A5064994528- Protein Structure and Dynamics
- Spectroscopy and Quantum Chemical Studies
- Photochemistry and Electron Transfer Studies
- DNA and Nucleic Acid Chemistry
- Enzyme Structure and Function
- Advanced Chemical Physics Studies
- Molecular Junctions and Nanostructures
- Advanced biosensing and bioanalysis techniques
- RNA and protein synthesis mechanisms
- Free Radicals and Antioxidants
- Hemoglobin structure and function
- T-cell and B-cell Immunology
- CRISPR and Genetic Engineering
- Supramolecular Chemistry and Complexes
- Computational Drug Discovery Methods
- Immune Cell Function and Interaction
- Lipid Membrane Structure and Behavior
- Protein Kinase Regulation and GTPase Signaling
- Supramolecular Self-Assembly in Materials
- Electron Spin Resonance Studies
- Molecular spectroscopy and chirality
- Microbial Metabolic Engineering and Bioproduction
- Redox biology and oxidative stress
- Biochemical and Molecular Research
- Machine Learning in Materials Science
Sapienza University of Rome
2016-2025
Università degli Studi Internazionali di Roma
2015
Cineca
2014
University of L'Aquila
2014
Spanish National Cancer Research Centre
2010-2012
Centro de Investigación del Cáncer
2010-2011
Universitat de Barcelona
2009-2010
Ikerbasque
2010
CIC bioGUNE
2010
Universitat Politècnica de Catalunya
2008-2010
Some years ago we developed a theoretical-computational hybrid quantum/classical methodology, the Perturbed Matrix Method (PMM), to be used in conjunction with molecular dynamics simulations for investigation of chemical processes complex systems, that proved valuable tool simulation relevant experimental observables, e.g., spectroscopic signals, reduction potentials, kinetic constants. In typical PMM calculations quantum sub-part system, centre, is embedded into an external perturbing field...
FlexServ is a web-based tool for the analysis of protein flexibility. The server incorporates powerful protocols coarse-grained determination dynamics using different versions Normal Mode Analysis (NMA), Brownian (BD) and Discrete Dynamics (DMD). It can also analyze user provided trajectories. allows complete flexibility large variety metrics, including basic geometrical analysis, B-factors, essential dynamics, stiffness collectivity measures, Lindemann's indexes, residue correlation,...
In this article we characterize, by means of the perturbed matrix method, response electronic states a chemical system to perturbing environment. theory section describe in detail basic derivations and implications extending its theoretical framework treat possible excitonic effects, show how characterize states. Finally, using set systems interacting with complex atomic-molecular environments, nature general features state mixing transitions as caused atomic molecular interactions.
The Trp53 gene is the most frequently mutated in all human cancers. Its protein product p53 a very powerful transcription factor that can activate different biochemical pathways and affect regulation of metabolism, senescence, DNA damage response, cell cycle death. understanding its function at molecular level could be pivotal relevance for therapy. Investigation long-range intra- interdomain communications tetramer–DNA complex was performed by means an atomistic model included...
Homing endonucleases recognize long target DNA sequences generating an accurate double-strand break that promotes gene targeting through homologous recombination. We have modified the homodimeric I-CreI endonuclease protein engineering to a specific sequence within human RAG1 gene. Mutations in produce severe combined immunodeficiency (SCID), monogenic disease leading defective immune response individuals, leaving them vulnerable infectious diseases. The structures of two engineered...
All-atom unbiased molecular dynamics simulations are now able to explore the microsecond millisecond time scale for simple biological macromolecules in an explicit solvent. This allows a careful comparison of efficiency and accuracy enhanced sampling methods versus long reconstructing conformational free energy surfaces. Here, we use equilibrium microsecond-long simulation as reference analyze convergence properties well-tempered metadynamics with two different sets collective variables. In...
A combined theoretical-experimental study of the hyperchromic effect as occurring in denaturation a double stranded polyA-polyT is presented. Our theoretical/computational procedure allows us to reproduce essential features experimental spectra and characterize those molecular interactions responsible for changes UV absorbance. We found that although excitonic intrastrand strongly affect absorbance, they are almost fully maintained single-stranded DNA. data indicate originates from higher...
Here, we extend a recently introduced theoretical-computational procedure [M. D’Alessandro, M. Aschi, C. Mazzuca, A. Palleschi, and Amadei, J. Chem. Phys. 139, 114102 (2013)] to include quantum vibrational transitions in modelling electronic spectra of atomic molecular systems condensed phase. The method is based on the combination Molecular Dynamics simulations chemical calculations within Perturbed Matrix Method approach. main aim presented approach reproduce as much possible spectral line...
In this paper we present a computational approach, based on <italic>NVT</italic> molecular dynamics trajectories, that allows the direct evaluation of protein partial volume.
Here, we present the theoretical–computational modeling of oxidation properties four DNA nucleosides and nucleotides a set dinucleotides in solutions. Our estimates vertical ionization energies reduction potentials, close to corresponding experimental data, show that an accurate calculation molecular electronic solutions requires proper treatment effect environment. In particular, found environment is stabilize oxidized state nucleobases resulting remarkable reduction—up 6.6 eV—of energy...
The charge transfer (CT) reactions in nucleic acids are crucial for genome damage and repair nanoelectronics using DNA as a molecular conductor. Previous experimental theoretical works underlined the significance of acid structural dynamics on CT kinetics, requiring models that incorporate acid, solvents, counterions. Here, we investigated hole kinetics poly adenine single double strands at various temperatures rate enhancement due to adenine-to-7-deazaadenine mutation by means QM/MM...
The oxidation of Met residues in proteins is a complex process, where protein-specific structural and dynamical features play relevant role determining the reaction kinetics. Aiming to full-side perspective, we report here comprehensive characterization kinetics by hydrogen peroxide leptin protein case study. To do that, estimated reaction-free energy profile via QM/MM approach, while formation reactive species were calculated using classical molecular dynamics (MD) simulations. Our data,...
Lymphocyte-specific protein tyrosine kinase (LCK) is essential for T cell antigen receptor (TCR)–mediated signal transduction. Here, we report two siblings homozygous a novel LCK variant (c.1318C&gt;T; P440S) characterized by lymphopenia with skewed memory phenotype, infant-onset recurrent infections, failure to thrive, and protracted diarrhea. The patients’ cells show residual TCR transduction proliferation following anti-CD3/CD28 phytohemagglutinin (PHA) stimulation. We demonstrate in...
Abstract The knowledge of the mechanism reactions occurring in solution is a primary research line both context theoretical‐computational chemistry and field organic bio‐organic chemistry. Given importance hydrolysis nucleic acids life‐related phenomena, here we present combined experimental computational study on cleavage an RNA model compound. This phosphodiester features rate strictly dependent pH with three different dependence domains. Such evidence, highlighted by in‐depth kinetic...
The chiral bile salt sodium cholate has been covalently linked to tetra-aryl-porphyrins, conferring them an extrinsic chirality and obtaining new molecules with high tendency aggregate in solution. transfer from the molecular nano- meso-scale investigated by promoting self-assembly of conjugates balancing ratio aqueous/organic solvent mixtures allowing a fine control dimensions morphology final supramolecular architectures. shift elongated structures helical ribbon features monodisperse...
We present here a molecular dynamics study on promising class of peptide nanotubes with partially hydrophobic inner cavity and an easy chemical functionalization the lumen cylindrical structure. The structural dynamical behavior nanotube in water, methanol, chloroform has been analyzed using state art theoretical methods. structure is always well preserved, but solvent-dependent dynamic alterations are evident. Such effects surprisingly more severe most viscous solvent (water), as...
The p53 protein is frequently mutated in a very large proportion of human tumors, where it seems to acquire gain-of-function activity that facilitates tumor onset and progression. A possible mechanism the ability mutant proteins physically interact with other proteins, including members same family, namely p63 p73, inactivating their function. Assuming this interaction might occurs at level monomer, investigate molecular basis for interaction, here, we sample structural flexibility wild-type...
Abstract Coordination polymers (CPs), including metal–organic frameworks (MOFs), are crystalline materials with promising applications in electronics, magnetism, catalysis, and gas storage/separation. However, the mechanisms pathways underlying their formation remain largely undisclosed. Herein, we demonstrate that diffusion‐controlled mixing of reagents at very early stages crystallization process (i.e., within ≈40 ms), achieved by using continuous‐flow microfluidic devices, can be used to...
By means of the conformational free energy surface and corresponding diffusion coefficients, as obtained by long time scale atomistic molecular dynamics simulations (μs scale), we model folding kinetics α-helix β-hairpin peptides a diffusive process over surface. The two systems studied in this paper (the α-helical temporin L prion protein H1 peptide) exhibit funnel-like almost barrierless profile, leading to nonexponential matching rather well available experimental data. Moreover, using...
Contradictory data in the huge literature on microwaves bio-effects may result from a poor understanding of mechanisms interaction between and biological systems. Molecular simulations biochemical processes seem to be promising tool comprehend microwave induced bio-effects. classical quantum events involved relevant enable follow dynamic evolution reaction presence fields. In this paper, action signal (1 GHz) covalent binding process ligand (carbon monoxide) protein (myoglobin) has been...
The hydrolysis of the phosphodiester bond is an important chemical reaction involved in several biological processes. Here, we study cleavage this by means a theoretical-computational method model system, dineopentyl phosphate. By such approach, reconstructed kinetics and related thermodynamics along isochore. In particular, evaluated kinetic constants all steps within wide range temperatures, mostly corresponding to conditions where no experimental measures are available due extremely slow...