bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA melting temperatures and renaturation rates in concentrated alkylammonium salt solutions
Authors: Orosz Jerry M. , Wetmur James G.
Published: May 2005

DNA melting temperatures and renaturation rates have been determined for Me2Et2NBr and a series of RMe3NBr and REt3NBr solvents where R is a linear hydrocarbon chain. The point of independence of DNA melting temperature on base composition has been investigated for each solvent system. Renaturation rates are compared with those found in other concentrated salt solutions. Solvent mixtures which accelerate DNA renaturation have also been investigated.
Analysis of periodic patterns in amino acid sequences: Collagen
Authors: McLachlan A. D.
Published: May 2005

Methods are given for analyzing regularly spaced patterns of amino acids in proteins and applied to the α1 chain of collagen. Fourier methods use the transform of the sequence either embedded in a very long array or folded onto a fundamental base period. Filtering through a moveable “window” of definite width is used to display almost regular features at any chosen frequency. A pattern detection method is described for patterns of general shape. Collagen has statistically significant periodicities at fractions of the stagger distance D = 670 Å. Hydrophobic groups show strong orders of 5, 6, 11; proline 5; charged groups 6, 18, 21. Charged residues mostly occur as neutral pairs. Their distribution has strong 6th and 21st orders which also appear in the changes which are paired at multiples of D. Charge pairs separated by (D + 3) residues show a strong 5D/89 pattern and may form a system of salt bridges across the fibril. There is no sign of any regular pattern of amino acids over the triple helix with a period close to its natural pitch of 30 residues. Supercoiled models with six relative turns of the contact edge between paired triple‐helical strands are examined.
Circular dichroism evidence for G·U and G·T base pairing in poly[r(G‐U)] and poly[d(G‐T)]
Authors: Gray Donald M. , Ratliff Robert L.
Published: May 2005

We have measured the circular dichroism (CD) and absorption properties of poly[r(G‐U)] and poly [d(G‐T)] over a wide range of Na+ concentrations and temperatures. We find evidence for self‐complexed forms of these polymers at lower temperatures and/or higher Na+ concentrations than generally needed for double‐strand formation in other DNA and RNA polymers. These self‐complexes could be composed of double‐stranded regions with weak G·U or G·T base pairs.
Cis‐Trans equilibrium and kinetic studies of acetyl‐L‐proline and glycyl‐L‐proline
Authors: Cheng H. N. , Bovey F. A.
Published: May 2005

By means of carbon‐13 nmr (at 25 MHz) the trans/cis conformer ratio in glycyl‐L‐proline has been measured in aqueous (D2O) solution over the temperature range 33–96°C. It is found that ΔH0 = −4.2 kJ/mole and ΔS0 = −9.7 J/mole/K.

Measurements of the T1 values for the proline ring carbons yielded values consistent with a fast puckering process involving both the β‐ and γ‐carbons.

Measurements of the rate of cis‐trans conformational interconversion in glycyl‐L‐proline, using complete line‐shape analysis for the glycyl α‐carbon resonance, gave values for the trans → cis isomerization as follows: ΔH≠ = 83.5 ± 0.2 kJ/mole; ΔS≠ = 0.0 ± 10 J/mole/K. A more approximate determination from coalescence temperature observations gave a value of ΔG≠ of 82.0 ± 0.4 kJ/mole for this process in acetyl‐L‐proline in aqueous solution. The presence of 12M NaSCN lowered this barrier by ca. 2.6 kJ/mole.

Such measurements are relevant to present theoretical models of the denaturation‐renaturation processes in proteins, in which proline residues may play a key role.
Circular dichroism of adenine and thymine containing synthetic polynucleotides
Authors: Greve J. , Maestre M. F. , Levin A.
Published: May 2005

Circular dichroism (CD) spectra of poly(dA), poly(dT), poly(dA)·poly(dT), and poly[d(A‐T)]·poly[d(T‐A)] have been measured as a function of temperature. From these data difference spectra have been calculated by subtracting the spectrum measured at low temperature from the spectra measured at higher temperatures. The CD difference spectra obtained upon melting of the two double‐stranded polymers are very similar. From a comparison of these difference spectra with calculated ones it is shown that optical transitions near 272 nm (on A) and 288 nm (most probably on T) are present. The premelting changes of the CD spectrum of poly[d(A‐t)]·poly[d(T‐A)] are due to a change in conformation in which the secondary structure goes from a C‐ to B‐type spectrum by increasing the A‐type nature of the polymer. Such a change is not observed for poly(dA)·poly(dT). Instead, a transition between two different B‐type geometries occurs.
Calorimetric investigation of some elastin‐solvent systems
Authors: Ceccorulli Giuseppina , Scandola Mariastella , Pezzin Giovanni
Published: May 2005

The interaction of ox ligamentum nuchae elastin (native, purified, and soluble) with different solvents (water, ethylene glycol, methanol, and 2,2,2‐trifluoroethanol) was investigated by means of differential scanning calorimetry. The unfreezable solvent content and the corresponding solvent to elastin residue molar ratio were determined from the melting endotherms of the freezable solvent present in these systems. The molar ratio obtained in the case of water and ethylene glycol agrees with hypothesis of a direct solvation of the main chain peptide group and is interpreted according to a model previously proposed for polyamides. Quite different molar ratios are obtained in the case of the two monofunctional solvents and no model can be proposed at present to explain their interaction with the protein.
Poly(L‐lysyl‐L‐alanyl‐α‐L‐glutamic acid). II. Conformational studies
Authors: Goren H. Joseph , McMillin Carl R. , Walton Alan G.
Published: May 2005

The solution characterization of poly(Lys‐Ala‐Glu) is described. This polytripeptide is zwitterionic at neutral pH and is shown to take on a conformation which is dictated by the state of ionization, molecular weight, temperature, and solvent. The polypeptide is almost entirely α‐helical at low pH and temperature for polymers of greater than 25,000 molecular weight. Melting profiles for these conditions show tm ∼ 20°C. Analysis of circular dichroism curves shows the α‐helical content to vary in a linear manner with molecular weight in the range 3000–30,000. At neutral pH the charged polypeptide is essentially random, but substantial α‐helix could be induced by addition of methanol or trifluoroethanol. At temperatures where the sequential polypeptide is a random coil, addition of trifluoroethanol produces a polymer which is mostly α‐helical but also contains an appreciable ammount of β‐structure. The infrared spectrum of a low‐molecular‐weight fraction assumed to be cyclo(Lys‐Ala‐Glu)2 was tentatively assigned a β‐pleated sheet structure.

A comparison of this polytripeptide in various ionization states with other polytripeptides containing L‐alanine and L‐glutamate or L‐lysine shows the α‐helix directing properties for the (uncharged) residues to lie in the order Ala > Glu > Lys.
Viscosity and potentiometric measurements of poly(L‐histidyl‐L‐alanyl‐α‐L‐glutamic acid) and poly(L‐lysyl‐L‐alanyl‐α‐L‐glutamic acid)
Authors: Goren H. Joseph , Grandan Loretta , Jay Alfred W. L. , Lotan Noah
Published: May 2005

Poly(His‐Ala‐Glu) and poly(Lys‐Ala‐Glu) were examined by viscosity and potentiometric titration. These measurements were interpreted in terms of the hydrodynamic size of the above sequential polypeptides. Effects of polymer, size and concentration, and solution‐salt concentration were demonstrated. Although the sequential polypeptides generally behave like polyampholytes, they do demonstrate some differences. These differences my be attributed to the ability of ionized side chains three residues apart to repel themselves, in the order His < Glu < Lys.
Kinetics of the renaturation of yeast tRNA3Leu
Authors: Hawkins E. R. , Chang S. H. , Mattice Wayne L.
Published: May 2005

Yeast tRNA3Leu is one of several tRNA molecules which can adopt a stable, biologically inactive, denatured conformation. The circular dichroism of the native and denatured conformers differs, providing the basis for the present study of the mechanism for the renaturation process. Conversion of the denatured structure to the native takes place in two steps: a rapid change occurring immediately on addition of Mg++, followed by a slower, strongly temperature‐dependent step which returns the molecule to its biologically active state. Optimal kinetic data for the second step could be obtained at 285 nm. Analysis of the time dependence of Δε285 by the Guggenheim method demonstrated that this step follows first‐order kinetics. The temperature dependence of the rate constants over the range 32–41°C yielded the following parameters for the rate‐limiting step: Ea = 69 kcal/mole, ΔH‡ = 69 kcal/mole, and ΔS‡ = 146 cal/mole deg. Values of this magnitude are typical of order—order transitions in nucleic acids.
Synthesis and conformational study of poly(0,0′‐dicarbobenzoxy‐L‐β‐3,4‐dihydroxyphenyl‐α‐alanine)
Authors: Yamamoto Hiroyuki , Hayakawa Tadao
Published: May 2005

High‐molecular‐weight poly(0,0′‐dicarbobenzoxy‐L‐β‐3,4‐dihydroxyphenyl‐α‐alanine) was prepared by the N‐carboxyanhydride method. From the results obtained by a study of the optical rotation, nuclear magnetic resonance, and solution infrared absorption, the conformation of poly(0,0′‐dicarbobenzoxy‐L‐β‐3,4‐dihydroxyphenyl‐α‐alanine) depended greatly on the solvent taking a right‐handed helix with [θ]225 = −13,600 ∼ −18,900 in alkyl halides, a left‐handed helix with [θ]228 = 22,100 ∼ 24,800 in cyclic ethers or trimethylphosphate, and a random coil structure in dichloroacetic acid, trifluoroacetic acid, or hexafluoroacetone sesquihydrate. The polypeptide underwent a right‐handed helix‐coil transition in chloroform/dichloroacetic acid (or trifluoroacetic acid) mixed solvents and a left‐handed helix‐coil transition in dioxane/dichloroacetic acid (or trifluoroacetic acid) mixed solvents. The results were compared with those of poly(0‐carbobenzoxy‐L‐tyrosine).
Unsaturated amino‐acid residues as probes for the conformation of polypeptides in solution
Authors: Pieroni Osvaldo , Fissi Adriano , Montagnoli Giorgio , Ciardelli Francesco
Published: May 2005

Acetyl‐(dehydro‐Phe) and acetyl‐bis(dehydro‐Phe) groups have been attached to the ε‐amino group of the lysine residues of the copolymer poly(Glu92Lys8) by reacting this last with acetyl‐(dehydro‐Phe)‐azlactone and acetyl‐bis(dehydro‐Phe)‐azlactone, respectively.

In the latter case induced CD is observed between 250 and 330 nm, due to the relative dissymmetric disposition of the two dehydro‐Phe groups under the chiral field of the polypeptide chain.

pH dependence of the induced CD, observed for the copolymer and lacking in the lowmolecular‐weight structural model, is related to the α‐helical and random coiled conformation of the polypeptide chain.
Nuclear magnetic resonance study of the impact of ribose 2′‐O‐methylation on the aqueous solution conformation of cytidylyl‐(3′ → 5′)‐cytidine
Authors: Cheng Doris M. , Sarma Ramaswamy H.
Published: May 2005

In order to obtain information about the conformational characteristics at the nearestneighbor level in the 2′‐O‐methylated region of t‐RNA, as well as in the bizarre 5′‐terminus of eucaryotic mRNA, a detailed nuclear magnetic resonance study of 2′‐O‐methyl‐cytidylyl‐(3′ → 5′)‐cytidine (CmpC) was conducted. Proton spectra were recorded at 270 MHz in the Fourier mode in D2O solutions, 0.01M, pD 7.3 in the temperature range 5–80°C. Complete accurate sets of nmr parameters were derived for each of the nucleotidyl units by a combination of homo‐nuclear decouplings and simulation iteration methods. The data were translated into conformational parameters using procedures developed in earlier studies from these laboratories.

It is shown that the ribofuranose ring exists at a 2E ⇄ 3E equilibrium with clear preference [(75–80)%] for the 3E mode. The C(4′)‐C(5′) and C(5′)‐O(5′) bonds form a stable conformational network with outspoken preference for conformers in which Ψ1, Ψ2 ≃ 60° and ϕ2 ≃ 180°. The orientation of the 3′‐phosphate and 2′‐O‐methyl groups is such that ϕ1′ ≃ 210° and ϕ″ ≃ 60°. The phosphodiester bonds are flexible and shift trends for base, H(1′), and H(5″) suggest the existence of a conformational blend of right‐handed stack (g−g−), left‐handed stack (g+g+), and unstacked arrays (tg− and tg+).

Elevation of temperature perturbs the 2E ⇄ 3E equilibrium accompanied with modest depopulation of ψ1, ψ2 ≃ 60° and ϕ2 ≃ 180° conformers. The major effect of elevation of temperature is in the increase of unstacked arrays at the expense of g−g− and g+g+ conformers. The shift trend of Cmp‐H(3′) with temperature shows that torsional variation about O(3′)‐P is facilitated by increase in temperature and the preferred rotamer about O(3′)‐P in the unstacked form is t (ω1′ = 180°).

A detailed comparison of the aqueous solution conformations of CpC and CmpC reveals that 2′‐O‐methylation causes: (i) a reduction in the magnitude of χ1; (ii) an increase in the population of 3E pucker at the 3′‐nucleotidyl unit; and (iii) modest perturbations in the O(3′)‐P and P‐O(5′) bond conformations. Comparison of the aqueous solution conformations of AmpA and CmpC makes clear that the conformational properties of pyrimidine‐pyrimidine and purine‐purine dimers which carry a 2′‐O‐methylated 3′‐nucleotidyl unit are significantly different.
Hydrodynamic properties of macromolecular complexes. I. Translation
Authors: De La Torre Jose Garcia , Bloomfield Victor A.
Published: May 2005

We have developed an improved theory for calculating the translational frictional coefficients of rigid macromolecular complexes composed of unequal spherical subunits. The Yamakawa hydrodynamic interaction tensor, which improves on the Oseen tensor by taking account of the finite sizes of the frictional subunits, has been generalized to accomodate nonidentical subunits. Iterative numerical methods are described for solving the set of simultaneous hydrodynamic interaction equations, thus avoiding preaveraging. The theory is applied to prolate ellipsoids of revolution, to lollipops, and to dumbbells, and comparison is made with earlier, more approximate theories.
Conformational properties of L‐leucine, L‐isoleucine, and L‐norleucine side chains in L‐lysine copolymers
Authors: Arfmann H.‐A. , Labitzke R. , Wagner K. G.
Published: May 2005

The structure inducing properties of L‐leucine, L‐isoleucine, and L‐norleucine residues incorporated into poly(L‐lysine) were investigated by the observation of the circular dichroism of the respective random copolypeptides. The comparison involves the coil‐helix transition in water/methanol mixtures, the formation of ordered structures at higher pH, and the kinetics of the α‐helix to β‐conformation transition of the leucine and norleucine copolymers induced by temperature changes at pH 10.5. The results confirm the known properties of the leucine residue, strongly supporting the α‐helix conformation. They also support the idea that the isoleucine residue is one of the most powerful candidates for β‐structure formation, and they show that the unbranched norleucine residue has intermediate properties. The results are discussed on the basis of steric and hydrophobic properties of the three side chains.
Low velocity gradient flow birefringence and viscosity changes in hyaluronate solutions as a function of pH
Authors: Barrett T. W. , Harrington R. E.
Published: May 2005

The flow birefringence and extinction angle over a velocity gradient range of approximately 5–100 sec−1, and the zero shear‐viscosity have been obtained from human umbilical cord hyaluronic acid at concentrations of 0.25, 0.125 and 0.0625%, and pHs 6.0, 6.5, 7.0, 7.5, 8.0, and 8.5 and constant ionic strength 0.1. The data indicate a large change in optical anisotropy as a function of pH, with most of the transition in the pH range 7.0–7.5, i.e., across the physiological range. The sign of the anisotropy changes between pH 8.0 and 8.5. These results, together with changes in the extinction angle and intrinsic viscosity as a function of pH, suggest a pH‐dependent structural change in the system. Due to the abruptness of the transition, as evidenced by the intrinsic viscosity and flow birefringence, it is probable that the structural transition is cooperative. If the data are interpreted in terms of the Rouse‐Zimm Gaussian subchain theory, a modification of the model in terms of the Haller‐Cerf concept of internal viscosity is required. Thus, the demonstrated properties of hyaluronate solutions indicate a system with memory of stress. Due to the presence of large concentration effects discernible in the extinction angle measurements, hyaluronic acid probably exists as a network in solution. The results are discussed with respect to the mechanoelectrical transducing properties of hyaluronates and stress‐dependent changes in ORD already reported.
Pyrene derivatives as fluorescent probes of conformation near the 3′ termini of polyribonucleotides
Authors: Koenig Paul , Reines Scott A. , Cantor Charles R.
Published: May 2005

When pyrene butyric acid hydrazide or pyrene acetic acid hydrazide is attached to single‐strand RNA 3′ termini a red shift in absorbance and substantial hypochromicity are observed. A strong induced CD is seen and the fluorescence intensity is quenched by an order of magnitude. In double‐stranded samples, a further 10‐fold quenching of fluorescence is seen. Several lines of evidence suggest that the residual fluorescence of pyrene butyric acid hydrazide‐duplex conjugates arises from a minor species. The most likely possibility is dye reacted at a site other than the 3′ end. Some indication exists that 3′‐attached pyrene may perturb the relative stability of nearby duplex. Within the limits of this reservation, it appears that 3′‐pyrene conjugates may be rather useful for detecting the existence of duplex regions accessible to a dye at the 3′ end of complex RNAs.
Molecular organization of DNA in chromosomes
Authors: Basu Samarendra
Published: May 2005

Metaphase chromosomes of Chinese hamster and lampbrush chromosomes of Triturus viridescens were studied for DNA arrangement by polarized fluorescence microscopy and by linear dichroic ratio measurements. Intact chromosomes showed a small but negative polarization (−8%) of fluorescence, while the dichroic ratio was negative and quite appreciable (0.85). On treatment with trypsin or RNase the polarization value increased to about −34% with no change in the polarization direction. The dichroic ratio on the other hand remained unchanged on such enzyme treatments. These results, along with the data of form dichroism and the change in fluorescence color following any enzyme action, suggest that basically the preexisting DNA arrangement was revealed by these enzymes. The fully enzyme‐treated chromosome–dye complexes showed cross‐bands. Quantitatively, the highest degree of DNA orientation across the above two chromosomes was in the range of 15–34%. This orientation fits well with a coiled coil‐DNA, which is mostly longitudinal in these chromosomes. It is suggested that this longitudinal coil may have occasional defects in DNA structure. Alternatively, this coil may terminate into regions of random DNA and unsupercoiled DNA showing lateral projections, such as loops. This alternating feature of the DNA arrangement would tandemly repeat in either metaphase and lampbrush chromosomes.
Protein conformational changes induced in human stratum corneum by organic sulfoxides: An infrared spectroscopic investigation
Authors: Oertel Richard P.
Published: May 2005

Formation of the antiparallel‐chain β‐sheet protein conformation is induced in in vitro human stratum corneum by three homologous organic sulfoxides known to enhance skin permeability: dimethylsulfoxide (Me2SO), hexylmethylsulfoxide (HxMeSO), and decylmethylsulfoxide (DecMeSO). Me2SO and HxMeSO apparently function by displacing water molecules bound to polar protein side‐chains, whereas DecMeSO probably interacts hydrophobically with the protein. The conformational transition does not result from lipid removal. The β‐sheet protein, most likely formed in normally α‐helical portions of the intracellular keratin filaments, is reconverted to α‐helix upon rehydration of the tissue. Though neat Me2SO produces the most β‐sheet of all treatments examined, the sequence of ability to promote β‐sheet formation at the 1M level is HxMeSO > DecMeSO > Me2SO. Spectroscopic evidence is presented regarding the dependence of β‐sheet formation on sulfoxide concentration, treatment duration, pH, and tissue hydration. The relationship of this conformational change to the enhancement of skin permeability is briefly discussed. The result of sulfoxide treatment is different from results of sodium dodecylsulfate and heat treatments of stratum corneum.
Proton transfer and polarizability of hydrogen bonds in proteins coupled with conformational changes. I. Infrared investigation of poly(glutamic acid) with various N Bases
Authors: Lindemann Rainald , Zundel Georg
Published: May 2005

The nature of hydrogen bonds formed between carboxylic acid residues and histidine residues in proteins is studied by ir spectroscopy. Poly(glutamic acid) [(Glu)n] is investigated with various monomer N bases. The position of the proton transfer equilibrium OH…︁N ⇌ O−…︁H+N is determined considering the bands of the carboxylic group.

It is shown that largely symmetrical double minimum energy surfaces are present in the OH…︁N ⇌ O−…︁H+N bonds when the pKa of the protonated N base is two values larger than that of the carboxylic groups of (Glu)n. Hence OH…︁N ⇌ O−…︁H+N bonds between glutamic and aspartic acid residues and histidine residues in proteins may be easily polarizable proton transfer hydrogen bonds. The polarizability of these bonds is one to two orders of magnitude larger than usual electron polarizabilities; therefore, these bonds strongly interact with their environment.

It is demonstrated that water molecules shift these proton transfer equilibria in favor of the polar proton boundary structure. The access of water molecules to such bonds in proteins and therefore the position of this proton transfer equilibrium is dependent on conformation.

The amide bands show that (Glu)n is α‐helical with all systems. The only exception is the (Glu)n‐n‐propylamine system. When this system is hydrated (Glu)n is α‐helical, too. When it is dried, however, (Glu)n forms antiparallel β‐structure. This conformational transition, dependent on degree of hydration, is reversible. An excess of n‐propylamine has the same effect on conformation as hydration.
13C and 1H NMR studies of helix‐coil transition of poly(β‐benzyl‐L‐aspartate) and poly(γ‐benzyl‐L‐glutamate): Behavior in nonprotonating solvent mixtures, and origin of solvent‐induced chemical shift
Authors: Suzuki Yasuyuki , Inoue Yoshio , Chûjô Riichirô
Published: May 2005

From the results of 13C‐nmr measurement of poly(β‐benzyl‐L‐aspartate) and its model compounds in dimethyl sulphoxide/deuterated chloroform mixtures, it was found that the side chain of poly(β‐benzyl‐L‐aspartate) is solvated by dimethyl sulphoxide in the region more than dimethyl sulphoxide 20% (v/v), where the backbone maintains the α‐helix. The chemical shift differences in the benzyl group carbons of poly(γ‐benzyl‐L‐glutamate) (trifluoroacetic acid/deuterated chloroform) accompanied by the helix‐coil transition, originate from the interaction between the ester group of the side chain and trifluoroacetic acid. The chemical shift difference in the ester carbon is similar. On the other hand, the chemical shift differences of the side‐chain carbons in the alkyl portion (Cβ, Cγ) originate not only from the interaction between the ester group of the side chain and trifluoroacetic acid, but also from some other unknown factors. The chemical shift differences of the side‐chain carbons of poly(β‐benzyl‐L‐aspartate) originate from the interaction between the ester group of the side chain and trifluoroacetic acid.
Helix–coil stability constants for amino acids in nonaqueous solvents. Studies of random poly(γ‐benzyl‐L‐glutamate‐co‐L‐alanine) and poly(γ‐benzyl‐L‐glutamate‐co‐L‐leucine) in a mixed solvent
Authors: Sridhara S. , Ananthanarayanan V. S. , Fredrickson R. A. , Zweifel B. O. , Taylor G. T. , Scheraga H. A.
Published: May 2005

The host–guest technique has been applied to the determination of the helix–coil stability constants of two naturally occurring amino acids, L‐alanine and L‐leucine, in a nonaqueous solvent system. Random copolymers containing L‐alanine and L‐leucine, respectively, as guest residues and γ‐benzyl‐L‐glutamate as the host residue were synthesized. The polymers were fractionated and characterized for their amino acid content, molecular weight, and helix–coil transition behavior in a dichloroacetic acid (DCA)–1,2‐dichloroethane (DCE) mixture. Two types of helix–coil transitions were carried out on the copolymers: solvent‐induced transitions in DCA–DCE mixtures at 25°C and thermally induced transitions in a 82:18 (wt %) DCA–DCE mixture. The thermally induced transitions were analyzed by statistical mechanical methods to determine the Zimm‐Bragg parameters, σ and s, of the guest residues. The experimental data indicate that, in the nonaqueous solvent, the L‐alanine residue stabilizes the α‐helical conformation more than the L‐leucine residue does. This is in contrast to their behavior in aqueous solution, where the reverse is true. The implications of this finding for the analysis of helical structures in globular proteins are discussed.
An equilibrium folding intermediate detected in the thermal unfolding transition of ribonuclease S by circular dichroism
Authors: Labhardt A. M.
Published: May 2005

The thermal‐denaturation transition of ribonuclease S (RNAase S) is measured by circular dichroism at 225 nm. Only conformational transitions involving the S‐peptide–S‐protein complex are detected at this wavelength. Different pathways of thermal unfolding at high and low concentrations are apparent: at low concentrations the temperature of half‐completion of denaturation (Tm) varies with concentration. Above a total enzyme concentration of 50 μM, Tm remains constant. The observed data can be explained on the basis of a model where the association–dissociation step occurs between S‐peptide and thermally (at least partly) unfolded S‐protein. The complex as a whole undergoes a major folding–unfolding transition in the course of which the S‐peptide μ‐helix appears to be formed. The unfolded complex is well populated in the unfolding transition region for enzyme concentrations of 100 μM or more. The model succeeds in deducing thermodynamic parameters from the thermal denaturation curves in various different ways. The values thus obtained are fully self‐consistent and, moreover, consistent with the values for the apparent association constant and apparent association enthalpy as measured in enzyme‐dilution experiments and by batch calorimetry.
Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains
Authors: Hagerman Paul J. , Zimm Bruno H.
Published: May 2005

A Monte Carlo analysis is presented which establishes a relationship between the rotational diffusion coefficients and the flexibility (persistence length, P) of short, wormlike chains. The results of this analysis are presented in terms of experimentally observable quantities; namely, the rotational relaxation times for the field‐free decay of optical anisotropy. The pertinent theoretical quantity is R, defined as the ratio of the longest rotational relaxation time of a wormlike chain to the transverse rotational relaxation time of a rigid cylinder having the same axial length (L) and segmental volume. R, so defined, is essentially independent of the axial ratio of the cylinder for any value of L/P within the range of validity of the present analysis (axial ratio > 20; 0.1 < L/P < 5). It is pointed out that P can be determined with reasonable accuracy even in the absence of a precise knowledge of the local hydrodynamic radius of the chain.
Isodichroic point and the β–random coil transition of poly(S‐carboxymethyl‐L‐cysteine) and poly(S‐carboxyethyl‐L‐cysteine) in the absence of added salt
Authors: Maeda Hiroshi , Ooi Kenta
Published: May 2005

The β‐coil transition of poly(S‐carboxymethyl‐L‐cysteine) (poly[Cys(CH2CO2H)]) and poly(S‐carboxyethyl‐L‐cysteine) (poly[Cys((CH2)2CO2H)]) was followed by CD, potentiometric titration, and viscosity in the absence of added salt. These different properties give consistent results for poly[Cys((CH2)2CO2H)]. The CD spectra of poly[Cys(CH2CO2H)] change considerably with the degree of neutralization α even for a low‐molecular‐weight sample incapable of forming the β‐structure. Because of the superposition of this additional effect, the dependence of CD on α is inconsistent with titration data for the case of poly[Cys(CH2CO2H)], particularly when the nπ transition is used to follow the β‐coil transition. The change of CD inherent to the β‐coil transition is characterized by an isodichroic point: 215 nm for poly[Cys((CH2)2CO2H)] and 218 nm for poly[Cys(CH2CO2H)]. A criterion supporting the stacking of the pleated sheet is suggested based on the isodichroic point.
Influence of interatomic interactions on the structure and stability of polypeptides and proteins
Authors: Scheraga Harold A.
Published: May 2005

Several examples are cited to demonstrate how conformational‐energy calculations provide information about the manner in which interatomic interactions influence the structure and stability of polypeptides and proteins, and of intermolecular complexes involving these same species. These include the screw senses of α‐helical polyamino acids, helix–coil transition parameters, properties of β‐bends, and the structures of gramicidin S and of synthetic poly‐(tripeptide) models of collagen. In all of these calculations, the multiple‐minimum problem has been surmounted. A description is provided as to how the multiple‐minimum problem is being approached in calculations on globular proteins. These computational methods have also been applied to protein structure refinement and to the calculation of structures of homologous proteins and of enzyme–substrate complexes.
Conformer equilibria of triostin A and its conformer‐specific interaction with nucleic acid bases
Authors: Kyogoku Yoshimasa , Higuchi Naoki , Watanabe Mayumi , Kawano Keiichi
Published: May 2005

A quinoxaline antibiotic triostin A has a bicyclic octadepsipeptide structure. Proton and carbon‐13 nmr spectra showed the presence of two symmetrical conformations favoring polar and nonpolar solvents, respectively. They interconvert slowly on the nmr time scale, and this slow interconversion is due to the cooperative effects of the presence of the quinoxaline ring and the N‐methyl peptide bonds. Reversal of the chirality of the disulfide bond as the origin of the slow exchange was excluded by the presence of two conformers for S‐benzyltriostin A. Conformer 2, which favors the polar solvent, can form hydrogen‐bonded complexes with purine nucleoside derivatives in organic solvents, but conformer 1 does not. The binding sites were elucidated and a mode of interaction with DNA proposed.
Design of protease inhibitors
Authors: Ondetti M. A. , Cushman D. W.
Published: May 2005

There is a general parallelism in the strategy followed in the design of hormonal peptide analogs and protease inhibitors. However, in the latter, one more dimension has been added with the development of mechanism‐based inhibitors, a dimension that is not yet available for hormonal peptides because of the lack of knowledge about receptor mechanisms. The recently advanced concepts of transition state and bi‐product analogs have made possible the development of highly potent active‐site directed reversible protease inhibitors of great therapeutic potential.
Application of the two‐dimensional nmr techniques on a des(Ala,Gly)‐somatostatin analog
Authors: Kobayashi Yuji , Kyogoku Yoshimasa , Emura Junji , Sakakibara Shumpei
Published: May 2005

Two‐dimensional nmr techniques have been carried out for the peak assignment of the spectrum of a somatostatin analog. Two‐dimensional J‐resolved spectroscopy simplified the rather broad and complicated spectrum to show the center of chemical shifts of each resonance and gave information on the coupling profiles. Another technique, two‐dimensional spin‐echo correlated spectroscopy, revealed the connectivities between protons which are correlated by weak spin–spin couplings. The combination of the results of these two complementary techniques made it possible for us to assign almost all peaks of the spectrum of the 11‐residue somatostatin analog.
Raman spectra of imino acids and poly‐L‐hydroxyproline
Authors: Deveney M. J. , Walton A. G. , Koenig J. L.
Published: May 2005

The Raman spectra of poly‐L‐hydroxyproline in the solid state and aqueous solution have been obtained. From the spectra, the conformations of the polypeptide in the solid and aqueous solution are found to be the same. Major differences in the spectra between the solid and solution are traced to environmental influences of the pyrrolidine group as indicated by studies of the monomers. The Raman spectra of the imino acids, proline and hydroxyproline, as the dipolar ions, the hydrochlorides, and the sodium salts are also reported.
Conformation of gramicidin S
Authors: De Santis P. , Liquori A. M.
Published: May 2005

A molecular conformation of Gramicidin S was derived on the basis of conformational calculations taking into account the available experimental data.

The conformation is characterized by a dyad axis which relates the two chemically equivalent halves of the molecule and contains four hydrogen bonds; other structural features agree with experimental results. X Ray Crystallographic evidences for the relative position of the Ornithine residues is also reported which supports an important feature of the structure of Gramicidin S.
A cooperative transition between two helical conformations in a linear system: poly‐L‐proline I ⇌ II. II. Kinetic studies
Authors: Winklmair D. , Engel J. , Ganser V.
Published: May 2005

The conformational transition between the two helical forms I and II of poly‐L‐proline serves as an experimental model for the study of the kinetic, behavior of cooperative systems. The slow I ⇌ II conversion after a sudden perturbation of the solvent composition was followed polarimetrically. The dependence of the mean relaxation times on chain length and the degree of conversion was compared with Schwarz's theory. In addition, a description of the entire relaxation curves was possible in three special cases: all‐or‐nothing, small perturbations of the I ⇌ II equilibrium in long chains, and conversions which start off with molecules completely in one or the other conformational state. The mathematical model on which the theory is based contains only one more adjustable parameter than the equilibrium model, but it adapts to the experimental results surprisingly well. The present kinetic results and equilibrium measurements on this system are described by the same values of those parameters which are common to both models. The found value of the rate constant of the propagation step, i.e. the cis ⇌ trans isomerization of a peptide bond at an existing I–II junction, agrees with the rate of isomerization in N,N‐dimethylacetamide reported in the literature. The rate of nucleation is up to 105 times smaller than the rate of propagation.
Model of the orientation symmetry of water molecules in biopolymers (by NMR Spectra)
Authors: Khanagov A. A.
Published: May 2005

Spectra of proton and deuteron magnetic resonance of water molecules in oriented biopolymer samples (collagen, DNA, cellulose) are interpreted on the basis of a model of molecular Schottki‐type diffusion. The presence of narrow splittings are shown to be the result of slight distortions of “ideal” symmetry of orientations of p‐p and O‐D vectors, corresponding to the point symmetry group of a tetrahedron, one of whose C3‐axes is oriented along the fiber axis.
Molecular beams of macroions. III. Zein and polyvinylpyrrolidone
Authors: Clegg G. A. , Dole M.
Published: May 2005

A 95% ethanol solution of the prolamin zein and of the synthetic polymer polyvinyl‐pyrrolidone (PVP) can be successfully electrosprayed and a molecular beam, containing ions of these substances in nitrogen carrier gas, formed. Similarly to polystyrene in benzene–acetone solvent, negative beams of zein and PVP have more substructure than beams containing positive ions. The results indicate considerable aggregation in the beam, possibly of six molecular units per aggregate, in addition to the singly charged single molecules.
Conformation of carboxymethyl amylose in aqueous solutions
Authors: Patel J. R. , Patel R. D.
Published: May 2005

Intrinsic viscosity and specific optical rotation measurements have been carried out for Carboxymethyl amylose (CMA) solutions in 0.15M sodium chloride at various pH values. Potentiometric titrations of CMA have been performed at various polymer concentrations as well as in presence of different divalent cations. The amount of divalent cation (Ni+2) bound to CMA has been determined by using a new method af analysis based on polyelectrolyte theory. Finally from the results it is shown that CMA may exist as a random coil in solution.
Relative effects of primary and tertiary structure on helix formation in myoglobin and α‐lactalbumin
Authors: Hermans Jan , Puett David
Published: May 2005

We have determined the ultraviolet optical rotatory properties of the cyanogen bromide peptides of myoglobin and reduced, S‐carboxymethylated α‐lactalbumin in both aqueous and aqueous alcohol solutions. Similar measurements were also made on the tryptic digests of apomyoglobin. In aqueous solutions the α‐helicity of the various peptides was between 5 and 15%, while in concentrated ethanol solutions the helicity could be increased significantly, but never to more than about 55%. The maximum helicity attained by the various peptides at high ethanol concentrations, as well as the cooperativity of the coil‐to‐helix transition (reflected in the slope at the steep portion of the helicity‐alcohol concentration curves), does not depend on the number of residues in the peptide in the manner expected. We have used a model which treats proline residues as absolute helix breakers, thus introducing the concept of effective chain length. By applying available theories of helix–coil transitions of short‐chain polypeptides to this model, one can satisfactorily describe most of the data on the myoglobin peptides. Significantly, it was possible to predict the helicity of acid‐denatured apomyoglobin from the behavior of the shorter fragments. By using the model, the peptides were found to have an equal intrinsic helix‐forming tendency which, with only two exceptions, was not raised by the formation of tertiary structure. The exceptions were apomyoglobin and peptide 56–131, which show, respectively, a considerable and a very small helicity attributable to tertiary structure formation in water at neutral pH. These results agree with the demonstrated absence of stable intermediates in protein unfolding equilibria. The results offer a further correlation between helical structure in the native molecule and the tendency to helix formation in isolated peptides. The results do not support the hypothesis that small folded regions are responsible for initiating the folding of the molecule, and an alternate description is proposed which envisages approximately half‐folded structures at the rate limiting step in the folding reaction. Helix formation in the 33‐residue C‐terminal peptide of α‐lactalbumin was found to be as easy as in the myoglobin peptides. If the proposed structural analogy between lysozyme and α‐lactalbumin is correct, then this is a case where helix formation occurs in a peptide which is not helical in the native protein. On the other hand, an α‐lactalbumin peptide corresponding to a region which has β‐structure in lysozyme did not lend to form α‐helices.
Interaction of magnesium ions with poly A and poly U
Authors: Willemsen A. M. , Van Os G. A. J.
Published: May 2005

The binding of Mg++ to poly A and poly U has been measured quantitatively by using the metallochromic indicator calmagite. The method is described in detail. It is shown that there is electrostatic interaction between the binding sites, viz., the phosphate groups, and the intrinsic association constant, for the specific binding can be determined. After extrapolation to zero ionic strength we find that, for the binding of Mg++ to poly A, kint = 4 × 104 and for that, to poly U, kint = 3 × 104. The intrinsic enthalpy of association is negative. The effect of Mg++ on the secondary structure of poly A and poly U has been studied by measuring the ultraviolet absorbance, optical rotatory dispersion and viscosity as a function of the amount of added Mg++ ions. It was found that Mg++ promotes the formation of a more ordered secondary structure by neutralizing or screening the negative charges. It is concluded from the absorbance measurements that for poly A at pH ⩾ 7 and for poly U at pH >xs 9 this ordering involves stacking of the bases. Likewise, in solutions of UDP with a pH around 10, base stacking occurs on addition of Mg++.
Simultaneous binding of adenosine and guanosine by polyuridylic acid: A further analysis
Authors: Schmitz Kenneth S. , Michael Schurr J.
Published: May 2005

The dialysis data of Pitha, Huang, and Ts'o for the simultaneous binding of adenosine and guanosine to polyuridylic acid are analyzed here using a grand‐partition function method described previously. The conclusion that the predominant mode of guanosine‐binding cannot be a competition with adenosine for the primary hydrogen‐bonding sites on the 2‐polyuridylic acid complex emerges from this analysis. By setting a reasonable upper limit to the amount of competitive binding that might occur, it is found that the difference in standard free energies for the binding of guanosine and adenosine must be at least FG − FA = 2400 cal/mole, provided the stacking energies for A − A, A − G, G − G interactions are all equal. This difference in binding free energies implies a specificity of at least 80: 1 in favor of A on the primary sites at 5°C. Since this is a lower limit, the actual binding specificity may well be much greater. The desirability of achieving specificity through repulsion of incorrect bases, rather than via attraction of correct bases, is discussed.
Conformations of cyclic peptides V. A proton magnetic resonance study of evolidine, cyclo‐Ser‐Phe‐Leu‐Pro‐Val‐Asn‐Leu
Authors: Kopple Kenneth D.
Published: May 2005

The 220 MHz proton magnetic resonance spectrum of the cyclic heptapeptide evoli‐dine, cyclo‐Ser‐Phe‐Leu‐Pro‐Val‐Asn‐Leu, has been analyzed. From the temperature dependence of chemical shift of the peptide protons in dimethyl sulfoxide, it is concluded that the peptide protons of the Asn and Phe residues are shielded from the solvent. This observation and H‐Cα‐N‐H dihedral angles, estimated from the corresponding coupling constants, are combined in a proposed conformation of the peptide backbone. The consistency of this conformation with other proton magnetic resonance observations is discussed.
Flow‐dichroic spectra of double‐stranded RNA
Authors: Wada Akiyoshi , Kawata Ikoi , Miura Kin‐Ichiro
Published: May 2005

Double stranded RNA from CPV and RDV have been studied by the flow‐dichroism technique. The flow orientation and dichroic spectra have shown that the molecular chain is flexible and has bases tilted slightly against the helix axis. It has been shown also that the wavelength dependency is similar to that of DNA, which strongly suggests the existence of an n − π* transition of bases around the 230 nm region.
Volume and sound velocity changes associated with coil‐β transition of poly (S‐carboxymethyl L‐cysteine) in aqueous solution
Authors: Makino Shio , Noguchi Hajime
Published: May 2005

The measurements were made for the volume and the sound velocity changes (ΔV and ΔU) on titrating the sodium salt of poly (S‐carboxymethyl L‐cysteine) with dilute HCl. For the reaction, COO− + H+ → COOH, ΔV per mole of H+ bound was + 12. 7 ml and +11. 4 ml in salt‐free and 0. 2 M NaCl solutions, respectively. Corresponding ΔU was about −13 cm/sec in salt‐free polymer solution where 11.5 mM carboxylate ion reacts with equimolar hydrogen ion. ΔV associated with the coil‐to‐β transition was found to be +2. 35 ml in H2O and +1. 90 ml in 0. 2 M NaCl per mole of amino acid residue, respectively. These values are larger than those obtained for the coil‐to‐helix transition of poly (L‐glutamic acid). ΔU for the transition was about −30 cm/sec in salt‐free solution of polymer concentration 0.0115 mole/liter. Possible sources of ΔV and ΔU for reaction; coil → β, are (1) the formation of void volume and (2) the changes in the extent of solvation in amide linkage and in side chain.
Base pairing equilibria between polynucleotides and complementary monomers
Authors: Davies R. J. H. , Davidson N.
Published: May 2005

Equilibrium dialysis measurements and optical melting curve data have been used to study the formation and stability of a number of complexes between polynucleotides and complementary monomers. The cooperativity parameter, (dθ/d ln c)θ = 0.5, where θ is the fraction of U or C residues complexed, and c is the concentration of free monomer has been measured as 1.4 for the 2:1 poly U:d‐adenosine‐complex, and 2.05 for the 2:1 poly C:d‐guanosiue complex at pH 7. The variation of Tm with c for several complexes has been used to calculate their partial molar enthalpies of formation at the midpoint of the transition: in 1.0 MNa + at pH 7, for the 2:1 complex of poly‐U with 2‐amino‐adenine, this is − 18.7 kcal/mole of 2‐amino‐adenine, for poly‐U with adenosine it is − 18.7 kcal/ mole; for poly‐C with dG, it is − 16.8 kcal/mole. These results do not agree very well with calorimetric integral heats of reaction reported in the literature.33 Complexes with random copolymers were also studied. The random copolymer, poly‐UC, can form a mixed complex with dG and either dA or 2‐amino‐adenosine; the binding of dG is enhanced by an adenine derivative and vice versa.Similarly, poly AC can form a mixed complex with dG and 3‐methyl‐xanthine. In each case, it appears that the ideal composition is a 2:1 hydrogen‐bonded complex, but the actual stoichiometry is such that each base on the random polynucleotide binds less than one‐half of a molecule of its complementary monomer. Poly UG can bind dG and dA, but in a less cooperative and specific way.
Circular dichroism of native and reconstituted nucleohistones
Authors: Frič I. , Šponar J.
Published: May 2005

Circular dichroism (CD) spectra of histone, DNA and native, partial and reconstituted nucleohistone complexes in 0.01 M Tris buffer in which nucleohistone complexes appear to be intact and in 2 M NaCl, in which complexes are mostly dissociated, have been compared. The CD spectra in the longwave region, where the protein contribution is negigible, reveal differences in the spectra for DNA in nucleohistone complexes as compared with that of free DNA, the difference being roughly proportional to the protein DNA ratio. An analysis of the shape of the first positive CD maximum suggests that we are probably dealing here with slight conformational changes on DNA. Minor differences between the behavior of native and reconstituted complexes may be due to the effect of different conformational states of the protein component.
Rotatory properties of molecules containing two peptide groups: experimental and theoretical results
Authors: Nielsen Eigil B. , Schellman John A.
Published: May 2005

Optical rotation studies were performed on five compounds containing two peptide groups. Four of the molecules were confined to restricted regions of conformational space by the presence of closed rings. Solvent and temperature were varied, and theoretical calculations were done for each compound covering the appropriate conformational space. The interpretation which results is qualitatively successful over the conformational regions covered by the compounds. Quantitative correlation between theory and experiment will require compounds of high rigidity.