***TASK***
the task is to simplify the input abstract of a biomedical literature

***INPUT***
the input is the abstract of a biomedical literature

***OUTPUT***
the output is the simplified abstract for the input abstract of a biomedical literature
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Input: Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation.
Output:  When species evolve, their genes duplicate and diverge to allow for adaptation of their functional repertoires to the changing environment. In this scenario, unrelated genes can convergently evolve to produce proteins with the same molecular function, termed “functionally analogous.” A quantitative determination of the reaction similarities among functionally analogous enzymes could provide insight about the different structural solutions nature has used to evolve similar catalysts. Bond changes between substrates and products, and between successive reaction intermediates, were used to compare the reactions catalyzed and the mechanisms of catalysis for 95 pairs of functionally analogous enzymes. Less than half of the reactions catalyzed by unrelated enzymes, but defined as similar by the Enzyme Commission (EC) classification, are similar in terms of bond changes, suggesting that this classification often fails to capture quantitative differences between many enzyme reactions. Furthermore, we addressed for the first time whether the chemical mechanisms by which similar overall reactions are achieved in functional analogs are also similar. We conclude that convergence of reaction is often accompanied by convergence of chemical mechanism. These results will be useful for classifying enzymes, guiding functional annotation of newly determined enzyme sequences and structures and for informing the engineering of enzymes with new functions.

Input:  The functional role of synchronization has attracted much interest and debate: in particular, synchronization may allow distant sites in the brain to communicate and cooperate with each other, and therefore may play a role in temporal binding, in attention or in sensory-motor integration mechanisms. In this article, we study another role for synchronization: the so-called “collective enhancement of precision”. We argue, in a full nonlinear dynamical context, that synchronization may help protect interconnected neurons from the influence of random perturbations—intrinsic neuronal noise—which affect all neurons in the nervous system. More precisely, our main contribution is a mathematical proof that, under specific, quantified conditions, the impact of noise on individual interconnected systems and on their spatial mean can essentially be cancelled through synchronization. This property then allows reliable computations to be carried out even in the presence of significant noise (as experimentally found e.g., in retinal ganglion cells in primates). This in turn is key to obtaining meaningful downstream signals, whether in terms of precisely-timed interaction (temporal coding), population coding, or frequency coding. Similar concepts may be applicable to questions of noise and variability in systems biology.


Output:

Synchronization phenomena are pervasive in biology, creating collective behavior out of local interactions between neurons, cells, or animals. On the other hand, many of these systems function in the presence of large amounts of noise or disturbances, making one wonder how meaningful behavior can arise in these highly perturbed conditions. In this paper we show mathematically, in a general context, that synchronization is actually a means to protect interconnected systems from effects of noise and disturbances. One possible mechanism for synchronization is that the systems jointly create and then share a common signal, such as a mean electrical field or a global chemical concentration, which in turn makes each system directly connected to all others. Conversely, extracting meaningful information from average measurements over populations of cells (as commonly used for instance in electro-encephalography, or more recently in brain-machine interfaces) may require the presence of synchronization mechanisms similar to those we describe.
