title: The complex folding behavior of HIV-1-protease monomer revealed by optical-tweezer single-molecule experiments and molecular dynamics simulations.
abstract: We have used optical tweezers and molecular dynamics simulations to investigate the unfolding and refolding process of a stable monomeric form of HIV-1-protease (PR). We have characterized the behavior under tension of the native state (N), and that of the ensemble of partially folded (PF) conformations the protein visits en route to N, which collectively act as a long-lived state controlling the slow kinetic phase of the folding process. Our results reveal a rich network of unfolding events, where the native state unfolds either in a two-state manner or by populating an intermediate state I, while the PF state unravels through a multitude of pathways, underscoring its structural heterogeneity. Refolding of mechanically denatured HIV-1-PR monomers is also a multiple-pathway process. Molecular dynamics simulations allowed us to gain insight into possible conformations the protein adopts along the unfolding pathways, and provide information regarding possible structural features of the PF state.
authors.affiliation: Dipartimento di Fisica, Università degli Studi di Milano and INFN, Milano, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Caldarini
authors.affiliation: Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Via Giuseppe Campi 213/A, 41125 Modena, Italy; CNR Institute of Nanoscience S3, Via Giuseppe Campi 213/A, 41125 Modena, Italy.
authors.forename: P
authors.initials: P
authors.lastname: Sonar
authors.affiliation: Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Via Giuseppe Campi 213/A, 41125 Modena, Italy; CNR Institute of Nanoscience S3, Via Giuseppe Campi 213/A, 41125 Modena, Italy.
authors.forename: I
authors.initials: I
authors.lastname: Valpapuram
authors.affiliation: Dipartimento di Fisica, Università degli Studi di Milano and INFN, Milano, Italy.
authors.forename: D
authors.initials: D
authors.lastname: Tavella
authors.affiliation: Dipartimento di Fisica, Università degli Studi di Milano and INFN, Milano, Italy.
authors.forename: C
authors.initials: C
authors.lastname: Volonté
authors.affiliation: Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
authors.forename: V
authors.initials: V
authors.lastname: Pandini
authors.affiliation: Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
authors.forename: M A
authors.initials: MA
authors.lastname: Vanoni
authors.affiliation: Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Aliverti
authors.affiliation: Dipartimento di Fisica, Università degli Studi di Milano and INFN, Milano, Italy; The Niels Bohr Institute, University of Copenhagen, Denmark.
authors.forename: R A
authors.initials: RA
authors.lastname: Broglia
authors.affiliation: Dipartimento di Fisica, Università degli Studi di Milano and INFN, Milano, Italy. Electronic address: tiana@mi.infn.it.
authors.forename: G
authors.initials: G
authors.lastname: Tiana
authors.affiliation: Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Via Giuseppe Campi 213/A, 41125 Modena, Italy; CNR Institute of Nanoscience S3, Via Giuseppe Campi 213/A, 41125 Modena, Italy. Electronic address: ciro.cecconi@gmail.com.
authors.forename: C
authors.initials: C
authors.lastname: Cecconi
mesh_terms: D016333:HIV Protease / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015497:HIV-1 / Q000201:enzymology*; D006801:Humans; D056004:Molecular Dynamics Simulation; D052898:Optical Tweezers; D011489:Protein Denaturation; D058849:Protein Refolding; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics
chemical_list: D011994:Recombinant Proteins; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1
keywords: HIV-1-protease; Intermediate states; Molecular dynamics simulations; Protein folding; Single-molecule studies