Xiongce Zhao

The O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase Is a Flexible, Disordered Protein

Fungi and bacteria secrete glycoprotein cocktails to deconstruct cellulose. Cellulose-degrading enzymes (cellulases) are often modular, with catalytic domains for cellulose hydrolysis and carbohydrate-binding modules connected by linkers rich in serine and threonine with O-glycosylation. Few studies have probed the role that the linker and O-glycans play in catalysis. Since different expression and growth conditions produce different glycosylation patterns that affect enzyme activity, the structure-function relationships that glycosylation imparts to linkers are relevant for understanding cellulase mechanisms. Here, the linker of the Trichoderma reesei Family 7 cellobiohydrolase (Cel7A) is examined by simulation. Our results suggest that the Cel7A linker is an intrinsically disordered protein with and without glycosylation. Contrary to the predominant view, the O-glycosylation does not change the stiffness of the linker, as measured by the relative fluctuations in the end-to-end distance; rather, it provides a 16xa0Å extension, thus expanding the operating range of Cel7A. We explain observations from previous biochemical experiments in the light of results obtained here, and compare the Cel7A linker with linkers from other cellulases with sequence-based tools to predict disorder. This preliminary screen indicates that linkers from Family 7 enzymes from other genera and other cellulases within T. reesei may not be as disordered, warranting further study.

Molecular dynamics study of carbon nanotube oscillators revisited

We performed molecular dynamics simulation of double walled carbon nanotube (DWCNT) oscillators under constant energy and constant temperatures with various commensurations and nanotube lengths. We clarify and resolve questions and differences raised by previous simulation results of similar systems. At constant energy, sustained oscillation is available for a wide range of initial temperatures. But low initial temperature is advantageous for DWCNTs to sustain oscillation under constant energy. We observed sustained oscillation at constant energy for both commensurate and incommensurate DWCNTs. On the other hand, under constant temperatures, both high and low temperatures are disadvantageous to sustain DWCNT oscillations. At constant low temperature, neither commensurate nor incommensurate DWCNTs can maintain oscillation. At appropriate constant temperatures, the oscillatory behavior of incommensurate nanotubes is much more sustained than that of commensurate tubes. The oscillatory frequency of DWCNTs depends significantly on the length of tubes. The initial oscillatory frequency is inversely proportional to the DWCNT lengths. The oscillation frequency of DWCNTs is insensitive to the initial temperatures at constant energy, but slightly dependent on the temperature at constant temperatures.

Molecular simulations of stretching gold nanowires in solvents.

The effect of solvent on the elongation of gold nanowires has been further studied through molecular simulations. For a simple Lennard-Jones solvent (propane), which is a non-bonded solvent, extensive molecular dynamics (MD) runs demonstrated that below the melting point of gold nanowires, the solvent effect on the elongation properties of Au nanowires is minimal. In thiol organic liquid, such as in benzenedithiol (BDT), the situation is much more complicated due to the Au-BDT chemical bonding. Here, we present the initial adsorption structure of BDT on a stretched gold nanowire through grand canonical Monte Carlo (GCMC) simulations. A recently developed force field for the BDT-Au chemical bonding was implemented in the simulations. We found that the packing density of the bonded BDT on the surface of Au nanowire is larger than that on an extended Au(111) surface. The results from this work are helpful in understanding the underlying mechanism of the formation of Au-BDT-Au junctions implemented in molecular conductance measurements.

Single-strand DNA molecule translocation through nanoelectrode gaps

Molecular dynamics simulations were performed to investigate the translocation of single-strand DNA through nanoscale electrode gaps under the action of a constant driving force. The application behind this theoretical study is a proposal to use nanoelectrodes as a screening gap as part of a rapid genomic sequencing device. Preliminary results from a series of simulations using various gap widths and driving forces suggest that the narrowest electrode gap that a single-strand DNA can pass is ∼1.5xa0nm. The minimum force required to initiate the translocation within nanoseconds is ∼0.3xa0nN. Simulations using DNA segments of various lengths indicate that the minimum initiation force is insensitive to the length of DNA. However, the average threading velocity of DNA varies appreciably from short to long DNA segments. We attribute such variation to the different nature of drag force experienced by the short and long DNA segments in the environment. Itxa0is found that DNA molecules deform significantly to fit in the shape of the nanogap during the translocation.

A molecular dynamics simulation study on trapping ions in a nanoscale Paul trap.

We found by molecular dynamics simulations that a low energy ion can be trapped effectively in a nanoscale Paul trap in both vacuum and aqueous environments when appropriate AC/DC electric fields are applied to the system. Using the negatively charged chlorine ion as an example, we show that the trapped ion oscillates around the center of the nanotrap with an amplitude dependent on the parameters of the system and applied voltages. Successful trapping of the ion within nanoseconds requires an electric bias of GHz frequency, in the range of hundreds of mV. The oscillations are damped in the aqueous environment, but polarization of water molecules requires the application of a higher voltage bias to reach improved stability of the trapping. Application of a supplemental DC driving field along the trap axis can effectively drive the ion off the trap center and out of the trap, opening up the possibility of studying DNA and other charged molecules using embedded probes while achieving a full control of their translocation and localization in the trap.

Molecular dynamics simulation of ss-DNA translocation between copper nanoelectrodes incorporating electrode charge dynamics.

Molecular dynamics simulations have been performed to study the translocation of single-stranded (ss)-DNA through the nanoscale gap between the nanoscale electrodes of a proposed genomic sequencing device. Using a fixed gap width between the electrodes and a small sample segment of ss-DNA as initial starting points in this project, the effect of applied electric fields on translocation velocity was studied. To describe the electrostatic interactions of the water, ions, and ss-DNA with the nanoscale electrodes, we applied the electrode charge dynamics (ECD) method. Through the density profile and comparison of translocation velocities to extrapolated experimental data, we found the ECD potential to be a better descriptor of the metal/nonmetal electrostatic interactions compared to the commonly used universal force field (UFF). Translocation velocities obtained using the ECD potential were consistent with simulated bulk data.

Electrophoresis of ssDNA through nanoelectrode gaps from molecular dynamics: impact of gap width and chain length.

Molecular dynamics simulations were performed to study the translocation of single-stranded (ss) DNA through the nanoscale gap between the nanoscale electrodes of a proposed genomic sequencing device. An applied electric field forces the ssDNA to move in the direction of the nanoscale gap in platinum electrodes. A series of simulations utilizing eight different nanoscale gap distances as well as seven different nucleotide chain lengths were performed to determine the impact of these variables on the overall design of the sequencing device and the translocation behavior of ssDNA. The results clearly indicate a threshold value of the gap width below which the ssDNA will readily enter and traverse the nanoscale gap. Translocation velocities obtained for various chain lengths were consistent with simulated bulk data; however, successful translocation was inconsistent, possibly related to the samples affinity for the metal electrodes. An attempt at overcoming this barrier was made through the implementation of shaped electrodes as well as pre-threading of the ssDNA sample.

Molecular simulations of DNA transport in solution

A proposed novel nanotechnology concept utilizes tunneling conductance measurements across nanoelectrodes to identify individual nucleotides as a DNA strand crosses its path. Such a device offers the possibility of unprecedented rapidity in the detection of DNA sequences. Preliminary simulations of this device have indicated that single-stranded (ss)-DNA sequences behave differently depending on the location of the molecule within the device. Motivated by the similarity of the comparison of the transport properties of the ss-DNA molecule in bulk solution to experimental capillary electrophoresis data, we performed molecular dynamics (MD) simulations of ss-DNA and double-stranded (ds)-DNA in free solution to directly compare electrophoretic mobility as calculated by simulation. Drift velocity at the lowest magnitude applied electric field was consistent with expected experimental data; however, at the larger applied fields necessary under timescale constraints, drift velocity appeared inconsistent with extrapolated experimental values. The simulated electrophoretic mobility values resulting from the drift velocity calculations were also smaller than experiment.