1
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Dos Santos Silva Araújo L, Chiappisi L. Effect of hydrostatic pressure on the supramolecular assembly of surfactant-cyclodextrin inclusion complexes. Phys Chem Chem Phys 2024. [PMID: 38982932 DOI: 10.1039/d4cp02043j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
The supramolecular assembly of simple colloids into complex, hierarchical structures arises from a delicate interplay of short-range directional and isotropic long-range forces. These assemblies are highly sensitive to environmental changes, such as temperature variations and the presence of specific molecules, making them promising candidates for nanomachine design. In this study, we investigate the effect of hydrostatic pressure, up to 1800 bar, on the supramolecular assemblies of cyclodextrin/surfactant complexes. Using small-angle neutron scattering, we demonstrate that while the overall structure of the supramolecular aggregates remains largely stable under pressure, the stiffness of the planar lattice formed by the inclusion complexes, the basic structural unit of the supramolecular assemblies, shows a fourfold increase between 250 and 1000 bar. These findings suggest that high-pressure studies can be exploited to better understand the mechanisms of supramolecular assembly processes, thereby aiding in the design of more robust and functional systems.
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Affiliation(s)
| | - Leonardo Chiappisi
- Institut Max von Laue - Paul Langevin (ILL), 71, avenue des Martyrs, 38042 Grenoble, France.
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2
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Le Brun AP, Gilbert EP. Advances in sample environments for neutron scattering for colloid and interface science. Adv Colloid Interface Sci 2024; 327:103141. [PMID: 38631095 DOI: 10.1016/j.cis.2024.103141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
This review describes recent advances in sample environments across the full complement of applicable neutron scattering techniques to colloid and interface science. Temperature, pressure, flow, tensile testing, ultrasound, chemical reactions, IR/visible/UV light, confinement, humidity and electric and magnetic field application, as well as tandem X-ray methods, are all addressed. Consideration for material choices in sample environments and data acquisition methods are also covered as well as discussion of current and potential future use of machine learning and artificial intelligence.
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Affiliation(s)
- Anton P Le Brun
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Elliot Paul Gilbert
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Road, Lucas Heights, NSW 2234, Australia.
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3
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Papadakis CM, Niebuur BJ, Schulte A. Thermoresponsive Polymers under Pressure with a Focus on Poly( N-isopropylacrylamide) (PNIPAM). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1-20. [PMID: 38149782 DOI: 10.1021/acs.langmuir.3c02398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Pressure is a key variable in the phase behavior of responsive polymers, both for applications and from a fundamental point of view. In this feature article, we review recent developments, particularly applications of neutron techniques such as small-angle neutron scattering (SANS) and quasi-elastic neutron scattering (QENS), across the temperature-pressure phase diagram. These are complemented by kinetic SANS experiments following pressure jumps. In the prototype system poly(N-isopropylacrylamide) (PNIPAM), QENS revealed the pressure-dependent characteristics of hydration water around the lower critical solution temperature transition. The size, water content, and inner structure of the mesoglobules formed in the two-phase region depend strongly on pressure, as shown by SANS. Beside these changes at the phase transition, the mesoglobule formation at low pressure is determined by kinetic factors, namely the formation of a polymer-rich, rigid shell, which hampers further growth by coalescence. At high pressure, in contrast, the growth proceeds by diffusion-limited coalescence without any kinetic hindrance. The disintegration of the mesoglobules evolves either via chain release from their surface or via swelling, depending on the osmotic pressure of the water. Moreover, we report on the profound influence of pressure on the cononsolvency effect. In the temperature-pressure frame, the one-phase region is hugely expanded upon the addition of the cosolvent methanol. SANS experiments unveil the enthalpic and entropic contributions to the effective Flory-Huggins interaction parameter between the segments and the solvent mixture. QENS experiments demonstrate an increase in polymer associated water with pressure, whereas methanol is released. Correspondingly, the solvent phase becomes enriched in methanol, providing a mechanism for the breakdown of cononsolvency at a high pressure. Finally, we outline future opportunities for high-pressure studies of thermoresponsive polymers, with a focus on neutron methods.
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Affiliation(s)
- Christine M Papadakis
- TUM School of Natural Sciences, Physics Department, Soft Matter Physics Group, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
| | - Bart-Jan Niebuur
- TUM School of Natural Sciences, Physics Department, Soft Matter Physics Group, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
| | - Alfons Schulte
- Department of Physics and College of Optics and Photonics, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816-2385, United States
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4
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Zheng N, Long M, Zhang Z, Du S, Huang X, Osire T, Xia X. Behavior of enzymes under high pressure in food processing: mechanisms, applications, and developments. Crit Rev Food Sci Nutr 2023:1-15. [PMID: 37243343 DOI: 10.1080/10408398.2023.2217268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
High pressure processing (HPP) offers the benefits of safety, uniformity, energy-efficient, and low waste, which is widely applied for microbial inactivation and shelf-life extension for foods. Over the past forty years, HPP has been extensively researched in the food industry, enabling the inactivation or activation of different enzymes in future food by altering their molecular structure and active site conformation. Such activation or inactivation of enzymes effectively hinders the spoilage of food and the production of beneficial substances, which is crucial for improving food quality. This paper reviews the mechanism in which high pressure affects the stability and activity of enzymes, concludes the roles of key enzymes in the future food processed using high pressure technologies. Moreover, we discuss the application of modified enzymes based on high pressure, providing insights into the future direction of enzyme evolution under complex food processing conditions (e.g. high temperature, high pressure, high shear, and multiple elements). Finally, we conclude with prospects of high pressure technology and research directions in the future. Although HPP has shown positive effects in improving the future food quality, there is still a pressing need to develop new and effective combined processing methods, upgrade processing modes, and promote sustainable lifestyles.
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Affiliation(s)
- Nan Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Mengfei Long
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zehua Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shuang Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xinlei Huang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Tolbert Osire
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Xiaole Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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5
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Smeller L. Pressure Tuning Studies of Four-Stranded Nucleic Acid Structures. Int J Mol Sci 2023; 24:ijms24021803. [PMID: 36675317 PMCID: PMC9866529 DOI: 10.3390/ijms24021803] [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: 12/06/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Four-stranded folded structures, such as G-quadruplexes and i-motifs in the genome, have attracted a growing interest nowadays since they have been discovered in the telomere and in several oncogene promoter regions. Their biological relevance is undeniable since their existence in living cells has been observed. In vivo they take part in the regulation of gene expression, in vitro they are used in the analytical biochemistry. They are attractive and promising targets for cancer therapy. Pressure studies can reveal specific aspects of the molecular processes. Pressure tuning experiments allow the determination of the volumetric parameters of the folded structures and of the folding-unfolding processes. Here, we review the thermodynamic parameters with a special focus on the volumetric ones, which were determined using pressure tuning spectroscopic experiments on the G-quadruplex and i-motif nucleic acid forms.
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Affiliation(s)
- László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, 1094 Budapest, Hungary
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6
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Knop JM, Mukherjee S, Jaworek MW, Kriegler S, Manisegaran M, Fetahaj Z, Ostermeier L, Oliva R, Gault S, Cockell CS, Winter R. Life in Multi-Extreme Environments: Brines, Osmotic and Hydrostatic Pressure─A Physicochemical View. Chem Rev 2023; 123:73-104. [PMID: 36260784 DOI: 10.1021/acs.chemrev.2c00491] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Elucidating the details of the formation, stability, interactions, and reactivity of biomolecular systems under extreme environmental conditions, including high salt concentrations in brines and high osmotic and high hydrostatic pressures, is of fundamental biological, astrobiological, and biotechnological importance. Bacteria and archaea are able to survive in the deep ocean or subsurface of Earth, where pressures of up to 1 kbar are reached. The deep subsurface of Mars may host high concentrations of ions in brines, such as perchlorates, but we know little about how these conditions and the resulting osmotic stress conditions would affect the habitability of such environments for cellular life. We discuss the combined effects of osmotic (salts, organic cosolvents) and hydrostatic pressures on the structure, stability, and reactivity of biomolecular systems, including membranes, proteins, and nucleic acids. To this end, a variety of biophysical techniques have been applied, including calorimetry, UV/vis, FTIR and fluorescence spectroscopy, and neutron and X-ray scattering, in conjunction with high pressure techniques. Knowledge of these effects is essential to our understanding of life exposed to such harsh conditions, and of the physical limits of life in general. Finally, we discuss strategies that not only help us understand the adaptive mechanisms of organisms that thrive in such harsh geological settings but could also have important ramifications in biotechnological and pharmaceutical applications.
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Affiliation(s)
- Jim-Marcel Knop
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Sanjib Mukherjee
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Michel W Jaworek
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Simon Kriegler
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Magiliny Manisegaran
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Zamira Fetahaj
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Lena Ostermeier
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Rosario Oliva
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany.,Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126Naples, Italy
| | - Stewart Gault
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, EH9 3FDEdinburgh, United Kingdom
| | - Charles S Cockell
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, EH9 3FDEdinburgh, United Kingdom
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
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7
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Micciulla S, Gutfreund P, Kanduč M, Chiappisi L. Pressure-Induced Phase Transitions of Nonionic Polymer Brushes. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c01979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Samantha Micciulla
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042Grenoble, France
| | - Philipp Gutfreund
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042Grenoble, France
| | - Matej Kanduč
- Jožef Stefan Institute, Jamova 39, SI-1000Ljubljana, Slovenia
| | - Leonardo Chiappisi
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042Grenoble, France
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8
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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9
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Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions. Molecules 2022; 27:molecules27206861. [PMID: 36296453 PMCID: PMC9610776 DOI: 10.3390/molecules27206861] [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: 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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10
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A High-Pressure, High-Temperature Flow Reactor Simulating the Hadean Earth Environment, with Application to the Pressure Dependence of the Cleavage of Avocado Viroid Hammerhead Ribozyme. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081224. [PMID: 36013404 PMCID: PMC9410335 DOI: 10.3390/life12081224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022]
Abstract
The RNA world hypothesis suggests that chemical networks consisting of functional RNA molecules could have constructed a primitive life-like system leading a first living system. The chemical evolution scenario of RNA molecules should be consistent with the Hadean Earth environment. We have demonstrated the importance of the environment at both high temperature and high pressure, using different types of hydrothermal flow reactor systems and high-pressure equipment. In the present study, we have attempted to develop an alternative easy-to-implement method for high-pressure measurements and demonstrate that the system is applicable as an efficient research tool for high-pressure experiments at pressures up to 30 MPa. We demonstrate the usefulness of the system by detecting the high-pressure influence for the self-cleavage of avocado hammerhead ribozyme (ASBVd(−):HHR) at 45–65 °C. A kinetic analysis of the high-pressure behavior of ASBVd(−):HHR shows that the ribozyme is active at 30 MPa and its activity is sensitive to pressures between 0.1–30 MPa. The surprising finding that such a short ribozyme is effective for self-cleavage at a high pressure suggests the importance of pressure as a factor for selection of adaptable RNA molecules towards an RNA-based life-like system in the Hadean Earth environment deep in the ocean.
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11
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Berger JE, Teixeira SCM, Reed K, Razinkov VI, Sloey CJ, Qi W, Roberts CJ. High-Pressure, Low-Temperature Induced Unfolding and Aggregation of Monoclonal Antibodies: Role of the Fc and Fab Fragments. J Phys Chem B 2022; 126:4431-4441. [PMID: 35675067 DOI: 10.1021/acs.jpcb.1c10528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effects of high pressure and low temperature on the stability of two different monoclonal antibodies (MAbs) were examined in this work. Fluorescence and small-angle neutron scattering were used to monitor the in situ effects of pressure to infer shifts in tertiary structure and characterize aggregation prone intermediates. Partial unfolding was observed for both MAbs, to different extents, under a range of pressure/temperature conditions. Fourier transform infrared spectroscopy was also used to monitor ex situ changes in secondary structure. Preservation of native secondary structure after incubation at elevated pressures and subzero ° C temperatures was independent of the extent of tertiary unfolding and reversibility. Several combinations of pressure and temperature were also used to discern the respective contributions of the isolated Ab fragments (Fab and Fc) to unfolding and aggregation. The fragments for each antibody showed significantly different partial unfolding profiles and reversibility. There was not a simple correlation between stability of the full MAb and either the Fc or Fab fragment stabilities across all cases, demonstrating a complex relationship to full MAb unfolding and aggregation behavior. That notwithstanding, the combined use of spectroscopic and scattering techniques provides insights into MAb conformational stability and hysteresis in high-pressure, low-temperature environments.
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Affiliation(s)
- Jordan E Berger
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Susana C M Teixeira
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States.,NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Kaelan Reed
- PharmBIO Products, W. L. Gore & Associates, Elkton, Maryland 21921, United States
| | - Vladimir I Razinkov
- Drug Product Technologies, Amgen, Thousand Oaks, California 91320, United States
| | - Christopher J Sloey
- Drug Product Technologies, Amgen, Thousand Oaks, California 91320, United States
| | - Wei Qi
- Drug Product Technologies, Amgen, Thousand Oaks, California 91320, United States
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
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12
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The Effects of High-Pressure Processing on pH, Thiobarbituric Acid Value, Color and Texture Properties of Frozen and Unfrozen Beef Mince. Molecules 2022; 27:molecules27133974. [PMID: 35807218 PMCID: PMC9268274 DOI: 10.3390/molecules27133974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 12/10/2022] Open
Abstract
In this study, beef mince (approximately 4% fat longissmus costarum muscle of approximately 2-year-old Holstein cattle) was used as a material. High-pressure processing (HPP) was applied to frozen and unfrozen, vacuum-packed minced meat samples. The pH and thiobarbituric acid (TBA) values of the samples were examined during 45 days of storage. Color values (L*, a* and b*) and texture properties were examined during 30 days of storage. After freezing and HPP (350 MPa, 10 min, 10 °C), the pH value of minced meat increased (p > 0.05) and its TBA value decreased (p < 0.05). The increase in pH may be due to increased ionization during HPP. Some meat peptides, which are considered antioxidant compounds, increased the oxidative stability of meat, so a decrease in TBA may have been observed after freezing and HPP. While the color change in unpressurized samples was a maximum of 3.28 units during storage, in the pressurized sample, it exceeded the limit of 10 units on the first day of storage and exceeded the limit of 10 units on the third day of storage in the frozen and pressurized sample. Freezing and HPP caused the color of beef mince to be retained longer. The hardness, gumminess, chewability, adherence, elasticity, flexibility values of the pressurized and pressurized after freezing samples were higher than those of the unpressurized samples during storage. On the other hand, the opposite was the case for the adhesiveness values. In industrial applications, meat must be pressurized after being vacuum packed. If HPP is applied to frozen beef mince, some of its properties such as TBA, color, and texture can be preserved for a longer period of time without extreme change.
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13
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Abdul Wazed M, Farid M. Denaturation kinetics and storage stability of Osteopontin in reconstituted infant milk formula. Food Chem 2022; 379:132138. [DOI: 10.1016/j.foodchem.2022.132138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/17/2021] [Accepted: 01/09/2022] [Indexed: 11/24/2022]
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14
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Tariq N, Kume T, Feroze UN, Macgregor RB. The Pressure Dependence of the Stability of the G-quadruplex Formed by d(TGGGGT). Life (Basel) 2022; 12:life12050765. [PMID: 35629431 PMCID: PMC9144232 DOI: 10.3390/life12050765] [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: 04/01/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/27/2022] Open
Abstract
The G-quadruplex (GQ), a tetrahelix formed by guanine-rich nucleic acid sequences, is a potential drug target for several diseases. Monomolecular GQs are stabilized by guanine tetrads and non-guanine regions that form loops. Hydrostatic pressure destabilizes the folded, monomolecular GQ structures. In this communication, we present data on the effect of pressure on the conformational stability of the tetramolecular GQ, d[5′-TGGGGT-3′]4. This molecule does not have loops linking the tetrads; thus, its physical properties presumably reflect those of the tetrads alone. Understanding the properties of the tetrads will aid in understanding the contribution of the other structural components to the stability of GQ DNA. By measuring UV light absorption, we have studied the effect of hydrostatic pressure on the thermal stability of the tetramolecular d[5′-TGGGGT-3′]4 in the presence of sodium ions. Our data show that, unlike monomolecular GQ, the temperature at which d[5′-TGGGGT-3′]4 dissociates to form the constituent monomers is nearly independent of pressure up to 200 MPa. This implies that there is no net molar volume difference (∆V) between the GQ and the unfolded random-coil states. This finding further suggests that the large negative ∆V values for the unfolding of monomolecular GQ are due to the presence of the loop regions in those structures.
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15
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Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques. Int J Mol Sci 2022; 23:ijms23105761. [PMID: 35628571 PMCID: PMC9144967 DOI: 10.3390/ijms23105761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 02/06/2023] Open
Abstract
Pressure is an equally important thermodynamical parameter as temperature. However, its importance is often overlooked in the biophysical and biochemical investigations of biomolecules and biological systems. This review focuses on the application of high pressure (>100 MPa = 1 kbar) in biology. Studies of high pressure can give insight into the volumetric aspects of various biological systems; this information cannot be obtained otherwise. High-pressure treatment is a potentially useful alternative method to heat-treatment in food science. Elevated pressure (up to 120 MPa) is present in the deep sea, which is a considerable part of the biosphere. From a basic scientific point of view, the application of the gamut of modern spectroscopic techniques provides information about the conformational changes of biomolecules, fluctuations, and flexibility. This paper reviews first the thermodynamic aspects of pressure science, the important parameters affecting the volume of a molecule. The technical aspects of high pressure production are briefly mentioned, and the most common high-pressure-compatible spectroscopic techniques are also discussed. The last part of this paper deals with the main biomolecules, lipids, proteins, and nucleic acids: how they are affected by pressure and what information can be gained about them using pressure. I I also briefly mention a few supramolecular structures such as viruses and bacteria. Finally, a subjective view of the most promising directions of high pressure bioscience is outlined.
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16
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Zhiguang C, Junrong H, Huayin P, Keipper W. The Effects of Temperature on Starch Molecular Conformation and Hydrogen Bonding. STARCH-STARKE 2022. [DOI: 10.1002/star.202100288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chen Zhiguang
- Xichang University Panxi Crops Research and Utilization Key Laboratory of Sichuan Province Xichang Sichuan Province 615000 P. R. China
- Shaanxi University of Science and Technology School of Food and Biological Engineering Xi'an Shaanxi Province 710021 P. R. China
| | - Huang Junrong
- Shaanxi University of Science and Technology School of Food and Biological Engineering Xi'an Shaanxi Province 710021 P. R. China
| | - Pu Huayin
- Shaanxi University of Science and Technology School of Food and Biological Engineering Xi'an Shaanxi Province 710021 P. R. China
| | - Wade Keipper
- Shaanxi University of Science and Technology School of Arts and Sciences Xi'an Shaanxi Province 710021 P. R. China
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17
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Rojas-Candelas LE, Chanona-Pérez JJ, Méndez JVM, Morales-Hernández JA, Benavides HAC. Characterization of Structural Changes of Casein Micelles at Different PH Using Microscopy and Spectroscopy Techniques. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-10. [PMID: 35156608 DOI: 10.1017/s1431927622000162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This study aimed to evaluate the influence of pH changes on morphometric parameters of casein micelles and a general overview of their conformational structure through microscopy techniques, Raman spectroscopy and multivariate analysis. It was found that casein micelles morphology and protein secondary structure depend strongly upon pH. The changes of arithmetic average roughness (Ra), size, and shape of casein micelles at different pH are properly characterized by atomic force and cryo-transmission electron microscopy. Morphometric changes of casein micelles were correlated correctly with folding and unfolding of casein molecules as evaluated by Raman spectroscopy when the pH was varied. The novelty of this contribution consists in demonstrating that there is a close structure-functionality relationship between the morphometric parameters of proteins and their secondary structure. Knowledge about casein micelles can help improve their use of its diverse applications.
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Affiliation(s)
- Liliana Edith Rojas-Candelas
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu Esq, Cda, Miguel Stampa s/n, C.P. 07738Mexico City, Mexico
| | - José Jorge Chanona-Pérez
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu Esq, Cda, Miguel Stampa s/n, C.P. 07738Mexico City, Mexico
| | - Juan Vicente Méndez Méndez
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu Esq, Cda, Miguel Stampa s/n, C.P. 07738Mexico City, Mexico
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Luis Enrique Erro s/n, Zacatenco, Gustavo A. Madero, C.P. 07738Mexico City, Mexico
| | - José Antonio Morales-Hernández
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), A. C. Av Normalistas #800, Guadalajara, Jalisco, México
| | - Héctor Alfredo Calderón Benavides
- Instituto Politécnico Nacional. Escuela Superior de Física y Matemáticas, Av. Instituto Politécnico Nacional Edificio 9, U. Profesional Adolfo Lopez Mateos, Gustavo A. Madero, C.P. 07738Mexico City, Mexico
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18
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Garcia AE. Atomistic Simulations of Thermal Unfolding. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2376:331-341. [PMID: 34845618 DOI: 10.1007/978-1-0716-1716-8_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This tutorial will provide a practical overview of the use of atomistic simulations to study thermal unfolding of biomolecules, in particular small proteins and RNA oligomers. The tutorial focuses on the use of atomistic, all atom simulations of biomolecules in explicit solvent, to study (reversible) thermal unfolding. The simulation methods described here have also been applied to study biomolecules using implicit solvent and coarse-grained models. We do not intend to provide an up-to-date review of the vast literature of biomolecular dynamics, enhanced sampling methods, force field developments, and applications of these methods. The purpose of this tutorial is to provide basic guidelines into the use of these methods to the starting scientist.
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Affiliation(s)
- Angel E Garcia
- Center for NonLinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA.
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19
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Eeckhoudt J, Bettens T, Geerlings P, Cammi R, Chen B, Alonso M, De Proft F. Conceptual Density Functional Theory under Pressure: Part I. XP-PCM Method Applied to Atoms. Chem Sci 2022; 13:9329-9350. [PMID: 36093025 PMCID: PMC9384819 DOI: 10.1039/d2sc00641c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
High pressure chemistry offers the chemical community a range of possibilities to control chemical reactivity, develop new materials and fine-tune chemical properties. Despite the large changes that extreme pressure brings to the table, the field has mainly been restricted to the effects of volume changes and thermodynamics with less attention devoted to electronic effects at the molecular scale. This paper combines the conceptual DFT framework for analyzing chemical reactivity with the XP-PCM method for simulating pressures in the GPa range. Starting from the new derivatives of the energy with respect to external pressure, an electronic atomic volume and an atomic compressibility are found, comparable to their enthalpy analogues, respectively. The corresponding radii correlate well with major known sets of this quantity. The ionization potential and electron affinity are both found to decrease with pressure using two different methods. For the electronegativity and chemical hardness, a decreasing and increasing trend is obtained, respectively, and an electronic volume-based argument is proposed to rationalize the observed periodic trends. The cube of the softness is found to correlate well with the polarizability, both decreasing under pressure, while the interpretation of the electrophilicity becomes ambiguous at extreme pressures. Regarding the electron density, the radial distribution function shows a clear concentration of the electron density towards the inner region of the atom and periodic trends can be found in the density using the Carbó quantum similarity index and the Kullback–Leibler information deficiency. Overall, the extension of the CDFT framework with pressure yields clear periodic patterns. Conceptual DFT has provided a framework in which to study chemical reactivity. Since high pressure is more and more a tool to control reactions and fine-tune chemical properties, this variable is introduced into the CDFT framework.![]()
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Affiliation(s)
- J Eeckhoudt
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| | - T Bettens
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| | - P Geerlings
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| | - R Cammi
- Department of Chemical Science, Life Science and Environmental Sustainability, University of Parma Parma Italy
| | - B Chen
- Donostia International Physics Center Donostia-San Sebastian Spain
- IKERBASQUE, Basque Foundation for Science Plaza Euskadi 5 48009 Bilbao Spain
| | - M Alonso
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| | - F De Proft
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
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20
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Somkuti J, Molnár OR, Grád A, Smeller L. Pressure Perturbation Studies of Noncanonical Viral Nucleic Acid Structures. BIOLOGY 2021; 10:1173. [PMID: 34827166 PMCID: PMC8615049 DOI: 10.3390/biology10111173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/16/2022]
Abstract
G-quadruplexes are noncanonical structures formed by guanine-rich sequences of the genome. They are found in crucial loci of the human genome, they take part in the regulation of important processes like cell proliferation and cell death. Much less is known about the subjects of this work, the viral G-quadruplexes. We have chosen three potentially G-quadruplex-forming sequences of hepatitis B. We measured the stability and the thermodynamic parameters of these quadruplexes. We also investigated the potential stabilization of these G-quadruplexes by binding a special ligand that was originally developed for cancer therapy. Fluorescence and infrared spectroscopic measurements were performed over wide temperature and pressure ranges. Our experiments indicate the small unfolding volume change of all three oligos. We found a difference between the unfolding of the 2-quartet and the 3-quartet G-quadruplexes. All three G-quadruplexes were stabilized by TMPyP4, which is a cationic porphyrin developed for stabilizing the human telomere.
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Affiliation(s)
| | | | | | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary; (J.S.); (O.R.M.); (A.G.)
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21
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Boosting the kinetic efficiency of formate dehydrogenase by combining the effects of temperature, high pressure and co-solvent mixtures. Colloids Surf B Biointerfaces 2021; 208:112127. [PMID: 34626897 DOI: 10.1016/j.colsurfb.2021.112127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
The application of co-solvents and high pressure has been shown to be an efficient means to modify the kinetics of enzyme-catalyzed reactions without compromising enzyme stability, which is often limited by temperature modulation. In this work, the high-pressure stopped-flow methodology was applied in conjunction with fast UV/Vis detection to investigate kinetic parameters of formate dehydrogenase reaction (FDH), which is used in biotechnology for cofactor recycling systems. Complementary FTIR spectroscopic and differential scanning fluorimetric studies were performed to reveal pressure and temperature effects on the structure and stability of the FDH. In neat buffer solution, the kinetic efficiency increases by one order of magnitude by increasing the temperature from 25° to 45 °C and the pressure from ambient up to the kbar range. The addition of particular co-solvents further doubled the kinetic efficiency of the reaction, in particular the compatible osmolyte trimethylamine-N-oxide and its mixtures with the macromolecular crowding agent dextran. The thermodynamic model PC-SAFT was successfully applied within a simplified activity-based Michaelis-Menten framework to predict the effects of co-solvents on the kinetic efficiency by accounting for interactions involving substrate, co-solvent, water, and FDH. Especially mixtures of the co-solvents at high concentrations were beneficial for the kinetic efficiency and for the unfolding temperature.
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22
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Barbhuiya RI, Singha P, Singh SK. A comprehensive review on impact of non-thermal processing on the structural changes of food components. Food Res Int 2021; 149:110647. [PMID: 34600649 DOI: 10.1016/j.foodres.2021.110647] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Non-thermal food processing is a viable alternative to traditional thermal processing to meet customer needs for high-quality, convenient and minimally processed foods. They are designed to eliminate elevated temperatures during processing and avoid the adverse effects of heat on food products. Numerous thermal and novel non-thermal technologies influence food structure at the micro and macroscopic levels. They affect several properties such as rheology, flavour, process stability, texture, and appearance at microscopic and macroscopic levels. This review presents existing knowledge and advances on the impact of non-thermal technologies, for instance, cold plasma treatment, irradiation, high-pressure processing, ultrasonication, pulsed light technology, high voltage electric field and pulsed electric field treatment on the structural changes of food components. An extensive review of the literature indicates that different non-thermal processing technologies can affect the food components, which significantly affects the structure of food. Applications of novel non-thermal technologies have shown considerable impact on food structure by altering protein structures via free radicals or larger or smaller molecules. Lipid oxidation is another process responsible for undesirable effects in food when treated with non-thermal techniques. Non-thermal technologies may also affect starch properties, reduce molecular weight, and change the starch granule's surface. Such modification of food structure could create novel food textures, enhance sensory properties, improve digestibility, improve water-binding ability and improve mediation of gelation processes. However, it is challenging to determine these technologies' influence on food components due to differences in their primary operation and equipment design mechanisms and different operating conditions. Hence, to get the most value from non-thermal technologies, more in-depth research about their effect on various food components is required.
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Affiliation(s)
- Rahul Islam Barbhuiya
- Department of Food Process Engineering, National Institute of Technology (NIT) Rourkela, Rourkela 769008, Odisha, India
| | - Poonam Singha
- Department of Food Process Engineering, National Institute of Technology (NIT) Rourkela, Rourkela 769008, Odisha, India.
| | - Sushil Kumar Singh
- Department of Food Process Engineering, National Institute of Technology (NIT) Rourkela, Rourkela 769008, Odisha, India.
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23
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Bai Y, Zeng X, Zhang C, Zhang T, Wang C, Han M, Zhou G, Xu X. Effects of high hydrostatic pressure treatment on the emulsifying behavior of myosin and its underlying mechanism. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111397] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins. Commun Chem 2021; 4:57. [PMID: 36697562 PMCID: PMC9814862 DOI: 10.1038/s42004-021-00499-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra-molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold denaturation and thus clarifies its absence in some proteins.
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25
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Lindeboom T, Zhao B, Jackson G, Hall CK, Galindo A. On the liquid demixing of water + elastin-like polypeptide mixtures: bimodal re-entrant phase behaviour. Phys Chem Chem Phys 2021; 23:5936-5944. [PMID: 33666204 DOI: 10.1039/d0cp05013j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water + elastin-like polypeptides (ELPs) exhibit a transition temperature below which the chains transform from collapsed to expanded states, reminiscent of the cold denaturation of proteins. This conformational change coincides with liquid-liquid phase separation. A statistical-thermodynamics theory is used to model the fluid-phase behavior of ELPs in aqueous solution and to extrapolate the behavior at ambient conditions over a range of pressures. At low pressures, closed-loop liquid-liquid equilibrium phase behavior is found, which is consistent with that of other hydrogen-bonding solvent + polymer mixtures. At pressures evocative of deep-sea conditions, liquid-liquid immiscibility bounded by two lower critical solution temperatures (LCSTs) is predicted. As pressure is increased further, the system exhibits two separate regions of closed-loop of liquid-liquid equilibrium (LLE). The observation of bimodal LCSTs and two re-entrant LLE regions herald a new type of binary global phase diagram: Type XII. At high-ELP concentrations the predicted phase diagram resembles a protein pressure denaturation diagram; possible "molten-globule"-like states are observed at low concentration.
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Affiliation(s)
- Tom Lindeboom
- Department of Chemical Engineering, Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Binwu Zhao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, USA.
| | - George Jackson
- Department of Chemical Engineering, Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, USA.
| | - Amparo Galindo
- Department of Chemical Engineering, Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
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26
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Molnár OR, Somkuti J, Smeller L. Negative volume changes of human G-quadruplexes at unfolding. Heliyon 2020; 6:e05702. [PMID: 33354631 PMCID: PMC7744710 DOI: 10.1016/j.heliyon.2020.e05702] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/22/2020] [Accepted: 12/08/2020] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes are tetrahelical structures. They are important targets for anti-cancer drugs, since they are situated at crucial positions within the genome. We studied the volumetric properties of the unfolding of three G-quadruplexes in the presence of potassium ion. The unfolding volume changes were determined using high-pressure fluorescence spectroscopy. The c-MYC, KIT, and VEGF sequences unfold with the transition volume of -17, -6 and -18 cm3/mol, respectively. The small magnitude of the unfolding volume of KIT could be explained by its unique structure and the lower amount of void volume. Since the cell interior is highly crowded, the available volume is restricted. Therefore the volumetric changes during the conformational transformations gain biological importance.
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Affiliation(s)
- Orsolya Réka Molnár
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Judit Somkuti
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
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27
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Dubois C, Herrada I, Barthe P, Roumestand C. Combining High-Pressure Perturbation with NMR Spectroscopy for a Structural and Dynamical Characterization of Protein Folding Pathways. Molecules 2020; 25:E5551. [PMID: 33256081 PMCID: PMC7731413 DOI: 10.3390/molecules25235551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
High-hydrostatic pressure is an alternative perturbation method that can be used to destabilize globular proteins. Generally perfectly reversible, pressure exerts local effects on regions or domains of a protein containing internal voids, contrary to heat or chemical denaturant that destabilize protein structures uniformly. When combined with NMR spectroscopy, high pressure (HP) allows one to monitor at a residue-level resolution the structural transitions occurring upon unfolding and to determine the kinetic properties of the process. The use of HP-NMR has long been hampered by technical difficulties. Owing to the recent development of commercially available high-pressure sample cells, HP-NMR experiments can now be routinely performed. This review summarizes recent advances of HP-NMR techniques for the characterization at a quasi-atomic resolution of the protein folding energy landscape.
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Affiliation(s)
| | | | | | - Christian Roumestand
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 34090 Montpellier, France; (C.D.); (I.H.); (P.B.)
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28
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Gault S, Jaworek MW, Winter R, Cockell CS. High pressures increase α-chymotrypsin enzyme activity under perchlorate stress. Commun Biol 2020; 3:550. [PMID: 33009512 PMCID: PMC7532203 DOI: 10.1038/s42003-020-01279-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/10/2020] [Indexed: 11/16/2022] Open
Abstract
Deep subsurface environments can harbour high concentrations of dissolved ions, yet we know little about how this shapes the conditions for life. We know even less about how the combined effects of high pressure influence the way in which ions constrain the possibilities for life. One such ion is perchlorate, which is found in extreme environments on Earth and pervasively on Mars. We investigated the interactions of high pressure and high perchlorate concentrations on enzymatic activity. We demonstrate that high pressures increase α-chymotrypsin enzyme activity even in the presence of high perchlorate concentrations. Perchlorate salts were shown to shift the folded α-chymotrypsin phase space to lower temperatures and pressures. The results presented here may suggest that high pressures increase the habitability of environments under perchlorate stress. Therefore, deep subsurface environments that combine these stressors, potentially including the subsurface of Mars, may be more habitable than previously thought. Gault et al. show that high pressures increase α-chymotrypsin enzyme activity in the presence of high perchlorate concentrations. These perchlorate salts shift the folded enzyme phase space to lower temperatures and pressure and may move the optimum enzyme activity towards lower temperatures in addition to higher pressures, which has implications for Martian habitability.
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Affiliation(s)
- Stewart Gault
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Michel W Jaworek
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, D-44227, Dortmund, Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, D-44227, Dortmund, Germany
| | - Charles S Cockell
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
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29
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Pruteanu CG, Naden Robinson V, Ansari N, Hassanali A, Scandolo S, Loveday JS. Squeezing Oil into Water under Pressure: Inverting the Hydrophobic Effect. J Phys Chem Lett 2020; 11:4826-4833. [PMID: 32496780 PMCID: PMC7467747 DOI: 10.1021/acs.jpclett.0c01410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
The molecular structure of dense homogeneous fluid water-methane mixtures has been determined for the first time using high-pressure neutron-scattering techniques at 1.7 and 2.2 GPa. A mixed state with a fully H-bonded water network is revealed. The hydration shell of the methane molecules is, however, revealed to be pressure-dependent with an increase in the water coordination between 1.7 and 2.2 GPa. In parallel, ab initio molecular dynamics simulations have been performed to provide insight into the microscopic mechanisms associated with the phenomenon of mixing. These calculations reproduce the observed phase change from phase separation to mixing with increasing pressure. The calculations also reproduce the experimentally observed structural properties. Unexpectedly, the simulations show mixing is accompanied by a subtle enhancement of the polarization of methane. Our results highlight the key role played by fine electronic effects on miscibility and the need to readjust our fundamental understanding of hydrophobicity to account for these.
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Affiliation(s)
- Ciprian G. Pruteanu
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E
6BT, United Kingdom
| | - Victor Naden Robinson
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Narjes Ansari
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Ali Hassanali
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Sandro Scandolo
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - John S. Loveday
- SUPA,
School of Physics and Astronomy and Centre for Science at Extreme
Conditions, The University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
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30
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Jaworek MW, Ruggiero A, Graziano G, Winter R, Vitagliano L. On the extraordinary pressure stability of the Thermotoga maritima arginine binding protein and its folded fragments - a high-pressure FTIR spectroscopy study. Phys Chem Chem Phys 2020; 22:11244-11248. [PMID: 32400824 DOI: 10.1039/d0cp01618g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The arginine binding protein from T. maritima (ArgBP) exhibits several distinctive biophysical and structural properties. Here we show that ArgBP is also endowed with a ramarkable pressure stability as it undergoes minor structural changes only, even at 10 kbar. A similar stability is also observed for its folded fragments (truncated monomer and individual domains). A survey of literature data on the pressure stability of proteins highlights the uncommon behavior of ArgBP.
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Affiliation(s)
- Michel W Jaworek
- Faculty of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn Str. 4a, D-44227 Dortmund, Germany.
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31
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Niebuur BJ, Ko CH, Zhang X, Claude KL, Chiappisi L, Schulte A, Papadakis CM. Pressure Dependence of the Cononsolvency Effect in Aqueous Poly(N-isopropylacrylamide) Solutions: A SANS Study. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bart-Jan Niebuur
- Physik-Department, Fachgebiet Physik weicher Materie, Technische Universität München, James-Franck-Str. 1, 85748 Garching, Germany
| | - Chia-Hsin Ko
- Physik-Department, Fachgebiet Physik weicher Materie, Technische Universität München, James-Franck-Str. 1, 85748 Garching, Germany
| | - Xiaohan Zhang
- Physik-Department, Fachgebiet Physik weicher Materie, Technische Universität München, James-Franck-Str. 1, 85748 Garching, Germany
| | - Kora-Lee Claude
- Physik-Department, Fachgebiet Physik weicher Materie, Technische Universität München, James-Franck-Str. 1, 85748 Garching, Germany
| | - Leonardo Chiappisi
- Large Scale Structures Group, Institut Laue-Langevin, 71, Avenue des Martyrs, CS 20 156, 38042 Grenoble, France
- Stranski Laboratorium für Physikalische Chemie und Theoretische Chemie, Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, Sekr. TC7, D-10623 Berlin, Germany
| | - Alfons Schulte
- Department of Physics and College of Optics and Photonics, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Christine M. Papadakis
- Physik-Department, Fachgebiet Physik weicher Materie, Technische Universität München, James-Franck-Str. 1, 85748 Garching, Germany
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32
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Avagyan S, Vasilchuk D, Makhatadze GI. Protein adaptation to high hydrostatic pressure: Computational analysis of the structural proteome. Proteins 2020; 88:584-592. [PMID: 31618488 DOI: 10.1002/prot.25839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/11/2019] [Accepted: 09/21/2019] [Indexed: 11/11/2022]
Abstract
Hydrostatic pressure has a vital role in the biological adaptation of the piezophiles, organisms that live under high hydrostatic pressure. However, the mechanisms by which piezophiles are able to adapt their proteins to high hydrostatic pressure is not well understood. One proposed hypothesis is that the volume changes of unfolding (ΔVTot ) for proteins from piezophiles is distinct from those of nonpiezophilic organisms. Since ΔVTot defines pressure dependence of stability, we performed a comprehensive computational analysis of this property for proteins from piezophilic and nonpiezophilic organisms. In addition, we experimentally measured the ΔVTot of acylphosphatases and thioredoxins belonging to piezophilic and nonpiezophilic organisms. Based on this analysis we concluded that there is no difference in ΔVTot for proteins from piezophilic and nonpiezophilic organisms. Finally, we put forward the hypothesis that increased concentrations of osmolytes can provide a systemic increase in pressure stability of proteins from piezophilic organisms and provide experimental thermodynamic evidence in support of this hypothesis.
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Affiliation(s)
- Samvel Avagyan
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York
| | - Daniel Vasilchuk
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York
| | - George I Makhatadze
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York
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33
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Baccile N, Zinn T, Laurent GP, Messaoud GB, Cristiglio V, Fernandes FM. Unveiling the Interstitial Pressure between Growing Ice Crystals during Ice-Templating Using a Lipid Lamellar Probe. J Phys Chem Lett 2020; 11:1989-1997. [PMID: 32101432 DOI: 10.1021/acs.jpclett.9b03347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
What is the pressure generated by ice crystals during ice-templating? This work addresses this crucial question by estimating the pressure exerted by oriented ice columns on a supramolecular probe composed of a lipid lamellar hydrogel during directional freezing. This process, also known as freeze-casting, has emerged as a unique processing technique for a broad class of organic, inorganic, soft, and biological materials. Nonetheless, the pressure exerted during and after crystallization between two ice columns is not known, despite its importance with respect to the fragility of the frozen material, especially for biological samples. By using the lamellar period of a glycolipid lamellar hydrogel as a common probe, we couple data obtained from ice-templated-resolved in situ synchrotron small-angle X-ray scattering (SAXS) with data obtained from controlled adiabatic desiccation experiments. We estimate the pressure to vary between 1 ± 10% kbar at -15 °C and 3.5 ± 20% kbar at -60 °C.
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Affiliation(s)
- Niki Baccile
- Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie de la Matière Condensée de Paris, LCMCP, F-75005 Paris, France
| | - Thomas Zinn
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38043 Grenoble, France
| | - Guillaume P Laurent
- Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie de la Matière Condensée de Paris, LCMCP, F-75005 Paris, France
| | - Ghazi Ben Messaoud
- Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie de la Matière Condensée de Paris, LCMCP, F-75005 Paris, France
| | - Viviana Cristiglio
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Francisco M Fernandes
- Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie de la Matière Condensée de Paris, LCMCP, F-75005 Paris, France
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34
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Gasic AG, Cheung MS. A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure. J Phys Chem B 2020; 124:1619-1627. [DOI: 10.1021/acs.jpcb.9b10734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andrei G. Gasic
- Department of Physics, University of Houston, Houston, Texas 77204, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Margaret S. Cheung
- Department of Physics, University of Houston, Houston, Texas 77204, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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35
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Jaworek MW, Möbitz S, Gao M, Winter R. Stability of the chaperonin system GroEL-GroES under extreme environmental conditions. Phys Chem Chem Phys 2020; 22:3734-3743. [PMID: 32010904 DOI: 10.1039/c9cp06468k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chaperonin system GroEL-GroES is present in all kingdoms of life and rescues proteins from improper folding and aggregation upon internal and external stress conditions, including high temperatures and pressures. Here, we set out to explore the thermo- and piezostability of GroEL, GroES and the GroEL-GroES complex in the presence of cosolvents, nucleotides and salts employing quantitative FTIR spectroscopy and small-angle X-ray scattering. Owing to its high biological relevance and lack of data, our focus was especially on the effect of pressure on the chaperonin system. The experimental results reveal that the GroEL-GroES complex is remarkably temperature stable with an unfolding temperature beyond 70 °C, which can still be slightly increased by compatible cosolutes like TMAO. Conversely, the pressure stability of GroEL and hence the GroEL-GroES complex is rather limited and much less than that of monomeric proteins. Whereas GroES is pressure stable up to ∼5 kbar, GroEl and the GroEl-GroES complex undergo minor structural changes already beyond 1 kbar, which can be attributed to a dissociation-induced conformational drift. Quite unexpectedly, no significant unfolding of GroEL is observed even up to 10 kbar, however, i.e., the subunits themselves are very pressure stable. As for the physiological relevance, the structural integrity of the chaperonin system is retained in a relatively narrow pressure range, from about 1 to 1000 bar, which is just the pressure range encountered by life on Earth.
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Affiliation(s)
- Michel W Jaworek
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Simone Möbitz
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Mimi Gao
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
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36
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Somkuti J, Molnár OR, Smeller L. Revealing unfolding steps and volume changes of human telomeric i-motif DNA. Phys Chem Chem Phys 2020; 22:23816-23823. [DOI: 10.1039/d0cp03894f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The i-motif structure of the human telomeric DNA was destabilized by pressure and unfolded with a negative volume change.
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Affiliation(s)
- Judit Somkuti
- Department of Biophysics and Radiation Biology
- Semmelweis University
- Tuzolto utca 37-47 1094
- Hungary
| | - Orsolya Réka Molnár
- Department of Biophysics and Radiation Biology
- Semmelweis University
- Tuzolto utca 37-47 1094
- Hungary
| | - László Smeller
- Department of Biophysics and Radiation Biology
- Semmelweis University
- Tuzolto utca 37-47 1094
- Hungary
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37
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Sung HL, Nesbitt DJ. DNA Hairpin Hybridization under Extreme Pressures: A Single-Molecule FRET Study. J Phys Chem B 2019; 124:110-120. [PMID: 31840514 DOI: 10.1021/acs.jpcb.9b10131] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Organisms have evolved to live in a variety of complex environments, which clearly has required cellular biology to accommodate to extreme conditions of hydraulic pressure and elevated temperature. In this work, we exploit single-molecule Forster resonance energy transfer (FRET) spectroscopy to probe structural changes in DNA hairpins as a function of pressure and temperature, which allows us to extract detailed thermodynamic information on changes in free energy (ΔG°), free volume (ΔV°), enthalpy (ΔH°), and entropy (ΔS°) associated with DNA loop formation and sequence-dependent stem hybridization. Specifically, time-correlated single-photon counting experiments on freely diffusing 40A DNA hairpin FRET constructs are performed in a 50 μm × 50 μm square quartz capillary cell pressurized from ambient pressure up to 3 kbar. By pressure-dependent van't Hoff analysis of the equilibrium constants, ΔV° for hybridization of the DNA hairpin can be determined as a function of stem length (nstem = 7-10) with single base-pair resolution, which further motivates a simple linear deconstruction into additive stem (ΔV°stem = ΔV°bp x nstem) and loop (ΔV°loop) contributions. We find that increasing pressure destabilizes the DNA hairpin stem region [ΔV°bp = +1.98(16) cm3/(mol bp)], with additional positive free volume changes [ΔV°loop = +7.0(14) cm3/mol] we ascribe to bending and base stacking disruption of the 40-dA loop. From a van't Hoff temperature-dependent analysis of the DNA 40A hairpin equilibria, the data support a similar additive loop/stem deconstruction of enthalpic (ΔH° = ΔH°loop + ΔH°stem) and entropic (ΔS° = ΔS°loop + ΔS°stem) contributions, which permits insightful comparison with predictions from nearest-neighbor thermodynamic models for DNA duplex formation. In particular, the stem thermodynamics is consistent with exothermically favored (ΔH°stem < 0) and entropically penalized (ΔS°stem < 0) hydrogen bonding but with additional enthalpic (ΔH°loop > 0) and entropic (ΔS°loop > 0) contributions due to loop bending effects consistent with distortion of dA base stacking in the 40-dA linker.
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Affiliation(s)
- Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
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38
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Fujiwara S, Matsuo T, Sugimoto Y, Shibata K. Segmental Motions of Proteins under Non-native States Evaluated Using Quasielastic Neutron Scattering. J Phys Chem Lett 2019; 10:7505-7509. [PMID: 31743029 DOI: 10.1021/acs.jpclett.9b03196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Characterization of the dynamics of disordered polypeptide chains is required to elucidate the behavior of intrinsically disordered proteins and proteins under non-native states related to the folding process. Here we develop a method using quasielastic neutron scattering, combined with small-angle X-ray scattering and dynamic light scattering, to evaluate segmental motions of proteins as well as diffusion of the entire molecules and local side-chain motions. We apply this method to RNase A under the unfolded and molten-globule (MG) states. The diffusion coefficients arising from the segmental motions are evaluated and found to be different between the unfolded and MG states. The values obtained here are consistent with those obtained using the fluorescence-based techniques. These results demonstrate not only feasibility of this method but also usefulness to characterize the behavior of proteins under various disordered states.
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Affiliation(s)
- Satoru Fujiwara
- Institute for Quantum Life Science , National Institutes for Quantum and Radiological Science and Technology , 2-4 Shirakata , Tokai , Ibaraki 319-1106 , Japan
| | - Tatsuhito Matsuo
- Institute for Quantum Life Science , National Institutes for Quantum and Radiological Science and Technology , 2-4 Shirakata , Tokai , Ibaraki 319-1106 , Japan
| | - Yasunobu Sugimoto
- Nagoya University Synchrotron Radiation Research Center , Furo-cho, Chikusa-ku, Nagoya , Aichi 464-8603 , Japan
| | - Kaoru Shibata
- Neutron Science Section, Materials and Life Science Division, J-PARC Center , Japan Atomic Energy Agency , 2-4 Shirakata , Tokai , Ibaraki 319-1195 , Japan
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39
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Teplukhin AV. Thermodynamic and Structural Characteristics of SPC/E Water at 290 K and under High Pressure. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619100044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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40
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Knierbein M, Wangler A, Luong TQ, Winter R, Held C, Sadowski G. Combined co-solvent and pressure effect on kinetics of a peptide hydrolysis: an activity-based approach. Phys Chem Chem Phys 2019; 21:22224-22229. [PMID: 31576857 DOI: 10.1039/c9cp03868j] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The application of co-solvents and high pressure has been reported to be an efficient means to tune the kinetics of enzyme-catalyzed reactions. Co-solvents and pressure can lead to increased reaction rates without sacrificing enzyme stability, while temperature and pH operation windows are generally very narrow. Quantitative prediction of co-solvent and pressure effects on enzymatic reactions has not been successfully addressed in the literature. Herein, we are introducing a thermodynamic approach that is based on molecular interactions in the form of activity coefficients of substrate and of enzyme in the multi-component solution. This allowed us to quantitatively predict the combined effect of co-solvent and pressure on the kinetic constants, i.e. the Michaelis constant KM and the catalytic constant kcat, of an α-CT-catalyzed peptide hydrolysis reaction. The reaction was studied in the presence of different types of co-solvents and at pressures up to 2 kbar, and quantitative predictions could be obtained for KM, kcat, and finally even primary Michaelis-Menten plots using activity coefficients provided by the thermodynamic model PC-SAFT.
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Affiliation(s)
- Michael Knierbein
- Laboratory of Thermodynamics, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany.
| | - Anton Wangler
- Laboratory of Thermodynamics, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany.
| | - Trung Quan Luong
- Physical Chemistry I, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Christoph Held
- Laboratory of Thermodynamics, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany.
| | - Gabriele Sadowski
- Laboratory of Thermodynamics, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany.
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41
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Vernon‐Carter EJ, Alvarez‐Ramirez J, Bello‐Perez LA, Hernandez‐Jaimes C, Reyes I. Role of Endogenous Protein in the Spherical Aggregation of Taro Starch Granules upon Spray‐Drying and in In Vitro Digestibility. STARCH-STARKE 2019. [DOI: 10.1002/star.201900087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Eduardo Jaime Vernon‐Carter
- Departamento de Ingeniería de Procesos e Hidráulica Universidad Autónoma Metropolitana, Iztapalapa Apartado, 55–534 Iztapalapa CDMX, C.P. 09340 México
| | - Jose Alvarez‐Ramirez
- Departamento de Ingeniería de Procesos e Hidráulica Universidad Autónoma Metropolitana, Iztapalapa Apartado, 55–534 Iztapalapa CDMX, C.P. 09340 México
| | - Luis A. Bello‐Perez
- CEPROBI. km 6 Carr. Yautepec‐Jojutla Calle Ceprobi No. 8, Apartado Postal 24, Yautepec Morelos 62731 México
| | | | - Isabel Reyes
- Universidad Autónoma del Estado de México Campus El Cerrillo Toluca 50200 México
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42
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Somkuti J, Adányi M, Smeller L. Self-crowding influences the temperature - pressure stability of the human telomere G-quadruplex. Biophys Chem 2019; 254:106248. [PMID: 31470349 DOI: 10.1016/j.bpc.2019.106248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 01/22/2023]
Abstract
We measured the effect of crowded environment on G-quadruplex structures, formed by guanine rich DNA sequences. Fluorescence and infrared spectroscopy were used to determine the temperature stability of G-quadruplex structure formed by the human telomere sequence. We determined the T-p phase diagram of Htel aptamer up to 1 GPa at different self-crowding conditions. The unfolding volume change was determined from the pressure induced shift of the unfolding temperature of the quadruplex form. The unfolding volume change decreased in magnitude, and even its sign changed from negative (-19 ml/mol) to positive (7 ml/mol) under self-crowded conditions. The possible explanations are the appearance of the parallel GQ structure at high concentration or the fact that the volume decrease caused by the released central K+ ion during the unfolding is less significant in crowded environment.
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Affiliation(s)
- J Somkuti
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - M Adányi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - L Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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43
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Semasaka C, Dekiwadia C, Buckow R, Kasapis S. Modeling counterion partition in composite gels of BSA with gelatin following high pressure treatment. Food Chem 2019; 285:104-110. [PMID: 30797324 DOI: 10.1016/j.foodchem.2019.01.125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 11/15/2022]
Abstract
We examine the morphology of hydrogels made of bovine serum albumin and gelatin following high pressure processing at 300 MPa for 15 min at 10 and 80 °C. Emphasis is on the distribution of added calcium counterions between the polymeric phases seen in changes in the structural properties of the composite gel. Protocol includes thermal and HPP treatments, dynamic oscillation rheology, ESEM, and modeling from the "synthetic polymer approach" to rationalize results. Pressurization at 10 °C produced continuous gelatin networks with dispersed BSA inclusions whereas pressurization at 80 °C yielded an inverse dispersion of BSA as the continuous phase supporting liquid gelatin inclusions. Lewis and Nielsen equations were adapted to predict the counterion distribution between the polymeric phases that profoundly affected the structural properties of the pressurized gels. The concept of counterion partition (pc) is introduced to the literature to follow the phase behavior of the composites in the presence of added calcium counterions.
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Affiliation(s)
- Carine Semasaka
- School of Science, RMIT University, Bundoora West Campus, Plenty Road, Melbourne, Vic 3083, Australia
| | - Chaitali Dekiwadia
- School of Science, RMIT University, Bundoora West Campus, Plenty Road, Melbourne, Vic 3083, Australia
| | - Roman Buckow
- CSIRO, Food and Nutrition, Werribee, VIC 3030, Australia
| | - Stefan Kasapis
- School of Science, RMIT University, Bundoora West Campus, Plenty Road, Melbourne, Vic 3083, Australia.
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44
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Knierbein M, Venhuis M, Held C, Sadowski G. Thermodynamic properties of aqueous osmolyte solutions at high-pressure conditions. Biophys Chem 2019; 253:106211. [PMID: 31280070 DOI: 10.1016/j.bpc.2019.106211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/20/2019] [Indexed: 12/25/2022]
Abstract
Living organisms can be encountered in nature under extreme conditions. At the seabed, pressure may reach 1000 bar. Yet microorganisms can be found that still function under these conditions. On the one hand, it is known that high pressure even has a positive effect on piezophile enzymes increasing their activity. On the other hand, such microorganisms might contain up to very high concentrations of osmolytes that counteract osmotic stress. To better understand high-pressure influences on biochemical systems, fundamental knowledge about pressure effects on thermodynamic properties of such osmolytes is important. However, literature data is scarce and experiments at high-pressure conditions are challenging. Hence, new high-pressure density data of aqueous osmolyte solutions were measured in this work at temperatures between 298.15 K and 318.15 K and at osmolyte concentrations up to 3 mol/kg water. Further, the thermodynamic model PC-SAFT has been applied recently to successfully model vapor pressures of water and density of water up to 10 kbar [M. Knierbein et al., Density variations of TMAO solutions in the kilobar range: experiments, PC-SAFT predictions, and molecular dynamics simulations, Biophysical chemistry, (2019)]. This allowed accurately predicting effects of temperature and osmolyte concentration on thermodynamic properties (especially mixture densities) up to very high pressures. Common osmolytes (trimethylamine-N-oxide, urea, ectoine, glycerol, glycine) as well as the dipeptides acetyl-N-methylglycine amide, acetyl-N-methylalanine amide, and acetyl-N-methylleucine amide were under investigation.
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Affiliation(s)
| | | | - Christoph Held
- Laboratory of Thermodynamics, TU Dortmund, 44227 Dortmund, Germany
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45
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Winter R. Interrogating the Structural Dynamics and Energetics of Biomolecular Systems with Pressure Modulation. Annu Rev Biophys 2019; 48:441-463. [DOI: 10.1146/annurev-biophys-052118-115601] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High hydrostatic pressure affects the structure, dynamics, and stability of biomolecular systems and is a key parameter in the context of the exploration of the origin and the physical limits of life. This review lays out the conceptual framework for exploring the conformational fluctuations, dynamical properties, and activity of biomolecular systems using pressure perturbation. Complementary pressure-jump relaxation studies are useful tools to study the kinetics and mechanisms of biomolecular phase transitions and structural transformations, such as membrane fusion or protein and nucleic acid folding. Finally, the advantages of using pressure to explore biomolecular assemblies and modulate enzymatic reactions are discussed.
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Affiliation(s)
- Roland Winter
- Faculty of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44227 Dortmund, Germany
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46
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Mahmoudinobar F, Urban JM, Su Z, Nilsson BL, Dias CL. Thermodynamic Stability of Polar and Nonpolar Amyloid Fibrils. J Chem Theory Comput 2019; 15:3868-3874. [DOI: 10.1021/acs.jctc.9b00145] [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)
- Farbod Mahmoudinobar
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Jennifer M. Urban
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Bradley L. Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L. Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
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47
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Xi S, Wang L, Liu J, Chapman W. Thermodynamics, Microstructures, and Solubilization of Block Copolymer Micelles by Density Functional Theory. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5081-5092. [PMID: 30855146 DOI: 10.1021/acs.langmuir.8b04336] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Block copolymer micelle is one of the most versatile self-assembled structures with applications in drug delivery, cosmetic products, and micellar-enhanced ultrafiltration. The key to design an effective block copolymer to form micelles is to understand how molecular architecture affects critical micelle concentrations, micellar dimensions, and partitioning of solute into the micelle. In this work, we studied micelles from nonionic block copolymers using interfacial statistical associating fluid theory a density functional theory, which explicitly includes block copolymer-water hydrogen bonding and water-water hydrogen bonding. We are able to predict and explain how micellar thermodynamic properties depend on polymer chain architecture. Dimension and aggregation of micelles are investigated for block copolymers with different hyrophobes and hydrophiles. The effects of temperature and pressure on micelle stability are also captured by the theory. The enhanced solubility of hydrophobic substance in water by micelle loading is demonstrated, and predicted solute distribution answers the question about the locus of benzene in micelles from a theoretical perspective.
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Affiliation(s)
- Shun Xi
- Department of Chemical and Biomolecular Engineering , Rice University , Houston , Texas 77005 , United States
| | - Le Wang
- Department of Chemical and Biomolecular Engineering , Rice University , Houston , Texas 77005 , United States
| | - Jinlu Liu
- Department of Chemical and Biomolecular Engineering , Rice University , Houston , Texas 77005 , United States
| | - Walter Chapman
- Department of Chemical and Biomolecular Engineering , Rice University , Houston , Texas 77005 , United States
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48
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Schummel PH, Anders C, Jaworek MW, Winter R. Cosolvent and Crowding Effects on the Temperature- and Pressure-Dependent Dissociation Process of the α/β-Tubulin Heterodimer. Chemphyschem 2019; 20:1098-1109. [PMID: 30829441 DOI: 10.1002/cphc.201900115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/01/2019] [Indexed: 11/09/2022]
Abstract
Tubulin is one of the main components of the cytoskeleton of eukaryotic cells. The formation of microtubules depends strongly on environmental and solution conditions, and has been found to be among the most pressure sensitive processes in vivo. We explored the effects of different types of cosolvents, such as trimethylamine-N-oxide (TMAO), sucrose and urea, and crowding agents to mimic cell-like conditions, on the temperature and pressure stability of the building block of microtubules, i. e. the α/β-tubulin heterodimer. To this end, fluorescence and FTIR spectroscopy, differential scanning and pressure perturbation calorimetry as well as fluorescence anisotropy and correlation spectroscopies were applied. The pressure and temperature of dissociation of α/β-tubulin as well as the underlying thermodynamic parameters upon dissociation, such as volume and enthalpy changes, have been determined for the different solution conditions. The temperature and pressure of dissociation of the α/β-tubulin heterodimer and hence its stability increases dramatically in the presence of TMAO and the nanocrowder sucrose. We show that by adjusting the levels of compatible cosolutes and crowders, cells are able to withstand deteriorating effects of pressure even up to the kbar-range.
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Affiliation(s)
- Paul Hendrik Schummel
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Christian Anders
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Michel W Jaworek
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
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Engstler J, Giovambattista N. Comparative Study of the Effects of Temperature and Pressure on the Water-Mediated Interactions between Apolar Nanoscale Solutes. J Phys Chem B 2019; 123:1116-1128. [PMID: 30592598 DOI: 10.1021/acs.jpcb.8b10296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We perform molecular dynamics simulations to study the effects of temperature and pressure on the water-mediated interaction (WMI) between two nanoscale (apolar) graphene plates at 240 ≤ T ≤ 400 K and -100 ≤ P ≤ 1200 MPa. These are thermodynamic conditions relevant to, for example, cooling-, heating-, compression-, and decompression-induced protein denaturation. We find that at all ( T, P) studied, the potential of mean force between the graphene plates, as a function of plate separation r, exhibits local minima at specific plate separations r = r n that can accommodate n water layers ( n = 0,1,2,3). In particular, our results show that isobaric cooling and isothermal compression have a similar effect on WMI between the plates; both processes tend to suppress the attraction and ultimate collapse of the graphene plates by kinetically trapping the plates at the metastable states with r = r n ( n > 0). In addition, isobaric heating and isothermal decompression also have a similar effect; both processes tend to reduce the range and strength of the interactions between the graphene plates. Interestingly, at low temperatures, the WMI between the plates is affected by crystallization. However, crystallization depends deeply on the water model considered, SPC/E and TIP4P/2005 water models, with the crystallization occurring at different ( T, P) conditions, into different forms of ice.
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Affiliation(s)
- Justin Engstler
- Department of Physics , Brooklyn College of the City University of New York , Brooklyn , New York 11210 , United States
| | - Nicolas Giovambattista
- Department of Physics , Brooklyn College of the City University of New York , Brooklyn , New York 11210 , United States.,Ph.D. Programs in Chemistry and Physics , The Graduate Center of the City University of New York , New York , New York 10016 , United States
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50
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Klamt A, Nagarathinam K, Tanabe M, Kumar A, Balbach J. Hyperbolic Pressure-Temperature Phase Diagram of the Zinc-Finger Protein apoKti11 Detected by NMR Spectroscopy. J Phys Chem B 2019; 123:792-801. [PMID: 30608169 DOI: 10.1021/acs.jpcb.8b11019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For a comprehensive understanding of the thermodynamic state functions describing the stability of a protein, the influence of the intensive properties of temperature and pressure has to be known. With the zinc-finger-containing Kti11, we found a suitable protein for this purpose because folding and unfolding transitions occur at an experimentally accessible temperature (280-330 °K) and pressure (0.1-240 MPa) range. We solved the crystal structure of the apo form of Kti11 to reveal two disulfide bonds at the metal-binding site, which seals off a cavity in the β-barrel part of the protein. From a generally applicable proton NMR approach, we could determine the populations of folded and unfolded chains under all conditions, leading to a hyperbolic pressure-temperature phase diagram rarely observed for proteins. A global fit of a two-state model to all derived populations disclosed reliable values for the change in Gibbs free energy, volume, entropy, heat capacity, compressibility, and thermal expansion upon unfolding. The unfolded state of apoKti11 has a lower compressibility compared to the native state and a smaller volume at ambient pressure. Therefore, a pressure increase up to 200 MPa reduces the population of the native state, and above this value, the native population increases again. Pressure-induced chemical-shift changes in two-dimensional 1H-15N NMR spectra could be employed for a molecular interpretation of the thermodynamic properties of apoKti11.
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Affiliation(s)
- Andi Klamt
- Institute of Physics, Biophysics , Martin-Luther University Halle-Wittenberg , Betty-Heimann Street 7 , 06120 Halle , Germany
| | - Kumar Nagarathinam
- HALOmem, Membrane Protein Biochemistry , Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Street 3 , 06120 Halle (Saale) , Germany.,Institute of Virology , Hannover Medical School , Carl-Neuberg-Straße 1 , D-30625 Hannover , Germany
| | - Mikio Tanabe
- HALOmem, Membrane Protein Biochemistry , Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Street 3 , 06120 Halle (Saale) , Germany.,Structural Biology Research Center, Institute of Materials Structure Science , KEK/High Energy Accelerator Research Organization , 1-1 Oho , Tsukuba , Ibaraki , 305-0801 , Japan
| | - Amit Kumar
- Institute of Physics, Biophysics , Martin-Luther University Halle-Wittenberg , Betty-Heimann Street 7 , 06120 Halle , Germany.,Department of Diabetes, Faculty of Lifesciences and Medicine , King's College London , Great Maze Pond , London SE1 1UL , U.K
| | - Jochen Balbach
- Institute of Physics, Biophysics , Martin-Luther University Halle-Wittenberg , Betty-Heimann Street 7 , 06120 Halle , Germany.,HALOmem, Membrane Protein Biochemistry , Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Street 3 , 06120 Halle (Saale) , Germany
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