bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational analysis of polytripeptides (Gly‐Pro‐Ala)n, (Gly‐Ala‐Hyp)n, and (Gly‐Ala‐Ala)n in connection with the problem of collagen structure
Authors: Tumanyan V. G. , Abagyan R. A. , Esipova N. G. 
Published: December 2004

AbstractConformational analysis of triple helics of a type of collagen was performed with typical collagen tripeptide sequences based on Gly‐Pro‐Ala, Gly‐Ala‐Hyp, and Gly‐Ala‐Ala. During energy minimization, the possibility of continual deformation of the pyrrolidine cycle was taken into account in order to achieve better accuracy in the resulting structure. The (Gly‐Pro‐Ala)n structure is almost isomorphic to the (Gly‐Pro‐Hyp)n structure obtained in the previous work [Tumanyan, V. G. & Esipova, N.G. (1982) Biopolymers 21, 475–497]. For a collagen‐type structure, the optimal conformation of (Gly‐Ala‐Hyp)n tends to have a decreased unit twist (t = 15°), although the energy advantage with respect to the conformation with t = 45° is not so significant. A similar situation is observed for (Gly‐Ala‐Ala)n. In this case, the energy decrease during unwinding to t = 15° from t = 45° is quite small. The conformations of (Gly‐Ala‐Hyp)n and (Gly‐Ala‐Ala)n with t = 15° exhibit a similarity with a triple complex of polyproline II helices—a noncoiled coil such as (Gly‐Pro‐Hyp)n and (Gly‐Pro‐Ala)n. A similar structure may be postulated for subcomponent cq1 of the first component of a human complement containing substantial Gly‐X‐Pro and Gly‐X‐Y tripeptide derivatives in the primary structure (X, Y = any amino acid). The results suggest that the observed helical symmetry of collagen (t = 36°) is a consequence of superposition of diffraction patterns (for sufficiently long segments) from various helices (t varies from ∼15° for Gly‐X‐Hyp and Gly‐X‐Y to ∼56° for Gly‐Pro‐Ala). For short alternating segments, some unification of different helical structures is possible.
Vibrational circular dichroism of polypeptides. III. Film studies of several α‐helical and β‐sheet polypeptides
Authors: Sen A. C. , Keiderling T. A. 
Published: December 2004

AbstractVibrational CD (VCD) of amides A, I, and II vibrations of a variety of polypeptide films have been measured. VCD of films of α‐helical and β‐sheet structures are compared in the three regions. Reproducible spectra could only be obtained for thin films free of orientation dependence. The sign and band shape of the VCD of films are not always the same as that in solution. However, the magnitude of the observed VCD seems to correlate with the secondary structure such that α‐helical molecules typically have much larger Δε/ε values than do β‐sheet molecules. The possibility of interference by artifacts owing to light‐scattering effects is discussed.
Vibrational analysis of peptides, polypeptides, and proteins. XXI. β‐Calcium‐poly(L‐glutamate)
Authors: Sengupta Pradeep K. , Krimm S. , Hsu S. L. 
Published: December 2004

AbstractThe observed Raman and ir spectra of Ca‐poly(L‐glutamate) in the β conformation have been analyzed by means of a normal mode calculation. The force field for the main chain was transferred without refinement from β‐poly(L‐alanine), yet it provides a good prediction of the observed bands and, in particular, explains subtle differences in the spectra of these two β‐sheet structures. Main‐ and side‐chain modes are well characterized, and the dependence of the amide III frequency on side‐chain composition is again demonstrated.
Differential electrostatic stabilization of A‐, B‐, and Z‐forms of DNA
Authors: Matthew James B. , Richards Frederic M. 
Published: December 2004

AbstractThe static accessibility discrete charge algorithm for protein charge interactions is extended to the case of linear polyelectrolytes. In this model, the effective dielectric value between surface charge sites depends predominantly on the solvent ionic strength and the solvent accessibilities of the charge sites. This treatment accounts for the phenomena of specific ion binding in the context of a general electrostatic effect [Matthew and Richards (1982) Biochemistry 21, 4989]. Specific ion sites are determined by locating areas of high electrostatic potential at the solvent interface of the macromolecule. At a given ionic strength the calculated potential at a site is taken to describe a binding constant and therefore the ion site occupancy. For a 20‐base‐pair fragment of B‐DNA, net charge of −40, 16 ion sites are indicated in the minor groove. The partial occupancy of each site increases from 0.2 to 0.5 as the ionic strength is increased from 0.01 to 0.50. Over the same range of ionic strength, the electrostatic free energy of this charge array is calculated to change from +0.6 to −0.05 kcal/bp. Parallel behavior is predicted for A‐ and Z‐DNA charge geometries. The most stable configuration, based on electrostatic criteria, at high ionic strength (I = 0.1–0.5) is that of Z‐DNA. In this range, the ratio of “bound” sodium to phosphate is predicted to be less than 0.4.
The conformational transition of κ‐carrageenan using microcalorimetry
Authors: Rochas Cyrille , Mazet Jean 
Published: December 2004

AbstractThe interactions between inorganic cations and κ‐carrageenan in aqueous solutions have been studied using microcalorimetry. The enthalpy of dilution and the enthalpy of mixing of κ‐carrageenan in the coil conformation with an alkaline metal chloride have been investigated and are in agreement with theoretical predictions. The formation of helical dimer in a K+ salt form in the absence of a gel formation is confirmed.
Interactions of molecules with nucleic acids. XI. Generalization of techniques to generate nucleic acid structures with applications to intercalation sites and kinked structures
Authors: Taylor Eric R. , Miller Kenneth J. 
Published: December 2004

AbstractA generalized procedure to generate nucleic acid structures is presented. In this procedure, the bases of a base pair are oriented first for characterization of particular DNA receptor sites. The resultant sites are then used in the study of specific molecule–DNA interactions. For example, intercalation sites, kinked DNA, and twisted and tilted bases are envisioned. Alterations of structures via anti → syn orientations of bases, as well as crankshaft motion about collinear bonds, provide additional conformations without disrupting the overall backbone structure. These approaches to the generation of nucleic acid structures are envisioned as required in studies of the intercalation phenomenon, minor adjustments of DNA to accommodate denaturation, binding of carcinogens to DNA, complex formation of transition metals with DNA, and antitumor agents as ligands. For these base‐pair and base orientations, backbone orientations are calculated by the AGNAS technique to yield physically meaningful conformations, namely, those conformations for which nonbonded contacts are favourable. A procedure is presented to generate dimer duplex units that are physically meaningful and to assemble these units into a polynucleotide duplex. Double helices that begin with B‐DNA, undergo a transition to one of the above‐mentioned receptor sites, and return to B‐DNA can be assembled from a catalog of dimer duplexes. Stereographic projections of the various receptor sites already being used to model binding to DNA are presented.
Molecular‐dynamics simulation of phenylalanine transfer RNA. I. Methods and general results
Authors: Harvey Stephen C. , Prabhakaran M. , McCammon J. Andrew 
Published: December 2004

AbstractA 24‐ps molecular‐dynamics simulation of motions in yeast tRNAPhe has been completed. The overall structure of the molecule is well preserved, for the motions represent fluctuations about an average structure that is very much like the crystallographic structure. The four helical stems remain intact, the structures of the loop regions do not deteriorate, and even the base stacking in the single‐stranded amino acid acceptor terminus is maintained. With two exceptions, none of the sugar puckers is significantly changed. The unconstrained floppy motions of base A76 are responsible for the repuckering of ribose 76. The other sugar that repuckers is ribose, 46, and this is the result of a very small structural change in the center of the molecule that is also responsible for the breakage of one tertiary hydrogen bond. This change in local structure does not seriously distort the base‐stacking and intercalation patterns where the variable loop and the D‐stem interact.
Solvent accessibility studies of β‐bends and application to cyclic hexapeptides
Authors: Soman K. V. , Ramakrishnan C. 
Published: December 2004

AbstractThe solvent‐accessible surface areas (ASAs), of the atoms in tripeptides around the minimum‐energy conformations of the β‐bend types I, I′, II, and II′ have been computed as a first step in the systematic solvent accessibiity study of secondary structures. The side chains chosen at the two middle positions of the bend are L‐Ala, D‐Ala, and Gly. The ASAs of the hydrogen atoms are reported here and are found useful in determining the type of β‐bends in six examples of cyclic hexapeptides whose crystal structures are known. Comparison with observation showed that all the β‐bends in these cyclic hexapeptides were correctly identified by the present method. This points to a possible use of the method in identifying β‐bend types in solution.
Simulation of the diffusion‐controlled reaction between superoxide and superoxide dismutase. I. Simple models
Authors: Allison S. A. , Ganti G. , McCammon J. A. 
Published: December 2004

AbstractA Brownian dynamics simulation method is used to study the diffusion‐influenced bimolecular reaction between superoxide and superoxide dismutase (SOD). Using simple models, the details of which are based on the crystallographic structure of SOD, it is found that the electrostatic charge distribution of SOD serves to guide superoxide into the active site and enhance the diffusion‐controlled rate constant by about 40%.
Conformations of blood group H‐active oligosacharides of ovarian cyst mucins
Authors: Rao B. N. Narasinga , Dua Virendra K. , Bush C. Allen 
Published: December 2004

AbstractSpectroscopic data and conformational energy calculations are reported for eight oligosaccharides from ovarian cyst mucins and from human milk, the nonreducing terminals of which have fucose (α1 → 2)galactose linked either (β1 → 3) (type I) or (β1 → 4)(type II) to N‐acetylglucosamine or in (β1 → 3) linkage to galactosaminitol. The fully assigned proton nmr spectra are reported along with nuclear Overhauser enhancement (NOE) data. Amide proton coupling constants and vacuum‐uv CD spectra provide information on the amide plane orientation and amide environment. Our results imply that the fucosidic dihedral angles are similar for all three cases and that the substantial differences in the chemical shifts of the fucosyl protons of type I, type II, and 3‐ol chains result from different perturbations by the amide group of the residue to which the β‐galactose is linked. Stereopair diagrams of conformational models for both type I and II H chains are presented that are consistent with NOE, coupling constants, conformational energy calculations, and the CD data. While the temperature dependence of the observed NOE of penta‐ and hexasaccharides indicates that their rotational correlation times are strongly temperature dependent, we conclude that the conformations are essentially independent of temperature.
Synthesis and nmr conformational studies of polyoxyethylene‐bound, α‐deuterated glutamate oligopeptides
Authors: Ribeiro Anthony A. , Saltman Robert , Goodman Murray 
Published: December 2004

AbstractThe syntheses of three series of glutamate oligopeptides attached to a macromolecular solubilizing polyoxyethylene (POE) group Boc‐[Glu(OMe)]n‐OPOE, Ac‐[Glu(OMe)]n‐OPOE, pGlu‐[Glu(OMe)]n−1‐OPOE (n − 1–7) and their various analogs specifically deuterated at individual α‐CH positions using the liquid‐phase method of peptide synthesis are described. It was shown that stepwise synthesis using the symmetrical anhydride gave homo‐oligopeptides that are analytically pure. Fragment condensation methods using DCC‐HOBt yield POE‐peptides with POE‐HOBt impurities but the peptide synthesis may be carried stoichiometrically with smaller quantities of amino acid derivatives. 360 MHz 1H‐nmr conformational studies of these homo‐oligopeptides in DMSO‐d6 are presented. The α‐deuterated peptides are shown to allow unequivocal homoligopeptide backbone NH assignments.
Conformational analysis of polyoxyethylene‐bound homo‐oligo‐L‐glutamates in aqueous environment
Authors: Ribeiro Anthony A. , Saltman Robert , Goodman Murray 
Published: December 2004

AbstractA detailed conformational analysis of homo‐oligo‐L‐glutamates was carried out in aqueous solution using 1H‐nmr spectroscopy. Three series of side‐chain protected (α‐OMe) glutamate oligopeptides, attached to polyoxyethylene (POE) to enhance their solubility, were synthesized. The effect of the N‐terminal blocking groups—Boc, Ac, and pGlu—on the conformations of these peptides in water is discussed. Unequivocal assignments were obtained for all amide NH resonances through use of selectively α‐deuterated oligo‐glutamates. Analysis of vicinal coupling constants, temperature dependence of NH chemical shifts, transfer of saturation experiments, and titration studies with a denaturing solvent (DMSO) were used to investigate the peptide structure. These data suggest that the Glu1 and Glu2 NH protons of each heptamer are solvent exposed, while the NH protons of interior glutamate residues chain are solvent sequestered. The nmr data are consistent with the onset of helical structure at the heptamer of each series in aqueous solution. The POE‐peptides with pGlu at the N‐terminus showed considerably reduced stability of structure than those with the Boc or acetyl blocking groups. Peptide conformations and their stability in water are compared to those in other solvents.
On the reptation theory of gel electrophoresis
Authors: Slater Gary W. , Noolandi Jaan 
Published: December 2004

AbstractWe introduce a new biased reptation theory that allows a qualitative and semiquantitative study of DNA gel electrophoresis. We prove that stretching of the end‐to‐end vector of a very long charged reptating chain in an electric field occurs in a short period of time during a typical electrophoresis experiment, and that this leads to a field‐dependent mobility only weaky dependent upon the size of the chain, in agreement with experiments on DNA. We also propose a practical technique to avoid chain stretching. Finally, many scaling laws are predicted, most of them being verifiable by experiment.
Models of thioredoxin hairpin structures: Conformational properties of β‐turn containing sequences
Authors: Azzena Ugo , Luisi Pier Luigi 
Published: December 2004

AbstractSequences 74–91 and 77–91 of E. coli thioredoxin, which according to x‐ray structure contain an irregular β‐turn, a hairpinlike structural element, have been synthesized and their conformational properties in solution have been investigated by means of CD spectroscopy. In addition, analogs of these sequences, containing the regular β‐turn element Gly‐Pro‐(Gly)2, have also been prepared and investigated. These are BOC‐Ile‐Gly‐Pro‐(Gly)2‐Val‐OMe (III) and BOC‐(Ile)3Gly‐Pro‐(Gly)2‐(Val)5‐OMe (IV) that on the basis of probability, should form hairpin structures stabilized by intramolecular interactions. While the natural sequences were shown to be unable to adopt structures characterized by an intrinsic conformational stability, the two analogs showed evidence of intramolecular folding in methanol and trifluoroethanol–water solution. In particular, the CD spectra are indicative of β‐structure. The most interesting case was observed for compound IV, as the highest degree of conformational order was present in solutions containing a large proportion of water. In addition, the formation of this structure took place in a highly cooperative manner. The results are utilized to discuss whether and to what extent conformationally stable folding peptide units of small size can be formed in aqueous solution.
A Raman spectroscopic study on 5′‐rGMP gel and self‐aggregate
Authors: Kim Kang Woo , Kim Sang Kyu , Kim Myung Soo , Suh Se Won 
Published: December 2004

AbstractIn order to analyze the melting behavior of 5′‐rGMP gel at acidic pH and self‐aggregate near neutral pH we have obtained Raman spectra of aqueous solutions of 5′‐rGMP at various temperatures. At low temperature the intensities of Raman peaks at 502, 585, 1083, 1179, 1322, 1366, 1487, and 1578 cm−1 decrease due to the formation of ordered structure (Raman hypochromism). In contrast, the peaks at 671, 725, 813, and 1338 cm−1 become stronger at low temperature (Raman hyperchromism). The Raman hyperchromism of the 671‐ and 813‐cm−1 peaks have been explained in terms of detailed structural models. Recently, the 668‐ and 682‐cm−1 peaks in the Raman spectrum of aqueous 5′‐rGMP solution have been attributed to the guanine ring breathing vibrations in C3′‐ and C2′‐endo conformers [Benevides, J. B., Lemur, D. & Thomas, G. J., Jr. (1984) Biopolymers 23, 1011–1024]. On the basis of this information our Raman data can be interpreted to suggest that the continuous helix model of 5′‐rGMP gel is right‐handed. The 1487‐cm−1 peak intensity has been used to monitor the melting profies at several pHs. Near neutral pH the melting profile shows a single transition, whereas at acidic pH it shows two transitions. From these observations we propose possible pathways for the melting of 5′‐rGMP gel formed at acidic pH and self‐aggregate formed near neutral pH.
Conformation of dioxopiperazines. III. Conformational‐energy calculations and evaluation of specific forces contributing to the intramolecular dioxopiperazine‐phenyl ring‐ring folding in cyclo(glycyl‐phenylalanyl)
Authors: Kołodziejczyk Aleksandra , Ciarkowski Jerzy 
Published: December 2004

AbstractConformational energy calculations on cyclo(glycyl‐L‐phenylalanyl), c(Gly‐Phe), were carried out by means of the semiempirical MO CNDO/2 method. They corroborated earlier experimental findings that in c(Gly‐Phe) the conformations with an aromatic side‐chain ring folded over the dioxopiperazine (DOP) ring contribute significantly to the overall equilibrium, provided that the empirical optimization of the DOP ring geometry, extracted from x‐ray data, rather than that of the CNDO/2‐derived data is used throughout the computations. Following these studies, more detailed calculations, based partly on CNDO/2‐derived data and partly on experimental data, were carried out to clarify the question, which are the forces responsible for this ring‐ring stacking? In contrast to early suggestions, it was found that the quadrupole‐quadrupole and dispersion interactions mainly contribute to folded conformations of c(Gly‐Phe). Some implications of this finding on devising force fields for molecular‐mechanics calculations of peptides are briefly outlined.
Molecular cartography of globular proteins with application to antigenic sites
Authors: Fanning David W. , Smith John A. , Rose George D. 
Published: December 2004

AbstractA method, molecular cartography, is introduced as a way to quantitate the topographic structure of a protein surface. The method is applied to the problem of antigenic determinants, and it is used to examine local and global topography of reported antigenic regions on the surface of myoglobin and lysozyme. In nine antigenic sites taken from the literature and studied in detail, no local property was found in sites that was not also found in remaining regions of the surface. However, a strong correlation was found between antigenic sites and regions of the surface that are globally exposed. This finding suggests that global exposure of the protein surface may play a primary role in determining the antigenic structure of the protein. Molecular cartography may be useful in other instances of protein–protein interactions such as those between proteolytic enzymes and their substrates.
Structural information from electric dichroism measurements of DNA and alternating GC nucleic acids in solution: The question of base tilt
Authors: Charney Elliot , Chen Holly Ho , Henry Eric R. , Rau Donald C. 
Published: December 2004

AbstractValues of the apparent intrinsic dichroism of the 260‐nm transition of duplex poly(dG‐dC) and poly(dG‐m5dC) in both B‐ and Z‐conformations are determined from electric dichroism (ED) measurements by extrapolation of the data at high field strengths. These values are compared to each other and to values of the intrinsic dichroism calculated for the Z‐ and B‐forms generated respectively from the crystal structure coordinates [(1981) A. H. J. Wang, G. J. Quigley, F. J. Kolpak, G. Van der Marel, T. H. Van Boom & A. Rich, Science 211, 171–176.] of the d(CpGpCpGpCpGp) hexamer and from the coordinates [(1982) A. V. Fratini, M. L. Kopka, H. R. Drew & R. E. Dickerson, J. Biol. Chem. 257, 14686–14707.]. of the terminal CpGpCpGp base pairs of the crystal of straight B‐form dodecamer d(CpGpCpGpApApTpTpCpGpCpGp). Direct association of the dichroism with the orientation of the optical transition moments with respect to the helix axis of poly(dG‐dC) implies that the average tilt of the bases is much different than the values calculated from the structural coordinates. The experimental values for both the B‐ and Z‐forms are, however, almost identical to those observed with fragments of “random” sequence B‐form DNA of the same molecular length. It is argued that this descrepancy and other anomalies reported in the literature are due to the theoretically predicted unusual high field behavior associated with diffuse ion atmosphere polarization. Unlike either permanent dipoles or induced moments based on bond polarizabilities, the orienting dipole energy from the polarization of the counterions surrounding DNA approaches a finite limiting value, dependent on DNA length, at very high field strengths. This can result in extrapolated dichroisms that do not reflect structure at perfect orientation, but rather structure at some limiting orientation. Consequently, we believe, the conclusion drawn from ED measurements on short fragments of DNA that the bases are highly tilted from the perpendicular to the helix axis by propeller twisting or otherwise is suspect.
Influence of different tripeptides on the stability of the collagen triple helix. I. Analysis of the collagen sequence and identification of typical tripeptides
Authors: Dölz R. , Heidemann E. 
Published: December 2004

AbstractThe amino acid sequence of the collagen α1(I) chain (calf) is analyzed. Deviations of random tripeptide distribution leads to the definition of clusters. Inside these regions, collagen‐typical tripeptides are located. Besides Gly‐Pro‐Hyp, Gly‐Pro‐Ala, and Gly‐Ala‐Hyp, the polar sequences Gly‐Glu‐Hyp, Gly‐Ala‐Arg, Gly‐Glu‐Arg, and Gly‐Pro‐Lys form typical sequences. The neighborhood of each tripeptide is analyzed and classified. The proximity to the collagen‐typical tripeptides is registered. Cluster theory: Less‐typical sequences also fold as members of the collagen triple helix and they are as reasonable as well as important for the collagen structure as the cluster tripeptides, but only the latter are important for the nucleation of the triple‐helical folding.