bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multinuclear magnetic resonance studies of collagen molecular structure and dynamics
Authors: Torchia D. A. , Hiyama Y. , Sarkar S. K. , Sullivan C. E. , Young P. E. 
Published: May 2005

AbstractWe have measured the percentages of cis and trans Gly‐Pro and X‐Hyp peptide bonds in thermally unfolded type I collagen. 13C‐nmr solution spectra show that 16% of the Gly‐Pro and 8% of the X‐Hyp bonds are cis in unfolded chick calvaria collagen. These results support the hypothesis that cis–trans isomerization is that rate‐limiting step in the propagation of the collagen triple helix. We have used multinuclear solid‐state nmr to study the molecular dynamics of the collagen backbone in tendon, demineralized bone, and intact bone as a function of temperature, hydration, and pH. These studies show that collagen backbone motions are characterized by a broad distribution of correlation times, τ, covering the range from 10−4 to 10−9 s. In the case of nonmineralized collagen, the root‐mean‐square fluctuations in azimuthal angle, γrms, range from ca. 10° when τ ∼ 10−9 s to ca. 30° when τ < 10−4 s; in the case of bone collagen, γrms values are about half as large as those found in nonmineralized collagen. Backbone motions are negligible at temperatures below −25°C. This is also the case at 22°C when demineralized bone collagen is lyophilized. In contrast, flexibility of hydrated demineralized bone collagen greatly increases as pH is lowered from 7 to 2. The more limited flexibility observed at neutral pH is a consequence of the intermolecular interactions that contribute to fibril organization and strength. However, the fibrils retain significant flexibility at physiological pH, enabling them to distribute stress and dissipate mechanical energy.
Applications of fluorescence spectroscopy to molecular cytogenetics
Authors: Latt Samuel A. , Lalande Marc , Kunkel Louis M. , Schreck Rhona , Tantravahi Umadevi 
Published: May 2005

AbstractPhenomena studied by fluorescence spectroscopy, including differential perturbations of dye fluorescence by variations in DNA composition and interdye energy transfer, can be applied to cytological studies of chromosome structure, replication, and repair. When combined with fluorescence‐activated flow sorting, fluorescent differentiation between metaphase chromosomes can be exploited to obtain recombinant DNA libraries enriched for all or parts of individual chromosomes. Cloned DNA segments from such libraries continue to find application in studies of human chromosome structure and function and in molecular linkage analyses, thus leading to molecular genetic investigations of human disease states.
Conformational analysis of lac promoters using the nuclease activity of 1,10‐phenanthroline‐copper ion
Authors: Sigman David S. , Spassky Annick , Rimsky Sylvia , Buc Henri 
Published: May 2005

AbstractThe artificial nuclease activity of (OP)2Cu+ and H2O2 has been used to analyze the DNA conformation of single‐stranded DNA form the coliphage M‐13, and the B‐type DNA of the promoter region of the lac operon. Despite the strong kinetic preference of the reaction of B‐DNA, demonstrated with synthetic polynucleotides, the reagent cannot distinguish the double‐stranded hairpin turns in M‐13 from the extensive single‐stranded region because the latter forms metastable hydrogen‐bonded structures that are readily cleaved.Analyses of the promoter regions of the lac operon of the wild‐type and of the Ps and UV‐5 mutations have demonstrated that the promoter‐specific sequence (Pribnow Box), extending from positions −12 to −6, exhibits a charactersitc hyperreactivity to the reagent. The wild‐type DNA has hypersensitive sites at the boundary of the region, at positions −13 and −12. The Ps and UV‐5 mutations, which support cyclic AMP protein‐independent transcription, have mutations at −9, and −9 and −8, respectively, and possess additional hyperreactive sites calibrated at −11 and −10 in the sequence. These experiments demonstrate that the local structure of the DNA of the these control regions is different. The unique structure of the promoter may govern recognition of the DNA by RNA polymerase. The artifical nuclease activity of (OP)2Cu+ may therefore be useful to identify functionally significant local variation in DNA structure.
Prolyl isomerization: How significant for in vivo protein folding?
Authors: Wetlaufer Don B. 
Published: May 2005

AbstractSuggestive but not decisive evidence indicates that in vivo peptide chain folding is completed in a time not much longer than that required for covalent peptide synthesis. Extrapolation of model peptide rates of the cis–trans prolyl isomerization leads to the prediction tht protein folding should be much slower than the apparent in vivo rates. On the assumption that rapid protein folding in vivo is the rule, three routes are suggested by which a protein undergoing biosynthesis can avoid a strongly slowed folding rate: (1) by a peptide chain‐elongation process that adds only trans peptide bonds, follwed by a rapid folding process that incorporates them into a three‐dimensional structure, raising the energy barrier to isomerization; (2) by folding to produce three dimensional structures that position prolyl residues largely in chain turns on the protein surface, where the residue may be either cis or trans without large effects on the protein structure and function; (3) prolyl cis–trans isomerization may be speeded by the formation of peptide loops.
Enzyme diffusion and action on soluble and insoluble substrate biopolymers
Authors: Katchalski‐Katzir Ephraim , Rishpon Judith , Sahar Elhanan , Lamed Raphael , Henis Yoav I. 
Published: May 2005

AbstractThe action of enzymes on soluble and insoluble substrate biopolymers is discussed, taking into account enzyme diffusion along the biopolymer “surface” and interaction with interspersed ligand groups that may be modified by the action of the enzyme. It is shown that movement of the enzyme under trhe combined effect of these two processes can be described as a diffusion process characterized by an apparent diffusion coefficient that generally depends on both time and position. Equations describing the system are formulated and some specific examples analyzed in terms of analytical or numerical solutions. The concentration distributions of both the enzyme and the substrate (or product ) were obtained for different systems for which the apparent diffusion coefficient is a function of time only, as well as of both time and position. The relevance of the formulation, as developed, to systems in which reduction in dimensionality leads to enhanced enzyme efficiency is discussed, and possible uses of the theory in studies of biopolymer structure and enzyme‐biopolymer interactions are suggested.
Temperature‐dependent conformational transitions in poly(dG‐dC) and poly(dG‐m5dC)
Authors: Behe Michael J. , Felsenfeld Gary , Szu Shousun Chen , Charney Elliot 
Published: May 2005

AbstractThe double‐stranded helical complexes of poly(dG‐dC) and of poly(dG‐m5dC) are shown to convert from B‐ to Z‐DNA‐type conformations at moderate or low ionic strengths, lower for the 5‐methyl than for the non‐methyl species, in a highly cooperative temperature‐dependent equilibrium. In the presence of low concentrations of divalent ion, e.g., Mg2+, the temperature at which the B → Z transition occurs is virtually independent of the salt concentration and the B‐conformation is favored at lower temperature, while the Z‐conformation is favored at higher temperature. Since the Debye‐Hückel screening parameter changes rapidly with ionic strength in this region, electrostatic interaction with the free ions appears to be only a small factor in the forces that promote the transition; the temperature dependence must derive principally from effects on the solvent. The temperature dependence at high salt concentrations is also reported.
Electron microscopy of the melting of sequenced DNA
Authors: Kalambet Yu. A. , Borovik A. S. , Lyamichev V. I. , Lyubchenko Yu. L. 
Published: May 2005

AbstractDifferential melting curves (DMCs) of DNAs pA03 and pBR322 in solutions of different ionic strength (0.02 and 0.2M Na+) were obtained. A previously developed procedure of glyxal fixation of partially denatured DNA molecules at temperatures within the melting range was used to construct electron‐microscopic melting maps for pBR322 and pAO3 plasmid DNA and for the replicative form of bacteriophage ϕX174 DNA, allowing the melting of these DNA molecules to be followed in solutions of low (0.1 × SSC) and high (1 × SSC) ionic strength. In spite of the fact that the melting was at nonequilibrium at the low ionic strength, the melting maps for the two kinds of solutions practically coincided. Experimental data are compared with theoretical calculations based on the Fixman‐Freire algorithm. The conclusion is that the melting pattern of these DNAs is, on the whole, correctly described by the theory, although there are appreciable differences between the theoretical and experimental differential melting curves. We have also determined the relation between the melting temperature of a region and its GC content, with allowances made for the boundary conditions of melting in 0.1 × SSC and 1 × SSC solutions, and have analyzed the theoretical shape of peaks of the DMCs.
Physical properties of rod‐shaped molecules in solution
Authors: Stimpson Donald I. , Bloomfield Victor A. 
Published: May 2005

AbstractSeveral theories describing the physical properties of solutions containing rod‐shaped molecules are reviewed. The results of the various theories are presented in a convenient form for implementation on a calculator or microcomputer. Expressions are derived for light scattering from thin rods using rational approximations for the sine and cosine integrals. These expressions apply to turbidity, Rayleigh, and dynamic light‐scattering measurements. Accurate approximating equations are given for the various diffusional motions involved in dynamic light scattering. For shear‐dependent viscosity and flow birefringence, empirically derived interpolation formulas are given. These provide values of the Simha factor, extinction angle and orientation function for a wide range of axial ratios and velocity gradients with relative errors less than 1%. We demonstrate how these equations can be applied to predict or model the properties of a solution containing thin rods of various lengths.
The size and shape of amylopectin: A study using pulsed‐field gradient nuclear magnetic resonance
Authors: Callaghan Paul T. , Lelievre John 
Published: May 2005

AbstractSelf‐diffusion coefficients have been obtained over a range of concentrations for both polymer and solvent in amylopectin/dimethylsulfoxide and amylopectin/water systems. The measurements were made using pulsed‐field gradient nuclear magnetic resonance (PFG‐nmr). The implications of macromolecule polydispersity to the interpretion of the PFG‐nmr experiment have been considered. Measurements of the self‐diffusion coefficients of solute and solvent are shown to provide an effective probe of polymer size and shape. Such measurements demonstrate that in dimethylsulfoxide, wheat starch amylopectin molecules are highly planar with Mw of order 106. In contrast, amylopectin in water is an aggregate with a more spherical shape and has a volume some 400 times larger than the single molecule.
Light‐scattering study on chick‐embryo cartilage proteoglycan type H (PGH)
Authors: Maeda Hiroshi , Oike Yasuteru 
Published: May 2005

AbstractLight‐scattering measurements were carried out on chick‐embryo cartilage proteoglycan type H (PG‐H) in three different media. The number of uronates per PG‐H was obtained as a measure of the molecular weight: 2.3 × 103 in 4M GdnHCl, 7.1 × 103 in 0.3M NaCl, and 5.7 × 103 in 0.04 g/dL SDS + 0.1M NaCl (GdnHCl, guanidine hydrochloride; SDS, sodium dodecylsulfate). Self‐association of PG‐H occurred in 0.3M NaCl and 0.04 g/dL SDS + 0.1M NaCl.
Reaction pathway for the quaternary structure change in hemoglobin
Authors: Janin Joël , Wodak Shoshana J. 
Published: May 2005

AbstractWe perform a computer simulation of the quaternary structure change during the allosteric transition of hemoglobin. The simulation is based on a docking procedure by which αβ dimers of human hemoglobin are associated into tetramers after being rotated in various orientations. The stability of tetramers thus reconstituted is estimated from the values of a simplified energy function describing nonbonded interactions and from the area of the surface buried in dimer–dimer contacts (their interface area), which we take to represent stabilizing interactions and solvent contribution. A systematic analysis of tetramers reconstituted with twofold symmetry reveals that when the dimers have the R tertiary structure, only tetramers having R‐like quaternary structures are stable. When the dimers have the T tertiary structure, they may associate into T‐like tetramers or a variety of quaternary structures ranging from T to near R, thus tracing a plausible reaction pathway for the allosteric transition. We subject intermediates of this pathway to energy refinement with rigid αβ dimers. The refinement demonstrates that symmetrical structures are more stable than non symmetrical ones. A detailed analysis of dimer–dimer contacts in intermediates shows how close packing is maintained over large interfaces throughout the quaternary structure change, especially in the “switch region” of contact between the C helix of α‐chains and the FG corner of β‐chains.
Properties of the aminotyrosine derivatives of calmodulin
Authors: Steiner R. F. , Marshall L. 
Published: May 2005

AbstractDerivatives of calmodulin have been prepared in which tyrosine‐99 and tyrosine‐138 have been converted to their aminotyrosine derivatives. Significant changes in microenvironment occur in the presence of Ca2+. Both groups have a significant degree of mobility with respect to the protein matrix; this is Ca2+ dependent.
Stereospecific assignments of 1H‐nmr methyl lines and conformation of valyl residues in the lac repressor headpiece
Authors: Zuiderweg E. R. P. , Boelens R. , Kaptein R. 
Published: May 2005

AbstractTwo‐dimensional 1H‐nmr methods are described to obtain information on the sidechain conformation of valyl residues of the lac repressor headpiece and to assign the resonances of their methyl groups stereospecifically. The spin–spin coupling constants (Jαβ) between Cαand Cβ protons are obtained from two‐dimensional correlated spectroscopy experiments. Large values for Jαβ(10–12 Hz) corresponding to trans orientations for these protons (g+ conformation) are found for all valyl residues in α‐helical segments. For these valyl residues, the distance between one methyl group (γ1)and the valyl amide proton is much shorter than for the other methyl group, so that stereospecific resonance assignments follow from relative intensities of the corresponding cross peaks in a two‐dimensional nuclear Overhauser enhancement spectrum. Thus, streospecific assignments could be made for the methyl groups of Val 9, 20, 23, and 38 (of a total of eight valyl residues).
Do parallel β‐strands have dipole moments? An ab initio molecular‐orbital‐direct reaction field study
Authors: Van Duijnen P. Th. , De Jager Jeltje C. , Thole B. T. 
Published: May 2005

AbstractRecently, it was suggested that parallel β‐sheets have a significant dipole moment, in contrast to antiparallel sheets. Ab initio molecular‐orbital (MO) calculations on parallel and antiparallel β‐strands of tetra(Gly) show that they have very similar charge distributions. Interaction energies between two and three strands of tetra(Gly), obtained using the direct reaction field Hamiltonian, show that a particular choice of point charges is probably not crucial for calculating interactions within β‐sheets, but that it might be for calculating interactions between these sheets and other parts of a protein, in particular, α‐helices. The point‐charge representation of our MO‐SCF results will probably reduce the hazard of introducing artefacts in electrostatic calculations of protein conformational energies, provided the short‐range interactions are treated in a more realistic way, i.e., such that intra‐ and interchain induction effects are included.
Domain characteristics of the carboxyl‐terminal fragment 206–316 of thermolysin: pH and ionic strength dependence of conformation
Authors: Dalzoppo Daniele , Vita Claudio , Fontana Angelo 
Published: May 2005

AbstractThe pH and ionic strength dependence of conformation of the COOH‐terminal fragment 206–316 (fragment FII) of thermolysin was monitored by far‐uv CD and difference absorption measurements. This fragment was shown previously to possess the properties of a protein domain, i.e., able to refold into a stable nativelike structure [Fontana, A., Vita, C. & Chaiken, I. M. (1983) Biopolymers 22, 69–78]. Analysis of the CD spectra in the pH range of 1–12 indicated that near pH 1, the conformation of fragment FII appears to be in an intermediate state (H) between the fully unfolded one (U) [the guanidine hydrochloride (Gdn · HCl)‐induced unfolded state] and the nativelike state (N—that attained at neutral pH). Quantitative analysis of secondary structure from CD spectra revealed that state H at 4°C is characterized by some 30% α‐helical structure, compared to 47% for state N. The heat‐ and Gdn · HCl‐mediated unfolding transitions of state H were fully reversible and characterized by little cooperativity, which is taken as an indication that state H corresponds to several species possessing different, and low, conformational stabilities. The midpoint transition from state H to N occurs near pH 2.5, implying that the acid transition results from the titration of carboxyl groups of the fragment with anomalously low pK, as would be expected for groups involved in specific salt bridges. Fragment FII at pH 1 (state H) may be induced to exhibit nearly the same degree of helicity of state N simply by increasing the ionic strength of the solution, thus reducing the repulsive interactions between positive charges within the highly charged fragment at pH 1. The results obtained emphasize the role of electrostatic interactions in the folding and stability of fragment FII and suggest a mechanism of folding of the fragment from U to N involving an intermediate state characterized by an assembly of fluctuating α‐helices.
Interactions of molecules with nucleic acids. XII. Theoretical model for the interaction of a fragment of bleomycin with DNA
Authors: Miller Kenneth J. , Lauer Michael , Caloccia William 
Published: May 2005

AbstractAn intercalation model of a complex between DNA and a bleomycin fragment (BLMF), consisting of the bithiazole core and an amide and a protonated amino substituent, is presented. The model, which shows a preference for BLMF with the protonated amine in the minor groove and the acetyl terminal inserted into either the minor and major grooves, respectively, agrees with recently obtained nmr data. The selection of sites I and II, which have the smallest unwinding of the three theoretical intercalation sites, is consistent with the experimental unwinding angle of 12°. The bithiazole moiety stacks between two base pairs of the double helix, while the protonated substituent interacts ionically with the negatively charged regions of the backbone in the minor groove of the DNA. The protonated amine also forms an intramolecular hydrogen bond with the carbonyl oxygen of the amide group on the same substituent. Analysis of drug complexes with different base‐pair sequences reveal four energetically defined groups. The relative energy of the dimer duplex complexes of BLMF correlates with bleomycin's observed base‐sequence specificity upon cleavage. The most stable intercalation complexes form adjacent to the bases cleaved most readily. This correlation suggests a primary connection between intercalation and cleavage. A model cleavage site based on these preliminary theoretical calculations and the experimental observations is proposed. It consists of an intercalation site in a trimer duplex. Pyrimidine(p)purine sequences are the predominant sites for intercalation, and the base adjacent to the site at the (3′) end is cleaved.
Deformational dynamics and nmr relaxation of supercoiled DNAs
Authors: Langowski Jörg , Fujimoto Bryant S. , Wemmer David E. , Benight Albert S. , Drobny Gary , Shibata John H. , Schurr J. Michael 
Published: May 2005

AbstractThe conformation and internal dynamics of supercoiled pUC 8 DNA (2717 bp) are examined by dynamic light scattering, and the magnitude and uniformity of its torsional rigidity are determined using time‐resolved fluorescence polarization anisotropy of intercalated ethidium dye. Neither measurement gives any indication of an appreciably reduced bending or twisting rigidity, or anomalously rapid internal motions. For 31P, in supercoiled pUC 8, we measure T2 = (2.0 ± 0.5) × 10−3 s. This lies within the range of present theoretical estimates obtained using normal rigidities. The proton linewidths observed for pUC 8 and pBR322 (4363 bp) DNAs are within a factor of 2–3 of those similarly estimated assuming ordinary rigidities.According to Bendel, Laub and James [(1982) J. Am. Chem. Soc. 104, 6748–6754], supercoiled pIns36 DNA (7200 bp) exhibits an astonishingly long T2 = 1.17 s for 31P, a slowest rotational relaxation time, τ = 5 × 10−9 s, and an enormously reduced bending rigidity. Serious questions raised by these findings are examined here. The 5 × 10−9 s slowest rotational relaxation time is shown to be physically inadmissible.The nmr relaxation theory developed previously by Allison, Shibata, Wilcoxon, and Schurr [(1982) Biopolymers 21, 729–762], is modified to incorporate new results for deformable filaments, which directly introduce the highly nonexponential tumbling correlation function for reorientation of the local helix axis. Essential requirements for a complete calculation of R2, including estimation of the tumbling correlation function and evaluation of the still unknown DIP/CSA cross‐term, are described in detail. Slow coil‐deformation modes analogous to the Rouse‐Zimm modes of linear DNAs are shown to make an important, if not dominant, contribution to the R2 relaxation rate. Geometrical parameters in the theory are chosen to provide good agreement with literature data for 600‐bp linear DNA. Using this theory and an informed guess for the tumbling correlation function, we find that the 31P‐nmr relaxation data of Bendel et al., if correct, necessarily impose on their DNA one or more extreme properties, such as enormously reduced bending or twisting rigidities. In contrast, the same theory yields reasonable agreement with the T2 reported here for 31P in supercoiled pUC 8 DNA when its rigidities are assumed to be quite ordinary.
Amide I band of IR spectrum and structure of collagen and related polypeptides
Authors: Lazarev Yu. A. , Grishkovsky B. A. , Khromova T. B. 
Published: May 2005

AbstractThe infrared amide I band of collagens (rat and cod skin) and related compounds (polyproline, polyglycine, and polytripeptides) was studied. Assignment of amide I‐band components for polyproline II and polytripeptides (Gly‐Pro‐Pro)n and (Gly‐Pro‐Gly)n in the solid state and water solution was made. Three amide I components observed in the polypeptide spectra were attributed to three different peptide CO groups in each triplet. On the basis of this assignment, the interpretation of the amide I multicomponent structure in collagen and isomorphous oligo‐ and polypeptides was attempted. The ordering of intra‐ and intermolecular hydrogen bonds involving peptide CO groups in collagen and related compounds was discussed.