1
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Datar PM, Joshi SY, Deshmukh SA, Marsh ENG. Probing the role of protein conformational changes in the mechanism of prenylated-FMN-dependent phenazine-1-carboxylic acid decarboxylase. J Biol Chem 2024; 300:105621. [PMID: 38176649 PMCID: PMC10850782 DOI: 10.1016/j.jbc.2023.105621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024] Open
Abstract
Phenazine-1-carboxylic acid decarboxylase (PhdA) is a prenylated-FMN-dependent (prFMN) enzyme belonging to the UbiD family of decarboxylases. Many UbiD-like enzymes catalyze (de)carboxylation reactions on aromatic rings and conjugated double bonds and are potentially valuable industrial catalysts. We have investigated the mechanism of PhdA using a slow turnover substrate, 2,3-dimethylquinoxaline-5-carboxylic acid (DQCA). Detailed analysis of the pH dependence and solvent deuterium isotope effects associated with the reaction uncovered unusual kinetic behavior. At low substrate concentrations, a substantial inverse solvent isotope effect (SIE) is observed on Vmax/KM of ∼ 0.5 when reaction rates of DQCA in H2O and D2O are compared. Under the same conditions, a normal SIE of 4.15 is measured by internal competition for proton transfer to the product. These apparently contradictory results indicate that the SIE values report on different steps in the mechanism. A proton inventory analysis of the reaction under Vmax/KM and Vmax conditions points to a "medium effect" as the source of the inverse SIE. Molecular dynamics simulations of the effect of D2O on PhdA structure support that D2O reduces the conformational lability of the enzyme and results in a more compact structure, akin to the active, "closed" conformer observed in crystal structures of some UbiD-like enzymes. Consistent with the simulations, PhdA was found to be more stable in D2O and to bind DQCA more tightly, leading to the observed rate enhancement under Vmax/KM conditions.
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Affiliation(s)
- Prathamesh M Datar
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Soumil Y Joshi
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Sanket A Deshmukh
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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2
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Haidar Y, Konermann L. Effects of Hydrogen/Deuterium Exchange on Protein Stability in Solution and in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37314114 DOI: 10.1021/jasms.3c00130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry (MS)-based techniques are widely used for probing protein structure and dynamics in solution. H/D exchange (HDX)-MS is one of the most common approaches in this context. HDX is often considered to be a "benign" labeling method, in that it does not perturb protein behavior in solution. However, several studies have reported that D2O pushes unfolding equilibria toward the native state. The origin, and even the existence of this protein stabilization remain controversial. Here we conducted thermal unfolding assays in solution to confirm that deuterated proteins in D2O are more stable, with 2-4 K higher melting temperatures than unlabeled proteins in H2O. Previous studies tentatively attributed this phenomenon to strengthened H-bonds after deuteration, an effect that may arise from the lower zero-point vibrational energy of the deuterated species. Specifically, it was proposed that strengthened water-water bonds (W···W) in D2O lower the solubility of nonpolar side chains. The current work takes a broader view by noting that protein stability in solution also depends on water-protein (W···P) and protein-protein (P···P) H-bonds. To help unravel these contributions, we performed collision-induced unfolding (CIU) experiments on gaseous proteins generated by native electrospray ionization. CIU profiles of deuterated and unlabeled proteins were indistinguishable, implying that P···P contacts are insensitive to deuteration. Thus, protein stabilization in D2O is attributable to solvent effects, rather than alterations of intraprotein H-bonds. Strengthening of W···W contacts represents one possible explanation, but the stabilizing effect of D2O can also originate from weakened W···P bonds. Future work will be required to elucidate which of these two scenarios is correct, or if both contribute to protein stabilization in D2O. In any case, the often-repeated adage that "D-bonds are more stable than H-bonds" does not apply to intramolecular contacts in native proteins.
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Affiliation(s)
- Yousef Haidar
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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3
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Tugarinov V, Baber JL, Clore GM. A methyl-TROSY based 13C relaxation dispersion NMR experiment for studies of chemical exchange in proteins. JOURNAL OF BIOMOLECULAR NMR 2023:10.1007/s10858-023-00413-8. [PMID: 37095392 DOI: 10.1007/s10858-023-00413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023]
Abstract
A methyl Transverse Relaxation Optimized Spectroscopy (methyl-TROSY) based, multiple quantum (MQ) 13C Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiment is described. The experiment is derived from the previously developed MQ 13C-1H CPMG scheme (Korzhnev in J Am Chem Soc 126: 3964-73, 2004) supplemented with a CPMG train of refocusing 1H pulses applied with constant frequency and synchronized with the 13C CPMG pulse train. The optimal 1H 'decoupling' scheme that minimizes the amount of fast-relaxing methyl MQ magnetization present during CPMG intervals, makes use of an XY-4 phase cycling of the refocusing composite 1H pulses. For small-to-medium sized proteins, the MQ 13C CPMG experiment has the advantage over its single quantum (SQ) 13C counterpart of significantly reducing intrinsic, exchange-free relaxation rates of methyl coherences. For high molecular weight proteins, the MQ 13C CPMG experiment eliminates complications in the interpretation of MQ 13C-1H CPMG relaxation dispersion profiles arising from contributions to exchange from differences in methyl 1H chemical shifts between ground and excited states. The MQ 13C CPMG experiment is tested on two protein systems: (1) a triple mutant of the Fyn SH3 domain that interconverts slowly on the chemical shift time scale between the major folded state and an excited state folding intermediate; and (2) the 82-kDa enzyme Malate Synthase G (MSG), where chemical exchange at individual Ile δ1 methyl positions occurs on a much faster time-scale.
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Affiliation(s)
- Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
| | - James L Baber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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4
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Khudozhitkov AE, Stange P, Paschek D, Stepanov AG, Kolokolov DI, Ludwig R. The Influence of Deuterium Isotope Effects on Structural Rearrangements, Ensemble Equilibria, and Hydrogen Bonding in Protic Ionic Liquids. Chemphyschem 2022; 23:e202200557. [PMID: 35944124 PMCID: PMC10087857 DOI: 10.1002/cphc.202200557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Indexed: 01/05/2023]
Abstract
We report strong isotope effects for the protic ionic liquid triethylammonium methanesulfonate [TEA][OMs] by means of deuterium solid-state NMR spectroscopy covering broad temperature ranges from 65 K to 313 K. Both isotopically labelled PILs differ in non-deuterated and fully deuterated ethyl groups of the triethyl ammonium cations. The N-D bond of both cations is used as sensitive probe for hydrogen bonding and structural ordering. The 2 H NMR line shape analysis provides the deuteron quadrupole coupling constants and the characteristics of a broad heterogeneous phase with simultaneously present static and mobile states indicating plastic crystal behavior. The temperatures where both states are equally populated differ by about 80 K for the two PILs, showing that deuteration of the ethyl groups in the trialkylammonium cations tremendously shifts the equilibrium towards the static state. In addition, it leads to a significant less cooperative transition, associated with a significantly reduced standard molar transition entropy.
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Affiliation(s)
- Alexander E Khudozhitkov
- Boreskov Institute of Catalysis, Siberian Branch of Russian Academy of Sciences, Prospekt Akademika Lavrentieva 5, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova Street 2, Novosibirsk, 630090, Russia
| | - Peter Stange
- Universität Rostock, Institut für Chemie, Abteilung für Physikalische Chemie, Albert-Einstein-Straße 27, 18059, Rostock, Germany
| | - Dietmar Paschek
- Universität Rostock, Institut für Chemie, Abteilung für Physikalische Chemie, Albert-Einstein-Straße 27, 18059, Rostock, Germany
| | - Alexander G Stepanov
- Boreskov Institute of Catalysis, Siberian Branch of Russian Academy of Sciences, Prospekt Akademika Lavrentieva 5, Novosibirsk, 630090, Russia
| | - Daniil I Kolokolov
- Boreskov Institute of Catalysis, Siberian Branch of Russian Academy of Sciences, Prospekt Akademika Lavrentieva 5, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova Street 2, Novosibirsk, 630090, Russia
| | - Ralf Ludwig
- Universität Rostock, Institut für Chemie, Abteilung für Physikalische Chemie, Albert-Einstein-Straße 27, 18059, Rostock, Germany.,Leibniz-Institut für Katalyse an der Universität Rostock e.V., Albert-Einstein-Str. 29a, 18059, Rostock, Germany
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5
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Fries MR, Skoda MWA, Conzelmann NF, Jacobs RMJ, Maier R, Scheffczyk N, Zhang F, Schreiber F. Bulk phase behaviour vs interface adsorption: Effects of anions and isotopes on β-lactoglobulin (BLG) interactions. J Colloid Interface Sci 2021; 598:430-443. [PMID: 33930747 DOI: 10.1016/j.jcis.2021.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 01/17/2023]
Abstract
HYPOTHESIS Protein adsorption is highly relevant in numerous applications ranging from food processing to medical implants. In this context, it is important to gain a deeper understanding of protein-protein and protein-surface interactions. Thus, the focus of this investigation is on the interplay of bulk properties and surface properties on protein adsorption. It was hypothesised that the type of solvent and ions in solution should significantly influence the protein's bulk and interface behaviour, which has been observed in literature and previous work for other net negatively charged, globular proteins such as bovine serum albumin (BSA). EXPERIMENTS The phase behaviour of β-lactoglobulin (BLG) with lanthanum chloride (LaCl3) and iodide (LaI3) in normal water H2O(l) and heavy water (D2O(l)) was established via optical microscopy and ultraviolet-visible spectroscopy. The formation of an adsorption layer and its properties such as thickness, density, structure, and hydration was investigated via neutron reflectivity, quartz-crystal microbalance with dissipation, and infra-red measurements. FINDINGS β-lactoglobulin does not show significant anion-induced or isotope-induced effects - neither in bulk nor at the solid-liquid interface, which deviates strongly from the behaviour of bovine serum albumin. We also provide a comprehensive discussion and comparison of protein-specific bulk and interface behaviour between bovine serum albumin and β-lactoglobulin dependent on anion, cation, solvent, and substrate properties. These findings pave the way for understanding the transition from adsorption to crystallisation.
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Affiliation(s)
- Madeleine R Fries
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Maximilian W A Skoda
- ISIS Facility, STFC, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom.
| | - Nina F Conzelmann
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Robert M J Jacobs
- Department for Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom.
| | - Ralph Maier
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Niels Scheffczyk
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Fajun Zhang
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Frank Schreiber
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
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6
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Bielskutė S, Garcia-Cabau C, Frigolé-Vivas M, Szulc E, De Mol E, Pesarrodona M, García J, Salvatella X. Low amounts of heavy water increase the phase separation propensity of a fragment of the androgen receptor activation domain. Protein Sci 2021; 30:1427-1437. [PMID: 33978290 DOI: 10.1002/pro.4110] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023]
Abstract
The phase equilibria of intrinsically disordered proteins are exquisitely sensitive to changes in solution conditions and this can be used to investigate the driving forces of phase separation in vitro as well as the biological roles of phase transitions in live cells. Here we investigate how using D2 O as co-solvent in an aqueous buffer changes the phase equilibrium of a fragment of the activation domain of the androgen receptor, a transcription factor that plays a role in the development of the male phenotype and is a therapeutic target for castration resistant prostate cancer. We show how replacing even small fractions of H2 O with D2 O increases the propensity of this fragment to undergo liquid-liquid phase separation, likely reflecting a stabilization of the hydrophobic interactions that drive condensation. Our results indicate that it is necessary to take this effect into consideration when studying phase separation phenomena with biophysical methods that require using D2 O as a co-solvent. In addition, they suggest that additions of D2 O may be used to enhance phase separation phenomena in cells, facilitating their observation.
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Affiliation(s)
- Stasė Bielskutė
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Marta Frigolé-Vivas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Elzbieta Szulc
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Eva De Mol
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Mireia Pesarrodona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Joint BSC-IRB Research Programme in Computational Biology, Barcelona, Spain.,ICREA, Barcelona, Spain
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7
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Liu F, Zhang J. Nano-second protein dynamics of key residue at Position 38 in catechol-O-methyltransferase system: a time-resolved fluorescence study. J Biochem 2020; 168:417-425. [DOI: 10.1093/jb/mvaa063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/17/2020] [Indexed: 02/02/2023] Open
Abstract
AbstractHuman catechol-O-methyltransferase, a key enzyme related to neurotransmitter metabolism, catalyses a methyl transfer from S-adenosylmethionine to catechol. Although extensive studies aim to understand the enzyme mechanisms, the connection of protein dynamics and enzyme catalysis is still not clear. Here, W38in (Trp143Phe) and W38in/Y68A (Trp143Phe with Tyr68Ala) mutants were carried out to study the relationship of dynamics and catalysis in nano-second timescale using time-resolved fluorescence lifetimes and Stokes shifts in various solvents. The comprehensive data implied the mutant W38in/Y68A with lower activity is more rigid than the ‘WT’−W38in, suggesting the importance of flexibility at residue 38 to maintain the optimal catalysis.
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Affiliation(s)
- Fan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jianyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
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8
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Li Y, Zhang Y, Cheng Y, Du T, Zhang J. Solvent inhibition profiles and inverse solvent isotope effects for enzymatic methyl transfer catalyzed by nicotinamide N‐methyltransferase. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yuping Li
- School of Pharmaceutical Science and Technology Tianjin University Tianjin China
| | - Yali Zhang
- School of Pharmaceutical Science and Technology Tianjin University Tianjin China
| | - Yiting Cheng
- School of Pharmaceutical Science and Technology Tianjin University Tianjin China
| | - Tianshu Du
- School of Pharmaceutical Science and Technology Tianjin University Tianjin China
| | - Jianyu Zhang
- School of Pharmaceutical Science and Technology Tianjin University Tianjin China
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9
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Tai Y, Takaba K, Hanazono Y, Dao HA, Miki K, Takeda K. X-ray crystallographic studies on the hydrogen isotope effects of green fluorescent protein at sub-ångström resolutions. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:1096-1106. [PMID: 31793903 DOI: 10.1107/s2059798319014608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/28/2019] [Indexed: 11/10/2022]
Abstract
Hydrogen atoms are critical to the nature and properties of proteins, and thus deuteration has the potential to influence protein function. In fact, it has been reported that some deuterated proteins show different physical and chemical properties to their protiated counterparts. Consequently, it is important to investigate protonation states around the active site when using deuterated proteins. Here, hydrogen isotope effects on the S65T/F99S/M153T/V163A variant of green fluorescent protein (GFP), in which the deprotonated B form is dominant at pH 8.5, were investigated. The pH/pD dependence of the absorption and fluorescence spectra indicates that the protonation state of the chromophore is the same in protiated GFP in H2O and protiated GFP in D2O at pH/pD 8.5, while the pKa of the chromophore became higher in D2O. Indeed, X-ray crystallographic analyses at sub-ångström resolution revealed no apparent changes in the protonation state of the chromophore between the two samples. However, detailed comparisons of the hydrogen OMIT maps revealed that the protonation state of His148 in the vicinity of the chromophore differed between the two samples. This indicates that protonation states around the active site should be carefully adjusted to be the same as those of the protiated protein when neutron crystallographic analyses of proteins are performed.
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Affiliation(s)
- Yang Tai
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kiyofumi Takaba
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuya Hanazono
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hoang Anh Dao
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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10
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Clark T, Heske J, Kühne TD. Opposing Electronic and Nuclear Quantum Effects on Hydrogen Bonds in H 2 O and D 2 O. Chemphyschem 2019; 20:2461-2465. [PMID: 31449714 PMCID: PMC6790677 DOI: 10.1002/cphc.201900839] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Indexed: 11/09/2022]
Abstract
The effect of extending the O-H bond length(s) in water on the hydrogen-bonding strength has been investigated using static ab initio molecular orbital calculations. The "polar flattening" effect that causes a slight σ-hole to form on hydrogen atoms is strengthened when the bond is stretched, so that the σ-hole becomes more positive and hydrogen bonding stronger. In opposition to this electronic effect, path-integral ab initio molecular-dynamics simulations show that the nuclear quantum effect weakens the hydrogen bond in the water dimer. Thus, static electronic effects strengthen the hydrogen bond in H2 O relative to D2 O, whereas nuclear quantum effects weaken it. These quantum fluctuations are stronger for the water dimer than in bulk water.
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Affiliation(s)
- Timothy Clark
- Computer-Chemie-Centrum, Department Chemie und PharmazieFriedrich-Alexander-Universität Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
| | - Julian Heske
- Chair of Theoretical Chemistry, Dynamics of Condensed Matter, Department of ChemistryUniversity of PaderbornWarburger Str. 10033098PaderbornGermany
| | - Thomas D. Kühne
- Chair of Theoretical Chemistry, Dynamics of Condensed Matter, Department of ChemistryUniversity of PaderbornWarburger Str. 10033098PaderbornGermany
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11
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Sheu SY, Liu YC, Zhou JK, Schlag EW, Yang DY. Surface Topography Effects of Globular Biomolecules on Hydration Water. J Phys Chem B 2019; 123:6917-6932. [PMID: 31282162 DOI: 10.1021/acs.jpcb.9b03734] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydration water serves as a microscopic manifestation of structural stability and functions of biomolecules. To develop bio-nanomaterials in applications, it is important to study how the surface topography and heterogeneity of biomolecules result in their diversity of the hydration dynamics and energetics. We here performed molecular dynamics simulations combined with the steered molecular dynamics and umbrella sampling to investigate the dynamics and escape process associated with the free energy change of water molecules close to a globular biomolecule, i.e., hemoglobin (Hb) and G-quadruplex DNA (GDNA). The residence time, power of long-time tail, and dipole relaxation time were found to display drastic changes within the averaged hydration shell of 3.0-5.0 Å. Compared with bulk water, in the inner hydration shell, the water dipole moment displays a slower relaxation process and is more oriented toward GDNA than toward Hb, forming a hedgehog-like structure when it surrounds GDNA. In particular, a spine water structure is observed in the GDNA narrow groove. The water isotope effect not only prolongs the dynamic time scales of libration motion in the inner hydration shell and the dipole relaxation processes in the bulk but also strengthens the DNA spine water structure. The potential of the mean force profile reflects the integrity of the hydration shell structure and enables us to obtain detailed insights into the structures formed by water, such as the caged H-bond network and the edge bridge structures; it also reveals that local hydration shell free energy (LHSFE) depends on H-bond rupture processes and ranges from 0.2 to 4.2 kcal/mol. Our results demonstrate that the surface topography of a biomolecule influences the integrity of the hydration shell structure and LHSFE. Our studies are able to identify various further applications in the areas of microfluid devices and nano-dewetting on bioinspired surfaces.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences , National Yang-Ming University , Taipei 112 , Taiwan.,Institute of Biomedical Informatics , National Yang-Ming University , Taipei 112 , Taiwan
| | - Yu-Cheng Liu
- Institute of Biomedical Informatics , National Yang-Ming University , Taipei 112 , Taiwan
| | - Jia-Kai Zhou
- Department of Life Sciences and Institute of Genome Sciences , National Yang-Ming University , Taipei 112 , Taiwan
| | - Edward W Schlag
- Institut für Physikalische und Theoretische Chemie , TU-München , Lichtenbergstr. 4 , 85748 Garching , Germany
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan
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12
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Brenner T, Tuvikene R, Cao Y, Fang Y, Rikukawa M, Price WS, Matsukawa S. Hydrogen isotope replacement changes hydration and large scale structure, but not small scale structure, of agarose hydrogel networks. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:53. [PMID: 31062106 DOI: 10.1140/epje/i2019-11816-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/20/2019] [Indexed: 05/24/2023]
Abstract
Agarose samples of low (Ag1) and high (Ag2) O -methyl content on position 6 of the galactose residue were studied in H2O and D2O. Differential scanning calorimetry, turbidity and rheological measurements showed a [Formula: see text] 2 ° C shift in the coil-to-helix transition temperature, indicating higher helix stability in D2O. The differential scanning calorimetry data could be superimposed using a temperature shift factor, suggesting similar extents of helix aggregation in both solvents. Small angle X-ray scattering of H2O and D2O gels were essentially identical, indicating no change in the small scale ( [Formula: see text] 0.05-20 nm) network structure on isotopic exchange. Larger ([Formula: see text] 1 μm) scale heterogeneities were more pronounced in deuterium gels. The 1HT2 relaxation times were measured at different H/D ratios. These relaxation times were analyzed using a model assuming regular solution mixing of H2O, HDO and D2O between the solvent and gel phases. The fit results suggested that H2O has higher affinity for the agarose network than HDO and D2O. The difference, however, was much larger for the Ag2 sample. This finding implies that the higher hydrophobic effect observed in D2O affects the hydration state much more strongly for the more hydrophobic (and more polarizable) agarose sample Ag2. As a consequence, Ag2 (but not Ag1) gels retained more H2O than D2O. In contrast, the bulk rheology of either hydrogel was not affected by the isotopic exchange.
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Affiliation(s)
- Tom Brenner
- Faculty of Science and Technology, Materials and Life Sciences, Sophia University, 7-1 Kioicho, Chiyoda, 102-8554, Tokyo, Japan.
| | - Rando Tuvikene
- School of Natural Sciences and Health, Tallinn University, Narva mnt 29, 10120, Tallinn, Estonia
| | - Yiping Cao
- Glyn O. Phillips Hydrocolloids Research Centre, School of Food and Pharmaceutical Engineering, Faculty of Light Industry, Hubei University of Technology, 430068, Wuchang, Wuhan, China
| | - Yapeng Fang
- Glyn O. Phillips Hydrocolloids Research Centre, School of Food and Pharmaceutical Engineering, Faculty of Light Industry, Hubei University of Technology, 430068, Wuchang, Wuhan, China
| | - Masahiro Rikukawa
- Faculty of Science and Technology, Materials and Life Sciences, Sophia University, 7-1 Kioicho, Chiyoda, 102-8554, Tokyo, Japan
| | - William S Price
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, 2751, Penrith, NSW, Australia
| | - Shingo Matsukawa
- Graduate School of Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-Ku, 108-8477, Tokyo, Japan
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13
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Korunur S, Zengin B, Yılmaz A. 400 MHz NMR Study of Isotope Effects on Albumin in H2O/D2O Solutions. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2018. [DOI: 10.1134/s003602441810014x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Stadmiller SS, Pielak GJ. Enthalpic stabilization of an SH3 domain by D 2 O. Protein Sci 2018; 27:1710-1716. [PMID: 30052291 PMCID: PMC6194290 DOI: 10.1002/pro.3477] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 06/30/2018] [Accepted: 07/02/2018] [Indexed: 01/06/2023]
Abstract
The stability of a protein is vital for its biological function, and proper folding is partially driven by intermolecular interactions between protein and water. In many studies, H2 O is replaced by D2 O because H2 O interferes with the protein signal. Even this small perturbation, however, affects protein stability. Studies in isotopic waters also might provide insight into the role of solvation and hydrogen bonding in protein folding. Here, we report a complete thermodynamic analysis of the reversible, two-state, thermal unfolding of the metastable, 7-kDa N-terminal src-homology 3 domain of the Drosophila signal transduction protein drk in H2 O and D2 O using one-dimensional 19 F NMR spectroscopy. The stabilizing effect of D2 O compared with H2 O is enthalpic and has a small to insignificant effect on the temperature of maximum stability, the entropy, and the heat capacity of unfolding. We also provide a concise summary of the literature about the effects of D2 O on protein stability and integrate our results into this body of data.
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Affiliation(s)
| | - Gary J. Pielak
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
- Department of Biochemistry and BiophysicsUniversity of North CarolinaChapel HillNorth Carolina27599
- Lineberger Comprehensive Cancer CenterUniversity of North CarolinaChapel HillNorth Carolina27599
- Integrative Program for Biological and Genome SciencesUniversity of North CarolinaChapel HillNorth Carolina27599
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15
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Brielle ES, Arkin IT. Site-Specific Hydrogen Exchange in a Membrane Environment Analyzed by Infrared Spectroscopy. J Phys Chem Lett 2018; 9:4059-4065. [PMID: 29957958 DOI: 10.1021/acs.jpclett.8b01675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hydrogen exchange is a powerful method to examine macromolecules. In membrane proteins, exchange can distinguish between solvent-accessible and -inaccessible residues due to shielding by the hydrophobic environment of the lipid bilayer. Herein, rather than examining which residues undergo hydrogen exchange, we employ a protocol that enables the full deuteration of all polar hydrogens in a membrane protein. We then measure the impact of hydrogen exchange on the shift of the amide I vibrational mode of individually labeled sites. The results enable us to correlate polarity with vibrational shifts, thereby providing a powerful tool to examine specific locations within a membrane protein in its native membrane environment.
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Affiliation(s)
- Esther S Brielle
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra Campus , Jerusalem 91904 , Israel
| | - Isaiah T Arkin
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra Campus , Jerusalem 91904 , Israel
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16
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Equilibrium folding dynamics of meACP in water, heavy water, and low concentration of urea. Sci Rep 2017; 7:16156. [PMID: 29170533 PMCID: PMC5700953 DOI: 10.1038/s41598-017-16449-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/13/2017] [Indexed: 12/21/2022] Open
Abstract
Many proteins fold in apparent two-state behavior, as partially folded intermediates only transiently accumulate and easily escape detection. Besides a native form and a mainly unfolded form, we captured a partially unfolded form of an acyl carrier protein from Micromonospora echinospora (meACP) in the folding/unfolding equilibrium using chemical exchange saturation transfer NMR experiments. The C-terminal region of the partially unfolded form is mainly folded and the N-terminal is unfolded. Furthermore, to understand how the folding process of meACP is influenced by solvent environments, we compared the folding dynamics of meACP in D2O, H2O and low concentration of urea. As the environment becomes more denaturing from D2O to H2O and then to urea, the unfolded state becomes increasingly populated, and the folding rate decreases. Adding a small amount of urea, which does not change solvent viscosity, has little effects on the unfolding rates, while changing H2O to D2O reduces the unfolding rates possibly due to the increase of solvent viscosity. The quantified solvent effects on the protein folding Gibbs energy and activation energy suggest that the transition state of folding may have a similar structure to the native state of the protein.
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17
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Bucciarelli S, Mahmoudi N, Casal-Dujat L, Jéhannin M, Jud C, Stradner A. Extended Law of Corresponding States Applied to Solvent Isotope Effect on a Globular Protein. J Phys Chem Lett 2016; 7:1610-1615. [PMID: 27077243 DOI: 10.1021/acs.jpclett.6b00593] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Investigating proteins with techniques such as NMR or neutron scattering frequently requires the partial or complete substitution of D2O for H2O as a solvent, often tacitly assuming that such a solvent substitution does not significantly alter the properties of the protein. Here, we report a systematic investigation of the solvent isotope effect on the phase diagram of the lens protein γB-crystallin in aqueous solution as a model system exhibiting liquid-liquid phase separation. We demonstrate that the observed strong variation of the critical temperature Tc can be described by the extended law of corresponding states for all H2O/D2O ratios, where scaling of the temperature by Tc or the reduced second virial coefficient accurately reproduces the binodal, spinodal, and osmotic compressibility. These findings highlight the impact of H2O/D2O substitution on γB-crystallin properties and warrant further investigations into the universality of this phenomenon and its underlying mechanisms.
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Affiliation(s)
- Saskia Bucciarelli
- Physical Chemistry, Department of Chemistry, Lund University , SE-22100 Lund, Sweden
| | - Najet Mahmoudi
- Physical Chemistry, Department of Chemistry, Lund University , SE-22100 Lund, Sweden
- Adolphe Merkle Institute (AMI), University of Fribourg , CH-1700 Fribourg, Switzerland
| | - Lucía Casal-Dujat
- Physical Chemistry, Department of Chemistry, Lund University , SE-22100 Lund, Sweden
| | - Marie Jéhannin
- Physical Chemistry, Department of Chemistry, Lund University , SE-22100 Lund, Sweden
| | - Corinne Jud
- Adolphe Merkle Institute (AMI), University of Fribourg , CH-1700 Fribourg, Switzerland
| | - Anna Stradner
- Physical Chemistry, Department of Chemistry, Lund University , SE-22100 Lund, Sweden
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18
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Ong WQ, Citron YR, Schnitzbauer J, Kamiyama D, Huang B. Heavy water: a simple solution to increasing the brightness of fluorescent proteins in super-resolution imaging. Chem Commun (Camb) 2015; 51:13451-3. [PMID: 26226621 PMCID: PMC4544551 DOI: 10.1039/c5cc04575d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoactivatable fluorescent proteins (PA-FPs) are widely used in live single-molecule super-resolution imaging but emit substantially fewer photons than organic dyes do. Herein, we show that in heavy water (D2O) instead of H2O, common PA-FPs emit 26-54% more photons, effectively improving the localization precision in super-resolution imaging.
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Affiliation(s)
- Wei Qiang Ong
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
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19
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Westberg M, Holmegaard L, Pimenta FM, Etzerodt M, Ogilby PR. Rational design of an efficient, genetically encodable, protein-encased singlet oxygen photosensitizer. J Am Chem Soc 2015; 137:1632-42. [PMID: 25575190 DOI: 10.1021/ja511940j] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Singlet oxygen, O(2)(a(1)Δ(g)), plays a key role in many processes of cell signaling. Limitations in mechanistic studies of such processes are generally associated with the difficulty of controlling the amount and location of O(2)(a(1)Δ(g)) production in or on a cell. As such, there is great need for a system that (a) selectively produces O(2)(a(1)Δ(g)) in appreciable and accurately quantifiable yields and (b) can be localized in a specific place at the suborganelle level. A genetically encodable, protein-encased photosensitizer is one way to achieve this goal. Through a systematic and rational approach involving mutations to a LOV2 protein that binds the chromophore flavin mononucleotide (FMN), we have developed a promising photosensitizer that overcomes many of the problems that affect related systems currently in use. Specifically, by decreasing the extent of hydrogen bonding between FMN and a specific amino acid residue in the local protein environment, we decrease the susceptibility of FMN to undesired photoinitiated electron-transfer reactions that kinetically compete with O(2)(a(1)Δ(g)) production. As a consequence, our protein-encased FMN system produces O(2)(a(1)Δ(g)) with the uniquely large quantum efficiency of 0.25 ± 0.03. We have also quantified other key photophysical parameters that characterize this sensitizer system, including unprecedented H(2)O/D(2)O solvent isotope effects on the O(2)(a(1)Δ(g)) formation kinetics and yields. As such, our results facilitate future systematic developments in this field.
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Affiliation(s)
- Michael Westberg
- Center for Oxygen Microscopy and Imaging, Chemistry Department and ‡Department of Molecular Biology and Genetics, Aarhus University , DK-8000, Aarhus, Denmark
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20
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Pokorna S, Jurkiewicz P, Vazdar M, Cwiklik L, Jungwirth P, Hof M. Does fluoride disrupt hydrogen bond network in cationic lipid bilayer? Time-dependent fluorescence shift of Laurdan and molecular dynamics simulations. J Chem Phys 2014; 141:22D516. [DOI: 10.1063/1.4898798] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sarka Pokorna
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Mario Vazdar
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, P.O.B. 180, HR-10002 Zagreb, Croatia
| | - Lukasz Cwiklik
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
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21
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Light-Induced Differences in Conformational Dynamics of the Circadian Clock Regulator VIVID. J Mol Biol 2014; 426:601-10. [DOI: 10.1016/j.jmb.2013.10.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 10/14/2013] [Accepted: 10/28/2013] [Indexed: 12/24/2022]
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22
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Lopez F, Cuomo F, Nostro PL, Ceglie A. Effects of solvent and alkaline earth metals on the heat-induced precipitation process of sodium caseinate. Food Chem 2013; 136:266-72. [DOI: 10.1016/j.foodchem.2012.07.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 10/28/2022]
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23
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Abstract
This Perspective is focused on amide groups of peptides interacting with water. The 2D IR spectroscopy has already enabled structural aspects of the peptide backbone to be determined through its ability to measure the coupling between different amide-I modes. Here we describe why nonlinear IR is emerging as the method of choice to examine the fast components of the water dynamics near peptides and how isotopically edited peptide links can be used to probe the local water at a residue level in proteins. This type of research necessarily involves an intimate mix of theory and experiment. The description of the results is underpinned by relatively well established quantum-statistical theories that describe the important manifestations of peptide vibrational frequency fluctuations.
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Affiliation(s)
- Ayanjeet Ghosh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Robin M. Hochstrasser
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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24
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Paesani F. Hydrogen bond dynamics in heavy water studied with quantum dynamical simulations. Phys Chem Chem Phys 2011; 13:19865-75. [PMID: 21892511 DOI: 10.1039/c1cp21863h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The structure and dynamics of the hydrogen-bond network in heavy water (D(2)O) is studied as a function of the temperature using quantum dynamical simulations. Our approach combines an ab initio-based representation of the water interactions with an explicit quantum treatment of the molecular motion. A direct connection between the calculated linear and nonlinear vibrational spectra and the underlying molecular dynamics is made, which provides new insights into the rearrangement of the hydrogen-bond network in heavy water. A comparison with previous calculations on liquid H(2)O suggests that tunneling does not effectively contribute to the dynamics of the water hydrogen-bond network above the melting point. However, the effects of nuclear quantization are not negligible at all temperatures and become increasingly important near the melting point, which is in agreement with recent experimental analysis of the structural properties of liquid water as well as of the proton momentum distribution in supercooled water.
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Affiliation(s)
- Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA 92093, USA.
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25
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Cuomo F, Ceglie A, Lopez F. Temperature dependence of calcium and magnesium induced caseinate precipitation in H2O and D2O. Food Chem 2011. [DOI: 10.1016/j.foodchem.2010.10.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Haward SJ, Shewry PR, Marsh J, Miles MJ, Mc Master TJ. Force spectroscopy of an elastic peptide: effect of D₂O and temperature on persistence length. Microsc Res Tech 2011; 74:170-6. [PMID: 21275005 DOI: 10.1002/jemt.20888] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This study explores the mechanical unfolding of elastic protein analogues as a function of temperature, in both H₂O and D₂O, using atomic force microscopy (AFM) force spectroscopy in a specially constructed AFM liquid cell. This represents the first time that the effect of D₂O on protein flexibility has been investigated at the single molecule level by this technique. Model elastic peptides, R6, were encoded from synthetic genes expressed in Escherichia coli. The peptides possess short N- and C-terminal domains with central repetitive domains containing 13 repeats of the motif PGQGQQ-plus-GYYPTSLQQ. These sequences mimic those in native high molecular weight subunit glutenin proteins which confer elasticity to bread dough. Fitting single molecule stretching events to the worm-like chain model, allows determination of the molecular persistence length under various experimental conditions. The effect of increasing the temperature is to increase the persistence length of the peptide in both H₂O and D₂O, consistent with the expected "thermal softening" effect. However, the effect is significantly enhanced in D₂O, in which the persistence length at 45°C is ∼25% greater than the value measured in H₂O at the same temperature. Stronger intrapeptide H-bonding due to isotopic substitution of hydrogen for deuterium is the most likely cause of the enhanced backbone rigidity.
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Affiliation(s)
- Simon J Haward
- H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom.
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27
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Ziegler BE, McMahon TB. Energetics and Structural Elucidation of Mechanisms for Gas Phase H/D Exchange of Protonated Peptides. J Phys Chem A 2010; 114:11953-63. [DOI: 10.1021/jp105170f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Blake E. Ziegler
- Department of Chemistry University of Waterloo Waterloo, Ontario
| | - Terry B. McMahon
- Department of Chemistry University of Waterloo Waterloo, Ontario
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28
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Single-molecule spectroscopy of protein folding in a chaperonin cage. Proc Natl Acad Sci U S A 2010; 107:11793-8. [PMID: 20547872 DOI: 10.1073/pnas.1002356107] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular chaperones are known to be essential for avoiding protein aggregation in vivo, but it is still unclear how they affect protein folding mechanisms. We use single-molecule Förster resonance energy transfer to follow the folding of a protein inside the GroEL/GroES chaperonin cavity over a time range from milliseconds to hours. Our results show that confinement in the chaperonin decelerates the folding of the C-terminal domain in the substrate protein rhodanese, but leaves the folding rate of the N-terminal domain unaffected. Microfluidic mixing experiments indicate that strong interactions of the substrate with the cavity walls impede the folding process, but the folding hierarchy is preserved. Our results imply that no universal chaperonin mechanism exists. Rather, a competition between intra- and intermolecular interactions determines the folding rates and mechanisms of a substrate inside the GroEL/GroES cage.
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29
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Absorption of light and heavy water vapours in polyelectrolyte multilayer films. Colloids Surf B Biointerfaces 2009; 74:462-7. [DOI: 10.1016/j.colsurfb.2009.08.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Revised: 08/17/2009] [Accepted: 08/21/2009] [Indexed: 11/21/2022]
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30
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Cho Y, Sagle LB, Iimura S, Zhang Y, Kherb J, Chilkoti A, Scholtz JM, Cremer PS. Hydrogen Bonding of β-Turn Structure Is Stabilized in D2O. J Am Chem Soc 2009; 131:15188-93. [DOI: 10.1021/ja9040785] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Younhee Cho
- Department of Chemistry, Texas A&M University, 3255 TAMU, and Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843, and Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - Laura B. Sagle
- Department of Chemistry, Texas A&M University, 3255 TAMU, and Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843, and Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - Satoshi Iimura
- Department of Chemistry, Texas A&M University, 3255 TAMU, and Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843, and Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - Yanjie Zhang
- Department of Chemistry, Texas A&M University, 3255 TAMU, and Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843, and Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - Jaibir Kherb
- Department of Chemistry, Texas A&M University, 3255 TAMU, and Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843, and Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - Ashutosh Chilkoti
- Department of Chemistry, Texas A&M University, 3255 TAMU, and Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843, and Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - J. Martin Scholtz
- Department of Chemistry, Texas A&M University, 3255 TAMU, and Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843, and Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - Paul S. Cremer
- Department of Chemistry, Texas A&M University, 3255 TAMU, and Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843, and Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
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31
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Paesani F, Voth GA. The properties of water: insights from quantum simulations. J Phys Chem B 2009; 113:5702-19. [PMID: 19385690 DOI: 10.1021/jp810590c] [Citation(s) in RCA: 189] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The properties of water play a central role in many phenomena of relevance to different areas of science, including physics, chemistry, biology, geology, and climate research. Although well studied for decades, the behavior of water under different conditions and in different environments still remains mysterious and often surprising. In this article, various efforts aimed at providing a comprehensive representation of the water properties at a molecular level through computer modeling and simulation will be described. In particular, the unique role played by the hydrogen-bond network will be examined, first in liquid water, then in the solvation of model biological compounds, and finally in ice, especially highlighting the important effects related to the quantization of the nuclear motion.
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Affiliation(s)
- Francesco Paesani
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112-0850, USA
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32
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Dougan L, Koti ASR, Genchev G, Lu H, Fernandez JM. A single-molecule perspective on the role of solvent hydrogen bonds in protein folding and chemical reactions. Chemphyschem 2009; 9:2836-47. [PMID: 19058277 DOI: 10.1002/cphc.200800572] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We present an array of force spectroscopy experiments that aim to identify the role of solvent hydrogen bonds in protein folding and chemical reactions at the single-molecule level. In our experiments we control the strength of hydrogen bonds in the solvent environment by substituting water (H(2)O) with deuterium oxide (D(2)O). Using a combination of force protocols, we demonstrate that protein unfolding, protein collapse, protein folding and a chemical reaction are affected in different ways by substituting H(2)O with D(2)O. We find that D(2)O molecules form an integral part of the unfolding transition structure of the immunoglobulin module of human cardiac titin, I27. Strikingly, we find that D(2)O is a worse solvent than H(2)O for the protein I27, in direct contrast with the behaviour of simple hydrocarbons. We measure the effect of substituting H(2)O with D(2)O on the force dependent rate of reduction of a disulphide bond engineered within a single protein. Altogether, these experiments provide new information on the nature of the underlying interactions in protein folding and chemical reactions and demonstrate the power of single-molecule techniques to identify the changes induced by a small change in hydrogen bond strength.
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Affiliation(s)
- Lorna Dougan
- Biological Sciences, Columbia University, New York 10027, USA.
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33
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Jasnin M, Tehei M, Moulin M, Haertlein M, Zaccai G. Solvent isotope effect on macromolecular dynamics in E. coli. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:613-7. [DOI: 10.1007/s00249-008-0281-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 12/20/2007] [Accepted: 01/30/2008] [Indexed: 10/22/2022]
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34
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Sheu SY, Schlag EW, Selzle HL, Yang DY. Molecular Dynamics of Hydrogen Bonds in Protein−D2O: The Solvent Isotope Effect. J Phys Chem A 2008; 112:797-802. [DOI: 10.1021/jp0771668] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences, National Yang-Ming University, Taipei 112, Taiwan, Institute für Physikalische und Theoretische Chemie, TU-München, Lichtenbergstrasse 4, 85748 Garching, Germany, and Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan
| | - E. W. Schlag
- Department of Life Sciences, National Yang-Ming University, Taipei 112, Taiwan, Institute für Physikalische und Theoretische Chemie, TU-München, Lichtenbergstrasse 4, 85748 Garching, Germany, and Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan
| | - H. L. Selzle
- Department of Life Sciences, National Yang-Ming University, Taipei 112, Taiwan, Institute für Physikalische und Theoretische Chemie, TU-München, Lichtenbergstrasse 4, 85748 Garching, Germany, and Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan
| | - Dah-Yen Yang
- Department of Life Sciences, National Yang-Ming University, Taipei 112, Taiwan, Institute für Physikalische und Theoretische Chemie, TU-München, Lichtenbergstrasse 4, 85748 Garching, Germany, and Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan
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35
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Guzzi R, Arcangeli C, Bizzarri AR. A molecular dynamics simulation study of the solvent isotope effect on copper plastocyanin. Biophys Chem 2007; 82:9-22. [PMID: 17030337 DOI: 10.1016/s0301-4622(99)00097-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/1999] [Revised: 07/29/1999] [Accepted: 07/29/1999] [Indexed: 11/24/2022]
Abstract
The effect of heavy water on the structure and dynamics of copper plastocyanin as well as on some aspects of the solvent dynamics at the protein-solvent interfacial region have been investigated by molecular dynamics simulation. The simulated system has been analyzed in terms of the atomic root mean square deviation and fluctuations, intraprotein H-bond pattern, dynamical cross-correlation map and the results have been compared with those previously obtained for plastocyanin in H2O (Ciocchetti et al. Biophys. Chem. 69 (1997), 185-198). The simulated plastocyanin structure in the two solvents, averaging 1 ns, is very similar along the beta-structure regions, while the most significant differences are registered, analogous to the turns and the regions likely involved in the electron transfer pathway. Moreover, plastocyanin in D2O shows an increase in the number of both the intraprotein H-bonds and the residues involved in correlated motions. An analysis of the protein-solvent coupling evidenced that D2O makes the H-bond formation more difficult with the solvent molecules for positively charged and polar residues, while an opposite trend is observed for negatively charged residues. On the other hand, the frequency of exchange of the solvent molecules involved in the protein-solvent H-bond formation is significantly depressed in D2O. The results are discussed also in connection with protein functionality and briefly with some experimental results connected with the thermostability of proteins in D2O.
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Affiliation(s)
- R Guzzi
- Unita' INFM, Dipartimento di Fisica, Universita' della Calabria, I-87030 Rende, Italy.
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36
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Sato S, Raleigh DP. Kinetic isotope effects reveal the presence of significant secondary structure in the transition state for the folding of the N-terminal domain of L9. J Mol Biol 2007; 370:349-55. [PMID: 17512540 DOI: 10.1016/j.jmb.2007.02.084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Revised: 02/20/2007] [Accepted: 02/22/2007] [Indexed: 11/26/2022]
Abstract
Our present understanding of the nature of the transition state for protein folding depends predominantly on studies where individual side-chain contributions are mapped out by mutational analysis (phi value analysis). This approach, although extremely powerful, does not in general provide direct information about the formation of backbone hydrogen bonds. Here, we report the results of amide H/D isotope effect studies that probe the development of hydrogen bonded interactions in the transition state for the folding of a small alpha-beta protein, the N-terminal domain of L9. Replacement of amide protons by deuterons in a solvent of constant isotopic composition destabilized the domain, decreasing both its T(m) and Delta G(0) of unfolding. The folding rate also decreased. The parameter Phi(H/D), defined as the ratio of the effect of isotopic substitution upon the activation free energy to the equilibrium free energy was determined to be 0.6 in a D(2)O background and 0.75 in a H(2)O background, indicating that significant intraprotein hydrogen bond interactions are developed in the transition state for the folding of NTL9. The value is in remarkably good agreement with more traditional measures of the position of the transition state, which report on the relative burial of surface area. The results provide a picture of a compact folding transition state containing significant secondary structure. Indirect analysis argues that the bulk of the kinetic isotope effect arises from the beta-sheet-rich region of the protein, and suggests that the development of intraprotein hydrogen bonds in this region plays a critical role in the folding of NTL9.
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Affiliation(s)
- Satoshi Sato
- Okayama Research Park Incubation Center, 5303 Haga Okayama 701-1223, Japan.
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37
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Sosnick TR, Krantz BA, Dothager RS, Baxa M. Characterizing the Protein Folding Transition State Using ψ Analysis. Chem Rev 2006; 106:1862-76. [PMID: 16683758 DOI: 10.1021/cr040431q] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tobin R Sosnick
- Department of Biochemistry, Institute for Biophysical Dynamics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA.
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38
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Mason JM, Cliff MJ, Sessions RB, Clarke AR. Low Energy Pathways and Non-native Interactions. J Biol Chem 2005; 280:40494-9. [PMID: 16216876 DOI: 10.1074/jbc.m509281200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Four versions of a beta-sheet protein (CD2.d1) have been made, each with a single artificial disulfide bond inserted into hairpin structures. Folding kinetics of reduced and oxidized forms shows bridge position strongly influences its effect on the folding reaction. Bridging residues 58 and 62 does not affect the rapidly formed intermediate (I) or rate-limiting transition (t) state, whereas bridging 33 and 38, or 31 and 41, lowers the t-state energy, with the latter having the stronger influence. Bridging residues 79 and 90 stabilizes both I- and t-states. To assess additivity in the energetic effects of these bridges, four double-bridge variants have also been made. All show precise additivity of overall stability, with two showing additivity when ground states and the rate-limiting t-state are assessed, i.e. no measurable change in the folding mechanism occurs. However, combining 31-41 and 79-90 bridges produces a molecule that folds through a different pathway, with a much more stable intermediate than expected and a much higher t-state barrier. This is explained by the artificial introduction of stabilizing, non-native contacts in the I-state. More surprisingly, for another double-bridge version (58-62 and 79-90) both I- and t-states are less stable than expected, showing that conformational constraints introduced by the two bridges prevent formation of non-native contacts that would otherwise stabilize the I- and t-states, thereby lowering the energy of the folding landscape in the wild-type (unbridged) molecule. We conclude that the lowest energy path for folding has I- and t-state structures that are stabilized by non-native interactions.
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Affiliation(s)
- Jody M Mason
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom.
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39
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Abstract
Density functional calculations (B3 LYP/6-31+G*) on molecular clusters and a quantum cluster equilibrium (QCE) model were used to calculate thermodynamic and structural properties of four isotopically labeled methanol species. The method allowed the reproduction of the characteristic differences in boiling points and heats of vaporization. Structural changes were also detected and related to recent experimental findings. It was shown that isotopic effects clearly have a quantum-mechanical origin.
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Affiliation(s)
- Ralf Ludwig
- Institut für Chemie, Abteilung Physikalische Chemie, Universität Rostock, 18051 Rostock, Germany.
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40
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Cliff MJ, Higgins LD, Sessions RB, Waltho JP, Clarke AR. Beyond the EX1 limit: probing the structure of high-energy states in protein unfolding. J Mol Biol 2004; 336:497-508. [PMID: 14757061 DOI: 10.1016/j.jmb.2003.12.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hydrogen exchange kinetics in native solvent conditions have been used to explore the conformational fluctuations of an immunoglobulin domain (CD2.domain1). The global folding/unfolding kinetics of the protein are unaltered between pH 4.5 and pH 9.5, allowing us to use the pH-dependence of amide hydrogen/deuterium exchange to characterise conformational states with energies up to 7.2kcal/mol higher than the folded ground state. The study was intended to search for discreet unfolding intermediates in this region of the energy spectrum, their presence being revealed by the concerted exchange behaviour of subsets of amide groups that become accessible at a given free energy, i.e. the spectrum would contain discreet groupings. Protection factors for 58 amide groups were measured across the pH range and the hydrogen-exchange energy profile is described. More interestingly, exchange behaviour could be grouped into three categories; the first two unremarkable, the third unexpected. (1) In 33 cases, amide exchange was dominated by rapid fluctuation, i.e. the free energy difference between the ground state and the rapidly accessed open state is sufficiently low that the contribution from crossing the unfolding barrier is negligible. (2) In 18 cases exchange is dominated by the global folding transition barrier across the whole pH range measured. The relationship between hydroxyl ion concentration and observed exchange rate is hyperbolic, with the limiting rate being that for global unfolding; the so-called EX1 limit. For these, the free energy difference between the folded ground state and any rapidly-accessed open state is too great for the proton to be exchanged through such fluctuations, even at the highest pH employed in this study. (3) For the third group, comprising five cases, we observe a behaviour that has not been described. In this group, as in category 2, the rate of exchange reaches a plateau; the EX1 limit. However, as the intrinsic exchange rate (k(int)) is increased, this limit is breached and the rate begins to rise again. This unintuitive behaviour does not result from pH instability, rather it is a consequence of amide groups experiencing two processes; rapid fluctuation of structure and crossing the global barrier for unfolding. The boundary at which the EX1 limit is overcome is determined by the equilibrium distribution of the fluctuating open and closed states (K(O/C)) and the rate constant for unfolding (k(u)). This critical boundary is reached when k(int)K(O/C)=k(u). Given that, in a simple transition state formalism: k(u)=K(#)k' (where K(#) describes the equilibrium distribution between the transition and ground state and k' describes the rate of a barrierless rearrangement), it follows that if the pH is raised to a level where k(int)=k', then the entire free energy spectrum from ground state to transition state could be sampled.
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Affiliation(s)
- Matthew J Cliff
- The Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, BS8 1TD, Bristol, UK.
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41
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Sasisanker P, Oleinikova A, Weingärtner H, Ravindra R, Winter R. Solvation properties and stability of ribonuclease A in normal and deuterated water studied by dielectric relaxation and differential scanning/pressure perturbation calorimetry. Phys Chem Chem Phys 2004. [DOI: 10.1039/b314070a] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Abstract
The effects of heavy water (D(2)O) on internal dynamics of proteins were assessed by both the intrinsic phosphorescence lifetime of deeply buried Trp residues, which reports on the local structure about the triplet probe, and the bimolecular acrylamide phosphorescence quenching rate constant that is a measure of the average acrylamide diffusion coefficient through the macromolecule. The results obtained with several protein systems (ribonuclease T1, superoxide dismutase, beta-lactoglobulin, liver alcohol dehydrogenase, alkaline phosphatase, and apo- and Cd-azurin) demonstrate that in most cases D(2)O does significantly increase the rigidity the native structure. With the exception of alkaline phosphatase, the kinetics of the structure tightening effect of deuteration are rapid compared with the rate of H/D exchange of internal protons, which would then assign the dampening of structural fluctuations in D(2)O to a solvent effect, rather than to stronger intramolecular D bonding. Structure tightening by heavy water is generally amplified at higher temperatures, supporting a mostly hydrophobic nature of the underlying interaction, and under conditions that destabilize the globular fold.
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Affiliation(s)
- Patrizia Cioni
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Area della Ricerca di Pisa, Pisa, Italy.
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43
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Abstract
Stopped-flow fluorescence studies on the N-terminal domain of rat CD2 (CD2.d1) have demonstrated that folding from the fully denatured state (U) proceeds via the transient accumulation of an apparent intermediate (I) in a so-called burst phase that precedes the rate-limiting transition leading to the native state (N). A previous pH-dependent equilibrium hydrogen exchange (HX) study identified a subset of amides in CD2.d1 which, under EX2 conditions, exchange from N with free energies greater than or equal to the free energy difference between the N and I states calculated from the stopped-flow data. Under EX1 conditions the rates of HX for these amides tend towards an asymptote that matches the global unfolding rate calculated from the stopped-flow data, suggesting that exchange for these amides requires traversing the N-to-I transition state barrier. Exchange for these amides presumably occurs from exchange-competent forms comprising the kinetic burst phase therefore. To explore this idea further, native state HX (NHX) data have been collected for CD2.d1 under EX2 conditions using denaturant concentrations which span either side of the denaturant concentration where, according to the stopped-flow data, the apparent U and I states are iso-energetic. The data fit to a two-component, sub-global (sg)/global (g) NHX mechanism, yielding Delta G and m value parameters (where the m value is a measure of hydrocarbon solvation). Regression analysis demonstrates that the (m(sg), Delta G(sg)) and (m(g), Delta G(g)) values calculated for this subset of amides correspond with those describing the kinetic burst phase transition. This result confirms the ability of the NHX technique to explore the structural and energetic properties of kinetic folding intermediates.
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Affiliation(s)
- M J Parker
- Department of Molecular and Cell Biology, University of California, Berkeley, 229 Stanley Hall, Berkeley, CA 94720, USA.
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44
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Poso D, Sessions RB, Lorch M, Clarke AR. Progressive stabilization of intermediate and transition states in protein folding reactions by introducing surface hydrophobic residues. J Biol Chem 2000; 275:35723-6. [PMID: 10938078 DOI: 10.1074/jbc.m001747200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
It can be argued from the principle of solvent exclusion that the introduction of hydrophobic residues onto the surface of a protein will not destabilize the folded state because the nonpolar side chain will be at least as exposed in the unfolded state as it is when the protein chain is folded. A comparison of the folding pathway of wild type and 11 site-directed mutants of CD2.d1 shows this to be true. In fact, owing to partial burial of nonpolar groups as folding proceeds, we find that the rapidly formed intermediate state and, to a greater extent, the transition state are generally stabilized by hydrophobic surface mutations. This effect is slightly moderated in the folded state presumably by the perturbation of van der Waals' contacts and/or local electrostatic interactions that have a greater influence in this fully compact structure. The fact that in all but one case we find that stabilization of the rapidly collapsed intermediate is accompanied by a faster acquisition of the folded state refutes the argument that I states are generally "off pathway" conformations or ensembles that lead to the inhibition of otherwise more rapid folding trajectories.
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Affiliation(s)
- D Poso
- Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, United Kingdom
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45
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Parker MJ, Marqusee S. A statistical appraisal of native state hydrogen exchange data: evidence for a burst phase continuum? J Mol Biol 2000; 300:1361-75. [PMID: 10903874 DOI: 10.1006/jmbi.2000.3922] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
For a number of proteins, folding occurs via the rapid accumulation of secondary and tertiary structural features in a so-called burst phase, preceding the relatively slow, highly activated transition leading to the native state. A fundamental question is: do these burst phase reactions comprise two phase-separated thermodynamic states or a continuum of states? Ribonuclease HI (RNase H) from Escherichia coli and phage T4 lysozyme (T4L) both exhibit such a phenomenon. Native-state hydrogen exchange (NHX) data have been collected for these proteins, providing residue-specific free energies and m-values (a measure of hydrocarbon solvation) for the manifold of partially unfolded, exchange-competent forms that are accessible from the native state (DeltaG(sg) and m(sg), where the sg subscript denotes sub-global). There is good evidence that these parameters pertain to exchange-competent species comprising the burst phase observed in the global folding kinetics. We combine the results from the global folding kinetics of these proteins with a statistical analysis of their NHX parameters to determine if the distribution of experimental (m(sg), DeltaG(sg)) values derive from a mechanism where the burst phase is two-state. For RNase H, this analysis demonstrates that the burst phase of this protein is not two-state; the results imply a distribution of states, m and DeltaG exhibiting a linear functional relationship consistent with the global folding parameters. For T4L, it is difficult to distinguish the observed distribution of m(sg), DeltaG(sg) values from that expected for a mechanism where the burst phase is two-state. The results for RNase H* lend support for the idea that the burst phase reaction of this protein comprises a continuum of states. This has important implications for how we model the process of structural acquisition in protein folding reactions.
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Affiliation(s)
- M J Parker
- Department of Molecular and Cell Biology, University of California, 229 Stanley Hall, Berkeley, CA 94720, USA.
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46
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Affiliation(s)
- O Bilsel
- Department of Chemistry, Pennsylvania State University, University Park 16802, USA
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47
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Hamill SJ, Cota E, Chothia C, Clarke J. Conservation of folding and stability within a protein family: the tyrosine corner as an evolutionary cul-de-sac. J Mol Biol 2000; 295:641-9. [PMID: 10623553 DOI: 10.1006/jmbi.1999.3360] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
What are the selective pressures on protein sequences during evolution? Amino acid residues may be highly conserved for functional or structural (stability) reasons. Theoretical studies have proposed that residues involved in the folding nucleus may also be highly conserved. To test this we are using an experimental "fold approach" to the study of protein folding. This compares the folding and stability of a number of proteins that share the same fold, but have no common amino acid sequence or biological activity. The fold selected for this study is the immunoglobulin-like beta-sandwich fold, which is a fold that has no specifically conserved function. Four model proteins are used from two distinct superfamilies that share the immunoglobulin-like fold, the fibronectin type III and immunoglobulin superfamilies. Here, the fold approach and protein engineering are used to question the role of a highly conserved tyrosine in the "tyrosine corner" motif that is found ubiquitously and exclusively in Greek key proteins. In the four model beta-sandwich proteins characterised here, the tyrosine is the only residue that is absolutely conserved at equivalent sites. By mutating this position to phenylalanine, we show that the tyrosine hydroxyl is not required to nucleate folding in the immunoglobulin superfamily, whereas it is involved to some extent in early structure formation in the fibronectin type III superfamily. The tyrosine corner is important for stability, mutation to phenylalanine costs between 1.5 and 3 kcal mol(-1). We propose that the high level of conservation of the tyrosine is related to the structural restraints of the loop connecting the beta-sheets, representing an evolutionary "cul-de-sac".
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Affiliation(s)
- S J Hamill
- Department of Chemistry, MRC Centre for Protein Engineering, Universityof Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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48
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Cota E, Clarke J. Folding of beta-sandwich proteins: three-state transition of a fibronectin type III module. Protein Sci 2000; 9:112-20. [PMID: 10739253 PMCID: PMC2144439 DOI: 10.1110/ps.9.1.112] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
An analysis of the folding of the 94 residue tenth fibronectin type III (fnIII) domain of human fibronectin (FNfn10) is presented. Use of guanidine isothiocyanate as a denaturant allows us to obtain equilibrium and kinetic data across a broad range of denaturant concentrations that are unavailable in guanidine hydrochloride. Equilibrium unfolding experiments show that FNfn10 is significantly more stable than has been reported previously. Comparison of equilibrium and kinetic parameters reveals the presence of an intermediate that accumulates at low denaturant concentrations. This is the first demonstration of three-state folding kinetics for a fnIII domain. We have previously shown that a homologous domain from human tenascin (TNfn3) folds by a two-state mechanism, but this does not necessarily indicate that the two proteins fold by different folding pathways.
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Affiliation(s)
- E Cota
- MRC Centre for Protein Engineering and Cambridge University Chemical Laboratory, United Kingdom
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49
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Abstract
In this paper, following our work on the two-state outer neighbor mixed bonding model of water, it is proposed that polar groups promote the formation of the low density ice Ih-type bonding in their neighborhood, whereas nonpolar groups tend to promote the higher density ice II-type structure. In a protein, because of the large numbers of exposed polar and nonpolar groups, large changes in the neighboring water structure can occur. These changes, of course, depend on whether the protein is in its native or its unfolded state and will be shown here to have a direct impact on the thermodynamics of protein unfolding at both high and low temperatures. For example, it is known that the polar hydration entropies become rapidly more negative with increasing temperature. This very unusual behavior can be directly related to the promotion in the outer bulk liquid of the more stable Ih-type bonding at the expense of II-type bonding by polar groups of the protein. In contrast, nonpolar groups have an opposite effect on the thermodynamics. It is the delicate balance created by these outer hydration contributions, mixed with ordinary thermodynamic contributions from the inner hydration shell and those from hydrogen-bond and van der Waals forces within the protein molecule itself that is responsible for both heat and cold denaturation of proteins.
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Affiliation(s)
- G W Robinson
- SubPicosecond and Quantum Radiation Laboratory, Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 USA.
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50
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Abstract
The denaturant-dependence of the major, observable relaxation rates for folding (kobs) of ribonuclease HI from Escherichia coli (RNase H) and phage T4 lysozyme (T4L) reveal that, for both proteins, folding begins with the rapid and transient accumulation of intermediate species in a "burst phase" which precedes the rate-limiting formation of the native state; this is evidenced by a "rollover" in the folding limb of the rate profiles (kobs versus denaturant, or chevron plot). These rate profiles are most simply described by a three-state mechanism (unfolded-to-intermediate-to-native), which implies that the burst phase represents a transition between two distinct thermodynamic states. It is shown here that the equilibrium properties of these burst phase reactions can be equally well modeled by a mechanism involving a continuum of states where the free energy of each state is linearly related to its m-value (the parameter describing the linear relationship between free energy and denaturant). A numerical model is also developed to describe the time evolution of such a system, which exhibits nearly perfect exponential behavior. Both models emphasize how a continuum of states operating under a linear free energy relationship may behave like a two state system. Such a scheme finds experimental justification from an interpretation of recent native state hydrogen exchange data. The analytical model described for a continuum can account for the observed kinetic profiles of several other model proteins. The results, however, appear context specific, suggesting that burst phase reactions are not entirely random and non-specific. The results reported in this study have important implications for the concept of cooperativity in protein folding reactions.
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Affiliation(s)
- M J Parker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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