Rafael Alves

An algorithm to enumerate all possible protein conformations verifying a set of distance constraints

BackgroundThe determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only.ResultsIn order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations.ConclusionsWe described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three α-helical peptides.

Vinasse fertirrigation alters soil resistome dynamics: an analysis based on metagenomic profiles

Every year around 300 Gl of vinasse, a by-product of ethanol distillation in sugarcane mills, are flushed into more than 9 Mha of sugarcane cropland in Brazil. This practice links fermentation waste management to fertilization for plant biomass production, and it is known as fertirrigation. Here we evaluate public datasets of soil metagenomes mining for changes in antibiotic resistance genes (ARGs) of soils from sugarcane mesocosms repeatedly amended with vinasse. The metagenomes were annotated using the ResFam database. We found that the abundance of open read frames (ORFs) annotated as ARGs changed significantly across 43 different families (p-value < 0.05). Co-occurrence network analysis revealed distinct patterns of interactions among ARGs, suggesting that nutrient amendment to soil microbial communities can impact on the coevolutionary dynamics of indigenous ARGs within soil resistome.

Modeling the Molecular Distance Geometry Problem Using Dihedral Angles

An alternative formulation based on dihedral angles to the molecular distance geometry problem with imprecise distance data is presented. This formulation considers the additional hypothesis of a particular ordering such that all distances \(||x_i-x_j||=d_{ij}\), \(|i-j|<3\), are known. Considering that bond length and angles are given a priori in a protein backbone, there is always at least one of such ordering in instances involving real protein data. This hypothesis reduces by 2/3 the number of variables of the problem and allows us to calculate the derivatives of the standard Cartesian coordinates representation with respect to the dihedral angles. Numerical experiments illustrate the correctness and viability of the proposed formulation.

Advances on the Geometric Algebra approach to the Discretizable Molecular Distance Geometry Problem (DMDGP)

We consider the Discretizable Molecular Distance Geometry Problem (DMDGP), which is a subclass of the Distance Geometry Problem (DGP), where the search space can be discretized. The DMDGP consists in finding a 3D protein structure for which some of the atomic distances are provided by Nuclear Magnetic Resonance (NMR) experiments. Due to the uncertainties in NMR data, some distances may not be precise, being represented by intervals of real numbers. We present recent results related to the use of Conformal Geometric Algebra to model the DMDGP with imprecise data.