Correlation effects on the structure and dynamics of the H3O+ hydrate: B3LYP/MM and MP2/MM MD simulations

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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Structure and Dynamics of Glycosphingolipids in Lipid Bilayers: Insights from Molecular Dynamics Simulations

International Journal of Carbohydrate Chemistry ◽

10.1155/2011/950256 ◽

2011 ◽

Vol 2011 ◽

pp. 1-9 ◽

Cited By ~ 4

Author(s):

Ronak Y. Patel ◽

Petety V. Balaji

Keyword(s):

Molecular Dynamics ◽

Lipid Bilayers ◽

Membrane Structure ◽

Lipid Membrane ◽

Biological Membranes ◽

Md Simulations ◽

Atomic Level ◽

Structure And Dynamics ◽

Hydrogen Bonding Interactions ◽

Dynamics Simulations

Glycolipids are important constituents of biological membranes, and understanding their structure and dynamics in lipid bilayers provides insights into their physiological and pathological roles. Experimental techniques have provided details into their behavior at model and biological membranes; however, computer simulations are needed to gain atomic level insights. This paper summarizes the insights obtained from MD simulations into the conformational and orientational dynamics of glycosphingolipids and their exposure, hydration, and hydrogen-bonding interactions in membrane environment. The organization of glycosphingolipids in raft-like membranes and their modulation of lipid membrane structure are also reviewed.

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Force field development and simulations of senior dialkyl sulfoxides

Physical Chemistry Chemical Physics ◽

10.1039/c5cp08006a ◽

2016 ◽

Vol 18 (15) ◽

pp. 10507-10515 ◽

Cited By ~ 8

Author(s):

Vitaly V. Chaban

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Ab Initio ◽

Md Simulations ◽

Field Development ◽

Force Field Development ◽

Structure And Dynamics ◽

Ethyl Methyl ◽

Methyl Sulfoxide ◽

Diethyl Sulfoxide

Thermodynamics, structure, and dynamics of diethyl sulfoxide (DESO) and ethyl methyl sulfoxide (EMSO) were investigated using ab initio calculations and non-polarizable potential based molecular dynamics (MD) simulations.

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Glycan synthesis, structure, and dynamics: A selection

Pure and Applied Chemistry ◽

10.1351/pac-con-12-10-17 ◽

2013 ◽

Vol 85 (9) ◽

pp. 1759-1770 ◽

Cited By ~ 9

Author(s):

Robert Pendrill ◽

K. Hanna M. Jonsson ◽

Göran Widmalm

Keyword(s):

Structural Information ◽

3D Structure ◽

Molecular Simulations ◽

Md Simulations ◽

Conformational Space ◽

Torsion Angles ◽

Structure And Dynamics ◽

Novel Approach ◽

Acetyl Group ◽

Experimental Spectroscopy

Glycan structural information is a prerequisite for elucidation of carbohydrate function in biological systems. To this end we employ a tripod approach for investigation of carbohydrate 3D structure and dynamics based on organic synthesis; different experimental spectroscopy techniques, NMR being of prime importance; and molecular simulations using, in particular, molecular dynamics (MD) simulations. The synthesis of oligosaccharides in the form of glucosyl fluorides is described, and their use as substrates for the Lam16A E115S glucosyl synthase is exemplified as well as a conformational analysis of a cyclic β-(1→3)-heptaglucan based on molecular simulations. The flexibility of the N-acetyl group of aminosugars is by MD simulations indicated to function as a gatekeeper for transitions of glycosidic torsion angles to other regions of conformational space. A novel approach to visualize glycoprotein (GP) structures is presented in which the protein is shown by, for example, ribbons, but instead of stick or space-filling models for the carbohydrate portion it is visualized by the colored geometrical figures known as CFG representation in a 3D way, which we denote 3D-CFG, thereby effectively highlighting the sugar residues of the glycan part of the GP and the position(s) on the protein.

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Insights into the structure and dynamics of liquid water: A comparative study of conventional QM/MM and ONIOM-XS MD simulations

Journal of Molecular Liquids ◽

10.1016/j.molliq.2012.07.024 ◽

2012 ◽

Vol 174 ◽

pp. 26-33 ◽

Cited By ~ 13

Author(s):

Sukhontip Thaomola ◽

Anan Tongraar ◽

Teerakiat Kerdcharoen

Keyword(s):

Comparative Study ◽

Liquid Water ◽

Md Simulations ◽

Structure And Dynamics

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

10.1101/2020.09.28.316596 ◽

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.

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Sequence-to-structure dependence of isolated IgG Fc complex biantennary N-glycans: A molecular dynamics study

10.1101/392001 ◽

2018 ◽

Author(s):

Aoife M Harbison ◽

Lorna P Brosnan ◽

Keith Fenlon ◽

Elisa Fadda

Keyword(s):

Molecular Dynamics ◽

Structural Integrity ◽

Md Simulations ◽

Structure And Dynamics ◽

Differential Recognition ◽

Dependent Cell ◽

Function Relationship ◽

Simulation Time ◽

Core Fucosylation

AbstractFc glycosylation of human immunoglobulins G (IgGs) is essential for their structural integrity and activity. Interestingly, the specific nature of the Fc glycoforms is known to modulate the IgG effector function. Indeed, while core-fucosylation of IgG Fc-glycans greatly affects the antibody-dependent cell-mediated cytotoxicity (ADCC) function, with obvious repercussions in the design of therapeutic antibodies, sialylation can reverse the antibody inflammatory response, and galactosylation levels have been linked to aging, to the onset of inflammation, and to the predisposition to rheumatoid arthritis. Within the framework of a structure-to-function relationship, we have studied the role of the N-glycan sequence on its intrinsic conformational propensity. Here we report the results of a systematic study, based on extensive molecular dynamics (MD) simulations in excess of 62 µs of cumulative simulation time, on the effect of sequence on the structure and dynamics of increasingly larger, complex biantennary N-glycoforms, i.e. from chitobiose to the larger N-glycan species commonly found in the Fc region of human IgGs. Our results show that while core fucosylation and sialylation do not affect the intrinsic dynamics of the isolated (unbound) N-glycans, galactosylation of the α(1-6) arm shifts dramatically its conformational equilibrium from an outstretched to a folded conformation. These findings are in agreement with and can help rationalize recent experimental evidence showing a differential recognition of positional isomers in glycan array data and also the preference of sialyltransferase for the more reachable, outstretched α(1-3) arm in both isolated and Fc-bound N-glycans.

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

10.1101/2022.01.06.475229 ◽

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.

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