All-atom molecular dynamics simulations were performed on partially folded states (with different secondary structure content) of the dimeric enzyme HIV-1 protease in aqueous solution. The calculations were based on previous simulations of the folding process of the protein based on a Go-model. The structures turn out to be stable, and the subunit-subunit contact surface is smaller than that of the native state. Interestingly, the flexibility of the partially folded states is similar to that observed for the monomer in the native state. The intersubunit contacts are formed by conserved residues, suggesting that these residues may play a role for the folding process. Docking a large set of molecules suggests that several ligands not yet associated to HIV-1 protease may bind to these partially unfolded structures. (c) 2006 Elsevier B.V. All rights reserved.

Partially folded states of HIV-1 protease: Molecular dynamics simulations and ligand binding / Cavallari, Manuela; C., Ghio; S., Monti; Ferrario, Mauro; A., Maritan; P., Carloni. - In: JOURNAL OF MOLECULAR STRUCTURE. THEOCHEM. - ISSN 0166-1280. - STAMPA. - 769:1-3(2006), pp. 111-121. [10.1016/j.theochem.2006.04.042]

Partially folded states of HIV-1 protease: Molecular dynamics simulations and ligand binding

CAVALLARI, Manuela;FERRARIO, Mauro;
2006

Abstract

All-atom molecular dynamics simulations were performed on partially folded states (with different secondary structure content) of the dimeric enzyme HIV-1 protease in aqueous solution. The calculations were based on previous simulations of the folding process of the protein based on a Go-model. The structures turn out to be stable, and the subunit-subunit contact surface is smaller than that of the native state. Interestingly, the flexibility of the partially folded states is similar to that observed for the monomer in the native state. The intersubunit contacts are formed by conserved residues, suggesting that these residues may play a role for the folding process. Docking a large set of molecules suggests that several ligands not yet associated to HIV-1 protease may bind to these partially unfolded structures. (c) 2006 Elsevier B.V. All rights reserved.
2006
769
1-3
111
121
Partially folded states of HIV-1 protease: Molecular dynamics simulations and ligand binding / Cavallari, Manuela; C., Ghio; S., Monti; Ferrario, Mauro; A., Maritan; P., Carloni. - In: JOURNAL OF MOLECULAR STRUCTURE. THEOCHEM. - ISSN 0166-1280. - STAMPA. - 769:1-3(2006), pp. 111-121. [10.1016/j.theochem.2006.04.042]
Cavallari, Manuela; C., Ghio; S., Monti; Ferrario, Mauro; A., Maritan; P., Carloni
File in questo prodotto:
Non ci sono file associati a questo prodotto.
Pubblicazioni consigliate

Licenza Creative Commons
I metadati presenti in IRIS UNIMORE sono rilasciati con licenza Creative Commons CC0 1.0 Universal, mentre i file delle pubblicazioni sono rilasciati con licenza Attribuzione 4.0 Internazionale (CC BY 4.0), salvo diversa indicazione.
In caso di violazione di copyright, contattare Supporto Iris

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11380/305288
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 5
  • ???jsp.display-item.citation.isi??? 3
social impact