bluuebunny/crossref_metadata_2025 huggingface dataset:
Brownian motion of highly charged poly(L‐lysine). Effects of salt and polyion concentration
Authors: Lin Sung‐Chang , Lee Wylie I. , Schurr J. Michael
Published: December 2004

The Brownian motion of a single sample of high‐molecular‐weight poly(L‐lysine) [(Lys)n, n = 955] has been studied by dynamic light scattering over a wide range of NaBr concentrations and at three different polyion concentrations. A substantial decrease in scattered intensity is associated with the transition from the ordinary phase to the low‐salt extraordinary phase. At the salt concentration where the transition takes place the relaxations are non‐exponential and appear to exhibit at all angles a rapid relaxation (τ ≅ 10 μsec) that is presumed to be a manifestation of the kinetics of the transition process. The K2 dependence of the slow relaxation rates in the extraordinary phase has been confirmed within the experimental error. The extrapolated infinite‐dilution values of the diffusion coefficients in the ordinary phase are observed to decline precipitously below 10−2M salt to astonishingly small values, indicating a dramatic rise in the friction factors of the isolated polyions. An extensive discussion of these findings in relation to the theory employed here and to existing data in the literature is also given.
Solubilities of amino acids
Authors: Bull Henry B. , Breese Keith , Swenson Charles A.
Published: December 2004

The Mettler/Paar precision density meter DMA‐02D has been used to determine the concentration of saturated solutions of amino acids at 20.0, 25.0, and 29.8 °C. The technique has proven itself an elegant and precise method. The solubilities of all of the amino acids with the exceptions of proline, lysine, and cystine have been measured. The Gibbs free energies of transfer from saturated water solution to 1M Na2SO4 and to 1M Gu·HCL along with the van't Hoff heats and entropies have been calculated. The van't Hoff heats have been compared with the calorimetrically determined heats for some of the amino acids. The Lumry‐Rajender relation between the entropy and heats has been observed. The process of transfer of the amino acids from water to the solvents is primarily enthalpic rather than entropic.
The antibody–antigen interaction at an aqueous–solid interface: A study by means of polarized infrared ATR spectroscopy
Authors: Ockman N.
Published: December 2004

The determination of structural changes in antibodies due to their specific interaction with antigenic proteins is an important problem in understanding immunological responses. The method of polarized ATR infrared spectroscopy applied to protein films adsorbed on an appropriate solid surface can give information about the conformation of the polypeptide chains, as well as their orientation with respect to the surface. The adsorption of anti‐rabbit serum albumin onto monomolecular films of rabbit serum albumin, bovine serum albumin, and ovalbumin, and of anti‐ovalbumin onto films of rabbit serum albumin and ovalbumin at a Ge‐aqueous interface have been studied by this technique. The intensity of the amide I absorption indicates that the strengths of binding of these three albumin proteins with anti‐rabbit serum albumin is, under appropriate conditions, in the order rabbit > bovine ≫ ovalbumin; with anti‐ovalbumin, it is ovalbumin ≫ rabbit. Since the frequencies of the amide I band appear near 1655 cm−1 for all the proteins and protein complexes studied, the major contributions to their conformation comes from α‐helix and random‐coil structures. The average orientation of the transition moments of the amide I and A bands has been shown to be about 75° with respect to the surface normal. This indicates that the polypeptides chains are on the average approximately parallel to the surface for all the systems studied. Consequently, the effect of the specific antibody‐antigen interaction on the conformation and orientation of the former seems negligible in these films.
Boundary analysis of sedimentation‐velocity experiments with monodisperse and paucidisperse solutes
Authors: Van Holde K. E. , Weischet Wolfgang O.
Published: December 2004

A method is presented which allows one to calculate a distribution of sedimentation coefficients from the boundries of sedimentation‐velocity experiments with mono‐ or pauci‐disperse solutes. With two solutes differences in S value as small as 20% can be resolved. In absence of heterogeneity and concentration‐dependent effects, the analysis also provides values for the diffusion coefficient within an accuracy of −10 to +5%. Tests with both simulated data and ultracentrifugation experiments on short DNA fragments show the value and the limitations of the method.
Optical properties of sugars. VI. Circular dichroism of amylose and glucose oligomers
Authors: Lewis Donald G. , Johnson W. Curtis
Published: December 2004

The CD spectra of amylose, the maltose oligomers, cellobiose, and the cyclodextrins are measured in aqueous solution to 1640 Å. Two bands are found in this region. An examination of chromophorically equivalent but conformationally different glucans demonstrates that the CD of glucans is sensitive to conformation. However, the conformation of the subunits in the maltose oligomer series appears independent of chainlength. The conformations of the interior maltosyl groups of this series are all approximately equivalent. A comparison of the amylose and cycloamylose spectra indicates that amylose is substantially biased in its chirality. Since there is little chainlength dependence, the oligomers should have a similar chirality bias. The butanol complex of amylose, which is believed to have a V‐form helical conformation, has a CD similar to free aqueous amylose. This is consistent with conformational calculations on amylose which predict that the maltosyl subunits of amylose are restricted to a small region on its conformational map which includes the V‐form helix. It is also consistent with the idea that amylose a loosely wound and extended helix in aqueous solution.
Studies on protein folding, unfolding, and fluctuations by computer simulation. II. A. Three‐dimensional lattice model of lysozyme
Authors: Ueda Yuzo , Taketomi Hiroshi , Gō Nobuhiro
Published: December 2004

A three‐dimensional lattice model of protein designed to assimilate lysozyme is introduced. An attractive interaction is assumed to work between preassigned specific pairs of units, when they occupy the nearest‐nighbor lattice points. The behavior of this lattice lysozyme is studied by a Monte Carlo simulation method. Because of the specific interunit interactions,“native state” of the lattice lysozyme is stable at low temperatures. Conformational fluctuations in the native state are observed to occur at both termini and loop regions of the main chain existing on the surface. The process of unfolding and denatured states of this model are discussed. Complete refolding from a denatured state was not observed. However, by starting from partially folded structures, the native conformation could be attained. From these observation it is concluded that, in the process of folding of proteins as simplified in a lattice model, nulceation is a rate‐limiting factor. The artificial character of this model and possible improvement are discussed.
Comparison of conformation and antimicrobial activity of synthetic analogs of gramicidin S: Stereochemical consideration of the role of D‐phenylalanine in the antibiotic
Authors: Kawai M. , Nagai U.
Published: December 2004

In order to study the role of D‐amino acid residues in keeping the stable β‐sheet conformation and in the antimicrobial activity of gramicidin S (GS), the four analogs of GS containing D‐Ala, L‐Ala, Gly, and Aib (α‐aminoisobutyric acid) in place of D‐Phe were synthesized. D‐Ala‐and Gly‐containing analogs showed antimicrobial activity, while those containing L‐Ala and Aib showed no activity. Conformation of these analogs and their derivatives were studied by comparison of ORD and CD spectra and by slective methylation method. It is concluded that the biologically active analogs have β‐sheet conformation while inactive analogs have a much different conformation from that of GS. This indicates that D‐Ala‐Pro and Gly‐Pro sequences favor taking a β‐bend form but L‐Ala‐Pro and Aib‐Pro sequences do not because the presence of L‐side methyl group on the α‐carbon atom of LAla and Aib residues destabilizes the β‐bend form. This would explain why the inactive analogs which take a different conformation from that of the active ones result in the loss of activity.
Photon correlation spectroscopy of hemoglobin: Diffusion of Oxy‐HbA and Oxy‐HbS
Authors: Jones C. Ronald , Jhonson Charles S. , Penniston John T.
Published: December 2004

Translation diffusion coefficients have been measured for oxyhemoglobin A and oxyhemoglobin S over the concentration range 0.1–37 g/dl by means of photon correlation spectroscopy. The solutions were 0.1 M in KCl and in each case the pH was adjusted to the isoelectric point of the hemoglobin species present. No significant differences were found between the HbA and HbS results; and after correction to water at 20°C, the diffusion coefficients could be described by the equation

where Do = (6.93 ± 0.06) × 10−7 cm2/sec and c ids the concentration in units of g/dl. No evidence was found for the aggregation of oxy‐HbS at high concentrations which was reported by Lindstrom et. al. [(1976) Biophys. J. 16, 679–689].
Model nucleoproteins: Binding of actinomycin D to complexes of DNA with lysine‐containing polypeptides
Authors: Votavoá H. , Bláha K. , Šponar J.
Published: December 2004

Complexes of DNA with histone H1 and random and sequential polypeptides containing 30–100% of lysine were studied using actinomycin D as a probe. The binding of actinomycin D was measured by spectrophotometric titration in 0.15M NaCl and in 0.01M Tris buffer. The excluded‐site model was used for the evaluation of binding data. Polypeptides reduce the number of binding sites on DNA available for actinomycin D binding. The extent of this change depends mainly on the content and distribution of basic lysine residues. Of the hydrophobic residues constituting the peptides, only leucine strongly depresses the actinomycin D binding. The helix‐forming and helix‐breaking amino acid residues are without effect.
Ellipsometry as a tool to study the adsorption behavior of synthetic and biopolymers at the air–water interface
Authors: De Feijter J. A. , Benjamins J. , Veer F. A.
Published: December 2004

The application of ellipsometry of the study of the adsorption behavior of proteins and synthetic macromolecules at the air‐water interface has been investigated. It is shown that for macromolecules the amount adsorbed per unit area, Γ, as determined by ellipsometry, only has a well‐defined physical meaning if the refractive‐index increment remains constant up to high concentrations present in the adsorbed layer. It has been found experimentally that this conditioned is fulfilled for proteins. The ellipsometric Γ values of some protein agree satisfactorily with those obtained by two independent techniques has been used to investigate the adsorption from solution of κ‐casein, bovine serum albumin, and polyvinyl alcohol. For bovine serum albumin, Γ reaches a plateau value of 2.9 mg/m2 for concentrations ≥ 0.05 wt%. The thickness of the adsorbed molecules. For κ‐casein, Γ steadily increases with increasing centration and multilayers are formed. The technique provides interesting information on conformational changes in adsorbed macromolecules, on the rate of the process, and on the conditions under which these occur.
Synthesis of sequential polypeptides containing lysine and tyrosine
Authors: St. Pierre S. , Ingwall R. T. , Goodman M.
Published: December 2004

Sequential polypeptides with the repeating units L‐tyrosyl‐L‐lysyl, L‐tyrosyl‐(L‐lysyl)2, and L‐tyrosyl‐(L‐lysyl)3 have been synthesized by solution polymerization of the N‐hydroxy‐succinimide esters of the corresponding di‐, tri‐, and tetrapeptides. The monomers for the polytripeptide and polytetrapeptide were prepared by fragment condensation, using the mixed carbonic anhydride coupoling method. Moderately high molecular weight polypeptides were obtained.
Proton magnetic relaxation in solid poly(L‐alanine), poly(L‐leucine), poly(L‐valine), and polyglycine
Authors: Andrew E. R. , Gaspar R. , Venart W.
Published: December 2004

Molecular motion in solid poly(L‐alanine), Poly(L‐leucine), poly(L‐valine), and polyglycine has been investigated through measurement of the portion spin‐lattice relaxation time at 30 and 60 MHz between 110 and 350°K. Rapid random reoriention of sied‐chain methyl groups provides the dominent source of relaxation in the first three; activation energies are 10.5 ± 1 1, 8.5 ± 1 kJ/mol, respectively, significantly lower than in the monomeric crystals. Relaxation times in poyglycine are two orders of magnitude longer than in the monomeric crystals. Relaxation times in polyglycine, significantly lower than in the monomeric crystals. Relaxation times in polyglycine are two orders of magnitude longer and are attributed mainly to segmental motions of the polymer chains. Evidence of nonexponential recovery of nuclear magnetization was encountered in the first three homopolyamino acids but not in polylycine, and was attributed to the correlated time to characterize these motions gave quite good agreement with the data; some improvement was obtained for two polymers using a Cole‐Davidson distribution of correlation times. For biopolymers using a Cole‐Davidson distribution of correlation times. For biopolymers generally it is concluded that rapid methyl group reorientation is a common dynamical feature and an important source of nuclear magnetic relaxation.
The structure of α‐amanitin in dimethylsulfoxide solution
Authors: Tonelli Alan E. , Patel Dinshaw J. , Wieland Th. , Faulstich H.
Published: December 2004

The backbone and side‐chain conformations of the bicyclic octapeptide α‐amanitin indimethylsulfoxide (DMSO) solution have ben deduced from analysis of the nmr spectrl parameters and conformational energy calculations. Several ambiguities in the nmr spectral assignments were resolved following a comparison with the recently published conformation of β‐amanitin in the crystalline state. The peptide proton exchange and temperature coefficient data demonstrate strong intramolecular hyfrogen bonds for the GLY5 and Cys8 peptide protons. The vicinal proton coupling constants are consistent with the cyclic octapeptide udergoing chain reversl at the Ile6‐Gly7 abd the Hyp2‐Hyi3 dipeptide segments. The upfield shifts of the glycine and isoleucine protons demonstrate the folding of the indole ring of the Trp4‐Cys8 brifge towards the Gly5‐Ile6‐Gly7 half of the Ile‐amanitin molecule. The structure af α‐amanitin in DMSO is defined by the (ϕψ) backbone rotation angles Trp4(−90, −60), Gly5 (+120, −120), Ile6(−6, +120), Gly7 (+45, +60), Cys8(−120, −60), Asn1 (+175, −175), Hyp2 (−160, −45), and Hyi3 (−90, −60). The study demonstrates that the structure of α‐amanitin in solution is similar to the structure f β‐amanitin in the crystalline state.
Study of DNA sequence supraorganization by intramolecular renaturation
Authors: Vizard Douglas L.
Published: December 2004

The method of DNA partial denaturation and intramolecular renaturation (in the absence of biomolecular reassociation) is developed analytically and presented as a means by which the supraorganization of the DNA sequences within large complex genomes may be studied. This analysis provides for the comparison of the actual borganization of DNA sequences with a random arrangement of the same sequences. The sequence organization of the E. coli genome does not appear to be very different from DNA sequences arranged along the genome without preference to sequence stabilities, whereas an orderly physical arrangement of DNA sequences is implicated for the human genoma.
Conformational features of oligocellulose acetates in the solid state and their implications for the structures of cellulose triacetate
Authors: Pérez S. , Brisse F.
Published: December 2004

The crystal data on cellobiose octaacetate and cellotriose undecaacetate are compared in an effort to analyze what information available from crystal structures of oligosaccharides can be used to arrive at the three‐dimensional structure of the related polysaccharides. This comparison points out the remarkable behavior of the reducing end of both molecules. The glycosidic torsion angles (ϕ,ψ) around the reducing and the middle residues in the disaccharide and in the trisaccharide have values around 45° and 14°, while the conformational angles about the nonreducing residues in cellotriose acetate are 24° and −20°. The conformations of the primary acetate groups on the two nonreducing residues are similar, but they differ from those observed for the acetate groups belonging to the reducing residues. The possibility of a 21 symmetry axis between contiguous triacetate residues within the oligosaccharide is examined, along with a comparison of the molecular packing found in the oligomer structures. Conformational energy calculations have been performed on two dimeric entities derived from cellotriose acetate. The isoenergy maps show the drastic influence of the relative orientations of the primary acetate groups. It is proposed that the nonreducing dimer, as found in the crystal structure of cellotriose acetate, most nearly expresses the “polymer averaged” interactions for contiguous residues in cellulose triacetate.
Theoretical studies on peptidoglycans. I. Effect of L‐alanyl, D‐butyl, or D‐valyl residuces at the positions 4 or 5 of the pentapeptide moiety of peptidoglycan on the cross‐linking reaction
Authors: Virudachalam R. , Rao V. S. R.
Published: December 2004

Possible conformations of X‐D‐alanyl4‐D‐alanine5 and its analogs X‐L‐analyl4‐D‐alanine5 X‐D‐alanyl4‐L‐alanine5, X‐D‐butyl4‐D‐alanine5, X‐D‐alanyl4‐D‐butyric acid5, X‐D‐valyl4‐D‐alanine5, and X‐D‐alanyl4‐D‐valine5 have been analyzed by theoretical methods. These studies suggest that L‐alanine and D‐valine at the 4 or 5 postion of the pentapeptide moiety of peptidoglycan will drastically reduce the cross‐linking in peptidoglycan biosynthesis, whereas the effect of D‐ butyric acid will be marked at the 4 postition and modeate at the 5 position. This is in good agreement with experimental results. The cross‐linking enzyme transpeptidase requires a specific confroamation for the 4th and 5th residues for optimal binding.
Rotating frame spin‐lattice relaxation experiments and the problem of intramolecular motions of peptides in solution
Authors: Bleich Hermann E. , Glasel Jay A.
Published: December 2004

The application of rotating frame spin‐lattice relaxtion to the determination of the intramolecular motions in peptides is discussed, and results are presented on the application of 13C T1p to peptide microdynamics in solution. The effective molecular rotational reorientation times at the amide and amino nitrogens may be derived from appropriate data onT1p of the carbons adjacent to them. We also show by theoretical caculations that 1H and 13C T1p experiments of suitable 2H and 15N substituted peptides will allow intramolecular main‐ and sidechain motions, characterized by times in the range 10−1–10−6 sec, to be investigated.
Conformational properties of the N‐terminal residues of S‐peptide. I. The ribonuclease S′ system
Authors: Filippi Bruno , Borin Gianfranco , Anselmi Ugo , Marchiori Fernando
Published: December 2004

The contribution of the 1–6 N‐terminal sequence to the conformational properties of the S‐peptide (the 1–20 sequence of ribonuclease A) was assessed by determining in the ribonuclease S′ system the helical content and the binding capability of synthetic [Orn10]‐S‐peptide analogs, in which lysine1, glutamic2 and threonine3 were progressively deleted, alanine4 and alanine5were alternatively replaced by serine, and alanine6 was substituted by serine or proline. Both the deletion of the three N‐terminal residues and the alanine6/proline replacement produces the loss of the helical structure up to lysine7. No or minor effects are found in all other cases. From the comparison of the binding data, the energy for the conformational stabilization of the N‐terminal region was calculated to amount to 1.4 kcal/mol. The results are discussed in comparison with the known x‐ray data of the enzyme, with some predictive rules of secondary structure which were applied to this region and with the known phylogenetic variance of the residues in this region.
Studies of the thyrotropin‐releasing factor. II. Conformations of TRF and some analogs
Authors: Flurry R. L. , Abdulnur S. F. , Bopp J. M.
Published: December 2004

The conformation of the thyrotropin‐releasing factor (TRF) and four analogs have been studied by the CNDO/2 molecular orbital method. The Nδ‐protonated tautomer of TRF is predicted to be the more stable of the two tautomeric forms; however, it is postulated that the Nε‐tautomer possesses the most active minimum‐energy conformation. The peptide backbone for the five compounds remains nearly constant. The conformations predicted from model fragments are very near to those found for the full compound.
13C‐NMR spectroscopic investigation of α‐ and β‐1,4‐D‐glucose homooligomers
Authors: Heyraud Alain , Rinaudo Marguerite , Vignon Michel , Vincendon Marc
Published: December 2004

A complete, unambiguous assignment of all the 13C signals of cellobiose and maltose has been achieved using methods such as selective proton decoupling, 13C selective spin labeling, and isotopic chemical shift induced by deuterium. The chemical‐shift variation of the 13C signals with the degree of polymerization in each α or β (1 → 4) series is discussed. The chemical‐shift dependence on temperature and solvent in these two series is shown and interpreted in terms of modifications of the solvation and of the conformation.
Interactions between bovine plasma albumin and sodium dodecyl sulfate studied by means of 13C‐nmr spectra
Authors: Inoue Yoshio , Sase Shigeru , Chûjô Riichiro , Nagaoka Shunji , Sogami Masaru
Published: December 2004

The interactions between the protein, bovine plasma albumin, and surfactant, sodium dodecyl sulfate, have been studied by 13C‐nmr spectroscopy at pH 5.4–6.8 in D2O solution. The 13C chemical shifts and the 13C spin‐lattice relaxation time of the individual carbons of the surfactant were measured as a function of the molar ratio of the surfactant to albumin in order to analyze the surfactant‐protein interaction and the molecular motion of the surfactant. It was found that in the region of initial binding of the surfactant to the high‐affinity sites on the protein, both the surfactant head group and alkyl chain interact with the protein. With an excess of high‐affinity sites at the beginning of the reaction, surfactant molecules are in a micellelike environment in which the surfactant's alkyl chains are associated with nonpolar groups of the protein. Even after the denaturation by many surfactant bindings, much of the secondary and higher structure seems to remain intact.
Thermodynamics and kinetics of the interaction of copper (II) ions with native DNA
Authors: Förster W. , Bauer E. , Schütz H. , Berg H. , Akimenko N. M. , Minchenkova L. E. , Evdokimov Yu. M. , Varshavsky Ya. M.
Published: December 2004

Based on equilibrium binding studies, as well as on kinetic investigations, two types of interactions of Cu2+ ions with native DNA at low ionic strength could be characterized, namely, a nondenaturing and a denaturing complex formation. During a fast nondenaturing complex formation at low relative ligand concentrations and at low temperatures, different binding sites at the DNA bases become occupied by the metal ions. This type of interaction includes chelate formation of Cu2+ ions with atoms N(7) of purine bases and the oxygens of the corresponding phosphate groups, chelation between atoms N(7) and O of C(6) of the guanine bases, as well as the formation of specific intestrand crosslink complexes at adjacent G°C pairs of the sequence dGpC. CD spectra of the resulting nondenatured complex (DNA–Cu2+)nat may be interpreted in terms of a conformational change of DNA from the B‐form to a C‐like form on ligand binding. A slow cooperative denaturing complex formation occurs at increased copper concentrations and/or at increased temperatures. The uv absorption and CD spectra of the resulting complex, (DNA–Cu2+)denat, indicate DNA denaturation during this type of interaction. Such a conclusion is confirmed by microcalorimetric measurements, which show that the reaction consumes nearly the same amount of heat as acid denaturation of DNA.

From these and the kinetic results, the following mechanism for the denaturing action of the ligands is suggested: binding of Cu2+ ions to atoms N(3) of the cytosine bases takes place when the cytosines come to the outside of the double helix as a result of statistical fluctuations. After the completion of the binding process, the bases cannot return to their initial positions, and thus local denaturation at the G·C pairs is brought about. The probability of the necessary fluctuations occurring is increased by chelation of Cu2+ ions between atoms N(7) and O of C(6) of the guanine bases during nondenaturing complex formation, which loosens one of the hydrogen bonds within the G·C pairs, as well as by raising the temperature. The implications of the new binding model, which comprises both the sequence‐specific interstand crosslinks and the described mechanism of denaturing complex formation, are discussed and some predictions are made. The model is also used to explain the different renaturation properties of the denatured complexes of Cu2+, Cd2+, and Zn2+ ions with DNA.

In temperature‐jump experiments with the nondenatured complex (DNA–Cu2+)nat, a specific kinetic effect is observed, namely, the appearance of a lag in the response to the perturbation. The resulting sigmoidal shape of the kinetic curves is considered to be a consequence of the necessity of disrupting a certain number of the crosslinks existing in the nondenatured complex before the local unwinding of the binding regions (a main step of denaturing complex formation) may proceed.
On the blue color of triiodide ions in starch and starch fractions. I. Characterization and assignment of absorption and circular dichroism spectra of triiodide ions in amylose
Authors: Handa Takashi , Yajima Hirofumi
Published: December 2004

Four fundamental Raman lines were observed at 159, 111, 55 and 27 cm‐1 corresponding to the I bound (I) in amyloses with DP from 20 to 100, regardless of the degree of polymerization of I and the excitation wavelength. The spectral resolution was based on the molar extinction coefficient and molar ellipticity spectra of I. Eight bands, named, S1, S2, ⃛, S8 from long to short wavelength, were isolated. These were found regardless of the DP. By a resonance excitation Raman study, the characteristics of S3 and S4, comprising the shoulder around 480 nm, were found to be different from those of S1 and S2, comprising the blue band. The assignment of the spectra was based on the electronic states of the monomeric I in the exciton‐coupled dimeric unit. It was concluded that the blue band (S1,S2) belonged to the long‐axis transitions and the shoulder band (S3,S4) to the short‐axis ones on the monmeric coordinate system.
Single crystals and oriented crystallization of ivory nut mannan
Authors: Chanzy Henri , Dube Michel , Marchessault R. H. , Revol J. F.
Published: December 2004

The preparation of lamellar single crystals of mannan[poly((1 → 4)‐β‐D‐mannose)] is described. Electron diffractograms clearly identify the perpendicular orientation of the chain axis with respect to the lamellar surface. Since the degree of polymerization is 40 or less, no conclusion is made as to chain folding. The unit cell corresponds to the mannan I structure derived from x‐ray fiber data on oriented algal mannan. The baseplane dimensions found were a = 7.22 Å and b = 8.92 Å, and the systematic absences observed confirm the proposed P212121 group. It was found that cellulose microfibrils from Valonia ventricosa and bacterial cellulose could serve as extended chain nuclei for inducing oriented crystallization of mannan on cellulose. This produces a shish‐kebab type of morphology.
Theoretical investigation of semiconductive properties in proteins. II. The possibility of charge transfer between proteins and different acceptor molecules
Authors: Suhai Sáandor , Collins Thomas C. , Ladik János
Published: December 2004

The results of theoretical investigations are reported concerning the possibility of impurity‐type charge carrier production in proteins. The energy band structures of the periodic protein model polyglycine calculated with the aid of the ab initio Hartree‐Fock crystal orbital method and corrected afterwards for long‐range correlation effects are compared with the empty levels of glyoxal, methyl‐glyoxal, acrolein, and croton‐aldehyde, suggested recently by Albert Szent‐Györgyi as possible acceptors against proteins. The comparison with previous supermolecule calculations shows that appreciable charge transfer can be expected to glyoxal, methyl‐glyoxal, and acrolein from the polypeptides, while croton‐aldehyde is probably less efficient in this relation.
Hydroxyproline content and location in relation to collagen thermal stability
Authors: Burjanadze Tengiz V.
Published: December 2004

A new analysis has been made on studies of the influence of imino acid content on the changes of collagen thermal stability (tm). It is shown that, for the interstitial vertebrate collagens, there is a strict regularity in the changes of tm depending on hydroxyproline content. No correlation is observed between tm and proline content. Also, no correlation between tm and hydroxyproline content is observed for invertebrate and basement membrane collagens. On the basis of the reported data, the dependence of tm on hydroxyproline content is considered to be not a correlation between tm and the total content of hydroxyproline, but only as the correlation between tm and the content of hydroxyproline occurring at the third position in the sequence (Gly‐R2‐R3)n. The results agree with the idea that the influence exerted by proline and hydroxyproline on the stabilization of the triple helix of collagen is different.
Salt‐induced conformational change of random copolymers (Lys50Tyr50)n and (Lys50Phe50)n studied by 1H‐ and 13C‐nuclear magnetic resonances. Aggregation behavior of helical segments
Authors: Saitô Hazime , Ohki Toyokazu , Kodama Masahiko , Nagata Chikayoshi
Published: December 2004

1H‐ and 13C‐nmr studies of conformational transitions of random amino acid copolymers containing aromatic residues (Lys50Tyr50)n and (Lys50Phe50)n in the presence of neutral salts were performed to serve as models of the aggregation behavior of polypeptides of biological significance. The 1H and 13C signal intensities of Tyr and Phe residues decreased preferentially with increasing concentration of neutral salts such as NaCl and NaClO4. This behavior contrasts with that of (Lys)n in the presence of similar neutral salts, where the displacement of the 13C signal is clearly seen on transition from the random‐coil to the helical conformation. On the basis of the previous conformational studies, the loss of the peak areas is ascribed to the presence of immobilized helical segments by hydrophobic interaction between aromatic side chains. The remaining resonances are due to the residual random‐coil regions, since the values of nuclear Overhauser enhancements and chemical shifts are unchanged in the presence and absence of the neutral salts.
Transport properties of particles with segmental flexibility. I. Hydrodynamic resistance and diffusion coefficients of a freely hinged particle
Authors: Harvey Stephen C.
Published: December 2004

Expressions are derived for the hydrodynamic resistance tensor and the diffusion tensor of a particle consisting of two rigid subunits connected by a free hinge. No restrictions are placed on the shapes of the subunits. The resistance tensor is obtained by using two independent approaches: first, from the Rayleigh dissipation function and, second, from an examination of the generalized forces for the appropriate seven‐dimensional coordinate system. For the derivation of the generalized Einstein equation connecting the diffusion and resistance tensors, the Brownian motion is treated as a stochastic process. That derivation is based on the assumption that the restoring force for bending is negligible, and the Einstein relation holds instantaneously only if that assumption is true. The relationship between these tensors and the macroscopically observable parameters is discussed, and it is shown that the separate measurement of resistance and diffusion coefficients can be used to detect macromolecular flexibility. One example is treated, the diffusion of a particle composed of two long rods joined at a free hinge. Those calculations are carried out with the first‐order assumption of negligible hydrodynamic interactions between the subunits. For the hinged rod, the bending degree of freedom produces a 34% increase in the translational diffusion coefficient over that of a stiff rod of the same total length, while the rotational diffusion coefficient about the axis perpendicular to the plane of bending is increased by 125%.
Adsorption of polypeptides on solid surfaces. I. Effect of chain stiffness
Authors: Birshtein T. M. , Zhulina E. B. , Skvortsov A. M.
Published: December 2004

The general method of obtaining the partition function and thermodynamic characteristics of polymer chains near an adsorbing surface, simulated by random walks on a lattice, is developed. The method takes into account the effect of short‐range interactions in polymer chains, in particular, the chain stiffness and secondary structure. The theory of adsorption of chains of different stiffness is developed, and the process of adsorption which occurs when the external conditions change is shown to be always a second‐order phase transition. The critical adsorption energy decreases and the sharpness of transition grows when the chain stiffness increases. A simple model of a chain with “virtual” steps is proposed which simplifies the treatment; the results obtained are in good agreement with exact theories. A general scheme of analysis of adsorption of chains with a given secondary structure is set forth and the analogy between the stiffness of a noncooperative chain and the presence of helical segments in a polypeptide chain is discussed.
Lysozyme film hydration events: An IR and gravimetric study
Authors: Careri G. , Giansanti A. , Gratton E. , Snamprogetti
Published: December 2004

By a combined gravimetric and ir technique, spectra of protein films are recorded during sorption isotherms at constant water content h (mg D2O/mg dry protein) in the range 0 les; h ⩽ 0.35 at 27 and 38°C. Computer‐aided differential analysis shows the effect of progressive hydration on some significant sites of the protein such as the ionizable acidic side chains and the backbone amide carbonyls, as well as the spectrum of the adsorbed water itself. In order to derive thermodynamic properties of these sites, the measured sorption isotherm is decomposed in terms of a model which postulates the existence of two classes of primary sorption sites only, and these two contributions are independently checked by the ir data. The free energy of binding of the strong and weak binding sites is found to be 2.0 ± 0.2 and 0.40 ± 0.1 kcal/mol, respectively. A water‐induced transition region is clearly detected in all the observed properties at 0.06 < h < 0.10 at 38°C and is shown to be due to changes involving both the structure of the absorbed water and the coverage of the absorption sites. A detailed picture of the hydration events is offered, and the relevance of these findings to protein dynamics is discussed.
The flexible DNA double helix. II. Superhelix formation
Authors: Olson Wilma K.
Published: December 2004

A simple super or s‐virtual bond scheme has been developed for the treatment of tertiary or superhelical structure in polynucleotide chains. The various spatial configurations accessible to the flexible double helix are rendered more readily intelligible by the introduction of these hypothetical bonds to replace real sequences of regular secondary structure. The scheme is utilized to examine the enormous variety of tertiary structure that can be generated by regularly bending a B‐DNA reference helix at the phosphodiester linkages. Of particular interest from the study are the large families of bends that generate superhelices of identical macroscopic dimensions. Various modes of folding the B‐type helix into superhelices that fit the experimentally measured dimensions of chromatin nucleosomes are illustrated.
An absolute method for the determination of the persistence length of native DNA from electron micrographs
Authors: Frontali C. , Dore E. , Ferrauto A. , Gratton E. , Bettini A. , Pozzan M. R. , Valdevit E.
Published: December 2004

Information on spatial correlation in the tangent direction along electron microscope images of filamentous molecule is shown to be obtainable by the analysis of statistical fluctuations in curvature, yielding an absolute measure of the persistence parameter amicro. The relationship of amicro, a local, microscopic parameter, to the persistence length introduced by Kratky and Porod is discussed. The hypotheses underlying the assumed theoretical model concern (1) the shape of the angle distribution, assumed to be Gaussian; (2) the passage from a three‐ to a two‐dimensional situation, which is supposed to occur by deformation of the flexible chain in a manner that preserves the memory of the spatial correlation in orientation (except for the blocking of one degree of freedom); and (3) the adsorption conditions, which should meet the equilibrium requirement as closely as possible. The analytical method has been checked on computer simulated “Gaussian” molecules: the study of the simulated sample was essential in solving the problems connected with minimum statistics requirements and the effect of the reading error. Experimental images obtained for T2 DNA fragments at different ionic strengths by Kleinschmidt's adsorption technique have been analyzed by means of an automatic flying spot digitizer, the “Precision Encoder and Pattern Recognition.” The results show that adsorbed molecules do in fact “remember” the rigidity they possessed in solution and that the Gaussian hypothesis is well verified. Consequently, the slopes of log cosθ(l) or θ2(l) may be used indifferently in the estimate of amicro. The dependence of this parameter on ionic strength in the range explored shows the expected behavior.
Polyelectrolyte behavior of carrageenans in aqueous solutions
Authors: Rinaudo M. , Karimian A. , Milas M.
Published: December 2004

Osmotic coefficients of sodium, potassium, and calcium counterions have been determined in aqueous solutions on kappa‐, iota‐, and lambda‐carrageenans at 25°C. The experimental results are correlated with the calculated ones from the limiting law of Manning. An orderd secondary structure exists in kappa‐ and iota‐carrageenans. Its stability is discussed as a function of temperature, ionic strength, and the nature of the counterions.
Effect of Mg++ and polyamines on proflavine binding to T2 DNA
Authors: Riemer Steven C. , Bloomfield Victor A.
Published: December 2004

Proflavine binding may be used as a probe of the environment and interactions of DNA. In this paper we report the effects of the divalent cations Mg++ and putrescine and the trivalent cation spermidine on the proflavine–Na DNA binding equilibrium. Difference spectroscopy at 430 nm was used to determine apparent proflavine–DNA binding constants K at several concentrations of each cation for temperatures between 15 and 43°C, and at a constant total ionic strength of 0.1M. Mg++, putrescine, and spermidine all have greater effects on K than expected on the basis of ionic strength alone in the order spermidine > Mg++ ≳ putrescine. van't Hoff analysis of K(T) enabled calculation of ΔH° and ΔS°, which are affected differently by each cation. These differences are discussed qualitatively in terms of such concepts as release of condensed counterions, localized or unlocalized condensation, hydration, and restriction of molecular and internal rotation.
Hydrodynamic properties of proteoglycan subunit from bovine nasal cartilage. Self‐association behaviour and interaction with hyaluronate studied by laser light scattering
Authors: Reihanian H. , Jamieson A. M. , Tang L. H. , Rosenberg L.
Published: December 2004

Measurements of translational diffusion coefficients by quasielastic laser light scattering, sedimentation coefficients, and intrinsic viscosities at zero shear of proteoglycan subunit fraction A1‐D1‐D1 isolated from bovine nasal septa are reported. Molecular weights and hydrodynamic dimensions are compared with those expected on the basis of structural models previously proposed. Comparison of the concentration dependence of the diffusion coefficient in the presence of NaCl and GdnHCl leads to the conclusion that significant self‐association behaviour of subunit occurs in the absence of GdnHCl. In the absence of added salt, anomalous nonlinear concentration dependence of Dt estimated from wide‐angle light‐scattering experiments is observed. In addition, Dt apparently becomes angle dependent. These results are interpreted in terms of the perturbation of normal translational diffusion of the monomer by strong repulsive intermolecular interactions due to the combined effects of long‐range electrostatic forces and macromolecular congestion at higher concentrations. By carrying out experiments at small scattering angles, it is possible to determine D for proteoglycan subunit in the absence of supporting electrolyte. Titration of a dilute solution of subunit with hyaluronic acid results in a sigmoidal behaviour of the Stokes radius, indicating the formation of complexes of higher molecular weight results from the noncovalent association of proteoglycan subunits with hyaluronate. Observation of Dt appears to provide a useful method for studying the proteoglycan subunit–hyaluronate interactions.
Effect of temperature on the limiting viscosity number of hyaluronic acid and chondroitin 4‐sulfate
Authors: Cleland Robert L.
Published: December 2004

The decrease in the limiting viscosity number [η] with temperature T for hyaluronic acid in nonalkaline solution and chondroitin 4‐sulfate in neutral and alkaline solutions may be expressed in terms of the temperature coefficient of the Kratky‐Porod persistence length a: d ln a/dT = −0.0040 (±0.0005). The result, while numerically somewhat smaller, resembles qualitatively that of cellulose derivatives. As in the latter case, standard conformational calculations underestimate the coefficient, which may be due to neglect of random occurrence of local conformational features of higher energy. In alkaline solution, large decreases in [η] of hyaluronic acid are accompanied by a positive temperature coefficient of [η]. This temperature effect is interpreted as an endothermal shift from the alkaline, low [η] form of the polymer to the neutral, high [η] form with increasing temperature.
Effect of some monohydric alcohols on the functional stability of bovine liver β‐galactosidase
Authors: Cordone Lorenzo , Izzo Vincenzo , Sgroi Giuseppe , Fornili Sandro L.
Published: December 2004

We report on experiments showing that the presence of some monohydric alcohols in the solution medium perturbs the kinetics of bovine liver β‐galactosidase. The effect increases with increasing alcohol concentration and alkyl group size. To explain this effect we suggest a model that considers the existence of functional and nonfunctional enzyme conformations in thermodynamical equilibrium. This equilibrium is dependent both on alcohol concentration and on alkyl group size.
Raman spectroscopic study of 2H‐ and 15N‐ substituted guanosines: Monomers, gels, and polymers
Authors: Delabar Jean‐Maurice , Guschlbauer Wilhelm
Published: December 2004

15N‐labeled guanosines were synthesized and studied by Raman spectroscopy. The isotopic substitution was either on nitrogens 1, 2, and 3 or on nitrogens 7 and 9. These substituted guanosines and their partially or totally deuterated derivatives were compared under a variety of experimental conditions: in aqueous solution in the presence of 0.1M KCl at pH 7 at 60 and 10°C, i.e., in solution and in gel form. The sensitivity to nitrogen isotopic substitution of some of the “hypochromic” bands was defined. These spectra were also compared with those in acidic and basic solution. The body of these data was compared with the results on poly(guanylic acid) and on guanine‐containing polynucleotides and nucleic acids.
Intermolecular association and molecular weight of aggregates of a monodisperse homohexapeptide, Nps‐[Glu(OBzl)]6‐NHEt, in solution
Authors: Ikeda Shoichi , Okahashi Kenji
Published: December 2004

Light scattering from the solutions of Nps‐[Glu(OBzl)]6‐NHEt in dioxane or ethylene dichloride has been measured at different concentrations, and a critical concentration of intermolecular association is found to exist, which is equal to the critical concentration of β‐form formation. The Debye plot of light scattering leads to the molecular weight of aggregates at the critical concentration, which corresponds to an aggregation number 15 in dioxane and 53 in ethylene dichloride. In the latter solvent the aggregates further associate into a larger aggregate consisting of 330 molecules when the concentration is increased beyond the critical concentration. The content of β‐form, which is a measure of number of hydrogen bonds, is derived from the ir data previously obtained. The results on the modes of intermolecular association and hydrogen bonding lead to possible structures of aggregates formed by both hydrogen bonds and other nonbonding side‐chain interactions.
The crystal and molecular structure of cyclo‐[‐(D‐Val‐Hyi‐Val‐D‐Hyi)3‐] (meso‐valinomycin, C60H102N6O18)
Authors: Pletnev V. Z. , Galitskii N. M. , Ivanov V. T. , Ovchinnikov Yu. A.
Published: December 2004

The crystal structure of the valinomycin analog, cyclo‐[(‐D‐Val‐Hyi‐Val‐D‐Hyi‐)3‐] (meso‐valinomycin, C60H102N6O18) has been determined by direct x‐ray diffraction procedures. The crystals are triclinic, space group P1, number of molecules per unit cell Z = 1, and cell parameters a = 11.831, b = 13.815, c = 14.889 Å, α = 109.54°, β = 116.10°, γ = 98.89°. The atomic coordinates for the C,N,O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation to R = 0.07.

The structure is centrosymmetric and has a threefold axis of pseudosymmetry. The depsipeptide chain is in the form of a bracelet stabilized by six identical intramolecular 4 → 1 hydrogen bonds between the amide CO and NH groups. The ester carbonyls are oriented towards the symmetry axis, their O atoms forming an ellipsoidal molecular cavity. The isopropyl side chains are located on the molecular periphery. The structure found differs considerably from the conformation of the crystalline naturally occurring antibiotic, valinomycin, but completely resembles that of valinomycin and meso‐valinomycin in nonpolar solvents. In the crystal, meso‐valinomycin molecules form stacks. The molecular cavities situated in the stacks one above the other along the pseudo‐C3 axis form a continuous channel, the internal surface of which is lined by O atoms. The possible conformations of depsipeptides of the valinomycin series and their mode of action in membranes are discussed in the light of the data obtained.