Charge-Changing Perturbations and Path Sampling via Classical Molecular Dynamic Simulations of Simple Guest–Host Systems
Currently, two different methods dominate the field of biomolecular free-energy calculations for the prediction of binding affinities. Pathway methods are frequently used for large ligands that bind on the surface of a host, such as protein–protein complexes. Alchemical methods, on the other hand, a...
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| Published in | Journal of chemical theory and computation Vol. 16; no. 12; pp. 7721 - 7734 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
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American Chemical Society
08.12.2020
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| Abstract | Currently, two different methods dominate the field of biomolecular free-energy calculations for the prediction of binding affinities. Pathway methods are frequently used for large ligands that bind on the surface of a host, such as protein–protein complexes. Alchemical methods, on the other hand, are preferably applied for small ligands that bind to deeply buried binding sites. The latter methods are also widely known to be heavily artifacted by the representation of electrostatic energies in periodic simulation boxes, in particular, when net-charge changes are involved. Different methods have been described to deal with these artifacts, including postsimulation correction schemes and instantaneous correction schemes (e.g., co-alchemical perturbation of ions). Here, we use very simple test systems to show that instantaneous correction schemes with no change in the system net charge lower the artifacts but do not eliminate them. Furthermore, we show that free energies from pathway methods suffer from the same artifacts. |
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| AbstractList | Currently, two different methods dominate
the field of biomolecular free-energy calculations for the prediction
of binding affinities. Pathway methods are frequently used for large
ligands that bind on the surface of a host, such as protein–protein
complexes. Alchemical methods, on the other hand, are preferably applied
for small ligands that bind to deeply buried binding sites. The latter
methods are also widely known to be heavily artifacted by the representation
of electrostatic energies in periodic simulation boxes, in particular,
when net-charge changes are involved. Different methods have been
described to deal with these artifacts, including postsimulation correction
schemes and instantaneous correction schemes (e.g., co-alchemical
perturbation of ions). Here, we use very simple test systems to show
that instantaneous correction schemes with no change in the system
net charge lower the artifacts but do not eliminate them. Furthermore,
we show that free energies from pathway methods suffer from the same
artifacts. Currently, two different methods dominate the field of biomolecular free-energy calculations for the prediction of binding affinities. Pathway methods are frequently used for large ligands that bind on the surface of a host, such as protein–protein complexes. Alchemical methods, on the other hand, are preferably applied for small ligands that bind to deeply buried binding sites. The latter methods are also widely known to be heavily artifacted by the representation of electrostatic energies in periodic simulation boxes, in particular, when net-charge changes are involved. Different methods have been described to deal with these artifacts, including postsimulation correction schemes and instantaneous correction schemes (e.g., co-alchemical perturbation of ions). Here, we use very simple test systems to show that instantaneous correction schemes with no change in the system net charge lower the artifacts but do not eliminate them. Furthermore, we show that free energies from pathway methods suffer from the same artifacts. |
| Author | Perthold, Jan Walther Lier, Bettina Öhlknecht, Christoph Oostenbrink, Chris |
| AuthorAffiliation | Institute of Molecular Modeling and Simulation |
| AuthorAffiliation_xml | – name: Institute of Molecular Modeling and Simulation |
| Author_xml | – sequence: 1 givenname: Christoph orcidid: 0000-0003-1847-1719 surname: Öhlknecht fullname: Öhlknecht, Christoph – sequence: 2 givenname: Jan Walther orcidid: 0000-0002-8575-0278 surname: Perthold fullname: Perthold, Jan Walther – sequence: 3 givenname: Bettina orcidid: 0000-0002-8032-0084 surname: Lier fullname: Lier, Bettina – sequence: 4 givenname: Chris orcidid: 0000-0002-4232-2556 surname: Oostenbrink fullname: Oostenbrink, Chris email: chris.oostenbrink@boku.ac.at |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33136389$$D View this record in MEDLINE/PubMed |
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| SubjectTerms | Binding sites Free energy Fullerenes - chemistry Ligands Molecular dynamics Molecular Dynamics Simulation Perturbation Proteins Static Electricity Thermodynamics |
| Title | Charge-Changing Perturbations and Path Sampling via Classical Molecular Dynamic Simulations of Simple Guest–Host Systems |
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