bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential polarization microscopy (cd and linear dichroism) of polytene chromosomes and nucleoli from the dipteran sarcophaga footpad
Authors: Livolant Françloise , Mickols William , Maestre Marcos F. 
Published: December 2004

AbstractCircular Dichroism (CD) and Linear Dichroism (LD) Microscopy measurements of single live polytene nuclei of the fleshfly Sarcophaga bullata suggest the existence of two groups of data. This was observed in both the linear and circular dichroism spectra indicating a difference in both the linear and chiral arrangements of the chromatin. The two groups of data were averaged separately and called nucleolus type 1 and type 2. The CD of nucleoli type 1 all show positive CD in the 260 nm wavelength. For the nucleoli type 2 the CD are very different, always negative, with maximum amplitude at 250 nm. The CD of the band, interband and transcriptionally active puffs show very similar CD spectra at 260 nm but differ at lower wavelength (between 245 and 260 nm). Differences are also observed in the LD measurements for nucleoli type 1 (LD maximum at 265 nm) vs. nucleoli type 2 (LD maximum centered at 250 nm). These differences are interpreted as a manifestation of large transcriptional activity for nucleolus type 1, and a more condensed structure and low transcriptional activity for nucleolus type 2.
Diffusion coefficients of segmentally flexible macromolecules with two subunits: A study of broken rods
Authors: Mellado P. , Iniesta A. , Diaz F. G. , De La Torre J. García 
Published: December 2004

AbstractA general treatment for the solution dynamics of segmentally flexible macromolecules having two subunits is presented. Bead modeling allows for a complete inclusion of hydrodynamic interactions in this treatment. The finite size of the beads is also considered, so that it is therefore possible to account properly for torsional motions of the subunits. Expressions for the components of the resistance matrix are derived. From them, the translational and rotational diffusion coefficients can be calculated. Distinction is made between hinged macromolecules, whose only internal motion is bending, and swivel‐jointed macromolecules, for which torsions of the subunits are also allowed. Numerical results are presented for broken rods with the two types of flexibility. The effects of hydrodynamic interaction between arms of broken rods are about 25% for translation and under 10% for rotation. These findings give support to the treatments of Harvey, Wegener, and co‐workers in which interactions were neglected. The rotational dynamics of hinged and swivel‐jointed rods are compared. Although there are differences in the short‐time behavior, the longest relaxation time is the same for the two cases. Finally, the validity of Wegener's rotational diffusion constants is discussed.
Structural and dynamic properties of the heme pocket in myoglobin probed by optical spectroscopy
Authors: Cupane Antonio , Leone Maurizio , Vitrano Eugenio , Cordone Lorenzo 
Published: December 2004

AbstractWe report the optical absorption spectra of sperm whale deoxy‐, oxy‐, and carbonmonoxymyoglobin in the temperature range 300–20 K and in 65% glycerol or ethylene glycol–water mixtures. By lowering the temperature, all bands exhibit half‐width narrowing and peak frequency shift; moreover, the near‐ir bands of deoxymyoglobin show a marked increase of the integrated intensities. Opposed to what has already been reported for human hemoglobin, the temperature dependence of the first moment of the investigated bands does not follow the behavior predicted by the harmonic Franck–Condon approximation and is sizably affected by the solvent composition; this solvent effect is larger in liganded than in nonliganded myoglobin. However, for all the observed bands the behavior of the second moment can be quite well rationalized in terms of the harmonic Franck–Condon approximation and is not dependent on solvent composition. On the basis of these data we put forward some suggestions concerning the structural and dynamic properties of the heme pocket in myoglobin and their dependence upon solvent composition. We also discuss the different behaviors of myoglobin and hemoglobin in terms of the different heme pocket structures and deformabilities of the two proteins.
Conformational characteristics of peptides and unanticipated results from crystal structure analyses
Authors: Karle Isabella L. 
Published: December 2004

AbstractPreferred conformation and types of molecular folding are some of the topics that can be addressed by structure analysis using x‐ray diffraction of single crystals. The conformations of small linear peptide molecules with 2–6 residues are affected by polarity of solvent, presence of water molecules, hydrogen bonding with neighboring molecules, and other packing forces. Larger peptides, both cyclic and linear, have many intramolecular hydrogen bonds, the effect of which outweighs any intermolecular attractions. Numerous polymorphs of decapeptides grown from a variety of solvents, with different cocrystallized solvents, show a constant conformation for each peptide.Large conformational changes occur, however, upon complexation with metal ions. A new form of free valinomycin grown from DMSO exhibits near three‐fold symmetry with only three intramolecular hydrogen bonds. The peptide is in the form of a shallow bowl with a hydrophobic exterior. Near the bottom of the interior of the bowl are three carbonyl oxygens, spaced and directed so that they are in position to form three ligands to a K+, e.g., complexation can be completed by the three lobes containing the β‐bends closing over and encapsulating the K+ ion. In another example, free antamanide and the biologically inactive perhydro analogue, in which four phenyl groups become cyclic hexyl groups, have essentially the same folding of backbone and side chains. The conformation changes drastically upon complexation with Li+ or Na+. However, the metal ion complex of natural antamanide has a hydrophobic globlar form whereas the metal ion complex of the inactive perhydro analogue has a polar band around the middle. The structure results indicate that the antamanide molecule is in a complexed form during its biological activity.Single crystal x‐ray diffraction structure analyses have identified the manner in which water molecules are essential to creating minipolar areas on apolar helices. Completely apolar peptides, such as membrane‐active peptides, can acquire amphiphilic character by insertion of a water molecule into the helical backbone of Boc‐Aib‐Ala‐Leu‐Aib‐Ala‐Leu‐Aib‐Ala‐Leu‐Aib‐OMe, for example. The C‐terminal half assumes an α‐helix conformation, whereas the N‐terminal half is distorted by an insertion of a water molecule W(1) between N(Ala5) and O(Ala2), forming and hydrogen bonds N(5)H ⃛ W(1) and W(1) ⃛ O(2). The distortion of the helix exposes CO (Aib1) and CO (Aib4) to the outside environment with the consequence of attracting additional water molecules. The leucyl side chains are on the other side of the molecule. Thus a helix with an apolar sequence can mimic an amphiphilic helix.
Cyclo(D‐Pro‐L‐Pro‐D‐Pro‐L‐Pro): Structural properties and cis/trans isomerization of the cyclotetrapeptide backbone
Authors: Mästle Werner , Weber Thomas , Thewalt Ulf , Rothe Manfred 
Published: December 2004

AbstractCombinations of L‐ and D‐proline residues are useful compounds for finding new structures and properties of cyclic peptides. This is demonstrated with one striking example, the cyclic tetrapeptide c(D‐Pro‐L‐Pro‐D‐Pro‐L‐Pro). For this molecule composed of strictly alternating D‐ and L‐configurated residues, a highly symmetrical structure is expected, which should be an optically inactive meso‐form. Cyclization of the enantiomeric pure linear precursor D‐Pro‐L‐Pro‐D‐Pro‐L‐Pro, however, yields a racemic mixture of two enantiomeric cyclotetrapeptides, both with twofold symmetry and a cis–trans–cis–trans sequence of the peptide bonds. Remarkably, this formation of a racemate was not caused by racemization, but by cis/trans isomerization of all peptide bonds in the ring. This process may occur in the linear precursor during the ring formation (cyclization of conformers with trans–cis–trans or cis–trans–cis arrangement of the amide bonds) as well as in the enantiomeric pure cyclic tetrapeptide at higher temperature. In the latter case, an all‐cis structure should exist as the intermediate, which can form a cis–trans–cis–trans sequence in two equivalent ways, leading finally to two enantiomeric cyclotetrapeptides. In the first one, the cis peptide bonds are attributed to the L‐residues and the trans peptide bonds to the D‐residues; in the second one, the cis bonds belong to the D and the trans bonds to the L‐residues. The mixture of these two enantiomers does not crystallize in the racemic form, but in enantiomeric pure separate crystals. The structural properties could be proved by 1H‐ and 13C‐nmr spectroscopy and x‐ray analysis. The cis/trans isomerization process was confirmed by optical rotation measurements and CD spectroscopy, as well as DREIDING model studies. Calorimetric measurements in the solid state suggest the existence of the expected all‐cis intermediate. The backbone conformation of the 12‐membered medium‐sized ring shows only slight deviations—up to 6° —from the planarity of the peptide bonds. On the other hand, the four pyrrolidine rings show different types of puckering of the Cγ or the Cβ atoms.
Regularly alternating L,D‐peptides. III. Hexacyclic peptides from valine or phenylalanine
Authors: Pavone Vincenzo , Benedetti Ettore , Di Blasio Benedetto , Lombardi Angela , Pedone Carlo , Tomasich Lera , Lorenzi Gian Paolo 
Published: December 2004

AbstractIn the present paper we describe the single‐crystal x‐ray analyses of two cyclic hexapeptides containing an equal number of alternating L,D‐residues as putative analogues of the metal binding compounds, enniatin and beauvericine. Both the molecules of c(L‐Val‐D‐Val)3 and c(L‐Phe‐D‐Phe)3 retain in the solid state the center of symmetry and crystallize with six and eight trifluoroacetic acid molecules, respectively. The peptides are strongly hydrogen bonded to the solvent molecules. We estimate, on the basis of the molecular geometry and spatial arrangement of the peptide carbonyl groups and in comparison with other metal binding cyclic peptides, the ability of these molecules to interact with metal ions as 1:1 complexes.
Structure of conformationally constrained peptides: From model compounds to bioactive peptides
Authors: Toniolo C. 
Published: December 2004

AbstractThe use of backbone conformational constraints has acquired increasing importance in the design and synthesis of structurally restricted agonists and antagonists of bioactive peptides. Here I discuss the preferred conformations of four among the most popular types of such peptide surrogates: (a) Peptides from Cα,α‐dialkylated residues, (b) tetrazolyl peptides, (c) (γ‐ and δ‐) lactam‐containing peptides, and (d) thiated peptides. Emphasis is given to conformational energy computations and x‐ray diffraction analyses of selected model compounds and analogues of small bioactive peptides such as the formylmethionyl tripeptide chemoattractant and MIF.
Structure and stability of the Boc(D‐Pro‐L‐Pro)2OCH3 Na+ complex: A model of poly(D,L‐proline), an alkali ion channel across membranes
Authors: De Santis P. , Scipioni A. , Palleschi A. , Savino M. 
Published: December 2004

AbstractIn order to elucidate the molecular mechanisms of alkali ions conduction of poly(D,L‐proline), which shows the typical behavior of an ion channel across membranes, conformations of the tetrameric derivative Boc(D‐Pro‐L‐Pro)2OCH3 in solution, in the presence of the Na+ ion, were investigated by CD and nmr spectroscopy. Both theoretical and experimental data indicate the formation in solution of a monomeric complex between the tetramer, in the all‐trans conformation, and the cation. The results allow to confirm the channel model, previously proposed on the phenomenological behavior of poly(D,L‐proline) in membranes.
Tooth enamel protein, amelogenin, has a probable β‐spiral internal channel, Gln112–Leu138, within a single polypeptide chain: Preliminary molecular mechanics and dynamics studies
Authors: Renugopalakrishnan V. , Pattabiraman N. , Prabhakaran M. , Strawich E. , Glimcher M. J. 
Published: December 2004

AbstractMolecular dynamics simulation, with backbone constraints for 20 ps of equilibration and simulation, of a repeating polypeptide segment, Gln‐Pro‐His‐Gln‐Pro‐Leu‐Gln‐Pro‐His‐Gln‐Pro‐Leu‐Gln‐Pro‐Met‐(Gln‐Pro‐Leu)4, constituting residues 112–138 of bovine amelolgenin, a 19.35 kD hydrophobic protein, are discussed. It is generally believed that the above polypeptide segment is important for the interaction of amelogenin with Ca++ ions, which occurs in the early phases of enamel mineralization. An energetically stable structure of the above polypeptide with recurrent β‐turns is observed and contains a pore of ∼ 1 Å radius along the helical that can accommodate an unhydrated Ca++ ion. The length of the polypeptide possesses correct dimensions to span a bilayer. The proposed structure is unique among known polypeptide and protein structures.
Conformation of bombesin in buffer and in the presence of lysolecithin micelles: Nmr, CD, and fluorescence studies
Authors: Cavatorta P. , Spisni A. , Szabo A. G. , Farruggia G. , Franzoni L. , Masotti L. 
Published: December 2004

AbstractThe conformation of the tetradecapeptide hormone bombesin has been studied in buffer and in the presence of lysolecithin micelles, using static and dynamic fluorescence, CD, and one‐ and two‐dimensional nmr. The results obtained show that in buffer bombesin is present in an extended flexible chain, with no evidence for any ordered secondary structure. A marked change in the CD spectrum is observed changing from buffer to the lipid suspension. Concomitantly, the 1H‐nmr spectrum of bombesin, in a D2O lipid dispersion, shows the persistence of resonances due to exchangeable protons and in similar conditions the fluorescence intensity increases. We think therefore that these results strongly support the hypothesis that bombesin interacts with the lipid phase, assuming ordered secondary structure. Finally, the marked dependence of tryptophan fluorescence quantum efficiency and order parameter from the hormone concentration in the presence of lysolecithin but not in buffer leads to the conclusion that bombesin can associate into the lipid matrix.
Molecular dynamics of the α‐helical epitope of a novel synthetic lipopeptide foot‐and‐mouth disease virus vaccine
Authors: Krug Michael , Folkers Gerd , Haas Bernd , Hess Günter , Wiesmüller Karl‐Heinz , Freund Stefan , Jung Günther 
Published: December 2004

AbstractA novel synthetic foot‐and‐mouth disease virus (FMDV) peptide vaccine consisting of a synthetic B‐cell and macrophage activator covalently linked to an amphiphilic α‐helical T‐cell epitope was developed. The low molecular weight vaccine of 3400 daltons is composed of virus VP1 antigenic determinant and the immunologically active lipotripeptide tripalmitoyl‐S‐glyceryl‐cysteinyl‐seryl‐serine (P3CSS) as built‐in adjuvant. The vaccine, tripalmitoyl‐S‐glyceryl‐cysteinyl‐seryl‐seryl‐FMDV‐VP1 (VP1 = serotype O1K 135–154) induces protection against homologous challenge and serotype‐specific virus neutralizing antibodies in guinea pigs after single administration without further adjuvants or carriers. A P3CSS conjugate with the FMDV‐VP1 segment 135–154 of strain O Wuppertal produced only poor cross‐protection against challenge with O1K virus.The antigenic determinant VP1(135–154) is an amphiphilic α‐helix, as shown by CD. Molecular dynamics simulations (MDS) carried out using the highly homologous α‐helical alcohol dehydrogenase (ADH) segment H3 as starting conformation for VP1(138–149) suggest that the FMDV segment 138–149 may adopt α‐helical conformation during binding to its T‐cell receptor, and that the development of the system during MDS may be considered as the dissociation step of the complex.
Comparison of the conformations of cyclolinopeptide a in the solid state and in solution
Authors: Tancredi T. , Zanotti G. , Rossi F. , Benedetti E. , Pedone C. , Temussi P. A. 
Published: December 2004

AbstractCyclolinopeptide A, a cyclic nonapeptide isolated from linseed, has lately attracted large interest for its cytoprotective activity. The recent elucidation of its solid state structure has prompted us to undertake a detailed conformational analysis in solution. Room‐temperature 1H‐nmr spectra in several solvents (DMSO‐d6, DMSO‐d6/D2O/H2O, CD3OH, (CD3)2CDOH, CDCl3) all show very broad lines, indicating the presence of chemical exchange among several conformers. It proved possible to freeze a single conformational state in CDCl3 at 214 K. Unusual chemical shifts and nuclear Overhauser enhancements are consistent with the main features of the solid state structure.
CH ⃛ O hydrogen bonding in solutions of methylated nucleic acid base analogs as revealed by nmr
Authors: Bruskov V. I. , Bushuev V. N. , Okon M. S. , Shulyupina N. V. , Poltev V. I. 
Published: December 2004

AbstractFormation and thermodynamic characteristics of CH ⃛ O hydrogen bonding of methylated uracils and caffeine have been studied by nmr along two lines.

The concentration and temperature dependencies of the PMR spectra of 1,3‐dimethyluracil (m2 1,3Ura), 1,3‐dimethylthymine (m2 1,3Thy), and 1,3,6‐trimethyluracil (m3 1,3,6Ura) in chloroform at high concentrations of base analogs indicated the self‐association of m2 1,3Ura and m2 1,3Thy via C(6)H ⃛ O hydrogen bonding and the competitive formation of CH ⃛ O bonds between carbonyl oxygens and chloroform. The intermolecular interaction energy and the arrangement of molecules in the local minima of various m2 1,3Ura dimers were calculated by the method of atom‐atom potentials. The deepest minimum for the m2 1,3Ura coplanar dimer corresponds to a C(6)H ⃛ O hydrogen‐bond formation.
At low concentration of m2 1,3Ura and caffeine in CCl4, C(6)H ⃛ O bonding for m2 1,3Ura and C(8)‐H ⃛ O bonding for caffeine with oxygens of dimethyl sulfoxide (DMSO) and acetone were observed. The association constants of these complexes were obtained at different temperatures. The enthalpies ΔH, of the m2 1,3Ura–DMSO, m2 1,3Ura–accetone, caffeine–DMSO, and caffeine–acetone complexes were −2 ⃛ 0.1 kcal/mol. The calculations showed that the deepest minimum of the caffeine‐acetone coplanar complex corresponds to C(8)H ⃛ O bonding with energy of −3.5 kcal/mol and that of the m2 1,3Ura‐acetone complexes corresponds to C(6)H ⃛ O bonding with energy of −3.4 kcal/mol. The approximate correction for the solvent effect provides good agreement of the experimental data with the calculations.
Proton nmr relaxation study of the dynamics of anthopleurin‐A in solution
Authors: Torda Andrew E. , Norton Raymond S. 
Published: December 2004

AbstractSpin–spin and spin–lattice 1H‐nmr relaxation times of the sea anemone polypeptide anthopleurin‐A were measured at frequencies of 200, 300, 400, and 500 MHz. Relaxation times were fitted iteratively by least squares regression to the isotropic tumbling model, Woessner's model for anisotropic motion, and Lipari and Szabo's “model‐independent” model. Data for aromatic and aliphatic methine protons could not be fitted satisfactority using the isotropic model. Good fits were obtained, however, using the model‐independent approach,‐indicating that high‐frequency internal motions of the polypeptide backbone were significant. In addition, a range of τC values from 2.2 to 3.2 ns was obtained for various methine protons, suggesting that overall rotational reorientation of the molecule was anisotropic. Methyl group relaxation data were fitted satisfactorily by Woessner's model. Some assessment has been made of the effect of experimental errors on the quality of fit to the data, as well as of the contribution of experimental values at certain frequencies to definition of the spectral density function.
Two‐dimensional proton NMR studies on poly(VPGVG) and its cyclic conformational correlate, cyclo(VPGVG)3
Authors: Urry D. W. , Chang D. K. , Krishna N. R. , Huang D. H. , Trapane T. L. , Prasad K. U. 
Published: December 2004

AbstractTwo‐dimensional nuclear Overhauser enhancement (2D NOESY) data are reported for the polypentapeptide of elastin, poly(VPGVG), and the cyclopentadecapeptide, cyclo(VPGVG)3. In both, the repeating type II Pro2‐Gly3 β‐turn can be derived from the NOE data, providing confirmation of many previous studies. In addition, other through‐space connectivities are detailed that also compare favorably with previously determined crystal and solution structures for cyclo(VPGVG)3. Also, near identical data for the cyclopentadecapeptide and the polypentapeptide demonstrate the cyclic conformation‐linear (helical) conformational correlate relationship between the two molecules. The 2D NOESY experiment is seen to be an effective means of establishing the presence or absence of a conformational relationship between a cyclic repeating sequence and its higher molecular weight linear counterpart. This is an approach of substantial practical value when developing the conformation of sequential polypeptides and when attempting to identify the presence of the conformation of a repeating peptide sequence within a more complex primary structure.Having established the basic conformational relationship between a cyclic conformation and its linear helical counterpart, cross peaks present in the linear helical structure that are not present in the cyclic conformational correlate can provide information on the interactions between adjacent turns of the helix. In this connection, a ValγCH3 ⟷ ProβCH2 interaction is reported that can be the basis for determining the number of pentamers per turn of helix once it is determined whether it is dominantly the Val1 or Val4γCH3 that is interacting with the Pro2βCH2.
Prediction of DNA structure from sequence: A build‐up technique
Authors: Hingerty Brian E. , Figueroa Samuel , Hayden Thomas L. , Broyde Suse 
Published: December 2004

AbstractA build‐up technique has been devised that permits prediction of DNA structure form sequence. No experimental information is employed other than the force field parameters. This strategy for dealing with the multiple minimum problem requires a supercomputer to make the necessary global searches. The number of energy minimization trials that were made for each of the 16 deoxydinucleoside monophosphate conformational building blocks of DNA was 1944. As a test case, the minimum energy conformations of d(GpC) and d(CpG) to 5.5 kcal/mole were then combined to generate energy‐minimized structures for d(CpGpC). The number of trials that were made for d(CpGpC) was 3752. Minima for this single‐stranded trimer to 15 kcal/mole were then employed to search for minimum energy conformations of the duplex d(CpGpC) · d(GpCpG). The number of starting conformations that were utilized at this stage was 1514. The lowest energy duplex had a Z‐II‐DNA conformation, followed by a B‐DNA form at 1.2 kcal/mole. The A‐ and Z‐I‐forms as well as many novel Watson–Crick base‐paired structures were found at higher energy. Finally, energy‐minimized structures of d(CG)6 in Z‐II and B‐DNA conformations were computed using torsion angles from the analogous duplex trimer minima.