1
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Jaufer AM, Bouhadana A, Fanucci GE. Hydrophobic Clusters Regulate Surface Hydration Dynamics of Bacillus subtilis Lipase A. J Phys Chem B 2024; 128:3919-3928. [PMID: 38628066 DOI: 10.1021/acs.jpcb.4c00405] [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: 04/26/2024]
Abstract
The surface hydration diffusivity of Bacillus subtilis Lipase A (BSLA) has been characterized by low-field Overhauser dynamic nuclear polarization (ODNP) relaxometry using a series of spin-labeled constructs. Sites for spin-label incorporation were previously designed via an atomistic computational approach that screened for surface exposure, reflective of the surface hydration comparable to other proteins studied by this method, as well as minimal impact on protein function, dynamics, and structure of BSLA by excluding any surface site that participated in greater than 30% occupancy of a hydrogen bonding network within BSLA. Experimental ODNP relaxometry coupling factor results verify the overall surface hydration behavior for these BSLA spin-labeled sites similar to other globular proteins. Here, by plotting the ODNP parameters of relative diffusive water versus the relative bound water, we introduce an effective "phase-space" analysis, which provides a facile visual comparison of the ODNP parameters of various biomolecular systems studied to date. We find notable differences when comparing BSLA to other systems, as well as when comparing different clusters on the surface of BSLA. Specifically, we find a grouping of sites that correspond to the spin-label surface location within the two main hydrophobic core clusters of the branched aliphatic amino acids isoleucine, leucine, and valine cores observed in the BSLA crystal structure. The results imply that hydrophobic clustering may dictate local surface hydration properties, perhaps through modulation of protein conformations and samplings of the unfolded states, providing insights into how the dynamics of the hydration shell is coupled to protein motion and fluctuations.
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Affiliation(s)
- Afnan M Jaufer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
- George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, Florida 32611, United States
| | - Adam Bouhadana
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
- George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, Florida 32611, United States
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2
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Frezza E, Laage D, Duboué-Dijon E. Molecular Origin of Distinct Hydration Dynamics in Double Helical DNA and RNA Sequences. J Phys Chem Lett 2024; 15:4351-4358. [PMID: 38619551 DOI: 10.1021/acs.jpclett.4c00629] [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: 04/16/2024]
Abstract
Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: first, the localization of the slowest hydration water molecules─in the minor groove in DNA, next to phosphates in RNA─and second, the markedly distinct hydration dynamics of the two phosphate oxygen atoms OR and OS in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges, and the presence of ions. We show that the slow hydration dynamics at RNA OR sites is not due to bridging water molecules but is caused by both the larger excluded volume and the stronger initial H-bond next to OR, due to the different phosphate orientations in A-form double helical RNA.
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Affiliation(s)
- Elisa Frezza
- Université Paris Cité, CNRS, CiTCoM, Paris 75006, France
| | - Damien Laage
- PASTEUR, Department of Chemistry, École Normale Supérieure-PSL, Sorbonne Université, CNRS, Paris 75005, France
| | - Elise Duboué-Dijon
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, Paris 75005, France
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3
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Mukherjee S, Ramos S, Pezzotti S, Kalarikkal A, Prass TM, Galazzo L, Gendreizig D, Barbosa N, Bordignon E, Havenith M, Schäfer LV. Entropy Tug-of-War Determines Solvent Effects in the Liquid-Liquid Phase Separation of a Globular Protein. J Phys Chem Lett 2024; 15:4047-4055. [PMID: 38580324 PMCID: PMC11033941 DOI: 10.1021/acs.jpclett.3c03421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/15/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024]
Abstract
Liquid-liquid phase separation (LLPS) plays a key role in the compartmentalization of cells via the formation of biomolecular condensates. Here, we combined atomistic molecular dynamics (MD) simulations and terahertz (THz) spectroscopy to determine the solvent entropy contribution to the formation of condensates of the human eye lens protein γD-Crystallin. The MD simulations reveal an entropy tug-of-war between water molecules that are released from the protein droplets and those that are retained within the condensates, two categories of water molecules that were also assigned spectroscopically. A recently developed THz-calorimetry method enables quantitative comparison of the experimental and computational entropy changes of the released water molecules. The strong correlation mutually validates the two approaches and opens the way to a detailed atomic-level understanding of the different driving forces underlying the LLPS.
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Affiliation(s)
- Saumyak Mukherjee
- Center
for Theoretical Chemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Sashary Ramos
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Simone Pezzotti
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Abhishek Kalarikkal
- Faculty
of Chemistry and Biochemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Tobias M. Prass
- Center
for Theoretical Chemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Laura Galazzo
- Faculty
of Chemistry and Biochemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Dominik Gendreizig
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
| | - Natercia Barbosa
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
| | - Enrica Bordignon
- Faculty
of Chemistry and Biochemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
| | - Martina Havenith
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Lars V. Schäfer
- Center
for Theoretical Chemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
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4
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Dunleavy KM, Li T, Milshteyn E, Jaufer AM, Walker SA, Fanucci GE. Charge Distribution Patterns of IA 3 Impact Conformational Expansion and Hydration Diffusivity of the Disordered Ensemble. J Phys Chem B 2023; 127:9734-9746. [PMID: 37936402 DOI: 10.1021/acs.jpcb.3c06170] [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: 11/09/2023]
Abstract
IA3 is a 68 amino acid natural peptide/protein inhibitor of yeast aspartic proteinase A (YPRA) that is intrinsically disordered in solution with induced N-terminal helicity when in the protein complex with YPRA. Based on the intrinsically disordered protein (IDP) parameters of fractional net charge (FNC), net charge density per residue (NCPR), and charge patterning (κ), the two domains of IA3 are defined to occupy different domains within conformationally based subclasses of IDPs, thus making IA3 a bimodal domain IDP. Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and low-field Overhauser dynamic nuclear polarization (ODNP) spectroscopy results show that these two domains possess different degrees of compaction and hydration diffusivity behavior. This work suggests that SDSL EPR line shapes, analyzed in terms of their local tumbling volume (VL), provide insights into the compaction of the unstructured IDP ensemble in solution and that protein sequence and net charge distribution patterns within a conformational subclass can impact bound water hydration dynamics, thus possibly offering an alternative thermodynamic property that can encode conformational binding and behavior of IDPs and liquid-liquid phase separations.
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Affiliation(s)
- Katie M Dunleavy
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Tianyan Li
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Eugene Milshteyn
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Afnan M Jaufer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Shamon A Walker
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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5
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Ramos S, Kamps J, Pezzotti S, Winklhofer KF, Tatzelt J, Havenith M. Hydration makes a difference! How to tune protein complexes between liquid-liquid and liquid-solid phase separation. Phys Chem Chem Phys 2023; 25:28063-28069. [PMID: 37840355 DOI: 10.1039/d3cp03299j] [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: 10/17/2023]
Abstract
Understanding how protein rich condensates formed upon liquid-liquid phase separation (LLPS) evolve into solid aggregates is of fundamental importance for several medical applications, since these are suspected to be hot-spots for many neurotoxic diseases. This requires developing experimental approaches to observe in real-time both LLPS and liquid-solid phase separation (LSPS), and to unravel the delicate balance of protein and water interactions dictating the free energy differences between the two. We present a vibrational THz spectroscopy approach that allows doing so from the point of view of hydration water. We focus on a cellular prion protein of high medical relevance, which we can drive to undergo either LLPS or LSPS with few mutations. We find that it is a subtle balance of hydrophobic and hydrophilic solvation contributions that allows tuning between LLPS and LSPS. Hydrophobic hydration provides an entropic driving force to phase separation, through the release of hydration water into the bulk. Water hydrating hydrophilic groups provides an enthalpic driving force to keep the condensates in a liquid state. As a result, when we modify the protein by a few mutations to be less hydrophilic, we shift from LLPS to LSPS. This molecular understanding paves the way for a rational design of proteins.
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Affiliation(s)
- Sashary Ramos
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany.
| | - Janine Kamps
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Simone Pezzotti
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany.
| | - Konstanze F Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr Unviersity Bochum, Bochum, Germany
| | - Jörg Tatzelt
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany.
- Department of Physics, TU Dortmund, Dortmund, Germany
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6
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Mukherjee S, Schäfer LV. Thermodynamic forces from protein and water govern condensate formation of an intrinsically disordered protein domain. Nat Commun 2023; 14:5892. [PMID: 37735186 PMCID: PMC10514047 DOI: 10.1038/s41467-023-41586-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) can drive a multitude of cellular processes by compartmentalizing biological cells via the formation of dense liquid biomolecular condensates, which can function as membraneless organelles. Despite its importance, the molecular-level understanding of the underlying thermodynamics of this process remains incomplete. In this study, we use atomistic molecular dynamics simulations of the low complexity domain (LCD) of human fused in sarcoma (FUS) protein to investigate the contributions of water and protein molecules to the free energy changes that govern LLPS. Both protein and water components are found to have comparably sizeable thermodynamic contributions to the formation of FUS condensates. Moreover, we quantify the counteracting effects of water molecules that are released into the bulk upon condensate formation and the waters retained within the protein droplets. Among the various factors considered, solvation entropy and protein interaction enthalpy are identified as the most important contributions, while solvation enthalpy and protein entropy changes are smaller. These results provide detailed molecular insights on the intricate thermodynamic interplay between protein- and solvation-related forces underlying the formation of biomolecular condensates.
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Affiliation(s)
- Saumyak Mukherjee
- Center for Theoretical Chemistry, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Ruhr University Bochum, D-44780, Bochum, Germany.
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7
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Liu A, Zhang L, Zhou A, Yang F, Yue Z, Wang J. Metabolomic and physiological changes of acid-tolerant Graesiella sp. MA1 during long-term acid stress. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:97209-97218. [PMID: 37589846 DOI: 10.1007/s11356-023-29295-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023]
Abstract
Algae plays a significant role for the primary production in the oligotrophic ecosystems such as the acid mine pit lakes. Graesiella sp. MA1 was a new acid-tolerant photosynthetic protist isolated from an acid mine pit lake. To understand the acid responses of Graesiella sp. MA1, its physiological changes and metabolomics were studied during long-term acid stress. Photosynthetic pigments, soluble proteins, and antioxidant systems of Graesiella sp. MA1 cells displayed two phases, the adaptation phase and the growth phase. During the adaptation phase, both photosynthetic pigments and soluble proteins were inhibited, while antioxidant activity of SOD, APX, and GSH were promoted to response to the organism's damage. Metabolomics results revealed lipids and organic acids were abundant components in Graesiella sp. MA1 cells. In response to acid stress, the levels of acid-dependent resistant amino acids, including glutamate, aspartate, arginine, proline, lysine, and histidine, accumulated continuously to maintain orderly intracellular metabolic processes. In addition, fatty acids were mainly unsaturated, which could improve the fluidity of the cell membranes under acid stress. Metabolomic and physiological changes showed that Graesiella sp. MA1 had tolerance during long-term acid stress and the potential to be used as a bioremediation strain for the acidic wastewater.
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Affiliation(s)
- Azuan Liu
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, 230009, Anhui, China
| | - Lu Zhang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, 230009, Anhui, China
| | - Ao Zhou
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, 230009, Anhui, China
| | - Fan Yang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, 230009, Anhui, China
| | - Zhengbo Yue
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, 230009, Anhui, China
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, 230009, Anhui, China
| | - Jin Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China.
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, 230009, Anhui, China.
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, 230009, Anhui, China.
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8
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Perillo MA, Burgos I, Clop EM, Sanchez JM, Nolan V. The role of water in reactions catalysed by hydrolases under conditions of molecular crowding. Biophys Rev 2023; 15:639-660. [PMID: 37681097 PMCID: PMC10480385 DOI: 10.1007/s12551-023-01104-2] [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: 04/11/2023] [Accepted: 07/23/2023] [Indexed: 09/09/2023] Open
Abstract
Under macromolecular crowding (MC) conditions such as cellular, extracellular, food and other environments of biotechnological interest, the thermodynamic activity of the different macromolecules present in the system is several orders of magnitude higher than in dilute solutions. In this state, the diffusion rates are affected by the volume exclusion induced by the crowders. Immiscible liquid phases, which may arise in MC by liquid-liquid phase separation, may induce a dynamic confinement of reactants, products and/or enzymes, tuning reaction rates. In cellular environments and other crowding conditions, membranes and macromolecules provide, on the whole, large surfaces that can perturb the solvent, causing its immobilisation by adsorption in the short range and also affecting the solvent viscosity in the long range. The latter phenomenon can affect the conformation of a protein and/or the degree of association of its protomers and, consequently, its activity. Changes in the water structure can also alter the enzyme-substrate interaction, and, in the case of hydrolytic enzymes, where water is one of the substrates, it also affects the reaction mechanism. Here, we review the evidence for how macromolecular crowding affects the catalysis induced by hydrolytic enzymes, focusing on the structure and dynamics of water.
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Affiliation(s)
- Maria A. Perillo
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Inés Burgos
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química Industrial y Aplicada, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
| | - Eduardo M. Clop
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Julieta M. Sanchez
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
- Institut de Biotecnologia I de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica I de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- CIBER de Bioingeniería Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, 08193 Barcelona, Spain
| | - Verónica Nolan
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
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9
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DeStefano A, Nguyen M, Fredrickson GH, Han S, Segalman RA. Design of Soft Material Surfaces with Rationally Tuned Water Diffusivity. ACS CENTRAL SCIENCE 2023; 9:1019-1024. [PMID: 37252353 PMCID: PMC10214527 DOI: 10.1021/acscentsci.3c00208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Indexed: 05/31/2023]
Abstract
Water structure and dynamics can be key modulators of adsorption, separations, and reactions at soft material interfaces, but systematically tuning water environments in an aqueous, accessible, and functionalizable material platform has been elusive. This work leverages variations in excluded volume to control and measure water diffusivity as a function of position within polymeric micelles using Overhauser dynamic nuclear polarization spectroscopy. Specifically, a versatile materials platform consisting of sequence-defined polypeptoids simultaneously offers a route to controlling the functional group position and a unique opportunity to generate a water diffusivity gradient extending away from the polymer micelle core. These results demonstrate an avenue not only to rationally design the chemical and structural properties of polymer surfaces but also to design and tune the local water dynamics that, in turn, can adjust the local activity for solutes.
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Affiliation(s)
- Audra
J. DeStefano
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - My Nguyen
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Glenn H. Fredrickson
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Materials
Research Laboratory, University of California, Santa Barbara, California 93106, United States
- Department
of Materials, University of California, Santa Barbara, California 93106, United States
| | - Songi Han
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Rachel A. Segalman
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Materials
Research Laboratory, University of California, Santa Barbara, California 93106, United States
- Department
of Materials, University of California, Santa Barbara, California 93106, United States
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
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10
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Negroni M, Kurzbach D. Missing Pieces in Structure Puzzles: How Hyperpolarized NMR Spectroscopy Can Complement Structural Biology and Biochemistry. Chembiochem 2023; 24:e202200703. [PMID: 36624049 DOI: 10.1002/cbic.202200703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
Structure determination lies at the heart of many biochemical research programs. However, the "giants": X-ray diffraction, electron microscopy, molecular dynamics simulations, and nuclear magnetic resonance, among others, leave quite a few dark spots on the structural pictures drawn of proteins, nucleic acids, membranes, and other biomacromolecules. For example, structural models under physiological conditions or of short-lived intermediates often remain out of reach of the established experimental methods. This account frames the possibility of including hyperpolarized, that is, dramatically signal-enhanced NMR in existing workflows to fill these spots with detailed depictions. We highlight how integrating methods based on dissolution dynamic nuclear polarization can provide valuable complementary information about formerly inaccessible conformational spaces for many systems. A particular focus will be on hyperpolarized buffers to facilitate the NMR structure determination of challenging systems.
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Affiliation(s)
- Mattia Negroni
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
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11
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Pezzotti S, König B, Ramos S, Schwaab G, Havenith M. Liquid-Liquid Phase Separation? Ask the Water! J Phys Chem Lett 2023; 14:1556-1563. [PMID: 36745512 DOI: 10.1021/acs.jpclett.2c02697] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Water is more than an inert spectator during liquid-liquid phase separation (LLPS), the reversible compartmentalization of protein solutions into a protein-rich and a dilute phase. We show that LLPS is driven by changes in hydration entropy and enthalpy. Tuning LLPS by adjusting experimental parameters, e.g., addition of co-solutes, is a major goal for biological and medical applications. This requires a general model to quantify thermodynamic driving forces. Here, we develop such a model based on the measured amplitudes of characteristic THz-features of two hydration populations: "Cavity-wrap" water hydrating hydrophobic patches is released during LLPS leading to an increase in entropy. "Bound" water hydrating hydrophilic patches is retained since it is enthalpically favorable. We introduce a THz-phase diagram mapping these spectroscopic/thermodynamic changes. This provides not only a precise understanding of hydrophobic and hydrophilic hydration driving forces as a function of temperature and concentration but also a rational means to tune LLPS.
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Affiliation(s)
- Simone Pezzotti
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
| | - Benedikt König
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
| | - Sashary Ramos
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
| | - Gerhard Schwaab
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
- Department of Physics, Technische Universität Dortmund, 44227Dortmund, Germany
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12
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Kalayan J, Chakravorty A, Warwicker J, Henchman RH. Total free energy analysis of fully hydrated proteins. Proteins 2023; 91:74-90. [PMID: 35964252 PMCID: PMC10087023 DOI: 10.1002/prot.26411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
The total free energy of a hydrated biomolecule and its corresponding decomposition of energy and entropy provides detailed information about regions of thermodynamic stability or instability. The free energies of four hydrated globular proteins with different net charges are calculated from a molecular dynamics simulation, with the energy coming from the system Hamiltonian and entropy using multiscale cell correlation. Water is found to be most stable around anionic residues, intermediate around cationic and polar residues, and least stable near hydrophobic residues, especially when more buried, with stability displaying moderate entropy-enthalpy compensation. Conversely, anionic residues in the proteins are energetically destabilized relative to singly solvated amino acids, while trends for other residues are less clear-cut. Almost all residues lose intraresidue entropy when in the protein, enthalpy changes are negative on average but may be positive or negative, and the resulting overall stability is moderate for some proteins and negligible for others. The free energy of water around single amino acids is found to closely match existing hydrophobicity scales. Regarding the effect of secondary structure, water is slightly more stable around loops, of intermediate stability around β strands and turns, and least stable around helices. An interesting asymmetry observed is that cationic residues stabilize a residue when bonded to its N-terminal side but destabilize it when on the C-terminal side, with a weaker reversed trend for anionic residues.
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Affiliation(s)
- Jas Kalayan
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Arghya Chakravorty
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jim Warwicker
- Manchester Institute of Biotechnology and School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Richard H Henchman
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
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13
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You X, Baiz CR. Importance of Hydrogen Bonding in Crowded Environments: A Physical Chemistry Perspective. J Phys Chem A 2022; 126:5881-5889. [PMID: 35968816 DOI: 10.1021/acs.jpca.2c03803] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells are heterogeneous on every length and time scale; cytosol contains thousands of proteins, lipids, nucleic acids, and small molecules, and molecular interactions within this crowded environment determine the structure, dynamics, and stability of biomolecules. For decades, the effects of crowding at the atomistic scale have been overlooked in favor of more tractable models largely based on thermodynamics. Crowding can affect the conformations and stability of biomolecules by modulating water structure and dynamics within the cell, and these effects are nonlocal and environment dependent. Thus, characterizing water's hydrogen-bond (H-bond) networks is a critical step toward a complete microscopic crowding model. This perspective provides an overview of molecular crowding and describes recent time-resolved spectroscopy approaches investigating H-bond networks and dynamics in crowded or otherwise complex aqueous environments. Ultrafast spectroscopy combined with atomistic simulations has emerged as a powerful combination for studying H-bond structure and dynamics in heterogeneous multicomponent systems. We discuss the ongoing challenges toward developing a complete atomistic description of macromolecular crowding from an experimental as well as a theoretical perspective.
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Affiliation(s)
- Xiao You
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 19104, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 19104, United States
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14
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Hu K, Matsuura H, Shirakashi R. Stochastic Analysis of Molecular Dynamics Reveals the Rotation Dynamics Distribution of Water around Lysozyme. J Phys Chem B 2022; 126:4520-4530. [PMID: 35675630 DOI: 10.1021/acs.jpcb.2c00970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water dynamics is essential to biochemical processes by mediating all such reactions, including biomolecular degeneration in solutions. To disentangle the molecular-scale distribution of water dynamics around a solute biomolecule, we investigated here the rotational dynamics of water around lysozyme by combining molecular dynamics (MD) simulations and broadband dielectric spectroscopy (BDS). A statistical analysis using the relaxation times and trajectories of every single water molecule was proposed, and the two-dimensional probability distribution of water at a distance from the lysozyme surface with a rotational relaxation time was given. For the observed lysozyme solutions of 34-284 mg/mL, we discovered that the dielectric relaxation time obtained from this distribution agrees well with the measured γ relaxation time, which suggests that rotational self-correlation of water molecules underlies the gigahertz domain of the dielectric spectra. Regardless of protein concentration, water rotational relaxation time versus the distance from the lysozyme surface revealed that the water rotation is severely retarded within 3 Å from the lysozyme surface and is nearly comparable to pure water when farther than 10 Å. The dimension of the first hydration layer was subsequently identified in terms of the relationship between the acceleration of water rotation and the distance from the protein surface.
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Affiliation(s)
- Kang Hu
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo 153-8505, Japan.,Department of Mechanical Engineering, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Matsuura
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo 153-8505, Japan.,Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Ryo Shirakashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo 153-8505, Japan
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15
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Lee G, Kageyama Y, Takeda S. Site-Selective Spin-Probe with a Photocleavable Macrocyclic Linker for Measuring the Dynamics of Water Surrounding a Liposomal Assembly. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Gyeorye Lee
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Yoshiyuki Kageyama
- Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Sadamu Takeda
- Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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16
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Hilty C, Kurzbach D, Frydman L. Hyperpolarized water as universal sensitivity booster in biomolecular NMR. Nat Protoc 2022; 17:1621-1657. [PMID: 35546640 DOI: 10.1038/s41596-022-00693-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
Abstract
NMR spectroscopy is the only method to access the structural dynamics of biomolecules at high (atomistic) resolution in their native solution state. However, this method's low sensitivity has two important consequences: (i) typically experiments have to be performed at high concentrations that increase sensitivity but are not physiological, and (ii) signals have to be accumulated over long periods, complicating the determination of interaction kinetics on the order of seconds and impeding studies of unstable systems. Both limitations are of equal, fundamental relevance: non-native conditions are of limited pharmacological relevance, and the function of proteins, enzymes and nucleic acids often relies on their interaction kinetics. To overcome these limitations, we have developed applications that involve 'hyperpolarized water' to boost signal intensities in NMR of proteins and nucleic acids. The technique includes four stages: (i) preparation of the biomolecule in partially deuterated buffers, (ii) preparation of 'hyperpolarized' water featuring enhanced 1H NMR signals via cryogenic dynamic nuclear polarization, (iii) sudden melting of the cryogenic pellet and dissolution of the protein or nucleic acid in the hyperpolarized water (enabling spontaneous exchanges of protons between water and target) and (iv) recording signal-amplified NMR spectra targeting either labile 1H or neighboring 15N/13C nuclei in the biomolecule. Water in the ensuing experiments is used as a universal 'hyperpolarization' agent, rendering the approach versatile and applicable to any biomolecule possessing labile hydrogens. Thus, questions can be addressed, ranging from protein and RNA folding problems to resolving structure-function relationships of intrinsically disordered proteins to investigating membrane interactions.
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Affiliation(s)
- Christian Hilty
- Chemistry Department, Texas A&M University, College Station, TX, USA.
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute for Biological Chemistry, University of Vienna, Vienna, Austria.
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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17
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Abstract
![]()
Water is essential
for the structure, dynamics, energetics, and
thus the function of biomolecules. It is a formidable challenge to
elicit, in microscopic detail, the role of the solvation-related driving
forces of biomolecular processes, such as the enthalpy and entropy
contributions to the underlying free-energy landscape. In this Perspective,
we discuss recent developments and applications of computational methods
that provide a spatially resolved map of hydration thermodynamics
in biomolecular systems and thus yield atomic-level insights to guide
the interpretation of experimental observations. An emphasis is on
the challenge of quantifying the hydration entropy, which requires
characterization of both the motions of the biomolecules and of the
water molecules in their surrounding.
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Affiliation(s)
- Saumyak Mukherjee
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
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18
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Moon H, Collanton RP, Monroe JI, Casey TM, Shell MS, Han S, Scott SL. Evidence for Entropically Controlled Interfacial Hydration in Mesoporous Organosilicas. J Am Chem Soc 2022; 144:1766-1777. [PMID: 35041412 DOI: 10.1021/jacs.1c11342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
At aqueous interfaces, the distribution and dynamics of adsorbates are modulated by the behavior of interfacial water. Hydration of a hydrophobic surface can store entropy via the ordering of interfacial water, which contributes to the Gibbs energy of solute binding. However, there is little experimental evidence for the existence of such entropic reservoirs, and virtually no precedent for their rational design in systems involving extended interfaces. In this study, two series of mesoporous silicas were modified in distinct ways: (1) progressively deeper thermal dehydroxylation, via condensation of surface silanols, and (2) increasing incorporation of nonpolar organic linkers into the silica framework. Both approaches result in decreasing average surface polarity, manifested in a blue-shift in the fluorescence of an adsorbed dye. For the inorganic silicas, hydrogen-bonding of water becomes less extensive as the number of surface silanols decreases. Overhauser dynamic nuclear polarization (ODNP) relaxometry indicates enhanced surface water diffusivity, reflecting a loss of enthalpic hydration. In contrast, organosilicas show a monotonic decrease in surface water diffusivity with decreasing polarity, reflecting enhanced hydrophobic hydration. Molecular dynamics simulations predict increased tetrahedrality of interfacial water for the organosilicas, implying increased ordering near the nm-size organic domains (relative to inorganic silicas, which necessarily lack such domains). These findings validate the prediction that hydrophobic hydration at interfaces is controlled by the microscopic length scale of the hydrophobic regions. They further suggest that the hydration thermodynamics of structurally heterogeneous silica surfaces can be tuned to promote adsorption, which in turn tunes the selectivity in catalytic reactions.
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Affiliation(s)
- Hyunjin Moon
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Ryan P Collanton
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Jacob I Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Thomas M Casey
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States.,Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Susannah L Scott
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States.,Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
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19
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Chen Q, Yang X, Meng Q, Zhao L, Yuan Y, Chi W, He L, Shi K, Liu S. Integrative multiomics analysis of the acid stress response of Oenococcus oeni mutants at different growth stages. Food Microbiol 2021; 102:103905. [PMID: 34809937 DOI: 10.1016/j.fm.2021.103905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Acid stress is one of the most important environmental stresses that adversely affect the growth of lactic acid bacteria (LAB), such as Oenococcus oeni which was isolated from grape-berries and mainly used in wine fermentation. The aim of this paper is to comprehensively characterize the mechanisms of acid stress regulation in O. oeni and to provide a viable theoretical basis for breed and improvement of existing LAB. METHOD First, six O. oeni mutants with acid-sensitive (strains b2, a1, c2) and acid-tolerant (strains b1, a3, c1) phenotypes were screened from three wild-type O. oeni, and then their genome (sequencing), transcriptome and metabolome (LC-MS/MS) were examined. RESULTS A total of 459 genes were identified with one or more intragenic single nucleotide polymorphisms (SNPs) in these mutants, and were extensively involved in metabolism and cellular functions with a high mutation rates in purine (46%) and pyrimidine (48%) metabolic pathways. There were 210 mutated genes that cause significant changes in expression levels. In addition, 446 differentially accumulated metabolites were detected, and they were consistently detected at relatively high levels in the acid-tolerant O. oeni mutant. The levels of intracellular differentially expressed genes and differential metabolites changed with increasing culture time. CONCLUSION The integrative pathways analysis showed that the intracellular response associated with acid regulation differed significantly between acid-sensitive and acid-tolerant O. oeni mutants, and also changed at different growth stages.
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Affiliation(s)
- Qiling Chen
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Xiangke Yang
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Henan University of Animal Husbandry and Economy, Zhenzhou, Henan, China
| | - Qiang Meng
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Lili Zhao
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuxin Yuan
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Wei Chi
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ling He
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Kan Shi
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of, Northwest A&F University, Yongning, Ningxia, 750104, China.
| | - Shuwen Liu
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of, Northwest A&F University, Yongning, Ningxia, 750104, China.
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20
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Päslack C, Das CK, Schlitter J, Schäfer LV. Spectrally Resolved Estimation of Water Entropy in the Active Site of Human Carbonic Anhydrase II. J Chem Theory Comput 2021; 17:5409-5418. [PMID: 34259506 DOI: 10.1021/acs.jctc.1c00554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A major challenge in understanding ligand binding to biomacromolecules lies in dissecting the underlying thermodynamic driving forces at the atomic level. Quantifying the contributions of water molecules is often especially demanding, although they can play important roles in biomolecular recognition and binding processes. One example is human carbonic anhydrase II, whose active site harbors a conserved network of structural water molecules that are essential for enzymatic catalysis. Inhibitor binding disrupts this water network and changes the hydrogen-bonding patterns in the active site. Here, we use atomistic molecular dynamics simulations to compute the absolute entropy of the individual water molecules confined in the active site of hCAII using a spectrally resolved estimation (SRE) approach. The entropy decrease of water molecules that remain in the active site upon binding of a dorzolamide inhibitor is caused by changes in hydrogen bonding and stiffening of the hydrogen-bonding network. Overall, this entropy decrease is overcompensated by the gain due to the release of three water molecules from the active site upon inhibitor binding. The spectral density calculations enable the assignment of the changes to certain vibrational modes. In addition, the range of applicability of the SRE approximation is systematically explored by exploiting the gradually changing degree of immobilization of water molecules as a function of the distance to a phospholipid bilayer surface, which defines an "entropy ruler". These results demonstrate the applicability of SRE to biomolecular solvation, and we expect it to become a useful method for entropy calculations in biomolecular systems.
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Affiliation(s)
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | | | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
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21
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Ahlers J, Adams EM, Bader V, Pezzotti S, Winklhofer KF, Tatzelt J, Havenith M. The key role of solvent in condensation: Mapping water in liquid-liquid phase-separated FUS. Biophys J 2021; 120:1266-1275. [PMID: 33515602 PMCID: PMC8059208 DOI: 10.1016/j.bpj.2021.01.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/21/2020] [Accepted: 01/19/2021] [Indexed: 01/09/2023] Open
Abstract
Formation of biomolecular condensates through liquid-liquid phase separation (LLPS) has emerged as a pervasive principle in cell biology, allowing compartmentalization and spatiotemporal regulation of dynamic cellular processes. Proteins that form condensates under physiological conditions often contain intrinsically disordered regions with low-complexity domains. Among them, the RNA-binding proteins FUS and TDP-43 have been a focus of intense investigation because aberrant condensation and aggregation of these proteins is linked to neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia. LLPS occurs when protein-rich condensates form surrounded by a dilute aqueous solution. LLPS is per se entropically unfavorable. Energetically favorable multivalent protein-protein interactions are one important aspect to offset entropic costs. Another proposed aspect is the release of entropically unfavorable preordered hydration water into the bulk. We used attenuated total reflection spectroscopy in the terahertz frequency range to characterize the changes in the hydrogen bonding network accompanying the FUS enrichment in liquid-liquid phase-separated droplets to provide experimental evidence for the key role of the solvent as a thermodynamic driving force. The FUS concentration inside LLPS droplets was determined to be increased to 2.0 mM independent of the initial protein concentration (5 or 10 μM solutions) by fluorescence measurements. With terahertz spectroscopy, we revealed a dewetting of hydrophobic side chains in phase-separated FUS. Thus, the release of entropically unfavorable water populations into the bulk goes hand in hand with enthalpically favorable protein-protein interaction. Both changes are energetically favorable, and our study shows that both contribute to the thermodynamic driving force in phase separation.
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Affiliation(s)
- Jonas Ahlers
- Department Physical Chemistry, Ruhr-University Bochum, Bochum, Germany
| | - Ellen M Adams
- Department Physical Chemistry, Ruhr-University Bochum, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Simone Pezzotti
- Department Physical Chemistry, Ruhr-University Bochum, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Martina Havenith
- Department Physical Chemistry, Ruhr-University Bochum, Bochum, Germany.
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22
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Juber S, Wingbermühle S, Nuernberger P, Clever GH, Schäfer LV. Thermodynamic driving forces of guest confinement in a photoswitchable cage. Phys Chem Chem Phys 2021; 23:7321-7332. [PMID: 33876092 DOI: 10.1039/d0cp06495e] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Photoswitchable cages that confine small guest molecules inside their cavities offer a way to control the binding/unbinding process through irradiation with light of different wavelengths. However, detailed characterization of the structural and thermodynamic consequences of photoswitching is very challenging to achieve by experiments alone. Thus, all-atom molecular dynamics (MD) simulations were carried out to gain insight into the relationship between the structure and binding affinity. Binding free energies of the B12F122- guest were obtained for all photochemically accessible forms of a photoswitchable dithienylethene (DTE) based coordination cage. The MD simulations show that successive photo-induced closure of the four individual DTE ligands that form the cage gradually decreases the binding affinity. Closure of the first ligand significantly lowers the unbinding barrier and the binding free energy, and therefore favours guest unbinding both kinetically and thermodynamically. The analysis of different enthalpy contributions to the free energy shows that binding is enthalpically unfavourable and thus is an entropy-driven process, in agreement with the experimental data. Separating the enthalpy into the contributions from electrostatic, van der Waals, and bonded interactions in the force field shows that the unfavourable binding enthalpy is due to the bonded interactions being more favourable in the dissociated state, suggesting the presence of structural strain in the bound complex. Thus, the simulations provide microscopic explanations for the experimental findings and provide a possible route towards the targeted design of switchable nanocontainers with modified binding properties.
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Affiliation(s)
- Selina Juber
- Theoretical Chemistry, Ruhr-University Bochum, D-44780 Bochum, Germany.
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23
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Päslack C, Schäfer LV, Heyden M. Protein flexibility reduces solvent-mediated friction barriers of ligand binding to a hydrophobic surface patch. Phys Chem Chem Phys 2021; 23:5665-5672. [PMID: 33656505 DOI: 10.1039/d1cp00181g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Solvent fluctuations have been explored in detail for idealized and rigid hydrophobic model systems, but so far it has remained unclear how internal protein motions and their coupling to the surrounding solvent affect the dynamics of ligand binding to biomolecular surfaces. Here, molecular dynamics simulations were used to elucidate the solvent-mediated binding of a model ligand to the hydrophobic surface patch of ubiquitin. The ligand's friction profiles reveal pronounced long-time correlations and enhanced friction in the vicinity of the protein, similar to idealized hydrophobic surfaces. Interestingly, these effects are shaped by internal protein motions. Protein flexibility modulates water density fluctuations near the hydrophobic surface patch and smooths out the friction profile of ligand binding.
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Affiliation(s)
- Christopher Päslack
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780 Bochum, Germany.
| | - Lars V Schäfer
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780 Bochum, Germany.
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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24
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Bolmatov D, Soloviov D, Zhernenkov M, Zav'yalov D, Mamontov E, Suvorov A, Cai YQ, Katsaras J. Molecular Picture of the Transient Nature of Lipid Rafts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4887-4896. [PMID: 32259453 DOI: 10.1021/acs.langmuir.0c00125] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In biological membranes, lipid rafts are now thought to be transient and nanoscopic. However, the mechanism responsible for these nanoscopic assemblies remains poorly understood, even in the case of model membranes. As a result, it has proven extremely challenging to probe the physicochemical properties of lipid rafts at the molecular level. Here, we use all-atom molecular dynamics (MD) simulations and inelastic X-ray scattering (IXS), an intrinsically nanoscale technique, to directly probe the energy transfer and collective short-wavelength dynamics (phonons) of biologically relevant model membranes. We show that the nanoscale propagation of stress in lipid rafts takes place in the form of collective motions made up of longitudinal (compression waves) and transverse (shear waves) molecular vibrations. Importantly, we provide a molecular picture for the so-called van der Waals mediated "force from lipid" [Anishkin, A. et al. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 7898], a key parameter for the ionic channel mechano-transduction and the mechanism for the lipid transfer of molecular level stress [Aponte-Santamarı́a, C. et al. J. Am. Chem. Soc. 2017, 139, 13588]. Specifically, we describe how lipid rafts are formed and maintained through the propagation of molecular stress, lipid raft rattling dynamics, and a relaxation process. Eventually, the rafts dissipate through the self-diffusion of lipids making up the rafts. We also show that the molecular stress and viscoelastic properties of transient lipid rafts can be modulated through the use of hydrophobic biomolecules such as melatonin and tryptophan. Ultimately, the herein proposed mechanism describing the molecular interactions for the formation and dissolution of lipid rafts may offer insights as to how lipid rafts enable biological function.
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Affiliation(s)
- Dima Bolmatov
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Dmytro Soloviov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russia
- Institute for Safety Problems of Nuclear Power Plants, NAS of Ukraine, Kyiv 03680, Ukraine
| | - Mikhail Zhernenkov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | | | - Eugene Mamontov
- Spectroscopy Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Alexey Suvorov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yong Q Cai
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - John Katsaras
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
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25
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Krah A, Huber RG, Bond PJ. How Ligand Binding Affects the Dynamical Transition Temperature in Proteins. Chemphyschem 2020; 21:916-926. [DOI: 10.1002/cphc.201901221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/03/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander Krah
- School of Computational SciencesKorea Institute for Advanced Study 85 Hoegiro, Dongdaemun-gu Seoul 02455 Republic of Korea
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
| | - Roland G. Huber
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
| | - Peter J. Bond
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
- National University of SingaporeDepartment of Biological Sciences 14 Science Drive 4 Singapore 117543
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26
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Mechanical Unfolding of Spectrin Repeats Induces Water-Molecule Ordering. Biophys J 2020; 118:1076-1089. [PMID: 32027822 DOI: 10.1016/j.bpj.2020.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 02/07/2023] Open
Abstract
Mechanical processes are involved at many stages of the development of living cells, and often external forces applied to a biomolecule result in its unfolding. Although our knowledge of the unfolding mechanisms and the magnitude of the forces involved has evolved, the role that water molecules play in the mechanical unfolding of biomolecules has not yet been fully elucidated. To this end, we investigated with steered molecular dynamics simulations the mechanical unfolding of dystrophin's spectrin repeat 1 and related the changes in the protein's structure to the ordering of the surrounding water molecules. Our results indicate that upon mechanically induced unfolding of the protein, the solvent molecules become more ordered and increase their average number of hydrogen bonds. In addition, the unfolded structures originating from mechanical pulling expose an increasing amount of the hydrophobic residues to the solvent molecules, and the uncoiled regions adapt a convex surface with a small radius of curvature. As a result, the solvent molecules reorganize around the protein's small protrusions in structurally ordered waters that are characteristic of the so-called "small-molecule regime," which allows water to maintain a high hydrogen bond count at the expense of an increased structural order. We also determined that the response of water to structural changes in the protein is localized to the specific regions of the protein that undergo unfolding. These results indicate that water plays an important role in the mechanically induced unfolding of biomolecules. Our findings may prove relevant to the ever-growing interest in understanding macromolecular crowding in living cells and their effects on protein folding, and suggest that the hydration layer may be exploited as a means for short-range allosteric communication.
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Srivastava A, Malik S, Karmakar S, Debnath A. Dynamic coupling of a hydration layer to a fluid phospholipid membrane: intermittency and multiple time-scale relaxations. Phys Chem Chem Phys 2020; 22:21158-21168. [DOI: 10.1039/d0cp02803g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the coupling of a hydration layer and a lipid membrane is crucial to gaining access to membrane dynamics and understanding its functionality towards various biological processes.
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Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
| | - Sheeba Malik
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
| | - Smarajit Karmakar
- Centre for Interdisciplinary Sciences
- Tata Institute of Fundamental Research
- Hyderabad 500107
- India
| | - Ananya Debnath
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
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28
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Honegger P, Steinhauser O. The protein-water nuclear Overhauser effect (NOE) as an indirect microscope for molecular surface mapping of interaction patterns. Phys Chem Chem Phys 2019; 22:212-222. [PMID: 31799520 DOI: 10.1039/c9cp04752b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this computational study, the intermolecular solute-solvent Nuclear Overhauser Effect (NOE) of the model protein ubiquitin in different chemical environments (free, bound to a partner protein and encapsulated) is investigated. Short-ranged NOE observables such as the NOE/ROE ratio reveal hydration phenomena on absolute timescales such as fast hydration sites and slow water clefts. We demonstrate the ability of solute-solvent NOE differences measured of the same protein in different chemical environments to reveal hydration changes on the relative timescale. The resulting NOE/ROE-surface maps are shown to be a central key for analyzing biologically relevant chemical influences such as complexation and confinement: the presence of a complexing macromolecule or a confining surface wall modulates the water mobility in the vicinity of the probe protein, hence revealing which residues of said protein are proximate to the foreign interface and which are chemically unaffected. This way, hydration phenomena can serve to indirectly map the precise influence (position) of other molecules or interfaces onto the protein surface. This proposed one-protein many-solvents approach may offer experimental benefits over classical one-protein other-protein pseudo-intermolecular transient NOEs. Furthermore, combined influences such as complexation and confinement may exert non-additive influences on the protein compared to a reference state. We offer a mathematical method to disentangle the influence of these two different chemical environments.
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Affiliation(s)
- Philipp Honegger
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, A-1090 Vienna, Austria.
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29
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Dey A, Banerjee A. Unusual Overhauser Dynamic Nuclear Polarization Behavior of Fluorinated Alcohols at Room Temperature. J Phys Chem B 2019; 123:10463-10469. [PMID: 31714083 DOI: 10.1021/acs.jpcb.9b08144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of fluorinated alcohols is a matter of considerable interest in view of wide-ranging biomolecular applications. The microheterogeneity of fluorinated alcohols in the liquid state, in particular, has been a matter of debate and discussion in recent years using experimental and theoretical methods, including neutron or X-ray diffraction, as well as density functional theory (DFT) and molecular dynamics (MD) simulations. Here, we show that 1H and 19F Overhauser dynamic nuclear polarization (ODNP) buildup curves in solution state at room temperature show unusual behavior that could offer a novel approach to investigate the structural heterogeneity and dynamics of such homogeneous liquids with improved sensitivity. A detailed analysis of multiexponential ODNP buildup curves as a function of microwave irradiation time is shown to evidence microheterogeneity in such systems. Experimental ODNP buildup rates are interpreted using simple motional models that yield the motional correlation times of the relevant species in solution. It may be emphasized that this information is not available from standard approaches of high-resolution nuclear magnetic resonance (NMR) spectroscopy. While the present study focuses on fluorinated alcohols, it is to be anticipated that this approach would be valuable in the study of molecular assemblies in the solution state, including peptides, surfactant systems, etc.
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Affiliation(s)
- Arnab Dey
- MRI-MRS Centre and Department of Chemistry , Indian Institute of Technology-Madras , Chennai 600036 , Tamil Nadu , India
| | - Abhishek Banerjee
- MRI-MRS Centre and Department of Chemistry , Indian Institute of Technology-Madras , Chennai 600036 , Tamil Nadu , India
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30
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Singh H, Vasa SK, Jangra H, Rovó P, Päslack C, Das CK, Zipse H, Schäfer LV, Linser R. Fast Microsecond Dynamics of the Protein–Water Network in the Active Site of Human Carbonic Anhydrase II Studied by Solid-State NMR Spectroscopy. J Am Chem Soc 2019; 141:19276-19288. [DOI: 10.1021/jacs.9b05311] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Himanshu Singh
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Suresh K. Vasa
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Harish Jangra
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Petra Rovó
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Christopher Päslack
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Chandan K. Das
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Hendrik Zipse
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Lars V. Schäfer
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Rasmus Linser
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
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31
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Heterogeneity in structure and dynamics of water near bilayers using TIP3P and TIP4P/2005 water models. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.110396] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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32
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Tao M, Pandey NK, Barnes R, Han S, Langen R. Structure of Membrane-Bound Huntingtin Exon 1 Reveals Membrane Interaction and Aggregation Mechanisms. Structure 2019; 27:1570-1580.e4. [PMID: 31466833 DOI: 10.1016/j.str.2019.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/23/2019] [Accepted: 08/09/2019] [Indexed: 02/08/2023]
Abstract
Huntington's disease is caused by a polyQ expansion in the first exon of huntingtin (Httex1). Membrane interaction of huntingtin is of physiological and pathological relevance. Using electron paramagnetic resonance and Overhauser dynamic nuclear polarization, we find that the N-terminal residues 3-13 of wild-type Httex1(Q25) form a membrane-bound, amphipathic α helix. This helix is positioned in the interfacial region, where it is sensitive to membrane curvature and electrostatic interactions with head-group charges. Residues 14-22, which contain the first five residues of the polyQ region, are in a transition region that remains in the interfacial region without taking up a stable, α-helical structure. The remaining C-terminal portion is solvent exposed. The phosphomimetic S13D/S16D mutations, which are known to protect from toxicity, inhibit membrane binding and attenuate membrane-mediated aggregation of mutant Httex1(Q46) due to electrostatic repulsion. Targeting the N-terminal membrane anchor using post-translational modifications or specific binders could be a potential means to reduce aggregation and toxicity in vivo.
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Affiliation(s)
- Meixin Tao
- Department of Neuroscience and Physiology, Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Nitin K Pandey
- Department of Neuroscience and Physiology, Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ryan Barnes
- Department of Chemistry and Biochemistry, Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Songi Han
- Department of Chemistry and Biochemistry, Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ralf Langen
- Department of Neuroscience and Physiology, Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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33
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Lai Y, Kuo Y, Chiang Y. Identifying Protein Conformational Dynamics Using Spin‐label ESR. Chem Asian J 2019; 14:3981-3991. [DOI: 10.1002/asia.201900855] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/02/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Yei‐Chen Lai
- Department of Chemistry National Tsing Hua University Hsinchu 30013 Taiwan
- Department of Chemistry&Biochemistry University of California Santa Barbara CA 93106-9510 USA
| | - Yun‐Hsuan Kuo
- Department of Chemistry National Tsing Hua University Hsinchu 30013 Taiwan
| | - Yun‐Wei Chiang
- Department of Chemistry National Tsing Hua University Hsinchu 30013 Taiwan
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34
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35
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Heyden M. Heterogeneity of water structure and dynamics at the protein-water interface. J Chem Phys 2019; 150:094701. [PMID: 30849897 DOI: 10.1063/1.5081739] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this molecular dynamics simulation study, we analyze the local structural and dynamic properties of water hydrating the protein ubiquitin on a spatial grid with 1 Å resolution. This allows for insights into the spatial distribution of water number densities, molecular orientations, translations, and rotations as a function of distance from the protein surface. Water molecule orientations follow a heterogeneous distribution with preferred local orientations of water dipoles and O-H bond vectors up to 10-15 Å distances from the protein, while local variations of the water number density converge to homogeneous bulk-like values within less than 8 Å. Interestingly, we find that the long-ranged orientational structure of water does not impact either the translational or rotational dynamics of water. Instead, heterogeneous distributions of local dynamical parameters and averaged dynamical retardation factors are only found close to the protein surface and follow a distance dependence comparable to heterogeneities in the local water number density. This study shows that the formation of nanodomains of preferred water orientations far from the protein does not significantly impact dynamical processes probed as a non-local average in most experiments.
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Affiliation(s)
- Matthias Heyden
- School of Molecular Sciences and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287-1604, USA
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36
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Dahanayake JN, Shahryari E, Roberts KM, Heikes ME, Kasireddy C, Mitchell-Koch KR. Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics. J Chem Inf Model 2019; 59:2407-2422. [PMID: 30865440 DOI: 10.1021/acs.jcim.9b00009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structure of the solvation layer around different regions of the enzyme Candida antarctica lipase B, wherein the radial distribution function (RDF) was used to calculate the pairwise entropy, providing a link between dynamics (diffusion) and thermodynamics (excess entropy) known as Rosenfeld scaling. Regions with higher RDF values/peaks in the hydration layer (the first peak, within 6 Å of the protein surface) have faster diffusion in the hydration layer. The finding thus hinted at a handle for rapid evaluation of hydration dynamics at different regions on the protein surface in molecular dynamics simulations. Such an approach may move the analysis of hydration dynamics from a specialized venture to routine analysis, enabling an informatics approach to evaluate the role of hydration dynamics in biomolecular function. This paper first confirms that the correlation between regional diffusive dynamics and hydration layer structure (via water center of mass around protein side-chain atom RDF) is observed as a general relationship across a set of proteins. Second, it seeks to devise an approach for rapid analysis of hydration dynamics, determining the minimum amount of information and computational effort required to get a reliable value of hydration dynamics from structural data in MD simulations based on the protein-water RDF. A linear regression model using the integral of the hydration layer in the water-protein RDF was found to provide statistically equivalent apparent diffusion coefficients at the 95% confidence level for a set of 92 regions within five different proteins. In summary, RDF analysis of 10 ns of data after simulation convergence is sufficient to accurately map regions of fast and slow hydration dynamics around a protein surface. Additionally, it is anticipated that a quick look at protein-water RDFs, comparing peak heights, will be useful to provide a qualitative ranking of regions of faster and slower hydration dynamics at the protein surface for rapid analysis when investigating the role of solvent dynamics in protein function.
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Affiliation(s)
- Jayangika N Dahanayake
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Elaheh Shahryari
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Kirsten M Roberts
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Micah E Heikes
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Chandana Kasireddy
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Katie R Mitchell-Koch
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
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37
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Functional Hydration Behavior: Interrelation between Hydration and Molecular Properties at Lipid Membrane Interfaces. J CHEM-NY 2019. [DOI: 10.1155/2019/4867327] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Water is an abundant commodity and has various important functions. It stabilizes the structure of biological macromolecules, controls biochemical activities, and regulates interfacial/intermolecular interactions. Common aspects of interfacial water can be obtained by overviewing fundamental functions and properties at different temporal and spatial scales. It is important to understand the hydrogen bonding and structural properties of water and to evaluate the individual molecular species having different hydration properties. Water molecules form hydrogen bonds with biomolecules and contribute to the adjustment of their properties, such as surface charge, hydrophilicity, and structural flexibility. In this review, the fundamental properties of water molecules and the methods used for the analyses of water dynamics are summarized. In particular, the interrelation between the hydration properties, determined by molecules, and the properties of molecules, determined by their hydration properties, are discussed using the lipid membrane as an example. Accordingly, interesting water functions are introduced that provide beneficial information in the fields of biochemistry, medicine, and food chemistry.
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38
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Capponi S, White SH, Tobias DJ, Heyden M. Structural Relaxation Processes and Collective Dynamics of Water in Biomolecular Environments. J Phys Chem B 2019; 123:480-486. [PMID: 30566356 DOI: 10.1021/acs.jpcb.8b12052] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this simulation study, we investigate the influence of biomolecular confinement on dynamical processes in water. We compare water confined in a membrane protein nanopore at room temperature to pure liquid water at low temperatures with respect to structural relaxations, intermolecular vibrations, and the propagation of collective modes. We observe distinct potential energy landscapes experienced by water molecules in the two environments, which nevertheless result in comparable hydrogen bond lifetimes and sound propagation velocities. Hence, we show that a viscoelastic argument that links slow rearrangements of the water-hydrogen bond network to ice-like collective properties applies to both, the pure liquid and biologically confined water, irrespective of differences in the microscopic structure.
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Affiliation(s)
| | | | | | - Matthias Heyden
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287-1604 , United States
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39
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Bordignon E, Kucher S, Polyhach Y. EPR Techniques to Probe Insertion and Conformation of Spin-Labeled Proteins in Lipid Bilayers. Methods Mol Biol 2019; 2003:493-528. [PMID: 31218631 DOI: 10.1007/978-1-4939-9512-7_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy of spin-labeled membrane proteins is a valuable biophysical technique to study structural details and conformational transitions of proteins close to their physiological environment, for example, in liposomes, membrane bilayers, and nanodiscs. Unlike in nuclear magnetic resonance (NMR) spectroscopy, having only one or few specific side chains labeled at a time with paramagnetic probes makes the size of the object under investigation irrelevant in terms of technique sensitivity. As a drawback, extensive site-directed mutagenesis is required in order to analyze the properties of the protein under investigation. EPR can provide detailed information on side chain dynamics of large membrane proteins or protein complexes embedded in membranes with an exquisite sensitivity for flexible regions and on water accessibility profiles across the membrane bilayer. Moreover, distances between the two spin-labeled side chains in membrane proteins can be detected with high precision at cryogenic temperatures. The application of EPR to membrane proteins still presents some challenges in terms of sample preparation, sensitivity and data interpretation, thus it is difficult to give ready-to-go methodological recipes. However, new technological developments (arbitrary waveform generators) and new spin labels spectroscopically orthogonal to nitroxides increased the range of applicability from in vitro toward in-cell EPR experiments. This chapter is an updated version of the one published in the first edition of the book and describes the state of the art in the application of nitroxide-based site-directed spin labeling EPR to membrane proteins, addressing new tools such as arbitrary waveform generators and spectroscopically orthogonal labels, such as Gd(III)-based labels. We will present challenges in sample preparation and data analysis for functional and structural membrane protein studies using site-directed spin labeling techniques and give experimental details on EPR techniques providing information on side chain dynamics and water accessibility using nitroxide probes. An updated optimal Q-band DEER setup for nitroxide probes will be described, and its extension to gadolinium-containing samples will be addressed.
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Affiliation(s)
- Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany.
| | - Svetlana Kucher
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
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40
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Päslack C, Schäfer LV, Heyden M. Atomistic characterization of collective protein–water–membrane dynamics. Phys Chem Chem Phys 2019; 21:15958-15965. [DOI: 10.1039/c9cp00725c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water mediates correlated vibrations of atoms of protein and membrane bilayer surfaces.
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Affiliation(s)
- Christopher Päslack
- Center for Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Lars V. Schäfer
- Center for Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Matthias Heyden
- School of Molecular Sciences
- Arizona State University
- Tempe
- USA
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41
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Päslack C, Smith JC, Heyden M, Schäfer LV. Hydration-mediated stiffening of collective membrane dynamics by cholesterol. Phys Chem Chem Phys 2019; 21:10370-10376. [DOI: 10.1039/c9cp01431d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydration water governs the cholesterol-induced changes in collective headgroup dynamics in lipid bilayers.
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Affiliation(s)
- Christopher Päslack
- Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr University Bochum
- D-44780 Bochum
- Germany
| | - Jeremy C. Smith
- Center for Molecular Biophysics
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Department of Biochemistry and Cellular and Molecular Biology
| | - Matthias Heyden
- School of Molecular Sciences
- Arizona State University
- Tempe
- USA
| | - Lars V. Schäfer
- Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr University Bochum
- D-44780 Bochum
- Germany
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42
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Honegger P, Heid E, Schmode S, Schröder C, Steinhauser O. Changes in protein hydration dynamics by encapsulation or crowding of ubiquitin: strong correlation between time-dependent Stokes shift and intermolecular nuclear Overhauser effect. RSC Adv 2019; 9:36982-36993. [PMID: 35539058 PMCID: PMC9075347 DOI: 10.1039/c9ra08008b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022] Open
Abstract
The local changes in protein hydration dynamics upon encapsulation of the protein or macromolecular crowding are essential to understand protein function in cellular environments. We were able to obtain a spatially-resolved picture of the influence of confinement and crowding on the hydration dynamics of the protein ubiquitin by analyzing the time-dependent Stokes shift (TDSS), as well as the intermolecular Nuclear Overhauser Effect (NOE) at different sites of the protein by large-scale computer simulation of single and multiple proteins in water and confined in reverse micelles. Besides high advanced space resolved information on hydration dynamics we found a strong correlation of the change in NOE upon crowding or encapsulation and the change in the integral TDSS relaxation times in all investigated systems relative to the signals in a diluted protein solution. Changes in local protein hydration dynamics caused by encapsulation or crowding are reflected in the TDSS and the intermolecular NOE alike.![]()
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Affiliation(s)
- Philipp Honegger
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Esther Heid
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Stella Schmode
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Christian Schröder
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
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43
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Franck JM, Han S. Overhauser Dynamic Nuclear Polarization for the Study of Hydration Dynamics, Explained. Methods Enzymol 2018; 615:131-175. [PMID: 30638529 DOI: 10.1016/bs.mie.2018.09.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We outline the physical properties of hydration water that are captured by Overhauser Dynamic Nuclear Polarization (ODNP) relaxometry and explore the insights that ODNP yields about the water and the surface that this water is coupled to. As ODNP relies on the pairwise cross-relaxation between the electron spin of a spin probe and a proton nuclear spin of water, it captures the dynamics of single-particle diffusion of an ensemble of water molecules moving near the spin probe. ODNP principally utilizes the same physics as other nuclear magnetic resonance (NMR) relaxometry (i.e., relaxation measurement) techniques. However, in ODNP, electron paramagnetic resonance (EPR) excites the electron spins probes and their high net polarization acts as a signal amplifier. Furthermore, it renders ODNP parameters highly sensitive to water moving at rates commensurate with the EPR frequency of the spin probe (typically 10GHz). Also, ODNP selectively enhances the NMR signal contributions of water moving within close proximity to the spin label. As a result, ODNP can capture ps-ns movements of hydration waters with high sensitivity and locality, even in samples with protein concentrations as dilute as 10 µM. To date, the utility of the ODNP technique has been demonstrated for two major applications: the characterization of the spatial variation in the properties of the hydration layer of proteins or other surfaces displaying topological diversity, and the identification of structural properties emerging from highly disordered proteins and protein domains. The former has been shown to correlate well with the properties of hydration water predicted by MD simulations and has been shown capable of evaluating the hydrophilicity or hydrophobicity of a surface. The latter has been demonstrated for studies of an interhelical loop of proteorhodopsin, the partial structure of α-synuclein embedded at the lipid membrane surface, incipient structures adopted by tau proteins en route to fibrils, and the structure and hydration profile of a transmembrane peptide. This chapter focuses on offering a mechanistic understanding of the ODNP measurement and the molecular dynamics encoded in the ODNP parameters. In particular, it clarifies how the electron-nuclear dipolar coupling encodes information about the molecular dynamics in the nuclear spin self-relaxation and, more importantly, the electron-nuclear spin cross-relaxation rates. The clarification of the molecular dynamics underlying ODNP should assist in establishing a connection to theory and computer simulation that will offer far richer interpretations of ODNP results in future studies.
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Affiliation(s)
- John M Franck
- Department of Chemistry, Syracuse University, Syracuse, NY, United States.
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, United States; Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, United States
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44
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Lippens JL, Egea PF, Spahr C, Vaish A, Keener JE, Marty MT, Loo JA, Campuzano ID. Rapid LC-MS Method for Accurate Molecular Weight Determination of Membrane and Hydrophobic Proteins. Anal Chem 2018; 90:13616-13623. [PMID: 30335969 PMCID: PMC6580849 DOI: 10.1021/acs.analchem.8b03843] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Therapeutic target characterization involves many components, including accurate molecular weight (MW) determination. Knowledge of the accurate MW allows one to detect the presence of post-translational modifications, proteolytic cleavages, and importantly, if the correct construct has been generated and purified. Denaturing liquid chromatography-mass spectrometry (LC-MS) can be an attractive method for obtaining this information. However, membrane protein LC-MS methodology has remained relatively under-explored and under-incorporated in comparison to methods for soluble proteins. Here, systematic investigation of multiple gradients and column chemistries has led to the development of a 5 min denaturing LC-MS method for acquiring membrane protein accurate MW measurements. Conditions were interrogated with membrane proteins, such as GPCRs and ion channels, as well as bispecific antibody constructs of variable sizes with the aim to provide the community with rapid LC-MS methods necessary to obtain chromatographic and accurate MW measurements in a medium- to high-throughput manner. The 5 min method detailed has successfully produced MW measurements for hydrophobic proteins with a wide MW range (17.5 to 105.3 kDa) and provided evidence that some constructs indeed contain unexpected modifications or sequence clipping. This rapid LC-MS method is also capable of baseline separating formylated and nonformylated aquaporinZ membrane protein.
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Affiliation(s)
- Jennifer L. Lippens
- Amgen Discovery Research, Amgen, Thousand Oaks, California 91320, United States
| | - Pascal F. Egea
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Chris Spahr
- Amgen Discovery Research, Amgen, Thousand Oaks, California 91320, United States
| | - Amit Vaish
- Amgen Discovery Research, Amgen, Thousand Oaks, California 91320, United States
| | - James E. Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Joseph A. Loo
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Iain D.G. Campuzano
- Amgen Discovery Research, Amgen, Thousand Oaks, California 91320, United States
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45
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Überrück T, Neudert O, Kreuer KD, Blümich B, Granwehr J, Stapf S, Han S. Effect of nitroxide spin probes on the transport properties of Nafion membranes. Phys Chem Chem Phys 2018; 20:26660-26674. [PMID: 30320331 DOI: 10.1039/c8cp04607g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Nafion is the most common material used as a proton exchange membrane in fuel cells. Yet, details of the transport pathways for protons and water in the inner membrane are still under debate. Overhauser Dynamic Nuclear Polarization (ODNP) has proven to be a useful tool for probing hydration dynamics and interactions within 5-8 Å of protein and soft material surfaces. Recently it was suggested that ODNP can also be applied to analyze surface water dynamics along Nafion's inner membrane. Here we interrogate the viability of this method for Nafion by carrying out a series of measurements relying on 1H nuclear magnetic resonance (NMR) relaxometry and diffusometry experiments with and without ODNP hyperpolarization, accompanied by other complementary characterization methods including small angle X-ray scattering (SAXS), thermal gravimetric analysis (TGA) of hydration, and proton conductivity by AC impedance spectroscopy. Our comprehensive study shows that commonly used paramagnetic spin probes-here, stable nitroxide radicals-for ODNP, as well as their diamagnetic analogues, reduce the inner membrane surface hydrophilicity, depending on the location and concentration of the spin probe. This heavily reduces the hydration of Nafion, hence increases the tortuosity of the inner membrane morphology and/or increases the activiation barrier for water transport, and consequently impedes water diffusion, transport, and proton conductivity.
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Affiliation(s)
- Till Überrück
- RWTH Aachen University, Institut für Technische und Makromolekulare Chemie, Worringerweg 2, 52074 Aachen, Germany.
| | - Oliver Neudert
- Dept. Technical Physics II/Polymer Physics, University of Technology Ilmenau, 98684 Ilmenau, Germany and GMBU e.V., Erich-Neuß-Weg 5, 06120 Halle (Saale), Germany
| | - Klaus-Dieter Kreuer
- Max-Planck-Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart, Germany
| | - Bernhard Blümich
- RWTH Aachen University, Institut für Technische und Makromolekulare Chemie, Worringerweg 2, 52074 Aachen, Germany.
| | - Josef Granwehr
- RWTH Aachen University, Institut für Technische und Makromolekulare Chemie, Worringerweg 2, 52074 Aachen, Germany. and Forschungszentrum Jülich, Institut für Energie- und Klimaforschung - Grundlagen der Elektrochemie (IEK-9), 52425 Jülich, Germany
| | - Siegfried Stapf
- Dept. Technical Physics II/Polymer Physics, University of Technology Ilmenau, 98684 Ilmenau, Germany
| | - Songi Han
- University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, CA 93106, USA
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46
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Buck ZN, Torres J, Miskowiec A, Mamontov E, Kaiser H, Hansen FY, Taub H, Tyagi M, Collins L, Herwig KW. Effect of melittin on water diffusion and membrane structure in DMPC lipid bilayers. ACTA ACUST UNITED AC 2018. [DOI: 10.1209/0295-5075/123/18002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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47
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Gallo PN, Iovine JC, Nucci NV. Toward comprehensive measurement of protein hydration dynamics: Facilitation of NMR-based methods by reverse micelle encapsulation. Methods 2018; 148:146-153. [PMID: 30048681 DOI: 10.1016/j.ymeth.2018.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 10/28/2022] Open
Abstract
Protein-water interactions are a fundamental determinant of protein structure and function. Despite their importance, the molecular details of water orientations and dynamics near protein surfaces remain poorly understood, largely due to the difficulty of measuring local water mobility near the protein in a site-resolved fashion. Solution NMR-based measurement of water mobility via the nuclear Overhauser effect was presented as a method for performing comprehensive, site-resolved measurements of water dynamics many years ago. Though this approach yielded extensive insight on the dynamics and locations of waters buried within proteins, its promise for measuring surface hydration dynamics was impeded by various technical barriers. Over the past several years, however, this approach has been pursued anew with the aid of reverse micelle encapsulation of proteins of interest. The confined environment of the reverse micelle resolves many of these barriers and permits site-resolved measurement of relative water dynamics across much of the protein surface. Here, the development of this strategy for measuring hydration dynamics is reviewed with particular focus on the important remaining challenges to its widespread application.
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Affiliation(s)
- Pamela N Gallo
- Department of Physics & Astronomy, Department of Molecular & Cellular Biosciences, Rowan University, 201 Mullica Hill Road, Glassboro, NJ 08028, United States
| | - Joseph C Iovine
- Department of Physics & Astronomy, Department of Molecular & Cellular Biosciences, Rowan University, 201 Mullica Hill Road, Glassboro, NJ 08028, United States
| | - Nathaniel V Nucci
- Department of Physics & Astronomy, Department of Molecular & Cellular Biosciences, Rowan University, 201 Mullica Hill Road, Glassboro, NJ 08028, United States.
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48
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New limits of sensitivity of site-directed spin labeling electron paramagnetic resonance for membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:841-853. [DOI: 10.1016/j.bbamem.2017.12.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/27/2017] [Accepted: 12/09/2017] [Indexed: 01/27/2023]
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49
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Srivastava A, Debnath A. Hydration dynamics of a lipid membrane: Hydrogen bond networks and lipid-lipid associations. J Chem Phys 2018. [DOI: 10.1063/1.5011803] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
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50
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Li Q, Zhou M, Yang M, Yang Q, Zhang Z, Shi J. Induction of long-lived room temperature phosphorescence of carbon dots by water in hydrogen-bonded matrices. Nat Commun 2018; 9:734. [PMID: 29467414 PMCID: PMC5821822 DOI: 10.1038/s41467-018-03144-9] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 01/23/2018] [Indexed: 11/08/2022] Open
Abstract
Phosphorescence shows great potential for application in bioimaging and ion detection because of its long-lived luminescence and high signal-to-noise ratio, but establishing phosphorescence emission in aqueous environments remains a challenge. Herein, we present a general design strategy that effectively promotes phosphorescence by utilising water molecules to construct hydrogen-bonded networks between carbon dots (CDs) and cyanuric acid (CA). Interestingly, water molecules not only cause no phosphorescence quenching but also greatly enhance the phosphorescence emission. This enhancement behaviour can be explained by the fact that the highly ordered bound water on the CA particle surface can construct robust bridge-like hydrogen-bonded networks between the CDs and CA, which not only effectively rigidifies the C=O bonds of the CDs but also greatly enhances the rigidity of the entire system. In addition, the CD-CA suspension exhibits a high phosphorescence lifetime (687 ms) and is successfully applied in ion detection based on its visible phosphorescence.
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Affiliation(s)
- Qijun Li
- State Key Laboratory of Tribology, School of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Ming Zhou
- State Key Laboratory of Tribology, School of Mechanical Engineering, Tsinghua University, Beijing, 100084, China.
| | - Mingyang Yang
- State Key Laboratory of Tribology, School of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Qingfeng Yang
- State Key Laboratory of Tribology, School of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Zhixun Zhang
- State Key Laboratory of Tribology, School of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Jing Shi
- State Key Laboratory of Tribology, School of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
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