Benedetto Di Blasio

The longest, regular polypeptide 310 helix at atomic resolution

A synthetic, terminally blocked homodecapeptide from the C alpha, alpha-dimethylated glycyl residue alpha-aminoisobutyric acid has been analyzed by single-crystal X-ray diffraction and the structure refined to R = 0.073. The compound crystallizes as a perfect 3(10) helix, stabilized by eight consecutive intramolecular N-H . . . O = C hydrogen bonds. This is the first observation at atomic resolution of a regular polypeptide 3(10) helix as long as three complete turns.

NMR Structure of the Single QALGGH Zinc Finger Domain from the Arabidopsis thaliana SUPERMAN Protein

Zinc finger domains of the classical type represent the most abundant DNA binding domains in eukaryotic transcription factors. Plant proteins contain from one to four zinc finger domains, which are characterized by high conservation of the sequence QALGGH, shown to be critical for DNA‐binding activity. The Arabidopsis thaliana SUPERMAN protein, which contains a single QALGGH zinc finger, is necessary for proper spatial development of reproductive floral tissues and has been shown to specifically bind to DNA. Here, we report the synthesis and UV and NMR spectroscopic structural characterization of a 37 amino acid SUPERMAN region complexed to a Zn2+ ion (Zn–SUP37) and present the first high‐resolution structure of a classical zinc finger domain from a plant protein. The NMR structure of the SUPERMAN zinc finger domain consists of a very well‐defined ββα motif, typical of all other Cys2‐His2 zinc fingers structurally characterized. As a consequence, the highly conserved QALGGH sequence is located at the N terminus of the α helix. This region of the domain of animal zinc finger proteins consists of hypervariable residues that are responsible for recognizing the DNA bases. Therefore, we propose a peculiar DNA recognition code for the QALGGH zinc finger domain that includes all or some of the amino acid residues at positions −1, 2, and 3 (numbered relative to the N terminus of the helix) and possibly others at the C‐terminal end of the recognition helix. This study further confirms that the zinc finger domain, though very simple, is an extremely versatile DNA binding motif.

Regularly alternatingL,D-peptides. II. The double-stranded right-handed antiparallel ?-helix in the structure oft-Boc-(L-Phe-D-Phe)4-OMe

The crystal structure of Boc‐(L‐Phe‐D‐Phe)4‐OMe has been determined by x‐ray diffraction analysis. The peptide crystallizes in the triclinic system, space group P1 with a = 15.290 Å, b = 15.163 Å, c = 19.789 Å, α = 102.49°, β = 96.59°, γ = 74.22°, and Z = 2. The structure has been solved by coupling of the molecular replacement technique and expansion by tangent formula refinement of the set of known phases. Several cycles of Fourier calculations and least‐squares refinement led to the location of 194 atoms of the two independent octapeptide chains and few molecules of cocrystallized solvent (chloroform, water, and methanol). The isotropic refinement converged to R = 0.13 for the 3077 “observed” reflections.

The prokaryotic Cys2His2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain.

The first putative prokaryotic Cys2His2 zinc-finger domain has been identified in the transcriptional regulator Ros from Agrobacterium tumefaciens, indicating that the Cys2His2 zinc-finger domain, originally thought to be confined to the eukaryotic kingdom, could be widespread throughout the living kingdom from eukaryotic, both animal and plant, to prokaryotic. In this article we report the NMR solution structure of Ros DNA-binding domain (Ros87), providing 79 structural characterization of a prokaryotic Cys2His2 zinc-finger domain. The NMR structure of Ros87 shows that the putative prokaryotic Cys2His2 zinc-finger sequence is indeed part of a significantly larger zinc-binding globular domain that possesses a novel protein fold very different from the classical fold reported for the eukaryotic classical zinc-finger. The Ros87 globular domain consists of 58 aa (residues 9–66), is arranged in a βββαα topology, and is stabilized by an extensive 15-residue hydrophobic core. A backbone dynamics study of Ros87, based on 15N R1, 15N R2, and heteronuclear 15N-{1H}-NOE measurements, has further confirmed that the globular domain is uniformly rigid and flanked by two flexible tails. Mapping of the amino acids necessary for the DNA binding onto Ros87 structure reveals the protein surface involved in the DNA recognition mechanism of this new zinc-binding protein domain.

Conformational Characterization of the 1-Aminocyclobutane-1-carboxylic Acid Residue in Model Peptides

A series of N‐ and C‐protected, monodispersed homo‐oligopeptides (to the dodecamer level) from the small‐ring alicyclic Cα,α‐dialkylated glycine 1‐aminocyclobutane‐1‐carboxylic acid (Ac4c) and two Ala/Ac4c tripeptides were synthesized by solution methods and fully characterized. The conformational preferences of all the model peptides were determined in deuterochloroform solution by FT‐IR absorption and 1H‐NMR. The molecular structures of the amino acid derivatives Z‐Ac4c‐OH and Z2‐Ac4c‐OH, the tripeptides Z‐(Ac4c)3‐OtBu, Z‐Ac4c‐(L‐Ala)2‐OMe and Z‐L‐Ala‐Ac4c‐L‐Ala‐OMe, and the tetrapeptide Z‐(Ac4c)4‐OtBu were determined in the crystal state by X‐ray diffraction. The average geometry of the cyclobutyl moiety of the Ac4c residue was assessed and the τ(N–Cα–C′) bond angle was found to be significantly expanded from the regular tetrahedral value. The conformational data are strongly in favour of the conclusion that the Ac4c residue is an effective β‐turn and helix former. A comparison with the structural propensities of α‐aminoisobutyric acid, the prototype of Cα,α‐dialkylated glycines, and the other extensively investigated members of the family of 1‐aminocycloalkane‐1‐carboxylic acids (Acnc, with n=3, 5–8) is made and the implications for the use of the Ac4c residue in conformationally constrained peptide analogues are briefly examined.

The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains

The recent characterization of the prokaryotic Cys2His2 zinc-finger domain, identified in Ros protein from Agrobacterium tumefaciens, has demonstrated that, although possessing a similar zinc coordination sphere, this domain is structurally very different from its eukaryotic counterpart. A search in the databases has identified ≈300 homologues with a high sequence identity to the Ros protein, including the amino acids that form the extensive hydrophobic core in Ros. Surprisingly, the Cys2His2 zinc coordination sphere is generally poorly conserved in the Ros homologues, raising the question of whether the zinc ion is always preserved in these proteins. Here, we present a functional and structural study of a point mutant of Ros protein, Ros56–142C82D, in which the second coordinating cysteine is replaced by an aspartate, 5 previously-uncharacterized representative Ros homologues from Mesorhizobium loti, and 2 mutants of the homologues. Our results indicate that the prokaryotic zinc-finger domain, which in Ros protein tetrahedrally coordinates Zn(II) through the typical Cys2His2 coordination, in Ros homologues can either exploit a CysAspHis2 coordination sphere, previously never described in DNA binding zinc finger domains to our knowledge, or lose the metal, while still preserving the DNA-binding activity. We demonstrate that this class of prokaryotic zinc-finger domains is structurally very adaptable, and surprisingly single mutations can transform a zinc-binding domain into a nonzinc-binding domain and vice versa, without affecting the DNA-binding ability. In light of our findings an evolutionary link between the prokaryotic and eukaryotic zinc-finger domains, based on bacteria-to-eukaryota horizontal gene transfer, is discussed.

Linear oligopeptides. Part 227. X-Ray crystal and molecular structures of two α-helix-forming (Aib-L-Ala)sequential oligopeptides, pBrBz-(Aib-L-Ala)5-OMe and pBrBz-(Aib-L-Ala)6-OMe

A crystal-state structutal analysis of pBrBz-(Aib-LAla)5-OMe tetrahydrate and pBrBz-(Aib-L-Ala)6-OMe dihydrate has been performed by X-ray diffraction. The decapeptide and dodecapeptide molecules are both basically α-helical with five and seven 1 â†� 5 intramolecular H-bonds, respectively. A similarity between the two structures is also seen near the C-terminus, where regularity of the α-helix is disrupted in favour of formation of intramolecular H-bonds of the 1 â†� 4 and 1 â†� 6 types. A brief comparison with parameters and interactions characteristic of the helices present in globular proteins has been made.

Long, Chiral Polypeptide 310-Helices at Atomic Resolution

The crystal-state preferred conformation of the terminally blocked hepta- and octapeptides with the general formula -(Aib)n L-Leu-(Aib)2- (n = 4 and 5, respectively), determined by X-ray diffraction, was found to be a right-handed 3(10)-helix stabilized by five and six consecutive intramolecular NH...O = C H-bonds of the C(10)-III type, respectively. The octapeptide structure represents the first observation at atomic resolution of a regular, chiral 3(10)-helix larger than two complete turns. In both cases the right handed screw sense of the helix is dictated by the presence of the single, internal L-residue. This study confirms the propensity of short peptides rich in Aib, the prototype of the amino acid residues dialkylated at the alpha carbon, to adopt a 3(10)-helical structure and is expected to help our understanding of the conformational preferences of the membrane-active, channel-forming, ion-transporting peptaibol antibiotics.

Structure of clathridine Zn-complex, a metabolite of the marine sponge Clathrina clathrus

Abstract The solid state structure of the Zn-complex of clathridine (1), a genuine metabolite of the sponge Clathrina clathrus, was established by X-ray diffraction analysis. In addition, the conformation of 1 in CDCl3 solution was investigated by NOE difference NMR experiments.

Linear oligopeptides — effect of lengthening of the main chain by one tetrahedral carbon atom in the -Aib-l-Ala- sequence: a solid-state conformational analysis of segments of polypeptide antibiotics

Abstract The infrared absorption and X-ray diffraction conformational analysis of t-Boc-Aib- l -Ala-Aib-OMe have shown the presence of the type-1 4→1 intramolecularly H-bonded peptide conformation (β-bend) in the solid state. Lengthening of the chain by one tetrahedral carbon atom, as in t-Boc-Aib-βAla-Aib-OMe, has a disruptive effect on this folded structure. It has also been found that two water molecules co-crystallize with each molecule of the l -Ala containing tripeptide. These results are discussed in comparison with those, previously reported, obtained in chloroform solution.