scholarly journals Structural and dynamical heterogeneity of water trapped inside Na+-pumping KR2 rhodopsin in the dark state

2020 ◽  
Author(s):  
Mantu Santra ◽  
Aniruddha Seal ◽  
Kankana Bhattacharjee ◽  
Suman Chakrabarty
Keyword(s):  
Md Simulations ◽  
Active Role ◽  
Water Molecules ◽  
Dark State ◽  
Dynamical Heterogeneity ◽  
Structure And Dynamics ◽  
Channel Opening ◽  
Conserved Water Molecules ◽  
Ion Proton ◽  
Ion Pumping

AbstractPhotoisomerisation in retinal leads to a channel opening in the rhodopsins that triggers translocation of an ion/proton. Crystal structures of rhodopsins contain several structurally conserved water molecules. It has been suggested that water plays an active role in facilitating the ion pumping/translocation process by acting as a lubricant in these systems. In this work, we investigate the localisation, local structure and dynamics of water molecules along the channel for the resting/dark state of KR2 rhodopsin. Employing 1.5 μs long atomistic molecular dynamics (MD) simulations of this trans-membrane protein system, we demonstrate the presence of five distinct water containing pockets/cavities separated by gateways controlled by the protein side-chains. We present evidence of significant structural and dynamical heterogeneity in the water molecules present in these cavities. The exchange time-scale of these buried water with bulk ranges from tens of nanoseconds to > 1.5 μs. The translational and rotational dynamics of buried water are found to be strongly dependent on protein cavity size and local interactions with possible functional significance.

scholarly journals Development and Validation of Fluorinated Amino Acid Parameters for use with the AMBER ff15ipq Protein Force Field

2022 ◽  
Author(s):  
Darian Yang ◽  
Angela Gronenborn ◽  
Lillian Chong
Keyword(s):  
Force Field ◽  
Aromatic Amino Acids ◽  
Md Simulations ◽  
Water Molecules ◽  
Relaxation Rates ◽  
Structure And Dynamics ◽  
Experimental Values ◽  
Development And Validation ◽  
Explicit Water ◽  
Good Agreement

We developed force field parameters for fluorinated aromatic amino acids enabling molecular dynamics (MD) simulations of fluorinated proteins. These parameters are tailored to the AMBER ff15ipq protein force field and enable the modeling of 4, 5, 6, and 7F-tryptophan, 3F- and 3,5F-tyrosine, and 4F- or 4-CF3-phenylalanine. The parameters include 181 unique atomic charges derived using the Implicitly Polarized Charge (IPolQ) scheme in the presence of SPC/Eb explicit water molecules and 9 unique bond, angle, or torsion terms. Our simulations of benchmark peptides and proteins maintain expected conformational propensities on the μs-timescale. In addition, we have developed an open-source Python program to calculate fluorine relaxation rates from MD simulations. The extracted relaxation rates from protein simulations are in good agreement with experimental values determined by 19F NMR. Collectively, our results illustrate the power and robustness of the IPolQ lineage of force fields for modeling structure and dynamics of fluorine containing proteins at the atomic level.

Temperature Dependence of the Air/Water Interface Revealed by Polarization Sensitive Sum-Frequency Generation Spectroscopy

2018 ◽  
Author(s):  
Daniel R. Moberg ◽  
Shelby C. Straight ◽  
Francesco Paesani
Keyword(s):  
Temperature Dependence ◽  
Low Frequency ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Sum Frequency Generation ◽  
Water Molecules ◽  
Water Interface ◽  
Sum Frequency ◽  
Air Water Interface ◽  
Frequency Generation

<div> <div> <div> <p>The temperature dependence of the vibrational sum-frequency generation (vSFG) spectra of the the air/water interface is investigated using many-body molecular dynamics (MB-MD) simulations performed with the MB-pol potential energy function. The total vSFG spectra calculated for different polarization combinations are then analyzed in terms of molecular auto-correlation and cross-correlation contributions. To provide molecular-level insights into interfacial hydrogen-bonding topologies, which give rise to specific spectroscopic features, the vSFG spectra are further investigated by separating contributions associated with water molecules donating 0, 1, or 2 hydrogen bonds to neighboring water molecules. This analysis suggests that the low frequency shoulder of the free OH peak which appears at ∼3600 cm−1 is primarily due to intermolecular couplings between both singly and doubly hydrogen-bonded molecules. </p> </div> </div> </div>

Dynamics and metastable surface structure of double atomic layer of water molecules and ions at the interface between KBr(c) and water

2004 ◽  
Vol 76 (1) ◽  
pp. 115-122 ◽  
Author(s):  
K. Ichikawa ◽  
S. Sato ◽  
N. Shimomura
Keyword(s):  
Surface Structure ◽  
Vertical Motion ◽  
Atomic Layer ◽  
Water Molecules ◽  
Potassium Ions ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
Atomic Force ◽  
Bromide Ions

The metastable surface structure and dynamics of water molecules, cations, and anions at the interface between KBr(001) and water have been demonstrated from the images in situ observed in atomic resolution using atomic force microscopy. The vertical motion of potassium ions, which means their own transfer from the equilibrium sites to the upper height right on the underlying bromide ions, has been observed at the interface. They are used to be located in some steady state stabilized by their interaction with water molecules in the double atomic layer at the interface. The observed water molecules bridge two bromide ions by hydrogen bond; the water molecules are sandwiched by the potassium ions and vice versa.

scholarly journals Molecular Dynamics Modellization and Simulation of Water Diffusion through Plant Cutin

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Structural Information ◽  
Md Simulations ◽  
Water Molecules ◽  
Plant Cuticle ◽  
X Ray Diffraction ◽  
Cross Link ◽  
X Ray ◽  
Good Agreement

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

scholarly journals Molecular Dynamics Study of Conserved Water Molecules in PrPc and Pathological Point Mutation T188R

2014 ◽  
Vol 106 (2) ◽  
pp. 612a
Author(s):  
Katsufumi Tomobe ◽  
Eiji Yamamoto ◽  
Takuma Akimoto ◽  
Masato Yasui ◽  
Kenji Yasuoka
Keyword(s):  
Molecular Dynamics ◽  
Point Mutation ◽  
Water Molecules ◽  
Conserved Water Molecules

Targeting conserved water molecules: Design of 4-aryl-5-cyanopyrrolo[2,3-d]pyrimidine Hsp90 inhibitors using fragment-based screening and structure-based optimization

2012 ◽  
Vol 20 (22) ◽  
pp. 6770-6789 ◽  
Author(s):  
Nicholas G.M. Davies ◽  
Helen Browne ◽  
Ben Davis ◽  
Martin J. Drysdale ◽  
Nicolas Foloppe ◽  
...  
Keyword(s):  
Water Molecules ◽  
Hsp90 Inhibitors ◽  
Conserved Water Molecules

scholarly journals Sorption, Structure and Dynamics of CO2 and Ethane in Silicalite at High Pressure: A Combined Monte Carlo and Molecular Dynamics Simulation Study

Molecules ◽  
2018 ◽  
Vol 24 (1) ◽  
pp. 99 ◽  
Author(s):  
Siddharth Gautam ◽  
Tingting Liu ◽  
David Cole
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Time Scales ◽  
Rotational Motion ◽  
High Pressures ◽  
Sorption Isotherms ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Structure And Dynamics ◽  
Low Pressures

Silicalite is an important nanoporous material that finds applications in several industries, including gas separation and catalysis. While the sorption, structure, and dynamics of several molecules confined in the pores of silicalite have been reported, most of these studies have been restricted to low pressures. Here we report a comparative study of sorption, structure, and dynamics of CO2 and ethane in silicalite at high pressures (up to 100 bar) using a combination of Monte Carlo (MC) and molecular dynamics (MD) simulations. The behavior of the two fluids is studied in terms of the simulated sorption isotherms, the positional and orientational distribution of sorbed molecules in silicalite, and their translational diffusion, vibrational spectra, and rotational motion. Both CO2 and ethane are found to exhibit orientational ordering in silicalite pores; however, at high pressures, while CO2 prefers to reside in the channel intersections, ethane molecules reside mostly in the sinusoidal channels. While CO2 exhibits a higher self-diffusion coefficient than ethane at low pressures, at high pressures, it becomes slower than ethane. Both CO2 and ethane exhibit rotational motion at two time scales. At both time scales, the rotational motion of ethane is faster. The differences observed here in the behavior of CO2 and ethane in silicalite pores can be seen as a consequence of an interplay of the kinetic diameter of the two molecules and the quadrupole moment of CO2.

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