title: The maturation of HIV-1 protease precursor studied by discrete molecular dynamics.
abstract: 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.
authors.affiliation: Department of Physics and INFN, Università degli Studi di Milano, Milano, 20133, Italy.
authors.forename: Sachie
authors.initials: S
authors.lastname: Kimura
authors.forename: Martina
authors.initials: M
authors.lastname: Caldarini
authors.forename: Ricardo A
authors.initials: RA
authors.lastname: Broglia
authors.forename: Nikolay V
authors.initials: NV
authors.lastname: Dokholyan
authors.forename: Guido
authors.initials: G
authors.lastname: Tiana
mesh_terms: D002151:Calorimetry; D004792:Enzyme Precursors / Q000737:chemistry* / Q000378:metabolism; D016333:HIV Protease / Q000737:chemistry* / Q000378:metabolism; D015497:HIV-1 / Q000201:enzymology*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D017510:Protein Folding; D055503:Protein Multimerization / Q000502:physiology*; D020836:Protein Structure, Quaternary
chemical_list: D004792:Enzyme Precursors; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1
keywords: MD simulations; computational model; equilibrium properties; non-native interactions; protein dimerization