2,719 research outputs found
Deciphering the folding kinetics of transmembrane helical proteins
Nearly a quarter of genomic sequences and almost half of all receptors that
are likely to be targets for drug design are integral membrane proteins.
Understanding the detailed mechanisms of the folding of membrane proteins is a
largely unsolved, key problem in structural biology. Here, we introduce a
general model and use computer simulations to study the equilibrium properties
and the folding kinetics of a -based two helix bundle fragment
(comprised of 66 amino-acids) of Bacteriorhodopsin. Various intermediates are
identified and their free energy are calculated toghether with the free energy
barrier between them. In 40% of folding trajectories, the folding rate is
considerably increased by the presence of non-obligatory intermediates acting
as traps. In all cases, a substantial portion of the helices is rapidly formed.
This initial stage is followed by a long period of consolidation of the helices
accompanied by their correct packing within the membrane. Our results provide
the framework for understanding the variety of folding pathways of helical
transmembrane proteins
Photocross-linking of nascent chains to the STT3 subunit of the oligosaccharyltransferase complex
In eukaryotic cells, polypeptides are N glycosylated after passing through the membrane of the ER into the ER lumen. This modification is effected cotranslationally by the multimeric oligosaccharyltransferase (OST) enzyme. Here, we report the first cross-linking of an OST subunit to a nascent chain that is undergoing translocation through, or integration into, the ER membrane. A photoreactive probe was incorporated into a nascent chain using a modified Lys-tRNA and was positioned in a cryptic glycosylation site (-Q-K-T- instead of -N-K-T-) in the nascent chain. When translocation intermediates with nascent chains of increasing length were irradiated, nascent chain photocross-linking to translocon components, Sec61α and TRAM, was replaced by efficient photocross-linking solely to a protein identified by immunoprecipitation as the STT3 subunit of the OST. No cross-linking was observed in the absence of a cryptic sequence or in the presence of a competitive peptide substrate of the OST. As no significant nascent chain photocross-linking to other OST subunits was detected in these fully assembled translocation and integration intermediates, our results strongly indicate that the nascent chain portion of the OST active site is located in STT3
Phosphatidylethanolamine mediates insertion of the catalytic domain of leader peptidase in membranes
AbstractLeader peptidase is an integral membrane protein of E. coli and it catalyses the removal of most signal peptides from translocated precursor proteins. In this study it is shown that when the transmembrane anchors are removed in vivo, the remaining catalytic domain can bind to inner and outer membranes of E. coli. Furthermore, the purified catalytic domain binds to inner membrane vesicles and vesicles composed of purified inner membrane lipids with comparable efficiency. It is shown that the interaction is caused by penetration of a part of the catalytic domain between the lipids. Penetration is mediated by phosphatidylethanolamine, the most abundant lipid in E. coli, and does not seem to depend on electrostatic interactions. A hydrophobic segment around the catalytically important residue serine 90 is required for the interaction with membranes
Identification of particles with Lorentz factor up to with Transition Radiation Detectors based on micro-strip silicon detectors
This work is dedicated to the study of a technique for hadron identification
in the TeV momentum range, based on the simultaneous measurement of the
energies and of the emission angles of the Transition Radiation (TR) X-rays
with respect to the radiating particles. A detector setup has been built and
tested with particles in a wide range of Lorentz factors (from about to
about crossing different types of radiators. The measured
double-differential (in energy and angle) spectra of the TR photons are in a
reasonably good agreement with TR simulation predictions.Comment: 31 pages, 12 figures, paper published on Nuclear Instruments &
Methods
The nucleotide and partial amino acid sequences of rat fetuin
Fetuins are among the major plasma proteins, yet their biological role has remained elusive. Here we report the molecular cloning of rat fetuin and the sequence analysis of a full-length clone, RF619 of 1456 bp with an open reading frame of 1056 bp encoding 352 amino acid residues. The coding part of RF619 was identical with the cDNA sequence of the natural inhibitor of the insulin receptor tyrosine kinase from rat (pp63) except for four substitutions and a single base insertion causing divergence of the predicted protein sequences. Partial amino acid sequences of rat plasma fetuin were in agreement with the predictions based on the RF619 cDNA. Purified rat fetuin inhibited the insulin receptor tyrosine kinase in vitro. Therefore, we conclude that RF619 and pp63 cDNA encode the same protein, i.e. authentic rat fetuin which is a functional tyrosine kinase inhibitor
Comparison of measurement and simulation of ATLAS cavern radiation background
Sixteen Medipix2 pixel detector based (MPX) devices were operated at various positions within the ATLAS detector and cavern continuously from early 2008 up to 2013. In addition to photons, each MPX detector is capable to detect charged particles, and neutrons as it is covered with a mask of converter materials dividing its area into regions sensitive to thermal or fast neutrons. The MPX detector network was effectively used for real-time measurements of the spectral characteristics and composition of complex radiation fields in ATLAS. This article reports comparison of the results of measurements performed with MPX detectors during the LHC operation period in 2010 and 2011 with Monte Carlo simulations results from the FLUGG and GCALOR codes. For the purpose of this comparison, the MPX detectors were operated in tracking mode with low threshold (8-10 keV) allowing one to distinguish among particle categories based on the recognition of track patterns left by the particles in the MPX sensitive layer. The comparison of measurements with simulations shows that the agreement between measured and simulated data is satisfactory in most cases within a factor of two
- …