bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrodynamic properties of mucous glycoproteins
Authors: Bloomfield Victor A. 
Published: May 2005

AbstractIn order to understand how mucous glycoproteins, or mucins, confer such striking rheological properties on mucous secretions, it is first necessary to understand the structures of the individual glycoproteins and their components. Although significant variability of structure among mucins from different sources is evident, the “bottlebrush” structure is a common motif. For purposes of hydrodynamic calculations, we take the typical mucin monomer to have a molecular weight of 5 × 105, 20% protein and 80% carbohydrate. About 25% of the polypeptide chain is unglycosylated or bare, while the remainder is densely substituted with oligosaccharide chains, averaging about eight sugar residues long. Unless the mucins are treated with S‐S reducing agents, proteases, and denaturants, they are often found to have molecular weights around 2 × 106. Thus, we model the normally occurring form as a tetramer, crosslinked like a star in the bare region.With these structural ideas as a basis, we have confronted published hydrodynamic data with modern hydrodynamic theories to obtain a picture of mucin molecular structure. To account for the oligosaccharide side chains, we used a treatment developed for partially porous spheres. To model the composite structure of glycosylated and bare regions, we used subunit hydrodynamic theory. To consider the effects of branching, we used published theories for branched random coils and extended the broken‐rod results of Wilemski to cover branched rodlike structures.The major conclusions are (1) the bare region is probably not highly extended, (2) the glycosylated region is more like a random coil than a rigid rod, and (3) comparison of hydrodynamic properties of monomers and branched tetramers suggests that the monomer is more rigid in the tetramer. This may be due either to understimation of aggregation in the analysis of the experimental data or to a real stiffening effect imposed by polyelectrolyte and steric repulsive interactions with the other chains in the branched mucin.
Polyelectrolyte complexes of glycol chitosan with some mucopolysaccharides: Dielectric properties and electrical conductivity
Authors: Pushpa S. , Srinivasan R. 
Published: May 2005

AbstractThe dielectric properties, DC electrical conductivity, and I‐V characteristics of thin films of polyelectrolyte complexes formed by glycol chitosan (GlChi) with mucopolysaccharides chondroitin sulfate A (CSA), chondroitin sulfate C (CSC), and hyaluronic acid (HA) have been studied at different temperatures. The dielectric constant and the loss factor were measured at frequencies ranging from 1 to 100 kHz at all temperatures. The behavior of GlChi–CSA and GlChi–CSC complexes resembles that of the GlChi–dextran sulfate complex reported earlier. The GlChi–HA complex behaves differently and is similar to the GlChi–alginic acid complex reported [Srinivasan, R. & Kamalam, R. (1982) Biopolymers 21, 251–263, 265–275].
Ethidium binding to deoxyribonucleic acid: Spectrophotometric analysis of analogs with amino, azido, and hydrogen substituents
Authors: Yielding Lerena W. , Yielding K. Lemone , Donoghue Jennifer E. 
Published: May 2005

AbstractThe DNA–ligand interactions of a series of phenanthridinium compounds with various combinations of amino, azido, and hydrogen functions at R3 and R8 were examined to determine the contribution of these particular substituents to ligand binding. Spectrophometric titrations using calf‐thymus DNA emphasized the importance of amino substituents in conferring a strong interaction and also stabilizing the interaction against reversal by high ionic strength. Although azido groups were not as effective as amino groups, they were more effective than hydrogen functions in enhancing the interaction. Furthermore, an amino substitution at R8 was consistently, though only slightly, more effective than an amino substituent at R3. The results from superhelical titrations using plasmid pBR322 DNA demonstrated that analogs with amino and/or azido functions at both R3 and R8 produced the greatest unwinding, and compounds with an amino or an azido function at R8 proved more effective than those with the corresponding amino or azido substituent at R3.
Kinetics of formation of fibrin oligomers. III. Ligation kinetics concurrent with and subsequent to oligomer assembly
Authors: Bale Marsha D. , Janmey Paul A. , Ferry John D. , Lorand Laszlo 
Published: May 2005

AbstractHuman fibrinogen was treated with thrombin in the presence of fibrinoligase (Factor XIIIa) and calcium ion at pH 8.5, ionic strength 0.45, and the ensuing polymerization was interrupted at various time intervals (t) both before and after the clotting time (tc) by solubilization with a solution of sodium dodecyl sulfate and urea. Aliquots of the solubilized protein were subjected to gel electrophoresis on polyacrylamide gels after disulfide reduction by dithiothreitol and on agarose gels without reduction. The degree of γ‐γ ligation was determined from the former. The latter provided the size distribution of ligated end‐to‐end sequences produced by splitting the ligated staggered overlapped oligomers down the middle, for degrees of polymerization, x, from 1 to 10. Addition of fibrinoligase (in which the activating thrombin had been inhibited by p‐nitrophenyl‐p′‐guanidinobenzoate, NPGB) to Kabi fibrinogen showed the presence of small amounts of ligatable oligomers. Addition of fibrinoligase to a polymerizing mixture in which the action of thrombin had been stopped before clotting by NPGB produced the same distribution of ligated end‐to‐end sequences that was obtained when fibrinoligase was originally present, at least for reaction times up to 0.7 of the clotting time. The kinetics of γ‐γ ligation by fibrinoligase acting on a polymerized mixture stabilized by NPGB were followed. The reaction was first order in the concentration of ligatable γ‐γ junctions and the initial velocity was proportional to the enzyme concentration. The time evolution of size distribution of ligated end‐to‐end sequences agreed with a theory based on random ligation of ligatable junctions.
Small‐angle x‐ray scattering studies on yeast inorganic pyrophosphatase and its interactions with divalent metal ions, inorganic phosphate, and hydroxymethane bisphosphonate
Authors: Thiyagarajan P. , Borso C. S. , Banerjee A. , Cooperman B. S. 
Published: May 2005

AbstractSmall‐angle x‐ray scattering studies have been carried out on the enzyme yeast inorganic pyrophosphatase (PPase), and its overall conformational changes on interaction with divalent metal ions (Mg2+ and Mn2+) and with phosphoryl ligands [inorganic phosphate (Pi) and hydroxymethane bisphosphonate (PCHOHP), a nonhydrolyzable inorganic pyrophosphate analog] were assessed. The enzyme undergoes an apparent reduction in size on simultaneous addition of Mg2+ and high Pi concentration, although neithough neither Mg2+ nor Pi added separately induced any measurable conformational changes. By contrast, simultaneous addition of Mn2+ and Pi to PPase does not result in an observable conformational change. However, the overall structure of the enzyme appears to enlarge in the simultaneous presence of Mn2+ ions and PCHOHP. The significance of the structural changes seen in PPase under various conditions is discussed.
Structure determination of the adduct formed between the signal nucleotide diadenosine 5′, 5‴‐P1, P4‐tetraphosphate (Ap4A) and cis‐[Pt(NH3)2Cl2]
Authors: Segal Evelyne , Girault Jean‐Pierre , Muzard Gabriel , Chottard Geneviève , Chottard Jean‐Claude , Le Pecq Jean‐Bernard 
Published: May 2005

AbstractDiadenosine 5′,5‴‐P1,P4‐tetraphosphate (Ap4A), an intracellular regulatory nucleotide, has been found to react with the antitumor drug cis‐diamminedichloroplatinum(II) and its aqua derivative to form a single complex. This complex has been purified by high‐performance liquid chromatography and characterized by 1H‐nmr and CD spectroscopy. In this complex, Ap4A takes a very particular conformation. It is an N7‐N7 chelate of the metal with the two adenines in a head‐to‐head arrangement and an anti–anti conformation of the adenosines. Platinum chelation leads to a large decrease of the Ap4A conformational flexibility.
Comments on the “ordinary–extraordinary phase transition” of poly(lysine)
Authors: Schmitz Kenneth S. , Lu Mei , Singh Narinder , Ramsay Donald J. 
Published: May 2005

AbstractThe “ordinary–extraordinary phase transition” of poly(lysine), first reported by Lin et al. [(1978) Biopolymers 17, 1041–1064], has been reexamined as a function of the data collection interval (Δt) and scattering angle (θ). These data suggest that the relaxation domains “split” as the ionic strength is lowered through the transition region. In contrast, fluorescence photobleaching recovery data of Ware and coworkers (personal communication) indicate the tracer diffusion coefficient is not sensitive to the “ordinary–extraordinary phase transition.” The apparent discrepancy between these two techniques is here proposed to be due to small ion effects on both the dynamics and the scattering power of the polyelectrolytes.
Sequential hydration of dry proteins: A direct difference IR investigation of sequence homologs lysozyme and α‐lactalbumin
Authors: Poole P. L. , Finney J. L. 
Published: May 2005

AbstractDirect difference ir spectra are presented as a function of hydration for lysozyme and α‐lactalbumin, and detailed sequential hydration molecular events identified. Despite the strong sequence homology between the two proteins, and their expected conformational similarity, the hydration behaviour of the polar groups is different for the two proteins. Using a Hill‐type analysis, we conclude that the acid groups ionize and hydrate rapidly and noncooperatively in both proteins, consistent with the known (lysozyme) and postulated (α‐lactalbumin) surface chemistry. The polar group hydration shows a clear cooperativity, which is quantitatively different in the two proteins. Complementary work suggests this cooperativity relates to a hydration‐induced “loosening up” of the lysozyme conformation at about 55 mol water/mol protein. α‐Lactalbumin appears to “open up” more easily for hydration than does lysozyme, consistent with its lower stability against thermal and acid denaturation.
Thermodynamic stability of the ordered conformations of carrageenan polyelectrolytes
Authors: Paoletti Sergio , Smidsrod Olav , Grasdalen Hans 
Published: May 2005

AbstractManning's counterion condensation theory has been applied to the temperature‐induced conformational transition of κ‐ and ι‐carrageenan in the solution and gel states. The formalism of the theory has been extended to transitions between conformations with charge densities below or across the counterion condensation threshold. Measurements of the dependence of the melting temperature on ionic strength, and of the enthalpy of melting, are interpreted with the theory as indicating that the conformational transition is intramolecular and that side‐by‐side dimerization of chains gives rise to the gel structure.
Twist and writhing in short circular DNAs according to first‐order elasticity
Authors: Le Bret Marc 
Published: May 2005

AbstractThe distribution of twist and writhing in a closed DNA shorter than its persistence length is examined. In this case, the only energy contribution is elastic. We have in tegrated the equations of elasticity for a homogeneous axially symmetric rod of undeformable infinitely small circular cross section with frictionless reactions, when there is no or only one self‐contact. In the absence of self‐contacts, the central line of the rod is drawn on a toroid. It makes ν turns around the axis of revolution of the toroid and m turns around its core. The integer, ν, is equal to one if the rod is unknotted. We prove that no infinitely thin rod with a positive Poisson ratio is stable in a toroidal conformation if there is no self‐contact. However, m‐leafed roses or rosettes, with but one multiple self‐contact, are shown to actually be stable when their writhing is not too great. When the integer, m, is equal to two, we have figure‐8 conformations. Buckling of the circle into a figure‐8 conformation occurs for the constraint such that the figure‐8 and the circular conformations have the same energy. This constraint is 1.845 turns for a bending‐to‐twisting elastic constants ratio of A/C = 1.5. For the same value of A/C, the figure‐8 conformation is unstable for a constraint greater than 2.4 turns. Corrections caused by a finite value of the radius ratio, a/L, of the cross section to the length of the rod, are estimated. For instance, both the circular conformation and the infinitesimally warped circle are simultaneous solutions for particular values of the β twist. β = A/C (m2 − ν2)½ [1 + (νπa/L)2/2]. The binding of ethidium to DNAs short enough to follow first‐order elasticity has been studied. Buckling occurs at an apparent average constraint of about 0.6. How the DNA molecules are distributed in figure‐8 conformations and circles has been determined as the ethidium concentration is varied.
Diffusion‐controlled protein–DNA association: Influence of segemental diffusion of the DNA
Authors: Berg Otto G. 
Published: May 2005

AbstractThe intrachain reaction theory of Wilemki and Fixman [(1974) J. Chem. Phys. 60, 866–877] is used to assess the influence of internal DNA motions on various protein–DNA association schemes. It is found that, for large proteins, the diffusional association rate can be totally dominated by these motions rather than by the free‐trans‐lational diffusion rates. Also, the time required for the diffusion together of two DNA segments is estimated. This estimate can be used to provide an upper limit for the rate of intrachain cyclization, and also for the effective intrachain transfer rate of a protein bound to a DNA chain.
Theoretical studies on protein–nucleic acid interactions. I. Interaction of positively charged amino acids with nucleic acid fragments
Authors: Kumar N. Vasant , Govil Girjesh 
Published: May 2005

AbstractCoulombic interactions between the side chains of charged amino acids (Arg+, Lys+, and His+) and negatively charged phosphate groups of nucleic acid fragments have been studied theoretically. Diribose monophosphate and dideoxyribose monophosphate are chosen as model systems for single‐stranded RNA and DNA, respectively. The interaction energies have been calculated by second‐order perturbation theory using simplified formulas for individual terms. The interaction energy in this formalism is a sum of electrostatic, polarization, dispersion, and repulsive energies. Our results show that about 90% of the total interaction energy is contributed by the electrostatic term alone. Contribution from the repulsive term exceeds that from the dispersion term. Calculated interaction energies suggest that Lys+ and His+ form more stable complexes with RNA than with single‐stranded DNA. On the other hand, Arg+ has a higher affinity for DNA than for RNA. The affinity of nucleic acids for the three amino acids is in the order Lys+ > His+ > Arg+. Further, the basic amino acid residues form more stable complexes with A‐DNA than with B‐DNA. The role of the Coulombic interactions in the specific recognition of nucleic acids by proteins is discussed.
Vibrational analysis of peptides, polypeptides, and proteins. XXIV. Conformation of poly(α‐aminoisobutyric acid)
Authors: Dwivedi Anil M. , Krimm S. , Malcolm B. R. 
Published: May 2005

AbstractRaman and polarized ir spectra have been obtained on built‐up monomolecular films of poly(α‐aminoisobutyric acid), and analyzed in the context of normal mode calculations on 310‐, α‐, and α′‐helix conformations of this molecule. The average discrepancy between observed and calculated frequencies is significantly smaller for the 310‐helix than for the other structures. This, together with the more satisfactory explanation of several special features of the spectra, indicates that this polypeptide adopts a 310‐helix conformation in such thin films.
Molecular design of an amplification cascade in vision
Authors: Stryer Lubert 
Published: May 2005

AbstractThe photoexcitation of rhodopsin triggers a cascade that results in the hydrolysis of a large number of molecules of cyclic GMP. The molecular mechanism of this amplification cascade has been delineated. Transducin, a multisubunit perpheral membrane protein, is the information‐carrying intermediate in the activation of the cyclic GMP phosphodiesterase. Photoexcited rhodopsin (R*) castalyzes the exchange of GRP for GDP bound to the α‐subunit of transducin (T). About 500 molecules of Tα‐GTP are formed per absorbed photon at low light levels. Tα‐GTP, rekeased from the β‐ and γ‐subunits of transducin, then activates the phosphodiesterase by relieving an inhibitory constraint imposed by its small sununit. Each actived phosphodiesterase molecule hydrolyzes more than 100 cyclic GMP/s, giving an overall gain of more than 500,000. Photoexcited rhodopsin triggers the activation of a molecule of transducin in a millisecond, which is sufficiently rapid to enable this cascade to participate in visual excitation. Hydrolysis of GTP bound to Tα seves to restore the system to the dark state. Transducin, like the G proteins of the adenylate cyclase casecade, can be specifically ADP‐ribosylated by cholera toxin and pertussis toxin. In both cascades, labling by pertussis toxin blocks the capacity of transducin to interact with the excited receptor, whereas labeling by cholera toxin inhibits the hydrolysis of bound GTP, leading to persistent activation. Moreover, the moleculaar design of the hormone‐triggered cyclic AMP cascade is similar to that of the light‐triggered cyclic GMP cascade. It seems likely that transducin, the stimulatory G protein, the inhibitor G protein, and the ras protein are members of the same family of signal amplifiers. The study of the cyclic nucleotide cascade of vision is providing rewarding views of recurring motifs of signal amplification in nature.
Conformation–function relationships in hydrophobic peptides: Interior turns and signal sequences
Authors: Gierasch L. M. , Rockwell A. L. , Thompson K. F. , Briggs M. S. 
Published: May 2005

AbstractTwo studies are diescribed in which synthetic peptides have been designed and examined to address biochemical problems inherent in hydorphobic environments: (1) The cyclic hexapeptide cyclo‐(D‐Tyr(Bzl)‐Gly‐Ile‐Leu‐Gln‐Pro) was synthesized as a model of an interior β‐turn from the protein lysozyme. Conformational analysis by proton nmr methods, including two‐dimensional nulcear Overhauser effect spectroscopy, revealed that the model peptide adopts one conformation in chloroform/dimethyl sulfoxide (98.2) and tetramethylene sulfone solutions. The conformation consists of two linked β‐turns, one with the same sequence (Gly‐Ile‐Leu‐Gln) and geometry (Type I) as the protein turn. (2) Major portions of the λ‐receptor protein (LamB) signal sequences from E. coli wildtype and mutant strains have been synthesized. The conformational properties and membrane interactions of these synthetic signal peptides correlate with the in vivo export function of the wild type and mutant strains. Functional signal sequences are significantly richer in α‐helix in aaqueous trifluoroethanol, lysolecithin, or sodium do‐decyl sulfate solution than is a nonfunctional mutant signal sequence.
Energetics of protein structure and folding
Authors: Goldenberg David P. , Creighton Thomas E. 
Published: May 2005

AbstractThe available experimental date on the kinetics of unfolding and refolding of small proteins are reviewed. Excluding slow transitions in the unfolded protein due to cis–trans isomerization of peptide bonds, the rate‐limiting transition state in both unfolding and refolding is concluded to be a high‐energy distortion of the fully folded state. Partially folded intermediates are undoubtedly important for folding, but their formation is normally not rate limiting. A simple model is used to illustrate some of the aspects of protein‐folding energetics.
Assembly of fibronection‐containing extracellular matrix: A glimpse of the machinery
Authors: Mosher Deane F. , McKeown‐Longo Paula J. 
Published: May 2005

AbstractSoluble fibronectin binds specifically and saturably to surfaces of substrate‐attached cells. Bound fibronection is then transferred to the deoxycholate‐insoluble extracellular matrix. During transfer, fibronectin is translocated from the cell surface and organized into disulfide‐bonded multimers by disulfide exchange. Binding is mediated by disulfidelooped, type I homology “fingers” in the amino‐terminal region. Exchange involves disulfides in the same amino‐terminal region.
Diffusion of bovine serum albumin in a neutral polymer solution
Authors: Phillies George D. J. 
Published: May 2005

AbstractThe diffusion coefficient D of bovine serum albumin through various solutions (pH 7.0, 0.5M NaCl) of polythylene oxide (Mw ∼ 1 × 105, 3 × 105) was studied with quasielastic light scattering. In solutions of the 1 × 105 polymer solution at polymer concentrations above 0.5 g/L, D is considerably greater than would have been expected from the viscosity of water:polymer mixtures, the deviations being larger at low protein concentration that at high protein concentration. With either polymer, D falls with increasing protein concentration.
A simple and novel interpretation of the three‐dimensional structure of globular proteins based on quantum‐mechanical computations on small model molecules. I
Authors: Peters David , Peters Jane 
Published: May 2005

AbstractIt is suggested that the three‐dimensional structure of globular proteins is partly determined by a framework of strengthened hydrogen bonds that involves both ionic side chains and water molecules in addition to the polypeptide backbone. This conclusion follows from a combination of the results of ab initio molecular‐orbital computations on small model molecules and high‐accuracy x‐ray data on the rubredoxin molecule. The computations yield the idea of hydrogen‐bonded bridges that are built from tens of atoms, and the experimental information yields the idea that the bridges are assembled into clusters, each of which is built from hundreds of atoms. Some 10 such clusters then form a globular protein.
Efficient monte carlo method for simulation of fluctuating conformations of native proteins
Authors: Noguti Tosiyuki , Gō Noguhiro 
Published: May 2005

AbstractA powerful Monte Carlo method is described to simulate thermal conformational fluctuations in native proteins by using an empirical conformational energy function in which bond lengths and bond angles are kept fixed and only dihedral angles are independent variables. In this method, collective variables corresponding to eigenvectors of the second‐derivative matrix of the energy function at its minimum point are scaled according to corresponding eigenvalues in such a way that the energy function in terms of the scaled collective variables is isotropic at the minimum point. Simulation is carried out with an isotropic step size in the space of these scaled collective variables. This simulation method is applied to a small protein, bovine pancreatic trypsin inhibitor (BPTI), and its model harmonic system defined by a quadratic energy function with the same second‐derivative matrix as that of BPTI at its minimum point. Efficiency of the simulation method with an isotropic step size in the space of the scaled collective variables is found to be about 500–50 times greater than the conventional method with with an isotropic step in the space of the usual nonscaled variables. One step of this new method generates conformational changes that occur in the real‐time range of 0.05 ps. In a record of 5 × 105 step simulation, the BPTI molecule is observed to migrate beyond a single minimum‐energy region.