1
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Pastore A, Temussi PA. Unfolding under Pressure: An NMR Perspective. Chembiochem 2023; 24:e202300164. [PMID: 37154795 DOI: 10.1002/cbic.202300164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/10/2023]
Abstract
This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this transition has been neglected for many years because of technical difficulties, it provides important information about the forces that keep protein structure together. We first analyse what pressure unfolding is, then provide a critical overview of how NMR spectroscopy has contributed to the field and evaluate the observables used in these studies. Finally, we discuss the commonalities and differences between pressure-, cold- and heat-induced unfolding. We conclude that, despite specific peculiarities, in both cold and pressure denaturation the important contribution of the state of hydration of nonpolar side chains is a major factor that determines the pressure dependence of the conformational stability of proteins.
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Affiliation(s)
- Annalisa Pastore
- European Synchrotron Radiation Facilities, 71 Ave des Martyrs, 38000, Grenoble, France
- The Wohl Institute, King's College London, 5 Cutcombe Rd, SE59RT, London, UK
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2
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Instability Challenges and Stabilization Strategies of Pharmaceutical Proteins. Pharmaceutics 2022; 14:pharmaceutics14112533. [PMID: 36432723 PMCID: PMC9699111 DOI: 10.3390/pharmaceutics14112533] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Maintaining the structure of protein and peptide drugs has become one of the most important goals of scientists in recent decades. Cold and thermal denaturation conditions, lyophilization and freeze drying, different pH conditions, concentrations, ionic strength, environmental agitation, the interaction between the surface of liquid and air as well as liquid and solid, and even the architectural structure of storage containers are among the factors that affect the stability of these therapeutic biomacromolecules. The use of genetic engineering, side-directed mutagenesis, fusion strategies, solvent engineering, the addition of various preservatives, surfactants, and additives are some of the solutions to overcome these problems. This article will discuss the types of stress that lead to instabilities of different proteins used in pharmaceutics including regulatory proteins, antibodies, and antibody-drug conjugates, and then all the methods for fighting these stresses will be reviewed. New and existing analytical methods that are used to detect the instabilities, mainly changes in their primary and higher order structures, are briefly summarized.
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Wu X, Tan M, Zhu Y, Duan H, Ramaswamy HS, Bai W, Wang C. The Influence of High Pressure Processing and Germination on Anti-Nutrients Contents, in Vitro Amino Acid Release and Mineral Digestibility of Soybeans. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kuwajima K, Yagi-Utsumi M, Yanaka S, Kato K. DMSO-Quenched H/D-Exchange 2D NMR Spectroscopy and Its Applications in Protein Science. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123748. [PMID: 35744871 PMCID: PMC9230524 DOI: 10.3390/molecules27123748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022]
Abstract
Hydrogen/deuterium (H/D) exchange combined with two-dimensional (2D) NMR spectroscopy has been widely used for studying the structure, stability, and dynamics of proteins. When we apply the H/D-exchange method to investigate non-native states of proteins such as equilibrium and kinetic folding intermediates, H/D-exchange quenching techniques are indispensable, because the exchange reaction is usually too fast to follow by 2D NMR. In this article, we will describe the dimethylsulfoxide (DMSO)-quenched H/D-exchange method and its applications in protein science. In this method, the H/D-exchange buffer is replaced by an aprotic DMSO solution, which quenches the exchange reaction. We have improved the DMSO-quenched method by using spin desalting columns, which are used for medium exchange from the H/D-exchange buffer to the DMSO solution. This improvement has allowed us to monitor the H/D exchange of proteins at a high concentration of salts or denaturants. We describe methodological details of the improved DMSO-quenched method and present a case study using the improved method on the H/D-exchange behavior of unfolded human ubiquitin in 6 M guanidinium chloride.
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Affiliation(s)
- Kunihiro Kuwajima
- Department of Physics, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Correspondence: (K.K.); (K.K.)
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
- Correspondence: (K.K.); (K.K.)
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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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Lameiras P, Nuzillard JM. Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 123:1-50. [PMID: 34078536 DOI: 10.1016/j.pnmrs.2020.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/06/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The nuclear Overhauser effect (NOE) is a consequence of cross-relaxation between nuclear spins mediated by dipolar coupling. Its sensitivity to internuclear distances has made it an increasingly important tool for the determination of through-space atom proximity relationships within molecules of sizes ranging from the smallest systems to large biopolymers. With the support of sophisticated FT-NMR techniques, the NOE plays an essential role in structure elucidation, conformational and dynamic investigations in liquid-state NMR. The efficiency of magnetization transfer by the NOE depends on the molecular rotational correlation time, whose value depends on solution viscosity. The magnitude of the NOE between 1H nuclei varies from +50% when molecular tumbling is fast to -100% when it is slow, the latter case corresponding to the spin diffusion limit. In an intermediate tumbling regime, the NOE may be vanishingly small. Increasing the viscosity of the solution increases the motional correlation time, and as a result, otherwise unobservable NOEs may be revealed and brought close to the spin diffusion limit. The goal of this review is to report the resolution of structural problems that benefited from the manipulation of the negative NOE by means of viscous solvents, including examples of molecular structure determination, conformation elucidation and mixture analysis (the ViscY method).
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Affiliation(s)
- Pedro Lameiras
- Université de Reims Champagne-Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
| | - Jean-Marc Nuzillard
- Université de Reims Champagne-Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
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Shapira R, Katalan S, Edrei R, Eichen Y. Chirality dependent inverse-melting and re-entrant gelation in α-cyclodextrin/1-phenylethylamine mixtures. RSC Adv 2020; 10:39195-39203. [PMID: 35518437 PMCID: PMC9057694 DOI: 10.1039/d0ra07643k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/16/2020] [Indexed: 01/14/2023] Open
Abstract
Solutions of cyclohexakis-(1→4)-α-d-glucopyranosyl, α-cyclodextrin, αCD, in R-(+)-1-phenylethylamine, αCD/R-PEA, and S-(−)-1-phenylethylamine, αCD/S-PEA, display abnormal phase transitions that strongly depend on supramolecular diastereomeric interactions. While αCD/R-PEA mixtures show one sol–gel inverse-melting phase transition, αCD/S-PEA mixtures show temperature dependent gel–sol–gel re-entrant behavior. NMR, Raman spectroscopy, microscopy and X-ray scattering measurements reveal that hydrogen bond weakening in solution, as well as changes in crystal composition are responsible for entropy increase and gel formation upon heating. Solutions of α-cyclodextrin in chiral 1-phenylethylamine display abnormal phase transitions. Depending on supramolecular diastereomeric interactions, inverse-melting and re-entrant gels are formed.![]()
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Affiliation(s)
- Reut Shapira
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- 3200008 Haifa
- Israel
| | - Sapir Katalan
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- 3200008 Haifa
- Israel
| | - Rachel Edrei
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- 3200008 Haifa
- Israel
| | - Yoav Eichen
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- 3200008 Haifa
- Israel
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8
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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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Pattni V, Heyden M. Pressure Effects on Protein Hydration Water Thermodynamics. J Phys Chem B 2019; 123:6014-6022. [DOI: 10.1021/acs.jpcb.9b04094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Viren Pattni
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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Levin A, Cinar S, Paulus M, Nase J, Winter R, Czeslik C. Analyzing protein-ligand and protein-interface interactions using high pressure. Biophys Chem 2019; 252:106194. [PMID: 31177023 DOI: 10.1016/j.bpc.2019.106194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 01/06/2023]
Abstract
All protein function is based on interactions with the environment. Proteins can bind molecules for their transport, their catalytic conversion, or for signal transduction. They can bind to each other, and they adsorb at interfaces, such as lipid membranes or material surfaces. An experimental characterization is needed to understand the underlying mechanisms, but also to make use of proteins in biotechnology or biomedicine. When protein interactions are studied under high pressure, volume changes are revealed that directly describe spatial contributions to these interactions. Moreover, the strength of protein interactions with ligands or interfaces can be tuned in a smooth way by pressure modulation, which can be utilized in the design of drugs and bio-responsive interfaces. In this short review, selected studies of protein-ligand and protein-interface interactions are presented that were carried out under high pressure. Furthermore, a perspective on bio-responsive interfaces is given where protein-ligand binding is applied to create functional interfacial structures.
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Affiliation(s)
- Artem Levin
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Süleyman Cinar
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Michael Paulus
- Technische Universität Dortmund, Fakultät Physik/Delta, D-44221 Dortmund, Germany
| | - Julia Nase
- Technische Universität Dortmund, Fakultät Physik/Delta, D-44221 Dortmund, Germany
| | - Roland Winter
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Claus Czeslik
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany.
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11
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Röder K, Joseph JA, Husic BE, Wales DJ. Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201800175] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Konstantin Röder
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - Jerelle A. Joseph
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - Brooke E. Husic
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - David J. Wales
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
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12
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Parui S, Jana B. Molecular Insights into the Unusual Structure of an Antifreeze Protein with a Hydrated Core. J Phys Chem B 2018; 122:9827-9839. [PMID: 30286600 DOI: 10.1021/acs.jpcb.8b05350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The primary driving force for protein folding is the formation of a well-packed, anhydrous core. However, recently, the crystal structure of an antifreeze protein, maxi, has been resolved where the core of the protein is filled with water, which apparently contradicts the existing notion of protein folding. Here, we have performed standard molecular dynamics (MD) simulation, replica exchange MD (REMD) simulation, and umbrella sampling using TIP4P water at various temperatures (300, 260, and 240 K) to explore the origin of this unusual structural feature. It is evident from standard MD and REMD simulations that the protein is found to be stable at 240 K in its unusual state. The core of protein has two layers of semi-clathrate water separating the methyl groups of alanine residues from different helical strands. However, with increasing temperature (260 and 300 K), the stability decreases as the core becomes dehydrated, and methyl groups of alanine are tightly packed driven by hydrophobic interactions. Calculation of the potential of mean force by an umbrella sampling technique between a pair of model hydrophobes resembling maxi protein at 240 K shows the stabilization of second solvent-separated minima (SSM), which provides a thermodynamic rationale of the unusual structural feature in terms of weakening of the hydrophobic interaction. Because the stabilization of SSMs is implicated for cold denaturation, it suggests that the maxi protein is so designed by nature where the cold denatured-like state becomes the biologically active form as it works near or below the freezing point of water.
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Affiliation(s)
- Sridip Parui
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Biman Jana
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
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Characterization of low-lying excited states of proteins by high-pressure NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:350-358. [PMID: 30366154 DOI: 10.1016/j.bbapap.2018.10.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/17/2018] [Accepted: 10/22/2018] [Indexed: 12/26/2022]
Abstract
Hydrostatic pressure alters the free energy of proteins by a few kJ mol-1, with the amount depending on their partial molar volumes. Because the folded ground state of a protein contains cavities, it is always a state of large partial molar volume. Therefore pressure always destabilises the ground state and increases the population of partially and completely unfolded states. This is a mild and reversible conformational change, which allows the study of excited states under thermodynamic equilibrium conditions. Many of the excited states studied in this way are functionally relevant; they also seem to be very similar to kinetic folding intermediates, thus suggesting that evolution has made use of the 'natural' dynamic energy landscape of the protein fold and sculpted it to optimise function. This includes features such as ligand binding, structural change during the catalytic cycle, and dynamic allostery.
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Caro JA, Wand AJ. Practical aspects of high-pressure NMR spectroscopy and its applications in protein biophysics and structural biology. Methods 2018; 148:67-80. [PMID: 29964175 PMCID: PMC6133745 DOI: 10.1016/j.ymeth.2018.06.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 01/15/2023] Open
Abstract
Pressure and temperature are the two fundamental variables of thermodynamics. Temperature and chemical perturbation are central experimental tools for the exploration of macromolecular structure and dynamics. Though it has long been recognized that hydrostatic pressure offers a complementary and often unique view of macromolecular structure, stability and dynamics, it has not been employed nearly as much. For solution NMR applications the limited use of high-pressure is undoubtedly traced to difficulties of employing pressure in the context of modern multinuclear and multidimensional NMR. Limitations in pressure tolerant NMR sample cells have been overcome and enable detailed studies of macromolecular energy landscapes, hydration, dynamics and function. Here we review the practical considerations for studies of biological macromolecules at elevated pressure, with a particular emphasis on applications in protein biophysics and structural biology.
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Affiliation(s)
- José A Caro
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6509, United States
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6509, United States.
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15
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Cinar S, Czeslik C. Inhibitor and peptide binding to calmodulin characterized by high pressure Fourier transform infrared spectroscopy and Förster resonance energy transfer. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:617-623. [DOI: 10.1016/j.bbapap.2018.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/09/2018] [Accepted: 03/15/2018] [Indexed: 10/17/2022]
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16
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Uralcan B, Kim SB, Markwalter CE, Prud’homme RK, Debenedetti PG. A Computational Study of the Ionic Liquid-Induced Destabilization of the Miniprotein Trp-Cage. J Phys Chem B 2018; 122:5707-5715. [DOI: 10.1021/acs.jpcb.8b01722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Betul Uralcan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Sang Beom Kim
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Chester E. Markwalter
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Robert K. Prud’homme
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G. Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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17
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Tischer A, Machha VR, Rösgen J, Auton M. "Cooperative collapse" of the denatured state revealed through Clausius-Clapeyron analysis of protein denaturation phase diagrams. Biopolymers 2018; 109:e23106. [PMID: 29457634 DOI: 10.1002/bip.23106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/20/2018] [Accepted: 01/23/2018] [Indexed: 11/09/2022]
Abstract
Protein phase diagrams have a unique potential to identify the presence of additional thermodynamic states even when non-2-state character is not readily apparent from the experimental observables used to follow protein unfolding transitions. Two-state analysis of the von Willebrand factor A3 domain has previously revealed a discrepancy in the calorimetric enthalpy obtained from thermal unfolding transitions as compared with Gibbs-Helmholtz analysis of free energies obtained from the Linear Extrapolation Method (Tischer and Auton, Prot Sci 2013; 22(9):1147-60). We resolve this thermodynamic conundrum using a Clausius-Clapeyron analysis of the urea-temperature phase diagram that defines how Δ H and the urea m-value interconvert through the slope of cm versus T, ( ∂ c m / ∂ T ) = Δ H / ( m T ) . This relationship permits the calculation of Δ H at low temperature from m-values obtained through iso-thermal urea denaturation and high temperature m-values from Δ H obtained through iso-urea thermal denaturation. Application of this equation uncovers sigmoid transitions in both cooperativity parameters as temperature is increased. Such residual thermal cooperativity of Δ H and the m-value confirms the presence of an additional state which is verified to result from a cooperative phase transition between urea-expanded and thermally-compact denatured states. Comparison of the equilibria between expanded and compact denatured ensembles of disulfide-intact and carboxyamidated A3 domains reveals that introducing a single disulfide crosslink does not affect the presence of the additional denatured state. It does, however, make a small thermodynamically favorable free energy (∼-13 ± 1 kJ/mol) contribution to the cooperative denatured state collapse transition as temperature is raised and urea concentration is lowered. The thermodynamics of this "cooperative collapse" of the denatured state retain significant compensations between the enthalpy and entropy contributions to the overall free energy.
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Affiliation(s)
- Alexander Tischer
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Venkata R Machha
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jörg Rösgen
- Department Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania, 17033
| | - Matthew Auton
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
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18
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Wang G, Bondarenko PV, Kaltashov IA. Multi-step conformational transitions in heat-treated protein therapeutics can be monitored in real time with temperature-controlled electrospray ionization mass spectrometry. Analyst 2018; 143:670-677. [PMID: 29303166 DOI: 10.1039/c7an01655g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heat-induced conformational transitions are frequently used to probe the free energy landscapes of proteins. However, the extraction of information from thermal denaturation profiles pertaining to non-native protein conformations remains challenging due to their transient nature and significant conformational heterogeneity. Previously we developed a temperature-controlled electrospray ionization (ESI) source that allowed unfolding and association of biopolymers to be monitored by mass spectrometry (MS) in real time as a function of temperature. The scope of this technique is now extended to systems that undergo multi-step denaturation upon heat stress, as well as relatively small-scale conformational changes that are precursors to protein aggregation. The behavior of two therapeutic proteins (human antithrombin and an IgG1 monoclonal antibody) under heat-stress conditions is monitored in real time, providing evidence that relatively small-scale conformational changes in each system lead to protein oligomerization, followed by aggregation. Temperature-controlled ESI MS is particularly useful for the studies of heat-stressed multi-domain proteins such as IgG, where it allows distinct transitions to be observed. The ability of native temperature-controlled ESI MS to monitor both the conformational changes and oligomerization/degradation with high selectivity complements the classic calorimetric methods, lending itself as a powerful experimental tool for the thermostability studies of protein therapeutics.
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Affiliation(s)
- Guanbo Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biomedical Materials, and School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu, China.
| | - Pavel V Bondarenko
- Attribute Sciences, Process Development, Amgen, Inc., Thousand Oaks, CA, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
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19
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Shapira R, Balazs YS, Kababya S, Edrei R, Eichen Y. Re-entrant supramolecular interactions in inverse-melting α-cyclodextrin·4-methylpyridine·water mixtures: an NMR study. Phys Chem Chem Phys 2018; 20:29610-29615. [DOI: 10.1039/c8cp04328k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Inverse freezing αCD·4MP·H2O turns into a gel as αCD loses its solvation shell. First, it loses its interaction with 4MP, and then its solvation by water.
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Affiliation(s)
- Reut Shapira
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- Haifa
- Israel
| | - Yael S. Balazs
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- Haifa
- Israel
| | - Shifi Kababya
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- Haifa
- Israel
| | - Rachel Edrei
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- Haifa
- Israel
| | - Yoav Eichen
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- Haifa
- Israel
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20
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Roche J, Royer CA, Roumestand C. Monitoring protein folding through high pressure NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:15-31. [PMID: 29157491 DOI: 10.1016/j.pnmrs.2017.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/31/2017] [Accepted: 05/31/2017] [Indexed: 06/07/2023]
Abstract
High-pressure is a well-known perturbation method used to destabilize globular proteins. It is perfectly reversible, which is essential for a proper thermodynamic characterization of a protein equilibrium. In contrast to other perturbation methods such as heat or chemical denaturant that destabilize protein structures uniformly, pressure exerts local effects on regions or domains of a protein containing internal cavities. When combined with NMR spectroscopy, hydrostatic pressure offers the possibility to monitor at a residue level the structural transitions occurring upon unfolding and to determine the kinetic properties of the process. High-pressure NMR experiments can now be routinely performed, owing to the recent development of commercially available high-pressure sample cells. This review summarizes recent advances and some future directions of high-pressure NMR techniques for the characterization at atomic resolution of the energy landscape of protein folding.
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Affiliation(s)
- Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Christian Roumestand
- Centre de Biochimie Structural INSERM U1054, CNRS UMMR 5058, Université de Montpellier, Montpellier 34090, France.
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21
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Krupa P, Sieradzan AK, Mozolewska MA, Li H, Liwo A, Scheraga HA. Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A. J Chem Theory Comput 2017; 13:5721-5730. [DOI: 10.1021/acs.jctc.7b00724] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paweł Krupa
- Baker
Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Adam K. Sieradzan
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Magdalena A. Mozolewska
- Baker
Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Huiyu Li
- Baker
Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Adam Liwo
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Harold A. Scheraga
- Baker
Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
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22
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Alderson TR, Charlier C, Torchia DA, Anfinrud P, Bax A. Monitoring Hydrogen Exchange During Protein Folding by Fast Pressure Jump NMR Spectroscopy. J Am Chem Soc 2017; 139:11036-11039. [PMID: 28766333 DOI: 10.1021/jacs.7b06676] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method is introduced that permits direct observation of the rates at which backbone amide hydrogens become protected from solvent exchange after rapidly dropping the hydrostatic pressure inside the NMR sample cell from denaturing (2.5 kbar) to native (1 bar) conditions. The method is demonstrated for a pressure-sensitized ubiquitin variant that contains two Val to Ala mutations. Increased protection against hydrogen exchange with solvent is monitored as a function of time during the folding process. Results for 53 backbone amides show narrow clustering with protection occurring with a time constant of ca. 85 ms, but slower protection is observed around a reverse turn near the C-terminus of the protein. Remarkably, the native NMR spectrum returns with this slower time constant of ca. 150 ms, indicating that the almost fully folded protein retains molten globule characteristics with severe NMR line broadening until the final hydrogen bonds are formed. Prior to crossing the transition state barrier, hydrogen exchange protection factors are close to unity, but with slightly elevated values in the β1-β2 hairpin, previously shown to be already lowly populated in the urea-denatured state.
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Affiliation(s)
- T Reid Alderson
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Cyril Charlier
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Dennis A Torchia
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Philip Anfinrud
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Ad Bax
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
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23
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Parui S, Jana B. Pairwise Hydrophobicity at Low Temperature: Appearance of a Stable Second Solvent-Separated Minimum with Possible Implication in Cold Denaturation. J Phys Chem B 2017; 121:7016-7026. [DOI: 10.1021/acs.jpcb.7b02676] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Sridip Parui
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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24
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Structural basis of urea-induced unfolding: Unraveling the folding pathway of hemochromatosis factor E. Int J Biol Macromol 2016; 91:1051-61. [DOI: 10.1016/j.ijbiomac.2016.06.055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 12/16/2022]
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25
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Kim SB, Palmer JC, Debenedetti PG. Computational investigation of cold denaturation in the Trp-cage miniprotein. Proc Natl Acad Sci U S A 2016; 113:8991-6. [PMID: 27457961 PMCID: PMC4987839 DOI: 10.1073/pnas.1607500113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The functional native states of globular proteins become unstable at low temperatures, resulting in cold unfolding and impairment of normal biological function. Fundamental understanding of this phenomenon is essential to rationalizing the evolution of freeze-tolerant organisms and developing improved strategies for long-term preservation of biological materials. We present fully atomistic simulations of cold denaturation of an α-helical protein, the widely studied Trp-cage miniprotein. In contrast to the significant destabilization of the folded structure at high temperatures, Trp-cage cold denatures at 210 K into a compact, partially folded state; major elements of the secondary structure, including the α-helix, are conserved, but the salt bridge between aspartic acid and arginine is lost. The stability of Trp-cage's α-helix at low temperatures suggests a possible evolutionary explanation for the prevalence of such structures in antifreeze peptides produced by cold-weather species, such as Arctic char. Although the 310-helix is observed at cold conditions, its position is shifted toward Trp-cage's C-terminus. This shift is accompanied by intrusion of water into Trp-cage's interior and the hydration of buried hydrophobic residues. However, our calculations also show that the dominant contribution to the favorable energetics of low-temperature unfolding of Trp-cage comes from the hydration of hydrophilic residues.
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Affiliation(s)
- Sang Beom Kim
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Jeremy C Palmer
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544;
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26
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Xia Q, Wang L, Xu C, Mei J, Li Y. Effects of germination and high hydrostatic pressure processing on mineral elements, amino acids and antioxidants in vitro bioaccessibility, as well as starch digestibility in brown rice (Oryza sativa L.). Food Chem 2016; 214:533-542. [PMID: 27507507 DOI: 10.1016/j.foodchem.2016.07.114] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 07/17/2016] [Accepted: 07/19/2016] [Indexed: 01/10/2023]
Abstract
The effects of germination and high hydrostatic pressure (HHP) processing on the in vitro bioaccessibility of mineral elements, amino acids (AAs), antioxidants and starch in brown rice (BR) were investigated. Germinated BR (GBR) was obtained by incubating at 37°C for 36h and then subjected to HHP treatments at 0.1, 100, 300 and 500MPa for 10min. The in vitro bioaccessibility of calcium and copper was increased by 12.59-52.17% and 2.87-23.06% after HHP, respectively, but bioaccessible iron was decreased. In addition, HHP significantly improved individual AAs, particularly indispensable AAs and gama-aminobutyric acid, as well as bioaccessible total antioxidant activities and starch resistance to enzymatic hydrolysis. However, germination greatly increased starch digestibility. Atomic force microscopy characterization suggested an obvious structural change in bran fraction at pressures above 300MPa. These results can help to understand the effects of germination and HHP technologies on nutrients bioaccessibility and develop appropriate processing conditions.
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Affiliation(s)
- Qiang Xia
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liping Wang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Congcong Xu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jun Mei
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yunfei Li
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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27
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Bothe JR, Tonelli M, Ali IK, Dai Z, Frederick RO, Westler WM, Markley JL. The Complex Energy Landscape of the Protein IscU. Biophys J 2016; 109:1019-25. [PMID: 26331259 PMCID: PMC4564936 DOI: 10.1016/j.bpj.2015.07.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 07/20/2015] [Accepted: 07/28/2015] [Indexed: 11/10/2022] Open
Abstract
IscU, the scaffold protein for iron-sulfur (Fe-S) cluster biosynthesis in Escherichia coli, traverses a complex energy landscape during Fe-S cluster synthesis and transfer. Our previous studies showed that IscU populates two interconverting conformational states: one structured (S) and one largely disordered (D). Both states appear to be functionally important because proteins involved in the assembly or transfer of Fe-S clusters have been shown to interact preferentially with either the S or D state of IscU. To characterize the complex structure-energy landscape of IscU, we employed NMR spectroscopy, small-angle x-ray scattering (SAXS), and differential scanning calorimetry. Results obtained for IscU at pH 8.0 show that its S state is maximally populated at 25°C and that heating or cooling converts the protein toward the D state. Results from NMR and DSC indicate that both the heat- and cold-induced S→D transitions are cooperative and two-state. Low-resolution structural information from NMR and SAXS suggests that the structures of the cold-induced and heat-induced D states are similar. Both states exhibit similar 1H-15N HSQC spectra and the same pattern of peptidyl-prolyl peptide bond configurations by NMR, and both appear to be similarly expanded compared with the S state based on analysis of SAXS data. Whereas in other proteins the cold-denatured states have been found to be slightly more compact than the heat-denatured states, these two states occupy similar volumes in IscU.
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Affiliation(s)
- Jameson R Bothe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ibrahim K Ali
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ziqi Dai
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ronnie O Frederick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - William M Westler
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin.
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28
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Del Galdo S, Amadei A. The unfolding effects on the protein hydration shell and partial molar volume: a computational study. Phys Chem Chem Phys 2016; 18:28175-28182. [DOI: 10.1039/c6cp05029h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes.
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Affiliation(s)
- Sara Del Galdo
- Department of Chemical Science and Technology
- University of Roma Tor Vergata
- 00133 Roma
- Italy
| | - Andrea Amadei
- Department of Chemical Science and Technology
- University of Roma Tor Vergata
- 00133 Roma
- Italy
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29
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Vanga SK, Singh A, Raghavan V. Review of conventional and novel food processing methods on food allergens. Crit Rev Food Sci Nutr 2015; 57:2077-2094. [DOI: 10.1080/10408398.2015.1045965] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Sai Kranthi Vanga
- Faculty of Agriculture and Environmental Studies, Department of Bioresource Engineering, McGill University, Quebec, Canada
| | - Ashutosh Singh
- Faculty of Agriculture and Environmental Studies, Department of Bioresource Engineering, McGill University, Quebec, Canada
| | - Vijaya Raghavan
- Faculty of Agriculture and Environmental Studies, Department of Bioresource Engineering, McGill University, Quebec, Canada
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30
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Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure. Proc Natl Acad Sci U S A 2015; 112:E2437-46. [PMID: 25918400 DOI: 10.1073/pnas.1506505112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Application of hydrostatic pressure shifts protein conformational equilibria in a direction to reduce the volume of the system. A current view is that the volume reduction is dominated by elimination of voids or cavities in the protein interior via cavity hydration, although an alternative mechanism wherein cavities are filled with protein side chains resulting from a structure relaxation has been suggested [López CJ, Yang Z, Altenbach C, Hubbell WL (2013) Proc Natl Acad Sci USA 110(46):E4306-E4315]. In the present study, mechanisms for elimination of cavities under high pressure are investigated in the L99A cavity mutant of T4 lysozyme and derivatives thereof using site-directed spin labeling, pressure-resolved double electron-electron resonance, and high-pressure circular dichroism spectroscopy. In the L99A mutant, the ground state is in equilibrium with an excited state of only ∼ 3% of the population in which the cavity is filled by a protein side chain [Bouvignies et al. (2011) Nature 477(7362):111-114]. The results of the present study show that in L99A the native ground state is the dominant conformation to pressures of 3 kbar, with cavity hydration apparently taking place in the range of 2-3 kbar. However, in the presence of additional mutations that lower the free energy of the excited state, pressure strongly populates the excited state, thereby eliminating the cavity with a native side chain rather than solvent. Thus, both cavity hydration and structure relaxation are mechanisms for cavity elimination under pressure, and which is dominant is determined by details of the energy landscape.
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31
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Holehouse AS, Garai K, Lyle N, Vitalis A, Pappu RV. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation. J Am Chem Soc 2015; 137:2984-95. [PMID: 25664638 PMCID: PMC4418562 DOI: 10.1021/ja512062h] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones, and therefore, backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations of denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of side chains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that side chains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of side chain-mediated interactions as determinants of the conformational properties of unfolded states in water and in influencing chain expansion upon denaturation.
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Affiliation(s)
- Alex S. Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, USA
| | - Kanchan Garai
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, USA
- TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad, 500075, India
| | - Nicholas Lyle
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, USA
| | - Andreas Vitalis
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-5807, Zurich, Switzerland
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32
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Mahmoudinobar F, Dias CL, Zangi R. Role of side-chain interactions on the formation of α-helices in model peptides. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:032710. [PMID: 25871147 DOI: 10.1103/physreve.91.032710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Indexed: 06/04/2023]
Abstract
The role played by side-chain interactions on the formation of α-helices is studied using extensive all-atom molecular dynamics simulations of polyalanine-like peptides in explicit TIP4P water. The peptide is described by the OPLS-AA force field except for the Lennard-Jones interaction between Cβ-Cβ atoms, which is modified systematically. We identify values of the Lennard-Jones parameter that promote α-helix formation. To rationalize these results, potentials of mean force (PMF) between methane-like molecules that mimic side chains in our polyalanine-like peptides are computed. These PMF exhibit a complex distance dependence where global and local minima are separated by an energy barrier. We show that α-helix propensity correlates with values of these PMF at distances corresponding to Cβ-Cβ of i-i+3 and other nearest neighbors in the α-helix. In particular, the set of Lennard-Jones parameters that promote α-helices is characterized by PMF that exhibit a global minimum at distances corresponding to i-i+3 neighbors in α-helices. Implications of these results are discussed.
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Affiliation(s)
- Farbod Mahmoudinobar
- New Jersey Institute of Technology, Physics Department, University Heights, Newark, New Jersey, 07102-1982, USA
| | - Cristiano L Dias
- New Jersey Institute of Technology, Physics Department, University Heights, Newark, New Jersey, 07102-1982, USA
| | - Ronen Zangi
- Department of Organic Chemistry I and POLYMAT, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
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33
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Fizil Á, Gáspári Z, Barna T, Marx F, Batta G. "Invisible" conformers of an antifungal disulfide protein revealed by constrained cold and heat unfolding, CEST-NMR experiments, and molecular dynamics calculations. Chemistry 2015; 21:5136-44. [PMID: 25676351 PMCID: PMC4464532 DOI: 10.1002/chem.201404879] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Indexed: 12/12/2022]
Abstract
Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two- and three-state analysis of thermal unfolding, that the population of hidden states may weight 20-40 % at 298 K in a disulfide-rich protein. In addition, sensitive (15) N-CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR "dark matter". Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction.
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Affiliation(s)
- Ádám Fizil
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen (Hungary)
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Larrea-Wachtendorff D, Tabilo-Munizaga G, Moreno-Osorio L, Villalobos-Carvajal R, Pérez-Won M. Protein Changes Caused by High Hydrostatic Pressure (HHP): A Study Using Differential Scanning Calorimetry (DSC) and Fourier Transform Infrared (FTIR) Spectroscopy. FOOD ENGINEERING REVIEWS 2015. [DOI: 10.1007/s12393-015-9107-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Kitahara R. High-Pressure NMR Spectroscopy Reveals Functional Sub-states of Ubiquitin and Ubiquitin-Like Proteins. Subcell Biochem 2015; 72:199-214. [PMID: 26174383 DOI: 10.1007/978-94-017-9918-8_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High-pressure nuclear magnetic resonance (NMR) spectroscopy has revealed that ubiquitin has at least two high-energy states--an alternatively folded state N2 and a locally disordered state I--between the basic folded state N1 and totally unfolded U state. The high-energy states are conserved among ubiquitin-like post-translational modifiers, ubiquitin, NEDD8, and SUMO-2, showing the E1-E2-E3 cascade reaction. It is quite intriguing that structurally similar high-energy states are evolutionally conserved in the ubiquitin-like modifiers, and the thermodynamic stabilities vary among the proteins. To investigate atomic details of the high-energy states, a Q41N mutant of ubiquitin was created as a structural model of N2, which is 71% populated even at atmospheric pressure. The convergent structure of the "pure" N2 state was obtained by nuclear Overhauser effect (NOE)-based structural analysis of the Q41N mutant at 2.5 kbar, where the N2 state is 97% populated. The N2 state of ubiquitin is closely similar to the conformation of the protein bound to the ubiquitin-activating enzyme E1. The recognition of E1 by ubiquitin is best explained by conformational selection rather than by induced-fit motion.
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Affiliation(s)
- Ryo Kitahara
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan,
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36
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Abstract
Proteins are essential players in the vast majority of molecular level life processes. Since their structure is in most cases substantial for their correct function, study of their structural changes attracted great interest in the past decades. The three dimensional structure of proteins is influenced by several factors including temperature, pH, presence of chaotropic and cosmotropic agents, or presence of denaturants. Although pressure is an equally important thermodynamic parameter as temperature, pressure studies are considerably less frequent in the literature, probably due to the technical difficulties associated to the pressure studies. Although the first steps in the high-pressure protein study have been done 100 years ago with Bridgman's ground breaking work, the field was silent until the modern spectroscopic techniques allowed the characterization of the protein structural changes, while the protein was under pressure. Recently a number of proteins were studied under pressure, and complete pressure-temperature phase diagrams were determined for several of them. This review summarizes the thermodynamic background of the typical elliptic p-T phase diagram, its limitations and the possible reasons for deviations of the experimental diagrams from the theoretical one. Finally we show some examples of experimentally determined pressure-temperature phase diagrams.
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Affiliation(s)
- László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary,
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Marion J, Trovaslet M, Martinez N, Masson P, Schweins R, Nachon F, Trapp M, Peters J. Pressure-induced molten globule state of human acetylcholinesterase: structural and dynamical changes monitored by neutron scattering. Phys Chem Chem Phys 2015; 17:3157-63. [DOI: 10.1039/c4cp02992e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We used neutron scattering to study the effects of high hydrostatic pressure on the structure and dynamics of human acetylcholinesterase (hAChE).
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Affiliation(s)
- J. Marion
- Univ. Grenoble Alpes
- IBS
- F-38044 Grenoble
- France
- Institut Laue Langevin
| | - M. Trovaslet
- Univ. Grenoble Alpes
- IBS
- F-38044 Grenoble
- France
- Institut de Recherche Biomédicale des Armées
| | - N. Martinez
- Univ. Grenoble Alpes
- IBS
- F-38044 Grenoble
- France
- Institut Laue Langevin
| | - P. Masson
- Univ. Grenoble Alpes
- IBS
- F-38044 Grenoble
- France
- Kazan Federal University
| | - R. Schweins
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
| | - F. Nachon
- Univ. Grenoble Alpes
- IBS
- F-38044 Grenoble
- France
- Institut Laue Langevin
| | - M. Trapp
- Angewandte Physikalische Chemie
- Universität Heidelberg
- 69120 Heidelberg
- Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie
| | - J. Peters
- Univ. Grenoble Alpes
- IBS
- F-38044 Grenoble
- France
- Institut Laue Langevin
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38
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Son I, Shek YL, Tikhomirova A, Baltasar EH, Chalikian TV. Interactions of Urea with Native and Unfolded Proteins: A Volumetric Study. J Phys Chem B 2014; 118:13554-63. [DOI: 10.1021/jp509356k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ikbae Son
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Yuen Lai Shek
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Anna Tikhomirova
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Eduardo Hidalgo Baltasar
- Department
of Physical Chemistry, Faculty of Chemistry, University Complutense of Madrid, 28040 Madrid, Spain
| | - Tigran V. Chalikian
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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39
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Process-induced undesirable compounds: Chances of non-thermal approaches. Meat Sci 2014; 98:392-403. [DOI: 10.1016/j.meatsci.2014.06.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/21/2014] [Accepted: 06/24/2014] [Indexed: 11/19/2022]
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40
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Dias CL, Chan HS. Pressure-Dependent Properties of Elementary Hydrophobic Interactions: Ramifications for Activation Properties of Protein Folding. J Phys Chem B 2014; 118:7488-7509. [DOI: 10.1021/jp501935f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Cristiano L. Dias
- Department
of Physics, New Jersey Institute of Technology, University Heights, Tiernan Hall, Room 463, Newark, New Jersey 07102, United States
- Departments
of Biochemistry, Molecular Genetics, and Physics, University of Toronto, 1 King’s College Circle, Toronto, Ontario Canada M5S 1A8
| | - Hue Sun Chan
- Departments
of Biochemistry, Molecular Genetics, and Physics, University of Toronto, 1 King’s College Circle, Toronto, Ontario Canada M5S 1A8
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41
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Abstract
Fluorescence is the most widely used technique to study the effect of pressure on biochemical systems. The use of pressure as a physical variable sheds light into volumetric characteristics of reactions. Here we focus on the effect of pressure on protein solutions using a simple unfolding example in order to illustrate the applications of the methodology. Topics covered in this review include the relationships between practical aspects and technical limitations; the effect of pressure and the study of protein cavities; the interpretation of thermodynamic and relaxation kinetics; and the study of relaxation amplitudes. Finally, we discuss the insights available from the combination of fluorescence and other methods adapted to high pressure, such as SAXS or NMR. Because of the simplicity and accessibility of high-pressure fluorescence, the technique is a starting point that complements appropriately multi-methodological approaches related to understanding protein function, disfunction, and folding from the volumetric point of view.
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42
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Shao Q, Shi J, Zhu W. Molecular dynamics simulation indicating cold denaturation of β-hairpins. J Chem Phys 2013; 138:085102. [DOI: 10.1063/1.4792299] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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43
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Volume of Hsp90 ligand binding and the unfolding phase diagram as a function of pressure and temperature. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:355-62. [DOI: 10.1007/s00249-012-0884-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 11/15/2012] [Accepted: 12/13/2012] [Indexed: 12/14/2022]
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44
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Buckow R, Sikes A, Tume R. Effect of High Pressure on Physicochemical Properties of Meat. Crit Rev Food Sci Nutr 2013; 53:770-86. [DOI: 10.1080/10408398.2011.560296] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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45
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Zhai Y, Winter R. Effect of molecular crowding on the temperature-pressure stability diagram of ribonuclease A. Chemphyschem 2012; 14:386-93. [PMID: 23281099 DOI: 10.1002/cphc.201200767] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/29/2012] [Indexed: 11/11/2022]
Abstract
FT-IR spectroscopic and thermodynamic measurements were designed to explore the effect of a macromolecular crowder, dextran, on the temperature and pressure-dependent phase diagram of the protein Ribonuclease A (RNase A), and we compare the experimental data with approximate theoretical predictions based on configuration entropy. Exploring the crowding effect on the pressure-induced unfolding of proteins provides insight in protein stability and folding under cell-like dense conditions, since pressure is a fundamental thermodynamic variable linked to molecular volume. Moreover, these studies are of relevance for understanding protein stability in deep-sea organisms, which have to cope with pressures in the kbar range. We found that not only temperature-induced equilibrium unfolding of RNase A, but also unfolding induced by pressure is markedly prohibited in the crowded dextran solutions, suggesting that crowded environments such as those found intracellularly, will also oppress high-pressure protein unfolding. The FT-IR spectroscopic measurements revealed a marked increase in unfolding pressure of 2 kbar in the presence of 30 wt % dextran. Whereas the structural changes upon thermal unfolding of the protein are not significantly influenced in the presence of the crowding agent, through stabilization by dextran the pressure-unfolded state of the protein retains more ordered secondary structure elements, which seems to be a manifestation of the entropic destabilization of the unfolded state by crowding.
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Affiliation(s)
- Yong Zhai
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry, TU Dortmund University, Germany
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46
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Sarma R, Paul S. Effect of trimethylamine-N-oxide on pressure-induced dissolution of hydrophobic solute. J Chem Phys 2012; 137:114503. [DOI: 10.1063/1.4752104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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47
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Sarma R, Paul S. The effect of aqueous solutions of trimethylamine-N-oxide on pressure induced modifications of hydrophobic interactions. J Chem Phys 2012; 137:094502. [DOI: 10.1063/1.4748101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Sarma R, Paul S. The effect of pressure on the hydration structure around hydrophobic solute: A molecular dynamics simulation study. J Chem Phys 2012; 136:114510. [DOI: 10.1063/1.3694834] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Maiti M, Weiner S, Buldyrev SV, Stanley HE, Sastry S. Potential of mean force between hydrophobic solutes in the Jagla model of water and implications for cold denaturation of proteins. J Chem Phys 2012; 136:044512. [DOI: 10.1063/1.3677187] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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Bianco V, Iskrov S, Franzese G. Understanding the role of hydrogen bonds in water dynamics and protein stability. J Biol Phys 2012; 38:27-48. [PMID: 23277668 PMCID: PMC3285729 DOI: 10.1007/s10867-011-9235-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 08/07/2011] [Indexed: 11/30/2022] Open
Abstract
The mechanisms of cold and pressure denaturation of proteins are a matter of debate, but it is commonly accepted that water plays a fundamental role in the process. It has been proposed that the denaturation process is related to an increase of hydrogen bonds among hydration water molecules. Other theories suggest that the causes of denaturation are the density fluctuations of surface water, or the destabilization of hydrophobic contacts as a consequence of water molecule inclusions inside the protein, especially at high pressures. We review some theories that have been proposed to give insight into this problem, and we describe a coarse-grained model of water that compares well with experiments for proteins' hydration water. We introduce its extension for a homopolymer in contact with the water monolayer and study it by Monte Carlo simulations in an attempt to understand how the interplay of water cooperativity and interfacial hydrogen bonds affects protein stability.
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Affiliation(s)
- Valentino Bianco
- Departament de Física Fonamental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain
| | - Svilen Iskrov
- École Normale Supérieure de Cachan, 61, avenue du Président Wilson, 94235 Cachan cedex, France
| | - Giancarlo Franzese
- Departament de Física Fonamental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain
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