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“Accurate prediction of protein-DNA complexes could provide an important

stepping stone towards a thorough comprehension of vital intracellular processes. Few attempts were made to tackle this issue, focusing on binding patch prediction, protein function classification and distance constraints-based docking. We introduce ParaDock: a novel ab initio protein-DNA docking algorithm. ParaDock combines short DNA fragments, which have been rigidly docked to the protein based on geometric complementarity, to create bent planar DNA molecules of arbitrary sequence. Our algorithm was tested on the bound and unbound targets of a protein-DNA benchmark comprised of 47 complexes. With neither addressing protein flexibility, nor applying any refinement procedure, CAPRI acceptable solutions were obtained among the 10 top ranked hypotheses in 83% of the bound BKM120 order complexes, and 70% of the unbound. Without requiring prior knowledge of DNA length and sequence, and within < 2 h per target on a standard 2.0 GHz single processor CPU, ParaDock offers a fast ab initio docking solution.”
“Large-scale (similar to 36,000 atoms) long-time (30 ns each) molecular dynamics (MD) simulations on the complex of imatinib and 16 common mutants of the ABL tyrosine kinase domain have been performed to study the imatinib resistance mechanisms at the atomic level. MD simulations show that long

time computational simulations could offer insight information that static find protocol models, simple homology modeling methods, or short-time check details simulations cannot provide for the BCR-ABL imatinib resistance

problem. Three possible types of mutational effects from those mutants are found: the direct effect on the contact interaction with imatinib (e. g. some P-loop mutations), the effect on the conformation of a remote region contacting with imatinib (e. g. T315I), and the effect on interaction between two regions within the BCR-ABL domain (e. g. H396P). Insights of possible imatinib resistance mechanisms, not consistent with current consensus, are revealed from various analyses and our findings suggest that drugs with different binding modes may be necessary to overcome the drug resistance due to T315I and other mutations. The relevant patents are discussed.”
“Flax phloem fibers achieve their length by intrusive-diffusive growth, which requires them to penetrate the extracellular matrix of adjacent cells. Fiber elongation therefore involves extensive remodelling of cell walls and middle lamellae, including modifying the degree and pattern of methylesterification of galacturonic acid (GalA) residues of pectin. Pectin methylesterases (PME) are important enzymes for fiber elongation as they mediate the demethylesterification of GalA in muro, in either a block-wise fashion or in a random fashion. Our objective was to identify PMEs and PMEIs that mediate phloem fiber elongation in flax.