bluuebunny/crossref_metadata_2025 huggingface dataset:
X‐Ray crystallographic analysis of a ternary intercalation complex between proflavine and the dinucleoside monophosphates CpA and UpG
Authors: Aggarwal A. , Islam S. A. , Kuroda R. , Neidle S.
Published: December 2004

We report the crystal‐structure analysis of a complex involving the drug proflavine and the two dinucleoside monophosphates cytidylyl‐3′,5′‐adenosine (CpA) and uridylyl‐3′,5′‐guanosine (UpG). The planar drug molecule is intercalated between C ⃛G and U ⃛A Watson‐Crick base pairs, in a double‐helical fragmentlike arrangement. Sugar conformations at the 3′‐ends of the two strands are dissimilar. The backbone conformations fall within the ranges of values noted previously for dinucleoside intercalation complexes, and some correlations involving these are noted. The separation of the two strands and the basic twist angle of 16°, compared to other reported complexes, are indicative of sequence‐dependent effects of the drug binding.
Quantitative aspects of the development of a hydrophobic binding site on calmodulin by calcium binding
Authors: Steiner Robert F.
Published: December 2004

The interactive binding by calmodulin of Ca2+ and 1‐anilinonaphthalene‐8‐sulfonate (1,8‐ANS) has been examined. In the presence of saturating levels of Ca2+, calmodulin develops one moderately strong binding site for 1,8‐ANS, plus one or more weaker sites. The binding of 1,8‐ANS by unliganded, or singly liganded, calmodulin is slight; the development of a strong binding site, as well as the characteristic fluorescence enhancement and CD spectrum, requires the binding of two Ca2+ ions. Little further change occurs on binding additional Ca2+ ions.
How alike are the shapes of two random chains?
Authors: McLachlan A. D.
Published: December 2004

Two completely flexible random chains containing N atoms joined by links of length L can be superimposed by rigid‐body motions to match their structures as closely as possible. The statistics of the root‐mean‐square best‐fit distance D are discussed. For long chains, D2 tends of 0.125L2N. Thus, for a protein of 100 residues, where the Cα‐Cα distance is L = 3.8 Å, the expected root‐mean‐square atomic distance is 13.4 Å. This result gives a surprisingly good fit to the observed results for unrelated structures.
Conformation of cyclic analogs of enkephalin. II. Analogs containing a cystine bridge
Authors: Hall David , Pavitt Nicola
Published: December 2004

A systematic survey has been made, using molecular mechanics, of the conformation of the ring entity of the enkephalin analogs, [D‐Cys2‐L‐Cys5]‐enkephalinamide and [D‐Cys2‐D‐Cys5]enkephalinamide. These molecules are considerably more flexible than the analog Tyr‐cyclo(Nγ‐D‐A2bu‐Gly‐Phe‐Leu‐), but the favored conformations of all three are very similar. The results of these studies are compatible with a Gly3‐Phe4 type II′ bend in the active conformation of enkephalin.
Precollapse of T7 DNA by spermidine at low ionic strength: A linear dichroism and intrinsic viscosity study
Authors: Baase Walter A. , Staskus Paul W. , Allison Stuart A.
Published: December 2004

At low salt ([Na+] = 10−3M), spermidine is capable of transforming DNA from a highly extended random coil to a compact particle. The transition takes place at a spermidine concentration of around 25 μM and the compact particle has been previously studied in considerable detail for several different DNAs. The objective of the present study is to see what effect, if any, spermidine has on T7 DNA conformation prior to collapse using flow dichroism and intrinsic viscosity. We conclude that increasing the spermidine concentration from 0 to the collapse transition point (above 20 μM) makes DNA increasingly nondraining. Furthermore, the persistence length dropped from 785 (±42) to 560 (±32) to 445 (±26) Å on increasing the ambient spermidine concentration from 0 to 1 to 10 μM. These results are in good agreement with counterion condensation theory and Odijk's theory of the electrostatic contribution to the persistence length of DNA. Nonetheless, it is concluded that counterion condensation is not entirely responsible for DNA collapse and that crosslinking promotes the transition to the compact state.
Anisotropic rotational motions of poly(L‐glutamic acid) in the α‐helix conformation
Authors: Hahn U. , Hanssum H. , Rüterjans H.
Published: December 2004

The anisotropic rotational motion of the backbone and the side chains of poly(L‐glutamic acid) in the α‐helical structure was investigated using the 13C‐T1 and T2 relaxation times of all carbon atoms with directly attached protons, obtained at a 13C‐Larmor frequency of 67.89 MHz. The evaluation of the nmr data was carried out according to the previously derived anisotropic diffusion model, in which the macromolecule is considered a rigid rod. The rotation of the backbone is characterized by two diffusion constants, D1 and D3, describing the rotation perpendicular to and around the symmetry axis. The additional internal motion of the Cβ‐methylene group is described as a jump process with a jump rate, k1, between two allowed rotametric states. Steric considerations indicate that the occupation of the third rotameric position is forbidden. The rotation of the Cγ‐methylene group is decribed as a one‐dimensional diffusion process around the Cβ–Cγ bond. Investigation of the temperature dependence of the relaxation parameters led to the temperature dependence of the dynamic parameters. Activation energies were determined from these data. The dynamic parameters obtained for poly(L‐glutamic acid) at 291 K are compared with the corresponding results of a previous study of poly(L‐lysine).

The development of an anisotropic diffusion model for the motions of the rod‐shaped poly(L‐lysine) α‐helix and its application to the interpretation of the 13C‐relaxation data of this molecule have already been published previously. In this model, both the overall molecular tumbling and the various internal motions have been characterized by diffusion constants or jump rates typical for each process. These dynamic parameters can be calculated from the spin–lattice relaxation times, the spin–spin relaxation times and the NOE factors of the Cα, Cβ, and Cγ nuclei of the polypetide.

In the present paper, we describe the application of the above‐mentioned dynamic model to the interpretation of 13C‐relaxation studies of a further homopolypeptide, poly(L‐glutamic acid), in the α‐helical structure. Furthermore, we studied the temperature dependence of the relaxation times of this polymer and determined the anisotropic diffusion parameters at each temperature. From their temperature dependence and from comparison of our present results with the data of our previous study of poly(L‐lysine), we were able to derive new insights into the intramolecular diffusion processes and the excitation of various motions.
QELS‐SEF study on poly(lysine) in the extraordinary phase: Effect of electric field strength on the apparent diffusion coefficient
Authors: Schmitz Kenneth S. , Ramsay Donald J.
Published: December 2004

The technique of quasielastic light scattering (QELS) in the presence of a sinusoidal electric field (QELS‐SEF) was used to examine the diffusion of poly(lysine) in the extraordinary phase, which is defined by the anomalously small value in the apparent diffusion coefficient (Dapp, obtained by QELS methods) as the added salt concentration is lowered below 10 mM. Spectra were obtained for high‐molecular‐weight poly(lysine) (800,000) in 0.5 mM KCl, using a driving frequency of 90 Hz. It was observed that the linewidth, hence apparent diffusion coefficient (DSF), increased with electric field strength (E) over the range 6 < E < 30 V/cm. As might be anticipated, the asymptotic limit, DSF(E = 0), was almost numerically equivalent to Dapp at this KCl concentration. As E approached the upper limit value of 31 V/cm, the value of DSF approached the high salt (500 mM KCl) value of Dapp. These observations are discussed in terms of small‐ion dispersion effects.
Adenine residue: A normal‐coordinate analysis of the vibrational spectra
Authors: Majoube Michel
Published: December 2004

The frequencies observed for adenine in the Raman spectra of adenosine monophosphate (AMP) and biopolymers such as poly(A), DNA, and RNA are compared with those calculated for a model compound, 9‐methyladenine, in which the methyl group is taken as a unit mass concentrated on the carbon. The force field used is a Urey‐Bradley field already tested on polycrystalline adenine and its analogs D‐substituted on the nitrogens, on the carbon at position 8, and on both. Assignments for adenine residue Raman bands are proposed and discussed on the basis of observed and calculated D‐shifts. These assignments are examined, in particular, for bands common to both adenine and guanine residues by analysis of their behavior for Raman hypochromism.
Preferred solution and calculated conformations of dermorphin and analysis of structure–conformation–activity relationships in the series [A1an]‐dermorphin
Authors: Toma Flavio , Dive Vincent , Fermandjian Serge , Darlak Krzysztof , Grzonka Zbigniew
Published: December 2004

We describe the solution (1H‐nmr) and calculated conformations of the opiatelike peptide dermorphin and the analysis of structure–conformation–activity relationships in the series [Alan]‐dermorphin. We used 1H‐nmr spectroscopy to study dermorphin and its analogs [Alan]‐dermorphin (with n = 1, 2…7) dissolved in dimethylsufoxide. Conformational energy calculations using semiempirical partitioned energy function methods were then carried out on dermorphin and its [L‐Ala2]‐analog. Agreement between calculation and experiment is satisfying, both suggesting predominance of a type I β‐turn around Pro6‐Ser7 at the C‐terminus and of an extended structure in the central sequence Phe3‐Gly4‐Tyr5. Detailed analysis by step‐by‐step substitutions with Ala indicates that intraresidue interactions dominate over medium‐range interactions (between adjacent residues), although the latter may also have a noticeable influence in shaping conformations. As a general feature, the effects of substitutions on the arrangement of side chains are always larger on the succeeding residue than on the preceding residue. Almost all the variations of activity observed in the analogs can be explained from conformational changes occurring in the aromatic side chains of the biologically important Tyr1, Phe3, and Tyr5 on substitutions effected on adjacent residues (fluctuations via medium‐range interactions).
Specific assignment of resonances in the 1H‐nmr spectrum of the polypeptide toxin I from Anemonia sulcata
Authors: Gooley Paul R. , Norton Raymond S.
Published: December 2004

The assignment of a large number of resonances in the 300‐MHz 1H‐nmr spectrum of the polypeptide neurotoxin Anemonia sulcata toxin I is described. The initial identification of spin systems is made using both one‐ and two‐dimensional nmr spectra. The subsequent assignment of these spin systems to specific residues in the molecule is based largely on the observation in two‐dimensional spectra of through‐space connectivities between Hα and NH resonances from adjacent residues in the amino acid sequence. Using these techniques, the full spin systems of 22 residues are specifically assigned, together with partial assignments for a further 8. Many of the spin systems from the remaining 16 residues have been defined, although not yet specifically assigned. From the pattern of through‐space connectivities between protons from adjacent residues in the sequence, some inferences may be drawn concerning the secondary structure of this polypeptide in aqueous solution.
2′5′‐linked polynucleotides do form a double‐stranded helical structure: A result from the energy minimization study of A2′p5′A
Authors: Anukanth A. , Ponnuswamy P. K.
Published: December 2004

Experimental results on 2′5′‐linked subunit systems of nucleic acids are interpreted to substantiate the view that the 2′5′‐linked polynucleotides cannot form double‐stranded helical structures. In order to look into this aspect of the 2′5′‐linked units, as well as to make a detailed comparison between the conformational characteristics of 3′5′‐ and 2′5′‐linked systems, we carried out an exhaustive theoretical study on A2′p5′A. The method was to compute the various terms of energy contributions to a conformational state and then to minimize the total energy, permitting all the relevant dihedral angles to adjust themselves. Four hundred thirty two probable starting conformations were considered for this treatment, but we found only 10 of them to come under low‐energy states, i.e., within 5 kcal/mol energy difference with reference to the global minimum energy state. The characteristic properties of these 10 conformations were compared in detail with those previously obtained on the corresponding 3′5′‐linked subunit, as well as such units with other base sequences. As a further step, a model‐building study was undertaken. Using the backbone‐course, base‐stacking, and hydrogen‐bonding possibilities of the 10 low‐energy conformations of the dimer A2′p5′A, double‐stranded helical structures were scrutinized for the 2′5′‐linked polynucleotide. Of a few reasonable forms, a right‐handed duplex structure satisfied our requirements. We describe this new duplex, making comparisons with the standard A‐ and B‐form states of DNA. The available experimental and theoretical results on 2′5′‐linked systems are also analyzed.
Conformational properties of poly[d(G‐T)]·poly[d(C‐A)] and poly[d(A‐T)] in low‐ and high‐salt solutions: Nmr and laser Raman analysis
Authors: Jenkins Bruce G. , Wartell Roger M. , Alderfer James L.
Published: December 2004

31P‐ and 1H‐nmr and laser Raman spectra have been obtained for poly[d(G‐T)]·[d(C‐A)] and poly[d(A‐T)] as a function of both temperature and salt. The 31P spectrum of poly[d(G‐T)]·[d(C‐A)] appears as a quadruplet whose resonances undergo separation upon addition of CsCl to 5.5M. 1H‐nmr measurements are assigned and reported as a function of temperature and CsCl concentration. One dimensional nuclear Overhauser effect (NOE) difference spectra are also reported for poly[d(G‐T)]·[d(C‐A)] at low salt. NOE enhancements between the H8 protons of the purines and the C5 protons of the pyrimidines, (H and CH3) and between the base and H‐2′,2″ protons indicate a right‐handed B‐DNA conformation for this polymer. The NOE patterns for the TH3 and GH1 protons in H2O indicate a Watson–Crick hydrogen‐bonding scheme. At high CsCl concentrations there are upfield shifts for selected sugar protons and the AH2 proton. In addition, laser Raman spectra for poly[d(A‐T)] and poly[d(G‐T)]·[d(C‐A)] indicate B‐type conformations in low and high CsCl, with predominantly C2′‐endo sugar conformations for both polymers. Also, changes in base‐ring vibrations indicate that Cs+ binds to O2 of thymine and possibly N3 of adenine in poly[d(G‐T)]·[d(C‐A)] but not in poly[d(A‐T)]. Further, 1H measurements are reported for poly[d(A‐T)] as a function of temperature in high CsCl concentrations. On going to high CsCl there are selective upfield shifts, with the most dramatic being observed for TH1′. At high temperature some of the protons undergo severe changes in linewidths. Those protons that undergo the largest upfield shifts also undergo the most dramatic changes in linewidths. In particular TH1′, TCH3, AH1′, AH2, and TH6 all undergo large changes in linewidths, whereas AH8 and all the H‐2′,2″ protons remain essentially constant. The maximum linewidth occurs at the same temperature for all protons (65°C). This transition does not occur for d(G‐T)·d(C‐A) at 65°C or at any other temperature studied. These changes are cooperative in nature and can be rationalized as a temperature‐induced equilibrium between bound and unbound Cs+, with duplex and single‐stranded DNA. NOE measurements for poly[d(A‐T)] indicate that at high Cs+ the polymer is in a right‐handed B‐conformation. Assignments and NOE effects for the low‐salt 1H spectra of poly[d(A‐T)] agree with those of Assa‐Munt and Kearns [(1984) Biochemistry 23, 791–796] and provide a basis for analysis of the high Cs+ spectra. These results indicate that both polymers adopt a B‐type conformation in both low and high salt. However, a significant variation is the ability of the phosphate backbone to adopt a repeat dependent upon the base sequence. This feature is common to poly[d(G‐T)]·[d(C‐A)], poly[d(A‐T)], and some other pyr–pur polymers [J. S. Cohen, J. B. Wouten & C. L Chatterjee (1981) Biochemistry 20, 3049–3055] but not poly[d(G‐C)].
Total optical activity of agarose: Relation to observable transitions in the vacuum ultraviolet
Authors: Morris E. R. , Stevens E. S. , Frangou S. A. , Rees D. A.
Published: December 2004

The changes in optical activity that accompany and characterize the coil‐helix and helix‐coil transitions of agarose in aqueous solutions and gels have been investigated by combined quantitative analysis of data from vacuum ultraviolet circular dichroism (VUCD) and optical rotary dispersion (ORD). VUCD of agarose in the high‐temperature coil state shows a single accessible Gaussian band centered at ∼183 nm. In the helix state this band is blue‐shifted by ∼9 nm, and the intensity is increased by a factor of ∼2.6. Spectra at intermediate temperatures can be fitted to within experimental error by linear combination of coil and helix spectra, the relative proportions required providing an index of the extent of conformational ordering. ORD spectra throughout the conformational transition have a common form and differ only in absolute magnitude. The temperature course of conformational ordering derived from ORD intensity is in close agreement with the values obtained from VUCD. In both the coil and helix states the accessible VUCD band is positive, while the overall ORD is negative, indicating strong negative CD activity at lower wavelength. The ORD contribution corresponding to the positive VUCD band was calculated by Kronig–Kramers transform, and it was subtracted from the total ORD to give the residual ORD from all other optically active transitions of the molecule. In both the coil and helix states, this residual ORD could be fitted to within experimental error by a single Gaussian CD band at ∼149 nm. A negative band at this wavelength has been reported previously for agarose films, but the observed intensity, relative to that of the lower energy positive band, is substantially smaller than the fitted value under hydrated conditions. In both the coil and helix states the total optical activity of agarose, characterized by observed ORD spectra, can be matched to within experimental error by Kronig‐Kramers transform of the 149‐nm negative band and the smaller positive band at higher wavelength, with no necessary involvement of deeper‐lying transitions. The significance of this conclusion for fundamental understanding of carbohydrate optical activity is discussed.
Synthesis of peptide gels for the investigation of oligopeptide–oligonucleotide interactions
Authors: Eckstein Heiner , Hu Zheng , Schott Herbert
Published: December 2004

Peptide gels usable as protein model systems have been synthesized by a cross‐linking copolymerization of acryloyl substituted peptides with 1,4‐tetramethylene dimethacrylate. A specially adapted approach to peptide synthesis allows the removal of the amino terminal Cbo group at the end of the peptide synthesis, followed by the introduction of an acryloyl group. The polymerizable peptide monomers obtained can be transferred into insoluble peptide gels by radical copoylmerization with cross‐linking agents. After cleavage of the protecting groups of the side chains, these peptide gels can be used both as protein model systems for investigating peptide–oligonucleotide interaction and as sorbents for affinity chromatography. The preparation and characterization of the peptide gels Ala‐Lys‐Glu‐Lys‐Ala‐OMe (I), Ala‐Arg‐Glu‐Arg‐Ala‐OMe (II), Ala‐Arg‐Glu‐Lys‐Ala‐OMe (III), and Ala‐Arg‐Ala‐Lys‐Ala‐OMe (IV) as well as the conditions for the removal of the protecting groups is presented. Gel III contains the natural peptide sequence Arg‐Glu‐Lys while the other gels are analogs of this sequence.
Chiral discrimination in the energetics of formation of diastereomeric adducts involving polypeptides
Authors: Paradossi G. , Pispisa B. , Rizzo R. , Barteri M.
Published: December 2004

Chiral discrimination in the energetics of formation of diastereomeric pairs between iron (III)‐complex ions bound to poly(L‐glutamate) or poly (D‐glutamate) and L‐catecholamines was measured by differential microcalorimetry at 25°C. When the association of substrates by Fe–polypeptide systems was virtually complete, diastereomeric discrimination energies of a few hundred calories per mol were observed, while diastereomeric discrimination entropies were found to be negligibly small. These results are consistent with the finding that the overall stereoselectivity in the electron transfer reaction between the optically active catecholamines and enantiomeric iron(III) materials—corresponding to Δ(ΔG≠) values around 900 cal/mol—is largely controlled by transition state effects in the kinetics.
Conformation and aggregation of melittin: Effect of pH and concentration of sodium dodecyl sulfate
Authors: Kubota Shigeo , Yang Jen Tsi
Published: December 2004

The conformation of melittin, a surface‐active polypeptide, in solution was studied by CD spectra between 190 and 240 nm. The molecule was essentially unordered (possibly with a trace of helix) in water without salt at neutral pH. Upon deprotonation of four of the six cationic groups at pH 12 the polypeptide became partially helical (about 35%). The addition of NaDodSO4 to an aqueous melittin solution first caused the solution to become turbid but it became clear again in excess surfactant solution. The conformational changes depended on the molar NaDodSO4/melittin ratio, R. With R from 2.34 to 23.4, the melittin solution was turbid and the polypeptide conformation was probably a mixture of α‐helix and β‐sheets. This was supported by the ir spectrum of the turbid solution, which indicated the presence of both conformations. With R = 46.8 or 468 (1 or 10 mM NaDodSO4) the polypeptide conformation was characteristic of an α‐helix, about 70–80% of the molecule, regardless of whether the surfactant was above or below its critical micelle concentration. This compared well with the x‐ray results of 92% helix in crystals. The lower helicity of melittin in NaDodSO4 solution might be attributed to the end effects that destabilize the first and last turn of an helix at its N‐ and C‐terminus, respectively.
Rate constants and activation parameters for the mobility of bulk and DNA‐associated glycol–water solvents
Authors: Milton John G. , Galley William C.
Published: December 2004

The decrease in mobility of viscous glycol–water solvents when associated with native DNA is quantified from a study of the loss of the exciting‐wavelength dependence of the phosphorescence spectrum of free and bound proflavin with increasing temperature. The data are interpreted in terms of a distribution of rate constants with an Arrhenius temperature dependence. Over the temperature range of the experiments a relative decrease of ∼ 104 in the average rate constant is observed for reorientation of the solvent when associated with DNA. The basis for this large reduction is found to derive from a large decrease in the pre‐exponential factors (i.e., activation entropy) associated with the reorientation rate constants. The changes in the distribution of rate constants and the activation parameters for solvent mobility induced by DNA do not resemble the changes observed for any one of a number of small ion or molecule perturbations. The results suggest the presence of disorganized, relatively immobile solvent in association with DNA.
A positron annihilation study of hydrated DNA
Authors: Warman John M. , Eldrup M.
Published: December 2004

Positron annihilation measurements are reported for hydrated DNA as a function of water content and as a function of temperature (20 to −180°C) for samples containing 10 and 50% wt of water. The ortho‐positronium mean lifetime and its intensity show distinct variations with the degree of hydration and with temperature for the 50% sample. The 10% water sample was relatively insensitive to temperature variation. The results indicate that hydrated DNA containing up to 10% water behaves as a rigid crystalline solid but that the rigidity markedly decreases with a further increase in water content until, for approximately 50% water, its properties resemble more those of a highly viscous fluid.
Scaled particle theory applied to gels of high molecular weight DNA in the ultracentrifuge
Authors: Richard Alfred J. , Westkaemper Richard B.
Published: December 2004

Equilibrium ultracentrifugation of high molecular weight DNA at moderate centrifuge speed leads to the formation of gel at the bottom of the centrifuge cell. The swelling pressures of the gels are strongly affected by the ionic strength of the medium and by polyvalent counterions in the medium. Scaled particle theory applied to the DNA gels gives values to the effective particle length and particle radius of the DNA. Different models for DNA conformations in the gels were required for the monovalent, the divalent, and the tetravalent cations used in this study.
ψ Compaction of poly[d(AT)] · poly[d(AT)]
Authors: Shin Yong A. , Feroli Susan L. , Eichhorn Gunther L.
Published: December 2004

The compaction of poly[d(A–T)] · poly[d(A–T)] by Co(III) is accompanied by the formation of ψ(+)‐ and ψ(‐)‐structures. The chirality of the ψ‐structure depends on the Co(III) concentration, ionic strength, temperature, pH, and the chain length of the polymer. The two forms can be readily interconverted by manipulating these factors. Phase diagrams have been constructed that demonstrate the regions of stability of the enantiomers as a function of two variables, while other factors are held constant. At critical points in the phase diagram the two forms are in such unstable equilibrium that mechanical motion will cause ψ(+) ⇆ ψ(‐) interconversion. The formation of both ψ(+)‐ and ψ(‐)‐structures by the action of Co(III) on poly[d(A–T)] · poly[d(A–T)] contrasts markedly with the behavior of poly[d(G–C)] · poly[d(G–C)] in similar circumstances by forming only the ψ(+)‐structure and that of native DNA to produce no ψ at all. Thus the base sequence is important in determining the structure of chirally associated DNA molecules.
Helix → β conformational transition of poly(L‐lysine) on dye binding
Authors: Scaria P. V. , Atreyi M. , Rao M. V. R.
Published: December 2004

Binding of an azo dye, 4′‐dimethyl amino azo benzene‐4‐carboxylic acid (DAAC) to poly(L‐lysine) (PLL) in basic aqueous solutions at 20°C has been studied. The azo dye was found to bind to PLL when its side‐chain amino groups are in the uncharged state. This was found to be a cooperative phenomenon, and the binding constant and cooperativity factor have been evaluated. The binding of the dye was found to result in a conformational transition of PLL from the α‐helix to the β‐sheet, which in turn helps in increased dye binding.
Local sequence patterns of hydrophobicity and solvent accessibility in soluble globular proteins
Authors: Lipman David J. , Pastor Richard W. , Lee B.
Published: December 2004

We examined the variation in the solvent accessibility and hydrophobicity of the amino acids along the sequences of 58 soluble globular proteins with known tertiary structure. We found that there is a significant tendency for the accessibilities to run in clusters along the sequence but that the hydrophobicities are distributed without such nonrandom clusters. Theseresults suggest severe limitations on the power of sequence analysis tools that use average hydrophobicity scores of overlapping subsequences to predict accessibility.
A model of the hydrodynamic behavior of irradiated DNA: Dependence on molecular conformation
Authors: Ostashevsky Joseph Y. , Lange Christopher S.
Published: December 2004

The model presented here describes the DNA viscosity and viscoelastometric responses to ionizing radiation‐induced molecular breakdown. Four DNA conformations are considered: (1) linear chain, (2) relaxed circle, (3) supercoiled circle, and (4) supercoiled linear. The model includes the systems of differential equations for calculating the size distributions of DNA molecules as functions of dose. Thedistributions are used in the usual hydrodynamic formulae for heterogeneouspopulations of polymer molecules. The sensitivity of viscoelastometry for the estimation of D37 is better than that of viscometry. The model predicts a considerable difference between the radiation responsesof linear and circular DNAs. The prediction is confirmed by experimental data for T4 DNA [C. S. Lange et al. (1984) Rad. Res. 100, 1–15] and E. coli DNA [S. E. Bresler et al. (1984) Biophys. J. 45, 749–754]. Thus, ionizing radiation can be used to determine the original conformation of DNA molecules.
Solid‐state conformations of α‐Aminoisobutyryl‐L‐prolyl sequences: Crystal structure of Boc‐Aib‐L‐Pro‐OBzl
Authors: Kawai Masao , Butsugan Yasuo , Fukuyama Keiichi , Taga Tooru
Published: December 2004

The protected dipeptide Boc‐Aib‐Pro‐OBzl, C21H30N2O5, crystallizes in the orthorhombic space group P212121, with a = 12.820, b = 10.529, c = 16.548Å, and Z = 4. The crystal structure has been solved by direct methods and refined to an R value of 0.074 for 1352 reflections. The Boc‐Aib‐Pro‐OBzl molecule has been shown to adopt an unfolded conformation in the solid state with ϕAib = 50.5°, ΨAib = 45.3°, ϕPro = −64.6°, and ΨPro = 148.1°. The result is in marked contrast with the reported crystal structure of Cbz‐Aib‐Pro‐NHMe, which adopts an intramolecularly hydrogen‐bonded β‐turn conformation. Comparison with 13 reported conformations of Aib‐Pro sequences in the crystalline state revealed that the Aib‐Pro sequence adopts an unfolded conformation if the residue that immediately follows the dipeptide sequence possesses no hydrogen available for hydrogen bonding, while a β‐turn conformation is preferred if the Pro residue is followed by an NH group. Correlation between pyrrolidine ring puckering of the Pro residue and main‐chain conformation in Aib‐Pro sequences is discussed.
On the CD helix band for long helical polymers
Authors: Rabenold David A. , Rhodes William
Published: December 2004

The CD helix bands for infinitely long helical polymers are shown tobe composed of two parts: a derivative‐shaped band plus an ordinary Gaussian‐like band. The derivative‐shaped band results from the zero‐order term of an expansion while the Gaussian‐like band results from the first‐order expansion term. However, the intensities of the two bands are shown to be of the same order of magnitude. They are both linear in the coulombic coupling of transition charge densities for polymer transitions. The sum yields a skewed derivative‐shaped band. The shapes of net CD helix bands are shown to not depend on the approximations used for averaging over orientations if the usual systems, such as polypeptides and polynucleotides, are considered in their long‐wave‐length spectral regions.
Vibrational spectroscopic analysis of LD‐sequential, bacterial cell wall peptides: An IR and raman study
Authors: Naumann Dieter , Labischinski Harald , Rönspeck Wolfgang , Barnickel Gerhard , Bradaczek Hans
Published: December 2004

The synthetic, zwitterionic bacterial cell wall peptides—D‐Gluγ‐L‐Lys, D‐Gluγ‐L‐Lys‐D‐Ala, D‐Gluγ‐L‐Lys‐D‐Ala‐D‐Ala, and L‐Ala‐D‐Gluγ‐L‐Lys‐D‐Ala‐D‐Ala—have been investigated in the crystalline and aqueous solution state applying ir and Raman spectroscopy. Additionally, aqueous solutions of the tetra‐ and pentapeptide have been investigated by CD spectroscopic techniques. Apart from the dipeptide, whose spectral features were dominated by end‐group vibrations, the corresponding ir and Raman active bands of the crystalline peptides in the amide and skeletal regions were found at similar wave numbers, thus suggesting an analogous three‐dimensional structure of these compounds. Dominant amide A, I, II, and III bands near 3275, 1630, 1540, and 1220–1250 cm−1, respectively, in the ir are interpreted in favor of an intermolecularly hydrogen‐bonded, β‐like structure. The absence of any amide components near 1680–1690 cm−1, together with the presence of strong amide bands near 1630 cm−1, and weak bands near 1660 cm−1 in the ir, which, conversely, were found in the Raman spectra as weak and strong bands, but at corresponding wave numbers, is taken as strong evidence for the presence of the unusual, parallel‐arranged β‐structure. On the basis of comparative theoretical considerations, a parallel‐arranged, “β‐type ring” conformation [P. De Santis, S. Morosetti, and R. Rizzo (1974) Macromolecules 7, 52–58] is hypothesized. The solubilized peptides exhibited distinct similarities with their crystalline counterparts in respect to frequency values and relative intensities of the corresponding ir and Raman‐active amide I/I′ components, and of some Raman bands in the skeletal region. This is interpreted in terms of residual short‐range order, persisting even in aqueous solution. We concluded that the peptides show a strong propensity to form hydrated, strongly associated aggregates in water. On the basis of amide I/I′ band positions, stable, intramolecular interactions via the amide groups are discarded for the solubilized peptides. Complementarily, the CD data obtained suggest the presence of weakly bent, “open‐turn”‐like structures for the tetra‐ and pentapeptide in aqueous solution.
Dynamic properties of oxy‐ and carbonmonoxyhemoglobin probed by optical spectroscopy in the temperature range of 300–20 K
Authors: Leone Maurizio , Cupane Antonio , Vitrano Eugenio , Cordone Lorenzo
Published: December 2004

We have studied the absorption bands of oxy‐ and carbonmonoxyhemoglobin in the wavelength range of 650–350 nm (visible and Soret bands) and in the temperature range of 300–20 K. The spectra in the whole temperature range have been successfully deconvoluted in terms of gaussian components. The analysis of the temperature dependence of the first and second moment of the bands enables us to compare dynamic properties of the heme group in oxy‐ and carbonmonoxyhemoglobin. The results of the analysis indicate that the “mean‐effective” frequency of the nuclear motion coupled to the electronic transition responsible for the visible bands is higher in carbonmonoxy‐ than in oxyhemoglobin. The possible functional relevance of this finding is discussed.
CD studies of synthetic polypeptides as histone models: Poly(L‐Arg‐L‐Ile‐Gly), poly(L‐Arg‐L‐Nva‐Gly), and poly(L‐Arg‐L‐Nle‐Gly)
Authors: Tsikaris Vassilios , Sakarellos‐Daitsiotis Maria , Sakarellos Constantinos , Marraud Michel
Published: December 2004

Sequential polypeptides (L‐Arg‐X‐Gly)n were prepared as synthetic models of arginine‐rich histones to study their structure and their stereospecific interactions with DNA. In our previous work the conformational characteristics of poly(L‐Arg‐L‐Ala‐Gly), poly(L‐Arg‐L‐Val‐Gly), and poly(L‐Arg‐L‐Leu‐Gly) have already been analyzed. To obtain further insight into the influence of the X residue side chain on the conformation of the (L‐Arg‐X‐Gly)n polytripeptides, we now report their synthesis and cd properties when X represents the amino acid residues Ile, Nva, and Nle. The pentachlorophenyl active esters of the appropriate tripeptides were used to perform the polymerization, and the toluene‐4‐sulfonyl group was used to protect the arginine guanido group. CD spectroscopy showed that, in 100% trifluoroethanol, the degree of helical conformation increased in the order Ile → Nle → Nva. An equilibrium between β‐turn, α‐helix, and random‐coil conformers occurred in 100% hexafluoroisopropyl alcohol, while a rise in the temperature or the addition of water favored the α‐helix, the highest percentage of which was observed in a mixture of hexafluoroisopropyl alcohol: water (20 : 80) and in the order Ile → Nle → Nva. In aqueous solutions (at pH 7 and 12) the polymers behaved as a random coil, but they were forced to a less aperiodic structure, over a range of ionic strengths (0–0.5M NaF). A rise in temperature of up to 70°C in 100% trifluoroethanol resulted in a decrease of the α‐helix percentage of the polymers, while in aqueous solutions the aperiodic structure decreased with increasing temperature. This study proved the importance of the nature of the X residue (length, Cβ branching) in relation to the structural order of the sequential polypeptides. We concluded that the polymers prepared are suitable models for arginine‐rich histones.
Helical formation of a 13‐residue C‐peptide analogue of ribonuclease a in sodium dodecyl sulfate solution
Authors: Wu Chuen‐Shang C. , Yang Jen Tsi
Published: December 2004

The conformation of a 13‐residue C‐peptide analogue of ribonuclease A——in surfactant solutions was studied by CD. The CD spectrum of the peptide in excess NaDodSO4 solution was typical for a helical conformation; the spectrum appeared to be virtually independent of pH (2.5–6) and temperature (3–25°C). Analysis of the CD data indicated a helicity of about 65–70% with no α‐sheet and β‐turn; this corresponded to 8 or 9 residues in the helical form or slightly more than two turns of α‐helix. This compares with an average of about one turn of α‐helix for the C‐peptide analogue in water at pH 4.7 and 7°C. The conformation of the peptide in cationic surfactant, dodecyl ammonium chloride, and nonionic surfactant, dodecyl heptaoxyethylene ether, solution resembled that in water. We concluded that the C‐peptide analogue can develop a maximum helicity close to the corresponding segment in ribonuclease A in hydrophobic environment provided by the clustering of NaDodSO4 molecules to the cationic side groups of the peptide, except that the end effects may destabilize two or three residues each at both ends of the helix. Thus, in the interior of a protein molecule this hydrophobic effect may overshadow the charged‐group effect than can be explained by the helix dipole model for the helical segments on the exterior of the protein molecule.
Polarized raman scattering from oriented single microcrystals of d(A5T5)2 and d(pTpT)
Authors: Patapoff Thomas W. , Thomas Gerald A. , Wang Yang , Peticolas Warner L.
Published: December 2004

Polarized Raman spectra have been obtained from single microcrystals of the duplex of the decamer d(A5T5)2 using a Raman microscope. This is the first report of Raman spectra from a crystal of a deoxyoligomer that contains only long, nonalternating sequences of adenine and thymine. Sequences containing d(A)n and d(T)n are of interest in view of recent suggestions that they induce bends in DNA and that they might exist in a nonstandard B‐conformation. Polarized Raman spectra of a crystal of d(pTpT) have also been obtained. Both crystals display Raman bands whose intensities are very sensitive to the orientation of the crystal with respect to the direction of polarization of the incident laser beam. These spectra indicate that the helical axes of the oligonucleotides are parallel to the long axes of the crystals and that the d(A5T5)2 is not appreciably bent in the crystal. The Raman spectrum from the d(pTpT) crystal indicates that all of the furanose ring puckers are in a C2′‐endo configuration since only the C2′‐endo marker band at 835 ± 5 cm−1 is present. Crystals of d(A5T5)2 show measurable Raman intensities in both the 838‐ and 816‐cm−1 bands. This indicates the presence of both the C2′‐endo and C3′‐endo, or possibly other non‐C2′‐endo, furanose conformations. The 816‐cm−1 band is weak so that only a small fraction of the residues are estimated to be in the non‐C2′‐endo conformation. In both the d(pTpT) and d(A5T5)2 crystals the intensity of the bands due to vibrations of the backbone show only a small dependence on orientation of the crystals. This result is explained by the low symmetry of the puckered sugar rings. It is concluded that Raman spectra obtained from oligonucleotide crystals in which the orientation of the crystal axes to the laser polarization is not carefully controlled may contain intensity artifacts that are due to polarization effects.
A 2H‐nmr study of the DNA hydration water in solid li‐DNA assemblies
Authors: Brandes Rolf , Kearns David R. , Rupprecht Allan
Published: December 2004

High‐resolution 2H‐nmr is employed to monitor the D2O in hydrated solids of Li‐DNA prepared from solution by three different methods: lyophilization, slow evaporation of the water, and wet spinning in alcohol. From the spectral shapes and spin–spin relaxation measurements, the DNA in the lyophilized samples is found to be locally ordered with a domain size of ∼ 0.4 μm. Much longer range macrosopic ordering is found in samples prepared by slow evaporation of the water. Here the DNA spontaneously assembles into a structure that is probably cholesteric, in which the pitch axis is perpendicular to the plane on which the DNA dried. The wet‐spinning method produces macroscopically, uniaxially oriented DNA molecules with a maximum helix axis disorder of 12°. To aid in the comparison between calculated and experimental line shapes, a two‐dimensional technique is employed to separate the contributions to the line width arising from DNA static disorder, magnetic inhomogeneities, and spin–spin relaxation.
Structure–Activity relationship of tetrapeptides related to dermorphin: A 500‐MHz 1H‐nmr study
Authors: Castiglione‐Morelli M. A. , Tancredi T. , Trivellone E. , Balboni G. , Marastoni M. , Salvadori S. , Tomatis R. , Temussi P. A.
Published: December 2004

Several tetrapeptide analogs of dermorphin have been studied by means of 1H‐nmr spectroscopy at 500 MHz in DMSO‐d6. In spite of the unfavorable properties of the solvent, it is possible to extract key structural information that, combined with the biological activity of the peptides, yields a structure–activity relationship that is consistent with our model of the μ receptor site. In particular, the importance of the orientation of the aromatic ring of the third residue, hypothesized in the theoretical model, is now substantiated. The shape of the P subsite of the receptor is also indirectly defined by the shape of several bulky side chains of the third residue.
Dynamic light‐scattering study of synthetic myosin filaments
Authors: Mochizuki‐Oda Noriko , Fujime Satoru
Published: December 2004

Synthetic myosin filaments of rabbit were prepared. Electron microscopy showed that the number‐average length (Ln = 470 nm) and sharpness in length distribution (Lw/Ln = 1.036) were independent of ionic strengths of 134, 74, and 44 mM, whereas the number ratio of M‐filaments (about 15 nm in diameter at the bare zone) to m‐filaments (about 10 nm) strongly depended on ionic strength (IS); the major filaments were M‐filaments at IS = 134 mM, m‐filaments at IS = 74 mM, and almost exclusively m‐filaments at IS = 44 mM. Dynamic light scattering showed that the change in diameter with the change in ionic strength by 2‐h dialysis was reversible. Combination of dynamic light scattering and sedimentation studies suggested a dynamic equilibrium between M‐ and m‐filaments. Dynamic light‐scattering spectra at IS = 134 and 74 mM could be analyzed by a theory for rigid rods, whereas those at IS = 44 mM only by introducing semiflexibility of filaments; m‐filaments are more flexible at IS = 44 than at 74 mM.
The amplitude of local angular motions of intercalated dyes and bases in DNA
Authors: Schurr J. Michael , Fujimoto Bryant S.
Published: December 2004

The orientation of ethidium dye in DNA and the amplitude of its local internal angular motion are estimated from fluorescence polarization anisotropy and reduced linear dichroism data. When the local internal motion is assumed to be isotropic, the acceptable range of polar angles of the transition dipole is ϵ = 70°−72°, and the acceptable range of root mean squared (rms) amplitudes of local internal motion is 〈δϵ2〉1/2 = 6.9°–8°, in agreement with earlier estimates. The nmr relaxation data reported by Kearns and co‐workers for the imino protons of duplex (dAdT)26.5 and (dGdC)30 are analyzed using recent theoretical results for flexible filaments. For typical, or reasonable, assumed geometrical parameters, large rms amplitudes of local internal motion of the bases are not required to be superimposed on the collective motions due to twisting and bending deformations. For the particular geometrical parameters considered herein, rms amplitudes greater than about 12° are precluded by the data, but values as low as 0° are not. The low precision of present knowledge about solution structures does not allow a definitive statement about the rms amplitudes of local angular motion of the bases to be made independent of any structural or geometric assumptions.
High‐Resolution solid‐state 13C‐nmr of peptides: A study of chain‐length dependence for 310‐helix formation
Authors: Saitô Hazime , Tabeta Ryoko , Formaggio Fernando , Crisma Marco , Toniolo Claudio
Published: December 2004

High‐resolution solid‐state 13C‐nmr spectra of two series of fully protected oligopeptides, Z‐(Aib)n‐OMe (n = 3−8) and Z‐(Aib)n‐L‐Leu‐(Aib)2‐OMe (n = 0−5), were recorded to gain insight into main‐chain length dependence for 310‐helix formation. We found that all the oligopeptides examined adopt an incipient or a fully developed 310‐helical structure, as judged from the characteristic splitting of the Cβ signals as well as the conformation‐dependent displacements of the Cα and CO peaks.
17O‐nmr studies of the conformational and dynamic properties of enkephalins in aqueous and organic solutions using selectively labeled analogues
Authors: Sakarellos Constantinos , Gerothanassis Ioannis P. , Birlirakis Nicolaos , Karayannis Theodoros , Sakarellos‐Daitsiotis Maria , Marraud Michel
Published: December 2004

The synthesis of Leu‐enkephalin selectively 17O‐enriched in Gly2 and Gly3 is reported. The 17O‐nmr chemical shifts of [17O‐Gly2, Leu5]‐ and [17O‐Gly3, Leu5]‐enkephalins in H2O are almost identical and independent of the pH. Since hydrogen bonding is the dominant factor governing the chemical shifts of the peptide oxygen, it can be concluded that the hydration state of both oxygens is identical and independent of the pH. The 17O chemical shifts of the [17O‐Leu5]‐enkephalin terminal carboxyl group at pH ∼ 1.9 and 5.6 are very different in H2O but very similar in CH3CN/DMSO (4:1) solution. This suggests that the protonation state of the carboxyl group at both pH values in CH3CN/DMSO solution is the same and consequently that Leu‐enkephalin exists in the neutral form at pH ∼ 5.6. In this organic mixed solvent system both Gly2 and Gly3 oxygen resonances exhibit a significant shift to high frequency by the same extent (Δδ ∼ 30 ppm). It is concluded that both peptide oxygens are not hydrogen bonded to an appreciable extent and that no specific 2 ← 5 hydrogen bonding exists to an appreciable extent. This conclusion is in agreement with the energy of activation for molecular rotation, as determined from T1 measurements, which was found to be almost identical for both [17O‐Gly2, Leu5]‐ and [17O‐Gly3, Leu5]‐enkephalins in CH3CN/DMSO (4:1) mixed solvent.
Conformationally constrained tachykinins: N‐methylated analogues of neurokinin A
Authors: Rovero P. , Pestellini V. , Patacchini R. , Santicioli P. , Maggi C. A. , Meli A.
Published: December 2004

Limited conformational constraints have been introduced in the sequence of the C‐terminal fragment of the peptide neurotransmitter neurokinin A by N‐methylation of individual peptide bonds, and the biological activities of the peptides thus obtained were evaluated in order to assess the effect of such conformational constraint on receptor selectivity. The analogue methylated in position 7 shows enhanced selectivity toward NK‐1 receptor.