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Abstract
Terahertz time-domain spectroscopy (THz-TDS) is a non-invasive, non-contact and label-free technique for biological and chemical sensing as THz-spectra are less energetic and lie in the characteristic vibration frequency regime of proteins and DNA molecules. However, THz-TDS is less sensitive for the detection of micro-organisms of size equal to or less than λ/100 (where, λ is the wavelength of the incident THz wave), and molecules in extremely low concentration solutions (like, a few femtomolar). After successful high-throughput fabrication of nanostructures, nanoantennas were found to be indispensable in enhancing the sensitivity of conventional THz-TDS. These nanostructures lead to strong THz field enhancement when in resonance with the absorption spectrum of absorptive molecules, causing significant changes in the magnitude of the transmission spectrum, therefore, enhancing the sensitivity and allowing the detection of molecules and biomaterials in extremely low concentration solutions. Herein, we review the recent developments in ultra-sensitive and selective nanogap biosensors. We have also provided an in-depth review of various high-throughput nanofabrication techniques. We also discussed the physics behind the field enhancements in the sub-skin depth as well as sub-nanometer sized nanogaps. We introduce finite-difference time-domain (FDTD) and molecular dynamics (MD) simulation tools to study THz biomolecular interactions. Finally, we provide a comprehensive account of nanoantenna enhanced sensing of viruses (like, H1N1) and biomolecules such as artificial sweeteners which are addictive and carcinogenic.
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Affiliation(s)
- Subham Adak
- Department of Physics, Birla Institute of Technology, Mesra, Ranchi - 835215, Jharkhand, India.
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2
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Mohanta D, Jana M. Effects of ethanol on the secondary structure specific hydration properties of Chymotrypsin Inhibitor 2 in its folded and unfolded forms. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1496246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Dayanidhi Mohanta
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, India
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3
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Gavrilov Y, Leuchter JD, Levy Y. On the coupling between the dynamics of protein and water. Phys Chem Chem Phys 2017; 19:8243-8257. [DOI: 10.1039/c6cp07669f] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The solvation entropy of flexible protein regions is higher than that of rigid regions and contributes differently to the overall thermodynamic stability.
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Affiliation(s)
- Yulian Gavrilov
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Jessica D. Leuchter
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yaakov Levy
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
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4
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Jose JC, Khatua P, Bansal N, Sengupta N, Bandyopadhyay S. Microscopic Hydration Properties of the Aβ1–42 Peptide Monomer and the Globular Protein Ubiquitin: A Comparative Molecular Dynamics Study. J Phys Chem B 2014; 118:11591-604. [DOI: 10.1021/jp505629q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Jaya C. Jose
- Physical Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune 411008, India
| | - Prabir Khatua
- Molecular
Modeling
Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Nupur Bansal
- Physical Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune 411008, India
| | - Neelanjana Sengupta
- Physical Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune 411008, India
| | - Sanjoy Bandyopadhyay
- Molecular
Modeling
Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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5
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Pal S, Bandyopadhyay S. Thermal unfolding of barstar and the properties of interfacial water around the unfolded forms. J Chem Phys 2013; 139:235101. [DOI: 10.1063/1.4844255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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6
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Sushko O, Dubrovka R, Donnan RS. Terahertz Spectral Domain Computational Analysis of Hydration Shell of Proteins with Increasingly Complex Tertiary Structure. J Phys Chem B 2013; 117:16486-92. [DOI: 10.1021/jp407580y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oleksandr Sushko
- School
of Electronic Engineering
and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Rostyslav Dubrovka
- School
of Electronic Engineering
and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Robert S. Donnan
- School
of Electronic Engineering
and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
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7
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Heyden M, Havenith M. Combining THz spectroscopy and MD simulations to study protein-hydration coupling. Methods 2010; 52:74-83. [PMID: 20685393 DOI: 10.1016/j.ymeth.2010.05.007] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 05/17/2010] [Accepted: 05/20/2010] [Indexed: 10/19/2022] Open
Abstract
THz spectroscopy is combined with MD simulations to study the dynamical properties of water in the solvation shell of proteins. The solvation dynamics is found to be influenced on length-scales of several hydration layers which is significantly more than what is found for static properties. Our experiments show that the properties of this dynamical solvation shell depend on the folding state of the protein. Kinetic THz absorption studies allow us to observe the formation of the dynamical solvation shell of the native protein upon folding. The experimental results can be reproduced using MD simulations which helps to develop a molecular understanding in terms of retardation of water dynamics.
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Affiliation(s)
- Matthias Heyden
- Physikalische Chemie II, Ruhr-Universität Bochum, 44780 Bochum, Germany
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8
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Agarwal M, Kushwaha HR, Chakravarty C. Local order, energy, and mobility of water molecules in the hydration shell of small peptides. J Phys Chem B 2010; 114:651-9. [PMID: 19863091 DOI: 10.1021/jp909090u] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The extent to which the presence of a biomolecular solute modifies the local energetics of water molecules, as measured by the tagged molecule potential energy (TPE), is examined using molecular dynamics simulations of the beta-hairpin of 2GB1 and the alpha-helix of deca-alanine in water. The CHARMM22 force field, in conjunction with the TIP3P solvent water model, is used for the peptides, with simulations of TIP3P and SPC/E water used as benchmarks for the behavior of bulk solvent. TIP3P water is shown to have significantly lower local tetrahedral order and higher binding energy than SPC/E at the same state point. The TIP3P and SPC/E water models show very similar dynamical correlations in the TPE fluctuations on frequency scales greater than 0.1 cm(-1). In addition, the two models show the same linear correlation between mean tetrahedral order and binding energy, suggesting that the relationship between choice of water models and simulated hydration behavior may involve a complex interplay of static and dynamic factors. The introduction of a peptide in water modifies the local TPE of water molecules as a function of distance from the biomolecular interface. There is an oscillatory variation in the TPE with distance from the peptide for water molecules lying outside a 3 A radius and extending to at least 10 A. These variations are of the order of 2-5% of the bulk TPE value and are anticorrelated with variations in local tetrahedral order in terms of locations of maxima and minima, which may be understood in terms of the relative contribution of van der Waals and Coulombic contributions to the TPE. The distance-dependent variations in local order and energetics are essentially the same for the beta-hairpin of 2GB1 as well as deca-alanine. Within a radius of 3 A, the perturbation of the solvent structure is very significant with local TPEs that are 10-15% lower than the bulk value. The chemical identity of side-chain residues and the secondary structure play an important role in determining residue-dependent variations in the TPEs. The variation in the residue-dependent tagged molecule potential energies is of the order of 3-5%, while the local residence times vary by a factor of approximately 5. The correlation of the local residence times with the local energetics within the innermost hydration layer is weak, though charged residues typically have low binding energies and large residence times.
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Affiliation(s)
- Manish Agarwal
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
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10
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Halle B, Nilsson L. Does the Dynamic Stokes Shift Report on Slow Protein Hydration Dynamics? J Phys Chem B 2009; 113:8210-3. [DOI: 10.1021/jp9027589] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bertil Halle
- Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden, and Department of Biosciences and Nutrition, Karolinska Institutet, SE-14157 Huddinge, Sweden
| | - Lennart Nilsson
- Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden, and Department of Biosciences and Nutrition, Karolinska Institutet, SE-14157 Huddinge, Sweden
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Hydration dynamics in a partially denatured ensemble of the globular protein human alpha-lactalbumin investigated with molecular dynamics simulations. Biophys J 2008; 95:5257-67. [PMID: 18775960 DOI: 10.1529/biophysj.108.136531] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Atomistic molecular dynamics simulations are used to probe changes in the nature and subnanosecond dynamical behavior of solvation waters that accompany partial denaturation of the globular protein, human alpha-lactalbumin. A simulated ensemble of subcompact conformers, similar to the molten globule state of human alpha-lactalbumin, demonstrates a marginal increase in the amount of surface solvation relative to the native state. This increase is accompanied by subtle but distinct enhancement in surface water dynamics, less favorable protein-water interactions, and a marginal decrease in the anomalous behavior of solvation water dynamics. The extent of solvent influx is not proportional to the increased surface area, and the partially denatured conformers are less uniformly solvated compared to their native counterpart. The observed solvation in partially denatured conformers is lesser in extent compared to earlier experimental estimates in molten globule states, and is consistent with more recent descriptions based on nuclear magnetic relaxation dispersion studies.
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12
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Sinha SK, Chakraborty S, Bandyopadhyay S. Thickness of the hydration layer of a protein from molecular dynamics simulation. J Phys Chem B 2008; 112:8203-9. [PMID: 18547099 DOI: 10.1021/jp8000724] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Water molecules around a protein exhibit slow dynamics with respect to that of pure bulk water. One important issue in protein hydration is the thickness of the hydration layer (i.e., the distance from the protein surface up to which the water dynamics is influenced by the protein). Estimation of thickness is crucial to understand better the properties of "biological water" and the role that it plays in guiding the protein's function. We have performed an atomistic molecular dynamics simulation of an aqueous solution of the protein villin headpiece subdomain or HP-36 to estimate the thickness of its hydration water. In particular, several dynamical properties of water around different segments (three alpha-helices) of the protein have been calculated by varying the thickness of the hydration layers. It is found that in general the influence of the helices on water properties extends beyond the first hydration layer. However, the heterogeneous nature of water among the first hydration layers of the three helices diminishes as the thickness is increased. It indicates that, for a small protein such as HP-36, the thickness of "biological water" is uniform for different segments of the protein.
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Affiliation(s)
- Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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13
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Godoy-Ruiz R, Henry ER, Kubelka J, Hofrichter J, Muñoz V, Sanchez-Ruiz JM, Eaton WA. Estimating free-energy barrier heights for an ultrafast folding protein from calorimetric and kinetic data. J Phys Chem B 2008; 112:5938-49. [PMID: 18278894 DOI: 10.1021/jp0757715] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Differential scanning calorimetry was used to measure the temperature dependence of the absolute heat capacity of the 35-residue subdomain of the villin headpiece, a protein that folds in 5 mus and is therefore assumed to have a small free-energy barrier separating folded and unfolded states. To obtain an estimate of the barrier height from the calorimetric data, two models, a variable-barrier model and an Ising-like model, were used to fit the heat capacity in excess of the folded state over the temperature range 15-125 degrees C. The variable-barrier model is based on an empirical mathematical form for the density of states, with four adjustable parameters and the enthalpy (H) as a reaction coordinate. The Ising-like model is based on the inter-residue contact map of the X-ray structure with exact enumeration of approximately 10(5) possible conformations, with two adjustable parameters in the partition function, and either the fraction of native contacts (Q) or the number of ordered residues (P) as reaction coordinates. The variable-barrier model provides an excellent fit to the data and yields a barrier height at the folding temperature ranging from 0.4 to 1.1 kcal mol(-1), while the Ising-like model provides a less good fit and yields barrier heights of 2.3 +/- 0.1 kcal mol(-1) and 2.1 +/- 0.1 kcal mol(-1) for the Q and P reaction coordinates, respectively. In both models, the barrier to folding increases with increasing temperature. Assuming a sufficiently large activation energy for diffusion on the free-energy surfaces, both models are consistent with the observation of a temperature-independent folding rate in previously published laser temperature-jump experiments. Analysis of this kinetic data, using an approximate form for the pre-exponential factor of Kramers theory and the 70 ns relaxation time for the fast phase that precedes the unfolding/refolding relaxation to determine the diffusion coefficient, results in a barrier height of 1.6 +/- 0.3 kcal mol-1 for an unspecified reaction coordinate. Although no independent test of the validity of the H, Q, or P reaction coordinates is given, the barrier-height estimates obtained with the three reaction coordinates are in quite good agreement with the value derived from a Kramers analysis of the kinetics that makes no assumptions about the reaction coordinate. However, the higher estimates obtained using Q or P appear more consistent with the finding of barrier-crossing kinetics of a villin mutant that folds in 700 ns, corresponding to a 1.3 kcal mol-1 reduction in the folding barrier relative to wild-type. All of the results suggest that the free-energy barrier to folding is sufficiently low that it should be possible to engineer this protein or find solution conditions that would eliminate the barrier to create the "downhill" folding scenario of Wolynes and Onuchic.
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Affiliation(s)
- Raquel Godoy-Ruiz
- Departamento de Quimica Fisica Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
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Chakraborty S, Bandyopadhyay S. Dynamics of water in the hydration layer of a partially unfolded structure of the protein HP-36. J Phys Chem B 2008; 112:6500-7. [PMID: 18433159 DOI: 10.1021/jp710904c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Atomistic molecular dynamics simulations of the folded native structure and a partially unfolded molten globule structure of the protein villin headpiece subdomain or HP-36 have been carried out with explicit solvent to explore the effects of unfolding on the dynamical behavior of water present in the hydration layers of different segments (three alpha-helices) of the protein. The calculations revealed that the unfolding of helix-2 influences the translational and rotational motions of water present in the hydration layers of the three helices in a heterogeneous manner. It is observed that a correlation exists between the unfolding of helix-2 and the microscopic kinetics of protein-water hydrogen bonds formed by its residues. This in turn has an influence on the rigidity of the hydration layers of the helices in the unfolded structure versus that in the folded native structure. These results should provide a microscopic explanation to recent solvation dynamics experiments on folded native and unfolded structures of proteins.
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Affiliation(s)
- Sudip Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur, India
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15
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Karunakaran V, Pfaffe M, Ioffe I, Senyushkina T, Kovalenko SA, Mahrwald R, Fartzdinov V, Sklenar H, Ernsting NP. Solvation oscillations and excited-state dynamics of 2-amino- and 2-hydroxy-7-nitrofluorene and its 2'-deoxyriboside. J Phys Chem A 2008; 112:4294-307. [PMID: 18386856 DOI: 10.1021/jp712176m] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Push-pull substituted fluorenes are considered for use as dynamic solvation probes in polynucleotides. Their fluorescence band is predicted (by simulations) to show weak spectral oscillations on the subpicosecond time scale depending on the nucleotide sequence. The oscillations reflect the local far-infrared spectrum of the environment around the probe molecule. A connection is provided by the continuum theory of polar solvation which, however, neglects molecular aspects. We examine the latter using acetonitrile solution as a test case. A collective librational solvent mode at 100 cm(-1) is observed with 2-amino-7-nitrofluorene, 2-dimethylamino-7-nitrofluorene, 2-hydroxy-7-nitrofluorene, and its 2'-deoxyriboside. Different strengths of the oscillation indicate that rotational friction of nearby acetonitrile molecules depends on the solute structure or that H bonding is involved in launching the librational coherence. Polar solvation in methanol is used for comparison. With hydroxynitrofluorenes, the observation window is limited by intersystem crossing for which rates are reported. A prominent excited-state absorption band of nitrofluorenes at 430 nm can be used to monitor polar solvation. Structural and electronic relaxation pathways are discussed with the help of quantum chemical calculations.
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Chakraborty S, Sinha SK, Bandyopadhyay S. Low-Frequency Vibrational Spectrum of Water in the Hydration Layer of a Protein: A Molecular Dynamics Simulation Study. J Phys Chem B 2007; 111:13626-31. [DOI: 10.1021/jp0746401] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sudip Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
| | - Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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Pizzitutti F, Marchi M, Sterpone F, Rossky PJ. How protein surfaces induce anomalous dynamics of hydration water. J Phys Chem B 2007; 111:7584-90. [PMID: 17564431 DOI: 10.1021/jp0717185] [Citation(s) in RCA: 194] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water around biomolecules slows down with respect to pure water, and both rotation and translation exhibit anomalous time dependence in the hydration shell. The origin of such behavior remains elusive. We use molecular dynamics simulations of water dynamics around several designed protein models to establish the connection between the appearance of the anomalous dynamics and water-protein interactions. For the first time we quantify the separate effect of protein topological and energetic disorder on the hydration water dynamics. When a static protein structure is simulated, we show that both types of disorder contribute to slow down water diffusion, and that allowing for protein motion, increasing the spatial dimensionality of the interface, reduces the anomalous character of hydration water. The rotation of water is, instead, altered by the energetic disorder only; indeed, when electrostatic interactions between the protein and water are switched off, water reorients even faster than in the bulk. The dynamics of water is also related to the collective structure--à voir the hydrogen bond (H-bond) network--formed by the solvent enclosing the protein surface. We show that, as expected for a full hydrated protein, when the protein surface offers pinning sites (charged or polar sites), the superficial water-water H-bond network percolates throughout the whole surface, hindering the water diffusion, whereas it does not when the protein surface lacks electrostatic interactions with water and the water diffusion is enhanced.
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Affiliation(s)
- Francesco Pizzitutti
- Commissariat a l'Energie Atomique, DSV-DBJC-SBFM, Centre d'Etudes, Saclay, 91191 Gif-sur-Yvette Cedex, France
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18
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Fedorov MV, Goodman JM, Schumm S. Solvent effects and hydration of a tripeptide in sodium halide aqueous solutions: an in silico study. Phys Chem Chem Phys 2007; 9:5423-35. [DOI: 10.1039/b706564g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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