Mapping the intramolecular signal propagation pathways in protein using Bayesian change point analysis of atomic motions

How water mediates the long-range interactions between remote protein molecules

A mechanism of the influence of the presence of one protein molecule on the internal dynamics of another is proposed.

Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations

Long time scale molecular dynamics (MD) simulations of biological systems are becoming increasingly commonplace due to the availability of both large-scale computational resources and significant advances in the underlying simulation methodologies. Therefore, it is useful to investigate and develop data mining and analysis techniques to quickly and efficiently extract the biologically relevant information from the incredible amount of generated data. Wavelet analysis (WA) is a technique that can quickly reveal significant motions during an MD simulation. Here, the application of WA on well-converged long time scale (tens of μs) simulations of a DNA helix is described. We show how WA combined with a simple clustering method can be used to identify both the physical and temporal locations of events with significant motion in MD trajectories. We also show that WA can not only distinguish and quantify the locations and time scales of significant motions, but by changing the maximum time scale of WA a more complete characterization of these motions can be obtained. This allows motions of different time scales to be identified or ignored as desired.

On the possible role of protein vibrations in information processing in the brain: three Russian dolls

Until recently it was held that the neurocomputations conducted by the brain involved only whole neurons as the operating units. This may however represent only a part of the mechanism. This theoretical and academic position article reviews the considerable evidence that allosteric interactions between proteins (as extensively described by Fuxe et al., 2014), and in particular protein vibrations in neurons, form small scale codes that are involved as parts of the complex information processing systems of the brain. The argument is then developed to suggest that the protein allosteric and vibration codes (that operate at the molecular level) are nested within a medium scale coding system whose computational units are organelles (such as microtubules). This medium scale code is nested in turn inside a large scale coding system, whose computational units are individual neurons. The hypothesis suggests that these three levels interact vertically in both directions thus materially increasing the computational capacity of the brain. The whole hierarchy is thus similar to three nested Russian dolls. This theoretical development may be of use in the design of experiments to test it.