bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction of poly(I) and poly(I)·poly(C) with chlorodiethylenetriamino platinum(II) chloride
Authors: Hermann Dominique , Fazakerley G. Victor , Guschlbauer Wilhelm
Published: December 2004

The fixation of dien‐Pt on poly(I)·poly(C) leads to only minor changes in the uv and CD spectra at ambient temperature, showing that there is little perturbation of the secondary structure in the rb range studied (up to 0.30). However, the melting profiles show two steps. The Tm for strand separation increases linearly from 61°C (rb = 0) to 80°C (rb = 0.18), after which it declines on further increasing the rb. The second melting step is not complete at 100°C, and the magnitude of the absorbance change in this second step also appears to be at a maximum at rb = 0.18. Although dien‐Pt can only coordinate to one base, the nmr spectra at 80°C also show a second type of interaction with the adjacent bases, which is only destroyed in the presence of a strong denaturing agent, 5M guanidinium hydrochloride. From these results and the spectrophotometric data, we observe that dien‐Pt forms a triple sandwich by hydrogen bonding of the platinum amino groups to the adjacent hypoxanthine bases (N7). The presence of these hydrogen bonds accounts for the increased stability (maximal at one Pt to three hypoxanthine bases) and their rupture is seen in the second melting step. No interaction has been observed with poly(C) strand. Reaction of dien‐Pt with poly(I) shows the formation of the same triple sandwich structure in the nmr spectra.
The effects of alkali‐metal chlorides and of spermidine and spermine on the swelling pressures of DNA gels in the ultracentrifuge
Authors: Richard Alfred J.
Published: December 2004

The effects is solution of the alkali‐metal chlorides on the gel‐like phase of DNA formed in the ultracentrifuge cell have been studied. The polycations, spermidine and spermine, also were shown to affect strongly the swelling pressure of the DNA gel, with evidence for the destabilization of DNA in very dilute spermine, below 10−6 M, and for the collapse of DNA in both spermine and spermidine solutions above 10−6 M.
Circular dichroism of core DNA in mononucleosomes: A theoretical model
Authors: Tobias Irwin
Published: December 2004

The observed difference between the CD spectrum of B‐DNA mononucleosomes and that of free DNA has been attributed to the tertiary structure of the core DNA. This conjecture is tested here. The tertiary structure is modeled as an optical system consisting of two identical, planar, linear retarders rotated with respect to each other. The retarders have the same linear birefringence and linear dichroism as oriented B‐DNA. Such an optical system is circularly dichroic. The predicted wavelength dependence and magnitude of the CD are in reasonably close agreement with the experimental results.
Antifreeze glycoproteins: Influence of polymer length and ice crystal habit on activity
Authors: Burcham Timothy S. , Knauf Michael J. , Osuga David T. , Feeney Robert E. , Yeh Yin
Published: December 2004

The effect of the ice crystalline habit and the length of the polymer on the ability of the antifreeze glycoproteins (AFGP) from polar fish to depress the freezing temperature of water was investigated. The low‐molecular‐weight components of the glycoproteins, AFGP‐ 6–8, are inactive when a solution of such a sample is nucleated at −6°C. A solution of large AFGP (1–4) is fully functional under the same conditions. The low‐molecular‐weight components differ from the height‐molecular‐weight components in that they contain some proline replacing the alanine in the Ala‐Ala‐Thr · disaccharide polymer unit. In the present experiments, antifreeze activity was examined in the presence of two different forms of ice crystal growth habits, and homodimders of AFGP 6 and 8 were prepared to investigate the function of polymer length and the on antifreeze activity at different degrees of supercooling. The results indicate that the ice crystal growth habit and the introduction of proline into the polymer unit may be responsible for the loss of activity at deep supercooling (−6°C) of AFGP 6–8. The loss in the ability of AFGP to depress the freezing temperature of water at deep supercooling is not solely due to polymer length, as carbodiimide‐linked dimers of AFGP 6 do not function under these freezing conditions. A Model of antifreezing action based on Langmuirian adsorption of AFGP on the ice surface and direct competition between water and AFGP molecules for the incorporation sites in the ice crystal lattice is presented.
Synthesis of oligopeptides consisting of L‐leucyl‐L‐leucyl‐L‐ananyl and L‐methionyl‐L‐methionyl‐L‐leucyl repeating units with an improved preparation of Nps‐amino acids
Authors: Katakai Ryoichi , Shida Hitoshi , Takada Toshiaki
Published: December 2004

Two series of peptides with hydrophobic side chains, Nps‐(L‐Leu‐L‐Leu‐L‐Ala)n‐OEt and Nps‐(L‐Met‐L‐Met‐LLeu)n‐OEt (n = 1–6), were synthesized by the fragment condensation method using dicyclohexylcarbodiimide in the presence of N‐hydroxysuccinimide. The tripeptide fragments were prepared stepwise by dicyclohexylcarbodiimide‐mediated reaction of Nps‐amino acids, which were synthesized by an improved rapid procedure.
Azobenzene‐Containing polypeptides: Photoregulation of conformation in solution
Authors: Ciardelli Francesco , Pieroni Osvaldo , Fissi Adriano , Houben Julien L.
Published: December 2004

Photochromic polypeptides, with 16 to 56% azobenzene groups in the side chains, have been prepared by reaction of poly(L‐glutamic acid) with p‐aminozaobenzene, both in the presence of dicyclohexyl carbodiimide/N‐hydroxybenzotriazole and of pivaloyl chloride. Analogous modification reactions carried out on poly(L‐aspartic acid) were unsuccessful owing to the formation of N‐succinimide rings. In trimethylphosphate, all the azopolypeptides exhibit the α‐helix CD pattern. Irradiation produces the trans‐to‐cis isomerization of the azo side chains, but does not induce any variations of the backbone conformation. In water, the CD spectra indicate the presence of appreciable amounts of α helix in 16 and 21% mol azo‐containing poly‐(Lglutamates), while a β structure is present in a 36% mol azopolypeptide. Light produces conformational changes of the polypeptide conformation which are completely reversed in the dark. The extent and kind of photobehavior depend on the azo content and the pH value at which irradiation is carried out. The light‐induced effects are discussed on the basis of the pH‐induced order‐disorder conformational transitions. In fact, the pK values and the transition curves of the dark‐adapted samples were found to be different from those of the irradiated ones.
Polypeptide matrices as active catalytic supports for stereoselective electron‐transfer reactions
Authors: Pispisa B. , Farinella M.
Published: December 2004

The oxidation of L‐adrenaline (epinephrine) in the presence of [Fe(tetpy)(OH)2]+ ions bound to poly(L‐glutamate) or to poly(D‐glutamate) has been studied at pH 7 (tetpy = 2,2′:6′,2″:6″,2‴‐tetrapyridyl). Electron transfer from the substrate to the central metal ion, which is rate‐determining, proceeds stereoselectively only when extensive and possibly specific interactions between adrenaline and the peptidic residues of the ordered polymer in the close environment of the active sites occur. This ensures different steric constraints for the two diastereomeric precursor complexes, which are thought to affect the separation and orientation of the redox centers differently, leading to the observed phenomena. Some data on the catalytic oxidation of L‐dopa(3,4‐dihydroxyphenylalanine) are also presented, showing stereoselective effects similar to those observed with L‐adrenaline, despite the diverse distance of the chiral center from the reacting OH groups. A mechanistic interpretation of the results is discussed in the light of a few general considerations concerning the structural features of the catalytic systems. Possible explanations for the finding that stereoselectivity occurs at the expense of the efficiency of catalysis are also considered.
Structural dynamics of melanin investigated by Rayleigh scattering of Mössbauer radiation
Authors: Albanese G. , Bridelli M. G. , Deriu A.
Published: December 2004

Measurements of Rayleigh scattering of Mössbauer radiation (RSMR) have been performed on synthetic L‐Dopa melanin as a function of the scattering vector, Q, and temperature, T, and are compared with the results of X‐ray diffraction analyses. The data obtained allow us to derive a radial distribution function for the atomic positions not affected by the dynamic disorder and determined only by the distribution of equilibrium interatomic distances. The mean‐square atomic displacements, , derived from the RSMR measurements, evidence a strong anisotropy of the atomic vibrations: even at room temperature,  reaches fairly high values for off‐plane displacements, as compared with those for motions within the planes of the structure. A connection is suggested between the observed dynamics and the biological screening action of melanins.
A consistent empirical potential for water–protein interactions
Authors: Hermans Jan , Berendsen Herman J. C. , Van Gunsteren Wilfred F. , Postma Johan P. M.
Published: December 2004

A simple point‐charge potential, developed earlier for the calculation of intermolecular forces in molecular‐dynamics simulations of liquid water, has been extended to include interactions between water molecules and polar groups of proteins. A complete potential for use in the simulation of protein dynamics in water is reported.
Vibrational circular dichroism of polypeptides. II. Solution amide II and deuteration results
Authors: Sen A. C. , Keiderling T. A.
Published: December 2004

Vibrational CD (VCD) of amide I and II vibrations of several α‐helical polypeptides have been measured in solution. For the amide II as well as the amide I [previously published: Lal, B.B. & Nafie, L.A. (1982) Biopolymers 21, 2161] we find the VCD to be characteristic of the polypeptide secondary structure. Amide II bands of right‐handed α helices were all found to have negative VCD and to have their maximum rotational strength for the parallel (low‐energy) component. However, left‐handed α helices formed from L‐amino acids gave positive amide II bands at higher frequencies than found for the right‐handed helices, indicating that the VCD was sensitive to the stereochemical difference. The amide‐I VCD spectra of some deuterated right‐handed α‐helical polypeptides have a new negative feature to low frequency that does not reflect theoretical predictions but also appears to be stereochemically sensitive. Amide‐II and amide‐A VCD of a few deuterated polypeptides imply retention of the secondary‐structure‐dependent characteristics seen in the hydrogenated VCD.
DNA gelation in concentrated solutions
Authors: Fried Michael G. , Bloomfield Victor A.
Published: December 2004

Sonicated calf‐thymus DNA (200 ± 30 base pairs) spontaneously forms viscoelastic gels over a wide range of concentration, temperature, and buffer conditions. Quasielastic light scattering (QLS) can be used to monitor this process, because the ratio of dynamic‐to‐static scattering intensity decreases dramatically as gelation occurs. Using QLS, we have explored the effects of DNA concentration and mono‐ and divalent cations on the thermal stability of DNA gels. We found that the gel–sol transition temperature (Tgel) varies linearly with [DNA] from 7.5 to 17 mg/mL. Both Na+ and Mg2+ strongly stabilize the gel state. The sharpness of the transition increases with increasing ionic and DNA concentrations. Analysis of the Na+‐dependent gelation indicates that the process requires the association of one Na+ per 118 base pairs. Mg2+ effectively stabilizes the gel at concentrations 10‐fold below those required for Na+. The unexpectedly large effect of Mg2+ suggests that ion‐specific interactions may play an important role in determining gel stability.
Conformation of control and acetylated HeLa stripped chromatin after reassociation with H1
Authors: Hüvös Piroskae , Sasi Ramakrishnan , Fasman Gerald D.
Published: December 2004

The effect of histone H1 on the conformation and stability of control and acetylated HeLa high‐molecular‐weight chromatin that had been stripped of H1 and nonhistone proteins was compared by circular dichroism (CD) and thermal denaturation measurements. Two different preparations of H1, originating from rat thymus and chicken erythrocyte, were used in the reconstitution studies. The control and acetylated stripped chromatin had identical CD and thermal denaturation properties, as did their reconstitutes with rat thymus H1. Reconstitutes of the two chromatins with chicken erythrocyte H1 had similar CD properties, but thermal denaturation studies showed that the acetylated reconstitute was destabilized compared to the control reconstitute. Reconstitutes of both chromatins with chicken erythrocyte H1 had a more condensed and stabilized structure than the reconstitutes with rat thymus H1. Thus, acetylation caused a decrease in the stability of chromatin in the presence of erythrocyte H1, but more marked differences were detected in the structure of stripped chromatin after reassociation with different H1 preparations.
Catalytic influence of heparin on auramine O hydrolysis: A basis for differentiating heparin from other glycosaminoglycans based on its properties as a polyelectrolyte
Authors: Band Philip , Lukton Aaron
Published: December 2004

The basis for heparin's ability to accelerate the conversion of auramine O (AuO) to Michlers ketone [P. Band & A. Lukton (1982) Anal. Biochem. 120, 19–24] is here explained in terms of well‐known polyelectrolyte phenomena. Acceleration of this acidcatalyzed hydrolysis appears to be due to colocalization of the cationic dye and hydronium ion within the microenvironment of heparin's electrostatic domain. The dependence of reaction rate on polymer, dye, and hydronium ion concentration, ionic strength, and various ratios of these parameters is consistent with what others have observed for polyelectrolyte catalysts. Dextran sulfate, polyvinyl sulfate, and polyanethole sulfonate likewise accelerate this reaction, thus precluding any explanation of the catalysis in terms of a specific catalytic site. A striking aspect about the polyanion–AuO system is the inability of all other natural glycosaminoglycans tested to catalyze this reaction, despite their analogous polyanionic nature. Manning's limiting laws describing counterion condensation in polyelectrolyte solutions provide a simple context within which to interpret these results. Calculation of the structural linear charge density parameter, ξ, based on analytically determined sulfate‐to‐hexosamine ratios, reveals that heparin is unique among the glycosaminoglycans in possessing an ξ value greater than unity under the conditions described. Thus, heparin's differential ability to catalyze AuO hydrolysis is a reflection of the fact that only heparin is sulfated to an extent great enough to maintain ξ > 1, even when the negative charge of carboxylate groups is neutralized. It is proposed that this distinction may be important to the unique biochemical attributes of heparin and that such considerations may prove useful in establishing structure–function relationships when comparing different glycosaminoglycan classes.
Synthesis and β‐conformation of sequential polypeptides containing arginine, histidine, and leucine
Authors: Barbier Bernard , Caille Anita , Brack André
Published: December 2004

Alternating poly(Arg‐Leu) and copolypeptides with Arg‐Leu and His‐Leu sequences were prepared by condensation of the corresponding p‐nitrophenyl dipeptide esters in the presence of 1‐hydroxybenzotriazole. Arginine was used without any protection and histidine side chains were protected using π‐benzyloxymethyl group recently introduced in peptide chemistry. The ability of these polypeptides with alternating hydrophilic and hydrophobic residues to form water‐soluble β‐sheets was investigated by CD.
Conformational effects on peptide aggregation in organic solvents: Spectroscopic studies of two chemotactic tripeptide analogs
Authors: Raj P. Antony , Balaram P.
Published: December 2004

The aggregation behavior of the chemotactic peptide analogs, Formyl‐Met‐Leu‐Phe‐OMe (1) and Formyl‐Met‐Aib‐Phe‐OMe (2), has been studied in chloroform and dimethylsulfoxide over the concentration range of 0.2–110 mM by 1H‐nmr spectroscopy. Both peptides associate in CDCl3 at concentrations ≥ 2 mM, while there is no evidence for aggregation in (CD3)2SO. Analog 1 adopts an extended conformation in both solvents favoring association to form β‐sheet structures. A folded, γ‐turn conformation involving a 3 → 1 hydrogen bond between Met CO and Phe NH is supported by 1H‐, 13C‐nmr, and ir studies of analog 2. The influence of backbone conformation on the ease of peptide aggregation is demonstrated by ir studies in CHCl3 and CD studies in dioxane.
Quantum‐mechanical theory of CD for infinite helical polymers
Authors: Pamuk H. Onder , Dougherty Anne M. , Johnson W. Curtis
Published: December 2004

Quantum‐mechanical equations are derived that are particularly well suited to actual computations of the CD for helical polymers. They make use of cyclic boundary conditions and helical symmetry, so that only two matrices with a size equal to the number of transitions considered need be diagonalized. The final equations are expressed directly in terms of monomer properties and helical parameters to invite the same input as earlier calculations, and are given as a rotational strength times a shape function for ease of comparison with the earlier work. The shape of the helix term is expressed as a derivative with respect to ω and depends on the distance between monomers along the helix axis. Other terms involving two electric transition dipoles depend on the distance from the helix axis to the transition center. These equations are directly comparable to the classical equations derived for cyclic boundary conditions and helical symmetry. We present an outline of the derivation and enough intermediate steps to clarify how the equations arise.
Random‐phase calculation of the low‐energy circular dichroism in glucans
Authors: Sathyanarayana B. K. , Stevens E. S. , Texter J.
Published: December 2004

The CD of the long‐wavelength electronic transition in the α‐(1 → 4)‐linked glucan dimer (maltose) and polymer (amylose), and in the β‐(1 → 6)‐linked dimer (gentiobiose) and polymer (pustulan), are calculated in the random‐phase approximation using time‐dependent Hartree theory. This long‐wavelength transition (180–190 nm) is assumed to be localized on the linkage oxygen atom and to be of a σ*/3 s ← n character. The zerothorder σ*/3s ← n magnetic‐dipole transition moment is coupled to the CC, CO, and CH bond density of states via a polarizability approximation. We assume this coupling is dominated energetically by the electric‐dipole, electric‐dipole interaction terms in the context of Schellman's μe‐μm coupling mechanism of rotatory power. The CD is calculated as a function of rotation about the two single bonds of the linkage oxygen atom and also as a function of rotation about the C(5)‐C(6) bond. For maltose, four rotational isomers are considered, resulting from combinations of the gg and gt C(6)H2OH group rotational isomers. The calculated CD values were then Boltzmann‐averaged over an empirical potential, and the resulting CD was found to compare satisfactorily with experiment. In the case of the polymers, only structures having periodicity (helicity) were examined.
Type I collagen segment long spacing banding patterns: Improved correlation with models using a variable h‐spacing
Authors: Bender Edward , Silver Frederick H.
Published: December 2004

Five models of collagen molecular structure incorporating a variable h‐spacing were evaluated by comparing theoretical densitometric scans of segment long spacing (SLS) banding patterns with experimental densitometric scans. The five models tested assumed a shift in the h‐spacing of different residues: (1) proline only, (2) hydroxyproline only, (3) proline and hydroxyproline (in the same direction), (4) proline and hydroxyproline (in opposite directions), and (5) all residues shifted depending on their relative hydrophobicity. The best correlation coefficients were obtained when, in the theoretical models, the proline residues were expanded axially and/or the hydroxyproline residues were contracted. Using the hydrophobic model, the results showed that in general the more hydrophobic a residue is, the larger its h‐spacing. Theorectical models with the α2‐chain in the A position of the triple helix (α2,α1,α1) correlated best with the experimental data. In conclusion, these studies suggest that variation exists in the h‐spacing of the amino acid residues proline and hydroxyproline in SLS prepared for electron microscopy and stained with phosphotungstic acid and uranyl acetate. Some of this variation may be due to drying and may not be present in hydrated molecules.
Two‐dimensional 1H‐nmr studies on the lac repressor DNA binding domain: Further resonance assignments and identification of nuclear overhauser enhancements
Authors: Zuiderweg E. R. P. , Scheek R. M. , Kaptein R.
Published: December 2004

The assignments of several 1H lines in the spectrum of the lac repressor DNA‐binding domain (or “headpiece”) are documented. These new assignments complement those obtained in a previous study [E.R.P. Zuiderweg, R. Kaptein, and K. Wüthrich (1983) Eur. J. Biochem. 137, 279] and were made from pure absorption phase two‐dimensional nuclear Overhauser enhancement (2D NOE) spectra and 1H 2D double‐quantum spectra of this protein. Based on the complete set of resonance assignments, a large number of interresidue NOEs are identified; these are documented and their relation with distance constraints is discussed. The identification of these NOEs is a prerequiste for the determination of the spatial structure of this protein, for which no crystallographic data are available.
Cross‐polarization/magic‐angle spinning 13C‐nmr of (1 → 6)‐β‐D‐glucan (pustulan): Mechanism of gelation
Authors: Stipanovic Arthur J. , Giammatteo Paul J. , Robie Stephen B.
Published: December 2004

13C‐nmr has been employed to probe the molecular conformation and crystal structure of (1 → 6)‐β‐D‐glucan (pustulan) in the solution, gel, and solid states. CP/MAS 13C‐nmr spectra recorded for partially crystalline solid pustulan display a resonance near 82 ppm that is absent in solution spectra. The intensity and peak width of this resonance were found to depend on relative crystallinity as determined by x‐ray diffraction. CP/MAS spectra of aqueous pustulan gels also exhibit the 82‐ppm resonance, suggesting that the gelation mechanism may involve microcrystalline junction zones. Since the 82‐ppm resonance is absent in the CP/MAS spectrum of the (1 → 6)‐β‐linked dimer gentiobiose, we tentatively conclude the crystal structure of this dimer does not adequately model the yet undetermined structure of pustulan.
Proton magnetic resonance studies on conformation and association of oligo‐γ‐benzyl‐L‐glutamates in solution
Authors: Imae Toyoko , Ikeda Shoichi , Kobayashi Yuji , Kyogoku Yoshimasa
Published: December 2004

The proton magnetic resonance spectra of o‐nitrophenylthio‐tetra‐ and hexa‐γ‐benzyl‐L‐glutamate ethylamides have been measured at different concentrations in CDCl3 and CD22C1. The NH and α‐CH resonances of the tetrapeptide show downfield shifts with increasing concentration, accompanying disappearance of their fine structure and line broadening. The apparent feature of chemical shifts against concentration is sigmoidal, and it can be interpreted by assuming the presence of a step or more of association–dissociation equilibria of tetrapeptide. With increasing concentration, small aggregates are formed by intermolecular hydrogen bonding, the size of which is not sufficiently large to exhibit critical micelle concentrations. In contrast to the tetrapeptide, the hexapeptide has constant chemical shifts of the NH and α‐CH resonances, independent of concentration, which implies that only the unassociated molecules show observable sharp resonances. In the hexapeptide, the phenyl CH and benzyl CH2 groups of the side chains exhibit new resonances above certain critical concentrations, indicating the restriction of rotational freedom of the side chains in the aggregated states.
Conformational analyses of polyoxyethylene‐bound homo‐oligo‐L‐glutamates in a helix‐supporting environment, trifluoroethanol
Authors: Ribeiro Anthony A. , Saltman Robert , Goodman Murray
Published: December 2004

A detailed conformational analysis of C‐terminal polyoxyethylene‐bound homo‐oligo‐L‐glutamates (dimer, penta‐heptamer) with N‐terminal blocking groups, X = Boc, Ac, or pGlu, was carried out in the helix‐supporting environment, trifluorethanol, using 1H‐nmr spectroscopy to observe backbone NH resonances. The nmr structural investigations for the three glutamate POE series were based on the assignment of individual amide NH resonances through deuteration, analyses of vicinal coupling constants (3JNH‐α‐CH), measurements of the temperature‐dependence of NH chemical shifts, saturation‐transfer experiments, stable free radical titration studies, and titration experiments using a denaturing solvent (DMSO). From these investigations, a detailed picture was derived for the possible conformations of these POE‐peptides.
Hydrogen‐bonding preferences in 2,6‐diaminopurine: uracil (thymine) and 8‐methyl adenine:uracil (thymine) complexes
Authors: Rao Shashidhar N. , Kollman Peter A.
Published: December 2004

We present molecular mechanical calculations on 2,6‐diaminopurine (2,6‐DAP):uracil (thymine) and 8‐methyladenine (8‐methyl A): uracil (thymine) hydrogen‐bonded complexes of various geometries, namely, Watson‐Crick (normal and reverse), Hoogsteen (normal and reverse), and purine N3 type. In contrast to earlier calculations [Ornstein, R. L. & Fresco, J. R. (1983) Proc. Natl. Acad. Sci. USA 80, 5171–5175], the 2,6‐DAP:uracil (thymine) complexes are predicted to be Watson‐Crick and the 8‐methyladenine:uracil (thymine) to be Hoogsteen. The results presented here are more consistent with the observed crystallographic preferences.
Examination of the secondary structure of proteins by deconvolved FTIR spectra
Authors: Byler D. Michael , Susi Heino
Published: December 2004

Fourier transform ir (FTIR) spectra of 21 globular proteins have been obtained at 2 cm−1 resolution from 1600 to 1700 cm−1 in deuterium oxide solution. Fourier self‐deconvolution was applied to all spectra, revealing that the amide I band of each protein except casein consists of six to nine components. The components are observed at 11 well‐defined frequencies, although all proteins do not exhibit components at every characteristic frequency. The root mean square (RMS) deviation of 124 individual values from the 11 average characteristic frequencies is 1.9 cm−1. The observed components are assigned to helical segments, extended beta‐segments, unordered segments, and turns. Segments with similar structures do not necessarily exhibit band components with identical frequencies. For instance, the lower frequency beta‐structure band can vary within a range of approximately 15 cm−1. The relative areas of the individual components of the deconvolved spectra were determined by a Gauss–Newton, iterative curve‐fitting procedure that assumed Gaussian band envelopes for the deconvolved components. The measured areas were used to estimate the percentage of helix and beta‐structure for each of 21 globular proteins. The results are in good general agreement with values derived from x‐ray data by Levitt and Greer. The RMS deviation between 22 values (alpha‐ and beta‐content of 11 beta‐rich proteins measured by both techniques) is 2.5 percentage points; the maximum absolute deviation is 4 percentage points.
Macroscopic polarity of connective tissue is due to discrete polar structures
Authors: Freund Isaac , Deutsch Moshe
Published: December 2004

Applying scanning optical harmonic microscopy to biological tissue for the first time, we have discovered that the macroscopic polarity of rat‐tail tendon is due to a coherent network of discrete polar structures. This finding permits isolation of these structures for further detailed analysis, which should lead to their complete characterization and thus to a solution of the twenty‐year‐old mystery of connective tissue polarity.
On an exact starting expression for macromolecular hydrodynamic models
Authors: Wegener William A.
Published: December 2004

A calculational method developed by G. K. Youngren and A. Acrivos [J. Fluid Mech. 75, 377 (1975)] expresses the fluid forces exerted over the surface of an immersed body in terms of differences between body and fluid motions. As opposed to bead‐model approaches, this method starts from an essentially exact hydrodynamic expression, and therefore should be of particular interest to those workers trying to obtain accurate coefficients needed to characterize the diffusive and viscoelastic behavior of macromolecules with complex shapes. However, Youngren and Acrivos's treatment has not been widely adopted nor even used as a proper starting place for higher order bead‐model methods. This is probably related to the unfamiliar appearance of their exact expression, which involves two surface integral terms as opposed to the single summation involved in bead models. We show that their expression may be rewritten in the expected analogous form involving one surface integral term whenever stick boundary conditions are applied to a rigid body or a flexible body composed of rigid segments. For spherical segments, we obtain Rotne–Prager‐type bead‐model results by following typical assumptions. Extensions to deformable particles are considered, in which internal friction can be represented by an arbitrarily viscous internal fluid.
Sequence‐dependent recognition of DNA duplexes: Netropsin complexation to the TATA site of the d(G‐G‐T‐A‐T‐A‐C‐C) duplex in aqueous solution
Authors: Patel Dinshaw J. , Shapiro Lawrence
Published: December 2004

We have recorded one‐dimensional exchangeable proton and two‐dimensional nonexchangeable proton nmr spectra on the complex of netropsin with the self‐complementary d(G‐G‐T‐A‐T‐A‐C‐C) duplex in aqueous solution between 25° and 35°C. The antibiotic amide, pyrrole, and methylene protons, and the nucleic acid base and sugar H1′, H2′, H2″, and H3′ protons, have been assigned from an analysis of the two‐dimensional nuclear Overhauser effect (NOESY) spectra of the complex. We observe intermolecular NOEs between the antibiotic concave face amide, pyrrole, and CH2 resonances, and the adenosine H2 and sugar H1′ protons of base‐pairs T3·A6 and A4·T5 in the central TATA core of the d(G1‐G2‐T3‐A4‐T5‐A6‐C7‐C8) duplex. We present a molecular model outlining these seven antibiotic‐DNA contacts for the complex in solution. The observed line‐broadening of several base and sugar protons at the TATA minor groove netropsin binding site in the complex at 35°C are interpreted in terms of intermediate exchange between two orientations of bound netropsin on the duplex.
Calorimetric studies of the polynucleotide analog poly(−)2‐[2‐(thymin‐1‐yl) propanamido]propenoic acid
Authors: Zand R. , Jiang Z. Z. , Overberger C. G.
Published: December 2004

The thermally elicited structural and conformational transitions of the polynucleotide analog, poly(‐)‐2‐[2‐(thymin‐1‐yl)propanamido]propenoic acid, P(‐)TDHA, have been studied using differential scanning calorimetry (DSC), differential thermal analysis (DTA), and thermogravmetric analysis (TGA). The differential scanning calorimetry curves obtained on solid P(‐)TDHA samples exhibited five distinct transitions. The transition occurring at 50°C is attributed to a disruption of interactions involving thymine–thymine stacking. In contrast the transition observed at 83°C is attributed to a hydrogen‐bonding interaction involving the thymine residues, whereas the transition occurring at 110°C is assigned to hydrogen bonding of the carboxylic acid side‐chain groups. The transitions observed at 50, 83, and 110°C are reversible if the heated and quenched sample is allowed to equilibrate in an atmosphere of high humidity. The transition occurring at 127°C is viewed as a structural rearrangement of the polymer backbone that does not involve the participation of water molecules. The transition observed at a temperature above 197°C is attributed to a structural modification of the polymer resulting from decomposition. Solutions of P(‐)TDHA in 0.1M phosphate buffer at pH 7.05 showed only a single transition at 50°C, which is in accord with an observed transition in the solid state assigned to the disruption of base‐stacking interactions. The average enthalpy for the transition at 50°C was 0.92 cal/g in the solid state and 1.08 cal/g for the solution, which provides additional support for the assignment.
A comparative study of lysozyme conformation in various reverse micellar systems
Authors: Steinmann Bettina , Jäckle Hans , Luisi Pier Luigi
Published: December 2004

The activity and conformation of lysozyme solubilized in apolar solvents via reverse micelles was investigated. The systems used were sodium di‐2‐ethylhexylsulfosuccinate (AOT)/isooctane/H2O, cetyltrioctylammoniumbromide (CTAB)/CHCl3, isooctane/H2O; tetraethyleneglycoldodecylether (EO4C12)/isooctane/H2O, and bulk water. CD spectra of lysozyme in reverse micellar solutions were investigated as a function of w0 (= [H2O]/[AOT]) and were compared to the spectra in aqueous solutions. No marked changes were found in the EO4C12 or in the CTAB systems with respect to water, which indicates that no sizeable conformational changes of the enzyme occurred upon solubilization in the reverse micellar systems. In agreement with previous studies [C. Grandi, R. E. Smith, and P. L. Luisi (1981) J. Biol. Chem. 256, 837–843] dramatic conformational changes can be inferred in the AOT system on the basis of CD studies. This is taken as an indication that the enzyme denatures in this micellar system. This is particularly striking because the enzyme is fully active in AOT reverse micelles. The apparent paradox is solved by the observation that the native CD spectrum (and by inference, the native conformation) is maintained when lysozyme is bound to NAG or NAG3, and by inference, when the substrate is bound, e.g., during enzyme turnover. However, in the absence of added NAG, NAG3, or substrate, the enzyme in the AOT reverse micellar system rapidly denatures. Together with CD studies, fluorescence and nmr data confirm the hypothesis of an irreversible denaturation of lysozyme in the AOT system, the denaturation being slowed down when the substrate is present. The activity of the enzyme has been studied as a function of pH and w0 using the chromophoric substrate 3,4‐dinitrophenyl‐tetra‐N‐acetyl‐β‐D‐chitotetraoside (3,4‐DNP‐NAG4). Generally speaking, the kinetic parameters are comparable to those found in bulk water solution. More detailed, in the CTAB system, kcat tends to be smaller than in aqueous solution (with quite similar KM), whereas in the EO4C12 system (at pH 7.0) the turnover number is larger and KM is smaller than in water. In the AOT system, the kinetic parameters at pH 7.0 are also quite comparable to those found in water.
Prediction of the native conformation of a polypeptide by a statistical‐mechanical procedure. II. average backbone structure of enkephalin
Authors: Paine Gregory H. , Scheraga Harold A.
Published: December 2004

The average conformation of Met‐enkephalin was determined by using an adaptive, importance‐sampling Monte Carlo algorithm (SMAPPS—Statistical Mechanical Algorithm for Predicting Protein Structure). In the calculation, only the backbone dihedral angles (ϕ and ψ) were allowed to vary; i.e., all side‐chain (χ) and peptide‐bond (ω) dihedral angles were kept fixed at the values corresponding to a low‐energy structure of the pentapeptide. The total conformational energy for each randomly generated structure of the polypeptide was obtained by summing over the interaction energies of all pairs of nonbonded atoms of the whole molecule. The interaction energies were computed by the program ECEPP/2 (Empirical Conformational Energy Program for Peptides). Solvent effects were not included in the computation. The calculation was repeated until a total of 10 independent average conformations were established. The regions of conformational space occupied by the average structures were compared with the regions of low conditional free energy obtained by SMAPPS in the first paper of this series. Such a comparison provides an analysis of the capacity of SMAPPS to adjust the Monte Carlo search to regions of highest probability. The results demonstrate that the ability of SMAPPS to focus the Monte Carlo search is excellent. Finally, the 10 independent average conformations and the mean of the 10 average structures were utilized as the initial conformations for a direct energy minimization of the pentapeptide. Of the 11 final energy‐minimized structures, three of the conformations were found to be equivalent to the conformation of lowest energy determined previously. In addition, all but two of the remaining energy‐minimized structures were found to correspond to one of the two other conformations of high probability obtained in the first paper of this series. These results indicate that a set of independent average conformations can provide a rational, unbiased choice for the initial conformation, to be used in a direct energy minimization of a polypeptide. The final energy‐minimized structures consequently constitute a set of low‐energy conformations, which include the global energy minimum.
Computer simulation of the folding–unfolding transition of island‐model proteins—folding pathway, transition process, and fluctuations
Authors: Segawa Shin‐Ichi , Kawai Toshikazu
Published: December 2004

Monte Carlo computer simulations were performed to elucidate the dynamic aspects of the folding and unfolding transitions of island‐model protein. Five different types of model proteins were designed, according to characteristics of backbone structure. The computer simulations clearly show that the unfolding and folding transitions are all‐or‐none processes between the N‐and U‐states. They are typical Poisson processes. From the Arrhenius plots of rate constants, the activation enthalpies of folding and unfolding were determined. In addition, the folding pathways were determined along the reaction coordinate. Formations of several local structures along a polypeptide chain are almost simultaneous, but the most probable time sequence of events exists at the moment of transition. That is the most probable folding pathway. The unfolding pathway was found to be just the reverse process of the most probable folding pathway. The relationship between the fluctuations in each equilibrium state and the transition process was considered. In contrast to the theory of absolute reaction rate, the transient states are widely distributed along the reaction coordinate. From analysis of the “transient process,” we tried to determine the critical states from which the transient process starts. As a result, we found that the unfolding transition occurs at the stage near the N‐state. During the U‐state, large joined blocks rarely appear, but they appear in the transient process towards the N‐state. However, the “branch point” between the N‐ and U‐states lies near the N‐state, and joined blocks tend to unfold prior to passing over the branch point. We concluded that the stability of later folding intermediates is important for selection of the folding pathway, while preferential selection of an early folding intermediate is important in acceleration of the folding rate. The effects of intrachain cross‐linking and peptide fragment binding on the rate constants were examined by using computer simulations of model proteins. In general, a small‐sized loop formed by cross‐linking accelerates the folding rate and a large‐sized loop contributes much to the stabilization of the native conformation. We also found that peptide fragment binding contributes little to the acceleration of the folding rate of the residual protein.
Structure and internal mobility of proteins: A molecular dynamics study of hen egg white lysozyme
Authors: Ichiye T. , Olafson B. D. , Swaminathan S. , Karplus M.
Published: December 2004

The structure and internal motions of the protein hen egg white lysozyme are studied by analysis of simulation and experimental data. A molecular dynamics simulation and an energy minimization of the protein in vacuum have been made and the results compared with high‐resolution structures and temperature factors of hen egg white lysozyme in two different crystal forms and of the homologous protein human lysozyme. The structures obtained from molecular dynamics and energy minimization have root‐mean‐square deviations for backbone atoms of 2.3 Å and 1.1–1.3 Å, respectively, relative to the crystal structures; the different crystal structures have root‐mean‐square deviations of 0.73–0.81 Å for the backbone atoms. In comparing the backbone dihedral angles, the difference between the dynamics and the crystal structure on which it is based is the same as that between any two crystal structures. The internal fluctuations of atomic positions calculated from the molecular dynamics trajectory agree well with the temperature factors from the three structures. Simulation and crystal results both show that there are large motions for residues involved in exposed turns of the backbone chain, relatively smaller motions for residues involved in the middle of helices or β‐sheet structures, and relatively small motions of residues near disulfide bridges. Also, both the simulation and crystal data show that side‐chain atoms have larger fluctuations than main‐chain atoms. Moreover, the regions that have large deviations among the x‐ray crystal structures, which indicates flexibility, are found to have large fluctuations in the simulation.
Rotational diffusion of short DNA fragments in polyacrylamide gels: An electric birefringence study
Authors: Wijmenga Sybren S. , Maxwell Anthony
Published: December 2004

Using electric birefringence we have examined the rotational diffusion of five short DNA fragments (55 to 256 base pairs) both in polyacrylamide gels as a function of gel concentration and in solution. The length dependence of the measured rotational relaxation times in the gels is in good agreement with the prediction from the Odijk theory for the dynamics of slightly flexible rods in a network. The rotational relaxation times were found to depend on the gel concentration, contrary to the prediction from the Odijk theory. Possible reasons for this observation are discussed. The birefringence decay curves for DNA fragments in the gel were single exponential only at small electric field strength.
Raman amide bands of type‐II β‐turns in cyclo‐(VPGVG)3 and poly‐(VPGVG), and implications for protein secondary‐structure analysis
Authors: Thomas George J. , Prescott Betty , Urry Dan W.
Published: December 2004

The cyclopentadecapeptide, c(VPGVG)3, a model structure for protein type‐II β‐turns [W. J. Cook et al. (1980) J. Am. Chem. Soc. 102, 5502–5505], has been investigated by laser Raman spectroscopy. Data obtained from both normal and deuterated crystals identify amide I, III, I′, and III′ bands characteristic of the β(II)turn. The structurally related polypentapeptide poly(VPGVG) in normal and deuterated forms has also been investigated, and exhibits the same Raman amide bands as c(VPGVG)3. The coacervate of poly(VPGVG), obtained by heating the solution to 40°C, likewise exhibits a Raman spectrum very similar to that of the c(VPGVG)3 crystal. Raman spectra thus indicate closely similar secondary structures for crystalline c(VPGVG)3 and aqueous poly(VPGVG), and provide an empirical basis for interpreting the conformation sensitive amide bands of globular proteins in terms of β(II)turn structures that may be present. An important conclusion from the present findings is that the amide I Raman profile of a protein may not be sufficient in general to distinguish turns from helix and sheet secondary structures, since the major amide I peaks of the β(II)turn at 1676 and 1652 cm−1 overlap, respectively, with amide I profiles generated by β‐sheet and α‐helix conformations.
Solvent effect on the stability of mannobiose conformers
Authors: Tvaroska I. , Perez S. , Noble O. , Taravel F.
Published: December 2004

The conformational equilibria of seven methyl β‐D‐mannobioside conformers have been studied theoretically in five solvents. The structure of each individual conformer has been refined by the PCILO quantum‐chemical method from the seven distinct low‐energy regions determined from (Φ, Ψ) maps calculated by a potential function method. The stability of the conformers in dilute solution has been evaluated by using a method that consists of electrostatic, dispersion, and cavity terms. The calculated abundance of conformers depends on the solvent and results indicate that the preponderant conformer in the solution may not be the one adopted by mannobiose in the crystalline form. Based on the determined abundance of conformers, thermodynamically averaged nmr parameters, dipole moment, and linkage rotation have been calculated. The solvation behavior of methyl β‐D‐mannobioside is compared to those previously estimated for cellobiose and maltose.
Conformational studies of diastereomeric cyclic enkephalins by 1H‐NMR and computer simulations
Authors: Mierke Dale F. , Lucietto Pierluigi , Goodman Murray , Schiller Peter W.
Published: December 2004

We report the solid‐phase synthesis and conformational analysis of a 14‐membered, cyclic enkephalin analog, HTyrc[DA2buGlyPheDLeu] (where A2bu represents α,γ‐diaminobutyric acid). The results from the guinea pig ileum (GPI) and mouse vas deferens (MVD) assays show that the analog, though active, has little selectivity for the μ or δ opioid receptors. Conformational analysis is carried out using 1H‐nmr and computer simulations, including molecular dynamics and energy minimizations. The results obtained here are compared with the findings of our studies carried out on the μ‐receptor‐selective diastereomer, HTyrc[DA2buGlyPheLeu] [N. Mammi, M. Hassan, and M. Goodman (1985) J. Am. Chem. Soc. 107, 4008–4013]. This comparison allows for insight into the regiospecificity of these cyclic enkephalin analogs.
Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves
Authors: Marky Luis A. , Breslauer Kenneth J.
Published: December 2004

In this paper, we derive the general forms of the equations required to extract thermodynamic data from equilibrium transition curves on oligomeric and polymeric nucleic acids of any molecularity. Significantly, since the equations and protocols are general, they also can be used to characterize thermodynamically equilibrium processes in systems other than nucleic acids. We briefly review how the reduced forms of the general equations have been used by many investigators to evaluate mono‐ and bimolecular transitions, and then explain how these equations can be generalized to calculate thermodynamic parameters from common experimental observables for transitions of higher molecularities. We emphasize the strengths and weaknesses of each method of data analysis so that investigators can select the approach most appropriate for their experimental circumstances. We also describe how to analyze calorimetric heat capacity curves and noncalorimetric differentiated melting curves so as to extract both model‐independent and model‐dependent thermodynamic data for transitions of any molecularity. The general equations and methods of analysis described in this paper should be of particular interest to laboratories that currently are investigating association and dissociation processes in nucleic acids that exhibit molecularities greater than two.