Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction

In protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies suggesting that function evolves fundamentally by recruitment, i.e., a same protein motif or fold can be used to perform different enzymatic functions and a few specific amino acids (AAs) are actually responsible for enzyme activity. These essential amino acids should belong to active sites and an effective method for predicting function should be able to recognize them. (C) 2012 Elsevier Ltd. All rights reserved.

Joint loading decreased by inexpensive and minimalist footwear in elderly women with knee osteoarthritis during stair descent

Objective Previous studies indicate that flexible footwear, which mimics the biomechanics of walking barefoot, results in decreased knee loads in patients with knee osteoarthritis (OA) during walking. However, the effect of flexible footwear on other activities of daily living, such as descending stairs, remains unclear. Our objective was to evaluate the influence of inexpensive and minimalist footwear (Moleca) on knee adduction moment (KAM) during stair descent of elderly women with and without knee OA. Methods. Thirty-four elderly women were equally divided into an OA group and a control group (CG). Stair descent was evaluated in barefoot condition, while wearing the Moleca, and while wearing heeled shoes. Kinematics and ground reaction forces were measured to calculate KAM by using inverse dynamics. Results. The OA group experienced a higher KAM during midstance under the barefoot condition (233.3%; P = 0.028), the Moleca (379.2%; P = 0.004), and heeled shoes (217.6%; P = 0.007). The OA group had a similar knee load during early, mid, and late stance with the Moleca compared with the barefoot condition. Heeled shoes increased the knee loads during the early-stance (versus barefoot [16.7%; P < 0.001] and versus the Moleca [15.5%; P < 0.001]), midstance (versus barefoot [8.6%; P = 0.014] and versus the Moleca [9.5%; P = 0.010]), and late-stance phase (versus barefoot [10.6%; P = 0.003] and versus the Moleca [9.2%; P < 0.001]). In the CG, the Moleca produced a knee load similar to the barefoot condition only during the early-stance phase. Conclusion. Besides the general foot protection, the inexpensive and minimalist footwear contributes to decreasing knee loads in elderly women with OA during stair descent. The loads are similar to the barefoot condition and effectively decreased when compared with heeled shoes.