36 research outputs found
Nanoscale temperature measurements using non-equilibrium Brownian dynamics of a levitated nanosphere
Einstein realised that the fluctuations of a Brownian particle can be used to
ascertain properties of its environment. A large number of experiments have
since exploited the Brownian motion of colloidal particles for studies of
dissipative processes, providing insight into soft matter physics, and leading
to applications from energy harvesting to medical imaging. Here we use
optically levitated nanospheres that are heated to investigate the
non-equilibrium properties of the gas surrounding them. Analysing the sphere's
Brownian motion allows us to determine the temperature of the centre-of-mass
motion of the sphere, its surface temperature and the heated gas temperature in
two spatial dimensions. We observe asymmetric heating of the sphere and gas,
with temperatures reaching the melting point of the material. This method
offers new opportunities for accurate temperature measurements with spatial
resolution on the nanoscale, and a new means for testing non-equilibrium
thermodynamicsComment: 5 pages, 4 figures, supplementary material available upon reques
Phenomenological analysis of ATP dependence of motor protein
In this study, through phenomenological comparison of the velocity-force data
of processive motor proteins, including conventional kinesin, cytoplasmic
dynein and myosin V, we found that, the ratio between motor velocities of two
different ATP concentrations is almost invariant for any substall, superstall
or negative external loads. Therefore, the velocity of motor can be well
approximated by a Michaelis-Menten like formula V=\atp k(F)L/(\atp +K_M),
with the step size, and the external load dependent rate of one
mechanochemical cycle of motor motion in saturated ATP solution. The difference
of Michaelis-Menten constant for substall, superstall and negative
external load indicates, the ATP molecule affinity of motor head for these
three cases are different, though the expression of as a function of
might be unchanged for any external load . Verifications of this
Michaelis-Menten like formula has also been done by fitting to the recent
experimental data
A seesaw model for intermolecular gating in the kinesin motor protein
Recent structural observations of kinesin-1, the founding member of the kinesin group of motor proteins, have led to substantial gains in our understanding of this molecular machine. Kinesin-1, similar to many kinesin family members, assembles to form homodimers that use alternating ATPase cycles of the catalytic motor domains, or “heads”, to proceed unidirectionally along its partner filament (the microtubule) via a hand-over-hand mechanism. Cryo-electron microscopy has now revealed 8-Å resolution, 3D reconstructions of kinesin-1•microtubule complexes for all three of this motor’s principal nucleotide-state intermediates (ADP-bound, no-nucleotide, and ATP analog), the first time filament co-complexes of any cytoskeletal motor have been visualized at this level of detail. These reconstructions comprehensively describe nucleotide-dependent changes in a monomeric head domain at the secondary structure level, and this information has been combined with atomic-resolution crystallography data to synthesize an atomic-level "seesaw" mechanism describing how microtubules activate kinesin’s ATP-sensing machinery. The new structural information revises or replaces key details of earlier models of kinesin’s ATPase cycle that were based principally on crystal structures of free kinesin, and demonstrates that high-resolution characterization of the kinesin–microtubule complex is essential for understanding the structural basis of the cycle. I discuss the broader implications of the seesaw mechanism within the cycle of a fully functional kinesin dimer and show how the seesaw can account for two types of "gating" that keep the ATPase cycles of the two heads out of sync during processive movement
Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control
Ribosome-associated quality control (RQC) pathways monitor and respond to stalling of the translating ribosome. Here the authors show that the ribosome associated RQC factor Hel2/ZNF598, an E3 ubiquitin ligase, generally interacts with mRNAs in the vicinity of stop codons
riboviz: analysis and visualization of ribosome profiling datasets
Abstract Background Using high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell. Since its introduction in 2009, this technique has played a key role in driving biological discovery, and yet it requires a rigorous computational toolkit for widespread adoption. Description We have developed a database and a browser-based visualization tool, riboviz, that enables exploration and analysis of riboseq datasets. In implementation, riboviz consists of a comprehensive and flexible computational pipeline that allows the user to analyze private, unpublished datasets, along with a web application for comparison with published yeast datasets. Source code and detailed documentation are freely available from https://github.com/shahpr/RiboViz . The web-application is live at www.riboviz.org. Conclusions riboviz provides a comprehensive database and analysis and visualization tool to enable comparative analyses of ribosome-profiling datasets. This toolkit will enable both the community of systems biologists who study genome-wide ribosome profiling data and also research groups focused on individual genes to identify patterns of transcriptional and translational regulation across different organisms and conditions
Ribosome profiling reveals the what, when, where and how of protein synthesis
Ribosome profiling, which involves the deep sequencing of ribosome-protected mRNA fragments, is a powerful tool for globally monitoring translation in vivo. The method has facilitated discovery of the regulation of gene expression underlying diverse and complex biological processes, of important aspects of the mechanism of protein synthesis, and even of new proteins, by providing a systematic approach for experimental annotation of coding regions. Here, we introduce the methodology of ribosome profiling and discuss examples in which this approach has been a key factor in guiding biological discovery, including its prominent role in identifying thousands of novel translated short open reading frames and alternative translation products