Computational Design of PDZ-Peptide Binding.
Implicit solvent
Ligand binding
MC simulation
Molecular mechanics
Protein design
Proteus program
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2021
2021
Historique:
entrez:
20
5
2021
pubmed:
21
5
2021
medline:
22
6
2021
Statut:
ppublish
Résumé
This chapter describes two computational methods for PDZ-peptide binding: high-throughput computational protein design (CPD) and a medium-throughput approach combining molecular dynamics for conformational sampling with a Poisson-Boltzmann (PB) Linear Interaction Energy for scoring. A new CPD method is outlined, which uses adaptive Monte Carlo simulations to efficiently sample peptide variants that tightly bind a PDZ domain, and provides at the same time precise estimates of their relative binding free energies. A detailed protocol is described based on the Proteus CPD software. The medium-throughput approach can be performed with standard MD and PB software, such as NAMD and Charmm. For 40 complexes between Tiam1 and peptide ligands, it gave high a2ccuracy, with mean errors of around 0.5 kcal/mol for relative binding free energies and no large errors. It requires a moderate amount of parameter fitting before it can be applied, and its transferability to other protein families is still untested.
Identifiants
pubmed: 34014526
doi: 10.1007/978-1-0716-1166-1_14
doi:
Substances chimiques
Ligands
0
Peptide Fragments
0
Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
237-255Références
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