Calculation of absolute protein–ligand binding free energy from computer simulations
Open accessAbstract
A general methodology for calculating the equilibrium binding constant of a flexible ligand to a protein receptor is formulated on the basis of potentials of mean force. The overall process is decomposed into several stages that can be computed separately: the free ligand in the bulk is first restrained into the conformation it adopts in the bound state, position, and orientation by applying biasing potentials, then it is translated into the binding site, where it is released completely. The conformational restraining potential is based on the root-mean-square deviation of the peptide coordinates relative to its average conformation in the bound complex. Free energy contributions from each stage are calculated by means of free energy perturbation potential of mean force techniques by using appropriate order parameters. The present approach avoids the need to decouple the ligand from its surrounding (bulk solvent and receptor protein) as is traditionally performed in the double-decoupling scheme. It is believed that the present formulation will be particularly useful when the solvation free energy of the ligand is very large. As an application, the equilibrium binding constant of the phosphotyrosine peptide pYEEI to the Src homology 2 domain of human Lck has been calculated. The results are in good agreement with experimental values.
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When applied to protein assemblies, MM-PBSA and MM-GBSA frequently produce binding free estimates with large statistical errors and make approximations, such as neglecting or partially accounting for the effects of changes in internal energy and entropy on protein association free energies, resulting in limited accuracy.
“However, when applied to protein assemblies, these methods frequently produce binding free estimates with large statistical errors53 and make a number of approximations, such as neglecting or partially accounting for the effects of changes in internal energy and entropy on protein association free energies, resulting in limited accuracy.54”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [54]
Woo and Roux pioneered the geometrical route for binding free energy calculations, where the binding process is decomposed into distinct, independent processes, each described by a unique CV corresponding to a specific slow degree of freedom of the system.
“To this end, Woo and Roux pioneered the so-called geometrical route for binding free energy calculations, where the binding process is decomposed into distinct, independent processes, each described by a unique CV, which corresponds to a specific slow degree of freedom of the system.”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [54]
The protocol has so far been successfully used in calculating the binding free energy of a variety of protein-protein complexes, in good agreement with experimental data, including a homodimeric α-helical complex.
“The protocol has so far been successfully used in calculating the binding free energy of a variety of protein–protein complexes, in good agreement with experimental data,54,62,64,65,67,73−76 including a homodimeric α-helical complex.69”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [54]
According to the geometrical route framework, the binding constant Keq can be expressed as a function of the free energy contributions from applied conformational, orientational and positional restraints in the bound and unbound states.
“According to the geometrical route framework proposed by Woo and Roux,54 the binding constant Keq can be expressed as a function of the free energy contributions from the applied conformational (c), orientational (o) and positional (a) restraints in the bound (site) and unbound (bulk) states (eq 2).”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [54]
More precise free energy changes can be obtained through the application of restraints which ensure that the relative orientation and position of the ligand with respect to the receptor is preserved and therefore the available phase space to be sampled during the simulations is reduced.
“More precise free energy changes can be obtained through the application of restraints which ensure that the relative orientation and position of the ligand with respect to the receptor is preserved and therefore the available phase space to be sampled during the simulations is reduced.54,63−65”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [54]
The separation PMF makes the largest contribution to the total binding free energy.
“The largest contribution is attributed to the separation PMF, as expected, reflecting the intermolecular interactions formed between “receptor” and “ligand” upon binding.54”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [54]
The RMSD term quantifies the loss of internal conformational freedom.
“By definition < 0 and > 0, so the term quantifies the loss of internal conformational freedom.54”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [54]
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“62,62,65,69 The protocol has so far been successfully used in calculating the binding free energy of a variety of protein − protein complexes, in good agreement with experimental data, 54,62,64,65,67,73 − 76 including a homodimeric α -helical complex.”
Influential
- Authors
- Woo, H.-J., & Roux, B.
- Affiliations
- Cornell University (US)
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2005-05-02
- Volume
- 102
- Issue
- 19
- Pages
- 6825-6830
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC1100764
- OpenAlex
- W2035672721
- Cited by
- 661
- References
- 1
- Citations by year
- 2026: 17 · 2025: 38 · 2024: 37 · 2023: 43 · 2022: 40 · 2021: 33 · 2020: 54 · 2019: 38 · 2018: 37 · 2017: 36 · 2016: 37 · 2015: 25 · 2014: 26 · 2013: 41 · 2012: 33
- FWCI
- 16.55
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (CA 93577, R01CA093577)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Keywords
- protein-ligand binding free energy, binding equilibrium constants, potential of mean force, free energy perturbation, flexible ligands, solvation free energy, SH2 domain, Lck, protein-peptide interactions
- MeSH terms
- Binding Sites, Computer Simulation, Humans, Kinetics, Ligands, Models, Molecular, Peptides, Protein Binding, Protein Conformation, Thermodynamics, Models, Statistical, Crystallography, X-Ray, src Homology Domains, Phosphotyrosine, Computational Biology, Lymphocyte Specific Protein Tyrosine Kinase p56(lck)
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