A deep attention network for predicting amino acid signals in the formation of [Formula: see text]-helices.

The secondary and tertiary structure of a protein has a primary role in determining its function. Even though many folding prediction algorithms have been developed in the past decades - mainly based on the assumption that folding instructions are encoded within the protein sequence - experimental techniques remain the most reliable to establish protein structures. In this paper, we searched for signals related to the formation of [Formula: see text]-helices. We carried out a statistical analysis on a large dataset of experimentally characterized secondary structure elements to find over- or under-occurrences of specific amino acids defining the boundaries of helical moieties. To validate our hypothesis, we trained various Machine Learning models, each equipped with an attention mechanism, to predict the occurrence of [Formula: see text]-helices. The attention mechanism allows to interpret the model's decision, weighing the importance the predictor gives to each part of the input. The experimental results show that different models focus on the same subsequences, which can be seen as codes driving the secondary structure formation.

On the dynamics of water molecules at the protein solute interfaces.

Proteins, with the large variety of chemical groups they present at their molecular surface, are a class of molecules which can be very informative on most of the possible solute-solvent interactions. Hen egg white lysozyme has been used as a probe to investigate the complex solvent dynamics occurring at the protein surface, by analysing the results obtained from Nuclear Magnetic Resonance, X-ray diffractometry and Molecular Dynamics simulations. A consistent overall picture for the dynamics of water molecules close to the protein is obtained, suggesting that a rapid exchange occurs, in a picosecond timescale, among all the possible hydration surface sites both in solution and the solid state, excluding the possibility that solvent molecules can form liquid-crystal-like supramolecular adducts, which have been proposed as a molecular basis of 'memory of water'.

NMR studies of protein surface accessibility.

Characterization of protein surface accessibility represents a new frontier of structural biology. A surface accessibility investigation for two structurally well-defined proteins, tendamistat and bovine pancreatic trypsin inhibitor, is performed here by a combined analysis of water-protein Overhauser effects and paramagnetic perturbation profiles induced by the soluble spin-label 4-hydroxy-2,2,6,6-tetramethyl-piperidine-1-oxyl on NMR spectra. This approach seems to be reliable not only for distinguishing between buried and exposed residues but also for finding molecular locations where a network of more ordered waters covers the protein surface. From the presented set of data, an overall picture of the surface accessibility of the two proteins can be inferred. Detailed knowledge of protein accessibility can form the basis for successful design of mutants with increased activity and/or greater specificity.

Mimicking the nicotinic receptor binding site by a single chain Fv selected by competitive panning from a synthetic phage library.

We have developed a novel competitive method to select from a phage display library a single chain Fv which is able to mimic the alpha-bungarotoxin binding site of the muscle nicotinic receptor. The single chain Fv was selected from a large synthetic library using alpha-bungarotoxin-coated magnetic beads. Toxin-bound phages were then eluted by competition with affinity purified nicotinic receptor. Recognition of the toxin by the anti-alpha-bungarotoxin single chain Fv was very similar to that of the receptor, such as indicated by the epitope mapping of alpha-bungarotoxin through overlapping synthetic peptides. Moreover, several positively charged residues located in the toxin second loop and in the C-terminal region were found to be critical, to a similar extent, for toxin recognition by the single chain Fv and the receptor. However, although the anti-alpha-bungarotoxin single chain Fv seems to mimic the toxin binding site of the nicotinic receptor, it does not bind other nicotinic agonists or antagonists. Our results suggest that competitive selection of anti-ligand antibody phages can allow the production of receptor-mimicking molecules directly and exclusively targeted at one specific ligand. Since physiologically and pharmacologically different ligands can produce opposite effects on receptor functions, such selective ligand decoys can have important therapeutic applications.

Probing the surface of a sweet protein: NMR study of MNEI with a paramagnetic probe.

The design of safe sweeteners is very important for people who are affected by diabetes, hyperlipemia, and caries and other diseases that are linked to the consumption of sugars. Sweet proteins, which are found in several tropical plants, are many times sweeter than sucrose on a molar basis. A good understanding of their structure-function relationship can complement traditional SAR studies on small molecular weight sweeteners and thus help in the design of safe sweeteners. However, there is virtually no sequence homology and very little structural similarity among known sweet proteins. Studies on mutants of monellin, the best characterized of sweet proteins, proved not decisive in the localization of the main interaction points of monellin with its receptor. Accordingly, we resorted to an unbiased approach to restrict the search of likely areas of interaction on the surface of a typical sweet protein. It has been recently shown that an accurate survey of the surface of proteins by appropriate paramagnetic probes may locate interaction points on protein surface. Here we report the survey of the surface of MNEI, a single chain monellin, by means of a paramagnetic probe, and a direct assessment of bound water based on an application of ePHOGSY, an NMR experiment that is ideally suited to detect interactions of small ligands to a protein. Detailed surface mapping reveals the presence, on the surface of MNEI, of interaction points that include residues previously predicted by ELISA tests and by mutagenesis.

Tendamistat surface accessibility to the TEMPOL paramagnetic probe.

TEMPOL, the soluble spin-label 4-hydroxy-2,2,6,6-tetramethyl-piperidine-1-oxyl, has been used to determine the surface characteristics of tendamistat, a small protein with a well-characterised structure both in solution and in the crystal. A good correlation has been found between predicted regions of exposed protein surface and the intensity attenuations induced by the probe on 2D NMR TOCSY cross peaks of tendamistat in the paramagnetic water solution. All the high paramagnetic effects have been interpreted in terms of more efficient competition of TEMPOL with water molecules at some surface positions. The active site of tendamistat coincides with the largest surface patch accessible to the probe. A strong hydration of protein N and C termini can also be suggested by this structural approach, as these locations exhibit reduced paramagnetic perturbations. Provided that the solution structure is known, the use of this paramagnetic probe seems to be well suited to delineate the dynamic behaviour of the protein surface and, more generally, to gain relevant information about the molecular presentation processes.

On the structural stability of a small bioactive peptide of potential use in biotechnology.

A tridecapeptide with the sequence CCEICCNPACFGC has been synthesized to reproduce the active moiety of a heat stable enterotoxin from Vibrio cholerae. The proton NMR analysis indicates, for the active synthetic fragment, a rigid secondary structure stabilised by three disulfide bridges. Such a rigid peptide, suitably detoxified and activated, could be a good candidate to be used as a carrier for linear bioactive peptides or other functional groups.

Identification of critical residues of staphylococcal enterotoxin B for lymphomonocyte proliferation and cytokine production.

Superantigens bind to major histocompatibility complex class II molecules and stimulate large numbers of T cells expressing particular Vbeta elements of the T-cell receptor. Staphylococcal enterotoxin B (SEB) is a bacterial superantigen that causes food poisoning and toxic-shock syndrome. The toxicity of SEB is thought to be mediated by T-cell stimulation and cytokine production. Different regions of the SEB molecule are important for mitogenic activity. To identify critical residues of SEB in the region 124-1 54, which competitively inhibits the mitogenic activity of the toxin, we used the synthetic peptide approach and alanine scanning mutagenesis as a probe. We synthesized eight peptides with alanine replacement of all residues in the SEB sequence 131-138 and tested them for the capacity to inhibit both SEB-induced proliferation of human lymphomonocytes and the production of tumor necrosis factor alpha and interferon gamma. Mutation to alanine of the residue Thr 133 improved the inhibition of SEB-induced proliferation and cytokine production, whereas the substitution of Ser 131 also increased the inhibition, albeit to a lesser degree. The peptide obtained by substitution of Val 136 with alanine was unable to inhibit SEB-induced proliferation and cytokine production, suggesting that Val 136 is essential for mitogenic activity. Thus hydrophobic interactions apparently are very important for mitogenic activity. The identification of critical residues in this active site in the SEB and the computer modeling based on crystal X-ray data contribute to a better understanding of the molecular mechanism of the superantigen and may be useful for therapeutical applications.

NMR studies on the structure/function correlations of T-cell-epitope analogs from pertussis toxin.

A synthetic tridecapeptide, corresponding to the 30-42 fragment of the S1 subunit of pertussis toxin, has been structurally characterised by using NMR spectroscopy. The molecule corresponds to a T-cell epitope of the bacterial toxin which has been extensively analysed with the alanine scanning approach to check the relevance of each residue for the biological activity of the peptide. Five of these Ala-substituted analogs have also been spectroscopically studied. In the experimental conditions used, different extents of helicity were found for the six peptides in a way which cannot be related to their capabilities of of binding to major histocompatibility complex (MHC) class II and inducing T-cell proliferation. Backbone flexibility around helical transient conformations seems to constitute the structural intermediate step between the structure of the corresponding sequence within the parental protein and in the MHC class II complex. A model of the latter complex, which accounts for the different biological activities of the analogs, is proposed.

The design of a specific ligand of HIV gp120.

The crystal structure of CD4 suggested that the C/G38 and C/L44 replacements with the consequent cystine bridge formation are compatible with the native structure of that molecular moiety. As the NQGSF sequence, corresponding to the 39-43 fragment of human CD4 protein, was found to be involved in the HIV gp120 interaction, it has been synthesized in a cyclic form by adding two cysteine residues at the amino and carboxy termini. 1H-NMR studies show that the predominant solution conformation of cyclo-[CNQGSFC] is a type II beta-turn centred on the NQGS segment. Structural and dynamic properties of the peptide are also analysed in relation to the in vitro activity.

Probing protein structure by solvent perturbation of NMR spectra: the surface accessibility of bovine pancreatic trypsin inhibitor.

In the absence of specific interactions, the relative attenuation of protein NMR signals due to added stable free radicals such as TEMPOL should reflect the solvent accessibility of the molecular surface. The quantitative correlation between observed attenuation and surface accessibility was investigated with a model system, i.e., the small protein bovine pancreatic trypsin inhibitor. A detailed discussion is presented on the reliability and limits of the approach, and guidelines are provided for data acquisition, treatment, and interpretation. The NMR-derived accessibilities are compared with those obtained from x-ray diffraction and molecular dynamics data. Although the time-averaged accessibilities from molecular dynamics are ideally suited to fit the NMR data, better agreement was observed between the paramagnetic attenuations of the fingerprint cross-peaks of homonuclear proton spectra and the total NH and H alpha accessibilities calculated from x-ray coordinates, than from time-averaged molecular dynamics simulations. In addition, the solvent perturbation response appears to be a promising approach for detecting the thermal conformational evolution of secondary structure elements in proteins.

CD and NMR structural characterization of ceratotoxins, natural peptides with antimicrobial activity.

Antibacterial properties of the secretion from the female reproductive accessory glands of medfly Ceratitis capitata are mostly ascribed to the presence of two peptides, ceratotoxin A and B, which exhibit a strong activity against gram-positive and gram-negative bacterial strains, and show sequence and function homology with cecropins, melittin, and magainins. CD experiments performed in different solvents indicate the presence of a significant content of helical structures in organic solvent. Two-dimensional nmr results for ceratotoxin A in methanol show a helical behavior for the 8-25 region of the peptide. A ramachandran classification of each residue for the structures obtained from distance geometry calculations lead to the definition of four structural families in which the central segment 10-19 is always helical and differences refer to residues 8-9 and 19-23. A sequence analysis of the two ceratotoxins and a systematic search on the protein data bank revealed the occurrence of a KX-hydrophobic-hydrophobic-P motif that seems to be important for helix stabilization.

Characterization of immunoreactive octapeptides of human-cytomegalovirus gp58.

We have mapped continuous epitopes, for positions 591-673 of the human cytomegalovirus 58-kDa glycoprotein using overlapping synthetic peptides and human sera. This region contains a fragment previously described as including the dominant site for induction of human-cytomegalovirus antibodies. Since the selected sequence is highly conserved among herpes viruses, we have considered the possible presence of antigenic cross-reactivity, particularly with the Epstein-Barr virus. Several peptides in the studied region were antigenic and two main continuous epitopes have been identified. Serological cross-reactions observed with Epstein-Barr virus are discussed, focusing on the possible implications of structural features and sequence similarity between human-cytomegalovirus and Epstein-Barr-virus glycoproteins.

A model of the rabies virus glycoprotein active site.

The glycoprotein from the neurotropic rabies virus shows a significant homology with the alpha neurotoxin that binds to the nicotinic acetylcholine receptor. The crystal structure of the alpha neurotoxins suggests that the Arg 37 guanidinium group and the Asp 31 side-chain carboxylate of the erabutoxin have stereochemical features resembling those of acetylcholine. Conformational studies on the Asn194-Ser195-Arg196-Gly197 tetrapeptide, an essential part of the binding site of the rabies virus glycoprotein, indicate that the side chains of Asn and Arg could also mimic the acetylcholine structure. This observation is consistent with the recently proposed mechanism of the viral infection.

Probing protein structure by solvent perturbation of NMR spectra. II. Determination of surface and buried residues in homologous proteins.

The experimental assignment of most residues in a protein to the surface or interior is in principle possible without prior solution of a complete three-dimensional structure. The method described is based on nmr measurements that determine the amino acid composition of the surface of a protein [A. Petros, L. Mueller, and K.D. Kopple (1990) Biochemistry, Vol. 29, pp. 10041-10048; G. Esposito, A. M. Lesk, H. Molinari, A. Motta, N. Niccolai, and A. Pastore (1992) Journal of Molecular Biology, Vol. 224, pp. 659-670]. If these measurements are carried out on several homologous proteins of known sequence, it is possible to combine the results to determine, in most cases, which positions in the sequence contain exposed residues.

Probing protein structure by solvent perturbation of nuclear magnetic resonance spectra. Nuclear magnetic resonance spectral editing and topological mapping in proteins by paramagnetic relaxation filtering.

Soluble spin labels, which "bleach" the surface proton resonances of a protein to n.m.r. measurements, can provide useful information about protein conformation and dynamics. The use of the soluble nitroxide, TEMPOL, has been explored to show the correlation of the paramagnetic perturbations of protein two-dimensional n.m.r. data with proton exposure to the free radical in hen egg-white lysozyme. The results demonstrate that the nitroxide approaches the protein randomly, and that the extent of the observed paramagnetic effects reflects the native folding pattern of the protein. A correlation of spectral simplification with the known tertiary structure establishes the feasibility of new strategies for topological mapping of surface and buried protons of the protein. Application to the elucidation of protein structure and to the study of dynamical processes is discussed.

1H- and natural abundance 15N-NMR studies of a derivative of a rabies glycoprotein fragment.

Using a combination of one- and two-dimensional methods, 1H- and 15N-nmr spectroscopy has been employed to perform the complete assignment and the structural determination of the immunogenic undecapeptide CTTTNSRGTTT in DMSO solution. Nuclear Overhauser enhancement spectroscopy experiments indicated the presence of secondary structures, mainly turn-like structures, which only represent a family, albeit a dominant one, of an ensemble of conformations available to the peptide. Since reverse turns may play an important role as intermediates in protein folding, the experimental observations described here may link the immunological and theoretical approaches to protein folding.

Solvent spin-labelling for investigating the interaction of biological ligands with macromolecules. A 1H paramagnetic relaxation study.

The paramagnetic contributions to the spin-lattice relaxation rates of khellin protons, induced by the presence in an aqueous solution of TEMPO nitroxide, have been analyzed in the interaction of the furochromone with DNA. The relaxation data obtained at different temperatures, nitroxide and DNA concentrations indicate that the average solvent exposure of the furanic moiety of khellin is lower than that of the pyranic group. This feature suggests that the former is the main site of approach of khellin to DNA.

Antipeptide monoclonal antibodies inhibit the binding of rabies virus glycoprotein and alpha-bungarotoxin to the nicotinic acetylcholine receptor.

It has been reported that binding to muscle nicotinic acetylcholine receptor at the post-synaptic membrane is an important event of the rabies virus neurotropism. The binding site can be located within the 190-203 region of the virus glycoprotein sharing a high degree of homology with the "toxic loop" of the curare-mimetic snake neurotoxins. We have synthesized a tetradecapeptide corresponding to this glycoprotein region and used it, following conjugation with an immunogenic carrier to raise MAbs. We found that some MAbs raised against the peptide were able to recognize both the virus glycoprotein and the snake neurotoxin alpha-bungarotoxin; moreover, they can inhibit the binding of rabies virus glycoprotein and alpha-bungarotoxin to the nicotinic acetylcholine receptor extracted from the electric organs of Torpedo marmorata. On the basis of this cross-reactivity, we suggest that rabies virus glycoprotein and curare-mimetic snake neurotoxins share three-dimensionally similar structures in order to bind to the nicotinic cholinergic receptor. The potential use of the immunogenic properties of the peptide for the rational design of a synthetic vaccine against rabies is proposed.