Studies of Disaccharide Solvation—Molecular Dynamics versus HPLC Retention

2005 ◽  
Vol 58 (11) ◽  
pp. 803 ◽  
Author(s):  
Norman W. H. Cheetham ◽  
Paramita Dasgupta
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modelling ◽  
High Dielectric Constant ◽  
Chromatographic Retention ◽  
Significant Finding ◽  
Oxygen Oxygen ◽  
Hydration Model ◽  
Dynamics Simulations ◽  
High Dielectric ◽  
Modelling Approach

Molecular dynamics simulations have been used to assess the conformational behaviour of seven disaccharides in aqueous solution. Solvation decreased the overall conformational fluctuations of the sugars, compared to in vacuo simulations using a high dielectric constant. The most significant finding was a linear correlation between the experimental chromatographic retention parameter K´ and a molecular modelling parameter based on the next-nearest oxygen–oxygen distances in the disaccharides. The results support previous proposals for a stereospecific hydration model for carbohydrates and demonstrate the utility of a combined experimental/molecular modelling approach to its study.

scholarly journals Molecular modelling of the nucleotide-binding domain of Wilson's disease protein: location of the ATP-binding site, domain dynamics and potential effects of the major disease mutations

2004 ◽  
Vol 382 (1) ◽  
pp. 293-305 ◽  
Author(s):  
Roman G. EFREMOV ◽  
Yuri A. KOSINSKY ◽  
Dmitry E. NOLDE ◽  
Ruslan TSIVKOVSKII ◽  
Alexander S. ARSENIEV ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Modelling ◽  
Wilson’S Disease ◽  
Wilson's Disease ◽  
Binding Domain ◽  
Atp Binding ◽  
Disease Mutations ◽  
Disease Protein ◽  
Dynamics Simulations

WNDP (Wilson's disease protein) is a copper-transporting ATPase that plays an essential role in human physiology. Mutations in WNDP result in copper accumulation in tissues and cause a severe hepato-neurological disorder known as Wilson's disease. Several mutations were surmised to affect the nucleotide binding and hydrolysis by WNDP; however, how the nucleotides bind to normal and mutated WNDP remains unknown. To aid such studies, we performed the molecular modelling of the spatial structure and dynamics of the ATP-binding domain of WNDP and its interactions with ATP. The three-dimensional models of this domain in two conformations were built using the X-ray structures of the Ca2+-ATPase in the E1 and E2 states. To study the functional aspects of the models, they were subjected to long-term molecular dynamics simulations in an explicit solvent; similar calculations were performed for the ATP-binding domain of Ca2+-ATPase. In both cases, we found large-scale motions that lead to significant changes of distances between several functionally important residues. The ATP docking revealed two possible modes of ATP binding: via adenosine buried in the cleft near residues H1069, R1151 and D1164, and via phosphate moiety ‘anchored’ by H-bonds with residues in the vicinity of catalytic D1027. Furthermore, interaction of ATP with both sites occurs if they are spatially close to each other. This may be achieved after relative domain motions of the ‘closure’ type observed in molecular dynamics simulations. The results provide a framework for analysis of disease mutations and for future mutagenesis studies.

scholarly journals Molecular modelling studies of quinazolinone derivatives as MMP-13 inhibitors by QSAR, molecular docking and molecular dynamics simulations techniques

MedChemComm ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 101-115 ◽  
Author(s):  
Shanshan Huang ◽  
Kairui Feng ◽  
Yujie Ren
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulations ◽  
Molecular Modelling ◽  
Molecular Modelling Studies ◽  
Qsar Models ◽  
Modelling Studies ◽  
Dynamics Simulations ◽  
Quinazolinone Derivatives

Reliable QSAR models for quinazolinones were constructed and eight novel MMP-13 inhibitors with higher predictive activity were identified.

The membranes of Gram-negative bacteria: progress in molecular modelling and simulation

2015 ◽  
Vol 43 (2) ◽  
pp. 162-167 ◽  
Author(s):  
Syma Khalid ◽  
Nils A. Berglund ◽  
Daniel A. Holdbrook ◽  
Yuk M. Leung ◽  
Jamie Parkin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Molecular Modelling ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Bacterial Membranes ◽  
Lipid Species ◽  
Membrane Models ◽  
Dynamics Simulations

Molecular modelling and simulations have been employed to study the membranes of Gram-negative bacteria for over 20 years. Proteins native to these membranes, as well as antimicrobial peptides and drug molecules have been studied using molecular dynamics simulations in simple models of membranes, usually only comprising one lipid species. Thus, traditionally, the simulations have reflected the majority of in vitro membrane experimental setups, enabling observations from the latter to be rationalized at the molecular level. In the last few years, the sophistication and complexity of membrane models have improved considerably, such that the heterogeneity of the lipid and protein composition of the membranes can now be considered both at the atomistic and coarse-grain levels of granularity. Importantly this means relevant biology is now being retained in the models, thereby linking the in silico and in vivo scenarios. We discuss recent progress in simulations of proteins in simple lipid bilayers, more complex membrane models and finally describe some efforts to overcome timescale limitations of atomistic molecular dynamics simulations of bacterial membranes.

Structure and molecular modelling of protected dipeptide fragment (Boc–Phe–Leu–OBzl) of enkephalin

1999 ◽  
Vol 55 (6) ◽  
pp. 975-984 ◽  
Author(s):  
S. Antolić ◽  
M. Teichert ◽  
G. Sheldrick ◽  
B. Kojić-Prodić ◽  
M. Čudić ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Molecular Modelling ◽  
Asymmetric Unit ◽  
Peptide Backbone ◽  
X Ray ◽  
The Family ◽  
Structural Database ◽  
Dynamics Simulations ◽  
Β Sheet

The conformational characteristics of a flexible totally protected C-terminal dipeptide fragment (Boc–Phe–Leu–OBzl) of enkephalin are studied using X-ray data, molecular modelling and data retrieved from the Cambridge Structural Database. The dipeptide crystallizes with seven conformers in the asymmetric unit. C27H36N2O5, T = 133 K, monoclinic, P21, a = 13.706 (3), b = 22.800 (3), c = 30.674 (5) Å, β = 97.15 (3)°, V = 9511 (3) Å3, Z = 14, D c = 1.145 Mg m−3. Six of the seven molecules exhibit folded conformations with hydrophobic groups disposed at the opposite side of the peptide backbone. The characteristic Φ1 and Ψ1 angles of the Phe residue and Φ2 of the Leu fragment are in the allowed region defined in the Ramachandran diagram. However, they do not belong to the family of the lowest energy conformations. In the crystal, molecules are interconnected via N—H...O hydrogen bonds of peptide groups forming an infinite sheet similar to a parallel β-sheet. Molecular dynamics simulations performed in vacuo reproduce the conformers and rotamers detected in the solid state.

Enhanced performance of supercapacitors by constructing a “mini parallel-plate capacitor” in an electrode with high dielectric constant materials

2020 ◽  
Vol 8 (32) ◽  
pp. 16661-16668
Author(s):  
Huayao Tu ◽  
Shouzhi Wang ◽  
Hehe Jiang ◽  
Zhenyan Liang ◽  
Dong Shi ◽  
...  
Keyword(s):  
Dielectric Constant ◽  
Carbon Fiber ◽  
Parallel Plate ◽  
Sandwich Structure ◽  
High Dielectric Constant ◽  
Parallel Plate Capacitor ◽  
Plate Capacitor ◽  
Fiber Metal ◽  
High Dielectric ◽  
Mini Plate

The carbon fiber/metal oxide/metal oxynitride layer sandwich structure is constructed in the electrode to form a mini-plate capacitor. High dielectric constant metal oxides act as dielectric to increase their capacitance.

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