Simple Selection Procedure to Distinguish between Static and Flexible Loops.
flexible loop
loop reconstruction
protein structure
static loop
structure prediction
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
26 Mar 2020
26 Mar 2020
Historique:
received:
10
03
2020
revised:
22
03
2020
accepted:
24
03
2020
entrez:
1
4
2020
pubmed:
1
4
2020
medline:
17
12
2020
Statut:
epublish
Résumé
Loops are the most variable and unorganized elements of the secondary structure of proteins. Their ability to shift their shape can play a role in the binding of small ligands, enzymatic catalysis, or protein-protein interactions. Due to the loop flexibility, the positions of their residues in solved structures show the largest B-factors, or in a worst-case scenario can be unknown. Based on the loops' movements' timeline, they can be divided into slow (static) and fast (flexible). Although most of the loops that are missing in experimental structures belong to the flexible loops group, the computational tools for loop reconstruction use a set of static loop conformations to predict the missing part of the structure and evaluate the model. We believe that these two loop types can adopt different conformations and that using scoring functions appropriate for static loops is not sufficient for flexible loops. We showed that common model evaluation methods, are insufficient in the case of flexible solvent-exposed loops. Instead, we recommend using the potential energy to evaluate such loop models. We provide a novel model selection method based on a set of geometrical parameters to distinguish between flexible and static loops without the use of molecular dynamics simulations. We have also pointed out the importance of water network and interactions with the solvent for the flexible loop modeling.
Identifiants
pubmed: 32225102
pii: ijms21072293
doi: 10.3390/ijms21072293
pmc: PMC7177474
pii:
doi:
Substances chimiques
Fungal Proteins
0
Insect Proteins
0
Epoxide Hydrolases
EC 3.3.2.-
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Narodowe Centrum Nauki
ID : DEC-2015/18/M/NZ1/00427
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