Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants

We present a framework for computing the gating properties of ligand-gated ion channel mutants using the Monod-Wyman-Changeux (MWC) model of allostery. We derive simple analytic formulas for key functional properties such as the leakiness, dynamic range, half-maximal effective concentration, and effective Hill coefficient, and explore the full spectrum of phenotypes that are accessible through mutations. Specifically, we consider mutations in the channel pore of nicotinic acetylcholine receptor (nAChR) and the ligand binding domain of a cyclic nucleotide-gated (CNG) ion channel, demonstrating how each mutation can be characterized as only affecting a subset of the biophysical parameters. In addition, we show how the unifying perspective offered by the MWC model allows us, perhaps surprisingly, to collapse the plethora of dose-response data from different classes of ion channels into a universal family of curves

Quasicontinuum representations of atomic-scale mechanics: From proteins to dislocations

Computation is one of the centerpieces of both the physical and biological sciences. A key thrust in computational science is the explicit mechanistic simulation of the spatiotemporal evolution of materials ranging from macromolecules to intermetallic alloys. However, our ability to simulate such systems is in the end always limited in both the spatial extent of the systems that are considered, as well as the duration of the time that can be simulated. As a result, a variety of efforts have been put forth that aim to finesse these challenges in both space and time through new techniques in which constraint is exploited to reduce the overall computational burden. The aim of this review is to describe in general terms some of the key ideas that have been set forth in both the materials and biological setting and to speculate on future developments along these lines. We begin by developing general ideas on the exploitation of constraint as a systematic tool for degree of freedom thinning. These ideas are then applied to case studies ranging from the plastic deformation of solids to the interactions of proteins and DNA

Bacteria are Stressed Out Too: The Physics of Mechanosensation

Many of the ways that cells talk and listen to the external world center on the presence of proteins on the cell surface. Indeed, the cell membrane is an amazingly diverse lipid environment, riddled in turn with a host of different proteins that perform tasks ranging from sensing and measuring chemical signals to the transport of sugars needed for cell division to the detection of potentially lethal osmotic pressures. This talk will focus on recent progress in the dissection of the mechanisms of mechanosensation in bacteria with special reference to the rich interplay between certain classes of ion channels and the surrounding lipids. Using simple arguments from elasticity theory, I will describe the membrane deformation footprint surrounding ion channels and how this deformation footprint contributes to the free energy of channel gating. In turn, I will show how these ideas can be parlayed into an experimental strategy for better understanding mechanosensation by watching individual cells as they are subjected to controlled levels of osmotic shock

Combinatorial Control through Allostery

Many instances of cellular signaling and transcriptional regulation involve switch-like molecular responses to the presence or absence of input ligands. To understand how these responses come about and how they can be harnessed, we develop a statistical mechanical model to characterize the types of Boolean logic that can arise from allosteric molecules following the Monod-Wyman-Changeux (MWC) model. Building upon previous work, we show how an allosteric molecule regulated by two inputs can elicit AND, OR, NAND and NOR responses, but is unable to realize XOR or XNOR gates. Next, we demonstrate the ability of an MWC molecule to perform ratiometric sensing - a response behavior where activity depends monotonically on the ratio of ligand concentrations. We then extend our analysis to more general schemes of combinatorial control involving either additional binding sites for the two ligands or an additional third ligand and show how these additions can cause a switch in the logic behavior of the molecule. Overall, our results demonstrate the wide variety of control schemes that biological systems can implement using simple mechanisms

Modelling diffusion in crystals under high internal stress gradients

Diffusion of vacancies and impurities in metals is important in many processes occurring in structural materials. This diffusion often takes place in the presence of spatially rapidly varying stresses. Diffusion under stress is frequently modelled by local approximations to the vacancy formation and diffusion activation enthalpies which are linear in the stress, in order to account for its dependence on the local stress state and its gradient. Here, more accurate local approximations to the vacancy formation and diffusion activation enthalpies, and the simulation methods needed to implement them, are introduced. The accuracy of both these approximations and the linear approximations are assessed via comparison to full atomistic studies for the problem of vacancies around a Lomer dislocation in Aluminium. Results show that the local and linear approximations for the vacancy formation enthalpy and diffusion activation enthalpy are accurate to within 0.05 eV outside a radius of about 13 Å (local) and 17 Å (linear) from the centre of the dislocation core or, more generally, for a strain gradient of roughly up to 6 × 10^6 m^-1 and 3 × 10^6 m^-1, respectively. These results provide a basis for the development of multiscale models of diffusion under highly non-uniform stress