Constant Domain-regulated Antibody Catalysis

Some antibodies contain variable (V) domain catalytic sites. We report the superior amide and peptide bond-hydrolyzing activity of the same heavy and light chain V domains expressed in the IgM constant domain scaffold compared with the IgG scaffold. The superior catalytic activity of recombinant IgM was evident using two substrates, a small model peptide that is hydrolyzed without involvement of high affinity epitope binding, and HIV gp120, which is recognized specifically by noncovalent means prior to the hydrolytic reaction. The catalytic activity was inhibited by an electrophilic phosphonate diester, consistent with a nucleophilic catalytic mechanism. All 13 monoclonal IgMs tested displayed robust hydrolytic activities varying over a 91-fold range, consistent with expression of the catalytic functions at distinct levels by different V domains. The catalytic activity of polyclonal IgM was superior to polyclonal IgG from the same sera, indicating that on average IgMs express the catalytic function at levels greater than IgGs. The findings indicate a favorable effect of the remote IgM constant domain scaffold on the integrity of the V-domain catalytic site and provide a structural basis for conceiving antibody catalysis as a first line immune function expressed at high levels prior to development of mature IgG class antibodies.     

Computational fluid dynamics simulations on a Devonian spiriferid Paraspirifer bownockeri (Brachiopoda): Generating mechanism of passive feeding flows

A mechanism of generating passive feeding flow for the Devonian spiriferide brachiopod Paraspirifer bownockeri was theoretically elucidated through fluid dynamics simulations for flow around rigid shells. The RANS equations were used as a turbulence model, and the unsteady incompressible flow was solved using the finite volume method. Two directions of ventral and dorsal flows were investigated as typical cases where little exchange flow occurs inside the shells. The digital model of the shell was constructed using image processing of X-ray CT images of a shell replica made by molding a polycarbonate plate to a well-preserved fossil specimen of Paraspirifer. To examine the effect of flow velocity, three conditions of ambient flow velocity were adopted for both the ventral and dorsal flows. The pressure distribution along the gape showed that a relatively high pressure occurred around the sulcus in all simulated cases. This high pressure generated inflow from the sulcus and subsequent spiral internal flow, especially in fast ambient flows. This means that the sulcus generated the considerable pressure gradient around the gape passively and generated the stable intake of seawater and a spiral flow of water inside the shell for feeding. We conclude that the shell form of certain spiriferides could generate spiral flows so as to promote passive feeding, and the sulcus is interpreted as an important form for the passive intake of water.     

Regulation of Translation by the Redox State of Elongation Factor G in the Cyanobacterium Synechocystis sp. PCC 6803

Elongation factor G (EF-G), a key protein in translational elongation, was identified as a primary target of inactivation by reactive oxygen species within the translational machinery of the cyanobacterium Synechocystis sp. PCC 6803 (Kojima, K., Oshita, M., Nanjo, Y., Kasai, K., Tozawa, Y., Hayashi, H., and Nishiyama, Y. (2007) Mol. Microbiol. 65, 936–947). In the present study, we found that inactivation of EF-G (Slr1463) by H₂O₂ was attributable to the oxidation of two specific cysteine residues and formation of a disulfide bond. Substitution of these cysteine residues by serine residues protected EF-G from inactivation by H₂O₂ and allowed the EF-G to mediate translation in a translation system in vitro that had been prepared from Synechocystis. The disulfide bond in oxidized EF-G was reduced by thioredoxin, and the resultant reduced form of EF-G regained the activity to mediate translation in vitro. Western blotting analysis showed that levels of the oxidized form of EF-G increased under strong light in a mutant that lacked NADPH-thioredoxin reductase, indicating that EF-G is reduced by thioredoxin in vivo. These observations suggest that the translational machinery is regulated by the redox state of EF-G, which is oxidized by reactive oxygen species and reduced by thioredoxin, a transmitter of reducing signals generated by the photosynthetic transport of electrons.Reactive oxygen species (ROS)² are produced as inevitable by-products of the light-driven reactions of photosynthesis. The superoxide radical, hydrogen peroxide (H₂O₂), and the hydroxyl radical are produced as a result of the photosynthetic transport of electrons, whereas singlet state oxygen (singlet oxygen) is produced by the transfer of excitation energy (1). Exposure of the photosynthetic machinery to strong light promotes the production of ROS and gives rise to oxidative stress (1).Strong light rapidly inactivates photosystem II (PSII). This phenomenon is referred to as photoinhibition (2–4), and it occurs when the rate of photodamage to PSII exceeds the rate of the repair of photodamaged PSII (5). The actions of ROS in the photoinhibition of PSII have been studied extensively, and several mechanisms for photoinhibition have been proposed (5). Recent studies of the effects of ROS on photodamage and repair have revealed that ROS act primarily by inhibiting the repair of photodamaged PSII and not by damaging PSII directly (5–9). Such studies have also shown that photodamage to PSII is an exclusively light-dependent event; photodamage is initiated by disruption of the manganese cluster of the oxygen-evolving complex upon absorption of light, in particular UV and blue light, with subsequent damage to the reaction center upon absorption of visible light by chlorophylls (10–12).Inhibition of the repair of PSII has been attributed to the suppression, by ROS, of the synthesis de novo of proteins that are required for the repair of PSII, such as the D1 protein, which forms a heterodimer with the D2 protein in the reaction center, in the cyanobacterium Synechocystis sp. PCC 6803 (hereafter referred to as Synechocystis) (6, 7), in Chlamydomonas (13), and in plants (14, 15). Analysis of polysomes in Synechocystis has demonstrated that ROS inhibit the synthesis de novo of proteins primarily at the elongation step of translation, suggesting that some proteins involved in translational elongation might be the targets of inactivation by ROS (6, 7).A translation system in vitro was successfully prepared from Synechocystis, and biochemical investigations using this translation system have revealed that elongation factor G (EF-G), a GTP-binding protein that catalyzes the translocation of peptidyl-tRNA (16), is a primary target of inactivation by ROS (17). EF-G is reversibly inactivated by ROS in a redox-dependent manner; it is inactive in the oxidized form and active in the reduced form (17). Moreover, it has been proposed that changes in the activity of EF-G might depend on and be regulated by the redox states of cysteine residues within EF-G (17). However, the specific cysteine residues within EF-G that might be the targets of ROS and might be responsible for redox regulation remain to be determined.In the present study, we investigated the redox state of Slr1463, the EF-G that is phylogenetically closest to chloroplast EF-G among three homologs of EF-G in Synechocystis (17). We determined that two specific cysteine residues in the EF-G of Synechocystis were targets of oxidation by ROS. The resultant disulfide bond between the two cysteine residues was efficiently reduced by thioredoxin. In addition, we observed that EF-G was reduced by thioredoxin in vivo. Our findings revealed the mechanism of the ROS-induced inactivation of EF-G and suggested a mechanism for the redox regulation of translation by electrons generated during photosynthesis.     

Antigen-specific Proteolysis by Hybrid Antibodies Containing Promiscuous Proteolytic Light Chains Paired with an Antigen-binding Heavy Chain

The antigen recognition site of antibodies consists of the heavy and light chain variable domains (V_L and V_H domains). V_L domains catalyze peptide bond hydrolysis independent of V_H domains (Mei, S., Mody, B., Eklund, S. H., and Paul, S. (1991) J. Biol. Chem. 266, 15571–15574). V_H domains bind antigens noncovalently independent of V_L domains (Ward, E. S., Güssow, D., Griffiths, A. D., Jones, P. T., and Winter, G. (1989) Nature 341, 544–546). We describe specific hydrolysis of fusion proteins of the hepatitis C virus E2 protein with glutathione S-transferase (GST-E2) or FLAG peptide (FLAG-E2) by antibodies containing the V_H domain of an anti-E2 IgG paired with promiscuously catalytic V_L domains. The hybrid IgG hydrolyzed the E2 fusion proteins more rapidly than the unpaired light chain. An active site-directed inhibitor of serine proteases inhibited the proteolytic activity of the hybrid IgG, indicating a serine protease mechanism. The hybrid IgG displayed noncovalent E2 binding in enzyme-linked immunosorbent assay tests. Immunoblotting studies suggested hydrolysis of FLAG-E2 at a bond within E2 located ∼11 kDa from the N terminus. GST-E2 was hydrolyzed by the hybrid IgG at bonds in the GST tag. The differing cleavage pattern of FLAG-E2 and GST-E2 can be explained by the split-site model of catalysis, in which conformational differences in the E2 fusion protein substrates position alternate peptide bonds in register with the antibody catalytic subsite despite a common noncovalent binding mechanism. These studies provide proof-of-principle that the catalytic activity of a light chain can be rendered antigen-specific by pairing with a noncovalently binding heavy chain subunit.Antibodies (Abs)² are composed of light and heavy chain subunits linked by intra- and inter-chain disulfide bonds. The noncovalent antigen binding site of Abs is formed mainly by amino acids located in the complementarity determining regions of the light and heavy chain variable domains (V_L and V_H domains). Physiological Ab-antigen binding reactions require both Ab subunits. The individual light and heavy chains can bind antigens independent of each other, but the binding affinity of the isolated subunits is often lower than the intact Abs from which they are derived (1–4). From crystallography analyses of Ab-antigen complexes, it appears that antigen contact areas with the V_H domain are somewhat greater than the V_L domain (5, 6). Recombinant IgG Abs composed of the heavy chain drawn from antigen-specific IgGs paired with irrelevant light chains retain antigen binding activity, albeit at reduced levels (1, 3).Following the initial noncovalent antigen binding step, some Abs proceed to catalyze hydrolysis of peptide bonds (7–12). The chemical catalysis step entails nucleophilic attack on the electrophilic carbonyl of peptide bonds by serine protease-like sites present in Ab V domains followed by hydrolysis of the covalent reaction intermediate if a water molecule is available (13–15). Unlike reversible binding, the catalytic function offers a means to permanently inactivate the antigen by its hydrolysis into smaller fragments. Reversibly binding Abs bind the antigen stoichiometrically (e.g. 2 antigen molecules/IgG molecule). As catalysts are reusable, a single catalytic Ab molecule can hydrolyze multiple antigen molecules. This offers the possibility of increased antigen neutralizing potency. Therefore, there is considerable interest in developing catalytic Abs directed to individual polypeptide antigens. The serine protease-like activity is a heritable trait encoded by germline Ab V genes, and Abs in the preimmune repertoire can hydrolyze peptides with diverse sequence promiscuously (13, 14, 16, 17). However, the adaptive immune system has evolved to maximize noncovalent binding affinity of Abs over the course of B cell differentiation. Physiological immune mechanisms do not favor retention and improvement of the catalytic function. B cell clonal proliferation is driven by antigen binding to B cell receptors (Abs associated with signal transducing proteins). Antigen hydrolysis by catalytic B cell receptors is followed by release of the antigen fragments, resulting in reduced B cell receptor occupancy and loss of the proliferative stimulus for the cells. Therefore, unlike the noncovalent antigen binding activity, the catalytic function is poorly selectable. Indeed, other than Abs to autoantigen and B cell superantigen substrates, there are no examples of antigen-specific catalytic Abs generated by physiological adaptive mechanisms (18).Much effort has been devoted to developing antigen-specific catalytic Abs by immune and protein engineering strategies. Based on the premise that binding to the transition state reduces the activation energy of the catalytic reaction, immunization with transition state analogs has been applied to raise Abs that catalyze ester bonds in small haptens (19). Attempts to improve the esterase activity by random mutagenesis followed by isolation of transition state analog-binding Abs have also been described (20). Developing antigen-specific proteolytic Abs, however, has been difficult because peptide bond hydrolysis is an energetically demanding reaction. Moreover, there is no viable engineering strategy available to render catalytic Abs specific for individual polypeptide antigens. We (8, 21, 22) and others (23, 24) have identified Ab light chains that hydrolyze peptide bonds promiscuously without participation from the heavy chain subunit. Disruption of the serine protease-like catalytic triad in an Ab light chain by site-directed mutagenesis was without effect on its ability to bind the polypeptide antigen by noncovalent means (13), and a discrete peptide epitope remote from the bond hydrolyzed by a proteolytic Ab preparation has been identified (25). This lead to a split-site model of proteolysis, in which distinct subsites present within the Ab combining site are responsible for initial noncovalent antigen binding and the ensuing peptide bond hydrolysis reaction (26). If this model is correct, it should be possible to develop hybrid proteolytic Abs specific for individual antigens by pairing light chains containing a promiscuous catalytic subsite with heavy chains that contribute the noncovalent subsite responsible for specific antigen binding. We describe proof-of-principle for this engineering approach using previously described catalytic light chains paired with the heavy chain of a monoclonal IgG that binds the hepatitis C virus (HCV) E2 coat protein. This protein is thought to be important in viral entry into hepatocytes and B cells by virtue of its ability to bind receptors expressed on the host cells (27, 28).     

Toward Effective HIV Vaccination: INDUCTION OF BINARY EPITOPE REACTIVE ANTIBODIES WITH BROAD HIV NEUTRALIZING ACTIVITY*

We describe murine monoclonal antibodies (mAbs) raised by immunization with an electrophilic gp120 analog (E-gp120) expressing the rare ability to neutralize genetically heterologous human immunodeficiency virus (HIV) strains. Unlike gp120, E-gp120 formed covalent oligomers. The reactivity of gp120 and E-gp120 with mAbs to reference neutralizing epitopes was markedly different, indicating their divergent structures. Epitope mapping with synthetic peptides and electrophilic peptide analogs indicated binary recognition of two distinct gp120 regions by anti-E-gp120 mAbs, the 421–433 and 288–306 peptide regions. Univalent Fab and single chain Fv fragments expressed the ability to recognize both peptides. X-ray crystallography of an anti-E-gp120 Fab fragment revealed two neighboring cavities, the typical antigen-binding cavity formed by the complementarity determining regions (CDRs) and another cavity dominated by antibody heavy chain variable (V_H) domain framework (FR) residues. Substitution of the FR cavity V_H Lys-19 residue by an Ala residue resulted in attenuated binding of the 421–433 region peptide probe. The CDRs and V_H FR replacement/silent mutation ratios exceeded the ratio for a random mutation process, suggesting adaptive development of both putative binding sites. All mAbs studied were derived from V_H1 family genes, suggesting biased recruitment of the V gene germ line repertoire by E-gp120. The conserved 421–433 region of gp120 is essential for HIV binding to host CD4 receptors. This region is recognized weakly by the FR of antibodies produced without exposure to HIV, but it usually fails to induce adaptive synthesis of neutralizing antibodies. We present models accounting for improved CD4-binding site recognition and broad HIV neutralizing activity of the mAbs, long sought goals in HIV vaccine development.Induction of neutralizing antibodies (Abs)² via adaptive immune processes is the cornerstone of vaccination against microbial antigens. The antigen-binding site is mostly formed by the complementarity determining regions (CDRs) of the light and heavy chain variable domains (V_L and V_H domains). Vaccine-induced adaptive Ab responses entail sequence diversification of Ab V domains expressed within the B cell receptor (BCR) complex, selective noncovalent antigen binding to the high affinity BCR mutants, and proliferation of the mutant B cell clones. No HIV vaccine is available. The surface of HIV is studded with noncovalently associated oligomers of gp120 complexed to gp41. HIV infection and experimental HIV vaccination attempts induce robust Ab responses to the immunodominant epitopes of gp120, which are structurally divergent in various HIV strains responsible for infection in different parts of the world. Abs to such epitopes express strain-specific neutralization (1, 2), i.e. they neutralize the HIV strain from which the immunogen was isolated but not strains genetically heterologous to the immunogen.The gp120 site responsible for binding host CD4 receptors (CD4BS) is structurally more conserved. Precise conformational details of the CD4BS expressed on the HIV surface are not available, but crystallography suggests a large, discontinuous determinant composed of regions distant from each other in the linear protein sequence (3, 4). The 421–433 peptide region is essential for CD4 binding by gp120, suggested by contacts in the crystallized complex and loss of CD4 binding function by site-directed mutagenesis in this region (5, 6). The 421–433 region is a member of a small group of microbial polypeptide sites recognized selectively by Abs produced by the immune system without prior infection by the microbe (preimmune Abs) (7–9). Such sites are designated B cell “superantigens” (SAgs) because of their selective and widespread recognition by the comparatively conserved framework regions (FRs) of Ab V domains (10, 11). Noncovalent SAg binding by preimmune Abs, however, is characterized by low-to-moderate binding strength (12). Most gp120-binding preimmune Abs from humans without infection display poor or no HIV neutralizing activity (13). Patients with the autoimmune disease lupus and no HIV infection produce increased amounts of Abs to the 421–433 CD4BS region (14). A single chain Fv (scFv; V_L and V_H domains linked by a flexible peptide) from the lupus Ab repertoire that binds the 421–433 region reversibly neutralizes genetically diverse strains of HIV (15). Following completion of the noncovalent binding step, certain Abs can hydrolyze polypeptides via nucleophilic attack on carbonyl groups (16–21). The proteolytic reaction imparts improved antigen inactivation potency to Abs (22). We reported the neutralization of HIV by secretory IgA from humans without infection, an Ab class distinguished by the ability to catalyze the hydrolysis of gp120 selectively because of initial noncovalent recognition of the 421–433 CD4BS region (13).The conserved character of the CD4BS in genetically diverse HIV strains renders it suitable as a vaccine target. The CD4BS, however, is poorly immunogenic. Traditional immunization methods do not stimulate the adaptive synthesis of neutralizing Abs to the 421–433 region or other CD4BS epitopes. Neutralizing Abs that bind the CD4BS are found in the blood of a subset of patients after years of HIV infection, but the target epitope is not identified, and Ab response is weak (23, 24). Certain monoclonal Abs (mAbs) that bind the CD4BS expressed by purified monomer gp120 do not neutralize HIV appreciably or display limited ability to neutralize genetically diverse HIV strains (25, 26). The CD4BS is a flexible structure expressed in differing conformational states by monomer gp120 and the native gp120 oligomers of the virus (27–30). Moreover, the process of binding CD4 may induce movements within the CD4BS (31). Reproducing the native CD4BS conformation in experimental vaccine candidates has been difficult. A CD4BS mimetic of the epitope recognized by a well known anti-CD4BS neutralizing mAb (clone b12) did not induce the synthesis of neutralizing Abs (32). Polyclonal Abs raised by immunization with synthetic peptides spanning the 421–433 CD4BS region neutralized laboratory-adapted, coreceptor CXCR4-dependent HIV strains inconsistently (33–35). Neutralization of coreceptor CCR5-dependent strains responsible for initiating most HIV infections was not studied. Importantly, small synthetic peptides are often more flexible than the corresponding native protein segments. Inducing a traditional adaptive immune response in which the Ab CDRs develop binding specificity for the peptide immunogen therefore does not ensure recognition of the native 421–433 CD4BS region (35, 36). From mutagenesis and sequence identity studies, the gp120-binding site of preimmune Abs, in contrast, is composed mainly of the V_H domain FR1 and FR3 (10, 11, 37). As certain preimmune Abs express HIV neutralizing activity attributable to recognition of the 421–433 region (13), the FR-dominated site must recognize the native state of this CD4BS epitope expressed on the viral surface.There is, however, substantial difficulty in amplifying and improving the subset of preimmune Abs with HIV neutralizing activity for vaccination against the virus; SAg binding to Ab FRs fails to stimulate adaptive B cell differentiation and synthesis of specific IgG class Abs (38, 39). Indeed, the binding at the FRs may even lead to premature death of the B cells (12, 40). The SAg character of the 421–433 CD4BS epitope is therefore predicted to render it hypoimmunogenic with respect to the adaptive synthesis of neutralizing Abs following infection or traditional vaccination procedures.We reported previously the induction of nucleophilic Abs by covalent immunization with full-length gp120 and a gp120 V3 peptide containing strongly electrophilic phosphonate groups (41–43). The electrophile reacts covalently with BCRs (44), resulting in adaptively strengthened nucleophilic reactivity coordinated with specific noncovalent recognition of gp120. The Abs obtained by covalent immunization formed very stable immune complexes with HIV resulting from pairing of Ab nucleophiles with the naturally occurring electrophilic groups of gp120 (e.g. the backbone and side chain carbonyls, see Refs. 42, 43). A minority of the Abs proceeded to catalyze the hydrolysis of gp120, aided by water attack on the covalent acyl-Ab complex (41). Here we report the neutralization of HIV strains heterologous to the full-length electrophilic gp120 immunogen (E-gp120) by mAbs with binary CD4BS and V3 loop recognition capability. We also present models that explain synthesis of the mAbs in response to immunization with E-gp120.     

Effects of vitamin C deficiency on the skin of the senescence marker protein-30 (SMP30) knockout mouse

Senescence marker protein-30 (SMP30) is a gluconolactonase required for vitamin C (VC) synthesis. We examined effects of VC deficiency on the mouse skin using SMP30 knockout (KO) mice. SMP30 KO or wild type male mice were weaned around day 30 of age, and fed VC-deficient diet. They were given either VC water or control water. VC deficiency for 36 days did not affect skin hydroxyproline contents, while VC deficiency for 60 days decreased the hydroxyproline levels. Levels of some collagen mRNAs were different among the groups, but did not correlate with skin VC levels. The epidermis was morphologically abnormal in VC-deficient SMP30 KO mouse at 60 days after the weaning. Interestingly, the hair cycle was not synchronized among the groups. These data suggest low susceptibility of the mouse skin to VC deficiency and involvement of VC in the regulation of keratinocyte function and hair cycle in vivo.     

Pressure-Induced Changes in the Structure and Function of the Kinesin-Microtubule Complex

Kinesin-1 is an ATP-driven molecular motor that “walks” along a microtubule by working two heads in a “hand-over-hand” fashion. The stepping motion is well-coordinated by intermolecular interactions between the kinesin head and microtubule, and is sensitively changed by applied forces. We demonstrate that hydrostatic pressure works as an inhibitory action on kinesin motility. We developed a high-pressure microscope that enables the application of hydrostatic pressures of up to 200 MPa (2000 bar). Under high-pressure conditions, taxol-stabilized microtubules were shortened from both ends at the same speed. The sliding velocity of kinesin motors was reversibly changed by pressure, and reached half-maximal value at ∼100 MPa. The pressure-velocity relationship was very close to the force-velocity relationship of single kinesin molecules, suggesting a similar inhibitory mechanism on kinesin motility. Further analysis showed that the pressure mainly affects the stepping motion, but not the ATP binding reaction. The application of pressure is thought to enhance the structural fluctuation and/or association of water molecules with the exposed regions of the kinesin head and microtubule. These pressure-induced effects could prevent kinesin motors from completing the stepping motion.