bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of peptides: Synthesis, crystal structure, molecular conformation, and conformational calculations of N‐Boc‐L‐Phe‐Dehydro‐Ala‐OCH3
Authors: Padmanabhan B. , Dey S. , Khandelwal B. , Rao G. Subba , Singh T. P. 
Published: December 2004

AbstractIt is noteworthy that the dehydro‐Ala residue adopts an extended conformation that is different than those observed in dehydro‐Phe, dehydro‐Leu, and dehydro‐Abu. The peptide N‐Boc‐L ‐Phe‐dehydro‐Ala‐OCH3 (C18H24N2O5) was synthesized by the usual workup procedure and finally by converting N‐Boc‐L‐Phe‐L‐Ser‐OCH3 to N‐Boc‐L‐Phe‐dehydro‐Ala‐OCH3. It was crystallized from its solution in a methanol–water mixture at room temperature. The crystals belong to the monoclinic space group P21 with a = 9.577(1) Å, b = 5.195 (3) Å, c = 19.563 (3) Å, β = 94.67 (5)°, V = 970.1(6) Å3, Z = 2, dm = 1.201(5) Mg m−3, dc = 1.197 (5) Mg m−3. The structure was determined using direct method procedures. It was refined by a full‐matrix least‐squares procedure to an R value of 0.048 for 1370 observed reflections. The C‐C distance is 1.327 (8) Å, while the bond angles N2‐C‐C and C‐N2‐C are 109.8 (5)° and 127.8 (5)°, respectively. The backbone adopts a nonspecific conformation with dehydro‐Ala in a fully extended conformation with the following torsion angles: θl = 175.2 (4)°, ω, 0 = 170.2 (4)°, ø1 = 135.8 (5)°, ψ 1 = ‐22.6(6)°, ω1 = 168.5 (5)°, ψ2,= ‐170.3(5)°, ψ = –178.6(5)°', θT = 178.4(7)°. The rigid planar and trans conformation of dehydro‐Ala forces Phe to adopt a strained conformation. The Boc group has a trans‐trans conformation. The side‐chain torsion angles of the Phe residue are χ1 = 63.3(6)°, χ = −92.1(6)°, χ12,2 = 89.5 (6)°. The observed conformation is stabilized by three nonlinear intramolecular C—H‐‐‐O type of interactions. The crystal structure is stabilized by an intermolecular hydrogen bond N1—H1‐‐‐O2 of distance 2.938(7) Å along the b axis while the van der Waals forces are the stabilizing interactions in the ac plane. The low‐energy conformation found by calculations corresponds to the solid state conformation established by the crystal structure analysis. © 1992 John Wiley & Sons, Inc.
Dipeptide backbone conformation and antibody recognition of a viral octapeptide epitope
Authors: Feller David C. , Collett Marc S. 
Published: December 2004

AbstractThe peptide YKGTMDSG (Tyr‐Lys‐Gly‐Thr‐Met‐Asp‐Ser‐Gly) represents an important antigenic determinant from the glycoprotein G2 of the pathogenic Rift Valley fever virus. By preparing a series of single‐residue substitution peptides, the importance to antigenicity of individual residues within this octapeptide has been determined. Here, we investigated a simple and rapid computational analysis to test for correlations between the observed antigenicity of the substitution analogue peptides and the calculated conformational preferences in local regions of the peptides. Conformational energy analyses were carried out on all dipeptide combinations represented in the wild‐type octapeptide and in the singleresidue substitution analogue peptides. Conformational similarities and differences between wild‐type and substitution dipeptide pairs were determined. The results of these computational analyses were then compared with the data on the relative antigenicity of the wild‐type octapeptide and the substitution analogues. This comparison revealed a positive correlation. Substitution peptides showing changes in antigenicity possessed significant changes in the calculated backbone conformation relative to wild type in the dipeptides encompassing the residue substitution. Substitution peptides showing no change in antigenicity similarly showed no significant changes in dipeptide conformation. The potential utility of dipeptide conformational energy analyses and this preliminary structure‐activity correlation are discussed. © 1992 John Wiley & Sons, Inc.
Measurement of restricted rotational diffusion of fluorescent lipids in supported planar phospholipid monolayers using angle‐dependent polarized fluorescence photobleaching recovery
Authors: Timbs Melanie M. , Thompson Nancy L 
Published: December 2004

AbstractA theory describing the shapes of polarized fluorescence photobleaching recovery (PFPR) curves for a population of fluorophores undergoing restricted rotational diffusion in two‐dimensional systems such as planar membranes has been developed. In this model, restricted rotational diffusion of the fluorophores is described by using reflective boundary conditions, in which the fluorophores are assumed to diffuse freely but only within an angular space of width 2ω. The magnitude and apparent rate of the PFPR postbleach fluorescence curves are a function of both ω and the angle between the bleaching and observation beam polarizations ψ. It is shown that estimates of the degree of rotational restriction ω may be obtained from changes in the ψ‐dependent postbleach fluorescence intensities.Using angle‐dependent PFPR, slow rotational reorientations of the fluorescent lipid analogue 1,1′‐dioctadecyl‐3,3,3′,3′‐tetramethylindocarbocyanine in distearoylphosphatidylcholine Langmuir–Blodgett monolayers deposited on octadecyltrichlorosilane‐treated fused quartz were measured. As theoretically predicted for a rotationally restricted fluorophore population, both the initial Fψ(0) and final Fψ(∞) postbleach fluorescence intensities varied as a function of ψ, and no measurable change in the postbleach fluorescence intensities was observed for ψ = 45°. Using the theory for restricted rotational motion, the ψ‐dependent variations of the final fluorescence intensities Fψ(∞) obtained at two bleaching intensities gave an average apparent ω ≈︁ 52°. However, to adequately fit the Fψ(0) data, inclusion of the theoretical effects of rapid (faster than the duration of the photobleaching pulse) fluorophore dynamics was also required. Best fits of the Fψ(0) and Fψ(∞) data were obtained when the fluorophores were assumed to rapidly wobble within a cone of semiangle δ ≈︁ 30°–50° while slowly rotating within an angular space defined by semiangle ω ≈︁ 35°–60°. Subsequent analysis of the time‐ and ψ‐dependent changes in the postbleach fluorescence curves Fψ(t) gave apparent diffusion coefficients ranging from D ≈︁ 10−3 s−1 to 4 × 10−2 s−1. © 1993 John Wiley & Sons, Inc.
Calculation and measurement of the dipole moment of small proteins: Use of protein data base
Authors: Takashima Shiro , Asami Koji 
Published: December 2004

AbstractThe dipole moments of small protein molecules were determined experimentally in order to validate the calculated dipole moments by previous investigators. We found that the agreements are satisfactory for some proteins. There are, however, many proteins for which the agreement is less than satisfactory. In order to find the cause of the disagreement, the dipole moments of these proteins were recalculated using the Brookhaven Protein Data Bank. We calculated the dipole moment due to fixed surface charges and the bond moments of all the carbonyl groups in main chain and side chains. The calculation consists of the mean moments and their mean square fluctuations. In addition, we investigated the effect of electrostatic interactions between charged sites for several proteins. These results show that incorporation of the interactions does not affect substantially the calculated dipole moments. The rms fluctuation of the dipole moment is found to be small but not negligible. In conclusion, recalculated dipole moments are in good agreement with the observed values. © 1993 John Wiley & Sons, Inc.
Linear dichroism demonstrates that the bases in poly[d(AC)] · poly[d(GT)] and poly[d(AG)] · poly[d(CT)] are inclined from perpendicular to the helix axis
Authors: Kang Hunseung , Curtis W. Johnson 
Published: December 2004

AbstractFlow linear dichroism is used to measure specific inclinations for each of the four bases in poly[d(AC)]·;poly[d(GT)] and poly[d(AG)]·poly[d(CT)] in both the B and A forms. For the B form in solution the bases are found to have a sizable inclination. Inclination is increased in the A form, as expected. In all cases the pyrimidines are more inclined than the purines. © 1993 John Wiley & Sons, Inc.
Permethylation alters the conformational transitions and the complexing ability of melittin: A model for methylated proteins
Authors: Ramalingam Kalaiyarasi , Bello Jake , Aimoto Saburo 
Published: December 2004

AbstractMelittin exhibits a transition from random‐coil monomer to helical tetramer as a function of peptide concentration [ J. Bello, H. R. Bello, and E. Granados (1982) Biochemistry, Vol. 21, pp. 461–465]. When permethylated on each of the four amino groups (Gly‐1 Nα and Lys‐7, 21, and 23 Nε) to yield trimethylammonium groups, melittin exists as a random coil and does not show any concentration‐dependent conformational transition (up to 290 μM). Acylation of the amino groups of melittin with glycine or 5‐aminopentanoic acid followed by permethylation increases helix formation, but to a lesser extent than for the unmethylated aminoacylmelittin derivatives. The results are discussed in relation to hydrophobicity, charge repulsions, and ion binding. Melittin, and more weakly, permethylated melittin (MLT‐Me) form helical hybrids with an anionic random‐coil melittin analogue (E‐MLT), in which all the lysine and arginine residues of melittin were replaced by glutamate residues. The hybrid between MLT‐Me and E‐MLT shows a concentration‐dependent increase in helicity. E‐MLT, when succinylated at the N‐terminal glycine (E‐MLT‐suc), forms a stronger hybrid with MLT‐Me, possibly as a result of increased electrostatic interaction between equal but opposite charges in E‐MLT‐suc (net charge –6) and MLT‐Me (net charge +6). The hybrids exhibit both cold‐ and heat‐induced denaturation, similar to the phenomenon exhibited by proteins. The hybrids also exhibit significant residual structures in the temperature range of 80–100°C, which may be similar to the molten globular states that have been suggested for proteins. © 1993 John Wiley & Sons, Inc.
The structure of the left‐handed antiparallel amylose double helix: Theoretical studies
Authors: Schulz Wolfgang , Sklenar Heinz , Hinrichs Winfried , Saenger Wolfram 
Published: December 2004

AbstractThe atomic coordinates from the crystal structure of a hexasaccharide complex accommodating a zigzag polyiodide [ W. Hinrichs, G. Büttner, M. Steifa, Ch. Betzel, V. Zabel, B. Pfannemüller, and W. Saenger (1987) Science Vol. 238, pp. 205–208; W. Hinrichs and W. Saenger (1990) Journal of the American Chemical Society, Vol. 112, pp. 2789–2796 ] served to construct an antiparallel‐stranded amylose double helix with a 5 Å wide central cavity. Using our methodology for the energetic optimization of polymer structures in the internal/ helical variable space [ H. Sklenar, R. Lavery, and B. Pullman (1986) Journal of Biomolecular Structure Dynamics, Vol. 3, pp. 967–987, 989–1014; 1015–1031], we have calculated a theoretical counterpart of this idealized double helix by constraining the helical twist and rise to their experimental values (−45° and 2.33 Å, respectively). Applying the same constraints to the parallel‐stranded duplex, this also leads to a low‐energy structure with wide central cavity. It is considered as an alternative model to accommodate iodine as observed in the starch–iodine complex.Release of the helical constraints leads to left‐handed antiparallel‐ and parallel‐stranded double helices, respectively, with narrow central cavities. Both structures have very similar helix parameters and correspond, in their main characteristics, to the experimentally derived parallel‐stranded structure of amylose in starch (6 residues per turn and a pitch height of about 21 Å). The intramolecular energy calculated for the optimized antiparallel‐stranded amylose double helix is comparable to that of the parallel‐stranded structure. This result raises the question why parallel‐stranded amylose seems to be favored in nature. © 1993 John Wiley & Sons, Inc.
Molecular dynamics simulations of B‐DNA: An analysis of the role of initial molecular configuration, randomly assigned velocity distribution, long integration times, and nonconstrained termini
Authors: Falsafi Sassan , Reich Norbert O. 
Published: December 2004

AbstractMolecular dynamics simulations of three DNA sequences using the AMBER 3.0 force field were performed with implicit inclusion of water through a distance‐dependent dielectric constant and solvated counterions. Simulations of the self‐complementary DNA dodecamer d(CGCGAATTCGCG) were started from a regular B‐DNA structure and the x‐ray single crystal B‐DNA structure. Although mean convergence during the 89‐ps calculation was confirmed, localized differences in backbone torsionals and base‐pair helicoidals were observed. A nanosecond simulation of the nonself‐complementary 14 base‐pair DNA d(GGCGGAATTGGCGG) indicates that most structural parameters stabilize within the first 100–200 ps, while isolated features show low‐frequency oscillations throughout the calculation. The lack of harmonic constraints on the ends of the molecules was shown not to perturb the structural dynamics of the internal oligonucleotide beyond the external 2 base pairs. Comparison of three simulations of the nonself‐complementary 14 base‐pair DNA d(GGCGAAATTCGCGG), identical in all respects other than the assignment of initial Maxwellian atomic velocity distributions, revealed the inherent systematic variability. The three calculations result in nearly superimposable global structures, with localized variations in torsionals and helicoidals. Our results provide a basis for performing a comparative analysis of the effect of DNA sequence on localized structure. © 1993 John Wiley & Sons, Inc.
Heat capacities of solid poly(amino acid)s. II. The remaining polymers
Authors: Roles K. A. , Xenopoulos A. , Wunderlich Bernhard 
Published: December 2004

AbstractIn the first paper heat capacities Cp, of polyglycine, poly(L‐alanine), and poly (L‐valine) were analyzed using approximate group vibrations and fitting the Cp contributions of the skeletal vibrations to a two‐parameter Tarasov function. In this second paper all other poly (amino acid) s are similarly analyzed. Heat capacities were measured by differential scanning calorimetry in the temperature range of 230–390 K for poly(L‐leucine), poly(L‐serine), poly (sodium‐L‐aspartate), poly(sodium‐L‐glutamate), poly(L‐asparagine), poly(L‐phenylalanine), poly(L‐tyrosine), poly(L‐methionine), poly (L‐tryptophane), poly(L‐proline), poly(L‐lysine · HBr), poly(L‐histidine), poly(L‐histidine‐ HCl), and poly(L‐arginine · HCl). Good agreement exists between experiment and calculation. Predictions of heat capacities were made for all not‐measured poly (amino acid) s. Enthalpies, entropies, and Gibbs functions for the solid state have been derived. © 1993 John Wiley & Sons, Inc.
1H‐ and 13C‐nmr investigations on cis–trans isomerization of proline peptide bonds and conformation of aromatic side chains in H‐Trp‐(Pro)n‐Tyr‐OH peptides
Authors: Poznański J. , Ejchart A. , Wierzchowski K. L. , Ciurak M. 
Published: December 2004

Abstract1H and 13C high‐resolution nmr spectra of cationic, zwitterionic, and anionic forms of the peptides: H‐Trp‐(Pro)n‐Tyr‐OH, n = 0‐5, and H‐Trp‐Pro‐OCH3 were obtained in D2O solution. Analysis of Hα(Pro1), Hα(Trp), Cγ(Pro), Hε(Tyr), and Hδ(Trp) resonances provided evidence for the presence of two predominant backbone isomers: the all‐trans one and another with the Trp‐Pro peptide bond in cis conformation; the latter constituted about 0.8 molar fraction of the total peptide (n > 1) concentration. Relative content of these isomers varied in a characteristic way with the number of Pro residues and the ionization state of the peptides. The highest content of the cis (Trp‐Pro) isomer, 0.74, was found in the anionic form of H‐Trp‐Pro‐Tyr‐OH; it decreased in the order of: anion ≫ zwitterion ≈ cation, and with the number of Pro residues to reach the value of 0.42 in the cationic form of H‐Trp‐ (Pro)5‐Tyr‐OH. Isomerization equilibria about Pro‐Pro bond(s) were found to be shifted far (⩾0.9) in favor of the trans conformation. Interpretation of the measured vicinal coupling constants Jα−β′ and Jα−β″ for CαH‐CβH2 proton systems of Trp and Tyr side chains in terms of relative populations of g+, g−, and t staggered rotamers around the χ1 dihedral angle indicated that in all the peptides studied (a) rotation of Trp indole ring in cis (Trp‐Pro) isomers is strongly restricted, and (b) rotation of Tyr phenol ring is relatively free. The most preferred χ1 rotamer of Trp (0.8‐0.9 molar fraction) was assigned as the t one on the basis of a large value of the vicinal coupling constant between the high‐field Hβ and carbonyl carbon atoms of Trp, estimated for the cis (Pro1) form of H‐Trp‐Pro‐Tyr‐OH from a 1H, 13C correlated spectroscopy 1H detected multiple quantum experiment. This indicates that cis ↔ trans equilibrium in the Trp‐Pro fragment is governed by nonbonding interactions between the pyrrolidine (Pro) and indole (Trp) rings. A molecular model of the terminal cis Trp‐Pro dipeptide fragment is proposed, based on the presented nmr data and the results of our molecular mechanics modeling of low‐energy conformers of the peptides, reported elsewhere. © 1993 John Wiley & Sons, Inc.
A method for studying the structure of uniaxially aligned biopolymers using solid state 15N‐nmr: Application to Bombyx mori silk fibroin fibers
Authors: Nicholson Linda K. , Asakura Tetsuo , Demura Makoto , Cross Timothy A. 
Published: December 2004

AbstractRecent advances in the application of solid state nmr spectroscopy to uniformly aligned biopolymers have opened a window through which to view the detailed structure of biological macromolecules that are unable to be seen with standard techniques for structure determination such as x‐ray diffraction. Atomic resolution structural details are obtained from solid state nmr data in the form of bond orientations, which yield the relative positions of specific atoms within the molecule. For static aligned systems such as fibers, in which rapid reorientation about the axis of alignment does not occur, it has generally been necessary to perform trial and error line‐shape simulations to extract structural details from nmr spectra arising from a single type of nuclear spin interaction. In the present work, a new method is developed in which solid state 15N‐nmr spectra obtained from uniaxially aligned molecules placed with the axis of alignment both parallel and perpendicular to the magnetic field are analyzed to yield the orientations of specific molecular bonds. Analytical expressions are derived that utilize spectral features read from 15N chemical shift anisotropy line shapes to calculate a discrete number of possible orientations for a specific site. The 15N‐1H dipolar interaction is employed to further narrow the number of unique orientations possible for a given site. With this method, a neighborhood of possible orientations is quickly determined, and full line‐shape simulations within this region of allowed space can be performed to refine the limits of orientation. This technique demonstrates the use of a single type of isotopic label to determine the orientation of a specific molecular group such as a peptide plane within a protein. Results from the application of this method to the Bombyx mori silk fibroin protein provide structural detail that is consistent with currently accepted structural models based on fiber diffraction studies. © 1993 John Wiley & Sons, Inc.
Improved molecular dynamics simulations for the determination of peptide structures
Authors: Mierke Dale F. , Kessler Horst 
Published: December 2004

AbstractIn this article a few methods or modifications proven to be useful in the conformational examination of peptides and related molecules by molecular dynamics are illustrated. The first is the explicit use of organic solvents in the simulations. For many cases such solvents are appropriate since the nmr measurements (or other experimental observations) were carried out in the same solvent. Here, the use of dimethylsulfoxide and chloroform in molecular dynamics is described, with some advantages of the use of these solvents highlighted.A constant allowing for the scaling of the nonbonded interactions of the force field, an idea previously employed in distance geometry and simulated annealing, has been implemented. The usefulness of this method is that when the nonbonded term is turned to zero, atoms can pass through each other, while the connectivity of the molecule is maintained. It will be shown that such simulations, if a sufficient driving force is present (i.e., nuclear Overhauser effects restraints), can produce the correct stereoconfiguration (i.e., chiral center) as well as configurational isomer (i.e., cis/trans isomers).Lastly, a penalty term for coupling constants directly related to the Karplus curve has been plemented into the potential energy force field. The advantages of this method over the commonly used dihedral angle restraining are discussed. In particular, it is shown that with more than one coupling constant about a dihedral angle a great reduction of the allowed conformational space is obtained. © 1993 John Wiley & Sons, Inc.
Effect of counterion concentration on the dielectric behavior of a polypeptidic chain in the helix–coil transition
Authors: Bordi F. , Cametti C. , Paradossi G. 
Published: December 2004

AbstractOn the basis of the two‐state model of a polyelectrolyte solution, the ion concentration in the polymer domain has been calculated by using the spherical Poisson–Boltzmann equation. The ion accumulation in the neighboring of the polyion influences, on different time scales, various electrical properties of the solution, in particular the low‐frequency electrical conductivity and the high‐frequency dielectric dispersion. These predictions have been compared with recent dielectric measurements on poly (L‐glutamic acid) aqueous solutions during the conformational transition from the α‐helix to random coil, and a satisfactory agreement has been found. This finding suggests that counterion distribution plays a different role in determining the electrical properties of charged polymer solutions, causing a electrophoretic contribution of the polymer domain to the electrical conductivity and influencing the high‐frequency dielectric dispersion. © 1993 John Wiley & Sons, Inc.
Z → B transition in poly[d(G‐m5C)2] induced by interaction with 4′,6‐diamidino‐2‐phenylindole
Authors: Kim Seog K. , Eriksson Svante , Nordén Bengt 
Published: December 2004

AbstractThe Z form of poly[d(G‐m5C)2], in presence of Mg2+ ion, is found to be transformed into B form upon interaction with 4′,6‐diamidino‐2‐phenylindole (DAPI). The Z → B transformation is complete at a mixing ratio of about 0.07 DAPI per DNA base pairs, i.e., each DAPI molecule may be related to the conversion of 6–7 base pairs. An interaction between DAPI and poly[d(G‐m5C)2] in its Z form at low drug: DNA ratios is suggested from optical dichroism and time‐resolved luminescence anisotropy results. The spectroscopic behaviour of DAPI indicates that the Z conformation of DNA does not provide normal binding sites for DAPI, such as groove or intercalation sites, but that the initial association may be of external nature. © 1993 John Wiley & Sons, Inc.