62 research outputs found
Shear-Wave Velocity Characterization of the USGS Hawaiian Strong-Motion Network on the Island of Hawaii and Development of an NEHRP Site-Class Map
No full textTo assess the level and nature of ground shaking in Hawaii for the purposes of earthquake hazard mitigation and seismic design, empirical ground-motion prediction models are desired. To develop such empirical relationships, knowledge of the subsurface site conditions beneath strong-motion stations is critical. Thus, as a first step to develop ground-motion prediction models for Hawaii, wspectral-analysis-of-surface-waves (SASW) profiling was performed at the 22 free-field U.S. Geological Survey (USGS) strong-motion sites on the Big Island to obtain shear-wave velocity (V(S)) data. Nineteen of these stations recorded the 2006 Kiholo Bay moment magnitude (M) 6.7 earthquake, and 17 stations recorded the triggered M 6.0 Mahukona earthquake. V(S) profiling was performed to reach depths of more than 100 ft. Most of the USGS stations are situated on sites underlain by basalt, based on surficial geologic maps. However, the sites have varying degrees of weathering and soil development. The remaining strong-motion stations are located on alluvium or volcanic ash. V(S30) (average V(S) in the top 30 m) values for the stations on basalt ranged from 906 to 1908 ft/s [National Earthquake Hazards Reduction Program (NEHRP) site classes C and D], because most sites were covered with soil of variable thickness. Based on these data, an NEHRP site-class map was developed for the Big Island. These new V(S) data will be a significant input into an update of the USGS statewide hazard maps and to the operation of ShakeMap on the island of Hawaii.George E. Brown, Jr. Network for Earthquake Engineering Simulation (NEES) under NSF CMS-0086605FEMA HSFEHQ-06-D-0162, HSFEHQ-04-D-0733U.S. Geological Survey, Department of the Interior 08HQGR0036Geotechnical Engineering Cente
MOLECULAR-CELL-D-20-00889
No full textRaw images of yeast spotting, western blots, and C. elegans experiments fromTuning Hsp104 specificity to selectively detoxify α-synucleinKorrie L. Mack, Hanna Kim, Edward M. Barbieri, JiaBei Lin, Sylvanne Braganza, Meredith E. Jackrel, Jamie E. DeNizio, Xiaohui Yan, Edward Chuang, Amber Tariq, Ryan R. Cupo, Laura M. Castellano, Kim A. Caldwell, Guy A. Caldwell, and James Shorter.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV
Examination Of The Dynamic Assembly Equilibrium For E. Coli Clpb
No full textAs a member of the Clp/Hsp 100 chaperone family, Escherichia coli ClpB is able to disaggregate denatured proteins with assistance of DnaKJE co-chaperones to help cell survive under stress. However, the working mechanism of ClpB disaggregation activity remains unclear. The active structure of ClpB is shown to be a hexameric ring and ATP binding and hydrolysis are required for ClpB to perform its chaperone activity. Thus, studying the energetics and kinetics of the ATP linked ClpB assembly equilibrium is essential for the quantitative examination of ClpB - protein substrate interaction to fully reveal its disaggregation mechanism. ATPgS (a slowly hydrolysable ATP analog) is used as a model for ATP in this study. In order to examine the ligand - linked ClpB assembly, ClpB self-assembly in the absence of nucleotide needs to be determined. In the first part of this study, we introduce to you the methods that were applied to perform this study using analytical ultracentrifugation. By performing NLLS analysis of the simulated sedimentation velocity data, we presented that both thermodynamic and kinetic parameters of a complex assembly system can be determined accurately with certain limitations. Further, the linkage of ligand binding can be determined by analyzing the assembly equilibrium constants as a function of [ligand]. In the second part, we applied the methods discussed in the first section into the determination of the assembly energetics and kinetics for ClpB in the absence of nucleotide. Here, we show that ClpB can form hexamers in the absence of nucleotide through two intermediates, dimers and tetramers. The assembly equilibrium constants and dissociation rate constants were determined for each oligomer in the absence of nucleotide. With the result of that, we examined the linkage of [ATPgS] binding to ClpB assembly. Not like assumed in many studies that ClpB forms hexamer only in the presence of ATP/ATPgS, here we show that ClpB exhibits a dynamic equilibrium in the presence of both limiting and excess ATPgS. ClpB monomer, dimer, tetramer, and hexamer were observed and their assembly equilibrium constants were determined. These interaction constants make it possible to predict the concentration of hexamers present and able to bind to co-chaperones and polypeptide substrates. Such information is essential for the interpretation of many in vitro studies. Moreover, the ATPgS bind equilibrium constant and stoichiometry for each oligomer were determined for the first time. All twelve NBDs of the hexameric ring are saturated with ATPgS binding, however, the binding stoichiometry of dimers and tetramers is one fewer than the maximum number of the NBDs, which suggests an open conformation. Our results are constant with the previously published structure studies. Finally, the strategies presented here are broadly applicable to a large number of AAA+ molecular motors that assemble upon nucleotide binding
Examination of ClpB Quaternary Structure and Linkage to Nucleotide Binding
No full textEscherichia coli caseinolytic peptidase B (ClpB)
is a molecular chaperone with the unique ability to catalyze protein
disaggregation in collaboration with the KJE system of chaperones.
Like many AAA+ molecular motors, ClpB assembles into hexameric rings,
and this reaction is thermodynamically linked to nucleotide binding.
Here we show that ClpB exists in a dynamic equilibrium of monomers,
dimers, tetramers, and hexamers in the presence of both limiting and
excess ATPγS. We find that ClpB monomer is only able to bind
one nucleotide, whereas all 12 sites in the hexameric ring are bound
by nucleotide at saturating concentrations. Interestingly, dimers
and tetramers exhibit stoichiometries of ∼3 and 7, respectively,
which is one fewer than the maximum number of binding sites in the
formed oligomer. This observation suggests an open conformation for
the intermediates based on the need for an adjacent monomer to fully
form the binding pocket. We also report the protein–protein
interaction constants for dimers, tetramers, and hexamers and their
dependencies on nucleotide. These interaction constants make it possible
to predict the concentration of hexamers present and able to bind
to cochaperones and polypeptide substrates. Such information is essential
for the interpretation of many in vitro studies. Finally, the strategies
presented here are broadly applicable to a large number of AAA+ molecular
motors that assemble upon nucleotide binding and interact with partner
proteins
Ligand-free Cu-catalyzed O-arylation of aliphatic diols
No full textCoupling reaction between aryl iodides and aliphatic diols was realized with a ligand-free copper catalyst under mild conditions. This method was successfully applied in the process of scale-up synthesis of medicinal candidate product EMB-3.Ministry of Science and Technology of China [2012ZX09103101-042]SCI(E)[email protected]
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