M-X-I motif of semliki forest virus capsid protein affects nucleocapsid assembly

Alphavirus budding is driven by interactions between spike and nucleocapsid proteins at the plasma membrane. The binding motif, Y-X-L, on the spike protein E2 and the corresponding hydrophobic cavity on the capsid protein were described earlier. The spike-binding cavity has also been suggested to bind an internal hydrophobic motif, M113-X-I115, of the capsid protein. In this study we found that replacement of amino acids M113 and I115 with alanines, as single or double mutations, abolished formation of intracellular nucleocapsids. The mutants could still bud efficiently, but the NCs in the released virions were not stable after removal of the membrane and spike protein layer. In addition to wild-type spherical particles, elongated multicored particles were found at the plasma membrane and released from the host cell. We conclude that the internal capsid motif has a biological function in the viral life cycle, especially in assembly of nucleocapsids. We also provide further evidence that alphaviruses may assemble and bud from the plasma membrane in the absence of preformed nucleocapsids.     

Molecular interactions of MnO2@RGO (manganese dioxide-reduced graphene oxide) nanocomposites with bovine serum albumin

Abstract

Graphene based materials have attracted global attention due to their excellent properties. GO-metal oxide nanocomposites have been conjugated with biomolecules for the development of novel materials and potentially used as biomarkers. Herein, a detailed study on the interaction of Bovine serum albumin (BSA) with MnO₂@RGO (manganese dioxide-reduced graphene oxide) nanocomposites (NC) has been carried out. MnO₂@RGO nanocomposites were prepared through a template/surfactant free hydrothermal route at 180?°C for 12?h by varying the graphene oxide (GO) concentration. Different biophysical experiments have been carried out to evaluate molecular interactions between BSA and NCs. Intrinsic fluorescence has been used to quantify the quenching efficiency of NCs and the binding association of BSA-NC complexes. NCs effectively quenched the intrinsic fluorescence of BSA via static and dynamic mechanism. Further, the results indicate that the molecular interactions of NC with BSA are dependent on the GO percentage in NC. Circular dichroism results demonstrate nominal changes in the secondary structure of BSA in presence of NCs. Also, the esterase-like activity of BSA was marginally affected after adsorption upon NCs. In addition, the FESEM micrographs reveal that the protein-NC complexes consist of nanorod and sheet-like morphologies are forming aggregates of different sizes. We hope that this study will provide a basis for the design of novel graphene based and other related nanomaterials for several biological applications.

Communicated by Ramaswamy H. Sarma     

Design, synthesis and biological evaluation of novel nitroaromatic compounds as potent glutathione reductase inhibitors

Discovery of GR inhibitors has become very popular recently due to antimalarial and anticancer activities. In this study, the synthesis and GR inhibitory capacities of novel nitroaromatic compounds (NCs) (1-3) were reported. Some commercially available molecules were also tested for comparison reasons. The novel NCs were obtained in high yields using simple chemical procedures and exhibited much potent inhibitory activities against GR at low micromolar concentrations with K(i) values ranging from 0.211 to 4.57 μM as compared with well-known agents. Inhibition mechanism was assessed as being due to occlusion of the active site entrance by means of the NCs. Molecular docking results have shown that docking poses of ligands are able to construct binding interactions with the essential amino acids.     

The application of Au nanoclusters in the fluorescence imaging of human serum proteins after native PAGE: enhancing detection by low-temperature plasma treatment

Proteins in human serum are increasingly being studied for their roles in a wide variety of biochemical interactions. To improve the sensitivity of the detection of human serum proteins after native polyacrylamide gel electrophoresis (PAGE), we have developed a fluorescence imaging detection technique for the detection. BSA (bovine serum albumin)-stabilized Au nanoclusters (NCs) were applied as fluorescent probes for imaging, and low-temperature plasma (LTP) treatment of the Au NCs was introduced to enhance the fluorescence imaging. Here, a series of optimization experiments (e.g. those to optimize for pH) were conducted for protein detection after 1-DE and 2-DE, and several types of discharge gases (He, O(2), and N(2)) were selected for the LTP treatment. The possible mechanism of interaction between the proteins and the Au NCs was demonstrated by an isothermal titration calorimetry experiment. Using the present method, a sensitivity of 7-14 times higher than that of traditional staining detection methods was observed in the oxygen LTP-treated Au NCs fluorescence images, and some relatively low abundance proteins (identified by the MS/MS technique) were easily detected. In addition, this fluorescence imaging method was applied to distinguish between the serum samples of patients with liver diseases and those of healthy people. Thus, this fluorescence imaging method is suitable for the highly sensitive detection of various serum proteins, and it shows potential capabilities for clinical diagnosis.     

The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture

All proteins require physical interactions with other proteins in order to perform their functions. Most of them oligomerize into homomers, and a vast majority of these homomers interact with other proteins, at least part of the time, forming transient or obligate heteromers. In the present paper, we review the structural, biophysical and evolutionary aspects of these protein interactions. We discuss how protein function and stability benefit from oligomerization, as well as evolutionary pathways by which oligomers emerge, mostly from the perspective of homomers. Finally, we emphasize the specificities of heteromeric complexes and their structure and evolution. We also discuss two analytical approaches increasingly being used to study protein structures as well as their interactions. First, we review the use of the biological networks and graph theory for analysis of protein interactions and structure. Secondly, we discuss recent advances in techniques for detecting correlated mutations, with the emphasis on their role in identifying pathways of allosteric communication.     

DNA-Ag nanoclusters as fluorescence probe for turn-on aptamer sensor of small molecules

As promising substitutes for organic dyes and quantum dots, few-atom fluorescent silver nanoclusters (Ag NCs) have recently gained much attention in a wide range from cellular imaging to chemical/biological detection applications owing to their ultrasmall size (<2 nm), excellent photostability, good biocompatibility and water solubility. Herein, we design an aptamer, guanine-rich (G-rich) DNA and Ag NCs nanocomplex to investigate its ability for the detection of small molecules. The design contains two DNA strands which are both chimeric conjugates of the DNA aptamer sequence fragment and G-rich sequence fragment. Using cocaine as a model molecule, the two DNA strands are in free state if there is no cocaine present, and the formed Ag NCs through the reduction of Ag(+) by NaBH(4) show weak fluorescence emission. In the presence of cocaine, however, the two aptamer fragments bind cocaine, which in turn puts the two G-rich sequence fragments in proximity and the fluorescent intensity of DNA-Ag NCs enhances greatly. As a result, DNA-Ag NCs are demonstrated as a novel, cost-effective and turn-on fluorescent probe for the analysis of cocaine, with a detection limit of 0.1 μM. Besides, successful detection of adenosine triphosphate (ATP) with detection limit of 0.2 μM demonstrates its potential to be a general method.     

Biosynthesis of flower-shaped Au nanoclusters with EGCG and their application for drug delivery

Background

In the last decade, the biosynthesis of metal nanoparticles using organisms have received more and more considerations. However, the complex composition of organisms adds up to a great barrier for the characterization of biomolecules involved in the synthesis process and their biological mechanisms.

Results

In this research, we biosynthesized a kind of flower-shaped Au nanoclusters (Au NCs) using one definite component—epigallocatechin gallate (EGCG), which was the main biomolecules of green tea polyphenols. Possessing good stability for 6 weeks and a size of 50 nm, the Au NCs might be a successful candidate for drug delivery. Hence, both methotrexate (MTX) and doxorubicin (DOX) were conjugated to the Au NCs through a bridge of cysteine (Cys). The introduction of MTX provided good targeting property for the Au NCs, and the conjugation of DOX provided good synergistic effect. Then, a novel kind of dual-drug loaded, tumor-targeted and highly efficient drug delivery system (Au-Cys-MTX/DOX NCs) for combination therapy was successfully prepared. The TEM of HeLa cells incubated with Au-Cys-MTX/DOX NCs indicated that the Au-Cys-MTX/DOX NCs could indeed enter and kill cancer cells. The Au-Cys-MTX/DOX NCs also possessed good targeting effect to the FA-receptors-overpressed cancer cells both in vitro and in vivo. Importantly, the Au-Cys-MTX/DOX NCs resulted in an excellent anticancer activity in vivo with negligible side effects.

Conclusions

These results suggest that the biosynthesized Au-Cys-MTX/DOX NCs could be a potential carrier with highly efficient anticancer properties for tumor-targeted drug delivery.

     

Preformed cytoplasmic nucleocapsids are not necessary for alphavirus budding.

According to the present model for assembly of alphaviruses, e.g. Semliki Forest virus (SFV), the viral genome is first encapsidated into a nucleocapsid (NC) in cytoplasm and this is then used for budding at plasma membrane (PM). The preformed NC is thought to act as a template on which the viral envelope can be organized. In the present work we have characterized two SFV deletion mutants which did not assemble NCs in the cytoplasm but which instead appeared to form NCs at the PM simultaneously with virus budding. The deletions were introduced in a conserved 14 residue long linker peptide that joins the amino-terminal RNA-binding domain with the carboxy-terminal serine-protease domain of the capsid protein. Despite the deletions and the change in morphogenesis, wild-type (wt)-like particles were produced with almost wt efficiency. It is suggested that the NC assembly defect of the mutants is rescued through spike-capsid interactions at PM. The results show that the preassembly of NCs in the cytoplasm is not a prerequisite for alphavirus budding. The apparent similarities of the morphogenesis pathways of wt and mutant SFV with those of type D and type C retroviruses are discussed.     

Prediction of protein-protein interactions using random decision forest framework

MOTIVATION: Protein interactions are of biological interest because they orchestrate a number of cellular processes such as metabolic pathways and immunological recognition. Domains are the building blocks of proteins; therefore, proteins are assumed to interact as a result of their interacting domains. Many domain-based models for protein interaction prediction have been developed, and preliminary results have demonstrated their feasibility. Most of the existing domain-based methods, however, consider only single-domain pairs (one domain from one protein) and assume independence between domain-domain interactions. RESULTS: In this paper, we introduce a domain-based random forest of decision trees to infer protein interactions. Our proposed method is capable of exploring all possible domain interactions and making predictions based on all the protein domains. Experimental results on Saccharomyces cerevisiae dataset demonstrate that our approach can predict protein-protein interactions with higher sensitivity (79.78%) and specificity (64.38%) compared with that of the maximum likelihood approach. Furthermore, our model can be used to infer interactions not only for single-domain pairs but also for multiple domain pairs.     

Membrane proteins organize a symmetrical virus

Alphaviruses are enveloped icosahedral viruses that mature by budding at the plasma membrane. According to a prevailing model maturation is driven by binding of membrane protein spikes to a preformed nucleocapsid (NC). The T = 4 geometry of the membrane is thought to be imposed by the NC through one-to-one interactions between spike protomers and capsid proteins (CPs). This model is challenged here by a Semliki Forest virus capsid gene mutant. Its CPs cannot assemble into NCs, or its intermediate structures, due to defective CP-CP interactions. Nevertheless, it can use its horizontal spike-spike interactions on membrane surface and vertical spike-CP interactions to make a particle with correct geometry and protein stoichiometry. Thus, our results highlight the direct role of membrane proteins in organizing the icosahedral conformation of alphaviruses.     

One‐step synthesis of cationic gold nanoclusters with high catalytic activity on luminol chemiluminescence reaction

The present study reports a one‐step synthesis method for the preparation of cationic gold nanoclusters (Au NCs). Polyethyleneimine (PEI), a positively charged hyperbranched polyamine, was selected as the capping reagent. Glutathione showed a synergistic effect on the formation of the small size of cationic Au NCs. The prepared cationic Au NCs have a size less than 2 nm and carry a positive charge in solution with pH less than 11. The cationic PEI–Au NCs‐triggered luminol chemiluminescence (CL) reactions showed slow and intense CL profiles. The maximum CL intensity can be obtained within 10 min and the CL signal maintained almost the same within 30 min. A linear increase of CL intensity was observed in the presence of an increasing concentration of cationic Au NCs ranging from 0.030 μM to 15 μM. The linear response of the cationic Au NCs in the CL reaction and the glow‐type CL profile make the proposed CL reaction have broad application prospects in the field of biological analysis and CL imaging.     

Protein chips for high-throughput doping screening in athletes

The biological significance of protein interactions, their method of generation and reliability is briefly reviewed. Protein interaction networks adopt a scale-free topology that explains their error tolerance or vulnerability, depending on whether hubs or peripheral proteins are attacked. Networks also allow the prediction of protein function from their interaction partners and therefore, the formulation of analytical hypotheses. Comparative network analysis predicts interactions for distantly related species based on conserved interactions, even if sequences are only weakly conserved. Finally, the medical relevance of protein interaction analysis is discussed and the necessity for data integration is emphasized.     

What do we learn from high-throughput protein interaction data?

The biological significance of protein interactions, their method of generation and reliability is briefly reviewed. Protein interaction networks adopt a scale-free topology that explains their error tolerance or vulnerability, depending on whether hubs or peripheral proteins are attacked. Networks also allow the prediction of protein function from their interaction partners and therefore, the formulation of analytical hypotheses. Comparative network analysis predicts interactions for distantly related species based on conserved interactions, even if sequences are only weakly conserved. Finally, the medical relevance of protein interaction analysis is discussed and the necessity for data integration is emphasized.     

Development of PEGylated Cu nanoclusters: A nontoxic,multifunctional colloidal system for bioimaging and peroxide sensing

This study introduces the development of blue-emitting colloidal Cu NCs through a novel and easy PEGylation method using different functional groups, including -SH and -COOH. The surface functionalization controls the size, cellular toxicity, and emission properties of Cu NCs. The combination of PEG, thiol, and carboxylic groups protects the particle surface from aggregation and oxidation. Among the samples, CAGP (Surface modified Cu NCs with -SH-COOH-PEG combination) emerges as an amazing candidate with the lowest toxicity and enhanced blue emission properties. The bright blue fluorescence emission from Hela cells after treatment with CAGP demonstrated this property. It also has excellent peroxide sensing potential, with a detection limit of 1.4 μM. Because of their excellent bioimaging and peroxide sensing properties, these Cu NCs could be a promising candidate for cellular oxidative stress sensing applications with high clinical relevance.     

Surface plasmon resonance spectroscopy in the study of membrane-mediated cell signalling.

Peptide-membrane interactions contribute to many important biological processes such as cellular signaling, protein trafficking and ion-channel formation. During receptor-mediated signalling, activated intracellular signalling molecules are often recruited into receptor-induced signaling complexes at the cytoplasmic surface of the cell membrane. Such recruitment can depend upon protein-protein and protein-lipid interactions as well as protein acylation. A wide variety of biophysical techniques have been combined with the use of model membrane systems to study these interactions and have provided important information on the relationship between the structure of these proteins involved in cell signalling and their biological function. More recently, surface plasmon resonance (SPR) spectroscopy has also been applied to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. This article provides an overview of these recent applications, which demonstrate the potential of SPR to enhance our molecular understanding of membrane-mediated cellular signalling.     

Biodistribution and long-term fate of silver nanoparticles functionalized with bovine serum albumin in rats

Silver nanocrystals (Ag NCs) hold promising antibiotic and antiviral properties in biological systems. The biodistribution of silver nanostructures injected into animals in vivo is currently unknown, remaining as a fundamental issue for potential therapeutic applications. Here, we injected Ag NCs capped with bovine serum albumin (BSA) in live rats to elucidate their fate in several organs including liver, heart and brain. Very significant accumulations of nanoparticles were confirmed by inductively coupled plasma mass spectroscopy (ICPMS) and transmission electron microscopy (TEM) techniques on the liver and heart. In contrast, the brain tissue did not reveal evidence of particles content. Our results suggest that Ag+ permeated across the blood-brain barrier (BBB), and followed swift clearance from the organ.     

Application of proteomics technology for analyzing the interactions between host cells and intracellular infectious agents

Host-pathogen interactions involve protein expression changes within both the host and the pathogen. An understanding of the nature of these interactions provides insight into metabolic processes and critical regulatory events of the host cell as well as into the mechanisms of pathogenesis by infectious microorganisms. Pathogen exposure induces changes in host proteins at many functional levels including cell signaling pathways, protein degradation, cytokines and growth factor production, phagocytosis, apoptosis, and cytoskeletal rearrangement. Since proteins are responsible for the cell biological functions, pathogens have evolved to manipulate the host cell proteome to achieve optimal replication. Intracellular pathogens can also change their proteome to adapt to the host cell and escape from immune surveillance, or can incorporate cellular proteins to invade other cells. Given that the interactions of intracellular infectious agents with host cells are mainly at the protein level, proteomics is the most suitable tool for investigating these interactions. Proteomics is the systematic analysis of proteins, particularly their interactions, modifications, localization and functions, that permits the study of the association between pathogens with their host cells as well as complex interactions such as the host-vector-pathogen interplay. A review on the most relevant proteomic applications used in the study of host-pathogen interactions is presented.     

Stomatal neighbor cell polarity and division in <Emphasis Type="Italic">Arabidopsis</Emphasis>

Asymmetric divisions are key to regulating the number and patterning of stomata in Arabidopsis thaliana (L.) Heynh. Many formative asymmetric divisions take place in neighbor cells (NCs), cells adjacent to a stoma or stomatal precursor. TOO MANY MOUTHS is a receptor-like protein required for the correct plane of NC division, resulting in the placement of the new precursor distal to the pre-existing stoma. Because plant cells usually become polarized before asymmetric division, we studied whether NCs display a cytological asymmetry as a function of cell stage and of possible division behavior. Cells that divided in the developing leaf epidermis were smaller than 400 micro m(-2) in area and included NCs as well as isolated cells. All NCs in the youngest complexes divided with comparable frequencies, but divisions became restricted to the smaller and most recently produced NCs as the stomatal complex matured. The majority of developing NCs had distally located nuclei, suggesting that nuclear position is actively regulated in NCs. NC stages exhibiting distally located nuclei were the likeliest to divide asymmetrically. However, a distal nucleus did not necessarily predict an asymmetric division, because more NCs had distal nuclei than were likely to divide. No defect was detected in nuclear distribution in tmm NCs. These data suggest that TMM uses intercellular signals to control the plane of asymmetric division after or independently of nuclear positioning.