The maturation of HIV-1 protease precursor studied by discrete molecular dynamics

Sachie Kimura, Martina Caldarini, Ricardo A. Broglia, Nikolay V. Dokholyan, Guido Tiana

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


The equilibrium properties of a HIV-1-protease precursor are studied by means of an efficient molecular dynamics scheme, which allows for the simulation of the folding of the protein monomers and their dimerization into an active form and compare them with those of the mature protein. The results of the model provide, with atomic detail, an overall account of several experimental findings, including the NMR conformation of the mature dimer, the calorimetric properties of the system, the effects of the precursor tail on the dimerization constant, the secondary chemical shifts of the monomer, and the paramagnetic relaxation enhancement data associated with the conformations of the precursor. It is found that although the mature protein can dimerize in a unique, single way, the precursor populates several dimeric conformations in which monomers are always native-like, but their binding can be non-native.

Original languageEnglish (US)
Pages (from-to)633-639
Number of pages7
JournalProteins: Structure, Function and Bioinformatics
Issue number4
StatePublished - Apr 2014

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology


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