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Bianco V, Franzese G, Coluzza I. In Silico Evidence That Protein Unfolding is a Precursor of Protein Aggregation. Chemphyschem 2020; 21:377-384. [DOI: 10.1002/cphc.201900904] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/01/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Valentino Bianco
- Faculty of Chemistry, Chemical Physics Department, Universidad Complutense de Madrid, Plaza de las Ciencias Ciudad Universitaria Madrid 28040 Spain
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària-Departament de Física de la Matèria Condensada, Facultat de Física & Institute of Nanoscience and Nanotechnology (IN2UB) Universitat de Barcelona Martí i Franquès 1 08028 Barcelona Spain
| | - Ivan Coluzza
- CIC biomaGUNE Paseo Miramon 182 20014 San Sebastian Spain
- IKERBASQUE, Basque Foundation for Science 48013 Bilbao Spain
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2
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Bianco V, Pagès-Gelabert N, Coluzza I, Franzese G. How the stability of a folded protein depends on interfacial water properties and residue-residue interactions. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.08.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wan R, Wang C, Lei X, Zhou G, Fang H. Enhancement of Water Evaporation on Solid Surfaces with Nanoscale Hydrophobic-Hydrophilic Patterns. PHYSICAL REVIEW LETTERS 2015; 115:195901. [PMID: 26588399 DOI: 10.1103/physrevlett.115.195901] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 05/13/2023]
Abstract
Using molecular dynamics simulations, we show that the evaporation of nanoscale water on hydrophobic-hydrophilic patterned surfaces is unexpectedly faster than that on any surfaces with uniform wettability. The key to this phenomenon is that, on the patterned surface, the evaporation rate from the hydrophilic region only slightly decreases due to the correspondingly increased water thickness; meanwhile, a considerable number of water molecules evaporate from the hydrophobic region despite the lack of water film. Most of the evaporated water from the hydrophobic region originates from the hydrophilic region by diffusing across the contact lines. Further analysis shows that the evaporation rate from the hydrophobic region is approximately proportional to the total length of the contact lines.
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Affiliation(s)
- Rongzheng Wan
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
| | - Chunlei Wang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
| | - Xiaoling Lei
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
| | - Guoquan Zhou
- School of Sciences, Zhejiang A & F University, Lin'an 311300, P. R. China
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
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Furlan AP, Fiore CE, Barbosa MC. Influence of disordered porous media on the anomalous properties of a simple water model. Phys Rev E 2015; 92:032404. [PMID: 26465479 DOI: 10.1103/physreve.92.032404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 11/06/2022]
Abstract
The thermodynamic, dynamic, and structural behavior of a water-like system confined in a matrix is analyzed for increasing confining geometries. The liquid is modeled by a two-dimensional associating lattice gas model that exhibits density and diffusion anomalies, similar to the anomalies present in liquid water. The matrix is a triangular lattice in which fixed obstacles impose restrictions to the occupation of the particles. We show that obstacles shorten all lines, including the phase coexistence, the critical and the anomalous lines. The inclusion of a very dense matrix not only suppresses the anomalies but also the liquid-liquid critical point.
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Affiliation(s)
- A P Furlan
- Instituto de Física, Univeridade Federal do Rio Grande do Sul, Caixa Postal 15051, 91501-570, Porto Alegre, RS, Brazil
| | - Carlos E Fiore
- Instituto de Física, Universidade de São Paulo, Caixa Postal 19044, 81531 São Paulo, SP, Brazil
| | - M C Barbosa
- Instituto de Física, Univeridade Federal do Rio Grande do Sul, Caixa Postal 15051, 91501-570, Porto Alegre, RS, Brazil
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Bianco V, Franzese G. Contribution of Water to Pressure and Cold Denaturation of Proteins. PHYSICAL REVIEW LETTERS 2015; 115:108101. [PMID: 26382703 DOI: 10.1103/physrevlett.115.108101] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 05/28/2023]
Abstract
The mechanisms of cold and pressure denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here, we study several cases of proteins, with or without a unique native state, with or without hydrophilic residues, by means of a coarse-grain protein model in explicit solvent. We show, using Monte Carlo simulations, that taking into account how water at the protein interface changes its hydrogen bond properties and its density fluctuations is enough to predict protein stability regions with elliptic shapes in the temperature-pressure plane, consistent with previous theories. Our results clearly identify the different mechanisms with which water participates to denaturation and open the perspective to develop advanced computational design tools for protein engineering.
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Affiliation(s)
- Valentino Bianco
- Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Giancarlo Franzese
- Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
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6
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Krott LB, Bordin JR, Barbosa MC. New Structural Anomaly Induced by Nanoconfinement. J Phys Chem B 2014; 119:291-300. [DOI: 10.1021/jp510561t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Leandro B. Krott
- Instituto
de Física, Universidade Federal do Rio Grande do Sul, Caixa
Postal 15051, CEP 91501-970, Porto Alegre, RS Brazil
| | - José Rafael Bordin
- Campus
Caçapava do Sul, Universidade Federal do Pampa, Av. Pedro Anunciação,
s/n, CEP 96570-000, Caçapava do Sul, RS Brazil
| | - Marcia C. Barbosa
- Instituto
de Física, Universidade Federal do Rio Grande do Sul, Caixa
Postal 15051, CEP 91501-970, Porto Alegre, RS Brazil
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Tomkins J, Hanna G. Signatures of nanoconfinement on the linear and nonlinear vibrational spectroscopy of a model hydrogen-bonded complex dissolved in a polar solvent. J Phys Chem B 2013; 117:13619-30. [PMID: 24079369 DOI: 10.1021/jp407469f] [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
The one-dimensional IR (1D-IR) absorption and IR pump-probe spectra of a hydrogen stretch in a model hydrogen-bonded complex dissolved in a polar solvent confined in spherical hydrophobic cavities of different sizes were simulated using ground-state mixed quantum-classical dynamics. Due to a thorough analysis of key properties of the complex and solvent from equilibrium trajectory data, we were able to gain insight into the microscopic details underlying the spectra. Both the 1D-IR and IR pump-probe spectra manifested the effects of confinement on the relative stabilities of the covalent and ionic forms of the complex through pronounced changes in their peak intensities and numbers. However, in contrast to the 1D-IR spectra, the time-resolved pump-probe spectra were found to be uniquely sensitive to the changes in the molecular dynamics as the cavity size is varied. In particular, it was found that the variations in the time evolutions of the peak intensities in the pump-probe spectra reflect the differences in the solvation dynamics associated with the various forms of the complex in different locations within the cavities. The ability to detect these differences underscores the advantage of using pump-probe spectroscopy for studying nanoconfined systems.
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Affiliation(s)
- Joseph Tomkins
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
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Kesselring TA, Lascaris E, Franzese G, Buldyrev SV, Herrmann HJ, Stanley HE. Finite-size scaling investigation of the liquid-liquid critical point in ST2 water and its stability with respect to crystallization. J Chem Phys 2013; 138:244506. [DOI: 10.1063/1.4808355] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Corradini D, Su Z, Stanley HE, Gallo P. A molecular dynamics study of the equation of state and the structure of supercooled aqueous solutions of methanol. J Chem Phys 2013; 137:184503. [PMID: 23163379 DOI: 10.1063/1.4767060] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We perform molecular dynamics computer simulations in order to study the equation of state and the structure of supercooled aqueous solutions of methanol at methanol mole fractions x(m) = 0.05 and x(m) = 0.10. We model the solvent using the TIP4P/2005 potential and the methanol using the OPLS-AA force field. We find that for x(m) = 0.05 the behavior of the equation of state, studied in the P - T and P - ρ planes, is consistent with the presence of a liquid-liquid phase transition, reminiscent of that previously found for x(m) = 0. We estimate the position of the liquid-liquid critical point to be at T = 193 K, P = 96 MPa, and ρ = 1.003 g/cm(3). When the methanol mole fraction is doubled to x(m) = 0.10 no liquid-liquid transition is observed, indicating its possible disappearance at this concentration. We also study the water-water and water-methanol structure in the two solutions. We find that down to low temperature methanol can be incorporated into the water structure for both x(m) = 0.05 and x(m) = 0.10.
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Affiliation(s)
- Dario Corradini
- Center for Polymer Studies and Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA.
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Krott LB, Barbosa MC. Anomalies in a waterlike model confined between plates. J Chem Phys 2013; 138:084505. [DOI: 10.1063/1.4792639] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Mazza MG, Stokely K, Stanley HE, Franzese G. Effect of pressure on the anomalous response functions of a confined water monolayer at low temperature. J Chem Phys 2012. [DOI: 10.1063/1.4767355] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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