bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational unfolding in the N‐terminal region of ribonuclease a detected by nonradiative energy transfer: Distribution of interresidue distances in the native, denatured, and reduced‐denatured states
Authors: Haas E. , McWherter C. A. , Scheraga H. A. 
Published: December 2004

AbstractTime‐dependent fluorescence measurements have been used to determine the distribution of distances between probes attached to residues 1 and (49 + 53) of bovine pancreatic ribonuclease A in the native, denatured, and reduced‐denatured states. Measurements were made on donor and on doubly labeled (donor + acceptor) protein in 50% aqueous glycerol solutions at −30°C and at room temperature. The fluorescence‐decay curves were used to compute distribution functions for the interprobe distances. The native protein has a narrow distribution of interprobe distances at −30°C (high‐viscosity medium); this distribution is narrower at room temperature (low‐viscosity medium), due primarily to the dynamic flexibility of the probes. Denaturation by 6M guanidine hydrochloride leads to a wider distribution of distances at −30°C, with a shift of the distribution curve to larger distances, because of the increased disorder of the protein. Reduction of the disulfide bonds by dithiothreitol leads to further decreases in transfer efficiency (a unique distribution curve for the reduced protein was not obtained because of the low transfer efficiency). Both the denatured and reduced‐denatured species have average interprobe distances of about 60 Å, compared to 36 Å for the native protein. Reduction of the solvent viscosity leads to nearly monoexponential decay of the donor fluorescence in the doubly labeled derivative. This is interpreted as a manifestation of fast local Brownian motions. It appears that large‐scale segmental motions do not take place in the denatured protein within the excited‐state lifetime of the donor (ca. 8 ns). The above results indicate that reduced‐denatured ribonuclease A has residual structure that limits segmental Brownian motion in the N‐terminal segment.
Identification of regions of potential flexibility in protein structures: Folding units and correlations with intron positions
Authors: Segawa Shin‐Ichi , Richards Frederic M. 
Published: December 2004

AbstractAn algorithm has been developed to estimate flexibility for potential hinge motion at specified residues, that is, the mutual movement of two domains by rotation around a set of main‐chain dihedral angles with torsion angles of neighboring side chains as variables. Such conformational changes must occur without severe atomic collisions. Flexible hinges have been found that satisfy such criteria. Sequence flexibility charts were obtained by plotting the flexibility of each residue against the residue number. Such charts were calculated for 10 proteins (ovomucoid third domain, cytochrome c, lysozyme, hemoglobin β‐chain, α‐chymotrypsin, elastase, carboxypeptidase A, dihydrofolate reductase, triosephosphate isomerase, and alcohol dehydrogenase) taken from the Protein Data Bank. The first step of unfolding is likely to occur at the hinge point with the largest flexibility. Following this idea, the polypeptide chain can be dissected into several folding units according to the sequence flexibility chart. When two domains are separated by conformational changes at such a hinge, the sequence flexibility chart for each domain changes, and it is recalculated and used to indicate subsequent unfolding steps. In this process of iterative estimation of flexibile hinges, some well‐isolated hinges, or the border line between flexible and inflexible regions, were found to be directly at or close to the positions of splice junctions in the eukaryotic genes. Of a total of 45 splice junctions in the 10 proteins examined in this paper, 38 junctions can be identified as flexible hinges between folding units. We suggest that the iterative estimation of flexible hinges may define an array of possible folding/unfolding paths, and that the exon–intron arrangement in the gene may be closely correlated with the folding process of the protein.
Effect of sequence‐specific interactions on the stability of helical conformations in polypeptides
Authors: Vásquez Max , Scheraga Harold A. 
Published: December 2004

AbstractA modification of the Zimm–Bragg two‐state model for the helix–coil transition in polypeptides, which considers the effect of charge–dipole, charge–charge, and other specific interactions on helix stability, is presented. The new model introduces a series of adjustable parameters whose values are estimated by fitting to recent spectroscopic results on medium‐sized peptides. This formalism, based on traditional two‐state helix–coil transition models, provides a framework in which data on the helix contents of peptides of specific sequence can be rationalized by a statistical mechanical theory.
Translational friction of a particle inside a vesicle studied by an extended shell method
Authors: Allison Stuart A. 
Published: December 2004

AbstractThe translational friction of a particle inside a rigid hollow sphere is determined in this work. This should be important in model studies of solute diffusion in cells or vesicles. An extended shell algorithm is developed and used in which the cell or vesicle is modeled as a large number of beads. In the extended algorithm, the shell is divided into groups of beads and the assumption is made that the force exerted by each bead on the solvent is constant within a group. The algorithm is tested by using it to determine the translational friction constants of spheres and prolate ellipsoids modeled as shells of beads.
Structural versatility of peptides from Cα,α‐dialkylated glycines. I. A conformational energy computation and x‐ray diffraction study of homo‐peptides from Cα,α‐diethylglycine
Authors: Benedetti E. , Barone V. , Bavoso A. , Di Blasio B. , Lelj F. , Pavone V. , Pedone C. , Bonora G. M. , Toniolo C. , Leplawy M. T. , Kaczmarek K. , Redlinski A. 
Published: December 2004

AbstractConformational energy computations on a derivative and a homo‐dipeptide of Cα,α‐diethylglycine were performed. In both cases the N‐ and C‐terminal groups are blocked as acetamido and methylamido moieties, respectively. It was found that the Cα,α‐diethylglycine residues are conformationally restricted and that the minimum energy conformation corresponds to the fully extended C5 structure when the NCαC′ bond angle is smaller than 108° (as experimentally observed). The results of the theoretical analysis are in agreement with the crystal‐state structural propensity of the complete series of N‐trifluoroacetylated homo‐peptides of this Cα,α‐dialkylated residue from monomer to pentamer, determined by x‐ray diffraction and also described in this work. Interestingly, for the first time, a crystallographically planar peptide backbone was observed (in the protected tripeptide). A comparison with peptides of Cα,α‐dimethylglycine, Cα‐methyl, Cα‐ethylglycine, and Cα,α‐di‐n‐propylglycine indicates that the fully extended conformation becomes more stable than the helical structures when both amino acid side‐chain Cβ atoms are substituted.
Structural versatility of peptides from Cα,α‐dialkylated glycines. II. An IR absorption and 1H‐nmr study of homo‐oligopeptides from Cα,α‐diethylglycine
Authors: Toniolo C. , Bonora G. M. , Bavoso A. , Benedetti E. , Di Blasio B. , Pavone V. , Pedone C. , Barone V. , Lelj F. , Leplawy M. T. , Kaczmarek K. , Redlinski A. 
Published: December 2004

AbstractThe conformational preferences of the N‐trifluoroacetylated homo‐peptides of Cα,α‐diethylglycine from monomer to pentamer in chloroform solution were determined by using ir absorption and 1H‐nmr. Intramolecular hydrogen bonding was found to be the dominant factor for all NH groups. The likely absence of a conformational transition upon increasing main‐chain length, and the remarkable stability to dilution, heating, and addition of perturbing agents, are additional relevant findings of this study. These results are in agreement with those of the fully extended, C5‐conformation‐forming homo‐peptides from the higher homolog Cα,α‐di‐n‐propylglycine, but contrast dramatically to those of the homo‐peptides from the lower homolog Cα,α‐dimethylglycine, which have been shown to adopt the 310‐helical structure.
Optical activity of saccharides—the vacuum‐uv origin of sodium‐D rotation
Authors: Stevens Eugene S. , Sathyanarayana Bangalore K. 
Published: December 2004

AbstractA semiempirical theory of saccharide optical activity indicates that the dominant source of NaD rotation is a vacuum‐uv CD band near 150 nm, a band observed experimentally in polysaccharide film CD spectra. The model is a modification of polarizability theory in which high‐energy electronic excitations are coupled by degenerate perturbation theory, giving rise to “molecular excitons.” The existence of an excitation mode well separated in energy from even higher energy modes arises from the local symmetry of tetrahedral carbon atoms in a puckered ring structure. Calculated NaD rotations correlate well with experimental values.
The effect of amino acid substitution on protein‐folding and ‐unfolding transition studied by computer simulation
Authors: Taketomi Hiroshi , Kanô Fumiaki , Gō Nobuhiro 
Published: December 2004

AbstractProtein‐folding and ‐unfolding transitions were studied by the method of computer simulation. The protein was modeled as a two‐dimensional lattice polymer. Various energy terms were assumed to be operative between units composing the polymer. But hydrophobic interactions were neglected explicitly. Both thermodynamic and kinetic quantities were obtained from the simulation, and from their temperature dependence in the transition zone characteristics of the conformational transition of proteins were discussed. Two amino acid substituted models, differing in the location of substitution, were studied and compared with the original in order to clarify the effect of substitution on conformational transition of proteins. The following conclusions were reached in this study: (1) The relaxation time of the slow mode, which reflects the overall folding and unfolding processes, shows a peak near the transition temperature, while that of the fast mode is almost independent of temperature. The peak of the slow mode occurs at a slightly lower temperature than the transition temperature. (2) The dependence of the logarithm of the rate constants on the inverse of temperature (Arrhenius plot) is linear. Therefore, the plot of the free energy of activation vs temperature is linear. (3) The values of kinetic parameters obtained suggest that in the activated state the intramolecular interactions are half broken, while the state is close to the native state on the entropy axis. (4) The amino acid substitution, which is modeled as having slightly unfavorable short‐range interactions, causes the substituted ones to be slightly unstable. Moreover, it causes the folding transition to slow. From the analysis of the way slowing down is observed in the two substituted models, we conclude that a structure, designed to model a β‐sheet, is formed before it gets assembled with other structures, which are designed to model α‐helices. The process of assembly occurs nearly at the activated state of the folding and unfolding transition. (5) It is suggested from this study that the maximum of folding rate constant in the Arrhenius plot that has been observed experimentally in real proteins is likely due to hydrophobic interactions.
A critical review of the nucleosidic vibration modes appearing in the 800–500‐cm−1 spectral region, based on new harmonic dynamics calculations
Authors: Ghomi M. , Letellier R. , Taillandier E. 
Published: December 2004

AbstractOn the basis of a harmonic dynamics calculation, it is shown that in the 800–500‐cm−1 spectral region of DNA vibrational spectra, the characteristic Raman peaks and ir bands do not arise from the same nucleosidic motions. The Raman spectra involve mainly the ring‐breathing modes of nucleic bases while the ir spectra reveal essentially their out‐of‐plane vibrations. Moreover, the calculated results show the splitting of the guanine‐ and adenine‐residue breathing modes upon their coupling with the sugar‐pucker motions. This fact is in agreement with the poly[d(G‐C)] and poly[d(A‐T)] Raman spectra.
Tanford–Kirkwood theory for concentric dielectric continua: Application to dimethylphosphate
Authors: Jayaram B. , Beveridge D. L. 
Published: December 2004

AbstractThe Tanford–Kirkwood theory for evaluating the electrostatic free energy of a discrete charge distribution in the presence of ion atmosphere is extended to concentric dielectric continua. The theory is applied to study the conformational preferences with respect to phosphodiester torsion angles in the dimethylphosphate anion (DMP−) and the sodium dimethylphosphate ion pair (Na+DMP−), in the absence and presence of ion atmosphere and at varying local dielectric constants. Results indicate that phosphodiester torsion angles in DMP− prefer the gauche‐gauche conformation in aqueous solutions.
Hydrogen exchange of the tryptophan residues in bovine α‐lactalbumin studied by uv spectroscopy
Authors: Harushima Yoshiaki , Kuwajima Kunihiro , Sugai Shintaro 
Published: December 2004

AbstractThe effect of Ca2+ ion on structural fluctuation of a milk Ca2+‐binding protein, α‐lactalbumin, under native conditions was investigated by comparing hydrogen‐exchange reactions of tryptophan residues in the apo‐form without Ca2+ and in the holo‐form at 1 mM CaCl2 at pH 7.0 in the presence of 0.1M Na+. The reactions were followed by measuring time‐dependent absorption changes at 298–300 nm due to the 2H‐1H exchange of the tryptophan imino protons and were found to be biphasic under all the conditions examined. Two of the four tryptophan protons are insensitive to Ca2+ concentration and show a relatively fast exchange rate. The other two protons are much more extensively protected (a protection degree of 103–105) and are markedly affected by the presence of Ca2+. Examinations of the temperature dependence and pH dependence of the individual exchange rates have been utilized for elucidating the exchange mechanism. The fast protons show a low activation energy reaction with so‐called EX2 kinetics. The exchange reaction of the slow protons is accompanied by a high activation energy, and the exchange mechanism of the protons depended on the presence or absence of stabilizing Ca2+ ions—the EX1 kinetics for the apo‐protein and the EX2 kinetics for the holo‐protein at 1 mM Ca2+. The exchange reaction in the thermally unfolded state was also found to be biphasic, but the fast phase, which has an exchange rate in the fully exposed state, becomes predominant with decreasing temperature. By taking this fact and using a structural unfolding model of hydrogen exchange, the present results are fully consistent with thermodynamic parameters of the thermal transition and kinetic parameters of refolding reactions induced by concentration jumps of guanidine hydrochloride obtained in previous studies. It is demonstrated that the reaction of the slow protons in the native state is mediated by a transient global unfolding equivalent to the “thermal” unfolding under a native condition and that switching of the exchange mechanism from the EX1 to EX2 kinetics results from acceleration of the refolding rate with an increase in Ca2+ concentration. The transient global unfolding takes place even under a strongly native condition, e.g., at a temperature 20° below the beginning of the thermal transition.
Moments for DNA topoisomers: The helical wormlike chain
Authors: Shimada Jiro , Yamakawa Hiromi 
Published: December 2004

AbstractThe mean‐square radius 〈S2〉N of gyration of the DNA topoisomer with the linking number N is evaluated as a function of N and chain length L on the basis of a (circular) twisted wormlike chain, i.e., a special case of the helical wormlike chain. Evaluation of 〈S2〉N and also of the moment 〈Wr2〉 of the writhe Wr is carried out over a wide range of L, following the Monte Carlo procedure of Frank‐Kamenetskii et al. It is found that the present Monte Carlo values of 〈Wr2〉 for large L are appreciably larger than the known Monte Carlo values for freely jointed chains. Thus, the empirical interpolation formula for 〈Wr2〉 previously constructed on the basis of the theoretical values for small L along with the latter Monte Carlo values for large L is revised with the present Monte Carlo values. By the use of the revised formula, a reanalysis of the experimental data for the distribution of topoisomers is made, and it is found that the present estimates of the torsional constant and the stiffness parameter are equal to and somewhat larger than the previous ones, respectively. It is shown that 〈S2〉N decreases with increasing |ΔN|, where ΔN = N − N, with N the number of helix turns in the linear DNA chain in its undeformed state. The mean‐square radii of gyration 〈S2〉Wr and 〈S2〉 of the original circular Kratky–Porod wormlike chain with and without Wr fixed are also evaluated.
Ligation of fibrinogen by factor XIIIa with dithiothreitol: Mechanical properties of ligated fibrinogen gels
Authors: Shimizu Akira , Ferry John D. 
Published: December 2004

AbstractHuman fibrinogen (concentration 8.4 mg/mL) was ligated (cross‐linked) with factor XIIIa and dithiothreitol (DTT) at pH 8.5, ionic strength 0.45. With 7.5 μg/mL of factor XIIIa alone, there was almost no γ‐γ ligation, but with 2 mM DTT added, oligomers appeared, and γ‐γ and Aα‐Aα ligation was nearly complete after 3 days. At 38 μg/mL of factor XIIIa, some γ‐γ and Aα‐Aα ligation occurred even without DTT. For fibrinogen concentrations of 4.0 and 8.4 mg/mL, 38 μ/mL factor XIIIa, 2.0 mM DTT, clot‐like gels formed and the shear modulus of elasticity increased slowly over several days to a constant value. The final modulus was similar in magnitude to those of ligated clots of α‐fibrin (clotted by thrombin) and α‐fibrin (clotted by batroxobin) under the same conditions. However, the opacity was somewhat higher; whereas in fine fibrin clots there is minimal lateral association of the protofibrils, in fibrinogen gels at the same pH and ionic strength the protofibrils (which are presumably single chains of fibrinogen monomers joined end to end at their D domains) are evidently associated in bundles (although not to the degree seen in coarse fibrin clots). Creep and creep recovery measurements showed almost perfect elastic behavior, with essentially no creep under stress and complete recovery after removal of stress. The modulus was scarcely affected by introduction of lithium bromide by diffusion to a concentration of 0.6M, which in unligated fibrin clots causes substantial softening. Whereas in fine fibrin clots (both αβ‐fibrin and α‐fibrin) factor XIIIa causes only γ‐γ ligation, addition of 2 mM DTT produced some α‐α ligation in these also.
Interaction of the fibrinogen‐binding tetrapeptide gly‐pro‐arg‐pro with fine clots and oligomers of α‐fibrin; comparison with αβ‐fibrin
Authors: Shimizu Akira , Schindlauer Günther , Ferry John D. 
Published: December 2004

AbstractThe tetrapeptide Gly‐Pro‐Arg‐Pro(GPRP) was introduced by diffusion into fine unligated clots formed from human fibrinogen at pH 8.5 and ionic strength 0.45 by batroxobin (αβ‐fibrin) and by thrombin (α‐fibrin). The α‐fibrin clots were essentially liquefied at GPRP concentrations above 1 mM and αβ‐fibrin clots above 15 mM, and the degree of polymerization of the resulting oligomers decreased progressively with increasing GPRP concentration as shown by γ‐γ ligation with factor XIIIa and subsequent gel electrophoresis. Much smaller concentrations of GPRP, when introduced into unligated clots by diffusion, were sufficient to modify their mechanical properties profoundly. The shear modulus of elasticity G25 measured 25 s after imposition of stress fell, for example, by a factor of 0.4 at 0.1 mM GPRP in α‐fibrin and at 1.1 mM in αβ‐fibrin. The rate of shear creep under constant stress and the proportion of irrecoverable deformation also increased enormously. This behavior, and the corresponding decrease in steady flow viscosity, may be interpreted in terms of competition of GPRP with A sites on the E domains of fibrin monomers for bidning to “a” sites on the D domains, resulting in a moderate increase with increasing GPRP concentration of the average proportion of severed network strands and an enormous increase in the rate at which all strands dissociate and reassociate. Reassociation of severed strands in new configurations is a necessary corollary since the differential modulus or compliance remains constant during creep and creep recovery. The greater susceptibility of α‐fibrin clots to interaction with GPRP is attributed to stabilization of contacts between monomer units by Bb associations in αβ‐fibrin. Ligated clots, with or without GPRP, exhibited essentially no time‐dependent creep and no irrecoverable deformation, corresponding to an absence of any severance of network strands.
1H‐nmr studies of the 20–31 fragment of calmodulin and of its cyclic analogue
Authors: Motta Andrea , Tancredi Teodorico , Borin Gianfranco , Marchiori Ferdinando , Peggion Evaristo , Temussi Pierandrea 
Published: December 2004

AbstractHigh‐resolution 1H‐nmr spectroscopy at 500 MHz has been used to study the Ca2+ binding domain I of bovine brain calmodulin in aqueous solution. All the resonances of the linear dodecapeptide Asp‐Lys‐Asp‐Gly‐Asn‐Gly‐Thr‐Ile‐Thr‐Thr‐Lys‐Glu and of its cyclic analogue, synthesized by classical solution methods, have been completely assigned using a combination of several one‐ and two‐dimensional nmr experiments, including the zero quantum correlation. Chemical shift values and 3JCHNH coupling constants indicate that, on the nmr time scale, both peptides are flexible and assume multiple conformations in rapid equilibrium, with no relevant contribution of structured features. Addition of Ca2+ causes only minor spectral changes in aqueous solution of both peptides, while larger effects are observed in more hydrophobic mixtures such as water/trifluoroethanol. The linear analogue shows nonspecific interactions, while only Asp3 and Asn5 are significantly perturbed in the cyclic peptide. This evidence, together with identical findings in La3+ titration studies of the cyclic analogue in pure water, suggest that loop I of calmodulin is endowed with an intrinsic binding ability.
Crystalline structure and packing of mannan I
Authors: Atkins E. D. T. , Farnell Sheila , Burden C. , Mackie W. , Sheldrick B. 
Published: December 2004

AbstractThe x‐ray fiber diffraction pattern of the mannan I polymorph has been reexamined using the linked atom least squares (LALS) model‐building program. The chain conformation and packing were refined using atomic coordinates derived from the x‐ray crystallographic structure of mannotriose. The study confirmed the conclusions of previous investigations and showed that, in mannan I, the chains are antiparallel. Mannan polymorphism is compared with other related polysaccharides and the biological significance of this result in relation to the biosynthesis of mannan is discussed.