Cn29, a novel orphan peptide found in the venom of the scorpion Centruroides noxius: Structure and function.

A peptide (Cn29) from the venom of the scorpion Centruroides noxius (about 2% of the soluble venom) was purified and its primary and three-dimensional structures were determined. The peptide contains 27 amino acids with primary sequence: LCLSCRGGDYDCRVKGTCENGKCVCGS. The peptide is tightly packed by three disulfide linkages formed between C2-C23, C5-C18 and C12-C25. Since the native peptide was obtained in limited amounts, the full synthetic peptide was prepared using the standard F-moc-based solid phase synthesis method of Merrifield. The native and synthetic peptides were shown to be identical by sequencing, HPLC separation and mass spectrometry. The solution structure of the peptide solved from NMR data shows that it consists of a well-defined N-terminal region without regular secondary structure extending from Leu 1 to Asp 9, followed by a short helical fragment from Tyr10 to Val14 and two short ß strands (Thr17-Glu19 and Lys22-Val24). The primary and tertiary structures of Cn29 are different from all other scorpion peptides described in the literature. Transcriptome analysis of RNA obtained from C. noxius confirmed the expression of a gene coding for Cn29 in its venom gland. Initial experiments were conducted to identify its possible function: lethality tests in mice and insects as well as ion-channel binding using in vitro electrophysiological assays. None of the physiological or biological tests displayed any activity for this peptide, which at present is considered to be another orphan peptide found in scorpion venoms. The peptide is thus the first example of a novel structural component present in scorpion venoms.

Dependence on solution conditions of aggregation and amyloid formation by an SH3 domain.

The formation of amyloid fibrils by the SH3 domain of the alpha-subunit of bovine phosphatidylinositol-3'-kinase (PI3-SH3) has been investigated under carefully controlled solution conditions. NMR and CD characterisation of the denatured states from which fibrils form at low pH show that their properties can be correlated with the nature of the resulting aggregates defined by EM and FTIR spectroscopy. Compact partially folded states, favoured by the addition of anions, are prone to precipitate rapidly into amorphous species, whilst well-defined fibrillar structures are formed slowly from more expanded denatured states. Kinetic data obtained by a variety of techniques show a clear lag phase in the formation of amyloid fibrils. NMR spectroscopy shows no evidence for a significant population of small oligomers in solution during or after this lag phase. EM and FTIR indicate the presence of amorphous aggregates (protofibrils) rich in beta-structure after the lag phase but prior to the development of well-defined amyloid fibrils. These observations strongly suggest a nucleation and growth mechanism for the formation of the ordered aggregates. The morphologies of the fibrillar structures were found to be highly sensitive to the pH at which the protein solutions are incubated. This can be attributed to the effect of small perturbations in the electrostatic interactions that stabilise the contacts between the protofilaments forming the amyloid fibrils. Moreover, different hydrogen bonding patterns related to the various aggregate morphologies can be distinguished by FTIR analysis.

Evidence concerning rate-limiting steps in protein folding from the effects of trifluoroethanol.

The refolding kinetics of 13 proteins have been studied in the presence of 2,2,2-trifluoroethanol (TFE). Low concentrations of TFE increased the folding rates of all the proteins, whereas higher concentrations have the opposite effect. The extent of deceleration of folding correlates closely with similar effects of guanidine hydrochloride and can be related to the burial of accessible surface area during folding. For those proteins folding in a two-state manner, the extent of acceleration of folding correlates closely with the number of local backbone hydrogen bonds in the native structure. For those proteins that fold in a multistate manner, however, the extent of acceleration is much smaller than that predicted from the data for two-state proteins. These results support the concept that for two-state proteins the search for native-like contacts is a key aspect of the folding reaction, whereas the rate-determining steps for folding of multistate proteins are associated with the reorganization of stable structure within a collapsed state or with the search for native-like interactions within less structured regions.

Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing.

Amyloid fibrils are assemblies of misfolded proteins and are associated with pathological conditions such as Alzheimer's disease and the spongiform encephalopathies. In the amyloid diseases, a diverse group of normally soluble proteins self-assemble to form insoluble fibrils. X-ray fibre diffraction studies have shown that the protofilament cores of fibrils formed from the various proteins all contain a cross-beta-scaffold, with beta-strands perpendicular and beta-sheets parallel to the fibre axis. We have determined the threedimensional structure of an amyloid fibril, formed by the SH3 domain of phosphatidylinositol-3'-kinase, using cryo-electron microscopy and image processing at 25 A resolution. The structure is a double helix of two protofilament pairs wound around a hollow core, with a helical crossover repeat of approximately 600 A and an axial subunit repeat of approximately 27 A. The native SH3 domain is too compact to fit into the fibril density, and must unfold to adopt a longer, thinner shape in the amyloid form. The 20x40-A protofilaments can only accommodate one pair of flat beta-sheets stacked against each other, with very little inter-strand twist. We propose a model for the polypeptide packing as a basis for understanding the structure of amyloid fibrils in general.

Does a peptide bound to a monoclonal antibody always adopt a unique conformation?

The conformation of a synthetic undecapeptide derived from the Escherichia coli tryptophan synthase beta2 subunit was studied by NMR spectroscopy when bound to a monoclonal antibody (mAb 164-2) Fab' fragment directed against the native protein. The peptide 1(H-G-R-V-G-I-Y-F-G-M-K)11, peptide 11, was recognized by the antibody and its corresponding Fab' fragments with high affinity (K(D) = 1.1+/-0.2* 10(-8) M). Peptide 11 was labelled with 15N and its structure at the binding site of the Fab' 164-2 fragment was studied by isotope-editing techniques. 1H-15N heteronuclear spectra indicated the presence of two Fab'-peptide 11 complexes with two different conformations in slow chemical exchange on the chemical shift time scale.

Amyloid fibril formation by an SH3 domain.

The SH3 domain is a well characterized small protein module with a simple fold found in many proteins. At acid pH, the SH3 domain (PI3-SH3) of the p85alpha subunit of bovine phosphatidylinositol 3-kinase slowly forms a gel that consists of typical amyloid fibrils as assessed by electron microscopy, a Congo red binding assay, and x-ray fiber diffraction. The soluble form of PI3-SH3 at acid pH (the A state by a variety of techniques) from which fibrils are generated has been characterized. Circular dichroism in the far- and near-UV regions and 1H NMR indicate that the A state is substantially unfolded relative to the native protein at neutral pH. NMR diffusion measurements indicate, however, that the effective hydrodynamic radius of the A state is only 23% higher than that of the native protein and is 20% lower than that of the protein denatured in 3.5 M guanidinium chloride. In addition, the A state binds the hydrophobic dye 1-anilinonaphthalene-8-sulfonic acid, which suggests that SH3 in this state has a partially formed hydrophobic core. These results indicate that the A state is partially folded and support the hypothesis that partially folded states formed in solution are precursors of amyloid deposition. Moreover, that this domain aggregates into amyloid fibrils suggests that the potential for amyloid deposition may be a common property of proteins, and not only of a few proteins associated with disease.

Folding kinetics of the SH3 domain of PI3 kinase by real-time NMR combined with optical spectroscopy.

The refolding kinetics of the chemically denatured SH3 domain of phosphatidylinositol 3'-kinase (PI3-SH3) have been monitored by real-time one-dimensional 1H NMR coupled with a variety of other biophysical techniques. These experiments indicate that the refolding kinetics of PI3-SH3 are biphasic. The slow phase (27 (+/- 8)% amplitude) is due to a population of substantially unfolded molecules with an incorrectly configured cis proline residue. The fast phase (73 (+/- 8)% amplitude) corresponds to the folding of protein molecules with proline residues in a trans configuration in the unfolded state. NMR experiments indicate that the first species populated after the initiation of folding exhibit poor chemical shift dispersion and have spectra very similar to that of the denatured protein in 8 M guanidine hydrochloride. Linear combinations of the first spectrum and of the spectrum of the native protein accurately reconstruct all of the spectra acquired during refolding. Consistent with this, native side-chain and backbone H alpha atom packing (NMR), secondary structure (far-UV circular dichroism), burial of aromatic residues (near-UV circular dichroism), intrinsic fluorescence and peptide binding activity are all recovered with effectively identical kinetics. Equilibrium unfolding and folding/unfolding kinetics yield, within experimental error, identical values for the free energy of unfolding (delta Gu-H2O = 3.38 kcal mol-1) and for the slope of the free energy of unfolding versus denaturant concentration (meq = 2.33 kcal mol-1 M-1). Together, these data provide strong evidence that PI3-SH3 folds without significant population of kinetic well-structured intermediates. That PI3-SH3 folds slowly (time constant 2.8 seconds in H2O at 20 degrees C) indicates that slow refolding is not always a consequence of kinetic traps but may be observed even when a protein appears to fold via a simple, two-state mechanism.

The folding kinetics and thermodynamics of the Fyn-SH3 domain.

The equilibrium unfolding and the kinetic folding and unfolding of the 67 residue Fyn-SH3 domain have been investigated. Equilibrium unfolding experiments indicate that, despite the lack of both disulfide bonds and prosthetic groups, Fyn-SH3 is relatively stable with a free energy of folding of -6.0 +/- 0.6 kcal mol-1 at 20 degrees C. Kinetic experiments indicate that the domain refolds in a rapid two-state manner without significant population of intermediates (k = 94.3 s-1 in H2O at 20 degrees C). Despite the presence of two proline residues, the refolding of the domain is monophasic, and no significant proline isomerization-like refolding phase is observed. This can be attributed to an extremely low level of the incorrect (cis) isomer of the structurally important Pro134 residue in the protein denatured in 8 M guanidine hydrochloride. Analysis of the temperature and guanidine hydrochloride dependence of the folding rate suggests that the folding transition state of this protein is relatively well organized. A comparison with the refolding kinetics and thermodynamics of other homologous SH3 domains indicates that these exhibit an equivalent degree of transition state organization. This potentially arises from conservation of key features of the transition state conformation despite sometimes relatively low overall sequence identity. Such a comparison further suggests that relative thermodynamic stability is an important factor in determining the relative folding rates of natural proteins with a common fold, but that specific details of the amino acid sequence can also play a significant role in individual cases.

The "pre-molten globule," a new intermediate in protein folding.

In vitro folding studies of several proteins revealed the formation, within 2-4 msec, of transient intermediates with a large far-UV ellipticity but no amide proton protection. To solve the contradiction between the secondary structure contents estimated by these two methods, we characterized the isolated C-terminal fragment F2 of the tryptophan synthase beta 2 subunit. In beta 2, F2 forms its tertiary interactions with the F1 N-terminal region. Hence, in the absence of F1, isolated F2 should remain at an early folding stage with no long-range interactions. We shall show that isolated F2 folds into, and remains in, a "state" called the pre-molten globule, that indeed corresponds to a 2- to 4-msec intermediate. This condensed, but not compact, "state" corresponds to an array of conformations in rapid equilibrium comprising native as well as nonnative secondary structures. It fits the "new view" on the folding process.

Chemical structure and translation inhibition studies of the antibiotic microcin C7.

Escherichia coli microcin C7 (MccC7) is an antibiotic that inhibits protein synthesis in vivo. It is a heptapeptide containing unknown modifications at the N and C termini (García-Bustos, J. F., Pezzi, N., and Méndez, E. (1985) Antimicrob. Agents Chemoth. 27, 791-797). The chemical structure of MccC7 has been characterized by use of 1H homonuclear and heteronuclear (13C, 15N, 31P) nuclear magnetic resonance spectroscopy as well as mass spectrometry (1177 +/- 1 Da). The heptapeptide Met-Arg-Thr-Gly-Asn-Ala-Asp is substituted at the N terminus by a N-formyl group. The C-terminal substituent consists of the phosphodiester of 5'-adenylic acid and n-aminopropanol (AMPap), which is linked via the phosphorus atom to an amide group, thus forming a phosphoramide. The main chain carbonyl of the C-terminal aspartic acid residue is connected via this amide bond to the modified nucleotide unit. MccC7 and the peptide unit inhibit protein translation in vitro while a synthetic analog of the AMPap substituent is not active. Neither the peptide nor the AMPap molecule has an effect on the growth of MccC7-sensible cells. Our results strongly suggest that the peptide is responsible for MccC7 antibiotic activity while the C-terminal substituent is needed for MccC7 transport. Implications of the structure determined in this work for MccC7 synthesis and mode of action are discussed.

Protein folding intermediates with rapidly exchangeable amide protons contain authentic hydrogen-bonded secondary structures.

Recent studies on protein folding intermediates by pulsed amide proton exchange and by far-ultraviolet circular dichroism have shown important discrepancies between the secondary structure contents estimated by these two methods at early folding stages. To solve these apparent discrepancies, structural studies have been performed on the isolated, 101 residue long, C-terminal proteolytic domain (F2) of the Escherichia coli tryptophan synthase beta chain, which had previously been reported to behave as an early folding intermediate [Chaffotte, A. F., Cadieux, C., Guillou, Y., & Goldberg, M. E. (1992) Biochemistry 31, 4303-4308]. The secondary structure of F2 has been investigated by far-UV circular dichroism (CD), Fourier transform infrared (FTIR) spectroscopy, and NMR. The CD and FTIR spectra clearly indicate that isolated F2 has about 30-45% of its residues involved in secondary structures stabilized by conventional hydrogen bonds. The characteristics of the NMR spectrum (line broadening, absence of structure-induced chemical shifts, absence of nuclear Overhauser effects in the amide region, few dipolar interactions between the side-chain protons) suggest that isolated F2 is oscillating between several conformations in rapid equilibrium. The rate of amide proton exchange has been studied by one-dimensional NMR, which indicates a significant extent of proton protection, with, however, protection factors that can be estimated to be at most 60 and more probably closer to 10. Thus, F2 appears to exist as a molten globule that exhibits very low amide proton protection and yet contains a large fraction of its residues involved in authentic secondary structures stabilized by hydrogen bonds. Such a state is likely to correspond to the earliest structured folding intermediates thus far characterized.