Changes In Torsion Angles Research Articles

Synthesis and Structural Characterization of 2′‐Fluoro‐α‐L‐RNA‐Modified Oligonucleotides

We describe the synthesis and binding properties of oligonucleotides that contain one or more 2'-fluoro-α-L-RNA thymine monomer(s). Incorporation of 2'-fluoro-α-L-RNA thymine into oligodeoxynucleotides decreased thermal binding stability slightly upon hybridization with complementary DNA and RNA with the smallest destabilization towards RNA. Thermodynamic data show that the duplex formation with 2'-fluoro-α-L-RNA nucleotides is enthalpically disfavored but entropically favored. 2'-Fluoro-α-L-RNA nucleotides exhibit very good base pairing specificity following Watson--Crick rules. The 2'-fluoro-α-L-RNA monomer was designed as a monocyclic mimic of the bicyclic α-L-LNA, and molecular modeling showed that this indeed is the case as the 2'-fluoro monomer adopts a C3'-endo/C2'-exo sugar pucker. Molecular modeling of modified duplexes show that the 2'-fluoro-α-L-RNA nucleotides partake in Watson--Crick base pairing and nucleobase stacking when incorporated in duplexes while the unnatural α-L-ribo configured geometry of the sugar is absorbed by changes in the sugar-phosphate backbone torsion angles. The duplex behavior of our new nucleotide follows that of α-L-LNA, by and large.

A general measure of conjugation in biphenyls and their radical cations

Changes in the amount of conjugation in the biphenyl system upon torsion have been investigated with quantum chemistry computations. For the unsubstituted biphenyl and its radical cation, the change in the energy for the first electronic transition as determined from time-dependent density functional theory, specifically TD-B3LYP, upon an imposed change in torsion angle appears to provide a good general measure of the delocalization of the π-electrons. Upon substitution, though, a relationship could not be established between the excitation energy and the twist across the C–C bond connecting the two phenyl rings. In contrast, the π-interaction energy, i.e., the π–π interaction across the central C–C bond, determined from a natural bond orbital analysis, provides a uniform description of conjugation in the electronically different systems, for an imposed twist as well as upon substitution. Substituent effects are found to be larger and more varied for the biphenyl radical cations. Of particular interest is the introduction of the oxidizable substituents OCH3(methoxyl) and SCH3(methylthio), as this leads to the smallest changes in torsion angle in the biphenyl unit upon removal of an electron from the molecule. The findings of this work could ultimately prove useful for the rational design of conductive polymer materials.

Theoretical study of hyaluronan oligosaccharides

The structure and energetics of hyaluronan oligomers from di- to decasaccharides have been studied by density functional theory calculations at the B3LYP/6-31G** level. The study covered selected conformers of the sodium salt, anionic disaccharides, and neutral acids in the isolated state and in aqueous solution using the PCM model approach. We investigated the structural changes of the hyaluronan chain when the Na+ ion is removed or replaced by proton. These processes result in some characteristic changes in the glycosidic torsional angles and hydrogen bonding interactions. We evaluated the folding for the hyaluronan chains and obtained values between 2.2 and 3.2, somewhat smaller than reported for the crystals. We found a contraction of the hyaluronan chains upon enlargement in most derivatives attributed partly to the helical character of hyaluronan. The energy consequences of the enlargement have been modeled by isodesmic reactions. The enlargement processes proved to be exothermal and the energies consistent within the gradual enlargement.

Solution Structure of the IIAChitobiose-IIBChitobiose Complex of the N,N′-Diacetylchitobiose Branch of the Escherichia coli Phosphotransferase System

The solution structure of the IIA-IIB complex of the N,N'-diacetylchitobiose (Chb) transporter of the Escherichia coli phosphotransferase system has been solved by NMR. The active site His-89 of IIA(Chb) was mutated to Glu to mimic the phosphorylated state and the active site Cys-10 of IIB(Chb) was substituted by serine to prevent intermolecular disulfide bond formation. Binding is weak with a K(D) of approximately 1.3 mm. The two complementary interaction surfaces are largely hydrophobic, with the protruding active site loop (residues 9-16) of IIB(Chb) buried deep within the active site cleft formed at the interface of two adjacent subunits of the IIA(Chb) trimer. The central hydrophobic portion of the interface is surrounded by a ring of polar and charged residues that provide a relatively small number of electrostatic intermolecular interactions that serve to correctly align the two proteins. The conformation of the active site loop in unphosphorylated IIB(Chb) is inconsistent with the formation of a phosphoryl transition state intermediate because of steric hindrance, especially from the methyl group of Ala-12 of IIB(Chb). Phosphorylation of IIB(Chb) is accompanied by a conformational change within the active site loop such that its path from residues 11-13 follows a mirror-like image relative to that in the unphosphorylated state. This involves a transition of the phi/psi angles of Gly-13 from the right to left alpha-helical region, as well as smaller changes in the backbone torsion angles of Ala-12 and Met-14. The resulting active site conformation is fully compatible with the formation of the His-89-P-Cys-10 phosphoryl transition state without necessitating any change in relative translation or orientation of the two proteins within the complex.

Molecular Adaptation in RNA Complexes

In this issue, Batey and colleagues show that the purine riboswitch is able to bind purine analogs by exploiting various strategies, including lateral shifts of the bases and, most importantly, changes in ligand tautomeric form.

Hydrophobic Dimerization and Thermal Dissociation of Perylenediimide-Linked DNA Hairpins

The structure and properties of hairpin-forming bis(oligonucleotide) conjugates possessing perylenediimide (PDI) chromophores as hairpin linkers have been investigated using a combination of spectroscopic and computational methods. These conjugates exist predominantly as monomer hairpins at room temperature in the absence of added salt and as head-to-head hairpin dimers in the presence of >50 mM NaCl. The hairpin dimer structure is consistent with the results of small-angle X-ray scattering in aqueous solution and molecular dynamics simulation. The structure of the nonconjugated PDI dimer in water is investigated using potential of mean force calculations. The salt dependence is attributed to increased cation condensation in the hairpin dimer vs monomer. Upon heating at low salt concentrations, the hairpin dimer undergoes sequential dissociation to form the monomer hairpin followed by conversion to a random coil structure; whereas at high salt concentrations both dissociation processes occur over the same temperature range. The monomer and dimer hairpins have distinct spectroscopic properties both in the ground state and excited singlet state. The UV and CD spectra provide evidence for electronic interaction between PDI and the adjacent base pair. Low fluorescence quantum yields are observed for both the monomer and dimer. The transient absorption spectrum of the dimer undergoes time-dependent spectral changes attributed to a change in the PDI-PDI torsional angle from ca. 20 degrees in the Franck-Condon singlet state to ca. 0 degrees in the relaxed singlet state, a process which occurs within ca. 40 ps.

The structural basis for peptide selection by the transport receptor OppA

Oligopeptide-binding protein A (OppA) from Lactococcus lactis binds peptides of an exceptionally wide range of lengths (4-35 residues), with no apparent sequence preference. Here, we present the crystal structures of OppA in the open- and closed-liganded conformations. The structures directly explain the protein's phenomenal promiscuity. A huge cavity allows binding of very long peptides, and a lack of constraints for the position of the N and C termini of the ligand is compatible with binding of peptides with varying lengths. Unexpectedly, the peptide's amino-acid composition (but not the exact sequence) appears to have a function in selection, with a preference for proline-rich peptides containing at least one isoleucine. These properties can be related to the physiology of the organism: L. lactis is auxotrophic for branched chain amino acids and favours proline-rich caseins as a source of amino acids. We propose a new mechanism for peptide selection based on amino-acid composition rather than sequence.

Electronic Properties and Conformation Analysis of Phytochromobilins, Chromophore in Phytochrome

Quantum-chemical investigation on the conformation analysis and electronic properties of phytochromobilins (PCBs), an open chain tetrapyrrole chromophore of phytochrome are performed. The PCB chromophore have two stable forms, which occur photoisomerization by visible light absorption. Structures for two stable forms, Pr and Pfr isomers were fully optimized by using semiempirical AM1, PM3 methods, ab initio HF/3-21G(d), and B3LYP/6-31G(d) methods. The potential energy curves with respect to the change of single torsion angle are obtained by using semiempirical methods, ab initio HF, and DFT calculations. It is shown that the conformations of the isomers are compromised between the steric repulsion interaction and the degree of the conjugation. Electronic properties of the molecules were obtained by applying the optimized structures and geometries to the Zindo/S method. Absorption wavelengths are predicted by Zindo/S analysis. The wavelengths which are calculated from optimized geometries by HF/3-21G(d) and B3LYP/6-31G(d) is reported. The absorption wavelength on the optimized geometries by B3LYP/6-31G(d) is much longer than that by HF/ 3-21G(d) level. The absorption wavelengths of Pfr form are longer than that of corresponding Pr form in the same torsion angle because of conjugation length difference. The absorption wavelengths of isomers with perpendicular linkage are shorter than those of planar linkage.

Effect of Hyperconjugation on Ionization Energies of Hydroxyalkyl Radicals

On the basis of electronic structure calculations and molecular orbital analysis, we offer a physical explanation of the observed large decrease (0.9 eV) in ionization energies (IE) in going from hydroxymethyl to hydroxyethyl radical. The effect is attributed to hyperconjugative interactions between the sigma CH orbitals of the methyl group in hydroxyethyl, the singly occupied p orbital of carbon, and the lone pair p orbital of oxygen. Analyses of vertical and adiabatic IEs and hyperconjugation energies computed by the natural bond orbital (NBO) procedure reveal that the decrease is due to the destabilization of the singly occupied molecular orbital in hydroxyethyl radical as well as structural relaxation of the cation maximizing the hyperconjugative interactions. The stabilization is achieved due to the contraction of the CO and CC bonds, whereas large changes in torsional angles bear little effect on the total hyperconjugation energies and, consequently, IEs.

Changes in the Isotropic Shielding of the17O Nucleus upon Torsion in Terminal Oxygen Systems: A Computational Study on Their Origin

We are presenting a computational study on the isotropic shielding, charge, and orbital contributions to the shielding of oxygen in benzaldehydes (Ar-CHO), nitrobenzenes (Ar-NO2), phenyl isocyanates (Ar-NCO), anilides (Ar-NHCOCH3), and N-sulfinylamines (Ar-NSO). In particular, changes upon ortho substitution of the aromatic ring and upon torsion of the unsubstituted parent molecules are examined. The experimentally observed changes in (17)O chemical shift, be they upfield or downfield, upon substitution by ortho-alkyl groups are reproduced well by the calculations. Relaxed torsional scans of the parent systems reveal that (a) charges change as expected from resonance arguments and (b) changes in isotropic shielding are monotonic and in line with changes upon substitution, with N-sulfinylaniline as an exception. In general, the changes in isotropic shieldings are explained in terms of changes in molecular orbitals, their energies, and relative alignments, whose mixing is magnetically active. Thus, for example, the observed deshielding of (17)O upon methyl substitution and upon torsion of benzaldehyde is mainly caused by a contribution from the pi-type oxygen lone pair, yet how these contributions change is fundamentally different. As a consequence, the experimentally observed downfield shift upon methyl substitution cannot be interpreted to imply a change in torsion angle between the phenyl ring and the aldehyde group. For N-sulfinylaniline, the consecutive downfield shifts upon methyl and tert-butyl substitution and the associated changes in torsion angle are in contrast to the 45 degrees maximum in isotropic shielding that is determined from a relaxed torsional scan.

A modified self-consistent computational model for an electrostrictive graft elastomer

An electrostrictive graft elastomer, as recently developed by NASA, is a type ofelectro-active polymer. In this paper, a 2D computational model with a self-consistentboundary is developed. Firstly, three-dimensional deformations, induced by both bendingangle and dihedral torsional angle changes, are projected onto a two-dimensional plane.Using both theoretical and numerical analyses, the projected 2D equilibrium bending angleis shown to have the same value as the 3D equilibrium bending angle. The 2D equivalentbending stiffness is derived using a series model based upon the fact that both bending anddihedral torsion produce a configurational change. Equivalent stiffness is justifiedby polymer chain end-to-end distance characteristics. Secondly, a self-consistentscheme is developed to eliminate the boundary effect. Eight images of the unitcell are created peripherally, with the original unit cell in the center. Thus theboundary can only affect the rotation of the eight images, not the central unit cell. Acomputational model is employed to determine the electromechanical properties of theelectrostrictive graft elastomer. Relations between electric field induced strain andelectric field strength are calculated. The effect of molecular scale factors, suchas free volume fraction, graft weight percentage and graft orientation, are alsodiscussed.

Theoretical study of 2,5-diphenyl-1,4-distyrylbenzene (A model compound of PPV): A comparison of the electronic structure and photophysical properties of cis- and trans-isomers

2,5-Diphenyl-1,4-distyrylbenzene (DPDSB), a model compound of PPV, have been synthesized with two isomers: cis- and trans-DPDSB in our lab. We have found three distinguishing features of photophysical properties between these two isomers. To explain these three special spectral behaviors, the quantum-chemical computations were performed to investigate the ground-state and excited-state molecular geometries, electronic structure, absorption and emission properties, potential–energy curve of the ground-state and excited-state, and so on. According to our calculated results, the nature causing above distinguishing photophysical properties is larger configuration displacement of cis-DPDSB than trans-DPDSB from the ground-state to the excited-state, especially for the changes in torsion angle along vinyl double bonds in cis-DPDSB.

Structurally-tolerant self-assembly of zinc pyridyl porphyrins

Zinc porphyrins equipped with pyridine ligands form macrocyclic assemblies in organic solvents. The assemblies have been characterised by 1H NMR, UV-visible spectroscopy, X-ray crystallography and vapour pressure osmometry. The self-assembly properties of six isomeric porphyrins are relatively insensitive to the geometry of the porphyrin monomer. Changes in the internal torsion angles allow all of the porphyrins to form macrocyclic dimers but with differences in the relative orientations of the porphyrin units. The associated strain reduces the effective molarities from the value of 6 M reported previously for an ‘ideal’ monomer to between 0.07 and 2 M leading to dimerisation constants in the 105–106 M−1 range. Only one isomer has a geometry that makes dimerisation impossible without severe distortion, and this compound self-assembles to give a tetrameric macrocycle at millimolar concentrations.

Structural Basis of Glyphosate Tolerance Resulting from Mutations of Pro101 in Escherichia coli 5-Enolpyruvylshikimate-3-phosphate Synthase

Glyphosate, the world's most used herbicide, is a massive success because it enables efficient weed control with minimal animal and environmental toxicity. The molecular target of glyphosate is 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which catalyzes the sixth step of the shikimate pathway in plants and microorganisms. Glyphosate-tolerant variants of EPSPS constitute the basis of genetically engineered herbicide-tolerant crops. A single-site mutation of Pro(101) in EPSPS (numbering according to the enzyme from Escherichia coli) has been implicated in glyphosate-resistant weeds, but this residue is not directly involved in glyphosate binding, and the basis for this phenomenon has remained unclear in the absence of further kinetic and structural characterization. To probe the effects of mutations at this site, E. coli EPSPS enzymes were produced with glycine, alanine, serine, or leucine substituted for Pro(101). These mutant enzymes were analyzed by steady-state kinetics, and the crystal structures of the substrate binary and substrate.glyphosate ternary complexes of P101S and P101L EPSPS were determined to between 1.5- and 1.6-A resolution. It appears that residues smaller than leucine may be substituted for Pro(101) without decreasing catalytic efficiency. Any mutation at this site results in a structural change in the glyphosate-binding site, shifting Thr(97) and Gly(96) toward the inhibitor molecule. We conclude that the decreased inhibitory potency observed for glyphosate is a result of these mutation-induced long-range structural changes. The implications of our findings concerning the development and spread of glyphosate-resistant weeds are discussed.

A Structural Hypothesis for the Transition between Bent and Extended Conformations of the Leukocyte β2 Integrins

Integrins mediate cell adhesion in response to activation signals that trigger conformational changes within their ectodomain. It is thought that a compact bent conformation of the molecule represents its physiological low affinity state and extended conformations its active state. We have determined the structure of two integrin fragments of the beta2 subunit. The first structure, consisting of the plexin-semaphorin-integrin domain, hybrid, integrin-epidermal growth factor 1 (I-EGF1), and I-EGF2 domains (PHE2), showed an L-shaped conformation with the bend located between the I-EGF1 and I-EGF2 domains. The second structure, which includes, in addition, the I-EGF3 domain, showed an extended conformation. The major reorientation of I-EGF2 with respect to the other domains in the two structures is accompanied by a change of torsion angle of the disulfide bond between Cys(461)-Cys(492) by 180 degrees and the conversion of a short alpha-helix (residues Ser(468)-Cys(475)) into a flexible coil. Based on the PHE2 structure, we introduced a disulfide bond between the plexin-semaphorin-integrin domain and I-EGF2 domains in the beta2 subunit. The resultant alphaLbeta2 integrin (leukocyte function-associated antigen-1) variant was locked in a bent state and could not be detected with the monoclonal antibody KIM127 in Mg(2+)/EGTA. However, it retained the binding activity to ICAM-1. These results provide a structural hypothesis for our understanding of the transition between the resting and active states of leukocyte function-associated antigen-1.

Conformational changes of glucose/galactose‐binding protein illuminated by open, unliganded, and ultra‐high‐resolution ligand‐bound structures

D-Glucose/D-Galactose-binding protein (GGBP) mediates chemotaxis toward and active transport of glucose and galactose in a number of bacterial species. GGBP, like other periplasmic binding proteins, can exist in open (ligand-free) and closed (ligand-bound) states. We report a 0.92 angstroms resolution structure of GGBP from Escherichia coli in the glucose-bound state and the first structure of an open, unbound form of GGBP (at 1.55 angstroms resolution). These structures vary in the angle between the two structural domains; the observed difference of 31 degrees arises from torsion angle changes in a three-segment hinge. A comparison with the closely related periplasmic receptors, ribose- and allose-binding proteins, shows that the GGBP hinge residue positions that undergo the largest conformational changes are different. Furthermore, the high-quality data collected for the atomic resolution glucose-bound structure allow for the refinement of specific hydrogen atom positions, the assignment of alternate side chain conformations, the first description of CO(2) trapped after radiation-induced decarboxylation, and insight into the role of the exo-anomeric effect in sugar binding. Together, these structures provide insight into how the hinge-bending movement of GGBP facilitates ligand binding, transport, and signaling.

Local motions in a benchmark of allosteric proteins

Allosteric proteins have been studied extensively in the last 40 years, but so far, no systematic analysis of conformational changes between allosteric structures has been carried out. Here, we compile a set of 51 pairs of known inactive and active allosteric protein structures from the Protein Data Bank. We calculate local conformational differences between the two structures of each protein using simple metrics, such as backbone and side-chain Cartesian displacement, and torsion angle change and rearrangement in residue-residue contacts. Thresholds for each metric arise from distributions of motions in two control sets of pairs of protein structures in the same biochemical state. Statistical analysis of motions in allosteric proteins quantifies the magnitude of allosteric effects and reveals simple structural principles about allostery. For example, allosteric proteins exhibit substantial conformational changes comprising about 20% of the residues. In addition, motions in allosteric proteins show strong bias toward weakly constrained regions such as loops and the protein surface. Correlation functions show that motions communicate through protein structures over distances averaging 10-20 residues in sequence space and 10-20 A in Cartesian space. Comparison of motions in the allosteric set and a set of 21 nonallosteric ligand-binding proteins shows that nonallosteric proteins also exhibit bias of motion toward weakly constrained regions and local correlation of motion. However, allosteric proteins exhibit twice as much percent motion on average as nonallosteric proteins with ligand-induced motion. These observations may guide efforts to design flexibility and allostery into proteins.

Formation of the Early Photoproduct Lumi-R of Cyanobacterial Phytochrome Cph1 Observed by Ultrafast Mid-Infrared Spectroscopy

The photoreactions of the Pr ground state of cyanobacterial phytochrome Cph1 from Synechocystis PCC 6803 have been investigated by picosecond time-resolved mid-infrared spectroscopy at ambient temperature. With femtosecond excitation of the Pr state at 640 nm, the photoisomerized Lumi-R product state is generated with kinetics and associated difference spectra indicative of vibrational cooling with tau(1) = 3 ps time constant and excited state decay with tau(1) = 3 ps, tau(2) = 14 ps, and tau(3) = 134 ps time constants. The Lumi-R state is characterized by downshifted absorption of three C=C modes assigned to C(15)=C(16), C(4)=C(6), and a delocalized C=C mode, in addition to the downshifted C(19)=O mode. The Lumi-R minus Pr difference spectrum is indicative of global restructuring of the chromophore on the ultrafast timescale, which is discussed in light of C(15) Z/E photoisomerization in addition to changes near C(5), which could be low bond order torsional angle changes.

High-pressure polymorphism in L-cysteine: the crystal structures of L-cysteine-III and L-cysteine-IV

The crystal structure of the orthorhombic phase of L-cysteine (hereafter L-cysteine-I) consists of chains of molecules linked via NH...O hydrogen bonds. The chains are linked into a layer by other NH...O hydrogen bonds, forming R4(4)(16) ring motifs. The layers are linked by further NH...O and disordered SH...S/SH...O interactions. The main effects of compression to 1.8 GPa are to contract voids in the middle of the R4(4)(16) rings and to reduce S...S distances from 3.8457 (10) to 3.450 (4) angstroms. The latter is at the lower limit for S...S distances and we suggest that strain about the S atom is responsible for the formation of a new phase of L-cysteine, L-cysteine-III, above 1.8 GPa. The phase transition is accompanied by a change in the NCCS torsion angle from ca 60 to ca -60 degrees and small positional displacements, but with no major changes in the orientations of the molecules. The structure of L-cysteine-III contains similar R-type ring motifs to L-cysteine-I, but there are no S...S contacts within 3.6 angstroms. L-Cysteine-III was found to be stable to at least 4.2 GPa. On decompression to 1.7 GPa, another single-crystal to single-crystal phase transition formed another previously uncharacterized phase, L-cysteine-IV. This phase is not observed on increasing pressure. The structure consists of two crystallographically independent cysteine molecules in the same conformations as those found in L-cysteine-I and L-cysteine-III. The structure separates into zones with are alternately phase I-like and phase III-like. L-Cysteine-IV can therefore be thought of as an unusual example of an intermediate phase. Further decompression to ambient pressure generates L-cysteine-I.

Additive effects in the modeling of oligosaccharides with mm3 at high dielectric constants: an approach to the ‘multiple minimum problem’

The production of an adiabatic map for a di- or trisaccharide requires the generation of many relaxed maps, ideally 59,049 for a disaccharide or 4,782,969 for a trisaccharide composed by hexose residues, due to a combination of exocyclic angle torsions. As the production of this amount of maps is usually ruled out for time considerations, different approaches were exploited. When working at low dielectric constants, starting points originated in cooperative hydrogen bonds through the rings are usually sufficient to produce an adiabatic map, but at higher dielectric constants those circuits are meaningless, and many low-energy conformers appear in each energy well. Herein, different conformations of four disaccharides (β-4-linked mannobiose, and three galactobioses, linked α-(1→3), α-(1→4), and β-(1→4)) and one trisaccharide (β-4-linked mannotriose) were minimized using mm3 at ε = 80, and the difference in energy produced by changes in torsional angles was recorded. A remarkable additive effect was found to occur when the exocyclics were gathered in groupings of two or three neighboring angles. Thus, in most cases, each grouping can be studied separately, and the minimum energy conformers can be predicted without the need of resorting to thousands of calculations. In some cases where two protons of different groups show steric interactions in some specific conformations, small deviations of the additivity were encountered. Anyway, a complex system with many variables can be transformed in one with many fewer variables, thus simplifying further studies. An attempt to calculate the same effect at ε = 3 shows that hydrogen bonding and electrostatic interactions make impossible to find those additive effects, thus precluding its utilization at such low dielectric constants.