Origins of the Intermediate Spectral Form in M100 Mutants of Photoactive Yellow Protein

Numerous single‐site mutants of photoactive yellow protein (PYP) from Halorhodospira halophila and as well as PYP homologs from other species exhibit a shoulder on the short wavelength side of the absorbance maximum in their dark‐adapted states. The structural basis for the occurrence of this shoulder, called the “intermediate spectral form,” has only been investigated in detail for the Y42F mutation. Here we explore the structural basis for occurrence of the intermediate spectral form in a M121E derivative of a circularly permuted H. halophila PYP (M121E‐cPYP). The M121 site in M121E‐cPYP corresponds to the M100 site in wild‐type H. halophila PYP. High‐resolution NMR measurements with a salt‐tolerant cryoprobe enabled identification of those residues directly affected by increasing concentrations of ammonium chloride, a salt that greatly enhances the fraction of the intermediate spectra form. Residues in the surface loop containing the M121E (M100E) mutation were found to be affected by ammonium chloride as well as a discrete set of residues that link this surface loop to the buried hydroxyl group of the chromophore via a hydrogen bond network. Localized changes in the conformational dynamics of a surface loop can thereby produce structural rearrangements near the buried hydroxyl group chromophore while leaving the large majority of residues in the protein unaffected.     

Bilinear electric field gradient focusing

Electric field gradient focusing (EFGF) uses an electric field gradient and a hydrodynamic counter flow to simultaneously separate and focus charged analytes in a channel. Previously, most EFGF devices were designed to form a linear field gradient in the channel. However, the peak capacity obtained using a linear gradient is not much better than what can be obtained using conventional CE. Dynamic improvement of peak capacity in EFGF can be achieved by using a nonlinear gradient. Numerical simulation results indicate that the peak capacity in a 4-cm long channel can be increased from 20 to 150 when changing from a linear to convex bilinear gradient. To demonstrate the increased capacity experimentally, an EFGF device with convex bilinear gradient was fabricated from poly(ethylene glycol) (PEG)-functionalized acrylic copolymers. The desired gradient profile was confirmed by measuring the focusing positions of a standard protein for different counter flow rates at constant voltage. Dynamically controlled elution of analytes was demonstrated using a monolith-filled bilinear EFGF channel. By increasing the flow rate, stacked proteins that were ordered but not resolved after focusing in the steep gradient segment were moved into the shallow gradient segment, where the analyte peak resolution increased significantly. In this way, the nonlinear field gradient was used to realize a dynamic increase in the peak capacity of the EFGF method.     

Quantum interface between an electrical circuit and a single atom

We show how to bridge the divide between atomic systems and electronic devices by engineering a coupling between the motion of a single ion and the quantized electric field of a resonant circuit. Our method can be used to couple the internal state of an ion to the quantized circuit with the same speed as the internal-state coupling between two ions. All the well-known quantum information protocols linking ion internal and motional states can be converted to protocols between circuit photons and ion internal states. Our results enable quantum interfaces between solid state qubits, atomic qubits, and light, and lay the groundwork for a direct quantum connection between electrical and atomic metrology standards.     

Quantum nanoscience

In this article we discuss the physical principles behind new quantum devices and materials that require some form of nanoscale fabrication. The two systems we discuss are superconducting quantum circuits and nanomechanical resonators. Both systems involve many-body systems of a special kind in which particular collective degrees of freedom can be factored out of the microscopic dynamics and subject to quantum control. We discuss applications to precision metrology.     

Measurement of unstable burning velocities of iso-octane–air mixtures at high pressure and the derivation of laminar burning velocities

A new technique is reported for measuring burning velocities at high pressures in the final stages of two inwardly propagating flame kernels in an explosion bomb. The flames were initiated at diametrically opposite spark electrodes, close to the wall, in quiescent mixtures. Measurements of pressure and flame kernel propagation speeds by high-speed photography showed the burning velocities to be elevated above the corresponding laminar burning velocities as a result of the developing flame instabilities. The enhancement increased with increase in pressure and decreased with increase in Markstein number. When the Markstein number was negative, instabilities could be appreciable, as could the enhancement. For the iso-octane–air mixtures investigated, where the mixtures had well-characterised Markstein numbers or critical Peclet numbers at the relevant pressures and temperatures, it was possible to explain the enhancement quantitatively by the spherical explosion flame instability theory of Bechtold and Matalon, provided the critical Peclet number was that observed experimentally, and allowance was made for the changing pressure. With this theoretical procedure, it was possible to derive values of laminar burning velocity from the measured values of burning velocity over a wide range of equivalence ratios, pressures, and temperatures. The values became less reliable at the higher temperatures and pressures as the data on Markstein and critical Peclet numbers became less certain. It was found that with iso-octane as the fuel the laminar burning velocity decreased during isentropic compression.     

Molecular structure calculations without clamping the nuclei

A number of recent papers have considered ways in which molecular structure may be calculated when both the electrons and the nuclei are treated from the outset as quantum particles. This is in contrast to the conventional approach in which the nuclei initially have their positions fixed and so merely provide a potential for electronic motion. The usual approach is generally assumed to be justified by the 1927 work of Born and Oppenheimer. In this paper we discuss what precisely might be anticipated in the way of molecular structure from a mathematical consideration of the spectral properties of the full Coulomb Hamiltonian, to what extent the very idea of molecular structure might be dependent upon treating the nuclei simply as providing a potential and the extent to which the work of Born and Oppenheimer can be used to support this position.     

Ion-permeable membrane for on-chip preconcentration and separation of cancer marker proteins

Cancer marker proteins have been electrophoretically concentrated and then separated in a microfluidic device. On-chip preconcentration was achieved using an ion-permeable membrane, consisting of acrylamide, N,N'-methylene-bisacrylamide and 2-(acrylamido)-2-methylpropanesulfonate. This negatively charged membrane was photopolymerized in the microdevice near the injection intersection. Anionic proteins were excluded from the porous membrane based on both size and charge, which concentrated target components in the injection intersection prior to separation by microchip capillary electrophoresis (μ-CE). Bovine serum albumin was used in the initial characterization of the system and showed a 40-fold enrichment in the μ-CE peak with 4 min of preconcentration. Adjustment of buffer pH enabled baseline resolution of two cancer biomarkers, α-fetoprotein (AFP) and heat shock protein 90 (HSP90), while fine control over preconcentration time limited peak broadening. Our optimized preconcentration and μ-CE approach was applied to AFP and HSP90, where enrichment factors of >10-fold were achieved with just 1 min of preconcentration. Overall, the process was simple and rapid, providing a useful tool for improving detection in microscale systems.     

In-channel atom-transfer radical polymerization of thermoset polyester microfluidic devices for bioanalytical applications

A new technique for polymer microchannel surface modification, called in-channel atom-transfer radical polymerization, has been developed and applied in the surface derivatization of thermoset polyester (TPE) microdevices with poly(ethylene glycol) (PEG). X-ray photoelectron spectroscopy, electroosmotic flow (EOF), and contact angle measurements indicate that PEG has been grafted on the TPE surface. Moreover, PEG-modified microchannels have much lower and more pH-stable EOF, more hydrophilic surfaces and reduced nonspecific protein adsorption. Capillary electrophoresis separation of amino acid and peptide mixtures in these PEG-modified TPE microchips had good reproducibility. Phosducin-like protein and phosphorylated phosducin-like protein were also separated to measure the phosphorylation efficiency. Our results indicate that PEG-grafted TPE microchips have broad potential application in biomolecular analysis.     

Photocontrol of DNA binding specificity of a miniature engrailed homeodomain

Control of DNA binding of HDH-3, a 18-residue polypeptide based on the recognition helix of the Q50K engrailed homeodomain, has been achieved. HDH-3 was linked to an azobenzene cross-linker through two cysteine residues in an i, i + 11 spacing. For the thermodynamically stable trans configuration of the cross-linker, the dark-adapted peptide (dad-HDH-3) adopted a mainly alpha-helical structure as judged by circular dichroism (CD) spectroscopy. After irradiation with light of 360 nm, the helical content of the peptide (irrad-HDH-3) was reduced significantly and the CD spectrum of the irradiated peptide resembled that of the largely unstructured, unalkylated peptide. Despite lacking helices-1 and -2 and the N-terminal arm of Q50K engrailed, dad-HDH-3 bound to its natural DNA target sequence TAATCC (QRE) with high affinity (K(D) = 7.5 +/- 1.3 nM). The binding affinity for the mutant DNA sequence, TAATTA (ERE), was reduced significantly (K(D) = 140 +/- 11 nM). Unlike irrad-HDH-3, which like the unalkylated parent peptide displayed only marginal DNA binding specificity, dad-HDH-3 specified base pairs 5 and 6 of QRE with an accuracy rivaling that of the intact wild-type Q50K engrailed homeodomain, making dad-HDH-3 the most specific designed DNA binding miniature homeodomain reported to date. Moreover, DNA binding affinity and specificity of HDH-3 could be controlled externally by irradiation with light.     

Electrically actuated, pressure-driven microfluidic pumps

In order to make the lab-on-a-chip concept a reality, it is desirable to have an integrated component capable of pumping fluids through microchannels. We have developed novel, electrically actuated micropumps and have integrated them with microfluidic systems. These devices utilize the build-up of electrolysis gases to achieve pressure-driven pumping, only require small voltages (approximately 10 V), and have approximate dimensions of 5 cm x 3 cm x 2 cm. Furthermore, these micropumps are composed of relatively inexpensive materials, and the reversible sealability of their poly(dimethylsiloxane) body to different microfluidic arrays enables repeated uses of the same pump. Under an applied potential of 10 V, three different micropumps had average flow rates of 8-13 microL min(-1) for water being pumped through five different 2 cm-long, 5500 microm(2) cross-sectional-area channels in poly(methyl methacrylate), in approximate agreement with predicted pump rates. We have also evaluated pump operation at the lower applied potential of 8 V and observed an average flow rate of 6.1 microL min(-1) for a pump-channel system. The current micropump design is capable of sustaining pumping pressures in the range of 300 kPa. The various advantages of these micropumps make them well suited for use in lab-on-a-chip analysis techniques.