Physical mechanisms of the Sec machinery operation.

The Sec complex, composed of a motor protein SecA and a channel SecYEG, is an ATP-driven molecular machine for the transport of proteins across the plasma membrane in bacteria. Today, there is a consensus about a general "rough" model of the complex activation and operation, which, however, lacks understanding of the physical mechanisms behind it. Molecular dynamics simulations were employed to address a way of allosteric activation, conformational transition of SecYEG from the closed to the open state, and driving forces of protein transport.

A unified framework for the numerical evaluation of the Q-subtractive Kramers-Kronig relations and application to the reconstruction of optical constants of quartz.

The direct usage of the Kramers-Kronig (KK) relations is complicated by two factors: limited frequency range of the available spectra and experimental errors. Here, we reconsider the application of the KK relations to experimental data for the construction of a self-consistent set of optical constants over a wide spectral range: the real part of the complex optical constant, F, is reconstructed using the imaginary part F, obtained from an experiment. The focus is on multiply (Q-)subtractive KK relations, which in contrast to the standard KK transformation, exploit information about F at a certain number Q of anchor frequencies.

Structural determinants of a permeation barrier of the SecYEG translocon in the active state.

The SecYEG translocon is a channel in bacteria, which provides a passage for secretory proteins across as well as integration of membrane proteins into the plasma membrane. The molecular mechanism, by which SecYEG manages protein transport while preventing water and ion leakage through the membrane, is still controversial. We employed molecular dynamics simulations to assess the contribution of the major structural elements - the plug and the pore ring (PR) - to the sealing of SecYEG in the active state, , with a signal sequence helix occupying the lateral gate.

ARGOS: An adaptive refinement goal-oriented solver for the linearized Poisson-Boltzmann equation.

An adaptive finite element solver for the numerical calculation of the electrostatic coupling between molecules in a solvent environment is developed and tested. At the heart of the solver is a goal-oriented a posteriori error estimate for the electrostatic coupling, derived and implemented in the present work, that gives rise to an orders of magnitude improved precision and a shorter computational time as compared to standard finite difference solvers. The accuracy of the new solver ARGOS is evaluated by numerical experiments on a series of problems with analytically known solutions.

Driving Forces of Translocation Through Bacterial Translocon SecYEG.

This review focusses on the energetics of protein translocation via the Sec translocation machinery. First we complement structural data about SecYEG's conformational rearrangements by insight obtained from functional assays. These include measurements of SecYEG permeability that allow assessment of channel gating by ligand binding and membrane voltage.

Theory of FRET "Spectroscopic Ruler" for Short Distances: Application to Polyproline.

Förster resonance energy transfer (FRET) is an important mechanism for the estimation of intermolecular distances, e.g., in fluorescent labeled proteins.