Caveolae: Formation,dynamics, and function

Caveolae are abundant surface pits formed by the assembly of cytoplasmic proteins on a platform generated by caveolin integral membrane proteins and membrane lipids. This membranous assembly can bud off into the cell or can be disassembled releasing the cavin proteins into the cytosol. Disassembly can be triggered by increased membrane tension, or by stress stimuli, such as UV. Here, we discuss recent mechanistic studies showing how caveolae are formed and how their unique properties allow them to function as multifunctional protective and signaling structures.     

Statistical measures on residue-level protein structural properties

The atomic-level structural properties of proteins, such as bond lengths, bond angles, and torsion angles, have been well studied and understood based on either chemistry knowledge or statistical analysis. Similar properties on the residue-level, such as the distances between two residues and the angles formed by short sequences of residues, can be equally important for structural analysis and modeling, but these have not been examined and documented on a similar scale. While these properties are difficult to measure experimentally, they can be statistically estimated in meaningful ways based on their distributions in known proteins structures. Residue-level structural properties including various types of residue distances and angles are estimated statistically. A software package is built to provide direct access to the statistical data for the properties including some important correlations not previously investigated. The distributions of residue distances and angles may vary with varying sequences, but in most cases, are concentrated in some high probability ranges, corresponding to their frequent occurrences in either α-helices or β-sheets. Strong correlations among neighboring residue angles, similar to those between neighboring torsion angles at the atomic-level, are revealed based on their statistical measures. Residue-level statistical potentials can be defined using the statistical distributions and correlations of the residue distances and angles. Ramachandran-like plots for strongly correlated residue angles are plotted and analyzed. Their applications to structural evaluation and refinement are demonstrated. With the increase in both number and quality of known protein structures, many structural properties can be derived from sets of protein structures by statistical analysis and data mining, and these can even be used as a supplement to the experimental data for structure determinations. Indeed, the statistical measures on various types of residue distances and angles provide more systematic and quantitative assessments on these properties, which can otherwise be estimated only individually and qualitatively. Their distributions and correlations in known protein structures show their importance for providing insights into how proteins may fold naturally to various residue-level structures.     

Electroblotting onto activated glass. High efficiency preparation of proteins from analytical sodium dodecyl sulfate-polyacrylamide gels for direct sequence analysis

We have developed a new method for the isolation of proteins for microsequencing. It consists of electrophoretic transfer (electroblotting) of proteins or their cleavage fragments onto activated glass filter paper sheets immediately after separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The proteins are immobilized on the glass fiber sheets by ionic interactions or by covalent attachment. A wide range of proteins can be prepared in this fashion with no apparent restriction due to solubility, size, charge, or other intrinsic properties of the proteins. As little as 50 ng of the transferred proteins can be detected using Coomassie Blue or fluorescent dye staining procedures and even smaller amounts of radiolabeled proteins by autoradiography. After detection, the protein-containing bands or spots are cut out and inserted directly into a gas-phase sequenator. The piece of glass fiber sheet acts as a support for the protein during the sequencing. Amounts of protein in the 5- to 150-pmol range can be sequenced, and extended runs can be obtained from the blotted samples because of improved stepwise yields and lower backgrounds. The method has been successfully applied to the sequencing of a variety of proteins and peptides isolated from one-dimensional and two-dimensional polyacrylamide gels.     

Solubility of proteins

A theory is presented on the solubility of proteins, in the hydrated as well as in the dry state, and in water as well as in organic solvents. To this effect, colloidal stability is assimilated with the solubility of the proteins, considered as hydrated entities. By means of a surface thermodynamic approach it can be shown that an increase in size of a hydrated protein must lead to insolubility, even in the absence of any change in a protein's surface properties. This can be substantiated experimentally by comparing the surface properties of immune complexes with those of their constituent immunoglobulins, as well as by comparing some of the properties of intact tobacco mosaic virus with those of its monomeric capsid subunits. Insolubilization of proteins by means of charge interactions as well as by dehydration is studied; an explanation is given of why precipitation caused by charge interactions is more likely to lead to partial irreversible denaturation than precipitation caused by protein-protein interactions brought about by partial dehydration (e.g., by “salting-out”). A link is established between the smallness (or even the negative value) of the interfacial tension between given proteins and various solvents and their solubility in these solvents. The energy of hydration of proteins can also be measured, and the differences between the free energies of interaction of dried and hydrated proteins with water point toward the additional processes underlying the solubilization, i.e., toward the conformational change of a protein in the process of becoming hydrated. The parameter of conformational change of a protein, while becoming hydrated, appears to be more closely linked to its degree of hydration than to its hydration energy.     

Membrane and protein interactions of oxysterols

PURPOSE OF REVIEW: Oxysterols, oxidation products of cholesterol, mediate numerous and diverse biological processes. The objective of this review is to explain some of the biochemical and cell biological properties of oxysterols based on their membrane biophysical properties and their interaction with integral and peripheral membrane proteins. RECENT FINDINGS: According to their biophysical properties, which can be distinct from those of cholesterol, oxysterols can promote or inhibit the formation of membrane microdomains or lipid rafts. Oxysterols that inhibit raft formation are cytotoxic. The stereo-specific binding of cholesterol to sterol-sensing domains in cholesterol homeostatic pathways is not duplicated by oxysterols, and some oxysterols are poor substrates for the pathways that detoxify cells of excess cholesterol. The cytotoxic roles of oxysterols are, at least partly, due to a direct physical effect on membranes involved in cholesterol-induced cell apoptosis and raft mediated cell signaling. Oxysterols regulate cellular functions by binding to oxysterol binding protein and oxysterol binding protein-related proteins. Oxysterol binding protein is a sterol-dependent scaffolding protein that regulates the extracellular signal-regulated kinase signaling pathway. According to a recently solved structure for a yeast oxysterol binding protein-related protein, Osh4, some members of this large family of proteins are likely sterol transporters. SUMMARY: Given the association of some oxysterols with atherosclerosis, it is important to identify the mechanisms by which their association with cell membranes and intracellular proteins controls membrane structure and properties and intracellular signaling and metabolism. Studies on oxysterol binding protein and oxysterol binding protein-related proteins should lead to new understandings about sterol-regulated signal transduction and membrane trafficking pathways in cells.     

Physical properties of ribosomal proteins isolated under different conditions from the Escherichia coli 50 S subunit

Physical properties of ribosomal proteins obtained with or without denaturating agents were compared. CD measurements and NMR studies have shown that proteins L2, L19, L24 and L30 isolated under denaturing conditions have the same properties as those prepared avoiding denaturating agents. CD and NMR spectra of proteins L1, L6, L11, L23, L25 and L29 obtained by us under denaturating conditions practically coincide with the data for the same proteins reported under 'mild' conditions. These findings suggest that the differences of reported physical properties can be due to different procedures of protein renaturation rather than to the methods of their isolation.     

Non-covalent interactions between proteins and polysaccharides

Foods with novel or improved properties can be created by utilizing non-covalent interactions between proteins and polysaccharides. In solution, either attractive or repulsive interactions between proteins and polysaccharides can be used to create microstructures that give foods novel textural and sensory properties. At interfaces, attractive electrostatic interactions can be used to create food emulsions with improved stability to environmental stresses or with novel encapsulation-release characteristics.     

Comparison of the physical properties of ribosomal proteins from Escherichia coli 50S subparticles isolated by different methods

Physical properties of ribosomal proteins obtained with or without denaturing agents were compared. CD measurements and PMR studies have shown that proteins L2, L19, L24 and L30 isolated under denaturing conditions have the same properties as those prepared avoiding denaturing agents. CD and PMR data of L1, L6, L11, L23, L25 and L29 obtained by us under denaturing conditions practically coincide with the data for these proteins obtained in "mild" conditions and published in the literature. These findings indicate that the differences of physical properties reported in the literature can be due to different procedures of protein renaturation rather than to the methods of their isolation.     

Spider silks: recombinant synthesis,assembly, spinning,and engineering of synthetic proteins

Since thousands of years humans have utilized insect silks for their own benefit and comfort. The most famous example is the use of reeled silkworm silk from Bombyx mori to produce textiles. In contrast, despite the more promising properties of their silk, spiders have not been domesticated for large-scale or even industrial applications, since farming the spiders is not commercially viable due to their highly territorial and cannibalistic nature. Before spider silks can be copied or mimicked, not only the sequence of the underlying proteins but also their functions have to be resolved. Several attempts to recombinantly produce spider silks or spider silk mimics in various expression hosts have been reported previously. A new protein engineering approach, which combines synthetic repetitive silk sequences with authentic silk domains, reveals proteins that closely resemble silk proteins and that can be produced at high yields, which provides a basis for cost-efficient large scale production of spider silk-like proteins.     

Modularity and functional plasticity of scaffold proteins as p(l)acemakers in cell signaling

Cells coordinate and integrate various functional modules that control their dynamics, intracellular trafficking, metabolism and gene expression. Such capacity is mediated by specific scaffold proteins that tether multiple components of signaling pathways at plasma membrane, Golgi apparatus, mitochondria, endoplasmic reticulum, nucleus and in more specialized subcellular structures such as focal adhesions, cell-cell junctions, endosomes, vesicles and synapses. Scaffold proteins act as "pacemakers" as well as "placemakers" that regulate the temporal, spatial and kinetic aspects of protein complex assembly by modulating the local concentrations, proximity, subcellular dispositions and biochemical properties of the target proteins through the intricate use of their modular protein domains. These regulatory mechanisms allow them to gate the specificity, integration and crosstalk of different signaling modules. In addition to acting as physical platforms for protein assembly, many professional scaffold proteins can also directly modify the properties of their targets while they themselves can be regulated by post-translational modifications and/or mechanical forces. Furthermore, multiple scaffold proteins can form alliances of higher-order regulatory networks. Here, we highlight the emerging themes of scaffold proteins by analyzing their common and distinctive mechanisms of action and regulation, which underlie their functional plasticity in cell signaling. Understanding these mechanisms in the context of space, time and force should have ramifications for human physiology and for developing new therapeutic approaches to control pathological states and diseases.     

High pressure simulations of biomolecules

Pressure is a thermodynamic variable which is particularly suitable for exploration of the properties of biological macromolecules. For proteins, in particular, denaturation induced by pressure is different from that induced by temperature or denaturants. The response of proteins to pressure changes can provide information on properties of their native and non-native states. This review focuses on molecular dynamics studies of the effect of pressure on detailed atomic models of proteins. It also reports on other theoretical approaches, such as Monte Carlo simulations, which have been used to study simplified models. Another purpose of this review is to try to point out potential future studies that may be both interesting and feasible, with constantly increasing computing power.     

Designing novel spectral classes of proteins with a tryptophan-expanded genetic code

Fluorescence methods are now well-established and powerful tools to study biological macromolecules. The canonical amino acid tryptophan (Trp), encoded by a single UGG triplet, is the main reporter of intrinsic fluorescence properties of most natural proteins and peptides and is thus an attractive target for tailoring their spectral properties. Recent advances in research have provided substantial evidence that the natural protein translational machinery can be genetically reprogrammed to introduce a large number of non-coded (i.e. noncanonical) Trp analogues and surrogates into various proteins. Especially attractive targets for such an engineering approach are fluorescent proteins in which the chromophore is formed post-translationally from an amino acid sequence, like the green fluorescent protein from Aequorea victoria. With the currently available translationally active fluoro-, hydroxy-, amino-, halogen-, and chalcogen-containing Trp analogues and surrogates, the traditional methods for protein engineering and design can be supplemented or even fully replaced by these novel approaches. Future research will provide a further increase in the number of Trp-like amino acids that are available for redesign (by engineering of the genetic code) of native Trp residues and enable novel strategies to generate proteins with tailored spectral properties.     

MASIA: recognition of common patterns and properties in multiple aligned protein sequences

SUMMARY: MASIA is a software tool for pattern recognition in multiple aligned protein sequences. MASIA converts a sequence to a properties matrix that can be scanned in both vertical and horizontal steps. Consistent patterns are recognized based on the statistical significance of their occurrence. Preset macros can be altered on-line to seek any combination of amino acid properties or sequence characteristics. MASIA output can be used directly by our programs to predict the 3D structure of proteins. AVAILABILITY: Access MASIA at http://www.scsb.utmb.edu/masia/ma sia.html.     

Structural analysis and classification of native proteins from E. coli commonly co-purified by immobilised metal affinity chromatography

Immobilised metal affinity chromatography (IMAC) is the most widely used technique for single-step purification of recombinant proteins. However, despite its use in the purification of heterologue proteins in the eubacteria Escherichia coli for decades, the presence of native E. coli proteins that exhibit a high affinity for divalent cations such as nickel, cobalt or copper has remained problematic. This is of particular relevance when recombinant molecules are not expressed at high levels or when their overexpression induces that of native bacterial proteins due to pleiotropism and/or in response to stress conditions. Identification of such contaminating proteins is clearly relevant to those involved in the purification of histidine-tagged proteins either at small/medium scale or in high-throughput processes. The work presented here reviews the native proteins from E. coli most commonly co-purified by IMAC, including Fur, Crp, ArgE, SlyD, GlmS, GlgA, ODO1, ODO2, YadF and YfbG. The binding of these proteins to metal-chelating resins can mostly be explained by their native metal-binding functions or their possession of surface clusters of histidine residues. However, some proteins fall outside these categories, implying that a further class of interactions may account for their ability to co-purify with histidine-tagged proteins. We propose a classification of these E. coli native proteins based on their physicochemical, structural and functional properties.     

Impact of Self-Association on the Architectural Properties of Bacterial Nucleoid Proteins

The chromosomal DNA of bacteria is folded into a compact body called the nucleoid, which is composed essentially of DNA (～80%), RNA (～10%), and a number of different proteins (～10%). These nucleoid proteins act as regulators of gene expression and influence the organization of the nucleoid by bridging, bending, or wrapping the DNA. These so-called architectural properties of nucleoid proteins are still poorly understood. For example, the reason why certain proteins compact the DNA coil in certain environments but make the DNA more rigid instead in other environments is the subject of ongoing debates. Here, we address the question of the impact of the self-association of nucleoid proteins on their architectural properties and try to determine whether differences in self-association are sufficient to induce large changes in the organization of the DNA coil. More specifically, we developed two coarse-grained models of proteins, which interact identically with the DNA but self-associate differently by forming either clusters or filaments in the absence of the DNA. We showed through Brownian dynamics simulations that self-association of the proteins dramatically increases their ability to shape the DNA coil. Moreover, we observed that cluster-forming proteins significantly compact the DNA coil (similar to the DNA-bridging mode of H-NS proteins), whereas filament-forming proteins significantly increase the stiffness of the DNA chain instead (similar to the DNA-stiffening mode of H-NS proteins). This work consequently suggests that the knowledge of the DNA-binding properties of the proteins is in itself not sufficient to understand their architectural properties. Rather, their self-association properties must also be investigated in detail because they might actually drive the formation of different DNA-protein complexes.     

Specification of the peroxisome targeting signals type 1 and type 2 of plant peroxisomes by bioinformatics analyses

To specify the C-terminal peroxisome targeting signal type 1 (PTS1) and the N-terminal PTS2 for higher plants, a maximum number of plant cDNAs and expressed sequence tags that are homologous to PTS1- and PTS2-targeted plant proteins was retrieved from the public databases and the primary structure of their targeting domains was analyzed for conserved properties. According to their high overall frequency in the homologs and their widespread occurence in different orthologous groups, nine major PTS1 tripeptides ([SA][RK][LM]> without AKM> plus SRI> and PRL>) and two major PTS2 nonapeptides (R[LI]x5HL) were defined that are considered good indicators for peroxisomal localization if present in unknown proteins. A lower but significant number of homologs contained 1 of 11 minor PTS1 tripeptides or of 9 minor PTS2 nonapeptides, many of which have not been identified before in plant peroxisomal proteins. The region adjacent to the PTS peptides was characterized by specific conserved properties as well, such as a pronounced incidence of basic and Pro residues and a high positive net charge, which probably play an auxiliary role in peroxisomal targeting. By contrast, several peptides with assumed peroxisomal targeting properties were not found in any of the 550 homologs and hence play--if at all--only a minor role in peroxisomal targeting. Based on the definition of these major and minor PTS and on the recognition of additional conserved properties, the accuracy of predicting peroxisomal proteins can be raised and plant genomes can be screened for novel proteins of peroxisomes more successfully.     

The use of deoxyribonucleic acid–cellulose chromatography and isoelectric focusing for the characterization and partial purification of steroid–receptor complexes

1. Two characteristic properties of the specific high-affinity steroid-binding proteins or receptors, their ability to bind to DNA-cellulose and their relatively acidic isoelectric point, have been exploited as a means of purification. These two fundamental properties distinguish the receptors from the steroid-binding proteins in serum and the non-specific low-affinity steroid-binding proteins in hormone-responsive cells. 2. A significant degree of purification of both cytoplasmic and nuclear steroid-receptor complexes can be achieved with practical facility by these procedures. The purity of the receptor complexes is sufficient to enable studies on their possible control of metabolic processes to be investigated in the future. 3. After extensive purification the physicochemical properties of the cytoplasmic androgen-receptor complex, such as sedimentation coefficient, were unchanged. Further, the purified complex fully retained at least one of its fundamental physiological properties, namely the ability to transfer 5alpha-dihydrotestosterone (17beta-hydroxy-5alpha-androstan-3-one) into chromatin in vitro. 4. The methods may also be employed for studying the changes in the structure and properties of the receptor complexes that are an essential prerequisite for the transfer of cytoplasmic receptor complexes into nuclear chromatin. The temperature-dependence of the binding of androgen-receptor complexes into chromatin is essentially due to a major change in cytoplasmic receptor complex before its attachment to nuclear chromatin. 5. The resolution of these analytical procedures was sufficient to enable a critical comparison of the receptor proteins from different male accessory glands to be undertaken. From these studies, no substantial evidence in support of the tissue specificity of androgen receptors could be established; rather the receptors from different androgen-dependent glands were remarkably similar in physicochemical properties. 6. Although the methods were initially developed for the partial purification of androgen-receptor complexes, they are equally suitable for the prompt and extensive purification of oestrogen-receptor and progesterone-receptor complexes.