The ends of a large RNA molecule are necessarily close

We show on general theoretical grounds that the two ends of single-stranded (ss) RNA molecules (consisting of roughly equal proportions of A, C, G and U) are necessarily close together, largely independent of their length and sequence. This is demonstrated to be a direct consequence of two generic properties of the equilibrium secondary structures, namely that the average proportion of bases in pairs is ∼60% and that the average duplex length is ∼4. Based on mfold and Vienna computations on large numbers of ssRNAs of various lengths (1000–10 000 nt) and sequences (both random and biological), we find that the 5′–3′ distance—defined as the sum of H-bond and covalent (ss) links separating the ends of the RNA chain—is small, averaging 15–20 for each set of viral sequences tested. For random sequences this distance is ∼12, consistent with the theory. We discuss the relevance of these results to evolved sequence complementarity and specific protein binding effects that are known to be important for keeping the two ends of viral and messenger RNAs in close proximity. Finally we speculate on how our conclusions imply indistinguishability in size and shape of equilibrated forms of linear and covalently circularized ssRNA molecules.     

Effects of limited input distance constraints upon the distance geometry algorithm.

In this paper we examine the distance geometry (DG) algorithm in the form used to determine the structure of proteins. We focus on three aspects of the algorithm: bound smoothing with the triangle inequality, the random selection of distances within the bounds, and the number of distances needed to specify a structure. Computational experiments are performed using simulated and real data for basic pancreatic trypsin inhibitor (BPTI) from nmr and crystallographic measurements. We find that the upper bounds determined by bound smoothing to be a linear function of the true crystal distance. A simple model that describes the results obtained with randomly selected trial distances is proposed. Using this representation of the trial distances, we show that BPTI DG structures are more compact than the true crystal structure. We also show that the DG-generated structures no longer resemble test structures when the number of these interresidue distance constraints is less than the number of degrees of freedom of the protein backbone. While the actual model will be sensitive the way distances are chosen, our conclusions are likely to apply to other versions of the DG algorithm.     

Communication over a large distance: enhancers and insulators.

Enhancers are regulatory DNA sequences that can work over a large distance. Efficient enhancer action over a distance clearly requires special mechanisms for facilitating communication between the enhancer and its target. While the chromatin looping model can explain the majority of the observations, some recent experimental findings suggest that a chromatin scanning mechanism is used to establish the loop. These new findings help to understand the mechanism of action of the elements that can prevent enhancer-promoter communication (insulators).     

Features of the geometry of a supercoiled DNA molecule

The features of the geometry of a supercoiled DNA molecule are considered. A model of supercoiled structure of DNA taking into account its natural helical structure has been constructed. Force factors arising in DNA has been calculated depending on winding angle.     

Controlling a system with redundant degrees of freedom. I. Torque distribution in still standing stick insects

The question is investigated as to how a stick insect solves the task of distributing its body weight onto its six legs, i.e., how are the torques coordinated that are produced by the 18 joints (3 per leg). Three-dimensional force measurements of ground reaction forces have been used to calculate the torques developed by each of the 18 joints. Torques were found to change considerably although the body and the legs of the animal did not move. This result implies a tight cooperation between the 18 joint controllers. Indeed, in each individual experiment, strong correlations could be observed between specific pairs of joints. However, in spite of thorough analysis, no general correlation rules between torques could be detected. The only common attribute found for all experiments was that high absolute torques observed at the beginning of the experiment tend to converge to some minimum over time. Thus, the insects tend to decrease the torques while standing still, but do not use fixed rules. Rather they appear to exploit their extra degrees of freedom and produce time courses that can strongly vary between experiments. Possible mechanisms underlying this behaviour are discussed in a companion paper [Lévy and Cruse (2008) Controlling a system with redundant degrees of freedom: ii. solution of the force distribution problem without a body model, submitted].     

Significance of kinetic degrees of freedom in operation of the actomyosin motor

The actomyosin motor as a principal functional component of cell motility is highly coordinated in regulating the participating molecular components. At the same time, it has to be flexible and plastic enough to accommodate itself to a wide variety of operational conditions. We prepared two different types of actomyosin systems. One is a natural intact actomyosin system with no artificial constraint on the kinetic degrees of freedom of the actin filaments, and the other is a regulated one with actin filaments supplemented by intra- and intermolecular crosslinking to suppress the kinetic degrees of freedom to a certain extent. Crosslinked actomyosin systems were found to remain almost insensitive to calcium regulation even when intact troponin-tropomyosin regulatory component was incorporated. Both the ATPase and the motile activities of the actin filaments sliding on myosin molecules were markedly lowered by the crosslinking. In contrast, once the crosslinking was cleaved, both properties returned to the normal as with intact actomyosin systems.     

Assessment of the accuracy of a human arm model with seven degrees of freedom

We are proposing a human arm model that consists of three rigid segments with seven degrees of freedom. The shoulder joint was modeled as a ball-and-socket joint and the elbow and wrist joints were modelled as skew-oblique joints. Optimal parameters for this model were calculated on the base of in vivo recordings with a spatial tracking system. The criterion of optimality was defined as the minimum of the mean-square deviation between the experimentally obtained sensor positions and orientations and their positions and orientations calculated by solving the direct kinematics problem. The minimal value of the direct kinematics error was found to be 0.5-0.6cm for sensor positions and 5-7 degrees for sensor orientations. We are proposing that these values serve as the assessment for the accuracy of the arm model.     

On the origin of the transfer RNA molecule.

Data and arguments are given in favour of the hypothesis that the primitive tRNA molecule may have originated from a direct duplication event involving one of the two halves of the tRNA molecule. It seems that a molecule capable of assuming a hairpin structure was involved as a precursor in this duplication. The two halves of the present tRNAs could, therefore, be considered as paralogous.     

Coherent conformational degrees of freedom as a structural basis for allosteric communication

Conformational changes in allosteric regulation can to a large extent be described as motion along one or a few coherent degrees of freedom. The states involved are inherent to the protein, in the sense that they are visited by the protein also in the absence of effector ligands. Previously, we developed the measure binding leverage to find sites where ligand binding can shift the conformational equilibrium of a protein. Binding leverage is calculated for a set of motion vectors representing independent conformational degrees of freedom. In this paper, to analyze allosteric communication between binding sites, we introduce the concept of leverage coupling, based on the assumption that only pairs of sites that couple to the same conformational degrees of freedom can be allosterically connected. We demonstrate how leverage coupling can be used to analyze allosteric communication in a range of enzymes (regulated by both ligand binding and post-translational modifications) and huge molecular machines such as chaperones. Leverage coupling can be calculated for any protein structure to analyze both biological and latent catalytic and regulatory sites.     

Polytomies and phylogenetically independent contrasts: examination of the bounded degrees of freedom approach

We examined the effect of soft polytomies on the performance (Type I error rate and bias) of Felsenstein's (1985; Am. Nat. 125:1-15) method of phylogenetically independent contrasts for estimating a bivariate correlation. We specifically tested the adequacy of bounding degrees of freedom, as suggested by Purvis and Garland (1993; Syst. Biol. 42:569-575). We simulated bivariate character evolution under Brownian motion (assumed by independent contrasts) and eight other models on five phylogenetic trees. For non-Brownian motion simulations, the adequacy of branch-length standardization was checked with a simple diagnostic (Garland et al., 1992; Syst. Biol. 41:18-32), and transformations were applied as indicated. Surprisingly, soft polytomies tended to have negligible effects on Type I error rates when models other than Brownian motion were used. Overall, and irrespective of evolutionary model, degrees of freedom were appropriately bounded for hypothesis testing, and unbiased estimates of the correlation coefficient were obtained. Our results, along with those of previous simulation studies, suggest that independent contrasts can reliably be applied to real data, even with phylogenetic uncertainty.     

Intramolecular RNA replicase: Possibly the first self-replicating molecule in the RNA world

Although there is more and more evidence suggested the existence of an RNA World during the origin of life, the scenario concerning the origin of the RNA World remains blurry. Usually it is speculated that it originated from a prebiotic nucleotide pool, during which a self-replicating RNA synthesis ribozyme may have emerged as the first ribozyme – the RNA replicase. However, there is yet no ersuasive supposition for the mechanism for the self-favouring feature of the replicase, thus the speculation remains unconvincing. Here we suggest that intramolecular catalysis is a possible solution. Two RNA synthesis ribozymes may be integrated into one RNA molecule, as two functional domains which could catalyze the copy of each other. Thus the RNA molecule could self-replicate and be referred to as “intramolecular replicase“ here. Computational simulation to get insight into the dynamic mechanism of emergence of the intramolecular replicase from a nucleotide pool is valuable and would be included in a following work of our group.     

RNA:RNA interactions in the large subunit ribosomal RNA of Euglena gracilis

In Euglena gracilis, the cytoplasmic large subunit (LSU) rRNA is composed of 14 discrete small RNA species that must somehow interact in the functional ribosome. We have isolated native complexes of Euglena rRNA and show here that the largest of these complexes contains eight of the 14 LSU rRNA species. Several of these small rRNA species are able to associate in vitro to reform an isolated domain of LSU rRNA structure.     

Two degrees of freedom quasi-static EMG-force at the wrist using a minimum number of electrodes

Surface electromyogram-controlled powered hand/wrist prostheses return partial upper-limb function to limb-absent persons. Typically, one degree of freedom (DoF) is controlled at a time, with mode switching between DoFs. Recent research has explored using large-channel EMG systems to provide simultaneous, independent and proportional (SIP) control of two joints—but such systems are not practical in current commercial prostheses. Thus, we investigated site selection of a minimum number of conventional EMG electrodes in an EMG-force task, targeting four sites for a two DoF controller. In a laboratory experiment with 10 able-bodied subjects and three limb-absent subjects, 16 electrodes were placed about the proximal forearm. Subjects produced 1-DoF and 2-DoF slowly force-varying contractions up to 30% maximum voluntary contraction (MVC). EMG standard deviation was related to forces via regularized regression. Backward stepwise selection was used to retain those progressively fewer electrodes that exhibited minimum error. For 1-DoF models using two retained electrodes (which mimics the current state of the art), subjects had average RMS errors of (depending on the DoF): 7.1–9.5% MVC for able-bodied and 13.7–17.1% MVC for limb-absent subjects. For 2-DoF models, subjects using four electrodes had errors on 1-DoF trials of 6.7–8.5% MVC for able-bodied and 11.9–14.0% MVC for limb-absent; and errors on 2-DoF trials of 9.9–11.2% MVC for able-bodied and 15.8–16.7% MVC for limb-absent subjects. For each model, retaining more electrodes did not statistically improve performance. The able-bodied results suggest that backward selection is a viable method for minimum error selection of as few as four electrode sites for these EMG-force tasks. Performance evaluation in a prosthesis control task is a necessary and logical next step for this site selection method.