bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct evidence for antifreeze glycoprotein adsorption onto an ice surface
Authors: Brown Robert A. , Yeh Yin , Burcham Timothy S. , Feeney Robert E. 
Published: December 2004

AbstractAqueous solutions of antifreeze glycoproteins (AFGP) exhibit hysteresis between the freezing and melting temperatures. Several recent studies on the mechanism of function of this protein system suggest that a likely model is for the antifreeze molecules to be adsorbed onto the surface of the crystals. However, direct proof of the presence of adsorbed AFGP has eluded previous researchers. In the present study, enhanced surface second‐harmonic generation (SSHG) was observed in the presence of an active AFGP solution in contact with a pure single crystal of ice. The enhancement of SSHG is a positive indication that active AFGP molecules adsorb to the surface of ice crystals.
Heavy‐atom effects on energy transfer from polynucleotides to terbium (III)
Authors: Burns Victor W. 
Published: December 2004

AbstractEnergy transfer in nucleic acids or polynucleotides at room temperature can be studied by using the fluorescence of complexed terbium (III) as a tool. Complexing the heavy atom thallium (I) enhances energy transfer from poly(G) to terbium (III). Thallium has no effect on transfer from GMP to terbium and a small negative effect on the transfer from single‐stranded DNA to terbium. Use of the Medinger‐Wilkinson model to analyze the poly(G) results provides an estimate of the room‐temperature intersystem crossing constant.
Conformational analysis of polyoxyethylene‐bound homo‐oligo‐L‐glutamates in a weakly interacting medium, CDCl3
Authors: Ribeiro Anthony A. , Saltman Robert , Goodman Murray 
Published: December 2004

AbstractA detailed conformational analysis of polyoxyethylene‐bound N‐t‐butyloxycarbonyl homo‐oligo‐L‐glutamates up to the heptamer was carried out in CDCl3 solution using high‐resolution 1H‐nmr spectroscopy. Unequivocal assignments of resolved backbone NH and α‐CH resonances were obtained with specifically deuterated oligomers. From nmr measurements, chemical‐shift dependencies with respect to temperature and solvent, and the line‐broadening effects of free radicals allowed the determination of hydrogen‐bonded residues. The nmr data, along with model‐building studies, suggest that seven‐membered rings may exist in the N‐terminal portion of these peptides. Replacement of the N‐t‐butyloxycarbonyl group by an acetyl or pyroglutamyl residue gave aggregated peptides, pointing to a special contribution by the Boc group to hydrogen bonding and solubility in CDCl3.
Fast approximations for accessible surface area and molecular volume of protein segments
Authors: Zehfus Micheal H. , Seltzer Jack P. , Rose George D. 
Published: December 2004

AbstractEquations are presented that approximate the accessible surface area of a continuous protein segment using the surface area of an inertial ellipsoid and that approximate the molecular volume from the number of non‐hydrogen atoms in the segment. These approximations, which are appropriate for segments of four or more residues in length, are much faster to calculate than the exact solutions, yet suffer only a 3–8% error. Included in an appendix are FORTRAN subroutines that calculate the surface area of an ellipsoid from its three principal moments of inertia.
Temperature dependence of dielectric constant at 10 GHz of Na‐DNA gels
Authors: Bonincontro A. , Di Biasio A. , Pedone F. 
Published: December 2004

AbstractPermittivity ε′ and dielectric loss ε″ of aqueous Na‐DNA gels have been measured at 10 GHz in the temperature interval −15 to + 45°C. The experimental results are analyzed in terms of a three‐component equation (Na‐DNA, interfacial water, bulk water) and yield a value of 35 water molecules/nucleotide interacting with DNA. According to theoretical and experimental data the presence of strongly bonded and weakly bonded water is considered. The modified water exhibits a mean dielectric relaxation time two‐or threefold greater than that of bulk water.
The properties of calmodulin at physiological temperature
Authors: Steiner Robert F. , Marshall Leda , Needleman Donna 
Published: December 2004

AbstractSeveral of the physical properties of calmodulin are changed significantly upon increasing the temperature from 25 to 37°C. Among the observed changes are a minor increase in intrinsic viscosity, a decrease in molecular ellipticity in the peptide region, the development of a difference spectrum in the aromatic region, and an increase in the mobility of extrinsic fluorescent labels. Except for the latter case, the magnitudes of the changes are substantially reduced in the presence of Ca2+. The above observations are consistent with an expanded and less tightly organized structure of calmodulin at the higher temperature.
Vacuum UV CD of the low‐salt Z‐forms of poly(rG‐dC)·poly(rG‐dC), and poly(dG‐m5dC)·poly(dG‐m5dC)
Authors: Behe Michael J. 
Published: December 2004

AbstractThe vacuum CD spectra of poly(rG‐dC)·poly(rG‐dC) and poly(dG‐m5dC)·poly(dG‐m5dC) have been obtained for the low‐salt Z‐conformations of both polymers. The spectra are very similar to those for the high‐salt Z‐forms. This behavior is consistent with the suggestion that the low‐ and high‐salt Z‐forms are comprised of different proportions of ZI‐ and ZII‐conformations.
Effect of NaCl on the association of thrombin with heparin
Authors: Oshima Genichiro , Uchiyama Hideki , Nagasawa Kinzo 
Published: December 2004

AbstractThe association of heparin with thrombin was investigated by fluorometric titration. A maximum of 25% of the fluorescence of fluorescein‐labeled heparin (FTC‐heparin) was quenched at thrombin saturation in the absence of NaCl. FTC‐heparin (H) associated tightly with thrombin (T) and the association constant of the ternary complex, H2T, formed in the absence of NaCl, was calculated to be 1.7 × 108M−1. However, the association was strongly influenced by the NaCl concentration, and the association constant of the equimolar complex, HT, formed in 0.15M NaCl was found to be 1 × 106M−1. The first‐order rate constant, kapp, for inactivation of thrombin by antithrombin III (AT III) and low‐affinity heparin (LA‐heparin) was comparable with that of high‐affinity heparin (HA‐heparin) in the absence of NaCl, but decreased with an increase in the concentration of NaCl. The decreased enhancement of the thrombin‐AT III reaction by LA‐heparin at high NaCl concentration appeared to result from a decreased association of thrombin with LA‐heparin, thus reducing the formation of the ternary complex, thrombin‐LA‐heparin‐AT III.
Models for the subunit arrangement in soluble and aggregated plasma fibronectin
Authors: Hörmann Helmut , Richter Hartmut 
Published: December 2004

AbstractFibronectin, consisting of two threadlike subunits connected close to their C‐terminal ends, exists in a soluble and a fibrous form. Models are presented that propose distinct foldings of the rodlike subunits in the soluble dimer and an extended arrangement in the aggregates. The proposed conformations are based on the analysis of electrostatic attractions and noncovalent affinities between domains. Electrofocusing of proteolytic fragments revealed a sequence of four domains with alternating charges in the N‐terminal half of each subunit and two domains with opposite charges close to the C‐terminus. Complementary sites with affinity to each other were localized by radioimmuno‐binding assay in the gelatin‐binding and in the subsequent DNA‐binding domain of the N‐terminal tetra‐domain sequence. Claiming that in soluble fibronectin electrostatic attractions and noncovalent affinities should be neutralized within the molecule resulted in the construction of a conformation with backfolded subunits, each containing an extra loop in which domains with complementary affinity sites are saturated by each other. The model is in accord with hydrodynamic and electronmicroscopic data. There is, however, an alternative folding in which electrostatic and noncovalent affinity sites in the N‐terminal half of each subunit are saturated by an interchain interaction within the molecule. Consequently, a rearrangement of the molecule without significant shape change cannot be excluded. In the aggregated form, the N‐terminal tetra‐domain sequence gives rise to an intermolecular interaction while the C‐terminal domains become available for binding ligands.
Dynamics of molecular organization in agarose sulphate
Authors: Norton I. T. , Goodall D. M. , Austen K. R. J. , Morris E. R. , Rees D. A. 
Published: December 2004

AbstractNongelling solutions of structurally regular chain segments of agarose sulphate show disorder–order and order–disorder transitions (as monitored by the temperature dependence of optical rotation) that are closely similar to the conformational changes that accompany the sol–gel and gel–sol transitions of the unsegmented polymer. The transition midpoint temperature (Tm) for formation of the ordered structure on cooling is ∼25 K lower than Tm for melting. Salt‐induced conformational ordering, monitored by polarimetric stopped‐flow, occurs on a millisecond time scale, and follows the dynamics expected for the process 2 coil ⇌ helix. The equilibrium constant for helix growth (s) was calculated as a function of temperature from the calorimetric enthalpy change for helix formation (ΔHcal = −3.0 ± 0.3 kJ per mole of disaccharide pairs in the ordered state), measured by differential scanning calorimetry. The temperature dependence of the nucleation rate constant (knuc), calculated from the observed second‐order rate constant (kobs) by the relationship kobs = knuc(1 − 1/s) gave the following activation parameters for nucleation of the ordered structure of agarose sulphate (1 mg mL−1; 0.5M Me4NCl or KCl): ΔH* = 112 ± 5 kJ mol−1; ΔS* = 262 ± 20 J mol−1 K−1; ΔG*298 = 34 ± 6 kJ mol−1; (knuc)298 = (7.5 ± 0.5) × 106 dm3 mol−1 s−1. The endpoint of the fast relaxation process corresponds to the metastable optical rotation values observed on cooling from the fully disordered form. Subsequent slow relaxation to the true equilibrium values (i.e., coincident with those observed on heating from the fully ordered state) was monitored by conventional optical rotation measurements over several weeks and follows second‐order kinetics, with rate constants of (2.25 ± 0.07) × 10−4 and (3.10 ± 0.10) × 10−4 dm3 mol−1 s−1 at 293.7 and 296.2 K, respectively. This relaxation is attributed to the sequential aggregation processes helix + helix → dimer, helix + dimer → trimer, etc., with depletion of isolated helix driving the much faster coil–helix equilibrium to completion. Light‐scattering measurements above and below the temperature range of the conformational transitions indicate an average aggregate size of 2–3 helices.
The proteoglycans of bovine nasal cartilage and human articular cartilage: A sedimentation equilibrium analysis
Authors: Hinnie J. , Serafini‐Fracassini A. 
Published: December 2004

AbstractCartilage proteoglycan was isolated from bovine nasal septum and fractionated according to buoyant density after dissociative CsCl density gradient centrifugation. Gel‐exclusion chromatography showed that hyaluronic acid was present in fractions of density lower than 1.69 g/mL. The molecular weight, assessed by sedimentation equilibrium analysis, of the proteoglycan present in the fractions with density > 1.69 g/mL, which appeared chromatographically homogeneous and constituted 54% of the preparation, ranged from 1.0 to 2.6 × 106 for v = 0.55 cm3 g−1. Carbodiimide‐induced modification of the carboxyl groups by methylamine resulted in a reduction of the molecular weight to 0.74 – 1.25 × 106. An analogous reduction in molecular weight was obtained after equilibration of this proteoglycan fraction with hyaluronic acid oligomers containing five disaccharide units. Since both procedures are known to cause inhibition of the interaction between proteoglycans and hyaluronic acid, it is suggested that this lower molecular‐weight range represents the true degree of polydispersity of the sub‐units of hyaline cartilage proteoglycan constituting this fraction, while the higher values obtained for the intact proteoglycan are the result of the presence of hyaluronic acid in the sample. The molecular‐weight range of the whole proteoglycan subunit preparation, assessed after carboxyl group modification, was 0.5–1.2 × 106. Apparently normal and abnormal cartilage was excised from single human osteoarthrosic femoral heads. Proteoglycans extracted by 4M guanidine hydrochloride were isolated after dissociative density gradient centrifugation and subjected to carboxyl group modification. Preparations from normal tissue exhibited molecular‐weight averages ranging from 5 to 9 × 105. A molecular‐weight reduction was observed with proteoglycans isolated from abnormal areas.
Gel formation by fibrin oligomers without addition of monomers
Authors: Janmey Paul A. , Ferry John D. 
Published: December 2004

AbstractSoluble fibrin oligomers were formed by reacting fibrinogen with thrombin under fine clotting conditions where the action of thrombin is the rate‐determining step for polymerization, and by inhibiting the reaction shortly before gelation. Oligomeric fibrin was separated from unreacted fibrinogen and small oligomers by gel permeation chromatography. Electron microscopy revealed that the largest soluble fibrin oligomers resemble the protofibrils present in fine clots, but are somewhat shorter and entirely lack the twisted, trifunctional junctions that contribute to the elastic properties of fine clots. When thrombin was added to the soluble fibrin oligomers, polymerization resumed and clots were formed at a more rapid rate than from fibrinogen at the same concentration and resulted in a less‐opaque clot under coarse clotting conditions. The results confirm a prediction of a theory for the polymerization of fibrin and provide additional evidence that the final state of a coarse fibrin clot depends on the mobility of protofibrils during its formation.
A study of apo‐ and holo‐forms of horse liver alcohol dehydrogenase in solution by diffuse X‐ray scattering
Authors: Yu. Pavlov M. , Sinev M. A. , Timchenko A. A. , Ptitsyn O. B. 
Published: December 2004

AbstractApo‐ and holo‐forms of horse liver alcohol dehydrogenase (LADH) in solution were studied by diffuse x‐ray scattering. Experimental scattering curves for apo‐ and holo‐forms coincide both with the curves calculated from the crystal structures of apo‐ and holo‐enzymes, and with each other. Thus the “sliding” of catalytical domains in LADH upon substrate binding, which has been shown by x‐ray analysis, cannot be detected by diffuse x‐ray scattering. Sensitivity of the scattering curves to the domain displacements of sliding and “locking” types has been investigated. It has been shown that the scattering curves of LADH are rather sensitive to the domain “unlocking.” However, these curves change only slightly upon sliding of domains, including the sliding of domains observed in LADH by x‐ray analysis.
Molecular structure of the cis‐syn photodimer of d(TpT) (cyanoethyl ester)
Authors: Hruska F. E. , Voituriez L. , Grand A. , Cadet J. 
Published: December 2004

AbstractThe three‐dimensional structure was determined by x‐ray crystallography for d(T[p](CE)T), a uv photoproduct of the cyanoethyl (CE) derivative of d(TpT), having the cis‐syn cyclobutane (CB) geometry and the S‐configuration at the chiral phosphorus atom. The crystals of C23H30N5O12P · 2H2O belong to the orthorhombic space group P212121 (Z = 4), with cell dimensions a = 11.596 Å, b = 14.834 Å, and c = 15.946 Å, containing two water molecules per asymmetric unit. The CB ring is puckered with a dihedral angle of 151°. The two pyrimidine bases are rotated by –29° from the position of direct overlap of their corresponding atoms. This represents a major distortion of DNA, since in DNA adjacent thymines are rotated by +36°. The pyrimidine rings are puckered with Cremer–Pople parameters for T[p] and in parentheses [p]T: Q: 0.24 Å (0.31 Å); θ: 123° (120°); ϕ: 141° (86°). These represent half‐chairs designated as 6H1 (T[p]) and 6H5 ([p]T). The CB and pyrimidine ring conformations are interrelated, and we postulate that they execute a coupled interconversion in solution. The T[p] segment has the syn glycosyl conformation, a 2T3 sugar pucker, and gauche− conformation at C4′‐C5′; the [p]T segment is anti, 3T4, trans. The C5′‐O5′ torsion of the [p]T unit is –124.5°, and the C3′‐O3′ torsion of the T[p] unit is –152.9°. Bond angles and bond lengths involving the phosphorus atom are similar to those of other phosphotriesters. The P‐O3′ and P‐05′ torsion angles are –138.1° and 58.6°, respectively. Several intermolecular (but no intramolecular) hydrogen bonds are found in the crystal.
Evolutionary similarity among peptide segments is a basis for prediction of protein folding
Authors: Sweet Robert M. 
Published: December 2004

AbstractShort segments of polypeptide, from a protein for which the primary sequence but not the three‐dimensional structure is known, are compared to a library of known structures. The basis of comparison is the probability with which residues in the unknown segment might substitute through evolution for residues in segments of known structure. In test cases, segments from known structures that are similar in sequence to those from a protein treated as unknown are often found to be similar in three‐dimensional structure to one another and to the true structure of the “unknown” segment. This provides a basis for prediction of the local configuration (secondary structure) of polypeptides.
The crystal structure of the photosynthetic inhibitors DCMU and DTPU
Authors: Gilon Chaim , Cohen Shmuel , Siderer Yona 
Published: December 2004

AbstractX‐ray diffraction studies have been carried out on a single crystal of the photosynthetic inhibitors N‐(3,4‐dichlorophenyl)‐N′‐dimethylurea (DCMU) and its newly synthesized spin‐labeled analog N‐(3,4‐dichlorophenyl)‐N′‐(3,3,5,5‐tetramethylpiperidine‐4‐oxyl)‐urea (DTPU). The synthesis of DTPU as well as its crystallographic data are reported. The crystal system of both compounds is monoclinic with a space group P21/c. The cell constants of DCMU are a = 7.759(1), b = 14.737(3), c = 9.233(2) Å, β = 100.99(6)°; of DTPU they are a = 6.976(1), b = 11.998(2), c = 23.585(3) Å, β = 91.38(5)°. Comparison of conformational parameters of DCMU and DTPU reveal differences in the dihedral angle between the aromatic ring and the ureido plane. The measured volumes of DCMU and DTPU are 259.1 and 493.3 Å3, respectively. These figures suggest the size of the binding site of the inhibitors in the photosynthetic membrane.
Stereochemistry of peptides containing 1‐aminocyclopentanecarboxylic acid (Acc5): Solution and solid‐state conformations of Boc‐Acc5‐Acc5‐NHMe
Authors: Bardi R. , Piazzesi A. M. , Toniolo C. , Sukumar M. , Balaram P. 
Published: December 2004

AbstractThe conformational analysis of a protected homodipeptide of 1‐aminocyclopentanecarboxylic acid (Acc5) has been carried out. 1H‐nmr studies establish a β‐turn conformation for Boc‐Acc5‐Acc5‐NHMe in chloroform and dimethylsulfoxide solutions involving the methylamide NH in an intramolecular hydrogen bond. Supportive evidence for the formation of an intramolecular hydrogen bond is obtained from ir studies. X‐ray diffraction studies reveal a type III β‐turn conformation in the solid state stabilized by a 4 → 1 hydrogen bond between the Boc CO and methylamide NH groups. The ϕ,ψ values for both Acc5 residues are close to those expected for an ideal 310‐helical conformation (ϕ≃ ± 60°, ψ∼ ±30°).
Pf1 virus particle dynamics
Authors: Tsang P. , Opella S. J. 
Published: December 2004

AbstractThe overall dynamics of the Pf1 filamentous bacteriophage particle in solution are characterized by nmr experiments. The chemical‐shift anisotropy powder‐pattern lineshapes from both DNA and protein backbone sites of the virus are motionally averaged in the same way, indicating that the entire particle undergoes rapid (< 104 Hz) reorientation about the long axis of the filament when the virus is in solution at high pH. In contrast, the virus particles in samples at low pH are immobile on this time scale.
Comparison between the unfolding rate and structural fluctuations in native lysozyme—effects of denaturants, ligand binding, and intrachain cross‐linking on hydrogen exchange and unfolding kinetics
Authors: Segawa Shin‐Ichi , Kume Katsuya 
Published: December 2004

AbstractThe hydrogen‐exchange reactions of peptide NH groups in lysozyme were studied by the change in the intensity of the amide II band in the ir spectrum. The slowest exchanging hydrogens, which are involved in intramolecular hydrogen bonding, are further divided into two groups at lower temperatures; half of them are exchanged through local unfolding and the other half through major cooperative unfolding. In order to study the correlation of the change in hydrogen‐exchange rates with the change in the unfolding rate constant, we observed the effects of intrachain cross‐linking, the addition of denaturant and ligand binding on the exchange rates through local unfolding. Although the exchange rate through major unfolding is greatly decreased by intrachain cross‐linking between Glu 35 and Trp 108 (1/22000), the exchange rate through local unfolding is only slightly decreased (1/20). Even at higher temperatures, where most intact lysozyme molecules unfold, the folded conformation of cross‐linked lysozyme remains compact, and no intermediate exists in which many side‐chain atoms are packed loosely so that the hydrogen‐exchange reaction occurs rapidly. Neither the addition of 2‐PrOD molecules nor (NAG)3 binding affects the exchange rates through local unfolding. Our experiments confirm that the change in the unfolding rate constant does not correlate with the change in fluctuations in the relatively flexible hydrogen‐bonded structure through which the exchange of peptide hydrogens takes place.
Concentration of protein in fibrin fibers and fibrinogen polymers determined by refractive index matching
Authors: Voter William A. , Lucaveche Carmen , Erickson Harold P. 
Published: December 2004

AbstractWe have used refractive index matching to determine the concentration of protein in the fibers in fibrin clots and of needlelike crystals of native fibrinogen. Our results are in agreement with those of Carr and Hermans [(1978) Macromolecules 11, 46–50], as determined by light scattering—namely, that protein makes up about 20% of the volume of the fiber. However, we have found that the protein concentration is strongly dependent on ionic strength. An increase in ionic strength caused a substantial drop in the protein concentration. In a buffer containing 100 mM NaCl, the protein concentration was 26.6–29.8 g of protein per 100 cm3 of polymer, and at 200 mM NaCl it was reduced to 22.1–23.1 g/100 cm3.