PubMed · 8164583
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M D Harpen. 1994. A mathematically based spread sheet application for compartmental analysis.. https://doi.org/10.1118/1.597244
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A new approach in implementing classical molecular dynamics simulation for parallel computers has enabled a simulation to be carried out on a protein with explicit representation of water an order of magnitude longer than previously reported and will soon enable such simulations to be carried into the microsecond time range. We have used this approach to study the folding of the villin headpiece subdomain, a 36-residue small protein consisting of three helices, from an unfolded structure to a molten globule state, which has a number of features of the native structure. The time development of the solvation free energy, the radius of gyration, and the mainchain rms difference from the native NMR structure showed that the process can be seen as a 60-nsec "burst" phase followed by a slow "conformational readjustment" phase. We found that the burial of the hydrophobic surface dominated the early phase of the folding process and appeared to be the primary driving force of the reduction in the radius of gyration in that phase.
Human mitochondrial RNase P does not distinguish itself from other RNase P enzymes by most of its basic properties. 5' phosphates on tRNA products, strict dependence on a divalent cation, independence of ATP or other cofactors, and sensitivity to puromycin are generally characteristic for RNase P. Slow sedimentation of human mitochondrial RNase P in glycerol gradients suggests a molecular weight considerably lower than that of bacterial or nuclear RNase P. In contrast to fungi, all putative components of mammalian mitochondrial RNase P are encoded by the nucleus. Intriguingly, no indication of the involvement of a trans-acting RNA was found in mammalian mitochondrial tRNA processing. Mitochondrial RNase P is resistant to rigorous treatments with nucleases and exhibits a protein-like density in Cs2SO4 gradients. Moreover, an analysis of copurifying RNAs revealed no putative RNase P RNA candidates. These data suggest that mammalian mitochondrial RNase P, unlike its nuclear counterpart or its bacterial relatives, is not a ribonucleoprotein but a protein enzyme.
Although the commonly used quadratic Hebbian-anti-Hebbian rules lead to successful models of plasticity and learning, they are inconsistent with neurophysiology. Other rules, more physiologically plausible, fail to specify the biological mechanism of bidirectionality and the biological mechanism that prevents synapses from changing from excitatory to inhibitory, and vice versa. We developed a synaptic bidirectional Hebbian rule that does not suffer from these problems. This rule was compared with physiological homosynaptic conditions in the hippocampus, with the results indicating the consistency of this rule with long-term potentiation (LTP) and long-term depression (LTD) phenomenologies. The phenomenologies considered included the reversible dynamics of LTP and LTD and the effects of N-methyl-D-aspartate blockers and phosphatase inhibitors.