A novel computer simulation method for simulating the multiscale transduction dynamics of signal proteins

Signal proteins are able to adapt their response to a change in the environment, governing in this way a broad variety of important cellular processes in living systems. While conventional molecular-dynamics (MD) techniques can be used to explore the early signaling pathway of these protein systems at atomistic resolution, the high computational costs limit their usefulness for the elucidation of the multiscale transduction dynamics of most signaling processes, occurring on experimental timescales. To cope with the problem, we present in this paper a novel multiscale-modeling method, based on a combination of the kinetic Monte-Carlo- and MD-technique, and demonstrate its suitability for investigating the signaling behavior of the photoswitch light-oxygen-voltage-2-Jα domain from Avena Sativa (AsLOV2-Jα) and an AsLOV2-Jα-regulated photoactivable Rac1-GTPase (PA-Rac1), recently employed to control the motility of cancer cells through light stimulus. More specifically, we show that their signaling pathways begin with a residual re-arrangement and subsequent H-bond formation of amino acids near to the flavin-mononucleotide chromophore, causing a coupling between β-strands and subsequent detachment of a peripheral α-helix from the AsLOV2-domain. In the case of the PA-Rac1 system we find that this latter process induces the release of the AsLOV2-inhibitor from the switchII-activation site of the GTPase, enabling signal activation through effector-protein binding. These applications demonstrate that our approach reliably reproduces the signaling pathways of complex signal proteins, ranging from nanoseconds up to seconds at affordable computational costs.     

Resonances in rotationally inelastic scattering of OH(X2Π) with helium and neon

We present detailed calculations on resonances in rotationally and spin-orbit inelastic scattering of OH (X(2)Π, j = 3/2, F(1), f) radicals with He and Ne atoms. We calculate new ab initio potential energy surfaces for OH-He, and the cross sections derived from these surfaces compare well with the recent crossed beam scattering experiment of Kirste et al. [Phys. Rev. A 82, 042717 (2010)]. We identify both shape and Feshbach resonances in the integral and differential state-to-state scattering cross sections, and we discuss the prospects for experimentally observing scattering resonances using Stark decelerated beams of OH radicals.     

Mechanism-inspired engineering of phenylalanine aminomutase for enhanced β-regioselective asymmetric amination of cinnamates

Turn to switch: A mutant of phenylalanine aminomutase was engineered that can catalyze the regioselective amination of cinnamate derivatives (see scheme, red) to, for example, β-amino acids. This regioselectivity, along with the X-ray crystal structures, suggests two distinct carboxylate binding modes differentiated by C(β)-C(ipso) bond rotation, which determines if β- (see scheme) or α-addition takes place.     

Convenient method for the functionalization of the 4- and 6-positions of the androgen skeleton

The preparation and reactivity of steroidal vinyldiazo compounds is reported, providing a convenient, substituent tolerant, chemo- and stereoselective entry into 4- and 6-substituted androgen analogues from a common precursor. Under dirhodium catalysis, O-H insertion occurs at the carbenoid site, leading to 4-substituted steroids, but under silver catalysis, O-H insertion occurs at the vinylogous position, leading to 6-substituted steroids.     

Expanding and testing a computational method for predicting the ground state reduction potentials of organic molecules on the basis of empirical correlation to experiment

A method for predicting the ground state reduction potentials of organic molecules on the basis of the correlation of computed energy differences between the starting S(0) and one-electron-reduced D(0) species with experimental reduction potentials in acetonitrile has been expanded to cover 3.5 V of potential range and 74 compounds across 6 broad families of molecules. Utilizing the conductor-like polarizable continuum model of implicit solvent allows a global correlation that is computationally efficient and has improved accuracy, with r(2) > 0.98 in all cases and root mean square deviation errors of <90 mV (mean absolute deviations <70 mV) for either B3LYP/6-311+G(d,p) or B3LYP//6-31G(d) with an appropriate choice of radii (UAKS or UA0). The correlations are proven to be robust across a wide range of structures and potentials, including four larger (27-28 heavy atoms) and more conformationally flexible photochromic molecules not used in calibrating the correlation. The method is also proven to be robust to a number of minor student "mistakes" or methodological inconsistencies.     

Exponential distance dependence of photoinitiated stepwise electron transfer in donor-bridge-acceptor molecules: implications for wirelike behavior

Donor-bridge-acceptor (D-B-A) systems in which a 3,5-dimethyl-4-(9-anthracenyl)julolidine (DMJ-An) chromophore and a naphthalene-1,8:4,5-bis(dicarboximide) (NI) acceptor are linked by oligomeric 2,7-fluorenone (FN(n)) bridges (n = 1-3) have been synthesized. Selective photoexcitation of DMJ-An quantitatively produces DMJ(+?)-An(-?), and An(-?) acts as a high-potential electron donor. Femtosecond transient absorption spectroscopy in the visible and mid-IR regions showed that electron transfer occurs quantitatively in the sequence: DMJ(+?)-An(-?)-FN(n)-NI → DMJ(+?)-An-FN(n)(-?)-NI → DMJ(+?)-An-FN(n)-NI(-?). The charge-shift reaction from An(-?) to NI(-?) exhibits an exponential distance dependence in the nonpolar solvent toluene with an attenuation factor (β) of 0.34 ?(-1), which would normally be attributed to electron tunneling by the superexchange mechanism. However, the FN(n)(-?) radical anion was directly observed spectroscopically as an intermediate in the charge-separation mechanism, thereby demonstrating conclusively that the overall charge separation involves the incoherent hopping (stepwise) mechanism. Kinetic modeling of the data showed that the observed exponential distance dependence is largely due to electron injection onto the first FN unit followed by charge hopping between the FN units of the bridge biased by the distance-dependent electrostatic attraction of the two charges in D(+?)-B(-?)-A. This work shows that wirelike behavior does not necessarily result from building a stepwise, energetically downhill redox gradient into a D-B-A molecule.     

Application of transmission electron microscopy to the clinical study of viral and bacterial infections: present and future

Transmission electron microscopy has had a profound impact on our knowledge and understanding of viruses and bacteria. The 1000-fold improvement in resolution provided by electron microscopy (EM) has allowed visualization of viruses, the existence of which had previously only been suspected as the causative agents of transmissible infectious disease. Viruses are grouped into families based on their morphology. Viruses from different families look different and these morphological variances are the basis for identification of viruses by EM. Electron microscopy initially came to prominence in diagnostic microbiology in the late 1960s when it was used in the rapid diagnosis of smallpox, by differentiating, on a morphological basis, poxviruses from the less problematic herpesviruses in skin lesions. Subsequently, the technique was employed in the diagnosis of other viral infections, such as hepatitis B and parvovirus B19. Electron microscopy has led to the discovery of many new viruses, most notably the various viruses associated with gastroenteritis, for which it remained the principal diagnostic method until fairly recent times. Development of molecular techniques, which offer greater sensitivity and often the capacity to easily process large numbers of samples, has replaced EM in many areas of diagnostic virology. Hence the role of EM in clinical virology is evolving with less emphasis on diagnosis and more on research, although this is likely only to be undertaken in specialist centres. However, EM still offers tremendous advantages to the microbiologist, both in the speed of diagnosis and the potential for detecting, by a single test, any viral pathogen or even multiple pathogens present within a sample. There is continuing use of EM for the investigation of new and emerging agents, such as SARS and human monkeypox virus. Furthermore, EM forms a vital part of the national emergency response programme of many countries and will provide a frontline diagnostic service in the event of a bioterrorism incident, particularly in the scenario of a deliberate release of smallpox virus. In the field of bacteriology, EM is of little use diagnostically, although some bacterial pathogens can be identified in biopsy material processed for EM examination. Electron microscopy has been used, however, to elucidate the structure and function of many bacterial features, such as flagellae, fimbriae and spores and in the study of bacteriophages. The combined use of EM and gold-labelled antibodies provides a powerful tool for the ultrastructural localisation of bacterial and viral antigens.     

A comment on "Prediction of protein structural classes by a new measure of information discrepancy"

Protein structural class describes the overall folding type of a protein or its domain. A number of methods were developed to predict protein structural class based on its primary sequence. The homology of the predicted sequences with respect to the training sequences is a key attribute for the prediction performance. In this article we investigated the FDOD method developed by Jin et al. [Jin, L., Fang, W., Tang, H., 2003. Prediction of protein structural classes by a new measure of information discrepancy. Comput. Biol. Chem. 27, 373-380], which gave high prediction accuracy on a low homology dataset, and we empirically confirmed that the reported results were an artifact of improper implementation.     

A continuous-flow crushing device for on-line delta2H analysis of fluid inclusion water in speleothems

A method for the isotope analysis of fluid inclusion water in speleothem calcite is presented. The technique is based on a commercially available continuous-flow pyrolysis furnace (ThermoFinnigan TC-EA). The main adaptation made to the standard TC-EA configuration is the addition of a crusher and cold trap unit, which is connected to the carrier gas inlet at the top of the TC-EA reactor tube. A series of tests conducted with this device shows that: (1) standard waters, injected in the crusher, and passed through a cryogenic trapping routine, yield accurate delta(2)H values; (2) crushed cubes of speleothem calcite from two Peruvian caves with rather dissimilar seepage water delta(2)H values yield fluid inclusion delta(2)H values in good accordance with these drip waters. The clear advantage of this continuous-flow technique for fluid inclusion isotope analysis is that it is relatively quick compared with other techniques. Since the conditions of water sample introduction into the TC-EA are identical for delta(2)H and delta(18)O analysis, we expect that only limited adaptations to the extraction procedure are required to provide delta(18)O analysis of fluid inclusion samples with the same device.     

QMC Rules of Arbitrary High Order: Reproducing Kernel Hilbert Space Approach

In this paper we consider numerical integration of smooth functions lying in a particular reproducing kernel Hilbert space. We show that the worst-case error of numerical integration in this space converges at the optimal rate, up to some power of a log?N factor. A similar result is shown for the mean square worst-case error, where the bound for the latter is always better than the bound for the square worst-case error. Finally, bounds for integration errors of functions lying in the reproducing kernel Hilbert space are given. The paper concludes by illustrating the theory with numerical results.