bluuebunny/crossref_metadata_2025 huggingface dataset:
Competition between native and monoacetylated polymyxin for charged adsorption sites
Authors: Miller I. R. , Teuber M. , Accad Y.
Published: December 2004

The native antibiotic polymyxin B, carrying five positive charges, displaces the monoacetylated on from its adsorbed state at the interface between negatively charged lipid layers ans water. A simulation model for asdorption, governed by electrostatic forces, is presented. The model adequently representes the competitive adsorption kinetics and equilibria.
Effects of solvent viscosity and different guanidine salts on the kinetics of ribonuclease A chain folding
Authors: Tsong Tian Y. , Baldwin Robert L.
Published: December 2004

The kinetics of folding of the two forms of unfolded ribonuclease A have been measured as a function of solvent viscosity by adding either glycerol or sucrose. The aim is to find out if either reaction is rate limited by segmental motion whose rate depends on external friction. The fast folding reaction (U2 ⇄ N) is known to be the direct folding process, and the slow folding reaction (U1 ⇌ N) is known to be rate limited by an interconversion between two forms (U1 ⇌ U2) which are present after unfolding in strongly denaturing conditions. No dependence on solvent viscosity is found, either for the direct folding reaction or for the interconversion reaction. Each folding reaction has also been tested to see if its rate depends on the concentration of one or more partly folded intermediates, by adding denaturants destabilize any partly folded structures. Different guanidine salts are used as denaturants to vary the denaturing effectiveness of the salt while holding the guanidinium ion concentration constant. The rates both of the direct folding reaction and of the interconversion reaction decrease in relation to the denaturing effectiveness of the salt. However, there is a basic difference between the responses of the fast and slow folding reactions to low concentrations of denaturants. Although each folding reaction produces native protein, there is an 800‐fold decrease in the rate of the fast folding reaction in 1M guanidine thiocyanate and only a 13‐fold decrease in the rate of the slow folding reaction. This is consistent with the fast reaction being the direct folding process and the slow reaction being rate limited by the initial conversion of the slowrefolding to the fast‐refolding form. Both the lack of viscosity dependence and the effects of denaturants indicate that the formation of structure is rate limiting in the direct folding reaction, U2 ⇌ N. The failure to find a viscosity dependence for the interconversion reaction, U1 ⇌ U2, indicates that in this reaction also friction‐limited segmental motion is not the rate‐limiting process. Since the U1 ⇌ U2 interconversion still occurs when the polypeptide chain is completely unfolded, the surprising result is that its rate in refolding conditions depends significantly on a reaction intermediate which is “denatured” by guanidine salts.
Interaction of alcohols with proteins
Authors: Bull Henry B. , Breese Keith
Published: December 2004

The kinetics of denaturation of egg albumin have been determined for methanol, ethanol, propanol, and butanol. The reactions are first order in respect to protein but between 11th and 18th order for the alcohols. The denaturation reaction is characterized by a large temperature coefficient with little or no dependence on pH. There is a marked change of pH when proteins are denatured. A series of eight proteins has been studied. There is surprisingly little difference in susceptibility to alcohol denaturation between the various proteins. Methanol, ethanol, propanol, and butanol are strongly bound to egg albumin—butanol being the most strongly bound. The binding of alcohol is probably accompanied by protein dehydration. The polyhydric alcohols' behavior is much different. These alcohols do not denature proteins and the protein is hydrated. Sucrose produces the greatest degree of hydration.
The effect of homologous amino acid replacement on the conformation of oligopeptides. II. Synthesis of co‐oligopeptides containing methionine and glycine
Authors: Champi Jim , Steinfeld Alvin S. , Naider Fred , Becker Jeffrey M.
Published: December 2004

The synthess of 18 co‐oligopeptides of L‐methionine and glycine is reported. A series of oligomers, Boc‐Gly‐Metn‐OMe (n = 1–6), and six hexamers‐containing five methionyl and one glycyl residue were synthesized using the mixed anhydride procedure. Polarimetric studies give evidence that oligomers in the Boc‐Gly‐Metn‐Ome series are essentially disordered in hexafluoroacetone sesquihydrate but begin forming secondry structures at n > 4 in trifluorethanol. Difference in the molar rotation values found for the six hexamers in hexafluoroacetone sesquihydrate may indicate that these compounds, while primirily disordered, are present in slightly different conformations.
The effect of homologos amini acid replacement on the conformation of oligopeptides. III. CD studies on co‐oligopeptides of methionine and valine or methionine and glycine in organic solution
Authors: Naider F. , Becker J. M. , Ribeiro A. , Goodman M.
Published: December 2004

A conformational analyis of co‐ologopeptides containing methionine and valine or methionine and glycine was carried out using circular dichrosim. The oligopeptides containing valine and methionine (dimer to hexamer) are disorder in hexafluoropropane diol·0.5 H2O and trimethyl phospate but become helical in trifluoroethanol at the heptamer. The CD spectra for hesamers and heptamers containing methionine or methionine and one valine give evidience that one valyl residue can be inserted into these peptides wothout affecting their secondry structure. Co‐oligomethionines. The effect of a glycyl residue are generally less ordered than the analogous homo‐oligomethionines. The effect of a glycl residue on the structure of the longer oligopeptides depends on its position in the chain. When inserted in the center of a hexamer or heptamer, the single glycyl residue destabilizes the ordered secondry structures in solution. Finally, evidence is presented that the CD patterns observed for various pentamers and hexamers are consistent with some order at these chain lenghts.
A model for the interrelationship between asymmetric interbase hydrogen bonding and base–base stacking in hemiprotonated polyribocytidylic acid: Crystal structure of 1‐methylcytosine hemihydroiodide hemihydrate
Authors: Kistemacher Thomas J. , Rossi Miriam , Marzilli Luigi G.
Published: December 2004

An x‐ray structural study of the 1‐methylcytosine H+ complex reveals asymmetrically hydrogen‐bonded dimers which are further stacked such that the molecular overlaps are between charged and neutral bases. This study supports the assignment of the asymmetry in the interbase hydrogen bonding in the cytidine–cytidine H+ hydrogen‐bonded complex. Furthermore, it is suggested that hemiprotonated, helical polyribocytidylic acid has as its translational repeat unit a set of highly stacked pairs of asymmetrically hydrogenbonded bases. The asymmetry in the interbase hydrogen bonding is stimulated, at least in part, by base‐stacking considerations.
The Raman spectra of Bence‐Jones proteins. Disulfide stretching frequencies and dependence of Raman intensity of tryptophan residues on their environments
Authors: Kitagawa T. , Azuma T. , Hamaguchi K.
Published: December 2004

The Raman spectra of Bence‐Jones proteins (BJP) were measured for their native and denatured states. All of the native BJPs investigated gave amide I at 1670–1675 cm−1 and amide III at 1242–1246 cm−1. Although the amide I was shifted to 1667 cm−1 upon the LiBr, acid, and thermal denaturation, as expected, the amide III frequency was unaltered, indicating that the antiparallel β‐ and disordered structures of BJP provide amide III at almost the same frequencies. The intensity of the 880‐cm−1 line of native BJP was relatively intense compared with that of amino acid mixed solution in which the mole ratios of Trp, Phe, and Tyr were adjusted to reproduce the corresponding ratios of BJP. However, the intensity was evidently reduced upon LiBr, acid, and thermal denaturation, approaching that of the amino acid mixture. Thus, the intensity of the 880‐cm−1 line is proposed as a practical probe for the environment of Trp residues. The pH dependence of the intensity of the 880‐cm−1 line suggests that one of two buried Trp residues is exposed between pH 4 and 3.2 and the other between pH 3.2 and 1.4. The variable fragment (VL) of BJP (Tod) exhibited a SS stretching Raman line at 525 cm−1. Provided that the crystallographic data of the VL of BJP is applicable to VL of BJP (Tod), the 525 cm−1 of the SS stretching frequency should be assigned to a TGG conformation of linkage, but not to the AGT or AGG conformation. This supports Sugeta's model rather than Scheraga's model.
1H‐ and 13C‐NMR studies of N‐acetyl‐L‐alanine methylester and N‐acetyl‐L‐alanine methylamide. I. Self‐association
Authors: Asakura Tetsuo , Kamio Masaru , Nishioka Atsuo
Published: December 2004

The 1H‐ and 13C‐NMR spectra of N‐acetyl‐L‐alanine methylester and N‐acetyl‐L‐alanine methylamide were measured to examine the modes of self‐association of these molecules in solution. The different dilution shifts between these molecules seem to correspond to the difference in the associated state for each molecule. Consequently, for the former molecule, a dimer model forming the intermolecular hydrogen bond through Ala NH hydrogen atom in one molecule to Ala CO oxygen atom in another molecule was proposed. Another dimer model, which coincides with that proposed recently by Neel and coworkers, was proposed for the latter molecule. This second dimer model forms an intermolecular hydrogen bond through the NH of the N‐methylamide group in one molecule to the acetyl CO in another molecule.
Association studies of N‐acetyl‐amino acid N,N‐dimethylamides in carbon tetrachloride
Authors: Mizuno Kazuko , Nishio Shigenori , Shindo Yohji
Published: December 2004

The self‐association of N‐acetylglycine N,N‐dimethylamide, N‐acetyl‐L‐valine N,N‐dimethylamide, and N‐acetyl‐L‐phenylalanine N,N‐dimethylamide in carbon tetrachloride was investigated by using ir and 1H‐nmr methods. It was concluded from ir measurements that the associated species is the dimer formed as a result of the simultaneous formation of two intermolecular hydrogen bonds. This is supported by the results of 1H‐nmr measurements. Thermodynamic quantities for the association were determined from the temperature and concentration dependence of the NH proton chemical shifts of the sample solutions. Compared with the Gly derivative, L‐Val and L‐Phe derivatives have larger values of −ΔH for association, which shows good correlation with ΔvNH values, the difference between the maxima of the monomer and dimer bands, obtained from ir spectra. This is due to the less stable monomer conformation and to the stronger intermolecular hydrogen bonding of the dimers in L‐Val and L‐Phe derivatives. The line shapes of both methyl proton resonances of L‐Val residue and methylene proton resonances of L‐Phe residue were found to vary with concentration and temperature of the sample solutions. These data indicate that the rotation about the Cα—Cβ bond is restricted by the steric hindrance present in the associated dimers. All these experimental results can be related to the fact that L‐Val and L‐Phe derivatives have a warped framework because of the bulky side chains, whereas the Gly derivative has a planar framework.
Salt‐concentration dependence of melting profiles of lambda phage DNAs: evidence for long‐range interactions and pronounced end effects
Authors: Gotoh Osamu , Wada Akiyoshi , Yabuki Sadato
Published: December 2004

Melting profiles of DNAs from wild‐type λ phage and a deletion mutant phage λb2 were examined in a wide range of salt concentration. The fine structure of the melting profiles changed sharply with salt concentration, especially in the range [Na+] ⩽ 10 mM. A comparison of the melting profiles between the wild‐type and the deletion mutant DNAs provided good evidence for extremely high melting cooperativity under low salt conditions, which is clearly manifested as the long‐range interactions and the pronounced end effects; a large melting peak appeared as a result of the b2 deletion without any inserted sequence in the salt range [Na+] ⩽ 2.8 mM. It was also suggested that in the further reduced salt range [Na+] ⩽ 2.0 mM, melting of a λ DNA molecule starts from its right end rather than the most (A + T)‐rich central region. The molecular basis of the high melting cooperativity at low salt concentrations can be explained in terms of the increased free energy associated with loop formation in the double‐helical structure of DNA.
The role of water in the crystal structure of N‐acetyl‐L‐4‐hydroxyproline
Authors: Hospital M. , Courseille C. , Leroy F. , Roques B. P.
Published: December 2004

The crystal structure of N‐acetyl‐L‐4‐hydroxyproline (Hyp) was determined by direct methods. (The crystal is orthorhombic with the space group P212121.) The acetyl group is in the trans conformation and the pyrrolidine ring puckers at Cγ (CsCγ envelope), as in most Hyp residues. According to the rotation angle ψ = −30°, the N‐acetyl‐L‐4Hyp has the same conformation as an α‐helix of prolyl residues. The crystal packing is stabilized by hydrogen bonds between three different molecules and the same molecule of water. One of the water bridges involves the carbonyl of the N‐acetyl group of one molecule and the hydrogen atom of the 4‐OH group of another. Such an arrangement has been proposed to explain the high stability of (Gly‐L‐Pro‐L‐4Hyp)n. A second bridge involves the two hydrogens of the water molecule and the carbonyl groups of two neighbouring molecules, as already proposed in a dihydrated model of collagen. These experimental features, which are discussed in relation to the different models of collagen, allow us to propose an hypothetical arrangement for the water molecule which is strongly retained in the triple helix of (Gly‐L‐Pro‐L‐4Hyp)n.
Energetics of intercalation specificity. I. Backbone unwinding
Authors: Ornstein Rick L. , Rein Robert
Published: December 2004

An empirical partitioned‐potential function with optimized parameters was employed to investigate the basis of intercalation specificity recently observed by experimental techniques. The nature of this specificity is discussed in terms of component interactions for all non‐truncated complementary dinucleoside triphosphate mini‐ (or miniature) helices. Our calculations agree with available evidence indicating the preference of Pyr(3′‐5′)Pur sequences over Pur(3′‐5′)Pyr sequences to change from the B‐DNA to the intercalated conformation. Base–base (stacking) and base–phosphate interactions control the specificity. The extent of net electrostatic charge on the phosphate groups play an important but limited role in establishing the observed specificity. These results should apply for the class of aromatic agents involved in nonspecific intercalation with nucleic acids but not necessarily for aromatic agents involved in specific reactions with a particular nucleotide base.
Influence of hydration on the conformational stability and formation of bends in terminally blocked dipeptides
Authors: Hodes Zachary I. , Némethy George , Scheraga Harold A.
Published: December 2004

The conformations of 23 terminally blocked dipeptide sequences were examined by conformational energy calculations that included the effects of the aqueous solvent. Starting structures were derived from combinations of minimum‐energy conformations of hydrated single residues. Their conformational energies were then minimized using the ECEPP potential (Empirical Conformational Energy Program for Peptides) with hydration included. Short‐range interactions dominate in stabilizing the conformations of the hydrated dipeptides. Differences between conformational stabilities of hydrated and unhydrated dipeptides in many cases are due to the competition of solute–water and intramolecular hydrogen bonds. In other cases, perturbation of the hydration shell of the solute by close approach of solute atoms alters conformational preferences. Probabilities of formation of bends were calculated and compared to the corresponding quantities for unhydrated dipeptides and to those calculated from x‐ray structures. For bends in dipeptides containing two nonpolar amino acids, computations omitting hydration yield better results. However, better agreement with experimental (x‐ray) bend probabilities for dipeptides containing glycine or polar amino acids is obtained only in some sequences when hydration is included. The results are rationalized by the observation that, in proteins, bends containing nonpolar sequences occur on the inside, shielded from the solvent. Bends containing glycine or polar amino acids occur frequently on the surface of the protein, but they are not completely hydrated.
Effect of inhibitor complex formation on the hydration properties of α‐chymotrypsin. Changes induced in protein hydration by tosylation of the native enzyme
Authors: Lüscher Madeleine , Schindler Paul , Rüegg Max , Rottenberg Max
Published: December 2004

The effect of enzyme‐inhibitor complex formation on the hydration properties of the macromolecular moiety was investigated on the model system of α‐chymotrypsin and its Ser‐195 tosyl derivative. The primary (A‐shell) hydration of the native and modified enzyme was compared by sorption measurements. The secondary (B‐shell) hydration water was investigated by differential scanning calorimetry. Tosylation is known to induce pronounced conformational changes in the chymotrypsin molecule. These structural modifications have the following effects on the hydration of the native enzyme.

The water binding capacity of the protein surface is significantly increased, as shown by both the calorimetric and the sorption results. The amount of unfreezable water of primary hydration is increased by 50 mol H2O/mol chymotrypsin.

The heats (ΔH) and entropies (ΔS) of the interaction of water with chymotrypsin are strongly reduced in the modified enzyme. This effect is interpretable by a reduction of the H bonding potential of the protein surface. Parallel to this decrease in δH, the heats of fusion of the secondary hydration water (Qfus) are significantly increased by tosylation (Qfus = 256.2 ± 7.8 and 294.2 ± 4.8 J g−1 H2O for the native and the tosylated enzyme, respectively). This increase in Qfus reflects an increase in the extent of H bonding in the B‐shell hydration sphere.

These changes in the hydration of the native enzyme, associated with the reaction: native chymotrypsin → tosylchymotrypsin, are interpreted by cooperative phase transitions of water molecules in the primary and secondary hydration water. One of these transitions was found to exhibit a significant, linear enthalpy–entropy compensation effect. The compensation temperature \documentclass{article}\pagestyle{empty}\begin{document}$ \hat{\beta} $\end{document} is 290.7 ± 2.8°K. This \documentclass{article}\pagestyle{empty}\begin{document}$ \hat{\beta} $\end{document} value agrees well with compensation temperatures reported in the literature for a series of biochemical reactions in aqueous solution (250–320° K). This agreement in \documentclass{article}\pagestyle{empty}\begin{document}$ \hat{\beta} $\end{document} may point to a common source of both compensation phenomena.
Electric field effect on the helix–coil transition of poly(L‐α,γ‐diaminobutyric acid hydrochloride) in methanol/water mixtures
Authors: Fujimori Mitsuo , Kikuchi Kazuo , Yoshioka Koshiro , Kubota Shigeo
Published: December 2004

Transient electric birefringence of poly(L‐α,γ‐diaminobutyric acid hydrochloride) in methanol/water mixtures has been measured over a wide range of field strengths and solvent compositions and at different polymer concentrations and temperatures. The molar ellipticity at 222 nm and the specific Kerr constant underwent an abrupt change between 75 and 80 vol % methanol at 25°C, accompanied by a solvent‐induced helix–coil transition. Anomalous birefringence transients were observed between 78 and 80 vol% methanol above threshold field strengths. The double logarithmic plots of the steady‐state specific birefringence versus the square of field strength for different solvent compositions and polymer concentrations could be superimposed by shifting them horizontally along the abscissa and vertically along the ordinate except for the range where anomalous transients were observed. The threshold field strength could be estimated from the point at which a downward deviation occurred. It increased with increasing polymer concentration and with increasing methanol content on the verge of the transition region. The results were interpreted as indicating that a conformational change from the charged helix to the charged coil is induced by high fields in this system, as in the case of poly(L‐lysine hydrobromide) in methanol/water mixtures.
Circular dichroism of complexes of NADH with self‐associating bovine liver glutamate dehydrogenase
Authors: Zeiri Leila , Reisler Emil
Published: December 2004

The CD of GDH–NADH complexes was measured in order to reexamine the binding of coenzyme to GDH. The existence of two distinct Cotton effects associated with two separate NADH binding sites/subunit was confirmed with native, polymerizing and crosslinked, unpolymerizing enzyme. CD titration of the high‐affinity NADH sites revealed significant dependence of the optical activity of the bound coenzyme on the state of protein association. Molar ellipticity of bound NADH decreased with the increasing degree of polymerization of GDH. It is suggested that the high‐affinity NADH sites are loacted at or near the association interface. Binding of NADH to the low‐affinity sites, in the presence of GTP, leads to an inversion of the CD spectrum of GDH–NADH complexes. This inversion is not related to the polymerization of GDH. However, for proper analysis of the CD of NADH bound to the low‐affinity sites, a correction for the effect of polymerization on the optical activity of NADH bound to the high‐affinity sites is required.
Nematic polymers: Excluded‐volume effects
Authors: Kim Y. H. , Pincus P.
Published: December 2004

We present a theoretical model which describes a cooperative helix–coil liquid‐crystal phase transition. We show that this model predicts a first‐order phase transition where certain types of chainlike macromolecules in solution make a transition from a nearly coiled to a nearly rigid conformation accompanied by a simultaneous development of long‐range nematic‐type liquid crystalline orientational order. From this model, the phase boundaries between nematic and isotropic phases are obtained as functions of concentration of macromolecules and of other physical parameters.
Dielectric relaxation of DNA solutions. III. Effects of DNA concentration, protein contamination, and mixed solvents
Authors: Sakamoto Masanori , Hayakawa Reinosuke , Wada Yasaku
Published: December 2004

As a continuation of previous papers [Biopolymers (1976) 15, 879; (1978) 17, 1508], the low‐frequency dielectric relaxation of DNA solutions was studied with a four‐electrode cell and the simultaneous two‐frequency measurement. Below a critical concentration, the dielectric relaxation time agrees with the rotational relaxation time estimated from the reduced viscosity and is almost independent of DNA concentration Cp, and the dielectric increment is proportional to Cp. The critical concentration is approximately 0.02% of DNA for molecular weight Mr 2 × 106 and 0.2% for Mr 4.5 × 105 in 1 mM NaCl. Dielectric relaxations are compared for samples before and after deproteinization, and the protein contamination is found to have a minor effect on the dipole moment of DNA. The effect of a mixed solvent of water and ethanol on the dielectric relaxation of DNA is well interpreted in terms of changes in viscosity and the dielectric constant of the solvent, assuming that the relaxation arises from rotation of the molecule with a quasi‐permanent dipole due to counterion fluctuation.
Analysis of cooperativity and ion effects in the interaction of quinacrine with DNA
Authors: Wilson W. David , Lopp Irene G.
Published: December 2004

The interaction of quinacrine with calf thymus DNA was monitored at several different ionic strengths using spectrophotometric and equilibrium dialysis techniques. The binding results can be explained, assuming each base pair is a potential binding site, using a model containing two negative cooperative effects: (1) ligand exclusion at binding sites adjacent to a filled binding site and (2) ligand–ligand negative cooperativity at adjacent filled binding sites. The logarithm of the observed equilibrium constant (Kobs) determined by this model varies linearily with log[Na+], as predicted by the ion condensation theory for polyelectrolytes. When the log Kobs plot is correlated for sodium release by DNA in the intercalation conformational change, the predicted number of ion pairs between the ligand and DNA is approximately two, as expected for the quinacrine dication. Even though Kobs depends strongly on ionic strength, the ligand negative cooperativity parameter ω was found to be indpendent of ionic strength within experimental error. This finding is also in agreement with the ion condensation theory, which predicts a relatively constant amount of condensed counterion on the DNA double helix over this ionic strength range. Drugs would, therefore, experience a relatively constant ionic environment when complexed to DNA even though the ionic conditions of the solvent could change considerably.
Relationship between conformation and physicochemical properties of polypeptides. I. Synthesis of homo‐ and co‐oligopeptides by the liquid‐phase method
Authors: El Rahman S. Abd , Anzinger H. , Mutter M.
Published: December 2004

The synthesis of the following oligo‐ and co‐oligopeptides by the liquid‐phase method is described: (L‐Met)15 (I), [L‐Glu(OBzl)]20 (II), (L‐Val)8‐Gly (IV), (L‐Ile)8‐Gly (V), (L‐Ile)4‐Gly‐(L‐Ile)4 (VI), (L‐Ile)4‐Pro‐(L‐Ile)4 (VII), (L‐Met)5‐L‐Pro‐(L‐Met)5 (VIII), [L‐Glu(OBzl)]7‐L‐Pro‐[L‐Glu(OBzl)]7 (IX). The oligomers are covalently bound to bifunctional polyethylene glycol (PEG) and monofunctional PEG‐M of Mr 5 × 103−2 × 104. Analytical controls were carried out after each step of synthesis in order to ensure quantitative coupling yields. All products could be obtained in high purity as indicated by amino acid analysis, thin‐layer chromatography and chiroptical methods. The solubility of the oligomers was strongly enhanced by the presence of the C‐terminal PEG group, enabling conformational investigations in a variety of solvents. A significant relationship between conformation and physicochemical properties of the oligopeptides was observed. Oligomers with tendencies to adopt α‐helical (I, II) or unordered structures (VI–IX) showed no pronounced change in solubility or coupling kinetics during chain elongation, whereas the onset of a β‐structure (IV, V) was paralleled by a drastic decrease in solubility and reactivity of the terminal amino groups. Most notably, the insertion of a proline or glycine in the middle of a β‐forming peptide chain (VI, VII) resulted in a considerable increase in solubility compared to the corresponding homo‐oligomers. The impact of the conformational properties of a peptide chain on strategic considerations of peptide synthesis in solution is delineated.
Circular dichroism and conformational analysis of the membrane‐modifying peptide ‐N‐t‐Boc‐(Aib‐L‐Ala)5‐Gly‐Ala‐Aib‐Pro‐Ala‐Aib‐Aib‐Glu‐(OBzl)‐Gln‐OMe with respect to alamethicin
Authors: Oekonomopulos R. , Jung G.
Published: December 2004

The conformational analysis of the CD spectrum is reported for the synthetic and membrane‐modifying nonadecapeptide analog of alamethicin N‐t‐Boc‐(Aib‐L‐Ala)5‐Gly‐Ala‐Aib‐Pro‐Ala‐Aib‐Aib‐Glu(OBzl)‐ Gln‐OMe. The CD data are evaluated according to three different methods and are discussed with respect to those obtained from natural alamethicin and suitable models such as N‐t‐Boc‐(Aib‐L‐Ala)7‐OPOE, fragments of the synthetic nonadecapeptide, and the hexadecapeptide N‐t‐Boc‐(Aib‐L‐Ala)5‐Pro‐Ala‐Aib‐Aib‐Glu(OBzl)‐Gln‐OMe. The synthetic nonadecapeptide with the longer helical region exhibits membrane activities comparable to those of alamethicin, whereas the hexadecapeptide with the shorter helix is inactive.
Heat capacities of transfer of some amino acids and peptides from water to aqueous urea solution
Authors: Prasad K. P. , Ahluwalia J. C.
Published: December 2004

Integral enthalpies of solution at low concentrations of several amino acids and peptides in 2 and 6M urea solutions have been determined at 25 and 35°C. These data have been used to derive the enthalpies of transfer (at 25 and 35°C) and heat capacities of transfer (at 30°C) of these amino acids and peptides from water to aqueous urea solutions. Furthermore, the enthalpies of transfer and heat capacities of transfer per CH2 group and per peptide group CONH have also been estimated. These results show that while the enthalpies and heat capacities of transfer per CH2 group are positive and negative, respectively, the reverse is true for CONH group. The implications of these results in the mechanism of the denaturation of proteins by urea are discussed.
Synthesis and ordered structure of amphipatic block copolymers with a saccharide and a peptide block
Authors: Douy André , Gallot Bernard
Published: December 2004

Amphipatic block copolymers (OβEb) with a hydrophilic saccharide block and a hydrophobic polypeptide block were synthesized. In these copolymers the saccharide block is the glyco‐amino acid Oβ from ovomucoid and the peptide block (Eb) is a poly(γ‐benzyl‐L‐glutamate) block. Copolymers OβEb exhibit, in the solid state and in Me2SO concentrated solutions, mesomorphic lamellar structures where the polypeptide chains are in an α‐helical conformation. Depending on the molecular weight of the polypeptide block, three types of lamellar structures are obtained, and they differ by the mode of organization of the polypeptide chains in their lamellae and by the T or Y conformation of the saccharide block.
Thermoelasticity of swollen elastin networks at constant composition
Authors: Andrady A. L. , Mark J. E.
Published: December 2004

Thermoelastic (force–temperature) measurements were carried out on elastin networks, swollen with a nonvolatile diluent, in elongation over the temperature range 8–35°C. The experiments were conducted at constant composition (thermodynamically closed system) rather than at swelling equilibrium (open system), thus avoiding the need for approximate corrections to account for the changes in swelling with temperature and with elongation. The results indicate that the elastic force is primarily of entropic origin and thus support the random‐network model rather than the liquid‐drop model for elastin in the rubberlike state. A significant energetic contribution to the force was observed, however, as is usually the case for a variety of elastomeric polymers.
Simulation methods for protein structure fluctuations
Authors: Northrup Scott H. , McCammon J. Andrew
Published: December 2004

Three numerical techniques for generating thermally accessible configurations of globular proteins are considered; these techniques are the molecular dynamics method, the Metropolis Monte Carlo method, and a modified Monte Carlo method which takes account of the forces acting on the protein atoms. The molecular dynamics method is shown to be more efficient than either of the Monte Carlo methods. Because it may be necessary to use Monte Carlo methods in certain important types of sampling problems, the behavior of these methods is examined in some detail. It is found that an acceptance ratio close to 1/6 yields optimum efficiency for the Metropolis method, in contrast to what is often assumed. This result, together with the overall inefficiency of the Monte Carlo methods, appears to arise from the anisotropic forces acting on the protein atoms due to their covalent bonding. Possible ways of improving the Monte Carlo methods are suggested.
Fluctuations of protein structure as expressed in the distribution of hydrogen exchange rate constants
Authors: Knox Donald G. , Rosenberg Andreas
Published: December 2004

Hydrogen exchange kinetics of proteins provide information about the dynamics of their structure. The interpretation of experiments has been limited by difficulty in identifying individual rate constants. In order to invert the kinetic data, and to gain information about the individual reacting sites, we introduce a Laplace inversion technique and obtain the distribution function of rate constants by which the intricate reaction proceeds. A series of carefully overlapped experiments were performed on lysozyme at 25°C, an exchange profile obtained, and a distribution function extracted. This function was composed of a product of two terms, indicating two parallel pathways. The first, a power‐law term, was attributed to exchange from the native state. This part of the distribution function thus describes the scope of the conformational fluctuations in proteins at constant temperature and pressure. The second, an exponential, was seen to be associated with the pathway involving thermal unfolding and subsequent free exchange with the solvent. The influence of trichlorethanol and glycerol on the total distribution function was measured. Trichloroethanol selectively increased the contribution from the thermal unfolding pathway, whereas glycerol, besides decreasing this type of contribution, increased the width of the distribution function attributed to structural fluctuations.
15N‐nmr spectroscopy. 20. Cis/trans isomerism and neighboring residue effects of proline‐containing peptides
Authors: Hull William E. , Kricheldorf Hans R.
Published: December 2004

Five N‐protected tetrapeptide esters of the structure Gly‐Pro‐X‐X*‐O‐methyl were synthesized in such a way that one of the two variable amino acid residues (X) was isotopically enriched in 15N (denoted by*). The variable amino acids are glycine, alanine, leucine, valine, and phenylalanine. For the natural abundance 15N‐nmr spectra of these tetrapeptide derivatives in methylene chloride only the signals of the Gly‐Pro trans isomer were found. In a 2:1 mixture of acetone and dimethylsulfoxide, signals for both the cis and trans isomers were observed. Three of the five tetrapeptide derivatives show cis/trans splitting of all four nitrogen signals. The 15N‐nmr spectra of Z‐Pro‐Pro‐OH and of (D,L‐proline)n were measured in a 2:1 mixture of acetone and dimethylsulfoxide as well as in water. The effects of solvents and neighboring residues and the influence of the cis/trans isomerism on the nmr spectra are discussed. The determination of the cis/trans equilibria and the assignment of the 15N‐nmr signals of all oligopeptides were achieved by selective isotopic enrichment and by means of 13C‐nmr spectra.
Effect of counterions on complex coacervation
Authors: Tainaka Kei‐Ichi
Published: December 2004

In a recent paper, we developed a thermodynamic theory on the complex coacervation in the absence of low molecular ions, under the assumption that the coacervation is a condensation phenomenon of aggregates of polyanion and polycation in the aqueous solution, by obtaining the interaction potential US between these aggregates on the basis of Flory's method. In this paper, we have extended the theory to a more complicated phenomenon of the counterion‐containing solutions. This treatment has led the interaction potential having an additional contribution to US resulting from an entropy increase by the counterion distribution. The phase diagram between solution (sol) and separated phase has been obtained as a function of the difference of charges between polyanion and polycation. It has been found that the presence of counterions sensitively suppresses the coacervation.
Thermal stability and renaturation of DNA in dimethyl sulfoxide solutions: Acceleration of the renaturation rate
Authors: Escara June F. , Hutton James R.
Published: December 2004

The thermal stability and renaturation kinetics of DNA have been studied as a function of dimethyl sulfoxide (DMSO) concentration. Increasing the concentration of DMSO lowers the melting temperature of DNA but results in an increased second‐order renaturation rate. For example, in a DNA solution containing 0.20M NaCl, 0.01M Tris (pH 8.0), and 0.001M EDTA, the addition of 40% DMSO lowers the melting temperature of the DNA by 27°C and approximately doubles the optimal renaturation rate. The effect of DMSO on the renaturation rate is shown to be at least partially due to its effect on the solution dielectric constant and to be consistent with the polyelectrolyte counterion condensation theory of Manning [(1976) Biopolymers 15, 1333–1343].
Dynamic light scattering studies of internal motions in DNA. II. Clean viral DNAs
Authors: Thomas J. C. , Allison S. A. , Schurr J. M. , Holder R. D.
Published: December 2004

Internal Brownian motions of clean ϕ29 and λ‐DNAs have been studied using photon‐correlation techniques at both visible (λ0 = 632.8 nm) and uv (λ0 = 363.8 nm) wavelengths. The present dynamic light scattering data, which extend to K2 = 19 × 1010 cm−2, can in every case be satisfactorily simulated by a Rouse‐Zimm model polymer with an appropriate choice of the three model parameters. The effects of pH, salt concentration, single‐strand breaks, and molecular weight on those model parameters have also been investigated. Intact clean DNAs exhibit surprisingly little variation with pH from 7.85 to 10.25, with salt concentration from 0.01 NaCl to 5.4M NH4Cl, or with molecular weight or GC content. The single‐strand breaks have no effect at pH 9.46, but produce dramatic changes in the model parameters at pH 10.0 and 10.25, indicating the introduction of titratable joints at those pHs. The failure of either single‐strand breaks or a large change in GC content to alter the model parameters in the neutral pH range is a strong indication that local denaturation is not required for those flexions and torsions that dominate the relaxation of fluctuations in the scattered light. The Langevin relaxation time for the slowest internal mode of a particular Rouse‐Zimm model derived from the dynamic light scattering data is compared with pertinent literature data extrapolated to the same molecular weight. The present algorithm for determining model parameters from the light‐scattering Dapp vs K2 curve actually yields a Langevin time in fairly good agreement with the literature value. For unknown reasons the light‐scattering D0 values generally exceed those obtained from the molecular weight and sedimentation coefficient by about 20%.
Activity coefficients of counterions and conformation in kappa‐carrageenan systems
Authors: Rochas C. , Rinaudo M.
Published: December 2004

The optical rotation and the conductivity of kappa‐carrageenans in aqueous solution have been investigated as functions of temperature in the presence of various electrolytes. The activity coefficients of sodium and potassium have been determined and correlated with the conformation. The potassium activity coefficient under ordered conformation is in agreement with a mechanism of dimerization.
1H‐nmr study of protected methionine homo‐oligopeptides in helix‐supporting environment
Authors: Naider Fred , Ribeiro Anthony A. , Goodman Murray
Published: December 2004

1H‐nmr spectra for a series of Boc‐L‐(Met)n‐OMe (n = 2–9) homo‐oligopeptides have been observed in the helix‐supporting solvent trifluoroethanol (TFE) at millimolar concentrations. Interfering solvent peaks were eliminated using two decoupling frequencies to selectively remove the methylene and hydroxyl protons of the solvent. Comparisons with specifically α‐deuterated homo‐oligopeptides gave complete assignments of the NH region of the Boc‐Metn‐OMe oligomers up to the heptapeptide. Analysis of chemical shifts, coupling constants, and temperature dependence of chemical shifts suggests that up to the hexapeptide, similar structures exist in deuterochloroform and TFE. In contrast, nmr parameters at the heptapeptide for several internal residues differ in these solvents. These results suggest that a C7 to α‐helix transition may occur in TFE as the chain length of the methionine oligopeptides increases.
Sedimentation‐equilibrium studies of the polysaccharide components of Pseudomonas aeruginosa
Authors: Horton Derek , Riley David A. , Hansen Poul M. T.
Published: December 2004

Mild acid hydrolysis of lipopolysaccharide antigens from seven different serotype strains antigen immunotypes nos. 1–7 [in the classification of Fisher, M. W., Devlin, H. B. & Gnabasik, F. J. (1969) J. Bacteriol. 98, 835–836] of Pseudomonas aeruginosa gave polysaccharide components of high molecular weight, which were isolated by gel filtration and dialysis. These components were examined by ultracentrifugation at equilibrium with the Rayleigh interferometric optical system. The partial specific volumes were calculated from densities obtained by using a mechanical oscillator. The average molecular weights (Mn, Mw, and Mz) were calculated and compared to evaluate the polydispersity of the polysaccharides. The nonideality was investigated by varying the rotor speed, the height of the solution column, and the concentrations of the polysaccharide fractions. The molar masses were found to range from 14,000 for the polysaccharide from immunotype two to 24,000 for that from immunotype one, when extrapolated to zero rotor speed and solution column height.
Hydrodynamic resistance and diffusion coefficients of a freely hinged rod
Authors: Wegener William A.
Published: December 2004

The seven‐dimensional hydrodynamic resistance and diffusion tensors are evaluated for a rod which is freely hinged at its center and immersed in a viscous fluid. The hydrodynamic resistance tensor is first determined at the hinge, then transformed to other points and inverted to obtain the diffusion tensor. Hydrodynamic interactions between rod halves are neglected, which is asymptotically correct for long rods. In the long‐rod limit, the diffusion coefficient characterizing translations over macroscopic distances is decreased by 3–6% from that for a rigid straight rod of same total length, while the average end‐over‐end rotational diffusion coefficient for each rod half is increased 4.67 times.
Conformational energy studies on N‐methylated analogs of thyrotropin releasing hormone, enkephalin, and luteinizing hormone‐releasing hormone
Authors: Manavalan Parthasarathy , Momany Frank A.
Published: December 2004

Empirical conformational energy calculations have been carried out for N‐methyl derivatives of alanine and phenylalanine dipeptide models and N‐methyl‐substituted active analogs of three biologically active peptides, namely thyrotropin‐releasing hormone (TRH), enkephalin (ENK), and luteinizing hormone‐releasing hormone (LHRH). The isoenergetic contour maps and the local dipeptide minima obtained, when the peptide bond (ω) preceding the N‐methylated residue is in the trans configuration show that (1) N‐methylation constricts the conformational freedom of both the ith and (i + 1)th residues; (2), the lowest energy position for both residues occurs around ϕ = −135° ± 5° and ψ = 75° ± 5°, and (3) the αL conformational state is the second lowest energy state for the (i + 1)th residue, whereas for the ith residue the C5 (extended) conformation is second lowest in energy. When the peptide bond (ωi) is in the cis configuration the ith residue is energetically forbidden in the range ϕ = 0° to 180° and ψ = −180° to +180°. Conformations of low energy for ωi = 0° are found to be similar to those obtained for the trans peptide bond. In all the model systems (irrespective of cis or trans), the αR conformational state is energetically very high. Significant deviations from planarity are found for the peptide bond when the amide hydrogen is replaced by a methyl group. Two low‐energy conformers are found for [(N‐Me)His2]TRH. These conformers differ only in the ϕ and ψ values at the (N‐Me)His2 residue. Among the different low‐energy conformers found for each of the ENK analogs [D‐Ala2,(N‐Me)Phe4, Met5]ENK amide and [D‐Ala2,(N‐Me)Met5]ENK amide, one low‐energy conformer was found to be common for both analogs with respect to the side‐chain orientations. The stability of the low‐energy structures is discussed in the light of the activity of other analogs. Two low‐energy conformers were found for [(N‐Me)Leu7]LHRH. These conformations differ in the types of bend around the positions 6 and 7 of LHRH. One bend type is eliminated when the active analog [D‐Ala6,(M‐Me)Leu7]LHRH is considered.
Effect of ionic strength on the pKa of ligands bound to DNA
Authors: Jones Robert L. , Wilson W. David
Published: December 2004

The pKa of 3,8‐diamino‐6‐phenyl‐phenanthridine (DAPP), a nonquaternary analog of ethidium bromide, has been determined spectrophotometrically as a function of sodium ion concentration both free in solution and complexed to DNA. Unwinding angle determinations with this compound were determined with Col El DNA using ethidium bromide as a standard. The unwinding angle for DAPP was 24 ± 2° relative to 26° for ethidium, and this suggests that DAPP binds in a manner quite similar to ethidium and with no significant outside bound DAPP under these experimental conditions. Isobestic behavior was obtained on spectrophotometric pH titration above pH 5 as long as the ratio of DNA‐phosphate to ligand was between 100 and 300 and the DNA phosphate concentration was approximately 0.01M or greater. The loss of isosbestic behavior which occurred below pH 5 is probably due to titration of the 8 amino group of the ligand complexed to DNA. To circumvent this problem, pKa values and the extinction coefficient of the acidic species were both determined by a computer program using experimental data obtained above pH 5. The pKa of the free compound has only a minor dependence on ionic strength, while the pKa of the ligand bound to DNA in an intercalated complex depends strongly on the sodium ion concentration. The pKa of the DAPP‐DNA complex is a linear function of –log[Na+] as predicted by the ion‐condensation theory of polyelectrolytes. It was determined that DAPP is essentially completely bound to DNA under the conditions of these experiments by (1) determination of apparent pKa values as a function of total DNA concentration, (2) calculation of binding constants for the neutral species of DAPP, and (3) spectral analysis of the protonated and neutral species of DAPP bound to DNA relative to DAPP free in solution. These results support the ion‐condensation theory; provide an independent method for measuring ψ*, the average number of counterions associated per phosphate of DNA in the intercalated conformation; and illustrate that there are no specific pH effects or absolute pKa values for ligands bound to DNA, but only ionic‐strength‐dependent results.