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Peters J, Oliva R, Caliò A, Oger P, Winter R. Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions. Chem Rev 2023; 123:13441-13488. [PMID: 37943516 DOI: 10.1021/acs.chemrev.3c00432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.
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Affiliation(s)
- Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, 140 rue de la physique, 38400 St Martin d'Hères, France
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France
- Institut Universitaire de France, 75005 Paris, France
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Antonino Caliò
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Philippe Oger
- INSA Lyon, Universite Claude Bernard Lyon1, CNRS, UMR5240, 69621 Villeurbanne, France
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Dortmund, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
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2
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Gupta MN, Uversky VN. Pre-Molten, Wet, and Dry Molten Globules en Route to the Functional State of Proteins. Int J Mol Sci 2023; 24:ijms24032424. [PMID: 36768742 PMCID: PMC9916686 DOI: 10.3390/ijms24032424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Transitions between the unfolded and native states of the ordered globular proteins are accompanied by the accumulation of several intermediates, such as pre-molten globules, wet molten globules, and dry molten globules. Structurally equivalent conformations can serve as native functional states of intrinsically disordered proteins. This overview captures the characteristics and importance of these molten globules in both structured and intrinsically disordered proteins. It also discusses examples of engineered molten globules. The formation of these intermediates under conditions of macromolecular crowding and their interactions with nanomaterials are also reviewed.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-494-5816
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3
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Gerlits O, Fajer M, Cheng X, Blumenthal DK, Radić Z, Kovalevsky A. Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering. Structure 2022; 30:1538-1549.e3. [PMID: 36265484 PMCID: PMC9637784 DOI: 10.1016/j.str.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/07/2022] [Accepted: 09/25/2022] [Indexed: 11/06/2022]
Abstract
Organophosphorus (OP) compounds, including nerve agents and some pesticides, covalently bind to the catalytic serine of human acetylcholinesterase (hAChE), thereby inhibiting acetylcholine hydrolysis necessary for efficient neurotransmission. Oxime antidotes can reactivate the OP-conjugated hAChE, but reactivation efficiency can be low for pesticides, such as paraoxon (POX). Understanding structural and dynamic determinants of OP inhibition and reactivation can provide insights to design improved reactivators. Here, X-ray structures of hAChE with unaged POX, with POX and oximes MMB4 and RS170B, and with MMB4 are reported. A significant conformational distortion of the acyl loop was observed upon POX binding, being partially restored to the native conformation by oximes. Neutron vibrational spectroscopy combined with molecular dynamics simulations showed that picosecond vibrational dynamics of the acyl loop soften in the ∼20-50 cm-1 frequency range. The acyl loop structural perturbations may be correlated with its picosecond vibrational dynamics to yield more comprehensive template for structure-based reactivator design.
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Affiliation(s)
- Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN 37303, USA
| | - Mikolai Fajer
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaolin Cheng
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Donald K Blumenthal
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Zoran Radić
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093-0657, USA.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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4
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Masson P, Lushchekina S. Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions. Molecules 2022; 27:6861. [PMID: 36296453 PMCID: PMC9610776 DOI: 10.3390/molecules27206861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.
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Affiliation(s)
- Patrick Masson
- Biochemical Neuropharmacology Laboratory, Kazan Federal University, Kremlievskaya Str. 18, 420111 Kazan, Russia
| | - Sofya Lushchekina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin Str. 4, 119334 Moscow, Russia
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5
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Unravelling the Adaptation Mechanisms to High Pressure in Proteins. Int J Mol Sci 2022; 23:ijms23158469. [PMID: 35955607 PMCID: PMC9369236 DOI: 10.3390/ijms23158469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 02/06/2023] Open
Abstract
Life is thought to have appeared in the depth of the sea under high hydrostatic pressure. Nowadays, it is known that the deep biosphere hosts a myriad of life forms thriving under high-pressure conditions. However, the evolutionary mechanisms leading to their adaptation are still not known. Here, we show the molecular bases of these mechanisms through a joint structural and dynamical study of two orthologous proteins. We observed that pressure adaptation involves the decoupling of protein–water dynamics and the elimination of cavities in the protein core. This is achieved by rearranging the charged residues on the protein surface and using bulkier hydrophobic residues in the core. These findings will be the starting point in the search for a complete genomic model explaining high-pressure adaptation.
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Wang Q, Zhang C, Li Z, Guo F, Zhang J, Liu Y, Su Z. High hydrostatic pressure refolding of highly hydrophobic protein: A case study of recombinant human interferon β-1b from inclusion bodies. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Lushchekina SV, Inidjel G, Martinez N, Masson P, Trovaslet-Leroy M, Nachon F, Koza MM, Seydel T, Peters J. Impact of Sucrose as Osmolyte on Molecular Dynamics of Mouse Acetylcholinesterase. Biomolecules 2020; 10:biom10121664. [PMID: 33322722 PMCID: PMC7763276 DOI: 10.3390/biom10121664] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 01/28/2023] Open
Abstract
The enzyme model, mouse acetylcholinesterase, which exhibits its active site at the bottom of a narrow gorge, was investigated in the presence of different concentrations of sucrose to shed light on the protein and water dynamics in cholinesterases. The study was conducted by incoherent neutron scattering, giving access to molecular dynamics within the time scale of sub-nano to nanoseconds, in comparison with molecular dynamics simulations. With increasing sucrose concentration, we found non-linear effects, e.g., first a decrease in the dynamics at 5 wt% followed by a gain at 10 wt% sucrose. Direct comparisons with simulations permitted us to understand the following findings: at 5 wt%, sugar molecules interact with the protein surface through water molecules and damp the motions to reduce the overall protein mobility, although the motions inside the gorge are enhanced due to water depletion. When going to 10 wt% of sucrose, some water molecules at the protein surface are replaced by sugar molecules. By penetrating the protein surface, they disrupt some of the intra-protein contacts, and induce new ones, creating new pathways for correlated motions, and therefore, increasing the dynamics. This exhaustive study allowed for an explanation of the detail interactions leading to the observed non-linear behavior.
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Affiliation(s)
- Sofya V. Lushchekina
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Gaetan Inidjel
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
- Université Grenoble Alpes, UFR PhITEM, LiPhy, CNRS, 38000 Grenoble, France
| | - Nicolas Martinez
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
- Université Grenoble Alpes, UFR PhITEM, LiPhy, CNRS, 38000 Grenoble, France
| | - Patrick Masson
- Neuropharmacology Laboratory, Kazan Federal University, Kremlevskaya str 18, 480002 Kazan, Russia;
| | - Marie Trovaslet-Leroy
- Institut de Recherche Biomédicale des Armées, 91223 Brétigny sur Orge, France; (M.T.-L.); (F.N.)
| | - Florian Nachon
- Institut de Recherche Biomédicale des Armées, 91223 Brétigny sur Orge, France; (M.T.-L.); (F.N.)
| | - Michael Marek Koza
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
| | - Tilo Seydel
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
| | - Judith Peters
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
- Université Grenoble Alpes, UFR PhITEM, LiPhy, CNRS, 38000 Grenoble, France
- Correspondence: ; Tel.: +33-4-7620-7560
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8
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Engelke J, Tuten BT, Schweins R, Komber H, Barner L, Plüschke L, Barner-Kowollik C, Lederer A. An in-depth analysis approach enabling precision single chain nanoparticle design. Polym Chem 2020. [DOI: 10.1039/d0py01045f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of single chain nanoparticles (SCNPs) is a vibrant field in macromolecular science. However, to achieve an in-depth understanding of the nature of intramolecular polymer folding, a step-change in the methodologies for SCNP analysis is required.
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Affiliation(s)
- Johanna Engelke
- School of Chemistry and Physics
- Queensland University of Technology (QUT)
- Brisbane
- Australia
- Leibniz-Institut für Polymerforschung Dresden
| | - Bryan T. Tuten
- School of Chemistry and Physics
- Queensland University of Technology (QUT)
- Brisbane
- Australia
- Centre for Materials Science
| | - Ralf Schweins
- Institut Laue-Langevin
- DS/LSS
- CS 20 156
- 38042 Grenoble CEDEX 9
- France
| | - Hartmut Komber
- Leibniz-Institut für Polymerforschung Dresden
- 01069 Dresden
- Germany
| | - Leonie Barner
- School of Chemistry and Physics
- Queensland University of Technology (QUT)
- Brisbane
- Australia
- Centre for Materials Science
| | - Laura Plüschke
- Leibniz-Institut für Polymerforschung Dresden
- 01069 Dresden
- Germany
- School of Science
- Technische Universität Dresden
| | - Christopher Barner-Kowollik
- School of Chemistry and Physics
- Queensland University of Technology (QUT)
- Brisbane
- Australia
- Centre for Materials Science
| | - Albena Lederer
- Leibniz-Institut für Polymerforschung Dresden
- 01069 Dresden
- Germany
- School of Science
- Technische Universität Dresden
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9
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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10
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Al-Ayoubi SR, Schummel PH, Cisse A, Seydel T, Peters J, Winter R. Osmolytes modify protein dynamics and function of tetrameric lactate dehydrogenase upon pressurization. Phys Chem Chem Phys 2019; 21:12806-12817. [PMID: 31165827 DOI: 10.1039/c9cp02310k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We present a study of the combined effects of natural cosolvents (TMAO, glycine, urea) and pressure on the activity of the tetrameric enzyme lactate dehydrogenase (LDH). To this end, high-pressure stopped-flow methodology in concert with fast UV/Vis spectroscopic detection of product formation was applied. To reveal possible pressure effects on the stability and dynamics of the enzyme, FTIR spectroscopic and neutron scattering measurements were carried out. In neat buffer solution, the catalytic turnover number of the enzyme, kcat, increases up to 1000 bar, the pressure range where dissociation of the tetrameric species to dimers sets in. Accordingly, we obtain a negative activation volume, ΔV# = -45.3 mL mol-1. Further, the enzyme substrate complex has a larger volume compared to the enzyme and substrate in the unbound state. The neutron scattering data show that changes in the fast internal dynamics of the enzyme are not responsible for the increase of kcat upon compression. Whereas the magnitude of kcat is similar in the presence of the osmolytes, the pressure of deactivation is modulated by the addition of cosolvents. TMAO and glycine increase the pressure of deactivation, and in accordance with the observed stabilizing effect both cosolvents exhibit against denaturation and/or dissociation of proteins. While urea does not markedly affect the magnitude of the Michaelis constant, KM, both 1 M TMAO and 1 M glycine exhibit smaller KM values of about 0.07 mM and 0.05 mM below about 1 kbar. Such positive effect on the substrate affinity could be rationalized by the effect the two cosolutes impose on the thermodynamic activities of the reactants, which reflect changes in water-mediated intermolecular interactions. Our data show that the intracellular milieu, i.e., the solution conditions that have evolved, may be sufficient to maintain enzymatic activity under extreme environmental conditions, including the whole pressure range encountered on Earth.
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Affiliation(s)
- Samy R Al-Ayoubi
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany.
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Al-Shabib NA, Khan JM, Malik A, Sen P, Alsenaidy MA, Husain FM, Alsenaidy AM, Khan RH, Choudhry H, Zamzami MA, Khan MI, Shahzad SA. A quercetin-based flavanoid (rutin) reverses amyloid fibrillation in β-lactoglobulin at pH 2.0 and 358 K. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 214:40-48. [PMID: 30763917 DOI: 10.1016/j.saa.2019.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 01/14/2019] [Accepted: 02/03/2019] [Indexed: 06/09/2023]
Abstract
β-lactoglobulin (BLG) is a well characterized milk protein and a model for folding and aggregation studies. Rutin is a quercetin based-flavanoid and a famous dietary supplement. It is a potential protector from coronary heart disease, cancers, and inflammatory bowel disease. In this study, amyloid fibrillation is reported in BLG at pH 2.0 and temperature 358 K. It is inhibited to some extent by rutin with a rate of 99.3 h-1 M-1. Amyloid fibrillation started taking place after 10 h of incubation and completed near 40 h at a rate of 16.6 × 10-3 h-1, with a plateau during 40-108 h. Disruption of tertiary structure of BLG and increased solvent accessibility of hydrophobic core seem to trigger intermolecular assembly. Increase in 7% β-sheet structure at the cost of 10% α-helical structures and the electron micrograph of BLG fibrils at 108 h further support the formation of amyloid. Although it could not block amyloidosis completely, and even the time required to reach plateau remains the same, a decrease of growth rate from 16.6 × 10-3 to 13.5 × 10-3 h-1 was observed in the presence of 30.0 μM rutin. Rutin seems to block solvent accessibility of the hydrophobic core of BLG. A decrease in the fibril population was observed in electron micrographs, with the increase in rutin concentration. All evidences indicate reversal of fibrillation in BLG in the presence of rutin.
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Affiliation(s)
- Nasser Abdulatif Al-Shabib
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia.
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Ajamaluddin Malik
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Priyankar Sen
- Centre for Bioseparation Technology, Vellore Institute of Technology, Vellore 632014, India
| | - Mohammad A Alsenaidy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Saudi Arabia
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Abdulrahman M Alsenaidy
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Rizwan Hasan Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohmmad Imran Khan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Syed Ali Shahzad
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
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12
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Golub M, Pieper J, Peters J, Kangur L, Martin EC, Hunter CN, Freiberg A. Picosecond Dynamical Response to a Pressure-Induced Break of the Tertiary Structure Hydrogen Bonds in a Membrane Chromoprotein. J Phys Chem B 2019; 123:2087-2093. [PMID: 30739452 DOI: 10.1021/acs.jpcb.8b11196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We used elastic incoherent neutron scattering (EINS) to find out if structural changes accompanying local hydrogen bond rupture are also reflected in global dynamical response of the protein complex. Chromatophore membranes from LH2-only strains of the photosynthetic bacterium Rhodobacter sphaeroides, with spheroidenone or neurosporene as the major carotenoids, were subjected to high hydrostatic pressure at ambient temperature. Optical spectroscopy conducted at high pressure confirmed rupture of tertiary structure hydrogen bonds. In parallel, we used EINS to follow average motions of the hydrogen atoms in LH2, which reflect the flexibility of this complex. A decrease of the average atomic mean square displacements of hydrogen atoms was observed up to a pressure of 5 kbar in both carotenoid samples due to general stiffening of protein structures, while at higher pressures a slight increase of the displacements was detected in the neurosporene mutant LH2 sample only. These data show a correlation between the local pressure-induced breakage of H-bonds, observed in optical spectra, with the altered protein dynamics monitored by EINS. The slightly higher compressibility of the neurosporene mutant sample shows that even subtle alterations of carotenoids are manifested on a larger scale and emphasize a close connection between the local structure and global dynamics of this membrane protein complex.
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Affiliation(s)
- Maksym Golub
- Institute of Physics , University of Tartu , W. Ostwald Str. 1 , 50411 Tartu , Estonia
| | - Jörg Pieper
- Institute of Physics , University of Tartu , W. Ostwald Str. 1 , 50411 Tartu , Estonia
| | - Judith Peters
- Institut Laue Langevin , F-38042 Grenoble Cedex 9 , France.,University Grenoble Alpes, CNRS, LIPhy , 38000 Grenoble , France
| | - Liina Kangur
- Institute of Physics , University of Tartu , W. Ostwald Str. 1 , 50411 Tartu , Estonia
| | - Elizabeth C Martin
- Department of Molecular Biology and Biotechnology , University of Sheffield , S10 2TN Sheffield , U.K
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology , University of Sheffield , S10 2TN Sheffield , U.K
| | - Arvi Freiberg
- Institute of Physics , University of Tartu , W. Ostwald Str. 1 , 50411 Tartu , Estonia.,Institute of Molecular and Cell Biology , University of Tartu , Riia 23 , 51010 Tartu , Estonia
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13
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Annighöfer B, Hélary A, Brûlet A, Colas de la Noue A, Loupiac C, Combet S. A high pressure cell using metallic windows to investigate the structure of molecular solutions up to 600 MPa by small-angle neutron scattering. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:025106. [PMID: 30831774 DOI: 10.1063/1.5051765] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
We report on a high pressure (HP) cell designed for the determination of the structure of molecular solutions by small-angle neutron scattering (SANS). The HP cell is fitted up with two thick metallic windows that make the device very resistant under hydrostatic pressures up to 600 MPa (or 6 kbar). The metallic windows are removable, offering the possibility to adapt the HP cell to a given study with the pressure desired on an appropriate spatial range to study the structure of various molecular solutions by SANS. In this context, we report the absorption, transmission, and scattering properties of different metallic windows. Finally, we describe, as a proof of principle, the solution structure changes of myoglobin, a small globular protein.
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Affiliation(s)
- Burkhard Annighöfer
- Laboratoire Léon-Brillouin (LLB), UMR 12 CEA-CNRS, Université Paris-Saclay, CEA-Saclay, F-91191 Gif-sur-Yvette CEDEX, France
| | - Arnaud Hélary
- Laboratoire Léon-Brillouin (LLB), UMR 12 CEA-CNRS, Université Paris-Saclay, CEA-Saclay, F-91191 Gif-sur-Yvette CEDEX, France
| | - Annie Brûlet
- Laboratoire Léon-Brillouin (LLB), UMR 12 CEA-CNRS, Université Paris-Saclay, CEA-Saclay, F-91191 Gif-sur-Yvette CEDEX, France
| | - Alexandre Colas de la Noue
- Laboratoire Léon-Brillouin (LLB), UMR 12 CEA-CNRS, Université Paris-Saclay, CEA-Saclay, F-91191 Gif-sur-Yvette CEDEX, France
| | - Camille Loupiac
- Laboratoire Léon-Brillouin (LLB), UMR 12 CEA-CNRS, Université Paris-Saclay, CEA-Saclay, F-91191 Gif-sur-Yvette CEDEX, France
| | - Sophie Combet
- Laboratoire Léon-Brillouin (LLB), UMR 12 CEA-CNRS, Université Paris-Saclay, CEA-Saclay, F-91191 Gif-sur-Yvette CEDEX, France
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14
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Cinar S, Al-Ayoubi S, Sternemann C, Peters J, Winter R, Czeslik C. A high pressure study of calmodulin-ligand interactions using small-angle X-ray and elastic incoherent neutron scattering. Phys Chem Chem Phys 2018; 20:3514-3522. [PMID: 29336441 DOI: 10.1039/c7cp07399b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calmodulin (CaM) is a Ca2+ sensor and mediates Ca2+ signaling through binding of numerous target ligands. The binding of ligands by Ca2+-saturated CaM (holo-CaM) is governed by attractive hydrophobic and electrostatic interactions that are weakened under high pressure in aqueous solutions. Moreover, the potential formation of void volumes upon ligand binding creates a further source of pressure sensitivity. Hence, high pressure is a suitable thermodynamic variable to probe protein-ligand interactions. In this study, we compare the binding of two different ligands to holo-CaM as a function of pressure by using X-ray and neutron scattering techniques. The two ligands are the farnesylated hypervariable region (HVR) of the K-Ras4B protein, which is a natural binding partner of holo-CaM, and the antagonist trifluoperazine (TFP), which is known to inhibit holo-CaM activity. From small-angle X-ray scattering experiments performed up to 3000 bar, we observe a pressure-induced partial unfolding of the free holo-CaM in the absence of ligands, where the two lobes of the dumbbell-shaped protein are slightly swelled. In contrast, upon binding TFP, holo-CaM forms a closed globular conformation, which is pressure stable at least up to 3000 bar. The HVR of K-Ras4B shows a different binding behavior, and the data suggest the dissociation of the holo-CaM/HVR complex under high pressure, probably due to a less dense protein contact of the HVR as compared to TFP. The elastic incoherent neutron scattering experiments corroborate these findings. Below 2000 bar, pressure induces enhanced atomic fluctuations in both holo-CaM/ligand complexes, but those of the holo-CaM/HVR complex seem to be larger. Thus, the inhibition of holo-CaM by TFP is supported by a low-volume ligand binding, albeit this is not associated with a rigidification of the complex structure on the sub-ns Å-scale.
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Affiliation(s)
- Süleyman Cinar
- Department of Chemistry and Chemical Biology, TU Dortmund University, D-44221 Dortmund, Germany.
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15
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Al-Ayoubi SR, Schummel PH, Golub M, Peters J, Winter R. Influence of cosolvents, self-crowding, temperature and pressure on the sub-nanosecond dynamics and folding stability of lysozyme. Phys Chem Chem Phys 2018; 19:14230-14237. [PMID: 28447688 DOI: 10.1039/c7cp00705a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We studied the effects of temperature and hydrostatic pressure on the dynamical properties and folding stability of highly concentrated lysozyme solutions in the absence and presence of the osmolytes trimethylamine-N-oxide (TMAO) and urea. Elastic incoherent neutron scattering (EINS) was applied to determine the mean-squared displacement (MSD) of the protein's hydrogen atoms to yield insights into the effects of these cosolvents on the averaged sub-nanosecond dynamics in the pressure range from ambient up to 4000 bar. To evaluate the additional effect of self-crowding, two protein concentrations (80 and 160 mg mL-1) were used. We observed a distinct effect of TMAO on the internal hydrogen dynamics, namely a reduced mobility. Urea, on the other hand, revealed no marked effect and consequently, no counteracting effect in an urea-TMAO mixture was observed. Different from the less concentrated protein solution, no significant effect of pressure on the MSD was observed for 160 mg mL-1 lysozyme. The EINS experiments were complemented by Fourier-transform infrared (FTIR) spectroscopy measurements, which led to additional insights into the folding stability of lysozyme under the various environmental conditions. We observed a stabilization of the protein in the presence of the compatible osmolyte TMAO and a destabilization in the presence of urea against temperature and pressure for both protein concentrations. Additionally, we noticed a slight destabilizing effect upon self-crowding at very high protein concentration (160 mg mL-1), which is attributable to transient destabilizing intermolecular interactions. Furthermore, a pressure-temperature diagram could be obtained for lysozyme at these high protein concentrations that mimics densely packed intracellular conditions.
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Affiliation(s)
- S R Al-Ayoubi
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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16
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Abstract
Protein dynamics is characterized by fluctuations among different conformational substates, i.e. the different minima of their energy landscape. At temperatures above ~200 K, these fluctuations lead to a steep increase in the thermal dependence of all dynamical properties, phenomenon known as Protein Dynamical Transition. In spite of the intense studies, little is known about the effects of pressure on these processes, investigated mostly near room temperature. We studied by neutron scattering the dynamics of myoglobin in a wide temperature and pressure range. Our results show that high pressure reduces protein motions, but does not affect the onset temperature for the Protein Dynamical Transition, indicating that the energy differences and barriers among conformational substates do not change with pressure. Instead, high pressure values strongly reduce the average structural differences between the accessible conformational substates, thus increasing the roughness of the free energy landscape of the system.
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17
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Wang Q, Liu Y, Zhang C, Guo F, Feng C, Li X, Shi H, Su Z. High hydrostatic pressure enables almost 100% refolding of recombinant human ciliary neurotrophic factor from inclusion bodies at high concentration. Protein Expr Purif 2017; 133:152-159. [PMID: 28323167 DOI: 10.1016/j.pep.2017.03.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/12/2017] [Accepted: 03/14/2017] [Indexed: 11/28/2022]
Abstract
Protein refolding from inclusion bodies (IBs) often encounters a problem of low recovery at high protein concentration. In this study, we demonstrated that high hydrostatic pressure (HHP) could simultaneously achieve high refolding concentration and high refolding yield for IBs of recombinant human ciliary neurotrophic factor (rhCNTF), a potential therapeutic for neurodegenerative diseases. The use of dilution refolding obtained 18% recovery at 3 mg/mL, even in the presence of 4 M urea. In contrast, HHP refolding could efficiently increase the recovery up to almost 100% even at 4 mg/mL. It was found that in the dilution, hydrophobic aggregates were the off-path products and their amount increased with the protein concentration. However, HHP could effectively minimize the formation of hydrophobic aggregates, leading to almost complete conversion of the rhCNTF IBs to the correct configuration. The stable operation range of concentration is 0.5-4.0 mg/mL, in which the refolding yield was almost 100%. Compared with the literatures where HHP failed to increase the refolding yield beyond 90%, the reason could be attributed to the structural difference that rhCNTF has no disulfide bond and is a monomeric protein. After purification by one-step of anionic chromatography, the purity of rhCNTF reached 95% with total process recovery of 54.1%. The purified rhCNTF showed similar structure and in vitro bioactivity to the native species. The whole process featured integration of solubilization/refolding, a high refolding yield of 100%, a high concentration of 4 mg/mL, and a simple chromatography to ensure a high productivity.
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Affiliation(s)
- Qi Wang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yongdong Liu
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China.
| | - Chun Zhang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China
| | - Fangxia Guo
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Cui Feng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China
| | - Xiunan Li
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China
| | - Hong Shi
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China
| | - Zhiguo Su
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China.
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18
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Siddiqi MK, Alam P, Chaturvedi SK, Nusrat S, Shahein YE, Khan RH. Attenuation of amyloid fibrillation in presence of Warfarin: A biophysical investigation. Int J Biol Macromol 2017; 95:713-718. [DOI: 10.1016/j.ijbiomac.2016.11.110] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/26/2016] [Accepted: 11/28/2016] [Indexed: 12/16/2022]
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19
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High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes. Sci Rep 2016; 6:32816. [PMID: 27595789 PMCID: PMC5011708 DOI: 10.1038/srep32816] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/12/2016] [Indexed: 12/12/2022] Open
Abstract
Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure.
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20
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Understanding the non-catalytic behavior of human butyrylcholinesterase silent variants: Comparison of wild-type enzyme, catalytically active Ala328Cys mutant, and silent Ala328Asp variant. Chem Biol Interact 2016; 259:223-232. [PMID: 27062896 DOI: 10.1016/j.cbi.2016.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/15/2016] [Accepted: 04/04/2016] [Indexed: 11/24/2022]
Abstract
Conformational dynamics of wild-type human butyrylcholinesterase (BChE), two mutants of residue Ala328, the catalytically active Ala328Cys, and the catalytically inactive (silent) Ala328Asp, and their interactions with butyrylcholine were studied. The aim was to understand the molecular mechanisms by which point mutations may lead to silent BChE variant or alter catalytic activity. Importance of BChE natural variants is due to medical consequences, i.e. prolonged apnea, following administration of the myorelaxant esters, succinylcholine and mivacurium. Comparison of molecular dynamics (MD) simulations for the three model systems showed that: 1) the active mutant Ala328Cys mutant has some changes in configuration of catalytic residues, which do not prevent binding of butyrylcholine to the active site; 2) in the naturally-occurring silent variant Ala328Asp, the Asp328 carboxylate may either form a salt bridge with Lys339 or a H-bond with His438. In the first case, the Ω-loop swings off the gorge, disrupting the π-cation binding site and the catalytic triad. In the second case, binding of cationic substrates in the catalytic center is also impaired. MD simulations carried out in 0.15 M NaCl, close to physiological ionic strength conditions, favored the second situation. It was seen that Asp328 forms a H-bond with the catalytic triad His438, which in turn disrupts the catalytic machinery. Therefore, we concluded that the Ala328Asp variant is not catalytically active because of that dramatic event. Computational results, consistent with in vitro biochemical data and clinical observations, validate our MD approach.
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21
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Stadler AM, Demmel F, Ollivier J, Seydel T. Picosecond to nanosecond dynamics provide a source of conformational entropy for protein folding. Phys Chem Chem Phys 2016; 18:21527-38. [DOI: 10.1039/c6cp04146a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Myoglobin can be trapped in fully folded structures, partially folded molten globules, and unfolded states under stable equilibrium conditions.
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Affiliation(s)
- Andreas M. Stadler
- Jülich Centre for Neutron Science JCNS and Institute for Complex Systems ICS
- Forschungszentrum Jülich GmbH
- 52425 Jülich
- Germany
| | | | | | - Tilo Seydel
- Institut Laue-Langevin
- 38042 Grenoble Cedex 9
- France
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22
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Erlkamp M, Marion J, Martinez N, Czeslik C, Peters J, Winter R. Influence of Pressure and Crowding on the Sub-Nanosecond Dynamics of Globular Proteins. J Phys Chem B 2015; 119:4842-8. [DOI: 10.1021/acs.jpcb.5b01017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- M. Erlkamp
- Physical
Chemistry I − Biophysical Chemistry, Department of Chemistry and Chemical
Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - J. Marion
- Université
Grenoble Alpes, IBS, 71 avenue des
Martyrs, CS 10090, 38044 Grenoble, France
- Institut Laue-Langevin, 71 avenue
des Martyrs, CS 20156, 38042 CEDEX 9 Grenoble, France
| | - N. Martinez
- Université
Grenoble Alpes, IBS, 71 avenue des
Martyrs, CS 10090, 38044 Grenoble, France
- Institut Laue-Langevin, 71 avenue
des Martyrs, CS 20156, 38042 CEDEX 9 Grenoble, France
| | - C. Czeslik
- Physical
Chemistry I − Biophysical Chemistry, Department of Chemistry and Chemical
Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - J. Peters
- Université
Grenoble Alpes, IBS, 71 avenue des
Martyrs, CS 10090, 38044 Grenoble, France
- Institut Laue-Langevin, 71 avenue
des Martyrs, CS 20156, 38042 CEDEX 9 Grenoble, France
| | - R. Winter
- Physical
Chemistry I − Biophysical Chemistry, Department of Chemistry and Chemical
Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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