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Konstantin Roeder

Publications and source records attributed to Konstantin Roeder.

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Polarization controlled second harmonic generation imaging of stretched collagen fibrils reveals collagen deformation pathway in situ

The tensile properties of single collagen fibrils, the building block of load-bearing tissues, have been studied extensively by nanomechanical techniques and molecular dynamics simulation. However, the deformation pathway of collagen molecules within fibrils has not yet been observed experimentally. In addition, the role played by divalent and trivalent enzymatic crosslinks in modulating this deformation pathway is poorly understood. Here we used polarization controlled second harmonic generation (SHG) imaging combined with atomic force microscopy (AFM) to characterize the molecular state of collagen triple helices within stretched single collagen fibrils. The fibrils were extracted from a pair of bovine leg tendons from the same animal in order to compare fibrils with a high amount of immature divalent crosslinks to fibrils with a high amount of mature trivalent crosslinks. By selecting fibrils with a large SHG intensity gradient along their length and then imaging the same fibrils by AFM we were able to link the observed intensity gradient with a gradient in D-band strain and a gradient in molecular strain as estimated from the SHG anisotropy parameter rho. In contrast to previous studies at the tendon scale, we observed that the SHG molecular strain is always larger than the D-band strain for all fibrils with this difference being largest for fibrils rich in divalent crosslinks. By analyzing the behavior of the relative density of SHG emitters as a function of molecular strain, we observe a two-state transition from an SHG producing to a non SHG producing state with a free energy barrier between 6 and 10 kBT that we propose corresponds to the local untwisting of the collagen triple helix superhelical twist which likely preceded bond rupture and loss of the SHG signal. We also show that trivalent crosslinks tend to delay the transition onset compared to divalent crosslinks.

q-bio.QM

Energy landscapes and dynamics of xylo-nucleic acids

Artificial analogues of the natural nucleic acids have attracted recent interest as a diverse class of information storage molecules capable of self-replication. In the present study, we use the computational potential energy landscape framework to investigate the structural and dynamical properties of xylo- and deoxyxylo-nucleic acids (XyNA and dXyNA), which are derived from their respective RNA and DNA analogues by an inversion of configuration at a single chiral center in the sugar moiety of the nucleotide unit. The free energy landscapes of an octameric XyNA sequence and its dXyNA analogue demonstrate the existence of a facile conformational transition between a left-handed helix that is the global free energy minimum, and a closely competing ladder-type structure with approximately zero helicity. The separation of the competing conformational ensembles is better-defined for the dXyNA system, whereas the XyNA analogue is inherently more flexible. The former therefore appear more suitable candidates for a molecular switch. The landscapes differ qualitatively from those reported in previous studies for evolved biomolecules: they are significantly more frustrated, so that XyNAs provide an example of an unnatural system for which the conditions constituting the principle of minimal frustration are, as may be expected, violated.

physics.bio-ph