bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural versatility of peptides from Cα,α‐disubstituted glycines: Preferred conformation of the Cα,α‐diphenylglycine residue
Authors: Crisma M. , Valle G. , Bonora G. M. , De Menego E. , Toniolo C. , Lelj F. , Barone V. , Fraternal F. 
Published: December 2004

AbstractThe preferred conformation of the Cα,α‐diphenylglycine residue was determined in simple derivatives and dipeptides. The dipeptides were synthesized by the 5(4H)‐oxazolone (from the N‐para‐bromobenzoylated amino acid) method. This activated intermediate and a reaction by‐product, para‐bromobenzoylbenzhydrylamine, were characterized inter alia by x‐ray diffraction. Conformational energy calculations on the Cα,α‐diphenylglycine mono‐peptide, Ac‐Døg‐NHMe, indicate that this Cα,α‐symmetrically disubstituted residue is conformationally restricted and that its minimum energy conformation falls in the fully extended (C5) region. The results of the theoretical analysis are in agreement with the solution and crystal‐state structural tendency of mClAc‐Døg‐OH, Z‐Døg‐OtBu, pBrBz‐Døg‐Gly‐OMe and its tert‐butyl ester analogue, determined by ir absorption, lH‐nmr, and x‐ray diffraction, and also described in this work. The implications for the use of the Døg residue in designing conformationally constrained analogues of bioactive peptides are briefly discussed.
Mechanical properties of DNA films
Authors: Gevorkian S. G. , Khudaverdian E. E. 
Published: December 2004

AbstractThe Young's dynamical modulus (E) and the DNA film logarithmic decrement (v) at frequencies from 50 Hz to 20 kHz are measured. These values are investigated as functions of the degree of hydration and temperature. Isotherms of DNA film hydration at 25°C are measured. The process of film hydration changing with temperature is studied. It is shown that the Young's modulus for wet DNA films (E = 0.02–0.025 GN m−2) strongly increases with decreasing hydration and makes E = 0.5–0.7 GN m−2. Dependence of E on hydration is of a complex character. Young's modulus of denatured DNA films is larger than that of native ones. All peculiarities of changing of E and v of native DNA films (observed at variation of hydration) vanish in the case of denatured ones. The native and denatured DNA films isotherms are different and depend on the technique of denaturation. The Young's modulus of DNA films containing > 1 g H2O/g dry DNA is found to decrease with increasing temperature, undergoing a number of step‐like changes accompanied by changes in the film hydration. At low water content (< 0.3 g H2O/g dry DNA), changing of E with increasing temperature takes place smoothly. The denaturation temperature is a function of the water content.
A hydrodynamic study with quasielastic light scattering and sedimentation of bacterial elongation factor EF‐Tu · guanosine‐5′‐diphosphate complex under nonassociating conditions
Authors: Sam Tom , Mandel Michel , Pley Cornelis 
Published: December 2004

AbstractThe hydrodynamics of the bacterial elongation factor EF‐Tu have been studied in the presence of its ligand guanosine‐5′‐diphosphate (GDP) by sedimentation in the ultracentrifuge and quasielastic light scattering. Sedimentation studies have made it possible to establish experimental conditions under which only negligible aggregation of the protein occurs (neutral pH, concentration < 3 mg/mL). Analysis of the light intensity autocorrelation functions under these conditions revealed two independent scattering species with diffusion coefficients of 0.71 × 10−6 and 0.04 × 10−6 cm2 s−1. The material with the lower diffusion coefficient, i.e., the aggregates, represented less than 1% of the total number of EF‐Tu particles. The other 99% diffused as monomeric molecules with a molar mass corresponding to the value calculated from the known primary structure of the protein. The hydrodynamic parameters derived from the experimental data suggest that EF‐Tu·GDP in solution is close to a spherical particle.
Global fluctuations of the immunoglobulin domains under physiological conditions
Authors: Kawata Yasushi , Hamaguchi Kozo 
Published: December 2004

AbstractHydrogen‐exchange rates of the indole NH proton of a tryptophan residue, buried fully in the interior of each of the constant (CL) and variable (VL) fragments of a type‐κ‐immunoglobulin light chain, were studied at various pH values and at 25°C under 1H‐nuclear magnetic resonance. The activation energies for the exchange reactions were determined also and compared with those for the unfolding reactions of these fragments induced by guanidine hydrochloride. The pH profiles of the exchange rates of the CL(κ) and VL(κ) fragments were very similar to that for a CL(λ) fragment reported previously.4 It was found that the CL(κ) and VL(κ) fragments as well as the CL(λ) fragment undergo a global unfolding transition with a conformation very similar to that of the fully unfolded state induced by guanidine hydrochloride even under physiological conditions.
Structure of the hydration shells of oligo(dA‐dT)·oligo(dA‐dT) and oligo(dA)·oligo(dT) tracts in B‐type conformation on the basis of Monte Carlo calculations
Authors: Eisenhaber F. , Tumanyan V. G. , Abagyan R. A. 
Published: December 2004

AbstractMonte Carlo simulations [(N, V, T)‐ensemble] were performed for the hydration shell of poly(dA‐dT)·poly(dA‐dT) in canonical B form and for the hydration shell of poly(dA) ·poly(dT) in canonical B conformation and in a conformation with narrow minor groove, highly inclined bases, but with a nearly zero‐inclined base pair plane (B′ conformation). We introduced helical periodic boundary conditions with a rather small unit cell and a limited number of water molecules to reduce the dimensionality of the configuration space. The coordinates of local maxima of water density and the properties of one‐ and two‐membered water bridges between polar groups of the DNA were obtained.The AT‐alternating duplex hydration mirrors the dyad symmetry of polar group distribution. At the dApdT step, a water bridge between the two carbonyl oxygens O2 of thymines is formed as in the central base‐pair step of Dickerson's dodecamer. In the major groove, 5‐membered water chains along the tetranucleotide pattern d (TATA) · d (TATA) are observed.The hydration geometry of poly (dA) · poly(dT) in canonical B conformation is distinguished by autonomous primary hydration of the base‐pair edges in both grooves. When this polymer adopts a conformation with highly inclined bases and narrow minor groove, the water density distribution in the minor groove is in excellent agreement with Dickerson's spine model. One local maximum per base pair of the first layer is located near the dyad axis between adjacent base pairs, and one local maximum per base pair in the second shell lies near the dyad axis of the base pair itself. The water bridge between the two strands formed within the first layer was observed with high probability. But the water molecules of the second layer do not have a statistically favored orientation necessary for bridging first layer waters. In the major groove, the hydration geometry of the (A · T) base‐pair edge resembles the main features of the AT‐pair hydration derived from other sequences for the canonical B form. The preference of the B′ conformation for oligo(dA) · oligo(dT) tracts may express the tendency to common hydration of base‐pair edges of successive base pairs in the grooves of B‐type DNA.The mean potential energy of hydration of canonical B‐DNA was estimated to be −60 to −80 kJ/mole nucleotides in dependence on the (G · C) contents. Because of the small system size, this estimation is preliminary.
Synthetic peptide helices in crystals: Structure and antiparallel and skewed packing motifs for α‐helices in two isomeric decapeptides
Authors: Karle Isabella L. , Flippen‐Anderson Judith L. , Uma K. , Balaram P. 
Published: December 2004

AbstractThe isomeric decapeptides Boc‐Aib‐Ala‐Leu‐Ala‐Aib‐Aib‐Leu‐Ala‐Leu‐Aib‐OMe (II) and Boc‐Aib‐Ala‐Aib‐Ala‐Leu‐Ala‐Leu‐Aib‐Leu‐Aib‐OMe (III), are predominantly a‐helical with little effect on the conformation with interchange of Aib/Ala residues or Aib/Leu residues. The packing motif of helices in crystal II is antiparallel, whereas the helices pack in a skewed fashion in crystal III, with a 40° angle between neighboring helix axes. Crystal III contains a water molecule in a hydrophobic hole that forms hydrogen bonds with two carbonyl oxygens that also participate in 5 → 1 type hydrogen bonds. Values for helical torsional angles ϕ and ψ assume a much wider range than anticipated. Crystal II: C49H88N10O13, space group P21 with a = 16.625(2) Å, b = 9.811(5) Å, c = 18.412(3) Å, β = 99.79(1)°, Z = 2, R = 5.7% for 4338 data with |F0 | > 3σ(F). Crystal III: C49H88N10O13. 1/2H2O, space group P21, with a = 11.072(2) Å, b = 34.663(5) Å, c = 16.446(3) Å, β = 107.85(1) °, Z = 4, R = 8.3% for 6087 data with |F0| > 3σ(F).
Randomness in the heparin polymer: Computer simulations of alternative action patterns of heparin lyase
Authors: Cohen David Marshall , Linhardt Robert J. 
Published: December 2004

AbstractHeparin is a mixture of linear polysaccharides of undetermined sequence. Both biosynthetic data and computer simulation studies have established that each heparin polymer chain is comprised of oligosaccharides of defined sequence, representing ordered domains. One such ordered domain is a pentasaccharide corresponding to heparin's antithrombin III binding site. Previous computer simulation studies, performed under the assumption that heparin lyase (heparinase, EC 4.2.2.7), has a random endolytic action pattern, suggested that certain of these ordered oligosaccharide domains may themselves be nonrandomly arranged in the heparin polymer. The present, work presents computer simulations of alternative action patterns for heparin lyase while assuming a random distribution of these oligosaccharide units within the heparin polymer. We consider action patterns that are determined solely by the primary structure of the substrate molecules. Results of the simulations are compared to (1) the experimental measurements of product chains formed throughout the reaction and (2) the change in weight average molecular weight Mw as a function of reaction completion as determined by absorbance at 232 nm.From the simulation of 60 action patterns for heparin lyase, we infer that one of the following statements concerning heparin and heparin lyase is true: (1) Heparin is a random arrangement of a small number of structurally defined oligosaccharide units. Heparin lyase changes its action pattern during the depolymerization of heparin (perhaps influenced by the secondary structure of substrate). (2) Heparin contains clusters of oligosaccharide sequences that are present in low concentrations (overall) in the polymer. Heparin lyase has a specificity for cleaving glycosidic linkages either exolytically at the nonreducing terminus of a chain or (endolytically) at the reducing side of these rare oligosaccharide sequences.
Environment‐dependent conformation of Boc‐Pro‐Ser‐NHCH3
Authors: Perczel A. , Hollósi M. , Fülöup V. , Kálmán A. , Sándor P. , Fasman G. D. 
Published: December 2004

AbstractThe conformation of Boc‐Pro‐Ser‐NHCH3 (1) was studied in the solid state and in solution. In the crystal, the steric structure of 1 is characterized by an E(cis) urethane tertiary amide bond and the lack of intramolecular H bonds. Four‐hundred megahertz 1H‐ and 101‐MHz 13C‐nmr studies in CDCl3 clearly show the presence of two conformers differing in the rotameric state of the tertiary‐amide bond. Selective 1H‐13C nuclear Overhauser enhancement experiments at −20°C as well as 1H‐nmr and ir data indicate that the major trans conformer (84% in CDC13) may adopt a type I β‐turn conformation with a possible Oγ  H‐N interaction, similarly to Piv‐Pro‐Ser HCH3 (2) [A. Aubry, N. Ghermani, and M. Mar‐raud (1984) Int. J. Peptide Protein Res. 23, 113‐122]. Molecular mechanics calculations on the cis rotamer show that the β‐pleated‐like backbone conformation of serine in the crystal of 1 is not a low‐energy state for the isolated molecule; it is caused by packing forces, particularly by the helical network of intermolecular H bonds.
Poly[d(Gm5C)·d(Gm5C)] can assume the Z′ form: A CD study
Authors: Zhong Lingxiu , Johnson W. Curtis 
Published: December 2004

AbstractPoly [d(Gm5C)·d(Gm5C)] can be titrated from the Z form in 30% ethanol to the Z′ form by adding either ethanol or divalents. Analysis by singular‐value decomposition of CD spectra recorded during the titration reveal that ethanol and transition metal induced changes are two state with a single‐step titration curve. When the change is induced by arkaline earth metals it is still two state, but in contrast the titration curve is complex, indicating two binding sites.
Correlation between dinucleotide periodicities and nucleosome positioning on mouse satellite DNA
Authors: Lowman Henry , Bina Minou 
Published: December 2004

AbstractPrevious studies demonstrated 16 well‐defined nucleosome locations (A–P) on a tandemly repeated prototype 234 base pair (bp) mouse satellite repeat unit. We have aligned the A–P fragments to search for DNA sequence elements that might contribute to nucleosome placement at these positions. Our results demonstrate a strikingly regular, uninterrupted, periodic pattern for the AA dinucleotide occurrences along the entire length of the aligned fragments. The periodicity of the AA occurrences is about 9.7 bp. The pattern exhibits a local minimum at position 74, near the nucleosome dyad axis of symmetry. Other dinucleotides—including AC : GT, CA : TG, and CC : GG—are also placed periodically, but their patterns of occurrence are less regular and less frequent than AA. The calculated spacings between consecutive preferred nucleosome locations on mouse satellite DNA are nearly identical, corresponding to multiples of 9.7 bp. The correlation between the periodicity of dinucleotide occurrences and the average spacing of nucleosome positions suggests that the preferred nucleosome locations recur at intervals that may correspond to the DNA helical repeat in the mouse satellite nucleosomes, and that the histone octamers sample (or slip along) the duplex in steps of 9.7 bp during nucleosome formation on mouse satellite DNA.
The thermal denaturation of nonpolymerizable αα‐tropomyosin and its segments as a function of ionic strength
Authors: Mo Jianming , Holtzer Marilyn Emerson , Holtzer Alfred 
Published: December 2004

AbstractNonpolymerizable tropomyosin (NPTm) is found to unfold thermally at high ionic strength almost exactly as the parent protein, but it does not aggregate at low ionic strength. Thus, NPTm can be used as a tropomyosin surrogate whose coiled‐coil structural stability can be probed by varying the ionic strength. Studies of NPTm by CD show that increasing ionic strength stabilizes the coiled‐coil structure. CD spectra over a wide range of helix content, obtained by varying either temperature or ionic strength, show an isodichroic point at 203 nm, suggesting a local, residue‐level, two‐state model. At given temperature, such a local helix ⇆ random equilibrium suggests In [Φh/(l − Φh)] = A1 + A2In, wherein Φh is the fraction helix, and A1, A2 and n are constants. In the low ionic strength region, theoretical limiting laws for ionic strength mediated charge–charge, dipole–dipole, and apolar–apolar (salting out) interactions give, respectively, n = 0.5, 1.0, and 1.0. Our experimental values for 40°C, where the data span a wide range of helix content, show n = 1.0, suggesting that ionic strength stabilizes either by reducing dipole–dipole repulsions or by enhancing hydrophobic interactions, both probably interhelix in nature. Two segments of tropomyosin, 11Tm127 and 142Tm281, neither of which aggregate at low ionic strength, give results similar to those for NPTm, i.e., n = 0.96 and 0.84, respectively.
The effect of the L‐azetidine‐2‐carboxylic acid residue on protein conformation. III. Collagen‐like poly(tripeptide)s
Authors: Zagari Adriana , Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractThe chemical and biological properties of collagen are altered by the biosynthetic substitution of the L‐azetidine‐2‐carboxylic acid (Aze) residue in the place of proline. The reasons for this alteration have been studied by means of conformational energy computations on single‐ and triple‐stranded structures formed by poly (GIy‐X‐Y) poly(tripeptide)s, where X and Y can be Pro or Aze. The most stable triple helix formed by Poly (Gly‐Pro‐Aze) is collagen‐like, but all low‐energy triple helices that can be formed by poly (Gly‐Aze‐Pro) and poly (Gly‐Aze‐Aze) are very different from collagen. Thus, the regular substitution of Aze for Pro in position X is not compatible with the collagen structure. In the absence of solvent effects, all of these triple helices are stable, relative to the statistical coil, but the substitutions reduce the stability of the collagen‐like triple helix, as compared with poly (Gly‐Pro‐Pro).
α‐Helix to random coil transitions of two‐chain coiled coils: Experiments on the thermal denaturation of isolated segments of αα‐tropomyosin
Authors: Holtzer Marilyn Emerson , Holtzer Alfred 
Published: December 2004

AbstractCircular dichroism (CD) experiments in the backbone (200–240 nm) region are reported for four isolated, excised two‐chain, coiled‐coil segments whose chains comprise, respectively, residues 11–127, 142–281, 1–189, and 190–284 of the rabbit αα‐tropomyosin (Tm) sequence. The uv and CD spectra for the noncross‐linked segments are very similar to those for parent Tm. At 3°C, all have a helix content of 90% or more; moreover, all thermal denaturation curves depend on concentration, as required by mass action, and are completely reversible. At comparable concentrations, solutions show values of T1/2 (the temperature at which the helix content is 50%) following the order of 11Tm127 ∼ 1Tm189 > 142Tm281 > 190Tm284. The thermal unfolding data for 11Tm127, 190Tm284, and 142Tm281 fall on apparently monophasic curves (single inflection point). However, curves for 1Tm189 show a heretofore unknown low temperature transition in which the helix content drops from ∼ 90% at 2°C to ∼ 73% at 20°C, indicating that this segment has one or more weak sections totaling approximately 50 residues per chain. Since thermal denaturation curves for noncross‐Iinked 11Tm127, 142Tm281, and Tm have no such low temperature transition, i.e., the helix content is not additive, the weak region probably comprises the bulk of the residues between 127 and 189 in 1Tm189, but is somehow stabilized in 142Tm281 and in parent Tm. This nonad‐ditivity may be explainable by a combination of lopp entropy and local adjustments in packing of hydrophobes in the helix–helix interface. For Cl90‐cross‐linked 142Tm281, the uv and CD spectra and helix content are very similar to those for other coiled‐coil species. In addition, the thermal unfolding curve shows a “pretransition” that is similar to but broader than that for cross‐linked parent Tm and a “posttransition” that is almost identical to that for cross‐linked parent Tm.
Partial molar volumes of polypeptides and their constituent groups in aqueous solution over a broad temperature range
Authors: Makhatadze G. I. , Medvedkin V. N. , Privalov P. L. 
Published: December 2004

AbstractThe partial molar volumes of various compounds that model protein constituent groups, such as tripeptides (Gly‐X‐Gly, where X = Gly, Ala, Val, Leu, Ile, Pro, Met, His, Ser), homopeptides (Glyn, n = 3, 4, 5), and simple organic analogues of amino acid side chains (methanol, acetamide, propanamide, acetic acid, propanoic acid, n‐butanamine, n‐butanamine nitrate, n‐propylguanidine nitrate, 4‐methylphenol), have been determined in aqueous solution with a vibrational densimeter in the temperature range of 5–85°C. The partial molar volumes of amino acid side chains and the peptide unit were estimated from the data obtained. Assuming additivity of component groups, the partial molar volumes of polypeptide chains of several proteins over a broad temperature range were calculated. The partial molar volume functions of four proteins (myoglobin, cytochrome C, ribonuclease A, lysozyme) were compared with those determined experimentally for the unfolded and native forms of these proteins. It has been shown that the average deviation of the calculated functions from the experimental ones does not exceed 3% over the temperature range studied.
The influence of macromolecular crowding on thermodynamic activity: Solubility and dimerization constants for spherical and dumbbell‐shaped molecules in a hard‐sphere mixture
Authors: Berg Otto G. 
Published: December 2004

AbstractMacromolecules in solution can have large effects on the properties of other solutes through nonideal excluded‐volume (crowding) interactions. Minton [(1983) Mol. Cell. Biochem. 55, 119–140] has calculated such effects by treating the macromolecules as a hard‐sphere fluid in a background of an inert structureless solvent. In the present paper these calculations are extended by including the primary solvent as a separate component in a hard‐sphere mixture. The results are in good agreement with experimental data. However, some predictions of this model differ drastically from those based on Minton's approach. Thus, much smaller effects from macromolecular crowding, particularly by smaller molecules, are expected. The present results also predict a much larger dependence on the shape of the molecules under study; notably for a dimerization reaction, it is found that the excluded‐volume effects actually can destabilize side‐by‐side binding of two spherical molecules, while a dimerization to a spherical complex is stabilized. Therefore there will exist intermediate shapes of complexes whose stability is insensitive to crowded‐volume effects. The consequences for crowding effects inside the living cell are also discussed.
Synthesis and peptide bond orientation in tetrapeptides containing L‐azetidine‐2‐carboxylic acid and L‐proline
Authors: Tsai F.‐H. , Overberger C. G. , Zand R. 
Published: December 2004

AbstractThe role of the amino acid proline in influencing the secondary and tertiary structure of proteins and polypeptides has been an area of active study for many years. We have investigated this problem by incorporating the four‐membered ring amino acid, azetidine‐2‐carboxylic acid, into some proline polypeptides. An adjunct to the synthesis of the peptides was the synthesis of azetidine‐2‐carboxylic acid and its resolution. We developed an improved synthesis of N‐benzhydryl‐2‐carbobenzyloxy azetidine, an essential intermediate required for the synthesis of Lazetidine‐2‐carboxylic acid. This amino acid was subsequently obtained via the partial hydrogenation of the N‐benzhydryl compound, under mild conditions. Our ability to isolate the intermediate N‐benzhydryl‐2‐carboxylic acid demonstrated that the rate of cleavage of the O‐benzyl ester group in this molecule is faster than the cleavage of the N‐benzhydryl group.The tetrapeptides, Boc‐(LPro)3‐LAze‐Opcp, and Boc‐(LAze‐LPro)2‐Opcp (Boc: t‐butoxycarbonyl; Pro: praline; Aze: azetidine‐2‐carboxyl acid; Opcp: pentachlorophenyl), were prepared using traditional solution peptide synthesis. They were characterized by direct chemical ionization‐mass spectrometry, CD spectra, and 13C‐ and 1H‐nmr spectroscopy. The assessment of the secondary structure assessment of the two peptides using the methods noted above has led us to conclude that the compound Boc‐(L‐Aze‐LPro)2‐Opcp, in trifluoroethanol, has an all‐cis peptide bond conformation with ϕ and ψ torsion angles compatible with a left‐handed helix. The secondary structure assessment of the peptide Boc‐(LPro)3‐LAze‐Opcp, in chloroform or trifluoroethanol, leads to an assignment of both cis and trans peptide bonds as being present in the peptide. We have interpreted this latter finding as indicating that the introduction of the azetidine group into a peptide containing three consecutive praline residues in a linear sequence perturbs the normal proline peptide secondary structure in this tetrapeptide.