bluuebunny/crossref_metadata_2025_split huggingface dataset:
Premelting and the hydrogen‐exchange open state in synthetic RNA duplexes
Authors: Preisler R. S. , Mandal C. , Englander S. W. , Kallenbach N. R. , Frazier J. , Miles H. T. , Howard F. B. 
Published: December 2004

AbstractHere we attempt to relate equilibrium temperature‐dependent spectral changes in two synthetic RNA homopolymer duplexes—poly(rA) · poly(rU) and poly(rI) · poly(rC)—to the conformational opening detected in stopped‐flow hydrogen–deuterium exchange experiments on these molecules. We are concerned with changes in several spectral properties that occur well below onset of the thermally induced helix‐coil “melting” transition in these systems. These are known as “premelting” transitions, and can be detected in uv CD spectra as well as in vibrational bands of the bases in the ir. Both CD and ir spectra exhibit isoelliptic or isosbestic points consistent with a well‐defined two‐state premelting process. Application of a least‐squares analysis to two‐state models for premelting using data from different bands in the CD and ir shows that the enthalpies are substantially greater than that of the hydrogen‐exchange opening. Thus the hydrogen‐exchange open state represents only one premelting reaction among several that lead to equilibrium changes in helix geometry or base vibrational modes. The latter include processes that occur on a rapid time scale, including potential base‐pair openings not productive for the exchange reaction. It appears that the former, and not the hydrogen‐exchange opening, dominates the premelting alterations monitored by ir and CD spectroscopy.
Proton magnetic resonance studies on dermorphin and its peptide fragments
Authors: Pastore A. , Temussi P. A. , Tancredi T. , Salvadori S. , Tomatis R. 
Published: December 2004

AbstractDermorphin (TyrD‐AlaPheGlyTyrProSerNH2), a potent natural peptide opioid, its synthetic L‐Ala2 analog, and all the N fragments from the tripeptide (TyrD‐AlaPheNH2) to the parent hexapeptide amide were characterized for the first time by means of proton nmr spectroscopy at 11.74 T. Assignments of most protons of dermorphin were facilitated by the study of the N‐terminal fragments. Comparison of spectroscopic parameters with relative pharmacological activity is proposed as a possible means of studying flexible agonists in solution.
Generalized Poisson‐Boltzmann calculation of the distribution of electrolyte ions around the B‐ and Z‐conformers of DNA
Authors: Pack George R. , Klein Brian J. 
Published: December 2004

AbstractA solution to the three‐dimensional Poisson‐Boltzmann equation, generalized to include the finite size of the ions, is presented for the environment of DNA in the B‐ and Z‐conformations. The results clearly indicate that despite the lower linear charge density of the left‐handed Z‐conformer, there is a higher concentration of Na+ at the immediate surface of the Z‐from than at the surface of the B‐form. The average concentration of counterions within a 12‐Å radius of the DNA is, nonetheless, higher for the B‐ than for the Z‐form. Calculations of the electrostatic interactions of these conformers with an environment of 0.01M monovalent salt show that the salt exerts a greater stabilizing effect on the left‐handed conformer than on the right‐handed form.
Low‐frequency dynamics of solid poly(L‐alanine) from Raman spectroscopy
Authors: Tipping M. , Viras K. , King T. A. 
Published: December 2004

AbstractRaman modes from amorphous α‐helical poly(L‐alanine) in the low‐frequency region < 150 cm−1 have been observed and assignments and values compared with mode‐analysis calculations. The temperature dependence of the complete Raman spectrum of α‐poly(L‐Ala) is also reported.
Synthesis and characterization of six sequential polypeptides containing tyrosine, glutamic acid, alanine, and glycine by circular dichroism and difference spectroscopy
Authors: Zeiger Allen R. , Ellis John S. , Maurer Paul H. 
Published: December 2004

AbstractSix sequential polytetrapeptides containing equimolar amounts of tyrosine, glutamic acid, alanine, and glycine were characterized by CD and difference spectroscopy over a wide range of pH. As the pH was lowered from physiological values, each of the polymers underwent pH‐sensitive transitions. The CD spectra indicated that two polymers, poly(Tyr‐Glu‐Ala‐Gly) and poly(Tyr‐Ala‐Glu‐Gly), had some α‐helical conformation at pH 7.0 and approached maximum helicity around pH 6.0; two others, poly(Ala‐Tyr‐Glu‐Gly) and poly(Glu‐Ala‐Tyr‐Gly), had no α‐helical conformation at pH 7.0 and about one‐third of the ellipticities of the above two polymers at pH 5.5; and the remaining two, poly(Ala‐Glu‐Tyr‐Gly) and poly(Glu‐Tyr‐Ala‐Gly) had little or no α‐helix, even at pH 5.5. Difference spectroscopy at 286 nm yielded results quite different. The molar extinction coefficients for poly(Tyr‐Glu‐Ala‐Gly) and poly(Tyr‐Ala‐Glu‐Gly) continued to change, even below pH 5.5, and the total changes in absorbance between pH 8.0 and 4.5 were of intermediate magnitudes among the six polymers. Poly(Ala‐Tyr‐Glu‐Gly) and poly(Glu‐Ala‐Tyr‐Gly), which had similar CD spectra, had the lowest and highest pH‐related changes in the molar extinction coefficients. It thus appears that amino acid composition alone cannot account for the apparent differences in conformation among the polytetrapeptides. Other factors, such as amno acid sequence, must play a major role in the determination of conformation.The intrinsic viscosity of poly(Tyr‐Glu‐Ala‐Gly) increased markedly between pH 6.0 and 5.5, which was below the pH of the CD transition but above the pH at which the largest absorption perturbation change, at 286 nm, took place. The model that can best account for the relatively low pH at which the absorption transition of tyrosine occurred is a progressive immobilization of side chains in the α‐helix as the pH decreases.
Stabilization of short helices by intramolecular cluster formation
Authors: Mattice Wayne L. 
Published: December 2004

AbstractThe intramolecular formation of multiple clusters of interacting helices has been characterized in a homopolymer. The configuration partition function permits the formation of clusters in which the number of interacting helices may be as large as the greatest integer in n/2, where n denotes the number of amino acid residues in the chain. The theoretical formulation has its origin in a recent [Mattice, W. L. & Scheraga, H. A. (1984) Biopolymers 23, 1701–1724], tractable matrix expression for the configuration partition function for intramolecular antiparallel β‐sheet formation. Reassignment of the expression for one of the n(n+3)/2 elements in the sparse statistical weight matrix, along with a simple change in notation, converts that treatment into a matrix formulation of the configuration partition function for a chain containing multiple clusters of interacting antiparallel helices. The five statistical weights used are δ, fl, w, and the Zimm‐Bragg σ and s. Each tight bend that connects two interacting helices contributes a factor of δ, fl is used in the weight for larger loops between interacting helices, and w arises from helix–helix interaction. The influence of the helix–helix interaction is well illustrated by two helix–coil transitions in a chain with n = 156 and σ = 0.001. In the absence of helix–helix interaction, the transition occurs by the nucleation and subsequent elongation of a small number of helices. When helix–helix interaction is attractive, the transition can occur by a different mechanism. Formation of a single pair of interacting helices is followed by addition of new helices to the initial cluster. In the latter process, individual helices experience relatively little growth after they are formed.
A molecular mechanical study of netropsin‐DNA interactions
Authors: Caldwell James , Kollman Peter 
Published: December 2004

AbstractWe present molecular mechanical calculations on the complexes of netropsin with dA6·dT6, d(TATATA)2, d(CGCGCG)2, and d(CGCGAATTCGCG)2. The complexes were model built using computer graphics and then completely energy refined. Our calculations are consistent with the observed AT preference for netropsin and suggest that mixed sugar pucker geometries should be more stable than uniform in netropsin complexes with poly[d(A‐T)]·poly[d(A‐T)] and poly(dA)·poly(dt). The netropsin·d(TATATA) and netropsin·dA6·dT6 complexes are significantly different in structure, leading to a possible reason why the observed thermodynamics of netropsin‐association with poly[d(A‐T)]·poly[d(A‐T)] and with poly(dA)·poly(dT) are so different. We also model built and energy refined a structure of netropsin‐d(CGCGAATTCGCG)2 using as a guide the nmr data of Patel [(1982) Proc. Natl. Acad. Sci. USA, 79, 6424–6428] and found a three‐dimensional structure qualitatively consistent with the NOE enhancements observed by him. After our calculations were completed, we learned of an x‐ray structure of a netropsin:d(CGCGAATTCGCG)2 complex, and we compared the structure found in our calculation with the x‐ray structure.
Self‐association and solubility of peptides: Solvent‐titration study of Nα‐protected C‐terminal sequences of substance P
Authors: Toniolo Claudio , Bonora Gian Maria , Stavropoulos George , Cordopatis Paul , Theodoropoulos Dimitrios 
Published: December 2004

AbstractSelf‐association of Nα‐protected peptides related to C‐terminal sequences of substance P in methylene chloride was disrupted by adding increasing amounts of various polar organic solvents. This process was monitored by the disappearance of the amide I CO stretching band (1630 cm−1) of strongly intermolecularly H‐bonded molecules in the irabsorption spectra. The effects induced by main‐chain length, incorporation at position 9 of a residue promoting folding (α‐aminoisobutyric acid), the nature of solvent, and peptide concentration were established. A corollary 1H‐nmr investigation provided detailed information on the NH protons involved in the self‐association process as H‐bonding donors. The increasing propensity to aggregate exhibited by these peptides is paralleled by a decrease in their solubility. The impact of these results on the synthesis of substance P short sequences is briefly outlined.
Dependence of oxygen quenching of intercalated methylene blue triplet lifetime on DNA base‐pair composition
Authors: Berkoff Bruce , Hogan Mike , Legrange Jane , Austin Robert 
Published: December 2004

AbstractWe utilize the dynamic quenching of the triplet state of methylene blue by molecular oxygen to observe changes in the rate at which oxygen can penetrate the helix as a function of base‐pair composition. The results indicate that the interior of the oligonucleotide dA‐dT is more accessible than dG‐dC to small molecules such as dioxygen.
The relation of ion pairs to protein hydration: An IR spectroscopic and X‐ray crystallographic survey
Authors: Poole P. L. , Barlow D. J. 
Published: December 2004

AbstractWe report here a novel ir technique that we use to determine the apparent van't Hoff's energy for the distillation of water from protein amide and acid groups. The method is used to study the hydration properties of ten different proteins. The results show that water removal from the environment of ion‐paired acid groups (those ⩽ 4 Å from a basic group on the protein surface) requires less energy than water removal from the environment of nonpaired acid groups. These observations are supported by an analysis of the solvent distributions in protein crystal structures. A model is proposed for the interaction between water and protein acid groups, and this model is used to account for the distributions and properties of certain eye‐lens proteins.
Conformational changes of pinellin in solution using intrinsic fluorescence and CD as probes
Authors: Lu Zi‐Xian , Shi Qing‐Luo , Xu Qing‐Yu 
Published: December 2004

AbstractPinellin is a plant protein extracted from the rhizome of the Chinese herb Pinellia. It has the ability to abort early pregnancy in mice as well as in rabbits. Studies on the conformational changes of pinellin have been carried out in our laboratory using intrinsic fluorescence and CD. Experimental results show that some tryptophanyl side chains are buried more deeply than others, which results in the heterogeneity of tryptophanyl emission. CD data indicated a high content of β‐pleated sheet and β‐turn for the backbone conformation. The results of fluorescence and CD measurements both demonstrated the presence of intermediates along the path of denaturation. The following was proposed as the unfolding mechanism of pinellin in 6M guanidine hydrochloride: native state → first intermediate → second intermediate → fully unfolded state.
A polynucleotide CD probe: Interactions with oligomers of a polycationic amine that exhibit positive extrinsic bands at > 300 nm
Authors: Zarlenga D. S. , Halsall H. B. , Day R. A. , Roth A. C. 
Published: December 2004

AbstractA set of large positive extrinsic CD bands ([θ]333 = 2.6 X 104 deg‐cm2/decimole phosphate) in the > 300 nm region as well as diminution of the intrinsic signals (θ275) have been observed in the CD spectra of various nucleic acids complexed with the achiral compound, N‐poly{α‐[N‐(4‐pyridylethylene‐4‐pyridyl‐N′‐)α′‐p‐xylyl]dibromide}‐4‐pyridylethylene‐4‐pyridinium bromide, (polymer X).1,2,5 The signal changes are attributed to the binding of polymer X chromophores isogeometrically to the DNA helix in an ordered chiral arrangement. Fractionation of polymer X gives 10 well‐separated oligomers. The oligomers were characterized by nmr. Their interactions with DNA have been investigated with respect to r(r = ratio of equivalents of polymer X charge/g‐atoms DNA phosphorus) and n (oligomer chain length). In all cases where n ≥ 1, [θ]333 increases linearly with increasing r between 0 and 0.32, and is accompanied by a corresponding decrease in [θ]275, which becomes negative as r approaches .32. Extrinsic band intensities reveal a dependence on n up to n = 5, above which increases in nonspecific binding result in a reduction in normalized band intensities. Polymer X shows a strong preference for B‐form nucleic acids and induces maximum extrinsic CD signal intensities with A‐T homopolymers. Alterations in helix hydration are believed to accompany complex formation. Inversions in [θ]275 of the octamer X‐poly(dA‐dT) complex have been attributed to the “alternating B” conformation of poly(dA‐dT).3 Similar inversions are not observed in other nucleic acid‐octamer X complexes. Visible and CD spectrometry data from competition studies in the presence of the antibiotics actinomycin D (AMD), daunomycin (DM), and distamycin A (DST) are consistent with “nonclassical” intercalation as the mode of binding, and these data place the potential binding site in or near the hydrophobic region of the minor groove. Reductions in [θ]333 with increasing urea further implicate the involvement of hydrophobic interactions in the formation of an asymmetric complex. Stabilization of the helix results in all cases as evidenced by alterations in Tm; corresponding changes, however, in cooperativity are not clearly discernable. Viscosity and light‐scattering data indicate no changes in molecular weight due to aggregation, and as such are not consistent with a transition to the ψ‐DNA upon complex formation.
Fluorescence decay of ethidium bromide in the presence of the Z‐conformation of poly‐(dG‐dC) and of poly(dG‐dC) modified by chlorodiethylenetriamine platinum(II) chloride
Authors: Genest D. , Malfoy B. 
Published: December 2004

AbstractA time‐resolved fluorescence study of ethidium bromide (EB) in the presence of poly(dG‐dC) and of poly(dG‐dC) modified by chlorodiethylenetriamine platinum(II) chloride is presented under solvent conditions in which these polymers adopt the Z‐conformation (high ionic strength). It is shown that these polynucleotides can intercalate a very small quantity of EB. The binding parameters have been determined. The fluorescence lifetime of EB is slightly higher when bound to the Z‐conformation (≃25 ns) than when bound to the B‐conformation (≃23.7 ns). The nature of the salt has been checked. In the presence of 2.5M NaClO4, no transition from the Z‐conformation to another conformation is observed when EB is added. On the contrary, in the presence of 4.25M NaCl, EB induces a cooperative transition from the Z‐conformation to a conformation characterized by a much higher affinity for EB intercalation. In the case of poly(dG‐dC) this last conformation is identical to the one observed at low ionic strength (B‐conformation), but in the case of the platinated polymer this conformation is slightly different, as judged by the smaller value of the fluorescence lifetime of the intercalated EB.
Structural studies of poly(α‐aminoisobutyric acid)
Authors: Malcolm B. R. , Walkinshaw M. D. 
Published: December 2004

AbstractThe electron‐diffraction pattern of an oriented film of poly(α‐aminoisobutyric acid) in the 310‐helical conformation has been analyzed. The conformation was obtained by a linked‐atom least‐squares refinement of average values from crystal structures. Specimens treated with dichloracetic acid, to improve their crystallinity, conform to space group R3c with a = 21.8 Å, c = 5.95 Å. The structure contains channels that can accommodate molecules of dichloracetic acid. One molecule of acid per six residues fills the channels, and the R‐factor then is 34% using 23 reflections. Ir evidence is presented to show that the acid may hydrogen bond to the peptide groups. Some reflections occasionally observed on the diffraction photographs are attributed to a 15/4 α‐helix. The significance of the results is considered in relation to Aib‐containing peptides.
The relationship of bound water to the IR amide I bandwidth of albumin
Authors: Jakobsen R. J. , Wasacz F. M. , Brasch J. W. , Smith K. B. 
Published: December 2004

AbstractFour different types of ir experiments, involving changes in pH, changes in pressure, and the use of nonaqueous solvents, and with either albumin molecules dissolved in saline or adsorbed albumin films, support the hypothesis that the bandwidth of the amide I vibration of albumin is directly related to the amount of bound water in this protein. From the amide I band narrowing and the amide I shift to higher frequencies, it is proposed that a more ordered helix structure results as the amount of bound water is decreased.
Adsorption of thionine on heparin studied by combining ultrafiltration and difference VIS spectroscopy
Authors: Nothelfer R. , Ruprecht J. , Heyl  , Baumgärtel H. 
Published: December 2004

AbstractThe combination of ultrafiltration and difference spectroscopy allows the quantitative determination of spectra of thionine bound to heparin. The spectra of the bound dye do not depend on the degree of coverage; this and the shape of the Scatchard plot show that “all‐or‐none” binding is valid. A calculus of variations based on a modification of the Hill plot shows that aggregates of seven thionine cations are bound. Tetrasaccharides with an average charge of two carboxylate and five sulfate groups are suggested to be the binding sites. The binding constant given for one mole thionine is 4.4 · 105 M−1. The Gibbs enthalpy for binding of one mole of thionine is −31.7 kJ·M−1 at 20°C.
Distribution of Mn2+ ions around poly(rI)·poly(rC)
Authors: Chang Ding‐Kwo , Kearns David R. 
Published: December 2004

AbstractThe distribution of bound Mn2+ ions about poly(rI)·poly(rC) has been studied by measuring the effect of this paramagnetic metal ion on the relaxation behavior of poly(rI)·poly(rC) protons. By combining selective spin – lattice and spin – spin relaxation rates for various protons, some of the principle regions of ion association can be identified. The relaxation data on the CH6 proton are consistent with a < 10% occupancy of phosphate inner‐sphere binding sites. The broadening of the imino proton resonance requires a substantial occupancy of sites located in the major groove, possibly near IN7. This would also be consistent with the observation that IH8 resonance is the proton most susceptible to relaxation by Mn2+. The relaxation data for the IH2 proton indicate a relatively low occupancy of minor‐groove binding sites (e.g., IN3).
Solution conformations of B. subtilis ribosomal 5S RNA: A calorimetric study
Authors: Chang Lee‐Hong , Marshall Alan G. 
Published: December 2004

AbstractThe unfolding of B. subtilis 5S RNA is examined by direct calorimetric measurement in the presence of various concentrations of Na+ and Mg2+. The composite differential scanning calorimetry (DSC) curve is analyzed into 3–5 individual two‐state melting transitions. In the absence of added Na+ or Mg2+, the 5S RNA segments melt together at Tm = 40°C. Addition of Na+ stabilizes the molecular structure (Tm = 56°C) and widens the melting temperature range, so that up to five component transitions are observed. Addition of Mg2+ alone produces a very stable structure (Tm = 75°C) with highly cooperative melting. Finally, addition of both Na+ and Mg2+ produces the highest stability (Tm = 76°C). The results are interpreted according to hypothetical secondary and tertiary base‐pairing schemes. The conformational changes demonstrated here may facilitate the movement of the protein synthesis machinery during RNA translation.
Interaction of fibrinogen‐binding tetrapeptides with fibrin oligomers and fine fibrin clots
Authors: Schindlauer Günther , Bale Marsha D. , Ferry John D. 
Published: December 2004

AbstractThe polymerization of fibrin, at pH 8.5 and ionic strength 0.45, and under conditions where the action of thrombin on fibrinogen was the rate‐determining step, was interrupted by inactivating thrombin with p‐nitrophenyl‐p′‐guanidinobenzoate (NPGB). Addition of the tetrapeptide Gly‐Pro‐Arg‐Pro (GPRP) partially dissociated the fibrin oligomers as shown by subsequent ligation with Factor XIIIa and calcium ion followed by denaturation and gel electrophoresis; polyacrylamide gel electrophoresis with reduction showed a decrease in the proportion of γ‐γ ligation compared with controls untreated by GPRP, and agarose gel electrophoresis showed a shift in the distribution of oligomer sizes. The dissociation was accomplished within 15 min and its extent was consistent with establishment of an equilibrium in which two molecules of GPRP react to sever an oligomer. When GPRP was introduced into fine unligated fibrin clots by diffusion, there was some dissociation as shown by differences in the degree of γ‐γ ligation after treatment by Factor XIIIa; but the action of GPRP was much slower and less complete than on soluble oligomers. However, even a small amount of dissociation affected the mechanical properties of fine clots profoundly. The shear modulus (measured 25 s after application of stress) decreased progressively with increasing concentration of GPRP introduced by diffusion. The rate of shear creep under constant stress and the proportion of irrecoverable deformation also increased enormously. If the steadystate creep rate is interpreted in terms of an effective viscosity, the latter is decreased by up to three orders of magnitude by the presence of GPRP. In terms of transient network theories of viscoelasticity, the average lifetime of a network strand is greatly diminished. However, the total density of strands remains constant during creep and creep recovery as shown by constancy of the differential modulus or compliance. Removal of GPRP by diffusion only partially restores the original shear modulus and creep behavior of the original clot. Some limited data on the effect of the tetrapeptide Gly‐His‐Arg‐Pro are also reported.