Understanding the avidin-biotin binding based on polarized protein-specific charge

2021 ◽  
Author(s):  
Dawei Zhang ◽  
Rui Duan
Keyword(s):  
Atomic Charges ◽  
Specific Charge ◽  
Biotin Binding ◽  
Biotin Molecule

In this study, charge updating schemes based on the local polarized protein-specific charge (LPPC) were introduced to vary the atomic charges of the biotin molecule and the residues in close...

Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin–biotin binding

Nanoscale ◽  
2020 ◽  
Vol 12 (13) ◽  
pp. 7134-7145 ◽  
Author(s):  
Yalong Cong ◽  
Kaifang Huang ◽  
Yuchen Li ◽  
Susu Zhong ◽  
John Z. H. Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Specific Charge ◽  
Wild Type ◽  
Double Mutation ◽  
Biotin Binding ◽  
Entropic Effect ◽  
Entropic Contribution

Molecular dynamics (MD) simulations were performed employing the polarized protein-specific charge (PPC) to explore the origin of the cooperativity in streptavidin–biotin systems (wild type, two single mutations and one double-mutation).

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

Partition Coefficients of Methylated DNA Bases Obtained from Free Energy Calculations with Molecular Electron Density Derived Atomic Charges.

2018 ◽  
Author(s):  
Alejandro Lara ◽  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Electron Density ◽  
Partition Coefficients ◽  
Dna Bases ◽  
Atomic Charges ◽  
Free Energies ◽  
Solvation Model ◽  
Minimal Basis ◽  
Methylated Dna ◽  
Implicit Solvation Model ◽  
Good Agreement

<div> <div> <div> <p>Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have been also used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in vac- uum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account deriving the atomic charges of polar DNA bases and when the energy needed to polarize the electron den- sity of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogues. Comparison of the two partitioning methods Hirsheld-I and Minimal Basis Iterative Stockholder (MBIS) revealed some deficiencies in the Hirshfeld-I method related to nonexistent isolated anionic nitrogen pro-atoms used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. </p> </div> </div> </div>

SAMPL6 Octanol-Water Partition Coefficients from Alchemical Free Energy Calculations with MBIS Atomic Charges

2019 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Electron Density ◽  
Free Energy Calculations ◽  
Basis Set ◽  
Energetic Cost ◽  
Atomic Charges ◽  
Free Energies ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of eleven molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder(MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed.

scholarly journals More on complex Sachdev-Ye-Kitaev eternal wormholes

2021 ◽  
Vol 2021 (3) ◽  
Author(s):  
Pengfei Zhang
Keyword(s):  
Black Hole ◽  
Ground State ◽  
Effective Action ◽  
Chemical Potential ◽  
Specific Charge ◽  
Zero Temperature ◽  
Small Coupling ◽  
Chemical Potentials ◽  
Quench Dynamics ◽  
Two Sides

Abstract In this work, we study a generalization of the coupled Sachdev-Ye-Kitaev (SYK) model with U(1) charge conservations. The model contains two copies of the complex SYK model at different chemical potentials, coupled by a direct hopping term. In the zero-temperature and small coupling limit with small averaged chemical potential, the ground state is an eternal wormhole connecting two sides, with a specific charge Q = 0, which is equivalent to a thermofield double state. We derive the conformal Green’s functions and determine corresponding IR parameters. At higher chemical potential, the system transit into the black hole phase. We further derive the Schwarzian effective action and study its quench dynamics. Finally, we compare numerical results with the analytical predictions.

Expression of various biotin-binding proteins in transgenic tobacco confers resistance to potato tuber moth, Phthorimaea operculella (Zeller) (fam. Gelechiidae)

2010 ◽  
Vol 19 (6) ◽  
pp. 1041-1051 ◽  
Author(s):  
Colleen Murray ◽  
Ngaire P. Markwick ◽  
Ryohei Kaji ◽  
Joanne Poulton ◽  
Harry Martin ◽  
...  
Keyword(s):  
Potato Tuber ◽  
Transgenic Tobacco ◽  
Binding Proteins ◽  
Phthorimaea Operculella ◽  
Potato Tuber Moth ◽  
Biotin Binding
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