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167 results on '"Fornili, Arianna"'

1. The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans

Author

Rehman, Saima, Antonovic, Anna Katarina, McIntire, Ian E., Zheng, Huaixin, Cleaver, Leanne, Baczynska, Maria, Adams, Carlton O., Portlock, Theo, Richardson, Katherine, Shaw, Rosie, Oregioni, Alain, Mastroianni, Giulia, Whittaker, Sara B-M., Kelly, Geoff, Lorenz, Christian D., Fornili, Arianna, Cianciotto, Nicholas P., and Garnett, James A.

Published
2024
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5. TheLegionellacollagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans

Author

Rehman, Saima, primary, Antonovic, Anna K., additional, McIntire, Ian E., additional, Zheng, Huaixin, additional, Cleaver, Leanne, additional, Adams, Carlton O., additional, Portlock, Theo, additional, Richardson, Katherine, additional, Shaw, Rosie, additional, Oregioni, Alain, additional, Mastroianni, Giulia, additional, Whittaker, Sara B-M, additional, Kelly, Geoff, additional, Fornili, Arianna, additional, Cianciotto, Nicholas P., additional, and Garnett, James A., additional

Published
2023
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7. Abnormal myosin post‐translational modifications and ATP turnover time associated with human congenital myopathy‐related RYR1 mutations

Author

Sonne, Alexander, primary, Antonovic, Anna Katarina, additional, Melhedegaard, Elise, additional, Akter, Fariha, additional, Andersen, Jesper L., additional, Jungbluth, Heinz, additional, Witting, Nanna, additional, Vissing, John, additional, Zanoteli, Edmar, additional, Fornili, Arianna, additional, and Ochala, Julien, additional

Published
2023
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10. Comparative study of binding pocket structure and dynamics in cardiac and skeletal myosin

Author

Antonovic, Anna Katarina, Ochala, Julien, Fornili, Arianna, Antonovic, Anna Katarina, Ochala, Julien, and Fornili, Arianna

Abstract

The development of small molecule myosin modulators has seen an increased effort in recent years due to their possible use in the treatment of cardiac and skeletal myopathies. Omecamtiv mecarbil (OM) is the first-in-class cardiac myotrope and the first to enter clinical trials. Its selectivity toward slow/beta-cardiac myosin lies at the heart of its function; however, little is known about the underlying reasons for selectivity to this isoform as opposed to other closely related ones such as fast-type skeletal myosins. In this work, we compared the structure and dynamics of the OM binding site in cardiac and in fasttype IIa skeletal myosin to identify possible reasons for OM selectivity. We found that the different shape, size, and composition of the binding pocket in skeletal myosin directly affects the binding mode and related affinity of OM, which is potentially a result of weaker interactions and less optimal molecular recognition. Moreover, we identified a side pocket adjacent to the OM binding site that shows increased accessibility in skeletal myosin compared with the cardiac isoform. These findings could pave the way to the development of skeletal-selective compounds that can target this region of the protein and potentially be used to treat congenital myopathies where muscle weakness is related to myosin loss of function.

Published
2023

11. Supplementary data for the manuscript: 'Binding pocket dynamics along the recovery stroke of human β-cardiac myosin'

Author

Akter, Fariha, Ochala, Julien, and Fornili, Arianna

Abstract

Supplementary data for the manuscript: Fariha Akter, Julien Ochala, Arianna Fornili: "Binding pocket dynamics along the recovery stroke of human β-cardiac myosin" The archive includes starting structures and plumed input files used for all 200-ns SMD simulations and all the US simulations described in the manuscript.

Published
2023
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13. N4BP1 is dimerization-dependent linear ubiquitin reader regulating TNFR1 signalling through linear ubiquitin binding and Caspase-8-mediated processing

Author

Kliza, Katarzyna Wiktoria, primary, Song, Wei, additional, Pinzuti, Irene, additional, Schaubeck, Simone, additional, Kunzelmann, Simone, additional, Kuntin, David, additional, Fornili, Arianna, additional, Pandini, Alessandro, additional, Hofmann, Kay, additional, Garnett, James, additional, Stieglitz, Benjamin, additional, and Husnjak, Koraljka, additional

Published
2021
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20. Structure and functional analysis of the Legionella pneumophila chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradation

Author

Rehman, Saima, primary, Grigoryeva, Lubov S., additional, Richardson, Katherine H., additional, Corsini, Paula, additional, White, Richard C., additional, Shaw, Rosie, additional, Portlock, Theo J., additional, Dorgan, Benjamin, additional, Zanjani, Zeinab S., additional, Fornili, Arianna, additional, Cianciotto, Nicholas P., additional, and Garnett, James A., additional

Published
2020
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24. Structural alphabets derived from attractors in conformational space

Author

Kleinjung Jens, Fornili Arianna, and Pandini Alessandro

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis. Results A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness. Conclusions The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics.

Published
2010
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30. Energy landscapes associated with macromolecular conformational changes from endpoint structures

Author

Fornili, Arianna, Giabbai, Barbara, Garau, Gianpiero, and Degano, Massimo

Subjects
Silicon compounds -- Chemical properties, Silicon compounds -- Electric properties, Chemistry
Abstract

A novel in silico approach based on the combined use of essential dynamics sampling and nonequilibrium free-energy calculations is introduced to obtain quantitative data on conformational energy landscapes. The proposed approach provides first evidence for a rate-limiting character of the conformational transition in this enzyme, and an unexpected role of the protonation state of a single residue in regulating substrate binding and product release.

Published
2010

31. Using local states to drive the sampling of global conformations in proteins

Author

Pandini, Alessandro and Fornili, Arianna

Subjects
Protein Conformation, Proteins, Molecular Dynamics Simulation, Article
Abstract

Conformational changes associated with protein function often occur beyond the time scale currently accessible to unbiased molecular dynamics (MD) simulations, so that different approaches have been developed to accelerate their sampling. Here we investigate how the knowledge of backbone conformations preferentially adopted by protein fragments, as contained in precalculated libraries known as structural alphabets (SA), can be used to explore the landscape of protein conformations in MD simulations. We find that (a) enhancing the sampling of native local states in both metadynamics and steered MD simulations allows the recovery of global folded states in small proteins; (b) folded states can still be recovered when the amount of information on the native local states is reduced by using a low-resolution version of the SA, where states are clustered into macrostates; and (c) sequences of SA states derived from collections of structural motifs can be used to sample alternative conformations of preselected protein regions. The present findings have potential impact on several applications, ranging from protein model refinement to protein folding and design. The computer resources, technical expertise, Red Española de Supercomputación, Cristian Micheletti, Michael Sadowski and Katarzyna Maksimiak

Published
2016

32. Structural basis for substrate specificity in group I nucleoside hydrolase

Author

Iovane, Elena, Giabbai, Barbara, Muzzolini, Laura, Matafora, Vittoria, Fornili, Arianna, Minici, Claudia, Giannese, Francesca, and Degano, Massimo

Subjects
Escherichia coli -- Genetic aspects, Hydrolases -- Genetic aspects, Enzymes -- Genetic aspects, Hydrolysis -- Research, X-ray crystallography -- Usage, Biological sciences, Chemistry
Abstract

Cryotrapping and X-ray crystallography were used to characterize the binding interactions between the slowly hydrolyzed substrate inosine and the Escherichia coli pyrimidine-specific nucloeside hydrolase (NH) YeiK. The results provided direct evidence for the distinct subsets of amino acid residues which are involved in the hydrolysis of purine or pyrimidine nucleosides in group I NHs.

Published
2008

34. Anatomy of protein disorder, flexibility and disease-related mutations

Author

Lu, Hui-Chun, Chung, Sun Sook, Fornili, Arianna, and Fraternali, Franca

Subjects
non-synonymous SNPs, protein flexibility, order-disorder propensity, Molecular Biosciences, disease-related mutations, Biochemistry, Genetics and Molecular Biology (miscellaneous), Molecular Biology, Biochemistry, protein disorder
Abstract

Integration of protein structural information with human genetic variation and pathogenic mutations is essential to understand molecular mechanisms associated with the effects of polymorphisms on protein interactions and cellular processes. We investigate occurrences of non-synonymous SNPs in ordered and disordered protein regions by systematic mapping of common variants and disease-related SNPs onto these regions. We show that common variants accumulate in disordered regions; conversely pathogenic variants are significantly depleted in disordered regions. These different occurrences of pathogenic and common SNPs can be attributed to a negative selection on random mutations in structurally highly constrained regions. New approaches in the study of quantitative effects of pathogenic-related mutations should effectively account for all the possible contexts and relative functional constraints in which the sequence variation occurs.

Published
2015
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44. A pH-Regulated Quality Control Cycle for Surveillance of Secretory Protein Assembly

Author

Vavassori, Stefano, primary, Cortini, Margherita, additional, Masui, Shoji, additional, Sannino, Sara, additional, Anelli, Tiziana, additional, Caserta, Imma R., additional, Fagioli, Claudio, additional, Mossuto, Maria F., additional, Fornili, Arianna, additional, van Anken, Eelco, additional, Degano, Massimo, additional, Inaba, Kenji, additional, and Sitia, Roberto, additional

Published
2013
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