Jorge Santoro

Solution structure of gamma 1-H and gamma 1-P thionins from barley and wheat endosperm determined by 1H-NMR: a structural motif common to toxic arthropod proteins.

The complete assignment of the proton NMR spectra of the homologous gamma 1-hordothionin and gamma 1-purothionin (47 amino acids, 4 disulfide bridges) from barley and wheat, respectively, has been performed by two-dimensional sequence-specific methods. A total of 299 proton-proton distance constraints for gamma 1-H and 285 for gamma 1-P derived from NOESY spectra have been used to calculate the three-dimensional solution structures. Initial structures have been generated by distance geometry methods and further refined by dynamical simulated annealing calculations. Both proteins show identical secondary and tertiary structure with a well-defined triple-stranded antiparallel beta-sheet (residues 1-6, 31-34, and 39-47), an alpha-helix (residues 16-28), and the corresponding connecting loops. Three disulfide bridges are located in the hydrophobic core holding together the alpha-helix and the beta-sheet and forming a cysteine-stabilized alpha-helical (CSH) motif. Moreover, a clustering of positive charges is observed on the face of the beta-sheet opposite to the helix. The three-dimensional structures of the gamma-thionins differ remarkably from plant alpha- and beta-thionins and crambin. However, they show a higher structural analogy with scorpion toxins and insect defensins which also present the CSH motif.

1H NMR detection of cerebral myo‐inositol

A previously unassigned group of prominent multiplets of the 360 MHz 1H NMR spectrum of acid stable metabolite extracts from rat brain is shown to arise from free myo‐inositol. This conclusion is derived from a systematic analysis of the high‐resolution 1H NMR spectra of brain acid extracts, in which appropriate conditions and optimal proton signals have been selected for the quantitative analysis of up to 15 metabolites. Developmental variations in the cerebral content of myo‐inositol could be readily detected using this approach, which provides a novel alternative to study myo‐inositol metabolism under physiological or pathological conditions.

1H NMR and CD evidence of the folding of the isolated ribonuclease 50-61 fragment

In our search for potential folding intermediates we have prepared and characterized the fragment of RNase A corresponding to residues 50–61. Proton chemical shift variations with temperature, addition of stabilizing (TFE) or denaturing agents (urea) provide a strong experimental basis for concluding that in aqueous solution this RNase fragment forms an α‐helix structure similar to that in the intact RNase A crystal. This conclusion lends strong support to the idea that elements of secondary structure (mainly α‐helices) can be formed in the absence of tertiary interactions and act as nucleation centers in the protein folding process.

Low‐temperature 1H‐NMR evidence of the folding of isolated ribonuclease S‐peptide

The temperature (−7°C to 45°C, pH 5.4) and pH (0°C) dependence of 1H chemical shifts of ribonuclease S‐peptide (5 mM, 1 M NaCl) has been measured at 360 MHz. The observed variations evidence the formation of a partial helical structure, involving the fragment Thr‐3—Met‐13. Two salt‐bridges stabilize the helix: those formed by Glu‐9−…His‐12+ and Glu‐2−…Arg‐10+. The structural features deduced from the 1H‐NMR at low temperature for the isolated S‐peptide are compatible with the structure shown by the same molecule in the ribonuclease S crystal.

Factors involved in the stability of isolated β-sheets: Turn sequence, β-sheet twisting, and hydrophobic surface burial

We have recently reported on the design of a 20‐residue peptide able to form a significant population of a three‐stranded up‐and‐down antiparallel β‐sheet in aqueous solution. To improve our β‐sheet model in terms of the folded population, we have modified the sequences of the two 2‐residue turns by introducing the segment DPro‐Gly, a sequence shown to lead to more rigid type II′ β‐turns. The analysis of several NMR parameters, NOE data, as well as ΔδCαH, ΔδCβ, and ΔδCβ values, demonstrates that the new peptide forms a β‐sheet structure in aqueous solution more stable than the original one, whereas the substitution of the DPro residues by LPro leads to a random coil peptide. This agrees with previous results on β‐hairpin‐forming peptides showing the essential role of the turn sequence for β‐hairpin folding. The well‐defined β‐sheet motif calculated for the new designed peptide (pair‐wise RMSD for backbone atoms is 0.5 ± 0.1 Å) displays a high degree of twist. This twist likely contributes to stability, as a more hydrophobic surface is buried in the twisted β‐sheet than in a flatter one. The twist observed in the up‐and‐down antiparallel β‐sheet motifs of most proteins is less pronounced than in our designed peptide, except for the WW domains. The additional hydrophobic surface burial provided by β‐sheet twisting relative to a “flat” β‐sheet is probably more important for structure stability in peptides and small proteins like the WW domains than in larger proteins for which there exists a significant contribution to stability arising from their extensive hydrophobic cores.

On the fundamental role of the Glu 2- ... Arg 10+ salt bridge in the folding of isolated ribonuclease A S-peptide.

The fundamental role of the Glu 2- ... Arg 10+ salt bridge in the folding of isolated S-peptide (1-19 N-terminal fragment of Ribonuclease A) is demonstrated from the comparison of the helix contents, at 0 degrees C, of S-peptide and related peptides. Helix contents have been determined from the analysis of proton chemical shift vs. temperature curves. The observed data can be accounted for by assuming that two side-chain interactions contribute to stabilize the 3-13 helix of S-peptide, the salt bridges Glu 2- ... Arg 10+ and Glu 9-... His 12+, the former being more effective. The salt bridge Glu 9- ... Arg 10+ turns to a weaker interaction, a hydrogen bond Glu 2 (C delta = 0) ... Arg 10+, on protonation or esterification of the Glu 2 carboxylate.

A study of the NH NMR signals of Gly-Gly-X-Ala tetrapeptides in H2O at low temperature.

Abstract The effect of temperature, pH and addition of denaturing agents on the amide and side chain NH δ values of a series of random coil linear tetrapeptides (Gly-Gly-X-Ala with X=Glu, Asp, His, Trp, Arg, Gly, Pro, Asn, Gln) has been measured in dilute aqueous solutions at two temperatures (24 and 0°C). Amide shift temperature coefficients were within the −5.8 to −9.1 ppb/K range. Amide δ changes following urea addition were ⩽ 0.03 ppm, with the exception of the Ala terminal residue of all peptides, and the His residue as well. Signs of a non-random structure near the COO − terminus were found for the Gly-Gly-His-Ala tetrapeptide.

NMR Spectroscopy Reveals that RNase A is Chiefly Denatured in 40% Acetic Acid: Implications for Oligomer Formation by 3D Domain Swapping

Protein self-recognition is essential in many biochemical processes and its study is of fundamental interest to understand the molecular mechanism of amyloid formation. Ribonuclease A (RNase A) is a monomeric protein that may form several oligomers by 3D domain swapping of its N-terminal alpha-helix, C-terminal beta-strand, or both. RNase A oligomerization is induced by 40% acetic acid, which has been assumed to mildly unfold the protein by detaching the terminal segments and consequently facilitating intersubunit swapping, once the acetic acid is removed by lyophilization and the protein is redissolved in a benign buffer. Using UV difference, near UV circular dichroism, folding kinetics, and multidimensional heteronuclear NMR spectroscopy, the conformation of RNase A in 40% acetic acid and in 8 M urea has been characterized. These studies demonstrate that RNase A is chiefly unfolded in 40% acetic acid; it partially retains the native helices, whereas the beta-sheet is fully denatured and all X-Pro peptide bonds are predominantly in the trans conformation. Refolding occurs via an intermediate, I(N), with non-native X-Pro peptide bonds. I(N) is known to be populated during RNase A refolding following denaturation in concentrated solutions of urea or guanidinium chloride, and we find that urea- or GdmCl-denatured RNase A can oligomerize during refolding. By revealing the importance of a chiefly denaturated state and a refolding intermediate with non-native X-Pro peptide bonds, these findings revise the model for RNase A oligomerization via 3D domain swapping and have general implications for amyloid formation.

3D structure of bovine pancreatic ribonuclease A in aqueous solution: An approach to tertiary structure determination from a small basis of1H NMR NOE correlations

SummaryA method is proposed to generate initial structures in cases where the distance geometry method may fail, such as when the set of1H NMR NOE-based distance constraints is small in relation to the size of the protein. The method introduces an initial correlation between the φ and ψ backbone angles (based on empirical observations) which is relaxed in later stages of the calculation. The obtained initial structures are refined by well-established methods of energy minimization and restrained molecular dynamics. The method is applied to determine the solution structure of Ribonuclease A (124 residues) from a NOE basis consisting of 467 NOE cross-correlations (97 intra-residue, 206 sequential, 23 medium-range and 141 long-range) obtained at 360 MHz. The global shape and backbone overall fold of the eight final refined structures are close to those shown by the crystal structure. A meaningful difference in the positioning of the catalytically important His119 side chain in the solution and crystal structures has been detected.

Structural basis for the catalytic mechanism and substrate specificity of the ribonuclease α-sarcin

α‐Sarcin is a ribosome‐inactivating protein which selectively cleaves a single phosphodiester bond in a universally conserved sequence of the major rRNA. The solution structure of α‐sarcin has been determined on the basis of 1898 distance and angular experimental constraints from NMR spectroscopy. It reveals a catalytic mechanism analogous to that of the T1 family of ribonucleases while its exquisite specificity resides in the contacts provided by its distinctive loops.