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Eskew MW, Reardon P, Benight AS. DNA-based assay for calorimetric determination of protein concentrations in pure or mixed solutions. PLoS One 2024; 19:e0298969. [PMID: 38427623 PMCID: PMC10906865 DOI: 10.1371/journal.pone.0298969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024] Open
Abstract
It was recently reported that values of the transition heat capacities, as measured by differential scanning calorimetry, for two globular proteins and a short DNA hairpin in NaCl buffer are essentially equivalent, at equal concentrations (mg/mL). To validate the broad applicability of this phenomenon, additional evidence for this equivalence is presented that reveals it does not depend on DNA sequence, buffer salt, or transition temperature (Tm). Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm values. In all cases, evaluated protein concentrations determined from the DNA standard curves agreed with the UV-Vis concentration for monomeric proteins. For multimeric proteins evaluated concentrations were greater than determined by UV-Vis suggesting the calorimetric approach can also be an indicator of molecular stoichiometry.
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Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
| | - Patrick Reardon
- OSU NMR Facility, Oregon State University, Corvallis, Oregon, United States of America
| | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
- Department of Physics, Portland State University, Portland, Oregon, United States of America
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2
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Saurabh S, Zhang Q, Li Z, Seddon JM, Kalonia C, Lu JR, Bresme F. Mechanistic Insights into the Adsorption of Monoclonal Antibodies at the Water/Vapor Interface. Mol Pharm 2024; 21:704-717. [PMID: 38194618 PMCID: PMC10848294 DOI: 10.1021/acs.molpharmaceut.3c00821] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 01/11/2024]
Abstract
Monoclonal antibodies (mAbs) are active components of therapeutic formulations that interact with the water-vapor interface during manufacturing, storage, and administration. Surface adsorption has been demonstrated to mediate antibody aggregation, which leads to a loss of therapeutic efficacy. Controlling mAb adsorption at interfaces requires a deep understanding of the microscopic processes that lead to adsorption and identification of the protein regions that drive mAb surface activity. Here, we report all-atom molecular dynamics (MD) simulations of the adsorption behavior of a full IgG1-type antibody at the water/vapor interface. We demonstrate that small local changes in the protein structure play a crucial role in promoting adsorption. Also, interfacial adsorption triggers structural changes in the antibody, potentially contributing to the further enhancement of surface activity. Moreover, we identify key amino acid sequences that determine the adsorption of antibodies at the water-air interface and outline strategies to control the surface activity of these important therapeutic proteins.
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Affiliation(s)
- Suman Saurabh
- Department
of Chemistry, Molecular Sciences Research
Hub Imperial College, London W12 0BZ, U.K.
| | - Qinkun Zhang
- Department
of Chemistry, Molecular Sciences Research
Hub Imperial College, London W12 0BZ, U.K.
| | - Zongyi Li
- Biological
Physics Group, School of Physics and Astronomy, Faculty of Science
and Engineering, the University of Manchester, Manchester M13 9PL, U.K.
| | - John M. Seddon
- Department
of Chemistry, Molecular Sciences Research
Hub Imperial College, London W12 0BZ, U.K.
| | - Cavan Kalonia
- Dosage
Form Design and Development, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Jian R. Lu
- Biological
Physics Group, School of Physics and Astronomy, Faculty of Science
and Engineering, the University of Manchester, Manchester M13 9PL, U.K.
| | - Fernando Bresme
- Department
of Chemistry, Molecular Sciences Research
Hub Imperial College, London W12 0BZ, U.K.
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3
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Eskew MW, Reardon PW, Benight AS. Calorimetric analysis using DNA thermal stability to determine protein concentration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559360. [PMID: 37808849 PMCID: PMC10557601 DOI: 10.1101/2023.09.25.559360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
It was recently reported for two globular proteins and a short DNA hairpin in NaCl buffer that values of the transition heat capacities, Cp,DNA and Cp,PRO, for equal concentrations (mg/mL) of DNA and proteins, are essentially equivalent (differ by less than 1%). Additional evidence for this equivalence is presented that reveals this phenomenon does not depend on DNA sequence, buffer salt, or Tm. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm's. For the molecules, in NaCl and CsCl buffer the evaluated Cp,PRO and Cp,DNA were equivalent. Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. In all cases, evaluated protein concentrations determined from the DNA standard curve agreed with the UV-Vis concentration for monomeric proteins. For samples of multimeric proteins, streptavidin (tetramer), Herpes Simplex Virus glycoprotein D (trimer/dimer), and a 16 base pair DNA duplex (dimer), evaluated concentrations were greater than determined by UV-Vis by factors of 3.94, 2.65, and 2.15, respectively.
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Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon
- Department of Chemistry, Portland State University, Portland, Oregon
| | | | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon
- Department of Chemistry, Portland State University, Portland, Oregon
- Department of Physics, Portland State University, Portland, Oregon
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4
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Ivanov YD, Tatur VY, Shumov ID, Kozlov AF, Valueva AA, Ivanova IA, Ershova MO, Ivanova ND, Stepanov IN, Lukyanitsa AA, Ziborov VS. The Effect of a Rotating Cone on Horseradish Peroxidase Aggregation on Mica Revealed by Atomic Force Microscopy. MICROMACHINES 2022; 13:1947. [PMID: 36363968 PMCID: PMC9697547 DOI: 10.3390/mi13111947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Our study reported herein aims to determine whether an electromagnetic field, induced triboelectrically by a metallic cone, rotating at a frequency of 167 Hz, has an effect on the properties of the horseradish peroxidase (HRP) enzyme. Atomic force microscopy (AFM) was employed to detect even the most subtle effects on single enzyme molecules. In parallel, a macroscopic method (spectrophotometry) was used to reveal whether the enzymatic activity of HRP in solution was affected. An aqueous solution of the enzyme was incubated at a distance of 2 cm from the rotating cone. The experiments were performed at various incubation times. The control experiments were performed with a non-rotating cone. The incubation of the HRP solution was found to cause the disaggregation of the enzyme. At longer incubation times, this disaggregation was found to be accompanied by the formation of higher-order aggregates; however, no change in the HRP enzymatic activity was observed. The results of our experiments could be of interest in the development of enzyme-based biosensors with rotating elements such as stirrers. Additionally, the results obtained herein are important for the correct interpretation of data obtained with such biosensors.
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Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| | - Vadim Y. Tatur
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, 109472 Moscow, Russia
| | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, 119991 Moscow, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
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5
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Eskew MW, Benight AS. Equivalence of the transition heat capacities of proteins and DNA. Biochem Biophys Res Commun 2022; 597:98-101. [PMID: 35134611 DOI: 10.1016/j.bbrc.2022.01.129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 01/31/2022] [Indexed: 01/18/2023]
Abstract
It has been reported for many globular proteins that the native heat capacity at 25 °C, per gram, is the same. This has been interpreted to indicate that heat capacity is a fundamental property of native proteins that provides important information on molecular structure and stability. Heat capacities for both proteins and DNA has been suggested to be related to universal effects of hydration/solvation on native structures. Here we report on results from thermal denaturation analysis of two well-known proteins, human serum albumin and lysozyme, and a short DNA hairpin. The transition heat capacities at the Tm for the three molecules were quantitatively evaluated by differential scanning calorimetry. When normalized per gram rather than per mol the transition heat capacities were found to be precisely equivalent. This observation for the transition heat capacities of the proteins is consistent with previous reports. However, an identical transition heat capacity for DNA has not been reported and was unexpected. Further analysis of the collected data suggested a mass dependence of hydration effects on thermal denaturation that is preserved at the individual protein amino acid and DNA base levels. Equivalence of transition heat capacities suggests the possibility of a universal role of hydration effects on the thermal stability of both proteins and DNA.
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Affiliation(s)
- Matthew W Eskew
- ThermoCap Laboratories Inc, Portland, OR, USA; Department of Chemistry, Portland State University, Portland, OR, USA.
| | - Albert S Benight
- ThermoCap Laboratories Inc, Portland, OR, USA; Department of Chemistry, Portland State University, Portland, OR, USA; Department of Physics, Portland State University, Portland, OR, USA
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6
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7
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Shiraga K, Urabe M, Matsui T, Kikuchi S, Ogawa Y. Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor. Phys Chem Chem Phys 2020; 22:19468-19479. [PMID: 32761010 DOI: 10.1039/d0cp02265a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.
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Affiliation(s)
- Keiichiro Shiraga
- RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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8
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Mechanical Unfolding of Spectrin Repeats Induces Water-Molecule Ordering. Biophys J 2020; 118:1076-1089. [PMID: 32027822 DOI: 10.1016/j.bpj.2020.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 02/07/2023] Open
Abstract
Mechanical processes are involved at many stages of the development of living cells, and often external forces applied to a biomolecule result in its unfolding. Although our knowledge of the unfolding mechanisms and the magnitude of the forces involved has evolved, the role that water molecules play in the mechanical unfolding of biomolecules has not yet been fully elucidated. To this end, we investigated with steered molecular dynamics simulations the mechanical unfolding of dystrophin's spectrin repeat 1 and related the changes in the protein's structure to the ordering of the surrounding water molecules. Our results indicate that upon mechanically induced unfolding of the protein, the solvent molecules become more ordered and increase their average number of hydrogen bonds. In addition, the unfolded structures originating from mechanical pulling expose an increasing amount of the hydrophobic residues to the solvent molecules, and the uncoiled regions adapt a convex surface with a small radius of curvature. As a result, the solvent molecules reorganize around the protein's small protrusions in structurally ordered waters that are characteristic of the so-called "small-molecule regime," which allows water to maintain a high hydrogen bond count at the expense of an increased structural order. We also determined that the response of water to structural changes in the protein is localized to the specific regions of the protein that undergo unfolding. These results indicate that water plays an important role in the mechanically induced unfolding of biomolecules. Our findings may prove relevant to the ever-growing interest in understanding macromolecular crowding in living cells and their effects on protein folding, and suggest that the hydration layer may be exploited as a means for short-range allosteric communication.
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9
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Gosink LJ, Overall CC, Reehl SM, Whitney PD, Mobley DL, Baker NA. Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies. J Phys Chem B 2017; 121:3458-3472. [PMID: 27966363 DOI: 10.1021/acs.jpcb.6b09198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper applies the Bayesian Model Averaging statistical ensemble technique to estimate small molecule solvation free energies. There is a wide range of methods available for predicting solvation free energies, ranging from empirical statistical models to ab initio quantum mechanical approaches. Each of these methods is based on a set of conceptual assumptions that can affect predictive accuracy and transferability. Using an iterative statistical process, we have selected and combined solvation energy estimates using an ensemble of 17 diverse methods from the fourth Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) blind prediction study to form a single, aggregated solvation energy estimate. Methods that possess minimal or redundant information are pruned from the ensemble and the evaluation process repeats until aggregate predictive performance can no longer be improved. We show that this process results in a final aggregate estimate that outperforms all individual methods by reducing estimate errors by as much as 91% to 1.2 kcal mol-1 accuracy. This work provides a new approach for accurate solvation free energy prediction and lays the foundation for future work on aggregate models that can balance computational cost with prediction accuracy.
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Affiliation(s)
| | | | | | | | - David L Mobley
- Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Nathan A Baker
- Division of Applied Mathematics, Brown University , Providence, Rhode Island 02912, United States
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10
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Barman A, Smitherman C, Souffrant M, Gadda G, Hamelberg D. Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. J Chem Inf Model 2015; 56:139-47. [DOI: 10.1021/acs.jcim.5b00560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Arghya Barman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Crystal Smitherman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Michael Souffrant
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Giovanni Gadda
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
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11
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Mirgorod YA, Dolenko TA. Liquid Polyamorphous Transition and Self-Organization in Aqueous Solutions of Ionic Surfactants. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:8535-8547. [PMID: 25797566 DOI: 10.1021/acs.langmuir.5b00479] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Polyamorphous transitions in supercooled water, porous substances, solutions of polyols, and proteins are studied intensively. They accompany the self-organization of hydrocarbons and surfactants. In this study, the methods of polyamorphous transition identification are proposed, and their dependence on hydrocarbons and surfactant concentration and sizes is investigated. The place of polyamorphous transitions in the general theory of phase separation is determined, and their bistability, self-oscillations, hysteresis, fluctuations, cooperative effect, enthalpy, and entropy are described. Surface, volume, and diffusion instabilities of polyamorphous transitions are analyzed. Technologies based on the properties of polyamorphous transitions are proposed.
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Affiliation(s)
| | - Tatiana A Dolenko
- ‡Department of Physics, M. V. Lomonosov Moscow State University, Moscow 119991, Russia
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12
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Espinosa-Marzal RM, Fontani G, Reusch FB, Roba M, Spencer ND, Crockett R. Sugars communicate through water: oriented glycans induce water structuring. Biophys J 2014; 104:2686-94. [PMID: 23790377 DOI: 10.1016/j.bpj.2013.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 04/16/2013] [Accepted: 05/06/2013] [Indexed: 01/13/2023] Open
Abstract
Cells are coated with a glycocalyx-a layer of carbohydrate-containing biomolecules, such as glycoproteins. Although the structure and orientation of the cell-surface glycans are frequently regarded as being random, we have found, using α-1-acid glycoprotein and antitrypsin as model systems for surface glycans, that this is not the case. A glycoprotein monolayer was adsorbed onto hydrophilic and hydrophobic substrates. Surface-force measurements revealed that the orientation of the glycans with respect to the aqueous solution has a profound effect on the structure of vicinal water. The glycan antennae of the surface-adsorbed glycoproteins apparently impose an ordering on the water, resulting in a strong repulsive force over some tens of nanometers with superposed film-thickness transitions ranging from ≈0.7 to 1.8 nm. When the glycan orientation is modified by chemical means, this long-range repulsion disappears. These results may provide an explanation as to why the multiantennary structure is ubiquitous in glycoproteins. Although direct, specific interactions between glycans and other biomolecules are essential for their functionality, these results indicate that glycans' long-range structuring of water may also influence their ability to interact with biomolecules in their vicinity.
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Affiliation(s)
- Rosa M Espinosa-Marzal
- Laboratory for Surface Science and Technology, Department of Materials, ETH Zurich, Zurich, Switzerland
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13
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Psychrophily and catalysis. BIOLOGY 2013; 2:719-41. [PMID: 24832805 PMCID: PMC3960892 DOI: 10.3390/biology2020719] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/18/2013] [Accepted: 03/18/2013] [Indexed: 11/24/2022]
Abstract
Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. Since the discovery that these ecosystems, contrary to what was initially expected, sustain a rather high density and broad diversity of living organisms, increasing efforts have been dedicated to the understanding of the molecular mechanisms involved in their successful adaptation to apparently unfavorable physical conditions. The first question that comes to mind is: How do these organisms compensate for the exponential decrease of reaction rate when temperature is lowered? As most of the chemical reactions that occur in living organisms are catalyzed by enzymes, the kinetic and thermodynamic properties of cold-adapted enzymes have been investigated. Presently, many crystallographic structures of these enzymes have been elucidated and allowed for a rather clear view of their adaptation to cold. They are characterized by a high specific activity at low and moderate temperatures and a rather low thermal stability, which induces a high flexibility that prevents the freezing effect of low temperatures on structure dynamics. These enzymes also display a low activation enthalpy that renders them less dependent on temperature fluctuations. This is accompanied by a larger negative value of the activation entropy, thus giving evidence of a more disordered ground state. Appropriate folding kinetics is apparently secured through a large expression of trigger factors and peptidyl–prolyl cis/trans-isomerases.
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14
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Luong TQ, Verma PK, Mitra RK, Havenith M. Do hydration dynamics follow the structural perturbation during thermal denaturation of a protein: a terahertz absorption study. Biophys J 2011; 101:925-33. [PMID: 21843484 DOI: 10.1016/j.bpj.2011.05.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 03/26/2011] [Accepted: 05/03/2011] [Indexed: 01/28/2023] Open
Abstract
We investigate the thermal denaturation of human serum albumin and the associated solvation using terahertz (THz) spectroscopy in aqueous buffer solution. Far- and near-ultraviolet circular dichroism spectroscopy reveal that the protein undergoes a native (N) to extended (E) state transition at temperature ≤55°C with a marginal change in the secondary and tertiary structure. At 70°C, the protein transforms into an unfolded (U) state with significant irreversible disruption of its structures. We measure the concentration- and temperature-dependent THz absorption coefficient (α) of the protein solution using a p-Ge THz difference spectrometer (2.1-2.8 THz frequency range), thereby probing the collective protein-water network dynamics. When the solvated protein is heated up to 55°C and cooled down again, a reversible change in THz absorption is observed. When increasing the temperature up to 70°C, we find a dramatic irreversible change of THz absorption. The increase in THz absorption compared to bulk water is attributed to a blue shift in the spectrum of the solvated protein compared to bulk water. This is supported by measurements of THz absorption coefficients using THz time-domain spectroscopy (0.1-1.2 THz frequency range). We also use picosecond-resolved fluorescence spectroscopy of the tryptophan 214 moiety of human serum albumin. All experimental observations can be explained by a change in the hydration dynamics of the solvated protein due to the additional exposure of hydrophobic residues upon unfolding.
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Affiliation(s)
- Trung Quan Luong
- Department of Physical Chemistry II, Ruhr-University Bochum, Bochum, Germany
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15
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Sanfeld A, Sefiane K, Steinchen A. Reactions of dipolar bio-molecules in nano-capsules--example of folding-unfolding process. Adv Colloid Interface Sci 2011; 169:26-39. [PMID: 21867984 DOI: 10.1016/j.cis.2011.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 07/22/2011] [Accepted: 07/24/2011] [Indexed: 11/29/2022]
Abstract
The confinement of chemical reactions in nano-capsules can lead to a dramatic effect on the equilibrium constant of these latter. Indeed, capillary effects due to the curvature and surface energy of nano-capsules can alter in a noticeable way the evolution of reactions occurring within. Nano-encapsulation of bio-materials has attracted lately wide interest from the scientific community because of the great potential of its applications in biomedical areas and targeted therapies. The present paper focuses one's attention on alterations of conformation mechanisms due to extremely confining and interacting solvated dipolar macromolecules at their isoelectric point. As a specific example studied here, the folding-unfolding reaction of proteins (particularly RNase A and creatine kinase CK) is drastically changed when encapsulated in solid inorganic hollow nano-capsules. The effects demonstrated in this work can be extended to a wide variety of nano-encapsulation situations. The design and sizing of nano-capsules can even make use of the effects shown in the present study to achieve better and more effective encapsulation.
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Affiliation(s)
- A Sanfeld
- ISM2-AD2M, UMR 6263, Universitė Paul Cezanne, Bd Escadrille Normandie Niemen, 13397, Marseille Cedex 20, France
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16
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Fita P, Fedoseeva M, Vauthey E. Hydrogen-bond-assisted excited-state deactivation at liquid/water interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:4645-4652. [PMID: 21405061 DOI: 10.1021/la104801h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The excited-state dynamics of eosin B (EB) at dodecane/water and decanol/water interfaces has been investigated with polarization-dependent and time-resolved surface second harmonic generation. The results of the polarization-dependent measurements vary substantially with (1) the EB concentration, (2) the age of the sample, and (3) the nature of the organic phase. All of these effects are ascribed to the formation of EB aggregates at the interface. Aggregation also manifests itself in the time-resolved measurements as a substantial shortening of the excited-state lifetime of EB. However, independently of the dye concentration used, the excited-state lifetime of EB at both dodecane/water and decanol/water interfaces is much longer than in bulk water, where the excited-state population undergoes hydrogen-bond-assisted non-radiative deactivation in a few picoseconds. These results indicate that hydrogen bonding between EB and water molecules at liquid/water interfaces is either much less efficient than in bulk water or does not enhance non-radiative deactivation. This strong increase of the excited-state lifetime of EB at liquid/water interfaces opens promising avenues of applying this molecule as a fluorescent interfacial probe.
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Affiliation(s)
- Piotr Fita
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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17
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Seker UOS, Ozel T, Demir HV. Peptide-mediated constructs of quantum dot nanocomposites for enzymatic control of nonradiative energy transfer. NANO LETTERS 2011; 11:1530-1539. [PMID: 21428276 DOI: 10.1021/nl104295b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A bottom-up approach for constructing colloidal semiconductor quantum dot (QDot) nanocomposites that facilitate nonradiative Förster-type resonance energy transfer (FRET) using polyelectrolyte peptides was proposed and realized. The electrostatic interaction of these polypeptides with altering chain lengths was probed for thermodynamic, structural, and morphological aspects. The resulting nanocomposite film was successfully cut with the protease by digesting the biomimetic peptide layer upon which the QDot assembly was constructed. The ability to control photoluminescence decay lifetime was demonstrated by proteolytic enzyme activity, opening up new possibilities for biosensor applications.
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18
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Norris V. Speculations on the initiation of chromosome replication in Escherichia coli: the dualism hypothesis. Med Hypotheses 2011; 76:706-16. [PMID: 21349650 DOI: 10.1016/j.mehy.2011.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Revised: 01/23/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
The exact nature of the mechanism that triggers initiation of chromosome replication in the best understood of all organisms, Escherichia coli, remains mysterious. Here, I suggest that this mechanism evolved in response to the problems that arise if chromosome replication does not occur. E. coli is now known to be highly structured. This leads me to propose a mechanism for initiation of replication based on the dynamics of large assemblies of molecules and macromolecules termed hyperstructures. In this proposal, hyperstructures and their constituents are put into two classes, non-equilibrium and equilibrium, that spontaneously separate and that are appropriate for life in either good or bad conditions. Maintaining the right ratio(s) of non-equilibrium to equilibrium hyperstructures is therefore a major challenge for cells. I propose that this maintenance entails a major transfer of material from equilibrium to non-equilibrium hyperstructures once per cell and I further propose that this transfer times the cell cycle. More specifically, I speculate that the dialogue between hyperstructures involves the structuring of water and the condensation of cations and that one of the outcomes of ion condensation on ribosomal hyperstructures and decondensation from the origin hyperstructure is the separation of strands at oriC responsible for triggering initiation of replication. The dualism hypothesis that comes out of these speculations may help integrate models for initiation of replication, chromosome segregation and cell division with the 'prebiotic ecology' scenario of the origins of life.
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Affiliation(s)
- Vic Norris
- AMMIS Laboratory, EA 3829, Department of Biology, University of Rouen, 76821 Mont Saint Aignan, France.
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19
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Mehrnejad F, Ghahremanpour MM, Khadem-Maaref M, Doustdar F. Effects of osmolytes on the helical conformation of model peptide: Molecular dynamics simulation. J Chem Phys 2011; 134:035104. [DOI: 10.1063/1.3530072] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Beauchamp DL, Khajehpour M. Probing the effect of water-water interactions on enzyme activity with salt gradients: a case-study using ribonuclease t1. J Phys Chem B 2010; 114:16918-28. [PMID: 21114308 DOI: 10.1021/jp107556s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water molecules interact with one another via hydrogen bonds. Experimental and theoretical evidence indicates that these hydrogen bonds occur in two modalities--high- and low-angle hydrogen bonding--and that the addition of various solutes to water affects only the number of water molecules participating in a specific type of hydrogen bond interactions, not the nature of the water-water interactions. In this work, we have investigated the effect of each of these hydrogen bonding types upon the activity of the enzyme ribonuclease t1. This was done through perturbation of the water hydrogen bonding distribution by using various salts. Our results indicate that various salts differ in their ability to reduce the enzymatic activity of ribonuclease t1, and this ability is well correlated with the ability of each salt to promote high-angle hydrogen bonding in water. By applying the two-phase model of liquid water (i.e., liquid water being modeled as an equilibrium existing between two phases, LD and HD water), we demonstrate that our results are compatible with the assumption that increasing the population of high-angle hydrogen bonds among water molecules stabilizes the more compact, less active conformations of the enzyme. This indicates that the structures that proteins adopt in water solution depend upon the nature of interactions between water molecules.
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Affiliation(s)
- David L Beauchamp
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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21
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Boucher V, Buitink J, Lin X, Boudet J, Hoekstra FA, Hundertmark M, Renard D, Leprince O. MtPM25 is an atypical hydrophobic late embryogenesis-abundant protein that dissociates cold and desiccation-aggregated proteins. PLANT, CELL & ENVIRONMENT 2010; 33:418-30. [PMID: 20002332 DOI: 10.1111/j.1365-3040.2009.02093.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Late embryogenesis-abundant (LEA) proteins are one of the components involved in desiccation tolerance (DT) by maintaining cellular structures in the dry state. Among them, MtPM25, a member of the group 5 is specifically associated with DT in Medicago truncatula seeds. Its function is unknown and its classification as a LEA protein remains elusive. Here, evidence is provided that MtPM25 is a hydrophobic, intrinsically disordered protein that shares the characteristics of canonical LEA proteins. Screening protective activities by testing various substrates against freezing, heating and drying indicates that MtPM25 is unable to protect membranes but able to prevent aggregation of proteins during stress. Prevention of aggregation was also found for the water soluble proteome of desiccation-sensitive radicles. This inhibition was significantly higher than that of MtEM6, one of the most hydrophilic LEA protein associated with DT. Moreover, when added after the stress treatment, MtPM25 is able to rapidly dissolve aggregates in a non-specific manner. Sorption isotherms show that when it is unstructured, MtPM25 absorbs up to threefold more water than MtEM6. MtPM25 is likely to act as a protective molecule during drying and plays an additional role as a repair mechanism compared with other LEA proteins.
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Affiliation(s)
- Virginie Boucher
- Université d'Angers, INRA, Agrocampus-Ouest, UMR1191 Physiologie Moléculaire des Semences, 16 Bd Lavoisier, F-49045 Angers, France
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22
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Guo F, Friedman JM. Charge density-dependent modifications of hydration shell waters by Hofmeister ions. J Am Chem Soc 2009; 131:11010-8. [PMID: 19603752 PMCID: PMC2745343 DOI: 10.1021/ja902240j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gadolinium (Gd(3+)) vibronic sideband luminescence spectroscopy (GVSBLS) is used to probe, as a function of added Hofmeister series salts, changes in the OH stretching frequency derived from first-shell waters of aqueous Gd(3+) and of Gd(3+) coordinated to three different types of molecules: (i) a chelate (EDTA), (ii) structured peptides (mSE3/SE2) of the lanthanide-binding tags (LBTs) family with a single high-affinity binding site, and (iii) a calcium-binding protein (calmodulin) with four binding sites. The vibronic sideband (VSB) corresponding to the OH stretching mode of waters coordinated to Gd(3+), whose frequency is inversely correlated with the strength of the hydrogen bonding to neighboring waters, exhibits an increase in frequency when Gd(3+) becomes coordinated to either EDTA, calmodulin, or mSE3 peptide. In all of these cases, the addition of cation chloride or acetate salts to the solution increases the frequency of the vibronic band originating from the OH stretching mode of the coordinated waters in a cation- and concentration-dependent fashion. The cation dependence of the frequency increase scales with charge density of the cations, giving rise to an ordering consistent with the Hofmeister ordering. On the other hand, water Raman spectroscopy shows no significant change upon addition of these salts. Additionally, it is shown that the cation effect is modulated by the specific anion used. The results indicate a mechanism of action for Hofmeister series ions in which hydrogen bonding among hydration shell waters is modulated by several factors. High charge density cations sequester waters in a configuration that precludes strong hydrogen bonding to neighboring waters. Under such conditions, anion effects emerge as anions compete for hydrogen-bonding sites with the remaining free waters on the surface of the hydration shell. The magnitude of the anion effect is both cation and Gd(3+)-binding site specific.
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Affiliation(s)
- Feng Guo
- Department of Biophysics and Physiology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, U.S.A. 10461
| | - Joel M. Friedman
- Department of Biophysics and Physiology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, U.S.A. 10461
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23
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Mitra T, Miró P, Tomsa AR, Merca A, Bögge H, Ávalos J, Poblet JM, Bo C, Müller A. Gated and Differently Functionalized (New) Porous Capsules Direct Encapsulates' Structures: Higher and Lower Density Water. Chemistry 2009; 15:1844-52. [DOI: 10.1002/chem.200801602] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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24
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Davidovic M, Mattea C, Qvist J, Halle B. Protein Cold Denaturation as Seen From the Solvent. J Am Chem Soc 2008; 131:1025-36. [DOI: 10.1021/ja8056419] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Monika Davidovic
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
| | - Carlos Mattea
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
| | - Johan Qvist
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
| | - Bertil Halle
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
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25
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Gonzalez L, Wess T. Use of attenuated total reflection-Fourier transform infrared spectroscopy to measure collagen degradation in historical parchments. APPLIED SPECTROSCOPY 2008; 62:1108-1114. [PMID: 18926020 DOI: 10.1366/000370208786049196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Developing a noninvasive method to assess the degraded state of historical parchments is essential to providing the best possible care for these documents. The conformational changes observed when collagen molecules, the primary constituent of parchment, unfold have been analyzed using attenuated total reflection-Fourier transform infrared (ATR-FT-IR) spectroscopy and the nanoscopic structural changes have been analyzed using X-ray diffraction (XRD). The relationship between the results obtained from these techniques was studied using principal component analysis, where correlation was found. The extent of gelatinization of historical parchments has been assessed using ATR-FT-IR and XRD and the frequency shifts observed as collagen degrades into gelatin have been reported. These results indicate that collagen degradation can be measured noninvasively in parchment and demonstrate the utility of ATR-FT-IR spectroscopy as a method to investigate historical documents.
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Affiliation(s)
- Lee Gonzalez
- School of Optometry and Vision Science, Maindy Road, Cardiff University, Cardiff, CF24 4LU, UK.
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26
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Djikaev YS, Ruckenstein E. Thermal denaturation of a native protein via spinodal decomposition in the framework of first-passage-time analysis. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:011909. [PMID: 18763984 DOI: 10.1103/physreve.78.011909] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Indexed: 05/26/2023]
Abstract
In this paper we present a kinetic model for the thermal unfolding of a native protein. Due to a sufficiently large temperature increase or decrease, the rate with which a cluster of native residues within a protein emits residues becomes larger than the rate of absorption of residues from the unfolded part of the protein in the whole range of cluster sizes up to the size of the whole protein. This leads to the unfolding of the protein in a barrierless way, i.e., as spinodal decomposition. Using the formalism of the first passage time analysis [previously applied also to the problem of protein folding via nucleation by the authors, J. Phys. Chem. B 111, 886 (2007); J. Chem. Phys. 126, 175103 (2007)], one can determine the temperature dependence of the rates of emission and absorption of residues by the cluster. Knowing these rates as functions of temperature and cluster size, one can find the threshold temperatures of cold and hot barrierless denaturation as well as the unfolding times at temperatures lower and higher, respectively, than those threshold values. For a numerical illustration, the method is applied to the thermal unfolding of a model protein consisting of 2500 residues.
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Affiliation(s)
- Y S Djikaev
- Department of Chemical and Biological Engineering, SUNY at Buffalo, Buffalo, New York 14260, USA.
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27
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Lopez CF, Darst RK, Rossky PJ. Mechanistic elements of protein cold denaturation. J Phys Chem B 2008; 112:5961-7. [PMID: 18181599 DOI: 10.1021/jp075928t] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Globular proteins undergo structural transitions to denatured states when sufficient thermodynamic state or chemical perturbations are introduced to their native environment. Cold denaturation is a somewhat counterintuitive phenomenon whereby proteins lose their compact folded structure as a result of a temperature drop. The currently accepted explanation for cold denaturation is based on an associated favorable change in the contact free energy between water and nonpolar groups at colder temperatures which would weaken the hydrophobic interaction and is thought to eventually allow polymer entropy to disrupt protein tertiary structure. In this paper we explore how this environmental perturbation leads to changes in the protein hydration and local motions in apomyoglobin. We do this by analyzing changes in protein hydration and protein motion from molecular dynamics simulation trajectories initially at 310 K, followed by a temperature drop to 278 K. We observe an increase in the number of solvent contacts around the protein and, in particular, distinctly around nonpolar atoms. Further analysis shows that the fluctuations of some protein atoms increase with decreasing temperature. This is accompanied by an observed increase in the isothermal compressibility of the protein, indicating an increase in the protein interior interstitial space. Closer inspection reveals that atoms with increased compressibility and larger-than-expected fluctuations are localized within the protein core regions. These results provide insight into a description of the mechanism of cold denaturation. That is, the lower temperature leads to solvent-induced packing defects at the protein surface, and this more favorable water-protein interaction in turn destabilizes the overall protein structure.
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Affiliation(s)
- Carlos F Lopez
- Center for Computational Molecular Sciences, Institute for Computational Engineering and Science, and Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712-1167, USA
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28
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Abstract
Background Many well-documented biochemical processes lack a molecular mechanism. Examples are: how ATP hydrolysis and an enzyme contrive to perform work, such as active transport; how peptides are formed from amino acids and DNA from nucleotides; how proteases cleave peptide bonds, how bone mineralises; how enzymes distinguish between sodium and potassium; how chirality of biopolymers was established prebiotically. Methodology/Principal Findings It is shown that involvement of water in all these processes is mandatory, but the water must be of the simplified configuration in which there are only two strengths of water-water hydrogen bonds, and in which these two types of water coexist as microdomains throughout the liquid temperature range. Since they have different strengths of hydrogen bonds, the microdomains differ in all their physical and chemical properties. Solutes partition asymmetrically, generating osmotic pressure gradients which must be compensated for or abolished. Displacement of the equilibrium between high and low density waters incurs a thermodynamic cost which limits solubility, depresses ionisation of water, drives protein folding and prevents high density water from boiling at its intrinsic boiling point which appears to be below 0°C. Active processes in biochemistry take place in sequential partial reactions, most of which release small amounts of free energy as heat. This ensures that the system is never far from equilibrium so that efficiency is extremely high. Energy transduction is neither possible and nor necessary. Chirality was probably established in prebiotic clays which must have carried stable populations of high density and low density water domains. Bioactive enantiomorphs partition into low density water in which they polymerise spontaneously. Conclusions/Significance The simplified model of water has great explanatory power.
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Goobes G, Goobes R, Shaw WJ, Gibson JM, Long JR, Raghunathan V, Schueler-Furman O, Popham JM, Baker D, Campbell CT, Stayton PS, Drobny GP. The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S32-S47. [PMID: 18172904 DOI: 10.1002/mrc.2123] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Proteins are found to be involved in interaction with solid surfaces in numerous natural events. Acidic proteins that adsorb to crystal faces of a biomineral to control the growth and morphology of hard tissue are only one example. Deducing the mechanisms of surface recognition exercised by proteins has implications to osteogenesis, pathological calcification and other proteins functions at their adsorbed state. Statherin is an enamel pellicle protein that inhibits hydroxyapatite nucleation and growth, lubricates the enamel surface, and is recognized by oral bacteria in periodontal diseases. Here, we highlight some of the insights we obtained recently using both thermodynamic and solid state NMR measurements to the adsorption process of statherin to hydroxyapatite. We combine macroscopic energy characterization with microscopic structural findings to present our views of protein adsorption mechanisms and the structural changes accompanying it and discuss the implications of these studies to understanding the functions of the protein adsorbed to the enamel surfaces.
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Affiliation(s)
- Gil Goobes
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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30
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Page RC, Li C, Hu J, Gao FP, Cross TA. Lipid bilayers: an essential environment for the understanding of membrane proteins. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S2-S11. [PMID: 18095258 DOI: 10.1002/mrc.2077] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 07/20/2007] [Accepted: 08/06/2007] [Indexed: 05/25/2023]
Abstract
Membrane protein structure and function is critically dependent on the surrounding environment. Consequently, utilizing a membrane mimetic that adequately models the native membrane environment is essential. A range of membrane mimetics are available but none generates a better model of native aqueous, interfacial, and hydrocarbon core environments than synthetic lipid bilayers. Transmembrane α-helices are very stable in lipid bilayers because of the low water content and low dielectric environment within the bilayer hydrocarbon core that strengthens intrahelical hydrogen bonds and hinders structural rearrangements within the transmembrane helices. Recent evidence from solid-state NMR spectroscopy illustrates that transmembrane α-helices, both in peptides and full-length proteins, appear to be highly uniform based on the observation of resonance patterns in PISEMA spectra. Here, we quantitate for the first time through simulations what we mean by highly uniform structures. Indeed, helices in transmembrane peptides appear to have backbone torsion angles that are uniform within ± 4°. While individual helices can be structurally stable due to intrahelical hydrogen bonds, interhelical interactions within helical bundles can be weak and nonspecific, resulting in multiple packing arrangements. Some helical bundles have the capacity through their amino acid composition for hydrogen bonding and electrostatic interactions to stabilize the interhelical conformations and solid-state NMR data is shown here for both of these situations. Solid-state NMR spectroscopy is unique among the techniques capable of determining three-dimensional structures of proteins in that it provides the ability to characterize structurally the membrane proteins at very high resolution in liquid crystalline lipid bilayers.
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Affiliation(s)
- Richard C Page
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
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31
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Li C, Qin H, Gao FP, Cross TA. Solid-state NMR characterization of conformational plasticity within the transmembrane domain of the influenza A M2 proton channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3162-70. [PMID: 17936720 DOI: 10.1016/j.bbamem.2007.08.025] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 08/11/2007] [Accepted: 08/29/2007] [Indexed: 11/27/2022]
Abstract
Membrane protein function within the membrane interstices is achieved by mechanisms that are not typically available to water-soluble proteins. The whole balance of molecular interactions that stabilize three-dimensional structure in the membrane environment is different from that in an aqueous environment. As a result interhelical interactions are often dominated by non-specific van der Waals interactions permitting dynamics and conformational heterogeneity in these interfaces. Here, solid-state NMR data of the transmembrane domain of the M2 protein from influenza A virus are used to exemplify such conformational plasticity in a tetrameric helical bundle. Such data lead to very high resolution structural restraints that can identify both subtle and substantial structural differences associated with various states of the protein. Spectra from samples using two different preparation protocols, samples prepared in the presence and absence of amantadine, and spectra as a function of pH are used to illustrate conformational plasticity.
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Affiliation(s)
- Conggang Li
- Department of Chemistry and Biochemistry, Florida State University, Florida, USA
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32
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Zhang L, Noda I, Czarnik-Matusewicz B, Wu Y. Multivariate estimation between mid and near-infrared spectra of hexafluoroisopropanol-water mixtures. ANAL SCI 2007; 23:901-5. [PMID: 17625338 DOI: 10.2116/analsci.23.901] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Multivariate regression based on partial least squares (PLS2) was applied to estimating one spectral dataset from another set having an intrinsic relationship with each other. An estimation was successfully carried out between mid-infrared (IR) spectra in the range of 2980 - 3800 cm(-1) and that of near-infrared (NIR) spectra in the range of 6000 - 7500 cm(-1) for hexafluoroisopropanol (HFIP)-water mixtures. The result demonstrates that, after building a suitable regression model, not only NIR spectra, but also well-resolved IR spectra of HFIP-water mixture can be estimated properly in this way. The use of IR and NIR spectroscopy together with PLS2 regression will not only alleviate laborious and costly measurements, but also open a way to provide easier assignments of generally weak and highly overlapped NIR spectral bands.
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Affiliation(s)
- Liping Zhang
- Key Lab for Supramolecular Structure and Material of Ministry of Education, Jilin University, Changchun, PR China
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33
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Miyawaki O. Hydration state change of proteins upon unfolding in sugar solutions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:928-35. [PMID: 17581805 DOI: 10.1016/j.bbapap.2007.05.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2007] [Revised: 05/16/2007] [Accepted: 05/17/2007] [Indexed: 10/23/2022]
Abstract
Change in hydration number of proteins upon unfolding, Deltan, was obtained from the analysis of thermal unfolding behavior of proteins in various sugar solutions with water activity, a(W), varied. By applying the reciprocal form of Wyman-Tanford equation, Deltan was determined to be 133.9, 124.1, and 139.2 per protein molecule for ribonuclease A at pH=5.5, 4.2, and 2.8, respectively, 201.4 for lysozyme at pH=5.5, and 100.1 for alpha-chymotripnogen A at pH=2.0. Among the sugars tested, reducing sugars gave the lower apparent Deltan as compared with nonreducing sugars probably because of the direct interaction of reducing terminal with amino group of proteins at a high temperature. From the knowledge of Deltan, a new thermodynamic model for protein stability was proposed with explicit consideration for hydration state change of protein upon unfolding. From this model, the contribution of a(W) was proven to be always positive for stabilization of proteins and its effect is not negligible depending on Deltan and a(W).
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Affiliation(s)
- Osato Miyawaki
- Department of Food Science, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan.
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34
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Mehrnejad F, Naderi-Manesh H, Ranjbar B. The structural properties of magainin in water, TFE/water, and aqueous urea solutions: molecular dynamics simulations. Proteins 2007; 67:931-40. [PMID: 17357162 DOI: 10.1002/prot.21293] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Here, the MD simulations and comparative structural analysis of Magainin in water, TFE/water, and 2M, 4M, and BM urea solutions is reported. For MAG-TFE/water and MAG-2M urea the largely alpha helical conformation of the peptide is maintained throughout the 9-ns simulation. While in water, 4M urea, and 8M urea, the helix length decreases and at the same time helix radius increases. This suggests a more destabilized magainin secondary structure. Our simulation data reveals that the stabilizing effect of TFE is induced by preferential accumulation of TFE molecules around the alpha helical peptide. These results indicate that an aqueous urea solution solvates the surface of polypeptide chain more favorably than pure water. Urea molecules interact more favorably with nonpolar groups of the peptide in comparison with water, and the presence of urea improves the interactions of water molecules with the hydrophilic groups of the peptide. At 8M urea, there are more direct interactions between the urea and solute, and the helix is destabilized. At 2M urea, the interaction of urea molecules and nonpolar residues are weak, therefore, the presence of urea molecules decreases the interactions of water molecules with hydrophilic groups. Urea could not deteriorate the peptide secondary structure with time from an initial helix structure.
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Affiliation(s)
- Faramarz Mehrnejad
- Faculty of Science, Department of Biophysics, Tarbiat Modarres University, Tehran, Iran
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35
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Hadi-Alijanvand H, Ahmad F, Moosavi-Movahedi AA. The correlation of cold denaturation temperature with surface stability factor of proteins. Protein J 2007; 26:395-402. [PMID: 17503164 DOI: 10.1007/s10930-007-9079-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cold denaturation is an intriguing phenomenon in protein denaturation for elucidating protein accessible surface area (ASA). Compared to the impact of protein surface, the importance of protein-water interactions in cold denaturation may be ruled out significantly. Here, based on the ASA, we have defined a new factor, the surface stability factor (SSF). From the SSF, in combination with the cold denaturation temperature (T(g')) or temperature at DeltaS = 0 (T(s)) of a given protein, one can predict the percent of hydrophobic surface area (H), percent of total surface there on positive and negative charge sum (effective charge) be zero (C), percent of patches hydrophobicity (HP) and others critical surface parameters without any need to the crystallographic data.
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36
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Rakhmanov SV, Makeev VJ. Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling. BMC STRUCTURAL BIOLOGY 2007; 7:19. [PMID: 17397537 PMCID: PMC1852318 DOI: 10.1186/1472-6807-7-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Accepted: 03/30/2007] [Indexed: 11/10/2022]
Abstract
Background Accurate description of protein interaction with aqueous solvent is crucial for modeling of protein folding, protein-protein interaction, and drug design. Efforts to build a working description of solvation, both by continuous models and by molecular dynamics, yield controversial results. Specifically constructed knowledge-based potentials appear to be promising for accounting for the solvation at the molecular level, yet have not been used for this purpose. Results We developed original knowledge-based potentials to study protein hydration at the level of atom contacts. The potentials were obtained using a new Monte Carlo reference state (MCRS), which simulates the expected probability density of atom-atom contacts via exhaustive sampling of structure space with random probes. Using the MCRS allowed us to calculate the expected atom contact densities with high resolution over a broad distance range including very short distances. Knowledge-based potentials for hydration of protein atoms of different types were obtained based on frequencies of their contacts at different distances with protein-bound water molecules, in a non-redundant training data base of 1776 proteins with known 3D structures. Protein hydration sites were predicted in a test set of 12 proteins with experimentally determined water locations. The MCRS greatly improves prediction of water locations over existing methods. In addition, the contribution of the energy of macromolecular solvation into total folding free energy was estimated, and tested in fold recognition experiments. The correct folds were preferred over all the misfolded decoys for the majority of proteins from the improved Rosetta decoy set based on the structure hydration energy alone. Conclusion MCRS atomic hydration potentials provide a detailed distance-dependent description of hydropathies of individual protein atoms. This allows placement of water molecules on the surface of proteins and in protein interfaces with much higher precision. The potentials provide a means to estimate the total solvation energy for a protein structure, in many cases achieving a successful fold recognition. Possible applications of atomic hydration potentials to structure verification, protein folding and stability, and protein-protein interactions are discussed.
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Affiliation(s)
- Sergei V Rakhmanov
- Institute of Genetics and Selection of Industrial Microorganisms, State Research Centre GosNIIgenetika, 1Dorozhny proezd, 1, Moscow, Russia
| | - Vsevolod J Makeev
- Institute of Genetics and Selection of Industrial Microorganisms, State Research Centre GosNIIgenetika, 1Dorozhny proezd, 1, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
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Goobes R, Goobes G, Campbell CT, Stayton PS. Thermodynamics of statherin adsorption onto hydroxyapatite. Biochemistry 2006; 45:5576-86. [PMID: 16634639 DOI: 10.1021/bi052321z] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Statherin is a salivary protein that inhibits the nucleation and growth of hydroxyapatite crystals in the supersaturated environment of the oral cavity. The thermodynamics of adsorption of statherin onto hydroxyapatite crystals have been characterized here by isothermal titration calorimetry and equilibrium adsorption isotherm analysis. At 25 degrees C, statherin adsorption is characterized by an exothermic enthalpy of approximately 3 kcal/mol that diminishes to zero at approximately 25% surface coverage. The initial heat of statherin adsorption increases with temperature, displaying a positive heat capacity change of 194 +/- 7 cal K(-)(1) mol(-)(1) at 25 degrees C. The heat of adsorption during this initial phase is strongly dependent on the buffer species, and from the differential heats of buffer ionization, it can be calculated that approximately one proton is taken up by the crystal or protein upon adsorption. The free energy of adsorption is dominated at all coverages by a large positive entropy (>or=23 cal K(-)(1) mol(-)(1)), which may be partially due to the loss of organized water that hydrates the protein and the mineral surface prior to adsorption. These results are interpreted using a two-site model for adsorption of statherin onto the hydroxyapatite crystals.
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Affiliation(s)
- Rivka Goobes
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-1721, USA
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Hill JJ, Shalaev EY, Zografi G. Thermodynamic and dynamic factors involved in the stability of native protein structure in amorphous solids in relation to levels of hydration. J Pharm Sci 2005; 94:1636-67. [PMID: 15965985 DOI: 10.1002/jps.20333] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The internal, dynamical fluctuations of protein molecules exhibit many of the features typical of polymeric and bulk small molecule glass forming systems. The response of a protein's internal molecular mobility to temperature changes is similar to that of other amorphous systems, in that different types of motions freeze out at different temperatures, suggesting they exhibit the alpha-beta-modes of motion typical of polymeric glass formers. These modes of motion are attributed to the dynamic regimes that afford proteins the flexibility for function but that also develop into the large-scale collective motions that lead to unfolding. The protein dynamical transition, T(d), which has the same meaning as the T(g) value of other amorphous systems, is attributed to the temperature where protein activity is lost and the unfolding process is inhibited. This review describes how modulation of T(d) by hydration and lyoprotectants can determine the stability of protein molecules that have been processed as bulk, amorphous materials. It also examines the thermodynamic, dynamic, and molecular factors involved in stabilizing folded proteins, and the effects typical pharmaceutical processes can have on native protein structure in going from the solution state to the solid state.
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Affiliation(s)
- John J Hill
- ICOS Corporation, 22021 20th Avenue SE, Bothell, WA 98021, USA.
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Scharnagl C, Reif M, Friedrich J. Stability of proteins: Temperature, pressure and the role of the solvent. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1749:187-213. [PMID: 15893966 DOI: 10.1016/j.bbapap.2005.03.002] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2004] [Revised: 02/23/2005] [Accepted: 03/02/2005] [Indexed: 10/25/2022]
Abstract
We focus on the various aspects of the physics related to the stability of proteins. We review the pure thermodynamic aspects of the response of a protein to pressure and temperature variations and discuss the respective stability phase diagram. We relate the experimentally observed shape of this diagram to the low degree of correlation between the fluctuations of enthalpy and volume changes associated with the folding-denaturing transition and draw attention to the fact that one order parameter is not enough to characterize the transition. We discuss in detail microscopic aspects of the various contributions to the free energy gap of proteins and put emphasis on how a cosolvent may either enlarge or diminish this gap. We review briefly the various experimental approaches to measure changes in protein stability induced by cosolvents, denaturants, but also by pressure and temperature. Finally, we discuss in detail our own molecular dynamics simulations on cytochrome c and show what happens under high pressure, how glycerol influences structure and volume fluctuations, and how all this compares with experiments.
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40
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41
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Arnórsdóttir J, Kristjánsson MM, Ficner R. Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation. FEBS J 2005; 272:832-45. [PMID: 15670163 DOI: 10.1111/j.1742-4658.2005.04523.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The crystal structure of a subtilisin-like serine proteinase from the psychrotrophic marine bacterium, Vibrio sp. PA-44, was solved by means of molecular replacement and refined at 1.84 A. This is the first structure of a cold-adapted subtilase to be determined and its elucidation facilitates examination of the molecular principles underlying temperature adaptation in enzymes. The cold-adapted Vibrio proteinase was compared with known three-dimensional structures of homologous enzymes of meso- and thermophilic origin, proteinase K and thermitase, to which it has high structural resemblance. The main structural features emerging as plausible determinants of temperature adaptation in the enzymes compared involve the character of their exposed and buried surfaces, which may be related to temperature-dependent variation in the physical properties of water. Thus, the hydrophobic effect is found to play a significant role in the structural stability of the meso- and thermophile enzymes, whereas the cold-adapted enzyme has more of its apolar surface exposed. In addition, the cold-adapted Vibrio proteinase is distinguished from the more stable enzymes by its strong anionic character arising from the high occurrence of uncompensated negatively charged residues at its surface. Interestingly, both the cold-adapted and thermophile proteinases differ from the mesophile enzyme in having more extensive hydrogen- and ion pair interactions in their structures; this supports suggestions of a dual role of electrostatic interactions in the adaptation of enzymes to both high and low temperatures. The Vibrio proteinase has three calcium ions associated with its structure, one of which is in a calcium-binding site not described in other subtilases.
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Affiliation(s)
- Jóhanna Arnórsdóttir
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August Universität Göttingen, Germany
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Melchionna S, Briganti G, Londei P, Cammarano P. Water induced effects on the thermal response of a protein. PHYSICAL REVIEW LETTERS 2004; 92:158101. [PMID: 15169320 DOI: 10.1103/physrevlett.92.158101] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2003] [Indexed: 05/24/2023]
Abstract
A model protein and surrounding water have been investigated at different temperatures. We have detected an anomalous compression of the protein near the freezing point of water-a compression not obviously related to the negative thermal expansion of the solvent. Moreover, the physiological protein working temperature (T=300 K) appears to be related to the activation of exchange of vicinal water with the bulk and the concomitant absorption of heat by hydrophilic amino acids. The inferred activation was interpreted on the basis of degenerate tetrahedral order between the hydration shell and the bulk. The results support the notion that the dynamics of vicinal water makes a substantial contribution to the activity optimum of proteins.
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Affiliation(s)
- Simone Melchionna
- Dipartimento di Fisica and INFM, Università La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
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Marqués MI, Borreguero JM, Stanley HE, Dokholyan NV. Possible mechanism for cold denaturation of proteins at high pressure. PHYSICAL REVIEW LETTERS 2003; 91:138103. [PMID: 14525339 DOI: 10.1103/physrevlett.91.138103] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2003] [Indexed: 05/24/2023]
Abstract
We study cold denaturation of proteins at high pressures. Using multicanonical Monte Carlo simulations of a model protein in a water bath, we investigate the effect of water density fluctuations on protein stability. We find that above the pressure where water freezes to the dense ice phase (approximately 2 kbars) the mechanism for cold denaturation with decreasing temperature is the loss of local low-density water structure. We find our results in agreement with data of bovine pancreatic ribonuclease A.
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Affiliation(s)
- Manuel I Marqués
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA.
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45
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Cho CH, Urquidi J, Singh S, Park SC, Robinson GW. Pressure Effect on the Density of Water. J Phys Chem A 2002. [DOI: 10.1021/jp0136260] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chul Hee Cho
- Department of Chemistry, Natural Science Campus, Sungkyunkwan University, Suwon 440-746, Korea, Intense Pulsed Neutron Source, Argonne National Laboratories, 9700 South Cass Avenue, Argonne, Illinois, 60439-4814, HNC Software, Inc., 5935 Cornerstone Court West, San Diego, California 92121, and SubPicosecond and Quantum Radiation Laboratory, Department of Chemistry and Biochemistry, P.O. Box 41061, Texas Tech University, Lubbock, Texas 79409-1061
| | - Jacob Urquidi
- Department of Chemistry, Natural Science Campus, Sungkyunkwan University, Suwon 440-746, Korea, Intense Pulsed Neutron Source, Argonne National Laboratories, 9700 South Cass Avenue, Argonne, Illinois, 60439-4814, HNC Software, Inc., 5935 Cornerstone Court West, San Diego, California 92121, and SubPicosecond and Quantum Radiation Laboratory, Department of Chemistry and Biochemistry, P.O. Box 41061, Texas Tech University, Lubbock, Texas 79409-1061
| | - Surjit Singh
- Department of Chemistry, Natural Science Campus, Sungkyunkwan University, Suwon 440-746, Korea, Intense Pulsed Neutron Source, Argonne National Laboratories, 9700 South Cass Avenue, Argonne, Illinois, 60439-4814, HNC Software, Inc., 5935 Cornerstone Court West, San Diego, California 92121, and SubPicosecond and Quantum Radiation Laboratory, Department of Chemistry and Biochemistry, P.O. Box 41061, Texas Tech University, Lubbock, Texas 79409-1061
| | - Seung C. Park
- Department of Chemistry, Natural Science Campus, Sungkyunkwan University, Suwon 440-746, Korea, Intense Pulsed Neutron Source, Argonne National Laboratories, 9700 South Cass Avenue, Argonne, Illinois, 60439-4814, HNC Software, Inc., 5935 Cornerstone Court West, San Diego, California 92121, and SubPicosecond and Quantum Radiation Laboratory, Department of Chemistry and Biochemistry, P.O. Box 41061, Texas Tech University, Lubbock, Texas 79409-1061
| | - G. Wilse Robinson
- Department of Chemistry, Natural Science Campus, Sungkyunkwan University, Suwon 440-746, Korea, Intense Pulsed Neutron Source, Argonne National Laboratories, 9700 South Cass Avenue, Argonne, Illinois, 60439-4814, HNC Software, Inc., 5935 Cornerstone Court West, San Diego, California 92121, and SubPicosecond and Quantum Radiation Laboratory, Department of Chemistry and Biochemistry, P.O. Box 41061, Texas Tech University, Lubbock, Texas 79409-1061
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Abstract
The hydrophobic effect is the major force driving protein folding. Around room temperature, small organic solutes and hydrophobic amino acids have low solubilities in water and the hydrophobic effect is the strongest. These facts suggest that globular proteins should be maximally stable around room temperature. While this fundamental paradigm has been expected, it has not actually been shown to hold. Toward this goal, we have collected and analyzed experimental thermodynamic data for 31 proteins that show reversible two-state folding <--> unfolding transitions at or near neutral pH. Twenty-six of these are unique, and 20 of the 26 are maximally stable around room temperature irrespective of their structural properties, the melting temperature, or the living temperatures of their source organisms. Their average temperature of maximal stability is 293 +/- 8 K (20 +/- 8 degrees C). These proteins differ in size, fold, and number of domains, hydrophobic folding units, and oligomeric states. They derive from the cold-loving psychrophiles, from mesophiles, and from thermophiles. Analysis of the single-domain proteins present in this set shows that the variations in their thermodynamic parameters are correlated in a way which may explain the adaptation of the proteins to the living temperatures of the organisms from which they derive. The average energetic contribution of the individual amino acids toward protein stability decreases with an increase in protein size, suggesting that there may be an upper limit for protein maximal thermodynamic stability. For the remaining proteins, deviation of the maximal stability temperatures from room temperature may be due to greater uncertainties in their heat capacity change (DeltaC(p)) values, a weaker hydrophobic effect, and/or a stronger electrostatic contribution.
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Affiliation(s)
- Sandeep Kumar
- Laboratory of Experimental and Computational Biology, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
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Bakk A, Høye JS, Hansen A. Apolar and polar solvation thermodynamics related to the protein unfolding process. Biophys J 2002; 82:713-9. [PMID: 11806913 PMCID: PMC1301880 DOI: 10.1016/s0006-3495(02)75433-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Thermodynamics related to hydrated water upon protein unfolding is studied over a broad temperature range (5-125 degrees C). The hydration effect arising from the apolar interior is modeled as an increased number of hydrogen bonds between water molecules compared with bulk water. The corresponding contribution from the polar interior is modeled as a two-step process. First, the polar interior breaks hydrogen bonds in bulk water upon unfolding. Second, due to strong bonds between the polar surface and the nearest water molecules, we assume quantization using a simplified two-state picture. The heat capacity change upon hydration is compared with model compound data evaluated previously for 20 different proteins. We obtain good correspondence with the data for both the apolar and the polar interior. We note that the effective coupling constants for both models have small variations among the proteins we have investigated.
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Affiliation(s)
- Audun Bakk
- Department of Physics, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
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48
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Kumar S, Tsai CJ, Nussinov R. Thermodynamic differences among homologous thermophilic and mesophilic proteins. Biochemistry 2001; 40:14152-65. [PMID: 11714268 DOI: 10.1021/bi0106383] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here, we analyze the thermodynamic parameters and their correlations in families containing homologous thermophilic and mesophilic proteins which show reversible two-state folding <--> unfolding transitions between the native and the denatured states. For the proteins in these families, the melting temperatures correlate with the maximal protein stability change (between the native and the denatured states) as well as with the enthalpic and entropic changes at the melting temperature. In contrast, the heat capacity change is uncorrelated with the melting temperature. These and additional results illustrate that higher melting temperatures are largely obtained via an upshift and broadening of the protein stability curves. Both thermophilic and mesophilic proteins are maximally stable around room temperature. However, the maximal stabilities of thermophilic proteins are considerably greater than those of their mesophilic homologues. At the living temperatures of their respective source organisms, homologous thermophilic and mesophilic proteins have similar stabilities. The protein stability at the living temperature of the source organism does not correlate with the living temperature of the protein. We tie thermodynamic observations to microscopics via the hydrophobic effect and a two-state model of the water structure. We conclude that, to achieve higher stability and greater resistance to high and low temperatures, specific interactions, particularly electrostatic, should be engineered into the protein. The effect of these specific interactions is largely reflected in an increased enthalpy change at the melting temperature.
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Affiliation(s)
- S Kumar
- Laboratory of Experimental and Computational Biology and Intramural Research Support Program-SAIC, Laboratory of Experimental and Computational Biology, National Cancer Institute-Frederick, Building 469, Room 151, Frederick, Maryland 21702, USA
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Affiliation(s)
- Tigran V. Chalikian
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada
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50
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Scatena LF, Richmond GL. Orientation, Hydrogen Bonding, and Penetration of Water at the Organic/Water Interface. J Phys Chem B 2001. [DOI: 10.1021/jp0132174] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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