title: Structure and dynamics of the multi-domain resuscitation promoting factor RpfB from Mycobacterium tuberculosis.
abstract: RpfB is multidomain protein that is crucial for Mycobacterium tuberculosis resuscitation from dormancy. This protein cleaves cell wall peptidoglycan, an essential bacterial cell wall polymer formed by glycan chains of β-(1-4)-linked-N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) cross-linked by short peptide stems. RpfB is structurally complex being composed of five distinct domains, namely a catalytic, a G5 and three DUF348 domains. Here, we have undertaken a combined experimental and computation structural investigations on the entire protein to gain insights into its structure-function relationships. CD spectroscopy and light scattering experiments have provided insights into the protein fold stability and into its oligomeric state. Using the available structure information, we modeled the entire protein structure, which includes the two DUF348 domains whose structure is experimentally unknown, and we analyzed the dynamic behavior of RpfB using molecular dynamics simulations. Present results highlight an intricate mutual influence of the dynamics of the different protein domains. These data provide interesting clues on the functional role of non-catalytic domains of RpfB and on the mechanism of peptidoglycan degradation necessary to resuscitation of M. tuberculosis.
authors.affiliation: a Institute of Biostructures and Bioimaging , CNR , Naples , Italy.
authors.forename: Alessia
authors.initials: A
authors.lastname: Ruggiero
authors.affiliation: a Institute of Biostructures and Bioimaging , CNR , Naples , Italy.
authors.forename: Flavia
authors.initials: F
authors.lastname: Squeglia
authors.affiliation: a Institute of Biostructures and Bioimaging , CNR , Naples , Italy.
authors.forename: Maria
authors.initials: M
authors.lastname: Romano
authors.affiliation: a Institute of Biostructures and Bioimaging , CNR , Naples , Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Vitagliano
authors.affiliation: b Division of Molecular Biosciences , Imperial College London , London , UK.
authors.forename: Alfonso
authors.initials: A
authors.lastname: De Simone
authors.affiliation: a Institute of Biostructures and Bioimaging , CNR , Naples , Italy.
authors.forename: Rita
authors.initials: R
authors.lastname: Berisio
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D056004:Molecular Dynamics Simulation; D009169:Mycobacterium tuberculosis / Q000378:metabolism; D011487:Protein Conformation; D000072417:Protein Domains; D054730:Protein Interaction Domains and Motifs; D055550:Protein Stability; D011994:Recombinant Proteins
chemical_list: D001426:Bacterial Proteins; D011994:Recombinant Proteins
keywords: dormancy; molecular dynamics; resuscitation; tuberculosis