bluuebunny/crossref_metadata_2025 huggingface dataset:
Spectroscopic studies on the structure of poly(8‐bromoadenylic acid): Effect of glycosidic torsion angle on the conformation and flexibility in polyribonucleotides
Authors: Govil Girjesh , Fisk Cherie L. , Howard Frank B. , Miles H. Todd
Published: December 2004

The helix–coil transition and conformational structure of poly(8‐bromoadenylic acid) [poly(8BrA)] have been investigated using 1H‐ and 13C‐nmr, CD, and ir spectroscopy. The results have been compared with the structure of the related 5′‐mono‐ and polynucleotides. The chemical shifts of H(2′), H(3′), C(2′), and C(3′) nmr signals show an interesting correlation with both the puckering of ribose ring and glycosidic bond torsion angle. Poly(8BrA) shows an upfield shift of the C(3′) signal and a downfield shift of the H(3′) signal compared to the chemical shifts in poly(A). These shifts are consistent with a C(3′) endo‐syn conformation for poly(8BrA). A similar effect has been reported previously and is also observed here on the C(2′) and H(2′) signals when the preferred conformation is C(2′)endo‐syn (e.g., in 5′‐8BrAMP). The chemical‐shift parameters thus act as a probe for studying syn ⇄ anti and N ⇄ S equilibria in solutions. The three‐bond 1H‐′13C coupling constants between H(1′) and C(8) and C(4) have been measured in poly(8BrA) and 5′‐8BrAMP and their structural implications have been discussed. The observed preference of a C(3′)endo‐syn conformation for poly(8BrA), coupled with other evidence, throws doubt on the validity of a correlation previously reported whereby a syn conformation is associated with a C(2′)endo ribose pucker. The backbone conformation of randomly coiled poly(8BrA) is very similar to the structures found in polyribonucleotides: poly(A) and poly(U). All three polymers show strong preferences for the backbone angles found in RNA helices. The CD spectrum of poly(8BrA) has a striking relationship to that of poly(A). The signs of all extrema are inverted, and the magnitudes are related by a constant factor. We suggest that these differences result from a change in the angle between coupled transition moment vectors in the two polymers. Infrared spectra of poly(8BrA) in H2O and D2O solution are reported for the frequency range below 1400 cm−1. The antisymmetric >PO stretching vibration is observed at an unusually low frequency in the helix (1214 cm−1). The symmetric >PO stretch occurs at ∼1095 cm−1 but is not resolved from a ring vibration near this frequency. A conformationally sensitive band, characteristic of helical RNA structures, is observed at 817 cm−1 and disappears when the helix is melted. This observation confirms the conclusion that ordered poly(8BrA) has a regular helical structure with an RNA backbone conformation. A stereochemical explanation is provided for the failure of poly(8BrA) (or other syn polymers) to form double helices with anti‐polyribonucleotides.
13C‐Nmr studies of ACTH: Assignment of resonances and conformational features
Authors: Toma Flavio , Fermandjian Serge , Löw Miklos , Kisfaludy Lajos
Published: December 2004

The biologically active ACTH(1–32) and ACTH(1–24) and other shorter peptide segments of the native hormone ACTH(1–39) were studied in aqueous solution by 13C‐nmr. In order to identify the 13C resonances—except those of the carbonyls—both high‐field nmr spectroscopy measurements and substitution of residues with amino acids enriched to 85% in 13C were carried out. The main results are (1) the direct characterization of the cis–trans isomerism of proline 24 and its effects on the directly connected and sequentially neighboring residues and (2) findings that the conformational features agree with an α‐helix type organization in the N‐terminal part of the ACTH molecule which is responsible for the biological activity.
Noninteracting local‐structure model of folding and unfolding transition in globular proteins. I. Formulation
Authors: GŌ Nobuhiro , Abe Haruo
Published: December 2004

A statistical‐mechanical model (a noninteracting local structure model) of folding and unfolding transition in globular proteins is described and a formulation is given to calculate the partition function. The process of transition is discussed in this model within the framework of equilibrium statistical mechanics. In order to clarify the range of applicability of such an approach, the characteristics of the folding and unfolding transition in globular proteins are analyzed from the statistical‐physical point of view. A theoretical advantage is pointed out in studying folding and unfolding processes taking place as conformational fluctuations in individual protein molecules under macroscopic equilibrium at the melting temperature. In this case, paths of folding and unfolding are shown to be identical in the statistical sense. A key to the noninteracting local structure model lies in the concept of local structures and the assumption of the absence of interactions between local structures. A local structure is defined as a continuous section of the chain which takes the same or similar local conformation as in the native conformation. The assumption of the absence of inter‐actions between local structures endows the model with the remarkable character that its partition function can be calculated exactly; thereby the equilibrium population of various conformations along the folding and unfolding paths can be discussed only by a knowledge of the folded native conformation.
X‐Pro peptides: Solution and solid‐state conformation of benzyloxycarbonyl‐(Aib‐Pro)2methyl ester, a type I β‐turn
Authors: Venkatachalapathi Y. V. , Nair C. M. K. , Vijayan M. , Balaram P.
Published: December 2004

The synthesis of the tetrapeptide benzyloxycarbonyl(α‐aminoisobutyryl‐L‐prolyl)2‐methyl ester (Z‐(Aib‐Pro)2‐OMe) and an analysis of its conformation in solution and the solid state are reported. Stepwise synthesis using dicyclohexylcarbodiimide leads to racemization at Pro(2). Evidence for the presence of diastereomeric tetrapeptides is obtained from 270‐MHz1H‐nmr and 67.89‐MHz 13C‐nmr. The all‐L tetrapeptide is obtained by fractional crystallization from ethyl acetate. The NH of Aib(3) is shown to be involved in an intramo‐lecular hydrogen bond by variable‐temperature 1H‐nmr and the solvent dependence of NH chemical shifts. The results are consistent with a β‐turn conformation with Aib(1) and Pro(2) at the corners stabilized by a 4 → 1 hydrogen bond. The molecule crystallizes in the space group P212121, with a = 8.839, b = 14.938, and c = 22.015 Å. The structure has been refined to an R value of 0.051. The peptide backbone is all‐trans, and a 4 → 1 hydrogen bond, between the CO group of the urethane moiety and Aib(3) NH, is observed. Aib(1) and Pro(2) occupy the corner positions of a type I β‐turn with ϕ = −55.4°, Ψ = −31.3° for Aib(1) and ϕ = −71.6°, Ψ = −38° for Pro(2). The tertiary amide unit linking Pro(2) and Aib(3) is significantly distorted from planarity (Δω = 14.3°).
Structure in solution of biscyclo(dipeptide) restricted by CSSC gauche effect
Authors: Ueyama Norikazu , Araki Takeo
Published: December 2004

Biscyclo(Cys‐Sar) [I] and biscyclo(Cys‐Pro) [II] were prepared by the extension of amino acid moieties from cystine. Compound I equilibrates between two rotamers around the CSSC bond of the cystine residue in methanol, showing dual negative CD transitions (CS‐SC) at 270 and 255 nm, and dual S‐S vibrations at 507 and 539 cm−1 in Raman spectra. In contrast, a conformation of P‐helix type is suggested in CH3CN, which shows a distinct negative CD at 270 nm and only one Raman band at 507 cm−1 for the S‐S bond. Compound II rotates freely in dimethylsulfoxide (Me2SO) but takes a relatively stable conformer of P‐helix type in methanol, chloroform/Me2SO (9:1), and chloroform/trifluoroacetic acid (9:1). The conformation in chloroform is retained even on addition of trifluoroacetic acid. A more complete conformation of compound II in water was determined from the negative CD of S‐S transition and 1H‐nmr spectra of the Cys‐β‐CH2 protons.
Conformation study of poly(γ‐methyl‐L‐glutamate) in helicogenic solvents by small‐angle X‐ray scattering
Authors: Ishimuro Yoshitaka , Yamaguchi Saburo , Hamada Fumiyuki , Nakajima Akio
Published: December 2004

Small‐angle x‐ray scattering of poly(γ‐methyl‐L‐glutamate), [Glu(OMe)]n, in m‐cresol and in pyridine was measured to determine the mass per unit length, Mq, and the radius of gyration of the cross section, 〈S〉1/2. It was confirmed from the values of Mq that [Glu(OMe)]n exists in an α‐helical conformation in these solvents. It was elucidated from the calculations on 〈S〉1/2 that the side chains come in moderately close contact with the main chain in these solvents. It was indicated from the analysis of the outer portion of the scattering curves that the side‐chain conformation varied depending on the solvent.
Conformational aspects of polypeptides. VIII. Helical assignments via far ultraviolet absorption spectra and optical activity
Authors: Goodman Murray , Listowsky Irving , Masuda Yukio , Boardman Franklin
Published: December 2004

We determined the onset of helical structures in solution for oligopeptides by means of the decrease in intensity of the 190 mμ band (hypochromism), and related these findings to optical rotatory dispersion data. Measurements of ultraviolet absorption spectra in trifluoroethanol show that helical conformations commence at about the tetradecamer for peptides derived from β‐methyl‐L‐aspartate. In the γ‐methyl‐L‐glutamate series the hypochromic effect starts at the nonamer, increasing in magnitude with peptide chain length. Essentially the same results were obtained by using optical rotatory dispersion. By dividing the b0 (Moffitt‐Yang constant) for the oligopeptides into helical and nonhelical components, we have better indications that in previous work for the onset of helicity. We have also studied the far ultraviolet spectra and optical rotatory dispersion for high polymers derived from β‐methyl‐L‐aspartate and γ‐methyl‐L‐glutamate. Assuming complete helicity for these high polymers, we assigned helical contents to the oligopeptides. In addition, ultraviolet spectra were measured for the polymer from γ‐methyl‐DL‐glutamate in order to determine its helical content.
Dialysis studies. V. The behavior of different preparations of bovine ribonuclease
Authors: Craig L. C. , King T. P. , Crestfield Arthur M.
Published: December 2004

Studies of different preparations of ribonuclease A by thin film dialysis and countercurrent distribution have shown the existence of conformational isomers. These forms are slowly interconvertible in a particular solvent environment. They show the minimum molecular weight of ribonuclease and do not differ enzymatically or by rotatory dispersion.
The orientation and dissociation field effect of DNA in solution
Authors: Ise N. , Eigen M. , Schwarz G.
Published: December 2004

By means of a previously described experimental technique the orientation field effect (orientation of polyions and anisotropy of conductivity in an electric field) has been found for a special sample of desoxyribonucleic acid (DNA) in aqueous solution. The results can be described fairly well by the theory. The fact that the polyions of undenatured DNA are rather rigid rods due to their helical structure is, as expected, clearly noticeable in the concentration dependence of the effect. This phenomenon is discussed in comparison with the data for the flexible polyphosphate ions. Also measurements of the dissociation field effect of the substance have been performed. The results can be understood in the light of the structure of the DNA.
Helix–coil stability constants for the naturally occurring amino acids in water. XXI. Glutamine parameters from random poly(hydroxypropylglutamine‐co‐L‐glutamine) and poly(hydroxybutylglutamine‐co‐L‐glutamine)
Authors: Denton J. B. , Powers S. P. , Zweifel B. O. , Scheraga H. A.
Published: December 2004

Water‐soluble, random copolymers containing L‐glutamine and either N5‐(3‐hydroxypropyl)‐L‐glutamine or N5‐(4‐hydroxybutyl)‐L‐glutamine were synthesized, fractionated, and characterized. The thermally induced helix–coil transitions of these copolymers were studied in water. A short‐range interaction theory was used to deduce the Zimm‐Bragg parameters σ and s for the helix–coil transition in poly(L‐glutamine) in water from an analysis of the melting curves of the copolymers in the manner described in earlier papers. The computed values of s indicate that L‐glutamine is helix‐indifferent at low temperature and a helix‐destabilizing residue at high temperature in water. At all temperatures in the range of 0–70°C, the glutamine residue promotes helix–coil boundaries since the computed value of σ is large.
Changes in Raman vibrational bands of calf thymus DNA during the B‐to‐A transition
Authors: Martin James C. , Wartell Roger M.
Published: December 2004

The B‐to‐A conformational transition of calf thymus DNA fibers was followed employing Raman spectroscopy. The transition was induced by soaking DNA fibers in water/ethanol mixtures increasing from 60 to 85% ethanol (v/v). Intensity changes of 17 Raman vibrational bands were quantified in the region from 400 to 860 cm−1. Two bands at 500 and 784 cm−1 were employed as internal standards. These bands do not appear to change in intensity with ethanol concentration. Large intensity changes relative to these two bands are observed between 70 and 74% ethanol for backbone vibrations at 708, 808, and 835 cm−1, and base vibrations at 682, 730, and 750 cm−1. These results indicate that a highly cooperative conformational change takes place between different portions of DNA in the B‐to‐A transition. Relative intensity changes preceding the onset of the major transition are observed in only two bands; at 835 cm−1, assigned to a ribose–phosphate vibration, and at 750 cm−1, assigned to thymine. The implications of these pretransition changes are discussed.
Adsorption of the polypeptides on a solid surface. III. Behavior of stiff chains in a pore
Authors: Zhulina E. B. , Gorbunov A. A. , Birshtein T. M. , Skvortsov A. M.
Published: December 2004

A strict analytical theory has been developed describing the behavior of a model lattice polymer chain of arbitrary stiffness in a slitlike pore at polymer–adsorbent interaction energies –ε. The thermodynamic characteristics of the system were calculated. It was shown that the transition of the macromolecule from the solution volume inside a pore occurs by the first‐order phase transition with evolution of latent heat of adsorption. The transition point –ε = –εc is determined by the chain stiffness and is independent of the pore width D. It is shown that in the precritical range, –ε < –εc, the free energy ΔF of the macromolecules in the pores is adequately described by the universal dependence ΔF = ΔF(D*/A), where D* is some effective pore width depending on the value of –ε, and A is the length of the Kuhn segment. At high attraction energies, –ε ≫ –εc, the macromolecules are bonded to the pore walls by a great number of units and their free energy depends only on –ε and the chain stiffness, ΔF = ΔF(A, ε). Close to the critical energy –ε ≃ –εc (transition range), ΔF is determined by both the stiffness of the macromolecule and the pore width D: ΔF ∼ A2D−1 for fairly high values of A and D. The possibilities of using porous media as protein stabilizers are discussed, and the value of the stabilizing effect depending on the chain stiffness is estimated.
Cyclodextrin–adamantanecarboxylate inclusion complexes: A model system for the hydrophobic effect
Authors: Harrison John C. , Eftink Maurice R.
Published: December 2004

Thermodynamic studies of the binding of adamantanecarboxylate to cyclodextrins have been made as a function of temperature and added organic cosolvent (methanol) using flow microcalorimetry. The negative heat capacity change associated with the adamantanecar‐boxylate/β‐cyclodextrin interaction and the fact that the interaction is weakened by the addition of methanol implicate the binding process as being a hydrophobically driven one. The negative enthalpy change (ΔH0 = −5.5 kcal/mol) and near‐zero entropy change (ΔS0 = 1.5 cal/mol deg) are quite different from the values normally expected for a hydrophobic bond, indicating that other bonding forces are important in addition to the hydrophobic effect. The relative contribution of the hydrophobic effect and other bonding forces (most likely van der Waals forces) to the overall binding was judged from an analysis of the dependence of the thermodynamics of the association process on the surface tension of the water–methanol mixtures following a model for “solvophobic” bonding described by Sinanoglu [Molecular Associations in Biology (1968) Academic Press, New York, pp. 427–445]. From this analysis, adamantane–carboxylate/cyclodextrin complex formation is found to be driven to the extent of −1.9 kcal/mol by the hydrophobic effect. Furthermore, the hydrophobic driving force is found to be characterized by a positive ΔS0 of 10 cal/mol deg. The remaining free energy of binding (and the ΔH0 of binding of ∼−6 kcal/mol) is then due to the intrinsic (surface‐tension‐independent) van der Waals interaction between the ligand and cyclodextrin cavity.
Equilibrium dialysis studies of polyamine binding to DNA
Authors: Braunlin W. H. , Strick T. J. , Record M. T.
Published: December 2004

Binding constants and binding site sizes for the interactions of the polyamines spermine (+4), spermidine (+3), and putrecine (+2) with helical DNA have been determined as a function of ionic conditions and temperature by equilibrium dialysis using 14C‐labeled polyamines. In addition, competition equilibrium dialysis has been used to determine binding parameters for the divalent cations putrescine and Mg2+ from the competitive effect of these ions on the binding of spermine or spermidine. In all cases, the logarithm of the binding constant (log Kobs) varies linearly with the logarithm of the monovalent salt concentration; the slopes d log Kobs/d log[NaCl] are proportional to the valence of the ligand, and values of the extrapolated binding constants at 1M NaCl obtained from the intercepts are small (of order 1–10M−1). In those cases examined, Kobs is insensitive to temperature; the free energy of binding is predominantly entropic. Consequently, polymines as DNA‐binding ligands behave analogously to the oligolysìnes investigated previously [cf. Record, Lohman & de Haseth (1976) J. Mol. Biol. 107, 145–158; Lohman, de Haseth & Record (1980) Biochemistry 19, 3522–3530]. The interactions of these oligocations with DNA are predominantly electrostatic and are driven by the release of thermodynamically bound electrolyte ions from the vicinity of the DNA. The extent to which these oligocations are localized at individual phosphate binding sites or delocalized on the DNA molecule is currently not known.
Helix–coil transition of poly(α,L‐glutamic acid) at an interface: Correlation with static and dynamic membrane properties
Authors: Pefferkorn Emile , Schmitt Adrien , Varoqui Raphaël
Published: December 2004

When adsorbed from an aqueous dilute solution at high pH into the pores of an inert cellulose acetate filter, poly(α,L‐glutamic acid) remains strongly anchored to the pore walls. The existence of the helix–coil transition for the adsorbed polypeptide in a certain pH range is evidenced by static and dynamic membrane properties displayed by the “activated” filter, such as excess cation uptake, membrane potential, and hyraulic permeability. In particular, the variations of the hydrodynamic thickeness present a sigmoidal shape characteristic of the helix–coil transition at the interface, a transition apparently less sharp than in solution.
Evidence for the role of 4‐hydroxyproline localized in the third position of the triplet (Gly‐X‐Y) in adaptational changes of thermostability of a collagen molecule and collagen fibrils
Authors: Burjanadze Tengiz V.
Published: December 2004

An analysis of the available data on the thermostability and imino acid content of various collagens has shown that the change of the denaturation temperature (tm) of the collagen triple helix, as well as the temperature of hydrothermic shrinkage (ts) of collagen fibrils, depends on the number of hydroxyproline residues localized in the third position of the collagen triplet. This change does not depend on the content of proline and 3‐ and 4‐hydroxyproline localized in the second position of the triplet. Empiric equations have been obtained connecting tm and ts with the content of 4‐hydroxyproline. The results of the analysis are in good agreement with one of the collagen structure models recently proposed by the Ramachandran school.
Studies of fibrin film. I. Stress relaxation and birefringence
Authors: Roska Fred J. , Ferry John D.
Published: December 2004

Measurements of stress relaxation in uniaxial extension and associated time‐dependent birefringence have been made on bovine fibrin film, prepared by gentle compaction of coarse fibrin clots, containing 13–22% fibrin plasticized with either aqueous buffer or glycerol. Both unligated and ligated (i.e., with α‐α and γ‐γ ligation by fibrinoligase, factor XIIIa) films were studied. Both types showed two stages of stress relaxation, with time scales of approximately 10 and 103–104 s, respectively, with a plateau region between. In the plateau, the nominal (engineering) stress for ligated glycerol‐plasticized film is proportional to In λ, where λ is the stretch ratio, up to λ ≅ 2, and it decreases with increasing temperature. For unligated glycerol‐plasticized film, the stresses are smaller by a factor of one‐half to one‐third. For ligated film, the second stage of relaxation is relatively slight, and recovery after release of stress is often nearly complete. For unligated film, the second stage involves a substantial drop in stress, and after recovery there is a significant permanent set. A second relaxation for ligated film reproduces the first, but for unligated film it reproduces the first only if the initial relaxation is terminated before the second stage; otherwise, the second relaxation shows a weaker structure. The behavior of water‐plasticized film is similar to that of glycerol‐plasticized except that the second stage of relaxation occurs at shorter times. During the first stage of stress relaxation, up to about 100 s, the birefringence and the stress‐optical coefficient increase; during the plateau zone of stress relaxation, the birefringence of ligated films is approximately constant and is proportional to 2λ2/(λ2 + 1) − 1, where λ is the stretch ratio. This dependence is predicted by a two‐dimensional model in which rodlike elements in the plane of the film are oriented with independent alignment. During the final stage of stress relaxation, the birefringence of ligated films decreases slightly; that of unligated films decreases substantially, but less rapidly than the stress, corresponding to a further increase in the stress‐optical coefficient. With additional information from small‐angle x‐ray scattering reported in an accompanying paper, the first stage of relaxation is attributed to partial release of bending forces in the fibers by orientation, accompanied by increased birefringence. The second stage is attributed, for ligated films, to an internal transition in the fibrin units accompanied by elongation of some of the fibers; and in the unligated films, to a combination of the latter transition with slippage of protofibrils lengthwise within the fiber bundles that causes some loss of orientation, which diminishes the birefringence.
Studies of fibrin film. II. Small‐angle x‐ray scattering
Authors: Roska Fred J. , Ferry John D. , Lin J. S. , Anderegg John W.
Published: December 2004

Measurements of small‐angle x‐ray scattering have been made on bovine fibrin film, prepared by gentle compaction of coarse fibrin clots, containing 12–15% fibrin plasticized with either aqueous buffer or glycerol. Most of the experiments were made with water‐plasticized films because of the better x‐ray contrast. Both unligated and ligated (i.e., with α‐α and λ‐λ ligation by fibrinoligase, factor XIIIa) films were studied. Theoretical angular scattering profiles were calculated for a simplified model of the fibrin protofibril as a function of stretch ratio in uniaxial elongation based on an orientation distribution derived in the preceding paper. Measurements were made on unstretched films both with slit geometry and with pinhole geometry and two‐dimensional position‐sensitive detection. From the former, which had better resolution, the fundamental peak corresponded to a repeat spacing of 230 ± 5 Å, in agreement with early results of Stryer et al. [(1963) Nature 197, 793–794] and electron micrographs of stained fibrin, and with the half‐staggered overlapping model of the protofibril. Measurements were made with pinhole geometry on film stretched up to a stretch ratio λ = 1.59 at different times after imposition of strain and after release and recovery. The changes in meridional and equatorial scattering profiles, including the more prominent appearance of a harmonic in the former, show the orientation of the protofibrils as previously deduced from birefringence and related quantitatively to stretch ratio. In addition, the original repeat spacing is gradually replaced by one of about 290 Å. The “internal” stretch ratio λx, averaging about 1.28, is independent of the macroscopic stretch ratio λ from 1.14 to 1.59. The change, which is more nearly complete for unligated film and is reversible on release and retraction of the stretched strips, is attributed to an internal transition in the fibrin monomer units, probably involving extension of either the helical connectors or the terminal nodules. The results of stress and birefringence relaxation reported in the preceding paper of this series are interpreted on this basis.
Crystal structures of diketopiperazines containing α‐aminoisobutyric acid: Cyclo(Aib‐Aib) and cyclo(Aib‐L‐Ile)
Authors: Suguna K. , Ramakumar S. , Shamala N. , Prasad B. V. Venkataram , Balaram P.
Published: December 2004

The crystal and molecular structures of two α‐aminoisobutyric acid (Aib)‐containing diketopiperazines, cyclo(Aib‐Aib) 1 and cyclo(Aib‐L‐Ile) 2, are reported. Cyclo(Aib‐Aib) crystallizes in the space group P1 with a = 5.649(3), b = 5.865(2), c = 8.363(1), α = 69.89(6), β = 113.04(8), γ = 116.0(3), and Z = 1, while 2 occurs in the space group P212121 with a = 6.177(1), b = 10.791(1), c = 16.676(1), and Z = 4. The structures of 1 and 2 have been refined to final R factors of 0.085 and 0.086, respectively. In both structures the diketopiperazine ring shows small but significant deviation from planarity. A very flat chair conformation is adopted by 1, in which the Cα atoms are displaced by 0.07 Å on each side of the mean plane, passing through the other four atoms of the ring. Cyclo(Aib‐Ile) favors a slight boat conformation, with Aib Cα and Ile Cα atoms displaced by 0.11 and 0.05 Å on the same side of the mean plane formed by the other ring atoms. Structural features in these two molecules are compared with other related diketopiperazines.
Strategy for trapping intermediates in the folding of ribonuclease and for using 1H‐NMR to determine their structures
Authors: Kuwajima Kunihiro , Kim Peter S. , Baldwin Robert L.
Published: December 2004

The major unfolded form of ribonuclease A is known to show well‐populated structural intermediates transiently during folding at 0°–10°C. We describe here how the exchange reaction between D2O and peptide NH protons can be used to trap folding intermediates. The protons protected from exchange during folding can be characterized by 1H‐nmr after folding is complete. The feasibility of using 1H‐nmr to resolve a set of protected peptide protons is demonstrated by using a specially prepared sample of ribonuclease S in D2O in which only the peptide protons of residues 7–14 are in the 1H‐form. All eight of these protected peptide protons are H‐bonded. Resonance assignments made on isolated peptides containing these residues have been used to identify the protected protons. Other sets of protected protons trapped in the 1H‐form can also be isolated by differential exchange, using either ribonuclease A or S. Earlier model compound studies have indicated that H‐bonded folding intermediates should be unstable in water unless stabilized by additional interactions. Nevertheless, peptides derived from ribonuclease A that contain residues 3–13 do show partial helix formation in water at low temperatures. We discuss the possibility that specific interactions between side chains can stabilize short α‐helixes by nucleating the helix, and that specific interactions may also define the helix boundaries at early stages in folding.
Multiphasic conformation transition of globular proteins under denaturating perturbation
Authors: Wada Akiyoshi , Saito Yoshio , Ohogushi Mikio
Published: December 2004

Denaturation profiles of 17 globular proteins were studied by the spectroscopic and chromatographic methods with high‐data‐point density. The denaturational transitions are broadly classified into three types according to their multiphasic characteristics. In general, more or less complex internal cooperative events seem to take place in the conformation transition of globular proteins.
Sequential individual resonance assignments in the 1H‐NMR spectra of polypeptides and proteins
Authors: Wüthrich Kurt
Published: December 2004

Recently, a new procedure for the assignment of protein 1H‐nmr spectra was introduced that relies on stereochemical considerations of proton–proton distances in polypeptides and on the use of two‐dimensional nmr for obtaining 1H‐1H through‐bond and through‐space connectivity maps. In the present paper a particular aspect of this assignment procedure is discussed in more detail, i.e., how to obtain individual resonance assignments from identification of amino acid side‐chain spin systems and identification of neighboring residues in the amino acid sequence.
The key role of residue 5 in angiotensin II
Authors: Fermandjian Serge , Sakarellos Constantin , Piriou Françlois , Juy Michel , Toma Flavio , Thanh Hung Lam , Lintner Karl , Khosla Mahesh C. , Smeby Robert R. , Bumpus F. Merlin
Published: December 2004

The conformation–biological activity relationships in a series of angiotensin II analogs substituted in position 5 were studied. Results indicated that only analogs with β‐branched residue in position 5 possess spectral and biological properties identical to that of parent angiotensin II.
Immunoassays of peptide hormones and their chemical aspects
Authors: Moroder L. , Nyfeler R. , Gemeiner M. , Kalbacher H. , Wüunsch E.
Published: December 2004

The N‐terminal maleoyl‐β‐alanyl derivative of human gastrin‐[2–17] has been synthesized as a model compound to investigate the usefulness of such peptide derivatives for their mild and selective conjugation, via reaction with thiol groups, to high‐molecular‐weight carrier molecules to produce antigens, as well as to radioiodinable or fluorogenic molecules to prepare tracers for immunoassays. In this context the examined enzyme substrate‐gastrin conjugate was found to exhibit the full immunoreactivity of the parent peptide and to be well suited as tracer in a gastrin fluorescence‐immunoassay.
Conformational study of ribonucleotides, 2′‐deoxyribonucleotides, and arabinonucleotides by carbon‐13 nuclear magnetic resonance
Authors: Blonski Wayne J. P. , Hruska Frank E. , Sadana Krishan L. , Loewen Peter C.
Published: December 2004

The geminal and vicinal 13C‐31P coupling constants have been monitored, as a function of pH, for a series of uracil and cytosine 3′‐ and 5′‐nucleotides with a ribose, arabinose, or 2′‐deoxyribose sugar. Data were also obtained for two 3′,5′‐diphosphates in the ribose and arabinose series. The geminal J(C5′‐P5′) and J(C3′‐P3′) couplings show only a small dependence on the ionization state of the phosphate, decreasing by < 0.5 Hz in the pH 5–7 range. For the ribose and arabinose 3′‐nucleotides, the vicinal J(C4′‐P3′) increase (up to 1.5 Hz) on secondary phosphate ionization in the pH 5–7 range, whereas their J(C2′‐P3′) couplings decrease (up to 1.5 Hz) over the same pH range. In contrast for the 2′‐deoxyribose molecules, both couplings decrease (∼0.5 Hz) on phosphate ionization. The titration curves provide information about the influence of the sugar on the conformation about the C3′O3′ bond. Some conformational trends could be rationalized by consideration of the sugar‐puckerdependent contact interactions between the 3′‐phosphate and the substituents on the furanose ring.
Tyrosine optical activity as a probe of the conformation and interactions of fibronectin
Authors: Welsh E. J. , Frangou S. A. , Morris E. R. , Rees D. A. , Chavin S. I.
Published: December 2004

A very intense negative band is observed at ∼ 183 nm in the CD spectrum of fibronectin from bovine plasma. This transition has not previously been reported, probably because it occurs in a spectral region that has not been readily accessible in earlier studies. At longer wavelength, the observed CD is very similar to spectra reported for human and chick material, having positive bands at ∼230 and ∼200 nm, and a negative band at ∼215nm. The low molar ellipticity of the negative band ([θ] ≈ −2.5 × 103 deg cm2 dmol−1) suggests little α‐helix or β‐sheet structure. The new transition, and the two positive bands at higher wavelength, do not correspond to known transitions of the peptide backbone, but all three are present in the CD of N‐acetyltyrosineamide. It is therefore suggested that the observed CD behavior of fibronectin arises predominantly from the optical activity of tyrosine side chains. The contribution of this side‐chain optical activity to the CD of other proteins is discussed.

On raising pH to ionize tyrosine residues, the positive CD band at ∼230 nm is lost in both N‐acetyltyrosineamide and in fibronectin. The spectral change is fully reversible in the model compound, but only partially reversible in fibronectin. From this evidence, and the magnitude of the 183‐nm band, it is suggested that some or all of the tyrosine residues in fibronectin may be present within ordered domains. The possible role of SS bonds in maintaining tertiary structure is discussed. The interaction of fibronectin with heparin is accompanied by a large increase in the 183‐nm band and by slight enhancement of the negative band at 215 nm, consistent with some limited formation of β‐sheet.

Present results indicate that CD may be of considerable value in characterization of the molecular organization and biologically relevant interactions of fibronectins and of related glycoproteins of the extracellular matrix.
Crystal structure of a tripeptide, L‐alanyl‐glycyl‐glycine and its relevance to the poly(glycine)‐II type of conformation
Authors: Subramanian E. , Lalitha V.
Published: December 2004

A tripeptide molecule, L‐alanyl‐glycyl‐glycine, crystallizes in the form of a left‐handed helix with (ϕ,ψ) = −83°, 170°. A pseudohexagonal packing arrangement and interchain hydrogen‐bonded interactions are reminiscent of the model for the structure of poly(glycine)‐II. Observations of certain intermolecular interactions appear to be relevant to the stereochemical assumptions incorporated in the models proposed for poly(glycine)‐II and related polypeptides.
Nmr studies on complex formation of poly(L‐lysine HBr) with carbonate ion in aqueous solution
Authors: Kakiuchi Kinji , Akutsu Hideo
Published: December 2004

Diemer formation of poly(L‐lysine HBr) in carbonate buffer at pD 10.5 was reported in our previous paper [Biopolymers(1981) 20, 345–357]. The mechanism of the dimer formation was investigated employing carbon‐13 and proton nmr. pD dependence of the 13C‐nmr spectrum of poly(L‐lysine HBr) in the presence of carbonate ion clearly shows that a complex formation between the CO ion and protonated ε‐amino group is involved in the stabilization of the dimer form. The lifetime of the complex is longer than 10−2 s. A stoichiometric evaluation suggests that CO bridges two lysyl side chains. A molecular model of the dimer form designated as a single antiparallel β‐ribbon was proposed and discussed in the light of hydrodynamic and ir spectroscopic properties reported earlier. Concentration change experiments indicate that CO binds not only to the dimer formation is inferred as stabilization of the single antiparallel β‐ribbon as an intermediate structure in the conversion between the α‐helix and β‐sheet. The α‐CH proton signal of the lysine residue located in the ordered structure (α‐helix and β‐form) was observed to be separate from that in the random‐coil region.
Collapse of DNA caused by trivalent cations: pH and ionic specificity effects
Authors: Thomas T. J. , Bloomfield V. A.
Published: December 2004

A comparison of the condensation of T4 phage DNA by spermidine and Co(NH3) at pH values between 5.1 and 10.2 has been made using quasielastic light scattering to determine translational diffusion coefficients and Stokes radii. Co(NH3) is more effective than spermidine in causing condensation at all pH, indicating that the differences observed in previous work were not due to pH effects, as might have been inferred from recent theories of intermolecular forces. The DNA particles collapsed with Co(NH3) are smaller than those obtained with spermidine. The hydrodynamic radius of spermide‐collapsed structures decreases slightly with increasing pH, while the size of the Co(NH3)collapsed structures is almost independent of pH. These results confirm that there are specific ion effects in DNA condensation by oligocations, in addition to the dominant general polyelectrolyte effects.
Mutual diffusion of crystallin proteins at finite concentrations: A light‐scattering study
Authors: Delaye M. , Gromiec A.
Published: December 2004

Both static and quasielastic light‐scattering measurements were performed on solutions of crystallin proteins extracted from calf lens cortex. The concentration range between ideal (c → O) and physiologic solutions (c up to 50%, w/w) was investigated. The intensity data are compatible with a model where the globular crystallins behave as “hard spheres,” the radius of which does not depend on concentration. The correlation function of the scattered intensity is correctly described by a single exponential (mutual diffusion) for 0 < c < 5%. For larger concentrations, a slowly relaxing component, whose amplitude increases with c, appears on top of the rapid component describing the mutual diffusion. Heterodyne detection is used to uncouple these two components. The mutual diffusion coefficient is then found to decrease linearly up to c ≃ 10% and to deviate sharply from linearity at larger concentrations.
Synthesis and conformation of the cyclic octapeptides cyclo(Phe‐Pro)4, cyclo(Leu‐Pro)4, and cyclo[Lys(Z)‐Pro]4
Authors: Kimura Shunsaku , Imanishi Yukio
Published: December 2004

Cyclic octapeptides, cyclo(X‐Pro)4, where X represents Phe, Leu, or Lys(Z), were synthesized and their conformations investigated. A C2‐symmetric conformer containing two cis peptide bonds was found in all of these cyclic octapeptides. The numbers of available conformations due to the cis–trans isomerization of Pro peptide bonds depended on the nature of the solvent and X residue: they decreased in the following order: cyclo[Lys(Z)‐Pro]4 > cyclo(Leu‐Pro)4 > cyclo(Phe‐Pro)4 in CDCl3. 13C spin‐lattice relaxation times (T1) of these cyclic octapeptides were measured, and the contribution of segmental mobility to T1 was found to vary with the nature of the X residue.
Circular dichroism studies of freeze‐drying‐induced conformational changes in human hemoglobin
Authors: Thirion Christian , Larcher Dominique , Chaillot Bernard , Labrude Pierre , Vigneron Claude
Published: December 2004

Freeze‐drying of hemoglobin leads to the formation of a significant amount of methemoglobin. It is possible to decrease this transformation in the presence of protective compounds. The mechanism of action of these protectors is presently unknown. Spectroscopic absorption and CD spectra between 190 and 700 nm are presented for samples of hemoglobin freeze‐dried with or without protection and for control solutions of oxyhemoglobin and methemoglobin. The interpretation of the dichroic spectra allows us to observe the secondary, tertiary, and quaternary structure changes that hemoglobin undergoes with freeze‐drying. The results indicate that the absence of a protector weakly influences the conformation in the vicinity of the heme and increases the helicity of protein chains from 75 to 81%. Furthermore, experimental data, in agreement with electron‐spin resonance measurements, suggest that the protective effect is not the result of a direct bond between the iron and the compound added.
Apparent molar volumes of some amino acids and peptides in aqueous urea solutions
Authors: Mishra A. K. , Prasad K. P. , Ahluwalia J. C.
Published: December 2004

Densities of solutions of several α‐amino acids and peptides in 3 and 6m aqueous urea solvents have been determined at 298.15 K. These data have been used to evaluate the infinite‐dilution apparent molar volumes of the solutes and the volume changes due to transfer (V) of the α‐amino acids and peptides at infinite dilution from water to aqueous urea solutions. The sign and magnitude of the V values have been rationalized in the framework of Friedman's cosphere‐overlap model. The V values for the glycyl group (CH2CONH) and alkyl side chains have been estimated.
CNDO/2 quantum‐mechanical calculations of the conformational flexibility of the diketopiperazine skeleton
Authors: Ciarkowski Jerzy
Published: December 2004

Eight conformers typical of diketopiperazine (DKP) ring folding were chosen for analysis. Conformational energy calculations were carried out using the semiempirical quantummechanical CNDO/2 method. The results obtained confirm considerable flexibility of the DKP skeleton. As the degree of folding increases, twisted boat conformations with the nonplanar peptide bonds tend to be more stable, while more rigid regular boat conformations with planar peptide bonds appear to be less stable than a flat one. The CNDO/2 method was found to be reliable enough for conformational studies of cyclic peptide skeletons with cis‐peptide bonds.
Relaxation kinetics of DNA–ligand binding including direct transfer
Authors: Ryan Dennis P. , Crothers Donald M.
Published: December 2004

The relaxation kinetics of binding of ethidium to calf‐thymus DNA as studied previously by the temperature‐jump method with absorption detection [Bresloff, J. & Crothers, D. M. (1975) J. Mol. Biol. 95, 103] is reanalyzed in terms of a series of models for DNA‐ligand interactions that include cases with and without internal and bimolecular direct transfer of ligands between different binding modes or different binding sites. The experimental results are shown to be consistent with two alternative binding mechanisms. Both models include bimolecular “direct transfer” steps and a site size of two base pairs per site. In the first model, there exist two distinct modes of binding to the DNA double helix at each binding site. In the second model, sites containing at least one GC base pair constitute a different and stronger class of binding sites than those containing only AT base pairs. The existence of a direct transfer pathway between two classes of bound ligands is supported by the linear increase of reciprocal relaxation times far beyond the concentration regions, where off‐rates should have become rate limiting. The second model, incorporating the notion of base selectivity, is in quantitative agreement with published work on ethidium binding to DNAs of different base compositions and with nmr measurements of bound ligand lifetimes.
Microwave dielectric absorption of DNA in aqueous solution
Authors: Foster Kenneth R. , Stuchly Maria A. , Kraszewski Andrzej , Stuchly Stanislaw S.
Published: December 2004

The dielectric properties of aqueous solutions of DNA were measured at frequencies ranging from 0.1 to 12 GHz. The results are analyzed using the Maxwell mixture theory and yield a value for the hydration of the DNA of about 0.4 g/g, which is in the range observed in other investigations. No evidence was found for an additional absorption effect at microwave frequencies, which has been predicted to occur in certain DNA analogs due to the vibrational excitation of the double helix by the applied microwave field.
1H‐ and 31P‐nuclear magnetic resonance studies on the conformation of d‐(CpGpCpG)2 and d‐(CpGpCpGpCpG)2 short helices in B‐conformation
Authors: Cheng Doris M. , Kan Lou‐Sing , Frechet Denise , Ts'O Paul O. P. , Uesugi Seiichi , Shida Toshio , Ikehara Morio
Published: December 2004

Two short DNA helices, d‐(CpGpCpG)2 and d‐(CpGpCpGpCpG)2, in dilute salt solutions have been studied thoroughly by 1H‐ and 31P‐nmr spectroscopy as model systems for the calibration of nmr theory in its application to nucleic acids research. All the nonexchangeable proton resonances of these two short helices have been assigned by the “incremental method,” “sequential homodecoupling” of the sugar protons, thermal perturbation, and computer spectral simulation, as well as the NOE technique.

The CD and uv data were also obtained at either identical or half concentrations of the oligomer used in the nmr studies in order to have comparable optical data for estimating helical content and for assigning conformation. The precise assignment of the sugar proton resonances and their corresponding coupling‐constant values provide valuable information about the backbone conformation. The sugar conformation was shown to be predominantly in the 2E‐form (>70%). The rotation of the C4′C5′ is in favor of the gg conformation (55–95%), the rotation of the C5′O5′ bond is highly in favor of g′g′ (83–91%), and the rotation of the C3′O3′ bond is restricted to the domain of ϕ′ ≃ 195°.

The CD data and the sugar conformational analyses indicate that these CG helices are in the B‐form in dilute salt solutions. The assignment of NHN hydrogen‐bonded resonances of these two helices are based on their thermal stability. The through‐space magnetic field effects on the base protons and the NHN protons in the helices were calculated and compared with the experimental values. This comparison yields two general conclusions: (1) For the base protons, application of both ring‐current effects and local anisotropic effects in the computations are preferred; but for the NHN protons, the application of the ring‐current effect alone is preferred over the application of both ring‐current effects and local anisotropic effects; and (2) while the computed values in the best theoretical treatment cited above did support the conclusion that these CG helices are in the B‐conformation, the differences among the computed values for the three conformations, A, A′, and B, are not very large, at least for the CG sequence. All the 31P resonances of these CG helices are unambiguously assigned through a specific heterodecoupling technique established previously [Cheng et al. (1982) Biopolymers 21, 697–701]. The complete assignment of all proton resonances and 31P resonance of d‐(CpGpCpG)2 and d‐(CpGpCpGpCpG)2 helices in the B‐form establishes these two deoxy CG helices as valuable model systems for the study of the nmr and polymorphism of nucleic acids.
Electrostatic interactions between α‐helix dipoles in crystals of an uncharged helical undecapeptide
Authors: Hol Wim G. J. , De Maeyer Marc C. H.
Published: December 2004

The electrostatic interactions between α‐helix dipoles in the crystals of an uncharged helical undecapeptide have been studied in detail. The electrostatic interaction energy between one helix dipole and its 26 nearest neighbors is approximately −23 kcal mol−1. A very similar result is obtained when calculating the interactions between one helix dipole and all 988 helix dipoles occurring within a distance of 75 Å. It therefore appears that in these crystals of completely uncharged molecules large, favorable electrostatic interactions occur.