Analysis Of Local Fluctuations Research Articles

Rate Estimates from Sampling Sparse Transitions: TRNA Motion Limits Transitions between Ribosomal Translocation Intermediates

During the elongation cycle, after peptide-bonds are formed in the ribosome, transfer RNAs translocate to their new binding sites. Resting on extensive MD simulations of 13 near-atomistically resolved translocation intermediates of the fully solvated ribosome, we have estimated the rates from transition state theory for the motions of the tRNAs, 30S head and body, as well as the L1-stalk. The Kramers pre-factor and transmission coefficient were determined from a statistical analysis of transitions observed in the simulations.To that aim, we first estimated all free energy barrier heights from a multidimensional quasi-harmonic approximation derived from local fluctuation analysis. Second, we introduced two model parameters, an attempt rate and a constant scaling factor for the estimated barrier heights. using the assumption that all barrier crossings occur at the same attempt rate, scaling factor and attempt rate were obtained through a least squares fitting of the transition probabilities observed in our simulation times to the respective transition probabilities from Kramers theory.The obtained rate estimates range from ns to ms and suggest that tRNA movement, rather than body and head rotation, is rate-limiting for most transitions between intermediate states of tRNA translocation.

Modulation of Elasticity in Functionally Distinct Domains of the Tropomyosin Coiled-Coil

Alpha-helical coiled-coils are common protein structural motifs. Whereas vast information is available regarding their structure, folding, and stability, far less is known about their elastic properties, even though they play mechanical roles in many cases such as tropomyosin in muscle contraction or neck stalks of kinesin or myosin motor proteins. Using computer simulations, we characterized elastic properties of coiled-coils, either globally or locally. Global bending stiffness of standard leucine zipper coiled-coils was calculated using normal mode analysis. Mutations in hydrophobic residues involved in the knob-into-hole interface between the two alpha-helices affect elasticity significantly, whereas charged side chains forming inter-helical salt bridges do not. This suggests that coiled-coils with less regular heptad periodicity may have regional variations in flexibility. We show this by the flexibility map of tropomyosin, which was constructed by a local fluctuation analysis. Overall, flexibility varies by more than twofold and increases towards the C-terminal region of the molecule. Describing the coiled-coil as a twisted tape, it is generally more flexible in the splay bending than in the bending of the broad face. Actin binding sites in alpha zones show local rigidity minima. Broken core regions due to acidic residues at the hydrophobic face such as the Asp137 and the Glu218 are found to be the most labile with moduli for splay and broad face bending as 70 nm and 116 nm respectively. Such variation in flexibility could be relevant to the tropomyosin function, especially for moving across the non-uniform surface of F-actin to regulate myosin binding.

Fluctuation dynamics of exchange rates on Polish financial market

We show results of local fluctuation analysis, probability distributions, and fractional integration analysis for nominal exchange rates of the Polish zloty versus two foreign currencies (US dollar and German mark/euro). The results confirm the rapid change of the volatility pattern in August 1997. We compare the type of the fluctuation behavior before and after this date.

Study of multiparticle spikes in central 4.5 A GeV/ c C-Cu collisions

An analysis of local fluctuations, or spikes, is performed for charged particles produced in central C-Cu collisions at 4.5 GeV/ c/nucleon. The distributions of spike centers and the maximum density distributions are investigated for different narrow pseudorapidity windows to search for multiparticle dynamical correlations. Two peaks over statistical background are observed in the spike-center distributions with the structure similar to that expected from the coherent gluon radiation model and recently found in hadronic interactions. The dynamical contribution to maximum density fluctuations is obtained to be hidden by statistical correlations, although behavior of the distributions shows qualitative agreement with that from the one-dimensional intermittency model. The observed features of the two different approaches, coherent vs. stochastic, to the formation of the local dynamical fluctuations are discussed.