simulation program and tested by examining elementary steps in the reaction mechanisms of three enzymes: citrate synthase, RasGAP, and lactate dehydrogenase. Good agreement is found for the energies and geometries of the species along the reaction profiles calculated using the new algorithm and previous versions of the NEB and string techniques, and also those obtained by the common method of adiabatic exploration of the potential energy surface as a function of predefined reaction coordinates. Precisely refined structures of the saddle points along the paths may be subsequently obtained with the climbing image variant of the NEB algorithm. Directions in which the utility of the methods that we have implemented can be further improved are discussed.
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Affiliation(s)
- Alexey Aleksandrov
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France.
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63
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Colletier JP, Aleksandrov A, Coquelle N, Mraihi S, Mendoza-Barbera E, Field M, Madern D. Sampling the Conformational Energy Landscape of a Hyperthermophilic Protein by Engineering Key Substitutions. Mol Biol Evol 2012; 29:1683-94. [DOI: 10.1093/molbev/mss015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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64
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Mahdavi A, Sajedi RH, Asghari SM, Taghdir M, Rassa M. An analysis of temperature adaptation in cold active, mesophilic and thermophilic Bacillus α-amylases. Int J Biol Macromol 2011; 49:1038-45. [PMID: 21907234 DOI: 10.1016/j.ijbiomac.2011.08.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 08/24/2011] [Accepted: 08/25/2011] [Indexed: 01/13/2023]
Affiliation(s)
- Atiyeh Mahdavi
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
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65
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Hayashi S, Akanuma S, Onuki W, Tokunaga C, Yamagishi A. Substitutions of coenzyme-binding, nonpolar residues improve the low-temperature activity of thermophilic dehydrogenases. Biochemistry 2011; 50:8583-93. [PMID: 21894900 DOI: 10.1021/bi200925f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although enzymes of thermophilic organisms are often very resistant to thermal denaturation, they are usually less active than their mesophilic or psychrophilic homologues at moderate or low temperatures. To explore the structural features that would improve the activity of a thermophilic enzyme at less than optimal temperatures, we randomly mutated the DNA of single-site mutants of the thermostable Thermus thermophilus 3-isopropylmalate dehydrogenase that already had improved low-temperature activity and selected for additional improved low-temperature activity. A mutant (Ile279 → Val) with improved low-temperature activity contained a residue that directly interacts with the adenine of the coenzyme NAD(+), suggesting that modulation of the coenzyme-binding pocket's volume can enhance low-temperature activity. This idea was further supported by a saturation mutagenesis study of the two codons of two other residues that interact with the adenine. Furthermore, a similar type of amino acid substitution also improved the catalytic efficiency of another thermophilic dehydrogenase, T. thermophilus lactate dehydrogenase. Steady-state kinetic experiments showed that the mutations all favorably affected the catalytic turnover numbers. Thermal stability measurements demonstrated that the mutants remain very resistant to heat. Calculation of the energetic contributions to catalysis indicated that the increased turnover numbers are the result of destabilized enzyme-substrate-coenzyme complexes. Therefore, small changes in the side chain volumes of coenzyme-binding residues improved the catalytic efficiencies of two thermophilic dehydrogenases while preserving their high thermal stabilities and may be a way to improve low-temperature activities of dehydrogenases in general.
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Affiliation(s)
- Sayaka Hayashi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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66
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Cayenne AP, Gabert B, Stillman JH. Identification of proteins interacting with lactate dehydrogenase in claw muscle of the porcelain crab Petrolisthes cinctipes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2011; 6:393-8. [PMID: 21968246 DOI: 10.1016/j.cbd.2011.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 09/08/2011] [Accepted: 09/08/2011] [Indexed: 01/11/2023]
Abstract
Biochemical adaptation of enzymes involves conservation of activity, stability and affinity across a wide range of intracellular and environmental conditions. Enzyme adaptation by alteration of primary structure is well known, but the roles of protein-protein interactions in enzyme adaptation are less well understood. Interspecific differences in thermal stability of lactate dehydrogenase (LDH) in porcelain crabs (genus Petrolisthes) are related to intrinsic differences among LDH molecules and by interactions with other stabilizing proteins. Here, we identified proteins that interact with LDH in porcelain crab claw muscle tissue using co-immunoprecipitation, and showed LDH exists in high molecular weight complexes using size exclusion chromatography and Western blot analyses. Co-immunoprecipitated proteins were separated using 2D SDS PAGE and analyzed by LC/ESI using peptide MS/MS. Peptide MS/MS ions were compared to an EST database for Petrolisthes cinctipes to identify proteins. Identified proteins included cytoskeletal elements, glycolytic enzymes, a phosphagen kinase, and the respiratory protein hemocyanin. Our results support the hypothesis that LDH interacts with glycolytic enzymes in a metabolon structured by cytoskeletal elements that may also include the enzyme for transfer of the adenylate charge in glycolytically produced ATP. Those interactions may play specific roles in biochemical adaptation of glycolytic enzymes.
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Affiliation(s)
- Andrea P Cayenne
- Romberg Tiburon Center and Department of Biology, San Francisco State University, 3152 Paradise Drive, Tiburon California 94920, USA
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67
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Cipolla A, D'Amico S, Barumandzadeh R, Matagne A, Feller G. Stepwise adaptations to low temperature as revealed by multiple mutants of psychrophilic α-amylase from Antarctic Bacterium. J Biol Chem 2011; 286:38348-38355. [PMID: 21900238 DOI: 10.1074/jbc.m111.274423] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The mutants Mut5 and Mut5CC from a psychrophilic α-amylase bear representative stabilizing interactions found in the heat-stable porcine pancreatic α-amylase but lacking in the cold-active enzyme from an Antarctic bacterium. From an evolutionary perspective, these mutants can be regarded as structural intermediates between the psychrophilic and the mesophilic enzymes. We found that these engineered interactions improve all the investigated parameters related to protein stability as follows: compactness; kinetically driven stability; thermodynamic stability; resistance toward chemical denaturation, and the kinetics of unfolding/refolding. Concomitantly to this improved stability, both mutants have lost the kinetic optimization to low temperature activity displayed by the parent psychrophilic enzyme. These results provide strong experimental support to the hypothesis assuming that the disappearance of stabilizing interactions in psychrophilic enzymes increases the amplitude of concerted motions required by catalysis and the dynamics of active site residues at low temperature, leading to a higher activity.
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Affiliation(s)
- Alexandre Cipolla
- Laboratories of Biochemistry, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium
| | - Salvino D'Amico
- Laboratories of Biochemistry, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium
| | - Roya Barumandzadeh
- Enzymology and Protein Folding, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium
| | - André Matagne
- Enzymology and Protein Folding, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium
| | - Georges Feller
- Laboratories of Biochemistry, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium.
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68
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Arai K, Ichikawa J, Nonaka S, Miyanaga A, Uchikoba H, Fushinobu S, Taguchi H. A molecular design that stabilizes active state in bacterial allosteric L-lactate dehydrogenases. J Biochem 2011; 150:579-91. [PMID: 21828088 DOI: 10.1093/jb/mvr100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
l-Lactate dehydrogenase (l-LDH) of Lactobacillus casei (LCLDH) is a typical bacterial allosteric l-LDH that requires fructose 1,6-bisphosphate (FBP) for its enzyme activity. A mutant LCLDH was designed to introduce an inter-subunit salt bridge network at the Q-axis subunit interface, mimicking Lactobacillus pentosus non-allosteric l-LDH (LPLDH). The mutant LCLDH exhibited high catalytic activity with hyperbolic pyruvate saturation curves independently of FBP, and virtually the equivalent K(m) and V(m) values at pH 5.0 to those of the fully activated wild-type enzyme with FBP, although the K(m) value was slightly improved with FBP or Mn(2+) at pH 7.0. The mutant enzyme exhibited a markedly higher apparent denaturating temperature (T(1/2)) than the wild-type enzyme in the presence of FBP, but showed an even lower T(1/2) without FBP, where it exhibited higher activation enthalpy of inactivation (ΔH(‡)). This result is consistent with the fact that the active state is more unstable than the inactive state in allosteric equilibrium of LCLDH. The LPLDH-like network appears to be conserved in many bacterial non-allosteric l-LDHs and dimeric l-malate dehydrogenases, and thus to be a key for the functional divergence of bacterial l-LDHs during evolution.
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Affiliation(s)
- Kazuhito Arai
- Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba, Japan
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69
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Luo Q, Meneely KM, Lamb AL. Entropic and enthalpic components of catalysis in the mutase and lyase activities of Pseudomonas aeruginosa PchB. J Am Chem Soc 2011; 133:7229-33. [PMID: 21504201 DOI: 10.1021/ja202091a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB) catalyzes two pericyclic reactions, demonstrating the eponymous activity and also chorismate mutase activity. The thermodynamic parameters for these enzyme-catalyzed activities, as well as the uncatalyzed isochorismate decomposition, are reported from temperature dependence of k(cat) and k(uncat) data. The entropic effects do not contribute to enzyme catalysis as expected from previously reported chorismate mutase data. Indeed, an entropic penalty for the enzyme-catalyzed mutase reaction (ΔS(++) = -12.1 ± 0.6 cal/(mol K)) is comparable to that of the previously reported uncatalyzed reaction, whereas that of the enzyme-catalyzed lyase reaction (ΔS(++) = -24.3 ± 0.2 cal/(mol K)) is larger than that of the uncatalyzed lyase reaction (-15.77 ± 0.02 cal/(mol K)) documented here. With the assumption that chemistry is rate-limiting, we propose that a reactive substrate conformation is formed upon loop closure of the active site and that ordering of the loop contributes to the entropic penalty for converting the enzyme substrate complex to the transition state.
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Affiliation(s)
- Qianyi Luo
- Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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70
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Tiberti M, Papaleo E. Dynamic properties of extremophilic subtilisin-like serine-proteases. J Struct Biol 2011; 174:69-83. [DOI: 10.1016/j.jsb.2011.01.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 12/19/2010] [Accepted: 01/20/2011] [Indexed: 10/18/2022]
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71
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Aleksandrov A, Field M. Efficient solvent boundary potential for hybrid potential simulations. Phys Chem Chem Phys 2011; 13:10503-9. [DOI: 10.1039/c0cp02828b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Coquelle N, Talon R, Juers DH, Girard É, Kahn R, Madern D. Gradual Adaptive Changes of a Protein Facing High Salt Concentrations. J Mol Biol 2010; 404:493-505. [DOI: 10.1016/j.jmb.2010.09.055] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 09/22/2010] [Accepted: 09/24/2010] [Indexed: 11/26/2022]
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73
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Bensel T, Stotz M, Borneff-Lipp M, Wollschläger B, Wienke A, Taccetti G, Campana S, Meyer KC, Jensen PØ, Lechner U, Ulrich M, Döring G, Worlitzsch D. Lactate in cystic fibrosis sputum. J Cyst Fibros 2010; 10:37-44. [PMID: 20947455 DOI: 10.1016/j.jcf.2010.09.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 09/16/2010] [Accepted: 09/20/2010] [Indexed: 11/26/2022]
Abstract
BACKGROUND Antibiotic therapy is thought to improve lung function in patients with cystic fibrosis (CF) by decreasing neutrophil-derived inflammation. We investigated the origin and clinical significance of lactate in the chronically inflamed CF lung. METHODS Lactate was measured in sputa of 18 exacerbated and 25 stable CF patients via spectrophotometry and gaschromatography. Lung function was assessed via spirometry. Seven patients with chronic obstructive pulmonary disease (COPD) and three patients with acute lung inflammation served as control groups. Neutrophil and bacterial lactate production was assessed under aerobic and anaerobic conditions. RESULTS In sputum specimens of patients with respiratory exacerbations lactate concentrations decreased significantly (p<0.005) from 3.4±2.3mmol/L to 1.4±1.4mmol/L after 2-3 weeks of intravenous antibiotics. Successful treatment was reflected in 16 patients (88.9%) by FVC increase associated with lactate decrease (p<0.05). In every single sputum lactate was detectable (3.0±3.1mmol/L, range 0.2-14.1mmol/L). Lactate was lower (1.6±0.8mmol/L) in sputa from seven COPD patients, and it was below the detection limit in three patients with acute lung inflammation. Neutrophil lactate production accumulated up to 10.5mmol/L after 4 days, whereas bacterial lactate production did not appear to contribute substantially to sputum lactate concentrations. CONCLUSIONS Successful antibiotic therapy is reflected by a decrease in lactate concentrations. Neutrophils are the most likely source for lactate in sputum of CF patients. Therefore lactate may be used to monitor responses to antibiotic therapy as an adjunct to lung function measurements.
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Affiliation(s)
- Tobias Bensel
- Institute of Hygiene, University Hospital of Halle-Wittenberg, Halle, Germany
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74
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Mekkawy IAA, Mahmoud UM, Osman AG, Sayed AEDH. Effects of ultraviolet A on the activity of two metabolic enzymes, DNA damage and lipid peroxidation during early developmental stages of the African catfish, Clarias gariepinus (Burchell, 1822). FISH PHYSIOLOGY AND BIOCHEMISTRY 2010; 36:605-626. [PMID: 19609701 PMCID: PMC2923706 DOI: 10.1007/s10695-009-9334-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Accepted: 05/11/2009] [Indexed: 02/07/2023]
Abstract
Many ultraviolet-A (UVA)-induced biochemical and physiological changes are valid as biomarkers using aquatic species for detection of the degree of stress. Changes in the concentration and activities of enzymes, such as glucose-6-phosphate dehyderogenase (G6PDH), lactate dehyderogenase (LDH), DNA damage and lipid peroxidation (LPO), can be used as biomarkers to identify possible environmental contamination in fish. This study aimed to investigate the impact of UVA on the activity of the selected enzymes, DNA damage and LPO during early developmental stages of the African catfish Clarias gariepinus. Embryo hemogenates were used for measurements of G6PDH, LDH, DNA damage and LPO concentrations and activities spectrophotometrically at 37 degrees C. The normal ontogenetic variations in enzyme activities, DNA damage and LPO of the early developmental stages (24-168 h-PFS; hours-post fertilization stage) were studied. There was a significant decrease in the activity of G6PDH till 120 h-PFS. Then after 120 h-PFS, the activity of such enzymes insignificantly increased toward higher stages. The LDH activity was recorded with a pattern of decrease till 96 h-PFS, followed by a significant increase toward 168 h-PFS. The polynomial pattern of variations in DNA damage and LPO was also evident. The patterns of the enzyme activities, corresponding DNA damage and LPO of the early ontogenetic stages under the influence of three different UVA doses (15, 30 and 60 min), were recorded. The pattern of variations in G6PDH activity in UVA-induced groups was similar to that of the control group with variation in the magnitude of such activity. In all treated groups, LDH activity decreased till 96 h-PFS, then increased till 168 h-PFS. Within each of the embryonic stages, the increase in UVA led to a significant increase in DNA damage. A significant increase in lipid peroxidation under UVA doses was recorded. The variability in number and molecular weight of proteins under exposure to UVA was evident, reflecting some of the genetic and transcriptional changes during exposure and development.
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Affiliation(s)
- Imam A A Mekkawy
- Zoology Department, Faculty of Science, Assiut University, 71516, Assiut, Egypt
| | - Usama M Mahmoud
- Zoology Department, Faculty of Science, Assiut University, 71516, Assiut, Egypt
| | - Alaa G Osman
- Zoology Department, Faculty of Science, Al Azhar University, 71524, Assiut, Egypt
| | - Alaa El-Din H Sayed
- Zoology Department, Faculty of Science, Assiut University, 71516, Assiut, Egypt.
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75
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Toth K, Amyes TL, Wood BM, Chan KK, Gerlt JA, Richard JP. An examination of the relationship between active site loop size and thermodynamic activation parameters for orotidine 5'-monophosphate decarboxylase from mesophilic and thermophilic organisms. Biochemistry 2009; 48:8006-13. [PMID: 19618917 DOI: 10.1021/bi901064k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Closure of the active site phosphate gripper loop of orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae (ScOMPDC) over the bound substrate orotidine 5'-monophosphate (OMP) activates the bound substrate for decarboxylation by at least 10(4)-fold [Amyes, T. L., Richard, J. P., and Tait, J. J. (2005) J. Am. Chem. Soc. 127, 15708-15709]. The 19-residue phosphate gripper loop of the mesophilic ScOMPDC is much larger than the nine-residue loop at the ortholog from the thermophile Methanothermobacter thermautotrophicus (MtOMPDC). This difference in loop size results in a small decrease in the total intrinsic phosphate binding energy of the phosphodianion group of OMP from 11.9 to 11.6 kcal/mol, along with a modest decrease in the extent of activation by phosphite dianion of decarboxylation of the truncated substrate 1-(beta-D-erythrofuranosyl)orotic acid. The activation parameters DeltaH(double dagger) and DeltaS(double dagger) for k(cat) for decarboxylation of OMP are 3.6 kcal/mol and 10 cal K(-1) mol(-1) more positive, respectively, for MtOMPDC than for ScOMPDC. We suggest that these differences are related to the difference in the size of the active site loops at the mesophilic ScOMPDC and the thermophilic MtOMPDC. The greater enthalpic transition state stabilization available from the more extensive loop-substrate interactions for the ScOMPDC-catalyzed reaction is largely balanced by a larger entropic requirement for immobilization of the larger loop at this enzyme.
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Affiliation(s)
- Krisztina Toth
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, USA
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76
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Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes. Comput Biol Chem 2009; 33:137-48. [DOI: 10.1016/j.compbiolchem.2008.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Accepted: 08/25/2008] [Indexed: 11/22/2022]
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77
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Silva A, Mateus M. Development of a polysulfone hollow fiber vascular bio-artificial pancreas device for in vitro studies. J Biotechnol 2009; 139:236-49. [DOI: 10.1016/j.jbiotec.2008.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 10/16/2008] [Accepted: 12/03/2008] [Indexed: 10/21/2022]
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78
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Functional and adaptive significance of differentially expressed lactate dehydrogenase isoenzymes in tissues of four obligatory air-breathing Channa species. Biologia (Bratisl) 2009. [DOI: 10.2478/s11756-009-0017-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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79
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Abstract
Cofactors are organic molecules, most of them originating from vitamins, that bind to enzymes making them able to catalyze defined reactions. A cofactor-based chemogenomics approach exploits the presence of a cofactor-binding domain to develop compound scaffolds tailored to mimic the cofactor and to replace it within target enzyme classes. As a result, a loss of function is observed. An expansion of the cofactor scaffold to include structural/chemical features derived from the substrate, that usually binds at cofactor adjacent sites, increases the specificity of the enzyme fishing. This approach has been so far applied only to NAD(P)(+)-dependent enzymes. However, it is suitable for all other cofactors, with difficulties, for some of them, originated by very tight binding. In the case of cofactors covalently bound to the enzyme, the competition between the natural cofactor and the cofactor scaffold mimic can only occur during enzyme folding.
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Affiliation(s)
- Ratna Singh
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy
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80
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Michaux C, Massant J, Kerff F, Frère JM, Docquier JD, Vandenberghe I, Samyn B, Pierrard A, Feller G, Charlier P, Van Beeumen J, Wouters J. Crystal structure of a cold-adapted class C beta-lactamase. FEBS J 2008; 275:1687-97. [PMID: 18312599 DOI: 10.1111/j.1742-4658.2008.06324.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In this study, the crystal structure of a class C beta-lactamase from a psychrophilic organism, Pseudomonas fluorescens, has been refined to 2.2 A resolution. It is one of the few solved crystal structures of psychrophilic proteins. The structure was compared with those of homologous mesophilic enzymes and of another, modeled, psychrophilic protein. The elucidation of the 3D structure of this enzyme provides additional insights into the features involved in cold adaptation. Structure comparison of the psychrophilic and mesophilic beta-lactamases shows that electrostatics seems to play a major role in low-temperature adaptation, with a lower total number of ionic interactions for cold enzymes. The psychrophilic enzymes are also characterized by a decreased number of hydrogen bonds, a lower content of prolines, and a lower percentage of arginines in comparison with lysines. All these features make the structure more flexible so that the enzyme can behave as an efficient catalyst at low temperatures.
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Affiliation(s)
- Catherine Michaux
- Chimie Biologique Structurale Laboratory, CPTS group, FUNDP, 61 rue de Bruxelles, Namur, Belgium.
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