bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractTwo 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

AbstractPolyriboadenylates 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

AbstractWe 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

AbstractResults 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

AbstractSalmon 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

AbstractSeveral 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

AbstractThe 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

AbstractThe 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

AbstractIn 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

AbstractGelled 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

AbstractUltraviolet 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

AbstractThe 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

AbstractModified 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

AbstractIndividual 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

AbstractWe 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

AbstractA 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.