List of Publications

    2017

    2016

    • Gruber R., Rogerson C., Windpassinger C., Banushi B., Straatman-Iwanowska A., Hanley J., Forneris F., Strohal R., Ulz P., Crumrine D., Menon G.K., Blunder S., Schmuth M., Müller T., Smith H., Mills K., Kroisel P., Janecke A.R., Gissen P.
      Autosomal recessive Keratoderma-Ichthyosis-Deafness (ARKID) syndrome is caused by VPS33B mutations affecting Rab protein interaction and collagen modification
      Journal of Investigative Dermatology, S0022-202X, 32800-32807. (2016) - PubMed

    • Israyilova A, Buroni S, Forneris F, Scoffone VC, Shixaliyev NQ, Riccardi G, Chiarelli LR.
      Biochemical characterization of Glutamate Racemase, a new candidate drug target against Burkholderia cenocepacia infections
      PLoS One, 11, e0167350. (2016) - PubMed

    • Speranzini V., Rotili D., Ciossani G., Pilotto S., Marrocco B., Forgione M., Lucidi A., Forneris F., Mehdipour P., Velankar S., Mai A., Mattevi A.
      Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features
      Science Advances, 2, e1601017. (2016) Watch the Movie - PubMed

    • Scoffone V.C.*, Chiarelli L.R.*, Makarov V.*, Brackman G., Israylova A., Azzalin A., Forneris F., Riabova O., Savina S., Coenye T., Riccardi G., Buroni S.
      Discovery of new diketopiperazines inhibiting Burkholderia cenocepacia quorum sensing in vitro and in vivo
      Scientific Reports, 6, 32487. (2016) *Equal Contribution - PubMed

    • Palamini M., Canciani A., Forneris F.
      Identifying and visualizing macromolecular flexibility in structural biology
      Frontiers in Molecular Biosciences, 3, 47. (2016) - PubMed
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      Structural biology comprises a variety of tools to obtain atomic resolution data for the investigation of macromolecules. Conventional structural methodologies including crystallography, NMR and electron microscopy often do not provide sufficient details concerning flexibility and dynamics, even though these aspects are critical for the physiological functions of the systems under investigation. However, the increasing complexity of the molecules studied by structural biology (including large macromolecular assemblies, integral membrane proteins, intrinsically disordered systems, and folding intermediates) continuously demands in-depth analyses of the roles of flexibility and conformational specificity involved in interactions with ligands and inhibitors. The intrinsic difficulties in capturing often subtle but critical molecular motions in biological systems have restrained the investigation of flexible molecules into a small niche of structural biology. Introduction of massive technological developments over the recent years, which include time-resolved studies, solution X-ray scattering, and new detectors for cryo-electron microscopy, have pushed the limits of structural investigation of flexible systems far beyond traditional approaches of NMR analysis. By integrating these modern methods with powerful biophysical and computational approaches such as generation of ensembles of molecular models and selective particle picking in electron microscopy, more feasible investigations of dynamic systems are now possible. Using some prominent examples from recent literature, we review how current structural biology methods can contribute useful data to accurately visualize flexibility in macromolecular structures and understand its important roles in regulation of biological processes.


    • Banushi B., Forneris F.*, Straatman-Iwanowska A., Strange A., Lyne A., Rogerson C., Burden J.J., Heywood W.E., Hanley J., Doykov I., Straatman K.R., Smith H., Bem D., Kriston-Vizi J., Ariceta G., Risteli M., Wang C., Ardill R.E., Zaniew M., Latka-Grot J., Waddington S.N., Howe S.J., Ferraro F., Gjinovci A., Lawrence S., Marsh M., Girolami M., Bozec L., Mills K., Gissen P.*
      Regulation of post-Golgi LH3 trafficking is essential for collagen homeostasis
      Nature Communications, 7, 12111. (2016) *Shared Corresponding Authors - PubMed
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      Post-translational modifications are necessary for collagen precursor molecules (procollagens) to acquire final shape and function. However, the mechanism and contribution of collagen modifications that occur outside endoplasmic reticulum and Golgi are not understood. We discovered that VIPAR, with its partner proteins, regulate sorting of Lysyl Hydroxylase 3 (LH3, also known as PLOD3) into newly-identified post-Golgi collagen IV carriers and that VIPAR-dependent sorting is essential for modification of lysines in multiple collagen types. Identification of structural and functional collagen abnormalities in cells and tissues from patients and murine models of the autosomal recessive multisystem disorder Arthrogryposis, Renal dysfunction and Cholestasis syndrome caused by VIPAR and VPS33B deficiencies confirmed our findings. Thus, regulation of post-Golgi LH3 trafficking is essential for collagen homeostasis and for the development and function of multiple organs and tissues.

      Press Release (in Italian) - Local Newspapers Articles (in Italian): 1, 2


    • Spadaro F.*, Scoffone V.C.*, Chiarelli L.R.**, Fumagalli M., Buroni S., Riccardi G., Forneris F.**
      The crystal structure of Burkholderia cenocepacia DfsA provides insights into substrate recognition and quorum sensing fatty acid biosynthesis
      Biochemistry, 55, 3241-3250. (2016) *Equal Contribution - **Shared Corresponding Authors - PubMed
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      Burkholderia cenocepacia is a major concern among respiratory tract infections in cystic fibrosis patients. This pathogen is particularly difficult to treat because of its high level of resistance to the clinically relevant antimicrobial agents. In B. cenocepacia, the quorum sensing cell-cell communication system is involved in different processes important for the bacterial virulence, such as biofilm formation or protease and siderophore production. Targeting the enzymes involved in this process represents a promising therapeutic approach. With the aim of finding effective quorum sensing inhibitors, we have determined the three-dimensional structure of B. cenocepacia diffusible factor synthase A, DfsA. This bifunctional crotonase (dehydratase/thioesterase) produces the characteristic quorum sensing molecule of B. cenocepacia, cis-2-dodecenoic acid or BDSF, starting from 3-hydroxydodecanoyl-acyl carrier protein. Unexpectedly, the crystal structure revealed the presence of a lipid molecule into the catalytic site of the enzyme, which was identified as dodecanoic acid. Our biochemical characterization shows that DfsA is able to use dodecanoyl-acyl carrier protein as a substrate, demonstrating that dodecanoic acid, the product of this reaction, is released very slowly from the DfsA active site, therefore acting as a DfsA inhibitor. This molecule shows an unprecedented conformational arrangement inside the DfsA active site. In contrast with previous hypotheses, our data illustrate how DfsA and closely-related homologous enzymes can recognize long hydrophobic substrates without large conformational changes or assistance by additional regulator molecules. The elucidation of the substrate binding mode in DfsA provides the starting point for structure-based drug discovery studies targeting B. cenocepacia quorum sensing-assisted virulence.


    • Forneris F., Wu J., Xue X., Ricklin D., Lin Z., Sfyroera G., Tzekou A., Volokhina E., Granneman J.C.M., Hauhart R., Bertram P., Liszewski M.K., Atkinson J.P., Lambris J.D., Gros P.
      Regulators of complement activity mediate inhibitory mechanisms through a common C3b-binding mode
      The EMBO Journal, 35, 1133-1149. (2016) - PubMed
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      Regulators of complement activation (RCA) inhibit complement-induced immune responses on healthy host tissues. We present crystal structures of humanRCA(MCP, DAF, andCR1) and a smallpox virus homolog (SPICE) bound to complement component C3b. Our structural data reveal that up to four consecutive homologousCCPdomains (i-iv), responsible for inhibition, bind in the same orientation and extended arrangement at a shared binding platform on C3b. Large sequence variations inCCPdomains explain the diverse C3b-binding patterns, with limited or no contribution of some individual domains, while all regulators show extensive contacts with C3b for the domains at the third site. A variation of ~100° rotation around the longitudinal axis is observed for domains binding at the fourth site on C3b, without affecting the overall binding mode. The data suggest a common evolutionary origin for both inhibitory mechanisms, called decay acceleration and cofactor activity, with variable C3b binding through domains at sites ii, iii, and iv, and provide a framework for understanding RCA disease-related mutations and immune evasion.


      More info about Structural Biology of the Complement System


    • Savino S., Ferrandi E., Forneris F., Rovida S., Riva S., Monti D., Mattevi A.
      Structural and biochemical insights into 7b-hydroxysteroid dehydrogenase stereoselectivity
      Proteins, 84, 859-865. (2016) Cover Image - PubMed
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      Hydroxysteroid dehydrogenases are of great interest as biocatalysts for transformations involving steroid substrates. They feature a high degree of stereo- and regio-selectivity, acting on a defined atom with a specific configuration of the steroid nucleus. The crystal structure of 7?-hydroxysteroid dehydrogenase from Collinsella aerofaciens reveals a loop gating active-site accessibility, the bases of the specificity for NADP+, and the general architecture of the steroid binding site. Comparison with 7?-hydroxysteroid dehydrogenase provides a rationale for the opposite stereoselectivity. The presence of a C-terminal extension reshapes the substrate site of the ?-selective enzyme, possibly leading to an inverted orientation of the bound substrate.

      An image from our paper was selected as cover image for this issue of proteins (Page C4):


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