scholarly journals Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions

2021 ◽  
Vol 22 (17) ◽  
pp. 9350
Author(s):  
Aneta Panuszko ◽  
Maciej Pieloszczyk ◽  
Anna Kuffel ◽  
Karol Jacek ◽  
Karol A. Biernacki ◽  
...  
Keyword(s):  
High Stability ◽  
Water Molecules ◽  
Hydration Water ◽  
Computational Results ◽  
Protein Surface ◽  
Structure Of Water ◽  
Hydration Shells ◽  
Dynamics Simulations ◽  
Proteins And Peptides ◽  
Main Factor

The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.

scholarly journals Origin and control of ionic hydration patterns in nanopores

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Miraslau L. Barabash ◽  
William A. T. Gibby ◽  
Carlo Guardiani ◽  
Alex Smolyanitsky ◽  
Dmitry G. Luchinsky ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Water Molecules ◽  
Surrounding Water ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Water Layers ◽  
Dynamics Simulations ◽  
And Control

AbstractIn order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. Here, we study the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in a graphene nanopore in terms of experimentally accessible radial distribution functions, giving results that agree well with molecular dynamics simulations. The patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the graphene membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

scholarly journals Impact of Sucrose as Osmolyte on Molecular Dynamics of Mouse Acetylcholinesterase

Biomolecules ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1664
Author(s):  
Sofya V. Lushchekina ◽  
Gaetan Inidjel ◽  
Nicolas Martinez ◽  
Patrick Masson ◽  
Marie Trovaslet-Leroy ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Sucrose Concentration ◽  
Water Dynamics ◽  
Water Molecules ◽  
Protein Surface ◽  
Incoherent Neutron Scattering ◽  
Enzyme Model ◽  
Non Linear ◽  
Model Mouse ◽  
Dynamics Simulations

The enzyme model, mouse acetylcholinesterase, which exhibits its active site at the bottom of a narrow gorge, was investigated in the presence of different concentrations of sucrose to shed light on the protein and water dynamics in cholinesterases. The study was conducted by incoherent neutron scattering, giving access to molecular dynamics within the time scale of sub-nano to nanoseconds, in comparison with molecular dynamics simulations. With increasing sucrose concentration, we found non-linear effects, e.g., first a decrease in the dynamics at 5 wt% followed by a gain at 10 wt% sucrose. Direct comparisons with simulations permitted us to understand the following findings: at 5 wt%, sugar molecules interact with the protein surface through water molecules and damp the motions to reduce the overall protein mobility, although the motions inside the gorge are enhanced due to water depletion. When going to 10 wt% of sucrose, some water molecules at the protein surface are replaced by sugar molecules. By penetrating the protein surface, they disrupt some of the intra-protein contacts, and induce new ones, creating new pathways for correlated motions, and therefore, increasing the dynamics. This exhaustive study allowed for an explanation of the detail interactions leading to the observed non-linear behavior.

A Molecular Dynamics Study of Ionic Hydration Near a Platinum Surface

1991 ◽  
Vol 46 (10) ◽  
pp. 876-886 ◽  
Author(s):  
J. Seitz-Beywl ◽  
M. Poxleitner ◽  
K. Heinzinger
Keyword(s):  
Boundary Layer ◽  
Molecular Dynamics ◽  
Distribution Functions ◽  
Water Molecules ◽  
Molecular Orbital Calculations ◽  
Platinum Surface ◽  
Average Temperature ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Dynamics Simulations

AbstractTwo Molecular Dynamics simulations have been performed where a Pt(100) surface is covered with three layers of water molecules and a lithium or an iodide ion is placed additionally in the boundary layer. The flexible BJH model of water is employed in the simulations and the ion-water, platinum-water and platinum-ion potentials are derived from molecular orbital calculations. The simulations extended over 7.5 ps at an average temperature of 298 K. The effect of the Pt(100) surface on the ionic hydration is demonstrated by the comparison of the radial distribution functions, the orientation of the water molecules and their geometrical arrangement in the first hydration shells of the ions in the boundary layer with those in a 2.2 molal bulk Lil solution.

scholarly journals Water-Protein Interactions: The Secret of Protein Dynamics

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Silvia Martini ◽  
Claudia Bonechi ◽  
Alberto Foletti ◽  
Claudio Rossi
Keyword(s):  
Protein Interactions ◽  
Nmr Relaxation ◽  
Spin Lattice Relaxation ◽  
Resonance Spectroscopy ◽  
Water Molecules ◽  
Hydration Water ◽  
Relaxation Rates ◽  
Relaxation Parameters ◽  
Hydration Shells ◽  
Dynamical Properties

Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R1NS) and selective (R1SE) spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.

scholarly journals Origin and control of ionic hydration patterns in nanopores

2020 ◽  
Author(s):  
Miraslau Barabash ◽  
William Gibby ◽  
Carlo Guardiani ◽  
Alex Smolyanitsky ◽  
Dmitry Luchinsky ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Molecules ◽  
Complex Interplay ◽  
Surrounding Water ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Water Layers ◽  
Dynamics Simulations ◽  
And Control

Abstract In order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. We now address the questions of the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in terms of experimentally accessible radial distributions functions, yielding results that agree well with molecular dynamics simulations. We show that the patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

scholarly journals Chemistry of cation hydration and conduction in a skeletal muscle ryanodine receptor

2019 ◽  
Author(s):  
Zhaolong Wu ◽  
Congcong Liu ◽  
Hua Yu ◽  
Duan Kang ◽  
Yinping Ma ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Binding Sites ◽  
Ryanodine Receptors ◽  
Cation Binding ◽  
Water Molecules ◽  
Ion Permeation ◽  
Multiscale Dynamics ◽  
Hydration Shells ◽  
Cation Hydration ◽  
Dynamics Simulations

AbstractRyanodine receptors (RyRs) are Ca2+-regulated Ca2+ channels of 2.2-megadalton in muscles and neurons for calcium signaling. How Ca2+ regulates ion conduction in the RyR channels remains elusive. We determined a 2.6-Å cryo-EM structure of rabbit skeletal muscle RyR1, and used multiscale dynamics simulations to elucidate cation interactions with RyR1. We investigated 21 potential cation-binding sites that may together rationalize biphasic Ca2+ response of RyR1. The selectivity filter captures a cation hydration complex by hydrogen-bonding with both the inner and outer hydration shells of water molecules. Molecular dynamics simulations suggest that adjacent Ca2+ ions moving in concert along ion-permeation pathway are separated by at least two cation-binding sites. Our analysis reveals that RyR1 has been evolved to favor its interactions with two hydration shells of cations.

scholarly journals Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for C-type inactivation

2017 ◽  
Vol 114 (42) ◽  
pp. 11145-11150 ◽  
Author(s):  
Jing Li ◽  
Jared Ostmeyer ◽  
Eliot Boulanger ◽  
Huan Rui ◽  
Eduardo Perozo ◽  
...  
Keyword(s):  
Md Simulations ◽  
Selectivity Filter ◽  
Time Dependent ◽  
Water Molecules ◽  
Computational Results ◽  
Structural Studies ◽  
X Ray ◽  
Chemically Modified ◽  
Dynamics Simulations ◽  
Rule Out

In many K+ channels, prolonged activating stimuli lead to a time-dependent reduction in ion conduction, a phenomenon known as C-type inactivation. X-ray structures of the KcsA channel suggest that this inactivated state corresponds to a “constricted” conformation of the selectivity filter. However, the functional significance of the constricted conformation has become a matter of debate. Functional and structural studies based on chemically modified semisynthetic KcsA channels along the selectivity filter led to the conclusion that the constricted conformation does not correspond to the C-type inactivated state. The main results supporting this view include the observation that C-type inactivation is not suppressed by a substitution of D-alanine at Gly77, even though this modification is believed to lock the selectivity filter into its conductive conformation, whereas it is suppressed following amide-to-ester backbone substitutions at Gly77 and Tyr78, even though these structure-conserving modifications are not believed to prevent the selectivity filter from adopting the constricted conformation. However, several untested assumptions about the structural and functional impact of these chemical modifications underlie these arguments. To make progress, molecular dynamics simulations based on atomic models of the KcsA channel were performed. The computational results support the notion that the constricted conformation of the selectivity filter corresponds to the functional C-type inactivated state of the KcsA. Importantly, MD simulations reveal that the semisynthetic KcsAD-ala77 channel can adopt an asymmetrical constricted-like nonconductive conformation and that the amide-to-ester backbone substitutions at Gly77 and Tyr78 perturb the hydrogen bonding involving the buried water molecules stabilizing the constricted conformation.

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