Circular dichroism calculations for polyinosinic acid in proposed multi-stranded geometries.

Circular dichroism spectra have been calculated for multi-stranded polyinosinic acid using three different right-handed structures proposed from X-ray diffraction studies. Agreement between calculated spectra and spectra measured at high salt concentration is best for a four strand structure in which the bases are tilted with respect to the helix axis, as proposed by Arnott et al. (1974). For structures in which the bases are perpendicular to the helix axis, the characteristic negative circular dichoroism of polyinosinic acid at long wavelength no longer appears in the calculated spectra. It is clear that a negative circular dichroism at long wavelength does not indicate a left-handed polynucleotide helix.     

Methylation of cytosine in the 5-position alters the structural and energetic properties of the supercoil-induced Z-helix and of B-Z junctions

The structural and energetic consequences of cytosine methylation in the 5-position on the supercoil-dependent B-Z equilibrium in alternating dC-dG sequences cloned into recombinant plasmids were investigated. The helical parameters determined with the band shift method for right-handed [10.7 base pairs (bp)/turn] and left-handed (12.8 bp/turn) 5MedC-dG inserts were different from the helical repeat values for unmethylated dC-dG inserts (10.5 bp/turn in the right-handed and 11.5 bp/turn in the left-handed form). We analyzed the thermodynamic parameters delta GBZ (free energy difference per base pair between right-handed and left-handed helix structure), delta Gjx (free energy for formation of one B-Z junction), and b (helix unwinding at a junction region) for varying lengths of dC-dG inserts by two-dimensional gel electrophoresis and application of a statistical mechanics model. A comparison of plasmids fully methylated in vitro with HhaI methylase and their unmethylated counterparts revealed that delta Gjx is not significantly changed by cytosine methylation. However, this base modification results in an approximate 3-fold decrease of delta GBZ and an approximate 2-fold decrease of the unwinding b at B-Z junction regions. Analysis of a pair of related plasmids, each containing two dC-dG blocks, revealed qualitatively different transition behaviors. When the two dC-dG blocks were separated by 95 bp of a mixed sequence, they underwent independent B to Z transitions with separate nucleation events and junction formations. When the two blocks were separated by only a 4 bp GATC sequence, only one nucleation event was necessary, and the Z-helix spread across the nonalternating GATC region.(ABSTRACT TRUNCATED AT 250 WORDS)     

2H nuclear magnetic resonance of the gramicidin A backbone in a phospholipid bilayer.

Solid-state 2H NMR spectroscopy has been employed to study the channel conformation of gramicidin A (GA) in unoriented 1,2-dimyristoyl-sn-glycerol-3-phosphocholine (DMPC) multilayers. Quadrupolar echo spectra were obtained at 44 degrees C and 53 degrees C, from gramicidin A labels in which the proton attached to the alpha carbon of residue 3, 4, 5, 10, 12, or 14 was replaced with deuterium. Because of the nearly axially symmetric electric field gradient tensor, the quadrupolar splittings obtained from an unoriented multilamellar dispersion of DMPC and singly labeled GA directly yield unambiguous orientational constraints on the C-2H bonds. The average of the ratios of the quadrupolar splittings of the left-handed amino acids to those of the right-handed amino acids, (delta vQL/delta vQD), is expected to be 0.97 +/- 0.04 for a relaxed right-handed beta 6.3LD helix, while a ratio of 0.904 +/- 0.003 is expected for a left-handed beta LD6.3 helix. Since we have experimentally determined this ratio to be 1.01 +/- 0.04, we conclude that that the helix sense of the channel conformation of GA is right-handed. Assuming that the dominant motions are fast axial diffusion of the gramicidin molecule and reorientation of the diffusion axis with respect to the local bilayer normal, then the theoretical splittings may all be scaled down by a constant motional narrowing factor. In this case, a relaxed right-handed beta LD6.3 helix, whose axis of motional averaging is roughly along the presumed helix axis, gave the best fit to experimental results. The reasonably uniform correspondence between the splittings predicted by the relaxed right-handed beta LD6.3 helix and the observed splittings, for labels from both the inner and outer turn of GA, did not reflect a peptide backbone flexibility gradient, since an outer turn (i.e., the turn of the helix closest to the interface with water) with greater flexibility would show additional motional narrowing for labels located there.     

Distinct structural changes detected by X-ray fiber diffraction in stabilization of F-actin by lowering pH and increasing ionic strength

Lowering pH or raising salt concentration stabilizes the F-actin structure by increasing the free energy change associated with its polymerization. To understand the F-actin stabilization mechanism, we studied the effect of pH, salt concentration, and cation species on the F-actin structure. X-ray fiber diffraction patterns recorded from highly ordered F-actin sols at high density enabled us to detect minute changes of diffraction intensities and to precisely determine the helical parameters. F-actin in a solution containing 30 mM NaCl at pH 8 was taken as the control. F-actin at pH 8, 30 to 90 mM NaCl or 30 mM KCl showed a helical symmetry of 2.161 subunits per turn of the 1-start helix (12.968 subunits/6 turns). Lowering pH from 8 to 6 or replacing NaCl by LiCl altered the helical symmetry to 2.159 subunits per turn (12.952/6). The diffraction intensity associated with the 27-A meridional layer-line increased as the pH decreased but decreased as the NaCl concentration increased. None of the solvent conditions tested gave rise to significant changes in the pitch of the left-handed 1-start helix (approximately 59.8 A). The present results indicate that the two factors that stabilize F-actin, relatively low pH and high salt concentration, have distinct effects on the F-actin structure. Possible mechanisms will be discussed to understand how F-actin is stabilized under these conditions.     

A conformational rearrangement in gramicidin A: from a double-stranded left-handed to a single-stranded right-handed helix.

A conformational transition is described for the polypeptide, gramicidin A, in which a dimer that forms a left-handed intertwined antiparallel helix is converted to a single-stranded amino terminus to amino terminus right-handed helix. The starting structure is determined here by solution NMR methods while reference is made to the well-established folding motif of gramicidin in a lipid bilayer for the ultimate conformation of this transition. Furthermore, an organic solvent system of benzene and ethanol in which gramicidin has a unique conformation is identified. This conformation is shown to be very similar to that derived from X-ray diffraction of crystals prepared from a similar solvent system.     

Filamentous bacterial viruses. XIL. Molecular architecture of the class I (fd, If1, IKe) virion

The X-ray diffraction patterns of the fd, If1 and IKe strains of filamentous bacterial viruses (class I) indicate that the arrangement of capsid proteins in the virion approximates a left-handed helix of 15 Å pitch with 4.5 units per turn. The protein molecules are each elongated in an axial direction, and also slope radially, so as to overlap each other and give an arrangement of molecules reminiscent of scales on a fish. This helix of capsid proteins is related to the class II helix by a small twist about the helix axis. The protein molecules are also perturbed (by a few Ångström units) away from the positions that they would occupy in a simple 4.5 units per turn helix. The perturbation repeats about every five protein molecules, and is mainly axial. This arrangement of proteins forms a tube with inner diameter about 20 Å and outer diameter about 60 Å, encapsulating the DNA.     

A critical analysis of a left-handed double helix model for B-DNA fibers.

A search for a left-handed double helix model for B-DNA fibers has been undertaken. The model has to present good stereochemistry and also to be in agreement with X-ray and infrared data. Dihedral angles as well as atomic coordinates and calculated intensities curves are given for the best model obtained. Comparison with experimental results shows that this model must be rejected as a candidate for the representation of B-DNA fibers.     

Energy-minimized conformation of gramicidin-like channels. I. Infinitely long poly-(L,D)-alanine beta 6.3-helix.

The energy-minimized conformation of an infinitely long poly-(L,D)-alanine in single-stranded beta 6.3-helix was calculated by the molecular mechanics method. When energy minimization was started from a wide range of initial geometries, six optimized conformations were obtained and identified as the right- and left-handed counterparts of the beta 4.5-, beta 6.3-, and beta 8.2-helices. It was found that their conformation energies increase in this order, the beta 4.5-helix having the lowest energy. The backbone dihedral angles of the energy-minimized beta 6.3-helix were: phi L = -116 degrees (or -131 degrees), psi L = 122 degrees (or 111 degrees), phi D = 131 degrees (or 116 degrees), psi D = -111 degrees (or -122 degrees), omega L = 173 degrees (or 173 degrees), and omega D = -173 degrees (or -173 degrees) for the right-handed (or left-handed) helix. This helix was composed of 6.30 residues/turn with a pitch of 4.97 A. All the alpha-carbons of L- and D-configurations appeared on one common circular helix. Interestingly, small deviations (approximately 7 degrees) of the peptide bonds from the planar structure caused a considerable lowering of the conformation energy, and, at the same time, they produced more favorable fitting of the hydrogen bonds; the carbonyl oxygens and the nearest-neighbor alpha-hydrogens also took more favorable relative positions.     

Fibre X-ray study of the helix-helix transitions of poly(dG-dC).poly(dG-dC).

Poly(dG-dC).poly(dG-dC) and poly(dG-m5dC).poly(dG-m5dC) present helix-helix transitions which are commonly assumed to be changes between the right-handed A- or B-DNA double helices and the left-handed Z-DNA structure. The mechanisms for such transconformations are highly improbable especially when they are supposed to be active in long polynucleotide chains organised in semicrystalline fibres. The present alternative possibility assumes that rather than the Z-DNA it is a right-handed double helix (S-DNA) which actually takes part in these form transitions. Two molecular models of this S form, in good agreement with X-ray measurements, are proposed. They present alternating C(2')-endo and C(3')-endo sugar puckering. Dihedral angles, sets of atomic co-ordinates and stereo views of the two S-DNA structures are given together with curves of calculated diffracted intensities.     

Conformational studies of polymers and copolymers of L-aspartate ester. II. Infrared studies and the factors involved in the formation of the omega-helix

It has already been show that the helix senses of poly(β-benzyl L -aspartate) and poly(β-methyl L -aspartate) are left-handed, while the poly esters of n-propyl, isopropyl, n-butyl, and phenethyl L -asparate are all right-handed. The effect of changes in helix sense from the left-handed to the right-handed α-helical form on the infrared spectra of copolymers of benzyl L -aspartate with ethyl, n-butyl, isopropyl, n-propyl, and phenethyl L -aspartate have been studied. Those show that for the right-handed helical form the amide band frequencies fall within the range given by Elliott,⁷ while for the left-handed form the frequencies are higher. The frequency ranges for the two helix senses are given and have been used to show that poly (β-n-propyl L -aspartate) in chloroform solution undergoes a transition from the right-handed to the left-handed helix form on heating. Polarized infrared studies of the different copolymers show that the disposition of the side chain ester groups is different for the two forms. Although methyl L -aspartate forms a left-handed α-helix similar to benzyl L -aspartate, the introduction of methyl L -aspartate residues into poly (β-benzyl L -aspartate) prevents the formation of the ω-helix. The factors involved in the formation of this helix form are discussed.     

Glycosaminoglycan conformation: do aqueous molecular dynamics simulations agree with x-ray fiber diffraction?

Glycosaminoglycan-protein interactions are biologically important and require an appreciation of glycan molecular shape in solution, which is presently unavailable. In previous studies we found strong similarity between aqueous molecular dynamics (MD) simulations and published x-ray diffraction refinements of hyaluronan. We have applied a similar approach here to chondroitin and dermatan, attempting to clarify some of the issues raised by the x-ray diffraction literature relating to chondroitin and dermatan sulfate. We predict that chondroitin has the same beta(1-->4) linkage conformation as hyaluronan, and that their average beta(1-->3) conformations differ. This is explained by changes in hydrogen-bonding across this linkage, resulting from its axial hydroxyl, causing a different sampling of left-handed helices in chondroitin (2.5- to 3.5-fold) as compared with hyaluronan (3.0- to 4.0-fold). Few right-handed helices, which lack intramolecular hydrogen-bonds, were sampled during our MD simulations. Thus, we propose that the 8-fold helix observed in chondroitin-6-sulfate, represented in the literature as an 8(3) helix (right-handed), though it has never been refined, is more likely to be 8(5) (left-handed) helix. Molecular dynamics simulations implied that (4)C(1) and (2)S(O), but not (1)C(4), forms of iduronate could be used in refinements of dermatan x-ray fiber diffraction patterns. Current models of 8-fold dermatan sulfate chains containing (4)C(1) iduronate refine to right-handed helices, which possess no intramolecular hydrogen-bonds. However, MD simulations predict that models containing (2)S(O) iduronate could provide better (8(5) helix) starting structures for refinement. Thus, the 8-fold dermatan sulfate refinement (8(3) helix) could be in error.     

Circular dichroism of polynucleotides: dimers as a function of conformation

Working within the restrictions of a model, we have calculated the circular dichroism of the dinucleoside phosphates ApA, CpC, and CpA for various conformations. Comparing the calculated curves with those measured in aqueous solution we find agreement for (1) ApA as a right-handed helix with both bases either as in B-form DNA, or else rotated 180° around the glycosidic bond, (2) CpC as the right-handed conformation with both bases as in DNA, (3) ApC as either the right-handed conformation with both bases as in DNA, or else as a left-handed helix with both bases rotated 180°, and (4) CpA as either a left-handed helix with both bases in a left-handed DNA, or else in the right-handed conformation with both bases rotated 180°. In addition, we have investigated circular dichroism as a measure of unstacking. We find that opening the bases to a 90° total angle (base planes perpendicular) reduces the intensity of the calculated bands to 20% of their original value. Further, we find that allowing the sliding of one base past the other does not lead to a temperature dependence consistent with experiment.     

Transition of bacterial flagella from helical to straight forms with different subunit arrangements.

We have found that several kinds of helical flagella from Salmonella and Escherichia become straight in the presence of 0·5 m-citric acid at pH values below 4·0, while the straight flagella from a mutant Salmonella (SJ814) are transformed into a helical shape under the same conditions. These transformations are reversible and transitional.Current models of bacterial flagella (Calladine, 1976,1978; Kamiya, 1976) predict that the family of distinct wave-forms should include two types of straight flagella, which have either an extreme right-handed twist (about 7 ° at the surface of the flagellum) or an extreme left-handed twist (2 ° to 3 °). As the inclination of the near-longitudinal rows of subunits in the Salmonella SJ814 flagellum (O'Brien &; Bennett, 1972) agrees closely with the degree of twisting predicted for the right-handed type, this flagellum has been considered to be the right-handed type. We have determined that the basic (1-start) helix in flagella is right-handed, using the method of Finch (1972). This fact, together with the selection rule (O'Brien &; Bennett, 1972), strongly suggests that the near-longitudinal rows in an SJ814 flagellum are right-handed, in agreement with the prediction. However, our optical diffraction and X-ray diffraction studies have revealed that the near-longitudinal rows of subunits in the citric acid-induced straight flagella and in the straight flagella from a mutant E. coli (Kondoh &; Yanagida, 1975) tilt at an angle of 2 ° to 3 ° with respect to the flagellar axis. This inclination is probably left-handed. Thus the predicted presence of the two types of straight flagella seems to be proved.     

Direct determination of the π-helix structure and helix transition behavior of poly(β-phenethyl l-aspartate) via synchrotron X-ray diffraction

The helix-sense inversions of poly(β-phenethyl l -aspartate) (2P) and diblock copolymers (2P-3P), with 2P and poly(β-phenylpropyl l -aspartate) (3P) blocks, were studied in their solid states using synchrotron wide-angle X-ray diffraction and small-angle X-ray scattering. The characteristic parameters of the π-helix structure of 2P were directly determined in situ after the helix transition at a high temperature. In the 2P-3P block copolymers, the main chains of the 3P blocks initially convert from right- to left-handed α-helices, and then the 2P blocks convert irreversibly from right-handed α-helices to left-handed π-helices. The chemical structures of the side chains of poly(l -aspartic acid ester)s significantly affect their helix transition behaviors.     

The influence of a chiral amino acid on the helical handedness of PNA in solution and in crystals

The X-ray structure of a self-complementary PNA hexamer (H-CGTACG-L-Lys-NH(2)) has been determined to 2.35 A resolution. The introduction of an L-lysine moiety has previously been shown to induce a preferred left-handedness of the PNA double helices in aqueous solution. However, in the crystal structure an equal amount of interchanging right- and left-handed helices is observed. The lysine moieties are pointing into large solvent channels and no significant interactions between this moiety and the remaining PNA molecule are observed. In contrast, molecular mechanics calculations show a preference for the left-handed helix of this hexameric PNA in aqueous solution as expected. The calculations indicate that the difference in the free energy of solvation between the left-handed and the right-handed helix is the determining factor for the preference of the left-handed helix in aqueous solution.     

Fibre and molecular structure of thymidylyl-3′,5′-deoxyadenosine

X-ray diffraction and molecular model building studies of an ordered structure of thymidylyl-3′,5′-deoxyadenosine which gives fibre-type diffraction patterns, are consistent with a seven-residues per turn, left-handed structure in which the adenine of one molecule and the thymine of the next are linked together by Hoogsteen type of hydrogen bonds. The structure thus resembles a macromolecule in which units are linked together by hydrogen bonds and stabilized by base stocking. Both nucleosides in the basic molecule are in the anti conformation and both sugar rings have C3′-endo puckers. The C5′-05′ bond of the deoxyadenosine is trans relative to C4′-C3′ and the conformations about the P-03′ and P-05′ bond are gauche^?, trans.     

Conformational studies of polymers and copolymers of L-aspartate esters. I. Preparation and solution studies

An alcoholysis method is described for the modification of high molecular weight poly(β-benzyl L -asparatate); by this method the benzyl groups in the polypeptide have been replaced by methyl, ethyl, isopropyl, n-propyl, and phenethyl groups to give a series of copolymers of each of the corresponding aspartate esters with benzyl L -aspartate. By repeating the reactions, replacement of better than 99% has been achieved in some cases to give in effect the homopolymer. Optical rotatory dispersion studies show that of all the systems studied only poly(β-methyl L -aspartate) has the left-handed helix sense, the others are right-handed. It is shown further that the helix sense is not an intrinsic property of the nature of the aspartate side chain. Raising the temperature of chloroform solutions of the right-handed form of the copolymers of benzyl L -aspartate and ethyl L -aspartate results in a transition to the left-handed helix, the temperature of the transition being dependent on the composition of the copolymer. Also poly(β-n-propyl L -aspartate) undergoes a transition from the right- to the left-handed helix form at 59°C. These results suggest a general pattern of behavior of poly(aspartate esters) and that with suitable conditions of solvent and temperature they may be in either the right- or left-handed helical form.     

Conformational Adaptability of Redβ during DNA Annealing and Implications for Its Structural Relationship with Rad52

Single-strand annealing proteins, such as Redβ from λ phage or eukaryotic Rad52, play roles in homologous recombination. Here, we use atomic force microscopy to examine Redβ quaternary structure and Redβ-DNA complexes. In the absence of DNA, Redβ forms a shallow right-handed helix. The presence of single-stranded DNA (ssDNA) disrupts this structure. Upon addition of a second complementary ssDNA, annealing generates a left-handed helix that incorporates 14 Redβ monomers per helical turn, with each Redβ monomer annealing ≈ 11 bp of DNA. The smallest stable annealing intermediate requires 20 bp DNA and two Redβ monomers. Hence, we propose that Redβ promotes base pairing by first increasing the number of transient interactions between ssDNAs. Then, annealing is promoted by the binding of a second Redβ monomer, which nucleates the formation of a stable annealing intermediate. Using threading, we identify sequence similarities between the RecT/Redβ and the Rad52 families, which strengthens previous suggestions, based on similarities of their quaternary structures, that they share a common mode of action. Hence, our findings have implications for a common mechanism of DNA annealing mediated by single-strand annealing proteins including Rad52.     

Helix-helix transitions in DNA: fibre X-ray study of the particular cases poly(dG-dC) · poly(dG-dC) and poly(dA) · 2poly(dT)

The helix-helix transitions which occur in poly(dG-dC) · poly(dG-dC) and in poly (dG-m⁵dC) · poly(dG-m⁵dC) are commonly assumed to be changes between the right-handed A- or B-DNA double helices and the left-handed Z-DNA structure. The mechanisms for such transconformations are highly improbable, especially when they are supposed to be active in long polynucleotide chains organised in semicrystalline fibres. The present alternative possibility assumes that rather than the Z-DNA it is a right-handed double helix (S-DNA) which actually takes part in these form transitions. Two molecular models of this S form, in good agreement with X-ray measurements, are proposed. They present alternating C(2′)-endo and C(3′)-endo sugar puckering like the “alternating B-DNA” put forward some years ago. Dihedral angles, sets of atomic coordinates and stereo views of the two S-DNA structures are given, together with curves of calculated diffracted intensities. Furthermore, we question the possibility of obtaining semicrystalline fibres with triple helices of poly(dA) · 2poly(dT) in a way which renders X-ray diffraction efficient. It is suggested that, up to now, only double helices of poly(dA) · poly(dT) can actually be observed by fibre X-ray diffraction measurements. Received: 30 March 1999 / Revised version: 30 June 1999 / Accepted: 30 June 1999     

Polarization selectivity of interaction of DNA molecules with X-ray radiation

The optimum form of a long helical molecule, which DNA is, has been calculated in terms of the classical electromagnetic theory. Three different methods of classical electrodynamics are used: the theory of dipole radiation of electromagnetic waves, the energetic power approach, and a helical model of molecules of chiral medium. In all three cases, an identical result for the optimum geometrical form of a long spiral molecule has been obtained. The lead angle between the tangent to the helix and the plane normal to the axis of the helix should be equal to 24.5 degrees. This condition imposes restrictions on the radius and the pitch of the helical molecule. The experimentally measured geometrical characteristics of the DNA molecule satisfy the theoretically calculated condition precisely enough. Having the optimum geometrical form, the DNA molecule is not influenced by a circularly right-polarized electromagnetic wave in the soft X-ray range λ = 7–8 nm. This wave, for which the right-handed DNA molecule is “transparent,” should propagate orthogonally to the helix axis and form a right-handed screw in space. The wave radiated by the right-handed DNA molecule orthogonally to helix axis in the range of λ ≈ 7–8 nm has, accordingly, the left-handed circular polarization. The polarization selectivity of the DNA molecule by the action of X-ray radiation is exhibited strongly enough in the wavelength range of λ ≈ 1–35 nm. The results obtained are valid for any distribution of electric currents in DNA, i.e., for any sequence of nitrogenous bases in DNA.