bluuebunny/crossref_metadata_2025 huggingface dataset:
Stereochemistry of nucleic acids and their constituents. X. solid‐slate base‐slacking patterns in nucleic acid constituents and polynucleotides
Authors: Bugg C. E. , Thomas J. M. , Sundaralingam M. , Rao S. T.
Published: December 2004

The base‐stacking patterns in over 70 published crystal structures of nucleic acid constituents and polynucleotides were examined. Several recurring stacking patterns were found. Base stacking in the solid state apparently is very specific, with particular modes of interaction persisting in various crystalline environments. The vertical stacking of purities and pyrimidines in polynucleotides is similar to that observed in crystals of nucleic acid constituents. Only partial base overlap was found in the majority of the structures examined. Usually, the base overlap is accomplished by positioning polar substituents over the ring system of an adjacent base. The stacking interactions are similar to those found in the crystal structures of other polar aromatic compounds, but are considerably different from the ring–ring interactions in nonpolar aromatic compounds. Apparently, dipole‐induced dipole forces are largely responsible for solid‐state base stacking. It is found that halogen substituents affect base‐stacking patterns. In general, the presence of a halogen substituent results in a stacking pattern which permits intimate contact between the halogen atom and adjacent purine or pyrimidine rings. Considering differences in the stacking patterns found for halogenated and nonhalogenated pyrimidines, a model is proposed to account for the mutagenic effects of halogenated pyrimidines.
Characteristic parameters and polydispersity elimination factors for hydrodynamic quantities of semirigid polymers, especially of DNA
Authors: Reinert K. E.
Published: December 2004

Relations are given allowing the calculation of intrinsic viscosity, diffusion constant, and related molecular weights of monodisperse subfractions of polydisperse samples from the measured averages of the hydrodynamic quantities and the individual (reduced) sedimentation constant distribution. The peculiarities resulting from the special behavior of semirigid polymers like DNA are treated. Expressions are derived which describe the dependence of the exponents as(aηs = aη/as), and aη of the relations so = ksMas [η] = kηs(so)aηs, and [η] = kηMaη on so and [η], respectively, and which are useful for practical and theoretical discussions of the wormlike chain. Furthermore, a generalized exponent rule for aη and as has been suggested, considering the dependence of the Mandelkern‐Flory‐Scheraga parameter β(≙Φ1/3P−1) on molecular weight. The results of this paper are applied extensively in the following paper to molecular weight and hydrodynamic properties of homogeneous DNA.
Helix–coil transition in copolypeptides. I. Poly (γ‐benzyl‐co‐γ‐methyl L‐glutamate)
Authors: Roig A. , Cortijo M.
Published: December 2004

The helix–coil transition in poly(γ‐benzyl L‐glutamate‐co‐γ‐methyl L‐glutamate) copolypeptides was studied experimentally in nonaqueous solvents and the results compared with theory. It is found that the transition can be described by the same theory as for the homopolypeptides, but the corresponding parameters are not related in the expected way to those of the homopolymers, due to the effect of the side chains on the stability of the helix, which is not taken into account explicitly by the theory.
Interaction of proflavine and 9‐aminoacridine with DNA at temperatures below and above the melting temperature
Authors: Jordan D. O. , Sansom L. N.
Published: December 2004

The influence of temperature on the binding of 9‐aminoacridine and of proflavine to E. coli DNA in 10−3M NaCl solution has been determined by a spectrophotometric technique. The inadequacy of the expression normally used for the determination of the extent of binding is discussed with reference to measurements at temperatures above which dissociation of the double helix occurs. A method of determining the relative extents of binding to native and denatured DNA at elevated temperatures is described.
Studies on the conformation of amino acids. IX. Conformations of butyl, seryl, threonyl, cysteinyl, and valyl residues in a dipeptide unit
Authors: Ponnuswamy P. K. , Sasisekharan V.
Published: December 2004

Potential energies of conformation of a dipeptide unit with butyl, seryl, threonyl, eysteinyl, and valyl side groups have been computed by using classical energy expressions. The presence of a γ‐atom introduces characteristic restrictions on the backbone rotational angles ϕ and ψ the γ‐atom itself is restricted to three staggered positions about the Cα—Cβ bond. The important results are that a γ‐carbon in position I (χ1 ≃ 60°) cannot be accommodated in the standard right‐and left‐handed α‐helices, whereas a γ‐oxygen or sulfur could easily be accommodated in the right‐handed α‐helix. Further, a γ‐carbon or a heteroatom in position II (χ1 ≃ 180°) does not favor a conformation ψ ≃ 180°, compared to two other positions. The valyl side group significantly reduces the allowed ϕ and ψ values and energetically prefers a β‐conformation compared to right‐or left‐handed α‐helical conformations. The less favorable α‐helical conformation is possible only for γ (III, II) combination of the valyl residue. The observed ϕ, ψ, and χ1 values of all the amino acid residues in the three protein molecules, lysozyme, myoglobin, and chymotrypsin are compared with the theoretical predictions and the agreement is excellent. The results bring out the important fact that even in large molecules, the conformation of local segments are predominantly governed by the short‐range intramolecular interactions.
Simple methods for the orientation of DNA molecules in films suitable for optical studies
Authors: Kurucsev T. , Zdysiewicz J. R.
Published: December 2004

Three methods are described for the preparation of oriented samples of DNA molecules in films. The methods involve simple equipment and produce films of good optical qualities, suitable for the determinations of dichroic spectra, for example. To illustrate the quality of the films the dichroism of DNA and of acridine orange–DNA complex are described. Evidence is given that native DNA structure is stabilized by poly‐(vinyl alcohol).
Thermal conformational transformations of tropocollagen. II. Viscometric and light‐scattering studies
Authors: Privalov P. L. , Serdyuk I. N. , Tiktopulo E. I.
Published: December 2004

It was shown by viscometric measurements that a tropocollagen solution at low shear gradients manifests elastic features which can be connected only with the existence of a labile spatial structure which develops in time in the solution. To judge by the concentration dependence of the rate of formation of this structure, it does not represent a molecular net formed by direct contact of macromolecules. Most likely this structure is a result of stabilization of macromolecules at a certain distance from each other. The study of light scattering by tropocollagen solutions demonstrated that it does not correspond with the scattering by rigid rod‐shaped units. Anomalies in the character of light scattering are probably the result of intermolecular interference produced by a spatial supermolecular structure and, in turn, indicate that this structure is to some extent regular. In the presence of salts the elastic features in the tropocollagen solution and anomalies in light scattering disappear in a narrow range of temperatures immediately before the process of denaturation which makes it possible to conclude that the supermolecular regular structure is disrupted in this temperature range.
The circular dichroism in the ultraviolet of aminoacridines and ethidium bromide bound to DNA
Authors: Dalglkish D. G. , Peacocke A. R. , Fey G. , Harvey C.
Published: December 2004

The circular dicrosim (CD) spectra of complexes of DNA with ethidiun bromnide, profiavine, 9‐aminoacridine and 4‐etliyl‐9‐amino‐acridine have been determined between 220 and 450 nm, the range lieing extended to 600 nm for ethidiufm bromide. The variation of the magnitude of the visible and near—ultraviolet CD spectra of ethidium bromide—DNA complexes with the amount of ligand bound (r) suggests a common binding position with profiavine. On the other hand, 4‐ethyl‐9‐aminoacndine complexed to DNA shows CD spectra not distinguishable from those of 9‐aminnoacnidmc in both the visible and ultraviolet. The interpretation of these results with respect to the stereochemistry of the DNA‐ligand complexes is discussed.
Consistent force field calculations on 2,5‐diketopiperazine and its 3.6‐dimethyl derivatives
Authors: Karplus Susan , Lifson Shneior
Published: December 2004

The minimum energy conformations are calculated for 2, 5‐diketopiperazine (DKP) and its 3,6‐dimethyl derivatives (DL‐DMDKP and LL‐DMDKP), using a consistent force field approach developed previously. The energy function parameters that were not required in earlier calculations on alkanes, amides, mid lactams are fitted to spectral and conformational data on the diketopiperazines. Vibrational assignments are suggested for DKP.

Conformational energies are also determined over a range of selected values for ring dihedral angles, and the shape of the potential energy functions is examined over deviations from planarity. DKP and LL‐DMDKP are found to have non‐planar minimum energy conformations, separated from planar by less than a kcal/mole. DL‐DMKP exhibits a nearly flat trough about the planar conformation. Calculations of minimum energies with one dihedral angle coordinate constrainted show a coupling between bond angles and dihedral angles in agreement with recent suggestions of Benedetti.
Molecular motion in poly(β‐benzyl‐L‐aspartate)
Authors: Happey F. , Jones D. W. , Watsox B. M.
Published: December 2004

As the temperature of solid poly(β‐benzyl‐L‐aspartate) (PBLA), (CO.NH.CH.‐CH2COOCH2C6H5)n, in the α‐helieal form is raised from −150 °C, tlie line width and second moment of the proton magnetic resonance (PMR) signal decrease in stages until the conformational transition to the ω‐helix occurs at about 90 °C. A similar temperature dependence of the PMR parameters is observed as the transformed polymer is cooled. Below −100°C (where the lattice is presumed to be rigid), the measured second moments are 9.5 Oe2 and 10.7 Oe2 for the α and ω forms, respectively. Second moments, calculated from the Van Vleck formula for the rigid lattice and also estimated for possible motional cases in which the polymer is taken to be in the ω form, are compared with the PMH data. By combination with the results of X‐ray diffraction and infrared spectroscopic measurements, a tentative explanation can be made of the types of motion occurring in PBLA.
Temperature dependence of the aminoacylation of tRNA by bacillus stearothermophilus aminoacyl‐tRNA synthetases
Authors: Johnson Lee , Söll Dieter
Published: December 2004

Valine specific transfer RNA (tRNAVal) was isolated from Bacillus stearothermophilus and Escherichia coli by chromatography on benzoylated DEAE–cellulose (BD–cellulose). Likewise isoleucine specific transfer RNA (tRNAIle) was isolated from B. stearothermophilus and from Mycoplasma sp. Kid. The thermal denaturation profiles (melting curves) of the two tRNAVal species in the presence of Mg+ + were nearly identical. However, the Tm for the Kid tRNAIle was about 10°C lower than that for the B. stearothermophilus tRNAIle. A nuclease and tRNA‐free aminoacyl‐tRNA synthetase (AA‐tRNA synthetase) preparation from B. stearothermophilus was able to function efficiently at temperatures up to 80°C in the aminoacylation of all four tRNA species. Determination of the amino acid‐acceptor activity of each tRNA species as a function of temperature of the aminoacylation reaction showed in each case a strong correlation between the loss of acceptor activity and the thermal denaturation profile of the tRNA. Evidence is presented that the loss in acceptor activity is most likely due to a change in structure of the tRNA as opposed to denaturation of the enzyme. These results further support the idea that correct secondary and/or tertiary structure must be maintained for tRNA to be active as a substrate for the AA‐tRNA synthetase.
Cis–Trans isomerism of the peptide bond
Authors: Andrews P. R.
Published: December 2004

The molecular orbital method PCILO is applied to eight. N‐monsubstituted amides. Experimentally known geometric properties are reasonably predicted by minimization of total energy with respect to molecular geometry. The same procedure shows that molecular deformations during rotation around the peptide bond significantly lower calculated barriers. Experimental heats of activation and the free‐energy changes associated with cis–trans isomerism are in good agreement with those calculated, which include qualitative estimates of configurational entropy contributions to the isomerism energies. Both the calculations and revised infrared data indicate that N‐phenylurethane, which has been used as a model for the cis peptide bond, should be predominantly trans. However the variations in rotational barriers and cis–trans isomerism energies among the N‐monosubstituted amides provide no reason to suppose that the cis peptide bond should be excluded from stable protein conformations.
Discontinuous volume transitions induced by calcium–sodium ion exchange in anionic gels and their neurobiological implications
Authors: Tasaki I. , Byrne P. M.
Published: December 2004

Discontinuous volume transitions in poly(acrylic acid) gels were studied by determining equilibrium swelling curves of small gel beads immersed in salt solutions containing varying concentrations of Ca2+ and Na+. Reversible contractions of gel membranes associated with Ca2+‐Na+ exchange were examined using both isometric and isotonic recording devices. A discontinuous change in electric conductance was demonstrated in association with Ca2+‐Na+ exchange in gel membranes. These experimental findings provide a sound physicochemical basis for elucidating the mechanism of nerve excitation. © 1994 John Wiley & Sons, Inc.
Condensation of DNA by basic protiens does not depend on protien composition
Authors: Garcia‐Ramírez Marta , Subirana Juan Antonio
Published: December 2004

We have studied by electron microscopy the size and morphology of the complexes obtained with different DNAs (between 500 and 5243 base pairs long) and four different proteins: sea urchin histone H1; sea cucumber histone ϕ0, chicken erythrocyte histone H5, and clupeine. Surprisingly, the type of protein used has only a marginal influence on the complexes formed. The molecular weight and topology of DNA do not show any influence. The size of the complexes depends strongly on the ratio of positive to negative charges and also on the ionic conditions. Our studies have been mainly carried out at a ratio of 0.4. Under these conditions the average thickness of rods and toroids observed varies between 165 Å at 1.5 mM salt to 290 Å at 100 mM salt, with minor variations around these values depending on the type of DNA and protein used. We conclude that the formation of DNA condensates is mainly determined by a balance of electrostatic and intermolecular forces, the influence of specific interactions is only marginal. This conclusion seems to apply not only to the complexes described here, but also to chromatin fibers and to DNA condensed by low molecular weight counterions and other compounds (polyamines, inorganic ions, ethanol, etc.). © 1994 John Wiley & Sons, Inc.
Low‐temperature IR spectroscopy reveals four stages of water loss during lyophilization of hen egg white lysozyme
Authors: Remmele Richard L. , Stushnoff Cecil
Published: December 2004

Water loss during lyophilization of a 49.4 mg/mL solution of lysozyme in D2O was studied with ir spectroscopy using a low‐temperature, single reflection, horizontal, attenuated, total reflectance accessory. Four regions of water loss were identified and assignable to different forms of bound water. The amide I band begins to shift to higher frequency while the amide II concurrently shifts to lower frequency and broadens after the first stage of water loss (sublimation) at −10°C. Additionally, the carboxylate band (at 1584 cm−1) shifts slightly to lower frequency. A second stage at 17°C is characterized by continued shifts in the carboxylate and amide II bands to low frequency, further broadening in the amide II and greater shift to high frequency in the amide I (ascribed to the removal of periphery water around the protein). At the third stage of water loss, the carboxylate band decreases substantially in relative absorbance (consistent with the removal of water from the carbonyl backbone). In the fourth and last stage, the carboxylate band nearly disappears and water loss is very slow. Based upon a final level of hydration of 0.037 h, the last stage corresponds to 25% completion of the removal of water associated with ionizable side chains. From start to finish, the amide I shifts 9 cm−1 to higher frequency. © 1994 John Wiley & Sons, Inc.
Filipin and its interaction with cholesterol in aqueous media studied using static and dynamic light scattering
Authors: Castanho Miguel A. R. B. , Brown Wyn , Prieto Manuel J. E.
Published: December 2004

Aggregation of filipin in aqueous medium and filipin‐induced changes in cholesterol micelles have been studied using intensity and dynamic light scattering. The dependencies of filipin aggregate dimensions on concentration, solvent, and temperature were studied, and revealed that the aggregates do not have a well‐defined geometry, i.e., a critical micelle concentration cannot be detected and stable structures are not formed. The aggregates are of size Rg ≈ 110 nm and Rh ≈ 63 nm, referring to the radius of gyration and hydrodynamic radius, respectively. In the concentration range studied (1 μM < C < 30 μM), a low molecular weight species (monomer/dimer) is always present together with the aggregates. In ethanol/ water mixtures, large (Rg ≈ 500 nm), narrow distribution aggregates are formed in the water volume fraction range 0.45 < ΦH2O < 0.65. Aggregation also occurs on changing the temperature; In the range 7–37°C, smaller aggregates (10–30 nm) form and the process is only partially reversible.

No pronounced effect of filipin on the structure of the cholesterol micelles was observed (a small increase in Rg and Rh is noted). These results rule out any “specificity” for the filipin interactions with cholesterol, which has been considered a key event in the filipin biochemical mode of action. A reevaluatiori Of this question is suggested and some alternatives are advanced. © 1994 John Wiley & Sons, Inc.
α‐Helical assembly of biologically active peptides and designed helix bundle protein
Authors: Morii Hisayuki , Honda Shinya , Ohashi Shinichi , Uedaira Hatsuho
Published: December 2004

The formation of α‐helical assembly by complexing biologically active peptides with de novo designed protein is described. The de novo designed protein described here is a cystinelinked 4‐helix bundle protein constructed with 80 amino acid residues and forms a hydrophobic core region surrounded by 4 helices in an aqueous solution. The biologically active peptides, such as melittin and human growth hormone releasing factor, contain the sequences that are able to form amphiphilic helices. These peptides alone do not form the α‐helix structure in a diluted solution with low ion strength. But on mixing with the designed helix bundle protein, the peptides are strongly bound to the protein with the induction of α‐helical structure in the biologically active peptides. The content of induced α‐helix is in accord with that estimated from the amphiphilic sequence. The results mean that a novel architecture composed of α‐helices is formed. Fluorescent and temperature‐scanning measurement revealed that the α‐helical assembly is constructed with hydrophobic interaction. Also, it is shown by means of fluorescence depolarization that the assembly has a compact globular form corresponding to 1 : 1 complex. © 1994 John Wiley & Sons, Inc.
Magnesium‐DNA interactions from interpretation of 25Mg‐nmr relaxation rates: Field and coion dependence
Authors: Wright Laura A. , Lerner Laura E.
Published: December 2004

We have used 25Mg‐nmr to investigate the binding of magnesium ions to double‐stranded DNA. We have measured line shapes for 25Mg in the presence of monodisperse calf thymus DNA (160 base pairs; b.p.) (magnesium : phosphate = 2.0) at two different field strengths, 11.75 T and 7.05 T, and used the isotropic model of two‐site exchange developed by Westlund and Wennerstrom to simultaneously fit the line shapes at both field strengths. This model does not reproduce the observed field dependence. This is in contrast to a previous study [E. Berggren, L. Nordenskiold, and W. H. Braunlin (1992), Biopolymers, Vol. 32, pp. 1339–1350] in which a similar model of isotropic two‐site exchange qualitatively reproduced the temperature dependence of the line widths.

Relaxation rates were also measured as a function of magnesium : phosphate ratio and colon type. These measurements were used to assess the sensitivity of magnesium relaxation measurements to small changes in DNA structure induced by changes in the solvent environment. The temperature dependence of the line shape varies with the type of coion (chloride or sulfate) present. This coion dependence of the line shape is consistent with the coion dependence of the aggregation midpoint temperature reported by Bloomfield and co‐workers [O. A. Knoll, M. G. Fried, and V. A. Bloomfield (1988) in Structure and Expres‐sion, Vol. 2, R. H. Sarma and M. H. Sarma, Eds., Adenine Press, New York] and attributed to a lyotropic effect. These results suggest that even at low magnesium : phosphate ratios, relaxation parameters are specific to each magnesium–coion–DNA system. © 1994 John Wiley & Sons, Inc.
A CD and an nmr study of multiple bradykinin conformations in aqueous trifluoroethanol solutions
Authors: Cann John R. , Liu Xiaohong , Stewart John M. , Gera Lajos , Kotovych George
Published: December 2004

CD and nmr studies have been carried out on aqueous trifluoroethanol (TFE) solutions of bradykinin (BK) and a bradykinin antagonist. The CD results exhibit a striking effect of TFE on the spectra of BK, with sequence Arg‐Pro‐Pro‐Gly‐Phe‐Ser‐Pro‐Phe‐Arg, and the BK antagonist, with sequence D‐Arg‐Arg‐Pro‐Hyp‐Gly‐Thi‐D‐Ser‐D‐Cpg‐Cpg‐Arg [where Hyp is 4‐hydroxy‐L‐proline; Thi refers to β‐(2‐thienyl)‐L‐alanine and Cpg refers to α‐cyclopentylglycine]. The effect of increasing concentration of TFE in water on the difference ellipticity at 222 nm was examined and showed that BK may be a mixture of at least two different conformers, one of which largely forms when the TFE concentration is increased beyond 80%. The linear extrapolation of 100% of the difference ellipticity of BK at low TFE concentrations yields a value in agreement with that shown by the BK antagonist, indicating that the conformation of BK at the lower TFE concentrations is similar to that of the BK antagonist. The conformational analysis was carried out using both one‐dimensional and two‐dimensional 1H‐nmr techniques. The total correlation spectroscopy (TOCSY) spectrum of BK in a 60/40% (v/v) TFE/H2O solution at 10°C and a nuclear Overhauser effect spectroscopy (NOESY) spectrum that shows only sequential Hα(i) – NH(i + 1) or the Hα(i) – Hδδ′(i + 1) NOEs indicate that the majority of the molecules adopt an all‐trans extended conformation. The TOCSY for BK in the 95/5% (v/v) TFE/H2O solution shows that there are two major conformations in the solution with about equal population. The NOESY experiment shows two new important cross peaks for one conformation, namely Pro2(α)‐Pro3 (α) and the Pro2(α)‐Gly4(NH), indicating a cis Pro2‐Pro3 bond and a type VI β‐turn between residues Arg1 and Gly4 involving cis proline at position 3, respectively. The low temperature coefficient of Gly4 for this conformation suggests the presence of an intramolecular hydrogen bond, therefore a type VIa β‐turn is present. The other conformation is all trans and extended.

The BK antafonist shows difference CD spectra in TFE solutions referred to H2O that are superficially indicative of a β‐bend. However, nmr speaks against this possibility, as only one set of peaks were observed in the TOCSY and NOESY experiments, indicating an all‐trans extended confirmation over the range of TFE concentrations. The BK‐antagonist CD data suggest that solvent perturbation of the CD of an extended confirmation perturbation of the optical activity of the thienyl moiety of the peptide since the CD spectrum of N‐acetyl‐β‐thienyl‐L‐alanine N‐methylamide is strongly perturbed by TFE. The present results again demonstrate the complementary relationship between CD and nmr. © 1994 John Wiley & Sons, Inc.
Three‐dimensional Hartree–Fock crystal‐orbital calculation on crystalline diprotonated deoxycytidine‐5′‐monophosphate monohydrate: Toward rationalizing nucleic acid semiconductivity
Authors: Starikov E. B.
Published: December 2004

A three‐dimensional Hartree–Fock crystal‐orbital calculation on the crystal of diprotonated deoxycytidine‐5′‐monophosphate monohydrate has been carried out using the CRYSTAL92 routine package. According to the calculation, this crystallohydrate can be considered a quasi one‐dimensional hole semiconductor with the indirect fundamental gap of 1.66 eV and with a possibility for the uv‐excited quasi one‐dimensional electron photoconductivity. The physical source for such properties is the charge transfer from the phosphate to the water molecule and cytosine residue, favored by the strong electrostatic interaction between nucleotide zwitterions and by the formation of the infinite spirals of hydrogen‐bonded zwitterions along one of the crystallographic axes. © 1994 John Wiley & Sons, Inc.
Conformation and sweet tastes of L‐aspartyl dipeptide methyl esters
Authors: Kim Young Ju , Han Seong Jun , Kim Shi Choon , Kang Young Kee
Published: December 2004

In order to investigate the conformational preferences to elicit tastes, conformational free energy calculations using an empirical potential (ECEPP/2) and the hydration shell model were carried out on the L‐aspartyl dipeptide methyl esters, L‐+HAsp−‐L‐Xaa‐OMe, in the hydrated state, where Xaa includes sweet (Phe, Tyr, Met, and Gly), bitter (Ala, Trp, Val, Leu, and Ile), and tasteless (Ser, Thr, and Abu) residues. The refined preferred conformation of the Phe dipeptide (aspartame) with side chain χ conformation g− is g−Fg− in the hydrated state, which is consistent with the structure deduced from 1H‐nmr experiments. Irrespective of the Xaa and taste, all the dipeptides have the same conformation for the Asp residue, which is attributable to the hydrogen bond between protonated amino hydrogen and carboxylate oxygen and the favored hydration of the carboxylate group. This implies that the L‐aspartyl residue is a necessary factor for the dipeptides to be sweet not a sufficient factor. The computed conformational preferences for sweet, bitter, and tasteless dipeptides in the hydrated state indicate to us that the conformation about the NCα bond of the Xaa residue, i.e., the orientation of the hydrophobic moiety with respect to the AH/B functionalities in the aspartyl moiety, seems to be crucial to elicit the tastes. In addition, the hydrophobicity and the size of the Xaa residue are found to play a major role in determining the tastes. These well accord with the related works reported previously. © 1994 John Wiley & Sons, Inc.
Conformational polymorphism in telomeric structures: Loop orientation and interloop pairing in d(G4TnG4)
Authors: Mohanty Debasisa , Bansal Manju
Published: December 2004

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded‐back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways—i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides—to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G4TnG4), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine–thymine pair. Our molecular mechanics calculations on various folded‐back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded‐back structures, while isolated stretches of guanines adopt a parallel tetraplex structure. © 1994 John Wiley & Sons, Inc.
Dynamic viscoelastic properties of glycinin and β‐conglycinin gels from soybeans
Authors: Nagano Takao , Akasaka Takeshi , Nishinari Katsuyoshi
Published: December 2004

The effects of heating temperature on gel properties and conformational changes were investigated in glycinin and β‐conglycinin gels using Theological and Fourier transform ir (FTIR) methods. Solutions of 15 wt % glycinin or β‐conglycinin in 35 mM phosphate buffer at pH 7.6 were heated at various temperatures for 30 min and rheological properties were measured at 20°C. The storage modulus G′ as a function of frequency changed from a monotonical decrease with decreasing frequency to a plateau in the range from 0.0018 to 40 Hz by heating at temperatures higher than 80°C for glycinin and 65°C for β‐conglycinin. A band at 1618 cm−1 (associated with the β‐sheet structure) on ir spectra increased with the formation of heat‐induced gels. The value of the storage modulus G′ correlated well with the increase in absorbance at 1618 cm−1. These results suggest that the formation of a β‐sheet structure may be closely related to the value of the storage modulus G′ for heat‐induced gels in soybean proteins and that heat‐induced gels of glycinin and β‐conglycinin are formed by cross‐links with intermolecular β‐sheet structures. © 1994 John Wiley & Sons, Inc.
Phosphophoryn, an “acidic” biomineralization regulatory protein: Conformational folding in the presence of Cd(II)
Authors: Evans John Spencer , Chiu Thomas , Chan Sunney I.
Published: December 2004

The divalent cation‐induced protein folding properties of the template macromolecule, bovine dentine phosphophoryn (BDPP), have been examined by 1H/31P/13C/113Cd‐nmr spectroscopy. Cd(II) was employed, exploiting the sensitivity of 113Cd‐nmr to ligand‐binding interactions and kinetics. Cation binding was studied over the stoichiometric range of 0–50 : 1 Cd(II) : protein (mole ratio), well below the range of Cd(II) concentration required to induce protein precipitation. The stepwise titration of divalent cation‐depleted phosphophoryn at pH 7.2 in H2O/D2O with 113CdCl2 revealed that (PSer)n, (PSerAsp)n, and (Asp)n polyelectrolyte cation‐binding domains undergo two major transitions in their secondary and tertiary structures: the first transition, occurring between 1 : 10 and 1 : 1 Cd(II) : protein stoichiometry, and the second, between 10 : 1 and 50 : 1. By monitoring the amide NH intensities, 31P‐nmr chemical shift, and 13C Asp‐C, resonances, it was concluded that Cd(II) ions exhibit a binding‐site preference for polyelectrolyte cation‐binding domains, in the order

This preference correlates with the degree of negative charge density for each sequence motif. Accompanying the backbone conformational transitions at the polyelectrolyte regions were conformational transitions in the flanking hinge domains, indicating that the hinge domains participate in the folding of the phosphophoryn molecule as divalent cation binding occurs at the polyelectrolyte domains.

We were unsuccessful in detecting phosphophoryn‐bound Cd (11) species by 113Cd‐nmr because of chemical exchange modulation. However, using a smaller 21‐residue peptide mimetic of phosphophoryn, we have observed three stoichiometric‐dependent 113Cd resonances that differ in terms of the oxoanion coordination number. Our observation of multiple Cd(II) species in the presence of the peptide supports our contention that Cd(II) has many chemically distinct coordination sites on phosphophoryn, each in multiple equilibria with H2O, Cl−, and side‐chain oxoatoms. © 1994 John Wiley & Sons, Inc.
Nmr and molecular modeling investigations of the neuropeptide substance P in the presence of 15 mM sodium dodecyl sulfate micelles
Authors: Young John K. , Hicks Rickey P. , Anklin Clemens
Published: December 2004

To better understand the structural basis of the biological activity of the neuropeptide substance P SP; (Arg‐Pro‐Lys‐Pro‐Gln‐Gln‐Phe‐Phe‐Gly‐Leu‐Met‐NH2), two‐dimensional nmr spectroscopy experiments and simulated annealing calculations were used to investigate the conformation adopted in the presence of the membrane model system sodium dodecyl sulfate. It was determined that SP in the presence of SDS micelles undergoes a conformational equilibrium between an α‐ and a 310‐helix involving the midregion (Pro4‐Gln5‐Gln6‐Phe7‐Phe8) of the peptide. The C‐terminus adopts an extended conformation while the N‐terminus remains quite flexible. The conformation adopted by SP in the presence of SDS micelles yields a structure that is consistent with the model of a neurokinin‐1 selective ligand proposed by Convert. © 1994 John Wiley & Sons, Inc.
A crystal structure with features of an antiparallel α‐pleated sheet
Authors: Di Blasio Benedetto , Saviano Michele , Fattorusso Roberto , Lombardi Angela , Pedone Carlo , Valle Valentina , Lorenzi Gian P.
Published: December 2004

A single‐crystal x‐ray diffraction analysis of Boc‐L‐Ala‐D‐aIle‐L‐Ile‐OMe has been carried out. The analysis has shown (a) that the tripeptide molecules have in part an α‐extended conformation, the torsion angles of the L‐Ala and D‐aIle residues being φ1 = −75.1° and ψ1 = −25.8° and φ2 = 67.3° and ψ2 = 44.1°, respectively, and (b) that the molecules are organized in rippled planes where they occur in relative antiparallel orientation linked together side by side by H bonds. This molecular organization of the tripeptide corresponds closely to that of an antiparallel α‐pleated sheet, and likely constitutes the first example of a structure of this kind for which a characterization at the atomic level has been achieved. A molecular dynamics study has shown that the molecular conformation of the tripeptide in the crystalline state is determined primarily by intermolecular interactions. © 1994 John Wiley & Sons, Inc.
β‐Alanine containing cyclic peptides with predetermined turned structure. V
Authors: Pavone Vincenzo , Lombardi Angelina , Saviano Michele , Di Blasio Benedetto , Nastri Flavia , Fattorusso Roberto , Maglio Ornella , Isernia Carla
Published: December 2004

In the present paper we describe the synthesis, purification, single crystal x‐ray analysis, and solution structural characterization by nmr spectroscopy, combined with restrained molecular dynamic simulations, of the cyclic hexapeptide cyclo‐(Pro‐Phe‐β‐Ala‐Phe‐Phe‐β‐Ala). The peptide was synthesized by classical solution methods and the cyclization of the free hexapeptide was accomplished in good yields in diluted methylenechloride solution using N, N‐dicyclohexyl‐carbodiimide. The compound crystallizes in the monoclinic space group P21 from methanol/ethyl acetate. The molecule adopts in the solid state a conformation characterized by cis β‐Ala6‐Pro1 peptide bond. The α‐amino acid residues are at the corner positions of turned structures. The Pro1‐Phe2 segment is incorporated in a pseudo type I β‐turn, while Phe4‐Phe5 is in a typical type I β‐turn. Assignment of all 1H and 13C resonances was achieved by homo‐ and heteronuclear two‐dimensional techniques in dimethylsulfoxide (DMSO) solutions. The conformational analysis was based on inter‐proton distances derived from rotating frame nuclear Overhauser effect spectroscopy spectra and homonuclear coupling constants. Restrained molecular dynamic simulation in vacuo was also performed to built refined molecular models. The molecule is present in DMSO solution as two slowly interconverting conformers, characterized by a cis‐tran isomerism around the β‐Ala6‐Pro1 peptide bond. This work confirms our expectations on the low propensity of β‐alanyl residues to be positioned at the corners of turned structure. © 1994 John Wiley & Sons, Inc.
Parallel nucleic acid helices with hoogsteen base pairing: Symmetry and structure
Authors: Raghunathan G. , Miles H. Todd , Sasisekharan V.
Published: December 2004

Molecular structures for parallel DNA and RNA double helices with Hoogsteen pairing are proposed for the first time. The DNA helices have sugars in the C2′‐endo region and the phosphodiester conformations are (trans, gauche−), and the RNA helices have sugars in the C3′‐endo region and the phosphodiester conformations are (gauche−, gauche−). A pseudorotational symmetry relates the two parallel strands of DNA helices and a screw symmetry relates the two strands of RNA helices, which have an associated tilt of the The conformational space of parallel helices with Hoogsteen base pairing, unlike the Watson‐Crick duplex, is highly restricted due to the unique positioning of the symmetry axis in the former case. The features of the parallel double helix with Hoogsteen pairing are compared with the Watson‐Crick duplex and the corresponding triple helix. © 1994 John Wiley & Sons, Inc.
Mixed conformation in Cα,α‐disubstituted tripeptides: X‐ray crystal structures of Z‐Aib‐Dph‐Gly‐Ome and Bz‐Dph‐Dph‐Gly‐Ome
Authors: Pavone V. , Lombardi A. , Saviano M. , Di Blasio B. , Nastri F. , Fattorusso R. , Zaccaro L. , Maglio O. , Yamada T. , Omote Y. , Kuwata S.
Published: December 2004

We report here the synthesis and molecular structure in the solid state of fully protected tripeptides containing Cα,α‐diphenylglycine (Dph), namely Z‐Aib‐Dph‐Gly‐OMe (Aib: Cα,α‐dimethylgrycine) and Bz‐Dph‐Dph‐Gly‐OMe. The molecular conformation around the Dph residue, containing two bulky substituents, is fully extended, while the Aib residue, containing two smaller groups on the Cα atom, adopts the typical 310/α‐helical conformation. Gly residues, without substituents on the Cα atom, show different conformational preferences. Each residue seems to behave, from a conformational point of view, independently from the presence of the other residues, and thus mixed local conformations (folded and extended) are present in the crystals. The nonconventional peptide synthesis, using the Ugi reaction, is also reported. © 1994 John Wiley & Sons, Inc.
Li+ counterion self‐diffusion in ordered DNA
Authors: Andreasson Bo , Nordenskiöld Lars , Eriksson Per‐Olof , Rupprecht Allan
Published: December 2004

The anisotropic self‐diffusion coefficient of 7Li+ (I = 3/2) counterions has been studied in hydrated, macroscopically oriented Li‐(B)DNA fibers at relatively high water contents, corresponding to approximate DNA‐DNA helix axis distances of 22–35 Å, using the pulsed field gradient hmr spin‐echo method. Self‐diffusion coefficients parallel (D∥) and perpendicular (D⟂) to the DNA helix axis increase with increasing salt content and with increasing DNA‐DNA helix axis distance. The observed anisotropy D∥/D⟂ decreases from 1.6 to 1.2 with the DNA‐DNA separation increasing from 22 to 35 Å in the salt‐free sample. This result can be understood by the obstruction effect caused by the DNA molecules themselves. The values of the Li+ self‐diffusion coefficients in the most water‐rich system with no added salt (corresponding to an approximate distance of 35 Å between the DNA helix axes) were D∥ ∼ 1.15 × 10−10 m2 s−1 and D⟂ ∼ 0.98 × 10−10 m2 s−1, compared to 9.14 × 10−10 m2 s−1 for the diffusion of Li+ in an aqueous solution of LiCl (∼ 2.1M). The possible occurrence of restriction effects in the DNA fibers have also been studied by determining the self‐diffusion coefficient at different effective diffusion times. The self‐diffusion coefficient of Li+ in the sample with the largest DNA‐DNA helix axis distance seems to be independent of the effective diffusion time, which indicates that the lithium ions are not trapped within impermeable barriers. The possibility of diffusion through permeable barriers has also been investigated, and is discussed. © 1994 John Wiley & Sons, Inc.
Crystal structure of guanylyl‐2′,5′‐cytidine dihydrate: An analogue of msDNA‐RNA junction in stigmatella aurantiaca
Authors: Krishnan R. , Seshadri T. P.
Published: December 2004

Sequence analysis of msDNA from bacterium such as Stigmatella aurantiaca, Myxococcus xanthus and Escherichia coli B revealed that the guanine residue of the single‐stranded RNA is linked to the cytosine residue of the msDNA through a 2′–5′ instead of a conventional 3′–5′ phosphodiester bond. We have now obtained the crystal structure of the self‐complementary dimer guanylyl‐2′,5′‐cytidine (G2′p5′C) that occurs at the msDNA‐RNA junction. G2′p5′C crystallizes in the orthorhombic space group P212121 with a = 8.376(2), b = 16.231(5), c = 18.671(4). CuK ∝ intensity data were collected on a diffractometer in the ω −2θ scan mode. The amount of 1699 out of 2354 reflections having I ≥ 3σ (F) were considered observed. The structure was solved by direct methods and refined by full‐matrix least squares to a R factor of 0.054. The conformation of the guanine base about the glycosyl bond is syn (χ1 = −54°) and that of cytosine is anti (χ2 = 156°). The 5′ and 2′ and ribose moieties show C2′‐endo and C3‐endo mixed puckering just like in A2′p5′A, A2′p5′C, A2′p5U, and dC3′p5′G. Charge neutralization in G2′p5′C is accomplished through protonation of the cytosine base. An important feature of G2′p5′C is the stacking of guanine on ribose 04′ of cytosine similar to that seen in other 2′–5′ dimers. G2′p5′C, unlike its 3′–5′ isomer, does not form a miniature double helix with the Watson‐Crick base‐pairing pattern. Comparison of G2′p5′C with A2′p5′C reveals that they are isostructural. A branched trinucleotide model for the msDNA‐RNA junction has been postulated. © 1994 John Wiley & Sons, Inc.
Thermal unfolding equilibria in homodimeric chicken gizzard tropomyosin coiled coils
Authors: Wrabl James , Holtzer Marilyn Emerson , Holtzer Alfred
Published: December 2004

CD studies are presented on thermal unfolding of coiled‐coil homodimers of two genetic variant chains of chicken gizzard tropomyosin (CG‐Tm). The experiments include the effects of cross‐linking both isoforms and the dependence on protein concentration of unfolding in both reduced isoforms, variables not examined in extant work. The general shapes of the unfolding curves for singly cross‐linked species depend on whether the crosslink is at C190 (its site on one isoform) or at C36 (its site on the other). These curves are compared with extant ones for various cross‐linked species of rabbit tropomyosin. The comparison supports the view that the unfolding behavior of cross‐linked species results from a complex interaction of strain at the cross‐link, local variations in structural stability, and loop entropy. The observed concentration dependence of the transition temperature for the uncross‐linked (reduced) species of CG‐Tm is very small (2.9°C) for one variant homodimer and unobservably small (< 2°C) for the other in the 100‐fold concentration range (∼ 0.01–1.0 mg/mL) accessible here. These experimental values of ΔTm are much smaller than are predicted from extant values of the van't Hoff transition enthalpies, calling the latter into question. © 1994 John Wiley & Sons, Inc.
Structural stability of short subsequences of the tropomyosin chain
Authors: Holtzer Marilyn Emerson , Crimmins Dan L. , Holtzer Alfred
Published: December 2004

The native tropomyosin molecule is a parallel, registered, α‐helical coiled coil made from two 284‐residiic chains. Long excised subsequences (≥ 95 residues) form the same structure with comparable thermal stability. Here, we investigate local stability using shorter subsequences (20‐50 residues) that are chemically synthesized or excised from various regions along the protein chain. Thermal unfolding studies of such shorter peptides by CD in the same solvent medium used in extant studies of the parent protein indicate very low helix content, almost no coiled‐coil formation, and high thermal lability of such secondary structure as does form. This behavior is in stark contrast to extant data on leucine‐zipper peptides and short “designed” synthetic peptides, many of which have high α‐helix content and form highly stable coiled coils. The existence of short coiled coils calls into question the older idea that short subsequences of a protein have little structure. The present study supports the older view, at least in its application to tropomyosin. The intrinsic local α‐helical propensity and helix–helix interaction in this prototypical α‐helical protein is sufficiently weak as to require not only dimerization, but macro‐molecular amplification in order to attain its native conformation in common benign media near neutral pH. © 1995 John Wiley & Sons, Inc.
Impact of moisture on thermally induced denaturation and decomposition of lyophilized bovine somatotropin
Authors: Bell Leonard N. , Hageman Michael J. , Bauer Juliane M.
Published: December 2004

The nonisothermal transitions of lyophilized recombinant bovine somatotropin (rbSt) as seen via differential scanning calorimetry were evaluated with respect to moisture content. The transition peak temperature of rbSt decreased with increasing moisture from 161°C in the dry state to a plateau of 65°C at 28% moisture, which is similar to that of rbSt in solution. Using high performance liquid chromatography, this irreversible endothermic transition consisted primarily of unfolding, hydrophobic aggregation, and some covalent modifications. In the dry state, covalent modifications, including polymerization into compounds of higher molecular weight, were more prominent, while in the presence of moisture, hydrophobic aggregation was most prominent. The irreversibility and scan rate dependence of the endothermic phenomena supports the kinetic nature of the transition rather than a simple equilibrium between globular and unfolded states. The apparent activation energy, for the net transition (i.e., unfolding, hydrophobic aggregation, and covalent modifications) was 57 kcal/mol for rbSt at 9.9% moisture. The observed enthalpy of the transition increased, decreased, then approximately leveled off as a function of increasing moisture content. This can be explained by the increasingly significant contribution of the exothermic aggregation at higher moisture contents. © 1995 John Wiley & Sons, Inc.