bluuebunny/crossref_metadata_2025 huggingface dataset:
Rotational relaxation of macromolecules determined by dynamic light scattering. II. Temperature dependence for DNA
Authors: Schmitz Kenneth S. , Schurr J. Michael
Published: December 2004

Correlation functions have been determined for the fluctuating intensity of the depolarized component of forward‐scattered laser light from solutions of DNA. The molecular correlation function of calf thymus DNA (mol wt ∼15 × 106) appears to exhibit a longest relaxation time (τ25,w, ∼ 18 msec) close to what one would predict from the flowdichroism measurements of Callis and Davidson and, in addition, manifests a spectrum of faster times down to tenths of milliseconds. Furthermore, a major fraction of the amplitude of fluctuations in the angular distribution of segment axes is relaxed on a very much shorter time scale (of the order of 20 microseconds) that appears to be relatively insensitive to molecular weight of the DNA, or to near‐melting temperatures.

The temperature profile of the longest relaxation time has been obtained and found to exhibit a peculiar spike near Tm, which, together with the absence of a corresponding spike in the (high shear) viscosity, has been interpreted as indicative of an increase in the molecular weight of the DNA in a narrow temperature region near Tm. Correlation functions for polarized light scattered at finite angles were obtained in an attempt to determine the temperature dependence of the translational diffusion coefficient. Although the data contain an extremely slow component that does not admit a simple interpretation, there is some indication of a decrease in the translational diffusion coefficient near Tm, thus supporting the notion of an aggregation occurring near Tm. Finally, a “counterion escape” mechanisn is proposed for the apparent aggregation.
On the interaction of lithium salts with model amides
Authors: Balasubramanian D. , Shaikh Rashid
Published: December 2004

Results of a study of the interaction of alkali metal salts on model aliphatic amides are reported. Lithium salts appear to interact more strongly with amides than those of other alkali metals. Spectroscopic investigations suggest that Li+ ion binds to the amide group at the carbonyl oxygen, causing a change in the spectroscopic properties and the geometry of the amide. Such binding of ions to amide groups may be of importance when one studies the spectral and conformational changes of polypeptides and proteins in high salt media.
The contribution of proton fluctuation to dielectric relaxation in protein solutions
Authors: South G. P. , Grant E. H.
Published: December 2004

Equations are derived which account for the effect of an applied electric field on the fluctuation of protons associated with a macromolecule. The contribution of this proton polarization to the complex permittivity of the macromolecules is evaluated in terms of its effect on both the dispersion due to proton fluctuation and the dispersion caused by dipolar rotation. An expression for the fluctuation correlation time τiδ is derived in terms of the mean lifetimes of the ionised and unionised state τ0 and τ+. If τiδ is very much less than the dipolar correlation time τi, the fluctuation dispersion will occur at much higher frequencies than the dispersion due to orientation polarization; hence the dispersions will be well separated. If τiδ » τi the two regions would overlap and would be indistinguishable as separate entities. At present insufficient data are available to test rigorously these conclusions but the potentialities of the theory in relation to small globular proteins is shown.
Occurrence of β‐chain conformation in poly‐γ‐methyl glutamate membranes
Authors: Nakajima Akio , Fujiwara Takashi , Hayashi Toshio , Kaji Keisuke
Published: December 2004

Molecular chain conformations of poly‐γ‐methyl‐L‐glutamate, poly‐γ‐methyl‐D‐glutamate, and poly‐γ‐methyl‐D,L‐glutamate in membranes prepared by using mainly trifluoroacetic acid and formic acid as solvents were investigated by infrared, X‐ray diffraction, and optical rotatory dispersion measurements. It was pointed that these polymers exist in the α‐helix form in membranes cast from trifluoroacetic acid solutions, but in the β‐chain form in membrances swollen in formic acid. The β‐chain structure was also observed in crystals precipitated from dilute solutions including formic acid. The formation of the β‐chain structure was discussed.
Structure of guanosine‐3′,5′‐cytidine monophosphate. I. Semi‐empirical potential energy calculations and model‐building
Authors: Stellman S. D. , Hingerty B. , Broyde S. B. , Subramanian E. , Sato T. , Langridge R.
Published: December 2004

The conformation and packing scheme for guanosine‐3′, 5′‐cytidine monophosphate, GpC, were computed by minimizing the classical potential energy. The lowest energy conformation of the isolated molecule had dihedral angles in the range of helical RNA's and the sugar pucker was C3′ endo. This was used as the starting conformation in a packing search over orientation space, the dihedral angles being flexible in this step also. The packing search was restricted by constraints from our x‐ray data, namely, (1) the dimensions of the monoclinic unit cell and its pseudo‐C2 symmetry (the real space group is P21), (2) the location of the phosphorous atom, and (3) the orientation of the bases. In addition, a geometric function was devised to impose Watson‐Crick base pairing. Thus, a trial structure could be sought without explicit inclusion of intermolecular potentials. An interactive computer graphics system was used for visualizing the calculated structures.

The packing searches yielded two lowest energy schemes in which the molecules had the same conformation (similar to double‐helical RNA) but different orientations within the unit cell. One of these was refined by standard x‐ray methods to a discrepancy index of 14.4% in the C2 pseudocell. This served as the starting structure for the subsequent refinement in the real P21 cell.5
Conformational analysis of a cyclic nucleotide: 3′−5′‐Adenosine monophosphate. A study based on the extended Hückel theory
Authors: Lespinasse Jean Noël , Vasilescu Dane
Published: December 2004

The extended Hückel theory (EHT) was used as a quantum mechanical approach for the determination of the best conformation of cyclic AMP. Both geometrical and quantum mechanical studies were necessary to ascertain the configuration of the sugar ring and phosphate ring. This was due to the fact that no crystallographic data are known for the ribose phosphate part of this nucleotide.

The calculations have shown that the sugar ring takes a 3T4 (C3′‐endo–C4′‐exo) configuration while the phosphate ring exhibits a chair form. Once the geometry of the rigid ribose–phosphate block is resolved, the problem of the determination of the best conformation for cyclic AMP is reduced to the determination of the position of the adenine base with respect to this ribose phosphate part.

The study of the rotation of the adenine base around the glycosidic bond C1′–N9 revealed that the two conformations anti (χ = 30°) and syn (ξ = 210°) are possible with an energy difference of only 1 kcal × mole−1. This theoretical calculation is in good agreement with experimental data.
Calorimetric investigation of the helix–coil conversion of polyuridylic acid
Authors: Heinecke Marion , Bode Diedrich , Schernau Ulrich
Published: December 2004

The heats of the conformational conversion ΔHc of polyuridylic acid (polyU) in the presence of various cations were determined using a differential scanning microcalorimeter and an isothermal mixing calorimeter. The first method yields a value of ΔHc = 5.2 kcal/mol of base pairs, the second one a value of ΔHc = 6.4 kcal/mol of base pairs. Knowing ΔHc and the maximal slope of the degree of conversion, which was determined from the temperature dependence of the absorbance of polyU solutions at 260 nm, we were able to evaluate the parameter of cooperativity σ. From the relation σ = e the stacking free energy ΔFstack could be calculated. Dividing the apparent enthalpy of conversion by the calorimetrically measured enthalpy yields the cooperative length N0 of one helical segment at the midpoint of conversion. The results show that the type of the cation has no influence on the magnitude of ΔHc, whereas the cooperativity of polyU is influenced by the various cations.
Raman spectra of copoly(D,L‐alanines)
Authors: Itoh Koichi , Hinomoto Tetsu , Shimanouchi Takehiko
Published: December 2004

Raman spectra in the region 1000–150 cm−1 were measured for copoly(D,L‐alanines) with the D‐residue contents, 3, 7, 10, and 20%, and compared with the spectrum of the α‐helical poly‐L‐alanine. The 532‐ and 378‐cm−1 peaks were assigned to the L‐residues with a right‐handed α‐helix‐like local conformation or to the D‐residues with a left‐handed α‐helix‐like local conformation. From the intensity of the latter peak the contents of these local conformations were estimated as a function of the D‐residue contents for the copolymers. The 264‐cm−1 peak, which has been assigned to the breathing vibration of the α‐helical poly‐L‐alanine, shows a marked decrease in its intensity upon the introduction of the D residues. This result suggests that the overall deformation vibration of the α‐helix arises from rather long sequences of the L‐ and D‐alanine residues with the α‐helical conformation and that the intensity of this vibration depends on the content of these sequences in the copolymers.
The infrared absorption spectrum of dextran and its bound water
Authors: Heyn Anton N. J.
Published: December 2004

Almost complete assignments are presented for the infrared absorption spectrum of dextran. These assignments were made by normal group analysis of the subaltern bands within the broad composite bands constituting the spectrum, and by examining the conclusions in the light of normal coordinate analysis of the repeat unit of this polymer.

The α‐1,6‐glycosidic linkages in dextran have been found to result in lower intermolecular hydrogen bonding than in other glucans and this explains many features of the spectrum, including the occurrence of a variety of bands originating from different types of bound water. Particularly, a very strong band at 800 cm−1 corresponding to the libration vibration of ice, which occurs in the spectrum of freeze‐dried dextran, is of great interest and has been ascribed to “organized” water.
The effect of thymine dimers on DNA: DNA hybridization
Authors: Kahn Michael
Published: December 2004

DNA from bacteriophage T7 was irradiated at long ultraviolet wavelengths in the presence of silver ions. Such treatment leads to selective production of thymine: thymine dimers in DNA. The DNA was melted and the renaturation rate was determined as a function of thymine dimer content and renaturation temperature. Under “normal” hybridization conditions little change in the renaturation rate was observed even when 30% of the thymine was dimerized. This result is consistent with the view that up to a 15% change in the primary sequence of DNA dose not appreciably change the renaturation rate.
Interactions between purine derivatives: Electronic spectral studies. II. Excition interactions in the dimer of 6‐methylpurine in aqueous solution
Authors: Kelly G. R. , Kurucsev T.
Published: December 2004

From a study of the concentration dependence of the ultraviolet absorption spectra of aqueous solutions of 6‐methylpurine, the spectra of monomeric and dimeric species have been derived. The dichroic spectrum of 6‐methylpurine in stretched poly(vinyl alcohol) films has been determined. The absorption envelope of 6‐methylpurine up to 44,000 cm−1 appears to include a low‐intensity nitrogen (π*,n) transition at the low wavenumber tail and two additional electronic transitions of dominant intensities. Both the experimental dichroic ratios and theoretical calculations suggest that the letter two transitions are in‐plane (π*,π) types. Analysis of the dimer species spectrum in terms of exciton interactions between molecules in “sandwich” conformation has been carried out. The interaction between the moments of the lowest energy (π*,π) transitions of the molecule in the dimer seems to result in transfer rates of energy of the order of 1013 sec−1 between the two molecules.
A circular dichroism study of the primary structures of three crab satellite DNA's rich in A:T base pairs
Authors: Gray Donald M. , Skinner Dorothy M.
Published: December 2004

We have measured the circular dichroism spectra and have obtained melting curves for samples of purified satellite DNA's from three species of crab, Cancer borealis, Gecarcinus lateralis, and Callinectes sapidus. Although all three satellite DNA's have the same density in neutral CsCl, their circular dichroism spectra and melting and reassociation characteristics are different, as are other properties of these DNA's. The circular dichroism spectra are analyzed to give estimates of nearest‐neighbor frequencies. We estimate that about 90% of the Cancer borealis satellite DNA and over 80% of the Gecarcinus lateralis satellite DNA consist of d(AT)n:d(AT)n sequences, while the serially repeating unit of the Callinectes sapidus satellite DNA may not contain any extended d(AT)n:d(AT)n sequences. The results from the circular dichroism spectra for the Cancer borealis, Gecarcinus lateralis, and the Callinectes sapidus satellite DNA's are in agreement with base composition analyses, which give 2.4, 8, and 25% G+C, respectively, for these DNA's.
A proposed solution for the determination of the ionization constants of sets of ionizing groups in proteins
Authors: Marini Mario A. , Martin Charles J. , Berger Robert L. , Forlani Luciano
Published: December 2004

A mixture of acids with known pK′ and in a known concentration was dissolved to simulate the ionic character of hemoglobin. The titration curves of the mixture were obtained in water and 3.6 M KCl at 20°C. These curves were subjected to analysis by a reiterative curve‐fitting procedure to determine if one could evaluate both the group ionization constants and the numbers of groups. This approach was successful in that the calculated parameters were within the experimental error encountered in obtaining these constants on each of the model compounds. However, analysis for the electrostatic interaction parameter w indicated that there was a possible effect on the ionization of formic acid, pyridine, imidazole, and the α‐amino group of glycylglycine in water and on imidazole and the α‐amino group of glycylglycine in 3.6 M KCl.
An electron microscopic method for studying nucleic acid–protein complexes. Visualization of RNA polymerase bound to the DNA of bacteriophages T7 and T3
Authors: Koller Th. , Sogo J. M. , Bujard H.
Published: December 2004

Double‐stranded DNA can be readily adsorbed on mica or directly on carbon coated grids from the surface of solutions containing ethidium bromide, actinomine, or propidium diiodide. The DNA molecules are unfolded, well separated, and show a length distribution similar to molecules prepared by protein monolayer techniques.

Since the intercalating dyes tested do not lead to an increased apparent diameter of the nucleic acid the method is useful for the study of nucleic acid–protein complexes. As a model, the binding of E. coli RNA polymerase to phage T7 and T3 DNA was examined under different conditions. The enzyme can easily be identified and its position along the DNA molecule can be mapped.
Syntheses and conformational studies of poly(Nε‐methyl‐L‐lysine), poly(Nδ‐methyl‐L‐ornithine), poly(Nδ‐ethyl‐L‐ornithine), and their carbobenzoxy derivatives
Authors: Yamamoto Hiroyuki , Yang Jen Tsi
Published: December 2004

The helix–coil transitions of poly(Nε‐methyl, Nε‐carbobenzoxy‐L‐lysine), poly(Nδ‐methyl, Nδ‐carbobenzoxy‐L‐ornithine), and poly(Nδ‐ethyl, Nδ‐carbobenzoxy‐L‐ornithine) in chloroform–dichloroacetic acid and their corresponding decarbobenzoxylated polypeptides in alkaline solutions were followed by optical rotation measurements. The introduction of a methyl or an ethyl group to the side chains of the carbobenzoxy derivatives of poly(L‐lysine) and poly(L‐ornithine) appeared to weaken the helical conformation at 25°C. The thermodynamic quantities of the three water‐soluble polypeptides were calculated from the data on potentiometric titrations at several temperatures. For uncharged coil‐to‐helix transition, ΔH = −370 cal/mol and ΔS = −1.1 eu/mol for poly(Nε‐methyl‐L‐lysine), and ΔH = −540 cal/mol and ΔS = −1.6 eu/mol for poly(Nδ‐ethyl‐L‐ornithine) (all on molar residue basis). The absolute values of ΔH and ΔS dropped in the region of pH‐induced transition and eventually both quantities became positive. The initiation factor σ was about 2 × 10−3, which was essentially independent of temperature. For poly(Nδ‐methyl‐L‐ornithine) the coil‐to‐helix transition was not complete even when the polymer was uncharged at high pH.
Synthesis and characterization of poly(LysAla3)
Authors: Wender D. B. , Treiber L. R. , Bensusan H. B. , Walton A. G.
Published: December 2004

The synthesis and characterization of poly(LysAla3) are described. The polytetrapeptide is a model for short sequences found in proelastin, and is presumably involved in desmosine or isodesmosine cross‐link formation in the native protein. Poly(LysAla3) is found to possess a mixture of conformations in aqueous solution dependent on molecular weight and pH. Low‐molecular‐weight (ca. 3000) material appears to be a mixture of random and extended helix at neutral pH. However, as the molecular weight is increased an increasing amount of α‐helix is observed rising to >50% for mol wt = 21,000. The α‐helical chain segments are thermally stable, melting to a mixture of extended and random forms at Tm = 25°C. High pH (10.5) promotes further α‐helix formation but at pH >11.0 the polypeptide becomes insoluble. The inference is that short chain segments of the peptide in elastin are unlikely to be α‐helical in the equilibrium state but may fluctuate through such a conformation.
The structure of native cellulose
Authors: Gardner K. H. , Blackwell J.
Published: December 2004

Native cellulose has been shown to consist of a crystalline array of parallel chains, based on the X‐ray diffraction data for specimens from the sea alga Valonia ventricosa. The unit cell is monoclinic with dimensions a = 16.34 Å, b = 15.72 Å, c = 10.38 Å (fiber axis), and β = 97.0°. The space group is P21 and the cell contains disaccharide segments of eight chains. Models containing chains with the same sense (parallel) or alternating sense (antiparallel) were refined against the intensity data using rigidbody least squares procedures. The results show a preference for a parallel chain structure with specific chain polarity with respect to the c axis. The refinement places the CH2OH side chains approximately 20′ from the so‐called tg conformation, with a result that an 02′H…06 intramolecular bond is formed. The structure also contains an 03H…05′ intramolecular bond and an 06H…03 intermolecular bond along the a axis. All these bonds lie in the 020 planes, and the structure is an array of hydrogen‐bonded sheets. A major consequence of this work is that regular chain folding can be ruled out and cellulose is seen as extended chain polymer single crystals.
Two proposed general configurations for bacterial cell wall peptidoglycans shown by space‐filling molecular models
Authors: Oldmixon E. H. , Glauser S. , Higgins M. L.
Published: December 2004

Bacterial cell wall peptidoglycans are built from unbranched β‐(1 → 4)‐linked glycan chains composed of alternately repeating units of N‐acetylglucosamine and N‐acetylmuramic acid residues, with peptide side chains attached to the muramic acid residues. The glycan chains are interconnected by peptide bonds formed between the peptide side chains. Through the use of three‐dimensional molecular models, two configurations of the glycan strands and the peptide side chains are described, which by their constancy of form reflect the fundamental constancies of the covalent structures. Each of these two models will accommodate any chemical modification that has been observed in bacteria without change in the configuration of the peptide backbone. Some alterations in the chemical structure, which have been sought in bacteria, but not found, would not be tolerated by the models. In these models, glycan strands are parallel, with their lengths and widths predominantly in the plane of the cell wall. The cross‐bridging portions of the peptide side chains are at right angles to the glycan strand, in a separate, parallel plane. A compact model is presented in which the peptide side chain is closely appressed to the glycan strand and is stabilized by three hydrogen bonds per disaccharide–peptide subunit. In a second model, the peptide side chain is raised away from the glycan strand in an entirely extended configuration. The compact and extended forms are interconvertible. The thickness of a sheet of peptidoglycan would be from 10.6 to 11.1 Å for the compact model, and 19.1 Å for the extended model.
Studies on deoxyribonucleoprotein structure. Sedimentation behaviour
Authors: Osipova T. N. , Vorob'ev V. I. , Sibileva M. A. , Frisman E. V.
Published: December 2004

The sedimentation behaviour of DNP samples from calf thymus partially depleted of protein was studied. Upon transition from DNP to DNA a twofold decrease of the sedimentation constant, S02 0,W was observed. The translational friction coefficient f of DNP calculated from S02 0,W does not change at deproteinization, whereas the intrinsic viscosity [η] increases notably. Such difference in the dependence of f and [η] on the protein content is interpreted in terms of the theories for semirigid coils. The application of different models of DNP structure for the description of the hydrodynamic behaviour of DNP is considered. A model of the semirigid coil formed by a DNP chain partly folded into the superhelix seems to be most preferable.
DNA conformation in N,N‐dimethyl formamide–H2O solutions
Authors: Bressan G. , Rampone R. , Bianchi E. , Ciferri A.
Published: December 2004

Optical density, viscosity, and light scattering measurements for calf thymus DNA in water–N,N dimethyl formamide (DMF) solutions are presented. DMF content varied between 0 and 60% (v/v) and DNA molecular weight varied between 15 × 106 and 0.5 × 106. Complementary measurements of the solubility of adenine, thymine, guanine, and cytosine in H2O–DMF mixtures are presented. The denaturation temperature of DNA, manifested by about a 35% increase of optical density, is gradually depressed by increasing DMF content. However, a significant increase of OD occurs even before (and even after) the denaturation point, when DMF content is increased isothermally. The intrinsic viscosity also exhibits a large decrease when DMF content is increased both before and after the denaturation point. Light scattering data for high‐molecular‐weight DNA in the predenaturation range indicate a decrease of the mean‐square radius and a constant molecular weight on increasing DMF content. The results, interpreted in terms of the wormlike chain of Kratky and Porod, indicate a large decrease of the persistence length of DNA. For low‐molecular‐weight DNA, radius and molecular weight increase with DMF content, indicating intermolecular aggregation. The formation of compact structures of native DNA is discussed in terms of an increased solubility of uncharged bases, and a decreased solubility of phosphate and deoxyribose groups, when a less polar environment is provided by the addition of DMF.
The interpretation of oligonucleotide maps. A theoretical study of nucleic acid digests with special reference to repeated diverged sequences
Authors: Slack Jonathan M. W.
Published: December 2004

Oligonucleotide mixtures produced by the digestion of RNA by specific nucleases can be defined in terms of isostichs (sets of common chain length), compositional isomers, and sequence isomers. Equations are derived to express the distribution of radioactivity on the isostich length, the distribution of compositional isomers on the isostich length, and the distribution of compositional isomers on the proportion of total radioactivity (“intensity”). It is shown how the properties of a “fingerprint” may be calculated from first principles, and conversely how the complexity of a sequence may be estimated from its fingerprint.

The equations are tested by means of computer simulations of RNA digestions and their range of applicability is determined.

The three distributions are used to analyze the digests of repetitious sequences. It is shown how the parameters of a diverged sequence family can, in a favorable case, be deduced from its fingerprint.
Buoyant densities of natural and synthetic DNA's in CsCl and Cs2SO4 considered as sequence‐dependent properties
Authors: Gray Donald M. , Gray Carla W. , Ratliff Robert L. , Smith David A.
Published: December 2004

The buoyant densities of natural and synthetic DNA's can be accurately interrelated if second‐neighbor influences are taken into account. We derive the following expressions, based partly on the buoyant densities of six synthetic DNA's, for the buoyant densities ρ (g/cm3) of DNA's having random sequences. In CsCl,

and in Cs2SO4,

.
In these equations, HG is the mole fraction of G : C base pairs in the DNA and the buoyant densities are calculated relative to densities for E. coli DNA of 1.703 and 1.426 (g/cm3) in CsCl and Cs2SO4, respectively.
Molecular weight and shape of the phycocyanin hexamer
Authors: Kato Masanori , Lee Wylie I. , Eichinger B. E. , Schurr J. M.
Published: December 2004

The hexamer of phycocyanin from Phormidium luridum has been isolated and purified by ammonium sulfate fractionation and gel chromatography. The protein is characterized by the sedimentation constant S°20, w = 10.2S, the diffusion coefficient D20, w = 4.73 × 10−7 cm2/sec, and intrinsic viscosity [η] = 3.89 ml/g. The molecular weight of the aggregate is 209,000. The shape and dimensions of the hexamer are discussed in terms of a model consisting of subunits arranged with C6 symmetry. The monomers, assumed to be spherical, are found to have a radius of 22 Å, and the diameter across the hexamer is 132 Å. The latter figure agrees closely with dimensions observed in electron micrographs.
Conformational change of the triple‐helical structure. III. Stabilizing forces in the triple helix
Authors: Sutoh Kazuo , Noda Haruhiko
Published: December 2004

The analysis of thermal melting curves of (PPG)n (n = 10, 12, 14, and 15) and (PPG)n(APG)m (PPG)n (2n + m = 15; m = 1, 3, and 5) revealed that the enthalpy and entropy changes accompanying the transition from the random coil to the triple helix are −2500 cal and −6.3 e.u. per one mole of the tripeptide of the form of Pro‐Pro‐Gly, and −3100 cal and −11.2 e.u. per one mole of the tripeptide of the form of Ala‐Pro‐Gly.

The thermal instability of the triple helix composed of Ala‐Pro‐Gly sequences, compared to the helix of Pro‐Pro‐Gly sequences, is due to the larger entropy change of Ala‐Pro‐Gly (−11.2 e.u.) compared to that of Pro‐Pro‐Gly (−6.3 e.u.), not from the difference in the enthalpy change.

The difference in the enthalpy change between Pro‐Pro‐Gly and Ala‐Pro‐Gly arises from the hydrophobic bond between two pyrrolidine rings of proline residues formed in the triple helix. Since the enthalpy change for the formation of hydrophobic bonds is positive, it is also concluded that only one hydrogen bond is formed in a tripeptide unit, regardless of the amino acid sequence. The enthalpy change for the formation of this hydrogen bond is −3100 cal/mol, and that of the hydrophobic bond between two pyrrolidine rings is +600 cal/mol.
Effect of agents affecting water structure on the uptake of saccharides by agar and polyacrylamide gels
Authors: Sigler K.
Published: December 2004

Uptake of D‐xylose, D‐glucose, lactose, and dextran 10 was studied in 3% and 12.5% polyacrylamide gels in the presence of 2 M LiCl, 2 M NaCl, 2 M KCl, 2 M RbCl, 2 M CsCl, 2 M MgCl2, 2 M CaCl2, 1 M NaF, 1 M NaI, 0.5 M guanidine thiocyanate, 0.5 M guanidine sulphate, and 0.5 M N,N′‐diethylurea. With the exception of N,N′‐diethylurea and, in some cases, LiCl, which had an accelerating effect, the compounds retarded considerably the uptake of saccharides by agar gel but had only a slight effect in polyacrylamide. The nature of the gel is thus of primary importance in interactions of this type. According to the magnitude of their effect on saccharide uptake, the salts used were arranged into several series. An attempt was made to correlate the effects of individual salts with their hydration properties. The strongest effect was found to be exerted by KCl, RbCl, and CsCl, i.e., by chlorides of cations possessing negative hydration shells.
A method for measuring sedimentation and diffusion of macromolecules in capillary tubes by total intensity and quasi‐elastic light‐scattering techniques
Authors: Loewenstein M. A. , Birnboim Meyer H.
Published: December 2004

Light scattered from a macromolecular solution in a capillary tube is used to determine both the sedimentation and translational diffusion coefficients. The capillary tube is spun in a preparative centrifuge, removed, and placed in a light‐scattering photometer equipped with a scanning mechanism. The intensity distribution of scattered light along the tube represents the concentration profile in the tube and provides the measure of boundary migration. The sedimentation coefficient is determined from this measure and the applied centrifugal field. The diffusion coefficient is obtained from a time‐autocorrelation analysis of fluctuations in intensity of light scattered from any fixed point of the profile. These coefficients were obtained for two monodisperse systems, R17 bacteriophage and 28s ribosomal rat liver RNA. The molecular weights obtained from ratios of these coefficients are in good agreement with literature values. In the sedimentation analysis, deviations from linearity between boundary displacement and applied field were found to be less than 1%. This precision confirms that the boundary is stable for the capillary geometry even in the absence of a preformed density gradient. The sedimentation coefficients of identical samples were also measured with the Spinco Model E analytical ultracentrifuge; results of the two methods agree to within 4%.

As a consequence of the capillary tube geometry and light‐scattering detection, sedimentation coefficients can be obtained from sample volumes of less than 100 μl. This detection techniques is thus far demonstrated to be at least an order of magnitude more sensitive than Schlieren optics, thereby useful when uv absorption is not applicable. For diffusion measurements there are also several inherent advantages. The diffusion coefficient is obtained from the identical sample, and scanning provides the capability to measure D from various parts of the sedimentation profiles and thereby directly explore concentration dependence, homogeneity, and integrity of the sample. The capillary tube with a layer of silicone oil over the sample and centrifugation provides an effective method to cleanse the solution and trap all dust.
Fluorescence correlation spectroscopy and nonideal solutions
Authors: Phillies George D. J.
Published: December 2004

The information that may be obtained from a fluorescence correlation spectroscopic study of a nonideal solution is considered. If all of the macromolecules in a two‐component solution are fluorescently labeled, the mutual diffusion coefficient will be measured. If only a few of the macromolecules in a solution are fluorescently labeled, the tracer diffusion coefficient will be obtained. Two nonideal systems that probably may usefully be studied with fluorescence correlation spectroscopy are proposed. The application of fluorescence correlation spectroscopy to studies of lateral diffusion in biological membranes is discussed; the form of the contribution to the fluorescence correlation spectrum of bulk motion within a membrane is noted.
Optical property of bovine plasma albumin between 2 and 82 eV
Authors: Inagaki T. , Hamm R. N. , Arakawa E. T. , Birkhoff R. D.
Published: December 2004

The optical constants of bovine plasma albumin in the form of a dry solid film have been determined in the 2–82 eV region of photon energy. The extinction coefficient k was obtained by transmission measurements on thin films on a calcium fluoride substrate and on ultrathin films of polystyrene supported by mesh screen. The refractive index n was determined by a Kramers–Kronig analysis using the measured values of k. The complex dielectric function ε and the energy‐loss function −Im(1/ε) for charged particles were derived from the data of n and k. The result for k exhibit, in addition to the well‐known absorptions at 4.4, 5.5, and 6.4 eV, a small peak at 7.6 eV, a shoulder around 9.7 eV, and a strong peak at 14.0 eV. A prominent peak at 22.7 eV in the energy‐loss function exhibits a large degree of collective nature.
Effects of metal ions on the structure and spectra of the peptide group
Authors: Balasubramanian D. , Misra B. C.
Published: December 2004

The interaction between salts of Groups IA and IIA and model aliphatic amides has been studied. The interaction has been monitored by calorimetry and spectroscopy. Among the alkali cations, lithium ion interacts strongest, while in Group II calcium appears to interact somewhat stronger than magnesium. The metal cation binds to the amide oxygen atom and causes alteration in the amide group geometry. As a consequence, significant alterations are seen in the infrared, nuclear magnetic resonance, ultraviolet, and circular dichroism spectra of the ligand peptide. These findings are suggested to be of importance to the conformational studies of polypeptides and proteins.
The buoyant and potentiometric titrations of human immuno‐gamma globulin
Authors: Ruark John E. , Ifft James B.
Published: December 2004

The buoyant density and potentiometric hydrogen ion titration curves of human immuno‐gamma globulin in 3M cesium chloride have been recorded. In addition, the amino acid analysis of the IgG employed has been completed. The hydration of the protein and the variation of the hydration with pH have been calculated from the buoyant density data. The potentiomtric hydrogen ion titration curve has been employed to estimate the intrinsic pK′s of the acidic and histidyl residues of the molecule, and to confirm the hypothesis that it does in fact conform to the oil drop model of protein conformation. Correlations have been drawn between the three sets of data in the following manner. The results of the potentiometric hydrogen ion titration have been checked against the amino acid analysis to determine whether the numbers of groups observed to titrate and the numbers of groups observed in the amino acid analysis do correspond. Second, previous hypotheses as to the direct correlation between potentiometric hydrogen ion titration behaviour and buoyant density titration behaviour have been investigated and substantially confirmed.
The effects of cooperativity, finite chain length, and field‐induced changes of the conformational equilibrium on the electric birefringence of polypeptides in the range of the helix–coil transition
Authors: Schwarz Gerhard , Schrader Uwe
Published: December 2004

An electric birefringence apparatus with an He–Ne laser is described, which permits a high sensitivity of measurement for field strengths up to 20 kV/cm and pulse durations between 10−5 to 1 sec. It is applied to poly(γ‐benzyl‐L‐glutamate) and poly(β‐benzyl‐L‐aspartate) in a nonaqueous solvent mixture, especially under the conditions of the helix‐coil equilibrium. A theoretical treatment of the problem shows that the usual neglect of end effects is only justified for comparatively long chains. On the basis of a computational procedure taking into account the finite chain lengths, the experimental data for 15 kV/cm reveal an obvious enhancement of the coil‐to‐helix transition caused by the electric field. This effect is quantitatively confirmed by a pertinent theory. The cooperative parameter σ may be best determined from the initial linear increase of the bire‐fringence versus the square of the field strength where the conformational equilibrium is not affected.
An X‐ray diffraction study of poly‐L‐homoarginine hydrochloride
Authors: Suwalsky M. , Bunster M. , Wagner K. G.
Published: December 2004

An X‐ray study of the synthetic polypeptide poly(L‐homoarginine hydrochloride) has been made to investigate whether, like the chemically related polypeptides poly(L‐lysine hydrochloride), poly(L‐arginine hydrochloride), and poly(L‐ornithine hydrobromide), it can undergo conformational transitions merely from variations in its degree of hydration. X‐ray photographs of powder and oriented specimens containing one to 15 molecules of water per L‐homoarginine hydrochloride residue showed that this polymer forms only a β‐pleated‐sheet structure. The pleated sheets, formed by antiparallel polypeptide chains hydrogen‐bonded to each other, are piled up along the b axis in an alternating sequence (“sandwich structure”). This structure did not appreciably change with variations of the degree of hydration, and the observed reflections at 56% relative humidity (1.8 molecules of water per residue) could be indexed satisfactorily in terms of a monoclinic unit cell, of space group P21, with a = 9.34 Å, b = 40.07 Å, c = 6.94 Å, and γ = 106°. These dimensions are shown by models to be compatible with the proposed structure, and the calculated density of 1.27 g/cm3 agrees well with the experimental value of 1.29 g/cm3. Removal of the last molecule of water results in a very diffuse pattern, while specimens containing 20 molecules of water per residue show only reflections due to water.
Characterization of the A ⇄ B transition of DNA in fibers and gels by laser Raman spectroscopy
Authors: Erfurth Stephen C. , Bond Peter J. , Peticolas Warner L.
Published: December 2004

Both Raman spectra and X‐ray diffraction patterns have been obtained from oriented fibers of sodium deoxyribonucleic acid (Na‐DNA) as a function of salt content and relative humidity. We have confirmed the previously reported X‐ray results that, for oriented fibers, the A‐form always exists between 75 and 92% relative humidity and that the conformation will change to the B‐form at 92% relative humidity only if an excess (3–5%) of added salt is present. Oriented fibers containing low amounts of added salt remain in the A‐type conformation at 92% relative humidity and higher. An exact correlation has been found between the familiar A‐ and B‐type X‐ray diffraction patterns of DNA fibers and the Raman spectra previously reported without X‐ray verification from this laboratory for the A‐ and B‐forms. In particular, a band at 807 cm−1 was always present when a fiber showed the A‐type diffraction pattern, and this band shifts to 790 cm−1 in the B‐form. Using the Raman spectrum to determine the specific conformation of DNA in samples less amenable to X‐ray analysis, we have studied the A ⇄ Btransformation in unoriented fibrous masses of DNA and in concentrated, oriented gels. We find that in unoriented fibrous masses, the A ⇄ B transition always occurs at 92% relative humidity even at very low salt concentration (0–4%). However, in oriented DNA gels at low salt, the A‐form can persist as a metastable state to concentration as low as 20% DNA. The origin of the bands at 807 and 790 cm−1 and the possible biological implications of these findings are discussed.
Analysis of the effects of chloride and 2,3‐diphosphoglycerate on the cooperative binding of oxygen to hemoglobin
Authors: Deal Walter J.
Published: December 2004

Analysis of experimental equilibrium constants for the oxygenation of hemoglobin leads to a plausible mechanism for the effect of pH and of chloride ions on cooperativity in hemoglobin. According to this mechanism, the structural changes responsible for cooperativity in chloride‐ and 2,3‐diphosphoglycerate‐free hemoglobin are affected only slightly by changes in pH, and the effect of chloride can be accounted for by sequential binding and release of chloride ions during oxygenation.
Magnetic susceptibility of various ferrihemoglobin species
Authors: Anusiem A. C. I.
Published: December 2004

Measurements of the magnetic susceptibility of guinea pig, human A, and pigeon ferrihemoglobins as a function of pH at 30°C demonstrate maxima very near the extrema found for the standard enthalpies and standard entropies of ligand binding, i.e., at the so‐called “characteristic pH” values, which are very different for these three species. Ligand binding is dependent on spin state, at least through the characteristic pH behavior, which is not yet understood.
Nature of amino acid side chain and α‐helix stability
Authors: Arfmann H.‐A. , Labitzke R. , Wagner K. G.
Published: December 2004

In order to investigate the ability of neutral amino acids to support the α‐helix conformation, the coil–helix transition of poly(L‐lysine) and of lysine copolymers with these amino acids was studied in water/methanol using circular dichroism. The transtions were recorded at constant pH adding buffer to the methanol/water mixtures. With poly(L‐lysine), experiments were performed at several constant pH's; the transition midpoint on the water (methanol) concentration scale was found to depend strongly upon pH; the helix stability region is shifted towards higher water concentrations, when the pH is increased. Copolymers of lysine and several neutral amino acids revealed the same effect in that increasing amounts of, for example, norleucine also shifted the transition midpoint to higher water concentrations. A series of copolymers containing L‐lysine as the host and different hydrophobic amino acids were synthesized and the helix–coil transition in water/methanol was observed at constant pH. Different copolymers of equal composition showed significant differences with respect to the nature of the amino acid incorporated into polylysine. From these studies an α‐helix‐philic scale (in decreasing order): Leu, Nle, Ile, Ala, Phe, Val, Gly is deduced and discussed; the results obtained were compared with those of different procedures.
Electron microscopy of ribosomal RNA mounted by adsorption in the absence of protein
Authors: Johnson Thomas R. , Caston J. Douglas
Published: December 2004

A method is described for visualizing ribosomal RNA in the electron microscope by an adsorption technique. The visual configuration of the molecules is sensitive to the composition of the medium from which they are adsorbed, and is reproducible under a given set of conditions. Regular structural features occur in the larger rRNA species similar to those observed with protein monolayer techniques. The dimensions of adsorbed molecules, however, are more consistent with current models of ribosomal RNA as it exists in solution.
Potentiometric titrations involving the β‐coil transition
Authors: Maeda Hiroshi , Ikeda Shoichi
Published: December 2004

Potentiometric titrations of poly(S‐carboxymethyl‐L‐cysteine) and poly(S‐carboxy‐ethyl‐L‐cysteine) were carried out in aqueous sodium chloride solutions and in water. For samples of both polymers of high molecular weight, a new pattern was observed concerning the change of titration curve with time; the β‐coil transition became sharper and the transition free energy increased by about 100 cal mole−1 as the equilibrium was approached. This suggests that equilibrium data were not obtained in most previous studies on the titration involving the β‐coil transition. It also shows that the reversbility is not necessarily sufficient to confirm the equilibrium. Another pattern, which was previously observed, was also confirmed with a low molecular weight sample of poly(S‐carboxymethytl‐L‐cysteine). The titration curves were shown to be insensitive to polymer concentration, even when aggregation or phase separation was present. The validity of the Gouy model to describe the titration curve of the β‐structure was found to depend on molecular weight as well as on the nature of the side chain.
Conformation of a rare nucleoside in the anti‐codon loop of tRNAs: Potential energy calculations for 2′‐O‐methyl cytidine
Authors: Stellman S. D. , Hingerty B. , Broyde S. , Langridge R.
Published: December 2004

The classical potential energy of 2′‐O‐methyl cytidine was calculated using contributions from van der Waals', electrostatic, and torsional terms. All five conformational angles, namely χ, Ψ, the methoxy angles m1 and m2 which are unique to O′‐methylated nucleosides, and the sugar pucker P were varied simultaneously, and the energy was minimized with respect to these parameters. An extensive search of conformation space was made, particularly with respect to the sugar pucker. At the predicted global minimum, χ and Ψ are anti‐gg, P is C(2′)‐endo‐C(3′)‐exo, and the methyl group is staggered with respect to the sugar. This calculated minimum agrees very well with the recently determined crystal structure of 2′‐O‐methyl cytidine. Thus, 2′‐O‐methylation still permits the conformational regions of the common nucleosides to be adopted. However, we infer that the predicted C(2′)‐endo sugar pucker results from the added methyl group, since cytidine is C(3′)‐endo in the crystal, and the common ribopyrimidine nucleosides generally favor C(3′)‐endo.
The interaction between two oppositely charged polyelectrolytes
Authors: Polderman A.
Published: December 2004

Mixtures of a weak polybase (polyethylenimine) and a weak polyacid acrylamide‐acrylic acid copolymer in aqueous solutions at several ionic strengths and polymer concentrations are studied potentiometrically. When the concentrations of the polyethylenimine and acrylamide‐acrylic acid copolymer charges are not too different, phase separation into two liquid phases (“complex coacervation”) is observed. In the pH region where no phase separation occurs, potentiometric titrations are performed on mixtures of both polymers. From the titrations of polyethylenimine solutions, acrylamide‐acrylic acid copolymer solutions, and the mixtures, the free energy of interaction has been evaluated according to the theory of Litan. The dependence of the free energy of interaction on pH, polymer concentrations, and ionic strength is explained quantitatively with a model of cooperative electrostatic physical association.
Synthesis of sequential polypeptides containing L‐azetidine‐2‐carboxylic acid residues
Authors: Boni R. , De Gregoriis E. , Di Blasi R. , Verdini A. S.
Published: December 2004

The synthesis and characterization of a series of sequential polypeptides with the repeating sequences Aze‐Pro‐Aze, Pro‐Aze‐Pro, Pro‐Aze‐Gly, Aze‐Pro‐Gly, Ala‐Aze‐Gly, Aze‐Ala‐Gly, and Pro‐Pro‐Gly are reported. The polymers were prepared by the active ester method, using the p‐nitrophenyl, pentachlorophenyl, and N‐hydroxysuccinimide esters as the polymerizable tripeptide derivatives. Except for poly(Ala‐Aze‐Gly) obtained via the N‐hydroxysuccinimide ester, all polymers were isolated in good yields and have weight‐average molecular weights in the range 10,000–30,000. The molecular weights have been determined by applying the calibrated gel chromatography system described by Fairweather et al. [J. Chromatogr. (1972) 67, 157] and by viscometry. All di‐ and tripeptide intermediates were chemically and optically pure.
Frictional properties of multisubunit structures
Authors: McCammon J. A. , Deutch J. M. , Felderhof B. U.
Published: December 2004

The translational drag, rotational drag, and intrinsic viscosity of spherical multisubunit structures have been calculated analytically using the Felderhof–Deutch theory of polymer frictional properties. The structures considered were hollow shells, spheres with uniform subunit density, and spheres covered with a subunit layer of different density. Changes in the transport coefficients resulting from the random removal of subunits and from the variation of subunit size are calculated. For the case of the shell, the results agree with the numerical computations of Bloomfield, Dalton, and Van Holde [Biopolymers 5, 135, 149 (1967)].