bluuebunny/crossref_metadata_2025 huggingface dataset:
Reversing‐pulse electric birefringence of poly (γ‐benzyl‐L‐glutamate). II. Field‐strength dependence of steady‐state and decay signals of well‐fractionated samples
Authors: Ueda Kazuyoshi , Mimura Masaharu , Yamaoka Kiwamu
Published: May 2005

The electric field dependence (up to 21 kV/cm) of the steady‐state and decay signals has been examined on the four well‐fractionated samples of poly(γ‐benzyl‐L‐glutamate), [Glu(OBzl)]n, in N,N‐dimethylformamide at 535 nm and 20°C. Together with the data previously obtained from the reversing‐pulse electric birefringence [Ueda, K., Nomura, M. & Yamaoka, K. (1983) Biopolymers 22, 2077–2090], the steady‐state birefringence and field‐free relaxation time were analyzed by a method that takes into account the polydispersity of the chain length. The weight‐average chain length, (lw), permanent dipole moment, (μw), electric polarizability anisotropy, (Δαw), and the length‐independent optical anisotropy factor were evaluated. The axial translation per residue was calculated for the [Glu(OBzl)]n helix, but the uncertainly involved in the weight‐average molecular weights, determined from light scattering by different investigators, makes the determination of the exact conformation of [Glu(OBzl)]n difficult. The contribution of Δαw to electric field orientation was found to be significant, since Δαw was approximately proportional to lw. A linear relationship also exists between μw and lw, when the [Glu(OBzl)]n helix is shorter than about 1200 Å.
Matrix formulation of the transition from a statistical coil to an intramolecular antiparallel β sheet
Authors: Mattice Wayne L. , Scheraga Harold A.
Published: May 2005

A tractible matrix formulation is developed for the formation of intramolecular antiparallel β sheets in a homopolymer chain molecule. The formulation is applicable to chains with a finite degree of polymerization. It can readily be extended to treat specific‐sequence heteropolymers. Individual sheets may contain any number of strands, the number of residues per strand can range upward from two, and there is no artificial constraint linking the numbers of residues in adjacent strands. The weighting scheme utilizes two end‐effect parameters, denoted by τ and δ. The first parameter is associated with each residue that does not have a partner in a proceding strand, and the latter is associated with each β bend. A third parameter, t, is associated with every residue in the sheet. Conditions are described which lead to the formation of different types of sheets: (1) “sheets” comprised of isolated extended strands; (2) cross‐β fibers in which a sheet contains a large number of very short strands; (3) fibers in which a few very long strands run parallel to the fiber axis; (4) sheets comprised of several strands in which the average strand contains five residues. The fourth type of sheet resembles those found in globular proteins. It is formed when τ and δ are both small, with the ratio, τ/δ, being slightly less than one.
Dielectric properties of slightly hydrated collagen: Time–water content superposition analysis
Authors: Sasaki Naoki
Published: May 2005

The frequency dependences of the dielectric constant, ε′, and the loss factor, ε″, in collagen were measured at several water contents from 0.1 to 0.3 g/g collagen over a frequency range of 30 Hz to 100 kHz and at a temperature of 20°C. Remarkable dispersion was observed at the lower frequencies for higher water contents. According to accumulated results on the thermodynamic and structural investigations, the dispersion has some analogy to the surface conduction proposed by B. V. Hamon [(1953) Aust. J. Phys. 6, 304–315]. An empirical relation bewteen ε″ and frequency, f, ε″ ∝︁ fn, where 0 < n < 1, suggests that the dielectric and conductive properties of hydrated collagen are related to carrier jumps between neighboring sites. For the polarization mechanism of this dispersion, we supposed a model of the transfer of protons between absorbed water molecules, and found that the time–water content superposition procedure is applicable to slightly hydrated collagen. The results derived from the superposition procedure show that the water content, ϕ, is related to the conductivity, σ, or the dielectric loss factor by the following equations: σ (ϕ, f) = const. × ϕnm−1f1−n and ε″ (ϕ, f) = const. ϕnmf−n, respectively, where m is a constant independent of ϕ and f. These results agree with that derived by another treatment of the same data. The role of water molecules in the conduction and polarization in slightly hydrated collagen is considered to be not far from that assumed in the model.
Mathematical models of depolymerization of amylose by α‐amylases
Authors: Mazur A. K.
Published: May 2005

For a long time the action pattern of depolymerizing enzymes was explored by examining the distribution of products. Some attempts to interpret the data on the action of α‐amylases on amylose quantitatively have led to conflicting results. In the present work, new mathematical models are developed based on the properties of the most‐probable distribution and on the recently established fact of its partial stability at enzyme depolymerization. Published data for several α‐amylases are reexamined in light of this theoretical analysis. The theory proposed permits us to resolve a controversy concerning the interpretation of experimental data in this field.
Calculation of the thermodynamic quantities of solvation for lysozyme and β‐lactoglobulin a in guanidinium chloride
Authors: Lapanje Savo
Published: May 2005

The thermodynamic quantities of solvation, that is, Gibbs free energy, enthalpy, and entropy for the transfer of lysozyme and β‐lactoglobulin A from water to 6M guanidinium chloride solution, were calculated from the respective contributions of constituent groups. Comparison of the calculated values with the experimental ones reveals satisfactory agreement for lysozyme, whereas for β‐lactoglobulin A, it is semiquantitative. Thus the method of calculation appears to be fundamentally sound. The reasons for the differences in calculated and experimental value are briefly discussed.
Theoretical studies on protein–nucleic acid interactions. II. Hydrogen bonding of amino acid side chains with bases and base pairs of nucleic acids
Authors: Kumar N. Vasant , Govil Girjesh
Published: May 2005

With a view to understanding the role of hydrogen bonds in the recognition of nucleic acids by proteins, hydrogen bonding between the bases and base pairs of nucleic acids and the amino acids (Asn, Gln, Asp and Glu, and charged residues Arg+, Glu−, and Asp−) has been studied by a second‐order perturbation theory. Binding energies have been calculated for all possible configurations involving a pair of hydrogen bonds between the base (or base pair) and the amino acid residue. Our results show that the hydrogen bonding in these cases has a large contribution from electrostatic interaction. In general, the charged amino acids, compared to the uncharged ones, form more stable complexes with bases or base pairs. The hydrogen‐bond energies are an order of magnitude smaller than the Coulombic interaction energies between basic amino acids (Lys+, Arg+, and His+) and the phosphate groups of nucleic acids. The stabilities of the complexes of amino acids Asn, Gln, Asp, and Glu with bases are in the order: G–X > C–X > A–X U–X or T–X, and G · C–X > A · T(U)–X, where X is one of these amino acid residues. It has been shown that Glu− and Asp− can recognize guanine in single‐stranded nucleic acids; Arg+ can recognize G · C base pairs from A · T base pairs in double‐stranded structures.
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

We 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

Phenomena 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

The 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

Suggestive 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

The 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

The 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

Differential 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

Several 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

Self‐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

Light‐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

We 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

Derivatives 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

Two‐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

Recently, 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

The 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

An 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

The 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

The 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.
Vibrational analysis of peptides, polypeptides, and proteins. XXXII. α‐Poly(L‐glutamic acid)
Authors: Sengupta Pradeep K. , Krimm S.
Published: May 2005

The Raman and ir spectra of α‐helical poly(L‐glutamic acid) have been assigned on the basis of a normal mode calculation for this structure. The force field was based on our previously refined main‐chain force constants for α‐poly(L‐alanine) and side‐chain force constants for β‐calcium–poly(L‐glutamate). Despite the identical backbone α‐helical structures, significantly different frequencies are calculated, and observed, in the amide III and backbone stretch regions of α‐poly(L‐glutamic acid), as compared with α‐poly(L‐alanine). This clearly demonstrates the influence of side‐chain structure on mainchain vibrational modes.
Binding of CC‐1065 to poly‐ and oligonucleotides
Authors: Krueger W. C. , Li L. H. , Moscowitz A. , Prairie M. D. , Petzold G. , Swenson D. H.
Published: May 2005

The binding of the antitumor agent CC‐1065 to a variety of poly‐ and oligonucleotides was studied by electronic absorption, CD, and resistance to removal by Sephadex column chromatography. Competitive binding experiments between CC‐1065 and netropsin were carried out with calf‐thymus DNA, poly(dI‐dC) · poly(dI‐dC), poly(dI) · poly(dC), poly(rA) · poly(dT), poly(dA‐ dC) · poly(dG‐dT), and poly(dA) · 2poly(dT). CC‐1065 binds to polynucleotides by three mechanisms. In the first, CC‐1065 binds only weakly, as judged by the induction of zero or very weak CD spectra and low resistance to extraction of drug from the polynucleotide by Sephadex chromatography. In the second and third mechanisms, CC‐1065 binds strongly, as judged by the induction of two distinct, intense CD spectra and high resistance to extraction of drug from the polynucleotide, by Sephadex chromatography in both cases. The species bound by the second mechanism converts to that bound by the third mechanism with varying kinetics, which depend both on the base‐pair sequence and composition of the polynucleotide. Competitive binding experiments with netropsin show that CC‐1065 binds strongly in the minor groove of DNA by the second and third mechanisms of binding. Netropsin can displace CC‐1065 that is bound by the second mechanism but not that bound by the third mechanism. CC‐1065 binds preferentially to B‐form duplex DNA and weakly (by the first binding mechanism) or not at all to RNA, DNA, and RNA–DNA polynucleotides which adopt the A‐form conformation or to single‐strand DNA. This correlation of strong binding of CC‐1065 to B‐form duplex DNA is consistent with x‐ray data, which suggest an anomalous structure for poly(dI) · poly(rC), as compared with poly(rI) · poly(dC) (A‐form) and poly(dI) · poly(dC) (B‐form). The binding data indicate that poly(rA) · poly(dU) takes the B‐form secondary structure like poly(rA) · poly(dT). Triple‐stranded poly(dA) · 2poly(dT) and poly(dA) · 2poly(dU), which are considered to adopt the A‐form conformation, bind CC‐1065 strongly. Netropsin, which also shows a binding preference for B‐form polynucleotides, also binds to poly(dA) · 2poly(dT) and occupies the same binding site as CC‐1065. These binding studies are consistent with results of x‐ray studies, which suggest that A‐form triplex DNA retains some structural features of B‐form DNA that are not present in A‐form duplex DNA; i.e., the axial rise per nucleotide and the base tilt. Triple‐stranded poly(dA) · 2poly(rU) does not bind CC‐1065 strongly but has nearly the same conformation as poly(dA) · 2poly(dT) based on x‐ray analysis. This suggests that the 2′‐OH group of the poly(rU) strands interferes with CC‐1065 binding to this polynucleotide. The same type of interference may occur for other RNA and DNA–RNA polynucleotides that bind CC‐1065 weakly.
Expressions for the interpretation of circular intensity differential scattering of chiral aggregates
Authors: Bustamante Carlos , Maestre Marcos F. , Keller David
Published: May 2005

The derivation of compact expressions of the circular intensity differential scattering (CIDS) of chiral molecules is presented in the first Born approximation of the fields. The expressions derived are valid for a suspension of scattering chiral particles free to adopt any orientation in solution. The connection is established between the preferential scattering cross section for right‐ vs left‐circularly polarized light for a given scattering angle and the geometrical parameters of the molecule. As observed experimentally, the equations predict that the circular differential scattering patterns must show as a function of the scattering angle a series of lobes of alternating sign. In between these lobes, zeros in the differential scattering cross section occur. For the case of two dipole moments arranged in chiral fashion, an expression is derived that shows how the relative arrangement of the dipoles and their separation relative to the wavelength of light control the number and the position of the zeros. A compact expression predicting the CIDS of a sample for very small angles of scattering is derived for a system of helices whose dimensions are small compared with the wavelength of light. Finally, the presence of CIDS in a sample is related to the appearance of anomalous signals in the CD spectrum of chiral systems. Expressions and computations of the magnitudes and sign of the anomalies are presented. The expressions obtained confirm the main features of the experimental CIDS patterns of chiral molecules previously published.
Temperature‐dependent optical rotatory dispersion properties of helical muscle proteins and homopolymers
Authors: Hvidt Søren , Rodgers Michael E. , Harrington William F.
Published: May 2005

Thermally induced helix–coil transitions of myosin rod, light meromyosin, and tropomyosin were studied by optical rotatory dispersion (ORD). Fractional helicity was calculated from both the Moffitt‐Yang parameter, b0, and the corrected mean residue rotation [m′] at 231.4 nm. Between 3 and 30°C, [m′] increases linearly with a slope of 59/°C, whereas b0 is virtually constant, indicating apparently different thermal melting behavior. Poly(L‐lysine) and poly(L‐glutamic acid) in their helical forms and myoglobin also show a nearly linear temperature dependence of [m′]231.4. Muscle proteins in 6M guanidine hydrochloride and the random‐coil forms of the homopolymers exhibit temperature‐dependent values of [m′]231.4 and b0. We conclude from these observations that ORD properties of both α‐helices and random‐coil polypeptides have significant intrinsic temperature dependencies. A new method of estimating fractional helicity as a function of temperature is proposed.
Structural analysis of carboxypeptidase A and its complexes with inhibitors as a basis for modeling enzyme recognition and specificity
Authors: Liebman Michael N. , Venanzi Carol A. , Weinstein Harel
Published: May 2005

A combination of novel methods of macrostructural analysis and theoretical chemistry were applied to study the metalloenzyme carboxypeptidase A and its complexes with two inhibitors—glycyl‐L‐tyrosine and a protein inhibitor isolated from potatoes. The methods of macrostructural analysis applied to the study of the crystal structures of these molecules include structural superposition, distance matrix analysis, and linear distance plot analysis, and the approach is complemented by the examination of computed physicochemical properties, including electrostatic potential surfaces, bulk hydrophobicity, and complementarity of van der Waals surfaces. The structural analysis identified folding domains in carboxypeptidase A that relate to such domains in carboxypeptidase B and are involved in the conformational changes following complexation with the inhibitors. The nature of these conformational changes and their relation to the physicochemical properties suggest their role in determining recognition and reactivity characteristics of the enzyme. The analysis also revealed a distinction between conformational changes in the secondary and tertiary structure of the protein that provides insight into the structure–function relationship in carboxypeptidase. Notably, some inhibitor‐induced changes in structure occur in regions in which the interacting molecules are not in contact, while some of the contact regions, such as the active site, incur only minor perturbation. The analysis reveals the interrelation between the enzyme–ligand interaction and the structural perturbation outside the active site, thus illuminating one aspect of the link between the structural organization of the protein and its function.
Low‐temperature glass transition in proteins
Authors: Morozov V. N. , Gevorkian S. G.
Published: May 2005

The viscoelastic properties of solid samples (crystals, amorphous films) of hen egg white lysozyme, bovine serum albumin, and sperm whale myoglobin were studied in the temperature range of 100–300 K at different hydration levels. Decreasing the temperature was shown to cause a steplike increase in the Young's modulus of highly hydrated protein samples (with water content exceeding 0.3 g/g dry weight of protein) in the temperature range of 237–251 K, followed by a large increase in the modulus in the broad temperature interval of 240–130 K, which we refer to as a mechanical glass transition.

Soaking the samples in 50% glycerol solution completely removed the steplike transition without significantly affecting the glass transition. The apparent activation energy determined from the frequency dependence of the glass‐transition temperature was found to be 18 kcal/mol for wet lysozyme crystals. Lowering the humidity causes both the change of the Young's modulus in response to the transition and the activation energy to decrease. The thermal expansion coefficient of amorphous protein films also indicates the glass transition at 150–170 K. The data presented suggest that the glass transition in hydrated samples is located in the surface layer of proteins and related to the immobilization of the protein groups and strongly bound water.
Poly(Pro‐Nle‐Gly): Can an amorphus polypeptide take up a supramolecular elastinlike structure?
Authors: Tamburro A. M. , Gordini D. Daga
Published: May 2005

Poly(Pro‐Nle‐Gly) was found to have a CD spectrum characteristic of a random polypeptide and an x‐ray powder pattern that does not reveal any regular secondary structure. In its electron micrograph, however, filaments and fibers were seen. This is a random polymer with supramolecular structure. It suggests that the supramolecular structure seen in electron micrographs of elastin preparations and related polypeptides does not necessarily imply an ordered structure at the molecular level.
Mechanism of intercalation: Ion effects on the equilibrium and kinetic constants for the interaction of propidium and ethidium with DNA
Authors: Wilson W. David , Krishnamoorthy C. R. , Wang Yueh‐Hwa , Smith J. C.
Published: May 2005

The effects of sodium ion concentration on the binding isotherms and association and dissociation reaction rates for the interaction of the closely related intercalating dication, propidium, and the monocation, ethidium, with DNA have been determined by spectrophotometric binding and stopped‐flow kinetics methods. The binding of propidium to DNA is best described by a neighbor‐exclusion binding isotherm (two base pairs per binding site) with negative ligand cooperatively on binding. The cooperativity parameter is fairly independent of salt concentration, while the log of the observed equilibrium binding constant varies with −log [Na+], with a slope of two for the propidium–DNA interaction. These effects of the sodium ion on the equilibrium binding of propidium with DNA are similar to those previously described for the dication, quinacrine [Wilson, W.D. & Lopp, I.G. (1979) Biopolymers, 18, 3025–3041]. Ethidium behaves, as a function of salt, as a monocation binding to DNA with neighbor exclusion and without ligand cooperativity. Equations are derived for two limiting kinetics models for intercalation involving binding of the intercalator to a preequilibrium, open state of DNA (model I) or binding form a preequilibrium externally associated state of the intercalator with DNA (model II). Model II gives the best fit to all of the kinetic results if it is assumed that the initial external interaction of the intercalator with DNA is similar to the exchange of free and condensed simple counterions. Intercalation then occurs from this state following an opening transition of the base pairs of the double helix. This model predicts a larger effect of salt concentration on the association than on the dissociation reaction, and that is what is experimentally observed. The intercalation conformational change makes a significant contribution to the ionic effects for both the equilibrium binding and the kinetic constants. The dissociation results and the association reaction results under pseudo‐first‐order conditions could be fit with single exponential curves under the conditions of our experiments.
Imino 1H‐ and 31P‐nmr analysis of the interaction of propidium and ethidium with DNA
Authors: Chandrasekaran Subramanian , Jones Robert L. , Wilson W. David
Published: May 2005

At low temperature and low salt concentration, both imino proton and 31p‐nmr spectra of DNA complexes with the intercalators ethidium and propidium are in the slow‐exchange region. Increasing temperature and/or increasing salt concentration results in an increase in the site exchange rate. Ring‐current effects from the intercalated phenanthridinium ring of ethidium and propidium cause upfield shifts of the imino protons of A · T and G · C base pairs, which are quite similar for the two intercalators. The limiting induced chemical shifts for propidium and ethidium at saturation of DNA binding sites are approximately 0.9 ppm for A · T and 1.1 ppm for G · C base pairs. The similarity of the shifts for ethidium and propidium, in both the slow‐ and fast‐exchange regions over the entire titration of DNA, shows that a binding model for propidium with neighbor‐exclusion binding and negative ligand cooperativity is correct. The fact that a unique chemical shift is obtained for imino protons at intercalated sites over the entire titration and that no unshifted imino proton peaks remain at saturation binding of ethidium and propidium supports a neighbor‐exclusion binding model with intercalators bound at alternating sites rather than in clusters on the double helix. Addition of ethidium and propidium to DNA results in downfield shifts in 31P‐nmr spectra. At saturation ratios of intercalator to DNA base pairs in the titration, a downfield shoulder (approximately −2.7 ppm) is apparent, which accounts for approximately 15% of the spectral area. The main peak is at −3.9 to −4.0 ppm relative to −4.35 in uncomplexed DNA. The simplest neighbor‐binding model predicts a downfield peak with approximately 50% of the spectral area and an upfield peak, near the chemical shift for uncomplexed DNA, with 50% of the area. This is definitely not the case with these intercalators. The observed chemical shifts and areas for the DNA complexes can be explained by models, for example, that involve spreading the intercalation‐induced unwinding of the double helix over several base pairs and/or a DNA sequence‐ and conformation‐dependent heterogeneity in intercalation‐induced chemical shifts and resulting exchange rates.
Short electric‐field pulses convert DNA from “condensed” to “free” conformation
Authors: Porschke Dietmar
Published: May 2005

Electric‐field pulses of e.g. 20 kV/cm and 100 μs induce a strong decrease in the scattered light intensity of DNA condensed by spermine. Analysis of this effect demonstrates that the decrease of the scattered light intensity results from decondensation of DNA. The decondensation reaction requires an electric‐field strength exceeding a threshold value. Complete decondensation can be achieved at field strength that are only slightly higher than the threshold value. The decondensation process is strongly accelerated at high electric‐field strengths. At 30 kV/cm, the decondensation time constant is ∼8 μs, corresponding to an acceleation factor of 105 relative to the field‐free decondensation reaction. The dependence of the time constants on the electric‐field strength suggests that the field‐induced decondensation is due to a dissociation field effect. The condensation process observed after electric‐field pulses at low concentrations of DNA and spermine shows a characteristic induction period, which strongly depends on the spermine concentration. This induction period reflects the time required for the binding of spermine to DNA, until the degree of binding is sufficiently high for the condensation reaction. The fast dissociation of condensed DNA by electric‐field pulses together with a relatively long lifetime of the free DNA results in a reaction cycle resembling a hysteresis loop.