Conformational changes in sperm-whale metmyoglobin due to combination with antibodies to apomyoglobin

The importance of conformation and of equilibria in the interaction of globular proteins and their fragments with antibodies

Oligopeptide fragments of globular proteins often inhibit the interaction of antibodies with native protein. Although such fragments appear to possess in aqueous solution an unfolded conformation it is apparent, in those cases where the protein's three-dimensional structure is known, that the antibody-bound fragment possesses a folded conformation mimicking that of the corresponding portion of the whole protein. The probable explanation of this dichotomy is that the fragment has various conformations in equilibrium including a small proportion of molecules whose shape is recognized and stabilized by the antibody. A related situation can exist in the interaction of antibody(ies) with the whole protein. Thus, antibodies against an altered form of the protein can induce the native antigen to adopt the conformation of the altered form. In this case, it appears that localized regions of the protein's surface are flexible, adopting various conformations in equilibrium, one of which is stabilized (selected) by interaction with the appropriate antibody. In both instances interaction with antibody perturbs an equilibrium, leading to the selection of a particular conformation. Such dynamic effects have profound implications on the choice of peptides as synthetic vaccines.

Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling

Regulation, recognition and cell signaling involve the coordinated actions of many players. To achieve this coordination, each participant must have a valid identification (ID) that is easily recognized by the others. For proteins, these IDs are often within intrinsically disordered (also ID) regions. The functions of a set of well-characterized ID regions from a diversity of proteins are presented herein to support this view. These examples include both more recently described signaling proteins, such as p53, alpha-synuclein, HMGA, the Rieske protein, estrogen receptor alpha, chaperones, GCN4, Arf, Hdm2, FlgM, measles virus nucleoprotein, RNase E, glycogen synthase kinase 3beta, p21(Waf1/Cip1/Sdi1), caldesmon, calmodulin, BRCA1 and several other intriguing proteins, as well as historical prototypes for signaling, regulation, control and molecular recognition, such as the lac repressor, the voltage gated potassium channel, RNA polymerase and the S15 peptide associating with the RNA polymerase S-protein. The frequent occurrence and the common use of ID regions in important protein functions raise the possibility that the relationship between amino acid sequence, disordered ensemble and function might be the dominant paradigm for the molecular recognition that serves as the basis for signaling and regulation by protein molecules.

Antibodies as specific chaperones

Protein folding is often accompanied by formation of non-native conformations leading to protein aggregation. A number of reports indicate that antibodies can facilitate folding and prevent aggregation of protein antigens. The influence of antibodies on folding is strictly antigen specific. Chaperone-like antibody activity may be due to the stabilization of native antigen conformations or folding transition states, or screening of aggregating hydrophobic surfaces. Taking advantage of chaperone-like activity of antibodies for immunotherapy may prove to be a promising approach to the treatment of Alzheimer's and prion-related diseases. Antibody-assisted folding may enhance renaturation of recombinant proteins from inclusion bodies.

Anti-PrP antibodies block PrPSc replication in prion-infected cell cultures by accelerating PrPC degradation

The use of anti-PrP antibodies represents one of the most promising strategies for the treatment of prion diseases. In the present study, we screened various anti-PrP antibodies with the aim of identifying those that would block PrP(Sc) replication in prion-infected cell culture. Two antibodies, SAF34 recognizing the flexible octarepeats region on HuPrP protein, and SAF61 directed against PrP amino acid residues (144-152), not only inhibited PrP(Sc) formation in prion-infected neuroblastoma cells but also decreased the PrP(C) levels in non-infected N2a cells. In addition, treatment with both SAF34 and SAF61 antibodies decreased PrP(C) and PrP(Sc) levels in the cells synergistically. In the presence of both antibodies, our results showed that the mode of action which leads to the disappearance of PrP(Sc) in cells is directly coupled to PrP(C) degradation by reducing the half-life of the PrP(C) protein.

Antiperoxidase antibodies enhance refolding of horseradish peroxidase

The effect of monoclonal antibodies on protein folding was studied using horseradish peroxidase refolding from guanidine hydrochloride as a model process. Among the five antiperoxidase clones tested, one was found to increase the yield of catalytically active peroxidase after guanidine treatment. The same clone also increased the activity of the native peroxidase by a factor of 2-2.5. While peroxidase refolding under standard conditions resulted in the recovery of only 7-8% of the initial catalytic activity, antibody-assisted refolding increased the yield to 50-100% (or 20-40% from the activity of native enzyme with antibodies). Kinetics of autorefolding and antibody-assisted refolding differed significantly. In the course of autorefolding the catalytic activity was recovered within the first 2.5 min and did not change further within a 2.5- to 60-min interval, whereas in the course of antibody-assisted refolding maximal catalytic activity was attained only in 60 min. The yield of active peroxidase for the antibody-assisted refolding depended linearly on the antibody concentration. The observed effect was strongly specific. Other antiperoxidase clones tested as well as nonspecific antithyroglobulin antibody affected neither kinetics, no the yield of peroxidase refolding.

Antibody-detected folding: kinetics of surface epitope formation are distinct from other folding phases

The rate of macromolecular surface formation in yeast iso-2 cytochrome c and its site-specific mutant, N52I iso-2, has been studied using a monoclonal antibody that recognizes a tertiary epitope including K58 and H39. The results indicate that epitope refolding occurs after fast folding but prior to slow folding, in contrast to horse cytochrome c where surface formation occurs early. The antibody-detected (ad) kinetic phase accompanying epitope formation has k(ad) = 0.2 s(-1) and is approximately 40-fold slower than the fastest detectable event in the folding of yeast iso-2 cytochrome c (k2f approximately 8 s(-1)), but occurs prior to the absorbance- and fluorescence-detected slow folding steps (k1a approximately 0.06 s(-1); k1b approximately 0.09 s(-1)). N5I iso-2 cytochrome c exhibits similar kinetic behavior with respect to epitope formation. A detailed dissection of the mechanistic differences between the folding pathways of horse and yeast cytochromes c identifies possible reasons for the slow surface formation in the latter. Our results suggest that non-native ligation involving H33 or H39 during refolding may slow down the formation of the tertiary epitope in iso-2 cytochrome c. This study illustrates that surface formation can be coupled to early events in protein folding. Thus, the rate of macromolecular surface formation is fine tuned by the residues that make up the surface and the interactions they entertain during refolding.

Antigen recognition by conformational selection

Conformational adaptation between antigen and antibody can modulate the antibody specificity. The phenomenon has often been proposed to result from an 'induced fit', which implies that the binding reaction induces a conformational change in the antigen and the antibody. Thus, an 'induced fit' requires initial complex formation followed by a conformational change in the complex. However, an antibody may select those antigen molecules that happen to be in a fitting conformational state. This leads to the same end result as an induced fit. Here, we demonstrate conformational selection by a single chain antibody fragment, raised against a random coil variant of the leucine zipper domain of transcription factor GCN4, when it cross-reacts with the wild-type dimeric leucine zipper. Kinetic and equilibrium data show that the single chain antibody fragment fragment selects monomeric peptides from the population in equilibrium with the leucine zipper dimer.

A monoclonal antibody to avidin dissociates quaternary structure and curtails biotin binding to avidin and streptavidin

An anti-avidin mAb, viz., H12G4, is shown to release bound biotin in a dose-dependent manner from holoavidin and holostreptavidin and inhibit the binding of ligand to the two apoproteins. The release of biotin by this mAb is accompanied by quenching of ligand-induced enhanced fluorescence of the FITC-avidin conjugate. In terms of mechanism of release of bound biotin, we demonstrate that on binding to the Fab fragment of the mAb, the native tetrameric holoavidin undergoes dissociation progressively with time to monomers with no bound biotin associated with the latter. Based on the immunoreactivity associated with defined overlapping fragments of avidin obtained by chemical cleavage, the epitope recognized by mAb H12G4 has been localized to residues 58-96 of the primary sequence. By pepscan method of epitope mapping, this mAb is shown to identify a minimal core sequence of 87RNGK90 in avidin and a corresponding sequence of 84RNAH87 in streptavidin.

Three-dimensional structure of an Fab-peptide complex: structural basis of HIV-1 protease inhibition by a monoclonal antibody

F11.2.32, a monoclonal antibody raised against HIV-1 protease (Kd = 5 nM), which inhibits proteolytic activity of the enzyme (K(inh) = 35(+/-3)nM), has been studied by crystallographic methods. The three-dimensional structure of the complex between the Fab fragment and a synthetic peptide, spanning residues 36 to 46 of the protease, has been determined at 2.2 A resolution, and that of the Fab in the free state has been determined at 2.6 A resolution. The refined model of the complex reveals ten well-ordered residues of the peptide (P36 to P45) bound in a hydrophobic cavity at the centre of the antigen-binding site. The peptide adopts a beta hairpin-like structure in which residues P38 to P42 form a type II beta-turn conformation. An intermolecular antiparallel beta-sheet is formed between the peptide and the CDR3-H loop of the antibody; additional polar interactions occur between main-chain atoms of the peptide and hydroxyl groups from tyrosine residues protruding from CDR1-L and CDR3-H. Three water molecules, located at the antigen-antibody interface, mediate polar interactions between the peptide and the most buried hypervariable loops, CDR3-L and CDR1-H. A comparison between the free and complexed Fab fragments shows that significant conformational changes occur in the long hypervariable regions, CDR1-L and CDR3-H, upon binding the peptide. The conformation of the bound peptide, which shows no overall structural similarity to the corresponding segment in HIV-1 protease, suggests that F11.2.32 might inhibit proteolysis by distorting the native structure of the enzyme.

Investigating protein conformation, dynamics and folding with monoclonal antibodies

Monoclonal antibodies with thoroughly characterized target specificities can be used as powerful probes of protein conformation. In addition to providing information on the relative arrangement of the domains in the native molecule, they can also be used to monitor both early and late stages of protein folding and conformational changes related to enzyme action.

Effect of glutaraldehyde-fixation on the immunogenicity, particle stability and antigenic reactivity of alfalfa mosaic virus, and the specificity of elicited antibodies

Glutaraldehyde-fixation was shown to stabilize the structural integrity of alfalfa mosaic virus (AMV) particles as well as to increase their immunogenicity and antigenic reactivity. The antigenic reactivity of the particles was substantially increased irrespective of whether the antibodies were from animals immunized with native or fixed AMV, or preparations of coat protein subunits isolated from the virus. No significant changes in the antigenic specificity of AMV particles were detected following glutaraldehyde-fixation. Thus it is possible to raise antisera to AMV with higher titres by using fixed virus as immunogen.

The conformation-sensitive immunoassay: a membrane based ELISA system for identifying antibodies sensitive to alterations of protein conformation

A Conformation-Sensitive Immunoassay (CSI) has been developed for identification of antibodies that are sensitive to alterations in protein conformation. The method involves covalently coupling proteins to an activated hydrophilic membrane support. The membrane bound proteins are then treated under conditions known to alter protein conformation, immobilized in a non-native state via additional covalent interactions with the support, and subsequently probed using conventional ELISA techniques. This method has been validated using several well characterized conformation-sensitive antibodies to horse cytochrome c and sperm whale myoglobin. A panel of monoclonal antibodies directed against bovine somatotropin (bSt) has been partially characterized using this validated CSI procedure. Each of these antibodies to bSt has been shown to detect conformational alterations of bSt structure. Data are also presented that demonstrates that the accuracy of CSI analysis is superior to that of Western blotting for characterizing conformation-sensitive antibodies.

Fine manipulation of antibody affinity for synthetic epitopes by altering peptide structure: antibody binding to looped peptides*

Linear peptides weakly imitate antibody binding sites on globular proteins when the peptides are shown to be effective at all. As a step toward enhancing the ability of peptides to mimic epitopes, we have examined the effects of various alterations in peptide structure on antibody binding. Synthetic peptides containing the core amino acid sequence of residues 41 to 48 from horse cytochrome c were examined for their ability to bind antibodies elicited against the 41-48 peptide coupled to bovine serum albumin (BSA). Since residues 41-48 in native cytochrome c are part of an omega loop, in some peptides cysteines were incorporated for intrachain disulfide bonding to stabilize loop structure. In additional cases, glycine was incorporated as a spacer between the natural sequence and the cysteine residues with the intent of relaxing loop structure slightly. Eleven analogues containing the 41-48 sequence were tested. These included native cytochrome c and the 1-80 and 1-65 cyanogen bromide-cleaved fragments. The native protein did not bind the anti-41-48 antibodies. The other analogues differed by over three orders of magnitude in their binding. The affinity of binding was inversely related to the extent of predicted loop structure indicating that the antibodies were elicited against the 41-48 sequence in a more unfolded conformation despite the Pro Gly sequence at positions 44 and 45 that generally favors a beta turn. Surprisingly, the immunizing peptide, containing residues 41-48 only, was the poorest binding peptide. The relative impotence of 41-48 was shown to be largely due to differences at the amino terminus between the free and BSA-coupled peptides as the antibodies were elicited against the latter. The distinctions among the synthetic peptides containing the 41-48 sequence show the exquisite sensitivity of antibody binding to amino acid changes that may occur outside of an epitope and suggest modifications in peptide structure at the periphery of an epitope that can lead to desired changes in antibody affinity.

Antigenic sites on cytochrome c2 from Rhodospirillum rubrum

The antigenic determinants for three monoclonal antibodies against cytochrome c2 from Rhodospirillum rubrum were partially characterized by differential chemical modification of free and antibody-bound cytochrome c2 and by cross-reactivity analysis with different antigens. Circular dichroism spectroscopy was used to probe the effect of antibody binding on the conformation of cytochrome c2. The binding of two antibodies was strongly dependent on the native folding of the antigen. The first antibody bound to a determinant around the exposed heme edge on the 'front side' of the molecule which is not antigenic in mitochondrial cytochrome c2. Binding of this antibody to cytochrome c increased the induced CD of the ferric heme in a manner similar to that observed previously when mitochondrial cytochrome-c oxidase bound to the front side of cytochrome c. This observation points to a subtle conformational adaptation of the antigen induced by the antibody. The determinant for the second antibody, which also affected the heme CD spectrum of the antigen, was on a polypeptide loop where cytochrome c2 differs from mitochondrial cytochrome c by an eight-residue insertion. The third antibody, which did not induce a change in CD, bound to a sequential determinant near the amino end of cytochrome c2. Only this antibody cross-reacted with isolated cytochrome-c-derived peptides and with apo-cytochrome c2. A preliminary analysis of the polyclonal immune response of five rats against cytochrome c2 indicates that, unlike in eukaryotic cytochrome c, antigenic determinants are distributed over the whole polypeptide chain of the prokaryotic immunogen.

Monoclonal antibody recognizes a conformational epitope in a random coil protein

The antigenic determinants for two monoclonal antibodies directed against horse apo-cytochrome c, a protein of disordered structure, as judged by spectroscopic and hydrodynamic criteria, have been studied by a combination of methods: antigen competition in solution by radio immunoassay and enzyme-linked immunoassay, and differential acetylation of free and antibody-bound antigen. In the latter method the accessibility of lysine residues of the antigen in the antigen-antibody complex is compared to the accessibility in the free antigen. The two antibodies against the heme-free protein do not recognize intact native cytochrome c, but they crossreact with the heme-containing peptides 1-38 and 1-65 of cytochrome c. The antigenic determinant recognized by monoclonal antibody SJL 2-4 is conformational and discontiguous, it is composed of residues close to the N-terminus and around position 25. The other monoclonal antibody, Cyt-1-59, seems to recognize a contiguous epitope close to the N-terminus. The present results show that even a seemingly disordered protein which is conventionally classified as a random coil may feature subtle spatial regularities. The presence of ordered conformational elements in apocytochrome c may be important for the enzyme-catalyzed covalent attachment of the heme and the import of cytochrome c into mitochondria. A discontiguous determinant for SJL 2-4 is particularly interesting because this antibody inhibits the proliferation of a T-cell clone specific for apo-cytochrome c [Corradin & Engers (1984) Nature (Lond.) 308, 547-548].

Assembly of the OmpF porin of Escherichia coli B. Immunological and kinetic studies of the integration pathway

The different conformations of the outer membrane protein OmpF of Escherichia coli B were studied with immunological probes. The antigenic determinants recognized by one monoclonal (MoF3) and two polyclonal antibodies were investigated under various conditions of solubilization which modify the association of OmpF with other membrane components, such as lipopolysaccharide. Several polymeric forms of the protein could be detected after extraction at 37 degrees C or 56 degrees C. The monoclonal antibody, which is specific to an exposed region of native OmpF, recognized various trimeric forms in an immunoprecipitation assay. Under the same conditions, the binding of polyclonal antibodies apparently induced strong conformational rearrangements, since the pattern of trimeric forms detected was greatly modified. The conversion of newly synthesized monomers of OmpF to the various trimer forms was investigated using these antibodies. The trimerization occurred rapidly but the appearance of the native conformation of OmpF was delayed. Some additional step was required to expose the MoF3-specific antigenic site at the surface of the trimeric form. These results are discussed in relation to the structure of OmpF and its association with lipopolysaccharide in the outer membrane.

Activation of low and null activity isozymes of maize alcohol dehydrogenase by antibodies

Antisera were raised against several purified, high specific activity isozymes of maize alcohol dehydrogenase (ADH1). The various antisera had different effects on the activity of immunoprecipitated ADH. One antiserum completely inactivated maize ADH. This inactivation could be blocked by preincubation of the enzyme with NAD+, its cofactor, or with NADP. The different antisera were used to analyze variant forms of ADH1. Isozymes having lowered specific activity were activated to wild-type levels by precipitation of the enzymes with noninactivating antisera. Isozymes having no detectable ADH activity (CRM+ nulls) were activated by immunoprecipitation with noninactivating antisera when preincubated with NAD+ or NADP. All of the CRM+ nulls were shown to be unable to bind NAD+, a flaw which can account for their lack of activity. The results indicate that a conformational equilibrium between active and inactive forms of maize ADH in solution controls the specific activity of the various isozymes. Both NAD+ and antibodies raised against high specific activity enzymes can interact with low activity isozymes to shift the balance of the equilibrium toward the active form, thus increasing their specific activity.

Three-dimensional structure of a complex of antibody with influenza virus neuraminidase

The structure of a complex between influenza virus neuraminidase and an antibody displays features inconsistent with the inflexible 'lock and key' model of antigen-antibody binding. The structure of the antigen changes on binding, and that of the antibody may also change; the interaction therefore has some of the character of a handshake.

Development of a screening system for detection of somatic mutations. II. The use of peptides and insoluble protein fragments in a non-competitive solid-phase enzyme immunoassay

A system proposed for measurement of mutational risk consists in detection of hemoglobin mutations expressed in erythrocytes. For this detection the production of antibodies specific for Hb variants is essential. Recently we reported a sensitive solid-phase EIA for the production and selection of polyclonal and monoclonal antibodies specific for hemoglobin determinants. An important characteristic of this EIA was the coating of water-insoluble proteins to polystyrene microtiter plates. Here we report that with this system, insoluble protein fragments and small peptides may also be covalently coated to a polystyrene surface. Coating is independent of the length of the peptides. This allows direct, non-competitive titration of the antibody response to small peptides and avoids the drawbacks of competitive assay.

Antibody-mediated activation of genetically defective Escherichia coli beta-galactosidases by monoclonal antibodies produced by somatic cell hybrids

Six hybridomas producing monoclonal antibodies against Escherichia coli beta-galactosidase (beta-D-galactoside galoctohydrolase, EC 3.2.1.23) have been derived from two separate somatic cell fusions. Three of these antibodies can activate defective enzymes produced by strains of E. coli carrying Z-gene point mutations. In antigen excess, one monoclonal antibody shows similar enzyme binding and mutant-activating capacity. Characteristically, the former reaction has a 200-fold higher equilibrium constant. These data provide direct evidence that the enzyme-activation reaction is a single-hit event in which one antibody site favors the correct conformation of one active center of the enzyme. Because each "activating" hybridoma is able to activate several but not all point mutant enzymes tested, it appears that the correction of the genetic defect is produced by binding key sites of the protein three-dimensional structure rather than the sites affected by the mutation.

Comparison of the structures of various eukaryotic ferricytochromes c and ferrocytochromes and their antigenic differences

The nuclear magnetic resonance spectra of various eukaryotic ferricytochromes c and ferrocytochromes c are described. The proteins from the species donkey, cow, dog, rabbit, chicken and pigeon were investigated. The conformations of these proteins detected by NMR were compared to those of horse and tuna cytochromes c and in some cases small differences were found. These differences in structure were shown to correlate with antigenic differences between the various proteins.

Cellular distrubtion, purification, and molecular nature of human Ia antigens

Human Ia antigens were extensively purified (1390-fold increase in specific activity) in 32% yield from BRI 8 cells, a lymphoblastoid B-cell line. Purification was monitored by using allogeneic antisera arising by foetal-maternal stimulation. The product, a glycoprotein fraction, contained the Ia antigens, the HLA-A and -B antigens, and a glycoprotein of unknown function. The glycoprotein fraction was composed of four glycosylated polypeptides with molecular weights of 43,000, 39,000, 33,000, and 28,000, and beta2-microglobulin; no polypeptide was linked to another by disulphide bridges. The A and B antigens only were absorbed by antibody against beta2-microglobulin. The Ia antigens comprised one each of the 33,000 and 28,000 molecular weight glycosylated polypeptides noncovalently linked together. Thus, only these chains were absorbed by xenogeneic anti-Ia antisera and were cross-linked by dimethyl-3-3'-dithiobispropionimidate dihydrochloride. The dimeric molecule bound deoxycholate (0.26 g/g of protein) and, when solubilized in deoxycholate, has a molecular weight of 77,000. The Ia allo- and xeno-antigenic activities were labile to heating and proteolysis and are probably determined by the polypeptide structure. Xenogeneic specific anti-Ia antisera were raised in rabbits and mice by immunizing with the glycoprotein fraction. These antisera reacted with B lymphocytes and monocytes but not T lymphocytes and fibroblasts. Their Fab fragments blocked the cytotoxicity of the allogeneic antisera for B lymphocytes and were potent inhibitors of the mixed lymphocyte reaction.