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Yang T, Zhang Y, Guo L, Li D, Liu A, Bilal M, Xie C, Yang R, Gu Z, Jiang D, Wang P. Antifreeze Polysaccharides from Wheat Bran: The Structural Characterization and Antifreeze Mechanism. Biomacromolecules 2024; 25:3877-3892. [PMID: 38388358 DOI: 10.1021/acs.biomac.3c00958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Exploring a novel natural cryoprotectant and understanding its antifreeze mechanism allows the rational design of future sustainable antifreeze analogues. In this study, various antifreeze polysaccharides were isolated from wheat bran, and the antifreeze activity was comparatively studied in relation to the molecular structure. The antifreeze mechanism was further revealed based on the interactions of polysaccharides and water molecules through dynamic simulation analysis. The antifreeze polysaccharides showed distinct ice recrystallization inhibition activity, and structural analysis suggested that the polysaccharides were arabinoxylan, featuring a xylan backbone with a majority of Araf and minor fractions of Manp, Galp, and Glcp involved in the side chain. The antifreeze arabinoxylan, characterized by lower molecular weight, less branching, and more flexible conformation, could weaken the hydrogen bonding of the surrounding water molecules more evidently, thus retarding the transformation of water molecules into the ordered ice structure.
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Affiliation(s)
- Tao Yang
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology, and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yining Zhang
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Li Guo
- School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Dandan Li
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, People's Republic of China
| | - Anqi Liu
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Muhammad Bilal
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Chong Xie
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, People's Republic of China
| | - Runqiang Yang
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, People's Republic of China
| | - Zhenxin Gu
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, People's Republic of China
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology, and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, People's Republic of China
| | - Pei Wang
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology, and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, People's Republic of China
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Alfonso T LL, Olmos-Asar JA, Mariscal MM, Avena MJ. Electronic-Level Insight into the Adsorption and Surface Diffusion Kinetics of a Simplified Glyphosate Model on a Goethite Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:11398-11405. [PMID: 37523487 DOI: 10.1021/acs.langmuir.3c01251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
The diffusive processes that occur in minerals involve chemical and physical surface phenomena of great interest that allow for understanding the mobility of different anions of environmental importance. One of them is glyphosate, which is widely used as a pesticide. In this work, we performed Hubbard-corrected density functional theory (DFT + U) calculations to study the adsorption and surface diffusion of methylphosphonic acid (MPA), as a model of glyphosate, on the (010) plane of goethite (GOT), one of the most important Fe(III) minerals in soils and sediments. In particular, the MPA adsorption was studied at the GOT-water interface, finding a strong covalent character in the bond. We also corroborated the occurrence of double proton transfer (MPA to GOT and GOT to GOT). Finally, activation energy barriers were calculated to estimate the half-lives for molecular diffusion, showing that MPA moves almost 3000 times slower than water at the GOT surface.
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Affiliation(s)
- Leslie L Alfonso T
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC-CONICET), X5000HUA Córdoba, Argentina
- Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
| | - Jimena A Olmos-Asar
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC-CONICET), X5000HUA Córdoba, Argentina
| | - Marcelo M Mariscal
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC-CONICET), X5000HUA Córdoba, Argentina
- Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
| | - Marcelo J Avena
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Av. Alem 1253, 8000 Bahía Blanca, Argentina
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Panahandeh N, Mohammadkhani S, Sedighi S, Nejadkarimi S, Ghasemi A. Comparative Effects of Three Bleaching Techniques on Tooth Discoloration Caused by Tea. Front Dent 2023; 20:25. [PMID: 37701654 PMCID: PMC10493118 DOI: 10.18502/fid.v20i25.13343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/24/2022] [Indexed: 09/14/2023] Open
Abstract
Objectives: This study aimed to investigate the impact of three different bleaching protocols on tooth discoloration caused by tea. Materials and Methods: Forty extracted sound premolars were cleaned, disinfected, and their initial color parameters were measured (T1). The teeth were then immersed in boiled tea solution for 24 hours, and their color was measured again (T2). The samples were divided into four groups of 10 teeth each. Group A was treated with an in-office bleaching gel followed by 30 seconds of light curing. Groups B, C, and D were respectively treated with 0.24M oxalic acid followed by bleaching gel, 5.25% sodium hypochlorite followed by bleaching gel, and a combination of 0.24M oxalic acid, 5.25% sodium hypochlorite, and bleaching gel. The color was measured once more after the interventions (T3). Data were analyzed using two-way repeated measures ANOVA, paired sample t-test, and Tukey's test. Results: The mean color change (∆E2) between T2 and T3 was significantly higher in group D compared to group A (P<0.05). However, there was no significant difference in color change between groups A, B, and C. Additionally, there was no significant difference in color change between groups B, C, and D. The groups also showed significant differences in ∆L (P=0.007), with the only significant difference found between groups B and C (P=0.001). Conclusion: The combined use of sodium hypochlorite and oxalic acid followed by in-office bleaching gel is more effective than bleaching alone in correcting tooth discoloration caused by tea. This protocol can further reduce yellow coloration.
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Affiliation(s)
- Narges Panahandeh
- Dental Research Center, Research Institute for Dental Sciences, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | | | - Sogol Nejadkarimi
- Department of Operative Dentistry, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Ghasemi
- Dental Research Center, Research Institute for Dental Sciences, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Peršin Fratnik Z, Plohl O, Kokol V, Fras Zemljič L. Using Different Surface Energy Models to Assess the Interactions between Antiviral Coating Films and phi6 Model Virus. J Funct Biomater 2023; 14:jfb14040232. [PMID: 37103322 PMCID: PMC10144987 DOI: 10.3390/jfb14040232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/04/2023] [Accepted: 04/16/2023] [Indexed: 04/28/2023] Open
Abstract
High molecular weight chitosan (HMWCh), quaternised cellulose nanofibrils (qCNF), and their mixture showed antiviral potential in liquid phase, while this effect decreased when applied to facial masks, as studied in our recent work. To gain more insight into material antiviral activity, spin-coated thin films were prepared from each suspension (HMWCh, qCNF) and their mixture with a 1:1 ratio. To understand their mechanism of action, the interactions between these model films with various polar and nonpolar liquids and bacteriophage phi6 (in liquid phase) as a viral surrogate were studied. Surface free energy (SFE) estimates were used as a tool to evaluate the potential adhesion of different polar liquid phases to these films by contact angle measurements (CA) using the sessile drop method. The Fowkes, Owens-Wendt-Rabel-Kealble (OWRK), Wu, and van Oss-Chaudhury-Good (vOGC) mathematical models were used to estimate surface free energy and its polar and dispersive contributions, as well as the Lewis acid and Lewis base contributions. In addition, the surface tension SFT of liquids was also determined. The adhesion and cohesion forces in wetting processes were also observed. The estimated SFE of spin-coated films varied between mathematical models (26-31 mJ/m2) depending on the polarity of the solvents tested, but the correlation between models clearly indicated a significant dominance of the dispersion components that hinder wettability. The poor wettability was also supported by the fact that the cohesive forces in the liquid phase were stronger than the adhesion to the contact surface. In addition, the dispersive (hydrophobic) component dominated in the phi6 dispersion, and since this was also the case in the spin-coated films, it can be assumed that weak physical van der Waals forces (dispersion forces) and hydrophobic interactions occurred between phi6 and the polysaccharide films, resulting in the virus not being in sufficient contact with the tested material during antiviral testing of the material to be inactivated by the active coatings of the polysaccharides used. Regarding the contact killing mechanism, this is a disadvantage that can be overcome by changing the previous material surface (activation). In this way, HMWCh, qCNF, and their mixture can attach to the material surface with better adhesion, thickness, and different shape and orientation, resulting in a more dominant polar fraction of SFE and thus enabling the interactions within the polar part of phi6 dispersion.
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Affiliation(s)
- Zdenka Peršin Fratnik
- Institute of Engineering Materials and Design, Faculty of Mechanical Engineering, University of Maribor, Smetanova ul. 17, SI-2000 Maribor, Slovenia
| | - Olivija Plohl
- Institute of Engineering Materials and Design, Faculty of Mechanical Engineering, University of Maribor, Smetanova ul. 17, SI-2000 Maribor, Slovenia
| | - Vanja Kokol
- Institute of Engineering Materials and Design, Faculty of Mechanical Engineering, University of Maribor, Smetanova ul. 17, SI-2000 Maribor, Slovenia
| | - Lidija Fras Zemljič
- Institute of Engineering Materials and Design, Faculty of Mechanical Engineering, University of Maribor, Smetanova ul. 17, SI-2000 Maribor, Slovenia
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Titus AR, Madeira PP, Ferreira LA, Belgovskiy AI, Mann EK, Mann JA, Meyer WV, Smart AE, Uversky VN, Zaslavsky BY. Arrangement of Hydrogen Bonds in Aqueous Solutions of Different Globular Proteins. Int J Mol Sci 2022; 23:ijms231911381. [PMID: 36232682 PMCID: PMC9570128 DOI: 10.3390/ijms231911381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/07/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
This work presents the first evidence that dissolved globular proteins change the arrangement of hydrogen bonds in water, with different proteins showing quantitatively different effects. Using ATR-FTIR (attenuated total reflection—Fourier transform infrared) spectroscopic analysis of OH-stretch bands, we obtain quantitative estimates of the relative amounts of the previously reported four subpopulations of water structures coexisting in a variety of aqueous solutions. Where solvatochromic dyes can measure the properties of solutions of non-ionic polymers, the results correlate well with ATR-FTIR measurements. In protein solutions to which solvatochromic dye probes cannot be applied, NMR (nuclear magnetic resonance) spectroscopy was used for the first time to estimate the hydrogen bond donor acidity of water. We found strong correlations between the solvent acidity and arrangement of hydrogen bonds in aqueous solutions for several globular proteins. Even quite similar proteins are found to change water properties in dramatically different ways.
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Affiliation(s)
- Amber R. Titus
- Cleveland Diagnostics, 3615 Superior Ave., Cleveland, OH 44114, USA
| | - Pedro P. Madeira
- Centro de Investigacao em Materiais Ceramicos e Compositos, Department of Chemistry, 3810-193 Aveiro, Portugal
| | | | | | | | - Jay Adin Mann
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, OH 44242, USA
| | | | | | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-974-5816
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Bruce‐Chwatt T, Naidoo KJ. Molecular mechanisms from reaction coordinate graph enabled multidimensional free energies illustrated on water dimer hydrogen bonding. J Comput Chem 2022; 43:1802-1813. [PMID: 36054751 PMCID: PMC9543413 DOI: 10.1002/jcc.26982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/10/2022] [Accepted: 07/22/2022] [Indexed: 11/11/2022]
Abstract
Computing the free energies of molecular mechanisms in multidimensional space relies on combinations of geometrically complex reaction coordinates. We show how a graph theory implementation reduces complexity, and illustrate this on the arrangements of hydrogen bonding of a water dimer. The reaction coordinates and forces are computed using graphs that define the dependencies on the atoms in the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) library. The library can be interfaced with classical molecular dynamics as well as quantum molecular dynamics packages. Multidimensional interdependent reaction coordinates are constructed to produce complex free energy hypersurfaces. The reaction coordinates are graphed from atomic and molecular components to define points, distances, vectors, angles, planes and combinations thereof. The resultant free energy surfaces that are a function of the distance, angles, planes, and so on, can represent molecular mechanisms in reduced dimensions from the component atomic Cartesian coordinate degrees of freedom. The FEARCF library can be interfaced with any molecular package. Here, we demonstrate the link to NWChem to compute a hyperdimensional DFT (aug‐cc‐pVDZ basis set and X3LYP exchange correlation functionals) free energy space of a water dimer. Analysis of the water dimer free energy hypervolume reveals that while the chain and cyclic hydrogen bonding configurations are located in stable minimum energy wells, the bifurcated hydrogen bond configuration is a gateway to instability and dimer dissociation.
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Affiliation(s)
- Tomás Bruce‐Chwatt
- Scientific Computing Research Unit, Department of Chemistry University of Cape Town Cape Town South Africa
| | - Kevin J. Naidoo
- Scientific Computing Research Unit, Department of Chemistry University of Cape Town Cape Town South Africa
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7
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Zuorro A. Water Activity Prediction in Sugar and Polyol Systems Using Theoretical Molecular Descriptors. Int J Mol Sci 2021; 22:11044. [PMID: 34681700 PMCID: PMC8540113 DOI: 10.3390/ijms222011044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/01/2022] Open
Abstract
Water activity is a key factor in the development of pharmaceutical, cosmetic, and food products. In aqueous solutions of nonelectrolytes, the Norrish model provides a simple and effective way to evaluate this quantity. However, it contains a parameter, known as the Norrish constant, that must be estimated from experimental data. In this study, a new strategy is proposed for the prediction of water activity in the absence of experimental information, based on the use of theoretical molecular descriptors for characterizing the effects of a solute. This approach was applied to the evaluation of water activity in the presence of sugars (glucose, fructose, xylose, sucrose) and polyols (sorbitol, xylitol, glycerol, erythritol). The use of two descriptors related to the constitutional and connectivity properties of the solutes was first investigated. Subsequently, a new theoretical descriptor, named the global information index (G), was developed. By using this index, the water activity curves in the binary systems were reconstructed. The positive results obtained support the proposed strategy, as well as the possibility of including, in a single information index, the main molecular features of a solute that determine its effects on water activity.
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Affiliation(s)
- Antonio Zuorro
- Department of Chemical Engineering, Materials and Environment, Sapienza University, 00185 Rome, Italy
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8
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Egorov GI, Makarov DM. Volumetric properties (water + 1,3-dimethylurea) mixture over the temperature range from 274.15 to 333.15 K at the ambient pressure – comparison with other methyl substituted analogues. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Szymaniec-Rutkowska A, Bugajska E, Kasperowicz S, Mieczkowska K, Maciejewska AM, Poznański J. Does the partial molar volume of a solute reflect the free energy of hydrophobic solvation? J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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11
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The Role of Water Homeostasis in Muscle Function and Frailty: A Review. Nutrients 2019; 11:nu11081857. [PMID: 31405072 PMCID: PMC6723611 DOI: 10.3390/nu11081857] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 07/31/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
Water, the main component of the body, is distributed in the extracellular and intracellular compartments. Water exchange between these compartments is mainly governed by osmotic pressure. Extracellular water osmolarity must remain within very narrow limits to be compatible with life. Older adults lose the thirst sensation and the ability to concentrate urine, and this favours increased extracellular osmolarity (hyperosmotic stress). This situation, in turn, leads to cell dehydration, which has severe consequences for the intracellular protein structure and function and, ultimately, results in cell damage. Moreover, the fact that water determines cell volume may act as a metabolic signal, with cell swelling acting as an anabolic signal and cell shrinkage acting as a catabolic signal. Ageing also leads to a progressive loss in muscle mass and strength. Muscle strength is the main determinant of functional capacity, and, in elderly people, depends more on muscle quality than on muscle quantity (or muscle mass). Intracellular water content in lean mass has been related to muscle strength, functional capacity, and frailty risk, and has been proposed as an indicator of muscle quality and cell hydration. This review aims to assess the role of hyperosmotic stress and cell dehydration on muscle function and frailty.
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Liang S, Hall KW, Laaksonen A, Zhang Z, Kusalik PG. Characterizing key features in the formation of ice and gas hydrate systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20180167. [PMID: 30982452 PMCID: PMC6501917 DOI: 10.1098/rsta.2018.0167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 05/16/2023]
Abstract
Crystallization in liquids is critical to a range of important processes occurring in physics, chemistry and life sciences. In this article, we review our efforts towards understanding the crystallization mechanisms, where we focus on theoretical modelling and molecular simulations applied to ice and gas hydrate systems. We discuss the order parameters used to characterize molecular ordering processes and how different order parameters offer different perspectives of the underlying mechanisms of crystallization. With extensive simulations of water and gas hydrate systems, we have revealed unexpected defective structures and demonstrated their important roles in crystallization processes. Nucleation of gas hydrates can in most cases be characterized to take place in a two-step mechanism where the nucleation occurs via intermediate metastable precursors, which gradually reorganizes to a stable crystalline phase. We have examined the potential energy landscapes explored by systems during nucleation, and have shown that these landscapes are rugged and funnel-shaped. These insights provide a new framework for understanding nucleation phenomena that has not been addressed in classical nucleation theory. This article is part of the theme issue 'The physics and chemistry of ice: scaffolding across scales, from the viability of life to the formation of planets'.
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Affiliation(s)
- Shuai Liang
- Key Laboratory of Gas Hydrate, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangdong Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, People's Republic of China
| | - Kyle Wm. Hall
- Department of Chemistry, Temple University, Philadelphia, PA, USA
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- Department of Chemistry-Ångström Laboratory, Uppsala University, 75121 Uppsala, Sweden
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Aleea Grigore Ghica-Voda, 41A, 700487 Iasi, Romania
| | - Zhengcai Zhang
- Department of Chemistry, University of Calgary, Calgary, Canada
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Brotzakis ZF, Bolhuis PG. Unbiased Atomistic Insight into the Mechanisms and Solvent Role for Globular Protein Dimer Dissociation. J Phys Chem B 2019; 123:1883-1895. [PMID: 30714378 PMCID: PMC6581425 DOI: 10.1021/acs.jpcb.8b10005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 01/30/2019] [Indexed: 12/18/2022]
Abstract
Association and dissociation of proteins are fundamental processes in nature. Although simple to understand conceptually, the details of the underlying mechanisms and role of the solvent are poorly understood. Here, we investigate the dissociation of the hydrophilic β-lactoglobulin dimer by employing transition path sampling. Analysis of the sampled path ensembles reveals a variety of mechanisms: (1) a direct aligned dissociation (2) a hopping and rebinding transition followed by unbinding, and (3) a sliding transition before unbinding. Reaction coordinate and transition-state analysis predicts that, besides native contact and neighboring salt-bridge interactions, solvent degrees of freedom play an important role in the dissociation process. Bridging waters, hydrogen-bonded to both proteins, support contacts in the native state and nearby lying transition-state regions, whereas they exhibit faster dynamics in further lying transition-state regions, rendering the proteins more mobile and assisting in rebinding. Analysis of the structure and dynamics of the solvent molecules reveals that the dry native interface induces enhanced populations of both disordered hydration water near hydrophilic residues and tetrahedrally ordered hydration water nearby hydrophobic residues. Although not exhaustive, our sampling of rare unbiased reactive molecular dynamics trajectories enhances the understanding of protein dissociation via complex pathways including (multiple) rebinding events.
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Affiliation(s)
| | - P. G. Bolhuis
- Van’t Hoff Institute
for Molecular Sciences, Universiteit van
Amsterdam, Science Park 904, 1090 GD Amsterdam, The Netherlands
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Brotzakis ZF, Voets IK, Bakker HJ, Bolhuis PG. Water structure and dynamics in the hydration layer of a type III anti-freeze protein. Phys Chem Chem Phys 2018; 20:6996-7006. [PMID: 29468240 DOI: 10.1039/c8cp00170g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on a molecular dynamics study on the relation between the structure and the orientational (and hydrogen bond) dynamics of hydration water around the ocean pout AFP III anti-freeze protein. We find evidence for an increasing tetrahedral structure from the area opposite to the ice binding site (IBS) towards the protein IBS, with the strongest signal of tetrahedral structure around the THR-18 residue of the IBS. The tetrahedral structural parameter mostly positively correlates with increased reorientation decay times. Interestingly, for several key (polar) residues that are not part of the IBS but are in its vicinity, we observe a decrease of the reorientation time with increasing tetrahedral structure. A similar anti-correlation is observed for the hydrogen-bonded water molecules. These effects are enhanced at a lower temperature. We interpret these results in terms of the structure-making and structure-breaking residues. Moreover, we investigate the tetrahedral structure and dynamics of waters at a partially dehydrated IBS, and for the protein adsorbed at the air-water interface. We find that the mutation changes the preferred protein orientation upon adsorption at an air-water interface. These results are in agreement with the water-air Vibration Sum Frequency Generation spectroscopic experiments showing a strongly reduced tetrahedral signal upon mutation at the IBS.
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Affiliation(s)
- Z Faidon Brotzakis
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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15
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Ma L, Cui X, Cai W, Shao X. Understanding the function of water during the gelation of globular proteins by temperature-dependent near infrared spectroscopy. Phys Chem Chem Phys 2018; 20:20132-20140. [PMID: 30027956 DOI: 10.1039/c8cp01431k] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water plays an indispensable role in the gelation of proteins, but its function still remains unclear. In this work, the variation of water species with the structural changes of globular proteins was investigated using temperature-dependent near infrared (NIR) spectroscopy. Ovalbumin (OVA) was used as a model protein, which forms a gel-like structure as the temperature increases through three phases, i.e., phase I (native), phase II (molten globule state), and phase III (gel state). The structural change and the content variation of different water species in the three phases of gelation were analyzed by two-dimensional correlation NIR spectroscopy and Gaussian fitting. A decrease in the water species with two hydrogen bonds (S2) was found and the change follows the same phases as OVA. In the first two phases, the change occurs after those of other water species but in the third phase, the change is faster than that of free water species. The result indicates that in the native and molten globule states, S2 is located in the hydration shell of OVA to maintain the stability of the protein structure, and then in the gel state, high temperature weakens the hydrogen bonding of S2 and leads to the destruction of the hydration shell, making OVA clusters form a gel structure.
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Affiliation(s)
- Li Ma
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China.
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16
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Das Mahanta D, Rana D, Patra A, Mukherjee B, Mitra RK. Heterogeneous structure and solvation dynamics of DME/water binary mixtures: A combined spectroscopic and simulation investigation. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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17
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Haider K, Cruz A, Ramsey S, Gilson MK, Kurtzman T. Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories. J Chem Theory Comput 2018; 14:418-425. [PMID: 29161510 PMCID: PMC5760325 DOI: 10.1021/acs.jctc.7b00592] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.
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Affiliation(s)
- Kamran Haider
- Department of Physics, City College of New York, The City University of New York, 160 Convent Ave, New York, NY 10031
| | - Anthony Cruz
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York, NY 10468
- Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, 365 Fifth Avenue, New York, New York, 10016, United States
| | - Steven Ramsey
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York, NY 10468
- Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York, 365 Fifth Avenue, New York, New York, 10016, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, CA, 92093-0736
| | - Tom Kurtzman
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York, NY 10468
- Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, 365 Fifth Avenue, New York, New York, 10016, United States
- Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York, 365 Fifth Avenue, New York, New York, 10016, United States
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18
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Hofer TS, Wiedemair MJ. Towards a dissociative SPC-like water model II. The impact of Lennard-Jones and Buckingham non-coulombic forces. Phys Chem Chem Phys 2018; 20:28523-28534. [DOI: 10.1039/c8cp04957b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dissociative water potential by Garofalini and coworkers has been re-formulated in the framework of the widely employed Lennard-Jones and Buckingham potentials, enhancing the transferability of the model to third party simulation programs.
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Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Martin J. Wiedemair
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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19
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Abstract
This review focuses on papers published since 2000 on the topic of the properties of solutes in water. More specifically, it evaluates the state of the art of our understanding of the complex relationship between the shape of a hydrophobe and the hydrophobic effect. To highlight this, we present a selection of references covering both empirical and molecular dynamics studies of small (molecular-scale) solutes. These include empirical studies of small molecules, synthetic hosts, crystalline monolayers, and proteins, as well as in silico investigations of entities such as idealized hard and soft spheres, small solutes, hydrophobic plates, artificial concavity, molecular hosts, carbon nanotubes and spheres, and proteins.
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Affiliation(s)
- Matthew B Hillyer
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118;
| | - Bruce C Gibb
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118;
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20
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Duereh A, Sato Y, Smith RL, Inomata H, Pichierri F. Does Synergism in Microscopic Polarity Correlate with Extrema in Macroscopic Properties for Aqueous Mixtures of Dipolar Aprotic Solvents? J Phys Chem B 2017; 121:6033-6041. [DOI: 10.1021/acs.jpcb.7b03446] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Alif Duereh
- Research
Center of Supercritical Fluid Technology, Graduate School of Engineering, Tohoku University, Aramaki Aza Aoba 6-6-11, Aoba-ku, Sendai 980-8579, Japan
| | - Yoshiyuki Sato
- Research
Center of Supercritical Fluid Technology, Graduate School of Engineering, Tohoku University, Aramaki Aza Aoba 6-6-11, Aoba-ku, Sendai 980-8579, Japan
| | - Richard Lee Smith
- Research
Center of Supercritical Fluid Technology, Graduate School of Engineering, Tohoku University, Aramaki Aza Aoba 6-6-11, Aoba-ku, Sendai 980-8579, Japan
- Graduate
School of Environmental Studies, Tohoku University, Aramaki Aza
Aoba 6-6-11, Aoba-ku, Sendai 980-8579, Japan
| | - Hiroshi Inomata
- Research
Center of Supercritical Fluid Technology, Graduate School of Engineering, Tohoku University, Aramaki Aza Aoba 6-6-11, Aoba-ku, Sendai 980-8579, Japan
| | - Fabio Pichierri
- Department
of Applied Chemistry, Graduate School of Engineering, Tohoku University, Aoba-yama
6-6-07, Aoba-ku, Sendai 980-8579, Japan
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21
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Sapir L, Harries D. Revisiting Hydrogen Bond Thermodynamics in Molecular Simulations. J Chem Theory Comput 2017; 13:2851-2857. [DOI: 10.1021/acs.jctc.7b00238] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liel Sapir
- Institute of Chemistry and The Fritz Haber
Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and The Fritz Haber
Research Center, The Hebrew University, Jerusalem 91904, Israel
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22
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Do guanidinium and tetrapropylammonium ions specifically interact with aromatic amino acid side chains? Proc Natl Acad Sci U S A 2017; 114:1003-1008. [PMID: 28096375 DOI: 10.1073/pnas.1618071114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Many ions are known to affect the activity, stability, and structural integrity of proteins. Although this effect can be generally attributed to ion-induced changes in forces that govern protein folding, delineating the underlying mechanism of action still remains challenging because it requires assessment of all relevant interactions, such as ion-protein, ion-water, and ion-ion interactions. Herein, we use two unnatural aromatic amino acids and several spectroscopic techniques to examine whether guanidinium chloride, one of the most commonly used protein denaturants, and tetrapropylammonium chloride can specifically interact with aromatic side chains. Our results show that tetrapropylammonium, but not guanidinium, can preferentially accumulate around aromatic residues and that tetrapropylammonium undergoes a transition at ∼1.3 M to form aggregates. We find that similar to ionic micelles, on one hand, such aggregates can disrupt native hydrophobic interactions, and on the other hand, they can promote α-helix formation in certain peptides.
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23
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Comez L, Paolantoni M, Sassi P, Corezzi S, Morresi A, Fioretto D. Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water. SOFT MATTER 2016; 12:5501-5514. [PMID: 27280176 DOI: 10.1039/c5sm03119b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
When a solute is dissolved in water, their mutual interactions determine the molecular properties of the solute on one hand, and the structure and dynamics of the surrounding water particles (the so-called hydration water) on the other. The very existence of soft matter and its peculiar properties are largely due to the wide variety of possible water-solute interactions. In this context, water is not an inert medium but rather an active component, and hydration water plays a crucial role in determining the structure, stability, dynamics, and function of matter. This review focuses on the collective dynamics of hydration water in terms of retardation with respect to the bulk, and of the number of molecules whose dynamics is perturbed. Since water environments are in a dynamic equilibrium, with molecules continuously exchanging from around the solute towards the bulk and vice versa, we examine the ability of different techniques to measure the water dynamics on the basis of the explored time scales and exchange rates. Special emphasis is given to the collective dynamics probed by extended depolarized light scattering and we discuss whether and to what extent the results obtained in aqueous solutions of small molecules can be extrapolated to the case of large biomacromolecules. In fact, recent experiments performed on solutions of increasing complexity clearly indicate that a reductionist approach is not adequate to describe their collective dynamics. We conclude this review by presenting current ideas that are being developed to describe the dynamics of water interacting with macromolecules.
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Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
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24
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Haider K, Wickstrom L, Ramsey S, Gilson MK, Kurtzman T. Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces. J Phys Chem B 2016; 120:8743-56. [PMID: 27169482 DOI: 10.1021/acs.jpcb.6b01094] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The principles underlying water reorganization around simple nonpolar solutes are well understood and provide the framework for the classical hydrophobic effect, whereby water molecules structure themselves around solutes so that they maintain favorable energetic contacts with both the solute and the other water molecules. However, for certain solute surface topographies, water molecules, due to their geometry and size, are unable to simultaneously maintain favorable energetic contacts with both the surface and neighboring water molecules. In this study, we analyze the solvation of ligand-binding sites for six structurally diverse proteins using hydration site analysis and measures of local water structure, in order to identify surfaces at which water molecules are unable to structure themselves in a way that maintains favorable enthalpy relative to bulk water. These surfaces are characterized by a high degree of enclosure, weak solute-water interactions, and surface constraints that induce unfavorable pair interactions between neighboring water molecules. Additionally, we find that the solvation of charged side chains in an active site generally results in favorable enthalpy but can also lead to pair interactions between neighboring water molecules that are significantly unfavorable relative to bulk water. We find that frustrated local structure can occur not only in apolar and weakly polar pockets, where overall enthalpy tends to be unfavorable, but also in charged pockets, where overall water enthalpy tends to be favorable. The characterization of local water structure in these terms may prove useful for evaluating the displacement of water from diverse protein active-site environments.
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Affiliation(s)
- Kamran Haider
- Department of Chemistry, Lehman College, The City University of New York , 250 Bedford Park Boulevard West, Bronx, New York 10468, United States
| | - Lauren Wickstrom
- Borough of Manhattan Community College, Department of Science, The City University of New York , 199 Chambers Street, New York, New York 10007, United States
| | - Steven Ramsey
- Department of Chemistry, Lehman College, The City University of New York , 250 Bedford Park Boulevard West, Bronx, New York 10468, United States.,Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York , 365 Fifth Avenue, New York, New York 10016, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Tom Kurtzman
- Department of Chemistry, Lehman College, The City University of New York , 250 Bedford Park Boulevard West, Bronx, New York 10468, United States.,Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York , 365 Fifth Avenue, New York, New York 10016, United States.,Ph.D. Program in Chemistry, The Graduate Center of The City University of New York , 365 Fifth Avenue, New York, New York 10016, United States
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25
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Affiliation(s)
- Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907;
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26
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Abstract
On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.
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Affiliation(s)
- Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes , D-66041 Saarbrücken, Germany
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27
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Abstract
Ice binding proteins (IBPs) are produced by various cold-adapted organisms to protect their body tissues against freeze damage. First discovered in Antarctic fish living in shallow waters, IBPs were later found in insects, microorganisms, and plants. Despite great structural diversity, all IBPs adhere to growing ice crystals, which is essential for their extensive repertoire of biological functions. Some IBPs maintain liquid inclusions within ice or inhibit recrystallization of ice, while other types suppress freezing by blocking further ice growth. In contrast, ice nucleating proteins stimulate ice nucleation just below 0 °C. Despite huge commercial interest and major scientific breakthroughs, the precise working mechanism of IBPs has not yet been unraveled. In this review, the authors outline the state-of-the-art in experimental and theoretical IBP research and discuss future scientific challenges. The interaction of IBPs with ice, water and ions is examined, focusing in particular on ice growth inhibition mechanisms.
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28
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Grossutti M, Dutcher JR. Correlation Between Chain Architecture and Hydration Water Structure in Polysaccharides. Biomacromolecules 2016; 17:1198-204. [DOI: 10.1021/acs.biomac.6b00026] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael Grossutti
- Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - John R. Dutcher
- Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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29
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Zhang Q, Hoogenboom R. Polymers with upper critical solution temperature behavior in alcohol/water solvent mixtures. Prog Polym Sci 2015. [DOI: 10.1016/j.progpolymsci.2015.02.003] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Duboué-Dijon E, Laage D. Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin. J Chem Phys 2015; 141:22D529. [PMID: 25494800 DOI: 10.1063/1.4902822] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hydration layer surrounding a protein plays an essential role in its biochemical function and consists of a heterogeneous ensemble of water molecules with different local environments and different dynamics. What determines the degree of dynamical heterogeneity within the hydration shell and how this changes with temperature remains unclear. Here, we combine molecular dynamics simulations and analytic modeling to study the hydration shell structure and dynamics of a typical globular protein, ubiquitin, and of the spruce budworm hyperactive antifreeze protein over the 230-300 K temperature range. Our results show that the average perturbation induced by both proteins on the reorientation dynamics of water remains moderate and changes weakly with temperature. The dynamical heterogeneity arises mostly from the distribution of protein surface topographies and is little affected by temperature. The ice-binding face of the antifreeze protein induces a short-ranged enhancement of water structure and a greater slowdown of water reorientation dynamics than the non-ice-binding faces whose effect is similar to that of ubiquitin. However, the hydration shell of the ice-binding face remains less tetrahedral than the bulk and is not "ice-like". We finally show that the hydrogen bonds between water and the ice-binding threonine residues are particularly strong due to a steric confinement effect, thereby contributing to the strong binding of the antifreeze protein on ice crystals.
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Affiliation(s)
- Elise Duboué-Dijon
- Département de Chimie, École Normale Supérieure-PSL Research University, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
| | - Damien Laage
- Département de Chimie, École Normale Supérieure-PSL Research University, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
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31
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Disalvo E, Pinto O, Martini M, Bouchet A, Hollmann A, Frías M. Functional role of water in membranes updated: A tribute to Träuble. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1552-62. [DOI: 10.1016/j.bbamem.2015.03.031] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 03/20/2015] [Accepted: 03/26/2015] [Indexed: 11/30/2022]
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32
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Duboué-Dijon E, Laage D. Characterization of the Local Structure in Liquid Water by Various Order Parameters. J Phys Chem B 2015; 119:8406-18. [PMID: 26054933 PMCID: PMC4516314 DOI: 10.1021/acs.jpcb.5b02936] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A wide
range of geometric order parameters have been suggested
to characterize the local structure of liquid water and its tetrahedral
arrangement, but their respective merits have remained elusive. Here,
we consider a series of popular order parameters and analyze molecular
dynamics simulations of water, in the bulk and in the hydration shell
of a hydrophobic solute, at 298 and 260 K. We show that these parameters
are weakly correlated and probe different distortions, for example
the angular versus radial disorders. We first combine these complementary
descriptions to analyze the structural rearrangements leading to the
density maximum in liquid water. Our results reveal no sign of a heterogeneous
mixture and show that the density maximum arises from the depletion
in interstitial water molecules upon cooling. In the hydration shell
of the hydrophobic moiety of propanol, the order parameters suggest
that the water local structure is similar to that in the bulk, with
only a very weak depletion in ordered configurations, thus confirming
the absence of any iceberg-type structure. Finally, we show that the
main structural fluctuations that affect water reorientation dynamics
in the bulk are angular distortions, which we explain by the jump
hydrogen-bond exchange mechanism.
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Affiliation(s)
- Elise Duboué-Dijon
- École Normale Supérieure-PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
| | - Damien Laage
- École Normale Supérieure-PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
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33
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Tookmanian EM, Fenlon EE, Brewer SH. Synthesis and Protein Incorporation of Azido-Modified Unnatural Amino Acids. RSC Adv 2014; 5:1274-1281. [PMID: 26478813 PMCID: PMC4603873 DOI: 10.1039/c4ra14244f] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Two new azidophenylalanine residues (3 and 4) have been synthesized and, in combination with 4-azido-L-phenylalanine (1) and 4-azidomethyl-L-phenylalanine (2), form a series of unnatural amino acids (UAAs) containing the azide vibrational reporter at varying distances from the aromatic ring of phenylalanine. These UAAs were designed to probe protein hydration with high spatial resolution by utilizing the large extinction coefficient and environmental sensitivity of the azide asymmetric stretch vibration. The sensitivity of the azide reporters was investigated in solvents that mimic distinct local protein environments. Three of the four azido-modified phenylalanine residues were successfully genetically incorporated into a surface site in superfolder green fluorescent protein (sfGFP) utilizing an engineered, orthogonal aminoacyl-tRNA synthetase in response to an amber codon with high efficiency and fidelity. SDS-PAGE and ESI-Q-TOF mass analysis verified the site-specific incorporation of these UAAs. The observed azide asymmetric stretch in the linear IR spectra of these UAAs incorporated into sfGFP indicated that the azide groups were hydrated in the protein.
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Affiliation(s)
- Elise M. Tookmanian
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003 USA
| | - Edward E. Fenlon
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003 USA
| | - Scott H. Brewer
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003 USA
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34
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Bandyopadhyay D, Mohan S, Ghosh SK, Choudhury N. Molecular Dynamics Simulation of Aqueous Urea Solution: Is Urea a Structure Breaker? J Phys Chem B 2014; 118:11757-68. [DOI: 10.1021/jp505147u] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dibyendu Bandyopadhyay
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Sadhana Mohan
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Swapan K. Ghosh
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Niharendu Choudhury
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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35
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Lascaris E, Hemmati M, Buldyrev SV, Stanley HE, Angell CA. Search for a liquid-liquid critical point in models of silica. J Chem Phys 2014; 140:224502. [DOI: 10.1063/1.4879057] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Nabeel Rashin M, Hemalatha J. Magnetic and ultrasonic studies on stable cobalt ferrite magnetic nanofluid. ULTRASONICS 2014; 54:834-840. [PMID: 24188514 DOI: 10.1016/j.ultras.2013.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 06/02/2023]
Abstract
Stable cobalt ferrite nanofluids of various concentrations have been prepared through co-precipitation method. Structural and morphological studies of nanoparticles are made with the help of X-ray diffraction technique and Transmission Electron Microscope respectively and it is found that the particles exhibit face centered cubic structure with an average size of 14 nm. The magnetic properties of the nanofluids have been analyzed at room temperature which revealed ferromagnetic behavior and also the very low value of coupling constant which ensures the negligible interparticle interaction in the absence of magnetic field. Ultrasonic investigations have been made for the nanofluids at different temperatures and magnetic fields. The temperature effects are explained with the help of open and close-packed water structure. The inter particle interactions of surface modified CoFe2O4 particles and the cluster formation at higher concentrations are realized through the variations in ultrasonic parameters.
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Affiliation(s)
- M Nabeel Rashin
- Advanced Materials Lab, Department of Physics, National Institute of Technology, Tiruchirappalli, Tamilnadu 620 015, India
| | - J Hemalatha
- Advanced Materials Lab, Department of Physics, National Institute of Technology, Tiruchirappalli, Tamilnadu 620 015, India.
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37
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Tripathy J, Mueller JJ, Shepherd NC, Beck WF. Dynamic solvation and coupling of the hydration shell of Zn(II)-substituted cytochrome c in the presence of guanidinium ions. J Phys Chem B 2013; 117:14589-98. [PMID: 24237324 DOI: 10.1021/jp404554t] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The fluorescence Stokes shift (FSS) response of Zn(II)-substituted cytochrome c (ZnCytc) is transformed from a monotonic red-shifting response in water to a bidirectional response with much slower time constants in the presence of low concentrations of guanidinium (Gdm(+)) ions. The FSS response in water observed over the 100 ps to 10 ns range has two exponential components with time constants of 135 ps and 1.6 ns that account for a total shift of 30 cm(-1), about one-half of the solvation reorganization energy. In contrast, in the presence of only 0.25 M Gdm(+), the FSS response initially shifts 21 cm(-1) to the blue with a 820 ps time constant and then shifts 60 cm(-1) back to the red with a 3.5 ns time constant. The effect of Gdm(+) on the FSS response effectively saturates at 1.0 M, well below the 1.75 M midpoint of the two-state unfolding transition. These results establish that the FSS response in ZnCytc includes a significant contribution from the surrounding hydration shell, which assumes a perturbed hydrogen-bonding network owing to the binding of Gdm(+) ions to the protein surface. The blue-shifting part of the FSS response arises from a light-induced conformational change that expands the protein- and solvent-derived cavity around the excited-state Zn(II) porphyrin. This non-polar part of the solvation response is enhanced in the presence of Gdm(+) because the protein/solvent surroundings of the Zn(II) porphyrin are effectively more flexible than in water. The enhanced flexibility in the presence of Gdm(+) increases the amplitudes and accordingly lengthens the correlation time scales for the protein and hydration-shell fluctuations that contribute to the FSS response.
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Affiliation(s)
- Jagnyaseni Tripathy
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
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38
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Kumar A, Venkatesu P. Does the stability of proteins in ionic liquids obey the Hofmeister series? Int J Biol Macromol 2013; 63:244-53. [PMID: 24211268 DOI: 10.1016/j.ijbiomac.2013.10.031] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 10/23/2013] [Accepted: 10/24/2013] [Indexed: 11/27/2022]
Abstract
Understanding the behavior of Hofmeister anions of ionic liquids (ILs) on protein stability helps to shed light on how the anions interact with proteins in aqueous solution and is a long standing object for chemistry and biochemistry. Ions effects play a major role in understanding the physicochemical and biological phenomenon that undertakes the protein folding/unfolding and refolding process. Despite the generality of these effects, our understanding of ions at the molecular-level is still limited. This review offers a tour through past successful investigations and presents a challenge in current research in the field to reassess the possibilities of ions and to apply new strategies. This review highlights on the stability behavior of the proteins and also comparisons of our past research work in the Hofmeister series of ILs. Furthermore, we specifically focus on the critical discussion on the recent findings with existing results and their implications, along with our understanding of the Hofmeister series of anions of ILs on biomolecular stability. A detailed examination of the difference between selective proteins can provide a better understanding of the molecular mechanism of protein folding/unfolding in the presence of the Hofmeister series of ions of ILs.
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Affiliation(s)
- Awanish Kumar
- Department of Chemistry, University of Delhi, Delhi 110 007, India
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39
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Ahmed M, Singh AK, Mondal JA, Sarkar SK. Water in the Hydration Shell of Halide Ions Has Significantly Reduced Fermi Resonance and Moderately Enhanced Raman Cross Section in the OH Stretch Regions. J Phys Chem B 2013; 117:9728-33. [DOI: 10.1021/jp403618x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mohammed Ahmed
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - Ajay K. Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - Jahur A. Mondal
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - Sisir K. Sarkar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
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40
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Carr JK, Buchanan LE, Schmidt JR, Zanni MT, Skinner JL. Structure and dynamics of urea/water mixtures investigated by vibrational spectroscopy and molecular dynamics simulation. J Phys Chem B 2013; 117:13291-300. [PMID: 23841646 DOI: 10.1021/jp4037217] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Urea/water is an archetypical "biological" mixture and is especially well-known for its relevance to protein thermodynamics as urea acts as a protein denaturant at high concentration. This behavior has given rise to an extended debate concerning urea's influence on water structure. On the basis of a variety of methods and of definitions of the water structure, urea has been variously described as a structure-breaker, a structure-maker, or as remarkably neutral toward water. Because of its sensitivity to microscopic structure and dynamics, vibrational spectroscopy can help resolve these debates. We report experimental and theoretical spectroscopic results for the OD stretch of HOD/H2O/urea mixtures (linear IR, 2DIR, and pump-probe anisotropy decay) and for the CO stretch of urea-D4/D2O mixtures (linear IR only). Theoretical results are obtained using existing approaches for water and a modification of a frequency map developed for acetamide. All absorption spectra are remarkably insensitive to urea concentration, consistent with the idea that urea only very weakly perturbs the water structure. Both this work and experiments by Rezus and Bakker, however, show that water's rotational dynamics are slowed down by urea. Analysis of the simulations casts doubt on the suggestion that urea immobilizes particular doubly hydrogen bonded water molecules.
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Affiliation(s)
- J K Carr
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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41
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Gruenbaum SM, Tainter CJ, Shi L, Ni Y, Skinner JL. Robustness of Frequency, Transition Dipole, and Coupling Maps for Water Vibrational Spectroscopy. J Chem Theory Comput 2013; 9:3109-17. [DOI: 10.1021/ct400292q] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S. M. Gruenbaum
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - C. J. Tainter
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - L. Shi
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - Y. Ni
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - J. L. Skinner
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
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42
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Disalvo EA, Frias MA. Water state and carbonyl distribution populations in confined regions of lipid bilayers observed by FTIR spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:6969-6974. [PMID: 23293989 DOI: 10.1021/la304390r] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
It has been suggested that water in confined regions presents different properties than bulk water, mainly because of the changes in water population species that may be induced by the adjacent walls of different polarities in terms of hydrogen bond formation. In this context, it would be expected that lipids in the gel and the fluid states should offer different templates for water organization. The presence of water pockets or defects in lipid bilayers has been proposed to explain the insertion of charged and polar peptides and amino acids in membranes. In this work, we provide direct evidence by means of FTIR spectroscopy that water band profiles are changed whether lipids are in the solid state, in the gel state after heating and cooling across the phase transition, or in the fluid state. The different bands found in each case were assigned to different H-bonded water populations in agreement with the exposure of carbonyl groups.
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Affiliation(s)
- E A Disalvo
- Laboratory of Biointerphases and Biomimetics Systems, CITSE (Universidad Nacional de Santiago del Estero, and CONICET), Santiago del Estero, Argentina.
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43
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Wu P, Chaudret R, Hu X, Yang W. Noncovalent Interaction Analysis in Fluctuating Environments. J Chem Theory Comput 2013; 9:2226-2234. [PMID: 23894230 DOI: 10.1021/ct4001087] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions play a central role in many chemical and biological systems. In a previous study, Johnson et al developed a NonCovalent Interaction (NCI) index to characterize and visualize different types of weak interactions. To apply the NCI analysis to fluctuating environments as in solution phase, we here develop a new Averaged NonCovalent Interaction (i.e., aNCI) index along with a fluctuation index to characterize magnitude of interactions and fluctuations. We applied aNCI for various systems including solute-solvent and ligand-protein noncovalent interactions. For water and benzene molecules in aqueous solution, solvation structures and the specific hydrogen bond patterns were visualized clearly. For the Cl-+CH3Cl SN2 reaction in aqueous solution, charge reorganization influences over solvation structure along SN2 reaction were revealed. For ligand-protein systems, aNCI can recover several key fluctuating hydrogen bond patterns that have potential applications for drug design. Therefore, aNCI, as a complementary approach to the original NCI method, can extract and visualize noncovalent interactions from thermal noise in fluctuating environments.
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Affiliation(s)
- Pan Wu
- Department of Chemistry, Duke University, Durham, NC 27708
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44
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Disalvo EA, Bouchet AM, Frias MA. Connected and isolated CH2 populations in acyl chains and its relation to pockets of confined water in lipid membranes as observed by FTIR spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1683-9. [PMID: 23500348 DOI: 10.1016/j.bbamem.2013.02.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 01/15/2013] [Accepted: 02/13/2013] [Indexed: 11/18/2022]
Abstract
Analysis of the band corresponding to the frequency of vibrational symmetric stretching mode of methylene groups in the lipid acyl chains and the bands of water below and above the phase transition of different lipids by Fourier transform infrared spectroscopy gives strong support to the formation of confined water pockets in between the lipid acyl chains. Our measures and analysis consolidate the mechanism early proposed by Traüble, in the sense that water is present in kinks formed by trans-gauche isomers along the hydrocarbon tails. The formation of these regions depends on the acyl lipid composition, which determines the presence of different populations of water species, characterized by its degree of H bond coordination in fluid saturated or unsaturated lipids. The free energy excess due to the reinforcement of the water structure along few water molecules in the adjacencies of exposed membrane residues near the phase transition is a reasonable base to explain the insertion and translocation of polar peptides and amino acid residues through the biomembrane on thermodynamic and structural grounds.
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Affiliation(s)
- E A Disalvo
- Universidad Nacional de Santiago del Estero, Santiago del Estero, Argentina.
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Abstract
Linear solvation theories are well established to describe electrostatic hydration of small solutes when the hydration free energy is dominated by the electrostatic free energy of the solute multipole. In contrast, hydration of nanometer solutes is driven by surface hydration. We address the question of whether the linear-response thermodynamics established for small multipolar solutes applies to surface hydration. To this end, molecular dynamics simulations are carried out on a model C180 solute that carries no global multipole, but the surface of which is decorated with radially pointing dipoles. Linear response is dramatically violated in this case. Further, two crossovers in the solvation thermodynamics are discovered as the surface polarity is increased. Both transformations produce strongly nonlinear solvation response. The second, more collective, crossover leads to a dramatic slowing down of the interfacial dynamics, reaching the time-scales of nanoseconds. Our picture offers the possibility of flipping water domains at interfaces of nanoparticles and biomolecules.
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Affiliation(s)
- Allan D Friesen
- Center for Biological Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
| | - Dmitry V Matyushov
- Center for Biological Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
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46
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Nabeel Rashin M, Hemalatha J. Magnetic and ultrasonic investigations on magnetite nanofluids. ULTRASONICS 2012; 52:1024-1029. [PMID: 22939116 DOI: 10.1016/j.ultras.2012.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 07/17/2012] [Accepted: 08/02/2012] [Indexed: 06/01/2023]
Abstract
Magnetite nanofluids of various concentrations have been prepared through co-precipitation method. The structural and magnetic properties of the magnetic nanofluids have been analyzed which respectively revealed their face centered cubic crystal structure and super paramagnetic behavior. Ultrasonic investigations have been made for the nanofluids at different temperatures and magnetic fields. Open- and close-packed water structure is considered to explain the temperature effects. The inter particle interactions of surface modified nanomagnetite particle and the cluster formation are realized through the variations in ultrasonic parameters.
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Affiliation(s)
- M Nabeel Rashin
- Advanced Materials Lab, Department of Physics, National Institute of Technology, Tiruchirappalli, Tamilnadu 620 015, India
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47
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Wang S, Tu Y, Wan R, Fang H. Evaporation of Tiny Water Aggregation on Solid Surfaces with Different Wetting Properties. J Phys Chem B 2012; 116:13863-7. [DOI: 10.1021/jp302142s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Shen Wang
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, P.O.
Box 800-204, Shanghai, 201800, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100080,
China
| | - Yusong Tu
- Institute of Systems
Biology, Shanghai University, Shanghai,
200444, China
| | - Rongzheng Wan
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, P.O.
Box 800-204, Shanghai, 201800, China
| | - Haiping Fang
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, P.O.
Box 800-204, Shanghai, 201800, China
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48
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Pazos IM, Gai F. Solute's perspective on how trimethylamine oxide, urea, and guanidine hydrochloride affect water's hydrogen bonding ability. J Phys Chem B 2012; 116:12473-8. [PMID: 22998405 PMCID: PMC3475735 DOI: 10.1021/jp307414s] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
While the thermodynamic effects of trimethylamine oxide (TMAO), urea, and guanidine hydrochloride (GdnHCl) on protein stability are well understood, the underlying mechanisms of action are less well characterized and, in some cases, even under debate. Herein, we employ the stretching vibration of two infrared (IR) reporters, i.e., nitrile (C≡N) and carbonyl (C═O), to directly probe how these cosolvents mediate the ability of water to form hydrogen bonds with the solute of interest, e.g., a peptide. Our results show that these three agents, despite having different effects on protein stability, all act to decrease the strength of the hydrogen bonds formed between water and the infrared probe. While the behavior of TMAO appears to be consistent with its protein-protecting ability, those of urea and GdnHCl are inconsistent with their role as protein denaturants. The latter is of particular interest as it provides strong evidence indicating that although urea and GdnHCl can perturb the hydrogen-bonding property of water their protein-denaturing ability does not arise from a simple indirect mechanism.
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Affiliation(s)
- Ileana M. Pazos
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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Brewer SH, Tang Y, Vu DM, Gnanakaran S, Raleigh DP, Dyer RB. Temperature dependence of water interactions with the amide carbonyls of α-helices. Biochemistry 2012; 51:5293-9. [PMID: 22680405 DOI: 10.1021/bi3006434] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydration is a key determinant of the folding, dynamics, and function of proteins. In this study, temperature-dependent Fourier transform infrared (FTIR) spectroscopy combined with singular value decomposition (SVD) and global fitting were used to investigate both the interaction of water with α-helical proteins and the cooperative thermal unfolding of these proteins. This methodology has been applied to an isolated α-helix (Fs peptide) and to globular α-helical proteins including the helical subdomain and full-length villin headpiece (HP36 and HP67). The results suggest a unique IR signature for the interaction of water with the helical amide carbonyl groups of the peptide backbone. The IR spectra indicate a weakening of the net hydrogen bond strength of water to the backbone carbonyls with increasing temperature. This weakening of the backbone solvation occurs as a discrete transition near the maximum of the temperature-dependent hydrophobic effect, not a continuous change with increasing temperature. Possible molecular origins of this effect are discussed with respect to previous molecular dynamics simulations of the temperature-dependent solvation of the helix backbone.
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Affiliation(s)
- Scott H Brewer
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604-3003, USA
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50
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King JT, Arthur EJ, Brooks CL, Kubarych KJ. Site-specific hydration dynamics of globular proteins and the role of constrained water in solvent exchange with amphiphilic cosolvents. J Phys Chem B 2012; 116:5604-11. [PMID: 22530969 DOI: 10.1021/jp300835k] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thermodynamic driving forces for protein folding, association, and function are often determined by protein-water interactions. With a novel covalently bound labeling approach, we have used sensitive vibrational probes, site-selectively conjugated to two lysozyme variants-in conjunction with ultrafast two-dimensional infrared (2D-IR) spectroscopy-to investigate directly the protein-water interface. By probing alternatively a topologically flat, rigid domain and a flexible domain, we find direct experimental evidence for spatially heterogeneous hydration dynamics. The hydration environment around globular proteins can vary from exhibiting bulk-like hydration dynamics to dynamically constrained water, which results from stifled hydrogen bond switching dynamics near extended hydrophobic surfaces. Furthermore, we leverage preferential solvation exchange to demonstrate that the liberation of dynamically constrained water is a sufficient driving force for protein-surface association reactions. These results provide an intuitive picture of the dynamic aspects of hydrophobic hydration of proteins, illustrating an essential function of water in biological processes.
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Affiliation(s)
- John T King
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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