Innate immune system damage in human immunodeficiency virus type 1 infection. Implications for acquired immunity and vaccine design.

HIV infection affects the innate as well as the acquired immune systems. Critically, it changes the function of macrophages, which link the innate and acquired responses through their ability to present antigen to CD4(+) T lymphocytes. Patients with HIV infection have a reduced capacity to deal with subsequent pathogen exposure and many suffer from chronic pulmonary infections. We have produced complex synthetic peptides that mimic the function of viral gp120 and may represent prototypes of molecules that can prevent or ameliorate HIV-induced damage to the immune system.

Inhibition of the ubiquitin-proteasome system in Alzheimer's disease.

Alzheimer's disease is the most common cause of dementia in the elderly. Although several genetic defects have been identified in patients with a family history of this disease, the majority of cases involve individuals with no known genetic predisposition. A mutant form of ubiquitin, termed Ub(+1), has been selectively observed in the brains of Alzheimer's patients, including those with nonfamilial Alzheimer's disease, but it has been unclear why Ub(+1) expression should be deleterious. Here we show that Ub(+1) is an efficient substrate for polyubiquitination in vitro and in transfected human cells. The resulting polyubiquitin chains are refractory to disassembly by deubiquitinating enzymes and potently inhibit the degradation of a polyubiquitinated substrate by purified 26S proteasomes. Thus, expression of Ub(+1) in aging brain could result in dominant inhibition of the Ub-proteasome system, leading to neuropathologic consequences.

Chemically synthesized ubiquitin extension proteins detect distinct catalytic capacities of deubiquitinating enzymes.

We have used solid-phase chemistry to synthesize proteins equivalent to a human ubiquitin precursor (ubiquitin-52-amino-acid ribosomal protein fusion; UBICEP52) and representative of isopeptide-linked ubiquitin-protein conjugates [ubiquitin-(epsilonN)-lysine]; these proteins were precisely cleaved by a purified recombinant Drosophila deubiquitinating enzyme (DUB), UCH-D. Along with the previously synthesized ubiquitin-(alphaN)-valine, these synthetic proteins were used as substrates to assess the catalytic capacities of a number of diverse DUBs expressed in Escherichia coli: human HAUSP; mouse Unp; and yeast Ubps 1p, 2p, 3p, 6p, 11p, and 15p and Yuh1p. Distinct specificities of these enzymes were detected; notably, in addition to UCH-D, isopeptidase activity [ubiquitin-(epsilonN)-lysine cleavage] was only associated with Yuh1p, Unp, Ubp1p, and Ubp2p. Additionally, human placental 26S proteasomes were only able to cleave UBICEP52 and ubiquitin-(epsilonN)-lysine, suggesting that 26S proteasome-associated DUBs are class II-like. This work demonstrates that the synthetic approach offers an alternative to recombinant methods for the production of small proteins in vitro.

Selective isopeptide bond formation: coupling ubiquitin(67-76) with histone 2A(114-128) by use of the transfer active ester condensation technique.

A peptide, ubiquitin(67-76)-histone 2A(114-128) fragment (UBH2AF), was synthesized by selective formation of an isopeptide bond between the C-terminus of ubiquitin(67-76) and the epsilon-amino group of lysine-119 in histone 2A(114-128) which contained 4 lysine residues at positions 118, 119, 125 and 127, respectively. The transfer active ester condensation technique, together with the Tnm amine protecting group, were used successfully in the peptide segment coupling reaction. [structure: see text]

A linear endothelin-1 analogue: solution structure of ET-1[Aib1,3,11,15, Nle7] by nuclear magnetic resonance spectroscopy and molecular modelling.

Two-dimensional nuclear magnetic resonance techniques and a combination of distance geometry and molecular dynamics calculations were utilised to determine the three dimensional solution structure of an ET-1 analogue, ET-1[Aib1,3,11,15, Nle7], in a methanol-d3/water co-solvent. The modelled structure shows that the peptide folds into a consistent alpha-helical conformation between residues Ser4-His16 while the C-terminus prefers no fixed conformation. Our studies confirm that the disulphide links which are normally associated with the endothelin family of neuropeptides are not important for the formation of a helical conformation in solution. This full length, modified, synthetic linear ET-1 analogue plays a vital role towards designing endothelin receptor agonists. Structure activity relationships are discussed in terms of the conformational features of the calculated structure.

Comparative studies of Nsc and Fmoc as N(alpha)-protecting groups for SPPS.

2-(4-Nitrophenyl)sulfonylethoxycarbonyl (Nsc) is an alternative base-labile N(alpha)-protecting group to 9-fluorenylmethoxycarbonyl (Fmoc) for amino acids. The UV spectrum of the Nsc group exhibits moderate absorption at 380 nm which is excellent for real-time monitoring of the deprotection process. It also decreases the rearrangement of X-Asp, which can be a serious problem in SPPS.

Solution structure of a novel ETB receptor selective agonist ET1-21 [Cys(Acm)1,15, Aib3,11, Leu7] by nuclear magnetic resonance spectroscopy and molecular modelling.

The solution structure of a biologically active modified linear endothelin-1 analogue, ET1-21[Cys(Acm)1,15, Aib3,11, Leu7], has been determined for the first time by two-dimensional nuclear magnetic resonance spectroscopy in a methanol-d3/water solvent mixture. Out of approximately one hundred linear peptide analogues tested by biological assay, this peptide, together with a dozen others, showed significant ETB selective agonist activity. Here we report the solution structure of an ETB selective agonist of a full-length, synthetic linear endothelin analogue. The calculated structures indicate that the peptide adopts an alpha-helical conformation between residues Ser5-His16, whilst both N- and C-termini show no preferred conformation. These results suggest that the disulphide bridges normally associated with endothelin and sarafotoxin peptides may not necessarily be important for either ETB receptor binding activity or the formation of a helical conformation in solution.

Electrophoretic separation of ubiquitin and single amino acid residue ubiquitin extensions using a commercial modified acrylamide gel electrophoresis system: an assay to determine catalytic capacities of deubiquitinating enzymes.

We have chemically synthesised a number of ubiquitin extension proteins, with carboxyl-terminal single amino acid residue extensions, to use as substrates to assess the catalytic capacities of deubiquitinating enzymes (DUBs). Here we describe a modified acrylamide gel electrophoresis system which allows separation of peptide- or isopeptide-linked ubiquitin-lysine from ubiquitin (77 and 76 residue proteins respectively) in only 2 h. Western blotting, using antibodies against ubiquitin, allows both substrate (i.e. ubiquitin-lysine) and product (i.e. ubiquitin) of DUB-catalyzed cleavage reactions to be detected. Catalytic capacities of DUBs may be indicative of in vivo functions of these proteases.

A functional, discontinuous HIV-1 gp120 C3/C4 domain-derived, branched, synthetic peptide that binds to CD4 and inhibits MIP-1alpha chemokine binding.

This paper describes a branched synthetic peptide [3.7] that incorporates sequence discontinuous residues of HIV-1 gp120 constant regions. The approach was to bring together residues of gp120 known to interact with human cell membranes such that the peptide could fold to mimic the native molecule. The peptide incorporates elements of both the conserved CD4 and CCR5 binding sites. The 3.7 peptide, which cannot be produced by conventional genetic engineering methods, is recognized by antiserum raised to native gp120. The peptide also binds to CD4 and competitively inhibits binding of QS4120 an antibody directed against the CDR2 region of CD4. When preincubated with the CD4+ve MM6 macrophage cell line, which expresses mRNA for the CCR3 and CCR5 chemokine receptors, both 3.7 and gp120 inhibit binding of the chemokine MIP-1alpha. The peptide also inhibits infection of primary macrophages by M-tropic HIV-1. Thus, 3.7 is a prototype candidate peptide for a vaccine against HIV-1 and represents a novel approach to the rational design of peptides that can mimic complex sequence discontinuous ligand binding sites of clinically relevant proteins.

Development of ET(B) selective agonists: solution structure of a linear endothelin-1 analogue, ET-1 [Cys(Acm)(1,15), Ala3, Leu7, dAsp8, Aib11].

The solution structure of a synthetic ET(B) selective agonist, ET-1[Cys(Acm)(1,15), Ala3, Leu7, dAsp8, Aib11] has been solved by 1H NMR and molecular modelling studies. Such solution structures of linear modified peptides in aqueous methanol are being used in an ongoing program of research designed to assist in an understanding of the basic structural requirements for the biological activity of vasoconstrictors. The resulting structure of this peptide is characterised by an alpha-helical conformation between residues Leu6-His16 and by N- and C-termini which assume no defined conformation. A knowledge of the solution structures of this and related peptides, which are ET(B) selective agonists, are proving to be important in the understanding of how they interact with the ET(B) receptor.

Synthetic peptides representing discontinuous CD4 binding epitopes of HIV-1 gp120 that induce T cell apoptosis and block cell death induced by gp120.

A vaccine against HIV-1 virus would block initial infection and must target conserved residues. Since initial infection depends on binding of the viral envelope protein gp120 to CD4 on the cell surface, the CD4 binding site of gp120 is a target for vaccine design. To identify the optimal biologically active site, we synthesized a series of 32-mer peptides, based on conserved residues in the C3 and C4 regions of gp120. These included three of five sequence discontinuous residues known to be involved in CD4 binding, one or two of which were substituted with alanine. We also synthesized a 44-mer peptide with an additional branch to incorporate an extra C4 region sequence including a fourth CD4 binding residue. All these peptides used an oxidized Cys-X-Cys bridge to link the discontinuous sequence elements in a manner suggested by the known conserved disulfide bridges in gp120. Polyclonal sera raised to these peptides indicate that they all contain both B and T lymphocyte epitopes. Binding of the peptides to CD4-transfected HeLa cells reveals a hierarchy dependent on the number of relevant CD4 binding residues present. Furthermore, antibody cross-linking of peptides bound to the surface of human T cells results in apoptosis that is similar to the known properties of gp120. The peptide incorporating three CD4 binding residues competitively inhibited gp 120-induced T lymphocyte apoptosis. Thus, we have synthesized novel, branched peptides incorporating conserved discontinuous sequences from two different conserved domains of HIV-1 gp120 that contain T and B lymphocyte epitopes and mimic biological functions of the native protein. These synthetic peptides are candidates for future vaccine development.

Solution conformation of an ET(B) selective agonist, ET-1[Cys(Acm)1,15,Ala3,Leu7,Aib11], in CD3OH/H2O by 1H NMR and molecular modelling.

To understand the basic structural requirements for the biological activity of endothelin peptides, the solution structure of an ETB selective agonist, ET-1[Cys-(Acm)1,15, Ala3,Leu7,Aib11, was investigated by 1H NMR spectroscopy and molecular modelling. The structure is characterised by an alpha-helical conformation between residues Ser5-His16 but is undefined at both the N and C termini. To date, neither the solution structures of linear modified peptides nor the effects of a methanol/water solvent system have been examined for endothelin or endothelin-like peptides. This structure plays an important role towards the design of endothelin receptor selective agonists and antagonists.

Alteration of the alpha helix region of cyanobacterial ribulose 1,5-bisphosphate carboxylase/oxygenase to reflect sequences found in high substrate specificity enzymes.

The sequence at the alpha helix region of the eight-stranded beta/alpha barrel domain of the large subunit of Synechococcus sp. strain PCC 6301 ribulosebisphosphate carboxylase/oxygenase (rubisco) was altered by site-directed mutagenesis. Changes were made to match the corresponding residues in the rubisco large subunit of chromophytic and rhodophytic algae, which have considerably higher substrate specificity factors (ratio of the rate constants for the carboxylase and oxygenase reactions). A set of cumulative mutations of one to eight amino acid residues was prepared and examined and it was found that mutant enzymes which contained from one to five substitutions all exhibited substantial decreases in carboxylase activity. Mutant enzymes which contained from six to eight amino acid substitutions were inactive and failed to maintain their native quarternary structure. For enzymes which maintained their native structure, consecutive changes in the alpha helix 6 region yielded a progressive increase in the K(m) for ribulosebisphosphate, confirming the importance of this region in substrate binding. Despite these results, and previous studies which indicated the importance and potential of residues in the alpha helix 6 region to influence the ability of loop 6 to affect rubisco catalysis, simple cumulative substitution did not significantly alter the substrate specificity factor of the enzyme. The results of this study lend further credence to the idea that engineered enhancement of rubisco specificity will likely require coordination of alterations at multiple sites in the primary structure.

Synthetic, structural and biological studies of the ubiquitin system: synthesis and crystal structure of an analogue containing unnatural amino acids.

Ubiquitin is a 76-amino acid protein involved in the targeting for destruction of proteins in the cell. The protein can readily be synthesized chemically affording an extra dimension to studies of protein stability. Ubiquitin with various modifications to the hydrophobic core has been synthesized. In particular, two core amino acids have been replaced by aminobutyric acid (Val-26) and norvaline (for Ile-30) and the product crystallized. The refined crystal structure shows an overall contraction of the molecule and the side chain of Nva-30 rotates relative to Ile-30. However, the side chain rotation is not sufficient to compensate for the effect of the loss of the methyl group and hence a small cavity is introduced into the structure, which decreases the stability of the protein. The biological behaviour of the modified protein is unaltered. The observed changes in stability are of the magnitude expected for the removal of methyl groups from the hydrophobic core of a protein. Interestingly, the effect appears to be independent of the position of the removed methyl group. The intact structure, but not its stability, is important for recognition by the biological conjugating system.

Capillary electrophoresis assay for ubiquitin carboxyl-terminal hydrolases with chemically synthesized ubiquitin-valine as substrate.

Ubiquitin is expressed in eukaryotic cells as precursors, fused via its carboxyl terminus either to other ubiquitin sequences in linear polyubiquitin arrays or to specific ribosomal proteins. In some of the polyubiquitin fusions a single amino acid (e.g., valine in humans) is attached to the carboxyl terminus. These gene products are rapidly (probably cotranslationally) cleaved by ubiquitin carboxyl-terminal hydrolase (UCH) enzymes; therefore, although ubiquitin precursors are suitable substrates for assays of UCH activity, they are difficult to isolate from nucleated cells. While the recombinant approach allows the production of ubiquitin precursors in prokaryotic cells (which do not contain the ubiquitin system), proteins produced in this manner require purification and may also be susceptible to modification by bacterial enzymes, e.g., adventitious proteolysis. As an alternative we have chemically synthesized human ubiquitin-valine. In the assay described here the cleavage of ubiquitin-valine to ubiquitin (77 and 76 residue proteins, respectively) by a purified recombinant Drosophila UCH was monitored by capillary electrophoresis. Mass spectrometry verified the precise cleavage of ubiquitin-valine, confirming that this synthetic protein is a UCH substrate. Synthetic ubiquitin-valine may serve as a generic substrate for UCHs allowing the purification and identification of new members of this enzyme family.

Solution structure determination of endothelin-1 in methanol/water by NMR and molecular modelling methods.

To understand the structural requirements for the biological activity of endothelin peptides and to develop receptor selective endothelin analogues further, the solution structure of the bicyclic 21 amino acid residue vasoactive peptide, endothelin-1, has been determined in methanol-d3/water using high-resolution 1H-NMR spectroscopy. To our knowledge, this solvent system has not previously been used in NMR studies of endothelin and/or endothelin-like peptides. Two-dimensional DQFCOSY, TOCSY and NOESY spectra were acquired along with a series of one-dimensional spectra. A total of 219 distance constraints and 5 angle constraints were derived from the NMR data. These were incorporated into structure calculations using distance geometry (DIANA) followed by simulated annealing and molecular dynamics. The resulting structures are characterized by an alpha-helical conformation, Lys9-His16, and residues Ser5-Asp8 form a type I beta-turn. The N-terminal region, which was not extensively constrained by NMR data, showed no preferred conformation. The C-terminal tail showed less extensive conformational averaging but no descriptive conformation could be observed. The results obtained in this study are in good agreement with previous proposals.

The impact of polystyrene resins in solid-phase organic synthesis.

A major objective of the DIVERSOMER technology is to provide pure and characterized compounds for biological testing in order to prevent 'false negatives' in our libraries. On several occasions, analysis of the final products by 1H-NMR and MS, has revealed by-products from the polystyrene solid support. Subsequently, three alternative methods were studied to remove polystyrene by-products; (i) prewashing of the resin prior to execution of the synthesis; (ii) pretreatment of the resin with the cleavage conditions consistent with the solid-phase synthesis reaction scheme; and (iii) parallel purification.

Design and synthesis of a highly immunogenic, discontinuous epitope of HIV-1 gp120 which binds to CD4+ve transfected cells.

Here we report the design and synthesis of a novel 32-mer peptide, Lys364-378Val445-459.oxidized (named GC-1), which represents a discontinuous epitope from the C3 and C4 domains of gp120 from the HIV-1 IIIB isolate. This peptide induces high titre IgG antibody responses in mice, indicating that it has both B and T cell epitopes. Epitope mapping using reduced GC-1 and appropriate linear peptides demonstrated that a large proportion of the antibodies raised in mice were directed against discontinuous epitope(s). Furthermore, antibodies to GC-1 peptide cross-reacted with purified HIV-1 strain IIIB gp120, indicating the GC-1 mimicked at least one epitope of the native protein. The peptide, which incorporates three gp120 residues Asp 368, Glu 370 and Asp 457, previously shown to be critical for CD4 ligation, bound to the surface of a CD4 transfected human epithelial cell line HeLa, but not to the parent cell line and inhibited binding of recombinant HIV-1 gp120 to recombinant soluble CD4. We have synthesized the first of a series of discontinuous peptides which will be useful for the probing of interactions of HIV-1 gp120 with the CD4 molecule.

The total chemical synthesis of monocyte chemotactic protein-1 (MCP-1).

The affinity-based N (alpha)-amino protecting group tetrabenzo[a,c,g,i]fluorenyl-17 methoxycarbonyl (Tbfmoc) has been utilized as a hydrophobic probe to allow the simple, quick and highly effective isolation of a 76 residue cysteine-containing protein (MCP-1). The base-labile Tbfmoc group can be removed under very mild conditions, which preserve the thiol-containing protein in the reduced state. Oxidative folding was then used to furnish the biologically active beta-chemokine MCP-1.