An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins

This is the published version. Copyright 2003 by Elsevier.Exploiting recent developments in generalized Born (GB) electrostatics theory, we have reformulated the calculation of the self-electrostatic solvation energy to account for the influence of biological membranes. Consistent with continuum Poisson-Boltzmann (PB) electrostatics, the membrane is approximated as an solvent-inaccessible infinite planar low-dielectric slab. The present membrane GB model closely reproduces the PB electrostatic solvation energy profile across the membrane. The nonpolar contribution to the solvation energy is taken to be proportional to the solvent-exposed surface area (SA) with a phenomenological surface tension coefficient. The proposed membrane GB/SA model requires minor modifications of the pre-existing GB model and appears to be quite efficient. By combining this implicit model for the solvent/bilayer environment with advanced computational sampling methods, like replica-exchange molecular dynamics, we are able to fold and assemble helical membrane peptides. We examine the reliability of this model and approach by applications to three membrane peptides: melittin from bee venom, the transmembrane domain of the M2 protein from Influenza A (M2-TMP), and the transmembrane domain of glycophorin A (GpA). In the context of these proteins, we explore the role of biological membranes (represented as a low-dielectric medium) in affecting the conformational changes in melittin, the tilt of transmembrane peptides with respect to the membrane normal (M2-TMP), helix-to-helix interactions in membranes (GpA), and the prediction of the configuration of transmembrane helical bundles (GpA). The present method is found to perform well in each of these cases and is anticipated to be useful in the study of folding and assembly of membrane proteins as well as in structure refinement and modeling of membrane proteins where a limited number of experimental observables are available

Implicit solvation based on generalized Born theory in different dielectric environments

Copyright 2004 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in The Journal of Chemical Physics and may be found at http://dx.doi.org/10.1063/1.1631258.In this paper we are investigating the effect of the dielectric environment on atomic Born radii used in generalized Born (GB) methods. Motivated by the Kirkwood expression for the reaction field of a single off-center charge in a spherical cavity, we are proposing extended formalisms for the calculation of Born radii as a function of external and internal dielectric constants. We demonstrate that reaction field energies calculated from environmentally dependent Born radii lead to much improved agreement with Poisson–Boltzmann solutions for low dielectric external environments, such as biological membranes or organic solvent, compared to previous methods where the calculation of Born radii does not depend on the environment. We also examine how this new approach can be applied for the calculation of transfer free energies from vacuum to a given external dielectric for a system with an internal dielectric larger than one. This has not been possible with standard GB theory but is relevant when scoring minimized or average structures with implicit solvent

Endogenous Nutritive Support after Traumatic Brain Injury: Peripheral Lactate Production for Glucose Supply via Gluconeogenesis.

We evaluated the hypothesis that nutritive needs of injured brains are supported by large and coordinated increases in lactate shuttling throughout the body. To that end, we used dual isotope tracer ([6,6-(2)H2]glucose, i.e., D2-glucose, and [3-(13)C]lactate) techniques involving central venous tracer infusion along with cerebral (arterial [art] and jugular bulb [JB]) blood sampling. Patients with traumatic brain injury (TBI) who had nonpenetrating head injuries (n=12, all male) were entered into the study after consent of patients' legal representatives. Written and informed consent was obtained from healthy controls (n=6, including one female). As in previous investigations, the cerebral metabolic rate (CMR) for glucose was suppressed after TBI. Near normal arterial glucose and lactate levels in patients studied 5.7±2.2 days (range of days 2-10) post-injury, however, belied a 71% increase in systemic lactate production, compared with control, that was largely cleared by greater (hepatic+renal) glucose production. After TBI, gluconeogenesis from lactate clearance accounted for 67.1% of glucose rate of appearance (Ra), which was compared with 15.2% in healthy controls. We conclude that elevations in blood glucose concentration after TBI result from a massive mobilization of lactate from corporeal glycogen reserves. This previously unrecognized mobilization of lactate subserves hepatic and renal gluconeogenesis. As such, a lactate shuttle mechanism indirectly makes substrate available for the body and its essential organs, including the brain, after trauma. In addition, when elevations in arterial lactate concentration occur after TBI, lactate shuttling may provide substrate directly to vital organs of the body, including the injured brain

Lactate: brain fuel in human traumatic brain injury: a comparison with normal healthy control subjects.

We evaluated the hypothesis that lactate shuttling helps support the nutritive needs of injured brains. To that end, we utilized dual isotope tracer [6,6-(2)H2]glucose, that is, D2-glucose, and [3-(13)C]lactate techniques involving arm vein tracer infusion along with simultaneous cerebral (arterial [art] and jugular bulb [JB]) blood sampling. Traumatic brain injury (TBI) patients with nonpenetrating brain injuries (n=12) were entered into the study following consent of patients' legal representatives. Written and informed consent was obtained from control volunteers (n=6). Patients were studied 5.7±2.2 (mean±SD) days post-injury; during periods when arterial glucose concentration tended to be higher in TBI patients. As in previous investigations, the cerebral metabolic rate for glucose (CMRgluc, i.e., net glucose uptake) was significantly suppressed following TBI (p<0.001). However, lactate fractional extraction, an index of cerebral lactate uptake related to systemic lactate supply, approximated 11% in both healthy control subjects and TBI patients. Further, neither the CMR for lactate (CMRlac, i.e., net lactate release), nor the tracer-measured cerebral lactate uptake differed between healthy controls and TBI patients. The percentages of lactate tracer taken up and released as (13)CO2 into the JB accounted for 92% and 91% for control and TBI conditions, respectively, suggesting that most cerebral lactate uptake was oxidized following TBI. Comparisons of isotopic enrichments of lactate oxidation from infused [3-(13)C]lactate tracer and (13)C-glucose produced during hepatic and renal gluconeogenesis (GNG) showed that 75-80% of (13)CO2 released into the JB was from lactate and that the remainder was from the oxidation of glucose secondarily labeled from lactate. Hence, either directly as lactate uptake, or indirectly via GNG, peripheral lactate production accounted for ∼70% of carbohydrate (direct lactate uptake+uptake of glucose from lactate) consumed by the injured brain. Undiminished cerebral lactate fractional extraction and uptake suggest that arterial lactate supplementation may be used to compensate for decreased CMRgluc following TBI

The Carina Nebula and Gum 31 molecular complex: II. The distribution of the atomic gas revealed in unprecedented detail

We report high spatial resolution observations of the HI 21cm line in the Carina Nebula and the Gum 31 region obtained with the Australia Telescope Compact Array. The observations covered $\sim$ 12 deg$^2$ centred on $l= 287.5\deg,b = -1\deg$, achieving an angular resolution of $\sim$ 35 arcseconds. The HI map revealed complex filamentary structures across a wide range of velocities. Several "bubbles" are clearly identified in the Carina Nebula Complex, produced by the impact of the massive star clusters located in this region. An HI absorption profile obtained towards the strong extragalactic radio source PMN J1032--5917 showed the distribution of the cold component of the atomic gas along the Galactic disk, with the Sagittarius-Carina and Perseus spiral arms clearly distinguishable. Preliminary calculations of the optical depth and spin temperatures of the cold atomic gas show that the HI line is opaque ($\tau \gtrsim$ 2) at several velocities in the Sagittarius-Carina spiral arm. The spin temperature is $\sim100$ K in the regions with the highest optical depth, although this value might be lower for the saturated components. The atomic mass budget of Gum 31 is $\sim35 \%$ of the total gas mass. HI self absorption features have molecular counterparts and good spatial correlation with the regions of cold dust as traced by the infrared maps. We suggest that in Gum 31 regions of cold temperature and high density are where the atomic to molecular gas phase transition is likely to be occurring.Comment: 20 pages, 1 table, 16 Figures, Accepted for Publication in the Monthly Notices of the Royal Astronomical Society Journa

Dehydration and ionic conductance quantization in nanopores

There has been tremendous experimental progress in the last decade in identifying the structure and function of biological pores (ion channels) and fabricating synthetic pores. Despite this progress, many questions still remain about the mechanisms and universal features of ionic transport in these systems. In this paper, we examine the use of nanopores to probe ion transport and to construct functional nanoscale devices. Specifically, we focus on the newly predicted phenomenon of quantized ionic conductance in nanopores as a function of the effective pore radius - a prediction that yields a particularly transparent way to probe the contribution of dehydration to ionic transport. We study the role of ionic species in the formation of hydration layers inside and outside of pores. We find that the ion type plays only a minor role in the radial positions of the predicted steps in the ion conductance. However, ions with higher valency form stronger hydration shells, and thus, provide even more pronounced, and therefore, more easily detected, drops in the ionic current. Measuring this phenomenon directly, or from the resulting noise, with synthetic nanopores would provide evidence of the deviation from macroscopic (continuum) dielectric behavior due to microscopic features at the nanoscale and may shed light on the behavior of ions in more complex biological channels.Comment: 13 pages, 10 figure

Electron Drift Velocities In Gas Mixtures Of He, N2, And CO 2

An electron swarm experiment has been used to obtain electron drift velocities in the He:CO2:N2 mixtures 0:1:1, 3:1:2, and 3:1:1. The E/N range of 3 to 57 Td was studied with total gas pressure varied from 50 to 200 Torr. These particular mixtures have not been previously studied experimentally. Good agreement is observed between theoretical calculations and experimental data