Accelerated molecular dynamics (aMD) protocols were assessed on predicting the secondary structure of eight peptides, of which two are helical, three are β-hairpins, and three are disordered. Protocols consisted of combinations of three force fields (ff99SB, ff14SB, ff19SB) and two explicit solvation models (TIP3P and OPC), and were evaluated in two independent aMD simulations, one starting from an extended conformation, the other starting from a misfolded conformation. The results of these analyses indicate that all three combinations performed well on helical peptides. As for β-hairpins, ff19SB performed well with both solvation methods, with a slight preference for the TIP3P solvation model, even though performance was dependent on both peptide sequence and initial conformation. The ff19SB/OPC combination had the best performance on intrinsically disordered peptides. In general, ff14SB/TIP3P suffered the strongest helical bias.

Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models / C. Coppa, A. Bazzoli, M. Barkhordari, A. Contini. - In: JOURNAL OF CHEMICAL INFORMATION AND MODELING. - ISSN 1549-9596. - 63:10(2023), pp. 3030-3042. [10.1021/acs.jcim.3c00138]

Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models

C. Coppa
Co-primo
;
A. Bazzoli
Co-primo
;
A. Contini
Ultimo
2023

Abstract

Accelerated molecular dynamics (aMD) protocols were assessed on predicting the secondary structure of eight peptides, of which two are helical, three are β-hairpins, and three are disordered. Protocols consisted of combinations of three force fields (ff99SB, ff14SB, ff19SB) and two explicit solvation models (TIP3P and OPC), and were evaluated in two independent aMD simulations, one starting from an extended conformation, the other starting from a misfolded conformation. The results of these analyses indicate that all three combinations performed well on helical peptides. As for β-hairpins, ff19SB performed well with both solvation methods, with a slight preference for the TIP3P solvation model, even though performance was dependent on both peptide sequence and initial conformation. The ff19SB/OPC combination had the best performance on intrinsically disordered peptides. In general, ff14SB/TIP3P suffered the strongest helical bias.
Molecular Dynamics; folding; peptides;
Settore CHIM/06 - Chimica Organica
   Functional Nano-Scaffolds for Regenerative Medicine
   NANOREMEDI
   European Commission
   Horizon Europe Framework Programme
   101072645

   One Health Action Hub: task force di Ateneo per la resilienza di ecosistemi territoriali (1H_Hub) Linea Strategica 3, Tema One health, one earth
   1H_Hub
   UNIVERSITA' DEGLI STUDI DI MILANO
2023
10-mag-2023
Article (author)
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/969223
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