Frank J. Lebeda

Prediction of a conserved, neutralizing epitope in ribosome-inactivating proteins

The secondary structures, side-chain solvent accessibilities, and superpositioned crystal structures of the A-chain of ricin and four other plant rRNA N-glycosidases (ribosome-inactivating proteins, RIPs) were examined. Previously, a 26-residue fragment from the A-chain of ricin was determined to bind to a neutralizing monoclonal antibody. The region in the native ricin A-chain, to which this peptide corresponds, is solvent-exposed and contains a negatively charged residue that has been hypothesized to participate in the toxins function, namely, rRNA binding and/or enzymatic activity. This region appears to be conserved in all of the structurally defined plant RIPs examined. Moreover, other plant RIPs, whose tertiary structures are, as yet, unknown, were predicted to have an analogous, solvent-exposed region containing a conserved, negatively charged residue. By analogy, these conserved structural and functional features lead to the suggestion that this exposed region represents a logical starting point for experiments designed to locate neutralizing epitopes in these RIPs. In contrast, the tertiary structure of the analogous region in a bacteria-derived RIP (Shiga toxin) is a less solvent-exposed, truncated loop and is a structure that is not as likely to be a neutralizing epitope. Because most of the amino acid residues are not conserved within this exposed region, these RIPs are predicted to be antigenically distinct.

Identifying the principal protective antigenic determinants of type A botulinum neurotoxin.

The neurotoxins from Clostridium botulinum (BoNT serotypes A-G) exert their lethal effect by preventing the release of acetylcholine at the neuromuscular junction. As with tetanus toxin, immunization with a non-toxic fragment, the 50 kDa C-terminal portion of BoNT/A (Hc; residues 861-1296), protects mice against lethal challenges with the intact toxin. To locate the neutralizing epitopes, several protective monoclonal antibodies (mAbs) against BoNT/A-Hc were isolated and cloned. Specific binding of the mAbs to BoNT/A-Hc was demonstrated by surface plasmon resonance, with Kas in the range of 10(-10) to 10(-11) M. These antibodies recognized a genetically engineered polypeptide (1150-1289) that was previously shown to induce protective immunity. Prior to the determination of the X-ray crystal structure of the tetanus neurotoxin Hc fragment, molecular modelling studies indicated that it contained two highly solvent-exposed loops. Based on these predictions, two 25-mer Hc-peptides corresponding to these two regions were synthesized and were demonstrated to bind the neutralizing mAbs. Mice immunized with the Hc-peptides had high levels of antibodies that recognized BoNT/A-Hc. However, immunizations with only one of the Hc peptides protected when mice were challenged with BoNT/A. On the basis of these analyses, it should be possible to develop small peptides that could be useful in the design of future vaccines against these neurotoxins.

Antagonism of botulinum toxin-induced muscle weakness by 3,4-diaminopyridine in rat phrenic nerve-hemidiaphragm preparations

The effects of the potassium channel inhibitor and putative botulinum toxin antagonist 3,4-diaminopyridine (3,4-DAP) were investigated in vitro on the contractile properties of rat diaphragm muscle. In the presence of 100 pM botulinum neurotoxin A (BoNT/A), twitches elicited by supramaximal nerve stimulation (0.1 Hz) were reduced to approximately 10% of control in 3 hr at 37 degrees C. Addition of 3,4-DAP led to a rapid reversal of the BoNT/A-induced depression of twitch tension. In the presence of 100 microM 3,4-DAP, antagonism of the BoNT/A-induced blockade began within 30-40 sec and reached 82% of control with a half-time of 6.7 min. The beneficial effect of 3,4-DAP was well maintained and underwent little or no decrement relative to control for at least 8 hr after addition. Application of 1 microM neostigmine 1 hr after 3,4-DAP led to a further potentiation of twitch tension, but this action lasted for < 20 min. Moreover, neostigmine caused tetanic fade during repetitive stimulation. In contrast to the efficacy of the parent compound, the quaternary derivative of 3,4-DAP, 3,4-diamino-1-methyl pyridinium produced little or no twitch potentiation up to a concentration of 1 mM. The potassium channel blocker, tetraethylammonium, generated a transient potentiation followed by a sustained depression of twitch tensions. It is concluded that 3,4-DAP is of benefit in antagonizing the muscle paralysis following exposure to BoNT/A. Co-application of neostigmine or tetraethylammonium with 3,4-DAP, however, appears to confer no additional benefit.

Structural predictions of the channel-forming region of botulinum neurotoxin heavy chain.

A novel combination of theoretical approaches was exploited to predict which amino acid residues of various botulinum neurotoxin serotypes participate in forming ion channels. Estimates of sequence hydrophobic moments were used initially to identify residues within amphipathic regions in the N-terminal half of the heavy chain. A neural network algorithm was then used to make additional secondary structural predictions for these regions. Together, these approaches predicted a complimentary pattern of four, adjacent amphipathic, possibly transmembrane, regions that may be separated by solvent-exposed loops. Both the hydrophobic moment and the neural net analyses predicted that at least one of these amphipathic segments may be in an extended conformation. These theoretical results are discussed in view of our current knowledge of other transmembrane structures.

Potentiometric measurements of hydrogen and cyanide ions in buffered media

Potentiometric measurements of hydrogen and cyanide levels were studied in different buffered media that are used in biological experiments. The addition of 1-10mM NaCN increased the pH (from 7.2-7.5 up to 9.5) of either bicarbonate/phosphate-buffered (artificial cerebrospinal fluid (ACSF), sera, and whole blood) or Hepes-buffered solutions in a concentration-dependent manner. While in aerated ACSF this increase was transient (half-relaxation time less than 4 min), the increase in pH was sustained in Hepes buffer. A mathematical model that predicts the maximum cyanide-induced increases in pH was derived. When NaCN was added to either ACSF or Hepes-buffered solutions, a Nernst relation was obtained, but deviations from Nernstian responses resulted when NaCN was added to sera or whole blood. These responses, however, differed substantially from the theoretical results that were based on the relative amounts of ionized cyanide present in the various pH environments. In addition, attempts were made to indirectly examine the formation and escape of HCN by calculating the time constants of decay (tau d) of the cyanide-induced potentiometric responses. With progressively higher NaCN concentrations in ACSF, the values of tau d did not decrease, but were constant. As predicted, however, the values of tau d were larger when solutions were covered or had higher initial pH values. These results suggest that in the solutions tested, the cyanide electrode used in the present study measured the total amount rather than the ionized portion of dissolved cyanide and that the values of tau d do not correspond to formation/escape rates of HCN.

Predicting differential antigen-antibody contact regions based on solvent accessibility.

A novel computational approach was examined tor predicting epitopes from primary structures of the seven immunologically distinct botulinum neurotoxins (BoNT/A-G) and tetanus toxin (TeTX). An artificial neural network [Rost and Sander (1994), Proteins20, 216] was used to estimate residue solvent accessibilities in multiple aligned sequences. A similar network trained to predict secondary structures was also used to examine this protein family, whose tertiary fold is presently unknown. The algorithm was validated by showing that it was 80% accurate in determining the secondary structure of avian egg-white lysozyme and that it correctly identified highly solvent-exposed residues that correspond to the major contact regions of lysozyme–antibody cocrystals. When sequences of the heavy (H) chains of TeTX and BoNT/A–G were analyzed, this algorithm predicted that the most highly exposed regions were clustered at the sequentially nonconserved N- and C-termini [Lebeda and Olson (1994), Proteins20, 293]. The secondary structures and the remaining highly solvent-accessible regions were, in contrast, predicted to be conserved. In experiments reported by others, H-chain fragments that induced immunological protection against BoNT/A overlap with these predicted most highly exposed regions. It is also known that the C-terminal halves of the TeTX and BoNT/A H-chains interfere with holotoxin binding to ectoacceptors on nerve endings. Thus, the present results provide a theoretical framework for predicting the sites that could assist in the development of genetically engineered vaccines and that could interact with neurally located toxin ectoacceptors. Finally, because the most highly solvent-exposed regions were not well conserved, it is hypothesized that nonconserved, potential contact sites partially account for the existence of different dominant binding regions for type-specific neutralizing antibodies.

Fold prediction of VP24 protein of Ebola and Marburg viruses using de novo fragment assembly

Virus particle 24 (VP24) is the smallest protein of the Ebola and Marburg virus genomes. Recent experiments show that Ebola VP24 blocks binding of tyrosine-phosphorylated STAT-1 homodimer (PY-STAT1) to the NPI-1 subfamily of importin alpha, thereby preventing nuclear accumulation of this interferon-promoting transcription factor which, in turn, reduces the innate immune response of the host target. Lacking an experimental structure for VP24, we applied de novo protein structure prediction using the fragment assembly-based Rosetta method to classify its fold topology and better understand its biological function. Filtering and ranking of models were performed with the DFIRE all-atom statistical potential and the CHARMM22 force field with a generalized Born solvent model. From 40,000 Rosetta-generated structures and selective comparisons with the SCOP database, a structural match to two of our top 10-ranking models was the Armadillo repeat fold topology. Specific members of this fold family include importin alpha, importin beta, and exportin. We propose that, unlike the nuclear import of host cargo, VP24 lacks a classical nuclear localization signal (NLS) and targets importin alpha in a similar manner to the observed heterodimeric complex with exportin, thereby interfering with the auto-inhibitory NLS on importin alpha and blocking peripheral docking sites for PY-STAT1 assembly.

Mechanism of action of sodium cyanide on rat diaphragm muscle.

The effects of sodium cyanide (NaCN) were investigated on the contractile and electrophysiological properties of rat diaphragm muscles in vitro. Sodium cyanide (0.1–1.0 mM) produced an initial potentiation of directly elicited twitch tensions, followed by a slow progressive depression. The potentiation and depression were both dependent on the NaCN concentration and stimulation frequency. Muscles exposed to NaCN exhibited marked reductions of creatine phosphate concentration, but ATP levels were not significantly lowered. Sodium cyanide had no effect on the resting potential, input resistance or action potential, indicating that the toxicity of the metabolic inhibitor is not mediated by alterations of membrane excitability or passive electrical properties. Sodium cyanide reduced the amplitude of contractures elicited by 70 mM K2SO4, suggesting that the actions of NaCN cannot be explained by a failure of action potentials to propagate across the muscle surface or within t‐tubular membranes. Sodium cyanide suppressed the first phase of the caffeine contracture, an observation consistent with an impaired release of, or reduced sensitivity to, sarcoplasmic reticular Ca2+, but did not alter the amplitude of the second phase, which represents rigor following ATP depletion. These results, in conjunction with those of previous studies, suggest that the depression in muscle tension following exposure to NaCN may result from alterations in Ca2+ homeostasis, intracellular acidosis or from accumulation of one or more products of phosphocreatine breakdown. Copyright

ACCURACY OF SECONDARY STRUCTURE AND SOLVENT ACCESSIBILITY PREDICTIONS FOR A CLOSTRIDIAL NEUROTOXIN C-FRAGMENT

Earlier studies used Rost and Sanders artificial neural network [(1993a), J. Mol. Biol.232, 584–599] to predict the secondary structures [Lebeda and Olson (1994), Proteins20, 293–300] and residue solvent accessibilities [Lebeda and Olson (1997), J. Protein Chem.16, 607–618] of the clostridial neurotoxins. Because the X-ray crystal structure of the 50-kDa C-terminal half of the heavy chain of tetanus toxin was recently determined, this report evaluates the accuracy of these network-derived predictions. For this predominantly β-strand-containing fragment, predictions, on a per-residue basis, for both secondary structure and solvent accessibility were about 70% accurate. A more flexible and realistic analysis based on overlapping segments yielded accuracies of over 80% for the three-state secondary structure and for the two-state accessibility predictions. Because the accuracies of these predictions are comparable to those made by Rost and Sander using a dataset of 126 nonhomologous globular proteins, our predictions provide a quantitative foundation for gauging the results when building by homology the structures of related proteins.

Kinetic and Reaction Pathway Analysis in the Application of Botulinum Toxin A for Wound Healing

A relatively new approach in the treatment of specific wounds in animal models and in patients with type A botulinum toxin is the focus of this paper. The indications or conditions include traumatic wounds (experimental and clinical), surgical (incision) wounds, and wounds such as fissures and ulcers that are signs/symptoms of disease or other processes. An objective was to conduct systematic literature searches and take note of the reactions involved in the healing process and identify corresponding pharmacokinetic data. From several case reports, we developed a qualitative model of how botulinum toxin disrupts the vicious cycle of muscle spasm, pain, inflammation, decreased blood flow, and ischemia. We transformed this model into a minimal kinetic scheme for healing chronic wounds. The model helped us to estimate the rate of decline of this toxins therapeutic effect by calculating the rate of recurrence of clinical symptoms after a wound-healing treatment with this neurotoxin.