bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthetic fragments and analogues of elastin. I. The synthesis
Authors: Guantieri V. , Grando S. , Pandolfo L. , Tamburro A. M.
Published: December 2004

The synthesis of some repetitive sequences of elastin and their simplified analogues, all comprising the structural unit Gly‐X‐Gly (X = Val, Leu, Ala), is described. In particular, the following peptides and polypeptides were synthesized and characterized: Boc‐Gly‐Val‐Gly‐Gly‐Leu‐OMe, Boc‐Gly‐Leu‐Gly‐Gly‐Val‐OMe, Boc‐(Gly‐Val‐Gly‐Gly‐Leu)2‐OMe, Boc‐(Gly‐Val‐Gly‐Gly‐Leu)3‐OMe, Boc‐Gly‐Val‐Gly‐Gly‐OEt, Boc‐Leu‐Gly‐Gly‐Leu‐OMe, Boc‐Val‐Gly‐Gly‐Val‐OMe, poly(Ala‐Gly‐Gly), poly(Val‐Gly‐Gly), and poly (Leu‐Gly‐Gly).

In every case, the synthesis was accomplished by classical procedures in solution, by using the p‐nitrophenyl ester method for the polycondensation step, and the mixed anhydride or the azide methods for the coupling steps.
Synthetic fragments and analogues of elastin. II. Conformational studies
Authors: Tamburro A. M. , Guantieri V. , Pandolfo L. , Scopa A.
Published: December 2004

Conformational studies on synthetic repetitive sequences and analogues of elastin are described.

CD and nmr measurements gave evidence of flexible β‐turns as the dominant structural feature whose stability was found to decrease by increasing the number of repetitive units. The sequences comprised the structural unit Gly‐X‐Gly (X = Val, Leu, Ala), with X‐Gly or Gly‐Gly located at the corners of the bend.

Based on that, it is proposed that these regions of elastin, unlike the proline‐containing sequences, contribute to the elasticity of the protein through a classical mechanism in terms of the rotational isomeric state theory.
The equilibrium partition function and base pair binding probabilities for RNA secondary structure
Authors: McCaskill J. S.
Published: December 2004

A novel application of dynamic programming to the folding problem for RNA enables one to calculate the full equilibrium partition function for secondary structure and the probabilities of various substructures. In particular, both the partition function and the probabilities of all base pairs are computed by a recursive scheme of polynomial order N3 in the sequence length N. The temperature dependence of the partition function gives information about melting behavior for the secondary structure. The pair binding probabilities, the computation of which depends on the partition function, are visually summarized in a “box matrix” display and this provides a useful tool for examining the full ensemble of probable alternative equilibrium structures. The calculation of this ensemble representation allows a proper application and assessment of the predictive power of the secondary structure method, and yields important information on alternatives and intermediates in addition to local information about base pair opening and slippage.

The results are illustrated for representative tRNA, 5S RNA, and self‐replicating and self‐splicing RNA molecules, and allow a direct comparison with enzymatic structure probes. The effect of changes in the thermodynamic parameters on the equilibrium ensemble provides a further sensitivity check to the predictions.
Block‐units method for conformational calculations of large nucleic acid chains. II. The two‐hierarchical approach and its application to conformational arrangement of the unusual TψC loop of rabbit tRNAval
Authors: Vorobjev YU. N.
Published: December 2004

The two‐level hierarchical methodology is suggested for conformational calculations of large fragments of nucleic acids. The method of the first level is intended for performing a fast screening of the conformational phase space. The high‐level method may be used to refine structurally important conformations. The method of the first level is the block‐units method, which has been developed specially for these purposes (see part I). It has been shown that the block‐units method allows the satisfactory calculation of the structure parameters of the optimal conformations of polynucleotides. The results of the conformational rerrangement calculations of the TψC loop of the tRNAPhe after modification of its sequence are represented.
Viscoelastic and rheological properties of concentrated solutions of proteoglycan subunit and proteoglycan aggregate
Authors: Soby L. , Jamieson A. M. , Blackwell J. , Choi H. U. , Rosenberg L. C.
Published: December 2004

The oscillatory and steady shear rheological properties of concentrated solutions of proteoglycan subunit (PGS) and aggregate (PGA) from bovine articular cartilage have been studied using a Rheometrics fluids spectrometer. At comparable concentrations in the physiological range tan δ increases from 0.5 to 1.0 for PGA as the oscillation frequency (ω) increases from 10−1 to 102 rads / s, compared to a decrease from 40 to 5 for PGS. Thus PGA solutions exhibit predominantly elastic response whereas those of PGS exhibit primarily viscous behavior. PGA solutions show pronounced shear‐thinning behavior at all shear rates (γ) in the range 10−2 < γ (s−1) < 10 2, whereas PGS solutions exhibit predominantly Newtonian flow. For PGA, the small‐strain complex viscosity η* (ω) is substantially smaller than the steady‐flow viscosity η (γ) at comparable values of ω and γ. These observations indicate that the presence of proteoglycan aggregates leads to formation of a transient or weak‐gel network. Since aggregation leads to a large increase in molecular hydrodynamic volume and hence in the relaxation times for macromolecular rotation, it appears that role of aggregate formation is to shift the linear viscoelastic response from the terminal viscous flow into the plateau elastomeric regime of relaxational behavior. Normal or pathological changes that produce a decrease in aggregation will result in a loss of elastomeric behavior of the proteoglycan matrix.
Distinct gelation mechanism between linear and branched (1 → 3)‐β‐D‐glucans as revealed by high‐resolution solid‐state 13C NMR
Authors: Saitô Hazime , Yoshioka Yûko , Yokoi Motoko , Yamada Junko
Published: December 2004

We have recorded high‐resolution 13C‐NMR spectra of linear (curdlan) and branched (lentinan, HA‐β‐glucan and its polyol and aldehyde derivatives) (1 → 3)‐β‐D‐glucans in hydrate and gel states, in order to gain insight into their gelation mechanism. Network structure of curdlan turned out to be highly heterogeneous from its motional state, from liquid‐like, through intermediate, to solid‐like domains. They are studied by a variety of experiments, conventional high‐resolution NMR by broad‐band decoupling, high‐power decoupling with magic angle spinning (MAS), and cross‐polarization‐magic‐angle‐spinning (CP‐MAS). Nevertheless, we found that conformations of these distinct liquid‐like and solid‐like do‐ mains exhibit an identical single helix conformation with a small proportion of a triple helix form, supporting our previous view as to the gelation mechanism. In contrast, the network structure of branched (1 → 3)‐β‐D‐glucans in the gel state arises mainly from the triple helix conformation. This means that gelation of branched (1 → 3)‐β‐D‐glucan proceeds from partial association of the triple helical chains, previously proposed for gelation of a linear glucan. Furthermore, we found that conversion from the single chain to the single helix was not achieved readily by hydration of over 8h at 96% R. H. for branched glucan but the triple helix form is obtained when these samples are hydrated fully as in gel state.
A ligand binding model of counterion condensation to finite length polyelectrolytes
Authors: Dewey T. G.
Published: December 2004

A ligand binding model of counterion association in finite length polyelectrolytes is presented. This model introduces counterion condensation features into a binding formalism. It agrees well with the predictions of other finite length models and is consistent with experimental data on helix–coil melting transitions for short nucleic acid oligomers. This model uses a discrete charge distribution for the polyelectrolyte. An expression for the electrostatic self‐energy of finite length polyelectrolytes is derived using the Euler–Maclaurin sum formula. This sum is shown to be accurate over a wide range of salt concentrations. This electrostatic term is used in an energy minimization analysis. The energy minimization is solved analytically using a Lagrange inversion formula. This general procedure gives a rapidly convergent series and requires no assumptions with regard to “limiting law” behavior. However, when used in the Manning minimization formalism [(1977) Biophysical Chemistry, 24, 2086], the volume of the condensed phase becomes unrealistically large at low ionic strength. The ligand binding model does not have a condensed phase volume as a parameter. It provides a single expression that agrees both with Manning's theory and with the theory of Ramanathan and Woodbury [(1982) Journal of Chemical Physics 77, 4133] under the respective conditions of these theories.
Solvent effects on the cooperative order–disorder transition of aqueous solutions of schizophyllan, a triple‐helical polysaccharide
Authors: Hirao Takayuki , Sato Takahiro , Teramoto Akio , Matsuo Takasuke , Suga Hiroshi
Published: December 2004

A triple‐helical polysaccharide schizophyllan in aqueous solution exhibited a highly cooperative transition between ordered and disordered states associated with the conformation of its side chains and nearby water molecules. The transition was followed by optical rotation and containing additives such as NaOH and DMSO as solvents. The ordered state was stabilized or destabilized or depending on the kind and amount of the additive employed; in particular, the addition of DMSO had a remarkable stabilizing effect. This effect was analyzed by means of a statistical mechanical theory of linear cooperative transitions, where DMSO was assumed to interact favorably with the ordered side chains. A small amount of NaOH in a solvent mixture stabilized the ordered state and made the transition curve very gradual. No molecular mechanism was elucidated to account for the role of NaOH.
Helix‐coil stability constants for the naturally occurring amino acids in water. XXIV. Half‐cystine parameters from random poly(hydroxybutylglutamine‐CO‐S‐methylthio‐L‐cysteine)
Authors: Wójcik J. , Altmann K.‐H. , Scheraga H. A.
Published: December 2004

Water‐soluble, random copolymers containing N5‐(4‐hydroxybutyl)‐L‐glutamine (host) and S‐methylthio‐L‐cysteine (guest) have been prepared, fractionated, and characterized, with S‐methylthio‐L‐cysteine serving as a model for cystine residues in proteins. From the thermally induced helix‐coil transition curves of these copolymers in water at neutral pH, the Zimm‐Bragg parameters σ and s for the helix‐coil transition of “poly(L‐cystine)” were deduced. The results show that the cystine model acts as a weak helix‐breaker over the entire temperature range from 0 to 60°C. The implications of this finding are evaluated in the context of a general discussion of the Zimm‐Bragg parameters for all the 20 naturally occurring amino acids.
Monte carlo method applied in the search for low‐energy conformations of βαβαβ structures
Authors: Carlacci Louis , Chou Kuo‐Chen
Published: December 2004

A Monte Carlo approach was used to find low‐energy conformations of sequentially linked βαβαβ structures to be used as initial conformations in energy minimizations. Only L‐type amino acids were used in the study. The composition of the linked polypeptide chain was H(Val)6(R)4(Ala)14(R)4(Val)6(R)4(Ala)14(R)4(Val)6OH. A loop region was represented by (R)4, where R was either Gly or Ala. Two types of connections were considered: connections between nearest neighbor strands in the β‐sheet, and connections between β‐strands separated by one intervening β‐strand. The loop energy and the total energy of the α‐helical and β‐strand segments in the energy‐minimized structures were analyzed. The orientations of the secondary structural elements were characterized. In agreement with the handedness observed by experiment, all right‐handed crossover conformations were computed to have lower conformational energies than the corresponding left‐handed crossover conformations. The energy gaps between the corresponding loop energies also favored right‐handed conformations. Furthermore, the packing angles between the α‐helix axis and the β‐sheet axis are also in good agreement with experimental observations. Therefore the right‐handedness of the observed βαβαβ structure can be understood from the viewpoint of energetics.
Polarized electronic spectra of Z‐DNA single crystals
Authors: Ho Pui S. , Zhou Guangwen , Clark Leigh B.
Published: December 2004

Polarized electronic absorption spectra of the (100) face of single crystals of the Z‐form double helical duplex of d(m5CGUAm5CG) have been obtained from Kramers‐Kronig analysis of reflection data. The c crystallographic axis is parallel to the helix axis and shows but weak absorption. The b axis is perpendicular to the helix axis and shows a structureless absorption band centered at 270 nm with an oscillator strength of 0.26. Calculations of the crystal spectra utilizing available transition moment data for the individual chromophores are carried through using the oriented gas model (no interbase interactions) and, again, employing all base‐base interactions (point dipole) in the duplex. The calculated hypochromism of the 270 nm band is much less than the experimental value obtained from the crystal data. The crystal spectra appear to be representative of Z‐form double helices of essentially infinite length and not of a collection of twelve base duplexes. No evidence for nπ* transitions polarized parallel to the helix axis is found.
Studies on the conformation of and metal ion binding by teichoic acid of Staphylococcus aureus
Authors: Pal Medini Kanta , Ghosh Tapash Chandra , Ghosh Jimut Kanti
Published: December 2004

Teichoic acid (TA) isolated from the gram‐positive bacteria S. aureus binds cationic dyes like pinacyanol (PCYN), 1,9‐dimethyl methylene blue, acridine orange, etc., depicting blue‐shifted metachromasia, and they bind the cationic dye carbocyanine depicting the red‐shifted J band. TAs do not show any uv absorption band, and exhibition of tailing CD in the short uv region hints at its chiral conformation. Chiral conformation of TA has been confirmed from the induction of strong biphasic CD in the TA–carbocyanine system.

Relative affinities for Ca2+, Mg2+, and Na+ have been probed from the disruption of metachromasia of the TA–dye system by these ions. Results show Ca2+ and Mg2+ to be almost equally effective in destroying the metachromasia of the TA–PCYN system, thus not supporting the hypothesis of special affinity for Mg2+ ion.
Theoretical analysis of deoxycytidine‐5′‐phosphate protonation
Authors: Starikov E. B. , Pedash Yu. F.
Published: December 2004

The electron density distribution in deoxycytidine‐5′‐monophosphate (5′‐dCMP) molecule and dianion has been studied by the method of CNDO/2. The comparison between the results of calculation for the neutral molecule and the data obtained by Pearlman and Kim13 shows that there is a linear correlation between the atomic charges calculated using quantum chemistry and those derived from X‐ray results. However, partial charges for the deoxyribose fragment are correlated in a nonlinear manner. The influence of the protons added to the cytosine and phosphate residues on the atomic charges and bond orders of deoxy‐cytidine‐5′‐monophosphate has been analyzed here. The conclusion has been drawn that the semiempirical quantum‐chemical CNDO/2 technique is applicable to the mono‐nucleotide studies.
Temporary network formation of hyaluronate under a physiological condition. 1. Molecular‐weight dependence
Authors: Yanaki Toshio , Yamaguchi Toshijiro
Published: December 2004

The dynamic shear moduli at various frequencies and stress growth after the sudden start of steady shear were measured for 1% HA (hyaluronic acid) solutions with different molecular weights. From the results of the zero shear viscosity, η0, the steady shear compliance, J and Δη defined as Δη = η0 − ηa (∞), where ηa(∞) is the apparent viscosity at the steady state, it was shown that the molecular mechanism of flow of 1% HA solutions was classified into four regions with respect to molecular weight: (I) the viscosity‐average molecular weight Mv < 35 × 104 HA chains are dispersed molecularly in solution; (II) 35 × 104 < Mv < 100 × 104, the polymer chains form a weak entanglement network observed only through η0 (HI) 100 × 104 < Mv < 160 × 104, the network is strengthened with increasing molecular weight and becomes detectable through both η0 and J and also through the overshoot phenomenon; and (IV) 160 × 104 < Mv, the network is “saturated” or “completed” dynamically. This is the conjecture presented for the first time by the present work.
Nmr conformational analysis of cyclopeptidic substrates of serine proteases, containing an ortho or meta aminobenzoic acid residue
Authors: Convert Odile , Mazaleyrat Jean‐Paul , Wakselman Michel , Morize Isabelle , Reboud‐Ravaux Michèle
Published: December 2004

Cyclopeptides I and II containing an ortho‐ or meta‐aminobenzoic acid residue are comparatively analysed by 1H‐ and 13C‐nmr. The 1H‐nmr results, i.e., the temperature coefficients ΔδNH/ΔT, the exchange rates of the amide protons, and nuclear Overhauser effects, suggest a predominant conformation for cyclopeptides I. The meta analogues II present a greater conformational mobility. This observation is related to the greater reactivity of peptides II toward enzymatic hydrolysis, compared to their ortho analogues I.
Condensation of DNA by trivalent cations. 2. Effects of cation structure
Authors: Plum G. Eric , Arscott Patricia G. , Bloomfield Victor A.
Published: December 2004

Electron microscopy is employed to examine DNA aggregates produced by three tripositively charged condensing agents. Spermidine, hexammine cobalt (III), and me8spermidine (in which the amine groups of spermidine are exhaustively methylated) all produce condensates. The predominant form of condensate observed is toroidal; however, me8spermidine produces a large fraction of rodlike condensates. Distributions of toroidal radii and estimated volumes suggest that the size of condensates depends on the condensing agent employed, its concentration, and the time elapsed after addition of condensing agent. While ligand charge seems to be the major factor in predicting condensing power, ligand structure influences the morphology and dimensions of the particles produced. The ability to form hydrogen bonds is not required to promote condensation, since me8spermidine has no NHs. There may be a kinetic barrier to condensation at low me8spermidine concentrations. The relative proportions of toroids and rods may depend on the energetic compensation between bending and binding in cyclic structures, or on rate‐limiting formation of sharply bent or kinked regions in rods.
Dynamics of F‐actin and F‐actin/filamin networks as studied by photon correlation spectroscopy
Authors: Seils J. , Jockusch B. M. , Dorfmuller Th.
Published: December 2004

Photon correlation spectroscopy was used to study both F‐actin and F‐actin/filamin networks in solution. The measured autocorrelation functions were analyzed with the inverse Laplace transform CONTIN. The resulting frequency distributions consist of maximal five relatively narrow peaks. This rather unexpected finding disagrees with the frequency spectra calculated for an entangled rigid rod model. For this model, we expect spectra consisting of a single broad peak. Factors like flexibility, deviation from an experimental length distribution, interference with chemical reactions, and translation rotation coupling that would influence the profile of the frequency distribution could be excluded by comparison of the data with model calculations or qualitative estimates. We conclude that our data for F‐actin are consistent with the dynamics of an infinite network stable on the time scale of the observed modes. Further support for this interpretation is provided by a comparison with frequency spectra of actin/filamin networks. These appear to be very similar in shape. The main peak of these spectra that corresponds to the slow motions shifts to lower frequencies with increasing cross‐link density. It appears that higher frequency modes of the gel are more efficiently damped with progressive cross‐link density, resulting in a predominance of the slow motions in the spectra. This behavior has been already found in other systems and seems to be a general feature of cross‐linked systems.
Hydration effects on dynamics of polyglycine and sodium poly(L‐glutamate)
Authors: Kennedy Scott D. , Bryant Robert G.
Published: December 2004

Solid state nmr methods were applied to the study of the motions and structural heterogeneity in polyglycine, sodium poly (L‐glutamate), and poly(L‐alanine). The response of both the main‐chain and side‐chain resonances to the addition of water was studied using static and magic‐angle sample‐spinning line shapes as well as the carbon spin‐lattice relaxation times, the proton spin‐lattice relaxation time in the rotating frame, and the proton‐carbon cross‐polarization time. The polyglycine motions are not drastically affected by the addition of water when the polymer is in the 31‐helix or the β‐sheet structure. The sodium poly(L‐glutamate), however, responds to increased hydration with little motion in the main‐chain carbon atoms, but considerable flexibility of the side‐chain atoms. The greatest motions are reported for the C5 carbon with rotational amplitudes about the C47‐C5 bond of about of 50°. In addition, motions somewhat less than half this size are required closer to the main chain.
Dynamic properties of the first enzymatic reaction steps of porcine pancreatic elastase. How rigid is the active site of the native enzyme? Molecular dynamics simulation
Authors: Geller Maciej , Carlson‐Golab Gail , Lesyng Bogdan , Swanson Stanley M. , Meyer Edgar F.
Published: December 2004

Two molecular dynamics simulations (100 and 50 ps) of native porcine pancreatic elastase i.e., without bound substrate and with the active site hydrated by a dome of water (630 molecules) have been performed. Dynamical properties of the catalytic tetrad have been examined. While relative conformations of the Asp 102, His 57, and Ser 214 are rather stable in time, the side chain of Ser 195 undergoes several conformational changes. No preferences are observed for the formation of a hydrogen bond between the OγH group (Ser 195) and nitrogen Nϵ (His 57). A cluster of ordered water molecules effectively competes with the HOγ group (Ser 195) and thereby prevents the formation of this H bond, which is generally agreed to be crucial for catalysis.
Saturation photodimerization of thymines in DNA
Authors: Texter John
Published: December 2004

Acetophenone sensitizes the uv photodimerization of adjacent thymines in nucleic acids and under steady state irradiation induces irreversible saturation dimerization. Monte Carlo and analytical techniques are used to calculate the saturation dimerization limits for various nucleic acids, under the assumption that acetophenone‐sensitized dimerization occurs by a random irreversible process. A comparison of these calculated results with experimental values indicates that sensitized dimerization occurs by an effectively random process only in single‐stranded DNA or in native DNA of very high A·T content. In general, nucleation phenomena operate in native DNA that serve to stereochemically restrict saturation dimerization limits below those expected for random dimerization.
Experimental evidence for predicted transmembrane peptide topography: Incorporation of hydrophobic peptide α‐helical rods with an N‐terminal positive charge having a length comparable to the thickness of lipid bilayers into the membranes
Authors: Katakai Ryoichi , Wanikawa Kunihiko , Saga Katsuyuki
Published: December 2004

Liposomes consisting of egg yolk phosphatidylcholine and hydrophobic peptides Nps‐ and Cl−·+H2−(Met‐Met‐Leu)n‐OEt (n = 6–10) with various polypeptide chain lengths were prepared by the sonication method. The conformation of the peptides incorporated into the liposomes was examined by CD spectroscopy. All the peptides incorporated assumed α‐helical conformation. Quantitative analyses of the peptides and lipids in the membranes showed that the concentration of the peptides with a positive charge at the N‐terminus in the liposomes decreased markedly as the peptide chain length increased, reaching zero for the peptides over n = 8. The peptides without a positive charge were hardly incorporated into the liposomes. Infrared attenuated reflection spectroscopy of multilayered membranes containing the peptides suggests that the axis of the α‐helical peptide rods is oriented in parallel with the molecular axis of lipids in the membranes. These results suggest that the hydrophobic peptides can be incorporated into the lipid bilayers of the liposomes in the α‐helical conformation, the rods of which have a length comparable to the thickness of the lipid bilayers, and the N‐terminal positive charge of the peptides is essential for the stable peptide incorporated into the membranes.
Ab initio self‐consistent field and potential‐dependent partial equalization of orbital electronegativity calculations of hydration properties of N‐acetyl‐N′‐methyl‐alanineamide
Authors: Grant J. A. , Williams R. L. , Scheraga H. A.
Published: December 2004

Using a recently developed parallel computation algorithm, ab initio self‐consistent field (SCF) calculations were carried out to estimate the relative hydration energies for 12 low‐energy conformations of N‐acetyl‐N′‐methyl‐alanineamide. The requisite SCF calculations were carried out using 6‐31G and 6‐31G* basis sets, both in the absence and presence of a perturbing potential arising from a model solvent. The αR, αL, polyproline II (PII), and π helical conformations were preferentially stabilized by the solvent potential, whereas conformations with intramolecular hydrogen‐bonding C5 and C7 were preferred in the gas phase. Average vicinal nmr coupling constants (J), calculated using the total energies of the various solvated conformations, were consistent with observed coupling constants for this peptide in aqueous solution. Substantial alteration of the solute charge density occurred upon equilibration with the reaction field, as was exemplified in changes both in the molecular dipole moments and in atom‐centered multipoles, when the molecule was transferred from a medium of low dielectric constant to one of high dielectric constant. In order to model these changes in charge density with an empirical scheme, we have implemented a novel monopolar representation of the solute charge density based on a potential‐dependent form of partial equalization of orbital electronegativities (PDPEOE). In the atom‐centered point charge PDPEOE representation, charge Hows from one region of the solute to another in response to external fields. Hydration energies calculated using the PDPEOE representation are similar to those calculated by the SCF procedure. Also, the PDPEOE calculations yielded changes in molecular dipole moments upon solvation that agreed closely with the changes in the calculated ab initio SCF dipole moments.
The effects of ligands on the conformation of phosphoglycerate kinase: Fluorescence anisotropy decay and theoretical interpretation
Authors: Mouawad Liliane , Desmadril Michel , Perahia David , Yon Jeannine M. , Brochon Jean‐Claude
Published: December 2004

Horse muscle phosphoglycerate kinase (PGK) is a monomer folded into two widely distant domains. In the glycolytic pathway, this enzyme catalyzes the first reaction that produces ATP. It was suggested, by analogy with yeast hexokinase, that a hinge‐bending motion may be induced by the binding of specific substrates to the protein. To analyze such a motion, or any structural changes induced by ligand binding, fluorescence anisotropy decay of tryptophan residues in free and liganded PGK was studied. At 293 K, for the free protein and the binary complex with 3‐phosphoglycerate, a single correlation time of 26 ns was observed, corresponding to the rotation of the overall protein, whereas upon addition of MgADP, this correlation time decreased to 10 ns. Such a decrease cannot be merely due to a change of the protein's shape and volume. To explain this, it was suggested that the fluorescence anisotropy decay of the PGK–MgADP complex corresponded to the rotation of the only buried tryptophan (Trp 335). The rotational paths of this tryptophan, in the presence and absence of the nucleotide, were established by potential energy minimization calculations. The results indicated that MgADP induces a displacement of helix α‐13 that decreases the rotational energy barrier of Trp 335 from 16 kcal/mol in the free protein to 8 kcal/mol in the complex.
A fourier transform IR study of the gelation of amylose and amylopectin
Authors: Goodfellow B. J. , Wilson R. H.
Published: December 2004

Fourier transform ir spectroscopy has been used to study the gelation and retrogradation of amylose and amylopectin. Results indicate that two processes occur: a fast change complete within 0.5 h shown by both samples and a much slower change that continues up to 400 h seen only for amylopectin. These processes are related to changes in molecular conformation, and are explained in terms of existing models for gelation and retrogradation in amylose and amylopectin.
Approach to the limit of counterion condensation
Authors: Fenley Marcia O. , Manning Gerald S. , Olson Wilma K.
Published: December 2004

According to counterion condensation theory, one of the contributions to the polyelectrolyte free energy is a pairwise sum of Debye–Hückel potentials between polymer charges that are reduced by condensed counterions. When the polyion model is taken as an infinitely long and uniformly spaced line of charges, a simple closed expression for the summation, combined with entropy‐derived mixing contributions, leads to the central result of the theory, a condensed fraction of counterions dependent only on the linear charge density of the polyion and the valence of the counterion, stable against increases of salt up to concentrations in excess of 0.1M. Here we evaluate the sum numerically for B‐DNA models other than the infinite line of B‐DNA charges. For a finite‐length line there are end effects at low salt. The condensation limit is reached as a flat plateau by increasing the salt concentration. At a fixed salt concentration the condensation limit is reached by increasing the length of the line. At moderate salt even very short B‐DNA line‐model oligomers have condensed fractions not far from the infinite polymer limit. For a long double‐helical array with charge coordinates at the phosphates of B‐DNA, the limiting condensed fraction appears to be approached at low salt. In contrast to the results for the line of charges, however, the computed condensed fraction varies strongly with salt in the range of experimentally typical concentrations. Salt invariance is restored, in agreement with both the line model and experimental data, when dielectric saturation is considered by means of a distance‐dependent dielectric function. For sufficiently long B‐DNA line and helical models, at typical salt concentrations, the counterion binding fraction approaches the polymer limit as a linear function of 1/P, where P is the number of phosphate groups of B‐DNA.
Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. III. Estimation of the protein secondary structure
Authors: Kalnin N. N. , Baikalov I. A. , Venyaminov S. Yu.
Published: December 2004

Infrared spectra of 13 globular proteins have been obtained in the 1800–1480‐cm−1 region for H2O solutions. A method for estimating protein secondary structure from the ir spectrum has been developed. The method can also be used for estimating polypeptide and fibrous protein conformation. For the globular and fibrous proteins and polypeptides analyzed, the correlation coefficients between the ir and x‐ray estimates of ordered helix, disordered helix, ordered β‐structure, disordered β‐structure, turns, and remainder were 0.98, 0.80, 0.99, 0.87, 0.90, and 0.92 respectively.
Polyiodine units in starch–iodine complex: INDO CI study of spectra and comparison with experiments
Authors: Minick Mark , Fotta Kristen , Khan Arshad
Published: December 2004

The starch–iodine blue complex formation does not involve negatively charged iodine species like I, I, or I; rather, neutral iodine units are involved. The heat of reaction is determined to be about −110 kJ for every mole of I‐I unit in the amylose helix, which suggests that the dissociation of I2 (binding energy 149 kJ/mol) does not take place during the complex formation. Quantum mechanical (INDO CI) calculations indicate that the linear as well as nonlinear polyiodine units, I6, with interiodine distance of 3.0 Å are responsible for characteristic absorbance bands of the starch–iodine complex. Based on our previous article [(1989) J. Polym. Sci. A 27, 4161] and the present studies we identify (C6H10O5)16.5I6 to be the polymeric unit responsible for the characteristic blue color of the complex.
Anomalous temperature dependence of the thermal expansion of proteins
Authors: Hiebl Manfred , Maksymiw Roman
Published: December 2004

The temperature dependence of the apparent expansibility of lysozyme and ovalbumin in Solution has been measured as a function of pH. This temperature dependence is explained in terms of suppressed fluctuations in bound water due to the protein. It is shown that the thermal expansion coefficient of bound water is different from bulk water. The pH dependence can be explained by increased hydration of side chains at lower pH. The amount in volume of hydration water in a typical protein–water system varies from 0.16 to 0.7. How the intrinsic thermal expansion coefficient of proteins can be derived from the apparent quantity is discussed. Intrinsic values of the thermal expansion coefficient for lysozyme at room temperature are between 1.7 and 4.4 × 10−4 K−1 for a 10% solution.
Vibrational analysis of crystalline tri‐L‐alanine
Authors: Qian Weili , Bandekar Jagdeesh , Krimm Samuel
Published: December 2004

We have found that tri‐L‐alanine (Ala3) can crystallize in a parallel‐chain β structure in addition to the previously known antiparallel‐chain β structure. Although the chain conformations in each structure are essentially similar, their and Raman spectra are distinctively different. We have calculated the normal modes of each structure, and can account in significant detail for these differences. This demonstrates the essential validity of our empirically refined force fields, as well as showing that deeper insights into polypeptide and protein structure can be achieved through the rigorous analyses of normal mode calculations.
Molecular conformation of a D,L stereoisomeric analogue of valinomycin, cyclo[‐(L‐Val‐L‐Hyi‐L‐Val‐D‐Hyi)2‐(D‐Val‐L‐Hyi‐L‐Val‐D‐Hyi)‐]
Authors: Langs D. A. , Grochulski P. , Duax W. L. , Pletnev V. Z. , Ivanov V. T.
Published: December 2004

The crystal structure of a synthetic analogue of valinomycin, cyclo[‐(L‐Val‐L‐Hyi‐L‐Val‐D‐Hyi)2‐(D‐Val‐L‐Hyi‐L‐Val‐D‐Hyi)‐] ([L‐Val1, L‐Val5]meso‐valinomycin), C60H102N6O18, has been determined. Crystals grown from petroleum ether are orthorhombic, space group P212121, with cell parameters a = 16.41(1), b = 18.76(1), c = 25.86(1) Å, and Z = 4. The atomic coordinates for nonhydrogen atoms, except those of terminal carbons on one side chain, were refined in the anisotropic thermal motion approximation. The coordinate parameters of the H atoms were incorporated into the structure factor calculations at geometrically expected positions. Values of the standard and weighted R factors after refinement are 0.074 and 0.083, respectively. The crystal structure of the molecule is asymmetric and adopts a conformation with four 4 → 1 type and one 6 → 1 type intramolecular hydrogen bonds between amide nitrogens and carbonyl oxygens. Valinomycin binds potassium more than 100 times strongly than the D,L Stereoisomeric analogue, as a result of a different spatial orientation of potentially interacting carbonyl groups.
Mobility models for stiff and flexible macromolecules in dilute gels
Authors: Arvanitidou Evangelia , Hoagland David , Smisek David
Published: December 2004

The effective sphere approximation for modeling electrophoretic transport of macromolecules in highly porous gels (the “Ogston model”) is examined, and contrasted with similar mobility models for stiff and flexible solutes. Calculation of segmental depletion near gel obstacles of various shapes demonstrates the limited applicability of the effective sphere approach. For highly flexible chains, both theory and experiment reveal a nonunique mapping between mobility and molecular size when the molecular radius is comparable to that of gel fibers. Turning to mobility behavior in more concentrated gels, neither flexible or stiff macromolecules behave as spheres; for the particular case of flexible chains, the presence of entropic barriers in concentrated gels can be understood in terms of a simple random planes model for the gel structure.
The solution conformation of tubulin‐β(422–434)‐NH2 and its Nac‐DATADEQG‐NH2 fragment based on nmr
Authors: Otter Albin , Scott Paul G. , Maccioni Ricardo B. , Kotovych George
Published: December 2004

The solution conformation of tubulin‐β(422–434)‐NH2 (YQQYQDATADEQG‐NH2) and its Nac‐DATADEQG‐NH2 fragment has been studied by two‐dimensional 1H‐nmr spectroscopy in CD3OH/H2O (90/10 v/v) at neutral and low pH. The 13 amino acid peptide is a segment of the C‐terminal region of tubulin, and is directly involved in the selective binding site with microtubule‐associated proteins MAP‐2 and the τ protein. Based on correlated spectroscopy, total correlation spectroscopy, and rotating frame nuclear Over‐hauser effect spectroscopy experiments, a complete assignment of all proton resonances was achieved, and the conformation of the backbone could be deduced from coupling constants, NH temperature coefficients, and nuclear Overhauser effects. The spectroscopic evidence indicates that the T8‐Q12 section of both molecules forms one complete α‐helical turn, stabilized by a NH(Q12)‐CO(T8) hydrogen bond. Furthermore, strong pH‐dependent backfolding of the E11 side chain to its own NH proton was found. In addition, close proximity between the aromatic side chains of Y1, Y4, and the α‐helical part, resulting in some substantial chemical shift changes when comparing the entire 13‐mer with the octamer, could be explained in terms of a nonclassical kink in the DATA section. The conformational space is dominated by extended structures and the nonextended conformers are only a minor, yet spectroscopically clearly discernible entity. The presence of the α‐helical region at the C‐terminus of the 13‐mer is important because binding studies of this peptide with MAP‐2 indicate that the D10‐E11‐Q12‐G13 fragment is critical for the binding interaction.
Structural determination of the vasoactive intestinal peptide by two‐dimensional 1H‐nmr spectroscopy
Authors: Theriault Y. , Boulancer Y. , St‐Pierre S.
Published: December 2004

The structure of the vasoactive intestinal peptide 1–28 in 40% 2,2,2‐trifluoroethanol was investigated by two‐dimensional 1H‐nmr spectroscopy. All 1H resonances, except the γ, δ, and ε protons of the lysine residues, could be sequentially assigned. Numerous intraresidual as well as short‐range interresidual nuclear Overhauser effect spectroscopy connectivities were observed. Using a variable‐target function minimization, a molecular model consisting of two helical stretches involving residues 7–15 and 19–27 connected by a region of undefined structure was calculated. The existence of an undefined structure between residues 16 and 18 confers mobility to the peptide molecule.
A scanning calorimetric study of the thermally induced unfolding of various forms of tropomyosin
Authors: Sturtevant Julian M. , Holtzer Marilyn Emerson , Holtzer Alfred
Published: December 2004

The reversible thermally induced unfolding of various forms of tropomyosin, a two‐chain α‐helical coiled coil, has been studied by high‐sensitivity differential scanning calorimetry (DSC). Included in the study are the reduced and oxidized (disulfide cross‐linked) forms of αα‐ and ββ tropomyosin, and the forms of αα‐tropomyosin in which all sulfhydryl groups have been blocked by carboxymethylation or carboxyamidomethylation. Oxidation or blocking of the sulfhydryl groups of tropomyosin strongly affect the thermotropic behavior of the protein in unpredictable ways. The empirical results presented here are in qualitative agreement with those from an earlier DSC study of the oxidized and carboxymethylated forms of αα‐tropomyosin [ S. A. Potekhin and P. L. Privalov (1982) Journal of Molecular Biology, Vol. 159, pp. 519‐535], but we find that a different decomposition into subtransitions is possible. Comparison of the αα and ββ species indicates, in agreement with extant CD studies, that the noncross‐linked ββ species is somewhat less stable than its αα counterpart, but that cross‐linking enhances the stability of the ββdoubly cross‐linked species by a greater amount and does not lead to the small low‐temperature transition (“pretransition”) seen in the singly cross‐linked αα species.
Local structures in unfolded lysozyme and correlation with secondary structures in the native conformation: Helix‐forming or ‐breaking propensity of peptide segments
Authors: Segawa Shin‐ichi , Fukuno Takuji , Fujiwara Keiro , Noda Yasuo
Published: December 2004

CD spectra of reduced and S‐3‐(trimethylated amino) propylated lysozyme (TMAP lysozyme) have been measured in various solutions containing guanidine hydrochloride or trifluoroethanol (TFE). The CD spectra indicate that there remain residual secondary structures in protein in aqueous solution. The addition of TFE further promotes the formation of secondary structures. In order to examine whether secondary structures are evenly induced over all the polypeptide chain, or locally at particular segments, the limited proteolysis of TMAP lysozyme by trypsin has been performed, and the CD spectra of all the final and intermediate products have been observed in solutions containing TFE. As a result, the fragments vary in a helix‐forming propensity. The CD spectra of peptide fragments T5, T7, T9T10, T12T13, T14T15T16, and T17T18 are not significantly affected by the addition of TFE, where T refers to the nomenclature of R. E. Canfield [(1963), Journal of Biological Chemistry, Vol. 238, pp. 2691–2697]. They are fragments of a helix‐breaking propensity. On the other hand, fragment 12 composed of T1‐T4, and fragments T6T7, T8, and T11, attain secondary structures with the addition of TFE. They are fragments of a helix‐forming propensity. Further, it is found that the fragments of a helix‐forming propensity just correspond to the helical segments in native lysozyme. We examine the interactions between neighboring fragments, which contribute to the stabilization of local structures along the polypeptide chain.
Oligopurine · oligopyrimidine tracts do not have the same conformation as analogous polypurine · polypyrimidines
Authors: Jayasena Vineetha K. , Behe Michael J.
Published: December 2004

The ability of tracts of synthetic oligopurine · oligopyrimidines containing both adenosine and guanosine residues to approach the conformation of analogous polypurine · polypyrimidines has been examined as a function of tract length by CD spectroscopy. Tracts of up to 19 contiguous, alternating dA and dG residues yield CD spectra that are distinctly different from that of the analogous alternating polymer. Thus the structural changes reflected in the unusual CD spectrum of poly[d(AG)] · poly [d(CT)] must require even longer tract lengths. Tracts of contiguous adenosines flanked by guanosine residues were seen to approach the CD spectrum of poly[dA] · poly[dT] quite slowly as a function of tract length, requiring more than 24 contiguous adenosines to give CD spectra similar to the homopolymer. These results lead us to the conclusion that oligopurine tracts in vivo are not well modeled by synthetic polypurine · polypyrimidines with one or two base pair repeating units.
Theoretical CD studies of polypeptide helices: Examination of important electronic and geometric factors
Authors: Manning Mark C. , Woody Robert W.
Published: December 2004

An improved model for calculating the CD of polypeptides has been developed. Excited state wavefunctions were derived from CNDO/S (complete neglect of differential overlap, spectroscopic) calculations on N‐methylacetamide. Four discrete peptide‐localized transitions were employed: π0π*(NV1), π+π* (NV2), nπ*, and n′π*. Inclusion of the π+π*transition (λ0 = 140 nm) significantly improves the accuracy of the calculated CD spectra in the 180‐250‐nm region. Spectra were computed for various helical structures, including right‐handed α‐, αII‐, ω‐, π‐, 310‐, and poly(proline)I‐helices, and the left‐handed poly(proline)II‐helix. Sensitivity to changes in the peptide backbone geometry and chain length are examined. Electronic factors such as ground‐state charge distribution, hybridization effects, and basis set deorthogonalization have been investigated. The nonconservative nature of the poly (Pro) I and II CD spectra is reproduced, and the helix band present in earlier exciton calculations on the α‐helix has been diminished.
Assignment of protein nmr spectra in the light of homonuclear 3D spectroscopy: An automatable procedure based on 3D TOCSY‐TOCSY and 3D TOCSY‐NOESY
Authors: Oschkinat H. , Holak T. A. , Cieslar C.
Published: December 2004

Automated assignment of proteins is greatly simplified using data from 3D‐nmr spectra. A strategy is presented which makes use of 3D‐TOCSY‐TOCSY and 3D‐TOCSY‐NOESY; its potential is demonstrated with the example of the spectra of BPTI.

The discussion of the potential of 3D‐nmr includes the introduction of a simple graph for the description of the information content of multidimensional nmr spectra.
Peptide–membrane interactions and a new principle in quantitative structure–activity relationships
Authors: Schwyzer Robert
Published: December 2004

Ideas about “active conformations” of peptides as the basis of their biological action are reviewed and put into perspective with recent work on the possible role of the lipid phase of the target cell membrane in mediating receptor subtype selectivity.
Antigen–antibody recognition by Fourier transform IR spectroscopy/attenuated total reflection studies: Biotin–avidin complex as an example
Authors: Barbucci R. , Magnani A. , Roncolini C. , Silvestri S.
Published: December 2004

Biotin–avidin recognition is studied by Fourier transform ir spectroscopy/attenuated total reflection (FTIR/ATR) under physiological conditions. The ureido portion of biotin is confirmed to be involved in the interaction with avidin, as previously found, but when the biotin–avidin complex forms, an electrostatic interaction occurs between the carboxylate group of the biotin molecule and the protonated aminic end group of the avidin amino acid side chains. Comparison of the biotin–avidin system with the biotin–1, 4‐diaminobutane and biotin–tryptophan systems confirms these findings.