bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correction of light‐scattering errors in spectrophotometric protein determinations
Authors: Winder A. F. , Gent W. L. G. 
Published: May 2005

AbstractErrors due to light scattering are a feature of spectrophotometrie methods of protein determination. The experimental conditions may be chosen to allow calculation of the scatter contribution, which is obtained essentially from the linear relationship between log turbidity and log incident wavelength, together with knowledge of the slope of such functions. Using this information, the scatter corrections may be obtained by various simple and rapid methods, applicable to single or multicomponent protein solutions.
Minor nucleosides in RNA: optical studies of dinucleoside phosphates containing dihydrouridine
Authors: Formoso Caul , Tinoco Ignacio 
Published: May 2005

AbstractPhotoreduction with NaBH4 was used to reduce the dinucleoside phosphates ApU, UpA, and GpU to the corresponding molecules containing dihydrouridine (H). Also obtained from this reaction are dinucleoside phosphates containing (β‐N‐ribosyl) ureido‐propanol, an open ring form of dihydrouridine. The results of CD and ultraviolet absorption studies with these compounds imply that HpA is strongly stacked, but that ApH and GpH are only slightly stacked. The temperature dependence of the CD suggests that the stacking in HpA is unusual. The results with compounds containing open ring forms of dihydrouridine indicate that there is more intramolecular interaction when the ring is open than when it is closed.
Nägeli amylodextrin and its relationship to starch granule structure. I. Preparation and properties of amylodextrins from various starch types
Authors: Kainuma Keiji , French Dexter 
Published: May 2005

AbstractNägeli‐type amylodextrins were prepared from various starch types: native starch granules from potato, waxy maize, wrinkled pea, and high‐amylose maize, and from a commercial amylose (“Superlose”). The granular starches and retrograded amylose were treated with 15% sulfuric acid at 22°–25° for 3 months, the undissolved residues were washed free of acid and air dried. X‐ray diffraction patterns showed that amylodextrin from waxy maize starch (A‐type) and potato starch (B‐type) retain the same diffraction type as that of the parent starch. On conversion of a starch to an amylodextrin, the sharpness and intensity of the diffraction patterns are either retained (waxy maize starch), improved (slightly with potato, significantly with high‐amylose maize, and very markedly with wrinkled pea) or developed (amylose). The results indicate that the crystalline regions of a native starch granule, retrograded amylose, or amylodextrin are exceedingly resistant to acidic hydrolysis at room temperature. In contrast to the parent starches, native amylodextrins stain little if at all with dilute iodine solution. The iodine stains of dissolved amylodextrins were red (waxy maize), red‐purple (potato), or purple (amylose, high‐amylose maize, and wrinkled pea).
Poly(dA‐dT) complexes with histone H1 and pancreatic ribonuclease: Specific base recognition evidenced by ultraviolet resonance Raman spectroscopy
Authors: Chinsky L. , Turpin P. Y. 
Published: May 2005

AbstractThe conformational changes of poly(dA‐dT) from random coil to ordered structure with stacked bases produce important changes in the Raman line intensities (hypochromism) when the polymer is excited under the preresonance Raman conditions (λ excitation = 300 nm). Poly(dA‐dT)–RNase and poly(dA‐dT)–histone H1 interactions have been studied as models of mechanisms of destabilization and stabilization by proteins of the DNA secondary structure, respectively, following this intense preresonance Raman hypochromism. In addition, the specific variation of the intensity of the 1582‐cm−1 line of adenine is interpreted in terms of the interaction of the amino group with the RNase (thus involving the large groove). In the poly(dA‐dT)–H1 complex, the intensity of the 1665‐cm−1 line of thymine increases. This increase appears to involve the C2O group of thymine, located in the narrow groove.
Three‐dimensional structure of actinoxanthin. IV. A 2.5‐Å resolution
Authors: Pletnev V. Z. , Kuzin A. P. , Trakhanov S. D. , Kostetsky P. V. 
Published: May 2005

AbstractThe protein actinoxanthin (isolated from Actinomyces globisporus—molecular weight, 10,300; 107 amino acid residues) crystallizes in space group P212121 with cell dimensions: a = 30.9 Å, b = 48.8 Å, c = 64.1 Å, and Z = 4. The three‐dimensional structure of actinoxanthin was determined by the x‐ray multiple isomorphous replacement method at 2.5‐Å resolution. The molecule is kidney‐shaped and has a well‐defined cavity. Its characteristic features are the absence of α‐helices and the presence of enhanced content of antiparallel β‐structure (∼55%). A cylinder‐shaped formation of seven antiparallel β‐strands comprises the main part of the protein structure. The established β‐supersecondary structure is characterized by a three‐dimensional topology similar to that of immunoglobulin domains, superoxide dismutase subunits, and azurin and plastocyanin proteins.
Crystallization behavior of glucomannan
Authors: Chanzy H. D. , Grosrenaud A. , Joseleau J. P. , Dubé M. , Marchessault R. H. 
Published: May 2005

AbstractFive different glucomannan samples were recrystallized from dilute solution. Depending on the experimental conditions, the crystals obtained could be identified as corresponding to the mannan I (anhydrous precipitate of more or less regular lozenge‐shaped crystals) or mannan II (hydrated gel‐forming pseudo‐fibrillar precipitate). High‐molecular‐weight material, low temperature of crystallization, or a polar crystallization medium favored the mannan II polymorph, whereas a low‐molecular weight, a high temperature of crystallization, and a crystallization medium of low polarity yielded the mannan I polymorph. Since the base‐plane unit‐cell dimensions are fairly constant with respect to variation of glucose, it is likely that isomorphous replacement of mannose by glucose occurs in glucomannan crystallization; the data also indicate that perfection of the glucomannan crystals was reduced in specimens having a high glucose:mannose ratio. The oriented crystallization of glucomannan on cellulose microfibrils was also studied under conditions where the mannan I polymorph was obtained. This gave shish‐kebab structures that were characterized.
1H‐nmr comparative studies of polynucleotides: Conformation and dynamic structure of polyribo(uridylic) and polyribo(cytidylic) acids in neutral solution
Authors: Neumann J. M. , Tran‐dinh S. 
Published: May 2005

AbstractThe conformation and the dynamic structure of single‐stranded poly(U) and poly(C) in neutral aqueous solution have been investigated by 1H‐nmr at two different frequencies (90 and 250 MHz) and at various temperatures. Measurements of proton chemical shifts, coupling constants JH‐H, and proton relaxation times, T1, T2, versus temperature show a striking difference in conformation and in dynamic structure between the two polynucleotides studied. The temperature effect on δ and JH‐H is found to be substantial for poly(C) and insignificant for poly(U). The S conformer is favored in poly(U), whereas the N conformer strongly predominates in poly(C) (≃90%), similar to the case for RNAs. These results suggest that single‐stranded poly(C) probably possesses a helical or partial helical structure, whereas poly(U) shows a clear preference for the random coil, in agreement with the optical results. The local motions of the ribose and base were studied at various temperatures by measurements on the relaxation times at 90 and 250 MHz. For a given temperature between 22 and 72°C, the ratio T1(90)/T1(250) is practically the same for all poly(U) protons, indicating that in this temperature interval the ribose base unit of poly(U) undergoes an isotropic motion characterized by a single correlation time τc. Above 52°C, poly(C) exhibits a dynamic structure similar to poly(U). Below this temperature, poly(C) exists in an equilibrium between randomly coiled and single‐stranded helix forms. This situation is characterized by a strong cross‐relaxation effect and T1 values corresponding to a relatively short apparent correlation time. An activation energy of 4 kcal/mol was determined for the motion of the ribose–base unit in both single‐stranded polynucleotides.
Influence of hemin on the conformation of cyanogen bromide‐cleaved peptides of apomyoglobin
Authors: Nakano Minoru , Iwamaru Hiroshi , Tobita Tohru , Yang Jen Tsi 
Published: May 2005

AbstractThe complexes of the three BrCN‐cleaved fragments of sperm whale apomyoglobin with hemin were studied by circular dichroism (CD). In native myoglobin, the heme is located in the middle fragment; the isolated peptide (residues 56–131), however, produces little extrinsic Cotton effects by the addition of hemin, although about four molecules of hemin are bound to this peptide. In marked contrast, the COOH‐terminal peptide (residues 132–153), which binds three hemin molecules, shows strong Cotton effects in the Soret bands and drastically changes its conformation from unordered to highly helical. The Arg‐modified or Lys‐deaminated peptide no longer undergoes conformational changes by the addition of hemin, suggesting that the two propionic acid groups of one hemin molecule interact with the Arg residue and one of the Lys residues, which stabilizes the induced helical conformation. The NH2‐terminal peptide (residues 1–55) binds one hemin molecules, and the helicity of this fragment is slightly enhanced by the addition of hemin. Both the CD and difference absorption spectra indicate that the mode of interaction between the peptides and hemin are different for the three apomyoglobin fragments.
Correlation between sugar pucker and the orientation around the C3′O3′ bond (Φ′) in 3′‐mononucleotides
Authors: Dhingra M. M. , Saran Anil 
Published: May 2005

AbstractClassical potential functions (CPF) calculations on 3′‐mononucleotides, the building blocks of nucleic acids, predict a correlation between the sugar ring pucker and the torsion angle Φ′ around the C3′O3′ bond. In ribonucleotides, the value of Φ′ depends on the sugar pucker, viz. the C2′‐endo sugar pucker is associated with Φ′ = 210° and 270°, while the C3′‐endo sugar pucker favors only Φ′ = 210°. On the other hand, in deoxyribonucleotides, both sugar puckers show a preference for Φ′ = 180°. These theoretical predictions are fully corroborated by the results obtained from x‐ray and nmr studies on mono‐, di‐, and polynucleotides.
Molecular dynamics of ferrocytochrome c: Anharmonicity of atomic displacements
Authors: Mao Boryeu , Pear Michael R. , McCammon J. A. , Northrup S. H. 
Published: May 2005

AbstractThe atomic position distributions obtained from a 32‐ps molecular‐dynamics simulation of tuna ferrocytochrome c at 297 K are analyzed in terms of their second, third, and fourth moments. Non‐Gaussian relations among these moments are found for the majority of atoms in the molecule, indicating anharmonicity in the effective potential functions for the atomic motions. Many atoms exhibit only slightly anharmonic mobility during the 32‐ps period, but about half of the atoms exhibit sizeable anharmonicity. For a typical atom, the anharmonic effects are largest for motions in the direction along which the largest displacements occur. Two classes of significantly anharmonic atoms are apparent: those whose effective potentials are distorted toward a square‐well shape and those whose effective potentials have secondary minima corresponding to conformational substates.
Flow dichroism of capsid DNA phages. I. Fast and slow T4B
Authors: Hall Stephen B. , Schellman John A. 
Published: May 2005

AbstractFlow linear dichroic studies have been conducted on phage T4B in its fast and slow forms. The behavior of the phages is well represented by an equivalent ellipsoid model using the Peterlin‐Stuart theory. The measurements permit the evaluation of the optical factor of the DNA in the phage and the rotary diffusion coefficient of the phage particle. Both these quantities change during the slow–fast conversion. The rotary diffusion results are in good agreement with those obtained by other workers with other methods. The optical factor is negative, indicating a net alignment of DNA helices parallel to the phage axis. The results exclude certain simplified models for the packaged DNA but do not lead to a unique structural conclusion. The flow dichroism experiment and its interpretation are described, and a simple method of calculating optical factors for complicated but cylindrically symmetric structures is presented.
Light‐scattering study of DNA condensation: Competition between collapse and aggregation
Authors: Post Carol Beth , Zimm Bruno H. 
Published: May 2005

AbstractLight‐scattering studies were done to investigate the DNA collapse transition, a large and discontinuous reduction in the radius of gyration. Of particular concern was differentiating the compaction of a single DNA molecule from aggregation. Solutions of RK2 plasmid DNA (Mr = 37 × 106) or bacteriophage T7 DNA (Mr = 25 × 106) were titrated with the condensing reagents spermidine in aqueous solvent or magnesium ion in ethanol–water solvent. The transition was followed by the change in scattering at a single angle or by the change in the angular dependence of scattering. At concentrations below 1 μg/mL, only aggregation could be detected by observation at a single angle; therefore, to study the collapse transition, it was necessary to measure the angular dependence of scattering. The intensities measured between the angles 30° and 60° were fit to known scattering functions. At low concentrations of the condensing reagent, the data were consistent with the scattering function of a random coil. On the other hand, during the transition at higher reagent concentrations, the curve that fit the data required two components—the scattering function for a random coil with a large radius of gyration, plus that for a sphere with a radius about one‐fifth of that of the coil. The fractional concentration of the sphere increased with increasing condensing‐reagent concentration. This two‐component behavior is in apparent contrast to the situation with a more flexible polymer such as polystyrene, in accord with theoretical predictions. At still higher reagent concentrations, aggregation was apparent. Condensation to a collapsed state was reversible without hysteresis, while dissolution of the aggregated state nearly always occurred with hysteresis. Qualitative agreement between the observed DNA collapse transition and the theoretical phase diagram presented in the preceding paper was found, although the light‐scattering results did not show quantitative agreement with the simple theoretical model.
Conformational study of poly(α,β‐L‐aspartic acid)
Authors: Saudek Vladimír , Štokrová Štěpánka , Schmidt Pavel 
Published: May 2005

AbstractThe conformation of several samples of poly(α,β‐L‐Asp) with a molar fraction of β‐bonds ranging from 0.1 to 0.55 was investigated by means of ir and CD spectroscopy and potentiometric titration and compared with the results obtained previously with poly(α‐L‐Asp). All samples investigated underwent a conformational change induced by changes in their degree of ionization: unpronounced ir absorption of amide V at 650 cm−1 was shifted to 620 cm−1 and substantially increased on deionization; CD spectra changed with the degree of ionization, passing through an isosbestic point; and the pattern of the titration curves was more complex than that of a simple polyelectrolyte. The conformation developing with the decreasing degree of ionization may be considered to be α‐helix, as deduced according to the analogous behavior of other polypeptides. The extent of the conformational change in the individual samples depends on the molar fraction of β‐bonds: the higher it is, the lower is the helix‐forming ability of the sample.
DNA bis‐intercalation: Theoretical analysis, including cooperativity of the interaction of echinomycin analogs with DNA
Authors: Shafer Richard H. , Waring Michael J. 
Published: May 2005

AbstractA theoretical analysis of the binding curves for the bifunctional peptide antibiotic echinomycin and its analogs interacting with a variety of DNAs is presented. The method is an extension of our previous work using the sequence‐generating‐function technique and has been modified to allow for consideration of cooperativity within the framework of the neighbor‐exclusion rule. Binding by both single and double intercalation is included, and the results are, in many cases, superior to the analysis based on single‐mode binding. In all cases the data are consistent with the neighbor‐exclusion principle for intercalation when analyzed with this approach, while data analysis, using a simpler method, often led to violation of this rule. Positive cooperativity is considered in the treatment of data for binding to poly(dA‐dT). Finally, we discuss the relationship between base specificity and binding site size.
Loop formation in polynucleotide chains. I. Theory of hairpin loop closure
Authors: Marky Nancy L. , Olson Wilma K. 
Published: May 2005

AbstractA theoretical model to determine the probability of loop formation, based on an elaborated form of the Jacobson‐Stockmayer theory of cyclization equilibria, has been developed and used on RNA chains of homogeneous puckering and lengths up to 27 residues. The probability Qx (q, γ0, ε0) of occurrence of hairpin loops of a particular chain x is given by Qx (q, γ0, ε0) = [W (q) δr][2Γq (γ0)δγ] [Eq,γ0 (ε0) δε] where W(q) is the three‐dimensional density distribution function of end‐to‐end vectors r centered about the ideal loop closure position q; Γq(γ0) is an angular correlation factor that restricts the orientation of terminal bonds (i.e., bond x and bond 1) in the loop to a specified value Δθ = cos−1 (γ0) when r adopts a value within a range δr from position q; and Eq,γ0(ε0) is the probability that ε falls within δε of ε0 when r and γ assume the values denoted by the respective subscripts. The parameter ε is related to the angle between a hypothetical bond (x + 1) and bond 1. In these calculations, Eqγ0(ε0) was set equal to 1. For randomly coiling models previously developed to reproduce polynucleotide unperturbed dimensions, loop closure probability is maximized with chains of length 22 residues. Larger hairpin loops of 24–25 residues, also favored in C3′‐endo random coils of this type, are potential models of tRNA unfolding. W(q) is a stronger determinant of loop closure than Γq(γ0). The angular correlation effect is most noticeable at chain lengths 22 and 23 where 2Γq(γ0) deviates from unity.
Molecular‐mechanics studies on d(CGCGAATTCGCG)2 and dA12·dT12: An illustration of the coupling between sugar repuckering and DNA twisting
Authors: Kollman Peter , Keepers Joe W. , Weiner Paul 
Published: May 2005

AbstractMolecular‐mechanics calculations have been carried out on the base‐paired deoxy dodecanucleoside undecaphosphates d(CGCGAATTCGCG)2 and d(A12)·d(T12). These refinements were carried out using the model‐built Arnott B‐DNA geometry as initial coordinates (with a helix repaeat of 10.0 residues/turn), as well as helix repeats ranging from 9 to 12 residues/turn. There was some variation in the optimum calculated helix repeat, depending on the dielectric model, the presence or absence of counterions, and the method used for inclusion for nonbonded interactions; the most interesting general result of these calculations was the coupling between furanose sugar puckering and twist. This coupling was observed for all models. With a helix repeat of 9.0 residues/turn, all sugars remain C(2′)endo after refinement; as the helix repear increases to 12.0 residues/turn, the number of sugars repuckering to O(1′)endo and C(3′)endo increases also. With our most rigorous model (i.e., a model with no cutoff distance for nonbonded interactions) and a helix repeat of 10.0 residues/turn, we find a greater tendency for pyrimidine than purine repuckering in d(CGCGAATTCGCG)2, in agreement with the x‐ray structural data of Drew et al. [(1981) Proc. Natl. Acad. Sci. USA 78, 2179–2185].We also carried out a number of calculations in which we “forced” one of two deoxy sugars to repucker or one of the C3′‐O3′‐P‐O5′ (ω) torsion angles to change from gauche− to trans using dihedral angle constraints. After the constraints were removed, some of these structures “reverted” to the sugar pucker of the initial structures, while others remained repuckered. In all cases, the energies for repuckered structures after refinement were very similar to energies of the initial structure. Experiments and theory suggest that local conformational fluctuations play an essential role in nmr relaxation of 31P and 13C atoms in double‐helical DNA. The results of our previous calculations on hexanucleoside phosphates and the calculations presented there are consistent with an important contribution to nmr relaxation processes of conformational changes in the torsion angle ω′ from gauche− to trans and deoxy sugar repuckering from C(2′)endo to C(3′)endo. Specifically, the calculations presented here indicate a very flexible phosphate backbone in helixes having an intermediate helix repeat of 10 to 11 residues/turn. These helixes may accommodate sugars of variable pucker without significantly disrupting base–base hydrogen‐bonding and stacking interactions. All of the variant structures are similar in energy, suggesting that conversion between them can occur on a nanosecond time scale, as observed in nmr relaxation experiments.
Vibrational analysis of peptides, polypeptides, and proteins. XV. Crystalline polyglycine II
Authors: Dwivedi A. M. , Krimm S. 
Published: May 2005

AbstractA force field has been refined for the 31‐helix structure of polyglycine II, using the polyglycine I force field plus previous CαHα…︁O force constants as a starting point. Besides force constants associated with the hydrogen bonds, which must change since the hydrogen‐bond characteristics are different in the two structures, we have had to modify only 10 force constants from the polyglycine I force field to make it suitable for reproducing the polyglycine II frequencies. Most involve the NCα bond, which is the torsion angle that changes from the I to the II structure. Calculations were done for parallel chain and antiparallel chain crystal structures of polyglycine II, the observed spectra being found to agree best with the latter structure. Since this provides strong evidence for the loss of strict threefold symmetry in the chain, our analysis strengthens the support for the existence of CαHα…︁O hydrogen bonds in the structure of polyglycine II.
Raman spectra and normal vibrations of dipeptides. I. Glycylglycine
Authors: Lagant P. , Vergoten G. , Loucheux‐Lefebvre M. H. , Fleury G. 
Published: May 2005

AbstractWe studied the Raman spectra of the zwitterionic glycylglycine crystal (GG) and its N‐deuterated analog. A normal coordinate analysis on its α‐crystalline form was performed and the effects of intra‐and intermolecular couplings are discussed. A modified Urey‐Bradley potential was used as a model of the intramolecular force field. Factor group splittings are described by the use of intermolecular potentials consisting of nonbonded atom‐atom interactions and dipole‐dipole interactions. Effects of hydrogen bonds on the vibrational frequencies of amino and carboxylate groups are also analyzed.