scholarly journals Correlated dipolar and dihedral fluctuations in a protein

2021 ◽  
Author(s):  
Abhik Ghosh Moulick ◽  
J. Chakrabarti
Keyword(s):  
Dihedral Angle ◽  
Spectral Density Function ◽  
Dynamics Simulation ◽  
Mutual Orientation ◽  
Amino Acid Residues ◽  
Strong Correlations ◽  
Dipole Orientation ◽  
Auto Correlation Function ◽  
Experimental Values ◽  
Zero Frequency

Correlation between dihedral fluctuations is a possible way to understand coordination between various amino acid residues of the protein. The nanosecond timescales of correlated fluctuations of dihedral angle do not allow direct probing by experimental methods. However, NMR experiments probe dipolar fluctuations given in terms of cross correlated relaxation (CCR) rates, expressed as zero frequency spectral density function (J) of the fluctuations of the mutual orientation of two spatially separated dipole vectors. Here we illustrate the correlation of protein dipolar and dihedral angle using molecular dynamics simulation of protein Ubiquitin (Ub) and GB3. We calculate CCR rates between protein bond vector from simulation and compare with CCR data obtained from NMR experiments. A good correlation between theoretical and experimental values is found. We further show that the zero frequency spectral functions of backbone dihedral ψ auto-correlation function and dipole orientation fluctuations show strong correlations. These correlations are not sensitive to protein and forcefield parameters. Hence, CCR may act as a marker for protein backbone dihedral fluctuations.

scholarly journals Design of peptides with strong binding affinity to poly(methyl methacrylate) resin by use of molecular simulation-based materials informatics

2021 ◽  
Author(s):  
Tomio Iwasaki ◽  
Masashi Maruyama ◽  
Tatsuya Niwa ◽  
Toshiki Sawada ◽  
Takeshi Serizawa
Keyword(s):  
Methyl Methacrylate ◽  
Binding Affinity ◽  
Molecular Simulation ◽  
Dynamics Simulation ◽  
Binding Affinities ◽  
Materials Informatics ◽  
Poly Methyl Methacrylate ◽  
Strong Binding ◽  
Experimental Values ◽  
Pmma Resin

AbstractPeptides with strong binding affinities for poly(methyl methacrylate) (PMMA) resin were designed by use of materials informatics technology based on molecular dynamics simulation for the purpose of covering the resin surface with adhesive peptides, which were expected to result in eco-friendly and biocompatible biomaterials. From the results of binding affinity obtained with this molecular simulation, it was confirmed that experimental values could be predicted with errors <10%. By analyzing the simulation data with the response-surface method, we found that three peptides (RWWRPWW, EWWRPWR, and RWWRPWR), which consist of arginine (R), tryptophan (W), and proline (P), have strong binding affinity to the PMMA resin. These amino acids were effective because arginine and tryptophan have strong binding affinities for methoxycarbonyl groups and methyl groups, which are the main constituents of the PMMA resin, and proline stabilizes the flat zigzag structures of the peptides in water. The strong binding affinities of the three peptides were confirmed by experiments (surface plasmon resonance methods).

scholarly journals Pushing and Pulling on OH-and H3O+ with Electric Fields Across Water’s Surface

2021 ◽  
Author(s):  
kamal ray ◽  
Aditya Limaye ◽  
Ankur Saha ◽  
Ka Chon Ng ◽  
Adam Willard ◽  
...  
Keyword(s):  
Electric Fields ◽  
Second Harmonic ◽  
Ionic Species ◽  
Dynamics Simulation ◽  
Dipole Orientation ◽  
Harmonic Intensity ◽  
Air Interface ◽  
Excess Surface ◽  
Internal Bias ◽  
Pushing And Pulling

<p>We use second harmonic generation spectroscopy, molecular dynamics simulation, and theoretical modeling to study the response of the neat liquid water-air interface to changes in the potential of an external electrode positioned above the liquid. We observe a parabolic dependence of second harmonic intensity on applied potential, indicating that water’s net interfacial dipole responds linearly. We also observe a minimum intensity when the potential is tuned to a specific positive value. Interpreting this minimum based on the macroscopic electrostatic potential profile yields misleading physical conclusions because it neglects the internal bias exerted on molecular orientations by the excess surface concentrations of OH<sup>-</sup> or H<sub>3</sub>O<sup>+</sup>. We thus find that water’s net interfacial dipole orientation is primarily responsive to the effects of these ionic species rather than the external electric field. </p>

scholarly journals Conformation and membrane interaction studies of the potent antimicrobial and anticancer peptide palustrin-Ca

2021 ◽  
Author(s):  
Patrick Brendan Timmons ◽  
Chandralal M Hewage
Keyword(s):  
Sodium Dodecyl ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Peptide Sequence ◽  
Helical Conformation ◽  
Dimensional Structure ◽  
Amino Acid Residues ◽  
Anticancer Activities ◽  
American Bullfrog ◽  
Α Helix

Palustrin-Ca (GFLDIIKDTGKEFAVKILNNLKCKLAGGCPP) is a host defense peptide with potent antimicrobial and anticancer activities, first isolated from the skin of the American bullfrog Lithobates catesbeianus. The peptide is 31 amino acid residues long, cationic and amphipathic. Two-dimensional NMR spectroscopy was employed to characterise its three-dimensional structure in a 50/50% water/2,2,2-trifluoroethanol-d3 mixture. The structure is defined by an α-helix that spans between Ile6-Ala26, and a cyclic disulphide bridged domain at the C-terminal end of the peptide sequence, between residues 23 and 29. A molecular dynamics simulation was employed to model the peptide's interactions with sodium dodecyl sulphate micelles, a widely used bacterial membrane-mimicking environment. Throughout the simulation, the peptide was found to maintain its α-helical conformation between residues Ile6-Ala26, while adopting a position parallel to the surface to micelle, which is energetically-favourable due to many hydrophobic and electrostatic contacts with the micelle.

scholarly journals Pushing and Pulling on OH-and H3O+ with Electric Fields Across Water’s Surface

2021 ◽  
Author(s):  
kamal ray ◽  
Aditya Limaye ◽  
Ankur Saha ◽  
Ka Chon Ng ◽  
Adam Willard ◽  
...  
Keyword(s):  
Electric Fields ◽  
Second Harmonic ◽  
Ionic Species ◽  
Dynamics Simulation ◽  
Dipole Orientation ◽  
Harmonic Intensity ◽  
Air Interface ◽  
Excess Surface ◽  
Internal Bias ◽  
Pushing And Pulling

<p>We use second harmonic generation spectroscopy, molecular dynamics simulation, and theoretical modeling to study the response of the neat liquid water-air interface to changes in the potential of an external electrode positioned above the liquid. We observe a parabolic dependence of second harmonic intensity on applied potential, indicating that water’s net interfacial dipole responds linearly. We also observe a minimum intensity when the potential is tuned to a specific positive value. Interpreting this minimum based on the macroscopic electrostatic potential profile yields misleading physical conclusions because it neglects the internal bias exerted on molecular orientations by the excess surface concentrations of OH<sup>-</sup> or H<sub>3</sub>O<sup>+</sup>. We thus find that water’s net interfacial dipole orientation is primarily responsive to the effects of these ionic species rather than the external electric field. </p>

scholarly journals Study of Caspase 8 Inhibition for the Management of Alzheimer’s Disease: A Molecular Docking and Dynamics Simulation

Molecules ◽  
2020 ◽  
Vol 25 (9) ◽  
pp. 2071
Author(s):  
Syed Sayeed Ahmad ◽  
Meetali Sinha ◽  
Khurshid Ahmad ◽  
Mohammad Khalid ◽  
Inho Choi
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Docking ◽  
Md Simulation ◽  
Simulation Analysis ◽  
Dynamics Simulation ◽  
Caspase 8 ◽  
Amino Acid Residues ◽  
The Stability ◽  
Molecular Docking And Dynamics

Alzheimer’s disease (AD) is the most common type of dementia and usually manifests as diminished episodic memory and cognitive functions. Caspases are crucial mediators of neuronal death in a number of neurodegenerative diseases, and caspase 8 is considered a major therapeutic target in the context of AD. In the present study, we performed a virtual screening of 200 natural compounds by molecular docking with respect to their abilities to bind with caspase 8. Among them, rutaecarpine was found to have the highest (negative) binding energy (−6.5 kcal/mol) and was further subjected to molecular dynamics (MD) simulation analysis. Caspase 8 was determined to interact with rutaecarpine through five amino acid residues, specifically Thr337, Lys353, Val354, Phe355, and Phe356, and two hydrogen bonds (ligand: H35-A: LYS353:O and A:PHE355: N-ligand: N5). Furthermore, a 50 ns MD simulation was conducted to optimize the interaction, to predict complex flexibility, and to investigate the stability of the caspase 8–rutaecarpine complex, which appeared to be quite stable. The obtained results propose that rutaecarpine could be a lead compound that bears remarkable anti-Alzheimer’s potential against caspase 8.

MOLECULAR MODELING OF THE INTERACTIONS BETWEEN HISTONE DEACETYLASE 8 AND INHIBITORS

2012 ◽  
Vol 11 (04) ◽  
pp. 907-924 ◽  
Author(s):  
DAWEI HUANG ◽  
XIAOHUI LI ◽  
ZHILONG XIU
Keyword(s):  
Molecular Dynamics ◽  
Histone Deacetylases ◽  
Hydrophobic Interactions ◽  
Binding Free Energy ◽  
Zinc Ion ◽  
Dynamics Simulation ◽  
Amino Acid Residues ◽  
Domain Docking ◽  
Dynamics Simulations ◽  
Linker Domain

Inhibitors of histone deacetylases (HDACs) have become an attractive class of anticancer agent. To understand the interaction between HDAC8 and inhibitors, including "pan-" inhibitors that inhibit many HDACs isoforms and selective inhibitors with no linker domain, docking and molecular dynamics simulation were conducted. Docking results showed the presence of π-π interactions between "linkerless" inhibitors and the aromatic amino acid residues of HDAC8 in the active site. Binding between HDAC8 and inhibitors was also stabilized by hydrogen bond and hydrophobic interaction. In molecular dynamics simulations, the zinc ion was shown to coordinate one more atom of HDAC8-"linkerless" inhibitor complexes than HDAC8-"pan-" inhibitor complexes. Persistent hydrogen bonds also existed between Tyr306 of HDAC8 and some inhibitors. When inhibitors with large cap groups bound to the active pocket of HDAC8, Phe152 and Met274 shifted from their initial positions and the entrance of the active pocket became more open, resulting in the formation of sub-pocket. Hydrophobic interactions contributed most favorably to the binding free energy between HDAC8 and inhibitors. Lys33, Asp178, Asp267, Tyr306 and Leu308 of HDAC8 were favorable for binding with all inhibitors.

scholarly journals Optical Measurements of Water Lenses in Ice

1987 ◽  
Vol 33 (114) ◽  
pp. 159-161 ◽  
Author(s):  
M.E.R. Walford ◽  
D.W. Roberts ◽  
I. Hill
Keyword(s):  
Grain Boundary ◽  
Specific Surface ◽  
Dihedral Angle ◽  
Focal Length ◽  
Water System ◽  
Optical Measurements ◽  
Free Energies ◽  
Minor Revision ◽  
Experimental Values ◽  
Ice Water

AbstractThe dihedral angle of water at a grain boundary in ice is found, by measuring the optical focal length of lenticular water inclusions, to be 33.6 ± 0.7°. The new result leads to only minor revision of published experimental values of specific surface free energies in the ice–water system (Ketcham and Hobbs, 1969).

Calculation of the isothermal susceptibility by the Kubo formula

1976 ◽  
Vol 54 (14) ◽  
pp. 1461-1464 ◽  
Author(s):  
T. Morita ◽  
T. Horiguchi
Keyword(s):  
Ising Model ◽  
Spectral Density ◽  
Density Function ◽  
Spectral Density Function ◽  
Kubo Formula ◽  
Frequency Limit ◽  
Frequency Dependent ◽  
Isothermal Susceptibility ◽  
Zero Frequency

The relation between the zero frequency limit of the frequency-dependent susceptibility and the isothermal susceptibility is made clearer by expressing them in terms of the spectral density function. The general formulas are illustrated for the perpendicular susceptibilities of the Ising model.

Far infrared reflectivity of liquid Ga–Te alloys

1983 ◽  
Vol 61 (11) ◽  
pp. 1503-1509 ◽  
Author(s):  
S. F. Johnston ◽  
E. D. Crozier ◽  
B. P. Clayman
Keyword(s):  
Fourier Transform ◽  
Composition Dependence ◽  
Far Infrared ◽  
Covalent Bonding ◽  
Band Model ◽  
Constant Density ◽  
Small Constant ◽  
Experimental Values ◽  
Molecular Clustering ◽  
Zero Frequency

The far infrared (FIR) reflectivities of liquid Ga–Te alloys as a function of composition, temperature, and frequency have been measured using both a far infrared laser and Fourier-transform spectroscopy. The reflectivity R is anomalously enhanced between the compositions GaTe and Ga2Te3, suggesting molecular clustering in this alloy range. The temperature dependence of R appears to correspond to an activated conductivity, and is strongest near Ga2Te3. The variation of R with frequency for the stoichiometric alloys is Drude-like at higher frequencies, but is nearly constant below 175 cm−1 for GaTe. The FIR conductivities extrapolated to zero frequency are significantly larger than the direct current (dc) values. The data are similar to liquid Mg–Bi measurements and to the spectra of several amorphous glasses. The composition dependence of R is consistent with a superposed band model for ionic constituents with some covalent bonding. Agreement of the frequency dependence of R with experimental values requires a small constant density of states at the Fermi energy.

DNA Transfection Efficiency of Antimicrobial Peptide as Revealed by Molecular Dynamics Simulation

2013 ◽  
Vol 1569 ◽  
pp. 109-114
Author(s):  
Namsrai Javkhlantugs ◽  
Janlav Munkhtsetseg ◽  
Chimed Ganzorig ◽  
Kazuyoshi Ueda
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Transfection Efficiency ◽  
Dynamics Simulation ◽  
Amino Acid Residues ◽  
Dna Transfection ◽  
Amphipathic Peptide ◽  
Endosomal Membrane ◽  
N Terminus ◽  
Dna Complex

ABSTRACTThe peptide-DNA complex was investigated by using molecular dynamics simulation to analyze the transfection efficiency of cationic amphipathic peptide. Previously, the cationic peptide, LFampinB, with positively charged amino acid residues of Lysines was used to investigate the orientation and interaction energies for entering the cell though disruption of the endosomal membrane. The same interactions were obtained for N-terminus of the LFampinB peptide with membrane and with plasmid DNA. The N-terminus of LFampinB can bind at minor groove of DNA to make complexation of the peptide with DNA.

Sign in / Sign up

Export Citation Format

Share Document