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Assessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum Mechanics Based Proposal

Ortiz Mahecha, Carlos A.; Bohórquez, Hugo Javier; Agudelo, William A.; Patarroyo, Manuel A.; Patarroyo, Manuel Elkin; Suárez, Carlos F. (2019)

Estimating peptide-major histocompatibility complex (pMHC) binding using structural computational methods has an impact on understanding overall immune function triggering adaptive immune responses in MHC class II molecules. ...
Exploring the electron density localization in single MoS2 monolayers by means of a localize-electrons detector and the quantum theory of atoms in molecules

Aray, Yosslen (2017)

The nature of the electron density localization in a MoS2 monolayer under 0 % to 11% tensile strain has been systematically studied by means of a localized electron detector function and the Quantum Theory of atoms in ...
Semi-empirical quantum evaluation of peptide – MHC class II binding

González, Ronald; Suárez, Carlos F.; Bohórquez, Hugo J.; Patarroyo, Manuel A.; Patarroyo, Manuel E. (2017)

Peptide presentation by the major histocompatibility complex (MHC) is a key process for triggering a specific immune response. Studying peptide-MHC (pMHC) binding from a structural-based approach has potential for reducing ...

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Assessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum Mechanics Based Proposal
...
Ortiz Mahecha, Carlos A. | 2019

Estimating peptide-major histocompatibility complex (pMHC) binding using structural computational methods has an impact on understanding overall immune function triggering adaptive immune responses in MHC class II molecules. We developed a strategy for optimizing pMHC structure interacting with water molecules and for calculating the binding energy of receptor + ligand systems, such as HLA-DR1 + HA, HLA-DR1 + CLIP, HLA-DR2 + MBP, and HLA-DR3 + CLIP, as well as a monosubstitution panel. Taking pMHC's structural properties, we assumed that ΔH ≫ -TΔS would generate a linear model for estimating relative free energy change, using three semiempirical quantum methods (PM6, PM7, and FMO-SCC-DFTB3) along with the implicit solvent models, and considering proteins in neutral and charged states. Likewise, we confirmed our approach's effectiveness in calculating binding energies having high correlation with experimental data and low root-mean-square error (<2 kcal/mol). All in all, our pipeline differentiates weak from strong peptide binders as a reliable method for studying pMHC interactions.

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Exploring the electron density localization in single MoS2 monolayers by means of a localize-electrons detector and the quantum theory of atoms in molecules
...
Aray, Yosslen | 2017

The nature of the electron density localization in a MoS2 monolayer under 0 % to 11% tensile strain has been systematically studied by means of a localized electron detector function and the Quantum Theory of atoms in molecules. At 10% tensile strain, this monolayer become metallic. It was found that for less than 6.5% of applied stress, the same atomic structure of the equilibrium geometry (0% strain) is maintained; while over 6.5% strain induces a transformation to a structure where the sulfur atoms placed on the top and bottom layer form S2 groups. The localized electron detector function shows the presence of zones of highly electron delocalization extending throughout the Mo central layer. For less than 10% tensile strain, these zones comprise the BCPs and the remainder CPs in separates regions of the space; while for the structures beyond 10% strain, all the critical points are involved in a region of highly delocalized electrons that extends throughout the material. This dissimilar electron localization pattern is like to that previously reported for semiconductors such as Ge bulk and metallic systems such as transition metals bulk. © 2017 Author(s).

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Semi-empirical quantum evaluation of peptide – MHC class II binding
...
González, Ronald | 2017

Peptide presentation by the major histocompatibility complex (MHC) is a key process for triggering a specific immune response. Studying peptide-MHC (pMHC) binding from a structural-based approach has potential for reducing the costs of investigation into vaccine development. This study involved using two semi-empirical quantum chemistry methods (PM7 and FMO-DFTB) for computing the binding energies of peptides bonded to HLA-DR1 and HLA-DR2. We found that key stabilising water molecules involved in the peptide binding mechanism were required for finding high correlation with IC50 experimental values. Our proposal is computationally non-intensive, and is a reliable alternative for studying pMHC binding interactions.

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Assessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum Mechanics Based Proposal ﻿

Exploring the electron density localization in single MoS2 monolayers by means of a localize-electrons detector and the quantum theory of atoms in molecules ﻿

Semi-empirical quantum evaluation of peptide – MHC class II binding ﻿

Envíos recientes

Assessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum Mechanics Based Proposal

Exploring the electron density localization in single MoS2 monolayers by means of a localize-electrons detector and the quantum theory of atoms in molecules

Semi-empirical quantum evaluation of peptide – MHC class II binding

Assessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum Mechanics Based Proposal

Exploring the electron density localization in single MoS2 monolayers by means of a localize-electrons detector and the quantum theory of atoms in molecules

Semi-empirical quantum evaluation of peptide – MHC class II binding