Aravind Rammohan

An actin-filament-binding interface on the Arp2/3 complex is critical for nucleation and branch stability.

The Arp2/3 complex polymerizes new actin filaments from the sides of existing filaments, forming Y-branched networks that are critical for actin-mediated force generation. Binding of the Arp2/3 complex to the sides of actin filaments is therefore central to its actin-nucleating and branching activities. Although a model of the Arp2/3 complex in filament branches has been proposed based on electron microscopy, this model has not been validated using independent approaches, and the functional importance of predicted actin-binding residues has not been extensively tested. Using a combination of molecular dynamics and protein-protein docking simulations, we derived an independent structural model of the interaction between two subunits of the Arp2/3 complex that are key to actin binding, ARPC2 and ARPC4, and the side of an actin filament. This model agreed remarkably well with the previous results from electron microscopy. Complementary mutagenesis experiments revealed numerous residues in ARPC2 and ARPC4 that were required for the biochemical activity of the entire complex. Functionally critical residues clustered together and defined a surface that was predicted by protein-protein docking to be buried in the interaction with actin. Moreover, key residues at this interface were crucial for actin nucleation and Y-branching, high-affinity F-actin binding, and Y-branch stability, demonstrating that the affinity of Arp2/3 complex for F actin independently modulates branch formation and stability. Our results highlight the utility of combining computational and experimental approaches to study protein-protein interactions and provide a basis for further elucidating the role of F-actin binding in Arp2/3 complex activation and function.

Design Principles for Functionalized Surfaces

ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels found within structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from aweb server tool MOLEonline (http://mole.upol.cz) detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores automatically within any given structure. Both database and tool gather information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability of detected channels. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB and MOLEonline provide invaluable resources for research related to deciphering the biological function of biomacromolecular channels.

Computational approaches for investigating interfacial adhesion phenomena of polyimide on silica glass

This manuscript provides a comprehensive study of adhesion behavior and its governing mechanisms when polyimide undergoes various modes of detachment from silica glass. Within the framework of steered molecular dynamics, we develop three different adhesion measurement techniques: pulling, peeling, and sliding. Such computational methodologies can be applied to investigate heterogeneous materials with differing interfacial adhesion modes. Here, a novel hybrid potential involving a combination of the INTERFACE force field in conjunction with ReaxFF and including Coulombic and Lennard-Jones interactions is employed to study such interfaces. The studies indicate that the pulling test requires the largest force and the shortest distance to detachment as the interfacial area is separated instantaneously, while the peeling test is observed to exhibit the largest distance for detachment because it separates via line-by-line adhesion. Two kinds of polyimides, aromatic and aliphatic type, are considered to demonstrate the rigidity dependent adhesion properties. The aromatic polyimide, which is more rigid due to the stronger charge transfer complex between chains, requires a greater force but a smaller distance at detachment than the aliphatic polyimide for all of the three methodologies.

Center or periphery? Modeling the effects of focal adhesion placement during cell spreading

Focal adhesions are often observed at the cell’s periphery. We provide an explanation for this observation using a system-level mathematical model of a cell interacting with a two-dimensional substrate. The model describes the biological cell as a hypoelastic continuum material whose behavior is coupled to a deformable, linear elastic substrate via focal adhesions that are represented by collections of linear elastic attachments between the cell and the substrate. The evolution of the focal adhesions is coupled to local intracellular stresses which arise from mechanical cell-substrate interactions. Using this model we show that the cell has at least three mechanisms through which it can control its intracellular stresses: focal adhesion position, size, and attachment strength. We also propose that one reason why focal adhesions are typically located on the cell periphery instead of its center is because peripheral focal adhesions allow the cell to be more sensitive to changes in the microenvironment. This increased sensitivity is caused by the fact that peripherally located focal adhesions allow the cells to modulate its intracellular properties over a much larger portion of the cell area.

Influence of Substrate Thickness and Stiffness on Cell Behavior

It is known that various cell types can sense and respond to the mechanical properties of their microenvironment. Specifically, cells have been known to spread more when cultured on stiff substrates and are able to match their internal stiffness to that of the substrate. It has also been recently reported that even some cells are cultured on soft but thin coatings attached to stiff supports, they can perceive an effective stiffness that is much larger than that of the bulk coating. Building on earlier models [1,2], we present a model and invoke arguments based on energetics that explain why stiff and thin substrates encourage some cells to spread more easily and why these cells can match their internal stiffness to external stiffness more efficiently than others.Figure : Traction energy as a function of coating thickness for different cell stiffnessesReference:1. U. S. Schwarz et al, Biosystems, 83, 225 (2006).2. J. M. Maloney et al, Phys. Rev. E, 78, 041923 (2008).View Large Image | View Hi-Res Image | Download PowerPoint Slide