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Decomposition of time-dependent fluorescence signals reveals codon-specific kinetics of protein synthesis
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Force-Dependent Unbinding Rate of Molecular Motors from Stationary Optical Trap Data
Get PDFMolecular
motors walk along filaments until they detach stochastically with
a force-dependent unbinding rate. Here, we show how this unbinding
rate can be obtained from the analysis of experimental data of molecular
motors moving in stationary optical traps. Two complementary methods
are presented, based on the analysis of the distribution for the unbinding
forces and of the motor’s force traces. In the first method,
analytically derived force distributions for slip bonds, slip-ideal
bonds, and catch bonds are used to fit the cumulative distributions
of the unbinding forces. The second method is based on the statistical
analysis of the observed force traces. We validate both methods with
stochastic simulations and apply them to experimental data for kinesin-1
Deducing the kinetics of protein synthesis in vivo from the transition rates measured in vitro.
Get PDFThe molecular machinery of life relies on complex multistep processes that involve numerous individual transitions, such as molecular association and dissociation steps, chemical reactions, and mechanical movements. The corresponding transition rates can be typically measured in vitro but not in vivo. Here, we develop a general method to deduce the in-vivo rates from their in-vitro values. The method has two basic components. First, we introduce the kinetic distance, a new concept by which we can quantitatively compare the kinetics of a multistep process in different environments. The kinetic distance depends logarithmically on the transition rates and can be interpreted in terms of the underlying free energy barriers. Second, we minimize the kinetic distance between the in-vitro and the in-vivo process, imposing the constraint that the deduced rates reproduce a known global property such as the overall in-vivo speed. In order to demonstrate the predictive power of our method, we apply it to protein synthesis by ribosomes, a key process of gene expression. We describe the latter process by a codon-specific Markov model with three reaction pathways, corresponding to the initial binding of cognate, near-cognate, and non-cognate tRNA, for which we determine all individual transition rates in vitro. We then predict the in-vivo rates by the constrained minimization procedure and validate these rates by three independent sets of in-vivo data, obtained for codon-dependent translation speeds, codon-specific translation dynamics, and missense error frequencies. In all cases, we find good agreement between theory and experiment without adjusting any fit parameter. The deduced in-vivo rates lead to smaller error frequencies than the known in-vitro rates, primarily by an improved initial selection of tRNA. The method introduced here is relatively simple from a computational point of view and can be applied to any biomolecular process, for which we have detailed information about the in-vitro kinetics
Biohybrid active matter -- the emergent properties of cell-mediated microtransport
Get PDFAs society paves its way towards device miniaturization and precision
medicine, micro-scale actuation and guided transport become increasingly
prominent research fields with high impact in both technological and clinical
contexts. In order to accomplish directed motion of micron-sized objects
towards specific target sites, active biohybrid transport systems, such as
motile living cells that act as smart biochemically-powered micro-carriers,
have been suggested as an alternative to synthetic micro-robots. Inspired by
the motility of leukocytes, we propose the amoeboid crawling of eukaryotic
cells as a promising mechanism for transport of micron-sized cargoes and
present an in-depth study of this novel type of composite active matter. Its
transport properties result from the interactions of an active element (cell)
and a passive one (cargo) and reveal an optimal cargo size that enhances the
locomotion of the load-carrying cells, even exceeding their motility in the
absence of cargo. The experimental findings are rationalized in terms of a
biohybrid active matter theory that explains the emergent cell-cargo dynamics
and enables us to derive the long-time transport properties of amoeboid
micro-carries. As amoeboid locomotion is commonly observed for mammalian cells
such as leukocytes, our results lay the foundations for the study of transport
performance of other medically relevant cell types and for extending our
findings to more advanced transport tasks in complex environments, such as
tissues.Comment: 11 pages, 5 figure
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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