Geometry of kinked protein helices from NMR data

Residual dipolar couplings between spin-1/2 and quadrupolar nuclei are often observed and exploited in the magic-angle spinning (MAS) NMR spectra of spin-1/2 nuclei. These orientation-dependent splittings contain information on the dipolar interaction, which can be translated into structural information. The same type of splittings may also be observed for pairs of quadrupolar nuclei, although information is often difficult to extract from the quadrupolar-broadened lineshapes. Here, the complete theory for describing the dipolar coupling between two quadrupolar nuclei in the frequency domain by Hamiltonian diagonalization is given. The theory is developed under MAS and double-rotation (DOR) conditions, and is valid for any spin quantum numbers, quadrupolar coupling constants, asymmetry parameters, and tensor orientations at both nuclei. All terms in the dipolar Hamiltonian become partially secular and contribute to the NMR spectrum. The theory is validated using experimental 11B and 35/37Cl NMR experiments carried out on powdered B-chlorocatecholborane, where both MAS and DOR are used to help separate effects of the quadrupolar interaction from those of the dipolar interaction. It is shown that the lineshapes are sensitive to the quadrupolar coupling constant of both nuclei and to the J coupling (including its sign). From these experiments, the dipolar coupling constant for a heteronuclear spin pair of quadrupolar nuclei may be obtained as well as the sign of the quadrupolar coupling constant of the perturbing nucleus; these are two parameters that are difficult to obtain experimentally otherwise.     

Cu(Ⅰ) and Cu (Ⅱ) helical complexes formed with oligobipyridine ligand

A new asymmetric oligobipyridine ligand, 1-(5'-methyl-2, 2'-bipyridin-5-yl)-2-(6'-methyl-2, 2'-bipyridin-6-yl)ethane (L), in which the bipyridine units are bridged by CH_2CH_2 at 5, 6'-position has been synthesized. The ligand L reacts with Cu(Ⅰ) and Cu(Ⅱ) ions giving double-stranded helical complexes [Cu_2~ⅠL_2] (ClO_4)_2·Et_2O (1) and [Cu_2~ⅡL_2 (OH) (H_2O)][ClO_4]_3(2), respectively. Complexes 1 and 2 were characterized by X-ray diffraction analyses, ES-MS, ESR and cyclic voltammetry, etc. Differing from the oligobipyridine ligands bridged by CH_2CH_2 at 6,6'-or 5,5'-position, the ligand L not only forms a double-stranded helicate with Cu(Ⅰ) ion, but also gives a double-stranded helicate with Cu(Ⅱ) ion. The results show that the linkage mode of the spacer group to the bipyridine units exerts a great impact on the formation of helix.     

Polymerization of optically active 2-fluorophenyl-4-fluorophenyl-2-pyridylmethyl methacrylate with anionic and radical initiators: Stereospecificity and helix-sense selection

Almost optically pure (+)- and (−)-2-fluorophenyl-4-fluorophenyl-2-pyridylmethyl methacrylate (2F4F2PyMA) monomers were obtained by HPLC resolution of the racemic monomer and polymerized with the use of anionic and free-radical initiators. Helix-sense selectivity during the polymerization seemed to be governed mainly by the chirality of the monomer itself, and the polymers obtained by using the complex of N,N′-diphenylethylenediamine monolithium amide with (S)-(+)-1-(2-pyrrolidinylmethyl)pyrrolidine (PMP) in toluene at −78°C appeared to possess single-handed helical conformation (+)-poly[(−)-2F4F2PyMA], [α]₃₆₅ + 1510°; (−)-poly[(+)-2F4F2PyMA], [α]₃₆₅ − 1610°]. The single-handed helical (+)-poly[(−)-2F4F2PyMA] and (−)-poly[(+)-2F4F2PyMA] obtained with the PMP complex exhibited better chiral recognition ability toward trans-stilbene oxide compared with the single-handed helical poly(rac-2F4F2PyMA) prepared previously. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 2645–2648, 1999     

Constraint dynamics algorithm for simulation of semiflexible macromolecules

Semiflexible models are often used to study macromolecules containing stable structural elements. Based on rigid body dynamics, we developed a rigid fragment constraint dynamics algorithm for the simulation of semiflexible macromolecules. Stable structural elements are treated as rigid fragments. Rigid fragment constraints, defined as combinations of distance constraints and position constraints, are introduced to limit internal molecular motion to the required mode. The constraint forces are solved separately for each rigid fragment constraint and iteratively until all constraint conditions are satisfied within a given tolerance at each time step, as is done for the bond length constraint in the SHAKE algorithm. The orientation of a rigid fragment is represented by the quaternion parameters, and both translation and rotation are solved by the leap-frog formulation. We tested the algorithm with molecular dynamics simulations of a series of peptides and a small protein. The computation cost for the constraints is roughly proportional to the size of the molecule. In the microcanonical ensemble simulation of polyvalines, the total energy was conserved satisfactorily with time steps as large as 20 fs. A helix folding simulation of a synthetic peptide was carried out to show the efficiency of the algorithm in a conformational search. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1555–1566, 1998     

The new science of protein mimetics

New chemistries have been developed for de novo protein design. Protein mimetics of different structural and functional properties such as synthetic peptide ligases and Dn symmetrical helical bundles have been reported. The Template-Assembled Synthetic Protein (TASP) method (as well as the ßMolecular Kit' approach) has also been utilized to prepare protein-like molecules. Here we report the synthesis of single chain, scaffold (TRIS)- and dendrimer-assembled collagen mimetics composed of the Gly-Nleu-Pro sequence where Nleu denotes N-isobutyl glycine. From the CD spectra and the thermal denaturation studies it can be seen that the collagen mimetics prepared form stable triple helices except the single chain structure. Furthermore, the 162-residue collagen mimetic dendrimer exhibits enhanced triple helical stability compared to the equivalent scaffold-terminated structure by an increase in the melting temperature in both H₂O and 2:1 ethylene glycol/H₂O (4°C and 12°C respectively). The concentration dependence for the melting transition of the collagen mimetic dendrimer was measured from which it was determined that the stabilization effect arises from the intramolecular clustering of the triple helical arrays about the core structure. This ensemble excludes solvent from the interior portion of the array which stabilizes the triple helix cluster.     

Synthesis and Characterization of Helix‐Coil Diblock Copolymers with Controlled Supramolecular Architectures in Aqueous Solution

Summary: A series of helix‐coil diblock copolymers based on poly(ethylene oxide) and optically active helical poly{(+)‐2,5‐bis[4′‐((S)‐2‐methylbutoxy)phenyl]styrene} (PMBPS) were synthesized via atom transfer radical polymerization (ATRP). The synthetic methodology permitted straightforward preparation of the diblock copolymers with relatively low polydispersities and a broad range of compositions and molecular weights. Depending on the composing block length and the initial concentration, the copolymers self‐assembled into different supramolecular structures in aqueous solution, including spherical micelles, vesicles, multilamellar vesicles, large compound vesicles, and tubules.

Schematic representation of the synthesis of PEO‐b‐PMBPS block copolymers and their aggregation in aqueous solution.     

Macromolecular helicity inversion of poly(phenylacetylene) derivatives induced by various external stimuli

Unique macromolecular helicity inversion of stereoregular, optically active poly(phenylacetylene) derivatives induced by external achiral and chiral stimuli is briefly reviewed. Stereoregular, cis-transoidal poly(phenylacetylene)s bearing an optically active substituent, such as (1R,2S)-norephedrine (poly- 1 ) and β-cyclodextrin residues (poly- 2 ), show an induced circular dichroism (ICD) in the UV-visible region of the polymer backbone in solution due to a predominantly one-handed helical conformation of the polymers. However, poly- 1 undergoes a helix-helix transition upon complexation with chiral acids having an R configuration, and the complexes exhibit a dramatic change in the ICD of poly- 1 . Poly- 2 also shows the inversion of macromolecular helicity responding to molecular and chiral recognition events that occurred at the remote cyclodextrin residues from the polymer backbone; the helicity inversion is accompanied by a visible color change. A similar helix-helix transition of poly((R)- or (S)-(4-((1-(1-naphthyl)ethyl)carbamoyl)phenyl)acetylene) is also briefly described.