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Selective flexible packaging pathways of the segmented genome of influenza A virus. Nat Commun 2020; 11:4355. [PMID: 32859915 PMCID: PMC7455735 DOI: 10.1038/s41467-020-18108-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
The genome of influenza A viruses (IAV) is encoded in eight distinct viral ribonucleoproteins (vRNPs) that consist of negative sense viral RNA (vRNA) covered by the IAV nucleoprotein. Previous studies strongly support a selective packaging model by which vRNP segments are bundling to an octameric complex, which is integrated into budding virions. However, the pathway(s) generating a complete genome bundle is not known. We here use a multiplexed FISH assay to monitor all eight vRNAs in parallel in human lung epithelial cells. Analysis of 3.9 × 105 spots of colocalizing vRNAs provides quantitative insights into segment composition of vRNP complexes and, thus, implications for bundling routes. The complexes rarely contain multiple copies of a specific segment. The data suggest a selective packaging mechanism with limited flexibility by which vRNPs assemble into a complete IAV genome. We surmise that this flexibility forms an essential basis for the development of reassortant viruses with pandemic potential.
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Munder MC, Midtvedt D, Franzmann T, Nüske E, Otto O, Herbig M, Ulbricht E, Müller P, Taubenberger A, Maharana S, Malinovska L, Richter D, Guck J, Zaburdaev V, Alberti S. A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy. eLife 2016; 5. [PMID: 27003292 PMCID: PMC4850707 DOI: 10.7554/elife.09347] [Citation(s) in RCA: 282] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 02/13/2016] [Indexed: 01/19/2023] Open
Abstract
Cells can enter into a dormant state when faced with unfavorable conditions. However, how cells enter into and recover from this state is still poorly understood. Here, we study dormancy in different eukaryotic organisms and find it to be associated with a significant decrease in the mobility of organelles and foreign tracer particles. We show that this reduced mobility is caused by an influx of protons and a marked acidification of the cytoplasm, which leads to widespread macromolecular assembly of proteins and triggers a transition of the cytoplasm to a solid-like state with increased mechanical stability. We further demonstrate that this transition is required for cellular survival under conditions of starvation. Our findings have broad implications for understanding alternative physiological states, such as quiescence and dormancy, and create a new view of the cytoplasm as an adaptable fluid that can reversibly transition into a protective solid-like state.
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Affiliation(s)
| | - Daniel Midtvedt
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Titus Franzmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Oliver Otto
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Maik Herbig
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Elke Ulbricht
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Paul Müller
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Anna Taubenberger
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Shovamayee Maharana
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Liliana Malinovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jochen Guck
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Williamson DM, Elferich J, Shinde U. Mechanism of Fine-tuning pH Sensors in Proprotein Convertases: IDENTIFICATION OF A pH-SENSING HISTIDINE PAIR IN THE PROPEPTIDE OF PROPROTEIN CONVERTASE 1/3. J Biol Chem 2015; 290:23214-25. [PMID: 26229104 DOI: 10.1074/jbc.m115.665430] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Indexed: 12/15/2022] Open
Abstract
The propeptides of proprotein convertases (PCs) regulate activation of cognate protease domains by sensing pH of their organellar compartments as they transit the secretory pathway. Earlier experimental work identified a conserved histidine-encoded pH sensor within the propeptide of the canonical PC, furin. To date, whether protonation of this conserved histidine is solely responsible for PC activation has remained unclear because of the observation that various PC paralogues are activated at different organellar pH values. To ascertain additional determinants of PC activation, we analyzed PC1/3, a paralogue of furin that is activated at a pH of ∼5.4. Using biophysical, biochemical, and cell-based methods, we mimicked the protonation status of various histidines within the propeptide of PC1/3 and examined how such alterations can modulate pH-dependent protease activation. Our results indicate that whereas the conserved histidine plays a crucial role in pH sensing and activation of this protease an additional histidine acts as a "gatekeeper" that fine-tunes the sensitivity of the PC1/3 propeptide to facilitate the release inhibition at higher proton concentrations when compared with furin. Coupled with earlier analyses that highlighted the enrichment of the amino acid histidine within propeptides of secreted eukaryotic proteases, our work elucidates how secreted proteases have evolved to exploit the pH of the secretory pathway by altering the spatial juxtaposition of titratable groups to regulate their activity in a spatiotemporal fashion.
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Affiliation(s)
- Danielle M Williamson
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239
| | - Johannes Elferich
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239
| | - Ujwal Shinde
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239
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Naiyer A, Hassan MI, Islam A, Sundd M, Ahmad F. Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques. J Biomol Struct Dyn 2015; 33:2267-84. [PMID: 25586676 DOI: 10.1080/07391102.2014.999354] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Almost all proteins fold via a number of partially structured intermediates such as molten globule (MG) and pre-molten globule states. Understanding the structure of these intermediates at atomic level is often a challenge, as these states are observed under extreme conditions of pH, temperature, and chemical denaturants. Furthermore, several other processes such as chemical modification, site-directed mutagenesis (or point mutation), and cleavage of covalent bond of natural proteins often lead to MG like partially unfolded conformation. However, the dynamic nature of proteins in these states makes them unsuitable for most structure determination at atomic level. Intermediate states studied so far have been characterized mostly by circular dichroism, fluorescence, viscosity, dynamic light scattering measurements, dye binding, infrared techniques, molecular dynamics simulations, etc. There is a limited amount of structural data available on these intermediate states by nuclear magnetic resonance (NMR) and hence there is a need to characterize these states at the molecular level. In this review, we present characterization of equilibrium intermediates by biophysical techniques with special reference to NMR.
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Affiliation(s)
- Abdullah Naiyer
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi - 110025 , India
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Axelsson J, Öberg CM, Rippe A, Krause B, Rippe B. Size-selectivity of a synthetic high-flux and a high cut-off dialyzing membrane compared to that of the rat glomerular filtration barrier. J Memb Sci 2012. [DOI: 10.1016/j.memsci.2012.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Qi PX, Nuñez A, Wickham ED. Reactions between β-lactoglobulin and genipin: kinetics and characterization of the products. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:4327-4335. [PMID: 22463374 DOI: 10.1021/jf300311k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this paper, we present the first detailed study of the reaction kinetics and the characterization of the products from the endothermic reactions between β-lactoglobulin and genipin. The effects of the concentration, temperature, and pH were investigated. In the temperature range studied, the reaction was approximately a pseudo-first-order with respect to genipin and 0.22-order and -0.24-order with respect to β-lactoglobulin for pH 6.75 and 10.5 with corresponding activation energy (E(a)) estimated to be 66.2 ± 3.8 and 9.40 ± 0.36 kJ/mol, respectively. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis studies, validated by matrix-assisted laser desorption ionization-time of flight mass spectrometry, showed the presence of oligomeric, i.e., di-, tri-, quadri-, and pentameric, forms of cross-linked β-lactoglobulin by genipin at neutral but not alkaline pH; however, an extensive cross-linked network was not observed, consistent with the atomic force microscopy images. It was demonstrated that the reaction temperature and the concentration of genipin but not that of β-lactoglobulin positively affected the extent of the cross-linking reactions.
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Affiliation(s)
- Phoebe X Qi
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center-ERRC, Agricultural Research Service-ARS, United States Department of Agriculture-USDA, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19038, USA.
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7
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Printz M, Kalonia DS, Friess W. Individual Second Virial Coefficient Determination of Monomer and Oligomers in Heat-Stressed Protein Samples Using Size-Exclusion Chromatography-Light Scattering. J Pharm Sci 2012; 101:363-72. [DOI: 10.1002/jps.22749] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 08/03/2011] [Accepted: 08/12/2011] [Indexed: 11/11/2022]
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8
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Ahmad SS, Dalby PA. Thermodynamic parameters for salt-induced reversible protein precipitation from automated microscale experiments. Biotechnol Bioeng 2010; 108:322-32. [DOI: 10.1002/bit.22957] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Seo JA, Hédoux A, Guinet Y, Paccou L, Affouard F, Lerbret A, Descamps M. Thermal denaturation of beta-lactoglobulin and stabilization mechanism by trehalose analyzed from Raman spectroscopy investigations. J Phys Chem B 2010; 114:6675-84. [PMID: 20411964 DOI: 10.1021/jp1006022] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The thermal denaturation process of beta-lactoglobulin has been analyzed in the 20-100 degrees C temperature range by Raman spectroscopy experiments simultaneously performed in the region of amide modes (800-1800 cm(-1)) and in the low-frequency range (10-350 cm(-1)). The analysis of amide modes reveals a two-step thermal denaturation process in the investigated temperature range. The first step corresponds to the dissociation of dimers associated with an increase of flexibility of the tertiary structure. In the second step, large conformational changes are detected in the secondary structure and described as a loss of alpha-helix structures and a concomitant formation of beta-sheets. Raman investigations in the low-frequency range provide important information on the origin of the denaturation process through the analysis of the solvent dynamics and its coupling with that of the protein. The softening of the tetrahedral structure of water induces the dissociation of dimers and makes the tertiary structure softer, leading to the water penetration in the protein interior. The methodology based on Raman investigations of amide modes and in the low-frequency region was used to analyze the mechanism of beta-lactoglobulin thermostabilization by trehalose. The main effect of trehalose is determined to be related to its capabilities to distort the tetrahedral organization of water molecules.
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Affiliation(s)
- Jeong-Ah Seo
- Unité Matériaux Et Transformations, UMR CNRS 8207, Université de Lille 1, 59655 Villeneuve d Ascq Cédex, France
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Lau EY, Krishnan VV. Temperature dependence of protein-hydration hydrodynamics by molecular dynamics simulations. Biophys Chem 2007; 130:55-64. [PMID: 17720293 DOI: 10.1016/j.bpc.2007.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 07/14/2007] [Accepted: 07/18/2007] [Indexed: 11/19/2022]
Abstract
The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.
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Affiliation(s)
- Edmond Y Lau
- Biology and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
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11
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Korolev VP, Kustov AV, Bekeneva AV. Thermodynamics of interaction of L-α-phenylalanine with urea and dimethylformamide in aqueous solution. RUSS J GEN CHEM+ 2007. [DOI: 10.1134/s1070363207070159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Affiliation(s)
- Valerie Daggett
- Department of Medicinal Chemistry, Box 357610, University of Washington, Seattle, Washington 98195-7610, USA
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13
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Esakova OA, Meshalkina LE, Kochetov GA. Effects of transketolase cofactors on its conformation and stability. Life Sci 2005; 78:8-13. [PMID: 16125202 DOI: 10.1016/j.lfs.2004.12.055] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2004] [Accepted: 12/14/2004] [Indexed: 11/24/2022]
Abstract
In studying transketolase (TK) from Saccharomyces cerevisiae, the majority of researchers use as cofactors Mg(2+) and thiamine diphosphate (ThDP) (by analogy with other ThDP-dependent enzymes), whereas the active site of native holoTK is known to contain only Ca(2+). Experiments in which Mg(2+) was substituted for Ca(2+) demonstrated that the kinetic properties of TK varied with the bivalent cation cofactor. This led to the assumption that TK species obtained by reconstitution from apoTK and ThDP in the presence of Ca(2+) or Mg(2+), respectively, adopt different conformations. Kinetic study of the H103A mutant yeast transketolase. FEBS Letters 567, 270-274]. Analysis of far-UV circular dichroism (CD) spectra and of data, obtained using methods of thermal denaturing, differential scanning calorimetry (DSC) and tryptophan fluorescence spectroscopy, corroborated this assumption. Indeed, the ratios of secondary structure elements in the molecule of apoTK, recorded in the presence of Ca(2+) or Mg(2+), respectively, turned out to be different. The two forms of the holoenzyme, obtained by reconstitution from apoTK and ThDP in the presence of Ca(2+) or Mg(2+), respectively, also differed in stability: the holoenzyme was more stable in the presence of Ca(2+) than Mg(2+).
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Affiliation(s)
- Olga A Esakova
- A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, GSP-2, Russia
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14
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Gosal WS, Clark AH, Ross-Murphy SB. Fibrillar β-Lactoglobulin Gels: Part 3. Dynamic Mechanical Characterization of Solvent-Induced Systems. Biomacromolecules 2004; 5:2430-8. [PMID: 15530060 DOI: 10.1021/bm0496615] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oscillatory shear rheometry has been used to study the gelation of beta-lactoglobulin at ambient in 50% v/v trifluoroethanol (TFE)/pH 7 aqueous buffer and in 50% v/v ethanol (EtOH)/water at pH 2. In contrast to what was found on heating aqueous solutions at pH 2 (Part 2 of this series), a more expected "chemical gelation"-like profile was found with modulus components G' and G' ' crossing over as the gels formed and then with G' ' passing through a maximum. In addition, for the EtOH system, there was a significant modulus increase at long time, suggestive of a more complex two-step aggregation scheme. Modulus-concentration relationships were obtained for both systems by extrapolating cure data to infinite time. For the TFE gels, this data was accurately described by classical branching theory, although it could also be approximated by a constant power--law relationship. Only the latter described the modulus--concentration data for the gels in ethanol, but there were problems here of greater frequency dependence of the modulus values and much less certain extrapolation. Gel times for the TFE systems showed higher power laws in the concentration than could be explained by the branching theory in its simplest form being similar, in this respect, to the heat-set systems at pH 2. Such power laws were harder to establish for the EtOH gels as for these there was evidence of gel time divergence close to a critical concentration. Reduced G'/G'inf versus t/tgel data were difficult to interpret for the gels in ethanol, but for the TFE system they were consistent with previous results for the heat-set gels and approximated master curve superposition. The frequency and temperature dependences of the final gel moduli were also studied. In general, the networks induced by alcohols appeared more flexible than those obtained by heating.
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Affiliation(s)
- Walraj S Gosal
- Department of Life Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NN, United Kingdom
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15
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Kim HJ, Decker EA, McClements DJ. Comparison of droplet flocculation in hexadecane oil-in-water emulsions stabilized by beta-lactoglobulin at pH 3 and 7. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2004; 20:5753-8. [PMID: 16459589 DOI: 10.1021/la048899b] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The influence of surface and thermal denaturation of adsorbed beta-lactoglobulin (beta-Lg) on the flocculation of hydrocarbon oil droplets was measured at pH 3 and compared with that at pH 7. Oil-in-water emulsions (5 wt % n-hexadecane, 0.5 wt % beta-Lg, pH 3.0) were prepared that contained different levels of salt (0-150 mM NaCl) added immediately after homogenization. The mean particle diameter (d43) and particle size distribution of diluted emulsions were measured by laser diffraction when they were either (i) stored at 30 degrees C for 48 h or (ii) subjected to different thermal treatments (30-95 degrees C for 20 min). In the absence of salt, little droplet flocculation was observed at pH 3 or 7 because of the strong electrostatic repulsion between the droplets. In the presence of 150 mM NaCl, a progressive increase in mean particle size with time was observed in pH 7 emulsions during storage at 30 degrees C, but no significant change in mean particle diameter with time (d43 approximately 1.4 +/- 0.2 microm) was observed in the pH 3 emulsions. Droplet aggregation became more extensive in pH 7 emulsions containing salt (added before thermal processing) when they were heated above 70 degrees C, which was attributed to thermal denaturation of adsorbed beta-Lg leading to interdroplet disulfide bond formation. In contrast, the mean particle size decreased and the creaming stability improved when pH 3 emulsions were heated above 70 degrees C. These results suggest that the droplets in the pH 3 emulsions were weakly flocculated at temperatures below the thermal denaturation temperature of beta-Lg (T < 70 degrees C) but that flocs did not form so readily above this temperature, which was attributed to a reduction in droplet surface hydrophobicity due to protein conformational changes. The most likely explanation for the difference in behavior of the emulsions is that disulfide bond formation occurs much more readily at pH 7 than at pH 3.
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Affiliation(s)
- H J Kim
- Biopolymers and Colloids Research Laboratory, Department of Food Science, University of Massachusetts, Amherst, Massachusetts 01003, USA
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16
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Dufour E, Hervé G, Haertle T. Hydrolysis of β-lactoglobulin by thermolysin and pepsin under high hydrostatic pressure. Biopolymers 2004. [DOI: 10.1002/bip.360350506] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Bennion BJ, Daggett V. The molecular basis for the chemical denaturation of proteins by urea. Proc Natl Acad Sci U S A 2003; 100:5142-7. [PMID: 12702764 PMCID: PMC154312 DOI: 10.1073/pnas.0930122100] [Citation(s) in RCA: 635] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2003] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics simulations of the protein chymotrypsin inhibitor 2 in 8 M urea at 60 degrees C were undertaken to investigate the molecular basis of chemical denaturation. The protein unfolded rapidly under these conditions, but it retained its native structure in a control simulation in water at the same temperature. The overall process of unfolding in urea was similar to that observed in thermal denaturation simulations above the protein's T(m) of 75 degrees C. The first step in unfolding was expansion of the hydrophobic core. Then, the core was solvated by water and later by urea. The denatured structures in both urea and at high temperature contained residual native helical structure, whereas the beta-structure was completely disrupted. The average residence time for urea around hydrophilic groups was six times greater than around hydrophobic residues and in all cases greater than the corresponding water residence times. Water self-diffusion was reduced 40% in 8 M urea. Urea altered water structure and dynamics, thereby diminishing the hydrophobic effect and encouraging solvation of hydrophobic groups. In addition, through urea's weakening of water structure, water became free to compete with intraprotein interactions. Urea also interacted directly with polar residues and the peptide backbone, thereby stabilizing nonnative conformations. These simulations suggest that urea denatures proteins via both direct and indirect mechanisms.
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Affiliation(s)
- Brian J Bennion
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, USA
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18
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Pace NC, Tanford C. Thermodynamics of the unfolding of β-lactoglobulin A in aqueous urea solutions between 5 and 55°. Biochemistry 2002; 7:198-208. [PMID: 5758543 DOI: 10.1021/bi00841a025] [Citation(s) in RCA: 182] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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D'Alfonso L, Collini M, Baldini G. Does beta-lactoglobulin denaturation occur via an intermediate state? Biochemistry 2002; 41:326-33. [PMID: 11772032 DOI: 10.1021/bi0115028] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The denaturation of beta-lactoglobulin (BLG) in the presence of urea and GuHCl has been investigated at different pH values with various spectroscopic techniques. The equilibrium denaturation free energy values, obtained by linearly extrapolating the data to vanishing denaturant (DeltaG(D)(H2O)), are compared and discussed. The fit of the spectroscopic data monitoring the denaturation of BLG has been approached, at first, with a two-state model that describes the protein transition from the folded state (at each pH and in the absence of denaturant) to the denatured state, but in particular, along the GuHCl denaturation pathway some evidence is found of the presence of an intermediate state. Time-resolved fluorescence experiments performed on the BLG-ANS (1-anilino-8-naphthalenesulfonate) complex help to understand the results. Fluorescence polarization anisotropy (FPA) measurements accompanying the denaturation process show the presence of a fast rotational diffusion of the ANS probe, and the data are interpreted in terms of local fluctuations of a still structured tract of the denatured protein where the probe is bound.
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Affiliation(s)
- Laura D'Alfonso
- Università degli Studi di Milano-Bicocca and INFM UdR Milano-Bicocca, P.za della Scienza, 3 I-20126 Milano, Italy
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20
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Timasheff SN. Control of protein stability and reactions by weakly interacting cosolvents: the simplicity of the complicated. ADVANCES IN PROTEIN CHEMISTRY 1998; 51:355-432. [PMID: 9615174 DOI: 10.1016/s0065-3233(08)60656-7] [Citation(s) in RCA: 436] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- S N Timasheff
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02254-9110, USA
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21
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Das M, Dasgupta D. Enhancement of transcriptional activity of T7 RNA polymerase by guanidine hydrochloride. FEBS Lett 1998; 427:337-40. [PMID: 9637252 DOI: 10.1016/s0014-5793(98)00458-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
T7 RNA polymerase shows an increase in processive transcription in the presence of low concentrations of guanidine hydrochloride (GdnCl) upto 60 mM, which is not observed when the enzyme is treated with urea. Higher concentrations of the denaturant lead to a progressive loss in the processive transcriptional activity of the enzyme. We have attempted to explain the above phenomenon in terms of the structural change in the enzyme. Fluorescence and CD studies suggest that the tertiary structure of the native enzyme undergoes an alteration upon addition of low concentration of guanidine hydrochloride. This is also indicated from the decreased susceptibility of the enzyme to limited proteolysis by trypsin.
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Affiliation(s)
- M Das
- Biophysics Division, Saha Institute of Nuclear Physics, Calcutta, India.
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22
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BECKWEITH AC, WALL JS, DIMLER RJ. AMIDE GROUPS AS INTERACTION SITES IN WHEAT GLUTEN PROTEINS: EFFECTS OF AMIDE-ESTER CONVERSION. Arch Biochem Biophys 1996; 103:319-30. [PMID: 14099542 DOI: 10.1016/0003-9861(63)90421-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Angelova M, Dimov N. Effect of mobile phase composition on selectivity in preparative hydrophobic interaction chromatographic purification of glucagon. Biomed Chromatogr 1996; 10:251-5. [PMID: 8879534 DOI: 10.1002/(sici)1099-0801(199609)10:5<251::aid-bmc601>3.0.co;2-o] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A weakly hydrophobic acrylester copolymer, Amberlite XAD-7, has been used in the purification process of glucagon production for elimination of protein impurities in the crude glucagon fractions, obtained from the industrial waste from insulin production. Varying the mobile phases composition, it was shown that suitable selectivity for the separation of proteins under non-denaturing conditions can be achieved. The purified glucagon, obtained at the proposed chromatographic conditions has a biological activity of above 1 IU/mg.
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Affiliation(s)
- M Angelova
- Chemical Pharmaceutical Research Institute, NIHFI, Sofia, Bulgaria
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24
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de Frutos M, Cifuentes A, Diez-Masa JC. Behavior of whey proteins in hydrophobic interaction chromatography. ACTA ACUST UNITED AC 1996. [DOI: 10.1002/jhrc.1240190910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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25
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Dufour E, Hoa GH, Haertlé T. High-pressure effects on beta-lactoglobulin interactions with ligands studied by fluorescence. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1206:166-72. [PMID: 8003521 DOI: 10.1016/0167-4838(94)90204-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The effects of pressure (0.1 MPa to 400 MPa) on intrinsic fluorescence of beta-lactoglobulin and on its binding of retinol and cis-parinaric acid have been studied at neutral and acid pHs. In neutral pH, fluorescence emission spectra of beta-lactoglobulin tryptophanes are characterized by an irreversible 14 nm red-shift indicating pressure-induced folding changes. The intensity of the fluorescence of retinol in beta-lactoglobulin-retinol complex is enhanced by a pressure increase up to 150 MPa. It decreases at higher pressures and disappears altogether at 300 MPa. beta-Lactoglobulin-retinol complex does not reassociate after decompression at neutral pH. At acid pH condition, the fluorescence quenching by pressure of beta-lactoglobulin tryptophans is coupled with a 2 nm spectral shift and is fully reversible demonstrating almost complete restoration of globulin folding. The evolution of retinol fluorescence in beta-lactoglobulin-retinol complex is also entirely reversible between 0.1 MPa and 400 MPa and the complex never dissociates in the studied pressure range. beta-lactoglobulin-cis-parinaric acid complexes at neutral and acid pH values dissociate irreversibly at 200 MPa and 350 MPa, respectively.
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Affiliation(s)
- E Dufour
- L.E.I.M.A. Institut National de la Recherche Agronomique, Nantes, France
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26
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Dufour E, Genot C, Haertlé T. beta-Lactoglobulin binding properties during its folding changes studied by fluorescence spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1205:105-12. [PMID: 8142474 DOI: 10.1016/0167-4838(94)90098-1] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The milk protein, beta-lactoglobulin (BLG) exhibits structural and binding properties which vary widely, depending on the medium. These properties of BLG are reflected in fluorescence intensities, steady-state anisotropies and phase lifetimes of BLG tryptophan residues and of retinol and diphenyl hexatriene (DPH) bound to BLG, as functions of pH, ethanol concentration and protein modifications (22% ethylated, 90% methylated and 85% acetylated BLGs). Tryptophan quenching experiments show that retinol and DPH bind to BLG in 1:1 molar ratios with apparent dissociation constants around 10(-7) - 10(-8) M. The strength of retinol binding is pH-dependent in the range 3-8, whereas that of DPH binding is not. Two different binding sites for these two ligands coexist on the protein. Modified BLGs exhibit higher affinities for DPH than the unmodified protein. At all pH values investigated, the fluorescence emission at 480 nm of retinol/BLG mixtures and retinol, DPH and tryptophan anisotropies and lifetimes change dramatically with midpoint at 27% ethanol for the first parameter and 35% for the others, suggesting simultaneous beta-strand to alpha-helix transition and the dissociation of BLG complexes at 35% ethanol. An intermediate state, possibly 'molten globular', occurs around 20% ethanol, as deduced from anisotropy and lifetime measurements.
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Affiliation(s)
- E Dufour
- L.E.I.M.A.-Institut National de la Recherche Agronomique, Nantes, France
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27
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Dufour E, Haertlé T. Temperature-induced folding changes of beta-lactoglobulin in hydro-methanolic solutions. Int J Biol Macromol 1993; 15:293-7. [PMID: 8251444 DOI: 10.1016/0141-8130(93)90029-l] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
It has been demonstrated using circular dichroism that methanol induces important structural changes of beta-lactoglobulin (BLG). The secondary structure of BLG dissolved in 45% methanol (v/v) at 30 degrees C (dielectric constant epsilon approximately 50) is predominantly alpha-helical and unable to complex retinol any more. However, when the dielectric constant of such a medium is raised back to epsilon approximately 70 by decreasing the temperature, both the refolding of BLG into a beta-structure and the formation of the retinol/BLG complex are observed. On the other hand, in the case of BLG solution in 30% methanol, the decrease of the dielectric constant from epsilon approximately 69 to epsilon approximately 53 by heating from 20 degrees C to 60 degrees C leads to the transition from a predominantly beta-structure into a predominantly random one and the dissociation of the retinol/BLG complex. The reversibility of the conformation changes by cooling was demonstrated by circular dichroism curves and tryptophan fluorescence. The retinol fluorescence intensity could not be completely recovered.
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Affiliation(s)
- E Dufour
- LEIMA, Institut National de la Recherche Agronomique, Nantes, France
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28
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Frapin D, Dufour E, Haertle T. Probing the fatty acid binding site of beta-lactoglobulins. JOURNAL OF PROTEIN CHEMISTRY 1993; 12:443-9. [PMID: 8251064 DOI: 10.1007/bf01025044] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The interactions of fatty acids with porcine and bovine beta-lactoglobulins were measured using tryptophan fluorescence enhancement. In the case of bovine beta-lactoglobulin, the apparent binding constants for most of the saturated and unsaturated fatty acids were in the range of 10(-7) M at neutral pH. Bovine beta-lactoglobulin displays only one high affinity binding site for palmitate with an apparent dissociation constant of 1 x 10(-7) M. The strength of the binding was decreasing in the following way: palmitate > stearate > myristate > arachidonate > laurate. Caprylic and capric acids are not bound at all. The affinity of beta-lactoglobulin for palmitate decreased as the pH of the incubation medium was lowered and BLG/palmitate complex was not observed at pH's lower than 4.5. Surprisingly, chemically modified bovine beta-lactoglobulin and porcine beta-lactoglobulin did not bind fatty acids in the applied conditions.
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Affiliation(s)
- D Frapin
- LEIMA, Institut National de la Recherche Agronomique, Nantes, France
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29
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Dufour E, Bertrand-Harb C, Haertlé T. Reversible effects of medium dielectric constant on structural transformation of beta-lactoglobulin and its retinol binding. Biopolymers 1993; 33:589-98. [PMID: 8467066 DOI: 10.1002/bip.360330408] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The secondary structure transformation of beta-lactoglobulin from a predominantly beta-structure into a predominantly alpha-helical one, under the influence of solvent polarity changes is reversible. Independent of the alcohol used--methanol, ethanol, or 2-propanol--the midpoints of the observed structural transformation occur around dielectric constant epsilon approximately 60. The structural change destroying the hydrophobic core formed by the beta-barrel structure leads, at room temperature, to the dissociation of the retinol/beta-lactoglobulin complex in the neighborhood of dielectric constant epsilon approximately 50. However, when the dielectric constant of the medium is raised back to epsilon approximately 70 by the decrease of the temperature, both the refolding of BLG into a beta-structure and the reassociation of the retinol/beta-lactoglobulin complex are observed. The esterification of beta-lactoglobulin carboxyl groups has two effects: on the one hand it accelerates the beta-strand<==>alpha-helix transition induced by alcohols. On the other hand, the esterification of beta-lactoglobulin strengthens its interaction with retinol as it may be deduced from the smaller apparent dissociation constant of retinol/methylated beta-lactoglobulin complex. The binding of retinol to modified or unmodified beta-lactoglobulin has no influence (stabilizing or destabilizing) on the folding changes induced by alcohol.
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Affiliation(s)
- E Dufour
- LEIMA, Institut National de la Recherche Agronomique, Nantes, France
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30
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Shibata A, Yamamoto M, Yamashita T, Chiou JS, Kamaya H, Ueda I. Biphasic effects of alcohols on the phase transition of poly(L-lysine) between alpha-helix and beta-sheet conformations. Biochemistry 1992; 31:5728-33. [PMID: 1610821 DOI: 10.1021/bi00140a006] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Poly(L-lysine) exists as a random-coil at neutral pH, an alpha-helix at alkaline pH, and a beta-sheet when the alpha-helix poly(L-lysine) is heated. The present Fourier-transform infrared (FTIR) study showed that short-chain alcohols (methanol, ethanol, and 2-propanol) partially transformed alpha-helix poly(L-lysine) to beta-sheet when their concentrations were low. At higher concentrations, however, these alcohols reversed the reaction, and the alcohol-induced beta-sheet was transformed back to alpha-helix structure. The reversal occurred at 1.40 M methanol, 0.96 M ethanol, and 0.55 M 2-propanol. The alcohol effects on the secondary structure were further investigated by circular dichroism (CD) on the thermally induced beta-sheet poly(L-lysine). Methanol, ethanol, and 1-propanol, but not 1-butanol, shifted the negative mean-residue ellipticity at 217 nm of the beta-sheet poly(L-lysine) to the positive side at low concentrations of the alcohols and to the negative side at high concentrations. With 1-butanol, only the positive-side shift was observed. The positive-side shift at low concentrations of alcohols indicates enhancement of the hydrophobic interactions among the side chains of the polypeptide in the beta-sheet conformation. The negative-side shift indicates a partial transformation to alpha-helix. The shift from the positive to negative side occurred at 7.1 M methanol, 4.6 M ethanol, and 3.1 M 1-propanol. The alcohol concentrations for the beta-to-alpha transition were higher in the CD study than in the IR study.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- A Shibata
- Faculty of Pharmaceutical Sciences, Tokushima University, Japan
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Watson DK, Moudrianakis EN. Histone-dependent reconstitution and nucleosomal localization of a nonhistone chromosomal protein: the H2A-specific protease. Biochemistry 1982; 21:248-56. [PMID: 7041960 DOI: 10.1021/bi00531a008] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We have described earlier a chromatin-bound protease with unique specificity for histone H2A [Eickbush, T. H., Watson, D. K., & Moudrianakis, E. N. (1976) Cell (Cambridge, Mass.) 9, 785--792]. In the present study, we explore the nature of interactions that form and stabilize the enzyme-chromatin system by using the activity of the protease to monitor its binding to DNA and DNA-histone complexes. During salt extraction of chromatin, the protease is released at an ionic strength between that required for the extraction of the slightly lysine-rich histones (H2A and H2B) and the arginine-rich histones (H3 and H4). The reassociation of this nonhistone protein to DNA has an absolute requirement for the H3--H4 tetramer and is only enhanced by the H2A--H2B dimer in the presence of the tetramer. We believe that the binding of the enzyme onto DNA requires some histone-elicited compaction of the helix. We have also examined the distribution of this enzyme within the chromatin fiber by isolating pools of monomer nucleosomes from micrococcal nuclease digests of 0.6 M NaCl extracted chromatin and from reconstituted DNA-protein complexes. The H2A-protease is found with these monomer nucleosome pools, and no activity can be detected in the low molecular weight products released during the digestion. Thus, by virtue of its extraction characteristics from chromatin and its association with isolated nucleosomes, this nonhistone protein exhibits properties hitherto assigned only to the inner histones.
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Pace CN, Marshall HF. A comparison of the effectiveness of protein denaturants for beta-lactoglobulin and ribonuclease. Arch Biochem Biophys 1980; 199:270-6. [PMID: 7356334 DOI: 10.1016/0003-9861(80)90281-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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PRADIPASENA PASAWADEE, RHA CHOKYUN. PSEUDOPLASTIC AND RHEOPECTIC PROPERTIES OF A GLOBULAR PROTEIN (?-LACTOGLOBULIN) SOLUTION. J Texture Stud 1977. [DOI: 10.1111/j.1745-4603.1977.tb01184.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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35
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Eftink MR, Zajicek JL, Ghiron CA. A hydrophobic quencher of protein fluorescence: 2,2,2-trichloroethanol. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 491:473-81. [PMID: 857905 DOI: 10.1016/0005-2795(77)90290-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Previously the neutral fluorescence quenching probe, acrylamide, was employed to determine the degree of exposure of tryptophan residues in proteins. A less polar neutral quencher 2,2,2-trichloroethanol (trichloroethanol) was used in the present work to investigate whether it would preferentially interact with apolar regions of proteins. For most proteins studied, the degree of quenching by trichloroethanol is found to be about the same as with acrylamide. However, for human and bovine serum albumin hydrophobic interactions between trichloroethanol and these proteins occur, leading to an exalted quenching. The fluorescence quencher thus senses the presence of a hydrophobic domain in the vicinity of the tryptophan residues in these proteins. Trichloroethanol is shown to induce conformational changes in certain proteins and to be a potentially useful quencher for proteins having predominantly tyrosine emission.
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Coffman RE, Stavens BW. Solvent-induced EPR anisotropy change of the non-heme chromophore of spinach ferredoxin. Biochem Biophys Res Commun 1970; 41:163-9. [PMID: 4318851 DOI: 10.1016/0006-291x(70)90483-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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39
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Nagwekar JB, Kostenbauder HB. Utilization of a model copolymer to evaluate the contribution of hydrophobic bonding in drug binding. J Pharm Sci 1970; 59:751-7. [PMID: 5423074 DOI: 10.1002/jps.2600590605] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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40
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Arakawa K, Takenaka N, Sasaki K. Ultrasonic Study of Dilute Aqueous Solutions of Urea, Guanidine Hydrochloride and Dioxane. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1970. [DOI: 10.1246/bcsj.43.636] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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41
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Puchtler H, Waldrop FS, Meloan SN, Terry MS, Conner HM. Methacarn (methanol-Carnoy) fixation. Practical and theoretical considerations. HISTOCHEMIE. HISTOCHEMISTRY. HISTOCHIMIE 1970; 21:97-116. [PMID: 4907154 DOI: 10.1007/bf00306176] [Citation(s) in RCA: 168] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Franklin JG, Leslie J. The kinetics of the reaction of n-ethylmaleimide with denatured beta-lactoglobulin and ovalbumin. BIOCHIMICA ET BIOPHYSICA ACTA 1968; 160:333-9. [PMID: 5680265 DOI: 10.1016/0005-2795(68)90206-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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46
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47
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Listowsky I, Betheil JJ, Englard S. Conformation of ferritin and apoferritin in solution. Optical rotatory dispersion properties. Biochemistry 1967; 6:1341-8. [PMID: 6036829 DOI: 10.1021/bi00857a017] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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48
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49
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Kientz ML, Bigelow CC. The effect of ethylene glycol on the structure of beta-lactoglobulin. Biochemistry 1966; 5:3494-500. [PMID: 5972330 DOI: 10.1021/bi00875a015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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50
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Bemis JA, Argus MF, Arcos JC. Studies on the denaturation of biological macromolecules by chemical carcinogens. 3. Optical rotatory dispersion and light-scattering changes of ovalbumin during denaturation and aggregation by water-soluble carcinogens. BIOCHIMICA ET BIOPHYSICA ACTA 1966; 126:274-85. [PMID: 5971853 DOI: 10.1016/0926-6585(66)90064-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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