Quantitative Limits on Small Molecule Transport via the Electropermeome - Measuring and Modeling Single Nanosecond Perturbations

The detailed molecular mechanisms underlying the permeabilization of cell membranes by pulsed electric fields (electroporation) remain obscure despite decades of investigative effort. To advance beyond descriptive schematics to the development of robust, predictive models, empirical parameters in existing models must be replaced with physics- and biology-based terms anchored in experimental observations. We report here absolute values for the uptake of YO-PRO-1, a small-molecule fluorescent indicator of membrane integrity, into cells after a single electric pulse lasting only 6 ns. We correlate these measured values, based on fluorescence microphotometry of hundreds of individual cells, with a diffusion-based geometric analysis of pore-mediated transport and with molecular simulations of transport across electropores in a phospholipid bilayer. The results challenge the drift and diffusion through a pore model that dominates conventional explanatory schemes for the electroporative transfer of small molecules into cells and point to the necessity for a more complex model

Determination of biomembrane bending moduli in fully atomistic simulations.

The bilayer bending modulus (Kc) is one of the most important physical constants characterizing lipid membranes, but precisely measuring it is a challenge, both experimentally and computationally. Experimental measurements on chemically identical bilayers often differ depending upon the techniques employed, and robust simulation results have previously been limited to coarse-grained models (at varying levels of resolution). This Communication demonstrates the extraction of Kc from fully atomistic molecular dynamics simulations for three different single-component lipid bilayers (DPPC, DOPC, and DOPE). The results agree quantitatively with experiments that measure thermal shape fluctuations in giant unilamellar vesicles. Lipid tilt, twist, and compression moduli are also reported

Laboratory-Reported Normal Value Ranges Should Not Be Used to Diagnose Periprosthetic Joint Infection.

INTRODUCTION: Clinical laboratories offer several multipurpose tests, such as the erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP), which are not intended to diagnose any specific disease but are used by clinicians in multiple fields. The results and laboratory interpretation (normal/abnormal) of these multipurpose tests are based on laboratory-reported normal thresholds, which vary across clinical laboratories. In 2018, the International Consensus Meeting on Musculoskeletal Infection (2018 ICM) provided a gold-standard definition to diagnose periprosthetic joint infection (PJI) which included many multipurpose laboratory tests, along with thresholds optimized to diagnose PJI. The discrepancy between laboratory-reported normal thresholds and 2018 ICM-recommended PJI-optimized test thresholds has never been studied. The purpose of this study was to assess the existing variation in laboratory-reported normal thresholds for tests commonly used to diagnose PJI and evaluate the potential diagnostic impact of using laboratory-reported normal thresholds instead of 2018 ICM-recommended PJI-optimized thresholds. METHODS: Clinical laboratories (N=85) were surveyed to determine the laboratory-reported units of measure and normal thresholds for common multipurpose tests to diagnose PJI, including the ESR, CRP, D-dimer, synovial fluid white blood cells (SF-WBC), and polymorphonuclear cell percent (SF-PMN%). The variability of units of measure and normal thresholds for each test was then assessed among the 85 included clinical laboratories. A representative dataset from patients awaiting a revision arthroplasty was used to determine the clinical significance of the existing discrepancy between laboratory-reported normal test interpretations and 2018 ICM-recommended PJI-optimized test interpretations. RESULTS: Two units of measure for the CRP and six units of measure for the D-dimer were observed, with only 59% of laboratories reporting the CRP in terms of mg/L and only 16% reporting the D-dimer in ng/ml, as needed to utilize the 2018 ICM definition of PJI. Across clinical laboratories surveyed, the mean laboratory-reported normal thresholds for the ESR (20 mm/h), CRP (7.69 mg/L), D-dimer (500 ng/mL), SF-WBC (5 cells/uL), and SF-PMN% (25%) were substantially lower than the 2018 ICM-recommended PJI-optimized thresholds of 30 mm/h, 10 mg/L, 860 ng/mL, 3,000 cells/uL, and 70%, respectively. Interpretation of test results from a representative PJI dataset using each laboratory\u27s normal test thresholds yielded mean false-positive rates of 14% (ESR), 18% (CRP), 42% (D-dimer), 93% (SF-WBC), and 36% (SF-PMN%) versus the ICM-recommended PJI-optimized thresholds. CONCLUSION: When reporting the results for multipurpose laboratory tests, such as the ESR, CRP, D-dimer, SF-WBC, and SF-PMN%, clinical laboratories utilize laboratory-reported units of measure and normal thresholds that are not intended to diagnose PJI, and therefore may not match the 2018 ICM recommendations. Our findings reveal that laboratory-reported normal thresholds for these multipurpose tests are well below the 2018 ICM recommendations to diagnose PJI. Clinical reliance on laboratory-reported results and interpretations, instead of strict use of the 2018 ICM-recommended units and PJI-optimized thresholds, may lead to false-positive interpretation of multipurpose laboratory tests

The October 2014 United States treasury bond flash crash and the contributory effect of mini flash crashes

We investigate the causal uncertainty surrounding the flash crash in the U.S. Treasury bond market on October 15, 2014, and the unresolved concern that no clear link has been identified between the start of the flash crash at 9:33 and the opening of the U.S. equity market at 9:30. We consider the contributory effect of mini flash crashes in equity markets, and find that the number of equity mini flash crashes in the three-minute window between market open and the Treasury Flash Crash was 2.6 times larger than the number experienced in any other three-minute window in the prior ten weekdays. We argue that (a) this statistically significant finding suggests that mini flash crashes in equity markets both predicted and contributed to the October 2014 U.S. Treasury Bond Flash Crash, and (b) mini-flash crashes are important phenomena with negative externalities that deserve much greater scholarly attention

Analyses of protein cores reveal fundamental differences between solution and crystal structures

There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality protein structures solved by both methods. We also find significant differences between NMR and crystal structures---in the root-mean-square deviations of the C$_{\alpha}$ atomic positions, identities of core amino acids, backbone and sidechain dihedral angles, and packing fraction of core residues. In contrast to prior studies, we identify the physical basis for these differences by modelling protein cores as jammed packings of amino-acid-shaped particles. We find that we can tune the jammed packing fraction by varying the degree of thermalization used to generate the packings. For an athermal protocol, we find that the average jammed packing fraction is identical to that observed in the cores of protein structures solved by x-ray crystallography. In contrast, highly thermalized packing-generation protocols yield jammed packing fractions that are even higher than those observed in NMR structures. These results indicate that thermalized systems can pack more densely than athermal systems, which suggests a physical basis for the structural differences between protein structures solved by NMR and x-ray crystallography.Comment: 9 pages, 4 figure

Using physical features of protein core packing to distinguish real proteins from decoys

The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a real protein. For example, it has long been appreciated that the hydrophobic cores of proteins contribute significantly to their stability. As a dataset of decoys to compare with real protein structures, we studied submissions to the bi-annual CASP competition (specifically CASP11, 12, and 13), in which researchers attempt to predict the structure of a protein only knowing its amino acid sequence. Our analysis reveals that many of the submissions possess cores that do not recapitulate the features that define real proteins. In particular, the model structures appear more densely packed (because of energetically unfavorable atomic overlaps), contain too few residues in the core, and have improper distributions of hydrophobic residues throughout the structure. Based on these observations, we developed a deep learning method, which incorporates key physical features of protein cores, to predict how well a computational model recapitulates the real protein structure without knowledge of the structure of the target sequence. By identifying the important features of protein structure, our method is able to rank decoys from the CASP competitions equally well, if not better than, state-of-the-art methods that incorporate many additional features.Comment: 7 pages, 5 figure

Picosecond to Terahertz Perturbation of Interfacial Water and Electropermeabilization of Biological Membranes

Non-thermal probing and stimulation with subnanosecond electric pulses and terahertz electromagnetic radiation may lead to new, minimally invasive diagnostic and therapeutic procedures and to methods for remote monitoring and analysis of biological systems, including plants, animals, and humans. To effectively engineer these still-emerging tools, we need an understanding of the biophysical mechanisms underlying the responses that have been reported to these novel stimuli. We show here that subnanosecond (≤500 ps) electric pulses induce action potentials in neurons and cause calcium transients in neuroblastoma-glioma hybrid cells, and we report complementary molecular dynamics simulations of phospholipid bilayers in electric fields in which membrane permeabilization occurs in less than 1 ns. Water dipoles in the interior of these model membranes respond in less than 1 ps to permeabilizing electric potentials by aligning in the direction of the field, and they re-orient at terahertz frequencies to field reversals. The mechanism for subnanosecond lipid electropore formation is similar to that observed on longer time scales-energy-minimizing intrusions of interfacial water into the membrane interior and subsequent reorganization of the bilayer into hydrophilic, conductive structures

Electric Field-Driven Water Dipoles: Nanoscale Architecture of Electroporation

<div><p>Electroporation is the formation of permeabilizing structures in the cell membrane under the influence of an externally imposed electric field. The resulting increased permeability of the membrane enables a wide range of biological applications, including the delivery of normally excluded substances into cells. While electroporation is used extensively in biology, biotechnology, and medicine, its molecular mechanism is not well understood. This lack of knowledge limits the ability to control and fine-tune the process. In this article we propose a novel molecular mechanism for the electroporation of a lipid bilayer based on energetics analysis. Using molecular dynamics simulations we demonstrate that pore formation is driven by the reorganization of the interfacial water molecules. Our energetics analysis and comparisons of simulations with and without the lipid bilayer show that the process of poration is driven by field-induced reorganization of water dipoles at the water-lipid or water-vacuum interfaces into more energetically favorable configurations, with their molecular dipoles oriented in the external field. Although the contributing role of water in electroporation has been noted previously, here we propose that interfacial water molecules are the main players in the process, its initiators and drivers. The role of the lipid layer, to a first-order approximation, is then reduced to a relatively passive barrier. This new view of electroporation simplifies the study of the problem, and opens up new opportunities in both theoretical modeling of the process and experimental research to better control or to use it in new, innovative ways.</p></div