Inactive cofilin has a low affinity for F-actin

es from 2B37 and 4OXN structures are 445.1 �3 and 2,032.8 �3, respectively, pointing out to significantly different volume values in the MD trajectory. Table 1. Fragment of the Cavity Attributes data set used for clustering the MD trajectory. For that, we developed a function based on a weight system. It gives weight 1 for the atoms whose residues determine the substrate analog in the crystal structure, and 3 for atoms whose residues surround the NADH nicotinamide ring. Remember that the substrate cavity is placed on the NADH coenzyme, which shapes the base of the target cavity and, for this reason, has more weight. The algorithm output is a set of cavities and their respective scores (sum of weights) for every conformation. Hence, we consider cavities with potential level of binding those that show high scores of weights. The number of heavy atoms summarized by the residues from the binding cavity are 2883-98-9 biological activity 19668191″ title=View Abstract(s)”>PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19668191 illustrated in Table 1. In this table, it is clear that the RMSD values are fully sensitive to conformational changes. However, the direction of internal motions is only detected by the volume and heavy atoms, which in turn recognizes small and localized changes that take place in the solvent-accessible surface of flexible systems. For instance, the first two and last two structures contain equal RMSD values; however there is a considerable PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19667298 difference between the volume value and the number of heavy atoms for each residues. The values from Table 1 are in different ranges since they correspond to the original information of each conformation. For clustering purposes, we created a CSV file with the data normalized within the interval [0,1]. It is noteworthy that this methodology is not specific for the InhA’s protein; it may