Vania Calandrini
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Featured researches published by Vania Calandrini.
Chemistry: A European Journal | 2014
Vania Calandrini; Trung Hai Nguyen; Fabio Arnesano; Angela Galliani; Emiliano Ippoliti; Paolo Carloni; Giovanni Natile
Cisplatin is one of the most used anticancer drugs. Its cellular influx and delivery to target DNA may involve the copper chaperone Atox1 protein. Although the mode of binding is established by NMR spectroscopy measurements in solution-the Pt atom binds to Cys12 and Cys15 while retaining the two ammine groups-the structural determinants of the adduct are not known. Here a structural model by hybrid Car-Parrinello density functional theory-based QM/MM simulations is provided. The platinated site minimally modifies the fold of the protein. The calculated NMR and CD spectral properties are fully consistent with the experimental data. Our in silico/in vitro approach provides, together with previous studies, an unprecedented view into the structural biology of cisplatin-protein adducts.
Journal of Physical Chemistry B | 2011
Paolo Calligari; Vania Calandrini; Gerald R. Kneller; Daniel Abergel
In a recent simulation study [J. Chem. Phys. 2010, 133, 145101], it has been shown that the time correlation functions probed by nuclear magnetic resonance (NMR) relaxation spectroscopy of proteins are well described by a fractional Brownian dynamics model, which accounts for the wide spectrum of relaxation rates characterizing their internal dynamics. Here, we perform numerical experiments to explore the possibility of using this model directly in the analysis of experimental NMR relaxation data. Starting from a molecular dynamics simulation of the 266 residue protein 6PGL in explicit water, we construct virtual (15)N R(1), R(2), and NOE relaxation rates at two different magnetic fields, including artificial noise, and test how far the parameters obtained from a fit of the model to the virtual experimental data coincide with those obtained from an analysis of the MD time correlation functions that have been used to construct these data. We show that in most cases, close agreement is found. Acceptance or rejection of parameter values obtained from relaxation rates are discussed on a physical basis, therefore avoiding overfitting.
Journal of Chemical Theory and Computation | 2017
Thomas Tarenzi; Vania Calandrini; Raffaello Potestio; Alejandro Giorgetti; Paolo Carloni
The recently proposed Hamiltonian adaptive resolution scheme (H-AdResS) allows the performance of molecular simulations in an open boundary framework. It allows changing, on the fly, the resolution of specific subsets of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the molecular mechanics/coarse-grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Toward this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.
Journal of Physical Chemistry B | 2017
Luca Pesce; Vania Calandrini; Henri-Baptiste Marjault; Colin H. Lipper; Giulia Rossetti; Ron Mittler; Patricia A. Jennings; Andreas Bauer; Rachel Nechushtai; Paolo Carloni
The NEET proteins are a novel family of iron–sulfur proteins characterized by an unusual three cysteine and one histidine coordinated [2Fe–2S] cluster. Aberrant cluster release, facilitated by the breakage of the Fe–N bond, is implicated in a variety of human diseases, including cancer. Here, the molecular dynamics in the multi-microsecond timescale, along with quantum chemical calculations, on two representative members of the family (the human NAF-1 and mitoNEET proteins), show that the loss of the cluster is associated with a dramatic decrease in secondary and tertiary structure. In addition, the calculations provide a mechanism for cluster release and clarify, for the first time, crucial differences existing between the two proteins, which are reflected in the experimentally observed difference in the pH-dependent cluster reactivity. The reliability of our conclusions is established by an extensive comparison with the NMR data of the solution proteins, in part measured in this work.
Archives of Biochemistry and Biophysics | 2015
Giulia Rossetti; Domenica Dibenedetto; Vania Calandrini; Alejandro Giorgetti; Paolo Carloni
G protein coupled receptors (GPCRs) and intrinsic disordered proteins (IDPs) are key players for neuronal function and dysfunction. Unfortunately, their structural characterization is lacking in most cases. From one hand, no experimental structure has been determined for the two largest GPCRs subfamilies, both key proteins in neuronal pathways. These are the odorant (450 members out of 900 human GPCRs) and the bitter taste receptors (25 members) subfamilies. On the other hand, also IDPs structural characterization is highly non-trivial. They exist as dynamic, highly flexible structural ensembles that undergo conformational conversions on a wide range of timescales, spanning from picoseconds to milliseconds. Computational methods may be of great help to characterize these neuronal proteins. Here we review recent progress from our lab and other groups to develop and apply in silico methods for structural predictions of these highly relevant, fascinating and challenging systems.
Journal of Chemical Physics | 2014
Vania Calandrini; Jens Dreyer; Emiliano Ippoliti; Paolo Carloni
Chloride anions permeate the bacterial NanC porin in physiological processes. Here we present a DFT-based QM/MM study of this porin in the presence of these anions. Comparison is made with classical MD simulations on the same system. In both QM/MM and classical approaches, the anions are almost entirely solvated by water molecules. However, the average water-Cl(-) distance is significantly larger in the first approach. Polarization effects of protein groups close to Cl(-) anion are sizeable. These effects might modulate the anion-protein electrostatic interactions, which in turn play a central role for selectivity mechanisms of the channel.
Dalton Transactions | 2014
Vania Calandrini; Fabio Arnesano; Angela Galliani; Trung Hai Nguyen; Emiliano Ippoliti; Paolo Carloni; Giovanni Natile
Journal of Physical Chemistry B | 2000
A. Bonincontro; Emanuele Bultrini; Vania Calandrini; Stefania Cinelli; G. Onori
Journal of Physical Chemistry B | 2015
Paolo Calligari; Vania Calandrini; Jacques Ollivier; Jean-Baptiste Artero; Mark R. Johnson; Gerald R. Kneller
Journal of Inorganic Biochemistry | 2015
Vania Calandrini; Giulia Rossetti; Fabio Arnesano; Giovanni Natile; Paolo Carloni