Biomedical subjects

Isabelle Navizet

Publications and source records attributed to Isabelle Navizet.

3 recordsLinked to original sources

PubMed2005

Vibrations in the B4 rhombic structure.

A double minimum six-dimensional potential energy surface (PES) is determined in symmetry coordinates for the most stable rhombic (D2h) B4 isomer in its 1Ag electronic ground state by fitting to energies calculated ab initio. The PES exhibits a barrier to the D4h square structure of 255 cm(-1). The vibrational levels (J=0) are calculated variationally using an approach which involves the Watson kinetic energy operator expressed in normal coordinates. The pattern of about 65 vibrational levels up to 1600 cm(-1) for all stable isotopomers is analyzed. Analogous to the inversion in ammonia-like molecules, the rhombus rearrangements lead to splittings of the vibrational levels. In B4 it is the B1g (D4h) mode which distorts the square molecule to its planar rhombic form. The anharmonic fundamental vibrational transitions of 11B4 are calculated to be (splittings in parentheses): G(0)=2352(22) cm(-1), nu1(A1g)=1136(24) cm(-1), nu2(B1g)=209(144) cm(-1), nu3(B2g)=1198(19) cm(-1), nu4(B2u)=271(24) cm(-1), and nu5(Eu)=1030(166) cm(-1) (D4h notation). Their variations in all stable isotopomers were investigated. Due to the presence of strong anharmonic resonances between the B1g in-plane distortion and the B2u out-of-plane bending modes, the higher overtones and combination levels are difficult to assign unequivocally.

Journal Article↗

PubMed2004

Myosin flexibility: structural domains and collective vibrations.

The movement of the myosin motor along an actin filament involves a directed conformational change within the cross-bridge formed between the protein and the filament. Despite the structural data that has been obtained on this system, little is known of the mechanics of this conformational change. We have used existing crystallographic structures of three conformations of the myosin head, containing the motor domain and the lever arm, for structural comparisons and mechanical studies with a coarse-grained elastic network model. The results enable us to define structurally conserved domains within the protein and to better understand myosin flexibility. Notably they point to the role of the light chains in rigidifying the lever arm and to changes in flexibility as a consequence of nucleotide binding.

Animals↗

PubMed2004

Probing protein mechanics: residue-level properties and their use in defining domains.

It is becoming clear that, in addition to structural properties, the mechanical properties of proteins can play an important role in their biological activity. It nevertheless remains difficult to probe these properties experimentally. Whereas single-molecule experiments give access to overall mechanical behavior, notably the impact of end-to-end stretching, it is currently impossible to directly obtain data on more local properties. We propose a theoretical method for probing the mechanical properties of protein structures at the single-amino acid level. This approach can be applied to both all-atom and simplified protein representations. The probing leads to force constants for local deformations and to deformation vectors indicating the paths of least mechanical resistance. It also reveals the mechanical coupling that exists between residues. Results obtained for a variety of proteins show that the calculated force constants vary over a wide range. An analysis of the induced deformations provides information that is distinct from that obtained with measures of atomic fluctuations and is more easily linked to residue-level properties than normal mode analyses or dynamic trajectories. It is also shown that the mechanical information obtained by residue-level probing opens a new route for defining so-called dynamical domains within protein structures.

Biophysics↗