Stereoelectronic and steric effects in the collagen triple helix: toward a code for strand association

Collagen is the most abundant protein in animals. The protein consists of a helix of three strands, each with sequence X-Y-Gly. Natural collagen is most stable when X is (2S)-proline (Pro) and Y is (2S,4R)-4-hydroxyproline (4R-Hyp). We had shown previously that triple helices in which X is (2S,4S)-4-fluoroproline (4S-Flp) or Y is (2S,4R)-4-fluoroproline (4R-Flp) display hyperstability. This hyperstability arises from stereoelectronic effects that preorganize the main-chain dihedral angles in the conformation found in the triple helix. Here, we report the synthesis of strands containing both 4S-Flp in the X-position and 4R-Flp in the Y-position. We find that these strands do not form a stable triple helix, presumably because of an unfavorable steric interaction between fluoro groups on adjacent strands. Density functional theory calculations indicate that (2S,3S)-3-fluoroproline (3S-Flp), like 4S-Flp, should preorganize the main chain properly for triple-helix formation but without a steric conflict. Synthetic strands containing 3S-Flp in the X-position and 4R-Flp in the Y-position do form a triple helix. This helix is, however, less stable than one with Pro in the X-position, presumably because of an unfavorable inductive effect that diminishes the strength of the interstrand 3S-FlpC=O...H-NGly hydrogen bond. Thus, other forces can counter the benefits derived from the proper preorganization. Although (Pro-Pro-Gly)7 and (4S-Flp-4R-Flp-Gly)7 do not form stable homotrimeric helices, mixtures of these two peptides form stable heterotrimeric helices containing one (Pro-Pro-Gly)7 strand and two (4S-Flp-4R-Flp-Gly)7 strands. This stoichiometry can be understood by considering the cross sections of the two possible heterotrimeric helices. This unexpected finding portends the development of a "code" for the self-assembly of determinate triple helices from two or three strands.     

Macrocyclic scaffold for the collagen triple helix

[structure: see text] Three strands of natural collagen are linked by covalent bonds prior to their folding into a triple helix. We report on a synthetic collagen in which the strands are pendent on a rigid macrocyclic scaffold of C(3) symmetry. The scaffold confers substantial conformational stability upon the collagen triple helix and makes its folding independent of concentration, both desirable attributes for exploring and exploiting synthetic collagens.     

The close-packed triple helix as a possible new structural motif for collagen

The one-dimensional problem of selecting the triple helix with the highest volume fraction is solved and hence the condition for a helix to be close-packed is obtained. The close-packed triple helix is shown to have a pitch angle of v _CP =?43.3°. Contrary to the conventional notion, we suggest that close packing form the underlying principle behind the structure of collagen, and the implications of this suggestion are considered. Further, it is shown that the unique zero-twist structure with no strain-twist coupling is practically identical to the close-packed triple helix. Some of the difficulties for the current understanding of the structure of collagen are reviewed: The ambiguity in assigning crystal structures for collagen-like peptides, and the failure to satisfactorily calculate circular dichroism spectra. Further, the proposed new geometrical structure for collagen is better packed than both the 10/3 and the 7/2 structure. A feature of the suggested collagen structure is the existence of a central channel with negatively charged walls. We find support for this structural feature in some of the early x-ray diffraction data of collagen. The central channel of the structure suggests the possibility of a one-dimensional proton lattice. This geometry can explain the observed magic angle effect seen in NMR studies of collagen. The central channel also offers the possibility of ion transport and may cast new light on various biological and physical phenomena, including biomineralization.     

The effect of a trans-locked Gly-Pro alkene isostere on collagen triple helix stability

An alkene isostere of Gly-trans-Pro was synthesized and incorporated into a host Ac-(Gly-Pro-Hyp)8-Gly-Gly-Tyr-NH2 peptide to investigate the effect of locking a proline amide bond. Proline amide bond isomerization is the slow step in collagen folding. By locking the amide, we hypothesized an increase in stability of the collagen triple helix. The substitution instead destabilized the collagen host peptide. The Tm value of the host control peptide was 50.0 degrees C, while the peptide containing the isostere, Ac-(Gly-Pro-Hyp)3-Gly-psi[(E)CH C]-Pro-Hyp-(Gly-Pro-Hyp)4-Gly-Gly-Tyr-NH2, had a Tm value of 28.3 degrees C. There are clearly factors that contribute to collagen stability and folding that we do not yet understand.     

Peptide bond isosteres: ester or (E)-alkene in the backbone of the collagen triple helix

[structure: see text] Collagen is the most abundant protein in animals. Interstrand N-H...O=C hydrogen bonds between backbone amide groups form a ladder in the middle of the collagen triple helix. Isosteric replacement of the hydrogen-bond-donating amide with an ester or (E)-alkene markedly decreases the conformational stability of the triple helix. Thus, this recurring hydrogen bond is critical to the structural integrity of collagen. In this context, an ester isostere confers more stability than does an (E)-alkene.     

Imino acids and collagen triple helix stability: characterization of collagen-like polypeptides containing Hyp-Hyp-Gly sequence repeats

The analysis of factors contributing to the stability of proteins is a subject of intense debate. Particularly challenging is the study of structural proteins, since their function is their structure. Among these is collagen, the key structural component of bones, skin, cartilage, tendons, and other connecting tissues. It is well established that the collagen triple helix is characterized by the presence of hydroxyproline, whose content modulates triple helix thermal stability according to the requirement of the host organism. Because of the complexity and the fibrous nature of collagen, data on the stability and structure of this protein have been mainly obtained by the use of collagen-like polypeptides. On the basis of CD characterization of collagen-like polypeptides we here show that the presence of Hyp at the X position of repeating triplets Hyp-Hyp-Gly stabilizes the triple helix significantly. This extra-stabilization has been ascribed, by using molecular modeling, to the formation of a hydrogen bond between Hyp residues belonging to the X and the Y positions of adjacent chains. This communication also provides a comprehensive interpretation of the ensemble of available data on polypeptides containing proline derivatives.     

Photocontrol of the collagen triple helix: synthesis and conformational characterization of bis-cysteinyl collagenous peptides with an azobenzene clamp

For the photomodulation of the collagen triple helix with an azobenzene clamp, we investigated various collagenous peptides consisting of ideal (Gly-Pro-Hyp) repeats and containing cysteine residues in various positions for a side chain-to-side chain crosslink with a suitable chromophore derivative. Comparative conformational analysis of these cysteine peptides indicated an undecarepeat peptide with two cysteine residues located in the central portion in i and i+7 positions and flanked by (Gly-Pro-Hyp) repeat sequences as the most promising for the cross-bridging experiments. In aqueous alcoholic solution the azobenzene-undecarepeat peptide formed a stable triple helix in equilibrium with the monomeric species as a trans-azobenzene isomer, whereas photoisomerization to the cis isomer leads to unfolding of at least part of the triple helix. Furthermore, the residual supercoiled structure acts like an intermolecular knot, thus making refolding upon cis-to-trans isomerization a concentration-independent fast event. Consequently, these photoswitchable collagenous systems should be well suited for time-resolved studies of folding/unfolding of the collagen triple helix under variable thermodynamic equilibria.     

Design of triple helix forming C-glycoside molecules

The modeling, synthesis, and characterization of oligomers containing 2-aminoquinazolin-5-yl 2'-deoxynucleotide residues are reported. The 2-aminoquinazoline residues sequence specifically bind via Hoogsteen base pairing as a third strand in the center of the major groove at T:A base pair Watson-Crick duplex sequences. Evidence for the formation of a sequence specific three-stranded structure is based on thermal denaturation UV-vis and fluorescence studies. The novel 2-aminoquinazoline C-nucleotide is a component of a system designed to overcome the homopurine requirement for triple helix structures.     

Bonded exciplex formation: electronic and stereoelectronic effects

As recently proposed, the singlet-excited states of several cyanoaromatics react with pyridine via bonded-exciplex formation, a novel concept in photochemical charge transfer reactions. Presented here are electronic and steric effects on the quenching rate constants, which provide valuable support for the model. Additionally, excited-state quenching in poly(vinylpyridine) is strongly inhibited both relative to that in neat pyridine and also to conventional exciplex formation in polymers, consistent with a restrictive orientational requirement for the formation of bonded exciplexes. Examples of competing reactions to form both conventional and bonded exciplexes are presented, which illustrate the delicate balance between these two processes when their reaction energetics are similar. Experimental and computational evidence is provided for the formation of a bonded exciplex in the reaction of the singlet excited state of 2,6,9,10-tetracyanoanthracene (TCA) with an oxygen-substituted donor, dioxane, thus expanding the scope of bonded exciplexes.     

PM3 semi-empirical study of stereoelectronic effects in the Baeyer-Villiger reaction

The Baeyer-Villiger reaction of polymethoxybenzaldehydes with peroxysuccinic acid (PSA) is studied theoretically. The semi-empirical SCF-MO/PM3 method has been used to study the reaction and to calculate the energy profiles. In addition, heat of formation computations and bond order analyses of the transition species along the reaction coordinates have been performed and are interpreted qualitatively in terms of electron flow through the system during aryl migration. Our results support the hypothesis that the second step is a concerted reaction. Our data support a definite effect of the substituent on the aryl migration. The theoretical predictions are in good agreement with experimental results.     

Dielectric assembly of a collagen-model polypeptide in a triple helix

In expectation of the formation of a thermally stable, dielectric supramolecular assembly of a polypeptide with an amino acid sequence similar to that of type-2 collagen, a sequential polypeptide consisting of the repetition of the Pro-Pro-Gly tripeptide was synthesized by solid-phase synthesis. Column chromatography of an ethanol solution of (Pro-Pro-Gly)₁₀ NH₂ showed the presence of a double helix or triple helix of the polypeptide. The pattern of a circular dichroism (CD) spectrum of an ethanol solution of (Pro-Pro-Gly)₁₀ NH₂ was very similar to that of an aqueous solution of (Pro-Pro-Gly)₁₀ OH, strongly suggesting the presence of a triple helix of the polypeptide in ethanol. An oriented monolayer assembly of (Pro-Pro-Gly)₁₀ NH₂ was formed on a thin gold film. The distribution of surface unevenness and the surface potential were investigated with Kelvin force microscopy. The rising spots carried an electric potential from room temperature to 150 °C. The correspondence showed the usefulness of the oriented monolayer of the sequential polypeptide materials for thermally stable, dielectric nanodevices. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 3632–3639, 2003     

Selective intercalation of six ligand molecules in a self-assembled triple helix

The addition of a ligand molecule to an artificial self-assembled triple helix leads to the selective intercalation of two hydrogen-bonded trimers in specific binding pockets. Furthermore, the triple helix suffers large conformational rearrangements in order to accommodate the ligand molecules in a highly organized manner.     

Cooperative ordering of collagen triple helices in the dense state

Extracellular matrixes such as bone, skin, cornea, and tendon have ordered structures comprised for the most part of collagen, an elongated protein of well-defined dimensions and composition. Here we show how the cooperative ordering of collagen triple helices in the dense fluid state is exploited to produce dense ordered collagen matrixes. The spontaneous formation of a birefringent phase occurs at critical concentrations that increase from 50-60 to 80-85 mg/mL as the acetic acid concentration of the solvent increases from 5 to 500 mM. We studied by small-angle X-ray scattering (SAXS) the local liquidlike positional order across the isotropic/anisotropic phase transition by unwinding the cholesteric phase with moderate shearing stress. Interparticle scattering gives rise to a broad interference peak. The average distance between triple helices, dav, is thus estimated and decreases linearly as a function of phi-1/2 from 12.7 +/- 0.9 nm (22.5 mg/mL) to 5.0 +/- 0.6 nm (166.4 mg/mL). Equilibrium concentrations and the order parameter of the nematic phase agree reasonably well with theoretical predictions for semiflexible macromolecules. Striated fibrils with a high degree of alignment were obtained by fine-tuning the delicately balanced electrostatic interactions, which yielded strong elastic gels with a hierarchical organization very similar to that of major biological tissues. Typical Bragg reflections corresponding to the 67 nm period characteristic of collagen fibrils in biological tissues were recorded by SAXS with ordered collagen matrixes reconstituted in vitro.     

Steric and stereoelectronic effects in the synthesis and photoisomerization of a dinitrone of 2,2,4,4-tetramethylcyclobutanedione

Peroxyacid oxidation of diimine (1) yielded only the $\text{trans}$ isomer of dinitrone (2) which upon photoisomerization gave dioxaziridines (3a) and (3b) and amide (4) as the only isolable isomers; an X-ray crystallographic investigation of (1) shows a considerable geometry distortion.     

Assessing stereoelectronic effects in dipolar cycloadditions yielding fused thiazolopyridone rings

We report a combined experimental and computational study on the cycloadditions of bicyclic 1,3-thiazolium-4-olates, derived from thiazolidin-2-thiones, with asymmetrically-substituted acetylenes. These results provide further mechanistic insights into the above dipolar cycloadditions and enable an unequivocal characterization by NMR spectroscopy of regiochemical patterns as previous derivatives had substituents at both C-2 (in the dipole) and C-6 (in products). Accordingly, new dihydrothiazolopyrid-2-ones have been obtained from a thioisomünchnone lacking substitution at C-2. With the aim of assessing the steric hindrance as well as the facial stereoselection induced by a bulky group on the Si face (relative to C-7a) of the mesoionic heterocycle, a chiral thioisomünchnone has also been obtained along with the resulting optically active thiazolopyridones. A computational study of these particular cycloadditions, largely based on an NBO analysis, allowed us to evaluate the influence of substituents on intermolecular steric repulsions, charge transfers, as well as solvent effects.