Protein Interaction

Quantitative analysis of the composition dependence of the concentration gradient of each species of macromolecule within a solution mixture at sedimentation equilibrium permits the quantitative characterization of self-and heterointeractions between sedimenting solutes. Sedimentation equilibrium experiments were conducted on solutions containing a trace concentration of FITClabeled BSA in varying concentrations of Ficoll 70 and on solutions containing a trace concentration of FITC-labeled Ficoll 70 in varying concentrations of BSA. The equilibrium gradient of each solute component in each mixture was measured independently. Analysis of the resulting gradients resulted in evaluation of the dependence of the activity coefficient of Ficoll upon the concentrations of Ficoll and BSA at concentrations of up to 100 g/L and the dependence of the activity coefficient of BSA upon the concentrations of Ficoll and BSA at concentrations of up to 100 g/L. The activity coefficients of both species increase significantly with increasing Ficoll and BSA concentration and do not vary with temperature, to within the precision of measurement, over the temperature range of 5-37 °C, indicating that the dominant interaction between Ficoll molecules and between BSA and Ficoll molecules is repulsive and probably due to steric volume exclusion. The measured dependences may be accounted for quantitatively by a simple model in which BSA and Ficoll 70 are represented by equivalent rigid particles.

Rapid synthesis and screening of compound libraries enables the accelerated identification of novel protein ligands in order to support processes like analysis of protein interactions, drug target discovery or lead structure discovery. SPOT synthesis-a well established method for the rapid preparation of peptide arrays-has recently been extended to the field of nonpeptides. In this contribution we report on the systematic evaluation of the SPOT technique for the assembly of N-alkylglycine (peptoid) library arrays. In the course of this investigation bromoacetic acid 2,4-dinitrophenylester (1a) was identified to be the most suited agent for bromoacetylation in terms of yield and N-selectivity enabling straightforward submonomer synthesis on hydroxy-group rich cellulose membranes. The potential of this method for the rapid identification of novel nonpeptidic protein ligands was demonstrated by synthesis and screening of a library consisting of 8000 peptoids and peptomers (i.e. their hybrids with a-substituted amino acids) allowing the identification of micromolar ligands for the monoclonal antibody Tab-2. q

One of the central problems in modern biology is to identify the complete set of interactions among the proteins in a cell. The structural interaction of proteins and their domains in networks is one of the most basic molecular mechanisms for biological cells. Structural evidence indicates that, interacting pairs of close homologs usually interact in the same way. In this article, we make use of both homology and inter-domain linker region knowledge to predict interaction between protein pairs solely by amino acid sequence information. High quality core set of 150 yeast proteins obtained from the Database of Interacting Proteins (DIP) was considered to test the accuracy of the proposed method. The strongest prediction of the method reached over 70% accuracy. These results show great potential for the proposed method.

Life depends on the interaction of proteins. The availability of the complete human genome sequence has highlighted the need for a tool to analyse protein interactions and several databases have been compiled for this purpose. These databases document, categorize, and analyze interacting proteins and the cellular functions of the interactions.

Protein-carbohydrate interactions play crucial roles in numerous biological processes. To study these interactions, we developed a simple and fast procedure for the biotinylation of carbohydrates based on reductive amination. The method allows complete and stable biotinylation of small quantities of oligosaccharides and includes a rapid and simple procedure to remove excess labeling reagent. After biotinylation, the structural and biological integrity of the glycans was intact as determined by HPLC, mass spectrometry, and a plant lectin assay. By using the human C-type lectin DC-SIGN (dendritic cell-speciWc ICAM-3-grabbing nonintegrin), we demonstrate that the biotinylated glycans can be used in a glycan array to determine binding speciWcities of lectins. Moreover, we show that Xuorescent beads coated with selected biotinylated glycans bind to DC-SIGN-expressing dendritic cells in vitro. Finally, by using biotinylated high-mannose N-glycans, we could visualize DC-SIGN-expressing cells in lymph node tissue. The availability of easy biotinylation methods for oligosaccharides such as those described here greatly facilitates the functional analysis of lectins. In addition, the biotinylated glycans will be great tools for investigating functional lectin receptors in situ.

We introduce a quantifiable structural motif, called dehydron, that is shown to be central to protein-protein interactions. A dehydron is a defectively packed backbone hydrogen bond suggesting preformed monomeric structure whose Coulomb energy is highly sensitive to binding-induced water exclusion. Such preformed hydrogen bonds are effectively adhesive, since water removal from their vicinity contributes to their stability. At the structural level, a significant correlation is established between dehydrons and sites for protein complexation, with the HIV-1 capsid protein P24 complexed with antibody light-chain FAB25.3 providing the most dramatic correlation. Furthermore, the number of dehydrons in homologous similar-fold proteins from different species is shown to be a signature of proteomic complexity. The techniques are then applied to higher levels of organization: The formation of the capsid and its organization in picornaviruses correlates strongly with the distribution of dehydrons on the rim of the virus unit. Furthermore, antibody contacts and crystal contacts may be assigned to dehydrons still prevalent after the capsid has been assembled. The implications of the dehydron as an encoded signal in proteomics, bioinformatics, and inhibitor drug design are emphasized.

Amelogenin-mineral interactions were investigated using an in vitro binding approach. Rat incisor enamel matrix proteins (mainly amelogenins) were dissolved in synthetic enamel fluid and allowed to equilibrate with deproteinised developing enamel crystals. The results showed that amlogenin proteins of 21, 23, 24, 26 and 27-kDa (corresponding to nascent and partially degraded amelogenins) were associated with the crystals whilst the lower Mr amelogenins (< 21 KDa) remained free in the synthetic enamel fluid. These data suggest the nascent and partially degraded amelogenins may interact with developing enamel crystals and could influence their growth. Albumin-mineral interactions were investigated by extracting developing rat incisor enamel with synthetic enamel fluid. Insoluble material (including the enamel crystals) was then further extracted with 0.1 M phosphate buffer (pH 7.4) to desorb any mineral bound proteins. Western blotting using anti-albumin antibodies showed that almost all of the albumin from the secretory stage enamel and a significant proportion of the albumin present in early transition stage was extractable in the synthetic enamel fluid. However, synthetic enamel fluid did not extract albumin from late transition or maturation stage tissue, which could only be removed following further extraction with phosphate buffer. Albumin degradation was apparent during the transition and maturation stages, where it is degraded and ultimately removed. This binding pattern may be related to amelogenin degradation and removal during the transition stage, permitting albumin access to the previously obscured crystal surfaces. That the secretory stage matrix appears to "protect" secretory stage crystals from albumin may be an important consideration in the aetiology of enamel hypoplasias (i.e. incomplete crystal growth) and when using dissociative extraction procedures for the identification of mineral bound proteins.

Acute inflammatory demyelinating polyneuropathy (AIDP) is a type of Guillain-Barré syndrome (GBS) characterized by primary nerve demyelination sometimes with secondary axonal degeneration. Studies on the fine structure of dorsal root ganglia in AIDP are lacking. Our aim was to investigate the cytology and nuclear organization of primary sensory neurons in AIDP with axonal injury using ultrastructural and immunohistochemical analysis. The light cytology of the L5 dorsal ganglion showed the characteristic findings of neuronal axonal reaction. The organization of chromatin, nucleolus, Cajal bodies, and nuclear pores corresponded to transcriptionally active neurons. However, the hallmark of the nuclear response to axonal injury was the formation of numerous nuclear bodies (NBs; 6.37 F 0.6, in the AIDP, vs. 2.53 F 0.2, in the control, mean F SDM), identified as promyelocytic leukemia (PML) bodies by the presence of the protein PML. In addition to PML protein, nuclear bodies contained SUMO-1 and the transcriptional regulators CREB-binding protein (CBP) and glucocorticoid receptor (GR). The presence of proteasome 19S was also detected in some nuclear bodies. We suggest that neuronal PML bodies could regulate the nuclear concentration of active proteins, a process mediated by protein interactions with PML and SUMO-1 proteins. In the AIDP case, the proliferation of PML bodies may result from the overexpression of some nuclear proteins due to changes in gene expression associated with axonal injury.

It is essential to catalog characterized hepatitis C virus (HCV) protein-protein interaction (PPI) data and the associated plethora of vital functional information to augment the search for therapies, vaccines and diagnostic biomarkers. In furtherance of these goals, we have developed the hepatitis C virus protein interaction database (HCVpro) by integrating manually verified hepatitis C virus-virus and virus-human protein interactions curated from literature and databases. HCVpro is a comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet, VirusMint, HCVdb and euHCVdb), and from BIND and other relevant biology repositories. HCVpro is further populated with information on hepatocellular carcinoma (HCC) related genes that are mapped onto their encoded cellular proteins. Incorporated proteins have been mapped onto Gene Ontologies, canonical pathways, Online Mendelian Inheritance in Man (OMIM) and extensively cross-referenced to other essential annotations. The database is enriched with exhaustive reviews on structure and functions of HCV proteins, current state of drug and vaccine development and links to recommended journal articles. Users can query the database using specific protein identifiers (IDs), chromosomal locations of a gene, interaction detection methods, indexed PubMed sources as well as HCVpro, BIND and VirusMint IDs.

Functional foods represent an emerging market of growing economic importance. The formulation of carotene fortified food emulsions involves the difficulty to transfer the carotenoids into the lipid phase. Usually, undesirable organic solvents are used to dissolve the carotenoid in the lipid phase, in particular astaxanthin and b-carotene. Here, we present a novel approach in which the carotenoid is first bound to bovine serum albumin (BSA) and then the carotenoid-protein complex is used to prepare an emulsion. Absorbance spectroscopy indicates the formation of the complex in the aqueous phase and provides first results of the carotenoid load, which is supported by the colour of the cream phase. The droplets in the emulsion are visualized by confocal laser scanning spectroscopy, indicating the protein layer. The laser diffraction spectroscopy and confocal laser scanning spectroscopy provide the particle size distribution and insight of the stability of emulsion interface.

We have studied a series of samples of bovine serum albumin (BSA) solutions with protein concentration, c, ranging from 2 to 500 mg/mL and ionic strength, I, from 0 to 2 M by small-angle X-ray scattering (SAXS). The scattering intensity distribution was compared to simulations using an oblate ellipsoid form factor with radii of 17 × 42 × 42 Å, combined with either a screened Coulomb, repulsive structure factor, S SC (q), or an attractive square-well structure factor, S SW (q). At pH ) 7, BSA is negatively charged. At low ionic strength, I < 0.3 M, the total interaction exhibits a decrease of the repulsive interaction when compared to the salt-free solution, as the net surface charge is screened, and the data can be fitted by assuming an ellipsoid form factor and screened Coulomb interaction. At moderate ionic strength (0.3-0.5 M), the interaction is rather weak, and a hard-sphere structure factor has been used to simulate the data with a higher volume fraction. Upon further increase of the ionic strength (I g 1.0 M), the overall interaction potential was dominated by an additional attractive potential, and the data could be successfully fitted by an ellipsoid form factor and a square-well potential model. The fit parameters, well depth and well width, indicate that the attractive potential caused by a high salt concentration is weak and long-ranged. Although the long-range, attractive potential dominated the protein interaction, no gelation or precipitation was observed in any of the samples. This is explained by the increase of a short-range, repulsive interaction between protein molecules by forming a hydration layer with increasing salt concentration. The competition between long-range, attractive and shortrange, repulsive interactions accounted for the stability of concentrated BSA solution at high ionic strength.

Figs. S1 to S35 Tables S1 to S5 References Second, AP/MS methods preferentially detect strong interactions within stable complexes, whereas Y2H methods can identify weaker, transient or condition-specific interactions (39). The MIPS complex catalog is biased towards large stable complexes (40). Thus, many interactions detectable by Y2H are

Since protein complex crystallization is expensive and time-consuming, computational docking tools provide a valuable method to investigate protein interactions. While the sampling of possible docked conformers of two proteins can be performed efficiently by Fast Fourier Transform (FFT) methods, the selection of near-native decoys from the pool of thousands of possible decoys is still far from being solved. Here, a new approach for docking decoy selection by Monte Carlo stability analysis is presented. In the course of replica exchange Monte Carlo simulations (REMC), replica from near-native decoys show a significantly lower structural diversity than replica from non-native decoys. The effect is successfully applied to rank docking decoys in a benchmark set of 59 protein complexes.

A study was made on the molecular and structural changes occurring in the protein and starch components of sorghum flour when fermented to prepare typical non-malted Sudanese foods. Protein solubility and SDS-PAGE studies indicated that water-soluble proteins are the main target of hydrolysis during fermentation. Proteolysis products are taken up for bacterial growth. Kafirins are among the proteins left intact by proteolytic events in the fermentation step. Upon cooking in boiling water kafirins are converted into protein aggregates almost insoluble even in the presence of 8 M urea and of disulphide-reducing agents. Viscoamylographic and microstructural studies indicate that fermentation leads to the release of starch granules from very compact structures in the original sorghum flour, in which proteolysis-sensitive, water-soluble proteins form an essential part of the outermost shell of large structures, where starch granules are embedded into a kafirin-rich protein matrix that is not affected by proteolytic events during fermentation.

In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi. nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez

The bioscience field has seen some spectacular advances in genomic and proteomic technologies that are able to deliver vast quantities of information on cellular activity. Such technologies are of critical importance to biology, medical science and in drug discovery. However, living systems are highly complex and to fully exploit these technologies requires knowledge at many different levels. Information such as genome sequence data, gene expression data, protein-to-protein interactions and metabolic pathways is required to understand the complexity of biological processes. The challenge for bioinformatics is to tackle the problem of fragmentation of knowledge by integrating the many sources of heterogeneous information into a coherent entity. Another problem is that the high level of biological complexity and the fragmented nature of biological research has meant that it is difficult to keep fully conversant with the latest research and discoveries. Progress in one area of biology may have implications for other areas but the dissemination of this knowledge is not straightforward; difficulties such as differences in naming conventions for genes and biological processes has led to confusion and the lack of productivity. This paper reviews the most recent research to overcome the fragmentation problem where technologies such as text mining and ontologies are used within the knowledge discovery process and the specific technical challenges they address.

After the success of human genome project, proteome is a new emerging field of biochemistry as it provides the knowledge of enzymes (proteins) interactions with different body organs and medicines administrated into human body. Therefore, the study of proteomics is very important for the development of new and effective drugs to control many lethal diseases. In proteomics study, analyses of proteome is essential and significant from the pathological point of views, i.e., in several serious diseases such as cancer, Alzheimer's disease and aging, heart diseases and also for plant biology. The separation and identification of proteomics is a challenging job due to their

Protein-carbohydrate interactions play crucial roles in numerous biological processes. To study these interactions, we developed a simple and fast procedure for the biotinylation of carbohydrates based on reductive amination. The method allows complete and stable biotinylation of small quantities of oligosaccharides and includes a rapid and simple procedure to remove excess labeling reagent. After biotinylation, the structural and biological integrity of the glycans was intact as determined by HPLC, mass spectrometry, and a plant lectin assay. By using the human C-type lectin DC-SIGN (dendritic cell-speciWc ICAM-3-grabbing nonintegrin), we demonstrate that the biotinylated glycans can be used in a glycan array to determine binding speciWcities of lectins. Moreover, we show that Xuorescent beads coated with selected biotinylated glycans bind to DC-SIGN-expressing dendritic cells in vitro. Finally, by using biotinylated high-mannose N-glycans, we could visualize DC-SIGN-expressing cells in lymph node tissue. The availability of easy biotinylation methods for oligosaccharides such as those described here greatly facilitates the functional analysis of lectins. In addition, the biotinylated glycans will be great tools for investigating functional lectin receptors in situ.

The objectives of this study were to determine the effect of pH on chemical, structural, and functional properties of Cheddar cheese, and to relate changes in structure to changes in cheese functionality. Cheddar cheese was obtained from a cheese-production facility and stored at 4 degrees C. Ten days after manufacture, the cheese was cut into blocks that were vacuum-packaged and stored for 4 d at 4 degrees C. Cheese blocks were then high-pressure injected one, three, or five times with a 20% (wt/wt) glucono-delta-lactone solution. Successive injections were performed 24 h apart. Cheese blocks were then analyzed after 40 d of storage at 4 degrees C. Acidulant injection decreased cheese pH from 5.3 in the uninjected cheese to 4.7 after five injections. Decreased pH increased the content of soluble calcium and slightly decreased the total calcium content of cheese. At the highest level, injection of acidulant promoted syneresis. Thus, after five injections, the moisture content of che...

During last decade there has been significant progress in the development of analytical techniques for evaluation of receptor-ligand interaction. Surface plasmon resonance (SPR)-based optical biosensors are now being used extensively to define the kinetics of wide variety of macromolecular interactions and high-and low-affinity small molecule interactions. The experimental design data analysis methods are evolving along with widespread applications in ligand fishing, microbiology, virology, host-pathogen interaction, epitope mapping, and protein-, cell-, membrane-, nucleic acid-protein interactions. SPR-based biosensors have strong impact on basic and applied research significantly. This brief review describes the SPR technology and few of its applications in relation to receptor-ligand interaction that has brought significant change in the methodology, analysis, interpretation, and application of the SPR technology.

During last decade there has been significant progress in the development of analytical techniques for evaluation of receptor-ligand interaction. Surface plasmon resonance (SPR)-based optical biosensors are now being used extensively to define the kinetics of wide variety of macromolecular interactions and high-and low-affinity small molecule interactions. The experimental design data analysis methods are evolving along with widespread applications in ligand fishing, microbiology, virology, host-pathogen interaction, epitope mapping, and protein-, cell-, membrane-, nucleic acid-protein interactions. SPR-based biosensors have strong impact on basic and applied research significantly. This brief review describes the SPR technology and few of its applications in relation to receptor-ligand interaction that has brought significant change in the methodology, analysis, interpretation, and application of the SPR technology.

... Wenhui Li, 1 * Swee-Kee Wong, 1 Fang Li, 2 Jens H. Kuhn, 1 ,3 I-Chueh Huang, 1 Hyeryun Choe, 4 and Michael ... Jackwood, MW, DA Hilt, SA Callison, CW Lee, H. Plaza, and E. Wade ... Kan, B., M. Wang, H. Jing, H. Xu, X. Jiang, M. Yan, W. Liang, H. Zheng, K. Wan, Q. Liu, B. Cui, Y ...

Transforming growth factor-␤ (TGF-␤) signaling requires the action of Smad proteins in association with other DNA-binding factors and coactivator and corepressor proteins to modulate target gene transcription. Smad2 and Smad3 both associate with the c-Ski and Sno oncoproteins to repress transcription of Smad target genes via recruitment of a nuclear corepressor complex.

Thymidylate synthase (TS) and dihydrofolate reductase (DHFR) play essential role in DNA synthesis, repair and cell division by catalyzing two subsequent reactions in thymidylate biosynthesis cycle. The lack of either enzyme leads to thymineless death of the cell, therefore inhibition of the enzyme activity is a common and successful tool in cancer chemotherapy and treatment of other diseases. However, the detailed mechanism of thymidylate synthesis cycle, especially the interactions between cycle enzymes and its role remain unknown.

The physiological responses of cells to external and internal stimuli are governed by genes and proteins interacting in complex networks whose dynamical properties are impossible to understand by intuitive reasoning alone. Recent advances by theoretical biologists have demonstrated that molecular regulatory networks can be accurately modeled in mathematical terms. These models shed light on the design principles of biological control systems and make predictions that have been verified experimentally.

One strategy to potentially improve the success of drug discovery is to apply computational approaches early in the process to select molecules and scaffolds with ideal binding and physicochemical properties. Numerous algorithms and different molecular descriptors have been used for modeling ligand-protein interactions as well as absorption, distribution, metabolism and excretion (ADME) properties. In most cases a single data set has been evaluated with one approach or multiple algorithms that have been compared for a single dataset. These models have been primarily evaluated by leave-one out analysis or boot strapping with groups representing 25-50% of the training set left out of the final model. In a very few examples a test set of molecules not included in the model has been used for an external evaluation. In the present study we have applied Sammon non-linear maps, Support Vector Machines and Kohonen Self Organizing Maps to modeling numerous datasets for ADME properties including human intestinal absorption, blood brain barrier permeability, cytochrome P450 binding, plasma protein binding, P-gp inhibition, volume of distribution and plasma half life.

Full quantum computation of the electronic state of proteins has recently become possible by the advent of the ab initio fragment molecular orbital (FMO) method. We applied this method to the analysis of the interaction between the Bombyx mori pheromone-binding protein and its ligand, bombykol. The protein-ligand interaction of this molecular complex was minutely analyzed by the FMO method, and the analysis revealed several important interactions between the ligand and amino acid residues.

Progress in identification of plant ion channels and development of electrophysiological analyses in heterologous expression systems and in planta, in combination with reverse genetic approaches, are providing the possibility of associating molecular entities with physiological functions. Recently, the first attempts to determine in vivo functions using knockout mutants demonstrated the roles of root ion channels. The search for proteins interacting with such channels leads to an even more complex view of the concerted action in protein networks.

Most important processes in cell life are regulated by calcium (Ca 2+ ). A number of mechanisms have thus been developed to maintain the concentration of free Ca 2+ inside cells at the level (100-200 nM) necessary for the optimal operation of the targets of its regulatory function. The systems that move Ca 2+ back and forth across membranes are important actors in its control. The plasma membrane calcium ATPase (PMCA pump) which ejects Ca 2+ from all eukaryotic cell types will be the topic of this contribution.

The review assesses current status and attempts to forecast trends in the development of lectin biorecognition technology. The progressive trend is characterized scientometrically and reflects the current transient situation, when standard low-throughput lectin-based techniques are being replaced by a novel microarray-based techniques offering high-throughput of detection. The technology is still in its infancy (validation phase), but already shows promise as an efficient tool to decipher the enormous complexity of the glycocode that influences physiological status of the cell. Further enhancement in robustness and flexibility of lectin microarrays is predicted by using recombinant and artificial lectins that will render production of lectin microarrays cost-effective and more affordable. Mass spectrometry is expected to play an important role to characterize the binding profile of new lectins. Differences in glycan recognition by lectins and anticarbohydrate antibodies are given on a molecular basis, and strong and weak points of both biorecognition molecules in diagnosis are briefly discussed.

The heat-induced interactions between whey proteins and casein micelles were investigated by de"ning the "nal product of the reaction when milk was heated at temperatures up to 903C. By looking at the changes of the interactions in skim milk and in resuspended casein micelles, to which di!erent amounts of whey protein had been added, information on the mechanisms that determine the heat-induced protein}protein interactions in milk was derived. The ratio of -lactalbumin and -lactoglobulin to -casein and the ratio of -lactalbumin to -lactoglobulin found in the micellar pellet were used as indices of these heat-induced reactions occurring in milk. The results suggested that at these low temperature (70}903C) with batch heating conditions, whey proteins form soluble complexes which act as intermediates in the heat-induced association of -lactalbumin and -lactoglobulin with the micelles. The presence of -lactoglobulin was necessary for any association of whey protein with casein micelles to occur; furthermore, the amount of -lactoglobulin found in the micellar pellet after heating seemed to be limited by a discrete number of binding sites available on the micelles.

Metal chelate affinity precipitation of proteins, a method combining metal-protein interaction and affinity precipitation is being discussed as a selective separation process for proteins. The technique utilizes a flexible soluble-insoluble thermo-responsive polymer with a covalently linked ligand loaded with metal ions. The affinity binding of the target protein varies with different metal ions. Copolymers of N-isopropylacrylamide with 1vinylimidazole loaded with Cu(II) ions are designed as a potential carriers for affinity purification and proved to be successful for purification of protein inhibitors from a variety of cereals.

The causative agent of anthrax, Bacillus anthracis, is capable of circumventing the humoral and innate immune defense of the host and modulating the blood chemistry in circulation to initiate a productive infection. It has been shown that the pathogen employs a number of strategies against immune cells using secreted pathogenic factors such as toxins. However, interference of B. anthracis with the innate immune system through specific interaction of the spore surface with host proteins such as the complement system has heretofore attracted little attention. In order to assess the mechanisms by which B. anthracis evades the defense system, we employed a proteomic analysis to identify human serum proteins interacting with B. anthracis spores, and found that plasminogen (PLG) is a major surface-bound protein. PLG efficiently bound to spores in a lysine-and exosporium-dependent manner. We identified a-enolase and elongation factor tu as PLG receptors. PLG-bound spores were capable of exhibiting anti-opsonic properties by cleaving C3b molecules in vitro and in rabbit bronchoalveolar lavage fluid, resulting in a decrease in macrophage phagocytosis. Our findings represent a step forward in understanding the mechanisms involved in the evasion of innate immunity by B. anthracis through recruitment of PLG resulting in the enhancement of anti-complement and anti-opsonization properties of the pathogen. Citation: Chung M-C, Tonry JH, Narayanan A, Manes NP, Mackie RS, et al. (2011) Bacillus anthracis Interacts with Plasmin(ogen) to Evade C3b-Dependent Innate Immunity. PLoS ONE 6(3): e18119.

The rapid proliferation of many different engineered nanomaterials (defined as materials designed and produced to have structural features with at least one dimension of 100 nanometers or less) presents a dilemma to regulators regarding hazard identification. The International Life Sciences Institute Research Foundation/Risk Science Institute convened an expert working group to develop a screening strategy for the hazard identification of engineered nanomaterials. The working group report presents the elements of a screening strategy rather than a detailed testing protocol. Based on an evaluation of the limited data currently available, the report presents a broad data gathering strategy applicable to this early stage in the development of a risk assessment process for Published: 06 October 2005 Particle and Fibre Toxicology 2005, 2:8 (page number not for citation purposes)

Visualization has long been key in helping to understand biological systems, such as metabolism 1 , signaling 2 and the regulation of gene expression 3 . In recent years, the study of such systems has been profoundly influenced by the development of a wide range of high-throughput experimental methods (Box 1), resulting in a greatly increased volume of complex, interconnected data. Remarkably, in spite of these changes, and in spite of the development of new methods for visualizing and analyzing these data, we still use the same primary visual metaphor to communicate ideas about biological systems: namely, pathways (graphs that show overall changes in state) or, more generally, networks (graphs that do not necessarily show state changes).

The effect of biotin binding on the thermal stability of streptavidin (STV) and avidin (AVD) was evaluated using differential scanning calorimetry. Biotin binding increases the midpoint of temperature T m of thermally induced denaturation of STV and AVD in phosphate buffer from 75 and 83°C to 112 and 117°C at full biotin saturation, respectively. This thermostability is the highest reported for proteins coming from either mesophilic or thermophilic organisms. In both proteins, biotin also increases the calorimetric enthalpy and the cooperativity of the unfolding. Thermal stability of STV was also evaluated in the presence of high concentrations of urea or guanidinium hydrochloride (GuHCl). In 6 M GuHCl, STV remains as a tetramer and the T m of the STV-biotin complex is centered at 108°C, a few degrees below the value obtained in phosphate buffer. On the contrary, STV under fully saturating condition remains mainly in its dimeric form in 8 M urea and the thermogram shows two endotherms. The main endotherm at a lower temperature has been ascribed to the dimeric liganded state with a T m of 87°C, and the higher temperature endotherm to the tetrameric liganded form with a T m of 106°C. As the thermostability of unliganded protein in the presence of urea is unchanged upon binding we related the extremely high thermal stability of this protein to both an increase in structural ordering and compactness with the preservation of the tetramer integrity.