Proton network flexibility enables robustness and large electric fields in the ketosteroid isomerase active site

Hydrogen bond networks play vital roles in biological functions ranging from protein folding to enzyme catalysis. Here we combine electronic structure calculations and ab initio path integral molecular dynamics simulations, which incorporate both nuclear and electronic quantum effects, to show why the network of short hydrogen bonds in the active site of ketosteroid isomerase is remarkably robust to mutations along the network and how this gives rise to large local electric fields. We demonstrate that these properties arise from the network's ability to respond to a perturbation by shifting proton positions and redistributing electronic charge density. This flexibility leads to small changes in properties such as the partial ionization of residues and $pK_a$ isotope effects upon mutation of the residues, consistent with recent experiments. This proton flexibility is further enhanced when an extended hydrogen bond network forms in the presence of an intermediate analog, which allows us to explain the chemical origins of the large electric fields in the enzyme's active site observed in recent experiments.Comment: 13 pages, 10 figures (7 main text and 3 SI

Doping driven structural distortion in the bilayer iridate (Sr1−x_{1-x}Lax_x)3_3Ir2_2O7_7

Neutron single crystal diffraction and rotational anisotropy optical second harmonic generation data are presented resolving the nature of the structural distortion realized in electron-doped (Sr$_{1-x}$La$_x$)$_3$Ir$_2$O$_7$ with $x=0.035$ and $x=0.071$. Once electrons are introduced into the bilayer spin-orbit assisted Mott insulator Sr$_3$Ir$_2$O$_7$, previous studies have identified the appearance of a low temperature structural distortion and have suggested the presence of a competing electronic instability in the phase diagram of this material. Our measurements resolve a lowering of the structural symmetry from monoclinic $C2/c$ to monoclinic $P2_1/c$ and the creation of two unique Ir sites within the chemical unit cell as the lattice distorts below a critical temperature $T_S$. Details regarding the modifications to oxygen octahedral rotations and tilting through the transition are discussed as well as the evolution of the low temperature distorted lattice as a function of carrier substitution.Comment: 8 pages, 4 figure

Clustering through post inhibitory rebound in synaptically coupled neurons

Post inhibitory rebound is a nonlinear phenomenon present in a variety of nerve cells. Following a period of hyper-polarization this effect allows a neuron to fire a spike or packet of spikes before returning to rest. It is an important mechanism underlying central pattern generation for heartbeat, swimming and other motor patterns in many neuronal systems. In this paper we consider how networks of neurons, which do not intrinsically oscillate, may make use of inhibitory synaptic connections to generate large scale coherent rhythms in the form of cluster states. We distinguish between two cases i) where the rebound mechanism is due to anode break excitation and ii) where rebound is due to a slow T-type calcium current. In the former case we use a geometric analysis of a McKean type model to obtain expressions for the number of clusters in terms of the speed and strength of synaptic coupling. Results are found to be in good qualitative agreement with numerical simulations of the more detailed Hodgkin-Huxley model. In the second case we consider a particular firing rate model of a neuron with a slow calcium current that admits to an exact analysis. Once again existence regions for cluster states are explicitly calculated. Both mechanisms are shown to prefer globally synchronous states for slow synapses as long as the strength of coupling is sufficiently large. With a decrease in the duration of synaptic inhibition both systems are found to break into clusters. A major difference between the two mechanisms for cluster generation is that anode break excitation can support clusters with several groups, whilst slow T-type calcium currents predominantly give rise to clusters of just two (anti-synchronous) populations