Diversification and distinctive structural features of S-RNase alleles in the genus Solanum.

The multigenic and multiallelic S-locus in plants is responsible for the gametophytic self-incompatibility system, which is important to prevent the detrimental effects of self-fertilization and inbreeding depression. Several studies have discussed the importance of punctual mutations, recombination, and natural selection in the generation of allelic diversity in the S-locus. However, there has been no wide-ranging study correlating the molecular evolution and structural aspects of the corresponding proteins in Solanum. Therefore, we evaluated the molecular evolution of one gene in this locus and generated a statistically well-supported phylogenetic tree, as well as evidence of positive selection, helping us to understand the diversification of S alleles in Solanum. The three-dimensional structures of some of the proteins corresponding to the major clusters of the phylogenetic tree were constructed and subsequently submitted to molecular dynamics to stabilize the folding and obtain the native structure. The positively selected amino acid residues were predominantly located in the hyper variable regions and on the surface of the protein, which appears to be fundamental for allele specificity. One of the positively selected residues was identified adjacent to a conserved strand that is crucial for enzymatic catalysis. Additionally, we have shown significant differences in the electrostatic potential among the predicted molecular surfaces in S-RNases. The structural results indicate that local changes in the three-dimensional structure are present in some regions of the molecule, although the general structure seems to be conserved. No previous study has described such structural variations in S-RNases.

Ascorbate peroxidase-related (APx-R) is a new heme-containing protein functionally associated with ascorbate peroxidase but evolutionarily divergent.

• Peroxidases are involved in several important processes, such as development and responses to environmental cues. In higher plants, most peroxidases are encoded by large, multigenic families that mainly originated from gene and chromosomal duplications. • Using phylogenetic, genomic and functional analyses, we have identified and characterized a new class of putative heme peroxidases, called ascorbate peroxidase-related (APx-R), which arose specifically in the lineage of plants. • The APx-R protein is structurally related to the ascorbate peroxidases, although the active site contains many conserved substitutions. Unlike all other plant peroxidases, which are encoded by gene families, APx-R is encoded by a single-copy gene in virtually all the species analyzed. APx-R proteins are targeted to the chloroplast and can physically interact with chloroplastic APx proteins. APx-R-knockdown rice (Oryza sativa) plants presented delayed development and a disturbed steady state of the antioxidant system compared with wild type. Moreover, the accumulation of APx-R transcripts was modulated by drought, UV irradiation, cold, and aluminum exposure in rice, suggesting the involvement of APx-R in the environmental stress response. • Our results reveal the existence of a new class of heme peroxidase which seems to play a role in the antioxidant system in plants, probably by modulating the activity of chloroplastic APx proteins.

GROMOS96 43a1 performance on the characterization of glycoprotein conformational ensembles through molecular dynamics simulations.

Considering the small number of papers assessing the conformational profile of glycoproteins through molecular dynamics (MD) simulations, the current work reports on a systematic analysis of the performance of the GROMOS96 43a1 force field and Löwdin HF/6-31G( * *)-derived atomic charges in the conformational description of glycoproteins. The results substantiate the accuracy of the computational representation of glycoprotein conformational ensembles in aqueous solution based on their agreement to available experimental information, supporting further contributions of computational techniques, mainly MD, in future studies on the characterization of glycoprotein structure and function.

A structural model for chorismate synthase from Mycobacterium tuberculosis in complex with coenzyme and substrate.

The enzymes of the shikimate pathway constitute an excellent target for the design of new antibacterial agents; chorismate synthase (CS) catalyzes the last step of this pathway. The prediction of Mycobacterium tuberculosis (MTB) CS three-dimensional structure and the geometric docking of the coenzyme FMN and the substrate EPSP were performed using the crystal structure of CS from Streptococcus pneumoniae as template. Energy minimization of the whole complex showed, as expected, that most of the template interactions are preserved in the MTB structure, except for HIS11, ARG139 and GLN255. However, novel interactions involving ARG111, GLY113 and SER317 were also observed.