bluuebunny/crossref_metadata_2025 huggingface dataset:
Solid‐phase synthesis of larger peptides by a new strategy of detachment from the resin
Authors: Niu Ching‐I , Yang Shi‐Zhen , Ma An‐Qing , Chen Yun‐Neng , Jiang Yong‐Qing , Huang Wei‐Teh
Published: May 2005

Attachment of the side‐chain carboxyl of the protected aspartic or glutamic acid ester to the resin support has been established for the solid‐phase synthesis of the asparagine or glutamine peptide. After further elongation of the α‐amino deprotected resin‐bound peptide ester with protected peptide fragments and the final detachment from the resin support by ammonolysis, the larger peptides containing, or preferably C‐terminated with, asparagine or glutamine could be obtained. Thus, the C‐peptide of human proinsulin was prepared by coupling to the resin‐bound dipeptide derivative, Leu‐Glu(OCH2Ph®)·OtBu, with six fragments consecutively. It was obtained in an overall yield of 36% after detaching from the resin with alcoholic ammonia, followed by mild acidolysis, DEAE cellulose chromatography, and gel filtration. This procedure has now been applied to the synthesis of the C‐terminal fragment of the insulin A chain ending in asparagine, and also to the synthesis of the threonine or serine peptide, where the anchorage to the resin was designed by the reaction of the sidechain hydroxyl with succinic anhydride in the presence of 4‐dimethylaminopyridine to form the hemiester of succinic acid, which in turn was condensed to the aminomethyl resin by the DCC‐HOBt procedure. Model experiments on the synthesis of the Z‐Thr(CO‐CH2CH2CONHCH2Ph®)·OtBu and Bpoc‐Lys(Boc)‐Thr(COCH2CH2CONHCH2Ph®)·OtBu, as well as their detachment from the resin by amminolysis or hydrazinolysis, have shown the potential for a milder process in the solid‐phase synthesis of larger peptides.
Semisynthesis and properties of some insulin analogs
Authors: Inouye Ken , Watanabe Kunio , Tochino Yoshihiro , Kobayashi Masashi , Shigeta Yukio
Published: May 2005

The trypsin‐catalyzed coupling of bovine (Boc)2‐desoctapeptide (B23‐B30)‐insulin with synthetic octapeptides, H‐Gly‐X2‐X3‐X4‐Thr‐Pro‐Lys(Boc)‐Thr‐OH (X2 = Phe or Ala, X3 = Phe or Ala, X4 = Tyr or Ala), followed by deprotection and purification produced the [AlaB24, ThrB30]‐, [AlaB25, ThrB30]‐, and [AlaB26, ThrB30]‐analogs of bovine insulin in yields of 32, 35, and 32%, respectively. The biological activity of these analogs decreased in the order, normal insulin ([ThrB30]‐bovine insulin) = AlaB26‐insulin > AlaB25‐insulin > AlaB24‐insulin, as assayed for receptor binding and some other biological effects, in contrast with the corresponding Leu‐analogs of human insulin, in which the activity decreased in the order, normal insulin > LeuB24‐insulin > LeuB25‐insulin. The affinity to insulin antibodies greatly diminished in both AlaB24‐insulin and LeuB24‐insulin but not in the B25‐substituted analogs. The CD spectra of the Leu‐ and the Ala‐analogs were compared with those of normal insulins to show that no apparent correlation seems to exist between the decrease in biological activity and the conformational changes observed in solution. The effects of organic solvents on the peptide‐bond equilibrium and on the stability of trypsin are also discussed.
A new method for the determination of optical purity of synthetic peptides
Authors: Kusumoto Shoichi , Matsukura Masayuki , Shiba Tetsuo
Published: May 2005

A novel and very accurate method was established for the determination of the optical purity of a peptide by use of the following procedure: (1) hydrolysis of the peptide in deuterium chloride, (2) gas chromatographic separation of each amino acid enantiomer on a chiral phase, and (3) determination of the D/L ratio by mass fragmentography. In this manner, one can estimate the true chiral purity of each amino acid residue with an accuracy of ∼0.2%. The recemization effected during hydrolysis could be eliminated in principle, since the artificially formed DL‐amino acids are necessarily labeled at the α‐position with deuterium and can thus be distinguished mass spectrometrically from the D‐ and L‐isomer originally present in the peptide. The versatility of the method was proven by analysis of model peptides, as well as by a racemization test in fragment condensation.
Cyclic peptides: Past, present, and future
Authors: Blout Elkan R.
Published: May 2005

After a brief review of the genesis of cyclic peptide research, some current areas of interest in this field are examined. The final section of this manuscript considers some possible future directions of research with cyclic peptides.
Mutations and protein stability
Authors: Schellman John A. , Lindorfer Margaret , Hawkes Richard , Grutter Markus
Published: May 2005

The comparative study of proteins which differ in primary structure by point mutations permits one to use thermodynamic experiments to obtain information about the role of specific amino acids in determining protein structure and stability. We have now determined the thermodynamic changes induced in six mutants of T4 lysozyme and have compared the results with the wildtype enzyme. Our work is in collaboration with B. Matthews and his colleagues, who have determined the crystal structure of T4 lysozyme and have obtained difference Fourier maps for four of the mutants. The ultimate aim is to correlate changes in protein stability with changes in the detailed structure of the protein. This paper discusses the thermodynamic results obtained from the mutants studied. All the mutants have a lower Tm than the wild‐type enzyme and changes in the enthalpy of denaturation are sometimes extraordinarily large. Changes in ΔH of denaturation are usually accompanied by compensating changes in ΔS. The general question of protein stability and the manner in which it varies with temperature and mutations is discussed.
Comparison of helix stabilities of poly‐L‐lysine, poly‐L‐ornithine, and poly(L‐diaminobutyric acid)
Authors: Grourke Martin J. , Gibbs Julian H.
Published: May 2005

The helix–coil transitions of aqueous solutions of poly‐α‐L‐lysine (PLL), poly‐α‐L‐ornithine (PLO), and poly(α,γ‐L‐diaminobutyric acid) (PLDBA) have been investigated as functions of pH at 25°C and of temperature at pH 11.75, where these polymers are uncharged; in the cases of the latter two polyamino acids, the transitions have also been studied as functions of apparent pH in methanol‐water solution (50/50 by volume). The helix stability of the polypeptides is shown to be a direct function of the number of methylene groups on the side chain. From an analysis of potentiometric titration data, we find that the difference between the helix stability of PLL and that of PLO is due to a difference of about 1 e.u. in the ΔS° of the transition. Combining the “melting curves” obtained from optical rotatory dispersion studies with the potentiometric titration data permits evaluation of the initiation parameter Z (or 1/σ½) of the statistical mechanical theories for these transitions. The value obtained for Z in the case of uncharged aqueous PLO is ca. 35.
Decay processes of electric birefringence in chemically reacting system
Authors: Kobayasi Syoyu
Published: May 2005

Analytical and numerical calculations of the decay processes of the electric birefringence in an isomerizing system have been performed. Two modes of isomerization are considered: in the first mode, the direction of the axis (of the optical anisotropy) of a molecule is conserved during isomerization; in the second mode, it is not. In the first mode, if GAis not equal to GB, and that, if kAopA2 is not equal to kBopB2 (when the orienting electric field is weak), in which GA, GB and pA, pb are the optical anisotropy and permanent electric dipole moments, of the molecule in two states A and B of the isomerization, and kAo and kBo are the rate constants for the transitions A → B and B → A, respectively, and if diffusion rates are very much slower than the chemical rates, the relaxation due to the chemical reaction can be detected in the decay of the electric birefringence. In the second mode, if diffusion rates are somewhat slower than the chemical rates, the relaxation due to the chemical reaction appears in the decay, even though there are no differences in optical anisotropy and electric moments in the two states. When the rotary diffusion coefficients are different in the two states, the decay process becomes almost one‐component, bringing the chemical rate about ten times higher to diffusion coefficients in both modes.
Conformational aspects of polypeptide structure. XXXIII. Infrared spectra and molecular conformations of γ‐ethyl L‐glutamate oligopeptides
Authors: Goodman Murray , Masuda Yukio , Verdini Axtonio S.
Published: May 2005

Infrared spectra of homo‐ and co‐oligopeptides containing glutamate residues were studied in both solution and solid state. Conformational analyses of these oligomers were carried out by using amide I and II band frequencies. Trimethyl phosphate supports the folded structure of oligomers above the heptamer. In chloroform solution, these oligomers assume the β‐extended structures above the pentamer.
The chain length dependence of the conformation for oligomers of L‐lysine in aqueous solution: Optical rotatory dispersion studies
Authors: Yaron A. , Katchalski E. , Berger A. , Fasman G. D. , Sober H. A.
Published: May 2005

The optical rotatory dispersion of L‐lysine oligopeptides (Lysn, n = 2–22) in solution was measured in water and in 50% methanol. A gradual change with increasing chain length in the ORD curves of the oligomers was observed at pH 4. 3. Not even a chain of 22 residues had ORD identical with that of high molecular weight poly‐L‐lysine. A plot of the average molar residue rotation at 233 nm versus 1/n (where n is the chain length) resulted in a straight line with an intercept of −1900, representing the internal residue rotation of a lysine residue in the random conformation, and a slope of +6200 representing the large end effect. At pH 11.9 a stright line is obtained up to n = 12 after which it deviates from the initial slope indicating onset of helicity. Extrapolation of the initially straight line to tire higher n's provided the necessary zero‐helicity values for calculation of helicity. The highest oligolysine (n = 22) showed at pH 11. 9 13% helicity, which on adding methanol to 50% increased to about 50% helicity. It is shown that helix‐coil data which are usually obtained from the temperature dependence of helicity can be obtained from the dependence of helicity on chain length applying the statistical theory. For the methanol‐water system the cooperativity parameter v was calculated to be in the range 0.024–0.060, with corresponding equilibrium constants w of 1.32–1.43. The helical structure was calculated to be less stable in water than in methanol‐water by about 250 calories per residue.
Estimation of the relative stiffness of the molecular chain in polyelectrolytes from measurements of viscosity at different ionic strengths
Authors: Smidsrød Olav , Haug Arne
Published: May 2005

A method was developed that allowed comparison of the stiffness of the chain in different polyelectrolyte from measurements of the intrinsic viscosity at different concentrations of added monovalent (sodium) salt. The response to salt was quantitatively expressed as the slope of straight lines relating the intrinsic viscosity to the reciprocal of the square‐root of the ionic strength. This slope increased considerably with increasing molecular weight of the polyelectrolyte, and could serve to characterize the response to salt of different substances only when comparison was made at a constant molecular weight. An empirical parameter, B, which is the slope corresponding to an intrinsic viscosity of 1.0 at an ionic strength of 0.1 M could be correlated to the unperturbed dimensions of the molecules. A method of extrapolation, enabling the determination of B from measurements of viscosity on only one sample of unknown molecular weight, was evaluated. The empirically found correlation between Band some well established parameters of stiffness did not contrast predictions from the “fuzzy‐sphere model” of Fixman, provided that reasonable assumptions regarding ion‐binding and the interaction between polymer and solvent were made.
Quenching of the emission of tryptophan, tyrosine, and serum albumins by cupric ion
Authors: Luk Chun Ka
Published: May 2005

The effect of cupric ion on the emission of tryptophan, tyrosine, and serum albumins is studied by emission spectroscopy and lifetime measurements. It is found that whenever cupric ion is bound to tryptophan or tyrosine, their emissions are quenched completely. The quenching may be due to an electron transfer mechanism. The fluorescence of complexes of cupric ions with serum albumins is partially quenched; this is because energy is transferred from tryptophan to the complexed cupric ions by a dipolar energy transfer mechanism. It is deduced from the present study that the tryptophan in the human serum albumin molecule is between 11 and 16 Å from the nearest eupric ion binding sites (assumed to be at the surface of the protein) and that one of the tryptophan in the bovine serum albumin molecule is very close to the cupric ion binding sites and the other is near the center of the bovine serum albumin molecule. It is also found that the deuterium solvent effect on serum albumin fluorescence is very small, and that the quenching of bovine serum albumin fluorescence at the N‐F transition is the result of quenching of the fluorescence of both tryptophans. The phosphorescence lifetime apparatus, capable of measuring decay times of signals with intensities changing over a few orders of magnitude, and the ratio spectrofluorometer, both of which were constructed in this laboratory, are also described.
Correction of light‐scattering errors in spectrophotometric protein determinations
Authors: Winder A. F. , Gent W. L. G.
Published: May 2005

Errors due to light scattering are a feature of spectrophotometrie methods of protein determination. The experimental conditions may be chosen to allow calculation of the scatter contribution, which is obtained essentially from the linear relationship between log turbidity and log incident wavelength, together with knowledge of the slope of such functions. Using this information, the scatter corrections may be obtained by various simple and rapid methods, applicable to single or multicomponent protein solutions.
Minor nucleosides in RNA: optical studies of dinucleoside phosphates containing dihydrouridine
Authors: Formoso Caul , Tinoco Ignacio
Published: May 2005

Photoreduction with NaBH4 was used to reduce the dinucleoside phosphates ApU, UpA, and GpU to the corresponding molecules containing dihydrouridine (H). Also obtained from this reaction are dinucleoside phosphates containing (β‐N‐ribosyl) ureido‐propanol, an open ring form of dihydrouridine. The results of CD and ultraviolet absorption studies with these compounds imply that HpA is strongly stacked, but that ApH and GpH are only slightly stacked. The temperature dependence of the CD suggests that the stacking in HpA is unusual. The results with compounds containing open ring forms of dihydrouridine indicate that there is more intramolecular interaction when the ring is open than when it is closed.
Nägeli amylodextrin and its relationship to starch granule structure. I. Preparation and properties of amylodextrins from various starch types
Authors: Kainuma Keiji , French Dexter
Published: May 2005

Nägeli‐type amylodextrins were prepared from various starch types: native starch granules from potato, waxy maize, wrinkled pea, and high‐amylose maize, and from a commercial amylose (“Superlose”). The granular starches and retrograded amylose were treated with 15% sulfuric acid at 22°–25° for 3 months, the undissolved residues were washed free of acid and air dried. X‐ray diffraction patterns showed that amylodextrin from waxy maize starch (A‐type) and potato starch (B‐type) retain the same diffraction type as that of the parent starch. On conversion of a starch to an amylodextrin, the sharpness and intensity of the diffraction patterns are either retained (waxy maize starch), improved (slightly with potato, significantly with high‐amylose maize, and very markedly with wrinkled pea) or developed (amylose). The results indicate that the crystalline regions of a native starch granule, retrograded amylose, or amylodextrin are exceedingly resistant to acidic hydrolysis at room temperature. In contrast to the parent starches, native amylodextrins stain little if at all with dilute iodine solution. The iodine stains of dissolved amylodextrins were red (waxy maize), red‐purple (potato), or purple (amylose, high‐amylose maize, and wrinkled pea).
Poly(dA‐dT) complexes with histone H1 and pancreatic ribonuclease: Specific base recognition evidenced by ultraviolet resonance Raman spectroscopy
Authors: Chinsky L. , Turpin P. Y.
Published: May 2005

The conformational changes of poly(dA‐dT) from random coil to ordered structure with stacked bases produce important changes in the Raman line intensities (hypochromism) when the polymer is excited under the preresonance Raman conditions (λ excitation = 300 nm). Poly(dA‐dT)–RNase and poly(dA‐dT)–histone H1 interactions have been studied as models of mechanisms of destabilization and stabilization by proteins of the DNA secondary structure, respectively, following this intense preresonance Raman hypochromism. In addition, the specific variation of the intensity of the 1582‐cm−1 line of adenine is interpreted in terms of the interaction of the amino group with the RNase (thus involving the large groove). In the poly(dA‐dT)–H1 complex, the intensity of the 1665‐cm−1 line of thymine increases. This increase appears to involve the C2O group of thymine, located in the narrow groove.
Three‐dimensional structure of actinoxanthin. IV. A 2.5‐Å resolution
Authors: Pletnev V. Z. , Kuzin A. P. , Trakhanov S. D. , Kostetsky P. V.
Published: May 2005

The protein actinoxanthin (isolated from Actinomyces globisporus—molecular weight, 10,300; 107 amino acid residues) crystallizes in space group P212121 with cell dimensions: a = 30.9 Å, b = 48.8 Å, c = 64.1 Å, and Z = 4. The three‐dimensional structure of actinoxanthin was determined by the x‐ray multiple isomorphous replacement method at 2.5‐Å resolution. The molecule is kidney‐shaped and has a well‐defined cavity. Its characteristic features are the absence of α‐helices and the presence of enhanced content of antiparallel β‐structure (∼55%). A cylinder‐shaped formation of seven antiparallel β‐strands comprises the main part of the protein structure. The established β‐supersecondary structure is characterized by a three‐dimensional topology similar to that of immunoglobulin domains, superoxide dismutase subunits, and azurin and plastocyanin proteins.
Crystallization behavior of glucomannan
Authors: Chanzy H. D. , Grosrenaud A. , Joseleau J. P. , Dubé M. , Marchessault R. H.
Published: May 2005

Five different glucomannan samples were recrystallized from dilute solution. Depending on the experimental conditions, the crystals obtained could be identified as corresponding to the mannan I (anhydrous precipitate of more or less regular lozenge‐shaped crystals) or mannan II (hydrated gel‐forming pseudo‐fibrillar precipitate). High‐molecular‐weight material, low temperature of crystallization, or a polar crystallization medium favored the mannan II polymorph, whereas a low‐molecular weight, a high temperature of crystallization, and a crystallization medium of low polarity yielded the mannan I polymorph. Since the base‐plane unit‐cell dimensions are fairly constant with respect to variation of glucose, it is likely that isomorphous replacement of mannose by glucose occurs in glucomannan crystallization; the data also indicate that perfection of the glucomannan crystals was reduced in specimens having a high glucose:mannose ratio. The oriented crystallization of glucomannan on cellulose microfibrils was also studied under conditions where the mannan I polymorph was obtained. This gave shish‐kebab structures that were characterized.
1H‐nmr comparative studies of polynucleotides: Conformation and dynamic structure of polyribo(uridylic) and polyribo(cytidylic) acids in neutral solution
Authors: Neumann J. M. , Tran‐dinh S.
Published: May 2005

The conformation and the dynamic structure of single‐stranded poly(U) and poly(C) in neutral aqueous solution have been investigated by 1H‐nmr at two different frequencies (90 and 250 MHz) and at various temperatures. Measurements of proton chemical shifts, coupling constants JH‐H, and proton relaxation times, T1, T2, versus temperature show a striking difference in conformation and in dynamic structure between the two polynucleotides studied. The temperature effect on δ and JH‐H is found to be substantial for poly(C) and insignificant for poly(U). The S conformer is favored in poly(U), whereas the N conformer strongly predominates in poly(C) (≃90%), similar to the case for RNAs. These results suggest that single‐stranded poly(C) probably possesses a helical or partial helical structure, whereas poly(U) shows a clear preference for the random coil, in agreement with the optical results. The local motions of the ribose and base were studied at various temperatures by measurements on the relaxation times at 90 and 250 MHz. For a given temperature between 22 and 72°C, the ratio T1(90)/T1(250) is practically the same for all poly(U) protons, indicating that in this temperature interval the ribose base unit of poly(U) undergoes an isotropic motion characterized by a single correlation time τc. Above 52°C, poly(C) exhibits a dynamic structure similar to poly(U). Below this temperature, poly(C) exists in an equilibrium between randomly coiled and single‐stranded helix forms. This situation is characterized by a strong cross‐relaxation effect and T1 values corresponding to a relatively short apparent correlation time. An activation energy of 4 kcal/mol was determined for the motion of the ribose–base unit in both single‐stranded polynucleotides.
Influence of hemin on the conformation of cyanogen bromide‐cleaved peptides of apomyoglobin
Authors: Nakano Minoru , Iwamaru Hiroshi , Tobita Tohru , Yang Jen Tsi
Published: May 2005

The complexes of the three BrCN‐cleaved fragments of sperm whale apomyoglobin with hemin were studied by circular dichroism (CD). In native myoglobin, the heme is located in the middle fragment; the isolated peptide (residues 56–131), however, produces little extrinsic Cotton effects by the addition of hemin, although about four molecules of hemin are bound to this peptide. In marked contrast, the COOH‐terminal peptide (residues 132–153), which binds three hemin molecules, shows strong Cotton effects in the Soret bands and drastically changes its conformation from unordered to highly helical. The Arg‐modified or Lys‐deaminated peptide no longer undergoes conformational changes by the addition of hemin, suggesting that the two propionic acid groups of one hemin molecule interact with the Arg residue and one of the Lys residues, which stabilizes the induced helical conformation. The NH2‐terminal peptide (residues 1–55) binds one hemin molecules, and the helicity of this fragment is slightly enhanced by the addition of hemin. Both the CD and difference absorption spectra indicate that the mode of interaction between the peptides and hemin are different for the three apomyoglobin fragments.
Correlation between sugar pucker and the orientation around the C3′O3′ bond (Φ′) in 3′‐mononucleotides
Authors: Dhingra M. M. , Saran Anil
Published: May 2005

Classical potential functions (CPF) calculations on 3′‐mononucleotides, the building blocks of nucleic acids, predict a correlation between the sugar ring pucker and the torsion angle Φ′ around the C3′O3′ bond. In ribonucleotides, the value of Φ′ depends on the sugar pucker, viz. the C2′‐endo sugar pucker is associated with Φ′ = 210° and 270°, while the C3′‐endo sugar pucker favors only Φ′ = 210°. On the other hand, in deoxyribonucleotides, both sugar puckers show a preference for Φ′ = 180°. These theoretical predictions are fully corroborated by the results obtained from x‐ray and nmr studies on mono‐, di‐, and polynucleotides.
Molecular dynamics of ferrocytochrome c: Anharmonicity of atomic displacements
Authors: Mao Boryeu , Pear Michael R. , McCammon J. A. , Northrup S. H.
Published: May 2005

The atomic position distributions obtained from a 32‐ps molecular‐dynamics simulation of tuna ferrocytochrome c at 297 K are analyzed in terms of their second, third, and fourth moments. Non‐Gaussian relations among these moments are found for the majority of atoms in the molecule, indicating anharmonicity in the effective potential functions for the atomic motions. Many atoms exhibit only slightly anharmonic mobility during the 32‐ps period, but about half of the atoms exhibit sizeable anharmonicity. For a typical atom, the anharmonic effects are largest for motions in the direction along which the largest displacements occur. Two classes of significantly anharmonic atoms are apparent: those whose effective potentials are distorted toward a square‐well shape and those whose effective potentials have secondary minima corresponding to conformational substates.
Flow dichroism of capsid DNA phages. I. Fast and slow T4B
Authors: Hall Stephen B. , Schellman John A.
Published: May 2005

Flow linear dichroic studies have been conducted on phage T4B in its fast and slow forms. The behavior of the phages is well represented by an equivalent ellipsoid model using the Peterlin‐Stuart theory. The measurements permit the evaluation of the optical factor of the DNA in the phage and the rotary diffusion coefficient of the phage particle. Both these quantities change during the slow–fast conversion. The rotary diffusion results are in good agreement with those obtained by other workers with other methods. The optical factor is negative, indicating a net alignment of DNA helices parallel to the phage axis. The results exclude certain simplified models for the packaged DNA but do not lead to a unique structural conclusion. The flow dichroism experiment and its interpretation are described, and a simple method of calculating optical factors for complicated but cylindrically symmetric structures is presented.
Light‐scattering study of DNA condensation: Competition between collapse and aggregation
Authors: Post Carol Beth , Zimm Bruno H.
Published: May 2005

Light‐scattering studies were done to investigate the DNA collapse transition, a large and discontinuous reduction in the radius of gyration. Of particular concern was differentiating the compaction of a single DNA molecule from aggregation. Solutions of RK2 plasmid DNA (Mr = 37 × 106) or bacteriophage T7 DNA (Mr = 25 × 106) were titrated with the condensing reagents spermidine in aqueous solvent or magnesium ion in ethanol–water solvent. The transition was followed by the change in scattering at a single angle or by the change in the angular dependence of scattering. At concentrations below 1 μg/mL, only aggregation could be detected by observation at a single angle; therefore, to study the collapse transition, it was necessary to measure the angular dependence of scattering. The intensities measured between the angles 30° and 60° were fit to known scattering functions. At low concentrations of the condensing reagent, the data were consistent with the scattering function of a random coil. On the other hand, during the transition at higher reagent concentrations, the curve that fit the data required two components—the scattering function for a random coil with a large radius of gyration, plus that for a sphere with a radius about one‐fifth of that of the coil. The fractional concentration of the sphere increased with increasing condensing‐reagent concentration. This two‐component behavior is in apparent contrast to the situation with a more flexible polymer such as polystyrene, in accord with theoretical predictions. At still higher reagent concentrations, aggregation was apparent. Condensation to a collapsed state was reversible without hysteresis, while dissolution of the aggregated state nearly always occurred with hysteresis. Qualitative agreement between the observed DNA collapse transition and the theoretical phase diagram presented in the preceding paper was found, although the light‐scattering results did not show quantitative agreement with the simple theoretical model.
Conformational study of poly(α,β‐L‐aspartic acid)
Authors: Saudek Vladimír , Štokrová Štěpánka , Schmidt Pavel
Published: May 2005

The conformation of several samples of poly(α,β‐L‐Asp) with a molar fraction of β‐bonds ranging from 0.1 to 0.55 was investigated by means of ir and CD spectroscopy and potentiometric titration and compared with the results obtained previously with poly(α‐L‐Asp). All samples investigated underwent a conformational change induced by changes in their degree of ionization: unpronounced ir absorption of amide V at 650 cm−1 was shifted to 620 cm−1 and substantially increased on deionization; CD spectra changed with the degree of ionization, passing through an isosbestic point; and the pattern of the titration curves was more complex than that of a simple polyelectrolyte. The conformation developing with the decreasing degree of ionization may be considered to be α‐helix, as deduced according to the analogous behavior of other polypeptides. The extent of the conformational change in the individual samples depends on the molar fraction of β‐bonds: the higher it is, the lower is the helix‐forming ability of the sample.
DNA bis‐intercalation: Theoretical analysis, including cooperativity of the interaction of echinomycin analogs with DNA
Authors: Shafer Richard H. , Waring Michael J.
Published: May 2005

A theoretical analysis of the binding curves for the bifunctional peptide antibiotic echinomycin and its analogs interacting with a variety of DNAs is presented. The method is an extension of our previous work using the sequence‐generating‐function technique and has been modified to allow for consideration of cooperativity within the framework of the neighbor‐exclusion rule. Binding by both single and double intercalation is included, and the results are, in many cases, superior to the analysis based on single‐mode binding. In all cases the data are consistent with the neighbor‐exclusion principle for intercalation when analyzed with this approach, while data analysis, using a simpler method, often led to violation of this rule. Positive cooperativity is considered in the treatment of data for binding to poly(dA‐dT). Finally, we discuss the relationship between base specificity and binding site size.
Loop formation in polynucleotide chains. I. Theory of hairpin loop closure
Authors: Marky Nancy L. , Olson Wilma K.
Published: May 2005

A theoretical model to determine the probability of loop formation, based on an elaborated form of the Jacobson‐Stockmayer theory of cyclization equilibria, has been developed and used on RNA chains of homogeneous puckering and lengths up to 27 residues. The probability Qx (q, γ0, ε0) of occurrence of hairpin loops of a particular chain x is given by Qx (q, γ0, ε0) = [W (q) δr][2Γq (γ0)δγ] [Eq,γ0 (ε0) δε] where W(q) is the three‐dimensional density distribution function of end‐to‐end vectors r centered about the ideal loop closure position q; Γq(γ0) is an angular correlation factor that restricts the orientation of terminal bonds (i.e., bond x and bond 1) in the loop to a specified value Δθ = cos−1 (γ0) when r adopts a value within a range δr from position q; and Eq,γ0(ε0) is the probability that ε falls within δε of ε0 when r and γ assume the values denoted by the respective subscripts. The parameter ε is related to the angle between a hypothetical bond (x + 1) and bond 1. In these calculations, Eqγ0(ε0) was set equal to 1. For randomly coiling models previously developed to reproduce polynucleotide unperturbed dimensions, loop closure probability is maximized with chains of length 22 residues. Larger hairpin loops of 24–25 residues, also favored in C3′‐endo random coils of this type, are potential models of tRNA unfolding. W(q) is a stronger determinant of loop closure than Γq(γ0). The angular correlation effect is most noticeable at chain lengths 22 and 23 where 2Γq(γ0) deviates from unity.
Molecular‐mechanics studies on d(CGCGAATTCGCG)2 and dA12·dT12: An illustration of the coupling between sugar repuckering and DNA twisting
Authors: Kollman Peter , Keepers Joe W. , Weiner Paul
Published: May 2005

Molecular‐mechanics calculations have been carried out on the base‐paired deoxy dodecanucleoside undecaphosphates d(CGCGAATTCGCG)2 and d(A12)·d(T12). These refinements were carried out using the model‐built Arnott B‐DNA geometry as initial coordinates (with a helix repaeat of 10.0 residues/turn), as well as helix repeats ranging from 9 to 12 residues/turn. There was some variation in the optimum calculated helix repeat, depending on the dielectric model, the presence or absence of counterions, and the method used for inclusion for nonbonded interactions; the most interesting general result of these calculations was the coupling between furanose sugar puckering and twist. This coupling was observed for all models. With a helix repeat of 9.0 residues/turn, all sugars remain C(2′)endo after refinement; as the helix repear increases to 12.0 residues/turn, the number of sugars repuckering to O(1′)endo and C(3′)endo increases also. With our most rigorous model (i.e., a model with no cutoff distance for nonbonded interactions) and a helix repeat of 10.0 residues/turn, we find a greater tendency for pyrimidine than purine repuckering in d(CGCGAATTCGCG)2, in agreement with the x‐ray structural data of Drew et al. [(1981) Proc. Natl. Acad. Sci. USA 78, 2179–2185].

We also carried out a number of calculations in which we “forced” one of two deoxy sugars to repucker or one of the C3′‐O3′‐P‐O5′ (ω) torsion angles to change from gauche− to trans using dihedral angle constraints. After the constraints were removed, some of these structures “reverted” to the sugar pucker of the initial structures, while others remained repuckered. In all cases, the energies for repuckered structures after refinement were very similar to energies of the initial structure. Experiments and theory suggest that local conformational fluctuations play an essential role in nmr relaxation of 31P and 13C atoms in double‐helical DNA. The results of our previous calculations on hexanucleoside phosphates and the calculations presented there are consistent with an important contribution to nmr relaxation processes of conformational changes in the torsion angle ω′ from gauche− to trans and deoxy sugar repuckering from C(2′)endo to C(3′)endo. Specifically, the calculations presented here indicate a very flexible phosphate backbone in helixes having an intermediate helix repeat of 10 to 11 residues/turn. These helixes may accommodate sugars of variable pucker without significantly disrupting base–base hydrogen‐bonding and stacking interactions. All of the variant structures are similar in energy, suggesting that conversion between them can occur on a nanosecond time scale, as observed in nmr relaxation experiments.
Vibrational analysis of peptides, polypeptides, and proteins. XV. Crystalline polyglycine II
Authors: Dwivedi A. M. , Krimm S.
Published: May 2005

A force field has been refined for the 31‐helix structure of polyglycine II, using the polyglycine I force field plus previous CαHα…︁O force constants as a starting point. Besides force constants associated with the hydrogen bonds, which must change since the hydrogen‐bond characteristics are different in the two structures, we have had to modify only 10 force constants from the polyglycine I force field to make it suitable for reproducing the polyglycine II frequencies. Most involve the NCα bond, which is the torsion angle that changes from the I to the II structure. Calculations were done for parallel chain and antiparallel chain crystal structures of polyglycine II, the observed spectra being found to agree best with the latter structure. Since this provides strong evidence for the loss of strict threefold symmetry in the chain, our analysis strengthens the support for the existence of CαHα…︁O hydrogen bonds in the structure of polyglycine II.
Raman spectra and normal vibrations of dipeptides. I. Glycylglycine
Authors: Lagant P. , Vergoten G. , Loucheux‐Lefebvre M. H. , Fleury G.
Published: May 2005

We studied the Raman spectra of the zwitterionic glycylglycine crystal (GG) and its N‐deuterated analog. A normal coordinate analysis on its α‐crystalline form was performed and the effects of intra‐and intermolecular couplings are discussed. A modified Urey‐Bradley potential was used as a model of the intramolecular force field. Factor group splittings are described by the use of intermolecular potentials consisting of nonbonded atom‐atom interactions and dipole‐dipole interactions. Effects of hydrogen bonds on the vibrational frequencies of amino and carboxylate groups are also analyzed.
Molecular dynamics of ferrocytochrome c: Time dependence of the atomic displacements
Authors: Morgan John D. , Andrew McCammon J. , Northrup Scott H.
Published: May 2005

The thermal motions of the atoms in a dynamical simulation of ferrocytochrome c are geometrically decomposed into local and highly collective components, and the contributions of these components to the net motion are determined for different intervals of time. It is found that the atomic displacement magnitudes and anisotropies are governed by local motions for times <10−12s, but that the highly collective motions tend to be dominant at longer times. Variations in this behavior are noted among different groups of atoms. Orientational correlations between the preferred directions of atomic displacement and elements of the protein structure are analyzed as a function of time scale. Finally, several sinificant implications of these results with respect to protein structure and function are considered.
Effects of calcium and manganese ions on the helix–coil transition of DNA
Authors: Blagoi Yu. P. , Sorokin V. A. , Valeev V. A. , Gladchenko G. O.
Published: May 2005

The thermal denaturation method was employed to study the effect of Ca2+ and Mn2+ ions on the DNA helix–coil transition parameters at Na+ concentrations of 10−3–10−1M. At low ion concentrations, thermal stability increases, the melting range passes through a maximum, and the denaturation curves become asymmetric. These changes are quantitatively similar for Mn2+ and Ca2+ ions. With a further increase in the concentration of bivalent ions, the conformational transition temperatures pass through a maximum, and the melting range first tends to saturation and then rapidly decreases to 1–2°C. The Mn2+ concentrations, at which the above effects occur, are an order of magnitude lower than the Ca2+ concentrations. Comparison of experimental results and calculation in terms of the ligand theory permitted estimation of binding constants characterizing association between Mn2+ and Ca2+ ions and bases of native and denatured DNA. We show that, unlike the interaction with phosphates, bivalent ion–DNA base binding is weakly dependent on monovalent ion concentration in the solution.
Solution properties of porcine submaxillary mucin
Authors: Shogren R. , Jamieson A. M. , Blackwell J. , Cheng P. W. , Dearborn D. G. , Boat T. F.
Published: May 2005

Porcine submaxillary mucin (PSM) is a glycoprotein composed of a protein core and frequent, short oligosaccharide side chains. We report static and dynamic light scattering experiments and intrinsic viscosities for PSM in aqueous solvent systems. In 0.1M NaCl solution, the data suggest PSM exists as large, internally branched, highly hydrated, polydisperse aggregates that slowly dissociate to give a stable species of weight‐average molecular weight (Mw) 7.4 × 106. In 6M GdnHCl solution, the noncovalent bonds between PSM molecules are broken, giving a highly elongated molecule of Mw = 2.0 × 106. The irreversible nature of this dissociation suggests that the forces that stabilize the native aggregates of PSM in 0.1M NaCl are specific in nature. On reduction of PSM with mercaptoethanol, the polydispersity decreases and Mw also decreases to 9 × 105. A discrete change is observed in the solution properties of PSM in 0.1M NaCl at a concentration of 2mg/mL, manifested by a sudden decrease in the translational diffusion coefficient, an increase in viscosity number, and a decrease in slope of the osmotic compressibility. We tentatively propose that a weak and reversible secondary association process occurs at this concentration, although a purely hydrodynamic interaction cannot be ruled out.
Relaxation processes on a picosecond time scale in hemoglobin and poly(L‐alanine) observed by millimeter‐wave spectroscopy
Authors: Genzel L. , Kremer F. , Poglitsch A. , Bechtold G.
Published: May 2005

Broadband measurements of the millimeter‐wave and far‐ir absorption (10–104 GHz) of lyophilized hemoglobin are reported. Additionally, the absorption of poly(L‐alanine) and crystalline L‐alanine at 70 GHz was measured for comparison. All measurements were extended over the temperature range from liquid helium to room temperature. For the millimeter range, this was attained by using the novel oversized‐cavity technique. It was found that the millimeter‐wave absorption of the materials increased nearly exponentially with temperature and increased as ν1.2–ν2 with frequency. The far‐ir absorption of hemoglobin showed broadbands with almost no temperature dependence. The frequency and temperature dependence of the millimeter‐wave absorption is quantitatively described as due to three distinct relaxation processes on a picosecond time scale occurring in asymmetric double‐well potentials. These processes are most probably assigned to the NH ⃛OC hydrogen bonds of the peptide backbone.
Kinetic studies of the interaction of methyl orange with poly(L‐lysine) by stopped‐flow with circular dichroism detection
Authors: Murakami Kiyofumi , Sano Takayuki , Kure Naohisa , Ishii Katsushi , Yasunaga Tatsuya
Published: May 2005

The interaction of methyl orange with poly(L‐lysine) was studied kinetically by the stopped‐flow technique with CD detection, as well as by static CD titration experiments. In the static experiments, the differences observed in the polymer‐to‐dye ratio dependences of the CD spectra and absorption spectra suggested at least two kinds of bound states of the methyl orange attached to the polymer. The kinetic experiments using the stopped‐flow apparatus, however, revealed four distinct reaction processes. The reaction mechanism was elucidated from the concentration dependence of the time constant for each process as follows: the first process was attributed to the bimolecular binding step of methyl orange to the side chain of poly(L‐lysine), the second and third process were ascribed to the intramolecular reaction of the polymer–dye complex, and the fourth process was found to be the intermolecular aggregation of the polymer–dye complex. The origin of the stacking of methyl orange on poly(L‐lysine) is discussed on the basis of the characteristics of signal amplitudes obtained from the kinetic experiments for these processes.
Counterion binding and hydration of hyaluronate and chondroitin in solution: An 17O, 23Na, and 25Mg nuclear‐magnetic‐relaxation study
Authors: Piculell Lennart , Lindman Björn , Einarsson Roland
Published: May 2005

Nuclear magnetic relaxation rates of H217O, 23Na+, and 25Mg2+ have been measured in aqueous hyaluronate solutions. The dependence on solution pH of the relaxation rates has been investigated, as well as the competition behavior of Na+ with Ca2+ and Mg2+. H217O and 23Na+ relaxation rates in chondroitin and hyaluronate solutions have been compared in the interval, 2 ≲ pH ≲ 12.5. The ion binding of hyaluronate can be fully accounted for by Coulomb interactions, with no need to involve chemical specificity. The hydration is only slighly pH dependent, and is comparable in magnitude to hydration of synthetic polyelectrolytes and monosaccharides. Ion‐binding and hydration properties of hyaluronate and chondroitin are quite similar, except at elevated pH. At alkaline pH, an increase in charge density with pH is seen in hyaluronate and, to a much lesser degree, in chondroitin, possibly due to the titration of hydroxy groups. H217O data indicate an alkali‐induced transition in both glycosaminoglycans.
Hetero‐α‐helical, two‐chain, coiled coils: αβ hybrid tropomysin
Authors: Holtzer Marilyn Emerson , Breiner Teresa , Holtzer Alfred
Published: May 2005

The nature of the interhelix interaction in two‐chain, α‐helical, coiled coils is studied by experiments on the formation of hydrid molecules in which one helical chain is an α‐tropomyosin and the other a β‐tropomoysin. By means of a recently developed assay, the population of heterohelical (i.e., αβ hybrid) molecules relative to their homohelical (αα and ββ) parent species is determined under a variety of conditions, both equilibrium and nonequilibrium. It is found that mixed intact αα and ββ molecules do not form hybrid species in detectible amounts even after incubation at room temperature (or below) for periods of over one week. That the lack of αβ species in this “native‐exchange” system is a result of a kinetic barrier is evident from experiments involving a thermal denaturation–renaturation cycle in which the largely dissociated, unfolded chains at higher temperature are annealed to benign temperatures over a period of 6 h, thus assuring an equilibrium population of two‐chain species. In the resulting equilibrium state, the αβ population is one‐half the total, indicating that recombination is random. Furthermore, this same (equilibrium) state is reached if the separated, mostly unfolded chains are renatured by a rapid (∼ 40 s) quench to benign temperatures. Some implications of these results for the thermodynamics of interhelix interation, for kinetics of chain dissociation and recombination, and for in vivo genesis of two‐chain coiled coils are discussed.
Head‐to‐head dimerization of parallel β helices in a synthetic model of the linear gramicidins
Authors: Lorenzi Gian Paolo , Gerber Christoph , Jäckle Hans
Published: May 2005

In chloroform solution, the D,L‐alternating stereo‐co‐oligopeptide HCO‐L‐Phe‐(D‐Phe‐L‐Phe)3‐OMe (I) forms three major species, two of which are dimeric and one tetrameric. One of the two dimeric species gives a specific set of 1H‐nmr signals at 25°C; the other, together with the tetrameric species, gives another set of resonance signals. In a carbon tetrachloride or cyclohexane solution at 25°C, I forms virtually only the tetrameric species. From the nmr data, it can be shown that the dimeric and tetrameric species, that are in rapid equilibrium with each other in chloroform solutions, are a right‐handed ↑↑β5.6 helical dimer and the head‐to‐head (formyl‐ends‐to‐formyl‐ends) dimerization product of this dimer. It is suggested that the linear gramicidins may also form head‐to‐head dimers of parallel β helices, as observed for the model oligopeptide I.
Determination of peptide conformation via vibrational coupling: Application to diastereoisomeric alanyl dipeptides
Authors: Diem Max , Oboodi M. Reza , Alva Carlos
Published: May 2005

Solution‐phase Raman spectra of diastereomeric alanyl dipeptides, D‐Ala‐L‐Ala and L‐Ala‐L‐Ala, and various mono‐ and dideuterated isotopomers in H2O and D2O, are reported. Spectral differences between the diastereomeric forms are interpreted, using the Raman analog of the coupled oscillator model, in terms of geometric differences between certain vibrations in the diastereomeric forms. Application of the coupled‐oscillator formalism allows the determination of a dihedral angle between the coupling vibrations. The results are compared with vibrational coupling employed by other workers in the determination of the vibrational spectra of peptides.