Iterative cluster-NMA: A tool for generating conformational transitions in proteins

Computational models provide insight into the structure–function relationship in proteins. These approaches, especially those based on normal mode analysis, can identify the accessible motion space around a given equilibrium structure. The large magnitude, collective motions identified by these methods are often well aligned with the general direction of the expected conformational transitions. However, these motions cannot realistically be extrapolated beyond the local neighborhood of the starting conformation. In this article, the iterative cluster-NMA (icNMA) method is presented for traversing the energy landscape from a starting conformation to a desired goal conformation. This is accomplished by allowing the evolving geometry of the intermediate structures to define the local accessible motion space, and thus produce an appropriate displacement. Following the derivation of the icNMA method, a set of sample simulations are performed to probe the robustness of the model. A detailed analysis of Β1,4-galactosyltransferase-T1 is also given, to highlight many of the capabilities of icNMA. Remarkably, during the transition, a helix is seen to be extended by an additional turn, emphasizing a new unknown role for secondary structures to absorb slack during transitions. The transition pathway for adenylate kinase, which has been frequently studied in the literature, is also discussed. Proteins 2009. © 2008 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/61529/1/22200_ftp.pd

Monophoton decay time fluorometry : theory, design, and application to biochemical systems

In the determination of binding heterogeneity and rotational diffusion relaxation times, fluorescence decay curves often take the form of sums of exponential decay times. An instrument is described which includes features permitting the collection of high precision time decay data, which may successfully be resolved into component decays. The instrument incorporates several novel features that significantly improve the monophoton technique. A decay curve is built up by successively adding to the memory.of a pulse height analyzer events, which represent the time between a brief excitation pulse and the detection of a single emitted photon from the sample. This decay curve represents the true probability of emission as a function of time only if the events measured are single photon events. By measuring the pulse height of the detected signals and rejecting all events not characteristic of single photons, we are able to collect single photon data at a rate significantly higher than that required for avoiding multi-photon events by using signal attenuation. The performance of the instrument is demonstrated by a number of tests. In all cases the experimental data are analyzed by a method of moments. We have successfully measured the decay time of NADH in water and obtained a value, 0.48 ± .05 nanoseconds, which is much shorter than the three nanosecond half width of our excitation pulse. Subnanosecond discrimination is demonstrated by the difference in the reproducible decay times of air equilibrated and deoxygenated solutions of anthracene in benzene, 3.65 and 4.00 nanoseconds respectively. We rigorously demonstrate the ability to resolve a double exponential decay curve by successively adding to the memory of the pulse height analyzer data from a solution of quinine and a solution of anthranilic acid. The data from each are analyzed and the results compared with a double exponential analysis of the summed decay curve. Finally we give the first example of the analysis of a single polarized component of emission yielding the zero point anisotropy, the excited state lifetime, and the rotational relaxation time of a dye protein complex. These values for an ANS-apomyoglobin complex are 0.33, 16.5 nanoseconds, and 28.4 nanoseconds respectively

Hubble Space Telescope WFPC2 Imaging of SN 1979C and Its Environment

The locations of supernovae in the local stellar and gaseous environment in galaxies contain important clues to their progenitor stars. As part of a program to study the environments of supernovae using Hubble Space Telescope (HST) imaging data, we have examined the environment of the Type II-L SN 1979C in NGC 4321 (M100). We place more rigorous constraints on the mass of the SN progenitor, which may have had a mass M \approx 17--18 M_sun. Moreover, we have recovered and measured the brightness of SN 1979C, m=23.37 in F439W (~B; m_B(max) = 11.6), 17 years after explosion. .Comment: 18 pages, 8 figures, submitted to PAS

52 Issues in Information Systems

ABSTRACT At IACIS 2007 we presented a pilot research project INTRODUCTION This paper describes the research and results of investigating Problem Formulation Ability (denoted PFA) and using it to predict the performance of first time students (those with no previous programming experience). A second factor, labeled Learning Technique (LT

The Formation of Kiloparsec-scale HI Holes in Dwarf Galaxies

The origin of kpc-scale holes in the atomic hydrogen (H i) distributions of some nearby dwarf irregular galaxies presents an intriguing problem. Star formation histories (SFHs) derived from resolved stars give us the unique opportunity to study past star-forming events that may have helped shape the currently visible Hi distribution. Our sample of five nearby dwarf irregular galaxies spans over an order of magnitude in both total Hi mass and absolute B-band magnitude and is at the low-mass end of previously studied systems. We use Very Large Array Hi line data to estimate the energy required to create the centrally dominant hole in each galaxy. We compare this energy estimate to the past energy released by the underlying stellar populations computed from SFHs derived from data taken with the Hubble Space Telescope. The inferred integrated stellar energy released within the characteristic ages exceeds our energy estimates for creating the holes in all cases, assuming expected efficiencies. Therefore, it appears that stellar feedback provides sufficient energy to produce the observed holes. However, we find no obvious signature of single star-forming events responsible for the observed structures when comparing the global SFHs of each galaxy in our sample to each other or to those of dwarf irregular galaxies reported in the literature. We also fail to find evidence of a central star cluster in FUV or Hα imaging. We conclude that large Hi holes are likely formed from multiple generations of star formation and only under suitable interstellar medium conditions

Japanese encephalitis virus co-opts the ER-stress response protein GRP78 for viral infectivity

The serum-free medium from Japanese encephalitis virus (JEV) infected Baby Hamster Kidney-21 (BHK-21) cell cultures was analyzed by liquid chromatography tandem mass spectrometry (LC-MS) to identify host proteins that were secreted upon viral infection. Five proteins were identified, including the molecular chaperones Hsp90, GRP78, and Hsp70. The functional role of GRP78 in the JEV life cycle was then investigated. Co-migration of GRP78 with JEV particles in sucrose density gradients was observed and co-localization of viral E protein with GRP78 was detected by immunofluorescence analysis in vivo. Knockdown of GRP78 expression by siRNA did not effect viral RNA replication, but did impair mature viral production. Mature viruses that do not co-fractionate with GPR78 displayed a significant decrease in viral infectivity. Our results support the hypothesis that JEV co-opts host cell GPR78 for use in viral maturation and in subsequent cellular infections

Disappearance of the Progenitor of Supernova iPTF13bvn

Supernova (SN) iPTF13bvn in NGC 5806 was the first Type Ib SN to have been tentatively associated with a progenitor candidate in pre-explosion images. We performed deep ultraviolet (UV) and optical Hubble Space Telescope (HST) observations of the SN site 740 days after explosion. We detect an object in the optical bands that is fainter than the pre-explosion object. This dimming is likely not produced by dust absorption in the ejecta; thus, our finding confirms the connection of the progenitor candidate with the SN. The object in our data is likely dominated by the fading SN, which implies that the pre-SN flux is mostly due to the progenitor. We compare our revised pre-SN photometry with previously proposed progenitor models. Although binary progenitors are favored, models need to be refined. In particular, to comply with our deep UV detection limit, any companion star must be less luminous than a late-O star or substantially obscured by newly formed dust. A definitive progenitor characterization will require further observations to disentangle the contribution of a much fainter SN and its environment.Comment: 8 pages, 3 tables, 3 figures. Accepted for publication in ApJ

SPIRITS 16tn in NGC 3556: A heavily obscured and low-luminosity supernova at 8.8 Mpc

We present the discovery by the SPitzer InfraRed Intensive Transients Survey (SPIRITS) of a likely supernova (SN) in NGC 3556 at only 8.8 Mpc, which, despite its proximity, was not detected by optical searches. A luminous infrared (IR) transient at $M_{[4.5]} = -16.7$ mag (Vega), SPIRITS 16tn is coincident with a dust lane in the inclined, star-forming disk of the host. Using IR, optical, and radio observations, we attempt to determine the nature of this event. We estimate $A_V \approx$ 8 - 9 mag of extinction, placing it among the three most highly obscured IR-discovered SNe to date. The [4.5] light curve declined at a rate of 0.013 mag day$^{-1}$, and the $[3.6] - [4.5]$ color grew redder from 0.7 to $\gtrsim$ 1.0 mag by 184.7 days post discovery. Optical/IR spectroscopy shows a red continuum, but no clearly discernible features, preventing a definitive spectroscopic classification. Deep radio observations constrain the radio luminosity of SPIRITS 16tn to $L_{\nu} \lesssim 10^{24}$ erg s$^{-1}$ Hz$^{-1}$ between 3 - 15 GHz, excluding many varieties of radio core-collapse SNe. A type Ia SN is ruled out by the observed red IR color, and lack of features normally attributed to Fe-peak elements in the optical and IR spectra. SPIRITS 16tn was fainter at [4.5] than typical stripped-envelope SNe by $\approx$ 1 mag. Comparison of the spectral energy distribution to SNe II suggests SPIRITS 16tn was both highly obscured, and intrinsically dim, possibly akin to the low-luminosity SN 2005cs. We infer the presence of an IR dust echo powered by a peak luminosity of the transient of $5 \times 10^{40}$ erg s$^{-1} < L_{\mathrm{peak}} < 4\times10^{43}$ erg s$^{-1}$, consistent with the observed range for SNe II. This discovery illustrates the power of IR surveys to overcome the compounding effects of visible extinction and optically sub-luminous events in completing the inventory of nearby SNe.Comment: 25 pages, 10 figures, submitted to Ap

Spitzer measurements of atomic and molecular abundances in the Type IIP SN 2005af

We present results based on Spitzer Space Telescope mid-infrared (3.6-30 micron) observations of the nearby IIP supernova 2005af. We report the first ever detection of the SiO molecule in a Type IIP supernova. Together with the detection of the CO fundamental, this is an exciting finding as it may signal the onset of dust condensation in the ejecta. From a wealth of fine-structure lines we provide abundance estimates for stable Ni, Ar, and Ne which, via spectral synthesis, may be used to constrain nucleosynthesis models.Comment: ApJ Letters (accepted