Based on the concepts of fractional Brownian dynamics and on the general theoretical framework for anomalous diffusion and relaxation processes, we have developed a so-called minimal model for the backbone dynamics of proteins (J. Chem. Phys. Editor’s choice 2012) and more recently a model-free interpretation of quasielastic neutron scattering spectra (QENS) from proteins proteins (J. Chem. Phys. Editor’s choice 2016). The basic features of protein dynamics, in particular its multiscale character, is here captured by essentially two parameters describing, respectively, the form and the scale of a spectrum. In case of the QENS analysis one uses in addition that high-resolution spectrometers can only detect the asymptotic for of the dynamics for long times and small frequencies.
Another type of minimal protein models, which has been developed in the group, concerns the characterization of their global fold. The ScrewFrame model uses the positions of the Cα-atoms along the backbone of a protein to construct a tube model for the protein under consideration. Such a tube model is essentially characterized by the bending and by the internal torsion of the tube. The model is based on Cα-based Frenet frames, which are constructed from the discrete trace of the Cα-positions, and a sequence of helix motions relating these frames. Current applications concern the structural characterization of “unstructured proteins” and the analysis of electron microscopy clichés.
Asymptotic neutron scattering laws for anomalously diffusing quantum particles
The Journal of Chemical Physics. 2016 Jul 28;145(4):44103
Kneller GR, Hinsen K
Protein secondary-structure description with a coarse-grained model
Acta Crystallogr D. 2015;71(7):1411–22
Kneller GR, Hinsen K, Calligari P
A minimal model for the diffusion-relaxation backbone dynamics of proteins
J Chem Phys. 2012;139(19):191101
Calligari PA, Kneller GR
ScrewFit: combining localization and description of protein secondary structure
Acta Cryst (2012) D68, 1690–1693 [doi:101107/S0907444912039029]. 2012;1–10