Monitoring the Activity of Single Translocons

Recent studies introduced a novel view that the SecYEG translocon functions as a monomer and interacts with the dimeric SecA ATPase, which fuels the preprotein translocation reaction. Here, we used nanodisc-reconstituted SecYEG to characterize the functional properties of single copies of the translocon. Using a method based on intermolecular Förster resonance energy transfer, we show for the first time that isolated nanodisc-reconstituted SecYEG monomers support preprotein translocation. When several copies of SecYEG were co-reconstituted within a nanodisc, no change in translocation kinetics was observed, suggesting that SecYEG oligomers do not facilitate enhanced translocation. In contrast, nanodisc-reconstituted monomers of the PrlA4 variant of SecYEG showed increased translocation rates. Experiments based on intramolecular Förster resonance energy transfer within the nanodisc-isolated monomeric SecYEG demonstrated a nucleotide-dependent opening of the channel upon interaction with SecA. In conclusion, the nanodisc-reconstituted SecYEG monomers are functional for preprotein translocation and provide a new prospect for single-molecule analysis of dynamic aspects of protein translocation.     

Evidence for Synchronous Activation of Neurons Located in Different Layers of Primary Somatosensory Cortex

Although many studies have examined the columnar organization of primary somatosensory (SI) cortex, the functional relationship among neurons in different layers remains unclear. To understand how activity is coordinated among different cortical layers, the present investigation tested the hypothesis that the initial part of a peripheral stimulus produces a serial pattern of laminar activation in SI cortex. Extracellular discharges of 334 histologically recovered neurons were recorded from the medial bank of the coronal sulcus in nine anesthetized cats during electrical or cutaneous stimulation of the distal forelimb. Mean responses during the initial 50-msec period following stimulus onset were largest in layers IIIb or IV for both types of stimulation, but laminar differences in the magnitude of onset responses were not statistically significant. Among 175 neurons with responses exceeding 0.5 spikes per stimulus, electrical Stimulation consistently produced shorter response latencies than mechanical indentation in the extragranular (II, IIIa, V, VI), but not in the middle (IIIb, IV), cortical layers. The average minimum latencies for different cortical layers ranged from 7.4 to 10.1 msec for responses to electrical stimulation and from 10.3 to 11.6 msec for responses to mechanical indentations, but these laminar differences were not statistically significant. In some experiments, neurons in different layers of a cortical column were recorded simultaneously with dual-electrode assemblies; among 37 neuron pairs in which both neurons responded with more than 0.5 spikes per stimulus, response latencies were similar, even though the neurons were separated by several hundred microns. Cross-correlation analysis of the onset responses for neurons recorded simultaneously from different layers also indicated that many cells throughout a cortical column were activated nearly simultaneously by the initial phase of a peripheral stimulus. Results from the present study are compared with previous reports examining laminar patterns of activation.     

Registration of pedobarographic image data in the frequency domain

Image registration has been used to support pixel-level data analysis on pedobarographic image data sets. Some registration methods have focused on robustness and sacrificed speed, but a recent approach based on external contours offered both high computational processing speed and high accuracy. However, since contours can be influenced by local perturbations, we sought more global methods. Thus, we propose two new registration methods based on the Fourier transform, cross-correlation and phase correlation which offer high computational speed. We found out that both proposed methods revealed high accuracy for the similarity measures considered, using control geometric transformations. Additionally, both methods revealed high computational processing speed which, combined with their accuracy and robustness, allows their implementation in near-real-time applications. Furthermore, we found that the current methods were robust to moderate levels of noise, and consequently, do not require noise removal procedure like the contours method does.     

Exploring a potential allosteric inhibition mechanism in the motor domain of human Eg-5

Kinesin-5 (Eg-5), microtubule motor protein, is one of the emerging drug targets in cancer research. Several inhibitors have been reported to bind the hEg-5 “motor domain” in two different locations that are potentially allosteric. Interestingly, the crystal structure of Eg-5 bound to benzimidazole unveils two chemically different allosteric pockets (PDB ID: 3ZCW). The allosteric modulators inhibit Eg-5 activity by causing conformational changes that affect nucleotide turnover rate. In the present work, three allosteric inhibitors were simulated along with the substrate nucleotides (ADP and ATP) to capture conformation changes induced by the allosteric inhibitors. To analyze the allosteric inhibition mechanism, we used dynamics cross-correlation, principal component analysis (PCA), and enthalpic calculations. The loop L5 interaction is determined by the type of substrate bind at the nucleotide binding site. The SW-II flexibility increased upon dual allosteric inhibition by SB-743921 and 6a. The ionic interaction between R221-E116 is observed only in the presence of two allosteric inhibitors. Also, we noticed that the α2/α3 helical orientation is responsible for the SW-1 loop position and substrate binding. Our simulation data suggest the critical chemical features required to block the motor domain by the allosteric inhibitors. The results summarized in this work will help the researchers to design better therapeutic agents targeting hEg-5.

Communicated by Ramaswamy H. Sarma     

High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus

The treatment of helical objects as a string of single particles has become an established technique to resolve their three-dimensional (3D) structure using electron cryo-microscopy. It can be applied to a wide range of helical particles such as viruses, microtubules and helical filaments. We have made improvements to this approach using Tobacco Mosaic Virus (TMV) as a test specimen and obtained a map from 210,000 asymmetric units at a resolution better than 5 A. This was made possible by performing a full correction of the contrast transfer function of the microscope. Alignment of helical segments was helped by constraints derived from the helical symmetry of the virus. Furthermore, symmetrization was implemented by multiple inclusions of symmetry-related views in the 3D reconstruction. We used the density map to build an atomic model of TMV. The model was refined using a real-space refinement strategy that accommodates multiple conformers. The atomic model shows significant deviations from the deposited model for the helical form of TMV at the lower-radius region (residues 88 to 109). This region appears more ordered with well-defined secondary structure, compared with the earlier helical structure. The RNA phosphate backbone is sandwiched between two arginine side-chains, stabilizing the interaction between RNA and coat protein. A cluster of two or three carboxylates is buried in a hydrophobic environment isolating it from neighboring subunits. These carboxylates may represent the so-called Caspar carboxylates that form a metastable switch for viral disassembly. Overall, the observed differences suggest that the new model represents a different, more stable state of the virus, compared with the earlier published model.     

用相关分析法研究家兔两类膈神经单位电活动差异的起源

家兔25只,乌拉坦静脉麻醉(1g/kg),三碘季铵酚制动,人工通气,切断双侧颈迷走神经干。分离双侧膈神经,右侧记录神经干放电;左侧分离细束,同时记录一对单位的放电。共记录到36对单位。神经电活动经放大后输入磁带记录仪,备作脱机处理;或将信号放大、限幅后输入计算机,作连机处理。单纤维根据其放电时程同神经干放电的关系分为时相性单位(PU)和紧张性单位(TU)。分别在TU同TU之间、PU同PU之间、PU同TU之间作相关分析。 在总共36对膈运动神经单位对中,有21对的互相关直方图上出现有显著意义的中心峰,表明它们之间存在着同步化活动,是接受共同的中枢传入所致。其中8对为2PU,,11对为2TU,2对为1PU和1TU。同步化活动的类型有短时程同步化、宽峰同步化和高频振荡同步化三种。在同类单位对(2PU或2TU)与不同类单位对(1PU和1TU)出现同步化的频数之间作x~2检验,结果表明同类单位对中出现同步化的比例显著高于不同类的单位对。 据此,我们认为膈运动神经元紧张性单位和时相性单位放电特性的不同可能是由于它们接受不同的中枢支配所致。     

Time lags for xylem and stem diameter variations in a Scots pine tree

Diameter variations in the xylem and whole stem (i.e. over bark) stem of a Scots pine (Pinus sylvestris L.) tree were measured at four heights over a 23 d period at 5 min intervals. Cross‐correlation analysis was used to calculate time lags between the measurements. Xylem diameter measurements at the different heights had time lags varying from 10 to 50 min, measurements at the lower heights lagging behind the most. This result was in good agreement with the cohesion theory of transpiration. For the whole stem diameter measurements, the treetop lagged behind all other heights and the shortest lags were midway along the stem. Changes in whole stem diameter always lagged behind those of xylem stem diameter (30–110 min), and at all heights. The considerable differences in the behaviour of xylem and whole stem diameter support the Münch hypothesis of phloem flow. Time lags calculated separately for the shrinkage (morning) and swelling (afternoon) periods indicated shorter time lags during the swelling periods. The non‐destructive methods used show promise in the simultaneous study of flow dynamics of xylem and phloem in trees.     

Cross-correlation between a carbonyl C' chemical shift anisotropy and a long-range dipolar C'HA coupling in proteins using symmetrical reconversion

A new sequence is described to measure the cross-correlation rates between the chemical shift anisotropy of the carbonyl carbon-13 nucleus and the dipole-dipole interaction between this carbonyl and the alpha-proton in proteins. The sequence is based on the symmetrical reconversion principle and is insensitive to experimental errors and to violations of the secular approximation. The cross-correlation rate depends on the backbone angle . The advantages and limitations of the sequence are discussed.     

Direct detection of caspase-3 activation in single live cells by cross-correlation analysis

Dual color fluorescence cross-correlation spectroscopy (FCCS) provides information about the coincidence of spectrally well-defined two fluorescent molecules in a small observation area at the single-molecule level. To evaluate the activity of caspase-3 in vivo directly, FCCS was applied to single live cells. We constructed chimeric proteins that consisted of tandemly fused enhanced green FP (EGFP) and monomeric red FP (mRFP). In control experiments, the protease reaction was monitored in solution, where a decrease in cross-correlation amplitude was observed due to specific cleavage of the amino acid sequence between EGFP and mRFP. Moreover, a decrease in cross-correlation amplitude could be detected in a live cell, where caspase-3 activation was induced by apoptosis. This is the first report of FP-based in vivo cross-correlation analysis. FP-based FCCS may become the most versatile method for analysis of protein-protein interactions in live cells.     

Measurement of 15N csa/dipolar cross-correlation rates by means of Spin State Selective experiments

We propose a method for the determination of (15)N csa/dipolar cross-correlation rates based on the measurement of the two apparent transverse (or longitudinal) relaxation rates associated with each component of the nitrogen doublet (N(alpha) and N(beta)). This is achieved by inserting a spin state selective scheme in conventional inverse Carr-Purcell-Meiboom-Gill (or inversion-recovery) pulse sequence which allows for the edition of a HSQC-type spectrum for each of the spin states. Transverse cross-correlation rates necessitate two independent sets of measurements (for N(alpha) and N(beta), respectively), whereas for longitudinal cross correlation rates, besides N(alpha) and N(beta) measurements, the method requires the knowledge of both the (15)N longitudinal auto-relaxation rate and the longitudinal two-spin order (2NzHz) auto-relaxation rate. These additional parameters are mandatory because of the non-exponential behavior of the N(alpha) and N(beta) longitudinal decays. Conversely, the present method does not require any complex manipulation of 2D spectra, the cross-correlation rates being obtained from the difference of the two (N(alpha) and N(beta)) apparent relaxation rates. This approach is applied to (15)N-labelled ubiquitin at two different magnetic fields (9.4 T and 14.1 T).