scholarly journals Complexation of 26-Mer Amylose with Egg Yolk Lipids with Different Numbers of Tails Using a Molecular Dynamics Simulation

Foods ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2355
Author(s):  
Shangyuan Sang ◽  
Xueming Xu ◽  
Xiao Zhu ◽  
Ganesan Narsimhan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Egg Yolk ◽  
Dynamics Simulation ◽  
Helical Conformation ◽  
Stable Complex ◽  
Tail Region ◽  
Cross Sectional ◽  
Average Binding Energy ◽  
Helical Region

A molecular dynamics simulation of mixtures of 26-mer amylose with three different egg yolk lipids, namely, cholesterol, triglyceride and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), demonstrated the formation of a stable complex. The 26-mer amylose fluctuated between a coiled and an extended helical conformation. The complex was a V-type amylose complex, with the hydrophobic tail of the lipids being inside the hydrophobic helical cavity of the amylose. The number of glucose units per turn was six for the two helical regions of the amylose-POPC complex and the palmitoyl tail region of the amylose-triglyceride complex. This value was eight for the cholesterol and the two-tail helical region in the amylose-triglyceride complex. Two tails of the POPC were in two different hydrophobic helical regions of the 26-mer amylose, whereas the palmitoyl tail of the triglyceride lay in one hydrophobic helical region and the linoleoyl and oleoyl tails both lay in another helical region, and the cross-sectional area of the latter was larger than the former to accommodate the two tails. The radii of the gyration of the complex were lower for all three cases compared to that of one single amylose. In addition, the stability of the complexes was ranked in the following order: POPC < cholesterol < triglyceride, with their average binding energy being −97.83, −134.09, and −198.35 kJ/mol, respectively.

THE EFFECT OF THE RANGE OF THE POTENTIAL ON THE MULTI-STEP CLUSTER MELTING PROCESS

2004 ◽  
Vol 15 (05) ◽  
pp. 649-658 ◽  
Author(s):  
SHI-WEI REN
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Morse Potential ◽  
Melting Process ◽  
Dynamics Simulation ◽  
Repulsive Core ◽  
Tail Region ◽  
Step Process

By using the microcanonical molecular dynamics simulation, the melting processes of the clusters bound by Morse potential are investigated. It is found that these clusters show a multi-step melting process as long as the range of the Morse potential is a suitable value. The origins of this multi-step process are analyzed. I find that not only the repulsive core of the potential but also the attractive tail range of the potential influences the melting process. Moreover, the occurrence of the multi-step melting process is more sensitive to the tail region of the Morse potential.

scholarly journals Computer simulation of complex of lysine dendrigraft with molecules of therapeutic KED peptide

2019 ◽  
Vol 24 ◽  
pp. 02008
Author(s):  
Igor Neelov ◽  
Valerii Bezrodnyi ◽  
Anna Marchenko ◽  
Emil Fatullaev ◽  
Sofia Miktaniuk
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Molecular Dynamics Simulation ◽  
Complex Formation ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Stable Complex ◽  
Target Organs ◽  
Therapeutic Peptides ◽  
Drug And Gene Delivery

Lysine dendrimers and dendrigrafts are often used in biomedicine for drug and gene delivery to different target organs or cells. In present paper the possibility of complex formation by lysine dendrigraft and 16 molecules of therapeutic KED peptide was investigated using molecular dynamics simulation method. A system containing of one dendrigraftt and 16 KED peptides in water were studied. It was shown that stable complex consisting of the dendrigraft and the peptide molecules formed and structure of this complex was studied. Similar complexes could be used in future for delivery of other therapeutic peptides to target organs.

scholarly journals High-Throughput Virtual Screening, Molecular Dynamics Simulation, and Enzyme Kinetics Identified ZINC84525623 as a Potential Inhibitor of NDM-1

2019 ◽  
Vol 20 (4) ◽  
pp. 819 ◽  
Author(s):  
Md Rehman ◽  
Mohamed AlAjmi ◽  
Afzal Hussain ◽  
Gulam Rather ◽  
Meraj Khan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Virtual Screening ◽  
Enzyme Kinetics ◽  
High Throughput ◽  
Md Simulation ◽  
Dynamics Simulation ◽  
Multi Drug Resistance ◽  
Stable Complex ◽  
High Throughput Virtual Screening

The bacteria expressing New Delhi Metallo-β-lactamase-1 (NDM-1) can hydrolyze all β-lactam antibiotics including carbapenems, causing multi-drug resistance. The worldwide emergence and dissemination of gene blaNDM-1 (produces NDM-1) in hospital and community settings, rising problems for public health. Indeed, there is an urgent need for NDM-1 inhibitors to manage antibiotic resistance. Here, we have identified novel non-β-lactam ring-containing inhibitors of NDM-1 by applying a high-throughput virtual screening of lead-like subset of ZINC database. The screened compounds were followed for the molecular docking, the molecular dynamics simulation, and then enzyme kinetics assessment. The adopted screening procedure funnels out five novel inhibitors of NDM-1 including ZINC10936382, ZINC30479078, ZINC41493045, ZINC7424911, and ZINC84525623. The molecular mechanics-generalized born surface area and molecular dynamics (MD) simulation showed that ZINC84525623 formed the most stable complex with NDM-1. Furthermore, analyses of the binding pose after MD simulation revealed that ZINC84525623 formed two hydrogen bonds (electrostatic and hydrophobic interaction) with key amino acid residues of the NDM-1 active site. The docking binding free energy and docking binding constant for the ZINC84525623 and NDM-1 interaction were estimated to be −11.234 kcal/mol, and 1.74 × 108 M−1 respectively. Steady-state enzyme kinetics in the presence of ZINC84525623 show the decreased catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics. The findings of this study would be helpful in identifying novel inhibitors against other β-lactamases from a pool of large databases. Furthermore, the identified inhibitor (ZINC84525623) could be developed as efficient drug candidates.

Effects of osmolytes on the helical conformation of model peptide: Molecular dynamics simulation

2011 ◽  
Vol 134 (3) ◽  
pp. 035104 ◽  
Author(s):  
Faramarz Mehrnejad ◽  
Mohammad Mehdi Ghahremanpour ◽  
Mahmoud Khadem-Maaref ◽  
Farahnoosh Doustdar
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Helical Conformation ◽  
Model Peptide

Ag wire and Ag alloy wire reliability and molding compounds

2013 ◽  
Vol 2013 (1) ◽  
pp. 000045-000049 ◽  
Author(s):  
Aya Mizushima ◽  
Shinichiro Kato ◽  
Hidenori Abe ◽  
Naoki Sadayori ◽  
Yoshinori Endo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Intermetallic Compound ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Ion Content ◽  
Cross Sectional ◽  
Alloy Wire ◽  
Molding Compounds ◽  
Accumulation Mechanism

Ag wire and Ag alloy wire reliability experiments were conducted on both 28-lead SOP and 96-pin PBGA packages. Biased HAST (b-HAST) of Ag-wired packages with higher ion content molding compouds generated obvious defects promoted by ion accumulation mechanism. Intermetallic compounds (IMCs) at the corroded interface are identified using cross-sectional TEM/EDX. Ion selective affinity of intermetallic compound is rationalized using ab initio molecular dynamics simulation.

scholarly journals Stability, Hydrogen Bond Occupancy Analysis and Binding Free Energy Calculation from Flavonol Docked in DAPK1 Active Site Using Molecular Dynamic Simulation Approaches

2020 ◽  
Author(s):  
Adi Tiara Zikri ◽  
Harno Dwi Pranowo ◽  
Winarto Haryadi
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Stable Complex ◽  
Energy Calculation ◽  
Compound C ◽  
C Complex

Stability and hydrogen bond occupancy analysis of flavonol derivative docked in DAPK1 have been carried out using molecular dynamics simulation approach. Six flavonol derivatives were docked in DAPK1 as protein target, then continued with molecular dynamics simulation. NVT and NPT ensembles were used to equilibrate the system, followed by 20 ns sampling time for each system. Structural stability and hydrogen bond occupancy analyses were carried out at the NVT ensemble, while free binding energy analysis was done at NPT ensemble. From all compounds used in this work, compound B (5,7-dihydroxy-2-(4-hydroxyphenyl)-6-methoxy-4H-chromen-4-one) has a similar interaction with reference ligands (quercetin, kaempferol, and fisetin), and the most stable complex system has the maximum RMSD around 2 Å. Compound C complex has -48.06 kJ/mol binding free energy score, and it was slightly different from quercetin, kaempferol, and fisetin complexes. Even though complex C has similar binding free energy with the reference compound, complex B shows more stable interactions due to their hydrogen bond and occupancy.

Identification of butyrylcholinesterase and monoamine oxidase B targeted ligands and their putative application in Alzheimer’s treatment: A computational strategy

2021 ◽  
Vol 27 ◽  
Author(s):  
Nasimudeen R Jabir ◽  
Md Tabish Rehman ◽  
Shams Tabrez ◽  
Raed F. Alserihi ◽  
Mohamed F AlAjmi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Monoamine Oxidase ◽  
Monoamine Oxidase A ◽  
Dynamics Simulation ◽  
Stable Complex ◽  
Monoamine Oxidase B ◽  
Mao B ◽  
Computational Screening ◽  
Mao A

Background: With the burgeoning worldwide aging population, the incidence of Alzheimer’s disease (AD) and its associated disorders is continuously rising. To appraise other relevant drug targets that could lead to potent enzyme targeting, 13 previously predicted ligands (shown favorable binding with AChE (acetylcholinesterase) and GSK-3 (glycogen synthase kinase) were screened for targeting 3 different enzymes namely butyrylcholinesterase (BChE), monoamine oxidase A (MAO-A), and monoamine oxidase B (MAO-B) to possibly meet the unmet medical need of better AD treatment. Materials and Methods: The study utilized in silico screening of 13 ligands against BChE, MAO-A and MAO-B using PyRx-Python prescription 0.8. The visualization of active interaction of studied compounds with targeted proteins was performed by Discovery Studio 2020 (BIOVIA). Results: The computational screening of studied ligands revealed the docking energies in the range of -2.4 to -11.3 kcal/mol for all the studied enzymes. Among the 13 ligands, 8 ligands (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed the binding energies of ≤ -8.0 kcal/mol towards BChE, MAO-A and MAO-B. The ligand 6Z5 was found to be the most potent inhibitor of BChE and MAO-B, with a binding energy of -9.7 and -10.4 kcal mol respectively. Molecular dynamics simulation of BChE-6Z5 and MAO-B-6Z5 complex confirmed the formation of a stable complex. Conclusion: Our computational screening, molecular docking, and molecular dynamics simulation studies revealed that the above-mentioned enzymes targeted ligands might expedite the future design of potent anti-AD drugs generated on this chemical scaffold.

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