Methods of virus formation

Viruses occur in a great variety of shapes and sizes, but for all their diversity in appearance they possess certain characteristics in common: all viruses contain a single nucleic acid molecule – deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) – surrounded by a protective protein coat. Among other things, the protein coat enables the genetic information stored in the nucleic acid to enter a host cell in a usable state, where it can initiate the reproduction of identical virus particles. After penetration of the cell the foreign genetic material of the virus particle first induces the synthesis of macromolecules not normally present in the cell: the viral nucleic acid undergoes replication and very many copies are produced, the protein of the virus coat is synthesized, and then these components are assembled to form a new generation of infectious virus particles. Most viruses also exhibit certain common structural features: their protein coat is built up from subunits arranged in helical or icosahedral fashion around the genetic material.     

Protein-RNA interactions during TMV assembly.

A review of the structural studies of tobacco mosaic virus (TMV) is given. TMV is essentially a flat helical microcrystal with 16 1/3 subunits per turn. A single strand of RNA runs along the helix and is deeply embedded in the protein. The virus particles form oriented gels from which high-resolution X-ray fiber diffraction data can be obtained. This may be interpreted by the use of six heavy-chain derivatives to give an electron density map at 0.4 nm resolution from which the RNA configuration and the form of the inner part of the protein subunit may be determined. In addition, the protein subunits form a stable 17-fold two-layered disk which is involved in virus assembly and which crystallizes. By the use of noncrystallographic symmetry and a single heavy-atom derivative, it has been possible to solve the structure of the double disk to 0.28 nm resolution. In this structure one sees that an important structural role is played by four alpha-helices, one of which (the LR helix) appears to form the main binding site for the RNA. The main components of the binding site appear to be hydrophobic interactions with the bases, hydrogen bonds between aspartate groups and the sugars, and arginine salt bridges to the phosphate groups. The binding site is between two turns of the virus helix or between the turns of the double disk. In the disk, the region proximal to the RNA binding site is in a random coil until the RNA binds, whereupon the 24 residues involved build a well-defined structure, thereby encapsulating the RNA.     

Covalent binding of human serum albumin and ovalbumin by chloramine-T and chemical modification of the proteins

The covalent binding of ³⁵S-chloramine-T to human resum albumin (HSA) and ovalbumin is described. At pH 6.5, up to 24 chloramine-T molecules were found to be covalently bound per molecule of HSA; with ovalbumin the binding was only 5–7 molecule per protein molecule. Binding was accompanied by extensive modification of methionine, cysteine, histidine, tyrosine and lysine. Three new peaks appeared in the amino acid profiles of the modified proteins; two were identified as 1-aminoadipic acid (oxidation of lysine) and 3-chlorotyrosine. The most sites for covalent binding are lysine residues.     

Substrate binding and sequence preference of the proteasome revealed by active-site-directed affinity probes

Background: The proteasome is a multicatalytic protease complex responsible for most cytosolic protein breakdown. The complex has several distinct proteolytic activities that are defined by the preference of each for the carboxyterminal (P1) amino acid residue. Although mutational studies in yeast have begun to define substrate specificities of individual catalytically active β subunits, little is known about the principles that govern substrate hydrolysis by the proteasome.Results: A series of tripeptide and tetrapeptide vinyl sulfones were used to study substrate binding and specificity of the proteasome. Removal of the aromatic amino-terminal cap of the potent tripeptide vinyl sulfone proteasome inhibitor 4-hydroxy-3-iodo-2-nitrophenyl-leucinyl-leucinyl-leucine vinyl sulfone resulted in the complete loss of binding and inhibition. Addition of a fourth amino acid (P4) to the tri-leucine core sequence fully restored inhibitory potency. 1251-labeled peptide vinyl sulfones were also used to examine inhibitor binding and to determine the correlation of subunit modification with inhibition of peptidase activity. Changing the amino acid in the P4 position resulted in dramatically different profiles of β-subunit modification.Conclusions: The P4 position, distal to the site of hydrolysis, is important in defining substrate processing by the proteasome. We observed direct correlations between subunit modification and inhibition of distinct proteolytic activities, allowing the assignment of activities to individual β subunits. The ability of tetrapeptides, but not tripeptide vinyl sulfones, to act as substrates for the proteasome suggests there could be a minimal length requirement for hydrolysis by the proteasome. These studies indicate that it is possible to generate inhibitors that are largely specific for individual β subunits of the proteasome by modulation of the P4 and carboxy-terminal vinyl sulfone moieties.     

Nanoassembly of Oligopeptides and DNA Mimics the Sequential Disassembly of a Spherical Virus

Protein subunits of a low aspect ratio (width over length) with stimuli‐responsiveness are hallmark building blocks of spherical viruses. The interaction of these repeating subunits enables hierarchical assembly for genome packaging and sequential disassembly for optimal genome release. Here, we mimicked these features and constructed a functional spherical artificial virus. The rationally designed 22‐amino acid peptide containing pH‐sensitive histidines and aromatic residues self‐assembled into homogenous nanodiscs of a low aspect ratio (≈7×7×4 nm). In the presence of DNA, the inter‐nanodisc interactions drove the formation of a viral capsid‐like structure enclosing DNA in the interior. This artificial virus roughly 50 nm in diameter underwent partial disassembly in response to acidic pH. The resulting intermediate with lowered DNA‐binding affinity continued to protect DNA from nuclease digestion. Such nanostructures, which mimic the intricate morphology and the intracellular transformation of spherical viruses, can be useful for constructing synthetic gene delivery vehicles, as evidenced by their efficient transgene expression.     

NMR studies of interactions between periplasmic chaperones from uropathogenic E. coli and pilicides that interfere with chaperone function and pilus assembly

Adherence of uropathogenic Escherichia coli to host tissue is mediated by pili, which are hair-like protein structures extending from the outer cell membrane of the bacterium. The chaperones FimC and PapD are key components in pilus assembly since they catalyse folding of subunits that are incorporated in type 1 and P pili, respectively, and also transport the subunits across the periplasmic space. Recently, compounds that inhibit pilus biogenesis and interfere with chaperone-subunit interactions have been discovered and termed pilicides. In this paper NMR spectroscopy was used to study the interaction of different pilicides with PapD and FimC in order to gain structural knowledge that would explain the effect that some pilicides have on pilus assembly. First relaxation-edited NMR experiments revealed that the pilicides bound to the PapD chaperone with mM affinity. Then the pilicide-chaperone interaction surface was investigated through chemical shift mapping using 15N-labelled FimC. Principal component analysis performed on the chemical shift perturbation data revealed the presence of three binding sites on the surface of FimC, which interacted with three different classes of pilicides. Analysis of structure-activity relationships suggested that pilicides reduce pilus assembly in E. coli either by binding in the cleft of the chaperone, or by influencing the orientation of the flexible F1-G1 loop, both of which are part of the surface by which the chaperone forms complexes with pilus subunits. It is suggested that binding to either of these sites interferes with folding of the pilus subunits, which occurs during formation of the chaperone-subunit complexes. In addition, pilicides that influence the F1-G1 loop also appear to reduce pilus formation by their ability to dissociate chaperone-subunit complexes.     

PROPERTIES OF THE RETINAL BINDING SITE IN BACTERIORHODOPSIN. USE OF RETINOL AND RETINYL MOIETIES AS FLUORESCENT PROBES

Abstract— The fluorescence spectra of various reduced bacteriorhodopsin chromophore species indicate energy transfer from aromatic amino acid side chains of the protein to the retinyl moiety. Binding studies with retinol reveal that energy transfer occurs only when the retinyl moiety is bound in the chromophoric site of the protein. Retroretinol is a fluorescent probe for the binding site.     

Study by means of high-performance liquid chromatography of solutes that decrease theophylline/protein binding in the serum of uremic patients.

Substantial changes in protein binding of drugs occur during the progression of renal insufficiency. Protein-bound uremic solutes play a role in the inhibition of drug protein binding. We previously demonstrated that hippuric acid in uremic ultrafiltrate was an inhibitor of the theophylline protein binding. The present study was undertaken to extend the yield of protein-bound uremic solutes by displacing ligands in uremic serum from their binding sites by five deproteinization methods. The inhibitory effect on theophylline protein binding of the deproteinized uremic serum was higher than with ultrafiltrate (p < 0.05). The influence of 30 semi-preparative HPLC fractions from deproteinized uremic serum on the theophylline protein binding was evaluated to identify the responsible compounds and to compare their relative individual impact. The theophylline protein binding was calculated as a percentage (bound versus total). The most important decrease of the protein binding was observed in HPLC fractions 6, 10 to 13, 15 and 28 with protein binding of: 61.5 +/- 10.8, 64.5 +/- 7.6, 60.9 +/- 10.1, 47.5 +/- 3.3, 60.0 +/- 6.7, 60.7 +/- 6.3 and 61.3 +/- 6.9%, respectively versus 69.1 +/- 2.4% for control serum (p < 0.05). The responsible compounds were characterized in the fractions by co-elution: 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF), indole-3-acetic acid, indoxyl sulfate, hippuric acid, p-hydroxyhippuric acid and tryptophan. Their concentration was determined by analytical HPLC and a solution containing these compounds at the same concentration as in deproteinized uremic serum was composed. This solution was added to control serum and decreased the theophylline protein binding from 69.0 +/- 4.4% to 61.3 +/- 1.3%, which was less important than in genuine uremic serum (44.4 +/- 3.8%, p < 0.05). Dose-response curves with the characterized compounds revealed that the most important role in binding inhibition could be attributed to hippuric acid and CMPF. Our data suggests that the yield of protein binding inhibiting compounds is more important with deproteinized uremic serum than with uremic ultrafiltrate. The identified uremic compounds are not entirely representative for the decreased protein binding of theophylline, indicating that additional factors than those identified in this study affect the protein binding as well.     

Translation of genetic information on the ribosome

The information for protein structure that is contained in the base sequence of the nucleic acids is translated on the ribosome into the amino acid sequence. This translation can be divided into chain initiation, chain growth, and chain termination. Several specific protein factors and nucleic acids are involved in each section.—For chain initiation, start complexes are formed from the initiating amino acyl-tRNA, mRNA carrying the start signal, and the small and large subunits of a ribosome. GTP and the initiating factors are also involved in this process.—In chain elongation, one amino acid at a time is transferred, in a reaction cycle, from the linkage with tRNA into a linkage with the polypeptide chain. The amino acid to be incorporated is initially bound to the ribosome as amino acyl-tRNA, a process for which GTP and protein factors are necessary. The subsequent formation of a peptide linkage is catalyzed by the peptidyl transferase of the large ribosomal subunit. The peptidyl-tRNA with its newly added amino acid residue is then transferred from the amino acyl-tRNA acceptor site A to the peptidyl donor site P of the ribosome. This requires another protein factor and cleavage of GTP into GDP and phosphate.–Ghain termination begins as soon as one of the three terminator triplets UAA, UAG, or UGA in the mRNA reaches the ribosome. The mRNA is moving in relation to the ribosome from the 5′ end to the 3′ end. Release of the completed polypeptide chain from the ribosome is dependent on release factors. Before initiation of a new polypeptide chain, the ribosomes dissociate into their subunits.     

Fluoride binding to humic acid

Fluoride (F^–) binding to humic acid has been measured as a function of pH (5–6.6). The pH dependent binding is attributed to the anion being trapped within the large structure (territorial bound) but is not bound to a particular functional group (site bound). Studying fluoride binding provides insight to cation, anion and neutral species interactions with humic acid.     

Erythropoietin mimetics derived from solution phase combinatorial libraries.

The erythropoietin receptor (EPOr) is activated by ligand-induced homodimerization, which leads to the proliferation and differentiation of erythroid progenitors. Through the screening of combinatorial libraries of dimeric iminodiacetic acid diamides, novel small molecule binders of EPOr were identified in a protein binding assay. Evaluation of a series of analogues led to optimization of binding subunits, and these were utilized in the synthesis of higher order dimer, trimer, and tetramer libraries. Several of the most active EPOr binders were found to be partial agonists and induced concentration-dependent proliferation of an EPO-dependent cell line (UT-7/EPO) while having no effect on a cell line lacking the EPOr (FDC-P1). An additional compound library, based on a symmetrical isoindoline-5,6-dicarboxylic acid template and including the optimized binding subunits, was synthesized and screened leading to the identification of additional EPO mimetics.     

Ultraviolet photoinactivation studies on hybrid viruses obtained by the cross-reconstitution of the protein and RNA components of U(1) and U(2) strains of TMV

The sensitivities of U(1) and U(2) TMV strains to inactivation by ultraviolet light at 253.7 nm were compared with those of hybrid viruses obtained by reconstituting the protein of either native strain with the RNA of the other. In each case, the hybrid virus was found to be virtually identical in sensitivity to the native strain which supplied the protein coat, indicating that the relative sensitivities of the two native strains to ultraviolet light are solely a function of their respective protein coats. Amino acid analysis of the U (2) protein reveals about thirteen or fourteen amino acid replacements compared with the U (1) strain, which is in agreement with earlier studies indicating that there are considerable differences in the protein subunits of the two proteins. Some of the ways in which the observed differences in proteins of the two strains may determine their respective ultraviolet sensitivities are discussed.     

Differences between G‐Protein‐Stabilized Agonist–GPCR Complexes and their Nanobody‐Stabilized Equivalents

Protein nanobodies have been used successfully as surrogates for unstable G‐proteins in order to crystallize G‐protein‐coupled receptors (GPCRs) in their active states. We used molecular dynamics (MD) simulations, including metadynamics enhanced sampling, to investigate the similarities and differences between GPCR–agonist ternary complexes with the α‐subunits of the appropriate G‐proteins and those with the protein nanobodies (intracellular binding partners, IBPs) used for crystallization. In two of the three receptors considered, the agonist‐binding mode differs significantly between the two alternative ternary complexes. The ternary‐complex model of GPCR activation entails enhancement of ligand binding by bound IBPs: Our results show that IBP‐specific changes can alter the agonist binding modes and thus also the criteria for designing GPCR agonists.     

Determining the topology of virus assembly intermediates using ion mobility spectrometry–mass spectrometry

We have combined ion mobility spectrometry–mass spectrometry with tandem mass spectrometry to characterise large, non‐covalently bound macromolecular complexes in terms of mass, shape (cross‐sectional area) and stability (dissociation) in a single experiment. The results indicate that the quaternary architecture of a complex influences its residual shape following removal of a single subunit by collision‐induced dissociation tandem mass spectrometry. Complexes whose subunits are bound to several neighbouring subunits to create a ring‐like three‐dimensional (3D) architecture undergo significant collapse upon dissociation. In contrast, subunits which have only a single neighbouring subunit within a complex retain much of their original shape upon complex dissociation. Specifically, we have determined the architecture of two transient, on‐pathway intermediates observed during in vitro viral capsid assembly. Knowledge of the mass, stoichiometry and cross‐sectional area of each viral assembly intermediate allowed us to model a range of potential structures based on the known X‐ray structure of the coat protein building blocks. Comparing the cross‐sectional areas of these potential architectures before and after dissociation provided tangible evidence for the assignment of the topologies of the complexes, which have been found to encompass both the 3‐fold and the 5‐fold symmetry axes of the final icosahedral viral shell. Such insights provide unique information about virus assembly pathways that could allow the design of anti‐viral therapeutics directed at the assembly step. This methodology can be readily applied to the structural characterisation of many other non‐covalently bound macromolecular complexes and their assembly pathways. Copyright © 2010 John Wiley & Sons, Ltd.     

Accurate evaluation method of the polymer content in Monomethoxy(polyethylene glycol) modified proteins based on Amino acid analysis

To overcome the uncertainty of the colorimetric or fluorimetric method so far employed for the evaluation of monomethoxy(polyethylene glycol) (MPEG) covalently bound to protein, a direct method based on amino acid analysis is proposed. The method exploits the use of MPEG, which was bounded with the unnatural amino acid norleucine (MPEG-Nle). MPEG-Nle was activated at its carboxylic group to succinimidyl ester for the binding to the amino groups of protein. After acid hydrolysis, the amino acid content is evaluated by conventional amino acid analyzer or by reverse-phase HPLC as phenylthiocarbamyl derivative. The number of bound MPEG chains is calculated from the amino acid composition, since one norleucine residue is released from each bound polymer chain. The method was verified with several proteins in comparison with colorimetric ones, also in the case of proteins that contain chromophores in the visible range, such cytocrome C. It was observed that in most of the cases, the colorimetric methods give an overestimation of the degree of protein modification.     

Refinement of the conformation of UDP-galactose bound to galactosyltransferase using the STD NMR intensity-restrained CORCEMA optimization

The STD NMR technique has originally been described as a tool for screening large compound libraries to identify the lead compounds that are specific to target proteins of interest. The application of this technique in the qualitative epitope mapping of ligands weakly binding to proteins, virus capsid shells, and nucleic acids has also been described. Here we describe the application of the STD NMR intensity-restrained CORCEMA optimization (SICO) procedure for refining the bound conformation of UDP-galactose in galactosyltransferase complex using STD NMR intensities recorded at 500 MHz as the experimental constraints. A comparison of the SICO structure for the bound UDP-galactose in solution with that in the crystal structure for this complex shows some differences in ligand torsion angles and V253 side-chain orientation in the protein. This work describes the first application of an STD NMR intensity-restrained CORCEMA optimization procedure for refining the torsion angles of a bound ligand structure. This method is likely to be useful in structure-based drug design programs since most initial lead compounds generally exhibit weak affinity (millimolar to micromolar) to target proteins of pharmaceutical interest, and the bound conformation of these lead compounds in the protein binding pocket can be determined by the CORCEMA-ST refinement.     

Decoration of discretely immobilized cowpea mosaic virus with luminescent quantum dots

This report describes two related methods for decorating cowpea mosaic virus (CPMV) with luminescent semiconductor nanocrystals (quantum dots, QDs). Variants of CPMV are immobilized on a substrate functionalized with NeutrAvidin using modifications of biotin-avidin binding chemistry in combination with metal affinity coordination. For example, using CPMV mutants expressing available 6-histidine sequences inserted at loops on the viral coat protein, we show that these virus particles can be specifically immobilized on NeutrAvidin functionalized substrates in a controlled fashion via metal-affinity coordination. To accomplish this, a hetero-bifunctional biotin-NTA moiety, activated with nickel, is used as the linker for surface immobilization of CPMV (bridging the CPMVs' histidines to the NeutrAvidin). Two linking chemistries are then employed to achieve CPMV decoration with hydrophilic CdSe-ZnS core-shell QDs; they target the histidine or lysine residues on the exterior virus surface and utilize biotin-avidin interactions. In the first scheme, QDs are immobilized on the surface-tethered CPMV via electrostatic attachment to avidin previously bound to the virus particle. In the second strategy, the lysine residues common to each viral surface asymmetric unit are chemically functionalized with biotin groups and the biotinylated CPMV is discretely immobilized onto the substrate via NeutrAvidin-biotin interactions. The biotin units on the upper exposed surface of the immobilized CPMV then serve as capture sites for QDs conjugated with a mixture of avidin and a second protein, maltose binding protein, which is also used for QD-protein conjugate purification. Characterization of the assembled CPMV and QD structures is presented, and the potential uses for protein-coated QDs functionalized onto this symmetrical virion nanoscaffold are discussed.     

Synthesis and Evaluation of a Cyclophane Receptor for Acetic Acid

A bicyclic cyclophane ( 2 ) containing one pyridine nitrogen and four amide N-H groups oriented toward the interior of the cavity was synthesized. The binding constants of various carboxylic acids with 2 were measured by UV/Vis spectroscopy. Acetic acid bound to 2 with a K a of 980 - 90 M m 1 in chloroform while branched carboxylic acids showed significantly lower binding. The data indicate that acetic acid was bound within the cavity of 2 . Only one acetic acid binds to two control hosts, whereas 2 shows definitive 1:1 binding. The results suggest that selectivity in the binding of carboxylic acids can be achieved via size constraints dictated by the receptor cavity, and that the same size restrictions lead to only one carboxylic acid bound to the cyclophane. The crystal structure of 2 is reported.