Self-association-driven transition of the β-peptidic H12 helix to the H18 helix

Various patterns of foldameric oligomers formed by trans-ABHC ((1S,2S,3S,5S)-2-amino-6,6-dimethylbicyclo[3.3.1]heptane-3-carboxylic acid) and β(3)-hSer residues were studied. NMR, ECD and molecular modelling demonstrated that octameric and nonameric sequences with multiple i-i+3 ABHC pair repulsions attain the β-H18 helix in CD(3)OH. As a close relative of the α-helix, this helix type is stabilized by i-i+4 backbone H-bond interactions. The formation of the β-H18 helix was found to be solvent- and concentration-dependent. Upon dilution, the β-H18 → β-H12 helix transition was revealed by concentration-dependent ECD, DOSY-NMR and TEM measurements.     

Genetic algorithms as a tool for helix design – computational and experimental studies on prion protein helix 1

Summary Evolutionary computing is a general optimization mechanism successfully implemented for a variety of numeric problems in a variety of fields, including structural biology. We here present an evolutionary approach to optimize helix stability in peptides and proteins employing the AGADIR energy function for helix stability as scoring function. With the ability to apply masks determining positions, which are to remain constant or fixed to a certain class of amino acids, our algorithm is capable of developing stable helical scaffolds containing a wide variety of structural and functional amino acid patterns. The algorithm showed good convergence behaviour in all tested cases and can be parameterized in a wide variety of ways. We have applied our algorithm for the optimization of the stability of prion protein helix 1, a structural element of the prion protein which is thought to play a crucial role in the conformational transition from the cellular to the pathogenic form of the prion protein, and which therefore poses an interesting target for pharmacological as well as genetic engineering approaches to counter the as of yet uncurable prion diseases. NMR spectroscopic investigations of selected stabilizing and destabilizing mutations found by our algorithm could demonstrate its ability to create stabilized variants of secondary structure elements.     

Supramolecular double helix from capped γ-peptide

The single crystal X-ray diffraction study of capped γ-peptide reveal that the peptide adopts helical conformation which self-assemble to form a supramolecular parallel double helical structure using intermolecular hydrogen bonding as well as π-π stacking interactions in the solid state.     

Hierarchical helix of helix in the crystal: formation of variable-pitch helical π-stacked array of single-helical dinuclear metal complexes

Unique helix of helix structures were formed via intermolecular π-stacking and metal-metal interactions in the crystal of single-helical dinuclear complexes [L(2)M(2)] (M = Pd, Ni) having an acyclic bis(N(2)O(2))-type ligand. The difference in the helical winding angle of the constituents (401.7° for [L(2)Pd(2)]; 421.3° for [L(2)Ni(2)]) led to variation of the helical pitches of the helical array (7(2) helix for [L(2)Pd(2)]; 6(2) helix for [L(2)Ni(2)]).     

Unwinding of ι-carrageenan double helix upon complex formation with polyethylaminophosphazene hydrochloride

The interaction of poly(ethylaminophosphazene) hydrochloride (M _SD = 3.2 × 10⁵) with potassium ι-carrageenan (M _w = 2.2 × 10⁵), which is a linear regular anionic polysaccharide, has been studied by high-sensitivity DSC at pH 3.8 in a 0.15 mol/l solution of KCl. The dependences of temperature, enthalpy, and the cooperativity parameter of the double helix-coil transition of polysaccharide on the concentration ratio of polyphosphazene and polysaccharide have been obtained. The presence of polyphosphazene has no effect on the temperature and cooperativity of transition, whereas the enthalpy of the transition decreases linearly with the content of polyphosphazene and turns to zero at a mass polymer-to-polysaccharide ratio of approximately 1: 1, which corresponds to the equivalent concentrations of polyphosphazene and polysaccharide with respect to charges. Our data indicate that the mixing of poly(ethylaminophosphazene) hydrochloride and potassium ι-carrageenan solutions gives rise to formation of the stoichiometric interpolyelectrolyte complex, in which the polysaccharide loses its ability to form double helix typical of ι-carrageenan in saline solution (0.15 M KCl).     

From helix to macrocycle: anion-driven conformation control of π-conjugated acyclic oligopyrroles

Anion-responsive pyrrole-based linear receptor oligomers were newly synthesized and their anion-driven dynamic conformation changes were investigated. Phenylene-bridged dimers and a tetramer of dipyrrolyldiketone boron complexes as π-conjugated acyclic anion receptors formed anion-driven helical structures in the solid and solution states. In fact, single-crystal X-ray analyses of the receptor-anion complexes exhibited various helical structures, such as [1+1]- and [1+2]-type single helices and a [2+2]-type double helix according to the lengths of oligomers and the existence of terminal aryl substituents. Anion-binding modes and behaviors of the oligomers in solution state were also examined by (1)H NMR and UV/Vis spectra along with ESI-TOF MS. Differences in the binding modes were observed in the solid and solution states. The oligomers showed augmented anion-binding constants and anion-tunable electronic and optical properties in comparison with the monomer receptor. A negative cooperative effect in the tetramer was observed in the second anion binding of the [1+2]-type single helix due to electrostatic repulsion between two anions captured in the helix. Further, an anion-template coupling reaction from the linear dimer provided a receptor macrocycle, which was obtained as a Cl(-) complex with distinct electronic and optical properties. The macrocycle exhibited extremely high anion-binding constants (>10(10) m(-1) in CH(2)Cl(2)) through multiple hydrogen bonding.     

Conformational and self-assembly studies of helix forming hexapeptides containing two α-amino isobutyric acids

Single crystal X-ray diffraction studies reveal that three hexapeptides with general formula Boc-Ile-Aib-Xx-Ile-Aib-Yy-OMe, where Xx and Yy are Leu in peptide I, Leu and Phe in peptide II, and Phe and Leu in peptide III, respectively, adopt equivalent conformations that can be described as mixed 3₁₀/α-helice with two 4→1 and two 5→1 intramolecular N-H?OC H-bonds. The peptides do not generate any helix-terminating Schellman motif despite having Aib at the penultimate position from C-terminus. In the crystalline state, the helices are packed in head-to-tail fashion through intermolecular hydrogen bonds to create supramolecular helical structures. The CD studies of the three hexapeptides in acetonitrile indicate that they are folded in well-developed 3₁₀-helical structures. NMR studies of peptide I in CDCl₃ also suggest the formation of a homogeneous 3₁₀-helical structure. The field emission scanning electron microscopic (FE-SEM) images of peptide II in the solid state reveal a non-twisted ribbon-like morphology, which is formed through lateral association of non-twisted filaments.     

Monte Carlo simulation of the kinetics of the helix—coil transition in a synthetic DNA

Values of the rate at which an alternating copolymeric nucleic acid melts after a temperature jump have been obtained with a Monte Carlo simulation. Using a Glauber—Ising scheme to model the dynamics, the helix—random coil transition shows a pure “monodispersive” relaxation in accord with previous analytical and experimental predictions.     

Supramolecular peptide helix from a novel double turn forming peptide containing a β-amino acid

A single-crystal X-ray diffraction study of the terminally protected tetrapeptide Boc-β-Ala-Aib-Leu-Aib-OMe 1 (Aib: α-aminoisobutyric acid; β-Ala: β-Alanine) reveals that it adopts a new type of double turn structure which self-associates to form a unique supramolecular helix through intermolecular hydrogen bonds. Scanning electron microscopic studies show that peptide 1 exhibits amyloid-like fibrillar morphology in the solid state.     

Water molecule adsorption on short alanine peptides: how short is the shortest gas-phase alanine-based helix?

Water adsorption measurements have been performed under equilibrium conditions for unsolvated Ac-A(n)K+H(+) and Ac-KA(n)+H(+) peptides with n = 4 - 10. Previous work on larger alanine peptides has shown that two dominant conformations (helices and globules) are present for these peptides and that water adsorbs much more strongly to the globules than to the helices. All the Ac-KA(n)+H(+) peptides studied here (which are expected to be globular) adsorb water strongly, and so do the Ac-A(n)K+H(+) peptides with n < 8. However, for Ac-A(n)K+H(+) with n = 8-10 there is a substantial drop in the propensity to adsorb water. This result suggests that Ac-A(8)K+H(+) is the smallest Ac-A(n)K+H(+) peptide to have a significant helical content in the gas phase. Water adsorption measurements for Ac-V(n)K+H(+) and Ac-L(n)K+H(+) with n = 5-10 suggest that the helix emerges at n = 8 for these peptides as well.     

Induced helix of 2-(2-aminophenoxy)alkanoic acid oligomers as a δ-peptidomimetic foldamer

Peptidomimetic foldamers were synthesized by oligomerizing derivatives of the δ-amino acid analogue, 2-(2-aminophenoxy)alkanoic acid. Single-crystal analysis of the tetramer reveals a 2₁-helical secondary structure stabilized by hydrogen bonding and the coiled stacking of aromatic rings. The M-helicity of 2-aminophenoxyacetic acid oligomers was induced by the incorporation of only a single chiral carbon of the N-terminal (R)-2-(2-nitrophenoxy)propionamide moiety. The solution state CD spectra demonstrated that the resulting helix induced a substantial Cotton effect. The secondary structure was further characterized by IR and NMR spectroscopy.     

Conformational control in a bipyridine linked π-conjugated oligomer: cation mediated helix unfolding and refolding

A chiral π-conjugated oligomer having alternate bipyridine and carbazole moieties connected through acetylinic bonds undergoes helical folding in chloroform-acetonitrile (40/60, v/v) as evident by fluorescence and circular dichroism changes. In the presence of transition metal cations such as Zn(2+) defolding of the helical conformation occurs. Upon decomplexation of the cation with EDTA, the helical conformation is regained.     

Substituent effects on CL···N, S···N, and P···N noncovalent bonds

Cl, S, and P atoms have previously been shown as capable of engaging in a noncovalent bond with the N atom on another molecule. The effects of substituents B on the former atoms on the strength of this bond are examined, and it is found that the binding energy climbs in the order B = CH(3) < NH(2) < CF(3) < OH < Cl < NO(2) < F. However, there is some variability in this pattern, particularly for the NO(2) group. The A···N bonds (A = Cl, S, P) can be quite strong, amounting to as much as 10 kcal/mol. The binding energy arises from approximately equal contributions from its induction and electrostatic components, although the former becomes more dominant for the stronger bonds. The induction energy is due in large measure to the transfer of charge from the N lone pair to a B-A σ* antibonding orbital of the electron-acceptor molecule containing Cl, S, or P. These A···N bonds typically represent the lowest-energy structure on each potential energy surface, stronger than H-bonds such as NH···F, CH···N, or SH···N.     

Weak H-bonds. Comparisons of CH···O to NH···O in proteins and PH···N to direct P···N interactions

Whereas CH···O H-bonds are usually weaker than interpeptide NH···O H-bonds, this is not necessarily the case within proteins. The nominally weaker CH···O are surprisingly strong, comparable to, and in some cases stronger than, the NH···O H-bonds in the context of the forces that hold together the adjacent strands in protein β-sheets. The peptide NH is greatly weakened as proton donor in certain conformations of the protein backbone, particularly extended structures, and forms correspondingly weaker H-bonds. The PH group is a weak proton donor, but will form PH···N H-bonds. However, there is a stronger interaction in which P can engage, in which the P atom, not the H, directly approaches the N electron donor to establish a direct P···N interaction. This approach is stabilized by the same sort of electron transfer from the N lone pair to the P-H σ* antibond that characterizes the PH···N H-bond.     

James D. Watson 88—the discovery of the double helix was an iconic event in structural chemistry

The ingenuity of James D. Watson and Francis Crick, the convergence of the advances in X-ray crystallography, the accumulated knowledge of structural chemistry, and the breakthroughs in chemical methods of analysis led to the discovery of the double helix structure of DNA. The discovery catapulted Watson to a career that helped DNA and the applications of the knowledge about its structure triumph in biomedical sciences. Watson’s eighty-eighth birthday is an occasion to have a look at his path to success, his personality, and assess his legacy.     

Cooper and Zinc Superoxide dismutase from Peking duck erythrocytes forms a supramolecular double－helix in the crystal

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Mechanism of intram olecular charge transfer in DNA helix as probed by the use of the fluorescent 2-aminopurine

~~Mechanism of intram olecular charge transfer in DNA helix as probed by the use of the fluorescent 2-aminopurine~~     

C-H···π interactions in the CHBrF2···HCCH weakly bound dimer

The microwave spectra of four isotopologues of the CHBrF(2)···HCCH weakly bound dimer have been measured in the 6-18 GHz region using chirped-pulse and Balle-Flygare Fourier-transform microwave spectroscopy. Spectra of (13)CH(79)BrF(2) and (13)CH(81)BrF(2) monomers have also been measured, and spectroscopic constants are reported. Measurement of spectra for the (79)Br and (81)Br isotopologues of CHBrF(2) complexed with both (12)C(2)H(2) and (13)C(2)H(2) have allowed the determination of a structure with C(s) symmetry for this complex. CHBrF(2) interacts with the triple bond of acetylene via a C-H···π contact (R(H···π) = 2.670(8) ?) with the Br atom lying in the ab plane, located 3.293(40) ? from a hydrogen atom of the HCCH molecule. The structure of CHBrF(2)···HCCH has been compared with recently studied related acetylene complexes, including a comparison with (and further structural analysis of) the CHClF(2)···HCCH complex.