The dynamics of polypeptide chain formation.

<p>(a) The average length of polypeptide chain d increases linearly with time. (b) With increasing time the overall occupation probability of polypeptides decreases near the initiation site and increases near the termination site. L denotes length of the lattice chain and m is the mean value of the underlying rate constant distribution, which is given by an exponential distribution for this figure.</p

The steady state distribution of proteins does not depend on the precise form of the underlying rate constant distributions for elongation.

<p>The plots show the simulated results for the steady state protein distributions in cases in which the underlying rate constant distributions along the entire chain follow (a) normal distribution (mean 50 and standard deviation 15), (b) exponential distribution (mean 100), (c) gamma distribution (shape parameter 10, scale parameter 5), and (d) log-normal distribution (derived from normal distribution with mean 3.5 and standard deviation 1). The parameters of the scaled rate constant (<i>ϵ</i>) distribution were chosen so that the system is in the steady state phase in all plots.</p

Schematic diagram of the stochastic random walk model for the translation of mRNAs.

<p>Following initiation the translation proceeds via elongation at different local rates on different mRNAs. The figure shows N copies of mRNA in a population of <i>N</i>_<i>c</i> cells undergoing elongation. Each mRNA is represented by a linear discrete lattice with individual nodes representing codons at which ribosomes add residues to the nascent polypeptide chain. At any given node <i>i</i> in an infinitesimal interval of time, the probability of a codon being translated or not is given by <i>p</i>_<i>i</i> and 1 − <i>p</i>_<i>i</i> respectively. The distribution of <i>p</i>_<i>i</i> at the <i>i</i>th node is given by <i>ρ</i>(<i>p</i>_<i>i</i>). <i>p</i>_{<i>i</i>;<i>j</i>} represents the scaled rate constant (drawn from probability distribution <i>ρ</i>(<i>p</i>_<i>i</i>)) for jth mRNA at the <i>i</i>th site. Once the ribosome reaches site <i>n</i>, the termination site, a completed protein is released and the ribosome moves back to the initiation site (the recycling step, found in eukaryotic cells.)</p

The effect of a low rate constant for elongation at a given residue.

<p>In this case it is expected that the elongation will stall at a site with a very low rate constant. (a) In order to simulate this condition the mean value for the rate constant distributions at various sites is allowed to vary between 50 and 150 except at site 20, where the mean value is set near zero. (b) The resulting distribution of the polypeptides across various sites clearly shows the stalling effect with resulting accumulation around the residue site 20. Although this example has been constructed to verify the validity of the model, the occurrence of pause sites has been reported in the literature.</p

A quantile-quantile (Q-Q) plot shows that the steady state protein distribution is well described by a log-normal except in the tail region where deviations arise.

<p>The histograms (a) and (b) show the simulated results for the steady state protein distributions in cases in which the <i>ϵ</i>_<i>i</i> follow: (a) a gamma distribution (shape parameter 10, scale parameter 5); or (b) a normal distribution (mean 50 and standard deviation 15). The solid (black) line in (a) and (b) represent the best unbiased fit for the corresponding data. The best unbiased fit for (a) is a sum of two log-normal distributions with weights 0.985935 and 0.0140649, and for (b) is a sum of log-normal and log-logistic distributions with weights 0.368091 and 0.631909 respectively. In the (Q-Q) plots (c) and (d), the log-transformed steady state distributions data corresponding to (a) and (b) respectively are plotted against a normal distribution. In the (Q-Q) plots (e) and (f), the log-transformed steady state distributions data corresponding to (a) and (b) respectively are plotted against the best unbiased fit distribution. The relative improvement of fit compared to (c) and (d) is noticeable.</p

The change in estimated variance of the occupation probability at different sites along the mRNA.

<p>(a) The variation of the estimated variance at different residues along the mRNA chain with time. (b) The changes in estimated variance at different times along the mRNA chain at different residue locations. The estimated variance is obtained by taking the log-transform of a log-normal distribution and calculating the variance of the resulting normal distribution.</p

The number of proteins per mRNA follows a log-normal distribution.

<p>The plot shows the histogram of the protein abundance (in fractional units) per template. For the simulation of this plot, the underlying rate constant (<i>ϵ</i>) distribution is taken to follow a gamma distribution with shape parameter 10 and scale parameter 5. Similar results are obtained in cases in which the underlying rate constant distributions are different.</p

The incorporation of correlation between individual rates has little effect on the resulting steady state distribution.

<p>(a) The spatial arrangement of rate constants at an arbitrarily chosen mRNA site across an ensemble of mRNA molecules encoding the same protein. For visual clarity, the moving averages of rate constants along 100 adjacent mRNAs is shown. (b) Steady state distribution corresponding to (a). (c) Spatially correlated rate constants at an arbitrarily chosen site of mRNA (moving average over 100 sites is plotted) across an ensemble of mRNA. (d) Steady state distribution corresponding to (b).</p

Deletion of the Murine Cytochrome P450 <i>Cyp2j</i> Locus by Fused BAC-Mediated Recombination Identifies a Role for <i>Cyp2j</i> in the Pulmonary Vascular Response to Hypoxia

<div><p>Epoxyeicosatrienoic acids (EETs) confer vasoactive and cardioprotective functions. Genetic analysis of the contributions of these short-lived mediators to pathophysiology has been confounded to date by the allelic expansion in rodents of the portion of the genome syntenic to human <i>CYP2J2</i>, a gene encoding one of the principle cytochrome P450 epoxygenases responsible for the formation of EETs in humans. Mice have eight potentially functional genes that could direct the synthesis of epoxygenases with properties similar to those of CYP2J2. As an initial step towards understanding the role of the murine <i>Cyp2j</i> locus, we have created mice bearing a 626-kb deletion spanning the entire region syntenic to <i>CYP2J2</i>, using a combination of homologous and site-directed recombination strategies. A mouse strain in which the locus deletion was complemented by transgenic delivery of BAC sequences encoding human CYP2J2 was also created. Systemic and pulmonary hemodynamic measurements did not differ in wild-type, null, and complemented mice at baseline. However, hypoxic pulmonary vasoconstriction (HPV) during left mainstem bronchus occlusion was impaired and associated with reduced systemic oxygenation in null mice, but not in null mice bearing the human transgene. Administration of an epoxygenase inhibitor to wild-type mice also impaired HPV. These findings demonstrate that <i>Cyp2j</i> gene products regulate the pulmonary vascular response to hypoxia.</p></div

Gene expression by quantitative RT-PCR.

<p>(A, B, C) <i>Cyp2c44</i>, <i>Cyp2c38</i>, and <i>Cyp2c29</i> mRNA levels in lung and heart of <i>Cyp2j^+/+</i>, <i>Cyp2j^−/−</i> and <i>Cyp2j^−/− -Tg</i> mice. Experiments were run in triplicate. Mouse tissue RNAs were pooled from three individual mice.</p