bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformations of model compounds of proteins II. Infrared spectra of n‐acetyl‐amino acid methylamides
Authors: Koyama Yasushi , Shimanouchi Takehiko , Sato Motomu , Tatsuno Takashi
Published: May 2005

N‐Acetyl‐amino acid methylamides CH3CONHCHRCONHCH3 were prepared from L‐ and DL‐alanine, L and DL‐α‐amino‐n‐butyric acid, L‐ and DL‐norvaline, DL‐norleucine, L‐ and DL‐methionine, L‐ and DL‐leucine, L‐aspartic acid and DL‐phenylalanine. The deuterium homologs of the type CH3CONDCHRCONDCH3, CD3CONHCHRCONHCH3, and CH3CONHCHRCONHCD3 were also prepared. The infrared spectra of these compounds were measured down to 300 cm−1 in the crystalline state. The infrared spectra of N‐isopropylacetamide CH3CONHCH(CH3)2, N‐methylisobutyramide (CH3)2CHCONHCH3 and their deuterium homologs were also measured. The CO in‐plane and out‐of‐plane bending vibration bands of the CH3CONHCα group (amide IVa and VIa) and those of the –CαCONHCH3 group (amide IVb and VIb) were assigned from these data. Two crystalline modifications, form I and form II, were found for the compounds prepared from L‐alanine, DL‐leucine, L‐aspartic acid and DL‐phenylalanine. The two forms show quite different skeletal vibrations, which suggest, rotational isomerism. Two distinct patterns were found as to the positions of the amide IVa and VIa bands for the above compounds. The two amide bands were found near 630 and 600 cm−1 in form I, whereas they were found near 600 cm−1 in form II. The crystals of the remaining compounds were also classified into form I or form II on the basis of the arrangement of the amide bands. The X‐ray structure analyses suggest that these two forms have different hydrogen‐bond structures.
A statistical mechanical theory of unfolding of globular proteins induced by preferential binding of solvent components in water‐organic solvent systems
Authors: Shindo Yohji
Published: May 2005

A statistical mechanical model was developed for use in connection with the problem of preferential binding of solvent components to proteins and of conformational transition in water‐organic solvent systems. The model is a statistical one for the conformational transition of globular proteins induced by the adsorption of solutes in the solution, considered as a nearest‐neighbor problem in statistical mechanics. Although a few illustrative examples are given, the actual interpretations of the experimental data using this theory are reserved for a later paper.
Stereochemistry of nucleic acids and polynucleotides III. Electronic charge distribution
Authors: Renugopalakrishnan V. , Lakshminarayanan A. V. , Sasisekharan V.
Published: May 2005

Calculation of σ‐ and π‐charges were made on nucleotides and nucleic acids. The σ‐charges were calculated using LCAO MO method suggested by Del Re, making use of Berthod and Pullman parameters. The π‐charges were calculated by Hückel's method, making use of suitable parameters which gave a good qualitative correlation of calculated bond orders with experimentally determined bond lengths. General features of the charge distribution are discussed.
The reaction between neutral salts and fibrous proteins. I. The model system sodium poly‐L‐glutamate‐LiBr‐H2O
Authors: Baddiel C. B. , Chaudhuri D. , Stage B. C.
Published: May 2005

The effects of concentrated aqueous solutions of a neutral salt, lithium bromide, on randomly coiled sodium poly‐L‐glutamate have been followed using high resolution infrared and nuclear magnetic resonance spectroscopy. The results suggest that two processes are taking place. First, at low concentrations 0–4M LiBr, a simple electrolyte effect occurs in which some water is removed from the polymer by an electrostriction effect. Second, a more intense interaction (>4M LiBr), apparently cooperative, occurs in which the competition for the available water in the system forces the electrolyte to form an association with the peptide group either as a fully or partially hydrated species. It is proposed that the anion is associated with the nitrogen atom of the peptide group and the cation is situated within the vicinity of the carbonyl oxygen.
Allosteric interactions in phospkorylase B
Authors: Bresler S. , Firsov L.
Published: May 2005

An allosteric model of phosphorylase B is proposed based on the following assumptions. The enzyme consists of two sub‐units and undergoes a concerted transition from the inactive T to the active R state. The binding of substrates, phosphate, and glycogen is regarded as exclusive, but the binding of the activator AMP is nonexclusive. The enzyme model is of the K, V type, i. e., the activator AMP is important, not only for the T‐R transition and the substrates binding, but also for the formation of the active site. Therefore, it displays a big influence on the maximal reaction rate. Calculations based on this model lead to an equation containing 5 constants, which can be easily computed from kinetic data. All kinetic measurements fit the expressions derived from the model. Independent methods for the measurement of all the constants involved were developed. They are based on the study of binding of phosphorylase with the substrates and the activator. These measurements are in satisfactory agreement with the data obtained from enzyme kinetics.
Optical properties of the polyglycine II helix
Authors: Rippon W. B. , Walton A. G.
Published: May 2005

The circular dichroism spectrum obtained from a dilute aqueous solution of poly (ala‐gly‐gly) resembles that described for charged polypeptides such as the salt form of poly glutamic acid. A similar spectrum is found for films cast from aqueous solution where x‐ray studies reported elsewhere have indicated a poly‐glycinc II conformation. Evidence is presented for a heat induced poly‐glycine II to unordered state transition similar to that described for collagen. The interpretation of this, the first observation of the optical properties of a poly‐amino acid in the poly glycine II conformation, is further rationalized on the basis of spectra obtained from a number of polypeptides whose conformation approaches that of a 31 helix.
Comparaison entre oligoribonucleotides et oligodesoxyribonucleotides. I. Formation des doubles helices
Authors: Mauriuzot J. C. , Blicharski J. , Brahms J.
Published: May 2005

The ability of oligodesoxyribonucleotides of various chain lengths to form complexes has been compared with that of oligoribonucleotides. Four series of oligonucleotidcs were prepared and investigated, i.e., dCn at acid pH versus rCn, dAn and dTn versus. rAn and rUn at neutral pH. The results indicate that in dilute solution, the formation of complexes is greatly facilitated in the case of desoxyoligomers and occurs for shorter oligomere than in the corresponding ribooligomers. The spectrophotometric titration of deoxyribooligo C indicates the appearance of two pK values in the 4–5 pH region characteristic of the double‐stranded form, which occurs for much shorter dCn than rCn. The circular dichroism (CD.) spectra of deoxycytidylies in dilute solution starting from the trimer are conservative, characteristic of the double‐stranded helical form of poly C at acid pH. In contrast, the CD spectra of a series of corresponding ribo Cn, under identical conditions is of nonconservative character similar to that of the single‐stranded form of poly C at neutral pH, but differs in the band position. This spectrum is called intermediate. Only at higher concentrations of oligonucleotidcs (i.e., 10−3Minstead of 10−4M) does the circular dichroism spectrum of longer ribocytidylics assume conservative character. Thermal denaturation of deoxycytidylces at acid pH are strongly dependent on chain length and concentration, its one would expect for a cooperative helix‐coil transition. The circular dichroism spectra measured at different temperatures shows one isosbestic point. In dilute solution, the standard‐state enthalpy change found was 5–6 kcal/mole for higher oligomers (dC7). These properties are all in agreement with a structural transition from the d‐Cn double‐stranded form to a coil for n > 3. Studies of dAn and dTn in solutions of high ionic strength at low temperature indicate that complex formation occurs already at the level of trimer and for high oligomers. Under identical conditions a complex between rAn and rUn is detected only for oligomers longer than the hexamer. The nature of the “intermediate” form of oligoribo C at acid pH and low temperature was investigated by sedimentation and circular dichroism. A model of rCn is proposed of linear molecules which are partially double‐stranded and partially single‐stranded, which probably are slowly rearranged by “slippage” into a regular‐double‐stranded helical form.
Conformational energy calculations on alginic acid I. Helix parameters and flexibility of the homopolymers
Authors: Whittington S. G.
Published: May 2005

Conformational energy maps have been calculated for the 1‐4‐linked dimers of β‐D‐mannuronic acid and α‐L‐guluronic acid. Helix parameters have been calculated for poly(mannuronic acid) and for poly(guluronic acid), which are in reasonable agreement with data from x‐ray fiber diffraction studies of these polysaccharides. The flexibility of the homopolymers was investigated by calculating the characteristic ratios, i.e., the ratio of the mean‐square end‐to‐end lengths of the unperturbed chains to the product of the number of residues in the chains and the virtual bond lengths. The general conclusions are that both polymers are very stiff and extended, but that poly(mannuronic acid) is less extended than poly(guluronic acid).
Conformational Studies of β‐glucans
Authors: Sathyanarayana B. K. , Rao V. S. K.
Published: May 2005

Steric and energy contour diagrams have been plotted for disaccharide‐like and for helical structures of linear β‐D‐glucans having (1 → 2), (1 → 3) and (1 → 4) linkages. The allowed conformations constitute only about. 4% of the total conformations, indicating that the freedom of rotation of glucose residues is highly restricted in all the three polysaccharides. The additional restrictions of the monomer unit, as one passes from disaccharide to polysaccaride structures, are severe in the case of (1 → 2) and (1 → 3) linked polysaccharides but not in (1 → 4) linked polysaccharide. The difference in the nature of linkages also has shown to affect the energetically preferred conformations: (1 → 2) linkages lead only to left handed helical conformations; (1 → 3) linkages lead to both right and left handed wide and extended helical conformations, (1 → 4) linkages lead to both right and left handed extended helical conformations. The possible hydrogen bonds between adjacent residues are also dependent on the nature of linkage.
The conformation of single‐strand polynucleotides in solution: sedimentation studies of apurinic acid
Authors: Achter Eugene K. , Kelsenfeld Gary
Published: May 2005

To elucidate the role of the bases in single‐strand polynucleolide conformation, we have studied apurinic acid, a single‐strand polydeoxyribonucleotide from which almost half the bases have been removed. The conformation of apurinic acid in aqueous solution near θ condition has been investigated by sedimentation velocity and sedimentation equilibrium measurements. The unperturbed coil dimensions of apurinic acid are essentially identical to those of poly rU of the same degree of polymerization. The dimensions are also similar to those of poly rA at high temperature, where the adenine residues are not stacked upon one another. We conclude that the considerable rigidity of these polynuclotides is conferred not by residual, undetected base stacking, but by restrictions in rotation about the bonds of the backbone. Furthermore, the rigidity of the ribose‐phosphate backbone cannot be attributed to interactions involving the 2'—OH group.
Circular dichroism studies of isoleucine oligopeptides in solution
Authors: Goodman Murray , Naider Fred , Toniolo Claudio
Published: May 2005

A conformational analysis was carried out on a series of L‐isoleucine oligomers having the general formula BOC‐(Ileu)n‐OMe (n = 2–8). These oligopeptides were examined in trifluoroethanol, trifluoroethanol‐acid and mixed organic‐water media. The results indicate that these oligomers form β‐conformations beginning at the heptamer. The stability of the β‐conformations was found to be greater than those formed by oligopeptides derived from L‐alanine.
Change in conformation of various DNAs on melting as followed by circular dichroism
Authors: Sprecher Cindy A. , Johnson W. Curtis
Published: May 2005

The intensities of the CD bands at about 275 and 190 nm were monitored for DNAs with different G + C contents as a function of temperature. The 190‐nm bands showed a nearly complete and cooperative collapse on melting of the DNA, demonstrating that the CD arises from base–base interactions. The small cooperative change on melting shown by the 275‐nm bands indicates that base–base interactions do not contribute much CD intensity here. No significant difference in melting temperature was found between the two wavelengths, but the lack of premelting in the 190‐nm bands contrasted with the significant premelting in the 275 nm bands. Since the 190‐nm bands are particularly sensitive to base–base interactions, the relative positions of the bases must not change much during premelting. Still, changes in such interactions would be noticeable on top of the low intensity of the 275‐nm bands. Premelting is discussed in the light of recent studies on DNA conformation.
Theoretical π‐π* absorption and circular dichroic spectra of polypeptide β‐structures
Authors: Applequist Jon
Published: May 2005

Absorption and circular dichroic (CD) spectra of the π‐π* transition near 200 nm are calculated for poly(Gly), poly(Ala), poly(Abu), and poly(Val) in the βP (paralle) and βA (antiparallel) pleated‐sheet structures using the dipole interaction model and including interactions among all atoms; optical parameters were obtained from previous studies of related molecules. Most of the calculations are for structures with one or three chains of six residues each. The oscillator strength and splitting of the π‐π* modes are found to be affected only to a small extent by variations in side‐chain structure and conformation, whereas the CD spectrum is very sensitive to these variations. Poly(Gly) and poly(Ala) β‐structures in uniform, planar lattices do not show sufficient rotational strength to account for observed CD spectra. Poly(Abu) and poly(Val) β‐structures in uniform, planar lattices show rotational strengths comparable to experiment when χ1 is near −60° for βA‐structures or in a broad range near 140° for βP‐structures. Poly(Ala) in uniformly twisted βA‐ and βP‐structures or in irregular βA‐structures corresponding to regions of the crystal structure of concanavalin A also show enhanced rotational strengths in the principal π‐π* CD band. Absorption and CD spectra calculated for poly(Abu) in uniform βA‐ and βP‐structures are compared with experimental data on poly(Lys) in the β‐form, assuming side‐chain conformations in Abu that maximize the intensity of the principal CD band. The calculations for the βA‐form show the better agreement with experiment for both types of spectra.
Hydrodynamics, size, and shape of bacteriophage T4D tails and baseplates
Authors: Benbasat Julyet A. , Bloomfield Victor A.
Published: May 2005

We have used translational diffusion coefficient measurements and subunit hydrodynamic theory to determine the dimensions and shape of bacterioophage T4D baseplates and tails. The diffusion coefficient of the baseplate, measured by quasielastic laser light scattering (QLS), was determined previously by Wagenknecht and Bloomfield to be D = 8.56 × 10−8 cm2/s. For the tail, we found D = 5.88 × 10−8 cm2/s by QLS, and D = 6.02 × 10−8 cm2/s by combining sedimentation coefficient and molecular weight in the Svedberg equation. These values, which have an uncertainty of ±2.7%, when combined with subunit hydrodynamic theory, enabled us to refine estimates of dimensions obtained by electron microscopy. For the hexagonal baseplate, the vertex‐to‐vertex distance is about 480 Å, the thickness is 160 Å, and there are six extended short fibers 320‐Å long and 40 Å in diameter. When a baseplate of these dimensions is attached to a tail tube‐sheath‐connector complex 1050‐Å long and 240 Å in diameter, the calculated D is 5.93 × 10−8 cm2/s, within 1% of experiment. This combined use of electron microscopy and hydrodynamics, using the former to ascertain shape, and the latter to obtain solution dimensions, is a powerful approach to the structure of biomolecular complexes.
On the interpretation and prediction of X‐ray scattering profiles of biomolecules in solution
Authors: Pickover C. A. , Engelman D. M.
Published: May 2005

If solution scattering curves can be accurately predicted from structural models, measurements can provide useful tests of predictions of secondary and tertiary structure. We have developed a computational technique for the prediction and interpretation of x‐ray scattering profiles of biomolecules in solution. The method employs a Monte Carlo procedure for the generation of length distribution functions and provides predictions to moderate resolution (∼5 Å). In addition to facilitating the assignment and interpretation of features in a solution scattering profile, the method also allows the elucidation of the role of protein motion in shaping the final scattering curve. The effect of protein motion on a scattering profile is investigated by generating scattering curves from several consecutive 0.147 ps atomic coordinate frames from a molecular dynamics simulation of the motion of bovine pancreatic trypsin inhibitor (BPTI) [McCammon, J. A. & Karplus, M. (1980) Annu. Rev. Phys. Chem. 31, 29–45]. The theoretical approach is applied to chicken egg white lysozyme and BPTI, and the overall features in the resulting theoretical scattering profiles match well with the experimental solution scattering curves recorded on film. It is apparent from this study that the scattering profile prediction technique in conjunction with other experimental methods may have value in testing ideas of conformational change based on crystallographic studies; investigations of this type would include a comparison of predicted scattering curves generated from a variety of crystallographic models with an actual scattering profile of the biomolecule in solution.
Fluoroquinacrine binding to nucleic acids: Investigation of the 19F‐nmr, optical, and fluorescence properties in the presence of DNA, poly(A), and tRNA
Authors: Mirau P. A. , Shafer R. H. , James T. L. , Bolton P. H.
Published: May 2005

The interaction of fluoroquinacrine, 3‐fluoro‐7‐chloro‐9‐(diethylamino‐1‐methylbutyl‐amino)acridine, with poly(A), DNA, and tRNA has been investigated by monitoring changes in the 19F‐nmr properties, the fluorescence, and the optical absorbance of the drug. The changes in the properties of fluoroquinacrine in the presence of nucleic acids are similar to those observed for quinacrine and suggest that the drugs bind in a similar fashion. The molecular dynamics of fluoroquinacrine bound to nucleic acids were determined by interpreting the data from a number of different nmr relaxation experiments with a two‐correlation‐time model. The two motions are the long‐range bending motion of the drug‐nucleic acid complex and the sliding of the drug between the base pairs. Both dipolar and chemical shift anisotropy contributions to the nmr relaxation parameters were taken into consideration. The binding of fluoroquinacrine to tRNA appears to be different from that observed for binding to DNA. Optical absorbance and 19F‐nmr were also used to examine the helix‐to‐coil transitions of the drug–nucleic acid complexes. In the DNA complex, the 19F chemical shift changes parallel the absorption changes that occur during the transition. 19F‐nmr and absorption show that the drug–tRNA complexes undergo a cooperative helix‐to‐coil transition, with the drug binding sites melting when the tRNA is 70% denatured.
Fluctuational base‐pair opening in DNA at temperatures below the helix–coil transition region
Authors: Wartell Roger M. , Benight Albert S.
Published: May 2005

The probability of DNA base‐pair opening was calculated at temperatures below the denaturation region. The helix–coil transition theory, modified to include different nearest‐neighbor interactions, was employed. Predictions of base‐pair opening employing DNA melting‐curve parameters differed considerably from predictions based on parameters evaluated from synthetic RNA oligomer data of Gralla and Crothers (G‐C) and formaldehyde–DNA binding experiments of McGhee and von Hippel (M‐vH). Calculations based on the latter parameters indicate a base‐pair‐opening probability of 10−2–10−3 at 35°C in 0.1M NaCl. DNA melting‐curve parameters predict values about 103 smaller. At a temperature 10°C below the transition midpoint of a specific DNA sequence, DNA melting parameters predict base‐pair opening of about 10−3, whereas the G‐C and M‐vH parameters predict that ≳0.16 of the DNA is melted. Experiments and theoretical assumptions relevant to the calculations are analyzed. Evidence suggests that DNA melting parameters are valid when the average loop size exceeds some minimum value, whereas the G‐C and M‐vH parameters appear more valid for single base‐pair loops. A reconciliation of the two sets of predictions can be made if interactions extending beyond neighboring base pairs are considered. Such interactions will make the parameters of the nearest‐neighbor model appear to change with the average loop size. Experiments that may provide further measurements of base‐pair opening are discussed.
Normal modes and structure of iodine in the starch–iodine complex
Authors: Kim Hyunyong
Published: May 2005

Normal modes of a linear array of iodine atoms with various repeat units, (I), (II), (II), and (I), have been calculated. The four resonance Raman bands (158, 107, 57, and 27 cm−1) observed with the starch–iodine complex can be assigned to the symmetric modes of either the (II)n or (I)n linear chain. However, the nature of the valence force fields of these two structures is very different: the former consists of a weakly coupled linear chain of (I) structure, while the latter, (I)n, is a tightly bound chain approaching equidistant iodine spacings. The nearly equivalent I‐I stretching force constants obtained in the present normal mode analysis of the (I)n structure is supported by the results of previous x‐ray and I‐129 Mössbauer effect measurements. A numerical method of calculating the frequency dispersions of one‐ and two‐dimensional molecular arrays is given.
Calorimetric determination of base‐stacking enthalpies in double‐helical DNA molecules
Authors: Marky Luis A. , Breslauer Kenneth J.
Published: May 2005

Differential scanning calorimetry was used to directly determine the transition enthalpies accompanying the duplex‐to‐single‐strand transition of poly[d(AT)], poly(dA)·poly(dT), poly[d(AC)]·poly[d(TG)], and d(GCGCGC). The calorimetric data allow us to define the following average base‐stacking enthalpies:

Interaction
ΔH (kcal/stack)

AC/TG, TG/AC
5.6

AT/TA, TA/AT
7.1

AA/TT
8.6

GC/CG, CG/GC
11.9

Comparison with published data on the corresponding RNA interactions reveals remarkably good agreement. By assuming transition enthalpies to result from the pairwise disruption of nearest‐neighbor stacking interactions, we used the enthalpy data listed above to predict the transition enthalpies for three oligomeric DNA duplexes. Excellent agreement was found between the predicted and the calorimetrically determined values.
The C‐terminal extrahelical peptide of type I collagen and its role in fibrillogenesis in vitro
Authors: Capaldi Michael J. , Chapman John A.
Published: May 2005

The formation in vitro of fibrils from type I acid‐soluble calf skin collagen has been studied before and after removal of the extrahelical peptides with carboxypeptidase and with pepsin. Turbidimetric studies show that the mechanism of fibril growth in undigested collagen is similar to that in pepsin‐digested collagen; following carboxypeptidase digestion, however, a different growth mechanism was apparent. The two mechanisms have been further characterized by electron microscopy. In the course of formation of fibrils from undigested collagen, “early fibrils” (short D‐periodic fibrils that have both ends visible) occurred in the lag phase under the precipitating conditions employed here. After pepsin or carboxypeptidase digestion of the collagen no “early fibrils” were seen. In carboxypeptidase‐digested collagen, lateral assembly was inhibited; after pepsin digestion, linear assembly was inhibited. Complete removal of the extrahelical peptides prevented fibril formation under the conditions used here. Electron‐optical examination of segment‐long‐spacing (SLS) dimers established a more complete removal of the C‐terminal peptide after carboxypeptidase digestion than after pepsin digestion. Analyses of staining patterns of SLS dimers and fibrils from undigested and digested samples showed that the C‐terminal peptide in SLS crystallites and fibrils formed from undigested collagen is in a condensed conformation. A proposed conformation, in which condensation occurs predominantly in a hydrophobic region at the proximal end of the C‐terminal peptide, is discussed in terms of a dual role for the C‐terminal peptide in fibrillogenesis. One role, shared with the N‐terminal peptide, is to participate in interactions between the 4D‐staggered molecules leading to the formation of linear aggregates; the other is to participate in interactions between these linear aggregates giving rise to D‐periodic aggregates and lateral (as well as linear) growth.
Kinetics of transfer in aqueous solution of ferriprotoporphyrin IX from human serum albumin to sperm whale apomyoglobin
Authors: Blauer G. , Silfen J.
Published: May 2005

Kinetic aspects of the transfer reaction of ferriprotoporphyrin IX (FP) from its complex with human serum albumin (HSA) to sperm whale apomyoglobin were investigated by spectrophotometry in aqueous solution. At molar ratios of 2:1 of both HSA and apomyoglobin to FP (1 × 10−5M), the initial rate of transfer at pH 7.4 (0.025M Tris buffer) and 25°C was virtually independent of the concentration of apomyoglobin up to a sixfold excess of the latter. The rate‐limiting step in the transfer reaction is considered to be the dissociation of FP from the FP‐HSA complex with an apparent rate constant of the order of 10−3 s−1 under the above conditions. The initial rate decreased with increasing concentrations of HSA, indicating competition between HSA and apomyoglobin for free FP in the recombination reactions. A steady‐state concentration of the order of 10−9M is estimated for free FP under the conditions given. The initial rate of transfer decreased markedly with pH in the range of pH 5–9 and was also dependent on the type and concentration of the buffer used. Also, various electrolytes at different concentrations showed very different and specific effects on the initial rate of reaction. Similarly, various drugs and analogous substances such as penicillins and salicylate affected the rates of dissociation in different concentration ranges. From the temperature dependence of the initial rate at pH 7.4 in the range of 5–25°C, an overall energy of activation of about 8 kcal/mol and an entropy of activation of about −50 e.u. are evaluated, indicating a much higher order of molecular groups around FP or other steric constraints in the transition state. It appears that kinetic parameters of the biopolymer–small molecule system are more sensitive to environmental changes than corresponding equilibrium data as measured by light absorption.
Flexibility of a labeled polymer chain: Time‐resolved fluorescence depolarization measurements and their interpretation by a Hinged‐Dumbbell model
Authors: Ricka J. , Amsler K. , Binkert Th.
Published: May 2005

Time‐resolved fluorescence depolarization was applied to investigate the dynamics of low‐molecular‐weight polyethylene glycols (MW 150, 400, 1000, 4000) labeled by fluorescein‐isothiocyanate. The analysis of measurements revealed considerable flexibility of the polymer chain. To interpret the observed dependence of the relaxation time of polarization anisotropy on the molecular weight of the polymer, a simple freely‐hinged dumbbell model was developed. The properties of the model were investigated by computer experiments. The model was found to account well for the measured data.
Secondary structure of peptides. 4: 13C‐Nmr CP/MAS investigation of solid oligo‐ and poly(L‐alanines)
Authors: Kricheldorf Hans R. , Mutter Manfred , Maser Franz , Müller Detlef , Förster Hans
Published: May 2005

Primary and tertiary amine‐initiated polymerizations of L‐alanine‐N‐carboxyanhydride (L‐Ala‐NCA) were conducted at 20 or 100°C in a variety of solvents. The 75.5‐MHz 13C‐nmr CP/MAS spectra of the resulting poly(L‐alanines) revealed that all samples contain both α‐helix and pleated‐sheet structures. Depending on the reaction conditions the α‐helix content varied between ca. 1 and 99%. Reprecipitation from aprotic nonsolvents does not change the α‐helix/β‐sheet ratio, indicating that this ratio is thermodynamically controlled. Since relatively large amounts of oligopeptides of degree of polymerization (DP) 4–6 can be extracted by means of acetic acid, it is concluded that (a) most poly(L‐alanines) possess a bimodal molecular weight distribution, (b) the oligopeptide fraction with DP ⩽ 11 is responsible for the β‐sheet fraction of all samples, and (c) the two‐stage crystal growth proposed by Komoto and Kawai is not correct. Solubilizing initiators such as poly(ethylene oxide) NH2 prevent the precipitation of oligoalanine and, thus, the formation of a β‐sheet structure. 13C‐nmr CP/MAS measurements also show that tri‐ and tetra‐L‐alanines form insoluble β‐sheet structures.
Mobility of oligopeptides on normal‐phase silica: Effect of positional isomerism
Authors: Naider Fred , Huchital Michael , Becker Jeffrey M.
Published: May 2005

Isomeric oligopeptides composed of five methionyl residues and one glycyl residue or of five γ‐methyl‐L‐glutamyl residues and one glycyl residue all exhibit marked differences in retention on normal‐phase silica. When the glycyl residue is at internal positions of hexa or heptapeptides, the peptide elutes most rapidly form the μPorasil column. Comparison of the effect of positional isomerism on retention in short oligopeptides with the effect on retention of hexamers and heptamers suggests that a change in peptide conformation may be responsible for the change in oligopeptide mobility.
Influence of base‐pair changes and cooperativity parameters on the melting curves of short DNAs
Authors: Benight Albert S. , Wartell Roger M.
Published: May 2005

Theoretical melting curves were calculated for four DNA restriction fragments, 157–257 base pairs (bp), and a series of hypothetical block DNAs with sequences d(C2xAxC2x). d(C2xTxG2x), 5 ⩽ x ⩽ 40. These DNAs provided a mixture of A·T/G·C sequence distributions with which to investigate the effects of parameters and base‐pair changes on the melting of short DNAs. The sensitivity of DNA melting curves to changes in internal loop melting parameters σ and κ was examined. As Expected, theoretical melting curves of short DNAs with a quasirandom base‐pair sequence vary little with changes in internal loop parameters. End melting dominates the transition behaviour of these moleucles. This was also observed for the block DNAs up to x = 22. Beyond this length, melting curves are highly sensitive to the internal loop parameters. Sensitivity is also predicted for a 157‐bp fragment with a block distribution of A·T and G·C pairs. These results indicate that accurate evaluation of internal loop parameters is possible with short DNAs (100–200 bp) containing a G·C/A·T/G·C block distribution with at least 22 bp in each block. Duplex‐to‐single‐strands dissociation parameters were reevaluated form experimental melting curve data of eight DNA fragments using a least squares fit approach. This analysis confirmed parameter values previously found with a simplified dissociation model. A Priori predictions are made on the effects of base‐pair changes on the melting curves of three characterized DNA restriction fragments. Single base‐pair changes are predicted to induce small but measurable changes in the melting curves. The characteristics of the altered melting curves depend on the location of the base‐pair change.
Improved technique for calculating X‐ray scattering intensity of biopolymers in solution: Evaluation of the form, volume, and surface of a particle
Authors: Pavlov M. Yu. , Fedorov B. A.
Published: May 2005

An improved cube method has been developed for calculating the intensity of diffuse x‐ray scattering of macromolecules in solution using a certain set of their atomic coordinates. The technique is based on the ideas of B. Lee and F. M. Richards [(1971) J. Mol. Biol. 55, 374–400] and Richards [(1977) Annu. Rev. Biophys. Bioeng. 6, 151–176] on the possibility of estimating the molecular and accessible surface of a particle by “rolling” a sphere, simulating a water molecule, on its molecular surface. It is shown that this technique is more advantageous than earlier versions of the cube methods. The improved technique for calculating scattering curves was utilized for several globular proteins, and for the first time, reliable scattering curves were obtained for protein‐“bound” water complexes. In the case of globular proteins and tRNA, this technique has permitted a strict evaluation of their accessible surfaces, their volumes, and, apparently for the first time, their complete molecular surfaces.
Model for the irreversible dissociation kinetics of cooperatively bound protein–nucleic acid complexes
Authors: Lohman Timothy M.
Published: May 2005

We present a quantitative model for the irreversible dissociation kinetics of cooperatively bound nonspecific protein–nucleic acid complexes. The model assumes that the major pathway of dissociation is via singly contiguously bound protein that “peels” off the ends of clusters of bound protein. It should therefore be most applicable for proteins that bind nucleic acids with high cooperativity (w > 103). Furthermore, the model assumes that no redistribution of bound protein occurs during the time course of the dissociation. Solutions to the rate equations are presented for the entire time course of the dissociation. Under initial conditions such that the nucleic acid is less than fully saturated with protein, a single‐exponential decay is predicted (if w is large). However, when the nucleic acid lattice is initially fully saturated, zero‐order kinetics, corresponding to a constant rate of protein dissociation, is predicted. The experimental observation of zero‐order dissociation kinetics in a cooperative protein–nucleic acid system is a good qualitative indicator for the dissociation mechanism discussed here. A discussion of the analysis of experimental data that enables one to extract molecular rate constants is presented. Furthermore, comparisons are made between the nonredistributing model presented here and Epstein's model [Epstein, I. R. (1979) Biopolymers 18, 2037–2050] in which protein can translocate infinitely quickly while bound to the nucleic acid, and hence protein clusters redistribute during dissociation and maintain an equilibrium distribution on the nucleic acid at all times.
Linear dichroism studies of nucleic acids. III. Reduced dichoism curves of DNA in ethanol–water and in poly(vinyl alcohol) films
Authors: Matsuoka Yukio , Nordén Bengt
Published: May 2005

The uv linear dichroism of calf thylus DNA has been studied at different degrees of orientation both in flow‐oriented ethanol–water solutions and in a stretched aqueous host of poly(vinyl alcohol) (PVA). The reduced dichroism (LDR) curves in the region 250–290 nm for DNA in PVA films at 75 and 100% relative humidity (r.h.) are in fair agreement with the curves calculated for the A‐ and B‐forms of DNA, based on the fiber structures and the π‐π* transitions of the free bases. This suggests that DNA adopts its A and B conformations in PVA at 75 and 100% r.h. In ethanol, on the other hand, a deviation from the A‐form spectrum shows that the conformation of DNA in the solution can differ from the fiber structure. At shorter wavelenghts, a positive contribution to LDR is explained in terms of an out‐of‐plane polarized n‐π* transition.
Localized vibrational modes at a double‐helix‐single‐strand junction
Authors: Putnam B. F. , Prohofsky E. W.
Published: May 2005

A vibrational analysis has been performed for a double‐helix–single‐strand junction. A Green's function technique has been used in treating the junction as a defect on an otherwise perfect system of infinite chain homopolymers. We calculate that the hydrogen‐bond stretching at the junction is amplified by a factor of two relative to the interior of the double helix, B poly(dG)–poly(dC). Breathing modes localized near the junction have also been predicted at 77 and 94 wave numbers. The calculated results are shown to be consistent with predictions from recent nmr studies.
Nmr studies of a free and protected tetrapeptide glycyl‐L‐prolylglycylglycine in β‐turn‐supporting environment
Authors: Perly B. , Helbecque N. , Forchioni A. , Loucheux‐Lefebvre M. H.
Published: May 2005

Nmr studies of the protected and free tetrapeptide Gly‐Pro‐Gly‐Gly were carried out in β‐turn‐supporting solvents, that is, in CDCl3 for Z‐Gly‐Pro‐Gly‐Gly‐OMe and in Me2SO‐d6 for H‐Gly‐Pro‐Gly‐Gly‐OH. Comparisons with specifically α‐deuterated analogs gave complete assignments of the NH and methylene regions. Analysis of chemical shifts, coupling constants, and the temperature dependence of chemical shifts show that the peptide adopts a type II β‐turn conformation. This turn is stabilized for the protected tetrapeptide by two hydrogen bonds between (i) CO (Gly1) and NH(Gly4), and (ii) urethane function NH and methyl ester CO.
Fluorescence correlation spectroscopy and photobleaching recovery of multiple binding reactions. II. FPR and FCS measurements at low and high DNA concentrations
Authors: Icenogle R. D. , Elson E. L.
Published: May 2005

The preceding paper develops the theory for the interpretation of fluorescence photobleaching recovery (FPR) measurements of multiple binding of a ligand to a multivalent substrate molecule. Based on a reasonable assumption about the mechanism of the photobleaching process, this analysis shows that the observed behavior of a multivalent system should be practically identical to that of a univalent binding system. This is in contrast to the expected and observed behavior of fluorescence correlation spectroscopy (FCS) measurments. Experimental FPR measurements of multivalent binding of ethidium bromide to DNA confirm these conclusions. The FCS and FPR measurements also reveal an apparently enhanced diffusion of ethidium at high DNA concentration. This enhancement might result from direct transfer of ethidium among DNA molecules.
New plot showing the existence of cooperativity, anticooperativity, and an arbitrary value of the neighbor‐exclusion parameter in systems of ligand binding to linear biopolymers
Authors: Tsuchiya Takashi
Published: May 2005

A new way of plotting the isotherm for ligand binding to linear biopolymers is presented. In this plot the isotherm for noncooperative binding of ligands of length n (n‐mers) becomes a straight line and the existence of cooperativity and anticooperativity between bound ligands is detected by appearance of opposite convexity of the curved isotherm. It is also usable for cases of fractional n values. Usefulness of the new plot in determining precise mechanisms of binding is shown using experimental data.
Correlation of Tm and sequence of DNA duplexes with ΔH computed by an improved empirical potential method
Authors: Ornstein Rick L. , Fresco Jacques R.
Published: May 2005

Tm values for 20 DNA duplexes with different repeating base sequences provided the data base for developing a rational and relatively simple methodology for computing apparent enthalpies for the helix → coil transitions of DNA helices, ΔHcalc. The computational variables and their range of acceptable values were selected on the basis of physically plausible arguments. Over 350,000 different combinations of the variables were tested for degree of fit. It was therby possible to find a combination giving a high degree of linear fit between Tm and ΔHcalc (correlation coefficient, 0.99), with Tm values deviating (on average) from the regression line by only ±2.17°C. Most of this uncertainty is attributed to experimental limitations, although computational approximations also contribute. With ΔHcalc for the melting of each of the unique complementary dinucleotide fragments computed by the method developed, it is possible to estimate Tm and (relative) ΔHcalc reliable for the melting of any particular DNA [with base pairs G(I)·C and A·T] given only its base sequence. The ΔHcalc values for the complementary dinucleotide fragments, together with statistical considerations, make it apparent that Tm of DNAs with repeating base sequence show only an approximate linear dependence on G·C content because A·T and G·G pairs do not contribute to helix stability independently of the base‐pair sequence in which they occur. In fact, the nearestneighbor stacking interactions are so significant that certain complementary dinucleotide fragment sequences with 0,50, and 100% G·C content have the same stability.
Possible observation of a defect resonance in DNA
Authors: Lindsay S. M. , Powell J.
Published: May 2005

A sharp feature is observed at about 600 MHz in the inelastic scattered light spectrum of fibers of calf thymus DNA. It broadens so as to be no longer distinctly resolved when the ordering of a fiber is disrupted by convection caused by laser heating. To within experimental uncertainties the frequency of this feature is wavevector independent. A possible origin of the feature lies in a defect resonance such as that associated with the chain terminus.
The heminucleotide scheme: An effective probe in the analysis and description of ordered polynucleotide structures
Authors: Malathi R. , Yathindra N.
Published: May 2005

The heminucleotide scheme formulated recently permits treatments of the repeating nucleotide backbone in terms of two conformationally similar moieties of constant magnitude spanning its 5′ and 3′ halves. The scheme is utilized in describing the conformational features of the ordered poly(mononucleotide) helices of A‐, B‐, and D‐DNA, polyadenylic acid, and poly(dinucleotide) helices of ZI and ZII types through distance diagonal plots. The unique feature of these diagonal plots lies in the fact that the variations in the observed patterns can be directly correlated with pairs of backbone bond rotations ψ,ψ′ (C5′—C4′ and C4′—C3′), of the sugar residue and ω′,ω (P—O3′ and P—O5′) of the phosphodiester, which determine the relative orientations of the heminucleotides and, therefore, the variety in the secondary structures. Thus, the heminucleotide scheme through its constant P˙C4′ and C4′˙P separations provides common premises for characterization and comparison of the observed secondary structures. It is not feasible otherwise through a distance plot of nucleotide P˙P separations or between any other atoms, since they vary depending on the backbone torsions, especially (ψ,ψ′) of the sugar residue. The plots afford identification at a glance of the secondary structural features such as the differences in the widths of the major and minor grooves, regions of closer separation, the parallel and antiparallel nature of the helical strand, and even the characteristic of the repeating motif, whether mono‐ or dinucleotide. A simple description such as the above may aid in better understanding the binding of metals, salts, solvents, etc., and hence of the conformational transitions among the different secondary structures.
Comparative study of GuHCl denaturation of globular proteins. I. Spectroscopic and chromatographic analysis of the denaturation curves of ribonuclease A, cytochrome c, and pepsinogen
Authors: Saito Yoshio , Wada Akiyoshi
Published: May 2005

Novel devices for the spectroscopic and chromatographic analysis of the denaturation curves of the protein are described. A multidimensional spectroscopic measuring system makes it possible to carry out simultaneous and continuous acquisition of a set of data of different spectroscopic dimensions at several wavelengths in the course of increasing or decreasing denaturational perturbation. GuHCl‐gradient chromatography can provide information about the progressive change of the protein volume in the course of increasing GuHCl concentration. Thus, denaturation curves with a high data‐point density can be obtained. The data‐storing function by a magnetic disk memory provides enough precision for a rigorous investigation of the correlation among the curves that probe different aspects of denaturation. The GuHCl denaturation of RNase A, cytochrome c, and pepsinogen are studied to demonstrate the high performance of these devices. Three types of transitions are found in these three proteins and the multiphasic nature of the transitions is clearly detected in the last two proteins.
Comparative study of GuHCl denaturation of globular proteins. II. A phenomenological classification of denaturation profiles of 17 proteins
Authors: Saito Yoshio , Wada Akiyoshi
Published: May 2005

GuHCl denaturation profiles of 17 proteins were studied by the spectroscopic and chromatographic methods described in the preceding report. The profiles are broadly classified into three types according to their multiphasic characteristics. It seems likely that more complex processes than those previously accepted take place in the denaturational conformation change of proteins.
Slow relaxational processes in the melting of linear biopolymers: A theory and its application to nucleic acids
Authors: Anshelevich V. V. , Vologodskii A. V. , Lukashin A. V. , Frank‐Kamenetskii M. D.
Published: May 2005

We treat the problem of the mean time of complete separation of complementary chains of a duplex containing N base pairs. A combination of analytical and computer methods is used to obtain the exact solution in the form of a compact expression. This expression is used to analyze the limits of application of the equilibrium theory of helix–coil transition in oligo‐ and polynucleotides. It also allows the melting behavior of a biopolymer to be predicted when its melting is nonequilibrium. In the case of oligonucleotides for which the equilibrium melting takes place at a high value of the stability constant s, the general expression turns into the equation of Craig, Crothers, and Doty, used by them to determine the rate constant kf of the growth of a helical region from temperature‐jump experiments. For the case of fragmented DNA with N ∼ 102, the melting process is shown to be completely nonequilibrium, and as a result, the observed melting temperature should be higher than that for the equilibrium. A simple equation is obtained that makes possible calculation of the real, “kinetic” melting temperature Tk. As N increases, the observed melting temperature should approach the equilibrium value, Tm. This analysis has explained quantitatively the peculiar chain‐length dependence of the experimentally observed shift in the DNA melting temperature during fragmentation. A thorough analysis is given of the nonequilibrium effects in the melting process of long DNA molecules (N ≳ 103). The main conclusion is that even in the presence of profound hysteresis phenomena, the melting profile observed on heating may differ only slightly from the equilibrium profile.