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Institute of Bioengineering

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Dr Arianna Fornili

Lecturer in Computational Organic Chemistry

Department School of Biological and Chemical Sciences
Email a.fornili@qmul.ac.uk
Homepage https://www.qmul.ac.uk/sbcs/staff/ariannafornili.html

IoB Highlights

My research activity is focused on the computational study of protein dynamics and its relationship to protein function.

The main interest of the group is the study of structural, dynamical and mechanical properties of proteins from the cardiac muscle. Heart contraction arises from a complex interplay of precisely timed molecular motions and the identification of new therapeutic targets for cardiomyopathies relies on a deep understanding of these mechanisms. Combining Molecular Modelling, Molecular Dynamics simulation and Bioinformatics techniques, we investigate how post-translational modifications and cardiomyopathy-related mutations affect the protein motion and stability.

The group is also involved in the development of computational methods for the study of conformational transitions in proteins. In addition to promoting the motion of molecular motors, conformational changes can be essential for many protein functions and they are often required for protein-protein interaction and allosteric regulation. The group aims at improving both the sampling and the detection of biologically relevant conformational transitions, which are usually beyond the timescale of traditional molecular simulations.

 

Research Interests

My research activity is focused on the computational study of protein dynamics and its relationship to protein function.

The main interest of the group is the study of structural, dynamical and mechanical properties of proteins from the cardiac muscle. Heart contraction arises from a complex interplay of precisely timed molecular motions and the identification of new therapeutic targets for cardiomyopathies relies on a deep understanding of these mechanisms. Combining Molecular Modelling, Molecular Dynamics simulation and Bioinformatics techniques, we investigate how post-translational modifications and cardiomyopathy-related mutations affect the protein motion and stability.

The group is also involved in the development of computational methods for the study of conformational transitions in proteins. In addition to promoting the motion of molecular motors, conformational changes can be essential for many protein functions and they are often required for protein-protein interaction and allosteric regulation. The group aims at improving both the sampling and the detection of biologically relevant conformational transitions, which are usually beyond the timescale of traditional molecular simulations.

2019

Tiberti M, Lechner B-D and Fornili A (2019). Binding Pockets in Proteins Induced by Mechanical Stress. J Chem Theory Comput  vol. 15, (1) 1-6. 10.1021/acs.jctc.8b00755

2017

Hashem S, Tiberti M and Fornili A (2017). Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil., Editors: Wei G. Plos Computational Biology  vol. 13, (11) e1005826-e1005826. 10.1371/journal.pcbi.1005826

2016

Pandini A and Fornili A (2016). Using Local States To Drive the Sampling of Global Conformations in Proteins. J Chem Theory Comput  vol. 12, (3) 1368-1379. 10.1021/acs.jctc.5b00992

Carluccio C, Fraternali F, Salvatore F, Fornili A and Zagari A (2016). Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase. J Biomol Struct Dyn  vol. 34, (3) 497-507. 10.1080/07391102.2015.1052016

2015

Lu H-C, Chung SS, Fornili A and Fraternali F (2015). Anatomy of protein disorder, flexibility and disease-related mutations. Front Mol Biosci  vol. 2, 10.3389/fmolb.2015.00047

2014

FORNILI A, Rostkova E, Fraternali F and Pfuhl M (2014). Phosphorylation Modulates the Dynamics of the N-Terminal Tail in Cardiac RLC., Editors: NA . Biophysical Society  Biophysical Journal  vol. 106, (2) 33A-33A. 10.1016/j.bpj.2013.11.253

2013

Carluccio C, Fraternali F, Salvatore F, Fornili A and Zagari A (2013). Structural features of the regulatory ACT domain of phenylalanine hydroxylase. Public Library of Science  Plos One  vol. 8, (11) 10.1371/journal.pone.0079482

Fornili A, Pandini A, Lu H-C and Fraternali F (2013). Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles. American Chemical Society  Journal of Chemical Theory and Computation  vol. 9, (11) 5127-5147. 10.1021/ct400486p

Pandini A, Fornili A, Fraternali F and Kleinjung J (2013). GSATools: Analysis of allosteric communication and functional local motions using a structural alphabet. Oxford Journals  Bioinformatics  vol. 29, (16) 2053-2055. 10.1093/bioinformatics/btt326

Vavassori S, Cortini M, Masui S, Sannino S, Anelli T, Caserta IR, Fagioli C, Mossuto MF, Fornili A, vanAnken E, Degano M, Inaba K and Sitia R (2013). A pH-Regulated Quality Control Cycle for Surveillance of Secretory Protein Assembly. Elsevier/Science Direct  Molecular Cell  vol. 50, (6) 783-792. 10.1016/j.molcel.2013.04.016

Chakroun N, Fornili A, Prigent S, Kleinjung J, Dreiss CA, Rezaei H and Fraternali F (2013). Decrypting prion protein conversion into a ?-rich conformer by molecular dynamics. American Chemical Society  Journal of Chemical Theory and Computation  vol. 9, (5) 2455-2465. 10.1021/ct301118j

Lu H-C, Fornili A and Fraternali F (2013). Protein-Protein interaction networks studies and importance of 3D structure knowledge. Informa Healthcare  Expert Review of Proteomics  vol. 10, (6) 511-520. 10.1586/14789450.2013.856764

2012

Pandini A, Fornili A, Fraternali F and Kleinjung J (2012). Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics. American Societies For Experimental Biology  Faseb Journal  vol. 26, (2) 868-881. 10.1096/fj.11-190868

Fornili A, Autore F, Chakroun N, Martinez P and Fraternali F (2012). Protein-water interactions in MD simulations: POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites. Springer Verlag  Methods in Molecular Biology  vol. 819, 375-392. 10.1007/978-1-61779-465-0_23

2010

Fornili A, Giabbai B, Garau G and Degano M (2010). Energy landscapes associated with macromolecular conformational changes from endpoint structures. American Chemical Society  Journal of The American Chemical Society  vol. 132, (49) 17570-17577. 10.1021/ja107640u

Autore F, Pagano B, Fornili A, Rittinger K and Fraternali F (2010). In silico phosphorylation of the autoinhibited form of p47phox: Insights into the mechanism of activation. Elsevier/Science Direct  Biophysical Journal  vol. 99, (11) 3716-3725. 10.1016/j.bpj.2010.09.008

Pandini A, Fornili A and Kleinjung J (2010). Structural alphabets derived from attractors in conformational space. Biomed Central  Bmc Bioinformatics  vol. 11, 10.1186/1471-2105-11-97

2008

Iovane E, Giabbai B, Muzzolini L, Matafora V, Fornili A, Minici C, Giannese F and Degano M (2008). Structural basis for substrate specificity in group I nucleoside hydrolases. Biochemistry  vol. 47, (15) 4418-4426. 10.1021/bi702448s

2007

Fornili A, Sironi M and Degano M (2007). Accurate description of nitrogenous base flexibility in classical molecular dynamics simulations of nucleotides bound to proteins. J Phys Chem B  vol. 111, (23) 6297-6302. 10.1021/jp0713357

Loos P-F, FORNILI A, Sironi M and Assfeld X (2007). Removing extra frontier parameters in QM/MM methods : a tentative with the Local Self-Consistent Field approach., Editors: NA . Brill  Computing Letters  vol. 3, (2) 473-486. 10.1163/157404007782913309

2006

Fornili A, Loos PF, Sironi M and Assfeld X (2006). Frozen core orbitals as an alternative to specific frontier bond potential in hybrid Quantum Mechanics/Molecular Mechanics methods. Chemical Physics Letters  vol. 427, (1-3) 236-240. 10.1016/j.cplett.2006.06.095

Fornili A, Moreau Y, Sironi M and Assfeld X (2006). On the suitability of strictly localized orbitals for hybrid QM/MM calculations. J Comput Chem  vol. 27, (4) 515-523. 10.1002/jcc.20366

2005

Genoni A, Fornili A and Sironi M (2005). Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals. J Comput Chem  vol. 26, (8) 827-835. 10.1002/jcc.20213

Morelli CF, Fornili A, Sironi M, Durì L, Speranza G and Manitto P (2005). Evidence for a nucleophilic anti-attack on the cleaved C(2)-oxygen bond in Cl2AlH-catalyzed ring-opening of 2-substituted 1,3-dioxolanes. Tetrahedron Letters  vol. 46, (11) 1837-1840. 10.1016/j.tetlet.2005.01.108

2003

Fornili A, Civera M, Sironi M and Fornili SL (2003). Molecular dynamics simulation of aqueous solutions of trimethylamine-N- oxide and tert-butyl alcohol. Physical Chemistry Chemical Physics  vol. 5, (21) 4905-4910. 10.1039/b308248b

Fornili A, Sironi M and Raimondi M (2003). Determination of extremely localized molecular orbitals and their application to quantum mechanics/molecular mechanics methods and to the study of intramolecular hydrogen bonding. Journal of Molecular Structure: Theochem  vol. 632, (1-3) 157-172. 10.1016/S0166-1280(03)00296-3

Civera M, Fornili A, Sironi M and Fornili SL (2003). Molecular dynamics simulation of aqueous solutions of glycine betaine. Chemical Physics Letters  vol. 367, (1-2) 238-244. 10.1016/S0009-2614(02)01707-4

2002

Morelli CF, Fornili A, Sironi M, Durì L, Speranza G and Manittoa P (2002). Regio- and diastereoselectivity in TiCl4-promoted reduction of 2-aryl-substituted cis-4-methyl-5-trifluoromethyl-1,3-dioxolanes. Tetrahedron Asymmetry  vol. 13, (23) 2609-2618. 10.1016/S0957-4166(02)00687-0

2001

FORNILI A (2001). Water interaction with glycine betaine: A hybrid QM/MM molecular dynamics simulation. Royal Society of Chemistry  Physical Chemistry Chemical Physics  vol. 3, 1081-1085. 10.1039/B009779I

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