bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of linear anisotropies on the CD spectrum: Is it true that the oriented polyvinyalcohol film has a magic chiral domain inducing optical activity in achiral molecules?
Authors: Shindo Yohji , Nishio Motohide
Published: December 2004

Recent publication of the induced CD studies by Ritcey and Gray [(1988) Biopolymers 27, 1363–1374] states that the Congo red dye bound to regenerated cellulose in highly swollen gel films formed shows induced optical activity, reflecting the chiral molecular arrangement of the cholesteric structure. In this paper, we show that this conclusion is erroneous owing to a misinterpretation of the experimental results. We point out in detail where the errors were committed, and present our experimental data to prove that the average CD signal obtained with using the method of Tunis‐Schneider and Maestre [(1970) J. Mol. Biol. 52, 521–541] can never be regarded as the true induced CD signal. We further present the result of analyzing our data with the Mueller matrix approach to confirm our conclusion. We repeat the conclusion of our previous paper [(1985) J. Am. Chem. Soc. 107, 91–97] that the CD spectra observed in cholesteric liquid structure cannot provide us with the proof showing the optical activity induced in achiral molecules.
Phase transitions of concentrated DNA solutions in low concentrations of 1 : 1 supporting electrolyte
Authors: Strzelecka Teresa E. , Rill Randolph L.
Published: December 2004

Transitions between isotropic and liquid crystalline phases of concentrated solutions of DNA with an average contour length (500 Å) near the persistence length were examined in 0.01 M supporting 1 : 1 electrolyte (predominantly NaCl). A quantitative phase diagram describing the transitions occurring over a DNA concentration range from 100 to 290 mg/mL and temperatures from 20 to 60°C was constructed from solid‐state31P‐nmr data and examination of the morphologies of the mesophases by polarized light microscopy. Three anisotropic phases were observed in solutions with DNA concentrations of 160–290 mg/mL: an unidentified, weakly birefringent phase termed “precholesteric” a true cholesteric phase with pitch ≈ 2 μm, and a third, presumably more highly ordered phase. Comparison with previous studies showed that the critical concentration for anisotropic phase formation and the nature of the phases formed by these DNA molecules are not strongly affected by decreasing the supporting electrolyte concentration from ∼ 0.2 M to 10 mM. There are, however, profound effects of decreasing the supporting electrolyte concentration on the width of the transition from isotropic to totally anisotropic solutions, and the nature of the transitions between phases. Decreasing the supporting electrolyte concentration significantly increases the concentration range of persistence of the isotrophic phase, and results in the formation of triphasic solutions (isotropic and two liquid crystalline phases).

Values of the critical DNA concentrations for anisotropic phase formation calculated from the theory of A. Stroobants et al. [(1986) Macromolecules 19, 2232 to 2238] were found to be significantly lower than the observed values for any reasonable estimate of the effective radius, probably because of the relatively short lengths of DNA fragments examined in the present study. Comparison of the experimentally determined DNA concentrations required for anisotropic phase formation with the values predicted from Flory's lattice statistics theory, which explicitly considers the rod length, permitted estimation of the effective DNA radius. The estimated radius was inconsistent with effective radii calculated from Poisson‐Boltzmann (P‐B) theory based on a supporting electrolyte concentration of 10 mM, but was in fair agreement with P‐B theory assuming that Na+ DNA contributes approximately 0.24 Na+ counterions/nucleotide to the effective free sodium ion concentration.
The solution conformations of ferrichrome and deferriferrichrome determined by 1H‐nmr spectroscopy and computational modeling
Authors: Constantine K. L. , De Marco A. , Madrid M. , Brooks C. L. , Llinás M.
Published: December 2004

We have applied computational procedures that utilize nmr data to model the solution conformation of ferrichrome, a rigid microbial iron transport cyclohexapeptide of known x‐ray crystallographic structure [D. van der Helm et al. (1980) J. Am. Chem. Soc. 102, 4224–4231]. The Al3+ and Ga3+ diamagnetic analogues, alumichrome and gallichrome, dissolved in d6‐dimethylsulfoxide (d6‐DMSO), were investigated via one‐ and two‐dimensional 1H‐nmr spectroscopy at 300, 600, and 620 MHz. Interproton distance constraints derived from proton Overhauser experiments were input to a distance geometry algorithm [T. F. Havel and K. Wüthrich (1984) Bull. Math. Biol. 46, 673–691] in order to generate a family of ferrichrome structures consistent with the experimental data. These models were subsequently optimized through restrained molecular dynamics/energy minimization [B. R. Brooks et al. (1983) J. Comp. Chem. 4, 187–217]. The resulting structures were characterized in terms of relative energies and conformational properties. Computations based on integration of the generalized Bloch equations for the complete molecule, which include the14N‐1H dipolar interaction, demonstrate that the x‐ray coordinates reproduce the experimental nuclear Overhauser effect time courses very well, and indicate that there are no significant differences between the crystalline and solution conformations of ferrichrome. A similar study of the metal free peptide, deferriferrichrome, suggests that at least two conformers are present in d6‐DMSO at 23°C. Both are different from the ferrichrome structure and explain, through conformational averaging, the observed amide NH and CHα multiplet splittings. The occurrence of interconverting peptide backbone conformations yields an increased number of sequential NH‐CHα and NH‐NH Overhauser connectivities, which reflects the 〈r−6〉 dependence of the dipolar interaction. Our results support the idea that, in the case of structurally rigid peptides, moderately accurate distance constraints define a conformational subspace encompassing the “true” structure, and that energy considerations reduce the size of this subspace. For flexible peptides, however, the straightforward approach can be misleading since the nmr parameters are averaged over substantially different conformational states.
Size, shape parameters, and Ca2+‐induced conformational change of the gelsolin molecule: A dynamic light scattering study
Authors: Patkowski A. , Seils J. , Dorfmüller Th. , Hinssen H.
Published: December 2004

We have investigated the size and shape of gelsolin, a calcium‐dependent actin‐binding protein, by means of combined photon correlation spectroscopy and depolarized dynamic light scattering. From the measured rotational and translational diffusion coefficients, a hydrodynamically equivalent ellipsoid of revolution with an axial ratio of 0.23 is obtained in the presence of EGTA. Such a distinctly elongated shape is suggested also by the depolarization ratio of 1.6 × 10−3. In the presence of Ca2+, when gelsolin has two Ca ions bound, a significant decrease in the translational diffusion coefficient and a smaller decrease in the rotational diffusion coefficient are observed. Both effects can be assigned to a change of shape from the elongated toward a more spherical form with an axial ratio of 0.37 and a hydrodynamic volume more than twice as large as in the absence of Ca2+. The apparent molecular mass as measured by static light scattering remains unchanged, indicating that the volume increase is not due to aggregation of gelsolin. The relatively large conformational changes observed upon binding of Ca2+, are probably related to an alteration of the surface charge of the molecule. As a result of these conformational changes, actin binding sites may become exposed and the molecule gains a high affinity for two actin molecules.
Excluded volume effects on the partition of macromolecules between two liquid phases
Authors: Zimmerman Steven B. , Trach Stefan O.
Published: December 2004

Partition parameters of several proteins and other macromolecules are measured in an aqueous two‐phase liquid system containing polyethylene glycol and phosphate buffer. Distribution of macromolecules is a function of the relative volume excluded to the macromolecules in the two phases. A simple model with no adjustable parameters yields covolumes of the macromolecules with the polyethylene glycol. Covolumes are used to estimate effective molecular volumes and the magnitudes of excluded volume effects. The same approach is applied to mixtures of macromolecules.
Counterion effects on the physical properties and the A to B transition of calf‐thymus DNA films
Authors: Lavalle N. , Lee S. A. , Rupprecht A.
Published: December 2004

We report measurements of the water content and swelling of wet‐spun films of Na‐, K‐, Rb‐, and Cs‐DNA as a function of relative humidity (rh). The water contents (number of water molecules per base pair of DNA) of these films are found to be quite similar, indicating that the identity of the counterion species is unimportant for the water content. Since the A to B transition for these DNAs occurs at different rhs, the corresponding water contents of the A to B transition are found to be quite different. These films swell as a function of rh in a very similar manner, implying that the changes in the intermolecular bonds in the different DNAs are similar. Dramatic changes are observed in the dimensions of the films above 84% rh for all types of DNA. Combining the water content and swelling measurements yields the dependence of the volume per base pair on water content. The volume per base pair is observed to be a nonlinear function of water content, indicating nonideal mixing of the water with the DNA.
Crystal and molecular structure of Boc‐D‐Ala‐ΔPhe‐Gly‐ΔPhe‐D‐Ala‐OMe: A 310‐helical dehydropeptide
Authors: Ciajolo M. Rosaria , Tuzi Angela , Pratesi Claudio R. , Fissi Adriano , Pieroni Osvaldo
Published: December 2004

The crystal and molecular structure of the pentapeptide Boc‐D‐Ala‐ΔPhe‐Gly‐ΔPhe‐D‐Ala‐OMe, containing two dehydrophenylalanine residues, was determined by x‐ray diffraction. The molecule crystallizes in the orthorombic P212121 space group, with a = 10.439(3), b = 15.319(3) and c = 21.099(4) Å.

In the solid state, the conformation of the pentapeptide is characterized by the presence of two type III′ β‐turns. Thus the peptide assumes a left‐handed 310‐helical conformation, the left sense being due to the D configuration of the alanine residues. The two unsaturated residues are located in the (i + 1) position of the first β‐turn and in the (i + 2) position of the second β‐turn, respectively.

In the crystal, the helical molecules are linked head to tail by hydrogen bonds. Lateral hydrogen bonds are also formed between molecules related by a twofold screw symmetry. This gives rise to a typical mode of packing characterized by infinite helical “chains,” smiliar to the packing found in other oligopeptides that adopt a 310‐helical structure.
Conformational search in enkephalin analogues containing a disulfide bond
Authors: Froimowitz Mark
Published: December 2004

A systematic Conformational search has been performed for the 14‐membered ring in model compounds for disulfide‐containing enkephalin analogues. The model compounds examined are , and the corresponding compounds with L‐amino acids at the C‐terminus. About 100 starting conformations were generated for each compound with the RNGCFM program and energy minimized with the AMBER program. Between 21 and 38 conformers within 3 kcal/mole of the apparent global minimum were found for each compound. There appeared to be fewer possible conformations of the disulfide‐containing side chain than of the main chain. , whose parent compound is selective for opioid δ receptors, was found to prefer conformers with a positive dihedral angle of the disulfide bond, which is consistent with the previous proposal that δ‐receptor selectivity may be associated with this conformational preference. Additional calculations were performed on the complete structure of (DPDPE) with various possible conformations of the tyrosine and phenylalanine side chains. Conformational free energies and entropies were computed for these conformers from the molecular vibrations obtained from a normal mode analysis. As was found previously, conformers with low energies tended to have lower entropies, which resulted in a narrowing of the free energy differences between conformers. A conformer is identified that has the lowest energy hitherto found for DPDPE. It is suggested that DPDPE may be a useful compound for evaluating conformational search strategies because of its relatively small size and the number of conformers that have already been identified. Conformational energy calculations are also reported for naltrindole using the MM2(87) program. Naltrindole, which incorporates two aromatic 6‐membered rings in a rigid structure, is a highly selective and potent opioid δ‐receptor antagonist and may be an important clue regarding the biologically active conformer of DPDPE. Various conformers of DPDPE have been superimposed quantitatively onto the structure of naltrindole using the SUPER program and those conformers of DPDPE that are the best fit to naltrindole are reported.
α‐Helix to random‐coil transitions of two‐chain coiled coils: The use of physical models in treating thermal denaturation equilibria of isolated subsequences of αα‐tropomyosin
Authors: Holtzer Alfred , Holtzer Marilyn Emerson
Published: December 2004

Two extant models of thermal folding/unfolding equilibria in two‐chain, α‐helical coiled coils are tested by comparison with experimental results on excised, isolated subsequences of rabbit αα‐tropomyosin (Tm). These substances are designated iTmj where i and j are, respectively, the residue numbers (in the 284‐residue parent chain) of the N‐ and C‐terminal residues of the subsequence. One model postulates that a coiled coil consists of segments, each denaturing in an all‐or‐none manner, like small globular proteins. Thus this model yields a small number of populated molecular species. In an extant calorimetry study of 11Tm127 and of 190Tm284, each required only two all‐or‐none‐segments, and their enthalpies and transition temperatures were assigned. These assignments are shown here to yield the concentration of all molecular species, and therefore the helix content, as a function of temperature. Such calculations for 190Tm284 are in tolerable agreement with CD experiments, but those for 11Tm127 are in gross disagreement. Thus, either the model itself or the calorimetric assignment is faulty. In the second model, all conformational states are counted and weighted, as in the Zimm–Bragg theory for single‐chain polypeptides. This theory has been extended (by Skolnick) to two‐chain coiled coils and is here used to fit CD data for 11Tm127, 142Tm281, and 190Tm284. The fit is tolerable for 11Tm127, good for 142Tm281, and quantitative for 190Tm284. Thus this comparison does not falsify this second model. The helix–helix interaction free energy, obtainable from the fit, shows nonadditivity when isolated subsequences are compared with the parent. This suggests that removal of a region from a long coiled coil allows energetically substantial adjustments in side‐chain packing in the helix–helix interface. Thus, the helix–helix interaction in long coiled coils is characteristic of a global free energy minimum and not just of the regional constellation of side chains.
Polyelectrolyte properties of biopolymers: Conductivity and secondary structure of polyriboadenylic acid and its salts in solutions
Authors: Kuznetsov I. A. , Vorontsova O. V. , Kozlov A. G.
Published: December 2004

Polyriboadenylates of alkali metals were obtained from (1) K+‐poly(A) (salts I) and (2) H+‐poly( A) (salts II) by the ion‐exchange method. The conductivity of these salts as well as of H+‐poly(A) were studied. Salts I and II of the same counterion were shown to have significantly different conductivity coefficients (f) and polyion conductances (λ). The charge density parameter (ζ) was 1.3 and 2.5, respectively, with λ equal to 44 and 83 ohm−1 cm2 mole−1 for poly(A)‐I and poly (A)‐II salts, respectively. This is credited to the difference in the conformations of corresponding polyions. The linear dependence of equivalent conductivity on the square root of polymer concentration (Kohlrausch coordinates), earlier obtained for DNA, is also satisfied for the studied polynucleotides. A comparison of the slopes of straight lines in Kohlrausch coordinates for poly(A), simple electrolytes, and for earlier studied polyribouridylic acid salts lends credence to the concepts, developed by a number of authors, that DNA can act as a “buffer” against the ion–ion interaction in concentrated electrolyte solutions. Using the approximation that the polyion conductance is independent of the counterion nature, parameter f (agreeing in this case with Eisenberg parameter ϕ) has been shown to decrease as the polynucleotide concentration is increased; the decrease is caused by the relaxation effect. The transference numbers of counterions, which have negative values in poly (A)‐II solutions, grow with the increase in polymer concentration; the higher the ζ, the more apparent is this increase. This is explained by the increase in the fraction of conductivity along the polyion chains (“surface” conductivity) with the growth of polyelectrolyte concentration.
Premelting thermal fluctuational base pair opening probability of poly(dA) · poly(dT) as predicted by the modified self‐consistent phonon theory
Authors: Chen Y. Z. , Feng Y. , Prohofsky W.
Published: December 2004

We employ a mean field, modified, self‐consistent phonon theory to evaluate the single base‐pair opening rate and the probability of a base pair in the amino proton exchangeable state for the homopolymer poly(dA) · poly(dT) at temperatures below the helix–coil transition region. Our calculated premelting single base‐pair opening probabilities are in general agreement with several available experimental estimates from imino proton exchange and formaldehyde‐induced DNA melting measurements. These calculated opening probabilities, however, are in disagreement with the prediction of the helix–coil transition theory. Possible reasons for the differences are discussed, especially the possible different definition of a meaningful open state in the premelting region. The premelting open state of the modified self‐consistent phonon approximation theory seems to be appropriate to describe a solvent‐accessible open configuration that is sufficient to facilitate important chemical reactions such as imino proton exchange and formaldehyde reaction with the bases. This can be compared with the completely unstacked open state of the helix–coil transition theory originally defined in the helix–coil transition region. We propose that the amino proton exchangeable state is different from the open state associated with melting and only involves the breaking of the amino interbase H bond. The agreement between the calculated and experimentally estimated probability of a base pair in the amino proton exchangeable state seems to support this hypothesis.
Shielding effects of small ions in gel electrophoresis of DNA
Authors: Stigter Dirk
Published: December 2004

Results of free electrophoresis and free sedimentation of charged rods are introduced to allow for electrical double‐layer effects in the gel electrophoresis of DNA, modeled as a Random flight sequence of rodlike Kuhn chain elements. The kinetics of DNA is shown to depend strongly on the orientation of the chain elements with respect to the external field and with respect to the direction of their velocity. The new theory gives approximate agreement between the DNA charge derived from electrophoresis of free and tethered DNA (close to 1.0e per DNA phosphate in both cases), compared with the earlier discrepancy of a factor 10 or 20 for the theory without shielding by salt. As part of a realistic force field for macromolecular dynamics simulation, the small ion effects are included in an expression for the gel forces restraining the DNA in gel electrophoresis from moving as in free electrophoresis.
Solution structure of salmon calcitonin
Authors: Meyer Jean‐Philippe , Pelton John T. , Hoflack Jan , Saudek Vladimir
Published: December 2004

Salmon calcitonin, a 32‐residue peptide with a 1–7 disulfide bridge, was synthesized by standard solid‐phase techniques, and studied by CD and two‐dimensional NMR experiments. The peptide was dissolved in pure trifluoroethanol (TFE) and in aqueous solutions containing various amounts of TFE. CD studies in pure TFE indicated the presence of an α‐helical structure comprising 40% of the constituent amino acids. This was fully confirmed by nmr. A detailed analysis was performed with the peptide in a 9 : 1 deuterated TFE/H2O mixture. A total of 365 nuclear Overhauser enhancements (154 intraresidual, 112 sequential and 99 long range) were compiled from the nuclear Overhauser enhancement spectroscopy spectra and used in the distance geometry calculations. The core of the peptide between residues 8 and 22 assumes an α‐helix like structure. The Cys 1–Cys 7 ring is well defined and in close association with the helix, while the C‐terminal decapeptide folds back toward the core, forming a loose loop.
Heteronuclear two‐and three‐dimensional nmr spectroscopy of 13C in natural abundance by multiplicity selection and editing: Application to peptides
Authors: Kessler H. , Schmieder P.
Published: December 2004

Several new proton‐detected heteronuclear two‐dimensional (2D) nmr techniques are presented that exhibit the features of selection and editing of multiplicity. The theoretical basis of the new features is briefly discussed and the application of the 2D techniques to a thioanalogon of Cyclosporin A [Thio‐(1)‐cyclosporin A] is shown. In addition, an extension of the experiments to three‐dimensional (3D) techniques is demonstrated and the application of two 3D techniques to Thio‐(1)‐cyclosporin A with 13C in natural abundance is presented. The new techniques can help simplify heteronuclear shift correlations and increase the resolution in the carbon dimension.
Conformation and formation tendency of the cyclotetrapeptide cyclo(D‐pro‐D‐pro‐L‐pro‐L‐pro): Experimental results and molecular modeling studies
Authors: Mästle Werner , Link Ulrich , Witschel Wolfgang , Thewalt Ulf , Weber Thomas , Rothe Manfred
Published: December 2004

The title compound represents the smallest member of cyclic proline peptides corresponding to the general formula c(DDLL‐Pro4)n with a strictly D, D, L, L double‐alternating sequence of the chiral amino acid residues. The cyclopeptides with n ⩾ 2 could be synthesized from both DDLL‐Pro4 (1) and DLLD‐Pro4 (2). The cyclic monomer (n = 1) resulted only from 2, whereas not even a trace could be found by cyclizntion of 1. The peptide exists in a strongly strained Ci symmetrical conformation (x‐ray analysis) with alternating cis and trans peptide bonds (ctct form I). The cis peptide bonds deviate from planarity (ω = 22°); two of the pyrrolidine rings show a “South” conformation (ϕ = −94°), whereas the other residues exhibit Cα‐endo puckering (ϕ = −124°). Two of the ψ angles surprisingly occur at +41° (anti‐cis), the others are located in the trans′region. A quantitative ring opening occurs with trifluoroacetic acid at room temperature. In solution the existence of an isomeric ctcc sequence (form Ia) is indicated. Dreiding model studies also suggested a favorable conformation with a tctc sequence (form II). Consequently, we performed molecular mechanics calculations, based on the CHARMM force field and semiempirical quantum mechanical AMI calculations (MOPAC program). Pronounced differences in the backbone parameters were found using these two methods. However, the theoretical studies evidenced the experimentally obtained differences in the cyclization tendencies of the linear precursors.
The solution structure of the lantibiotic gallidermin
Authors: Freund Stefan , Jung Günther , Gutbrod Oliver , Foikers Gerd , Gibbons William A. , Allgaier Hermann , Werner Rolf
Published: December 2004

The 21‐peptide amide antibiotic gallidermin is a potential therapeutic against acne disease. It belongs to the class of polycyclic lanthionine and α,β‐clidehydroamino acids containing polypeptides, which were named “lantibiotics.” The structural gene of the recently elucidated lantibiotic gallidermin encodes a precursor peptide containing Ser, Thr, and Cys residues in the Oterminal prolantibiotic part, and an unusually hydrophilic leader peptide. The ribosomally synthesized pregallidermin is posttranslationally modified and processed to a complex peptide antibiotic with four/sulfide rings and two unsaturated residues.

The complete solution structure of gallidermin was determined in triffuoroethanol : water (95 : 5) and dimethylsulfoxide by two‐dimensional 1H‐nmr at 500 MHz, using a combination of double quantum filtered correlated spectroscopy, homonuclear Hartman‐Hahn, and nuclear Overhauser enhancement spectroscopy experiments. Using a total number of 152 distance constraints from NOEs and 14 torsional constraints, derived from coupling constants, we obtained a screwlike solution structure of gallidermin. Restrained molecular dynamics simulations yielded a set of five converging structures with an atomic rms difference of 1.7 Å for the backbone atoms, not dependent on the starting structure. The spatial structure model is in excellent agreement with the amphiphilic and channel‐forming properties of gallidermin on membranes and its tryptic cleavage at the exposed site between residues 13 and 14.
Conformational studies of stereoisomeric 14‐membered cyclic enkephalin analogues containing 1‐naphthyialanine at the fourth position: Chirality effect of leucine at the fifth position on biological activity and receptor selectivity
Authors: Yamazaki Toshimasa , Said‐Nejad Odile E. , Schiller Peter W. , Goodman Murray
Published: December 2004

In order to study structure‐activity relationships of enkephalin‐related analogues, we report the biological activity and conformational analysis of four 14‐membered cyclic enkephalin analogues with β‐(1‐naphthyl)alanine in place of phenylalanine at the fourth position, Tyr‐c[D‐A2bu‐Gly‐(L and D)‐βNal(1)‐(L and D)‐Leu]. The L‐βNal(1)‐containing analogues display higher activity at both the μ and δ receptors than the corresponding analogues with the L‐Phe residue. In contrast to the linear enkephalins, the cyclic analogues with the D‐βNal(1) residue are also active at the μ receptor since the relative spatial arrangement of functional groups required for biological activity is achieved by the constrained nature of the cyclic molecules. A comparison of the findings from the conformational analysis and biological assays establishes that relatively extended structures, in which the two aromatic side chains are oriented in opposite directions with a ∼ 14Å separation, is required for activity at the μ receptor. On the other hand, folded conformations with nearly parallel orientations and a close proximity ( < 10Å) of the aromatic rings of the Tyr and βNal(1) residues are required for activity at the δ receptor. It should be noted that the overall structures and thus the biological profiles of the 14‐membered cyclic enkephalin analogues are strongly dependent on the conformation of the second residue. The folded conformations with parallel orientation of the two aromatic side chains of Tyr‐c [D‐A2bu‐Gly‐L‐βNal (1)‐D‐Leu] is stabilized by an interaction between the Tyr phenolic OH proton and βNal(1) C*O groups. This analogue, which shows the highest activity at both the μ and δ receptors among the four stereoisomers studied, displays an increase of the fraction of the side‐chain χ1 = t conformer for the βNal(1) residue. It is concluded that the incorporation of the D‐Leu residue at the fifth position increases the relative fraction of the folded conformations with parallel orientation of the aromatic side chains, and hence enhances activity at the δ receptor as compared to the corresponding L‐Leu containing analogue.
The substructure of agarose gels as prepared for electrophoresis
Authors: Whytock Susan , Finch John
Published: December 2004

Gelled agarose was observed by freeze‐fracture and electron microscopy. Aggregated double helices of agarose form a fibrous network that showed conformational variations over a range of agarose concentrations (0.3–2%). Diameters of fibers tend to increase with rising concentrations and the appearance of protuberances or cul‐de‐sacs in the network increases with falling concentration.
A stable antiparallel cytosine–thymine base pair occurring only at the end of a duplex
Authors: Vanhommerig Sylvia A. M. , van Genderen Marcel H. P. , Buck Henk M.
Published: December 2004

Ultraviolet hyperchromicity experiments indicate that in DNA duplex formation, a C–T mismatch is destabilizing in the center of a duplex, but behaves as a stable base pair at the terminus of a duplex. The C–T base pair is thought to contain two hydrogen bonds, but has thermodynamic parameters (ΔH° and ΔG° of dissociation) that are similar to a G‐C base pair. AMBER molecular mechanics calculations were performed to study the possible structural properties of DNA duplexes with central and terminal C–T combinations. These calculations also indicate that a central C–T pair destabilizes a duplex, while terminal C–T forms a stable base pair. Hydrogen bonding between cytosine and thymine occurs only in the energy‐minimized structures when the helix diameter decreases and the propeller twist angle between the bases increases. These changes are found to occur only at the end of a duplex in the calculations, which may explain the experimental results.
Valinomycin and its interaction with ions in organic solvents, detergents, and lipids studied by Fourier transform IR spectroscopy
Authors: Jackson Michael , Mantsch Henry H.
Published: December 2004

The structure of valinomycin in a range of organic solvents of varying polarity and in detergent and lipid dispersions has been studied by Fourier transform ir Spectroscopy. In solvents of low polarity such as chloroform, ir spectra of valinomycin are fully consistent with the bracelet structure proposed on the basis of nmr Spectroscopy, showing a single narrow amide I component attributable to the presence of β‐turns and a single band arising from nonhydrogen‐bonded ester CO groups. K+ complexation results in a downward shift in the amide I band frequency, indicating an increase in the strength of the amide hydrogen bonds, along with a shift to lower frequencies of the ester CO absorption due to a reduction in electron density in these bonds upon complexation. Identical results were obtained with NH, a finding not previously reported.

In solvents of both medium (CHCl3/DMSO 3 : 1) and high (pure DMSO) polarity, we find evidence of significant disruption of the internal hydrogen‐bonding network of the peptide and the appearance of a band suggesting the presence of free amide CO groups. In such solvents, complexation with K+ and NH was not observed.

The structure of valinomycin in detergent micelles resembles that in nonpolar organic solvents. However, changes were found in the amide I and ester carbonyl maxima as 2H2O penetrated the micelle which suggest significant interaction between the solvent and peptide. Complexation with K+ was reduced in cationic detergent micelles as a result of a decrease in the effective K+ concentration due to charge repulsion at the micelle surface.

In lipid bilayers the structure again appears identical to that found in chloroform. As in detergent micelles, the amide I and ester carbonyl bands exhibit shifts that indicate interactions with solvent. Complexation with both K+ and NH is efficient, producing spectral changes similar to those seen in organic solvents.
Premelting thermal fluctuational interbase hydrogen‐bond disrupted states of a B‐DNA guanine–cytosine base pair: Significance for amino and imino proton exchange
Authors: Chen Y. Z. , Zhuang W. , Prohofsky E. W.
Published: December 2004

Modified self‐consistent phonon theory when applied to the DNA double helix indicates the existence of fairly long‐lived states in which single interbase H bonds are disrupted. One can then postulate a number of situations in which particular disrupted H bonds can enhance particular proton exchange. In this paper we postulate a number of such partially open states for a B‐conformation GC base pair and calculate the probability of each of these states for a B‐conformation poly(dG) · poly(dC). We compare these probabilities to those probabilities needed to explain various observed proton exchange rates. We propose that, for a GC base pair in B conformation, there are two amino proton exchangeable states—a cytosine amino proton exchangeable state and a guanine amino proton exchangeable state; both require the disruption of only the corresponding inter base H bond. The imino proton exchange, however, requires the disruption of all three inter base H bonds and this defines a third open state. Our calculated probabilities for a GC base pair in these three states are in fair agreement with available experimental estimates from measurements of amino and imino proton exchange.
Conformational correlatives of DNA band compression and bidirectional migration during field inversion gel electrophoresis, detected by quantitative video epifluorescence microscopy
Authors: Rampino Nicholas J. , Chrambach Andreas
Published: December 2004

Individual DNA molecules in the Mb size range were monitored by epifluorescence video microscopy during field inversion gel electrophoresis (FIGE). DNA migrating in an agarose gel gives rise to characteristic V‐conformational elements and when doing so exhibits a reduced mobility. When the V‐conformational elements per DNA molecule are few, the degree of retardation appears proportional to the number of V's, and since larger DNA species exhibit more V's, to DNA size. For a particular pulse frequency, the proportionality breaks down progressively as the number of V‐conformational elements per DNA molecule increases. The loss of proportionality between DNA length and migration rate is being correlated with the macroscopically observed loss of electrophoretic size discrimination known as band compression. For a particular pulsing frequency and size class of DNA, the loss of size discrimination is thought to be due to the different orientations of migration, caused by the asymmetric distribution of V‐conformational elements when the number of these elements is moderate. Small and very large DNA by contrast migrate with the direction of the biased field. These events, analyzed by microscopic measurement, are consistent with the known macroscopically observed double‐valued mobilities in FIGE.
Assignment of the 1H‐nmr resonances of the four rotamers of β‐casomorphin‐5 in DMSO
Authors: Delaet Nancy G. J. , Verheyden Patricia M. F. , Tourwé Dirk , Van Binst Georges
Published: December 2004

We report the complete assignment of the 1H‐nmr spectrum of β–casomorphin‐5 in DMSO‐d6 solution. With a combination of one‐dimensional, double quantum filtered correlated spectroscopy, homonuclear Hartmann–Hahn, and rotating frame nuclear Overhauser enhancement spectroscopy (ROESY) spectra, we were able to differentiate the four conformers originating from two Xxx‐Pro bonds present in the sequence. Exchange peaks in the ROESY spectra confirmed the presence of four interchanging conformational isomers. Based on integrations, the relative populations of the four species were estimated, while characteristic sequential nuclear Overhauser enhancements (NOEs) were used to determine the orientation of the Xxx‐Pro bonds. This orientation was also shown to correlate with the chemical shift changes for the α protons of both the Xxx and Pro residues. Finally, interresidue NOEs indicate conformational preferences for the aromatic side chains, especially in the all‐trans conformer.
DNA interpolyelectrolyte complexes as a tool for efficient cell transformation
Authors: Kabanov Alexander V. , Astafyeva Irina V. , Chikindas Mikhail L. , Rosenblat Gennadii F. , Kiselev Vsevolod I. , Severin Eugenii S. , Kabanov Victor A.
Published: December 2004

A tool was developed for enhancement of plasmid penetration into an intact cell, based on increasing DNA hydrophobicity via inclusion into a soluble interpolyelectrolyte complex (IPC) with polycations. The characteristics of formation of DNA IPC with synthetic polycations [poly(N‐ethyl‐4‐vinylpyridinium)bromide (PVP) and PVP modified with 3% of N‐cetyl‐4‐vinylpyridinium units (PVP‐C)] were studied using ultracentrifugation and polyacrylamide gel electrophoresis methods. The conditions were established under which the mixing of DNA and polycation aqueous solutions results in the selfassembly of soluble IPC species. Incorporation of DNA into IPC results in the enhancement of DNA binding with isolated Bacillus subtilis membranes. A considerable increase in the efficiency of transformation of B. subtilis cells with pBC16 plasmid resulted from incorporation of the plasmid into the IPC with PVP and CVP.
Pair distribution functions in small systems: Implications for protein structure analysis
Authors: Edelman Jay
Published: December 2004

A general formula is derived for the relation between the pair correlation function and the histogram of interparticle distances in small nonuniform systems. The formula is applied to random packings of spheres in a spherical container, which are generated by a Monte Carlo method. When measured properly, the resultant correlation functions are very similar to ones in bulk systems with the same volume fraction of particles. In contrast, the density is very nonuniform as a function of distance from the center of the container. The variation is an order of magnitude for the number density of particle centers, or several fold for the occupied volume fraction. It is described how these results can be used to analyze the forces that determine protein structure.
Fourier transform IR attenuated total reflectance study on the secondary structure of poly(γ ‐methyl L‐glutamate) surfaces treated with formic acid
Authors: Kugo Kohei , Okuno Masaki , Kitayama Koji , Kitaura Tatsuro , Nishino Jun , Ikuta Nobuo , Nishio Etsuo , Iwatsuki Makoto
Published: December 2004

Fourier transform ir attenuated total reflectance (FTIR ATR) spectra have been obtained to investigate the secondary structure of poly(γ ‐methyl L‐glutamate) (PMLG) surfaces untreated and treated with formic acid in a quantitative manner. Curve analysis including Fourier self‐deconvolution and the band fitting was applied to the ir spectra in the amide II region, revealing that the amide II band of those surfaces consists of five components. The essentially α‐helical form in the PMLG surface layer transformed readily into the β‐structure by the formic acid treatment, and the β‐structure content increased with increasing time of the treatment. The content of random coil structure of treated PMLG was generally very little and/or negligible. The depth profile obtained by considering the depth of ir beam penetration indicated that the β‐structure content also increased with approaching the outermost surface.
High osmotic stress behavior of hyaluronate and heparin
Authors: Peitzsch Robert M. , Reed Wayne F.
Published: December 2004

Using polyethylene glycol and dextran as osmotic stressing agents, the concentrations of hyaluronate and heparin were measured as a function of osmotic pressure II over the range of 0.03 to nearly 50 atmospheres. The experimental results were analyzed in terms of the Donnan osmotic pressure, the virial expansion, and Flory's first neighbor interaction parameter. In addition, II was looked at as a function of the reciprocal cube root of the concentration, which represents an average intermonomer spacing at high concentrations. The decay lengths in the so‐called hydration region were found to be around 2.6 Å and negligibly salt dependent. In the electrostatically dominated region the decay lengths were found to be dependent on the ionic strength, but not simply so. The osmotic compressibilities were also calculated, and were compared to compressibility data of corneal stroma and articular cartilage. These latter compressibilities were close to those for the pure hyaluronate and heparin, strengthening the evidence that glycosaminoglycans (GAGs) are largely responsible for connective tissue compressibility. Higher compressibilities for previously reported GAG data is thought to be related to the protein content of those samples.
Stereochemical studies on nucleic acid analogues. I. Conformations of α‐nucleosides and α‐nucleotides: Interconversion of sugar puckers via O4′‐exo
Authors: Latha Y. Swarna , Yathindra N.
Published: December 2004

The preferred conformations of ribo and deoxyribo α‐nucleosides and β‐nucleotides, the stereoisomers of the naturally occurring β‐isomers, are worked out by minimizing the conformational energy as a function of all the major parameters including the sugar ring conformations along the pseudorotation path. The results of the studies bring out certain distinct conformational features that are at variance with their β counterparts. The range of glycosyl conformations are found to be not only quite restricted here but favor predominantly the anti conformation. The syn glycosyl conformation for the entire region of α values are found to be energetically less favorable, with the barrier to anti ⇆ syn interconversion being higher especially in α‐ribonucleosides. The energetically preferred range of pseudorotation phase angles (P) is also considerably restricted and P values corresponding to the C1′‐exo range of sugars are highly unfavorable for α‐nucleosides, in sharp contrast to the broad range of sugar ring conformations favored by β‐isomers. While both trans ≃ 180° and skew ≃ 270° conformations around the C3′‐O3′ (ϕ′) bond are favored for β‐3′‐nucleotides with deoxyribose sugars, ribose sugars seem to favor only the skew values of ϕ′. Most interestingly and in sharp contrast to β‐stereoisomers, an energy barrier is encountered at P values corresponding to O4′‐endo sugars. This suggests that the possible sugar pucker interconversion between C2′‐endo/C3′‐exo and C3′‐endo/C2′‐exo in a‐anomers could take place only through the O4′‐exo region. Likewise the possible path of anti ⇆ syn interconversion in α‐nucleosides is not via high anti, in sharp contrast to α‐nucleosides. These observations should be borne in mind while assigning the sugar ring conformers in α‐nucleosides and those containing them from nmr investigations. Comparison of the results with α‐anomers seem to suggest on the whole a lack of conformational variability or the restricted nature of α‐stereoisomers. This could be one of the reasons for its nonselection in the naturally occurring nucleic acids.
Normal mode refinement: Crystallographic refinement of protein dynamic structure applied to human lysozyme
Authors: Kidera Akinori , Inaka Koji , Matsushima Masaaki , Gō Nobuhiro
Published: December 2004

A new method of dynamic structure refinement of protein x‐ray crystallography, normal mode refinement; is developed. In this method the Debye–Waller factor is expanded in terms of the low‐frequency normal modes and external normal modes, whose amplitudes and couplings are optimized in the process of crystallographic refinement. By this method, internal and external contributions to the atomic fluctuations can be separated. Also, anisotropic atomic fluctuations and their interatomic correlations can be determined experimentally even with a relatively small number of adjustable parameters. The method is applied to the analysis of experimental data of human lysozyme to reveal its dynamic structure.
Identification of structured peptide segments in folding proteins
Authors: Pincus Matthew R.
Published: December 2004

Prediction of the structures of long polypeptides and small proteins has been carried out using conformational energy calculations. These calculations can be applied to large proteins if structured regions of their sequences can be identified. Three different approaches to identifying such sequences are presented. First, sequences of five or more contiguous hydrophobic residues tend to nucleate α‐helices. Second, peptide sequences from parent proteins that have the same biological activities as the parent proteins are highly structured. Third, structured synthetic peptide segments from proteins inhibit the folding of the parent proteins by competing with the corresponding segment of the protein chain for associating with complementary regions. Examples of each of these approaches are presented.
Perturbation of peptide conformations induced in anisotropic environments
Authors: Büttner K. , Blondelle S. E. , Ostresh J. M. , Houghten R. A.
Published: December 2004

Reversed‐phase high performance liquid chromatography (RP HPLC) has been found to be a convenient and powerful tool for the study of the secondary structure of peptides. Here, the ability of proline to perturb the secondary structures of peptides induced at aqueous‐lipid interfaces and the induced conformation of polyproline peptides were investigated by means of RP HPLC. For these studies, four different complete sets of substitution analogues of model peptides expected to have specific induced conformations were used. In the first two studies, a single lysine was “walked” through two 18‐residue polyproline sequences (one N‐acetylated, the other not). In the remaining two studies, a proline was “walked” through two different sequences that had been found earlier to be induced into an α‐helical conformation during RP HPLC (an 18‐residue polyalanine sequence and the amphipathic 14‐residue sequence Ac‐LLKLLKKLLKKLKK‐NH2). Sixty‐eight individual analogues were synthesized for this study and the effect of the respective substitutions on retention times was determined. The results are consistent with the concept that, upon interaction with the C‐18 of the stationary phase during RP HPLC, polyproline is induced into a type II helical conformation, polyalanine into an α‐helical conformation, and Ac‐LLKLLKKLLKKLKK‐NH2 into an amphipathic α‐helical array. In an extension of this study, the antimicrobial activities of Ac‐LLKLLKKLLKKLKK‐NH2 and its 18 proline substitution analogues were found to be inversely correlated with their RP HPLC retention times.
Protein: Nucleic acid interactions. I. Electronic structures of cytosine, indole, and guanine complexes
Authors: Ilich P. , Prendergast F. G.
Published: December 2004

Low singlet transition energies and line strengths were calculated for the cytosine : in‐dole : guanine complex by the INDO/1S‐CI method. The chromophores were arranged in three sets of 270 intercalating geometries. Calculations were executed in the supermolecule model with single excited configurations. Errors due to basis set extension and incomplete configuration representation were assessed, for all chromophore pairs, by full BSSE correction calculations and inclusion of double‐excited configurations. The intercalation‐induced perturbations of the principal transitions are characterized by but not limited to (a) a decrease in strength of {π*,π} transitions, (b) increase in strength in {π*,n} transitions, (c) splitting of {π*,π} transitions into components of unequal strength, and (d) energy and strength dependence in mixed transitions on rise and shift movements of the nucleic acid bases. These predictions are in accord with absorption, fluorescence emission, and scattering, and resonance Raman spectroscopic data on oligonucleotides and analogous aromatic complexes. The calculations suggest that major differences in intercalating coordinations are discernible in the near‐uv spectroscopic domain of proteins and nucleic acids.