Exploring the electronic structure of knotted proteins: the case of two ornithine transcarbamylase family.
Knotted proteins
Protein electronic structure
Quantum chemical descriptors
Structural fluctuations
Journal
Journal of molecular modeling
ISSN: 0948-5023
Titre abrégé: J Mol Model
Pays: Germany
ID NLM: 9806569
Informations de publication
Date de publication:
15 Jul 2024
15 Jul 2024
Historique:
received:
31
01
2024
accepted:
06
06
2024
medline:
15
7
2024
pubmed:
15
7
2024
entrez:
15
7
2024
Statut:
epublish
Résumé
Geometrical knots are rare structural arrangements in proteins in which the polypeptide chain ties itself into a knot, which is very intriguing due to the uncertainty of their impact on the protein properties. Presently, classical molecular dynamics is the most employed technique in the few studies found on this topic, so any information on how the presence of knots affects the reactivity and electronic properties of proteins is even scarcer. Using the electronic structure methods and quantum chemical descriptors analysis, we found that the same amino-acid residues in the knot core have statistically larger values for the unknotted protein, for both hard-hard and soft-soft interaction descriptors. In addition, we present a computationally feasible protocol, where we show it is possible to separate the contribution of the geometrical knot to the reactivity and other electronic structure properties. In order to investigate these systems, we used PRIMoRDiA, a new software developed by our research group, to explore the electronic structure of biological macromolecules. We evaluated several local quantum chemical descriptors to unveil relevant patterns potentially originating from the presence of the geometrical knot in two proteins, belonging to the ornithine transcarbamylase family. We compared several sampled structures from these two enzymes that are highly similar in both tertiary structure and function, but one of them has a knot whereas the other does not. The sampling was carried out through molecular dynamics simulations using ff14SB force field along 50 ns, and the semiempirical convergence was performed with PM7 Hamiltonian.
Identifiants
pubmed: 39008190
doi: 10.1007/s00894-024-06009-9
pii: 10.1007/s00894-024-06009-9
doi:
Substances chimiques
Ornithine Carbamoyltransferase
EC 2.1.3.3
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
265Subventions
Organisme : Universidade Federal da Paraíba
ID : PIA14864-2021
Organisme : Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
ID : AUXPE1375/2014
Organisme : Conselho Nacional de Desenvolvimento Científico e Tecnológico
ID : 440363/2022-5
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
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