1
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Lim LZ, Song J. NMR Dynamic View of the Destabilization of WW4 Domain by Chaotropic GdmCl and NaSCN. Int J Mol Sci 2024; 25:7344. [PMID: 39000450 PMCID: PMC11242413 DOI: 10.3390/ijms25137344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
GdmCl and NaSCN are two strong chaotropic salts commonly used in protein folding and stability studies, but their microscopic mechanisms remain enigmatic. Here, by CD and NMR, we investigated their effects on conformations, stability, binding and backbone dynamics on ps-ns and µs-ms time scales of a 39-residue but well-folded WW4 domain at salt concentrations ≤200 mM. Up to 200 mM, both denaturants did not alter the tertiary packing of WW4, but GdmCl exerted more severe destabilization than NaSCN. Intriguingly, GdmCl had only weak binding to amide protons, while NaSCN showed extensive binding to both hydrophobic side chains and amide protons. Neither denaturant significantly affected the overall ps-ns backbone dynamics, but they distinctively altered µs-ms backbone dynamics. This study unveils that GdmCl and NaSCN destabilize a protein before the global unfolding occurs with differential binding properties and µs-ms backbone dynamics, implying the absence of a simple correlation between thermodynamic stability and backbone dynamics of WW4 at both ps-ns and µs-ms time scales.
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Affiliation(s)
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
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2
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Panuszko A, Śmiechowski M, Pieloszczyk M, Malinowski A, Stangret J. Weakly Hydrated Solute of Mixed Hydrophobic-Hydrophilic Nature. J Phys Chem B 2024; 128:6352-6361. [PMID: 38913837 PMCID: PMC11228977 DOI: 10.1021/acs.jpcb.4c02429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/26/2024]
Abstract
Infrared (IR) spectroscopy is a commonly used and invaluable tool in studies of solvation phenomena in aqueous solutions. Concurrently, density functional theory calculations and ab initio molecular dynamics simulations deliver the solvation shell picture at the molecular detail level. The mentioned techniques allowed us to gain insights into the structure and energy of the hydrogen bonding network of water molecules around methylsulfonylmethane (MSM). In the hydration sphere of MSM, there are two types of populations of water molecules: a significant share of water molecules weakly bonded to the sulfone group and a smaller share of water molecules strongly bonded to each other around the methyl groups of MSM. The very weak hydrogen bond of water molecules with the hydrophilic group causes the extended network of water hydrogen bonds to be not "anchored" on the sulfone group, and consequently, the MSM hydration shell is labile.
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Affiliation(s)
- Aneta Panuszko
- Department of Physical Chemistry, Faculty
of Chemistry, Gdańsk University of
Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Maciej Śmiechowski
- Department of Physical Chemistry, Faculty
of Chemistry, Gdańsk University of
Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Maciej Pieloszczyk
- Department of Physical Chemistry, Faculty
of Chemistry, Gdańsk University of
Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Adrian Malinowski
- Department of Physical Chemistry, Faculty
of Chemistry, Gdańsk University of
Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Janusz Stangret
- Department of Physical Chemistry, Faculty
of Chemistry, Gdańsk University of
Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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3
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Song J. Adenosine Triphosphate: The Primordial Molecule That Controls Protein Homeostasis and Shapes the Genome-Proteome Interface. Biomolecules 2024; 14:500. [PMID: 38672516 PMCID: PMC11048592 DOI: 10.3390/biom14040500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Adenosine triphosphate (ATP) acts as the universal energy currency that drives various biological processes, while nucleic acids function to store and transmit genetic information for all living organisms. Liquid-liquid phase separation (LLPS) represents the common principle for the formation of membrane-less organelles (MLOs) composed of proteins rich in intrinsically disordered regions (IDRs) and nucleic acids. Currently, while IDRs are well recognized to facilitate LLPS through dynamic and multivalent interactions, the precise mechanisms by which ATP and nucleic acids affect LLPS still remain elusive. This review summarizes recent NMR results on the LLPS of human FUS, TDP-43, and the viral nucleocapsid (N) protein of SARS-CoV-2, as modulated by ATP and nucleic acids, revealing the following: (1) ATP binds to folded domains overlapping with nucleic-acid-binding interfaces; (2) ATP and nucleic acids interplay to biphasically modulate LLPS by competitively binding to overlapping pockets of folded domains and Arg/Lys within IDRs; (3) ATP energy-independently induces protein folding with the highest efficiency known so far. As ATP likely emerged in the prebiotic monomeric world, while LLPS represents a pivotal mechanism to concentrate and compartmentalize rare molecules for forming primordial cells, ATP appears to control protein homeostasis and shape genome-proteome interfaces throughout the evolutionary trajectory, from prebiotic origins to modern cells.
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Affiliation(s)
- Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
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4
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Zhang Y, Borch LA, Fischer NH, Meldal M. Hydrodynamic Control of Alzheimer Aβ Fibrillation with Glucosaminic Acid Containing Click-Cyclized β-Bodies. J Am Chem Soc 2024; 146:2654-2662. [PMID: 38126710 DOI: 10.1021/jacs.3c12118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
It is well established that the dynamic hydration shell plays a vital role in macromolecular functions such as protein-ligand, protein-protein, protein-DNA, and protein-lipid interactions. Here we investigate how the water modality affects conformational changes, solubility, and motion of fibrillar proteins. The hypothesis is that the introduction of a poly hydroxyl amino acid would increase solvation of the fibril forming peptides, preventing their misfolding and aggregation. For the amyloid β (Aβ) peptide, which is considered to be connected with nervous system diseases, including dementia and cognitive decline in Alzheimer's disease, the formation of β-sheet fibrils always occurs with a conformational change and a decrease in the dynamic hydration shell around Aβ(1-42). We present novel cyclic d-amino acid peptides that effectively inhibit fibrillation through affecting the dynamic hydration shell of Aβ(1-42) in vitro. Using de novo design within the software Molecular Operating Environment (MOE), five different peptides that recognize Alzheimer's fibrils were designed and synthesized. Three of them were cyclic all-d-amino acid peptides incorporating the same polyhydroxy building block derived from d-glucosaminic acid (GA). One peptide was the parent cyclic all d-amino acid inhibitor with no GA incorporated, and another was an all l-amino acid linear fibrillation inhibitor. The GA-containing peptides were found to show significantly improved inhibition of Aβ(1-42) aggregation. The inhibition was dramatically improved by the synergistic application of two GA peptides targeting each end of the growing fibril. The present study may facilitate future developments of intervention strategies for Alzheimer's disease and similar neurodegenerative diseases.
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Affiliation(s)
- Yuan Zhang
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Line A Borch
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Niklas H Fischer
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Morten Meldal
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
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5
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Grimm LM, Setiadi J, Tkachenko B, Schreiner PR, Gilson MK, Biedermann F. The temperature-dependence of host-guest binding thermodynamics: experimental and simulation studies. Chem Sci 2023; 14:11818-11829. [PMID: 37920355 PMCID: PMC10619620 DOI: 10.1039/d3sc01975f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 09/24/2023] [Indexed: 11/04/2023] Open
Abstract
The thermodynamic parameters of host-guest binding can be used to describe, understand, and predict molecular recognition events in aqueous systems. However, interpreting binding thermodynamics remains challenging, even for these relatively simple molecules, as they are determined by both direct and solvent-mediated host-guest interactions. In this contribution, we focus on the contributions of water to binding by studying binding thermodynamics, both experimentally and computationally, for a series of nearly rigid, electrically neutral host-guest systems and report the temperature-dependent thermodynamic binding contributions ΔGb(T), ΔHb(T), ΔSb(T), and ΔCp,b. Combining isothermal titration calorimetry (ITC) measurements with molecular dynamics (MD) simulations, we provide insight into the binding forces at play for the macrocyclic hosts cucurbit[n]uril (CBn, n = 7-8) and β-cyclodextrin (β-CD) with a range of guest molecules. We find consistently negative changes in heat capacity on binding (ΔCp,b) for all systems studied herein - as well as for literature host-guest systems - indicating increased enthalpic driving forces for binding at higher temperatures. We ascribe these trends to solvation effects, as the solvent properties of water deteriorate as temperature rises. Unlike the entropic and enthalpic contributions to binding, with their differing signs and magnitudes for the classical and non-classical hydrophobic effect, heat capacity changes appear to be a unifying and more general feature of host-guest complex formation in water. This work has implications for understanding protein-ligand interactions and other complex systems in aqueous environments.
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Affiliation(s)
- Laura M Grimm
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Jeffry Setiadi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego 9255 Pharmacy Lane La Jolla CA 92093 USA
| | - Boryslav Tkachenko
- Institute of Organic Chemistry, Justus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego 9255 Pharmacy Lane La Jolla CA 92093 USA
| | - Frank Biedermann
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
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6
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Zytkiewicz E, Shkel IA, Cheng X, Rupanya A, McClure K, Karim R, Yang S, Yang F, Record MT. Quantifying Amide-Aromatic Interactions at Molecular and Atomic Levels: Experimentally Determined Enthalpic and Entropic Contributions to Interactions of Amide sp 2O, N, C and sp 3C Unified Atoms with Naphthalene sp 2C Atoms in Water. Biochemistry 2023; 62:2841-2853. [PMID: 37695675 DOI: 10.1021/acs.biochem.3c00367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
In addition to amide hydrogen bonds and the hydrophobic effect, interactions involving π-bonded sp2 atoms of amides, aromatics, and other groups occur in protein self-assembly processes including folding, oligomerization, and condensate formation. These interactions also occur in aqueous solutions of amide and aromatic compounds, where they can be quantified. Previous analysis of thermodynamic coefficients quantifying net-favorable interactions of amide compounds with other amides and aromatics revealed that interactions of amide sp2O with amide sp2N unified atoms (presumably C═O···H-N hydrogen bonds) and amide/aromatic sp2C (lone pair π, n-π*) are particularly favorable. Sp3C-sp3C (hydrophobic), sp3C-sp2C (hydrophobic, CH-π), sp2C-sp2C (hydrophobic, π-π), and sp3C-sp2N interactions are favorable, sp2C-sp2N interactions are neutral, while sp2O-sp2O and sp2N-sp2N self-interactions and sp2O-sp3C interactions are unfavorable. Here, from determinations of favorable effects of 14 amides on naphthalene solubility at 10, 25, and 45 °C, we dissect amide-aromatic interaction free energies into enthalpic and entropic contributions and find these vary systematically with amide composition. Analysis of these results yields enthalpic and entropic contributions to intrinsic strengths of interactions of amide sp2O, sp2N, sp2C, and sp3C unified atoms with aromatic sp2C atoms. For each interaction, enthalpic and entropic contributions have the same sign and are much larger in magnitude than the interaction free energy itself. The amide sp2O-aromatic sp2C interaction is enthalpy-driven and entropically unfavorable, consistent with direct chemical interaction (e.g., lone pair-π), while amide sp3C- and sp2C-aromatic sp2C interactions are entropy-driven and enthalpically unfavorable, consistent with hydrophobic effects. These findings are relevant for interactions involving π-bonded sp2 atoms in protein processes.
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Affiliation(s)
- Emily Zytkiewicz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Irina A Shkel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Xian Cheng
- Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Anuchit Rupanya
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kate McClure
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rezwana Karim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Sumin Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Felix Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - M Thomas Record
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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7
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Zytkiewicz E, Shkel IA, Cheng X, Rupanya A, McClure K, Karim R, Yang S, Yang F, Record MT. Quantifying Amide-Aromatic Interactions at Molecular and Atomic Levels: Experimentally-determined Enthalpic and Entropic Contributions to Interactions of Amide sp 2 O, N, C and sp 3 C Unified Atoms with Naphthalene sp 2 C Atoms in Water. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548600. [PMID: 37503153 PMCID: PMC10370101 DOI: 10.1101/2023.07.12.548600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In addition to amide hydrogen bonds and the hydrophobic effect, interactions involving π-bonded sp 2 atoms of amides, aromatics and other groups occur in protein self-assembly processes including folding, oligomerization and condensate formation. These interactions also occur in aqueous solutions of amide and aromatic compounds, where they can be quantified. Previous analysis of thermodynamic coefficients quantifying net-favorable interactions of amide compounds with other amides and aromatics revealed that interactions of amide sp 2 O with amide sp 2 N unified atoms (presumably C=O···H-N hydrogen bonds) and amide/aromatic sp 2 C (lone pair-π, n-π * ) are particularly favorable. Sp 3 C-sp 3 C (hydrophobic), sp 3 C-sp 2 C (hydrophobic, CH-π), sp 2 C-sp 2 C (hydrophobic, π-π) and sp 3 C-sp 2 N interactions are favorable, sp 2 C-sp 2 N interactions are neutral, while sp 2 O-sp 2 O and sp 2 N-sp 2 N self-interactions and sp 2 O-sp 3 C interactions are unfavorable. Here, from determinations of favorable effects of fourteen amides on naphthalene solubility at 10, 25 and 45 °C, we dissect amide-aromatic interaction free energies into enthalpic and entropic contributions and find these vary systematically with amide composition. Analysis of these results yields enthalpic and entropic contributions to intrinsic strengths of interactions of amide sp 2 O, sp 2 N, sp 2 C and sp 3 C unified atoms with aromatic sp 2 C atoms. For each interaction, enthalpic and entropic contributions have the same sign and are much larger in magnitude than the interaction free energy itself. The amide sp 2 O-aromatic sp 2 C interaction is enthalpy-driven and entropically unfavorable, consistent with direct chemical interaction (e.g. lone pair-π) while amide sp 3 C- and sp 2 C-aromatic sp 2 C interactions are entropy-driven and enthalpically unfavorable, consistent with hydrophobic effects. These findings are relevant for interactions involving π-bonded sp 2 atoms in protein processes. Table of Contents Graphic
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Affiliation(s)
- Emily Zytkiewicz
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Irina A. Shkel
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Xian Cheng
- Biophysics Program, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Anuchit Rupanya
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Kate McClure
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Rezwana Karim
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Sumin Yang
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Felix Yang
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - M. Thomas Record
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
- Biophysics Program, University of Wisconsin – Madison, Madison, Wisconsin 53706
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
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8
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López‐Pérez E, de Gómez‐Puyou MT, Nuñez CJ, Zapién DM, Guardado SA, Beltrán HI, Pérez‐Hernández G. Ordered-domain unfolding of thermophilic isolated β subunit ATP synthase. Protein Sci 2023; 32:e4689. [PMID: 37252686 PMCID: PMC10273367 DOI: 10.1002/pro.4689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 05/31/2023]
Abstract
The flexibility of the ATP synthase's β subunit promotes its role in the ATP synthase rotational mechanism, but its domains stability remains unknown. A reversible thermal unfolding of the isolated β subunit (Tβ) of the ATP synthase from Bacillus thermophilus PS3, tracked through circular dichroism and molecular dynamics, indicated that Tβ shape transits from an ellipsoid to a molten globule through an ordered unfolding of its domains, preserving the β-sheet residual structure at high temperature. We determined that part of the stability origin of Tβ is due to a transversal hydrophobic array that crosses the β-barrel formed at the N-terminal domain and the Rossman fold of the nucleotide-binding domain (NBD), while the helix bundle of the C-terminal domain is the less stable due to the lack of hydrophobic residues, and thus the more flexible to trigger the rotational mechanism of the ATP synthase.
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Affiliation(s)
- Edgar López‐Pérez
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
| | - Marietta Tuena de Gómez‐Puyou
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología Celular, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Concepción José Nuñez
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología Celular, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Denise Martínez Zapién
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
| | - Salomón Alas Guardado
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
| | - Hiram Isaac Beltrán
- División de Ciencias Básicas e Ingeniería, Departamento de Ciencias BásicasUniversidad Autónoma Metropolitana, Unidad AzcapotzalcoCiudad de MéxicoMexico
| | - Gerardo Pérez‐Hernández
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
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9
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Fleming PJ, Correia JJ, Fleming KG. Revisiting macromolecular hydration with HullRadSAS. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:215-224. [PMID: 36602579 DOI: 10.1007/s00249-022-01627-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023]
Abstract
Hydration of biological macromolecules is important for their stability and function. Historically, attempts have been made to describe the degree of macromolecular hydration using a single parameter over a narrow range of values. Here, we describe a method to calculate two types of hydration: surface shell water and entrained water. A consideration of these two types of hydration helps to explain the "hydration problem" in hydrodynamics. The combination of these two types of hydration allows accurate calculation of hydrodynamic volume and related macromolecular properties such as sedimentation and diffusion coefficients, intrinsic viscosities, and the concentration-dependent non-ideality identified with sedimentation velocity experiments.
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Affiliation(s)
- Patrick J Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - John J Correia
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Karen G Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
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10
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Roterman I, Stapor K, Konieczny L. New insights on the catalytic center of proteins from peptidylprolyl isomerase group based on the FOD-M model. J Cell Biochem 2023. [PMID: 37139783 DOI: 10.1002/jcb.30407] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 05/05/2023]
Abstract
Generating the structure of the hydrophobic core is based on the orientation of hydrophobic residues towards the central part of the protein molecule with the simultaneous exposure of polar residues. Such a course of the protein folding process takes place with the active participation of the polar water environment. While the self-assembly process leading to the formation of micelles concerns freely moving bi-polar molecules, bipolar amino acids in polypeptide chain have limited mobility due to the covalent bonds. Therefore, proteins form a more or less perfect micelle-like structure. The criterion is the hydrophobicity distribution, which to a greater or lesser extent reproduces the distribution expressed by the 3D Gaussian function on the protein body. The vast majority of proteins must ensure solubility, so a certain part of it-as it is expected-should reproduce the structuring of micelles. The biological activity of proteins is encoded in the part that does not reproduce the micelle-like system. The location and quantitative assessment of the contribution of orderliness to disorder is of critical importance for the determination of biological activity. The form of maladjustment to the 3D Gauss function may be varied-hence the obtained high diversity of specific interactions with strictly defined molecules: ligands or substrates. The correctness of this interpretation was verified on the basis of the group of enzymes Peptidylprolyl isomerase-E.C.5.2.1.8. In proteins representing this class of enzymes, zones responsible for solubility-micelle-like hydrophobicity system-the location and specificity of the incompatible part in which the specific activity of the enzyme is located and coded were identified. The present study showed that the enzymes of the discussed group show two different schemes of the structure of catalytic center (taking into account the status as defined by the fuzzy oil drop model).
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Kraków, Poland
| | - Katarzyna Stapor
- Department of Applied Informatics, Faculty of Automatic, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University-Medical College, Kraków, Poland
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11
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Light, Water, and Melatonin: The Synergistic Regulation of Phase Separation in Dementia. Int J Mol Sci 2023; 24:ijms24065835. [PMID: 36982909 PMCID: PMC10054283 DOI: 10.3390/ijms24065835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
The swift rise in acceptance of molecular principles defining phase separation by a broad array of scientific disciplines is shadowed by increasing discoveries linking phase separation to pathological aggregations associated with numerous neurodegenerative disorders, including Alzheimer’s disease, that contribute to dementia. Phase separation is powered by multivalent macromolecular interactions. Importantly, the release of water molecules from protein hydration shells into bulk creates entropic gains that promote phase separation and the subsequent generation of insoluble cytotoxic aggregates that drive healthy brain cells into diseased states. Higher viscosity in interfacial waters and limited hydration in interiors of biomolecular condensates facilitate phase separation. Light, water, and melatonin constitute an ancient synergy that ensures adequate protein hydration to prevent aberrant phase separation. The 670 nm visible red wavelength found in sunlight and employed in photobiomodulation reduces interfacial and mitochondrial matrix viscosity to enhance ATP production via increasing ATP synthase motor efficiency. Melatonin is a potent antioxidant that lowers viscosity to increase ATP by scavenging excess reactive oxygen species and free radicals. Reduced viscosity by light and melatonin elevates the availability of free water molecules that allow melatonin to adopt favorable conformations that enhance intrinsic features, including binding interactions with adenosine that reinforces the adenosine moiety effect of ATP responsible for preventing water removal that causes hydrophobic collapse and aggregation in phase separation. Precise recalibration of interspecies melatonin dosages that account for differences in metabolic rates and bioavailability will ensure the efficacious reinstatement of the once-powerful ancient synergy between light, water, and melatonin in a modern world.
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12
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Stefaniuk A, Gawinkowski S, Golec B, Gorski A, Szutkowski K, Waluk J, Poznański J. Isotope effects observed in diluted D 2O/H 2O mixtures identify HOD-induced low-density structures in D 2O but not H 2O. Sci Rep 2022; 12:18732. [PMID: 36333587 PMCID: PMC9636167 DOI: 10.1038/s41598-022-23551-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
Normal and heavy water are solvents most commonly used to study the isotope effect. The isotope effect of a solvent significantly influences the behavior of a single molecule in a solution, especially when there are interactions between the solvent and the solute. The influence of the isotope effect becomes more significant in D2O/H2O since the hydrogen bond in H2O is slightly weaker than its counterpart (deuterium bond) in D2O. Herein, we characterize the isotope effect in a mixture of normal and heavy water on the solvation of a HOD molecule. We show that the HOD molecule affects the proximal solvent molecules, and these disturbances are much more significant in heavy water than in normal water. Moreover, in D2O, we observe the formation of low-density structures indicative of an ordering of the solvent around the HOD molecule. The qualitative differences between HOD interaction with D2O and H2O were consistently confirmed with Raman spectroscopy and NMR diffusometry.
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Affiliation(s)
- Anna Stefaniuk
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Sylwester Gawinkowski
- grid.425290.80000 0004 0369 6111Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Barbara Golec
- grid.425290.80000 0004 0369 6111Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Aleksander Gorski
- grid.425290.80000 0004 0369 6111Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Kosma Szutkowski
- grid.5633.30000 0001 2097 3545Adam Mickiewicz University, NanoBioMedical Centre, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland
| | - Jacek Waluk
- grid.425290.80000 0004 0369 6111Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland ,grid.440603.50000 0001 2301 5211Faculty of Mathematics and Science, Cardinal Stefan Wyszyński University, Dewajtis 5, 01-815 Warsaw, Poland
| | - Jarosław Poznański
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
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13
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Acharya N, Jha SK. Dry Molten Globule-Like Intermediates in Protein Folding, Function, and Disease. J Phys Chem B 2022; 126:8614-8622. [PMID: 36286394 DOI: 10.1021/acs.jpcb.2c04991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The performance of a protein depends on its correct folding to the final functional native form. Hence, understanding the process of protein folding has remained an important field of research for the scientific community for the past five decades. Two important intermediate states, namely, wet molten globule (WMG) and dry molten globule (DMG), have emerged as critical milestones during protein folding-unfolding reactions. While much has been discussed about WMGs as a common unfolding intermediate, the evidence for DMGs has remained elusive owing to their near-native features, which makes them difficult to probe using global structural probes. This Review puts together the available literature and new evidence on DMGs to give a broader perspective on the universality of DMGs and discuss their significance in protein folding, function, and disease.
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Affiliation(s)
- Nirbhik Acharya
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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14
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Sun Q, Fu Y, Wang W. Temperature effects on hydrophobic interactions: Implications for protein unfolding. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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15
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Cong Y, Li M, Qi Y, Zhang JZH. A fast-slow method to treat solute dynamics in explicit solvent. Phys Chem Chem Phys 2022; 24:14498-14510. [PMID: 35665790 DOI: 10.1039/d2cp00732k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aiming to reduce the computational cost in the current explicit solvent molecular dynamics (MD) simulation, this paper proposes a fast-slow method for the fast MD simulation of biomolecules in explicit solvent. This fast-slow method divides the entire system into two parts: a core layer (typically solute or biomolecule) and a peripheral layer (typically solvent molecules). The core layer is treated using standard MD method but the peripheral layer is treated by a slower dynamics method to reduce the computational cost. We compared four different simulation models in testing calculations for several small proteins. These include gas-phase, implicit solvent, fast-slow explicit solvent and standard explicit solvent MD simulations. Our study shows that gas-phase and implicit solvent models do not provide a realistic solvent environment and fail to correctly produce reliable dynamic structures of proteins. On the other hand, the fast-slow method can essentially reproduce the same solvent effect as the standard explicit solvent model while gaining an order of magnitude in efficiency. This fast-slow method thus provides an efficient approach for accelerating the MD simulation of biomolecules in explicit solvent.
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Affiliation(s)
- Yalong Cong
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University at Shanghai, 200062, China.
| | - Mengxin Li
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University at Shanghai, 200062, China.
| | - Yifei Qi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University at Shanghai, 200062, China.
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University at Shanghai, 200062, China. .,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Department of Chemistry, New York University, NY, NY 10003, USA.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, 030006, China
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16
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Pulavarti SVSRK, Maguire JB, Yuen S, Harrison JS, Griffin J, Premkumar L, Esposito EA, Makhatadze GI, Garcia AE, Weiss TM, Snell EH, Kuhlman B, Szyperski T. From Protein Design to the Energy Landscape of a Cold Unfolding Protein. J Phys Chem B 2022; 126:1212-1231. [PMID: 35128921 PMCID: PMC9281400 DOI: 10.1021/acs.jpcb.1c10750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein-water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ∼0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.
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Affiliation(s)
- Surya V S R K Pulavarti
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Jack B Maguire
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Shirley Yuen
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jermel Griffin
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Edward A Esposito
- Malvern Panalytical Inc, Northhampton, Massachsetts 01060, United States
| | - George I Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 08544, United States
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center, Stanford University, Menlo Park, California 94025, United States
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, United States.,Department of Materials Design and Innovation, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Thomas Szyperski
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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17
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Ishihara A, Tsukamoto Y, Inoue H, Noda Y, Koizumi S, Joko K. Analysis of water distribution in delipidated human hair by small-angle neutron scattering (SANS). Int J Cosmet Sci 2021; 43:653-661. [PMID: 34665889 DOI: 10.1111/ics.12741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 09/08/2021] [Accepted: 10/11/2021] [Indexed: 12/01/2022]
Abstract
OBJECTIVE It is known that damaged hair has a part of its internal structure damaged, and its water absorption and desorption behavior are different. In recent years, it has been reported that internal lipids play an important role in the adsorption and desorption of water to the hair. Therefore, we investigate whether the water distribution in hair and the amount of internal lipids are related. METHODS To investigate the effect of internal lipid on water distribution, we prepare human hair samples with and without a partial lack of internal lipids. Internal lipids have been removed using formic acid. The distribution of D2 O in the hair is investigated using small angle neutron scattering (SANS) under the wet and dry conditions of each hair sample. RESULTS It is found from the obtained SANS data that formic acid-treated hairs tended to have fewer 40Å-sized water clusters that were periodically present along the fibre axis in the wet condition. On the other hand, in the dry condition, there were no differences in water distribution between samples. CONCLUSION These observations are believed to have been caused by the reduction of 40Å-sized water clusters existing on the constituents removed by formic acid treatment, especially the hydrophobic (lipid) constituent tissues. Consequently, it is clarified that internal lipids are deeply involved in the state of water distribution on hair in wet conditions.
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Affiliation(s)
| | | | | | - Yohei Noda
- Institute of Quantum Beam Science, Ibaraki University, Ibaraki, Japan
| | - Satoshi Koizumi
- Institute of Quantum Beam Science, Ibaraki University, Ibaraki, Japan
| | - Kyohei Joko
- Sugiyama Jogakuen University, Chikusa-ku, Japan
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18
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Ki H, Choi S, Kim J, Choi EH, Lee S, Lee Y, Yoon K, Ahn CW, Ahn DS, Lee JH, Park J, Eom I, Kim M, Chun SH, Kim J, Ihee H, Kim J. Optical Kerr Effect of Liquid Acetonitrile Probed by Femtosecond Time-Resolved X-ray Liquidography. J Am Chem Soc 2021; 143:14261-14273. [PMID: 34455778 DOI: 10.1021/jacs.1c06088] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Optical Kerr effect (OKE) spectroscopy is a method that measures the time-dependent change of the birefringence induced by an optical laser pulse using another optical laser pulse and has been used often to study the ultrafast dynamics of molecular liquids. Here we demonstrate an alternative method, femtosecond time-resolved X-ray liquidography (fs-TRXL), where the microscopic structural motions related to the OKE response can be monitored using a different type of probe, i.e., X-ray solution scattering. By applying fs-TRXL to acetonitrile and a dye solution in acetonitrile, we demonstrate that different types of molecular motions around photoaligned molecules can be resolved selectively, even without any theoretical modeling, based on the anisotropy of two-dimensional scattering patterns and extra structural information contained in the q-space scattering data. Specifically, the dynamics of reorientational (libration and orientational diffusion) and translational (interaction-induced motion) motions are captured separately by anisotropic and isotropic scattering signals, respectively. Furthermore, the two different types of reorientational motions are distinguished from each other by their own characteristic scattering patterns and time scales. The measured time-resolved scattering signals are in excellent agreement with the simulated scattering signals based on a molecular dynamics simulation for plausible molecular configurations, providing the detailed structural description of the OKE response in liquid acetonitrile.
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Affiliation(s)
- Hosung Ki
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Seungjoo Choi
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Jungmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Eun Hyuk Choi
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Seonggon Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Kihwan Yoon
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Chi Woo Ahn
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Doo-Sik Ahn
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Jae Hyuk Lee
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Jaeku Park
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Intae Eom
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Minseok Kim
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Sae Hwan Chun
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Joonghan Kim
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
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19
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Sumi T, Imamura H. Water-mediated interactions destabilize proteins. Protein Sci 2021; 30:2132-2143. [PMID: 34382697 PMCID: PMC8442971 DOI: 10.1002/pro.4168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 01/29/2023]
Abstract
Proteins are folded to avoid exposure of the nonpolar groups to water because water‐mediated interactions between nonpolar groups are a promising factor in the thermodynamic stabilities of proteins—which is a well‐accepted view as one of the unique effects of hydrophobic interactions. This article poses a critical question for this classical view by conducting an accurate solvation free‐energy calculation for a thermodynamic cycle of a protein folding using a liquid‐state density functional theory. Here, the solvation‐free energy for a leucine zipper formation was examined in the coiled‐coil protein GCN4‐p1, a typical model for hydrophobic interactions, which demonstrated that water‐mediated interactions were unfavorable for the association of nonpolar groups in the native state, while the dispersion forces between them were, instead, responsible for the association. Furthermore, the present analysis well predicted the isolated helical state stabilized by pressure, which was previously observed in an experiment. We reviewed the problems in the classical concept and semiempirical presumption that the energetic cost of the hydration of nonpolar groups is a driving force of folding.
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Affiliation(s)
- Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, Kita-ku, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Kita-ku, Japan
| | - Hiroshi Imamura
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
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20
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Almeida FCL, Sanches K, Pinheiro-Aguiar R, Almeida VS, Caruso IP. Protein Surface Interactions-Theoretical and Experimental Studies. Front Mol Biosci 2021; 8:706002. [PMID: 34307462 PMCID: PMC8298896 DOI: 10.3389/fmolb.2021.706002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
In this review, we briefly describe a theoretical discussion of protein folding, presenting the relative contribution of the hydrophobic effect versus the stabilization of proteins via direct surface forces that sometimes may be overlooked. We present NMR-based studies showing the stability of proteins lacking a hydrophobic core which in turn present hydrophobic surface clusters, such as plant defensins. Protein dynamics measurements by NMR are the key feature to understand these dynamic surface clusters. We contextualize the measurement of protein dynamics by nuclear relaxation and the information available at protein surfaces and water cavities. We also discuss the presence of hydrophobic surface clusters in multidomain proteins and their participation in transient interactions which may regulate the function of these proteins. In the end, we discuss how surface interaction regulates the reactivity of certain protein post-translational modifications, such as S-nitrosation.
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Affiliation(s)
- Fabio C L Almeida
- Institute of Medical Biochemistry-IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Karoline Sanches
- Institute of Medical Biochemistry-IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Multiuser Center for Biomolecular Innovation (CMIB), Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São Paulo, Brazil
| | - Ramon Pinheiro-Aguiar
- Institute of Medical Biochemistry-IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vitor S Almeida
- Institute of Medical Biochemistry-IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Icaro P Caruso
- Institute of Medical Biochemistry-IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Multiuser Center for Biomolecular Innovation (CMIB), Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São Paulo, Brazil
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21
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Song J. Adenosine triphosphate energy-independently controls protein homeostasis with unique structure and diverse mechanisms. Protein Sci 2021; 30:1277-1293. [PMID: 33829608 PMCID: PMC8197423 DOI: 10.1002/pro.4079] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 02/06/2023]
Abstract
Proteins function in the crowded cellular environments with high salt concentrations, thus facing tremendous challenges of misfolding/aggregation which represents a pathological hallmark of aging and an increasing spectrum of human diseases. Recently, intrinsically disordered regions (IDRs) were recognized to drive liquid-liquid phase separation (LLPS), a common principle for organizing cellular membraneless organelles (MLOs). ATP, the universal energy currency for all living cells, mysteriously has concentrations of 2-12 mM, much higher than required for its previously-known functions. Only recently, ATP was decoded to behave as a biological hydrotrope to inhibit protein LLPS and aggregation at mM. We further revealed that ATP also acts as a bivalent binder, which not only biphasically modulates LLPS driven by IDRs of human and viral proteins, but also bind to the conserved nucleic-acid-binding surfaces of the folded proteins. Most unexpectedly, ATP appears to act as a hydration mediator to antagonize the crowding-induced destabilization as well as to enhance folding of proteins without significant binding. Here, this review focuses on summarizing the results of these biophysical studies and discussing their implications in an evolutionary context. By linking triphosphate with unique hydration property to adenosine, ATP appears to couple the ability for establishing hydrophobic, π-π, π-cation and electrostatic interactions to the capacity in mediating hydration of proteins, which is at the heart of folding, dynamics, stability, phase separation and aggregation. Consequently, ATP acquired a category of functions at ~mM to energy-independently control protein homeostasis with diverse mechanisms, thus implying a link between cellular ATP concentrations and protein-aggregation diseases.
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Affiliation(s)
- Jianxing Song
- Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
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22
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Beyerle ER, Dinpajooh M, Ji H, von Hippel PH, Marcus AH, Guenza MG. Dinucleotides as simple models of the base stacking-unstacking component of DNA 'breathing' mechanisms. Nucleic Acids Res 2021; 49:1872-1885. [PMID: 33503257 PMCID: PMC7913701 DOI: 10.1093/nar/gkab015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/22/2020] [Accepted: 01/07/2021] [Indexed: 01/11/2023] Open
Abstract
Regulatory protein access to the DNA duplex ‘interior’ depends on local DNA ‘breathing’ fluctuations, and the most fundamental of these are thermally-driven base stacking-unstacking interactions. The smallest DNA unit that can undergo such transitions is the dinucleotide, whose structural and dynamic properties are dominated by stacking, while the ion condensation, cooperative stacking and inter-base hydrogen-bonding present in duplex DNA are not involved. We use dApdA to study stacking-unstacking at the dinucleotide level because the fluctuations observed are likely to resemble those of larger DNA molecules, but in the absence of constraints introduced by cooperativity are likely to be more pronounced, and thus more accessible to measurement. We study these fluctuations with a combination of Molecular Dynamics simulations on the microsecond timescale and Markov State Model analyses, and validate our results by calculations of circular dichroism (CD) spectra, with results that agree well with the experimental spectra. Our analyses show that the CD spectrum of dApdA is defined by two distinct chiral conformations that correspond, respectively, to a Watson–Crick form and a hybrid form with one base in a Hoogsteen configuration. We find also that ionic structure and water orientation around dApdA play important roles in controlling its breathing fluctuations.
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Affiliation(s)
- Eric R Beyerle
- Institute for Fundamental Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Mohammadhasan Dinpajooh
- Institute for Fundamental Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Huiying Ji
- Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA.,Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Peter H von Hippel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Andrew H Marcus
- Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA.,Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Marina G Guenza
- Institute for Fundamental Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA.,Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA.,Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
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23
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Camino JD, Gracia P, Cremades N. The role of water in the primary nucleation of protein amyloid aggregation. Biophys Chem 2021; 269:106520. [PMID: 33341693 DOI: 10.1016/j.bpc.2020.106520] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022]
Abstract
The understanding of the complex conformational landscape of amyloid aggregation and its modulation by relevant physicochemical and cellular factors is a prerequisite for elucidating some of the molecular basis of pathology in amyloid related diseases, and for developing and evaluating effective disease-specific therapeutics to reduce or eliminate the underlying sources of toxicity in these diseases. Interactions of proteins with solvating water have been long considered to be fundamental in mediating their function and folding; however, the relevance of water in the process of protein amyloid aggregation has been largely overlooked. Here, we provide a perspective on the role water plays in triggering primary amyloid nucleation of intrinsically disordered proteins (IDPs) based on recent experimental evidences. The initiation of amyloid aggregation likely results from the synergistic effect between both protein intermolecular interactions and the properties of the water hydration layer of the protein surface. While the self-assembly of both hydrophobic and hydrophilic IDPs would be thermodynamically favoured due to large water entropy contributions, large desolvation energy barriers are expected, particularly for the nucleation of hydrophilic IDPs. Under highly hydrating conditions, primary nucleation is slow, being facilitated by the presence of nucleation-active surfaces (heterogeneous nucleation). Under conditions of poor water activity, such as those found in the interior of protein droplets generated by liquid-liquid phase separation, however, the desolvation energy barrier is significantly reduced, and nucleation can occur very rapidly in the bulk of the solution (homogeneous nucleation), giving rise to structurally distinct amyloid polymorphs. Water, therefore, plays a key role in modulating the transition free energy of amyloid nucleation, thus governing the initiation of the process, and dictating the type of preferred primary nucleation and the type of amyloid polymorph generated, which could vary depending on the particular microenvironment that the protein molecules encounter in the cell.
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Affiliation(s)
- José D Camino
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR(CSIC), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Pablo Gracia
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR(CSIC), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Nunilo Cremades
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR(CSIC), Universidad de Zaragoza, Zaragoza 50018, Spain.
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24
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Tamoliu Nas K, Galamba N. Protein Denaturation, Zero Entropy Temperature, and the Structure of Water around Hydrophobic and Amphiphilic Solutes. J Phys Chem B 2020; 124:10994-11006. [PMID: 33201713 DOI: 10.1021/acs.jpcb.0c08055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The hydrophobic effect plays a key role in many chemical and biological processes, including protein folding. Nonetheless, a comprehensive picture of the effect of temperature on hydrophobic hydration and protein denaturation remains elusive. Here, we study the effect of temperature on the hydration of model hydrophobic and amphiphilic solutes, through molecular dynamics, aiming at getting insight on the singular behavior of water, concerning the zero-entropy temperature, TS, and entropy convergence, TS*, also observed for some proteins, upon denaturation. We show that, similar to hydrocarbons, polar amphiphilic solutes exhibit a TS, although strongly dependent on solute-water interactions, opposite to hydrocarbons. Further, the temperature dependence of the hydration entropy, normalized by the solvent accessible surface area, is shown to be nearly solute size independent for hydrophobic but not for amphiphilic solutes, for similar reasons. These results are further discussed in the light of information theory (IT) and the structure of water around hydrophobic groups. The latter shows that the tetrahedral enhancement of some water molecules around hydrophobic groups, associated with the reduction of water defects, leads to the strengthening of the weakest hydrogen bonds, relative to bulk water. In addition, a larger tetrahedrality is found in low density water populations, demonstrating that pure water has encoded structural information, similar to that associated with hydrophobic hydration. The reversal of the hydration entropy dependence on the solute size, above TS*, is also analyzed and shown to be associated with a greater loss of water molecules exhibiting enhanced orientational order, in the coordination sphere of large solutes. Finally, the source of the differences between Kauzmann's "hydrocarbon model" on protein denaturation and hydrophobic hydration is discussed, with relatively large amphiphilic hydrocarbons seemingly displaying a more similar behavior to some globular proteins than aliphatic hydrocarbons.
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Affiliation(s)
- Kazimieras Tamoliu Nas
- Centre of Chemistry and Biochemistry and Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
| | - Nuno Galamba
- Centre of Chemistry and Biochemistry and Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
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Cheng X, Shkel IA, O'Connor K, Record MT. Experimentally determined strengths of favorable and unfavorable interactions of amide atoms involved in protein self-assembly in water. Proc Natl Acad Sci U S A 2020; 117:27339-27345. [PMID: 33087561 PMCID: PMC7959557 DOI: 10.1073/pnas.2012481117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Folding and other protein self-assembly processes are driven by favorable interactions between O, N, and C unified atoms of the polypeptide backbone and side chains. These processes are perturbed by solutes that interact with these atoms differently than water does. Amide NH···O=C hydrogen bonding and various π-system interactions have been better characterized structurally or by simulations than experimentally in water, and unfavorable interactions are relatively uncharacterized. To address this situation, we previously quantified interactions of alkyl ureas with amide and aromatic compounds, relative to interactions with water. Analysis yielded strengths of interaction of each alkylurea with unit areas of different hybridization states of unified O, N, and C atoms of amide and aromatic compounds. Here, by osmometry, we quantify interactions of 10 pairs of amides selected to complete this dataset. An analysis yields intrinsic strengths of six favorable and four unfavorable atom-atom interactions, expressed per unit area of each atom and relative to interactions with water. The most favorable interactions are sp2O-sp2C (lone pair-π, presumably n-π*), sp2C-sp2C (π-π and/or hydrophobic), sp2O-sp2N (hydrogen bonding) and sp3C-sp2C (CH-π and/or hydrophobic). Interactions of sp3C with itself (hydrophobic) and with sp2N are modestly favorable, while sp2N interactions with sp2N and with amide/aromatic sp2C are modestly unfavorable. Amide sp2O-sp2O interactions and sp2O-sp3C interactions are more unfavorable, indicating the preference of amide sp2O to interact with water. These intrinsic interaction strengths are used to predict interactions of amides with proteins and chemical effects of amides (including urea, N-ethylpyrrolidone [NEP], and polyvinylpyrrolidone [PVP]) on protein stability.
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Affiliation(s)
- Xian Cheng
- Program in Biophysics, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Irina A Shkel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Kevin O'Connor
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - M Thomas Record
- Program in Biophysics, University of Wisconsin-Madison, Madison, WI 53706;
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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27
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Dongmo Foumthuim CJ, Carrer M, Houvet M, Škrbić T, Graziano G, Giacometti A. Can the roles of polar and non-polar moieties be reversed in non-polar solvents? Phys Chem Chem Phys 2020; 22:25848-25858. [DOI: 10.1039/d0cp02948c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using thermodynamic integration, we study the solvation free energy of 18 amino acid side chain equivalents in solvents with different polarities, ranging from the most polar water to the most non-polar cyclohexane.
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Affiliation(s)
- Cedrix J. Dongmo Foumthuim
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Campus Scientifico
- Edificio Alfa
- via Torino 155
| | - Manuel Carrer
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences
- University of Oslo
- 0315 Oslo
- Norway
| | - Maurine Houvet
- Polytech Nantes–Engineering School of the University of Nantes
- Rue Christian Pauc
- 44306 Nantes Cedex 3
- France
| | - Tatjana Škrbić
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Campus Scientifico
- Edificio Alfa
- via Torino 155
| | - Giuseppe Graziano
- Department of Science and Technology
- University of Sannio-Benevento
- via Francesco de Sanctis
- 82100 Benevento
- Italy
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Campus Scientifico
- Edificio Alfa
- via Torino 155
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28
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Szymaniec-Rutkowska A, Bugajska E, Kasperowicz S, Mieczkowska K, Maciejewska AM, Poznański J. Does the partial molar volume of a solute reflect the free energy of hydrophobic solvation? J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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29
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Stephens AD, Kaminski Schierle GS. The role of water in amyloid aggregation kinetics. Curr Opin Struct Biol 2019; 58:115-123. [PMID: 31299481 DOI: 10.1016/j.sbi.2019.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/30/2019] [Accepted: 06/06/2019] [Indexed: 12/16/2022]
Abstract
The role of water in protein function and aggregation is highly important and may hold some answers to understanding initiation of misfolding diseases such as Parkinson's, Alzheimer's and Huntington's where soluble intrinsically disordered proteins (IDPs) aggregate into fibrillar structures. IDPs are highly dynamic and have larger solvent exposed areas compared to globular proteins, meaning they make and break hydrogen bonds with the surrounding water more frequently. The mobility of water can be altered by presence of ions, sugars, osmolytes, proteins and membranes which differ in different cell types, cell compartments and also as cells age. A reduction in water mobility and thus protein mobility enhances the probability that IDPs can associate to form intermolecular bonds and propagate into aggregates. This poses an interesting question as to whether localised water mobility inside cells can influence the propensity of an IDP to aggregate and furthermore whether it can influence fibril polymorphism and disease outcome.
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Affiliation(s)
- Amberley D Stephens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Gabriele S Kaminski Schierle
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
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30
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Islam MM, Kobayashi K, Kidokoro S, Kuroda Y. Hydrophobic surface residues can stabilize a protein through improved water–protein interactions. FEBS J 2019; 286:4122-4134. [DOI: 10.1111/febs.14941] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/19/2019] [Accepted: 05/28/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Mohammad M. Islam
- Department of Biochemistry and Molecular Biology University of Chittagong Chittagong Bangladesh
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Tokyo Japan
| | - Kei Kobayashi
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Tokyo Japan
| | - Shun‐Ichi Kidokoro
- Department of Bioengineering Nagaoka University of Technology Niigata Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Tokyo Japan
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31
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Arya S, Singh AK, Bhasne K, Dogra P, Datta A, Das P, Mukhopadhyay S. Femtosecond Hydration Map of Intrinsically Disordered α-Synuclein. Biophys J 2019; 114:2540-2551. [PMID: 29874605 DOI: 10.1016/j.bpj.2018.04.028] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 10/14/2022] Open
Abstract
Protein hydration water plays a fundamentally important role in protein folding, binding, assembly, and function. Little is known about the hydration water in intrinsically disordered proteins that challenge the conventional sequence-structure-function paradigm. Here, by combining experiments and simulations, we show the existence of dynamical heterogeneity of hydration water in an intrinsically disordered presynaptic protein, namely α-synuclein, implicated in Parkinson's disease. We took advantage of nonoccurrence of cysteine in the sequence and incorporated a number of cysteine residues at the N-terminal segment, the central amyloidogenic nonamyloid-β component (NAC) domain, and the C-terminal end of α-synuclein. We then labeled these cysteine variants using environment-sensitive thiol-active fluorophore and monitored the solvation dynamics using femtosecond time-resolved fluorescence. The site-specific femtosecond time-resolved experiments allowed us to construct the hydration map of α-synuclein. Our results show the presence of three dynamically distinct types of water: bulk, hydration, and confined water. The amyloidogenic NAC domain contains dynamically restrained water molecules that are strikingly different from the water molecules present in the other two domains. Atomistic molecular dynamics simulations revealed longer residence times for water molecules near the NAC domain and supported our experimental observations. Additionally, our simulations allowed us to decipher the molecular origin of the dynamical heterogeneity of water in α-synuclein. These simulations captured the quasi-bound water molecules within the NAC domain originating from a complex interplay between the local chain compaction and the sequence composition. Our findings from this synergistic experimental simulation approach suggest longer trapping of interfacial water molecules near the amyloidogenic hotspot that triggers the pathological conversion into amyloids via chain sequestration, chain desolvation, and entropic liberation of ordered water molecules.
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Affiliation(s)
- Shruti Arya
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India
| | - Avinash K Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Karishma Bhasne
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India
| | - Priyanka Dogra
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India
| | - Anindya Datta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India.
| | - Payel Das
- Data Science Department, IBM Thomas J. Watson Research Center, Yorktown Heights, New York.
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India.
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32
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Binding of norharmane with RNA reveals two thermodynamically different binding modes with opposing heat capacity changes. J Colloid Interface Sci 2019; 538:587-596. [DOI: 10.1016/j.jcis.2018.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/26/2018] [Accepted: 12/03/2018] [Indexed: 02/01/2023]
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33
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Larocca M, Foglia F, Cilibrizzi A. Dihedral Angle Calculations To Elucidate the Folding of Peptides through Its Main Mechanical Forces. Biochemistry 2019; 58:1032-1037. [PMID: 30719916 DOI: 10.1021/acs.biochem.8b01101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study reports a general method to calculate dihedral angles (φ and ψ) of a given amino acid sequence, focusing on potential energy and torque moment concepts. By defining these physical measures in relation to the chemical interactions that occur on each single amino acid residue within a peptide, we analyze the folding process as the result of main mechanical forces (MMFs) exerted in the specific amino acid chain of interest. As a proof of concept, Leu-enkephalin was initially used as a model peptide to carry out the theoretical study. Our data show agreement between calculated Leu-enkephalin backbone dihedral angles and the corresponding experimentally determined X-ray values. Hence, we used calcitonin to validate our MMF-based method on a larger peptide, i.e., 32 amino acid residues forming an α-helix. Through a similar approach (although simplified with regard to electrostatic interactions), the calculations for calcitonin also demonstrate a good agreement with experimental values. This study offers new opportunities to analyze peptides' amino acid sequences and to help in the prediction of how they must fold, assisting in the development of new computational techniques in the field.
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Affiliation(s)
- Michele Larocca
- Institute of Pharmaceutical Science , King's College London , Stamford Street , London SE1 9NH , U.K
| | - Fabrizia Foglia
- Institute of Pharmaceutical Science , King's College London , Stamford Street , London SE1 9NH , U.K
| | - Agostino Cilibrizzi
- Institute of Pharmaceutical Science , King's College London , Stamford Street , London SE1 9NH , U.K
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34
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Parui S, Jana B. Factors Promoting the Formation of Clathrate-Like Ordering of Water in Biomolecular Structure at Ambient Temperature and Pressure. J Phys Chem B 2019; 123:811-824. [PMID: 30605607 DOI: 10.1021/acs.jpcb.8b11172] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Clathrate hydrate forms when a hydrophobic molecule is entrapped inside a water cage or cavity. Although biomolecular structures also have hydrophobic patches, clathrate-like water is found in only a limited number of biomolecules. Also, while clathrate hydrates form at low temperature and moderately higher pressure, clathrate-like water is observed in biomolecular structure at ambient temperature and pressure. These indicate presence of other factors along with hydrophobic environment behind the formation of clathrate-like water in biomolecules. In the current study, we presented a systematic approach to explore the factors behind the formation of clathrate-like water in biomolecules by means of molecular dynamics simulation of a model protein, maxi, which is a naturally occurring nanopore and has clathrate-like water inside the pore. Removal of either confinement or hydrophobic environment results in the disappearance of clathrate-like water ordering, indicating a coupled role of these two factors. Apart from these two factors, clathrate-like water ordering also requires anchoring groups that can stabilize the clathrate-like water through hydrogen bonding. Our results uncover crucial factors for the stabilization of clathrate-like ordering in biomolecular structure which can be used for the development of new biomolecular structure promoting clathrate formation.
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Affiliation(s)
- Sridip Parui
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Biman Jana
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
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35
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Robalo JR, Vila Verde A. Unexpected trends in the hydrophobicity of fluorinated amino acids reflect competing changes in polarity and conformation. Phys Chem Chem Phys 2019; 21:2029-2038. [DOI: 10.1039/c8cp07025c] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The hydration free energy of fluorinated amino acids is calculated with molecular simulations and explained with an analytical model.
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Affiliation(s)
- João R. Robalo
- Max Planck Institute for Colloids and Interfaces
- Department of Theory & Bio-systems
- Science Park
- Potsdam 14424
- Germany
| | - Ana Vila Verde
- Max Planck Institute for Colloids and Interfaces
- Department of Theory & Bio-systems
- Science Park
- Potsdam 14424
- Germany
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36
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Sato T, Sasaki T, Ohnuki J, Umezawa K, Takano M. Hydrophobic Surface Enhances Electrostatic Interaction in Water. PHYSICAL REVIEW LETTERS 2018; 121:206002. [PMID: 30500220 DOI: 10.1103/physrevlett.121.206002] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Indexed: 06/09/2023]
Abstract
A high dielectric constant is one of the peculiar properties of liquid water, indicating that the electrostatic interaction between charged substances is largely reduced in water. We show by molecular dynamics simulation that the dielectric constant of water is decreased near the hydrophobic surface. We further show that the decrease in the dielectric constant is due to both the decreased water density and the reduced water dipole correlation in the direction perpendicular to the surface. We finally demonstrate that electrostatic interaction in water is actually strengthened near the hydrophobic surface.
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Affiliation(s)
- Takato Sato
- Department of Pure and Applied Physics, Waseda University, Ohkubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Tohru Sasaki
- Department of Pure and Applied Physics, Waseda University, Ohkubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Jun Ohnuki
- Department of Pure and Applied Physics, Waseda University, Ohkubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Koji Umezawa
- Department of Biomedical Engineering/Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano, 399-4598, Japan
| | - Mitsunori Takano
- Department of Pure and Applied Physics, Waseda University, Ohkubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan
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37
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Leśniewski M, Śmiechowski M. Communication: Inside the water wheel: Intrinsic differences between hydrated tetraphenylphosphonium and tetraphenylborate ions. J Chem Phys 2018; 149:171101. [DOI: 10.1063/1.5056237] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mateusz Leśniewski
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Maciej Śmiechowski
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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38
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Raghuwanshi VS, Cohen Y, Garnier G, Garvey CJ, Russell RA, Darwish T, Garnier G. Cellulose Dissolution in Ionic Liquid: Ion Binding Revealed by Neutron Scattering. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01425] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Vikram Singh Raghuwanshi
- Bioresource Processing Research Institute of Australia (BioPRIA), Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Yachin Cohen
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Guillaume Garnier
- Bioresource Processing Research Institute of Australia (BioPRIA), Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Christopher J. Garvey
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd., Lucas Heights, NSW 2234, Australia
| | - Robert A. Russell
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd., Lucas Heights, NSW 2234, Australia
| | - Tamim Darwish
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd., Lucas Heights, NSW 2234, Australia
| | - Gil Garnier
- Bioresource Processing Research Institute of Australia (BioPRIA), Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
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39
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Daschakraborty S. How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction. J Chem Phys 2018; 148:134501. [PMID: 29626866 DOI: 10.1063/1.5019239] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.
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40
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Dimova M, Devedjiev YD. Protein crystal lattices are dynamic assemblies: the role of conformational entropy in the protein condensed phase. IUCRJ 2018; 5:130-140. [PMID: 29765602 PMCID: PMC5947717 DOI: 10.1107/s2052252517017833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 12/13/2017] [Indexed: 05/03/2023]
Abstract
Until recently, the occurrence of conformational entropy in protein crystal contacts was considered to be a very unlikely event. A study based on the most accurately refined protein structures demonstrated that side-chain conformational entropy and static disorder might be common in protein crystal lattices. The present investigation uses structures refined using ensemble refinement to show that although paradoxical, conformational entropy is likely to be the major factor in the emergence and integrity of the protein condensed phase. This study reveals that the role of shape entropy and local entropic forces expands beyond the onset of crystallization. For the first time, the complete pattern of intermolecular interactions by protein atoms in crystal lattices is presented, which shows that van der Waals interactions dominate in crystal formation.
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Affiliation(s)
- Margarita Dimova
- Department of Anesthesiology, University of Virginia, 1215 Lee Street, Charlottesville, VA 22908, USA
| | - Yancho D. Devedjiev
- Department of Anesthesiology, University of Virginia, 1215 Lee Street, Charlottesville, VA 22908, USA
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41
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Cerdeiriña CA, Debenedetti PG. Water’s Thermal Pressure Drives the Temperature Dependence of Hydrophobic Hydration. J Phys Chem B 2017; 122:3620-3625. [DOI: 10.1021/acs.jpcb.7b11100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Claudio A. Cerdeiriña
- Departamento de Física Aplicada, Universidad de Vigo—Campus del Agua, Ourense 32004, Spain
| | - Pablo G. Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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42
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Sung SS. Dielectric screening effect of electronic polarization and intramolecular hydrogen bonding. Protein Sci 2017; 26:2003-2009. [PMID: 28726339 DOI: 10.1002/pro.3238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 07/12/2017] [Indexed: 01/11/2023]
Abstract
Recent site-resolved hydrogen exchange measurements have uncovered significant discrepancies between simulations and experimental data during protein folding, including the excessive intramolecular hydrogen bonds in simulations. This finding indicates a possibility that intramolecular charge-charge interactions have not included sufficient dielectric screening effect of the electronic polarization. Scaling down peptide atomic charges according to the optical dielectric constant is tested in this study. As a result, the number of intramolecular hydrogen bonds is lower than using unscaled atomic charges while reaching the same levels of helical contents or β-hairpin backbone hydrogen bonds, because van der Waals interactions contribute substantially to peptide folding in water. Reducing intramolecular charge-charge interactions and hydrogen bonding increases conformational search efficiency. In particular, it reduces the equilibrium helical content in simulations using AMBER force field and the energy barrier in folding simulations using CHARMM force field.
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Affiliation(s)
- Shen-Shu Sung
- Department of Pharmacology, College of Medicine, Penn State University, Hershey, Pennsylvania, 17033
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43
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Cheng X, Shkel IA, O'Connor K, Henrich J, Molzahn C, Lambert D, Record MT. Experimental Atom-by-Atom Dissection of Amide-Amide and Amide-Hydrocarbon Interactions in H 2O. J Am Chem Soc 2017; 139:9885-9894. [PMID: 28678492 PMCID: PMC5580340 DOI: 10.1021/jacs.7b03261] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Quantitative information about amide interactions in water is needed to understand their contributions to protein folding and amide effects on aqueous processes and to compare with computer simulations. Here we quantify interactions of urea, alkylated ureas, and other amides by osmometry and amide-aromatic hydrocarbon interactions by solubility. Analysis of these data yields strengths of interaction of ureas and naphthalene with amide sp2O, amide sp2N, aliphatic sp3C, and amide and aromatic sp2C unified atoms in water. Interactions of amide sp2O with urea and naphthalene are favorable, while amide sp2O-alkylurea interactions are unfavorable, becoming more unfavorable with increasing alkylation. Hence, amide sp2O-amide sp2N interactions (proposed n-σ* hydrogen bond) and amide sp2O-aromatic sp2C (proposed n-π*) interactions are favorable in water, while amide sp2O-sp3C interactions are unfavorable. Interactions of all ureas with sp3C and amide sp2N are favorable and increase in strength with increasing alkylation, indicating favorable sp3C-amide sp2N and sp3C-sp3C interactions. Naphthalene results show that aromatic sp2C-amide sp2N interactions in water are unfavorable while sp2C-sp3C interactions are favorable. These results allow interactions of amide and hydrocarbon moieties and effects of urea and alkylureas on aqueous processes to be predicted or interpreted in terms of structural information. We predict strengths of favorable urea-benzene and N-methylacetamide interactions from experimental information to compare with simulations and indicate how amounts of hydrocarbon and amide surfaces buried in protein folding and other biopolymer processes and transition states can be determined from analysis of urea and diethylurea effects on equilibrium and rate constants.
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Affiliation(s)
- Xian Cheng
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Irina A Shkel
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Kevin O'Connor
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - John Henrich
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Cristen Molzahn
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - David Lambert
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - M Thomas Record
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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Abstract
Szent-Győrgi called water the "matrix of life" and claimed that there was no life without it. This statement is true, as far as we know, on our planet, but it is not clear whether it must hold throughout the cosmos. To evaluate that question requires a close consideration of the many varied and subtle roles that water plays in living cells-a consideration that must be free of both an assumed essentialism that gives water an almost mystical life-giving agency and a traditional tendency to see it as a merely passive solvent. Water is a participant in the "life of the cell," and here I describe some of the features of that active agency. Water's value for molecular biology comes from both the structural and dynamic characteristics of its status as a complex, structured liquid as well as its nature as a polar, protic, and amphoteric reagent. Any discussion of water as life's matrix must, however, begin with an acknowledgment that our understanding of it as both a liquid and a solvent is still incomplete.
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45
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Islam MM, Yohda M, Kidokoro SI, Kuroda Y. Crystal structures of highly simplified BPTIs provide insights into hydration-driven increase of unfolding enthalpy. Sci Rep 2017; 7:41205. [PMID: 28266637 PMCID: PMC5339861 DOI: 10.1038/srep41205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 12/16/2016] [Indexed: 11/15/2022] Open
Abstract
We report a thermodynamic and structural analysis of six extensively simplified bovine pancreatic trypsin inhibitor (BPTI) variants containing 19–24 alanines out of 58 residues. Differential scanning calorimetry indicated a two-state thermal unfolding, typical of a native protein with densely packed interior. Surprisingly, increasing the number of alanines induced enthalpy stabilization, which was however over-compensated by entropy destabilization. X-ray crystallography indicated that the alanine substitutions caused the recruitment of novel water molecules facilitating the formation of protein–water hydrogen bonds and improving the hydration shells around the alanine’s methyl groups, both of which presumably contributed to enthalpy stabilization. There was a strong correlation between the number of water molecules and the thermodynamic parameters. Overall, our results demonstrate that, in contrast to our initial expectation, a protein sequence in which over 40% of the residues are alanines can retain a densely packed structure and undergo thermal denaturation with a large enthalpy change, mainly contributed by hydration.
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Affiliation(s)
- Mohammad Monirul Islam
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan.,Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong-4331, Bangladesh
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
| | - Shun-Ichi Kidokoro
- Department of Bioengineering, Nagaoka University of Technology, Kamitomioka-cho, Nagaoka, Niigata 940-2188, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
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46
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Cheng L, Sun DW, Zhu Z, Zhang Z. Effects of high pressure freezing (HPF) on denaturation of natural actomyosin extracted from prawn (Metapenaeus ensis). Food Chem 2017; 229:252-259. [PMID: 28372171 DOI: 10.1016/j.foodchem.2017.02.048] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 02/08/2017] [Accepted: 02/10/2017] [Indexed: 12/22/2022]
Abstract
Effects of protein denaturation caused by high pressure freezing, involving Pressure-Factors (pressure, time) and Freezing-Factors (temperature, phase transition, recrystallization, ice crystal types), are complicated. In the current study, the conformation and functional changes of natural actomyosin (NAM) under pressure assisted freezing (PAF, 100,150,300,400,500MPaP-20°C/25min), pressure shift freezing (PSF, 200MPaP-20°C/25min), and immersion freezing (0.1MPaP-20°C/5min) after pressure was released to 0.1MPa, as compared to normal immersion freezing process (IF, 0.1MPaP-20°C/30min). Results indicated that PSF (200MPaP-20°C/30min) could reduce the denaturation of frozen NAM and a pressure of 300MPa was the critical point to induce such a denaturation. During the periods of B→D in PSF or B→C→D in PAF, the generation and growth of ice crystals played an important role on changing the secondary and tertiary structure of the treated NAM.
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Affiliation(s)
- Lina Cheng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Food Refrigeration and Computerized Food Technology (FRCFT), University College Dublin, National University of Ireland, Agriculture and Food Science Centre, Belfield, Dublin 4, Ireland. http://www.ucd.ie/refrig,http://www.ucd.ie/sun
| | - Zhiwei Zhu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Zhihang Zhang
- Food Refrigeration and Computerized Food Technology (FRCFT), University College Dublin, National University of Ireland, Agriculture and Food Science Centre, Belfield, Dublin 4, Ireland
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47
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Yeh YQ, Liao KF, Shih O, Shiu YJ, Wu WR, Su CJ, Lin PC, Jeng US. Probing the Acid-Induced Packing Structure Changes of the Molten Globule Domains of a Protein near Equilibrium Unfolding. J Phys Chem Lett 2017; 8:470-477. [PMID: 28067527 DOI: 10.1021/acs.jpclett.6b02722] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Using simultaneously scanning small-angle X-ray scattering (SAXS) and UV-vis absorption with integrated online size exclusion chromatography, supplemental with molecular dynamics simulations, we unveil the long-postulated global structure evolution of a model multidomain protein bovine serum albumin (BSA) during acid-induced unfolding. Our results differentiate three global packing structures of the three molten globule domains of BSA, forming three intermediates I1, I2, and E along the unfolding pathway. The I1-I2 transition, overlooked in all previous studies, involves mainly coordinated reorientations across interconnected molten globule subdomains, and the transition activates a critical pivot domain opening of the protein for entering into the E form, with an unexpectedly large unfolding free energy change of -9.5 kcal mol-1, extracted based on the observed packing structural changes. The revealed local packing flexibility and rigidity of the molten globule domains in the E form elucidate how collective motions of the molten globule domains profoundly influence the folding-unfolding pathway of a multidomain protein.
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Affiliation(s)
- Yi-Qi Yeh
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Kuei-Fen Liao
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Ying-Jen Shiu
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Wei-Ru Wu
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - Po-Chang Lin
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan
- Department of Chemical Engineering, National Tsing Hua University , Hsinchu 30013, Taiwan
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48
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Origin of hydrophobicity and enhanced water hydrogen bond strength near purely hydrophobic solutes. Proc Natl Acad Sci U S A 2016; 114:322-327. [PMID: 28028244 DOI: 10.1073/pnas.1612480114] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrophobicity plays an important role in numerous physicochemical processes from the process of dissolution in water to protein folding, but its origin at the fundamental level is still unclear. The classical view of hydrophobic hydration is that, in the presence of a hydrophobic solute, water forms transient microscopic "icebergs" arising from strengthened water hydrogen bonding, but there is no experimental evidence for enhanced hydrogen bonding and/or icebergs in such solutions. Here, we have used the redshifts and line shapes of the isotopically decoupled IR oxygen-deuterium (O-D) stretching mode of HDO water near small purely hydrophobic solutes (methane, ethane, krypton, and xenon) to study hydrophobicity at the most fundamental level. We present unequivocal and model-free experimental proof for the presence of strengthened water hydrogen bonds near four hydrophobic solutes, matching those in ice and clathrates. The water molecules involved in the enhanced hydrogen bonds display extensive structural ordering resembling that in clathrates. The number of ice-like hydrogen bonds is 10-15 per methane molecule. Ab initio molecular dynamics simulations have confirmed that water molecules in the vicinity of methane form stronger, more numerous, and more tetrahedrally oriented hydrogen bonds than those in bulk water and that their mobility is restricted. We show the absence of intercalating water molecules that cause the electrostatic screening (shielding) of hydrogen bonds in bulk water as the critical element for the enhanced hydrogen bonding around a hydrophobic solute. Our results confirm the classical view of hydrophobic hydration.
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49
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Abstract
How hydrophobicity (HY) drives protein folding is studied. The 1971 Nozaki-Tanford method of measuring HY is modified to use gases as solutes, not crystals, and this makes the method easy to use. Alkanes are found to be much more hydrophobic than rare gases, and the two different kinds of HY are termed intrinsic (rare gases) and extrinsic (alkanes). The HY values of rare gases are proportional to solvent-accessible surface area (ASA), whereas the HY values of alkanes depend on special hydration shells. Earlier work showed that hydration shells produce the hydration energetics of alkanes. Evidence is given here that the transfer energetics of alkanes to cyclohexane [Wolfenden R, Lewis CA, Jr, Yuan Y, Carter CW, Jr (2015) Proc Natl Acad Sci USA 112(24):7484-7488] measure the release of these shells. Alkane shells are stabilized importantly by van der Waals interactions between alkane carbon and water oxygen atoms. Thus, rare gases cannot form this type of shell. The very short (approximately picoseconds) lifetime of the van der Waals interaction probably explains why NMR efforts to detect alkane hydration shells have failed. The close similarity between the sizes of the opposing energetics for forming or releasing alkane shells confirms the presence of these shells on alkanes and supports Kauzmann's 1959 mechanism of protein folding. A space-filling model is given for the hydration shells on linear alkanes. The model reproduces the n values of Jorgensen et al. [Jorgensen WL, Gao J, Ravimohan C (1985) J Phys Chem 89:3470-3473] for the number of waters in alkane hydration shells.
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50
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Hydration of proteins and nucleic acids: Advances in experiment and theory. A review. Biochim Biophys Acta Gen Subj 2016; 1860:1821-35. [PMID: 27241846 DOI: 10.1016/j.bbagen.2016.05.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/21/2022]
Abstract
BACKGROUND Most biological processes involve water, and the interactions of biomolecules with water affect their structure, function and dynamics. SCOPE OF REVIEW This review summarizes the current knowledge of protein and nucleic acid interactions with water, with a special focus on the biomolecular hydration layer. Recent developments in both experimental and computational methods that can be applied to the study of hydration structure and dynamics are reviewed, including software tools for the prediction and characterization of hydration layer properties. MAJOR CONCLUSIONS In the last decade, important advances have been made in our understanding of the factors that determine how biomolecules and their aqueous environment influence each other. Both experimental and computational methods contributed to the gradually emerging consensus picture of biomolecular hydration. GENERAL SIGNIFICANCE An improved knowledge of the structural and thermodynamic properties of the hydration layer will enable a detailed understanding of the various biological processes in which it is involved, with implications for a wide range of applications, including protein-structure prediction and structure-based drug design.
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