900 research outputs found
Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast
A combined multidimensional chromatography-mass spectrometry approach known as "MudPIT" enables rapid identification of proteins that interact with a tagged bait while bypassing some of the problems associated with analysis of polypeptides excised from SDS-polyacrylamide gels. However, the reproducibility, success rate, and applicability of MudPIT to the rapid characterization of dozens of proteins have not been reported. We show here that MudPIT reproducibly identified bona fide partners for budding yeast Gcn5p. Additionally, we successfully applied MudPIT to rapidly screen through a collection of tagged polypeptides to identify new protein interactions. Twenty-five proteins involved in transcription and progression through mitosis were modified with a new tandem affinity purification (TAP) tag. TAP-MudPIT analysis of 22 yeast strains that expressed these tagged proteins uncovered known or likely interacting partners for 21 of the baits, a figure that compares favorably with traditional approaches. The proteins identified here comprised 102 previously known and 279 potential physical interactions. Even for the intensively studied Swi2p/Snf2p, the catalytic subunit of the Swi/Snf chromatin remodeling complex, our analysis uncovered a new interacting protein, Rtt102p. Reciprocal tagging and TAP-MudPIT analysis of Rtt102p revealed subunits of both the Swi/Snf and RSC complexes, identifying Rtt102p as a common interactor with, and possible integral component of, these chromatin remodeling machines. Our experience indicates it is feasible for an investigator working with a single ion trap instrument in a conventional molecular/cellular biology laboratory to carry out proteomic characterization of a pathway, organelle, or process (i.e. "pathway proteomics") by systematic application of TAP-MudPIT
Charting the protein complexome in yeast by mass spectrometry
It has become evident over the past few years that many complex cellular processes, including control of the cell cycle and ubiquitin-dependent proteolysis, are carried out by sophisticated multisubunit protein machines that are dynamic in abundance, post-translational modification state, and composition. To understand better the nature of the macromolecular assemblages that carry out the cell cycle and ubiquitin-dependent proteolysis, we have used mass spectrometry extensively over the past few years to characterize both the composition of various protein complexes and the modification states of their subunits. In this article we review some of our recent efforts, and describe a promising new approach for using mass spectrometry to dissect protein interaction networks
Measuring Temperature Gradients over Nanometer Length Scales
When a quantum dot is subjected to a thermal gradient, the temperature of
electrons entering the dot can be determined from the dot's thermocurrent if
the conductance spectrum and background temperature are known. We demonstrate
this technique by measuring the temperature difference across a 15 nm quantum
dot embedded in a nanowire. This technique can be used when the dot's energy
states are separated by many kT and will enable future quantitative
investigations of electron-phonon interaction, nonlinear thermoelectric
effects, and the effciency of thermoelectric energy conversion in quantum dots.Comment: 6 pages, 5 figure
Corepressors: custom tailoring and alterations while you wait
A diverse cadre of metazoan transcription factors mediate repression by recruiting protein complexes containing the SMRT (silencing mediator of retinoid and thyroid hormone receptor) or N-CoR (nuclear receptor corepressor) corepressors. SMRT and N-CoR nucleate the assembly of still larger corepressor complexes that perform the specific molecular incantations necessary to confer transcriptional repression. Although SMRT and N-CoR are paralogs and possess similar molecular architectures and mechanistic strategies, they nonetheless exhibit distinct molecular and biological properties. It is now clear that the functions of both SMRT and N-CoR are further diversified through alternative mRNA splicing, yielding a series of corepressor protein variants that participate in distinctive transcription factor partnerships and display distinguishable repression properties. This review will discuss what is known about the structure and actions of SMRT, N-CoR, and their splicing variants, and how alternative splicing may allow the functions of these corepressors to be adapted and tailored to different cells and to different developmental stages
Theory of biopolymer stretching at high forces
We provide a unified theory for the high force elasticity of biopolymers
solely in terms of the persistence length, , and the monomer spacing,
. When the force f>\fh \sim k_BT\xi_p/a^2 the biopolymers behave as Freely
Jointed Chains (FJCs) while in the range \fl \sim k_BT/\xi_p < f < \fh the
Worm-like Chain (WLC) is a better model. We show that can be estimated
from the force extension curve (FEC) at the extension
(normalized by the contour length of the biopolymer). After validating the
theory using simulations, we provide a quantitative analysis of the FECs for a
diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and
unstructured PEVK domain of titin) for . The success of a specific
polymer model (FJC or WLC) to describe the FEC of a given biopolymer is
naturally explained by the theory. Only by probing the response of biopolymers
over a wide range of forces can the -dependent elasticity be fully
described.Comment: 20 pages, 4 figure
Negative Thermal Expansion Coefficient of Graphene Measured by Raman Spectroscopy
The thermal expansion coefficient (TEC) of single-layer graphene is estimated
with temperature-dependent Raman spectroscopy in the temperature range between
200 and 400 K. It is found to be strongly dependent on temperature but remains
negative in the whole temperature range, with a room temperature value of
-8.0x10^{-6} K^{-1}. The strain caused by the TEC mismatch between graphene and
the substrate plays a crucial role in determining the physical properties of
graphene, and hence its effect must be accounted for in the interpretation of
experimental data taken at cryogenic or elevated temperatures.Comment: 17 pagese, 3 figures, and supporting information (4 pages, 3
figures); Nano Letters, 201
New insights into electron spin dynamics in the presence of correlated noise
The changes of the spin depolarization length in zinc-blende semiconductors
when an external component of correlated noise is added to a static driving
electric field are analyzed for different values of field strength, noise
amplitude and correlation time. Electron dynamics is simulated by a Monte Carlo
procedure which keeps into account all the possible scattering phenomena of the
hot electrons in the medium and includes the evolution of spin polarization.
Spin depolarization is studied by examinating the decay of the initial spin
polarization of the conduction electrons through the D'yakonov-Perel process,
the only relevant relaxation mechanism in III-V crystals. Our results show
that, for electric field amplitude lower than the Gunn field, the dephasing
length shortens with the increasing of the noise intensity. Moreover, a
nonmonotonic behavior of spin depolarization length with the noise correlation
time is found, characterized by a maximum variation for values of noise
correlation time comparable with the dephasing time. Instead, in high field
conditions, we find that, critically depending on the noise correlation time,
external fluctuations can positively affect the relaxation length. The
influence of the inclusion of the electron-electron scattering mechanism is
also shown and discussed.Comment: Published on "Journal of Physics: Condensed Matter" as "Fast Track
Communications", 11 pages, 9 figure
Deciphering the nuclear bile acid receptor FXR paradigm
Originally called retinoid X receptor interacting protein 14 (RIP14), the farnesoid X receptor (FXR) was renamed after the ability of its rat form to bind supra-physiological concentrations of farnesol. In 1999 FXR was de-orphanized since primary bile acids were identified as natural ligands. Strongly expressed in the liver and intestine, FXR has been shown to be the master transcriptional regulator of several entero-hepatic metabolic pathways with relevance to the pathophysiology of conditions such as cholestasis, fatty liver disease, cholesterol gallstone disease, intestinal inflammation and tumors. Furthermore, given the importance of FXR in the gut-liver axis feedbacks regulating lipid and glucose homeostasis, FXR modulation appears to have great input in diseases such as metabolic syndrome and diabetes. Exciting results from several cellular and animal models have provided the impetus to develop synthetic FXR ligands as novel pharmacological agents. Fourteen years from its discovery, FXR has gone from bench to bedside; a novel nuclear receptor ligand is going into clinical use
Screening of suitable cationic dopants for solar absorber material CZTS/Se: A first principles study
The earth abundant and non-toxic solar absorber material kesterite Cu2ZnSn(S/Se)(4) has been studied to achieve high power conversion efficiency beyond various limitations, such as secondary phases, antisite defects, band gap adjustment and microstructure. To alleviate these hurdles, we employed screening based approach to find suitable cationic dopant that can promote the current density and the theoretical maximum upper limit of the energy conversion efficiency (P(%)) of CZTS/Se solar devices. For this task, the hybrid functional (Heyd, Scuseria and Ernzerhof, HSE06) were used to study the electronic and optical properties of cation (Al, Sb, Ga, Ba) doped CZTS/Se. Our in-depth investigation reveals that the Sb atom is suitable dopant of CZTS/CZTSe and also it has comparable bulk modulus as of pure material. The optical absorption coefficient of Sb doped CZTS/Se is considerably larger than the pure materials because of easy formation of visible range exciton due to the presence of defect state below the Fermi level, which leads to an increase in the current density and P(%). Our results demonstrate that the lower formation energy, preferable energy gap and excellent optical absorption of the Sb doped CZTS/Se make it potential component for relatively high efficient solar cells
Study of Thermal Properties of Graphene-Based Structures Using the Force Constant Method
The thermal properties of graphene-based materials are theoretically
investigated. The fourth-nearest neighbor force constant method for phonon
properties is used in conjunction with both the Landauer ballistic and the
non-equilibrium Green's function techniques for transport. Ballistic phonon
transport is investigated for different structures including graphene, graphene
antidot lattices, and graphene nanoribbons. We demonstrate that this particular
methodology is suitable for robust and efficient investigation of phonon
transport in graphene-based devices. This methodology is especially useful for
investigations of thermoelectric and heat transport applications.Comment: 23 pages, 9 figures, 1 tabl
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