Virtual bond probe to study ordered and random coil conformations of nucleic acids

Recognition of the stereochemical features inherent to a nucleotide, viz., the preferred trans character of the two C? O bonds and the approximate chemical and conformational symmetry, has facilitated the representation of a nucleotide in terms of two nearly equal blocks or two virtual bonds spanning the atoms P to C4' on the 5' side and C4' to P on the 3' side. The scheme, by virtue of its unique ability to account for the main sources of flexibility and to incorporate their interdependence, could be effectively applied to probe ordered, as well as random coil conformations of polynucleotide chains. Using this scheme, conformations of nucleotide, dinucleotides, helices, and yeast tRNA^Phe have been characterized by virtual bond parameters. The two blocks of nucleotide have also been described in terms of two approximate planes similar to peptides. Unperturbed end-to-end dimensions and persistence lengths of random coil polynucleotides have been computed by considering short-range as well as near-neighbor bond long-range correlations and are in excellent agreement with the experimentally determined values. A striking finding of these studies is the relevation that random coils comprise of a large proportion of stacked A-type helical segments in sharp contrast to earlier interpretations which invoked a high fraction of unstacked extended conformations.     

Conformational studies of poly(cis-5-ethyl-D-proline)

Two possible conformations for poly(cis-5-ethyl-D -proline) have been identified and characterized by using combinations of ¹H- and ¹³C-NMR, CD, and ORD spectroscopic techniques. Both forms have helical conformations similar to those of poly(L -proline) characterized by different amide bonds (cis and trans). However, the carbonyl group of the amide in poly(cis-5-ethyl-D -proline) form II (trans) seems to be closer to perpendicular orientation with respect to the helical axis than in poly(L -proline) form II. The pyrrolidine ring conformation of form I (cis) is probably β⁺γ^?-puckered, whereas for form II it is probably β⁺-puckered in nature. The side-chain ethyl groups prefer to adopt anti conformations to the C₅? H bond, or prefer to have χ = 180°, regardless which of the two forms poly(cis-5-ethyl-D -proline) may like to assume. The experimental results agree well with our previous theoretical conformational energy calculations.     

Crystalline poly(4‐methyl‐1‐pentene): Structure and solubility of gas molecules

Monte Carlo (MC) simulations have been used to study the crystal structure of isotactic poly(4‐methyl‐1‐pentene). Four different tetragonal packing models, each one containing two right‐handed and two left‐handed 7/2 helices, have been considered in an investigation of the up‐and‐down chain statistical disorder proposed on the basis of X‐ray data. Simulations have been performed with the isotropic united‐atom parameterization of the AMBER force field. The influence on the more stable packing models of the force‐field parameterization has been investigated with respect to the anisotropic united‐atom and all‐atom models. Results reveal that packing consisting of two upward and two downward helices arranged at random is more stable than packing with three or four helices with the same sense. Furthermore, the fiber period length for the 7/2 helix is predicted to be 0.56 Å larger than that experimentally determined. The microstructures generated from MC simulations have been employed to study the solubility of gas molecules (He, H₂, Ar, O₂, CH₄, and CO₂) with Widom's test‐particle insertion method. Special attention has been paid to the solubility of CH₄ and CO₂ because experimental data are available for these penetrants, the latter being described by both spherical and explicit models. The results are in good agreement with experimental measures only when a suitable model is used for the penetrant. The solubility of gas molecules in crystalline poly(4‐methyl‐1‐pentene) has been correlated with that measured for the crystal phases of other helical polymers. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2037–2049, 2002     

alpha and piDL helical states of alternating poly(gamma-benzyl D-L-glutamate) in solution.

As in solid state, strictly alternating poly(gamma-benzyl D-L-glutamate) in solution can adopt two different helical conformations. Besides the alpha helix, a second helical conformation is found at higher temperatures in dioxane and chloroform, the properties of which correspond to that of the piDL4 helix. As the molecules have a finite length a screw sense is favored for both helical forms thus giving rise to optical activity allowing the study of the transconformation by optical rotatory dispersion and circular dichroism besides infrared and dielectric measurements. Thus, as the temperature is raised the equilibria right-left handed alpha helices and alpha-piDL helical forms can be followed. The favored screw senses are determined by the number of interacting side chains for the alpha helix and by the number of hydrogen bonds which are formed in the piDL helical conformation. The side chain-side chain interactions in the alpha helix are experimentally shown to be attractive.     

Long‐range effects of chirality in aromatic poly(isocyanide)s

The preparation of optically active atropoisomeric polymers which present chiral backbones, thanks to induction during their synthesis from stereogenic centers, located far away from the skeleton is possible, thanks principally to semirigid conformations of the promesogenic spacers between them. The result is that chiral “information” can be passed as far as 21 Å from the asymmetric center to the carbon atom that forms the polymeric chain in poly(isocyanide)s. The sense of chiral induction in these conformationally rigid polymers parallels the helical sense of the cholesteric phases, as well as to the helical senses of chiral smectic C phases, induced by the monomers in nematic and smectic C phases, respectively. All these phenomena obey the odd–even rules proposed for chiral sense changes in these liquid crystalline phases. Noncovalent interactions play an important part in the induction process, in which steric arguments can be used to justify the inductions observed. The methodology can be used to prepare macromolecules, which display switching behavior upon thermal or electrochemical stimulus. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 3161–3174, 2006     

α‐Peptide–Oligourea Chimeras: Stabilization of Short α‐Helices by Non‐Peptide Helical Foldamers

Short α‐peptides with less than 10 residues generally display a low propensity to nucleate stable helical conformations. While various strategies to stabilize peptide helices have been previously reported, the ability of non‐peptide helical foldamers to stabilize α‐helices when fused to short α‐peptide segments has not been investigated. Towards this end, structural investigations into a series of chimeric oligomers obtained by joining aliphatic oligoureas to the C‐ or N‐termini of α‐peptides are described. All chimeras were found to be fully helical, with as few as 2 (or 3) urea units sufficient to propagate an α‐helical conformation in the fused peptide segment. The remarkable compatibility of α‐peptides with oligoureas described here, along with the simplicity of the approach, highlights the potential of interfacing natural and non‐peptide backbones as a means to further control the behavior of α‐peptides.     

Helical conformations of isotactic polyacetaldehyde and other isotactic polytrihaloacetaldehydes

Minimum potential energy helical conformations for a family of four isotactic polyacetaldehydes have been determined. Our results indicate that all of the polymers form irrational helices. Comparisons have been made with the reported structures for two of these stereoregular polymers based on earlier X-ray diffraction data. c-Axis values associated with the pitch of the helix for polyacetaldehyde and for polytrichloroacetaldehyde (polychloral) were experimentally measured to be 0.48 and 0.51 nm, respectively. Our calculated conformations afforded values for a helix pitch of 0.47 and 0.52 nm, respectively, which derive from a 3.9/1 helix for polyacetaldehyde and a 3.7/1 helix for polychloral. The structure for polytribromoacetaldehyde (polybromal) was predicted to be similar to that for polychloral. For polytrifluoroacetaldehyde (polyfluoral) and polyacetaldehyde, a number of helical conformations with similar energies were found. All of these conformations could be related to the polychloral helical structure. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 1855–1860, 1998     

Monte Carlo simulations on short single-stranded oligonucleotides. I. Application to RNA trimers

Monte Carlo (MC) structural simulation of short RNA sequences has been carried out by random variations of the nucleotide conformational angles (i.e., phosphodiester chain torsional angles and sugar pucker pseudorotational angles). All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker ring. In this article we present the simulated structures of RNA trimers—r(AAA) and r(AAG)—obtained at 11°C and 70°C. The influence of various initial conformations (selected as starting points in the MC simulations) on the equilibrium conformations has been discussed. The simulated conformational angles have been compared with those estimated by nuclear magnetic resonance (NMR) spectroscopy. For both of the oligonucleotides studied here, the most stable structures are helical conformations with stacked bases, at 11°C and 70°C. However, when the starting point is a stretched chain, it is found that r(AAA) adopts a reverse-stacked structure at low temperature (11°C), in which the A3 base is located between the A1 and A2 bases. Although the energies of these conformations (helical and reverse stacked) are very close to each other, the potential barrier between them is extremely high (close to 30 kcal/mol). This hinders the conformational transition from one structure to the other at a given temperature (and in the course of a same MC simulation). However, it is possible to simulate this structural transition by heating the reverse-stacked structure up to 500°C and cooling down progressively to 70°C and 11°C: Canonical helical structures have been obtained by this procedure. © 1994 by john Wiley & Sons, Inc.     

Rigid assembly and Monte Carlo models of stable and unstable chromatin structures: the effect of nucleosomal spacing

Coarse-grained models are used to assess the packing of the 30-nm chromatin fiber. First, rigid assembly models for nucleosomal repeats from 155 to 211 bp are built using the crystal structure of the mononucleosome and attached straight stretches of B-DNA. The resulting fiber conformations are analyzed for static clashes and classified into stable and unstable structures. The effect of flexibility and thermal fluctuations is then taken into account by conducting Monte Carlo simulations of chromatin fiber models. Here the DNA is approximated by a flexible polymer chain with Debye–Hückel electrostatics, the geometry of the linker DNA connecting the nucleosomes is based on a two-angle zigzag model, and nucleosomes are represented by flat ellipsoids interacting via an attractive Gay–Berne potential. Unstable fibers occur at a particular repeat length period of 10 bp. Also, the regions of densely compacted fibers repeat at intervals of 10 bp. Besides one- and two-start helical zigzag structures, we show evidence for possible three-start structures, which have not been reported in experiments yet. Finally, we show that a local opening of the linker DNA at the nucleosome core—as probably occurs upon histone acetylation—leads to more open and flexible structures.     

Analysis of stacking overlap in nucleic acid structures: algorithm and application

RNA contains different secondary structural motifs like pseudo-helices, hairpin loops, internal loops, etc. in addition to anti-parallel double helices and random coils. The secondary structures are mainly stabilized by base-pairing and stacking interactions between the planar aromatic bases. The hydrogen bonding strength and geometries of base pairs are characterized by six intra-base pair parameters. Similarly, stacking can be represented by six local doublet parameters. These dinucleotide step parameters can describe the quality of stacking between Watson–Crick base pairs very effectively. However, it is quite difficult to understand the stacking pattern for dinucleotides consisting of non canonical base pairs from these parameters. Stacking interaction is a manifestation of the interaction between two aromatic bases or base pairs and thus can be estimated best by the overlap area between the planar aromatic moieties. We have calculated base pair overlap between two consecutive base pairs as the buried van der Waals surface between them. In general, overlap values show normal distribution for the Watson–Crick base pairs in most double helices within a range from 45 to 50 Å² irrespective of base sequence. The dinucleotide steps with non-canonical base pairs also are seen to have high overlap value, although their twist and few other parameters are rather unusual. We have analyzed hairpin loops of different length, bulges within double helical structures and pseudo-continuous helices using our algorithm. The overlap area analyses indicate good stacking between few looped out bases especially in GNRA tetraloop, which was difficult to quantitatively characterise from analysis of the base pair or dinucleotide step parameters. This parameter is also seen to be capable to distinguish pseudo-continuous helices from kinked helix junctions.     

Crystal structure of double helical hexitol nucleic acids

A huge variety of chemically modified oligonucleotide derivatives has been synthesized for possible antisense applications. One such derivative, hexitol nucleic acid (HNA), is a DNA analogue containing the standard nucleoside bases, but with a phosphorylated 1',5'-anhydrohexitol backbone. Hexitol nucleic acids are some of the strongest hybridizing antisense compounds presently known, but HNA duplexes are even more stable. We present here the first high-resolution structure of a double helical nucleic acid with all sugars being hexitols. Although designed to have a restricted conformational flexibility, the hexitol oligomer h(GTGTACAC) is able to crystallize in two different double helical conformations. Both structures display a high x-displacement, normal Watson-Crick base pairing, similar base stacking patterns, and a very deep major groove together with a minor groove with increased hydrophobicity. One of the conformations displays a major groove which is wide enough to accommodate a second HNA double helix resulting in the formation of a double helix of HNA double helices. Both structures show most similarities with the A-type helical structure, the anhydrohexitol chair conformation thereby acting as a good mimic for the furanose C3'-endo conformation observed in RNA. As compared to the quasi-linear structure of homo-DNA, the axial position of the base in HNA allows efficient base stacking and hence double helix formation.     

Study of low-frequency molecular motions in polydimethylsiloxane polymers by neutron inelastic scattering

The intrachain and interchain vibrations below 900 cm^?1 of polydimethylsiloxane (PDMS) have been studied by slow neutron inelastic scattering. A composite motion observed at +25°C for the methyl groups corresponds to nearly free rotation about the threefold axis of symmetry together with a large-amplitude rotation of the entire methyl group. At ?123°C, rotation about the threefold axis evolves to a torsional oscillation. The large-amplitude rotation evolves to the skeletal vibrations of a helical conformation. Vestiges of the cooperative skeletal vibrations of the conformation at ?123°C persist into the 25°C spectrum. The results indicate the presence of interrupted helical conformations at 25°C, which result from thermal disordering of the low temperature helices. The effects of crosslinking, low molecular-weight oils, and silica filler on the freedom of the methyl group motions and on skeletal vibrations have been determined. The effects of different crosslinking agents and different relative amounts of filler and oil on both the macroscopic physical properties and the observed molecular motions of PDMS can also be interpreted in terms of an interrupted helix.     

Structure factor calculations of various DNA duplexes

Based upon a stereochemical guideline, both right- and left-handed duplexes were generated for A, B, and D forms of DNA using a mononucleotide as the repeat. Structure factor amplitudes were computed following two methods: (i) one employed an infinite helix as the motif and (ii) the other had an exact crystallographic repeat (e.g., 10 b.p. for B-DNA) as the motif. Both the procedures showed that DNA in either handedness for A, B, and D forms of DNA are consistent with the observed fiber data. This observation is attributed to the fact that fibre pattern (resolved only upto 3 Å) only gives the image of the gross structure of the molecule. Thus, when the gross structure is suitably fitted to match the observed pattern, it is immaterial as to what the precise stereochemistry of the repeating unit (fine structure) and handedness of a model are. Sequence specific helical conformations were obtained using dinucleotide as the repeating unit. Helices fell into two classes: (i) right-handed uniform (RU ) and (ii) left-handed zig-zag (LZ ) structures. A few aspects concerning the scattering profile of these helices are discussed.     

Raman spectra of extended-chain syndiotactic poly(vinyl chloride)

Raman spectra have been obtained for a typical poly(vinyl chloride) (PVC) of low crystallinity and for a highly crystalline sample of syndiotactic PVC obtained by irradiation of a urea-canal complex. Raman measurements have been made on the three different ordered chain structures possible for ordinary PVC. Extended and folded conformations for the syndiotactic structure and a helical structure for the isotactic molecule obey different selection rules and have different dichroic properties in the infrared and Raman spectra. The observed Raman spectrum is consistent with the model of the extended syndiotactic conformation for crystalline PVC. With the new Raman data some additional assignments can be made in the vibrational spectra of PVC.     

Computational prediction of kink properties of helices in membrane proteins

We have combined molecular dynamics simulations and fold identification procedures to investigate the structure of 696 kinked and 120 unkinked transmembrane (TM) helices in the PDBTM database. Our main aim of this study is to understand the formation of helical kinks by simulating their quasi-equilibrium heating processes, which might be relevant to the prediction of their structural features. The simulated structural features of these TM helices, including the position and the angle of helical kinks, were analyzed and compared with statistical data from PDBTM. From quasi-equilibrium heating processes of TM helices with four very different relaxation time constants, we found that these processes gave comparable predictions of the structural features of TM helices. Overall, 95 % of our best kink position predictions have an error of no more than two residues and 75 % of our best angle predictions have an error of less than 15°. Various structure assessments have been carried out to assess our predicted models of TM helices in PDBTM. Our results show that, in 696 predicted kinked helices, 70 % have a RMSD less than 2 Å, 71 % have a TM-score greater than 0.5, 69 % have a MaxSub score greater than 0.8, 60 % have a GDT-TS score greater than 85, and 58 % have a GDT-HA score greater than 70. For unkinked helices, our predicted models are also highly consistent with their crystal structure. These results provide strong supports for our assumption that kink formation of TM helices in quasi-equilibrium heating processes is relevant to predicting the structure of TM helices.     

Effect of sodium poly(styrene sulfonate) on thermoreversible gelation of gelatin

The effect of an added polyanion, sodium poly(styrene sulfonate) (NaPSS), on the thermoreversible gelation and remelting of gelatin gels has been investigated by polarimetry and rheology. The presence of NaPSS can either enhance or reduce collagenlike helix formation, depending on the polymer concentration relative to that of gelatin and the gelation temperature. At temperatures < 20°C, the helical content is reduced by increasing the amount of added NaPSS, demonstrating the disruption of helical structure of gelatin by the polyanion. Synchronous measurements of optical rotation and modulus at 25°C, in both gelation and remelting, indicate that the optical rotation at the gel point for the pure gelatin is lowered on addition of NaPSS. At low frequency, the storage modulus of gelatin is increased by the addition of a small amount of NaPSS relative to that of gelatin, but decreased with excess NaPSS. The mechanical properties of gelatin with and without NaPSS will be discussed in light of the competition between network junction formation by strands of triple helices among gelatin chains and temporary ionic crosslinking between gelatin and the polyanion. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 2287–2295, 1999     

Polypeptide helices in hybrid peptide sequences

A new class of polypeptide helices in hybrid sequences containing alpha-, beta-, and gamma-residues is described. The molecular conformations in crystals determined for the synthetic peptides Boc-Leu-Phe-Val-Aib-betaPhe-Leu-Phe-Val-OMe 1 (betaPhe: (S)-beta3-homophenylalanine) and Boc-Aib-Gpn-Aib-Gpn-OMe 2(Gpn: 1-(aminomethyl)cyclohexaneacetic acid) reveal expanded helical turns in the hybrid sequences (alpha alphabeta)n and (alphagamma)n. In 1, a repetitive helical structure composed of C14 hydrogen-bonded units is observed, whereas 2 provides an example of a repetitive C12 hydrogen-bonded structure. Using experimentally determined backbone torsion angles for the hydrogen-bonded units formed by hybrid sequences, we have generated energetically favorable hybrid helices. Conformational parameters are provided for C11, C12, C13, C14, and C15 helices in hybrid sequences.     

A novel type of optically active helical polymers: Synthesis and characterization of poly(N‐propargylureas)

This article presents two novel artificial helical polymers, substituted polyacetylenes with urea groups in side chains. Poly( 4 ) and poly( 5 ) can be obtained in high yields (≥97%) and with moderate molecular weights (11,000–14,000). Poly( 4 ) contains chiral centers in side chains, and poly( 5 ) is an achiral polymer. Both of the two polymers adopted helical structures under certain conditions. More interestingly, poly( 4 ) exhibited large specific optical rotations, resulting from the predominant one‐handed screw sense. The helical conformation in poly( 5 ) was stable against heat, while poly( 4 ) underwent conformational transition from helix to random coil upon increasing temperature from 0 to 55 °C. Solvents had considerable influence on the stability of the helical conformation in poly( 4 ). The screw sense adopted by the helices was also largely affected by the nature of the solvent. Poly( 4 ‐co‐ 5 )s formed helical conformation and showed large optical rotations, following the Sergeants and Soldiers rule. By comparing the present two polymers (with one ? N? H groups) with the three polymers previously reported (with two ? N? H groups in side chains), the nature of the hydrogen bonds formed between the neighboring urea groups played big roles in the formation of stable helical conformation. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4112–4121, 2008     

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 of polyisocyanide derived from phenylalanine and its temperature‐dependent helical conformation

Screw‐sense‐selective polymerization of the chiral isocyanide monomers derived from phenylalanine with NiCl₂ as a catalyst in methanol to yield helical‐conjugated polyisocyanide was investigated with respect to the thermal stability of its helical conformation. Poly(1‐tert‐butoxycarbonyl‐2‐phenylethyl isocyanide) (poly 1c ) took a stable helical conformer independent of the polymerization temperature. In poly(1‐ethoxycarbonyl‐2‐phenylethyl isocyanide) (poly 2c ), which had slightly smaller side groups, the helical conformation was thermally destabilized. The specific rotation and circular dichroism of poly 2c prepared at temperatures greater than 40 °C were considerably depressed in comparison with the values for poly 2c prepared at or below room temperature. Additionally, poly 2c prepared at low temperatures exhibited reversible temperature‐dependent specific rotation and circular dichroism, whereas poly 1c showed few changes. It is suggested that polyisocyanide derived from phenylalanine takes various helical conformers (i.e., from tightly to loosely coiled helices), the thermal stability of which depends on the size of the side group. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 40: 399–408, 2002