Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals.

To enable a sustainable supply of chemicals, novel biotechnological solutions are required that replace the reliance on fossil resources. One potential solution is to utilize tailored biosynthetic modules for the metabolic conversion of CO2 or organic waste to chemicals and fuel by microorganisms. Currently, it is challenging to commercialize biotechnological processes for renewable chemical biomanufacturing because of a lack of highly active and specific biocatalysts. As experimental methods to engineer biocatalysts are time- and cost-intensive, it is important to establish efficient and reliable computational tools that can speed up the identification or optimization of selective, highly active, and stable enzyme variants for utilization in the biotechnological industry. Here, we review and suggest combinations of effective state-of-the-art software and online tools available for computational enzyme engineering pipelines to optimize metabolic pathways for the biosynthesis of renewable chemicals. Using examples relevant for biotechnology, we explain the underlying principles of enzyme engineering and design and illuminate future directions for automated optimization of biocatalysts for the assembly of synthetic metabolic pathways.

How many states can the motor molecule, prestin, assume in an electric field?

By using an analogy between the magnetization of a paramagnetic material in an external magnetic field and the electric polarization of the lateral wall of outer hair cells in response to the transmembrane potential, we show that, based on experimental data on the charge transfer across the membrane, it is impossible to make a statement about the number of possible conformational states of the motor molecule, prestin. Although the choice of model affects the values of derived parameters, such as total charge and motor charge, this is frequently overlooked in the literature.

Vibration pattern of the organ of Corti up to 50 kHz: evidence for resonant electromechanical force.

Electromechanical force derived from the soma of the outer hair cell has long been postulated as the basis of the exquisite sensitivity of the cochlea. The problem with this postulate is that the electrical source and mechanical load for the electromechanical outer hair cell might be severely attenuated and phase-shifted by the electrical impedance of the cell and the mechanical impedance of the organ of Corti, respectively. Until now, it has not been possible to experimentally derive the high-frequency electrically induced force at the reticular lamina when the cells are embedded within the organ of Corti. In the study reported here, we succeeded in determining the frequency spectrum of the force up to 50 kHz. This was achieved by measuring both the electrically induced velocity and the mechanical impedance at different radial positions on the reticular lamina without tectorial membrane and with clamped basilar membrane. Velocity was measured with a laser interferometer and impedance, with a magnetically driven atomic force cantilever. The electromechanical force, normalized to the electric current density, exhibited a broad amplitude maximum at 7-20 kHz with a quality factor, Q(3dB), of 0.6 - 0.8. The displacement response was independent of frequency up to 10-20 kHz. The force response compensates for the viscoelastic impedance of the organ of Corti, extending the amplitude response of the organ to high frequencies. It is proposed that the electrical phase response of the cell is compensated with Zwislocki's original mechanism of a parallel resonance in the tectorial membrane-stereocilia complex.

Impedance analysis of the organ of corti with magnetically actuated probes.

An innovative method is presented to measure the mechanical driving point impedance of biological structures up to at least 40 kHz. The technique employs an atomic force cantilever with a ferromagnetic coating and an external magnetic field to apply a calibrated force to the cantilever. Measurement of the resulting cantilever velocity using a laser Doppler vibrometer yields the impedance. A key feature of the method is that it permits measurements for biological tissue in physiological solutions. The method was applied to measure the point impedance of the organ of Corti in situ, to elucidate the biophysical basis of cochlear amplification. The basilar membrane was mechanically clamped at its tympanic surface and the measurements conducted at different radial positions on the reticular lamina. The tectorial membrane was removed. The impedance was described by a generalized Voigt-Kelvin viscoelastic model, in which the stiffness was real-valued and independent of frequency, but the viscosity was complex-valued with positive real part, which was dependent on frequency and negative imaginary part, which was independent of frequency. There was no evidence for an inertial component. The magnitude of the impedance was greatest at the tunnel of Corti, and decreased monotonically in each of the radial directions. In the absence of inertia, the mechanical load on the outer hair cells causes their electromotile displacement responses to be reduced by only 10-fold over the entire range of auditory frequencies.

Mechanical transduction in outer hair cells.

The outer hair cells are responsible for the exquisite sensitivity, frequency selectivity and dynamic range of the cochlea. These cells are part of a mechanical feedback system involving the basilar membrane and tectorial membrane. Transverse displacement of the basilar membrane results in relative motion between the tectorial membrane and the reticular lamina, causing deflection of the stereocilia and modulation of the open probability of their transduction channels. The resulting current causes a change of membrane potential, which in turn produces mechanical force, that is fed back into the motion of the basilar membrane. Experiments were conducted to address mechanical transduction mechanisms in both the stereocilia and the basolateral cell membrane, as well as modes of coupling of the outer hair cell force to the organ of Corti.