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Bianchi G, Mangiagalli M, Barbiroli A, Longhi S, Grandori R, Santambrogio C, Brocca S. Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins. Biomolecules 2022; 12:biom12040561. [PMID: 35454150 PMCID: PMC9031945 DOI: 10.3390/biom12040561] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/29/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are ensembles of interconverting conformers whose conformational properties are governed by several physico-chemical factors, including their amino acid composition and the arrangement of oppositely charged residues within the primary structure. In this work, we investigate the effects of charge patterning on the average compactness and shape of three model IDPs with different proline content. We model IDP ensemble conformations as ellipsoids, whose size and shape are calculated by combining data from size-exclusion chromatography and native mass spectrometry. For each model IDP, we analyzed the wild-type protein and two synthetic variants with permuted positions of charged residues, where positive and negative amino acids are either evenly distributed or segregated. We found that charge clustering induces remodeling of the conformational ensemble, promoting compaction and/or increasing spherical shape. Our data illustrate that the average shape and volume of the ensembles depend on the charge distribution. The potential effect of other factors, such as chain length, number of proline residues, and secondary structure content, is also discussed. This methodological approach is a straightforward way to model IDP average conformation and decipher the salient sequence attributes influencing IDP structural properties.
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Affiliation(s)
- Greta Bianchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
| | - Alberto Barbiroli
- Departement of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy;
| | - Sonia Longhi
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, 13288 Marseille, France;
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
- Correspondence: (C.S.); (S.B.); Tel.: +39-02-6448-3363 (C.S.); +39-02-6448-3518 (S.B.)
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
- Correspondence: (C.S.); (S.B.); Tel.: +39-02-6448-3363 (C.S.); +39-02-6448-3518 (S.B.)
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2
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Hande VR, Chakrabarty S. How Far Is "Bulk Water" from Interfaces? Depends on the Nature of the Surface and What We Measure. J Phys Chem B 2022; 126:1125-1135. [PMID: 35104127 DOI: 10.1021/acs.jpcb.1c08603] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using systematic molecular dynamics (MD) simulations, we revisit the question: At what distance from an interface do the properties of "bulk water" get recovered? We have considered three different kinds of interfaces: nonpolar (hydrophobic; isooctane-water interface), charged (negative; AOT bilayer), and polar (zwitterionic; POPC bilayer). In order to interrogate the extent of perturbation of the interfacial water molecules as a function of the distance from the interface, we utilize a diverse range of structural and dynamical parameters. To capture the structural perturbations, we look into local density (translational order), local tetrahedral order parameter, and dipolar orientation of the water molecules. We also explore the anisotropic diffusion of the water molecules in the direction perpendicular to the interface as well as the planar diffusion parallel to the interface in a distance dependent manner. In addition, the orientational time correlation functions have been computed to understand the extent of slowdown in the rotational dynamics. As expected, the electrostatic field emanating from the charged AOT interface seems to have the highest long-range effect on the orientational order and dynamics of the water molecules, whereas specific interactions like hydrogen bonding and electrostatic interaction lead to significant trapping and kinetic slowdown for both AOT and POPC (zwitterionic) very close to the interface. Our analysis highlights that not only the length-scale of perturbation depends on the nature of the interfaces and specific interactions but also the type of water property that we measure/calculate. Different water properties seem to have widely different length-scale of perturbation. Orientational order parameters seem to be perturbed to a much longer length-scale as compared to translational order parameters. The global orientational order of water can be perturbed even up to ∼4-5 nm near the negatively charged AOT surface in the absence of any extra electrolyte. This observation has significant implication toward the interpretation of experimental measurements as well since different spectroscopic techniques would probe different parameters or water properties with possible mutual disagreement and inconsistency between different types of measurements. Thus, our study provides a broader and unifying perspective toward the aspect of "context dependent" structural and dynamical perturbation of "interfacial water".
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Affiliation(s)
- Vrushali R Hande
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suman Chakrabarty
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
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3
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Wu H, Ghaani MR, Nandi PK, English NJ. Investigation of Dipolar Response of the Hydrated Hen-Egg White Lysozyme Complex under Externally Applied Electric Fields: Insights from Non-equilibrium Molecular Dynamics. J Phys Chem B 2022; 126:858-868. [PMID: 35060735 PMCID: PMC8819654 DOI: 10.1021/acs.jpcb.1c07096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- HaoLun Wu
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mohammad Reza Ghaani
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Prithwish K. Nandi
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
- Irish Centre for High-End Computing, Trinity Enterprise Centre, Pearse Street, Dublin 2, Ireland
| | - Niall J. English
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
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4
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The thermodynamic and kinetic mechanisms of a Ganoderma lucidum proteoglycan inhibiting hIAPP amyloidosis. Biophys Chem 2021; 280:106702. [PMID: 34741991 DOI: 10.1016/j.bpc.2021.106702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/17/2021] [Accepted: 10/26/2021] [Indexed: 12/14/2022]
Abstract
Ganoderma lucidum is a valuable medicinal herbal which has been reported to prevent type 2 diabetes (T2D). A natural hyperbranched proteoglycan extracted from Ganoderma lucidum, namely, FYGL, has been demonstrated to inhibit the amyloidosis of human islet amyloid polypeptide (hIAPP) previously by our lab. However, the effective active components and the mechanisms of FYGL in inhibiting hIAPP amyloidosis are unknown. To identify the effective active components, different components from FYGL were isolated: the polysaccharide FYGL-1, the proteoglycans of FYGL-2 and FYGL-3. We further separated and sequenced the protein moieties of FYGL-2 and FYGL-3, namely, FYGL-2-P and FYGL-3-P, respectively, and compared their abilities to inhibit hIAPP amyloidosis, and systematically explored the inhibitory mechanisms by spectroscopy, microscopy and molecular dynamic simulation methods. Results showed that the protein moieties of FYGL played essential roles in inhibiting hIAPP amyloidosis. The strong, specific, and enthalpy-driven interaction by π-π stacking and electrostatic forces between hIAPP and FYGL-3-P dramatically inhibited hIAPP amyloidosis. These results suggested that FYGL-3-P had enormous potential to prevent hIAPP misfolding-induced diabetes and structurally helped researchers to seek or design inhibitors against polypeptide amyloidosis.
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5
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Wu B, Wang H, Dai X, Chai X. Influential mechanism of water occurrence states of waste-activated sludge: specifically focusing on the roles of EPS micro-spatial distribution and cation-dominated interfacial properties. WATER RESEARCH 2021; 202:117461. [PMID: 34343872 DOI: 10.1016/j.watres.2021.117461] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/30/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
The highly hydrated colloidal structure of waste-activated sludge (WAS) is the main obstacle of enhanced dewatering for sludge volume minimization. Extracellular polymeric substances (EPS) maintain the colloidal stability of bio-flocs in a three-dimensional matrix due to bindings with bivalent cations (i.e., Ca2+ and Mg2+) and hydrophobic interactions. However, few studies specifically focused on the quantitative relationships among spatial distribution of EPS, microstructure of bio-flocs and fractions of bound water (e.g. vicinal water and interstitial water). Thus, there may be still some debates on whether and what extent of the lysis or flocculation of sludge flocs is optimal for the dewaterability improvement. This study applied the gradient addition of cation exchange resin (CER) to remove EPS-complexed cations and loosen the spatial distribution of EPS. Consequently, how the spatial extension of EPS layers with relief of complex cations influenced the particle size distribution, fractal dimension, interfacial free energy and water occurrence states of WAS was systematically investigated. The quartz crystal microbalance with dissipation (QCM-D) was also applied to analyze the water-EPS interactions with and without the presence of Ca2+ and Mg2+. All the results confirmed that the dispersed EPS adhering layers led to the higher fractal dimension (Df) but the lower space filling degree of bio-flocs. Also, the 4-fold reduction in the polar/acid-based interfacial free energy could be induced by the removal of cations from EPS matrix, which indicated the significant increase in hydrophobicity. Predictably, the fractions of vicinal water and interstitial water were dominated by the polar/acid-based interfacial free energy and pore structure of microbial aggregates, respectively, which were confirmed by the strong Pearson correlation (Rp>0.80, p-value<0.04). These findings are expected to provide the improved mechanistic insights into the relationship between water occurrence states and colloidal structure of WAS, and can serve as the basis for the optimal combination of various sludge conditioning approaches towards regulating aggregation states of bio-flocs.
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Affiliation(s)
- Boran Wu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Hao Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| | - Xiaoli Chai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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6
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Jafari M, Mojtabavi S, Faramarzi MA, Mehrnejad F, Soleimani M, Mirjani R. Molecular level insight into stability, activity, and structure of Laccase in aqueous ionic liquid and organic solvents: An experimental and computational research. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Mondal S, Bandyopadhyay S. Heterogeneous Dynamical Environment at the Interface of a Protein-DNA Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4567-4581. [PMID: 32267701 DOI: 10.1021/acs.langmuir.9b03175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Binding between protein and DNA is an essential process to regulate different biological activities. Two puzzling questions in protein-DNA recognition are (i) how the protein's binding domain identifies the DNA sequence in an aqueous solution and (ii) how the formation of the complex alters the dynamical environment around it. In this work, we present results obtained from molecular dynamics simulations of the N-terminal α-helical domain of the λ-repressor protein (in dimeric form) bound to the corresponding operator DNA. Effects of formation of the complex in modifying the microscopic dynamics of water as well as the kinetics of hydrogen bonds at the interface have been explored. Locally heterogeneous restricted water motions at the complex interface have been observed, the extent of restriction being more significant around the directly bound residues of the protein and the DNA. In particular, the calculation revealed the existence of significantly constrained motionally restricted water layer that can form either bridges around the directly bound residues of the protein and DNA or are engaged in forming water-mediated contacts between a fraction of the unbound residues. More importantly, it is observed that the restricted water motion around the complex is correlated with the hydrogen bond relaxation time scale at the interface. It is further demonstrated that the kinetics of water-water hydrogen bonds involving the bridged water are influenced more due to complex formation.
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Affiliation(s)
- Sandip Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
- Centre for Computational and Data Sciences, Indian Institute of Technology, Kharagpur 721302, India
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8
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Wu H, Zhang R, Zhang W, Hong J, Xiang Y, Xu W. Rapid 3-dimensional shape determination of globular proteins by mobility capillary electrophoresis and native mass spectrometry. Chem Sci 2020; 11:4758-4765. [PMID: 34122932 PMCID: PMC8159243 DOI: 10.1039/d0sc01965h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Established high-throughput proteomics methods provide limited information on the stereostructures of proteins. Traditional technologies for protein structure determination typically require laborious steps and cannot be performed in a high-throughput fashion. Here, we report a new medium throughput method by combining mobility capillary electrophoresis (MCE) and native mass spectrometry (MS) for the 3-dimensional (3D) shape determination of globular proteins in the liquid phase, which provides both the geometric structure and molecular mass information of proteins. A theory was established to correlate the ion hydrodynamic radius and charge state distribution in the native mass spectrum with protein geometrical parameters, through which a low-resolution structure (shape) of the protein could be determined. Our test data of 11 different globular proteins showed that this approach allows us to determine the shapes of individual proteins, protein complexes and proteins in a mixture, and to monitor protein conformational changes. Besides providing complementary protein structure information and having mixture analysis capability, this MCE and native MS based method is fast in speed and low in sample consumption, making it potentially applicable in top–down proteomics and structural biology for intact globular protein or protein complex analysis. Using native mass spectrometry and mobility capillary electrophoresis, the ellipsoid dimensions of globular proteins or protein complexes could be measured efficiently.![]()
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Affiliation(s)
- Haimei Wu
- School of Life Science, Beijing Institute of Technology No. 5 South Zhongguancun Street, Haidian Dist Beijing China
| | - Rongkai Zhang
- School of Life Science, Beijing Institute of Technology No. 5 South Zhongguancun Street, Haidian Dist Beijing China
| | - Wenjing Zhang
- School of Life Science, Beijing Institute of Technology No. 5 South Zhongguancun Street, Haidian Dist Beijing China
| | - Jie Hong
- School of Life Science, Beijing Institute of Technology No. 5 South Zhongguancun Street, Haidian Dist Beijing China
| | - Ye Xiang
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University Beijng China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology No. 5 South Zhongguancun Street, Haidian Dist Beijing China
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9
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Abstract
Terahertz time-domain spectroscopy (THz-TDS) is a non-invasive, non-contact and label-free technique for biological and chemical sensing as THz-spectra are less energetic and lie in the characteristic vibration frequency regime of proteins and DNA molecules. However, THz-TDS is less sensitive for the detection of micro-organisms of size equal to or less than λ/100 (where, λ is the wavelength of the incident THz wave), and molecules in extremely low concentration solutions (like, a few femtomolar). After successful high-throughput fabrication of nanostructures, nanoantennas were found to be indispensable in enhancing the sensitivity of conventional THz-TDS. These nanostructures lead to strong THz field enhancement when in resonance with the absorption spectrum of absorptive molecules, causing significant changes in the magnitude of the transmission spectrum, therefore, enhancing the sensitivity and allowing the detection of molecules and biomaterials in extremely low concentration solutions. Herein, we review the recent developments in ultra-sensitive and selective nanogap biosensors. We have also provided an in-depth review of various high-throughput nanofabrication techniques. We also discussed the physics behind the field enhancements in the sub-skin depth as well as sub-nanometer sized nanogaps. We introduce finite-difference time-domain (FDTD) and molecular dynamics (MD) simulation tools to study THz biomolecular interactions. Finally, we provide a comprehensive account of nanoantenna enhanced sensing of viruses (like, H1N1) and biomolecules such as artificial sweeteners which are addictive and carcinogenic.
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Affiliation(s)
- Subham Adak
- Department of Physics, Birla Institute of Technology, Mesra, Ranchi - 835215, Jharkhand, India.
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10
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Pedregal-Cortés R, Toriz G, Delgado E, Pollack GH. Interfacial water and its potential role in the function of sericin against biofouling. BIOFOULING 2019; 35:732-741. [PMID: 31468985 DOI: 10.1080/08927014.2019.1653863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Silk sericin is a globular protein whose resistance against fouling is important for applications in biomaterials and water-purification membranes. Here it is shown how sericin generates a water-exclusion zone that may facilitate antifouling behavior. Negatively charged microspheres were used to mimic the surface charge and hydrophobic domains in bacteria. Immersed in water, regenerated silk sericin formed a 100-µm-sized exclusion zone (for micron-size foulants), along with a proton gradient with a decrease of >2 pH-units. Thus, when in contact with sericin, water molecules near the surface restructure to form a physical exclusionary barrier that might prevent biofouling. The decreased pH turns the aqueous medium unviable for neutrophilic bacteria. Therefore, resistance to biofouling seems explainable, among other factors, on the basis of water-exclusionary phenomena. Furthermore, sericin may play a role in triggering the fibroin assembly process by lowering the pH to the required value.
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Affiliation(s)
- Ricardo Pedregal-Cortés
- Departamento de Madera, Celulosa y Papel, Universidad de Guadalajara , Zapopan , Jalisco , Mexico
| | - Guillermo Toriz
- Instituto Transdiciplinar de Investigación y Servicios/Departamento de Madera, Celulosa y Papel, Universidad de Guadalajara , Zapopan , Jalisco , México
| | - Ezequiel Delgado
- Departamento de Madera, Celulosa y Papel, Universidad de Guadalajara , Zapopan , Jalisco , Mexico
| | - Gerald H Pollack
- Department of Bioengineering, University of Washington , Seattle , WA , USA
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11
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Liu X, Amini K, Steinle T, Sanchez A, Shaikh M, Belsa B, Steinmetzer J, Le AT, Moshammer R, Pfeifer T, Ullrich J, Moszynski R, Lin CD, Gräfe S, Biegert J. Imaging an isolated water molecule using a single electron wave packet. J Chem Phys 2019; 151:024306. [PMID: 31301712 DOI: 10.1063/1.5100520] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Observing changes in molecular structure requires atomic-scale Ångstrom and femtosecond spatio-temporal resolution. We use the Fourier transform (FT) variant of laser-induced electron diffraction (LIED), FT-LIED, to directly retrieve the molecular structure of H2O+ with picometer and femtosecond resolution without a priori knowledge of the molecular structure nor the use of retrieval algorithms or ab initio calculations. We identify a symmetrically stretched H2O+ field-dressed structure that is most likely in the ground electronic state. We subsequently study the nuclear response of an isolated water molecule to an external laser field at four different field strengths. We show that upon increasing the laser field strength from 2.5 to 3.8 V/Å, the O-H bond is further stretched and the molecule slightly bends. The observed ultrafast structural changes lead to an increase in the dipole moment of water and, in turn, a stronger dipole interaction between the nuclear framework of the molecule and the intense laser field. Our results provide important insights into the coupling of the nuclear framework to a laser field as the molecular geometry of H2O+ is altered in the presence of an external field.
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Affiliation(s)
- Xinyao Liu
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Kasra Amini
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Tobias Steinle
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Aurelien Sanchez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Moniruzzaman Shaikh
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Blanca Belsa
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Johannes Steinmetzer
- Institute of Physical Chemistry, Friedrich-Schiller University, 07743 Jena, Germany
| | - Anh-Thu Le
- Missouri University of Science and Technology, Rolla, Missouri 65409, USA
| | - Robert Moshammer
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117, Heidelberg, Germany
| | - Thomas Pfeifer
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117, Heidelberg, Germany
| | - Joachim Ullrich
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117, Heidelberg, Germany
| | - Robert Moszynski
- Department of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - C D Lin
- Abbe Center of Photonics, Friedrich-Schiller University, 07745 Jena, Germany
| | - Stefanie Gräfe
- Institute of Physical Chemistry, Friedrich-Schiller University, 07743 Jena, Germany
| | - Jens Biegert
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
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12
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Zheng L, Xia K, Mu Y. Ligand Binding Induces Agonistic-Like Conformational Adaptations in Helix 12 of Progesterone Receptor Ligand Binding Domain. Front Chem 2019; 7:315. [PMID: 31134186 PMCID: PMC6514052 DOI: 10.3389/fchem.2019.00315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 04/23/2019] [Indexed: 01/28/2023] Open
Abstract
Progesterone receptor (PR) is a member of the nuclear receptor (NR) superfamily and plays a vital role in the female reproductive system. The malfunction of it would lead to several types of cancers. The understanding of conformational changes in its ligand binding domain (LBD) is valuable for both biological function studies and therapeutically intervenes. A key unsolved question is how the binding of a ligand (agonist, antagonist, or a selective modulator) induces conformational changes of PR LBD, especially its helix 12. We applied molecular dynamics (MD) simulations to explore the conformational adaptations of PR LBD with or without a ligand or the co-repressor peptides binding. From the simulations, both the agonist progesterone (P4) and the selective PR modulator (SPRM) asoprisnil induces agonistic-like helix 12 conformations (the "closed" states) in PR LBD and the complex of LBD-SPRM is less stable, comparing to the agonist-liganded PR LBD. The results, therefore, explain the partial agonism of the SPRM, which could induce weak agonistic effects in PR. We also found that co-repressor peptides could be stably associated with the LBD and stabilize the LBD in a "semi-open" state for helix 12. These findings would enhance our understanding of PR structural and functional relationships and would also be useful for future structure and knowledge-based drug discovery.
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Affiliation(s)
- Liangzhen Zheng
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kelin Xia
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
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13
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Zhang R, Wu H, He M, Zhang W, Xu W. Mobility Capillary Electrophoresis-Restrained Modeling Method for Protein Structure Analysis in Mixtures. J Phys Chem B 2019; 123:2335-2341. [PMID: 30807169 DOI: 10.1021/acs.jpcb.9b01148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein stereostructure analysis in mixtures still remains challenging, especially large-scale analysis such as in proteomics. With the capability of measuring the hydrodynamic radius of ions in the liquid phase, mobility capillary electrophoresis (MCE) has been applied to study the structure of peptides. In this study, MCE was extended for protein mixture separation and their corresponding hydrodynamic radius analyses. After ellipsoid approximation, the results obtained by MCE experiments were then used as a restraint in molecular dynamics simulations to predict the most probable structure of each protein. Besides a three-protein mixture, a mixture of disulfide bond reduced insulin was also studied by this MCE-restrained modeling method. The results obtained by this method agree with literature studies, and mass spectrometry experiments were also carried out to confirm our findings.
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Affiliation(s)
- Rongkai Zhang
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
| | - Haimei Wu
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
| | - Muyi He
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
| | - Wenjing Zhang
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
| | - Wei Xu
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
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14
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Abstract
Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by 17O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)-the integral rotational correlation time. Numerous 17O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. This rotational perturbation factor (RPF) has been corroborated by molecular dynamics simulations, which can also reveal the underlying molecular mechanisms. Here, we address several outstanding problems in this area by analyzing an extensive set of molecular dynamics data, including four globular proteins and three water models. The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index. We conclude that the previously observed correlation of the RPF with surface polarity is a secondary effect of the correlation between polarity and confinement. Water rotation interpolates between a perturbed but bulk-like collective mechanism at low confinement and an exchange-mediated orientational randomization (EMOR) mechanism at high confinement. The EMOR process, which accounts for about half of the RPF, was not recognized in previous simulation studies, where only the early part of the TCF was examined. Based on the analysis of the experimentally relevant TCF over its full time course, we compare simulated and measured RPFs, finding a 30% discrepancy attributable to force field imperfections. We also compute the full 17O MRD profile, including the low-frequency dispersion produced by buried water molecules. Computing a local RPF for each hydration shell, we find that the perturbation decays exponentially with a decay "length" of 0.3 shells and that the second and higher shells account for a mere 3% of the total perturbation measured by 17O MRD. The only long-range effect is a weak water alignment in the electric field produced by an electroneutral protein (not screened by counterions), but this effect is negligibly small for 17O MRD. By contrast, we find that the 17O TCF is significantly more sensitive to the important short-range perturbations than the other two TCFs examined here.
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Affiliation(s)
- Filip Persson
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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15
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Abstract
Proteins interact with their aqueous surroundings, thereby modifying the physical properties of the solvent. The extent of this perturbation has been investigated by numerous methods in the past half-century, but a consensus has still not emerged regarding the spatial range of the perturbation. To a large extent, the disparate views found in the current literature can be traced to the lack of a rigorous definition of the perturbation range. Stating that a particular solvent property differs from its bulk value at a certain distance from the protein is not particularly helpful since such findings depend on the sensitivity and precision of the technique used to probe the system. What is needed is a well-defined decay length, an intrinsic property of the protein in a dilute aqueous solution, that specifies the length scale on which a given physical property approaches its bulk-water value. Based on molecular dynamics simulations of four small globular proteins, we present such an analysis of the structural and dynamic properties of the hydrogen-bonded solvent network. The results demonstrate unequivocally that the solvent perturbation is short-ranged, with all investigated properties having exponential decay lengths of less than one hydration shell. The short range of the perturbation is a consequence of the high energy density of bulk water, rendering this solvent highly resistant to structural perturbations. The electric field from the protein, which under certain conditions can be long-ranged, induces a weak alignment of water dipoles, which, however, is merely the linear dielectric response of bulk water and, therefore, should not be thought of as a structural perturbation. By decomposing the first hydration shell into polarity-based subsets, we find that the hydration structure of the nonpolar parts of the protein surface is similar to that of small nonpolar solutes. For all four examined proteins, the mean number of water-water hydrogen bonds in the nonpolar subset is within 1% of the value in bulk water, suggesting that the fragmentation and topography of the nonpolar protein-water interface has evolved to minimize the propensity for protein aggregation by reducing the unfavorable free energy of hydrophobic hydration.
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Affiliation(s)
- Filip Persson
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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16
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Chakravorty A, Jia Z, Peng Y, Tajielyato N, Wang L, Alexov E. Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents. Front Mol Biosci 2018; 5:25. [PMID: 29637074 PMCID: PMC5881404 DOI: 10.3389/fmolb.2018.00025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/05/2018] [Indexed: 12/04/2022] Open
Abstract
Conventional modeling techniques to model macromolecular solvation and its effect on binding in the framework of Poisson-Boltzmann based implicit solvent models make use of a geometrically defined surface to depict the separation of macromolecular interior (low dielectric constant) from the solvent phase (high dielectric constant). Though this simplification saves time and computational resources without significantly compromising the accuracy of free energy calculations, it bypasses some of the key physio-chemical properties of the solute-solvent interface, e.g., the altered flexibility of water molecules and that of side chains at the interface, which results in dielectric properties different from both bulk water and macromolecular interior, respectively. Here we present a Gaussian-based smooth dielectric model, an inhomogeneous dielectric distribution model that mimics the effect of macromolecular flexibility and captures the altered properties of surface bound water molecules. Thus, the model delivers a smooth transition of dielectric properties from the macromolecular interior to the solvent phase, eliminating any unphysical surface separating the two phases. Using various examples of macromolecular binding, we demonstrate its utility and illustrate the comparison with the conventional 2-dielectric model. We also showcase some additional abilities of this model, viz. to account for the effect of electrolytes in the solution and to render the distribution profile of water across a lipid membrane.
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Affiliation(s)
- Arghya Chakravorty
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
| | - Zhe Jia
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
| | - Yunhui Peng
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
| | - Nayere Tajielyato
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
| | - Lisi Wang
- Department of Chemistry, Clemson University, Clemson, SC, United States
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
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17
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Chakravorty A, Jia Z, Li L, Zhao S, Alexov E. Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling. J Chem Theory Comput 2018; 14:1020-1032. [PMID: 29350933 PMCID: PMC9885857 DOI: 10.1021/acs.jctc.7b00756] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Typically, the ensemble average polar component of solvation energy (ΔGpolarsolv) of a macromolecule is computed using molecular dynamics (MD) or Monte Carlo (MC) simulations to generate conformational ensemble and then single/rigid conformation solvation energy calculation is performed on each snapshot. The primary objective of this work is to demonstrate that Poisson-Boltzmann (PB)-based approach using a Gaussian-based smooth dielectric function for macromolecular modeling previously developed by us (Li et al. J. Chem. Theory Comput. 2013, 9 (4), 2126-2136) can reproduce that ensemble average (ΔGpolarsolv) of a protein from a single structure. We show that the Gaussian-based dielectric model reproduces the ensemble average ΔGpolarsolv(⟨ΔGpolarsolv⟩) from an energy-minimized structure of a protein regardless of the minimization environment (structure minimized in vacuo, implicit or explicit waters, or crystal structure); the best case, however, is when it is paired with an in vacuo-minimized structure. In other minimization environments (implicit or explicit waters or crystal structure), the traditional two-dielectric model can still be selected with which the model produces correct solvation energies. Our observations from this work reflect how the ability to appropriately mimic the motion of residues, especially the salt bridge residues, influences a dielectric model's ability to reproduce the ensemble average value of polar solvation free energy from a single in vacuo-minimized structure.
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Affiliation(s)
- Arghya Chakravorty
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Zhe Jia
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Shan Zhao
- Departement of Mathematics, College of Arts and Sciences, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.,Corresponding Author Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.
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18
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Jafari M, Mehrnejad F, Rahimi F, Asghari SM. The Molecular Basis of the Sodium Dodecyl Sulfate Effect on Human Ubiquitin Structure: A Molecular Dynamics Simulation Study. Sci Rep 2018; 8:2150. [PMID: 29391595 PMCID: PMC5794983 DOI: 10.1038/s41598-018-20669-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/16/2018] [Indexed: 01/01/2023] Open
Abstract
To investigate the molecular interactions of sodium dodecyl sulfate (SDS) with human ubiquitin and its unfolding mechanisms, a comparative study was conducted on the interactions of the protein in the presence and absence of SDS at different temperatures using six independent 500 ns atomistic molecular dynamics (MD) simulations. Moreover, the effects of partial atomic charges on SDS aggregation and micellar structures were investigated at high SDS concentrations. The results demonstrated that human ubiquitin retains its native-like structure in the presence of SDS and pure water at 300 K, while the conformation adopts an unfolded state at a high temperature. In addition, it was found that both SDS self-assembly and the conformation of the resulting protein may have a significant effect of reducing the partial atomic charges. The simulations at 370 K provided evidence that the SDS molecules disrupted the first hydration shell and expanded the hydrophobic core of ubiquitin, resulting in complete protein unfolding. According to these results, SDS and temperature are both required to induce a completely unfolded state under ambient conditions. We believe that these findings could be useful in protein folding/unfolding studies and structural biology.
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Affiliation(s)
- Majid Jafari
- Nanobiotechnology Lab, Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561, Tehran, Iran
| | - Faramarz Mehrnejad
- Nanobiotechnology Lab, Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561, Tehran, Iran.
| | - Fereshteh Rahimi
- Nanobiotechnology Lab, Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561, Tehran, Iran
| | - S Mohsen Asghari
- Department of Biology, Faculty of Sciences, University of Guilan, 4193833697, Rasht, Iran
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19
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Sharma S, Biswas P. Hydration water dynamics around a protein surface: a first passage time approach. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:035101. [PMID: 29192889 DOI: 10.1088/1361-648x/aa9eab] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A stochastic noise-driven dynamic model is proposed to study the diffusion of water molecules around a protein surface, under the effect of thermal fluctuations that arise due to the collision of water molecules with the surrounding environment. The underlying dynamics of such a system may be described in the framework of the generalized Langevin equation, where the thermal fluctuations are assumed to be algebraically correlated in time, which governs the non-Markovian behavior of the system. Results of the calculations of mean-square displacement and the velocity autocorrelation function reveal that the hydration water around the protein surface follows subdiffusive dynamics at long times. Analytical expressions for the first passage time distribution, survival probability, mean residence time and mean first passage time of water molecules are derived for different boundary conditions, to analyze hydration water dynamics under the effect of thermally correlated noise. The results depict a unimodal distribution of the first passage time unlike Brownian motion. The survival probability of hydration water follows a stretched exponential decay for both boundary conditions. The mean residence time of the hydration water molecule for different initial positions increases with increase in the complexity/heterogeneity of the surrounding environment for both boundary conditions. The mean first passage time of the water molecule to reach the absorbing/reflecting boundary follows an asymptotic power law with respect to the thickness of the hydration layer, and increases with increase in the complexity/heterogeneity of the environment.
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Affiliation(s)
- Shivangi Sharma
- Department of Chemistry, University of Delhi, Delhi 110007, India
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20
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Biswas R, Bagchi B. Anomalous water dynamics at surfaces and interfaces: synergistic effects of confinement and surface interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:013001. [PMID: 29205175 DOI: 10.1088/1361-648x/aa9b1d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small on a macroscopic scale. Examples include lipid bilayers and reverse micelles as well as biomolecules like proteins, DNA and zeolites, to name a few. While the presence of surfaces and interfaces interrupts the continuous hydrogen bond network of liquid water, confinement on a mesoscopic scale introduces new features. Even when extended on a molecular scale, natural and biological surfaces often have features (like charge, hydrophobicity) that vary on the scale of the molecular diameter of water. As a result, many new and exotic features, which are not seen in the bulk, appear in the dynamics of water close to the surface. These different behaviors bear the signature of both water-surface interactions and of confinement. In other words, the altered properties are the result of the synergistic effects of surface-water interactions and confinement. Ultrafast spectroscopy, theoretical modeling and computer simulations together form powerful synergistic approaches towards an understanding of the properties of confined water in such systems as nanocavities, reverse micelles (RMs), water inside and outside biomolecules like proteins and DNA, and also between two hydrophobic walls. We shall review the experimental results and place them in the context of theory and simulations. For water confined within RMs, we discuss the possible interference effects propagating from opposite surfaces. Similar interference is found to give rise to an effective attractive force between two hydrophobic surfaces immersed and kept fixed at a separation of d, with the force showing an exponential dependence on this distance. For protein and DNA hydration, we shall examine a multitude of timescales that arise from frustration effects due to the inherent heterogeneity of these surfaces. We pay particular attention to the role of orientational correlations and modification of the same due to interaction with the surfaces.
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21
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Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
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22
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Pal S, Chakraborty K, Khatua P, Bandyopadhyay S. Microscopic dynamics of water around unfolded structures of barstar at room temperature. J Chem Phys 2016; 142:055102. [PMID: 25662668 DOI: 10.1063/1.4907007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The breaking of the native structure of a protein and its influences on the dynamic response of the surrounding solvent is an important issue in protein folding. In this work, we have carried out atomistic molecular dynamics simulations to unfold the protein barstar at two different temperatures (400 K and 450 K). The two unfolded forms obtained at such high temperatures are further studied at room temperature to explore the effects of nonuniform unfolding of the protein secondary structures along two different pathways on the microscopic dynamical properties of the surface water molecules. It is demonstrated that though the structural transition of the protein in general results in less restricted water motions around its segments, but there are evidences of formation of new conformational motifs upon unfolding with increasingly confined environment around them, thereby resulting in further restricted water mobility in their hydration layers. Moreover, it is noticed that the effects of nonuniform unfolding of the protein segments on the relaxation times of the protein-water (PW) and the water-water (WW) hydrogen bonds are correlated with hindered hydration water motions. However, the kinetics of breaking and reformation of such hydrogen bonds are found to be influenced differently at the interface. It is observed that while the effects of unfolding on the PW hydrogen bond kinetics seem to be minimum, but the kinetics involving the WW hydrogen bonds around the protein segments exhibit noticeably heterogeneous characteristics. We believe that this is an important observation, which can provide valuable insights on the origin of heterogeneous influence of unfolding of a protein on the microscopic properties of its hydration water.
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Affiliation(s)
- Somedatta Pal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Kaushik Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Prabir Khatua
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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23
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Chatterjee P, Sengupta N. Signatures of protein thermal denaturation and local hydrophobicity in domain specific hydration behavior: a comparative molecular dynamics study. MOLECULAR BIOSYSTEMS 2016; 12:1139-50. [PMID: 26876051 DOI: 10.1039/c6mb00017g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We investigate, using atomistic molecular dynamics simulations, the association of surface hydration accompanying local unfolding in the mesophilic protein Yfh1 under a series of thermal conditions spanning its cold and heat denaturation temperatures. The results are benchmarked against the thermally stable protein, Ubq, and behavior at the maximum stability temperature. Local unfolding in Yfh1, predominantly in the beta sheet regions, is in qualitative agreement with recent solution NMR studies; the corresponding Ubq unfolding is not observed. Interestingly, all domains, except for the beta sheet domains of Yfh1, show increased effective surface hydrophobicity with increase in temperature, as reflected by the density fluctuations of the hydration layer. Velocity autocorrelation functions (VACF) of oxygen atoms of water within the hydration layers and the corresponding vibrational density of states (VDOS) are used to characterize alteration in dynamical behavior accompanying the temperature dependent local unfolding. Enhanced caging effects accompanying transverse oscillations of the water molecules are found to occur with the increase in temperature preferentially for the beta sheet domains of Yfh1. Helical domains of both proteins exhibit similar trends in VDOS with changes in temperature. This work demonstrates the existence of key signatures of the local onset of protein thermal denaturation in solvent dynamical behavior.
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Affiliation(s)
- Prathit Chatterjee
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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24
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Chakraborty K, Bandyopadhyay S. Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules. J Chem Phys 2015; 143:045106. [DOI: 10.1063/1.4927568] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Kaushik Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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25
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Dutta P, Botlani M, Varma S. Water Dynamics at Protein–Protein Interfaces: Molecular Dynamics Study of Virus–Host Receptor Complexes. J Phys Chem B 2014; 118:14795-807. [DOI: 10.1021/jp5089096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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26
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Jose JC, Khatua P, Bansal N, Sengupta N, Bandyopadhyay S. Microscopic Hydration Properties of the Aβ1–42 Peptide Monomer and the Globular Protein Ubiquitin: A Comparative Molecular Dynamics Study. J Phys Chem B 2014; 118:11591-604. [DOI: 10.1021/jp505629q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Jaya C. Jose
- Physical Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune 411008, India
| | - Prabir Khatua
- Molecular
Modeling
Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Nupur Bansal
- Physical Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune 411008, India
| | - Neelanjana Sengupta
- Physical Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune 411008, India
| | - Sanjoy Bandyopadhyay
- Molecular
Modeling
Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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27
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Aniket, Gaul DA, Rickard DL, Needham D. MicroglassificationTM: A Novel Technique for Protein Dehydration. J Pharm Sci 2014; 103:810-20. [DOI: 10.1002/jps.23847] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/11/2013] [Accepted: 12/12/2013] [Indexed: 11/11/2022]
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28
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Sushko O, Dubrovka R, Donnan RS. Terahertz Spectral Domain Computational Analysis of Hydration Shell of Proteins with Increasingly Complex Tertiary Structure. J Phys Chem B 2013; 117:16486-92. [DOI: 10.1021/jp407580y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oleksandr Sushko
- School
of Electronic Engineering
and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Rostyslav Dubrovka
- School
of Electronic Engineering
and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Robert S. Donnan
- School
of Electronic Engineering
and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
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29
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Pal S, Bandyopadhyay S. Effects of protein conformational motions in the native form and non-uniform distribution of electrostatic interaction sites on interfacial water. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.04.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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30
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Pal S, Bandyopadhyay S. Effects of Protein Conformational Flexibilities and Electrostatic Interactions on the Low-Frequency Vibrational Spectrum of Hydration Water. J Phys Chem B 2013; 117:5848-56. [DOI: 10.1021/jp402662v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Somedatta Pal
- Molecular Modeling Laboratory, Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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31
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Pal S, Bandyopadhyay S. Importance of protein conformational motions and electrostatic anchoring sites on the dynamics and hydrogen bond properties of hydration water. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:1162-1173. [PMID: 23289748 DOI: 10.1021/la303959m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The microscopic dynamic properties of water molecules present in the vicinity of a protein are expected to be sensitive to its local conformational motions and the presence of polar and charged groups at the surface capable of anchoring water molecules through hydrogen bonds. In this work, we attempt to understand such sensitivity by performing detailed molecular dynamics simulations of the globular protein barstar solvated in aqueous medium. Our calculations demonstrate that enhanced confinement at the protein surface on freezing its local motions leads to increasingly restricted water mobility with long residence times around the secondary structures. It is found that the inability of the surface water molecules to bind with the protein residues by hydrogen bonds in the absence of protein-water (PW) electrostatic interactions is compensated by enhanced water-water hydrogen bonds around the protein with uniform bulklike behaviors. Importantly, it is further noticed that in contrast to the PW hydrogen bond relaxation time scale, the kinetics of the breaking and formation of such bonds are not affected on freezing the protein's conformational motions.
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Affiliation(s)
- Somedatta Pal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India
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32
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Record MT, Guinn E, Pegram L, Capp M. Introductory lecture: interpreting and predicting Hofmeister salt ion and solute effects on biopolymer and model processes using the solute partitioning model. Faraday Discuss 2013; 160:9-44; discussion 103-20. [PMID: 23795491 PMCID: PMC3694758 DOI: 10.1039/c2fd20128c] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding how Hofmeister salt ions and other solutes interact with proteins, nucleic acids, other biopolymers and water and thereby affect protein and nucleic acid processes as well as model processes (e.g. solubility of model compounds) in aqueous solution is a longstanding goal of biophysical research. Empirical Hofmeister salt and solute "m-values" (derivatives of the observed standard free energy change for a model or biopolymer process with respect to solute or salt concentration m3) are equal to differences in chemical potential derivatives: m-value = delta(dmu2/dm3) = delta mu23, which quantify the preferential interactions of the solute or salt with the surface of the biopolymer or model system (component 2) exposed or buried in the process. Using the solute partitioning model (SPM), we dissect mu23 values for interactions of a solute or Hofmeister salt with a set of model compounds displaying the key functional groups of biopolymers to obtain interaction potentials (called alpha-values) that quantify the interaction of the solute or salt per unit area of each functional group or type of surface. Interpreted using the SPM, these alpha-values provide quantitative information about both the hydration of functional groups and the competitive interaction of water and the solute or salt with functional groups. The analysis corroborates and quantifies previous proposals that the Hofmeister anion and cation series for biopolymer processes are determined by ion-specific, mostly unfavorable interactions with hydrocarbon surfaces; the balance between these unfavorable nonpolar interactions and often-favorable interactions of ions with polar functional groups determine the series null points. The placement of urea and glycine betaine (GB) at opposite ends of the corresponding series of nonelectrolytes results from the favorable interactions of urea, and unfavorable interactions of GB, with many (but not all) biopolymer functional groups. Interaction potentials and local-bulk partition coefficients quantifying the distribution of solutes (e.g. urea, glycine betaine) and Hofmeister salt ions in the vicinity of each functional group make good chemical sense when interpreted in terms of competitive noncovalent interactions. These interaction potentials allow solute and Hofmeister (noncoulombic) salt effects on protein and nucleic acid processes to be interpreted or predicted, and allow the use of solutes and salts as probes of
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Affiliation(s)
- M Thomas Record
- Department of Chemistry, University of Wisconsin, Madison WI 53706, USA
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Deshmukh SA, Sankaranarayanan SKRS, Mancini DC. Vibrational spectra of proximal water in a thermo-sensitive polymer undergoing conformational transition across the lower critical solution temperature. J Phys Chem B 2012; 116:5501-15. [PMID: 22490002 DOI: 10.1021/jp211831x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The vibrational spectrum of water near a thermo-sensitive polymer poly(N-isopropylacrylamide) (PNIPAM) undergoing conformational transition through the lower critical solution temperature (LCST) is calculated using molecular dynamics simulations. The characteristic structural features observed at the atomic scale for these proximal water molecules in a solvated polymer chain while undergoing the conformational transition are strongly correlated to their vibrational densities of states. Comparison of the vibrational spectrum below LCST for the proximal water with the vibrational spectrum obtained for bulk water reveals a significant fraction of the hydrogen bonding between the proximal water molecules and the polymer side groups. Hydrogen-bonded bridges of water molecules are formed between two adjacent and alternate monomers. This network of hydrogen bonding results in formation of locally ordered water molecules at temperatures below the LCST. Analysis of the simulation trajectories confirms the presence of a quasi-stable solvation structure near the PNIPAM. The calculated vibrational spectra for proximal water above the LCST suggest significantly reduced hydrogen bonding with the polymer and indicate a reduction in the structural stability of proximal water around a collapsed polymer chain. Systematic trends in the observed peak intensities and frequency shifts at the low- and high-frequency ends of the spectrum can be correlated with the structural and dynamical changes of water molecules below and above the LCST transition, respectively, for various polymer chain lengths. The simulations reveal that, compared to bulk water, the libration bands are blue shifted and OH stretch bands red shifted for water in proximity to PNIPAM with 30 monomer units below the LCST. The simulations suggest that vibrational spectra can be used as a predictive tool for quantifying atomic-scale structural transitions in solvation of thermo-sensitive polymers such as PNIPAM.
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Affiliation(s)
- Sanket A Deshmukh
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, USA
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Calorimetric and spectroscopic studies of the interactions between insulin and (−)-epigallocatechin-3-gallate. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2012.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Sinha SK, Bandyopadhyay S. Local heterogeneous dynamics of water around lysozyme: a computer simulation study. Phys Chem Chem Phys 2012; 14:899-913. [DOI: 10.1039/c1cp22575h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Jana M, Bandyopadhyay S. Kinetics of hydrogen bonds in aqueous solutions of cyclodextrin and its methyl-substituted forms. J Chem Phys 2011; 134:025103. [PMID: 21241151 DOI: 10.1063/1.3530781] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Molecular dynamics simulations of β-cyclodextrin (BCD) and its two methyl-substituted derivatives, namely, heptakis(2,6-di-O-methyl)-β-cyclodextrin (DIMEB) and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TRIMEB) have been performed in aqueous solutions. Detailed analyses were carried out to investigate the effects of substitution on the kinetics of cyclodextrin-water and water-water hydrogen bonds formed by water present in the hydration layers around these macromolecules as well as those formed by water inside their cavities. It is observed that increased geometrical constraints due to substitution of the OH groups of the glucose rings of the BCD molecule result in rapid establishment of hydrogen bond breaking and reformation equilibria for DIMEB and TRIMEB. This has been found to be the microscopic origin of highly rigid arrangement of water around TRIMEB and inside its cavity, as against water in and around BCD and DIMEB.
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Affiliation(s)
- Madhurima Jana
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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Sinha SK, Bandyopadhyay S. Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules. J Chem Phys 2011; 134:115101. [DOI: 10.1063/1.3560442] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Jana M, Bandyopadhyay S. Microscopic investigation of the hydration properties of cyclodextrin and its substituted forms. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:13084-91. [PMID: 19739659 DOI: 10.1021/la902003y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Substitution of the hydroxyl (OH) groups of cyclodextrins (CDs) by methoxy (OCH(3)) groups is likely to influence the microscopic properties of water inside the cavities of these molecules and in the surrounding hydration layers. We have performed atomistic molecular dynamics (MD) simulations of aqueous solutions of beta-cyclodextrin (BCD) and its two methyl-substituted forms, dimethyl beta-cyclodextrin (DIMEB) and trimethyl beta-cyclodextrin (TRIMEB). The calculations reveal that the translational and rotational motions of water present either in the hydration layers or in the cavities of these macrocyclic molecules are slower than that of pure bulk water. Interestingly, it is noticed that the effect of confinement inside the cavity increases with substitution of the OH groups of the BCD molecule. Most importantly, it is revealed that the time scale of relaxation of the CD-water (CW) and water-water (WW) hydrogen bonds are correlated with the microscopic dynamics of water and their degree of confinement within the cavities of these molecules.
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Affiliation(s)
- Madhurima Jana
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India
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Pieniazek PA, Lin YS, Chowdhary J, Ladanyi BM, Skinner JL. Vibrational Spectroscopy and Dynamics of Water Confined inside Reverse Micelles. J Phys Chem B 2009; 113:15017-28. [DOI: 10.1021/jp906784t] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Piotr A. Pieniazek
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Yu-Shan Lin
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Janamejaya Chowdhary
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Branka M. Ladanyi
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - J. L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
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Sasmal DK, Dey S, Das DK, Bhattacharyya K. Deuterium isotope effect on femtosecond solvation dynamics in methyl β-cyclodextrins. J Chem Phys 2009; 131:044509. [DOI: 10.1063/1.3176020] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Pegram LM, Record MT. Using surface tension data to predict differences in surface and bulk concentrations of nonelectrolytes in water. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2009; 113:2171-2174. [PMID: 19436772 PMCID: PMC2680307 DOI: 10.1021/jp8073305] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Recently, we developed a quantitative interpretation of surface tension increments (STI) of salts, acids, and bases in terms of the solute (or salt ion) partitioning model (SPM). Here, we obtain an analogous SPM-based interpretation of surface tension increments of nonelectrolytes, which yields local-bulk partition coefficients (K(p)) quantifying the accumulation or exclusion of these solutes in the local region near the air-water surface, and the amount of water per unit area of that region (b1σ). Sucrose exhibits the largest positive STI (approximately 1.4 ergs cm(-2) Osm(-1)). Assuming that K(p) = 0 for sucrose (i.e. that it is completely excluded from the surface of water), these STI provide a minimum estimate of b1σ of 0.20 H(2)O/Å(2), or a minimum thickness of the surface region of approximately two layers of water at bulk density. This is the same value as obtained previously from analysis of surface tension and hydrocarbon solubility increments of Na(2)SO(4) and also for the interaction of glycine betaine with anionic carboxylate surface, indicating that this quantity is not a function of the type of solute or surface investigated and therefore that it may represent the molecular thickness of the region. Partition coefficients of other nonelectrolytes investigated range from moderately excluded (e.g urea) to moderately accumulated (e.g. glycerol, ethylene glycol); strongly accumulated surface active solutes (e.g. mono-substituted alcohols) were not included in this analysis. Partition coefficients for many salt ions obtained from STI and hydrocarbon solubility increments fall in a rank order which corresponds to the Hofmeister series for protein folding and protein solubility, indicating a common pattern of accumulation or exclusion of salt ions at the air-water surface and nonpolar surfaces of dissolved hydrocarbons and proteins; no such patterns are observed for nonelectrolytes.
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Affiliation(s)
- Laurel M. Pegram
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - M. Thomas Record
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Lebard DN, Matyushov DV. Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:061901. [PMID: 19256862 DOI: 10.1103/physreve.78.061901] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Indexed: 05/27/2023]
Abstract
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of electrostatic fluctuations, expressed in terms of the reorganization energy of changing the redox state of the protein, is related to the formation of the hydrophobic protein-water interface, allowing large-amplitude collective fluctuations of the water density in the protein's first solvation shell. On top of the monotonic increase of the reorganization energy with increasing temperature, we have observed a spike at approximately 220 K also accompanied by a significant slowing of the exponential collective Stokes shift dynamics. In contrast to the local density fluctuations of the hydration-shell waters, these spikes might be related to the global property of the water solvent crossing the Widom line or undergoing a weak first-order transition.
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Affiliation(s)
- David N Lebard
- Center for Biological Physics, Arizona State University, P.O. Box 871604, Tempe, Arizona 85287-1604, USA
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Pegram LM, Record MT. Quantifying accumulation or exclusion of H +, HO -, and Hofmeister salt ions near interfaces. Chem Phys Lett 2008; 467:1-8. [PMID: 23750042 PMCID: PMC3673785 DOI: 10.1016/j.cplett.2008.10.090] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recently, surface spectroscopies and simulations have begun to characterize the non-uniform distributions of salt ions near macroscopic and molecular surfaces. The thermodynamic consequences of these non-uniform distributions determine the often-large ion-specific effects of Hofmeister salts on a very wide range of processes in water. For uncharged surfaces, where these nonuniform ion distributions are confined to the first few layers of water at the surface, a two-state approximation to the distributions of water and ions, called the salt ion partitioning model (SPM) has both molecular and thermodynamic signiicance. Here, we summarize SPM results quantifying the local accumulation of H+, exclusion of HO-, and range of partitioning behavior of Hofmeister anions and cations near macroscopic and molecular interfaces. These results provide a database to interpret or predict Hofmeister salt effects on aqueous processes in terms of structural information regarding amount and composition of the surface exposed or buried in these processes.
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Affiliation(s)
- L. M. Pegram
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - M. T. Record
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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