Michalski, P. J. | Search bioRxiv

bioRxiv2018

mol2sphere: Spherical Decomposition of Multi-Domain Molecules for Visualization and Coarse Grained Spatial Modeling

SummaryProteins, especially those involved in signaling pathways are composed of functional modules consisting of long strings of amino acids. These functional \"domains\" are linked together in geometric arrangements that can be rigid or flexible, depending on the nature of the linker domains. To understand the structure-function relationships in these macromolecules, it would be helpful to visualize the geometric arrangement of domains. Furthermore, accurate spatial representation of domain structure is necessary for coarse-grain models of the multi-molecular interactions that comprise signaling pathways. Here we introduce a new tool, mol2sphere, that transforms the atomistic structure of a macromolecule into a series of linked spheres corresponding to domains. mol2sphere does this with a k-means clustering algorithm. It may be used for visualization or for coarse grain modeling and simulation.\n\nAvailability and implementationmol2sphere is available as both a plugin for PyMOL and as a new feature within the SpringSaLaD modeling and simulation software. They run on all desktop platforms and are available with documentation at, respectively, https://nmrbox.org/registry/mol2sphere and http://vcell.org/ssalad. Source code is available for the PyMOL (and python) implementations on the NMRbox platform and for the SpringSaLaD implementation at https://github.com/jmasison/SpringSaLaD.

biophysics↗

bioRxiv2017

Langevin Dynamics Simulation of AKAP-PKA Complex: Re-Envisioning the Local Concentration Mechanism for Directing PKA Phosphorylation

The second messenger cAMP and its effector cAMP-dependent protein kinase A (PKA) constitute a ubiquitous cell signaling system. In its inactive state PKA is composed of two regulatory subunits that dimerize, and two catalytic subunits that are inhibited by the regulatory subunits. Activation of the catalytic subunits occurs upon binding of two molecules of cAMP to each regulatory subunit. Although many receptor types existing within the same cell may use this signaling system, compartmentation of signaling is thought to occur due to A-Kinase Anchoring Proteins (AKAPs), which act to co-localize PKA with specific substrates. However, the molecular mechanism allowing AKAPs to direct PKA phosphorylation to a particular substrate remained elusive, as prior evidence suggested that the catalytic subunit, which is highly diffusible, is released after cAMP binding to the regulatory subunit. Recent evidence from Smith et al. suggests that in the cell, the catalytic subunit may in fact not be released from the AKAP complex [1, 2]. They further demonstrated that alterations in the structure of the PKA regulatory subunit tether affect substrate phosphorylation. We use a novel computational software based on Langevin dynamics, SpringSaLaD, to simulate the AKAP-PKA complex in order to determine a molecular mechanism for the changes in phosphorylation seen with alteration in tether length and flexibility, and to demonstrate whether or not AKAPs can effectively direct PKA phosphorylation to a particular substrate upon release of the catalytic subunit from the complex. We find that short and flexible tethers contribute to a decrease in the average characteristic time of binding, allowing the catalytic subunit to spend more time in a bound state with the substrate, which yields faster characteristic times of phosphorylation. We further demonstrate that release of the catalytic subunit from the AKAP complex abrogates the effect of tethering, with characteristic times of phosphorylation similar to non-AKAP bound PKA. The data demonstrates that AKAPs likely do not release the catalytic subunit in directing PKA phosphorylation to AKAP bound substrates. In combination with the changes in characteristic time of phosphorylation which are driven by tether structure, this work indicates that the purpose of AKAPs may be to increase the efficiency of phosphorylation of particular AKAP substrates.

cell biology↗