Related Experiment Video
Updated: Jun 4, 2025
10:29
Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
Published on: May 9, 2025
371
Absolute and Relative Binding Free Energy Calculations of Nucleotides to Multiple Protein Classes
Apoorva Purohit1, Xiaolin Cheng1
1Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United States.
Journal of Chemical Theory and Computation
|December 19, 2024
Summary
Alchemical free energy simulations accurately predict nucleotide-protein binding for many enzymes. However, challenges remain with charged ligands, conformational changes, and divalent ions, requiring further simulation refinement.
Area of Science:
- Biochemistry
- Computational Chemistry
- Structural Biology
Background:
- Polyphosphate nucleotides like ATP and GTP are vital for protein function.
- Calculating their binding free energies is challenging due to ligand flexibility and charge.
- Existing computational methods face limitations with these complex interactions.
Purpose of the Study:
- To assess the accuracy of alchemical free energy simulations for nucleotide-protein binding.
- To evaluate fixed-charge force fields in modeling these interactions.
- To identify limitations and guide future computational strategies.
Main Methods:
- Alchemical free energy simulations were performed for four nucleotides binding to nine diverse proteins.
- Fixed-charge force fields were employed to model the interactions.
- Experimental binding free energies were used for validation.
Main Results:
- Simulations accurately reproduced experimental binding free energies for proteins without significant conformational changes (87.5% within ±2 kcal/mol absolute, 88.9% within ±3 kcal/mol relative).
- Inaccuracies were observed when divalent ions were included, indicating limitations of nonpolarizable force fields.
- Extensive conformational sampling is needed for highly charged, flexible ligands.
Conclusions:
- Alchemical simulations are reliable for predicting nucleotide-protein binding when conformational changes are minimal.
- Current force fields struggle with divalent ion interactions in these systems.
- The validated simulation strategy can aid in predicting nucleotide analog binding to protein targets.
Related Concept Videos
02:18The Equilibrium Binding Constant and Binding Strength
12.8K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
12.8K
02:13Nuclear Binding Energy
12.3K
The difference between the calculated and experimentally measured masses is known as the mass defect of the atom. In the case of helium-4, the mass defect indicates a “loss” in mass of 4.0331 amu – 4.0026 amu = 0.0305 amu. The loss in mass accompanying the formation of an atom from protons, neutrons, and electrons is due to the conversion of that mass into energy that is evolved as the atom forms. The nuclear binding energy is the energy produced when the atoms’ nucleons...
12.3K
00:49Ligand Binding and Linkage
4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K
01:49Conserved Binding Sites
4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K
02:49Calculating Standard Free Energy Changes
20.7K
The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
20.7K
01:19Allosteric Proteins-ATCase
5.7K
Binding sites linkages can regulate a protein's function. For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
5.7K