COMPUTER SIMULATIONS TO INVESTIGATE STABILITY AND STRUCTURAL PROPERTIES OF PEPTIDE AMPHIPHILE NANOFIBERS

2007 ◽  
Vol 06 (03) ◽  
pp. 621-630
Author(s):  
RUO-YU CHEN ◽  
LING-YING WU ◽  
JUN-MIN LIAO ◽  
CHENG-LUNG CHEN
Keyword(s):  
Molecular Dynamics ◽  
Disulfide Bonds ◽  
Md Simulation ◽  
Intermolecular Hydrogen Bond ◽  
Intermolecular Distance ◽  
Peptide Amphiphile ◽  
Hydrogen Bond Interactions ◽  
Self Assembling ◽  
Polar Groups ◽  
The Stability

Molecular mechanics (MM) method followed by molecular dynamics (MD) simulation was carried out to investigate the stability of an aggregate formed by self-assembling of peptide amphiphile (PA) molecules. The MM + MD simulation confirms that the cylindrical shaped aggregate is very stable. The analysis showed that the remarkable stability of the aggregate was partly due to various intermolecular hydrogen-bond interactions between polar groups of PA molecules. The hydrophobic alkyl tails of PA molecules are packed loosely inside the interior of the aggregates. The packing of alkyl tails contribute further stability of the PA aggregate. Our simulations reproduce qualitatively experimental observations and support the fact that PA molecules are self-assembled within closed intermolecular distance to favor the forming of disulfide bonds.

Design of potential IKK-β inhibitors using molecular docking and molecular dynamics techniques for their anti-cancer potential

2020 ◽  
Vol 16 ◽  
Author(s):  
Salam Pradeep Singh ◽  
Iftikar Hussain ◽  
Bolin Kumar Konwar ◽  
Ramesh Chandra Deka ◽  
Chingakham Brajakishor Singh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Md Simulation ◽  
Inflammatory Diseases ◽  
Binding Free Energy ◽  
Anti Cancer ◽  
Dietary Phytochemicals ◽  
Toxicity Analysis ◽  
The Stability ◽  
Stable Trajectory

Aim and Objective: To evaluate a set of seventy phytochemicals for their potential ability to bind the inhibitor of nuclear factor kappaB kinase beta (IKK-β) which is a prime target for cancer and inflammatory diseases. Materials and Methods: Seventy phytochemicals were screened against IKK-β enzyme using DFT-based molecular docking technique and the top docking hits were carried forward for molecular dynamics (MD) simulation protocols. The adme-toxicity analysis was also carried out for the top docking hits. Results: Sesamin, matairesinol and resveratrol were found to be the top docking hits with a total score of -413 kJ/mol, -398.11 kJ/mol and 266.73 kJ/mol respectively. Glu100 and Gly102 were found to be the most common interacting residues. The result from MD simulation observed a stable trajectory with a binding free energy of -107.62 kJ/mol for matairesinol, -120.37 kJ/mol for sesamin and -40.56 kJ/mol for resveratrol. The DFT calculation revealed the stability of the compounds. The ADME-Toxicity prediction observed that these compounds fall within the permissible area of Boiled-Egg and it does not violate any rule for pharmacological criteria, drug-likeness etc. Conclusion: The study interprets that dietary phytochemicals are potent inhibitors of IKK-β enzyme with favourable binding affinity and less toxic effects. In fact, there is a gradual rise in the use of plant-derived molecules because of its lesser side effects compared to chemotherapy. The study has also provided an insight by which the phytochemicals inhibited the IKK-β enzyme. The investigation would also provide in understanding the inhibitory mode of certain dietary phytochemicals in treating cancer.

scholarly journals Optimized structure of monoubiquitinated FANCD2 (human) at Lys 561: a theoretical approach

2021 ◽  
Author(s):  
Sudipa Mondal ◽  
Subba Reddy ◽  
Sudit S. Mukhopadhyay
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Theoretical Approach ◽  
Md Simulation ◽  
Docking Studies ◽  
Fanconi Anaemia ◽  
Cross Linking ◽  
Structural Differences ◽  
The Stability ◽  
Dna Docking

AbstractFanconi anaemia pathway repairs inter-strand cross linking damage (ICL) of the DNA. Monoubiquitination of FANCD2 and FANCI is very crucial for ICL repairing. In this work we have tried to understand the monoubiquitinated FANCD2 structure, which facilitates the FANCD2 for binding the damage part of the chromatin. Crystal structure of the monoubiquitinated FANCD2 alone is not available, therefore we have developed the optimized structure of the human monoubiquitinated (Lys 561) FANCD2. As there is no suitable software or web server we have developed a method for building up monoubiquitinated product and validated on simplest monoubiquitinated protein, diubiquitin. We have predicted the structure of human monoubiquitinated FANCD2 by using our method and studied the interaction with DNA by docking studies. Molecular Dynamics (MD) simulation was used to understand the stability of the structure. Large structural differences have been observed between FANCD2 and monoubiquitinated FANCD2. DNA docking studies suggest that the binding site varies for the FANCD2 and monoubiquitinated FANCD2.

scholarly journals New Insights Into the Structure of Hydroxylated and Alkylated Glycols: A Comparative X-ray Diffraction, Raman and Molecular Dynamics Study of Ethane-1,2-Diol, 2-Methoxyethan-1-ol and 1,2-Dimethoxy Ethane

2020 ◽  
Author(s):  
Lorenzo Gontrani ◽  
Pietro Tagliatesta ◽  
Antonio Agresti ◽  
Sara Pescetelli ◽  
Marilena Carbone
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Room Temperature ◽  
Intermolecular Hydrogen Bond ◽  
Hydroxyl Groups ◽  
Gauche Conformation ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Diffraction Patterns ◽  
Intramolecular Hydrogen

In this study, we report a detailed experimental and theoretical investigation of three glycols, namely ethane-1,2-diol, 2-methoxyethan-1-ol and 1,2-dimethoxy ethane. For the first time, the X-Ray spectra of the latter two liquids was measured at room temperature, and they were compared with the newly measured spectrum of ethane-1,2-diol. The experimental diffraction patterns were interpreted very satisfactorily with molecular dynamics calculations, and suggest that in liquid ethane-1,2-diol most molecules are found in gauche conformation, with intramolecular hydrogen bond between the two hydroxyl groups. Intramolecular H-bonds are established in the mono-alkylated diol, but the interaction is weaker. The EDXD study also evidences strong intermolecular hydrogen-bond interactions, with short O···O correlations in both systems, while longer methyl-methyl interactions are found in 1,2-dimethoxy ethane. X-Ray studies are complemented by micro Raman investigations at room temperature and at 80°C, that confirm the conformational analysis predicted by X-Ray experiments and simulations.

scholarly journals DFT Studies and Molecular Dynamics of the Molecular and Electronic Structure of Cu (II) and Zn (II) Complexes with the Symmetric Ligand (Z)-2-((3,5-dimethyl-2H-pyrrol-2-yl) methylene)-3,5-dimethyl-2H-pyrrole

2021 ◽  
Vol 12 (5) ◽  
pp. 5953-5968
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Nbo Analysis ◽  
Docking Studies ◽  
Binding Motifs ◽  
Ligand Coordination ◽  
Dependent Protein ◽  
The Stability ◽  
Symmetric Ligands ◽  
Molecular And Electronic Structure

The binding patterns of the metal cations Cu 2+ and Zn 2+ with the symmetric ligands (Z)-2-((3,5-dimethyl-2H-pyrrol-2-yl) methylene)-3,5-dimethyl-2H-pyrrole (L1) and (Z)-2-(1-(3,5-dimethyl-2H-pyrrol-2-yl)ethylidene)-3,5-dimethyl-2H-pyrrole (L2), have been investigated at B3LYP and MM2 level of theories in the gas phase and a solution respectively. Natural bond orbital (NBO) analysis has been applied to explore the character of metal-ligand coordination. The stability of the most favorable binding motifs of the metal ions has also been investigated by the molecular dynamics (MD) simulation. Finally, the inhibition activity of the complexes (L1Cu2+), (L2Cu2+), (L1Zn2+), and (L2Zn2+) against the DNA dependent protein kinase also have been investigated by molecular docking studies.

scholarly journals An All-Atomistic Molecular Dynamics Study to Determine the Structural Importance of Disulfide Bonds in Immunoglobulin G and Bovine Serum Albumin

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Akshay Mathavan ◽  
Akash Mathavan ◽  
Michael Fortunato ◽  
Coray Colina
Keyword(s):  
Molecular Dynamics ◽  
Bovine Serum Albumin ◽  
Serum Albumin ◽  
Immunoglobulin G ◽  
Bovine Serum ◽  
Disulfide Bonds ◽  
Structural Changes ◽  
Conformational Stability ◽  
The Stability

A fully-atomistic molecular dynamics study was performed to determine the importance of disulfide bonds on the stability of immunoglobulin G (IgG) and bovine serum albumin (BSA).The transferability of a previous prescreening methodology to assess contributions from individual disulfide bonds on conformational stability was tested on both proteins. In IgG, it was apparent that inter-chain and intra-chain disulfide bonds play different roles in maintaining structure, evidenced by clear separation of inter-chain cysteine residues upon cleavage of disulfide bonds. In BSA, a set of double disulfide bonds required both to be broken in order to observe significant structural changes, equivalently seen in a previous study of human serum albumin (HSA), a structurally similar protein. Structural analysis of IgG showed deviations in distances between domains, while analysis of BSA suggested more local structural changes. This work helps confirm the efficacy and reproducibility of the prescreening methodology on both a novel, larger protein such as IgG and a more homologous (to HSA), globular protein such as BSA. The results provide insight into the role of specific disulfide bonds in the stability of IgG and BSA. KEYWORDS: Molecular Dynamics; Atomistic Simulations; Immunoglobulin G; Bovine Serum Albumin; Disulfide Bonds

scholarly journals Conjugated β-Cyclodextrin Enhances the Affinity of Folic Acid towards FRα: Molecular Dynamics Study

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5304
Author(s):  
Mohammad G. Al-Thiabat ◽  
Amirah Mohd Gazzali ◽  
Noratiqah Mohtar ◽  
Vikneswaran Murugaiyah ◽  
Ezatul Ezleen Kamarulzaman ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Folic Acid ◽  
Root Mean Square ◽  
Active Site ◽  
Md Simulation ◽  
Binding Free Energy ◽  
Cancer Drug ◽  
Radius Of Gyration ◽  
Mean Square ◽  
The Stability

Drug targeting is a progressive area of research with folate receptor alpha (FRα) receiving significant attention as a biological marker in cancer drug delivery. The binding affinity of folic acid (FA) to the FRα active site provides a basis for recognition of FRα. In this study, FA was conjugated to beta-cyclodextrin (βCD) and subjected to in silico analysis (molecular docking and molecular dynamics (MD) simulation (100 ns)) to investigate the affinity and stability for the conjugated system compared to unconjugated and apo systems (ligand free). Docking studies revealed that the conjugated FA bound into the active site of FRα with a docking score (free binding energy < −15 kcal/mol), with a similar binding pose to that of unconjugated FA. Subsequent analyses from molecular dynamics (MD) simulations, root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg) demonstrated that FA and FA–βCDs created more dynamically stable systems with FRα than the apo-FRα system. All systems reached equilibrium with stable RMSD values ranging from 1.9–2.4 Å and the average residual fluctuation values of the FRα backbone atoms for all residues (except for terminal residues ARG8, THR9, THR214, and LEU215) were less than 2.1 Å with a consistent Rg value of around 16.8 Å throughout the MD simulation time (0–100 ns). The conjugation with βCD improved the stability and decreased the mobility of all the residues (except residues 149–151) compared to FA–FRα and apo-FRα systems. Further analysis of H-bonds, binding free energy (MM-PBSA), and per residue decomposition energy revealed that besides APS81, residues HIS20, TRP102, HIS135, TRP138, TRP140, and TRP171 were shown to have more favourable energy contributions in the holo systems than in the apo-FRα system, and these residues might have a direct role in increasing the stability of holo systems.

Synthesis, Photophysics and Theoretical Calculation of (E)-2-(benzo[d] thiazol-2-yl)-3-(3-methoxyphenyl)acrylonitrile

2020 ◽  
Vol 17 (9) ◽  
pp. 688-693
Author(s):  
Pei-Chieh Wu ◽  
Chih-Hsien Chen
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Emission Intensity ◽  
Intermolecular Hydrogen Bond ◽  
Aromatic Rings ◽  
Organic Nanoparticles ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
New Type ◽  
The Stability

In this study, a new type of luminogen with aggregation-induced-emission (AIE) behavior was designed and synthesized. The result of single-crystal X-ray structure showed a planar structure in which the dihedral angle between two aromatic rings is less than 30o. Moreover, two different intermolecular hydrogen bond interactions supported the stability of the crystal structure. After the formation of organic nanoparticles in poor solubility solvent, the emission intensity of the desired product was increased and the enhancement achieved was 14-fold. This new design of luminogen provided further understanding of the AIE mechanism.

scholarly journals New Insights into the Structure of Glycols and Derivatives: A Comparative X-Ray Diffraction, Raman and Molecular Dynamics Study of Ethane-1,2-Diol, 2-Methoxyethan-1-ol and 1,2-Dimethoxy Ethane

Crystals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1011
Author(s):  
Lorenzo Gontrani ◽  
Pietro Tagliatesta ◽  
Antonio Agresti ◽  
Sara Pescetelli ◽  
Marilena Carbone
Keyword(s):  
Molecular Dynamics ◽  
Room Temperature ◽  
Intermolecular Hydrogen Bond ◽  
Hydroxyl Groups ◽  
Gauche Conformation ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Molecular Dynamics Calculations ◽  
Diffraction Patterns ◽  
Intramolecular Hydrogen

In this study, we report a detailed experimental and theoretical investigation of three glycol derivatives, namely ethane-1,2-diol, 2-methoxyethan-1-ol and 1,2-dimethoxy ethane. For the first time, the X-ray spectra of the latter two liquids was measured at room temperature, and they were compared with the newly measured spectrum of ethane-1,2-diol. The experimental diffraction patterns were interpreted very satisfactorily with molecular dynamics calculations, and suggest that in liquid ethane-1,2-diol most molecules are found in gauche conformation, with intramolecular hydrogen bonds between the two hydroxyl groups. Intramolecular H-bonds are established in the mono-alkylated diol, but the interaction is weaker. The EDXD study also evidences strong intermolecular hydrogen-bond interactions, with short O···O correlations in both systems, while longer methyl-methyl interactions are found in 1,2-dimethoxy ethane. X-ray studies are complemented by micro Raman investigations at room temperature and at 80 °C, that confirm the conformational analysis predicted by X-ray experiments and simulations.

Molecular Dynamics Simulation of Nanobubbles

2003 ◽  
Author(s):  
Shu Takagi ◽  
Gota Kikugawa ◽  
Yoichiro Matsumoto
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Pure Water ◽  
Simulation Method ◽  
Bubble Nucleation ◽  
Liquid Interface ◽  
Dynamics Simulation ◽  
Hydroxyl Groups ◽  
Surfactant System ◽  
The Stability

Some results have been reported recently related to the bubble formation with Molecular Dynamics (MD) simulation method. Some of them conduct the MD simulations of the bubble nucleation including impurity molecules with L-J potential [1,2]. In the present study, we investigate the stability of the nanometer size bubble in water, using molecular dynamics (MD) simulation method. MD simulation of an aqueous surfactant system: water liquid and alcohols below the liquid saturation density is carried out to investigate the stability of “nanobubbles” and the structure of the gas-liquid interface. To analyze the effect of surfactant structure, volume, and polarization on the stability of bubble nuclei, we use water by SPC/E model as the solvent molecules and 1-propanol, 1-pentanol, 1-heptanol as the surfactant molecules. Fig.1 shows the numerical result of instantaneous behavior of nanobubbles under the presence of surfactant in water. The calculation system is the cubic cell which has a side length of 25.057[Å], and a three-dimensional periodic boundary condition is applied. To include the intramolecular motion, AMBER force field [3] is adopted as a potential function. The momentum equations are integrated by velocity-Verlet argorithm [4]. Further, the time integration is extended to the Multi Time Scale algorithm by r-RESPA method [5]. As the surfactant molecules, to evaluate the influence of the hydrophobic effect of surfactants on the stability of bubble nuclei, we adopt 1-propanol (C3H7OH), 1-pentanol (C5H11OH), and 1-heptanol (C7H15OH), and to investigate the influence of the polarization of hydrophilic groups (-OH), “pseudo” 1-pentanol of which charge is cancelled away is also calculated. As a result, it was found that from the MD simulation at the condition that the bubble nuclei could not exist stably in pure water, a stable bubble is formed in aqueous surfactant system and hydroxyl groups of surfactants tend to point to the liquid phase at the gas-liquid interface. It is also shown that the longer hydrophobic chains the surfactants have, the more stably the bubble nuclei can exist.

Theoretical study of inclusion complexes of dopamine with β-cyclodextrin based on PM6, ONIOM, and natural bonding orbital analysis

2011 ◽  
Vol 89 (12) ◽  
pp. 1519-1524 ◽  
Author(s):  
Rayenne Djemil ◽  
Djameleddine Khatmi
Keyword(s):  
Intermolecular Hydrogen Bond ◽  
Inclusion Process ◽  
Hydrogen Bond Interactions ◽  
Complex Orientation ◽  
Optimum Position ◽  
Natural Bonding Orbital ◽  
Donor Acceptor ◽  
The Stability ◽  
Cpcm Model ◽  
Orbital Analysis

The inclusion process involving β-cyclodextrin (β-CD) with dopamine (DA) was investigated by using PM6, HF, and ONIOM methods. The most stable structure was obtained at the optimum position and angle. The complex orientation in which the catechol ring of dopamine penetrates into the β-CD cavity near primary hydroxyls is preferred in energy. The structures show the presence of several intermolecular hydrogen bond interactions that were studied on the basis of natural bonding orbital analysis, employed to quantify the donor–acceptor interactions between dopamine and β-CD. A study of these complexes in solution was carried out using the CPCM model to examine the influence of solvation on the stability of the dopamine β-CD complex.

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