A model for ribosome translocation based on the alternated displacement of its subunits.

A meaningful dilemma in ribosome translocation arising from experimental facts is that, although the ribosome-mRNA interaction force always has a significant magnitude, the ribosome still moves to the next codon on the mRNA. How does the ribosome move to the next codon in the sequence while holding the mRNA tightly? The hypothesis proposed here is that ribosome subunits alternate the grip of the ribosome on the mRNA, freeing the other subunit of such interaction for a while, thus allowing its motion to the following codon. Based on this assumption, a single-loop cycle of ribosome configurations involving the relative position of its subunits is elaborated. When its dynamic is modeled as a Markov network, it gives expressions for the average ribosome translocation speed and stall force as functions of the equilibrium constants among the proposed ribosome configurations. The calculations have a reasonable agreement with experimental results, and the succession of molecular events considered here is consistent with current biomolecular concepts of the ribosome translocation process. Thus, the alternative displacements hypothesis developed in the present work suggests a feasible explanation of ribosome translocation.

Theoretical estimate of the effect of thermal agitation on ribosome motion generated by stochastic microswimming.

The effect of thermal agitation on ribosome motion is evaluated through the Péclet number, assuming that the ribosome is self-propelled along the mRNA during protein synthesis by a swimming stroke consisting of a cycle of stochastically-generated ribosome configurations involving its two subunits. The ribosome velocity probability distribution function is obtained, giving an approximately normal distribution. Its mean and variance together with an estimate of the in vivo free diffusion coefficient of the ribosome and using only configuration changes of small size, give a Péclet number similar to motor proteins and microorganisms. These results suggest the feasibility of the stochastic microswimming hypothesis to explain ribosome motion.

Stochastic microswimming model for the average translational velocity of the ribosome.

The motion of the ribosome is modeled here, assuming that its two subunits are subject to stochastic rearrangements, thus producing different conformations constituting its deformation cycle, or swimming stroke. Using a general statistical mechanical formulation, the mean propulsion velocity of the ribosome is obtained as a function of the transition rates among the different conformations and of the relevant deformation variables. A calculation with reasonable parameter estimations shows that the ribosome can match the average protein synthesis speed with deformations of a size comparable to its radius.

Information theory and the ethylene genetic network.

The original aim of the Information Theory (IT) was to solve a purely technical problem: to increase the performance of communication systems, which are constantly affected by interferences that diminish the quality of the transmitted information. That is, the theory deals only with the problem of transmitting with the maximal precision the symbols constituting a message. In Shannon's theory messages are characterized only by their probabilities, regardless of their value or meaning. As for its present day status, it is generally acknowledged that Information Theory has solid mathematical foundations and has fruitful strong links with Physics in both theoretical and experimental areas. However, many applications of Information Theory to Biology are limited to using it as a technical tool to analyze biopolymers, such as DNA, RNA or protein sequences. The main point of discussion about the applicability of IT to explain the information flow in biological systems is that in a classic communication channel, the symbols that conform the coded message are transmitted one by one in an independent form through a noisy communication channel, and noise can alter each of the symbols, distorting the message; in contrast, in a genetic communication channel the coded messages are not transmitted in the form of symbols but signaling cascades transmit them. Consequently, the information flow from the emitter to the effector is due to a series of coupled physicochemical processes that must ensure the accurate transmission of the message. In this review we discussed a novel proposal to overcome this difficulty, which consists of the modeling of gene expression with a stochastic approach that allows Shannon entropy (H) to be directly used to measure the amount of uncertainty that the genetic machinery has in relation to the correct decoding of a message transmitted into the nucleus by a signaling pathway. From the value of H we can define a function I that measures the amount of information content in the input message that the cell's genetic machinery is processing during a given time interval. Furthermore, combining Information Theory with the frequency response analysis of dynamical systems we can examine the cell's genetic response to input signals with varying frequencies, amplitude and form, in order to determine if the cell can distinguish between different regimes of information flow from the environment. In the particular case of the ethylene signaling pathway, the amount of information managed by the root cell of Arabidopsis can be correlated with the frequency of the input signal. The ethylene signaling pathway cuts off very low and very high frequencies, allowing a window of frequency response in which the nucleus reads the incoming message as a varying input. Outside of this window the nucleus reads the input message as an approximately non-varying one. This frequency response analysis is also useful to estimate the rate of information transfer during the transport of each new ERF1 molecule into the nucleus. Additionally, application of Information Theory to analysis of the flow of information in the ethylene signaling pathway provides a deeper insight in the form in which the transition between auxin and ethylene hormonal activity occurs during a circadian cycle. An ambitious goal for the future would be to use Information Theory as a theoretical foundation for a suitable model of the information flow that runs at each level and through all levels of biological organization.

Comparison of efficiency of translation between a deformable swimmer versus a rigid body in a bounded fluid domain: consequences for subcellular transport.

In this paper, we compare the translation efficiencies of a deformable circle that swims by means of low amplitude periodic tangential surface waves versus a rigid circle, moving in a bounded fluid domain. The swimmer is found to be much more efficient than the rigid body. We believe that this result gives some support to the active hypothesis of subcellular transport, where it is supposed that the organelle can generate by itself a propulsive flux, (by changes of form or metabolic activities) instead of just being carried by the motion of an external agent, like a molecular motor.