Annular anionic lipids stabilize the integrin αIIbβ3 transmembrane complex

Cationic membrane-proximal amino acids determine the topology of membrane proteins by interacting with anionic lipids that are restricted to the intracellular membrane leaflet. This mechanism implies that anionic lipids interfere with electrostatic interactions of membrane proteins. The integrin αIIbβ3 transmembrane (TM) complex is stabilized by a membrane-proximal αIIb(Arg(995))-β3(Asp(723)) interaction; here, we examine the influence of anionic lipids on this complex. Anionic lipids compete for αIIb(Arg(995)) contacts with β3(Asp(723)) but paradoxically do not diminish the contribution of αIIb(Arg(995))-β3(Asp(723)) to TM complex stability. Overall, anionic lipids in annular positions stabilize the αIIbβ3 TM complex by up to 0.50 ± 0.02 kcal/mol relative to zwitterionic lipids in a headgroup structure-dependent manner. Comparatively, integrin receptor activation requires TM complex destabilization of 1.5 ± 0.2 kcal/mol, revealing a sizeable influence of lipid composition on TM complex stability. We implicate changes in lipid headgroup accessibility to small molecules (physical membrane characteristics) and specific but dynamic protein-lipid contacts in this TM helix-helix stabilization. Thus, anionic lipids in ubiquitous annular positions can benefit the stability of membrane proteins while leaving membrane-proximal electrostatic interactions intact.

Insight into α-synuclein plasticity and misfolding from differential micelle binding

Misfolded species of the 140-residue protein α-synuclein (αS) are implicated in the demise of dopaminergic neurons, resulting in fatal neurodegeneration. The intrinsically unstructured protein binds curved synaptic vesicle membranes in helical conformations but misfolds into amyloid fibrils via β-sheet interactions. Breaks in helical αS conformation may offer a pathway to transition from helical to sheet conformation. Here, we explore the evolution of broken αS helix conformations formed in complex with SDS and SLAS micelles by molecular dynamics simulations. The population distribution of experimentally observed αS conformations is related to the spatial concentration of intrinsic micelle shape perturbations. For the success of micelle-induced αS folding, we posit the length of the first helical segment formed, which controls micelle ellipticity, to be a key determinant. The degree of micelle curvature relates to the arrangement and segmental motions of helical secondary structure elements. A criterion for assessing the reproduction of such intermediate time scale protein dynamics is introduced by comparing the sampling of experimental and simulated spin label distributions. Finally, at the sites of breaks in the elongated, marginally stable αS helix, vulnerability to forming a transient, intramolecular β-sheet is identified. Upon subsequent intermolecular β-sheet pairing, pathological αS amyloid formation from initial helical conformation is thus achievable.

Construction of covalent membrane protein complexes and high-throughput selection of membrane mimics

The association of transmembrane (TM) helices underlies membrane protein structure and folding. Structural studies of TM complexes are limited by complex stability and the often time-consuming selection of suitable membrane mimics. Here, methodology for the efficient, preparative scale construction of covalent TM complexes and the concomitant high-throughput selection of membrane mimics is introduced. For the employed integrin αIIbβ3 model system, the methodology identified phospholipid bicelles, including their specific composition, as the best membrane mimic. The method facilitates structure determination by NMR spectroscopy as exemplified by the measurement of previously inaccessible residual dipolar couplings and (15)N relaxation parameters.

Human immunodeficiency virus in injecting drug users in Europe following a reported increase of cases in Greece and Romania, 2011

Greece and Romania reported an increased number of HIV cases among injecting drug users (IDUs) during 2011. Most European countries reported no changes in the rate of newly diagnosed cases of HIV or HIV prevalence in IDUs; however, six countries did report increases and several additional countries reported increases in injecting risk indicators or low coverage of prevention services. These indicate a potential risk for increased HIV transmission and future outbreaks unless adequate prevention is implemented.

Human immunodeficiency virus in injecting drug users in Europe following a reported increase of cases in Greece and Romania, 2011

Greece and Romania reported an increased number of HIV cases among injecting drug users (IDUs) during 2011. Most European countries reported no changes in the rate of newly diagnosed cases of HIV or HIV prevalence in IDUs; however, six countries did report increases and several additional countries reported increases in injecting risk indicators or low coverage of prevention services. These indicate a potential risk for increased HIV transmission and future outbreaks unless adequate prevention is implemented.

The clustering and spatial arrangement of beta-sheet sequence, but not order, govern alpha-synuclein fibrillogenesis

The intrinsically unstructured protein alpha-synuclein (aS) is prone to misfold into cytotoxic beta-sheet-rich oligomers and amyloid fibrils that underlie the pathogenesis of Lewy body diseases such as Parkinson's disease. An important, recognized fibrillogenesis parameter is amino acid content, whereas the influence of amino acid sequence distribution is not as well understood. The fibril core of aS encompasses five regions of high beta-sheet propensity, termed beta1-beta5. Using four aS variants with identical amino acid compositions but rearranged pseudorepeat motifs, we show that beta2-beta5 sequence clustering, but not order, is important for efficient fibrillogenesis. For molecular species progressing toward the fibrillar state, order invariably increases; i.e., the spatial arrangement of sequence elements becomes restricted. By introducing disulfide bonds in a fibril structure-based manner, we demonstrated that a successful protofibril-to-fibril conversion is dependent upon the spatial arrangement of sequence elements of high beta-sheet propensity. Moreover, a disulfide-linked aS dimer is shown to fibrillize rapidly. We propose that a conformational search underlies the emergence of a fibrillar aS nucleus that is directed by gaps in sequence between beta-sheet regions and the accessible range of spatial beta-sheet arrangements in soluble, prefibrillar oligomers. On the basis of the universal cross-beta-sheet structure of amyloid fibrils, these principles are expected to apply to a wide range of amyloidogenic proteins.

Antiviral compounds discovered by virtual screening of small-molecule libraries against dengue virus E protein

Infection by the mosquito-borne dengue virus causes dengue fever and the sometimes fatal dengue hemorrhagic fever. The increasing number of dengue infections per year suggests that the virus is becoming more virulent and its transmission is expanding. Nevertheless, no effective treatment for dengue infection currently exists. In a search for antiviral agents effective against dengue virus, we investigated the potential of targeting a structural protein site rather than an enzymatic one. Using this approach, we now report the discovery of a small molecule ligand that inhibits viral growth. Our results also provide the first evidence that the binding site, a pocket located at the hinge between domains 1 and 2 of the envelope protein (E protein) on the virus surface, is a valid target for antiviral therapy. Ligand candidates were identified from libraries of approximately 142,000 compounds using a computational high-throughput screening protocol targeting this pocket of the E protein. Cell-based assays were conducted on 23 top-ranked compounds. Among four with good antiviral activity profiles, the compound P02 was found to inhibit viral reproduction at micromolar concentrations. Using saturation transfer difference NMR spectroscopy, we also show that the compound binds virus and competes for binding E protein with the known ligand N-octyl-beta-D-glucoside. Together, the results are consistent with an inhibition mechanism against maturation or host-cell entry mediated by ligand binding to the E-protein pocket. P02 is a promising lead compound for future development of an effective treatment against dengue virus and related flaviviruses.

Mapping the future dynamics of disease transmission: risk analysis in the United Kingdom Foresight Programme on the detection and identification of infectious diseases

This paper reflects on the qualitative risk analysis framework developed for a Foresight study on the Detection and Identification of Infectious Diseases, which was coordinated in 2005 by the United Kingdom (UK) under what is now the Government Office for Science, Department for Innovation, Universities and Skills. The risk assessment covered human, plant and animal diseases in the UK and Africa in the years 2015 and 2030. Through engaging a diverse pool of experts, we developed a model conceptualising disease spread as the outcome of interactions among sources, pathways and drivers. We then used this model to conduct a Delphi survey of experts. The factors perceived most likely to contribute to infectious disease spread in 2015 and 2030 included geographic extension of existing pathogens (partially due to climate change), over-use of antibiotics/antivirals/pesticides leading to drug resistance, and zoonoses. Our methodology provides a framework for those who need to integrate a wide range of perspectives and factors into their planning and analyses.

Solution conformation of alphaA-conotoxin EIVA, a potent neuromuscular nicotinic acetylcholine receptor antagonist from Conus ermineus

We report the solution three-dimensional structure of an alphaA-conotoxin EIVA determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. The alphaA-conotoxin EIVA consists of 30 amino acids representing the largest peptide among the alpha/alphaA-family conotoxins discovered so far and targets the neuromuscular nicotinic acetylcholine receptor with high affinity. alphaA-Conotoxin EIVA consists of three distinct structural domains. The first domain is mainly composed of the Cys3-Cys11-disulfide loop and is structurally ill-defined with a large backbone root mean square deviation of 1.91 A. The second domain formed by residues His12-Hyp21 is extremely well defined with a backbone root mean square deviation of 0.52 A, thus forming a sturdy stem for the entire molecule. The third C-terminal domain formed by residues Hyp22-Gly29 shows an intermediate structural order having a backbone root mean square deviation of 1.04 A. A structurally ill-defined N-terminal first loop domain connected to a rigid central molecular stem seems to be the general structural feature of the alphaA-conotoxin subfamily. A detailed structural comparison between alphaA-conotoxin EIVA and alphaA-conotoxin PIVA suggests that the higher receptor affinity of alphaA-conotoxin EIVA than alphaA-conotoxin PIVA might originate from different steric disposition and charge distribution in the second loop "handle" motif.

Solution conformation of alpha-conotoxin EI, a neuromuscular toxin specific for the alpha 1/delta subunit interface of torpedo nicotinic acetylcholine receptor

A high resolution structure of alpha-conotoxin EI has been determined by (1)H NMR spectroscopy and molecular modeling. alpha-Conotoxin EI has the same disulfide framework as alpha 4/7 conotoxins targeting neuronal nicotinic acetylcholine receptors but antagonizes the neuromuscular receptor as do the alpha 3/5 and alpha A conotoxins. The unique binding preference of alpha-conotoxin EI to the alpha(1)/delta subunit interface of Torpedo neuromuscular receptor makes it a valuable structural template for superposition of various alpha-conotoxins possessing distinct receptor subtype specificities. Structural comparison of alpha-conotoxin EI with the gamma-subunit favoring alpha-conotoxin GI suggests that the Torpedo delta-subunit preference of the former originates from its second loop. Superposition of three-dimensional structures of seven alpha-conotoxins reveals that the estimated size of the toxin-binding pocket in nicotinic acetylcholine receptor is approximately 20 A (height) x 20 A (width) x 15 A (thickness).

Local structural elements in the mostly unstructured transcriptional activation domain of human p53

DNA transcription is initiated by a small regulatory region of transactivators known as the transactivation domain. In contrast to the rapid progress made on the functional aspect of this promiscuous domain, its structural feature is still poorly characterized. Here, our multidimensional NMR study reveals that an unbound full-length p53 transactivation domain, although similar to the recently discovered group of loosely folded proteins in that it does not have tertiary structure, is nevertheless populated by an amphipathic helix and two nascent turns. The helix is formed by residues Thr(18)-Leu(26) (Thr-Phe-Ser-Asp-Leu-Trp-Lys-Leu-Leu), whereas the two turns are formed by residues Met(40)-Met(44) and Asp(48)-Trp(53), respectively. It is remarkable that these local secondary structures are selectively formed by functionally critical and positionally conserved hydrophobic residues present in several acidic transactivation domains. This observation suggests that such local structures are general features of acidic transactivation domains and may represent "specificity determinants" (Ptashne, M., and Gann, A. A. F. (1997), Nature 386, 569-577) that are important for transcriptional activity.