Inhibiting protein-protein interactions: a model for antagonist design.

Protein-protein interactions (PPI) are a ubiquitous mode of transmitting signals in cells and tissues. We are testing a stepwise, generic, structure-driven approach for finding low molecular weight inhibitors of protein-protein interactions. The approach requires development of a high-affinity, single chain antibody directed specifically against the interaction surface of one of the proteins to obtain structural information on the interface. To this end, we developed a single chain antibody (sc1E3) against hIL-1beta that exhibited the equivalent affinity of the soluble IL-1 receptor type I (sIL-1R) for hIL-1beta and competitively blocked the sIL-1R from binding to the cytokine. The antibody proved to be more specific for hIL-1beta than the sIL-1R in that it failed to bind to either murine IL-1beta or human/murine IL-1alpha proteins. Additionally, failure of sc1E3 to bind to several hIL-1beta mutant proteins, altered at receptor site B, indicated that the antibody interacted preferentially with this site. This, coupled with other surface plasmon resonance and isothermal titration calorimetry measurements, shows that sc1E3 can achieve comparable affinity of binding hIL-1beta as the receptor through interactions at a smaller interface. This stable single chain antibody based heterodimer has simplified the complexity of the IL-1/IL-1R PPI system and will facilitate the design of the low molecular weight inhibitors of this interaction.

Identification, characterization, and crystal structure of the Omega class glutathione transferases.

A new class of glutathione transferases has been discovered by analysis of the expressed sequence tag data base and sequence alignment. Glutathione S-transferases (GSTs) of the new class, named Omega, exist in several mammalian species and Caenorhabditis elegans. In humans, GSTO 1-1 is expressed in most tissues and exhibits glutathione-dependent thiol transferase and dehydroascorbate reductase activities characteristic of the glutaredoxins. The structure of GSTO 1-1 has been determined at 2.0-A resolution and has a characteristic GST fold (Protein Data Bank entry code ). The Omega class GSTs exhibit an unusual N-terminal extension that abuts the C terminus to form a novel structural unit. Unlike other mammalian GSTs, GSTO 1-1 appears to have an active site cysteine that can form a disulfide bond with glutathione.

Inclusion body formation by interleukin-1 beta depends on the thermal sensitivity of a folding intermediate.

We show that sequence and growth temperature effects on IB formation in the small, monomeric beta-barrel protein interleukin-1 beta (IL-1 beta) can be quantitatively reproduced in an in vitro system in which IL-1 beta is refolded from denaturant at different temperatures. The results suggest that temperature and mutational effects on IB formation may be based on intrinsic properties of the protein sequence rather than interactions with chaperones or other cellular factors. We also report striking correlations of IB formation with mutation-dependent changes in residue hydrophobicity. The nature of these trends differs considerably with residue position, however, suggesting that they are mediated by particular local environments created by an ordered structure.

Nativelike secondary structure in interleukin-1 beta inclusion bodies by attenuated total reflectance FTIR.

Attenuated total reflectance FTIR has been used to study the structure of human interleukin-1 beta in inclusion bodies (IBs) and other aggregated forms. The secondary structure composition of native wild-type IL-1 beta determined by FTIR is in excellent agreement with that previously determined by crystallography and NMR: 52% beta-sheet, 25% loop/irregular structure, and 23% turn. Remarkably, IL-1 beta inclusion bodies exhibit secondary structural composition very similar to that of the native protein. The results indicate that the IBs form from a folding intermediate that has nativelike secondary structure. The secondary structure content of aggregated IL-1 beta, formed either in refolding or by thermal denaturation, was identical within experimental error to that of the IB, indicating that these aggregates were formed from intermediates with structures similar to that of the inclusion body.

Breakdown in the relationship between thermal and thermodynamic stability in an interleukin-1 beta point mutant modified in a surface loop.

Sequence variants of the beta-barrel protein interleukin-1 beta have been analyzed for their stabilities toward irreversible thermal inactivation by monitoring the generation of light scattering aggregates on heating. The derived temperatures for the onset of aggregation (T(agg) values) correlate well with the free energies of unfolding of these proteins with the exception of one variant, Lys97-->Val (K97V), which undergoes aggregation at a temperature 7 degrees C lower than expected based on its thermodynamic stability. This lower than expected thermal stability may be due to generation of an aggregation-prone unfolding intermediate at a temperature lower than the Tm of the global transition. This hypothesis is supported by the location of residue 97 in the long 86-99 loop which has structural features suggesting it may comprise a small, independent folding unit or microdomain. The excellent correlation of thermal and thermodynamic stabilities of seven of the eight variants tested is consistent with accepted models for thermal inactivation of proteins. At the same time the poor fit of the K97V variant underscores the risk in using thermal stability data in quantitative analysis of mutational studies of the folding stability of proteins.

Inclusion body formation and protein stability in sequence variants of interleukin-1 beta.

Inclusion body formation during recombinant protein expression in bacteria is of both fundamental interest and practical importance. To elucidate molecular mechanisms of this process, we are examining the in vitro folding and stability properties of a series of human interleukin-1 beta (IL-1 beta) sequence variants which exhibit widely differing tendencies to form inclusion bodies. Of 67 variants surveyed, nine, including wild type, were purified and their in vitro stability properties determined. One of these, a high inclusion body mutant, exhibited very low solubility in native buffer after purification and was not pursued further. For the other eight sequence variants, no strong correlations were observed between extent of inclusion body formation and either thermodynamic or thermal stability. In particular, a Lys97-->Val mutation produces substantially more IL-1 beta in inclusion bodies than the wild type (61 versus 8%) despite generating a protein more thermodynamically stable than wild type. Furthermore, the Lys97-->Val mutant forms substantial levels of inclusion bodies at 32 degrees C but requires incubation at temperatures greater than 48 degrees C for thermally induced aggregation in vitro. This and other data suggest that the tendency of at least some IL-1 beta variants to form inclusion bodies is most likely related to the stability or solubility of folding intermediates rather than native states. Implications of the structural locations of these mutations are also discussed.

Mutagenic analysis of the interior packing of an alpha/beta barrel protein. Effects on the stabilities and rates of interconversion of the native and partially folded forms of the alpha subunit of tryptophan synthase.

A series of single and double amino acid replacements in four beta strands of the alpha subunit of tryptophan synthase from Salmonella typhimurium, and alpha/beta barrel protein, was made to study the interior packing of the barrel and to clarify its folding mechanism. The urea-induced unfolding of the alpha subunit is thought to involve a stable intermediate in which the amino folding unit (residues 1-188; helices 0-5, strands 1-6) remains folded while the carboxy folding unit (residues 189-268; helices 6-8, strands 7-8) becomes disordered [Beasty, A. M., & Matthews, C. R. (1985) Biochemistry 24, 3547; Miles, E. W., Yutani, K., & Ogasahara, K. (1982) Biochemistry 21, 2586]. Mutations in strands 1 (A18G and A18V), 6 (Y175Q), 7 (L209V), and 8 (G230A, G230V, and I232V) at the interface between these two folding units show that the effects on the stabilities of the native and intermediate conformations critically depend on the site of the replacement. Although all of these mutations decrease the stability of the native conformation, only the replacements in strand 6, Y175Q, and possibly strand 8, I232V, also perturb the intermediate. Comparisons of the effects of three pairs of double mutants with the effects of the constituent single mutants on stability show that strands 6 and 7 interact in both the intermediate and native conformations, while strands 1 and 8 interact only in the native conformation. Kinetic studies of unfolding indicate that the interactions which occur in the native conformation arise in the preceding transition state. These results demonstrate that the carboxy folding unit adopts an organized structure in the intermediate, contrary to our previous interpretation. The general implication is that the state of folding of one segment of a protein can depend on the presence of another, more stable element of structure.

Multiple replacements at position 211 in the alpha subunit of tryptophan synthase as a probe of the folding unit association reaction.

Equilibrium and kinetic studies on the folding of a series of amino acid replacements at position 211 in the alpha subunit of tryptophan synthase from Escherichia coli were performed in order to determine the role of this position in the rate-limiting step in folding. Previous studies [Beasty, A. M., Hurle, M. R., Manz, J. T., Stackhouse, T., Onuffer, J. J., & Matthews, C. R. (1986) Biochemistry 25, 2965-2974] have shown that the rate-limiting step corresponds to the association/dissociation of the amino (residues 1-188) and carboxy (residues 189-268) folding units. In terms of the secondary structure, the amino folding unit consists of the first six strands and five alpha helices of this alpha/beta barrel protein. The carboxy folding unit comprises the remaining two strands and three alpha helices; position 211 is in strand 7. Replacement of the wild-type glycine at position 211 with serine, valine, and tryptophan at most alters the rate of dissociation of the folding units; association is not changed significantly. In contrast, glutamic acid and arginine dramatically decelerate and accelerate, respectively, both association and dissociation. The difference in effects is attributed to long-range electrostatic interactions for these charged side chains; steric effects and/or hydrogen bonding play lesser roles. When considered with previous data on replacements at other positions in the alpha subunit [Hurle, M. R., Tweedy, N. B., & Matthews, C. R. (1986) Biochemistry 25, 6356-6360], it is clear that beta strands 6 (in the amino folding unit) and 7 (in the carboxy folding unit and containing position 211) dock late in the folding process.

Role of diffusion in the folding of the alpha subunit of tryptophan synthase from Escherichia coli.

The rate-limiting step in the folding of the alpha subunit of tryptophan synthase has been proposed to be the association of two folding units. To probe the role of diffusion in this rate-limiting step, the urea-induced unfolding and refolding of the protein was examined in the presence of a number of viscosity-enhancing agents. The analysis was simplified by studying the effect of these agents on folding unit dissociation, the rate-limiting unfolding reaction, and the reverse of the rate-limiting step in refolding. In the presence of ethylene glycol, the relaxation times for unfolding to the same final conditions increased with increasing concentration of the cosolvent. When the effects of the cosolvent on protein stability were taken into account, the rates were found to show a unitary linear dependence on the viscosity of the solution. Similar results were obtained with glycerol and low concentrations of glucose, demonstrating that the effect is general and not specific to any viscogenic agent. These results clearly demonstrate that the rate-limiting folding unit association/dissociation reaction in the alpha subunit of tryptophan synthase involves a diffusional process.