Plant cytochromes P450 (P450s) participate in a variety of biochemical pathways to produce a vast diversity of plant natural products. The number of P450 genes in plant genomes is estimated to be up to 1% of the total gene annotations of each plant species, implying that plants are huge sources for various P450-dependent reactions. Plant P450s catalyze a wide variety of monooxygenation/hydroxyl...

Many protein and mRNA species occur at low molecular counts within cells, and hence are subject to large stochastic fluctuations in copy numbers over time. Development of computationally tractable frameworks for modelling stochastic fluctuations in population counts is essential to understand how noise at the cellular level affects biological function and phenotype. We show that stochastic hybr...

Biochemical pathways or networks are generic representations used to model many different types of complex functional and physical interactions in biological systems. Models based on experimental results are often incomplete, e.g., reactions may be missing and only some products are observed. In such cases, one would like to reason about incomplete network representations and propose candidate ...

Stochasticity is an essential aspect of biochemical processes at the cellular level. We now know that living cells take advantage of stochasticity in some cases and counteract stochastic effects in others. Here we propose a method that allows us to calculate contributions of individual reactions to the total variability of a system's output. We demonstrate that reactions differ significantly in...

Molecular crowding is a critical feature distinguishing intracellular environments from idealized solution-based environments and is essential to understanding numerous biochemical reactions, from protein folding to signal transduction. Many biochemical reactions are dramatically altered by crowding, yet it is extremely difficult to predict how crowding will quantitatively affect any particular...

Two ;multitest'(1) media for biochemical classification of the genus Proteus into species were developed. The species so determined were checked with conventional methods. Results show that these media were useful for rapid identification of species. The biochemical reactions of four Proteus species isolated from clinical specimens as tested by conventional methods are reviewed and the occurren...

The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like 'how much Gibbs energy is released by ATP hydrolysis at pH 5?' are complicated excessively by the search for accurate data. To address this problem, ...

Twenty-five isolates of nutritionally variant streptococci submitted to the Streptococcus Laboratory of the Center for Disease Control over a 2-year period were tested for growth requirements and for biochemical reactions. After they were recovered from storage in blood at -170 degrees C, all isolates grew within 48 h in both thioglycollate broth and Todd-Hewitt broth supplemented with 0.001% p...

Motor enzymes catalyse chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific biochemical steps in their catalysed reactions, challenging the classical view that work can only be performed within a biochemical state. To address these studies an alternative class of models, often referred to...

The parallel simulation of biochemical reactions is a very interesting problem: biochemical systems are inherently parallel, yet the majority of the algorithms to simulate them, including the well-known and widespread Gillespie SSA, are strictly sequential. Here we investigate, in a general way, how to characterize the simulation of biochemical systems in terms of Discrete Event Simulation. We ...