A heterogeneous tRNA granule structure exhibiting rapid, bi-directional neuritic transport.

mRNA translation is regulated by diverse mechanisms that converge at the initiation and elongation steps to determine the rate, profile, and localization of proteins synthesized. A consistently relevant feature of these mechanisms is the spatial re-distribution of translation machinery, a process of particular importance in neural cells. This process has, however, been largely overlooked with respect to its potential role in regulating the local concentration of cytoplasmic tRNAs, even as a multitude of data suggest that spatial regulation of the tRNA pool may help explain the remarkably high rates of peptide elongation. Here, we report that Cy3/Cy5-labeled bulk tRNAs transfected into neural cells distribute into granule-like structures - "tRNA granules" - that exhibit dynamic mixing of tRNAs between granules and rapid, bi-directional vectorial movement within neurites. Imaging of endogenous tRNAgly and tRNAlys by fluorescent in situ hybridization revealed a similar granular distribution of tRNAs in somata and neurites; this distribution was highly overlapping with granules imaged by introduction of exogenous Cy5-tRNAthr and Cy3-tRNAval. A subset of tRNA granules located in the cell body, neurite branch points and growth cones displayed fluorescence resonance energy transfer (FRET) between Cy3 and Cy5-labeled tRNAs indicative of translation, and co-localization with elongation machinery. A population of smaller, rapidly trafficked granules in neurites lacked FRET and showed poor colocalization with translation initiation and elongation factors, suggesting that they are a translationally inactive tRNA transport particle. Our data suggest that tRNAs are packaged into granules that are rapidly transported to loci where translation is needed, where they may greatly increase the local concentration of tRNAs in support of efficient elongation. The potential implications of this newly described structure for channeling of elongation, local translation, and diseases associated with altered tRNA levels or function are discussed.

A cell-free expression and purification process for rapid production of protein biologics.

Cell-free protein synthesis has emerged as a powerful technology for rapid and efficient protein production. Cell-free methods are also amenable to automation and such systems have been extensively used for high-throughput protein production and screening; however, current fluidic systems are not adequate for manufacturing protein biopharmaceuticals. In this work, we report on the initial development of a fluidic process for rapid end-to-end production of recombinant protein biologics. This process incorporates a bioreactor module that can be used with eukaryotic or prokaryotic lysates that are programmed for combined transcription/translation of an engineered DNA template encoding for specific protein targets. Purification of the cell-free expressed product occurs through a series of protein separation modules that are configurable for process-specific isolation of different proteins. Using this approach, we demonstrate production of two bioactive human protein therapeutics, erythropoietin and granulocyte-macrophage colony-stimulating factor, in yeast and bacterial extracts, respectively, each within 24 hours. This process is flexible, scalable and amenable to automation for rapid production at the point-of-need of proteins with significant pharmaceutical, medical, or biotechnological value.

15N-labeled brain enables quantification of proteome and phosphoproteome in cultured primary neurons.

Terminally differentiated primary cells represent a valuable in vitro model to study signaling events associated within a specific tissue. Quantitative proteomic methods using metabolic labeling in primary cells encounter labeling efficiency issues hindering the use of these cells. Here we developed a method to quantify the proteome and phosphoproteome of cultured neurons using (15)N-labeled brain tissue as an internal standard and applied this method to determine how an inhibitor of an excitatory neural transmitter receptor, phencyclidine (PCP), affects the global phosphoproteome of cortical neurons. We identified over 10,000 phosphopeptides and made accurate quantitative measurements of the neuronal phosphoproteome after neuronal inhibition. We show that short PCP treatments lead to changes in phosphorylation for 7% of neuronal phosphopeptides and that prolonged PCP treatment alters the total levels of several proteins essential for synaptic transmission and plasticity and leads to a massive reduction in the synaptic strength of inhibitory synapses. The results provide valuable insights into the dynamics of molecular networks implicated in PCP-mediated NMDA receptor inhibition and sensorimotor deficits.

Roaming dynamics in formaldehyde-d2 dissociation.

State-resolved photodissociation dynamics of formaldehyde-d(2), i.e., D(2)CO, at energies slightly above the deuterium atom elimination channel have been studied both experimentally and theoretically. The results showed a clear bimodal distribution of energy into molecular photofragments. Substantial translational excitation of products at high rotational levels of CO was observed together with the D(2) cofragment in moderately excited vibrational levels, whereas rather small translational energy release of CO in low rotational levels was matched by a large degree of vibrational excitation in the D(2) molecule. An analogous distribution of energy in two distinct channels has been recently observed under similar conditions in H(2)CO photolysis and attributed to two different dissociation pathways, namely, a pathway via the conventional transition state geometry and the previously unobserved pathway, deemed "roaming". Our experimental and theoretical data indicated that the same two dissociation pathways were responsible for the bimodal energy distribution into the molecular fragments resulting from the photolysis of D(2)CO. Energy partitioning into molecular products was compared between photolysis of H(2)CO and D(2)CO at energies slightly above the H/D atom abstraction threshold.

Phase space analysis of formaldehyde dissociation branching and comparison with quasiclassical trajectory calculations.

We investigate the dependence of the branching ratio of formaldehyde dissociation to molecular and radical products on the total energy and angular momentum and the HCO rotational state distributions by using a combination of transition state/Rice-Ramsperger-Kassel-Marcus theory and phase space theory. Comparisons are made with recent quasiclassical trajectory (QCT) calculations [Farnum, J. D.; Zhang, X.; Bowman, J. M. J. Chem. Phys. 2007, 126, 134305]. The combined phase-space analysis is in semiquantitative agreement with the QCT results for the rotational distributions of HCO but is only in qualitative agreement for the branching ratio. Nevertheless, that level of agreement serves to provide insight into the QCT results, which showed suppression of the radical channel with increasing total angular momentum for a fixed total energy.

Formaldehyde photodissociation: dependence on total angular momentum and rotational alignment of the CO product.

Quasiclassical trajectory calculations are reported to investigate the effects of rotational excitation of formaldehyde on the branching ratios of the fragmentation products, H2+CO and H+HCO. The results of tens of thousands of trajectories show that increased rotational excitation causes suppression of the radical channel and enhancement of the molecular channel. Decomposing the molecular channel into "direct" and "roaming" channels shows that increased rotation switches from suppressing to enhancing the roaming products across our chosen energy range. However, decomposition into these pathways is difficult because the difference between them does not appear to have a distinct boundary. A vector correlation investigation of the CO rotation shows different characteristics in the roaming versus direct channels and this difference is a potentially useful signature of the roaming mechanism, as first speculated by Kable and Houston in their experimental study of photodissociation of acetaldehyde [P. L. Houston and S. H. Kable, Proc. Nat. Acad. Sci. 103, 16079 (2006)].

The roaming atom pathway in formaldehyde decomposition.

We present a detailed experimental and theoretical investigation of formaldehyde photodissociation to H(2) and CO following excitation to the 2(1)4(1) and 2(1)4(3) transitions in S(1). The CO velocity distributions were obtained using dc slice imaging of single CO rotational states (v=0, j(CO)=5-45). These high-resolution measurements reveal the correlated internal state distribution in the H(2) cofragments. The results show that rotationally hot CO (j(CO) approximately 45) is produced in conjunction with vibrationally "cold" H(2) fragments (v=0-5): these products are formed through the well-known skewed transition state and described in detail in the accompanying paper. After excitation of formaldehyde above the threshold for the radical channel (H(2)CO-->H+HCO) we also find formation of rotationally cold CO (j(CO)=5-28) correlated to highly vibrationally excited H(2) (v=6-8). These products are formed through a novel mechanism that involves near dissociation followed by intramolecular H abstraction [D. Townsend et al., Science 306, 1158 (2004)], and that avoids the region of the transition state entirely. The dynamics of this "roaming" mechanism are the focus of this paper. The correlations between the vibrational states of H(2) and rotational states of CO formed following excitation on the 2(1)4(3) transition allow us to determine the relative contribution to molecular products from the roaming atom channel versus the conventional molecular channel.

Modeling the influence of a laser pulse on the potential energy surface in optimal molecular control theory.

Understanding and modeling the interaction between light and matter is essential to the theory of optical molecular control. While the effect of the electric field on a molecule's electronic structure is often not included in control theory, it can be modeled in an optimal control algorithm by a set or toolkit of potential energy surfaces indexed by discrete values of the electric field strength where the surfaces are generated by Born-Oppenheimer electronic structure calculations that directly include the electric field. Using a new optimal control algorithm with a trigonometric mapping to limit the maximum field strength explicitly, we apply the surface-toolkit method to control the hydrogen fluoride molecule. Potential energy surfaces in the presence and absence of the electric field are created with two-electron reduced-density-matrix techniques. The population dynamics show that adjusting for changes in the electronic structure of the molecule beyond the static dipole approximation can be significant for designing a field that drives a realistic quantum system to its target observable.

Spectral difference Lanczos method for efficient time propagation in quantum control theory.

Spectral difference methods represent the real-space Hamiltonian of a quantum system as a banded matrix which possesses the accuracy of the discrete variable representation (DVR) and the efficiency of finite differences. When applied to time-dependent quantum mechanics, spectral differences enhance the efficiency of propagation methods for evolving the Schrodinger equation. We develop a spectral difference Lanczos method which is computationally more economical than the sinc-DVR Lanczos method, the split-operator technique, and even the fast-Fourier-Transform Lanczos method. Application of fast propagation is made to quantum control theory where chirped laser pulses are designed to dissociate both diatomic and polyatomic molecules. The specificity of the chirped laser fields is also tested as a possible method for molecular identification and discrimination.