The continuing story of class IIa bacteriocins.

Many bacteria produce antimicrobial peptides, which are also referred to as peptide bacteriocins. The class IIa bacteriocins, often designated pediocin-like bacteriocins, constitute the most dominant group of antimicrobial peptides produced by lactic acid bacteria. The bacteriocins that belong to this class are structurally related and kill target cells by membrane permeabilization. Despite their structural similarity, class IIa bacteriocins display different target cell specificities. In the search for new antibiotic substances, the class IIa bacteriocins have been identified as promising new candidates and have thus received much attention. They kill some pathogenic bacteria (e.g., Listeria) with high efficiency, and they constitute a good model system for structure-function analyses of antimicrobial peptides in general. This review focuses on class IIa bacteriocins, especially on their structure, function, mode of action, biosynthesis, bacteriocin immunity, and current food applications. The genetics and biosynthesis of class IIa bacteriocins are well understood. The bacteriocins are ribosomally synthesized with an N-terminal leader sequence, which is cleaved off upon secretion. After externalization, the class IIa bacteriocins attach to potential target cells and, through electrostatic and hydrophobic interactions, subsequently permeabilize the cell membrane of sensitive cells. Recent observations suggest that a chiral interaction and possibly the presence of a mannose permease protein on the target cell surface are required for a bacteria to be sensitive to class IIa bacteriocins. There is also substantial evidence that the C-terminal half penetrates into the target cell membrane, and it plays an important role in determining the target cell specificity of these bacteriocins. Immunity proteins protect the bacteriocin producer from the bacteriocin it secretes. The three-dimensional structures of two class IIa immunity proteins have been determined, and it has been shown that the C-terminal halves of these cytosolic four-helix bundle proteins specify which class IIa bacteriocin they protect against.     

A dataset of human cornea proteins identified by Peptide mass fingerprinting and tandem mass spectrometry

Diseases of the cornea are extremely common and cause severe visual impairment worldwide. To explore the basic molecular mechanisms involved in corneal health and disease, the present study characterizes the proteome of the normal human cornea. All proteins were extracted from the central 7-mm region of 12 normal human donor corneas containing all layers: epithelium, Bowman's layer, stroma, Descemet's membrane, and endothelium. Proteins were fractionated and identified using two different procedures: (i) two-dimensional gel electrophoresis and protein identification by MALDI-MS and (ii) strong cation exchange or one-dimensional SDS gel electrophoresis followed by LC-MS/MS. All together, 141 distinct proteins were identified of which 99 had not previously been identified in any mammalian corneas by direct protein identification methods. The characterized proteins are involved in many processes including antiangiogenesis, antimicrobial defense, protection from and transport of heme and iron, tissue protection against UV radiation and oxidative stress, cell metabolism, and maintenance of intracellular and extracellular structures and stability. This proteome study of the healthy human cornea provides a basis for further analysis of corneal diseases and the design of bioengineered corneas.     

Inductive characteristics of proteins secreted by retinal cells

The studies of the development of eye rudiments and formation of adult eye tissues have always been among priorities in developmental biology and then in developmental genetics, which is associated with the peculiarities of the development and structure of the eye. In the late 80s, it was established by the group of developmental factors of the Institute of Gene Biology of RAS that many differentiated tissues are able to produce proteins causing homologous differentiations in polypotent cells of early gastrula ectoderm. The aim of our present study was isolation of proteins secreted by mammalian and fish retinal cells and determination of their inductive properties in early gastrula ectoderm of Xenopus laevis. The sets of proteins secreted by retina induce tissues homologous to the inducer, that is, neural tissue, brain, retina, pigmented epithelium, and also lenses and ear vesicles. The retinal inductive proteins retain their homologous inductive capacity after lyophilization. Biological testing shows that a total mixture of proteins secreted by retinal cells induces in polypotent gastrula ectoderm of X. laevis a narrower spectrum of tissues than the fractions obtained from this mixture. The above-outlined results obtained in thecourse of investigations of inductive peculiarities of retina and its fractions help in the elucidation of questions concerning embryonic induction and factors determining it, as well as questions concerning the maintenance of tissue specifity and regenerative capacity of the tissue studied.     

Changes of extracellular matrix of rat cornea after exposure to hypoxia

The purpose of the study was to check whether hypoxia of corneal tissue increases the collagenolytic activity due to release of reactive oxygen and nitrogen species. Rats were exposed to hypoxia 10% O(2) for 4, 14, and 21 days. The radical tissue injury was measured by the level of nitrotyrosine and changes in the lipoperoxide-related fluorophores. Collagen protein composition was analyzed by slab gel electrophoresis. The activity of gelatinolytic enzymes was studied using the zymography. The vascularization of the corneas was measured. We found no differences in the corneal tissue in the gel electrophoretic profile of collagenous proteins and gelatinolytic activity between normoxic and hypoxic rats. We did not find any sign of radical tissue injury. There were no changes in the vascularization of corneas after exposition to hypoxia. The environmental 10% hypoxia does not induce radical tissue injury and an increase of collagenolytic activity in the rat cornea.     

Novel two-stage hybrid neural discriminant model for predicting proteins structural classes

In order to establish novel hybrid neural discriminant model, linear discriminant analysis (LDA) was used at the first stage to evaluate the contribution of sequence parameters in determining the protein structural class. An in-house program generated parameters including single amino acid and all dipeptide composition frequencies for 498 proteins came from Zhou [An intriguing controversy over protein structural class prediction, J. Protein Chem. 17(8) (1998) 729-738]. Then, 127 statistically effective parameters were selected by stepwise LDA and were used as inputs of the artificial neural networks (ANNs) to build a two-stage hybrid predictor. In this study, self-consistency and jackknife tests were used to verify the performance of this hybrid model, and were compared with some of prior works. The results showed that our two-stage hybrid neural discriminant model approach is very promising and may play a complementary role to the existing powerful approaches.     

Structural elements, mechanism, and evolutionary convergence of Rho protein-guanine nucleotide exchange factor complexes

Rho GTPases act as key regulators of cellular biochemistry by determining the timing, direction, and amplitude of signal transduction in a number of important pathways. The rate of activation of a GTPase-controlled reaction is limited by the rate of GTP binding to the Rho protein, and this, in turn, depends on the rate that GDP dissociates from the GTPase. The latter is controlled by the action of guanine nucleotide exchange factors (GEFs) that catalyze GDP-GTP exchange by increasing the rate of GDP dissociation. Here, the recently reported structural information for Rho GTPase-GEF complexes and the molecular basis for the specificity of their interactions are discussed. Underscoring the importance of regulating the Rho GTPase activation pathway, genetically unrelated proteins have evolved which complement or mimic the Dbl homology-Pleckstrin homology (DH-PH) domain-containing family of proteins in their ability to catalyze GDP-GTP exchange. In particular, the structure of the mammalian Cdc42 protein bound to the SopE protein from Salmonella typhimurium illustrates how two unrelated protein folds are able to carry out guanine nucleotide exchange by a remarkably similar mechanism. It will be interesting to see if this conservation of mechanism extends to a newly recognized class of GEFs related to the DOCK180 family.     

Quantitative metabolomic analysis of the human cornea and aqueous humor

Introduction

Cornea is the outermost part of the eye supplied mostly by aqueous humor (AH). Therefore, the comparison of the metabolomic compositions of AH and cornea may help to determine which compounds are produced inside the cornea, and which penetrate into cornea from AH for intra-corneal consumption. Keratoconus (KC) is the most common form of the cornea dystrophy, and the analysis of KC corneas can unravel the metabolomic changes occurring in AH and cornea of KC patients.

Objectives

The work is aimed at the determination of concentrations of a wide range of metabolites in the human cornea and AH, the comparison of the metabolomic profiles of cornea and AH, and the comparison of the metabolomic compositions of samples taken from KC patients and normal donors (post-mortem).

Methods

The quantitative metabolomic profiling was carried out with the use of two independent methods—high-frequency ¹H NMR spectroscopy and HPLC with high-resolution ESI-MS detection.

Results

The concentrations of 71 most abundant metabolites in cornea and AH from keratoconus patients and from human cadavers have been measured. It is found that the concentrations of purines and organic acids in cornea are significantly higher than in AH. The KC corneas are characterized by the enhanced levels of acetate and citrate, and also by low values of GSH/GSSG ratios.

Conclusion

A significant difference in the metabolomic compositions of the human AH and cornea has been revealed. The concentrations of glucose and some amino acids in cornea are significantly lower than in AH, indicating their fast consumption inside the cornea. The high levels of organic acids, purines and GSH in cornea should be attributed to their production in the cornea. The enhanced levels of acetate and citrate as well as the low values of GSH/GSSG ratios in KC corneas are the indicators of the oxidative stress.

     

Human cornea proteome: identification and quantitation of the proteins of the three main layers including epithelium, stroma, and endothelium

Diseases of the cornea are common and refer to conditions like infections, injuries and genetic defects. Morphologically, many corneal diseases affect only certain layers of the cornea and separate analysis of the individual layers is therefore of interest to explore the basic molecular mechanisms involved in corneal health and disease. In this study, the three main layers including, the epithelium, stroma and endothelium of healthy human corneas were isolated. Prior to analysis by LC-MS/MS the proteins from the different layers were either (i) separated by SDS-PAGE followed by in-gel trypsinization, (ii) in-solution digested without prior protein separation or, (iii) in-solution digested followed by cation exchange chromatography. A total of 3250 unique Swiss-Prot annotated proteins were identified in human corneas, 2737 in the epithelium, 1679 in the stroma, and 880 in the endothelial layer. Of these, 1787 proteins have not previously been identified in the human cornea by mass spectrometry. In total, 771 proteins were quantified, 157 based on in-solution digestion and 770 based on SDS-PAGE separation followed by in-gel digestion of excised gel pieces. Protein analysis showed that many of the identified proteins are plasma proteins involved in defense responses.     

Structural analysis of botulinum neurotoxin serotype F light chain: implications on substrate binding and inhibitor design

The seven serologically distinct Clostridium botulinum neurotoxins (BoNTs A-G) are zinc endopeptidases which block the neurotransmitter release by cleaving one of the three proteins of the soluble N-ethylmaleimide-sensitive-factor attachment protein receptor complex (SNARE complex) essential for the fusion of vesicles containing neurotransmitters with target membranes. These metallopeptidases exhibit unique specificity for the substrates and peptide bonds they cleave. Development of countermeasures and therapeutics for BoNTs is a priority because of their extreme toxicity and potential misuse as biowarfare agents. Though they share sequence homology and structural similarity, the structural information on each one of them is required to understand the mechanism of action of all of them because of their specificity. Unraveling the mechanism will help in the ultimate goal of developing inhibitors as antibotulinum drugs for the toxins. Here, we report the high-resolution structure of active BoNT/F catalytic domain in two crystal forms. The structure was exploited for modeling the substrate binding and identifying the S1' subsite and the putative exosites which are different from BoNT/A or BoNT/B. The orientation of docking of the substrate at the active site is consistent with the experimental BoNT/A-LC:SNAP-25 peptide model and our proposed model for BoNT/E-LC:SNAP-25.     

Method for Lyophilizing Brain Proteolipid Preparation That Increases Subsequent Solubilization by Detergent

Abstract: A frozen mixture of solubilized brain proteolipid proteins in chloroform-methanol is not sublimable in a vacuum. However, when 7 to 10 volumes of benzene were added to a chloroform-methanol solution containing 5 mg of proteolipid protein per ml, the proteolipid proteins remained in solution for a while and the frozen mixture was easily sublimated at 2 mm Hg. Before the addition of benzene, higher concentrations of protein required the acidification of the medium to avoid precipitation of proteolipid proteins. In contrast to what happens when proteolipid proteins are obtained by the evaporation of the organic mixture at room temperature, the protein obtained by lyophilization was soluble in aqueous solutions of ionic and nonionic detergents. Sodium dodecyl sulfate at 0.6 to 0.7% concentration completely solubilized the proteolipid protein obtained by lyophilization. With the nonionic detergents Lubrol WX and Triton X-100, a solubilization between 50 and 65% was achieved. Sodium deoxycholate was practically ineffective. Triton X-100 showed selectivity in solubilizing certain proteins. The role of lipids in the solubilization of proteolipid proteins with detergents is discussed.     

Hierarchy of inductive events

Examination of data on the inducing capacity of mesoderm-inducing factors shows that none of them induces mesoderm alone, but that they also induce endoderm and neural tissues, while in the mesoderm itself, they induce tissues belonging to its main levels. Tests on the inducing capacity of living retina have shown that it does not induce mesoderm, but does induce a spectrum of tissues, including retina, pigmented epithelium, lens and a piece of brain. This situation seems to be indispensable because if it evokes only one differentiation, an increase of diversity in development would be impossible. Selectivity occurs only at the end of the sequence of inductions, as it does in the induction of lens tissue by lens epithelium. Such mechanisms, however, are insufficient for the development of different kinds of cells into homogeneous tissues. This is achieved through the aggregation or separation of initially induced cells, their own products determining (or not) their further fate and leading to homogeneity of tissues. These mechanisms of the first two levels of inductive interactions overlap with events that allow or prevent the access of inducing factors and are, therefore, also involved in the manifestation of competence of potentially reactive cells.     

Structural biology of the Bcl-2 family and its mimicry by viral proteins

Intrinsic apoptosis in mammals is regulated by protein–protein interactions among the B-cell lymphoma-2 (Bcl-2) family. The sequences, structures and binding specificity between pro-survival Bcl-2 proteins and their pro-apoptotic Bcl-2 homology 3 motif only (BH3-only) protein antagonists are now well understood. In contrast, our understanding of the mode of action of Bax and Bak, the two necessary proteins for apoptosis is incomplete. Bax and Bak are isostructural with pro-survival Bcl-2 proteins and also interact with BH3-only proteins, albeit weakly. Two sites have been identified; the in-groove interaction analogous to the pro-survival BH3-only interaction and a site on the opposite molecular face. Interaction of Bax or Bak with activator BH3-only proteins and mitochondrial membranes triggers a series of ill-defined conformational changes initiating their oligomerization and mitochondrial outer membrane permeabilization. Many actions of the mammalian pro-survival Bcl-2 family are mimicked by viruses. By expressing proteins mimicking mammalian pro-survival Bcl-2 family proteins, viruses neutralize death-inducing members of the Bcl-2 family and evade host cell apoptosis during replication. Remarkably, structural elements are preserved in viral Bcl-2 proteins even though there is in many cases little discernible sequence conservation with their mammalian counterparts. Some viral Bcl-2 proteins are dimeric, but they have distinct structures to those observed for mammalian Bcl-2 proteins. Furthermore, viral Bcl-2 proteins modulate innate immune responses regulated by NF-κB through an interface separate from the canonical BH3-binding groove. Our increasing structural understanding of the viral Bcl-2 proteins is leading to new insights in the cellular Bcl-2 network by exploring potential alternate functional modes in the cellular context. We compare the cellular and viral Bcl-2 proteins and discuss how alterations in their structure, sequence and binding specificity lead to differences in behavior, and together with the intrinsic structural plasticity in the Bcl-2 fold enable exquisite control over critical cellular signaling pathways.     

In vivo sensing of rabbit cornea by terahertz technology

A Novel scalable approach using Terahertz (THz) waves together with the electromagnetic field simulation was applied to investigate four rabbits of eight rabbit corneas in vivo. One eye of each rabbits’ corneas was edema induced; the other eye of the corneas served as the control. The simulation revealed the propagation of THz waves at a certain distance along the sub-surface of the cornea. THz spectra have been collected close to the corneal surface by deviating the direct reflection of the THz beam for the edema cornea, the reflected wave intensity for edema corneas is generally larger compared with the control cornea. Upon edema becomes severe at the end of the observation, the reflected wave intensities obtained by detector corresponding to the corneal deep stroma layer approach to the same value for all observed corneas. Good correlation is observed between central corneal thickness measurements and THz wave reflection signal intensities. Our results demonstrated that THz spectroscopy technique could obtain the information from different corneal sublayers.     

Cross-validation of protein structural class prediction using statistical clustering and neural networks.

We present an approach to predicting protein structural class that uses amino acid composition and hydrophobic pattern frequency information as input to two types of neural networks: (1) a three-layer back-propagation network and (2) a learning vector quantization network. The results of these methods are compared to those obtained from a modified Euclidean statistical clustering algorithm. The protein sequence data used to drive these algorithms consist of the normalized frequency of up to 20 amino acid types and six hydrophobic amino acid patterns. From these frequency values the structural class predictions for each protein (all-alpha, all-beta, or alpha-beta classes) are derived. Examples consisting of 64 previously classified proteins were randomly divided into multiple training (56 proteins) and test (8 proteins) sets. The best performing algorithm on the test sets was the learning vector quantization network using 17 inputs, obtaining a prediction accuracy of 80.2%. The Matthews correlation coefficients are statistically significant for all algorithms and all structural classes. The differences between algorithms are in general not statistically significant. These results show that information exists in protein primary sequences that is easily obtainable and useful for the prediction of protein structural class by neural networks as well as by standard statistical clustering algorithms.     

The roles of contact residue disorder and domain composition in characterizing protein-ligand binding specificity and promiscuity

Most protein chains interact with only one ligand but a small number of protein chains can bind several ligands, and many examples are available in the protein-ligand complex database of PDB. Among these proteins, some show preferences for the ligands or types of ligands they bind; however, so far we have only poor understanding of what determines protein-ligand binding and its specificity. Here we investigate the structural and functional properties of proteins in protein-ligand complexes. Analysis of the protein-ligand complex dataset from the PDB structure database reveals that proteins with more interactions have more disordered contact residues. Those proteins containing few disordered contact residues that bind multiple ligands have a tendency to consist of several domains. Analysis of physicochemical properties of hub contact residues binding multiple ligands indicates that they are enriched for hydrophilic, charged, polar and His-Asp catalytic triad residues. Finally, in order to differentiate proteins binding different classes of ligands, we mapped the three most prominent classes of ligands onto different superfamily domains. Our results demonstrate that contact residue disorder and ordered multiple domains are complementary factors that play a crucial role in determining ligand binding specificity and promiscuity.     

Microtubule organization by cross-linking and bundling proteins.

To understand microtubule function the factors regulating their spatial organization and their interaction with cellular organelles, including other microtubules, must be elucidated. Many proteins are implicated in these organizational events and the known consequences of their actions within the cell are increasing. For example, the function of microtubule bundles at the surfaces of polarized cells has recently received attention, as has the action in cortical rotation of a transient arrangement of microtubules found beneath the vegetal surface of fertilized frog eggs. The in vivo association of microtubules during early Xenopus oogenesis has added interest as microtubules bundled in cell-free extracts are protected against the action of a severing protein found in this animal. A 52 kDa F-actin bundling protein purified from Physarum polycephalum organizes microtubules and causes the cobundling of microtubules and microfilaments. These observations, in concert with others that are presented, emphasize the diversity within the family of microtubule cross-linking proteins. The challenge is to determine which proteins are relevant from a physiological perspective, to ascertain their molecular mechanisms of action and to describe how they affect cytoplasmic organization and cell function. To realize this objective, the proteins which cross-link and bundle microtubules must be investigated by techniques which reveal different but related aspects of their properties. Cloning and sequencing of genes for cross-linking proteins, their subcellular localization especially as microtubule-related changes in cell morphology are occurring and the application of genetic studies are necessary. Study of the neural MAP provides the best example of just how powerful current experimental approaches are and at the same time shows their limits. The neural MAP have long been noted for their enhancement of tubulin assembly and microtubule stability. Their spatial distribution has been studied during the morphogenesis of neural cells. Sequencing of cloned genes has revealed the functional domains of neural MAP including carboxy-terminal microtubule-binding sites. Similarities to microtubule binding proteins from other cell types stimulate interest in the neural MAP and further suggest their importance in microtubule organization. For example, MAP4 enjoys a wide cellular distribution and has microtubule-binding sequences very similar to those in the neural MAP. Moreover, the nontubulin proteins of marginal bands are immunologically related to neural MAP, indicating shared structural/functional domains. Even with these findings the mechanism by which neural MAP cross-link microtubules remains uncertain. Indeed, some researchers express doubt that microtubule cross-linking is actually a function of neural MAP in vivo.(ABSTRACT TRUNCATED AT 400 WORDS)     

Recognition in the face of diversity: interactions of heterotrimeric G proteins and G protein-coupled receptor (GPCR) kinases with activated GPCRs

G protein-coupled receptors (GPCRs) represent the largest class of integral membrane protein receptors in the human genome. Despite the great diversity of ligands that activate these GPCRs, they interact with a relatively small number of intracellular proteins to induce profound physiological change. Both heterotrimeric G proteins and GPCR kinases are well known for their ability to specifically recognize GPCRs in their active state. Recent structural studies now suggest that heterotrimeric G proteins and GPCR kinases identify activated receptors via a common molecular mechanism despite having completely different folds.     

Expression of SFRP Family Proteins in Human Keratoconus Corneas

We investigated the expression of the secreted frizzled-related proteins (SFRPs) in keratoconus (KC) and control corneas. KC buttons (∼8 mm diameter) (n = 15) and whole control corneas (n = 7) were fixed in 10% formalin or 2% paraformaldehyde and subsequently paraffin embedded and sectioned. Sections for histopathology were stained with hematoxylin and eosin, or Periodic Acid Schiff’s reagent. A series of sections was also immunolabelled with SFRP 1 to 5 antibodies, visualised using immunofluorescence, and examined with a Zeiss LSM700 scanning laser confocal microscope. Semi-quantitative grading was used to compare SFRP immunostaining in KC and control corneas. Overall, KC corneas showed increased immunostaining for SFRP1 to 5, compared to controls. Corneal epithelium in all KC corneas displayed heterogeneous moderate to strong immunoreactivity for SFRP1 to 4, particularly in the basal epithelium adjacent to cone area. SFRP3 and 5 were localised to epithelial cell membranes in KC and control corneas, with increased SFRP3 cytoplasmic expression observed in KC. Strong stromal expression of SFRP5, including extracellular matrix, was seen in both KC and control corneas. In control corneas we observed differential expression of SFRP family proteins in the limbus compared to more central cornea. Taken together, our results support a role for SFRPs in maintaining a healthy cornea and in the pathogenesis of epithelial and anterior stromal disruption observed in KC.