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Rai DK, Gillilan RE, Huang Q, Miller R, Ting E, Lazarev A, Tate MW, Gruner SM. High-pressure small-angle X-ray scattering cell for biological solutions and soft materials. J Appl Crystallogr 2021; 54:111-122. [PMID: 33841059 PMCID: PMC7941318 DOI: 10.1107/s1600576720014752] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/06/2020] [Indexed: 11/10/2022] Open
Abstract
Pressure is a fundamental thermodynamic parameter controlling the behavior of biological macromolecules. Pressure affects protein denaturation, kinetic parameters of enzymes, ligand binding, membrane permeability, ion trans-duction, expression of genetic information, viral infectivity, protein association and aggregation, and chemical processes. In many cases pressure alters the molecular shape. Small-angle X-ray scattering (SAXS) is a primary method to determine the shape and size of macromolecules. However, relatively few SAXS cells described in the literature are suitable for use at high pressures and with biological materials. Described here is a novel high-pressure SAXS sample cell that is suitable for general facility use by prioritization of ease of sample loading, temperature control, mechanical stability and X-ray background minimization. Cell operation at 14 keV is described, providing a q range of 0.01 < q < 0.7 Å-1, pressures of 0-400 MPa and an achievable temperature range of 0-80°C. The high-pressure SAXS cell has recently been commissioned on the ID7A beamline at the Cornell High Energy Synchrotron Source and is available to users on a peer-reviewed proposal basis.
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Affiliation(s)
- Durgesh K. Rai
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Richard E. Gillilan
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Robert Miller
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Department of Chemistry, Cornell University, Ithaca, NY 14853, USA
| | - Edmund Ting
- Pressure BioSciences Inc., South Easton, MA 02375, USA
| | | | - Mark W. Tate
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - Sol M. Gruner
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
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Maurel MC, Leclerc F, Hervé G. Ribozyme Chemistry: To Be or Not To Be under High Pressure. Chem Rev 2019; 120:4898-4918. [DOI: 10.1021/acs.chemrev.9b00457] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS, Sorbonne Université, Muséum National d’Histoire Naturelle, EPHE, F-75005 Paris, France
| | - Fabrice Leclerc
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, F-91198 Gif-sur-Yvette, France
| | - Guy Hervé
- Laboratoire BIOSIPE, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Campus Pierre et Marie Curie, F-75005 Paris, France
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3
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Low crowding agent concentration destabilizes against pressure unfolding. Biophys Chem 2017; 231:125-134. [PMID: 28502485 DOI: 10.1016/j.bpc.2017.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/28/2017] [Accepted: 04/29/2017] [Indexed: 02/05/2023]
Abstract
The concentration of macromolecules inside a cell is very high, which can affect the behavior of the enzymes, and consequently influence vital biological processes. This is called macromolecular crowding. Since the most important effect of macromolecular crowding is the excluded volume, we performed pressure experiments, where the volume (as conjugate parameter to the pressure) is the crucial factor. We measured the temperature and pressure stability of bovine serum albumin and lysozyme with various concentrations of crowding agents, dextran, Ficoll™ and lysozyme itself. Our most interesting finding is that low concentration of all the studied crowding agents decreases the pressure stability of the proteins. We explain this by the reduced hydration volume change in the crowded environment. Furthermore, we discuss the volumetric parameters and emphasize the difference between the partial volume of the protein and the volume it influences, and their relation to the excluded volume which is responsible for the macromolecular crowding.
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Zhang X, Jia R, Zhou J, Wang M, Yin Z, Cheng A. Capsid-Targeted Viral Inactivation: A Novel Tactic for Inhibiting Replication in Viral Infections. Viruses 2016; 8:E258. [PMID: 27657114 PMCID: PMC5035972 DOI: 10.3390/v8090258] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/08/2016] [Accepted: 09/15/2016] [Indexed: 12/18/2022] Open
Abstract
Capsid-targeted viral inactivation (CTVI), a conceptually powerful new antiviral strategy, is attracting increasing attention from researchers. Specifically, this strategy is based on fusion between the capsid protein of a virus and a crucial effector molecule, such as a nuclease (e.g., staphylococcal nuclease, Barrase, RNase HI), lipase, protease, or single-chain antibody (scAb). In general, capsid proteins have a major role in viral integration and assembly, and the effector molecule used in CTVI functions to degrade viral DNA/RNA or interfere with proper folding of viral key proteins, thereby affecting the infectivity of progeny viruses. Interestingly, such a capsid-enzyme fusion protein is incorporated into virions during packaging. CTVI is more efficient compared to other antiviral methods, and this approach is promising for antiviral prophylaxis and therapy. This review summarizes the mechanism and utility of CTVI and provides some successful applications of this strategy, with the ultimate goal of widely implementing CTVI in antiviral research.
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Affiliation(s)
- Xingcui Zhang
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
| | - Jiakun Zhou
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
| | - Zhongqiong Yin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, Sichuan Province, China.
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
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Erlkamp M, Grobelny S, Winter R. Crowding effects on the temperature and pressure dependent structure, stability and folding kinetics of Staphylococcal Nuclease. Phys Chem Chem Phys 2015; 16:5965-76. [PMID: 24549181 DOI: 10.1039/c3cp55040k] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
FT-IR spectroscopic, small-angle X-ray scattering and calorimetric measurements have been applied to explore the effect of the macromolecular crowder agent Ficoll on the temperature- and pressure-dependent stability diagram and folding reaction of the protein Staphylococcal Nuclease (SNase). Additionally, we compare the experimental data with approximate theoretical predictions. We found that temperature- and pressure-induced equilibrium unfolding of SNase is markedly shifted to higher temperatures and pressures in 30 wt% Ficoll solutions. The structure of the unfolded state ensemble does not seem to be strongly influenced in the presence of the crowder. Self-crowding effects have been found to become important at SNase concentrations above 10 wt% only. Our kinetic results show that the folding rate of SNase decreases markedly in the presence of Ficoll. These results indicate that besides the commonly encountered excluded volume effect, other factors need to be considered when assessing confinement effects on protein folding kinetics. Among those, crowder-induced viscosity changes seem to be prominent.
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Affiliation(s)
- M Erlkamp
- TU Dortmund University, Department of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, D-44221 Dortmund, Germany.
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Abstract
Fluorescence is the most widely used technique to study the effect of pressure on biochemical systems. The use of pressure as a physical variable sheds light into volumetric characteristics of reactions. Here we focus on the effect of pressure on protein solutions using a simple unfolding example in order to illustrate the applications of the methodology. Topics covered in this review include the relationships between practical aspects and technical limitations; the effect of pressure and the study of protein cavities; the interpretation of thermodynamic and relaxation kinetics; and the study of relaxation amplitudes. Finally, we discuss the insights available from the combination of fluorescence and other methods adapted to high pressure, such as SAXS or NMR. Because of the simplicity and accessibility of high-pressure fluorescence, the technique is a starting point that complements appropriately multi-methodological approaches related to understanding protein function, disfunction, and folding from the volumetric point of view.
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Hatch HW, Stillinger FH, Debenedetti PG. Computational Study of the Stability of the Miniprotein Trp-Cage, the GB1 β-Hairpin, and the AK16 Peptide, under Negative Pressure. J Phys Chem B 2014; 118:7761-9. [DOI: 10.1021/jp410651u] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Harold W. Hatch
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Frank H. Stillinger
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G. Debenedetti
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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Zhai Y, Winter R. Effect of molecular crowding on the temperature-pressure stability diagram of ribonuclease A. Chemphyschem 2012; 14:386-93. [PMID: 23281099 DOI: 10.1002/cphc.201200767] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/29/2012] [Indexed: 11/11/2022]
Abstract
FT-IR spectroscopic and thermodynamic measurements were designed to explore the effect of a macromolecular crowder, dextran, on the temperature and pressure-dependent phase diagram of the protein Ribonuclease A (RNase A), and we compare the experimental data with approximate theoretical predictions based on configuration entropy. Exploring the crowding effect on the pressure-induced unfolding of proteins provides insight in protein stability and folding under cell-like dense conditions, since pressure is a fundamental thermodynamic variable linked to molecular volume. Moreover, these studies are of relevance for understanding protein stability in deep-sea organisms, which have to cope with pressures in the kbar range. We found that not only temperature-induced equilibrium unfolding of RNase A, but also unfolding induced by pressure is markedly prohibited in the crowded dextran solutions, suggesting that crowded environments such as those found intracellularly, will also oppress high-pressure protein unfolding. The FT-IR spectroscopic measurements revealed a marked increase in unfolding pressure of 2 kbar in the presence of 30 wt % dextran. Whereas the structural changes upon thermal unfolding of the protein are not significantly influenced in the presence of the crowding agent, through stabilization by dextran the pressure-unfolded state of the protein retains more ordered secondary structure elements, which seems to be a manifestation of the entropic destabilization of the unfolded state by crowding.
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Affiliation(s)
- Yong Zhai
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry, TU Dortmund University, Germany
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Krüger B, Liang C, Prell F, Fieselmann A, Moya A, Schuster S, Völker U, Dandekar T. Metabolic adaptation and protein complexes in prokaryotes. Metabolites 2012; 2:940-58. [PMID: 24957769 PMCID: PMC3901225 DOI: 10.3390/metabo2040940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 11/10/2012] [Accepted: 11/12/2012] [Indexed: 02/07/2023] Open
Abstract
Protein complexes are classified and have been charted in several large-scale screening studies in prokaryotes. These complexes are organized in a factory-like fashion to optimize protein production and metabolism. Central components are conserved between different prokaryotes; major complexes involve carbohydrate, amino acid, fatty acid and nucleotide metabolism. Metabolic adaptation changes protein complexes according to environmental conditions. Protein modification depends on specific modifying enzymes. Proteins such as trigger enzymes display condition-dependent adaptation to different functions by participating in several complexes. Several bacterial pathogens adapt rapidly to intracellular survival with concomitant changes in protein complexes in central metabolism and optimize utilization of their favorite available nutrient source. Regulation optimizes protein costs. Master regulators lead to up- and downregulation in specific subnetworks and all involved complexes. Long protein half-life and low level expression detaches protein levels from gene expression levels. However, under optimal growth conditions, metabolite fluxes through central carbohydrate pathways correlate well with gene expression. In a system-wide view, major metabolic changes lead to rapid adaptation of complexes and feedback or feedforward regulation. Finally, prokaryotic enzyme complexes are involved in crowding and substrate channeling. This depends on detailed structural interactions and is verified for specific effects by experiments and simulations.
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Affiliation(s)
- Beate Krüger
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany.
| | - Chunguang Liang
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany.
| | - Florian Prell
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany.
| | - Astrid Fieselmann
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany.
| | - Andres Moya
- Unidad Mixta de Investigación en Genómica y Salud CSISP-UVEG, University of València José Beltrán 2, 46980 Paterna, Valencia, Spain.
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich-Schiller-University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Friedrich-Ludwig-Jahn-Straße 15a, 17487, Greifswald, Germany.
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany.
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Roche J, Dellarole M, Caro JA, Guca E, Norberto DR, Yang Y, Garcia AE, Roumestand C, García-Moreno B, Royer CA. Remodeling of the folding free energy landscape of staphylococcal nuclease by cavity-creating mutations. Biochemistry 2012; 51:9535-46. [PMID: 23116341 DOI: 10.1021/bi301071z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The folding of staphylococcal nuclease (SNase) is known to proceed via a major intermediate in which the central OB subdomain is folded and the C-terminal helical subdomain is disordered. To identify the structural and energetic determinants of this folding free energy landscape, we have examined in detail, using high-pressure NMR, the consequences of cavity creating mutations in each of the two subdomains of an ultrastable SNase, Δ+PHS. The stabilizing mutations of Δ+PHS enhanced the population of the major folding intermediate. Cavity creation in two different regions of the Δ+PHS reference protein, despite equivalent effects on global stability, had very distinct consequences on the complexity of the folding free energy landscape. The L125A substitution in the C-terminal helix of Δ+PHS slightly suppressed the major intermediate and promoted an additional excited state involving disorder in the N-terminus, but otherwise decreased landscape heterogeneity with respect to the Δ+PHS background protein. The I92A substitution, located in the hydrophobic OB-fold core, had a much more profound effect, resulting in a significant increase in the number of intermediate states and implicating the entire protein structure. Denaturant (GuHCl) had very subtle and specific effects on the landscape, suppressing some states and favoring others, depending upon the mutational context. These results demonstrate that disrupting interactions in a region of the protein with highly cooperative, unfrustrated folding has very profound effects on the roughness of the folding landscape, whereas the effects are less pronounced for an energetically equivalent substitution in an already frustrated region.
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Affiliation(s)
- Julien Roche
- Centre de Biochimie Structurale, INSERM U554, CNRS UMR 5048, Universités de Montpellier, Montpellier, France
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