Defining the Structural Consequences of Mechanism-Based Inactivation of Mammalian Cytochrome P450 2B4 Using Resonance Raman Spectroscopy

In view of the potent oxidizing strength of cytochrome P450 intermediates, it is not surprising that certain substrates can give rise to reactive species capable of attacking the heme or critical distal-pocket protein residues to irreversibly modify the enzyme in a process known as mechanism-based (MB) inactivation, a result that can have serious physiological consequences leading to adverse drug−drug interactions and toxicity. While methods exist to document the attachment of these substrate fragments, it is more difficult to gain insight into the structural basis for the altered functional properties of these modified enzymes. In response to this pressing need to better understand MB inhibition, we here report the first application of resonance Raman spectroscopy to study the inactivation of a truncated form of mammalian CYP2B4 by the acetylenic inhibitor 4-(tert-butyl)phenylacetylene, whose activated form is known to attach to the distal-pocket T302 residue of CYP2B4

Basic linear algebra subprograms for FORTRAN usage

A package of 38 low level subprograms for many of the basic operations of numerical linear algebra is presented. The package is intended to be used with FORTRAN. The operations in the package are dot products, elementary vector operations, Givens transformations, vector copy and swap, vector norms, vector scaling, and the indices of components of largest magnitude. The subprograms and a test driver are available in portable FORTRAN. Versions of the subprograms are also provided in assembly language for the IBM 360/67, the CDC 6600 and CDC 7600, and the Univac 1108

Phase behavior of a system of particles with core collapse

The pressure-temperature phase diagram of a one-component system, with particles interacting through a spherically symmetric pair potential in two dimensions is studied. The interaction consists of a hard core plus an additional repulsion at low energies. It is shown that at zero temperature, instead of the expected isostructural transition due to core collapse occurring when increasing pressure, the system passes through a series of ground states that are not triangular lattices. In particular, and depending on parameters, structures with squares, chains, hexagons and even quasicrystalline ground states are found. At finite temperatures the solid-fluid coexistence line presents a zone with negative slope (which implies melting with decreasing in volume) and the fluid phase has a temperature of maximum density, similar to that in water.Comment: 11 pages, 15 figures included. To appear in PRE. Some figures in low quality format. Better ones available upon request from [email protected]

Theorem on the Distribution of Short-Time Particle Displacements with Physical Applications

The distribution of the initial short-time displacements of particles is considered for a class of classical systems under rather general conditions on the dynamics and with Gaussian initial velocity distributions, while the positions could have an arbitrary distribution. This class of systems contains canonical equilibrium of a Hamiltonian system as a special case. We prove that for this class of systems the nth order cumulants of the initial short-time displacements behave as the 2n-th power of time for all n>2, rather than exhibiting an nth power scaling. This has direct applications to the initial short-time behavior of the Van Hove self-correlation function, to its non-equilibrium generalizations the Green's functions for mass transport, and to the non-Gaussian parameters used in supercooled liquids and glasses.Comment: A less ambiguous mathematical notation for cumulants was adopted and several passages were reformulated and clarified. 40 pages, 1 figure. Accepted by J. Stat. Phy

Extracting the time-dependent transmission rate from infection data via solution of an inverse ODE problem

The transmission rate of many acute infectious diseases varies significantly in time, but the underlying mechanisms are usually uncertain. They may include seasonal changes in the environment, contact rate, immune system response, etc. The transmission rate has been thought difficult to measure directly. We present a new algorithm to compute the time-dependent transmission rate directly from prevalence data, which makes no assumptions about the number of susceptible or vital rates. The algorithm follows our complete and explicit solution of a mathematical inverse problem for SIR-type transmission models. We prove that almost any infection profile can be perfectly fitted by an SIR model with variable transmission rate. This clearly shows a serious danger of overfitting such transmission models. We illustrate the algorithm with historic UK measles data and our observations support the common belief that measles transmission was predominantly driven by school contacts

The Explanatory Value of Abstracting Away from Idiosyncratic and Messy Detail

Some explanations are relatively abstract: they abstract away from the idiosyncratic or messy details of the case in hand. The received wisdom in philosophy is that this is a virtue for any explanation to possess. I argue that the apparent consensus on this point is illusory. When philosophers make this claim, they differ on which of four alternative varieties of abstractness they have in mind. What's more, for each variety of abstractness there are several alternative reasons to think that the variety of abstractness in question is a virtue. I identify the most promising reasons, and dismiss some others. The paper concludes by relating this discussion to the idea that explanations in biology, psychology and social science cannot be replaced by relatively micro explanations without loss of understanding.This work has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant agreement no 284123.This is the author accepted manuscript. The final version is available from Springer via http://dx.doi.org/10.1007/s11098-015-0554-

Metastable liquid-liquid phase transition in a single-component system with only one crystal phase and no density anomaly

We investigate the phase behavior of a single-component system in 3 dimensions with spherically-symmetric, pairwise-additive, soft-core interactions with an attractive well at a long distance, a repulsive soft-core shoulder at an intermediate distance, and a hard-core repulsion at a short distance, similar to potentials used to describe liquid systems such as colloids, protein solutions, or liquid metals. We showed [Nature {\bf 409}, 692 (2001)] that, even with no evidences of the density anomaly, the phase diagram has two first-order fluid-fluid phase transitions, one ending in a gas--low-density liquid (LDL) critical point, and the other in a gas--high-density liquid (HDL) critical point, with a LDL-HDL phase transition at low temperatures. Here we use integral equation calculations to explore the 3-parameter space of the soft-core potential and we perform molecular dynamics simulations in the interesting region of parameters. For the equilibrium phase diagram we analyze the structure of the crystal phase and find that, within the considered range of densities, the structure is independent of the density. Then, we analyze in detail the fluid metastable phases and, by explicit thermodynamic calculation in the supercooled phase, we show the absence of the density anomaly. We suggest that this absence is related to the presence of only one stable crystal structure.Comment: 15 pages, 21 figure

Liquid State Anomalies for the Stell-Hemmer Core-Softened Potential

We study the Stell-Hemmer potential using both analytic (exact $1d$ and approximate $2d$) solutions and numerical $2d$ simulations. We observe in the liquid phase an anomalous decrease in specific volume and isothermal compressibility upon heating, and an anomalous increase in the diffusion coefficient with pressure. We relate the anomalies to the existence of two different local structures in the liquid phase. Our results are consistent with the possibility of a low temperature/high pressure liquid-liquid phase transition.Comment: 4 pages in one gzipped ps file including 11 figures; One RevTex and 11 gzipped eps figure

Stable Propagation of a Burst Through a One-Dimensional Homogeneous Excitatory Chain Model of Songbird Nucleus HVC

We demonstrate numerically that a brief burst consisting of two to six spikes can propagate in a stable manner through a one-dimensional homogeneous feedforward chain of non-bursting neurons with excitatory synaptic connections. Our results are obtained for two kinds of neuronal models, leaky integrate-and-fire (LIF) neurons and Hodgkin-Huxley (HH) neurons with five conductances. Over a range of parameters such as the maximum synaptic conductance, both kinds of chains are found to have multiple attractors of propagating bursts, with each attractor being distinguished by the number of spikes and total duration of the propagating burst. These results make plausible the hypothesis that sparse precisely-timed sequential bursts observed in projection neurons of nucleus HVC of a singing zebra finch are intrinsic and causally related.Comment: 13 pages, 6 figure

Folding transitions of the triangular lattice with defects

A recently introduced model describing the folding of the triangular lattice is generalized allowing for defects in the lattice and written as an Ising model with nearest-neighbor and plaquette interactions on the honeycomb lattice. Its phase diagram is determined in the hexagon approximation of the cluster variation method and the crossover from the pure Ising to the pure folding model is investigated, obtaining a quite rich structure with several multicritical points. Our results are in very good agreement with the available exact ones and extend a previous transfer matrix study.Comment: 16 pages, latex, 5 postscript figure