An MD View of Ligand Binding
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F25%3A00643899" target="_blank" >RIV/61388971:_____/25:00643899 - isvavai.cz</a>
Result on the web
<a href="https://www.mdpi.com/1420-3049/30/24/4678" target="_blank" >https://www.mdpi.com/1420-3049/30/24/4678</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3390/molecules30244678" target="_blank" >10.3390/molecules30244678</a>
Alternative languages
Result language
angličtina
Original language name
An MD View of Ligand Binding
Original language description
Protein-ligand complexes in crystal structures are well described by an array of bonding interactions among precisely defined functional groups. The present work examines how one representative complex behaves in one-microsecond molecular dynamics simulations, starting from a crystal structure with a native biological ligand bound, and proceeding to simulations of structures derived by docking of that native ligand, and then to docking of selected ligand analogs. The MD behaviors and system energies calculated in RMSD plateau regions using MM/GBSA are similar when initiated from the crystal structure or the structure with the docked native ligand, although independent replicate simulations differ. Despite these similarities, interatomic contact frequencies indicate that some contacts observed in the crystal structure are rarely sampled again, others are sampled only intermittently, and new contacts are recruited that can be more persistent. Docked structures of non-native ligand analogs were chosen for simulation by screening manually for features consistent with known binding interactions, and these displayed behaviors similar to those for the native ligand and, in some cases, similar calculated energies. Overall, ligands appear to cooperate dynamically with the protein in forming the observed interactions.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10606 - Microbiology
Result continuities
Project
—
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Molecules
ISSN
1420-3049
e-ISSN
1420-3049
Volume of the periodical
30
Issue of the periodical within the volume
24
Country of publishing house
CH - SWITZERLAND
Number of pages
43
Pages from-to
4678
UT code for WoS article
001647067400001
EID of the result in the Scopus database
2-s2.0-105025753415