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Shadrin NV, Anufriieva EV, Belyakov VP, Bazhora AI. Chironomidae larvae in hypersaline waters of the Crimea: diversity, distribution, abundance and production. EUROPEAN ZOOLOGICAL JOURNAL 2017. [DOI: 10.1080/11250003.2016.1273974] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- N. V. Shadrin
- Kovalevsky Institute of Marine Biological Research, Russian Academy of Sciences, Sevastopol, Russia
| | - E. V. Anufriieva
- Kovalevsky Institute of Marine Biological Research, Russian Academy of Sciences, Sevastopol, Russia
| | - V. P. Belyakov
- Institute of Limnology, Russian Academy of Sciences, St.-Petersburg, Russia
| | - A. I. Bazhora
- Institute of Limnology, Russian Academy of Sciences, St.-Petersburg, Russia
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2
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Shukla N, Pomarico E, Chen L, Chergui M, Othon CM. Retardation of Bulk Water Dynamics by Disaccharide Osmolytes. J Phys Chem B 2016; 120:9477-83. [DOI: 10.1021/acs.jpcb.6b07751] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nimesh Shukla
- Department
of Physics, Wesleyan University, Middletown, Connecticut 06457, United States
| | - Enrico Pomarico
- Laboratoire
de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast
Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Lee Chen
- Department
of Physics, Wesleyan University, Middletown, Connecticut 06457, United States
| | - Majed Chergui
- Laboratoire
de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast
Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Christina M. Othon
- Department
of Physics, Wesleyan University, Middletown, Connecticut 06457, United States
- Molecular
Biophysics Program, Wesleyan University, Middletown, Connecticut 06457, United States
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3
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Eiberweiser A, Nazet A, Kruchinin SE, Fedotova MV, Buchner R. Hydration and Ion Binding of the Osmolyte Ectoine. J Phys Chem B 2015; 119:15203-11. [PMID: 26565946 DOI: 10.1021/acs.jpcb.5b09276] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ectoine is a widespread osmolyte enabling halophilic bacteria to withstand high osmotic stress that has many potential applications ranging from cosmetics to its use as a therapeutic agent. In this contribution, combining experiment and theory, the hydration and ion-binding of this zwitterionic compound was studied to gain information on the functioning of ectoine in particular and of osmolytes in general. Dielectric relaxation spectroscopy was used to determine the effective hydration number of ectoine and its effective dipole moment in aqueous solutions with and without added NaCl. The obtained experimental data were compared with structural results from 1D-RISM and 3D-RISM calculations. It was found that ectoine is strongly hydrated, even in the presence of high salt concentrations. Upon addition of NaCl, ions are bound to ectoine but the formed complexes are not very stable. Interestingly, this osmolyte strongly rises the static relative permittivity of its solutions, shielding thus effectively long-range Coulomb interactions among ions in ectoine-containing solutions. We believe that via this effect, which should be common to all zwitterionic osmolytes, ectoine protects against excessive ions within the cell in addition to its strong osmotic activity protecting against ions outside.
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Affiliation(s)
- Andreas Eiberweiser
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg , D-93040 Regensburg, Germany
| | - Andreas Nazet
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg , D-93040 Regensburg, Germany
| | - Sergey E Kruchinin
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences , Akademicheskaya st. 1, Ivanovo, Russia
| | - Marina V Fedotova
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences , Akademicheskaya st. 1, Ivanovo, Russia
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg , D-93040 Regensburg, Germany
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4
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Kim J, Bertozzi CR. A Bioorthogonal Reaction of N-Oxide and Boron Reagents. Angew Chem Int Ed Engl 2015; 54:15777-81. [PMID: 26568479 DOI: 10.1002/anie.201508861] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Indexed: 12/15/2022]
Abstract
The development of bioorthogonal reactions has classically focused on bond-forming ligation reactions. In this report, we seek to expand the functional repertoire of such transformations by introducing a new bond-cleaving reaction between N-oxide and boron reagents. The reaction features a large dynamic range of reactivity, showcasing second-order rate constants as high as 2.3×10(3) M(-1) s(-1) using diboron reaction partners. Diboron reagents display minimal cell toxicity at millimolar concentrations, penetrate cell membranes, and effectively reduce N-oxides inside mammalian cells. This new bioorthogonal process based on miniscule components is thus well-suited for activating molecules within cells under chemical control. Furthermore, we demonstrate that the metabolic diversity of nature enables the use of naturally occurring functional groups that display inherent biocompatibility alongside abiotic components for organism-specific applications.
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Affiliation(s)
- Justin Kim
- Department of Chemistry and Howard Hughes Medical Institute, Stanford University, 380 Roth Way, Stanford, CA 94305 (USA)
| | - Carolyn R Bertozzi
- Department of Chemistry and Howard Hughes Medical Institute, Stanford University, 380 Roth Way, Stanford, CA 94305 (USA).
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5
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Affiliation(s)
- Justin Kim
- Department of Chemistry and Howard Hughes Medical Institute, Stanford University, 380 Roth Way, Stanford, CA 94305 (USA)
| | - Carolyn R. Bertozzi
- Department of Chemistry and Howard Hughes Medical Institute, Stanford University, 380 Roth Way, Stanford, CA 94305 (USA)
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6
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Paul S, Paul S. Investigating the Counteracting Effect of Trehalose on Urea-Induced Protein Denaturation Using Molecular Dynamics Simulation. J Phys Chem B 2015; 119:10975-88. [DOI: 10.1021/acs.jpcb.5b01457] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Subrata Paul
- Department
of Chemistry, Indian Institute of Technology, Guwahati, Assam India-781039
| | - Sandip Paul
- Department
of Chemistry, Indian Institute of Technology, Guwahati, Assam India-781039
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7
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Verma PK, Lee H, Park JY, Lim JH, Maj M, Choi JH, Kwak KW, Cho M. Modulation of the Hydrogen Bonding Structure of Water by Renal Osmolytes. J Phys Chem Lett 2015; 6:2773-2779. [PMID: 26266862 DOI: 10.1021/acs.jpclett.5b01087] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Osmolytes are an integral part of living organism, e.g., the kidney uses sorbitol, trimethylglycine, taurine and myo-inositol to counter the deleterious effects of urea and salt. Therefore, knowing that the osmolytes' act either directly to the protein or mediated through water is of great importance. Our experimental and computational results show that protecting osmolytes, e.g., trimethylglycine and sorbitol, significantly modulate the water H-bonding network structure, although the magnitude and spatial extent of osmolyte-induced perturbation greatly vary. In contrast, urea behaves neutrally toward local water H-bonding network. Protecting osmolytes studied here show strong concentration-dependent behaviors (vibrational frequencies and lifetimes of two different infrared (IR) probes), while denaturant does not. The H-bond donor and/or acceptor (OH/NH) in a given osmolyte molecule play a critical role in defining their action. Our findings highlight the significance of the alteration of H-bonding network of water under biologically relevant environment, often encountered in real biological systems.
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Affiliation(s)
- Pramod Kumar Verma
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
- ‡Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Hochan Lee
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
- ‡Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Joon-Young Park
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
- ‡Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Joon-Hyung Lim
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
- ‡Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Michał Maj
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
- ‡Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Jun-Ho Choi
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
| | - Kyung-Won Kwak
- §Department of Chemistry, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Minhaeng Cho
- †Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 136-701, Republic of Korea
- ‡Department of Chemistry, Korea University, Seoul 136-701, Republic of Korea
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8
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How Can a Free Amino Acid Stabilize a Protein? Insights from Molecular Dynamics Simulation. J SOLUTION CHEM 2015. [DOI: 10.1007/s10953-015-0291-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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9
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Moosa MM, Ferreon ACM, Deniz AA. Forced folding of a disordered protein accesses an alternative folding landscape. Chemphyschem 2014; 16:90-4. [PMID: 25345588 DOI: 10.1002/cphc.201402661] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Indexed: 11/12/2022]
Abstract
Intrinsically disordered proteins (IDPs) are involved in diverse cellular functions. Many IDPs can interact with multiple binding partners, resulting in their folding into alternative ligand-specific functional structures. For such multi-structural IDPs, a key question is whether these multiple structures are fully encoded in the protein sequence, as is the case in many globular proteins. To answer this question, here we employed a combination of single-molecule and ensemble techniques to compare ligand-induced and osmolyte-forced folding of α-synuclein. Our results reveal context-dependent modulation of the protein's folding landscape, suggesting that the codes for the protein's native folds are partially encoded in its primary sequence, and are completed only upon interaction with binding partners. Our findings suggest a critical role for cellular interactions in expanding the repertoire of folds and functions available to disordered proteins.
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Affiliation(s)
- Mahdi Muhammad Moosa
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 (USA)
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10
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Baturin S, Galka JJ, Piyadasa H, Gajjeraman S, O'Neil JD. The effects of a protein osmolyte on the stability of the integral membrane protein glycerol facilitator. Biochem Cell Biol 2014; 92:564-75. [PMID: 25387032 DOI: 10.1139/bcb-2014-0076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Osmolytes are naturally occurring molecules used by a wide variety of organisms to stabilize proteins under extreme conditions of temperature, salinity, hydrostatic pressure, denaturant concentration, and desiccation. The effects of the osmolyte trimethylamine N-oxide (TMAO) as well as the influence of detergent head group and acyl chain length on the stability of the Escherichia coli integral membrane protein glycerol facilitator (GF) tetramer to thermal and chemical denaturation by sodium dodecyl sulphate (SDS) are reported. TMAO promotes the association of the normally tetrameric α-helical protein into higher order oligomers in dodecyl-maltoside (DDM), but not in tetradecyl-maltoside (TDM), lyso-lauroylphosphatidyl choline (LLPC), or lyso-myristoylphosphatidyl choline (LMPC), as determined by dynamic light scattering (DLS); an octameric complex is particularly stable as indicated by SDS polyacrylamide gel electrophoresis. TMAO increases the heat stability of the GF tetramer an average of 10 °C in the 4 detergents and also protects the protein from denaturation by SDS. However, it did not promote re-association to the tetramer when added to SDS-dissociated protein. TMAO also promotes the formation of rod-like detergent micelles, and DLS was found to be useful for monitoring the structure of the protein and the redistribution of detergent during thermal dissociation of the protein. The protein is more thermally stable in detergents with the phosphatidylcholine head group (LLPC and LMPC) than in the maltoside detergents. The implications of the results for osmolyte mechanism, membrane protein stability, and protein-protein interactions are discussed.
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Affiliation(s)
- Simon Baturin
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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11
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Nakagawa Y, Sehata S, Fujii S, Yamamoto H, Tsuda A, Koumoto K. Mechanistic study on the facilitation of enzymatic hydrolysis by α-glucosidase in the presence of betaine-type metabolite analogs. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.06.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Sacchi R, Gardell AM, Chang N, Kültz D. Osmotic regulation and tissue localization of themyo-inositol biosynthesis pathway in tilapia (Oreochromis mossambicus) larvae. ACTA ACUST UNITED AC 2014; 321:457-66. [DOI: 10.1002/jez.1878] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/16/2014] [Accepted: 06/05/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Romina Sacchi
- EcoPhysiological Proteomics Laboratory; Department of Animal Science; University of California; Davis; Davis California
| | - Alison M. Gardell
- EcoPhysiological Proteomics Laboratory; Department of Animal Science; University of California; Davis; Davis California
| | - Nicole Chang
- EcoPhysiological Proteomics Laboratory; Department of Animal Science; University of California; Davis; Davis California
| | - Dietmar Kültz
- EcoPhysiological Proteomics Laboratory; Department of Animal Science; University of California; Davis; Davis California
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13
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Liu L, Shi Y, Liu C, Wang T, Liu G, Zhang G. Insight into the amplification by methylated urea of the anion specificity of macromolecules. SOFT MATTER 2014; 10:2856-2862. [PMID: 24667999 DOI: 10.1039/c3sm52778f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Methylated urea and sugar are chaotropic and kosmotropic osmolytes, respectively. In the present work, we have investigated the specific anion effect on the lower critical solution temperature (LCST) behavior of poly(N-isopropylacrylamide) (PNIPAM) in the presence of methylated urea or sugars. Differential scanning calorimetry studies revealed that tetramethylurea can adsorb onto the PNIPAM surface, but glucose is excluded from the PNIPAM surface. The specific anion effect on the LCST behavior of PNIPAM is amplified by methylated urea but not by sugars. The amplification of the anion specificity by methylated urea is attributed to an increased difference in the anion-specific polarization of hydrogen bonds, induced by the formation of PNIPAM/methylated urea complexes via hydrophobic interactions. As the number of methyl groups on the methylated urea increases, the extent of amplification of the anion specificity increases due to increasing hydrophobic interactions between the PNIPAM and methylated urea. Additionally, no amplification of the anion specificity is observed in the presence of urea because a PNIPAM/urea complex cannot be formed via hydrophobic interactions.
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Affiliation(s)
- Lvdan Liu
- Department of Chemical Physics, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, P.R. China.
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14
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Sepasi Tehrani H, Moosavi-Movahedi A, Ghourchian H, Ahmad F, Kiany A, Atri M, Ariaeenejad S, Kavousi K, Saboury A. Effect of compatible and noncompatible osmolytes on the enzymatic activity and thermal stability of bovine liver catalase. J Biomol Struct Dyn 2013; 31:1440-54. [DOI: 10.1080/07391102.2012.742460] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Denning EJ, Thirumalai D, MacKerell AD. Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure. Biophys Chem 2013; 184:8-16. [PMID: 24012912 DOI: 10.1016/j.bpc.2013.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/08/2013] [Accepted: 08/08/2013] [Indexed: 01/10/2023]
Abstract
The osmolyte trimethylamine N-oxide (TMAO) stabilizes the tertiary but not the secondary structures of RNA. However, molecular dynamics simulations performed on the PreQ1 riboswitch showed that TMAO destabilizes the tertiary riboswitch structure, leading us to hypothesize that the presence of RNA could result in enhanced population of the protonated form, TMAOP. Constant pH replica exchange simulations showed that a percentage of TMAO is indeed protonated, thus contributing to the stability of the tertiary but not the secondary structure of PreQ1. TMAOP results in an unfavorable dehydration of phosphodiester backbone, which is compensated by electrostatic attraction between TMAOP and the phosphate groups. In addition, TMAOP interacts with specific sites in the tertiary RNA structure, mimicking the behavior of positively charged ions and of the PreQ1 ligand in stabilizing RNA. Finally, we predict that TMAO-induced stabilization of RNA tertiary structures should be strongly pH dependent.
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Affiliation(s)
- Elizabeth J Denning
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
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16
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Hidalgo K, Laparie M, Bical R, Larvor V, Bouchereau A, Siaussat D, Renault D. Metabolic fingerprinting of the responses to salinity in the invasive ground beetle Merizodus soledadinus at the Kerguelen Islands. JOURNAL OF INSECT PHYSIOLOGY 2013; 59:91-100. [PMID: 23123259 DOI: 10.1016/j.jinsphys.2012.10.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 10/03/2012] [Accepted: 10/04/2012] [Indexed: 06/01/2023]
Abstract
Salinity is an abiotic factor that may impact survival and fitness of terrestrial insects in coastal environments. Meanwhile, some terrestrial arthropods can survive in hypersaline environments, and counterbalance osmotic stress by intra- and extracellular buildups of organic osmolytes. The ground beetle Merizodus soledadinus originates from South America and it is distributed in forests and riparian zones, where salinity levels are considerably low. This species has been introduced at the Kerguelen Islands a century ago, where it colonized coastal areas (tide drift lines), and must thus withstand salinity variations due to tide, spray, and organic matter deposited therein. In the present study, we addressed the physiological plasticity of M. soledadinus to saline conditions, by monitoring body water content and survival in adults experimentally subjected to different salinities. We also investigated possible metabolic adjustments involved at three contrasted salinity levels (0‰, 35‰, 70‰) at 4 and 8°C. We hypothesized that this invasive ground beetle can withstand a broad range of salinity conditions thanks to the plastic accumulation of compatible solutes. The study revealed a progressive drop in body water content in individuals exposed to 35‰ and 70‰, as opposed to the controls. Metabolic fingerprints showed compatible solute (erythritol, alanine, glycine and proline) accumulation at medium and high salinity conditions (35‰ and 70‰). We concluded that the osmo-induced accumulation of amino acids and polyols was likely to modulate the ground beetles' body water balance on medium saline substrates, thus enhancing their survival ability.
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Affiliation(s)
- K Hidalgo
- Université de Rennes 1, UMR CNRS 6553 Ecobio, Campus de Beaulieu, 263 avenue du Gal Leclerc, CS 74205, 35042 Rennes, France
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17
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Sarma R, Paul S. The effect of aqueous solutions of trimethylamine-N-oxide on pressure induced modifications of hydrophobic interactions. J Chem Phys 2012; 137:094502. [DOI: 10.1063/1.4748101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Venkatesan S, Lee SL. Computational investigation on microsolvation of the osmolyte glycine betaine [GB (H(2)O)(1-7)]. J Mol Model 2012; 18:5017-28. [PMID: 22736222 DOI: 10.1007/s00894-012-1501-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 06/08/2012] [Indexed: 11/30/2022]
Abstract
The preferential interactions of glycine betaine (GB) with solvent components and the effect of solvent on its stability have been examined. In particular, the microsolvation of organic osmolyte and widely important osmoprotectant in nature as glycine betaine has been reported by using M06 method. A number of configurations (b(X) (a-z)) of the clusters for one to seven water molecules (× = 1-7) have been considered for the microsolvation. Structures of stable conformers are obtained and denoted as b1a, b2a, b3a, b4a, b5a, b6a and b7a. It is observed from the interaction energy difference (∆E) that only seven water molecules can be accommodated in the first solvation shell to stabilize GB. It is also observed that the calculated relative energy using M06 is in close agreement with calculations at the MP2 level of theory.
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19
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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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20
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Lemos GSD, Márquez-Bernardes LF, Arvelos LR, Paraíso LF, Penha-Silva N. Influence of Glucose Concentration on the Membrane Stability of Human Erythrocytes. Cell Biochem Biophys 2011; 61:531-7. [DOI: 10.1007/s12013-011-9235-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Panuszko A, Śmiechowski M, Stangret J. Fourier transform infrared spectroscopic and theoretical study of water interactions with glycine and its N-methylated derivatives. J Chem Phys 2011; 134:115104. [PMID: 21428668 DOI: 10.1063/1.3567202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aneta Panuszko
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11∕12, 80-233 Gdańsk, Poland
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22
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Salinity regulates N-methylation of phosphatidylethanolamine in euryhaline crustaceans hepatopancreas and exchange of newly-formed phosphatidylcholine with hemolymph. J Comp Physiol B 2011; 181:731-40. [DOI: 10.1007/s00360-011-0562-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 02/15/2011] [Accepted: 02/19/2011] [Indexed: 10/18/2022]
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23
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McMeekin T, Hill C, Wagner M, Dahl A, Ross T. Ecophysiology of food-borne pathogens: Essential knowledge to improve food safety. Int J Food Microbiol 2010; 139 Suppl 1:S64-78. [DOI: 10.1016/j.ijfoodmicro.2010.01.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 01/26/2010] [Accepted: 01/27/2010] [Indexed: 10/19/2022]
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24
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Nayak A, Lee CC, McRae GJ, Belfort G. Osmolyte controlled fibrillation kinetics of insulin: New insight into fibrillation using the preferential exclusion principle. Biotechnol Prog 2010; 25:1508-14. [PMID: 19653270 DOI: 10.1002/btpr.255] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Amyloid proteins are converted from their native-fold to long beta-sheet-rich fibrils in a typical sigmoidal time-dependent protein aggregation curve. This reaction process from monomer or dimer to oligomer to nuclei and then to fibrils is the subject of intense study. The main results of this work are based on the use of a well-studied model amyloid protein, insulin, which has been used in vitro by others. Nine osmolyte molecules, added during the protein aggregation process for the production of amyloid fibrils, slow-down or speed up the process depending on the molecular structure of each osmolyte. Of these, all stabilizing osmolytes (sugars) slow down the aggregation process in the following order: tri > di > monosaccharides, whereas destabilizing osmolytes (urea, guanidium hydrochloride) speed up the aggregation process in a predictable way that fits the trend of all osmolytes. With respect to kinetics, we illustrate, by adapting our earlier reaction model to the insulin system, that the intermediates (trimers, tetramers, pentamers, etc.) are at very low concentrations and that nucleation is orders of magnitude slower than fibril growth. The results are then collated into a cogent explanation using the preferential exclusion and accumulation of osmolytes away from and at the protein surface during nucleation, respectively. Both the heat of solution and the neutral molecular surface area of the osmolytes correlate linearly with two fitting parameters of the kinetic rate model, that is, the lag time and the nucleation rate prior to fibril formation. These kinetic and thermodynamic results support the preferential exclusion model and the existence of oligomers including nuclei and larger structures that could induce toxicity.
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Affiliation(s)
- Arpan Nayak
- Howard P. Isermann Dept. of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Coughlan BM, Moroney GA, van Pelt FNAM, O'Brien NM, Davenport J, O'Halloran J. The effects of salinity on the Manila clam (Ruditapes philippinarum) using the neutral red retention assay with adapted physiological saline solutions. MARINE POLLUTION BULLETIN 2009; 58:1680-1684. [PMID: 19664787 DOI: 10.1016/j.marpolbul.2009.06.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 06/25/2009] [Accepted: 06/26/2009] [Indexed: 05/28/2023]
Abstract
This study investigated the internal osmotic regulatory capabilities of the Manila clam (Ruditapes philippinarum) following in vivo exposure to a range of salinities. A second objective was to measure the health status of the Manila clam following exposure to different salinities using the neutral red retention (NRR) assay, and to compare results using a range of physiological saline solutions (PSS). On exposure to seawater of differing salinities, the Manila clam followed a pattern of an osmoconformer, although they seemed to partially regulate their circulatory haemolytic fluids to be hyperosmotic to the surrounding aqueous environment. Significant differences were found when different PSS were used, emphasizing the importance of using a suitable PSS to reduce additional osmotic stress. Using PSS in the NRR assay that do not exert additional damage to lysosomal membrane integrity will help to more accurately quantify the effects of exposure to pollutants on the organism(s) under investigation.
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Affiliation(s)
- B M Coughlan
- Environmental Research Institute, University College Cork, Cork, Ireland.
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Krywka C, Sternemann C, Paulus M, Tolan M, Royer C, Winter R. Effect of Osmolytes on Pressure-Induced Unfolding of Proteins: A High-Pressure SAXS Study. Chemphyschem 2008; 9:2809-15. [DOI: 10.1002/cphc.200800522] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Santivarangkna C, Higl B, Foerst P. Protection mechanisms of sugars during different stages of preparation process of dried lactic acid starter cultures. Food Microbiol 2008; 25:429-41. [DOI: 10.1016/j.fm.2007.12.004] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 12/16/2007] [Accepted: 12/30/2007] [Indexed: 11/29/2022]
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Chebotareva NA, Meremyanin AV, Makeeva VF, Livanova NB, Kurganov BI. Cooperative self-association of phosphorylase kinase from rabbit skeletal muscle. Biophys Chem 2008; 133:45-53. [DOI: 10.1016/j.bpc.2007.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Revised: 12/03/2007] [Accepted: 12/04/2007] [Indexed: 11/15/2022]
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Koumoto K, Ochiai H, Sugimoto N. Structural effect of synthetic zwitterionic cosolutes on the stability of DNA duplexes. Tetrahedron 2008. [DOI: 10.1016/j.tet.2007.10.060] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Okazaki RK, Gillins MA, Duerden BJ, Hodges C, Record NR. Osmotic induction of stress proteins in nemerteans. J NAT HIST 2006. [DOI: 10.1080/00222930600834196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Somero GN. Protein adaptations to temperature and pressure: complementary roles of adaptive changes in amino acid sequence and internal milieu. Comp Biochem Physiol B Biochem Mol Biol 2003; 136:577-91. [PMID: 14662287 DOI: 10.1016/s1096-4959(03)00215-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Retention of required structural and functional properties of proteins in species adapted to different temperatures and pressures is achieved through variation in amino acid sequence and accumulation of small organic solutes that stabilize protein traits. Conservation of ligand binding and catalytic rate can be achieved by minor differences in sequence. For orthologs of lactate dehydrogenase-A (A(4)-LDH) temperature adaptation may involve only a single amino acid substitution. Adaptation involves changes in conformational mobility of regions of A(4)-LDH that undergo movement during ligand binding, movements that are rate-limiting to catalysis. A model that integrates adaptations in sequence and intracellular milieu is developed on the basis of conformational microstates. Although orthologs of different thermally adapted species vary in stability, at physiological temperatures it is hypothesized that a similar ensemble of conformational microstates exists for all orthologs. Organic solutes stabilize this ensemble of microstates. Differences among orthologs in responses to organic solutes at a common temperature lead to similar responses at normal body temperatures. Because protein stability increases at high protein concentrations, intrinsic stabilities of proteins may reflect the protein concentrations of the cellular compartments in which they occur. Protein-stabilizing solutes like trimethylamine-N-oxide (TMAO) conserve protein function and structure at elevated hydrostatic pressures.
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Affiliation(s)
- George N Somero
- Department of Biological Sciences, Hopkins Marine Station, Stanford University, Oceanview Blvd, Pacific Grove, CA 93950, USA.
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Kinsey ST, Lee BC. The effects of rapid salinity change on in vivo arginine kinase flux in the juvenile blue crab, Callinectes sapidus. Comp Biochem Physiol B Biochem Mol Biol 2003; 135:521-31. [PMID: 12831772 DOI: 10.1016/s1096-4959(03)00121-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The effect of acclimation salinity and salinity changes on the concentration of high-energy phosphate metabolites and arginine kinase (AK) flux was examined in vivo in juvenile blue crabs using 31P-nuclear magnetic resonance (NMR). Crabs were acclimated for 7 days to a salinity of 5 or 35 per thousand and then placed in a flow apparatus that could sustain the animals while NMR spectra were acquired. Crabs were subjected to either hyperosmotic salinity changes, where an animal acclimated to 5 per thousand was exposed to a salinity of 35 per thousand, or hyposmotic changes, which involved the reciprocal exchange. Neither acclimation salinity nor salinity change had a significant effect on the concentrations of arginine phosphate, inorganic phosphate or ATP. 31P-NMR saturation transfer experiments were used to determine the effect of salinity on the forward and reverse flux of the AK reaction. There was no significant effect of acclimation salinity or salinity change on the flux rate through this reaction. This is in contrast to previous results, which showed that AK flux in isolated muscle was sensitive to prevailing osmotic conditions (Holt and Kinsey, J. Exp. Biol. 205 (2002) 1775-1785). The present study indicates that the integrated osmoregulatory capacity of the intact animal is sufficient to preserve cellular energy status and enzyme function during acute salinity changes.
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Affiliation(s)
- Stephen T Kinsey
- Department of Biological Sciences, University of North Carolina at Wilmington, 601 South College Road, 28403-5915, Wilmington, NC, USA.
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Yancey PH, Blake WR, Conley J. Unusual organic osmolytes in deep-sea animals: adaptations to hydrostatic pressure and other perturbants. Comp Biochem Physiol A Mol Integr Physiol 2002; 133:667-76. [PMID: 12443924 DOI: 10.1016/s1095-6433(02)00182-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Shallow-living marine invertebrates use free amino acids as cellular osmolytes, while most teleosts use almost no organic osmolytes. Recently we found unusual osmolyte compositions in deep-sea animals. Trimethylamine N-oxide (TMAO) increases with depth in muscles of some teleosts, skates, and crustaceans (up to 300 mmol/kg at 2900 m). Other deep-sea animals had high levels of (1). scyllo-inositol in echinoderms, gastropods, and polychaetes, (2). that polyol plus beta-alanine and betaine in octopods, (3). hypotaurine, N-methyltaurine, and unidentified methylamines in vestimentiferans from hydrothermal vents and cold seeps, and (4). a depth-correlated serine-phosphate osmolyte in vesicomyid clams from trench seeps. We hypothesize that some of these solutes counteract effects of hydrostatic pressure. With lactate dehydrogenase, actin, and pyruvate kinase, 250 mM TMAO (but not glycine) protected both ligand binding and protein stability against pressure. To test TMAO in living cells, we grew yeast under pressure. After 1 h at 71 MPa, 3.5 h at 71 MPa, and 17 h at 30 MPa, 150 mM TMAO generally doubled the number of cells that formed colonies. Sulfur-based osmolytes which are not correlated with depth, such as hypotaurine and thiotaurine, are probably involved in sulfide metabolism and detoxification. Thus deep-sea osmolytes may have at least two other roles beyond acting as simple compatible osmotica.
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Affiliation(s)
- Paul H Yancey
- Biology Department, Whitman College, Walla Walla, WA 99362, USA.
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Ferraris JD, GarcÍa-Pérez A. Osmotically Responsive Genes: The Mammalian Osmotic Response Element (ORE)1. ACTA ACUST UNITED AC 2001. [DOI: 10.1668/0003-1569(2001)041[0734:orgtmo]2.0.co;2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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