Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K

The conformational space annealing (CSA) method for global optimization has been applied to the 10-55 fragment of the B-domain of staphylococcal protein A (protein A) and to a 75-residue protein, apo calbindin D9K (PDB ID code 1CLB), by using the UNRES off-lattice united-residue force field. Although the potential was not calibrated with these two proteins, the native-like structures were found among the low-energy conformations, without the use of threading or secondary-structure predictions. This is because the CSA method can find many distinct families of low-energy conformations. Starting from random conformations, the CSA method found that there are two families of low-energy conformations for each of the two proteins, the native-like fold and its mirror image. The CSA method converged to the same low-energy folds in all cases studied, as opposed to other optimization methods. It appears that the CSA method with the UNRES force field, which is based on the thermodynamic hypothesis, can be used in prediction of protein structures in real time.

Low dimensionality of supraspinally induced force fields

Recent experiments using electrical and N-methyl-d-aspartate microstimulation of the spinal cord gray matter and cutaneous stimulation of the hindlimb of spinalized frogs have provided evidence for a modular organization of the frog’s spinal cord circuitry. A “module” is a functional unit in the spinal cord circuitry that generates a specific motor output by imposing a specific pattern of muscle activation. The output of a module can be characterized as a force field: the collection of the isometric forces generated at the ankle over different locations in the leg’s workspace. Different modules can be combined independently so that their force fields linearly sum. The goal of this study was to ascertain whether the force fields generated by the activation of supraspinal structures could result from combinations of a small number of modules. We recorded a set of force fields generated by the electrical stimulation of the vestibular nerve in seven frogs, and we performed a principal component analysis to study the dimensionality of this set. We found that 94% of the total variation of the data is explained by the first five principal components, a result that indicates that the dimensionality of the set of fields evoked by vestibular stimulation is low. This result is compatible with the hypothesis that vestibular fields are generated by combinations of a small number of spinal modules.

Methylation is not the main force repressing the retrotransposon MAGGY in Magnaporthe grisea

We have introduced the LTR-retrotransposon MAGGY into a naive genome of Magnaporthe grisea and estimated the copy number of MAGGY in a cell by serial isolation of fungal protoplasts at certain time intervals. The number of MAGGY elements rapidly increased for a short period following introduction. However, it did not increase geometrically and reached equilibrium at 20–30 copies per genome, indicating that MAGGY was repressed or silenced during proliferation. De novo methylation of MAGGY occurred immediately following invasion into the genome but the degree of methylation was constant and did not correlate with the repression of MAGGY. 5-Azacytidine treatment demethylated and transcriptionally activated the MAGGY element in regenerants but did not affect transpositional frequency, suggesting that post-transcriptional suppression, not methylation, is the main force that represses MAGGY proliferation in M.grisea. Support for this conclusion was also obtained by examining the methylation status of MAGGY sequences in field isolates of M.grisea with active or inactive MAGGY elements. Methylation of the MAGGY sequences was detected in some isolates but not in others. However, the methylation status did not correlate with the copy numbers and activity of the elements.