☆ 4.5 Article

Molecular Modeling of the Deamidation Reaction in Solution: A Theoretical-Computational Study

JOURNAL OF PHYSICAL CHEMISTRY B (2023)

相关参考文献

注意：仅列出部分参考文献，下载原文获取全部文献信息。

Article Chemistry, Physical

PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method

Cheng Giuseppe Chen et al.

Summary: PyMM is a Python software package that applies the QM/MM approach using the perturbed matrix method in a simple and efficient way. It accurately describes the electronic properties of the system and provides various perturbed calculations and analyses for common electronic properties.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2023)

添加到收藏夹

Article Biochemistry & Molecular Biology

Modelling Complex Bimolecular Reactions in a Condensed Phase: The Case of Phosphodiester Hydrolysis

Alessandro Nicola Nardi et al.

Summary: In this study, the kinetics of hydroxide-promoted hydrolysis of phosphoric diesters were modeled using a hybrid quantum/classical approach. The results suggest that the hydrolysis occurs through a concerted A(N)D(N) mechanism, with no formation of penta-coordinated intermediates. This modeling method has the potential to predict rate constants and reactivities/selectivities in complex environments.

MOLECULES (2023)

添加到收藏夹

Article Chemistry, Medicinal

Oxidation and Deamidation of Monoclonal Antibody Products: Potential Impact on Stability, Biological Activity, and Efficacy

Surbhi Gupta et al.

Summary: Therapeutic proteins, especially monoclonal antibodies (mAbs), play a significant role in human health. The physical and chemical degradation, particularly oxidation and deamidation, can affect the properties and efficacy of the products.

JOURNAL OF PHARMACEUTICAL SCIENCES (2022)

添加到收藏夹

Review Medicine, Research & Experimental

In silico prediction of post-translational modifications in therapeutic antibodies

Shabdita Vatsa

Summary: This article reviews the application of computational methods in predicting modifications of antibodies, including deamidation, isomerization, and oxidation. Although progress has been made, the accuracy of predictions can be improved using machine learning and molecular dynamic simulations. Opportunities for improvement and development are also discussed.

MABS (2022)

添加到收藏夹

Article Biochemistry & Molecular Biology

Theoretical Evaluation of Sulfur-Based Reactions as a Model for Biological Antioxidant Defense

Maria Laura De Sciscio et al.

Summary: Sulfur-containing amino acids play a crucial role in maintaining cellular redox homeostasis and modulating signaling cascades. This study successfully simulated sulfur-based reactions using a theoretical-computational approach, providing a foundation for studying these mechanisms in complex biological systems.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

添加到收藏夹

Article Medicine, Research & Experimental

Deciphering deamidation and isomerization in therapeutic proteins: Effect of neighboring residue

Flaviyan Jerome Irudayanathan et al.

Summary: In this study, the mechanisms of spontaneous degradation of Asn and Asp residues in 131 clinical-stage therapeutic antibodies were investigated using proton-affinity calculations and molecular dynamics simulations. The secondary structure of the backbone, the conformation of the side-chain rotamer, and the solvent accessibility were found to be key indicators of Asp isomerization and Asn deamidation. A mechanistic explanation for the influence of the identity of the n + 1 residue on the rate of degradation was proposed based on the analysis of backbone dihedral angles and N-H proton affinity calculations. Based on these findings, a physics-based classification model was proposed to predict the propensity of deamidation and isomerization in proteins.

MABS (2022)

添加到收藏夹

Article Chemistry, Multidisciplinary

Deamidation reaction network mapping of pharmacologic and related proteins: impact of solvation dielectric on the degradation energetics of asparagine dipeptides

Katherine E. Lawson et al.

Summary: This study mapped out the deamidation of Asn-X dipeptides into Asp-X dipeptides using density functional theory (DFT). The researchers predicted the selectivity of the deamidation reaction and identified the most likely deamidation reaction mechanism for each dipeptide.

REACTION CHEMISTRY & ENGINEERING (2022)

添加到收藏夹

Article Chemistry, Physical

Q-Force: Quantum Mechanically Augmented Molecular Force Fields

Selim Sami et al.

Summary: The Q-Force protocol enhances transferable force fields with molecule-specific parameters derived from quantum mechanical calculations, improving the accuracy of molecular dynamics simulations. Its molecular fragmentation procedure allows treatment of large molecules with low computational cost, making it widely applicable for atomistic molecular dynamics simulations.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

添加到收藏夹

Article Chemistry, Physical

DNA cleavage by endonuclease I-DmoI: a QM/MM study and comparison with experimental data provide indications on the environmental effects

Giuseppe E. Segreto et al.

THEORETICAL CHEMISTRY ACCOUNTS (2020)

添加到收藏夹

Article Biochemistry & Molecular Biology

Altered Protein Dynamics and Increased Aggregation of Human γS-Crystallin Due to Cataract-Associated Deamidations

Heather M. Forsythe et al.

BIOCHEMISTRY (2019)

添加到收藏夹

Article Medicine, Research & Experimental

Machine Learning Enables Accurate Prediction of Asparagine Deamidation Probability and Rate

Jared A. Delmar et al.

MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT (2019)

添加到收藏夹

Review Pharmacology & Pharmacy

Biopharmaceutical Informatics: supporting biologic drug development via molecular modelling and informatics

Sandeep Kumar et al.

JOURNAL OF PHARMACY AND PHARMACOLOGY (2018)

添加到收藏夹

Article Medicine, Research & Experimental

Structure Based Prediction of Asparagine Deamidation Propensity in Monoclonal Antibodies

Qingrong Yan et al.

MABS (2018)

添加到收藏夹

Article Chemistry, Physical

Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory

Laura Zanetti-Polzi et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2018)

添加到收藏夹

Article Chemistry, Physical

Quantifying the Risks of Asparagine Deamidation and Aspartate Isomerization in Biopharmaceuticals by Computing Reaction Free Energy-Surfaces

Nikolay V. Plotnikov et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2017)

添加到收藏夹

Review Biotechnology & Applied Microbiology

Protein deamidation in biopharmaceutical manufacture: understanding, control and impact

David Gervais

JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (2016)

添加到收藏夹

Article Biochemistry & Molecular Biology

Why Does Asn71 Deamidate Faster Than Asn15 in the Enzyme Triosephosphate Isomerase? Answers from Microsecond Molecular Dynamics Simulation and QM/MM Free Energy Calculations

Ilke Ugur et al.

BIOCHEMISTRY (2015)

添加到收藏夹

Article Chemistry, Physical

Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

Michael J. Robertson et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

添加到收藏夹

Article Chemistry, Physical

In silico characterization of protein partial molecular volumes and hydration shells

Sara Del Galdo et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2015)

添加到收藏夹

Article Multidisciplinary Sciences

Structure-Based Prediction of Asparagine and Aspartate Degradation Sites in Antibody Variable Regions

Jasmin F. Sydow et al.

PLOS ONE (2014)

添加到收藏夹

Article Computer Science, Interdisciplinary Applications

A flexible algorithm for calculating pair interactions on SIMD architectures

Szilard Pall et al.

COMPUTER PHYSICS COMMUNICATIONS (2013)

添加到收藏夹

Article Chemistry, Medicinal

Asparagine deamidation dependence on buffer type, pH, and temperature

Amanda L. Pace et al.

JOURNAL OF PHARMACEUTICAL SCIENCES (2013)

添加到收藏夹

Article Chemistry, Physical

Initiation of the Reaction of Deamidation in Triosephosphate Isomerase: Investigations by Means of Molecular Dynamics Simulations

Ilke Ugur et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2012)

添加到收藏夹

Article Chemistry, Physical

Free Energy Barriers for the N-Terminal Asparagine to Succinimide Conversion: Quantum Molecular Dynamics Simulations for the Fully Solvated Model

Ilya Kaliman et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

添加到收藏夹

Article Chemistry, Physical

Deamidation of Asparagine Residues: Direct Hydrolysis versus Succinimide-Mediated Deamidation Mechanisms

Saron Catak et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2009)

添加到收藏夹

Article Chemistry, Physical

Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the Haem carbon monoxide binding-unbinding reaction in Myoglobin

Andrea Amadei et al.

THEORETICAL CHEMISTRY ACCOUNTS (2007)

添加到收藏夹

Article Chemistry, Physical

Canonical sampling through velocity rescaling

Giovanni Bussi et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

添加到收藏夹

Article Biochemical Research Methods

Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: Does deamidation contribute to crystallin insolubility?

P. A. Wilmarth et al.

JOURNAL OF PROTEOME RESEARCH (2006)

添加到收藏夹

Article Chemistry, Organic

Theoretical modeling of chemical reactions in complex environments: The intramolecular proton transfer in aqueous malonaldehyde

Massimiliano Aschi et al.

JOURNAL OF PHYSICAL ORGANIC CHEMISTRY (2006)

添加到收藏夹

Article Biochemistry & Molecular Biology

Asparagine deamidation: pH-dependent mechanism from density functional theory

B Peters et al.

BIOCHEMISTRY (2006)

添加到收藏夹

Article Chemistry, Physical

Statistical mechanical modeling of chemical reactions in complex systems: The reaction free energy surface

A Amadei et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2004)

添加到收藏夹

Article Biochemical Research Methods

Structure-dependent nonenzymatic deamidation of glutaminyl and asparaginyl pentapeptides

NE Robinson et al.

JOURNAL OF PEPTIDE RESEARCH (2004)

添加到收藏夹

Article Biochemical Research Methods

Prediction of primary structure deamidation rates of asparaginyl and glutaminyl peptides through steric and catalytic effects

NE Robinson et al.

JOURNAL OF PEPTIDE RESEARCH (2004)

添加到收藏夹

Article Chemistry, Physical

Electronic properties of formaldehyde in water: a theoretical study

A Amadei et al.

CHEMICAL PHYSICS LETTERS (2003)

添加到收藏夹

Article Chemistry, Physical

Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K

P Mark et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2001)

添加到收藏夹

Article Chemistry, Multidisciplinary

Neighboring side chain effects on asparaginyl and aspartyl degradation: An ab initio study of the relationship between peptide conformation and backbone NH acidity

JL Radkiewicz et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)

添加到收藏夹

Article Multidisciplinary Sciences

Molecular clocks

NE Robinson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

添加到收藏夹

Article Biochemical Research Methods

Kinetic and thermodynamic control of the relative yield of the deamidation of asparagine and isomerization of aspartic acid residues

S Capasso et al.

JOURNAL OF PEPTIDE RESEARCH (2000)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.