arXiv subjects

Fabio Pichierri

Publications and source records attributed to Fabio Pichierri.

8 recordsLinked to original sources

arXiv2019

IYPt is a highly polar, nonlinear triatomic molecule

An explorative quantum chemical study of the triatomic molecule IYPt, its isomers, group 17 congeners, and dimer is carried out. The results indicate that IYPt is a ground-state singlet with a bent geometry and a large electric dipole moment of magnitude 4.8 D. The IPtY isomer also is bent but 33.5 kcal/mol higher in energy whereas the isomer with the central iodine atom is not stable a molecule. Furthermore, the calculations indicate that only the dimer of IYPt, made of a (PtY)2 rhombus with the iodine atoms bonded to Y, is characterized by positive vibrational frequencies.

physics.chem-ph↗

arXiv2018

Giulio Fermi's contributions to biophysics and molecular biology

This paper presents a comprehensive list of the scientific articles of Giulio Fermi (1936-1997), son of the Italian-American physicist Enrico Fermi, published between 1962 and 1997. The initial research activity of Giulio was concerned with virology and biological cybernetics while, from 1975 onward, his work was completely devoted to protein crystallography. The crystallographic research was carried out in collaboration with Nobel laureate Max Perutz at the Medical Research Council (MRC) Laboratory of Molecular Biology in Cambridge (United Kingdom). A short biography of Giulio (Judd) Fermi appears inside John Finch's book A Nobel Fellow on Every Floor: A History of the Medical Research Council Laboratory of Molecular Biology published by the MRC in 2008.

physics.hist-ph↗

arXiv2013

Protein conformational dynamics and electronic structure

Quantum mechanical calculations are performed on 116 conformers of the protein ubiquitin (Lange et al., Science 2008, 320, 1471-1475). The results indicate that the heat of formation (HOF), dipole moment, energy of the frontier orbitals HOMO and LUMO, and HOMO-LUMO gap fluctuate within their corresponding ranges. This study thus provides a link between the conformational dynamics of a protein and its electronic structure.

q-bio.BM↗

arXiv2013

Dipole-dipole interactions in protein-protein complexes: a quantum mechanical study of the ubiquitin-Dsk2 complex

Quantum mechanical calculations are performed on the proteins that constitute the ubiquitin-Dsk2 complex whose atomic structure has been experimentally determined by NMR spectroscopy (PDB id 1WR1). The results indicate that the dipole moment vectors of the two proteins are aligned in a head-to-tail orientation while forming and angle of ~130°. Hence, attractive dipole-dipole interactions not only stabilize the protein-protein complex but they are likely to favor the correct orientation of the proteins during the formation of the complex.

q-bio.BM↗

arXiv2011

Quantum Proteomics

We put forward the idea of establishing a novel interdisciplinary field of research at the interface between quantum mechanics and proteomics. The new field, called quantum proteomics, is defined as the large-scale study of the electronic structure of the proteins that define an organism's proteome. The electronic structure of proteins is unveiled with the aid of linear-scaling quantum mechanical calculations. Such calculations provide information about the energy levels of the proteins, the charges of their amino acid side chains, their electrostatic potentials and permanent dipole moments (μ). Since the magnitude of the electric dipole moment of any protein is not null (μ\neq0 Debye), the dipole moment can be employed to characterize the electronic structure of each protein that belongs to an organism's proteome. As an example, we investigate six proteins from the thermophilic bacterium Methanobacterium thermoautotrophicum (Mth) whose atomic structures were characterized by solution NMR spectroscopy.

q-bio.BM↗

arXiv2010

A quantum mechanical analysis of the light-harvesting complex 2 from purple photosynthetic bacteria. Insights into the electrostatic effects of transmembrane helices

We perform a quantum mechanical study of the peptides that are part of the LH2 complex from Rhodopseudomonas acidophila, a non-sulfur purple bacteria that has the ability of producing chemical energy from photosynthesis. The electronic structure calculations indicate that the transmembrane helices of these peptides are characterized by dipole moments with a magnitude of ~150 D. When the full nonamer assembly made of eighteen peptides is considered, then a macrodipole of magnitude 704 D is built up from the vector sum of each monomer dipole. The macrodipole is oriented normal to the membrane plane and with the positive tip toward the cytoplasm thereby indicating that the electronic charge of the protein scaffold is polarized toward the periplasm. The results obtained here suggest that the asymmetric charge distribution of the protein scaffold contributes an anisotropic electrostatic environment which differentiates the absorption properties of the bacteriochlorophyll pigments, B800 and B850, embedded in the LH2 complex.

q-bio.BM↗

arXiv2010

The electronic structure and dipole moment of charybdotoxin, a scorpion venom peptide with K+ channel blocking activity

The electronic structure of charybdotoxin (ChTX), a scorpion venom peptide that is known to act as a potassium channel blocker, is investigated with the aid of quantum mechanical calculations. The dipole moment vector (145 D) of ChTX can be stirred by the full length KcsA potassium channel's macrodipole (403 D) thereby assuming the proper orientation before binding the ion channel on the cell surface. The localization of the frontier orbitals of ChTX has been revealed for the first time. HOMO is localized on Trp14 while the three lowest-energy MOs (LUMO, LUMO+1, and LUMO+2) are localized on the three disulfide bonds that characterize this pepetide. An effective way to engineer the HOMO-LUMO (H-L) gap of ChTX is that of replacing its Trp14 residue with Ala14 whereas deletion of the LUMO-associated disulfide bond with the insertion of a pair of L-alpha-aminobutyric acid residues does not affect the H-L energy gap.

q-bio.BM↗

arXiv2009

Macrodipoles of potassium and chloride ion channels as revealed by electronic structure calculations

With the aid of quantum mechanical calculations we investigate the electronic structure of the full length (FL) potassium channel protein, FL-KcsA, in its closed conformation, and the electronic structure of the ClC chloride channel. The results indicate that both ion channels are strongly polarized towards the extracellular region with respect to the membrane mean plane. FL-KcsA possesses an electric dipole moment of magnitude 403 Debye while ClC has a macrodipole whose magnitude is about five times larger, 1983 Debye, thereby contributing to differentiate their membrane electric barriers. The dipole vectors of both proteins are aligned along the corresponding selectivity filters. This result suggests that potassium and chloride ion channels are not passive with respect to the movement of ions across the membrane and the ionic motion might be partially driven by the electric field of the protein in conjunction with the electrochemical potential of the membrane.

q-bio.BM↗