Symmetry-breaking transitions in the early steps of protein self-assembly.

Protein misfolding and subsequent self-association are complex, intertwined processes, resulting in development of a heterogeneous population of aggregates closely related to many chronic pathological conditions including Type 2 Diabetes Mellitus and Alzheimer's disease. To address this issue, here, we develop a theoretical model in the general framework of linear stability analysis. According to this model, self-assemblies of peptides with pronounced conformational flexibility may become, under particular conditions, unstable and spontaneously evolve toward an alternating array of partially ordered and disordered monomers. The predictions of the theory were verified by atomistic molecular dynamics (MD) simulations of islet amyloid polypeptide (IAPP) used as a paradigm of aggregation-prone polypeptides (proteins). Simulations of dimeric, tetrameric, and hexameric human-IAPP self-assemblies at physiological electrolyte concentration reveal an alternating distribution of the smallest domains (of the order of the peptide mean length) formed by partially ordered (mainly ß-strands) and disordered (turns and coil) arrays. Periodicity disappears upon weakening of the inter-peptide binding, a result in line with the predictions of the theory. To further probe the general validity of our hypothesis, we extended the simulations to other peptides, the Aß(1-40) amyloid peptide, and the ovine prion peptide as well as to other proteins (SOD1 dimer) that do not belong to the broad class of intrinsically disordered proteins. In all cases, the oligomeric aggregates show an alternate distribution of partially ordered and disordered monomers. We also carried out Surface Enhanced Raman Scattering (SERS) measurements of hIAPP as an experimental validation of both the theory and in silico simulations.

Design of Hydrated Porphyrin-Phospholipid Bilayers with Enhanced Magnetic Resonance Contrast.

Computer simulations are used to design more hydrated bilayers, formed from amine-modified porphyrin-phospholipids (PoPs). Experiments confirm that the new constructs give rise to bilayers with greater water content. When chelated with manganese, amine-modified PoPs provide improved contrast for magnetic resonance and are safely used for imaging in vivo.

The Relationship Between Methamphetamine Use, Sexual Sensation Seeking and Condomless Anal Intercourse Among Men Who Have Sex With Men in Vietnam: Results of a Community-Based, Cross-Sectional Study.

This study assessed the relationship between methamphetamine use and condomless anal intercourse (CAI) among men who have sex with men (MSM) in Hanoi and Ho Chi Minh City, Vietnam. Of 622 MSM participants, 75.7% reported any CAI in the last three months, 23.2% reported engaging in sex work in the last three months, 21.1% reported group sex in the last twelve months (21.1%) and 14.3% had used methamphetamine for sex in the last three months. CAI was associated with living in Ho Chi Minh City vs. Hanoi, being versatile during anal sex, a greater degree of sexual sensation-seeking, and more strongly agreeing that withdrawal before ejaculation is effective in preventing HIV. Effect-modification analysis showed that recent sex-related methamphetamine use was related to a higher probability of CAI for men with low sexual sensationseeking scores. Methamphetamine assessment and/or interventions should be incorporated into HIV prevention and research with Vietnam's MSM population.

GRAS1 non-coding RNA protects against DNA damage and cell death by binding and stabilizing NKAP.

Non-coding RNA (ncRNA) gene products are involved in diverse biological processes including splicing, epigenetic regulation, gene expression, proliferation, and metabolism. The biological mechanisms by which ncRNAs contribute to cell survival remain poorly understood. We found that the Growth Regulator Antisense 1 (GRAS1) long non-coding RNA (lncRNA) transcript promotes growth in multiple human cell types by protecting against DNA damage. Knockdown of GRAS1 induced DNA damage and cell death, along with significant expression changes in DNA damage response, intrinsic apoptotic signaling, and cellular response to environmental stimulus genes. Extensive DNA damage occurred after GRAS1 knockdown, with numerous double strand breaks occurring in each cell. The number of cells undergoing apoptosis and with fragmented nuclei increased significantly after GRAS1 knockdown. We used RNA antisense purification and mass spectrometry (RAP-MS) to identify the NF-κB activating protein (NKAP) as a direct protein interaction partner of GRAS1 lncRNA. NKAP protein was degraded after GRAS1 knockdown, in a proteasome-dependent manner. Overexpression of GRAS1 or NKAP mitigated the DNA damage effects of GRAS1 knockdown. In summary, GRAS1 and NKAP directly interact to protect against DNA damage and cell death in multiple human cell lines.

Streamlined Purification of RNA-Protein Complexes Using UV Cross-Linking and RNA Antisense Purification.

RNA-protein interactions are important in development and disease, but identification of novel RNA-protein interactions remains challenging. Here, we describe an updated capture method to identify direct and specific RNA-protein interactions. First, RNA and protein are covalently cross-linked in living cells by treatment with UV light at 254 nanometers wavelength. The antisense purification approach is dependent upon nucleic acid hybridization between biotinylated DNA probes and a target RNA. Target protein:RNA:DNA complexes are enriched by capture on streptavidin magnetic beads and purified through several denaturing washes that remove nonspecific protein and nucleic acid interactors. Mass spectrometry is used to identify proteins that are specifically enriched in the target RNA capture. This method has been applied to discover the protein interactions of noncoding RNAs but can be used to capture any RNA where the target sequence is known.

Development of a Subunit Vaccine against Duck Hepatitis A Virus Serotype 3.

In this study, we sought to develop a subunit vaccine against the increasingly prevalent Duck hepatitis A virus serotype 3 (DHAV-3). The VP1 protein of DHAV-3 and a truncated version containing the C-terminal region of VP1, termed VP1-C, were expressed recombinantly in Escherichia coli as vaccine antigens. For enhanced immune response, a truncated version of flagellin, nFliC, was included as vaccine adjuvant. Ducklings were vaccinated once for immune response analysis and challenge test. Results showed that VP1-C elicited a higher level of virus-specific antibody response and neutralization titer than VP1. The addition of nFliC further enhanced the antibody response. In terms of cellular immune response, the VP1-C + nFliC vaccine elicited the highest level of T cell proliferation among the vaccine formulations tested. Examination of the cytokine expression profile showed that peripheral blood mononuclear cells from the VP1-C + nFliC vaccine group expressed the highest levels of pro-inflammatory (IL-6) and TH-1 type (IL-12 and IFN-γ) cytokines. Finally, in a DHAV-3 challenge test, the VP1-C + nFliC vaccine provided a 75% protection rate (n = 8), in contrast to 25% for the VP1 vaccine. In conclusion, E. coli-expressed VP1-C has been shown to be a promising antigen when combined with nFliC and may be further developed as a single-dose subunit vaccine against DHAV-3.

Cytotoxic Coumarins from the Bark of Mammea siamensis.

A new geranylated coumarin, (E)-4-(1-hydroxypropyl)-5,7-dihydroxy-6-(3,7-dimethyl-2,6-octadienyl)-8-(3-methyl-1-oxobutyl)coumarin (named surangin D), was isolated from the bark of Mammea siamensis collected in Vietnam, along with four known coumarins, surangins B and C, and theraphins B and C, and seven xanthones, 1,7-dihydroxyxanthone, 7-hydroxy-1-methoxyxanthone, 1,7-dimethoxyxanthone, 1,7-dimethoxy-6-hydroxyxanthone, 1,6,7-trihydroxyxanthone, 1,3,7-trihydroxyxanthone, and 1,7-dihydroxy-3-methoxyxanthone. Their structures were determined by spectroscopic methods (mainly 1D- and 2D-NMR) and preparation of methylated derivatives. The four coumarins, surangins C and D and theraphins B and C, were tested for inhibition of cell proliferation in DLD-1 (colon cancer), MCF-7 (breast adenocarcinoma), HeLa (human cervical cancer) and NCI-H460 (human lung cancer) cell lines using the sulforhodamine B (SRB) assay. In all four cell lines, theraphin C showed the strongest activity (IC50 in the range of 1.6-5.7 µM). Testing the anti-proliferative effect of the methylated derivatives showed reduced cellular effects of all derivatives, indicating that the number and position of free hydroxyl groups were very important for the anti-proliferative effect.

Binding of Disordered Peptides to Kelch: Insights from Enhanced Sampling Simulations.

Keap1 protein plays an essential role in regulating cellular oxidative stress response and is a crucial binding hub for multiple proteins, several of which are intrinsically disordered proteins (IDP). Among Kelch's IDP binding partners, NRF2 and PTMA are the two most interesting cases. They share a highly similar binding motif; however, NRF2 binds to Kelch with a binding affinity of approximately 100-fold higher than that of PTMA. In this study, we perform an exhaustive sampling composed of 6 µs well-tempered metadynamics and 2 µs unbiased molecular dynamics (MD) simulations aiming at characterizing the binding mechanisms and structural properties of these two peptides. Our results agree with previous experimental observations that PTMA is remarkably more disordered than NRF2 in both the free and bound states. This explains PTMA's lower binding affinity. Our extensive sampling also provides valuable insights into the vast conformational ensembles of both NRF2 and PTMA, supports the hypothesis of coupled folding-binding, and confirms the essential role of linear motifs in IDP binding.

Amphetamine-type stimulant use among men who have sex with men (MSM) in Vietnam: Results from a socio-ecological, community-based study.

INTRODUCTION: Amphetamine-type-stimulants (ATS) use is associated with HIV-related sexual risk behaviours and is an emergent problem among men who have sex with men (MSM) in Vietnam. The purpose of this study is to describe ATS use patterns and understand the correlates of recent methamphetamine use from a socio-ecological perspective. METHODS: From September through December, 2014, 622 MSM were recruited in Hanoi and Ho Chi Minh City, Vietnam. We collected information on demographic characteristics, HIV testing behaviours, use of ATS and other recreational drugs (ever and recently), sexual sensation seeking, depressive mood, experienced and internalized stigma related to homosexuality, social involvement with other MSM, and perceptions of ATS use in MSM networks. We performed descriptive statistics to describe ATS use patterns and multivariate logistic regression to establish independent correlates of recent methamphetamine use. RESULTS: Nearly one-third (30.4%) had ever used ATS, including 23.6% who had used methamphetamine, 4.3% who had used amphetamine ('speed') and 20.9% who had used ecstasy. 20.1% and 11.9% had ever used methamphetamine and ecstasy, respectively, during sex. Eighteen percent of methamphetamine users were classified as engaged in high-risk use. Recent methamphetamine use (in the last 3 months) was associated with participants perceiving more methamphetamine use in their MSM network, recent sex work, and higher sexual sensation seeking scores. CONCLUSIONS: ATS use is relatively prevalent among MSM sampled in Vietnam's main cities. Interventions to address methamphetamine are warranted for MSM in Vietnam. Methamphetamine treatments are needed for high-risk users.

Accelerating the Conformational Sampling of Intrinsically Disordered Proteins.

Intrinsically disordered proteins (IDPs) are a class of proteins lacking a well-defined secondary structure. Instead, they are able to attain multiple conformations, bind to multiple targets, and respond to changes in their surroundings. Functionally, IDPs have been associated with molecular recognition, cell regulation, and signal transduction. The dynamic conformational ensemble of IDPs is highly environmental and binding partner dependent, rendering the characterization of IDPs extremely challenging. Here, we compare the sampling efficiencies of conventional molecular dynamics (MD), well-tempered metadynamics (WT-META), and bias-exchange metadynamics (BE-META). The total simulation time was over 10 µs, and a 20-mer peptide derived from the Neh2 domain of the Nuclear factor erythroid 2-related factor 2 (Nrf2) protein was simulated. BE-META, with a neutral replica and seven biased replicas employing a set of seven relevant collective variables (CVs), provided the most reliable and efficient sampling. Finally, we propose a free-energy reconstruction method based on the probability distribution of the secondary structure contents. This postprocessing analysis confirms the presence of not only the ß-hairpin conformation of the free Neh2 peptide but also its rare bound-state-like conformation, both of that have been experimentally observed. In addition, our simulations also predict other possible conformations to be verified with future experiments.

Stabilizing additives added during cell lysis aid in the solubilization of recombinant proteins.

Insoluble recombinant proteins are a major issue for both structural genomics and enzymology research. Greater than 30% of recombinant proteins expressed in Escherichia coli (E. coli) appear to be insoluble. The prevailing view is that insolubly expressed proteins cannot be easily solubilized, and are usually sequestered into inclusion bodies. However, we hypothesize that small molecules added during the cell lysis stage can yield soluble protein from insoluble protein previously screened without additives or ligands. We present a novel screening method that utilized 144 additive conditions to increase the solubility of recombinant proteins expressed in E. coli. These selected additives are natural ligands, detergents, salts, buffers, and chemicals that have been shown to increase the stability of proteins in vivo. We present the methods used for this additive solubility screen and detailed results for 41 potential drug target recombinant proteins from infectious organisms. Increased solubility was observed for 80% of the recombinant proteins during the primary and secondary screening of lysis with the additives; that is 33 of 41 target proteins had increased solubility compared with no additive controls. Eleven additives (trehalose, glycine betaine, mannitol, L-Arginine, potassium citrate, CuCl(2), proline, xylitol, NDSB 201, CTAB and K(2)PO(4)) solubilized more than one of the 41 proteins; these additives can be easily screened to increase protein solubility. Large-scale purifications were attempted for 15 of the proteins using the additives identified and eight (40%) were prepared for crystallization trials during the first purification attempt. Thus, this protocol allowed us to recover about a third of seemingly insoluble proteins for crystallography and structure determination. If recombinant proteins are required in smaller quantities or less purity, the final success rate may be even higher.