Richard N. Perham

Pulling geometry defines the mechanical resistance of a β-sheet protein

Proteins show diverse responses when placed under mechanical stress. The molecular origins of their differing mechanical resistance are still unclear, although the orientation of secondary structural elements relative to the applied force vector is thought to have an important function. Here, by using a method of protein immobilization that allows force to be applied to the same all-β protein, E2lip3, in two different directions, we show that the energy landscape for mechanical unfolding is markedly anisotropic. These results, in combination with molecular dynamics (MD) simulations, reveal that the unfolding pathway depends on the pulling geometry and is associated with unfolding forces that differ by an order of magnitude. Thus, the mechanical resistance of a protein is not dictated solely by amino acid sequence, topology or unfolding rate constant, but depends critically on the direction of the applied extension.

Multiple display of foreign peptides on a filamentous bacteriophage: Peptides from Plasmodium falciparum circumsporozoite protein as antigens

We describe here two systems for encoding foreign amino acid sequences in the exposed N-terminal segment of the major coat protein of bacteriophage fd. Small peptides can be encoded directly; larger peptides are encoded in hybrid bacteriophage particles, in which the capsid is formed from a mixture of wild-type and modified coat proteins. In both cases, the peptides are present in multiple copies per phage particle. Peptides that represent the circumsporozoite protein, the major surface antigen of the sporozoites of the malaria parasite, Plasmodium falciparum, were inserted in this way and found to be highly immunogenic. These systems should prove to be valuable in displaying specific or random peptides as antigens, and could lead to cheap and effective vaccines. They will also allow rapid screening of peptides as potential agents of other biological effects, with important applications in biomolecular design.

A common structural motif in thiamin pyrophosphate-binding enzymes

The amino acid sequences of a wide range of enzymes that utilize thiamin pyrophosphate (TPP) as cofactor have been compared. A common sequence motif approximately 30 residues in length was detected, beginning with the highly conserved sequence ‐GDG‐ and concluding with the highly conserved sequence ‐NN‐. Secondary structure predictions suggest that the motif may adopt a βαβ fold. The same motif was recognised in the primary structure of a protein deduced from the DNA sequence of a hitherto unassigned open reading frame of Rhodobacter capsulata. This putative protein exhibits additional homology with some but not all of the TPP‐binding enzymes.

Immunological properties of foreign peptides in multiple display on a filamentous bacteriophage

The genome of bacteriophage fd has been engineered to permit construction of hybrid virus particles in which the wild-type major coat protein (gpVIII) subunits were interspersed with coat proteins displaying one or other of two foreign peptides (fdMAL1, sequence NANPNANPNANP or fdMAL2, sequence NDDSYIPSAEKI) in the exposed N-terminal segments [Greenwood et al., J. Mol. Biol. 220 (1991) 821-827]. These sequences represent major antigenic determinants of the circumsporozoite protein of the malaria parasite, Plasmodium falciparum. The peptide epitopes in the hybrid bacteriophages were found to be strongly immunogenic in four different strains of mice without the use of external adjuvants, and the antibodies (Ab) were highly specific to the individual epitopes in ELISA assays. When tested in nude (nu/nu) and heterozygote (nu +/-) BALB/c mice, the immune response was found to be T-cell dependent and to undergo class-switching from IgM to IgG. Proliferation assays of T-cells taken from lymph nodes of BALB/c mice injected with bacteriophage particles in the presence or absence of Freunds complete adjuvant indicated no difference in the immune response. This way of generating Ab against peptide epitopes is simpler and much less expensive than the conventional method of peptide synthesis and coupling to a carrier protein for injection. The specificity of the immune response, the ability to recruit helper T-cells and the lack of need for external adjuvants suggest that it will also be an inexpensive and simple route to the production of effective vaccines.

Protein–protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase

BACKGROUND The ubiquitous pyruvate dehydrogenase multienzyme complex is built around an octahedral or icosahedral core of dihydrolipoamide acetyltransferase (E2) chains, to which multiple copies of pyruvate decarboxylase (E1) and dihydrolipoamide dehydrogenase (E3) bind tightly but non-covalently. E2 is a flexible multidomain protein that mediates interactions with E1 and E3 through a remarkably small binding domain (E2BD). RESULTS In the Bacillus stearothermophilus complex, the E2 core is an icosahedral assembly of 60 E2 chains. The crystal structure of the E3 dimer (101 kDa) complexed with E2BD (4 kDa) has been solved to 2.6 A resolution. Interactions between E3 and E2BD are dominated by an electrostatic zipper formed by Arg135 and Arg139 in the N-terminal helix of E2BD and Asp344 and Glu431 of one of the monomers of E3. E2BD interacts with both E3 monomers, but the binding site is located close to the twofold axis. Thus, in agreement with earlier biochemical results, it is impossible for two molecules of E2BD to bind simultaneously to one E3 dimer. CONCLUSIONS Combining this new structure for the E3-E2BD complex with previously determined structures of the E2 catalytic domain and the E2 lipoyl domain creates a model of the E2 core showing how the lipoyl domain can move between the active sites of E2 and E3 in the multienzyme complex.

Domain structure of bacteriophage fd adsorption protein

Received 13 October 1981 1. Introduction Bacteriophage fd is one of a group of closely-related filamentous male-specific coliphages (others are M 13 and fl). The virion consists of a closed single-stranded loop of DNA, 6408 nucleotides in length [1], within a tubular array of 2700 subunits of coat protein [2]. At one end of the viral filament are ~5 copies of a second protein, the adsorption protein or A-protein [3 ]; there are also a few copies of 2 or 3 other, smaller proteins [4,5 ]. Much is known about the life cycle of the virus (review [6]). The A-protein is required for adsorption of the phage to the host receptor, which is probably the tip of the F-pilus [7]. Treatment of the phage with the proteinase subtilisin results in digestion of the A-pro- tein but not the coat protein, leaving a particle which is stable but not infectious [7,8]. Electron microscopy reveals that such a particle has lost several small knob- like structures located at one end of the native virion [9]. The amino acid sequence of the A-protein has been deduced by alignment of the N-terminal residues of the protein [3] with the translated DNA sequence of the phage [1,10]. Further analysis of the structure of the A-protein, and its role in adsorption to the host cell, has been hindered by its low abundance (~1% of the virus (w/w)) and its extreme insolubility; isolation of the protein requires complete denaturation of the virus with detergent [3,4]. Here, we show that mild digestion of phage fd with subtilisin releases a large, soluble N-terminal fragment of the A-protein. The fragment appears to compete with intact phage for attachment sites on the host cell. These results suggest models for the structure of * Present address: European Molecular Biology Laboratory, Postfach 10 2209, Meyerhofstrasse 1,6900 Heidelberg, FRG the A-protein and its assembly into the virion at the host cell membrane. 2. Materials and methods

Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine

Electron cryo‐microscopy of ‘single particles’ is a powerful method to determine the three‐dimensional (3D) architectures of complex cellular assemblies. The pyruvate dehydrogenase multi‐enzyme complex couples the activity of three component enzymes (E1, E2 and E3) in the oxidative decarboxylation of pyruvate to generate acetyl‐CoA, linking glycolysis and the tricarboxylic acid cycle. We report here a 3D model for an 11 MDa, icosahedral pyruvate dehydrogenase sub‐complex, obtained by combining a 28 Å structure derived from electron cryo‐microscopy with previously determined atomic coordinates of the individual E1 and E2 components. A key feature is that the E1 molecules are located on the periphery of the assembly in an orientation that allows each of the 60 mobile lipoyl domains tethered to the inner E2 core to access multiple E1 and E2 active sites from inside the icosahedral complex. This unexpected architecture provides a highly efficient mechanism for active site coupling and catalytic rate enhancement by the motion of the lipoyl domains in the restricted annular region between the inner core and outer shell of the complex.

Phage display of peptide epitopes from HIV-1 elicits strong cytolytic responses

Although much effort has been expended on evaluating recombinant proteins and synthetic peptides as immunogens, they have generally proved incapable of inducing an efficient cytotoxic T-cell (CTL) response. Filamentous bacteriophage fd can display multiple copies of foreign peptides in the N-terminal region of its major coat protein pVIII, 2,700 copies of which make up the virus capsid. Here we show that fd virions displaying peptide RT2 (ILKEPVHGV), corresponding to residues 309–317 of the reverse transcriptase (RTase) of HIV-1, are able to prime a CTL response specific for this HIV-1 epitope in human cell lines. Successful priming also requires a T-helper epitope, pep23 (KDSWTVNDIQKLVGK), corresponding to residues 249–263 of HIV-1 RTase. Supplying this by displaying it on either the same or a separate bacteriophage virion led to activation of antigen-specific CD4+ T cells. Likewise, HLA-A2 transgenic mice immunized with bacteriophage virions displaying peptide RT2 were shown to mount an effective, specific anti-HIV-RT2 CTL response. This unexpected ability to elicit a designated cytolytic T-cell response, in addition to a B-cell response, has important implications for access to the class I major histocompatibility complex (MHC) loading compartment and the development of recombinant vaccines.

Genetic reconstruction and functional analysis of the repeating lipoyl domains in the pyruvate dehydrogenase multienzyme complex of Escherichia coli

The dihydrolipoamide acetyltransferase component (E2p) of the pyruvate dehydrogenase complex of Escherichia coli contains three highly homologous sequences of about 100 residues that are tandemly repeated to form the N-terminal half of the polypeptide chain. All three sequences include a lysine residue that is a site for lipoylation and they appear to form independently folded functional domains. These lipoyl domains are in turn linked to a much larger (about 300 residues) subunit-binding domain of the E2p chain that aggregates to form the octahedral inner core of the complex and also contains the acetyltransferase active site. In order to investigate whether individual lipoyl domains play different parts in the enzymic mechanism, selective deletions were made in vitro in the dihydrolipoamide acetyltransferase gene (aceF) so as to excise one or two of the repeating sequences. This was facilitated by the high degree of homology in these sequences, which allowed the creation of hybrid lipoyl domains that closely resemble the originals. Pyruvate dehydrogenase complexes incorporating these genetically reconstructed E2p components were purified and their structures were confirmed. It was found that the overall catalytic activity, the system of active site coupling, and the ability to complement pyruvate dehydrogenase complex mutants, were not significantly affected by the loss of one or even two lipoyl domains per E2p chain. No special role can be attached thus far to individual lipoyl domains. On the other hand, certain genetic deletions affecting the acetyltransferase domain caused inactivation of the complex, highlighting particularly sensitive areas of that part of the E2p chain.

The pyruvate dehydrogenase multienzyme complex

Abstract During the review period, several structures of component enzymes and domains of enzymes of this multienzyme complex were determined. Three structures of the flavoprotein component, dihydrolipoamide dehydrogenase, became available. The structure of the core component, dihydrolipoyl acetyltransferase, can in principle be constructed from the known structures of its modules: the lipoyl, the peripheral subunit-binding and the catalytic domain. Dynamic aspects, such as the structure and function of the inter-domain linkers in dihydrolipoyl acetyltransferase and the conformational changes invlved in the mechanism of electron transfer in dihydrolipoamide dehydrogenase, remain to be clarified. Although several questions concerning the structure of the individual components of the complex have been solved, there is still much to learn about the assembly pathway. In mammalian complexes, the structure and function of protein X remains something of a riddle.