bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural analysis of purified human tracheobronchial mucins
Authors: Gupta R. , Jentoft N. , Jamieson A. M. , Blackwell J. 
Published: December 2004

AbstractLight scattering has been used to investigate the structure of human tracheobronchial mucin glycoproteins (HTBM) from the sputum of cystic fibrosis patients. The specimen was extracted using 6M guanidinium hydrochloride solution and fractionated by gel exclusion chromatography on Sephacryl S‐1000. The fractionated HTBM was purified by density gradient ultracentrifugation. Purity of the resulting material was confirmed by SDS polyacrylamide gel electrophoresis and uv spectroscopy. Light scattering measurements on the fractionated mucins yield weight‐average molecular weights Mw, and z‐average radii of gyration Rg, z. The native cystic fibrosis HTBM consisted of a high molecular weight fraction with Mw = 9.3 × 106 daltons and a lower molecular weight fraction contanining partly degraded mucins. After reduction and carboxymethylation of the high molecular weight native fraction, the resulting material was separated into three pools with Mw values of 5.1 × 106, 1.6 × 106, and 400,000. The derived molecular weights for the protein cores Mp,w, and the experimental radii of gyration are found to be consistent with the Mp,w – Rg relation established previously for submaxillary, cervical, and gastric mucins. These results imply that HTBM has the same extended‐coil conformation reported for other mucins and has a molecular structure consisting of subunits, linked into linear chains via covalent (disulfide) bonds.
CD of the synthetic RNA duplexes poly[r(A‐T)] and poly[r(A‐U)] in salt and ethanolic solutions
Authors: Voriíčková Michaela , Kypr Jaroslav , Jovin Thomas M. , Planck Max 
Published: December 2004

AbstractSynthetic RNA poly[r(A‐T)] has been synthesized and its CD spectral properties compared to those of poly[r(A‐U)], poly[d(A‐T)], and poly[d(A‐U)] in various salt and ethanolic solutions. The CD spectra of poly[r(A‐T)] in an aqueous buffer and of poly[d(A‐T)] in 70.8% v/v ethanol are very similar, suggesting that they both adopt the same A conformation. On the other hand, the CD spectra of poly[r(A‐T)] and of poly[r(A‐U)] differ in aqueous, and even more so in ethanolic, solutions. We have recently observed a two‐state salt‐induced isomerization of poly[r(A‐U)] into chiral condensates, perhaps of Z‐RNA [M. Vorlíčková, J. Kypr, and T. M. Jovin, (1988) Biopolymers 27, 351–354]. It is shown here that poly[r(A‐T)] does not undergo this isomerization. Both the changes in secondary structure and tendency to aggregation are different for poly[r(A‐T)] and poly[r(A‐U)] in aqueous salt solutions. In most cases, the CD spectrum of poly[r(A‐U)] shows little modification of its CD spectrum unless the polymer denatures or aggregates, whereas poly[r(A‐T)] displays noncooperative alterations in its CD spectrum and a reduced tendency to aggregation. At high NaCl concentrations, poly[r(A‐T)] and poly[r(A‐U)] condense into ψ (‐) and ψ (+) structures, respectively, indicating that the type of aggregation is dictated by the polynucleotide chemical structure and the corresponding differences in conformational properties.
Synthesis and conformational studies by 1H‐ and 13C‐nmr spectroscopy of a novel, sterically constrained analogue of thyrotropin‐releasing hormone
Authors: Mapelli Claudio , Halbeek Herman Van , Stammer Charles H. 
Published: December 2004

AbstractA novel thyrotropin‐releasing hormone (TRH) analogue, [2, 4‐MePro3]‐TRH (2, 4‐MePro: 2‐carboxy‐2, 4‐methanopyrrolidine), has been synthesized using a rapid solid phase peptide synthesis method, and its conformational properties investigated by one‐ and two‐ dimensional (2D) nmr spectroscopy and by proton Overhauser measurements. Following a published approach, calibrated interproton Overhauser effects were used together with distance geometry analysis to deduce that the single conformation of the His‐2, 4‐MePro tertiary amide bond is trans in aqueous solution. This conclusion was corroborated by 2D dipolar‐correlated (NOESY) spectroscopy. A preferentially extended conformation is indicated by the nmr data, similar to that of TRH. The ϕ, ψ conformational space of 2, 4‐MePro is, however, significantly different from that of trans proline and the structural consequences of these differences at the C‐terminus are discussed. The distribution of histidine side‐chain conformation in the TRH analogue was deduced from coupling constants and from the short‐range interaction between the imidazole ring and one of the prochiral faces of the 2, 4‐MePro side chain.
Uv resonance Raman spectroscopy of nucleic acid duplexes containing A‐U and A‐T base pairs
Authors: Grygon Christine A. , Spiro Thomas G. 
Published: December 2004

AbstractResonance Raman spectra have been obtained at several uv wavelengths (200–266 nm) for poly(rA)‐poly(rU), poly(dA‐dU), poly(dA)‐poly(dT), and poly(dA‐dT), representing nucleic acid duplexes containing A‐U and A‐T base pairs with different stacking interactions and different backbone conformations. Frequency shifts are seen in the exocyclic modes corresponding to coupled C4O and C5C6 stretching of U and T, although the NH2 scissors frequency of A is unshifted relative to that of the mononucleotide. These frequency patterns are interpreted as the superposition of H bonding and dipole–dipole coupling effects. Strong hypochromism is seen for most of the ring modes, resulting from the absorption hypochromism and from shifts in the electronic transitions due to stacking. The effects are larger for A bands in the homopolymers than in the heteropolymer duplexes, reflecting the larger influence of A/A than A/U(T) stacking. Poly(rA)‐poly(rU) stands out among these polymers in showing 10 cm−1 downshifts in one U and several A modes. These shifts may be related to the A form structural parameters of this duplex, but the physical mechanism is not obvious.
Ir and Raman spectroscopic studies on coulombic interaction between water‐soluble porphyrins and nucleic acids
Authors: Nonaka Y. , Lu D. S. , Dwivedi A. , Strommen D. P. , Nakamoto K. 
Published: December 2004

AbstractWe have shown previously that the N‐methylpridyl group vibrations of water‐soluble porphyrins, M(TMpy‐P4), are shifted to lower frequencies (0.5–2.6 cm−1) as a result of coulombic interaction between the N+‐CH3 group of M(TMpy‐P4) and the PO2 group of a nucleic acid. We have now turned over our attention to the effect of this coulombic interaction on the PO2 group vibrations of nucleic acids. Using Fourier transform ir and Raman spectroscopy, we found that the νa(PO2) at 1221 cm−1 is shifted 12 ∼ 17 cm−1 to higher frequencies, whereas the νs(PO2) at 1087 cm−1 is shifted 18 ∼ 26 cm−1 to lower frequencies, when DNA is mixed with M(TMpy‐P4). These results indicate that the N+‐CH3 group of M(TMpy‐P4) interacts preferentially with one of the two oxygen atoms of the PO2 group of the DNA duplex.
The calculated free energy effects of 5‐methyl cytosine on the B to Z transition in DNA
Authors: Pearlman David A. , Kollman Peter A. 
Published: December 2004

AbstractWe have examined the free energy effects of 5‐methylation of cytosine on the B ⟷ Z conformational equilibrium in DNA. Free energy differences were calculated using the free energy perturbation approach, which uses an easily derived equation from classical statistical mechanics to relate the free energy difference between two states to the ensemble average of the potential energy difference between the states. Calculations were carried both in explicit solvent and (for comparison) in vacuo. The free energy values obtained for the explicit solvent systems are total free energies, with contributions from all parts of the system (solvent + solute), and so are relevant to the B ⟷ Z transitions observed under real(physiological) conditions. We calculate that in solution, methylation makes the B → Z transition more favorable by about −0.4 kcal/mole base pair (bp) in free energy. This value compares well with approximate experimentally derived values of about −0.3 kcal/ mole‐bp. We also discuss a method for determining the free energy difference between conformational states poorly maintained by a potential energy model. Finally, the effects of methylation on the melting temperature of DNA are examined.
Solvent effect on the conformation of the hydroxymethyl group established by molecular dynamics simulations of methyl‐β‐D‐glucoside in water
Authors: Kroon‐Batenburg L. M. J. , Kroon J. 
Published: December 2004

AbstractMolecular dynamics simulations of methyl‐β‐D‐glucoside in water are performed. Although the tg conformation of the hydroxymethylgroup is found to be the lowest in energy for the isolated molecule, it appears to be unstable in water. The well‐known absence of a significant amount of the tg conformation in polar solvents can therefore be explained as a solvent effect.
Structural principles of B‐DNA grooves hydration in fibers as revealed by Monte Carlo simulations and x‐ray diffraction
Authors: Eisenhaber F. , Mannik J. H. , Tumanyan V. G. 
Published: December 2004

AbstractBeing interested in possible effects of sequence‐dependent hydration of B‐DNA with mixed sequence in fibers, we performed a series of Monte Carlo calculations of hydration of polydeoxyribonucleotides in B form, considering all sequences with dinucleotide repeat. The computational results allow the ten base‐stacking types to be classified in accordance with their primary hydration in the minor groove. As a rule, the minor groove is occupied by two water molecules per base pair in the depth of the groove, which are located nearly midway between the planes of successive base pairs and symmetrically according to the dyad there. The primary hydration of the major groove depends on the type of the given base pair. The coordinates of 3 water molecules per base pair in the depth of the major groove are determined by the type of this pair together with its position and orientation in the helix, and are practically independent on the adjacent base pairs. A/T‐homopolymer tracts do not fit into this hydration pattern; the base pair edges are hydrated autonomously in both grooves.Analysis of the Li‐B‐DNA x‐ray diffraction intensities reveals those two water positions in the minor groove. In the major groove, no electronic density peaks in suffiecient distance from the base edges were found, thus confirming the absence of any helical invariance of primary hydration in this region.With the help of the rules proposed in this paper it is possible to position the water molecules of the first hydration shell in the grooves of canonical B‐DNA for any given sequence.
Molecular dynamics simulation provides a possible structure for substance P‐like peptides in aqueous solution
Authors: Teleman Olle , Von Der Lieth Claus‐Wilhelm 
Published: December 2004

AbstractA hypothetical conformation of the undecapeptide Substance P in aqueous solution is generated by molecular dynamics simulation for 284 ps. The conformation takes explicit solvent interactions into account as well as entropic effects to the extent that phase space is sampled in simulation. The initial conformation is taken from energy minimization studies and modified. In spite of fluctuations through 180° in some backbone dihedral angles, the peptide settles with all backbone dihedrals within ± 60° from the initial values. In 130 ps, the radius of gyration decreases from 6.2 Å to 5.5 Å, whereas only fluctuation (± .2 Å) is observed during the last 150 ps. The root‐mean‐square deviation at optimal superposition for a pair of conformations from the last 150 ps is 0.6 Å, based on backbone atoms. The final structure is close‐knit, nearly globular, and stabilized by several long‐lived hydrogen bonds. The simulation conformation agrees with the scarce experimental data including a large number of structure‐activity relationships. Thus, the simulation conformation is a likely candidate for one of the several conformations, the existence of which has been deduced from nuclear magnetic resonance data. Simulation results and experimental modification studies suggest that Phe 8 and Leu 10 are involved in the primary binding of SP to its receptors.
Helix‐coil stability constants for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly(hydroxybutylglutamine‐CO‐L‐proline)
Authors: Altmann K.‐H. , Wójcik J. , Vásquez M. , Scheraga H. A. 
Published: December 2004

AbstractWater‐soluble random copolymers containing L‐proline and N5‐(4‐hydroxybutyl)‐L‐glutamine were synthesized by copolymerization of the tripeptides H‐L‐Glu(OBzl)‐L‐Glu(OBzl)‐L‐Glu(OBzl)‐OH and H‐L‐Glu(OBzl)‐L‐Pro‐L‐Glu(OBzl)‐OH, using ben‐zotriazolyl‐N‐oxy‐tris(dimethylamino)‐phosphonium hexafluorophosphate as condensing reagent, and subsequent aminolysis of the Bzl ester groups with 4‐amino‐1‐butanol. These copolymers were found to contain significant amounts of N5‐(4‐hydroxybutyl)‐D‐glutamine, thus requiring the synthesis of a binary copolymer containing only D‐ and L‐N5‐(4‐hydroxybutyl)glutamine residues in order to evaluate the possible effects of the D‐residues on the conformational properties of poly(hydroxybutylglutamine‐co‐L‐proline). The different copolymers were fractionated, and their thermally induced helix‐coil transition curves were obtained in water at neutral pH. When proper corrections were applied for the helix‐destabilizing properties of N5‐(4‐hydroxybutyl)‐D‐glutamine, the Zimm‐Bragg parameters σ and s for L‐proline could be deduced from the melting curves of poly (hydroxybutylglutamine‐co‐L‐proline). The results indicate that L‐proline acts as a very strong helix breaker over the entire temperature range from 0 to 60°C.
On the multiple‐minima problem in the conformational analysis of polypeptides. IV. Application of the electrostatically driven monte carlo method to the 20‐residue membrane‐bound portion of melittin
Authors: Ripoll Daniel R. , Scheraca Harold A. 
Published: December 2004

AbstractThe conformational space of the membrane‐bound portion of melittin has been searched using the electrostatically driven Monte Carlo (EDMC) method with the ECEPP/2 (em‐pirical conformational energy program for peptides) algorithm. The former methodology assumes that a polypeptide or protein molecule is driven toward the native structure by the combined action of electrostatic interactions and stochastic conformational changes associated with thermal movements. The algorithm produces a Monte Carlo search in the conformational hyperspace of the polypeptide using electrostatic predict ions and a random sampling technique, combined with local minimization of the energy function, to locate low‐energy conformations. As a result of 8 test calculations on the 20‐residue membrane‐bound portion of melittin, starting from six arbitrary and two completely random conformations, the method was able to locate a very low‐energy region of the potential with a well‐defined structure for the backbone. In all of the cases under study, the method found a cluster of similar low‐energy conformations that agree well with the structure deduced from x‐ray diffraction experiments and with one computed earlier by the build‐up procedure.
A simple statistical field theory of heteropolymer collapse with application to protein folding
Authors: Bryngelson Joseph D. , Wolynes Peter G. 
Published: December 2004

AbstractA simple statistical extension of the Flory theory of excluded volume is developed, and applied to random heteropolymer collapse and a simple model of protein folding. Sequence heterogeneity is found to lead to new effects. The nucleation of protein folding is also briefly considered.
Thermal unfolding of helices of a C‐peptide analogue of ribonuclease A in sodium dodecyl sulfate solution
Authors: Wu Chuen‐Shang C. , Yang Jen Tsi 
Published: December 2004

AbstractThe conformation of a 13‐residue C‐peptide analogue of ribonuclease A, \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm suc - A}\mathop {\rm E}\limits^ - {\rm T - AAA}\mathop {\rm K}\limits^{\rm + } {\rm FL}\mathop {\rm R}\limits^{\rm + } {\rm A}\mathop {\rm H}\limits^{\rm + } {\rm A - CONH}_2 $\end{document}, in NaDodSo4 solutions with respect to temperature was studied with CD. The equilibrium constant of unfolding yielded a straight line in a van't Hoff plot. In 10 mM NaDodSo4, ΔGu = 120 cal/mol, ΔHu = 700 cal/mol, and ΔSu = 2.0 entropy units all on per helical residue. These values compared fairly well with the thermodynamic parameters of the uncharged helix‐coil transition of (Glu)n in 0.1 M NaCl based on the theories of Zimm and Bragg and Zimm and Rice. The peptide was not unfolded at 75°C completely. Even in water without surfactant it was not a “random coil.”
Problems of CD spectrometers (V): Can we measure CD and LD simultaneously? Comments on differential polarization microscopy (CD and linear dichroism)
Authors: Shindo Yohji , Nishio Motohide , Maeda Shiro 
Published: December 2004

AbstractAn interesting paper on circular dichroism (CD) and linear dichroism (LD) microscopy by Livolant, Mickols, and Maestre [(1988) Biopolymers 27, 1761–1969] has attracted our attention. They reported that they have succeeded in deconvoluting mathematically true CD and LD from signals obtained for their samples of strong and incompatible anisotropies. If this is true, then their method of mathematical deconvolution will open new possibilities in polarization‐modulation spectroscopy. However, after carefully reading through their paper, we found the following obscure points in their results: (1) the hardware of their spectrometer; (2) the sensitivity matrix; (3) the method for separation of CD and LD by using two standards; (4) average CD curves; and (5) circular intensity differential scattering (CIDS) and linear intensity differential scattering (LIDS) in the wavelength range from 300 to 330 nm. Making use of the Mueller matrix analysis, we present our comments on the above subjects together with our data. In conclusion, we maintain that it is difficult to accept their claim of having a general and useful approach to separating true CD and LD from signals observed in macroscopically anisotropic samples.
Complete assignment of the noncarbonylic carbon‐13 resonances of Tendamistat
Authors: Kessler H. , Schmieder P. , Bermel W. 
Published: December 2004

AbstractThe complete assignment of all noncarbonylic carbon‐13 resonances at natural abundance of the α‐amylase inhibitor Tendamistat is presented. Such an assignment can help solve ambiguities in the proton spectrum and forms the basis for further measurements to obtain more structural or dynamic information. Using a nonenriched sample, the low sensitivity due to the small gyromagnetic ratio of 13C to 1H and the low natural abundance of 13C requires sensitive methods to obtain interpretable spectra. Thus all the NMR techniques used incorporate proton detection. With three different techniques, the HMQC, the HMQC with TOCSY‐transfer, and the HMBC, a complete assignment based on the published proton chemical shifts (A. D. Kline, K. Wüthrich J. Mol. Biol. 192(1986)) was possible with spectra recorded in a reasonable time. Especially the HMBC, which yields correlations via 1H‐13C long‐range couplings, proved to be extremely valuable in the assignment procedure.
An optimal formulation of the matrix method in statistical mechanics of one‐dimensional interacting units: Efficient iterative algorithmic procedures
Authors: Yeramian E. , Schaeffer F. , Caudron B. , Claverie P. , Buc H. 
Published: December 2004

AbstractStatistical mechanical calculations for one‐dimensional interacting units have undergone great development in many fields of macromolecular science. The partition function is the most rigorous description of an ensemble of molecules in equilibrium. Specific methodological formulations and algorithms were developed to handle numerically the inclusion of long‐range effects (as compared to usual nearest neighbor Ising models) and known sequence‐dependent heterogeneities of biological macromolecules. The most successful approach in formulating these problems in a very general and tractable framework was the so‐called matrix method. Despite several improvements, it was claimed that in practical applications this approach had fundamental limitations inherent to any “matrix” formulation. We show here that a new conceptual formulation allows us to overcome these limitations completely. We propose a general iterative procedure that combines the theoretical advantages of the matrix method with the possibility of highly optimized and efficient numerical algorithms.
Conformational analysis and helical preferences of normal and α,α‐dialkyl amino acids
Authors: Hodgkin Edward E. , Clark John D. , Miller Katherine R. , Marshall Garland R. 
Published: December 2004

AbstractEnergy calculations have been performed on right‐handed helical structures of L‐alanine and α‐methylalanine oligomers. A new ′3.610′‐helix is described for α‐methylalanine peptides. The dependence of the relative stability of the α, 310, and 3.610 structural forms on helix length, dielectric, and force‐field, in the gas phase, has been studied. Potential energy surfaces for the interconversion of helices have been generated. The 310‐helix in α‐methylalanine oligomers exhibits a degree of enthalpic and entropic stabilization not observed for alanine. The relevance of the results to the formation of voltage‐sensitive ion channels is discussed.
Amide III frequencies for Ala‐X peptides depend on the X amino acid size
Authors: Weaver James L , Williams Robert W. 
Published: December 2004

AbstractRaman spectra of series of aqueous solutions of peptides containing two amino acids, glycine‐X, alanine‐X, and serine‐X, where X is an uncharged amino acid, show that the amide III band shifts systematically to lower frequencies as the side chain of the X amino acid becomes larger. The range of this shift is about 20cm−1, starting at 1275cm−1 for alanine‐glycine and moving to 1251 cm−1 for alanine‐tryptophan, with a correlation coefficient of 0.93 with the mass of the X amino acid side chain for 10 peptides. The amide I frequencies remain constant as the X amino acid is changed. This shift may result from a change in the average conformational preference of the peptide, a change in vibrational coupling of the amide III modes with the X amino acid side chain, a change in molecular force constants, or a combination of these. These results present a test for computational methods.
Synthesis and1H‐nmr studies of α‐deuterated analogues ofdes‐Trp1, Nle12‐human minigastrin
Authors: Amonraksa Kitti , Simonetti Mario , Da Rin‐Fioretto Silvio , Mammi Stefano , Peggion Evaristo 
Published: December 2004

AbstractThree analogues of the tridecapeptide amide H‐Leu‐(Glu)5‐Ala‐Tyr‐Gly‐Nle‐Asp‐Phe‐NH2were synthetized with α‐deuterated glutamate residues in specific positions in order to assign unambiguously the1H nmr spectrum of the parent peptide in water and in water‐trifluoroethanol mixtures. The synthetic route is described and the assignment illustrated. A previous, tentative assignment based solely on indirect evidence [Mammi, S., Mammi, N. J. & Peggioa, E. (1988)Biochemistry27, 1374–1379] was partially modified.