Protein-lipid interactions: correlation of a predictive algorithm for lipid-binding sites with three-dimensional structural data

BACKGROUND: Over the past decade our laboratory has focused on understanding how soluble cytoskeleton-associated proteins interact with membranes and other lipid aggregates. Many protein domains mediating specific cell membrane interactions appear by fluorescence microscopy and other precision techniques to be partially inserted into the lipid bilayer. It is unclear whether these protein-lipid-interactions are dependent on shared protein motifs or unique regional physiochemistry, or are due to more global characteristics of the protein. RESULTS: We have developed a novel computational program that predicts a protein's lipid-binding site(s) from primary sequence data. Hydrophobic labeling, Fourier transform infrared spectroscopy (FTIR), film balance, T-jump, CD spectroscopy and calorimetry experiments confirm that the interfaces predicted for several key cytoskeletal proteins (alpha-actinin, Arp2, CapZ, talin and vinculin) partially insert into lipid aggregates. The validity of these predictions is supported by an analysis of the available three-dimensional structural data. The lipid interfaces predicted by our algorithm generally contain energetically favorable secondary structures (e.g., an amphipathic alpha-helix flanked by a flexible hinge or loop region), are solvent-exposed in the intact protein, and possess favorable local or global electrostatic properties. CONCLUSION: At present, there are few reliable methods to determine the region of a protein that mediates biologically important interactions with lipids or lipid aggregates. Our matrix-based algorithm predicts lipid interaction sites that are consistent with the available biochemical and structural data. To determine whether these sites are indeed correctly identified, and whether use of the algorithm can be safely extended to other classes of proteins, will require further mapping of these sites, including genetic manipulation and/or targeted crystallography

Proteinase 3 associated with Wegener's granulomatosis

Abstract Wegener's granulomatosis (WG) is a form of systemic vasculitis characterized by granulomatous inflammation of the upper and lower airways, vasculitis, and necrotizing glomerulonephritis. It is strongly associated with anti‐neutrophil cytoplasmic antibodies against proteinase 3 (PR3‐ANCAs). Various in vitro observations provided strong evidence that autoimmune PR3‐ANCAs are directly involved in glomerular and vascular inflammation. However, little is known about the pathogenic significance of PR3‐ANCAs in vivo. Therefore, the generation of animal models helped to validate the suggested autoimmune origin and pathophysiology in WG. To characterize and improve the models, numerous studies were carried out to elucidate the effect of mouse/rat PR3‐ANCAs on neutrophil function as well as the role of CD4/CD8 in T and B cells and antibodies in the pathogenesis of the disease. Understanding the pathogenesis is therefore critical to relate these models to human studies hoping that they will be useful for better insight of WG and the development of specific therapies for the disease

Electron mean free path from angle-dependent photoelectron spectroscopy of aerosol particles

We propose angle-resolved photoelectron spectroscopy of aerosol particles as an alternative way to determine the electron mean free path of low energy electrons in solid and liquid materials. The mean free path is obtained from fits of simulated photoemission images to experimental ones over a broad range of different aerosol particle sizes. The principal advantage of the aerosol approach is twofold. Firstly, aerosol photoemission studies can be performed for many different materials, including liquids. Secondly, the size-dependent anisotropy of the photoelectrons can be exploited in addition to size-dependent changes in their kinetic energy. These finite size effects depend in different ways on the mean free path and thus provide more information on the mean free path than corresponding liquid jet, thin film, or bulk data. The present contribution is a proof of principle employing a simple model for the photoemission of electrons and preliminary experimental data for potassium chloride aerosol particles

Implications of troponin testing in clinical medicine

During the past decade considerable research has been conducted into the use of cardiac troponins, their diagnostic capability and their potential to allow risk stratification in patients with acute chest pain. Determination of risk in patients with suspected myocardial ischaemia is known to be as important as retrospective confirmation of a diagnosis of myocardial infarction (MI). Therefore, creatine kinase (CK)-MB - the former 'gold standard' in detecting myocardial necrosis - has been supplanted by new, more accurate biomarkers.Measurement of cardiac troponin levels constitute a substantial determinant in assessment of ischaemic heart disease, the presentations of which range from silent ischaemia to acute MI. Under these conditions, troponin release is regarded as surrogate marker of thrombus formation and peripheral embolization, and therefore new therapeutic strategies are focusing on potent antithrombotic regimens to improve long-term outcomes. Although elevated troponin levels are highly sensitive and specific indicators of myocardial damage, they are not always reflective of acute ischaemic coronary artery disease; other processes have been identified that cause elevations in these biomarkers. However, because prognosis appears to be related to the presence of troponins regardless of the mechanism of myocardial damage, clinicians increasingly rely on troponin assays when formulating individual therapeutic plans

Physical and Antibacterial Properties of Peppermint Essential Oil Loaded Poly (ε-caprolactone) (PCL) Electrospun Fiber Mats for Wound Healing

The aim of this study was to fabricate and characterize various concentrations of peppermint essential oil (PEP) loaded on poly(ε-caprolactone) (PCL) electrospun fiber mats for healing applications, where PEP was intended to impart antibacterial activity to the fibers. SEM images illustrated that the morphology of all electrospun fiber mats was smooth, uniform, and bead-free. The average fiber diameter was reduced by the addition of PEP from 1.6 ± 0.1 to 1.0 ± 0.2 μm. Functional groups of the fibers were determined by Raman spectroscopy. Gas chromatography-mass spectroscopy (GC-MS) analysis demonstrated the actual PEP content in the samples. In vitro degradation was determined by measuring weight loss and their morphology change, showing that the electrospun fibers slightly degraded by the addition of PEP. The wettability of PCL and PEP loaded electrospun fiber mats was measured by determining contact angle and it was shown that wettability increased with the incorporation of PEP. The antimicrobial activity results revealed that PEP loaded PCL electrospun fiber mats exhibited inhibition against Staphylococcus aureus (gram-positive) and Escherichia coli (gram-negative) bacteria. In addition, an in-vitro cell viability assay using normal human dermal fibroblast (NHDF) cells revealed improved cell viability on PCL, PCLPEP1.5, PCLPEP3, and PCLGEL6 electrospun fiber mats compared to the control (CNT) after 48 h cell culture. Our findings showed for the first time PEP loaded PCL electrospun fiber mats with antibiotic-free antibacterial activity as promising candidates for wound healing applications

Lifetime of d-holes at Cu surfaces: Theory and experiment

We have investigated the hole dynamics at copper surfaces by high-resolution angle-resolved photoemission experiments and many-body quasiparticle GW calculations. Large deviations from a free-electron-like picture are observed both in the magnitude and the energy dependence of the lifetimes, with a clear indication that holes exhibit longer lifetimes than electrons with the same excitation energy. Our calculations show that the small overlap of d- and sp-states below the Fermi level is responsible for the observed enhancement. Although there is qualitative good agreement of our theoretical predictions and the measured lifetimes, there still exist some discrepancies pointing to the need of a better description of the actual band structure of the solid.Comment: 15 pages, 7 figures, 1 table, to appear in Phys. Rev.

Deep Time-Delay Reservoir Computing: Dynamics and Memory Capacity

The Deep Time-Delay Reservoir Computing concept utilizes unidirectionally connected systems with time-delays for supervised learning. We present how the dynamical properties of a deep Ikeda-based reservoir are related to its memory capacity (MC) and how that can be used for optimization. In particular, we analyze bifurcations of the corresponding autonomous system and compute conditional Lyapunov exponents, which measure the generalized synchronization between the input and the layer dynamics. We show how the MC is related to the systems distance to bifurcations or magnitude of the conditional Lyapunov exponent. The interplay of different dynamical regimes leads to a adjustable distribution between linear and nonlinear MC. Furthermore, numerical simulations show resonances between clock cycle and delays of the layers in all degrees of the MC. Contrary to MC losses in a single-layer reservoirs, these resonances can boost separate degrees of the MC and can be used, e.g., to design a system with maximum linear MC. Accordingly, we present two configurations that empower either high nonlinear MC or long time linear MC

Biomembrane-mimicking lipid bilayer system as a mechanically tunable cell substrate

Cell behavior such as cell adhesion, spreading, and contraction critically depends on the elastic properties of the extracellular matrix. It is not known, however, how cells respond to viscoelastic or plastic material properties that more closely resemble the mechanical environment that cells encounter in the body. In this report, we employ viscoelastic and plastic biomembrane-mimicking cell substrates. The compliance of the substrates can be tuned by increasing the number of polymer-tethered bilayers. This leaves the density and conformation of adhesive ligands on the top bilayer unaltered. We then observe the response of fibroblasts to these property changes. For comparison, we also study the cells on soft polyacrylamide and hard glass surfaces. Cell morphology, motility, cell stiffness, contractile forces and adhesive contact size all decrease on more compliant matrices but are less sensitive to changes in matrix dissipative properties. These data suggest that cells are able to feel and respond predominantly to the effective matrix compliance, which arises as a combination of substrate and adhesive ligand mechanical properties

Wigner Crystalline Edges in nu < 1 Quantum Dots

We investigate the edge reconstruction phenomenon believed to occur in quantum dots in the quantum Hall regime when the filling fraction is nu < 1. Our approach involves the examination of large dots (< 40 electrons) using a partial diagonalization technique in which the occupancies of the deep interior orbitals are frozen. To interpret the results of this calculation, we evaluate the overlap between the diagonalized ground state and a set of trial wavefunctions which we call projected necklace (PN) states. A PN state is simply the angular momentum projection of a maximum density droplet surrounded by a ring of localized electrons. Our calculations reveal that PN states have up to 99% overlap with the diagonalized ground states, and are lower in energy than the states identified in Chamon and Wen's study of the edge reconstruction.Comment: 8 pages, 8 figures, to be published in Phys. Rev.