bluuebunny/crossref_metadata_2025_split huggingface dataset:
Approach to the limit of counterion condensation
Authors: Fenley Marcia O. , Manning Gerald S. , Olson Wilma K. 
Published: December 2004

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

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

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

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

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

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

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

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

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

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

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

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

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

AbstractAutomated assignment of proteins is greatly simplified using data from 3D‐nmr spectra. A strategy is presented which makes use of 3D‐TOCSY‐TOCSY and 3D‐TOCSY‐NOESY; its potential is demonstrated with the example of the spectra of BPTI.The discussion of the potential of 3D‐nmr includes the introduction of a simple graph for the description of the information content of multidimensional nmr spectra.
Antigen–antibody recognition by Fourier transform IR spectroscopy/attenuated total reflection studies: Biotin–avidin complex as an example
Authors: Barbucci R. , Magnani A. , Roncolini C. , Silvestri S. 
Published: December 2004

AbstractBiotin–avidin recognition is studied by Fourier transform ir spectroscopy/attenuated total reflection (FTIR/ATR) under physiological conditions. The ureido portion of biotin is confirmed to be involved in the interaction with avidin, as previously found, but when the biotin–avidin complex forms, an electrostatic interaction occurs between the carboxylate group of the biotin molecule and the protonated aminic end group of the avidin amino acid side chains. Comparison of the biotin–avidin system with the biotin–1, 4‐diaminobutane and biotin–tryptophan systems confirms these findings.
A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins
Authors: Wade Rebecca C. , Mazor Michael H. , McCammon J. Andrew , Quiocho Florante A. 
Published: December 2004

AbstractThe structure and activity of a protein molecule are strongly influenced by the extent of hydration of its cavities. This is, in turn, related to the free energy change on transfer of a water molecule from bulk solvent into a cavity. Such free energy changes have been calculated for two cavities in a sulfate‐binding protein. One of these cavities contains a crystallo graphically observed water molecule while the other does not. Thermodynamic integration and perturbation methods were used to calculate free energies of hydration for each of the cavities from molecular dynamics simulations of two separate events: the removal of a water molecule from pure water, and the introduction of a water molecule into each protein cavity. From the simulations for the pure water system, the excess chemical potential of water was computed to be −6.4 ± 0.4 kcal/mol, in accord with experiment and with other recent theoretical calculations. For the protein cavity containing an experimentally observed water molecule, the free energy change on hydrating it with one water molecule was calculated as −10.0 ± 1.3 kcal/mol, indicating the high probability that this cavity is occupied by a water molecule. By contrast, for the cavity in which no water molecules were experimentally observed, the free energy change on hydrating it with one water molecule was calculated as 0.2 ± 1.5 kcal/mol, indicating its low occupancy by water. The agreement of these results with experiment suggests that thermodynamic simulation methods may become useful for the prediction and analysis of internal hydration in proteins.
Topographical requirements for δ‐selective opioid peptides
Authors: Nikiforovich Gregory V. , Hruby Victor J. , Prakash Om , Gehrig Catherine A. 
Published: December 2004

AbstractThe conformational possibilities of three different δ‐selective opioid peptides, which are DPDPE magnified image, and DRE (Tyr‐D‐Met‐Phe‐His‐Leu‐Met‐Asp‐NH2, dermenkephalin), were explored using energy calculations. Sets of low‐energy conformers were obtained for each of these peptides. The sets consisted of 61 structures for DPDPE, 32 for DCFPE, and 38 for DRE, including various types of rotamers of the Tyr and Phe side‐chain groups. Comparison of the geometrical shapes of the conformers was performed for these sets using topographical considerations, i.e., examination of the mutual spatial arrangement of the N‐terminal α‐amino group, and of the Tyr and Phe side‐chain groups. The results obtained suggest a model for the δ‐receptor‐bound conformer(s) for opioid peptides. The model suggests the placement of the Phe side chain in a definite position in space corresponding to the g− rotamer of Phe for peptides containing Phe4 and to the t rotamer for peptides containing Phe.3 The position of the Tyr1 side chain cannot be specified so precisely. The proposed model is in a good agreement with the results of biological testing of β‐Me‐Phe4‐substituted DPDPE analogues that were not considered in the process of model construction.
Molecular dynamics simulation in vacuo and in solution of cyclolinopeptide A: A conformational study
Authors: Saviano Michele , Aida Misako , Corongiu Giorgina 
Published: December 2004

AbstractThe conformation of cyclolinopeptide A [c‐(Pro‐Pro‐Phe‐Phe‐Leu‐Ile‐Ile‐Leu‐Val)], a naturally occurring peptide with remarkable cytoprotective activity, has been investigated by means of molecular dynamics simulations in various molecular environments. Structural and dynamical properties have been analyzed and compared with those experimentally determined. A detailed analysis of hydrogen bonds is reported.
A molecular dynamics simulation of polyalanine: An analysis of equilibrium motions and helix–coil transitions
Authors: Daggett Valerie , Kollman Peter A. , Kuntz Irwin D. 
Published: December 2004

AbstractAn understanding of helix dynamics can aid in interpreting the motions of proteins. The conformational transitions that occur also appear to play a role in protein folding. Structural studies of isolated peptides in solution are just becoming available. However, detailed analysis of the helix–coil transition is still not available and will be difficult to obtain experimentally. For these reasons, we performed a long molecular dynamics simulation of polyalanine at high temperature. Using this approach, we obtain a description of the overall structure and inherent flexibility of the chain as well as a structural picture of the conformational changes that occur. In this way, we can address both equilibrium properties of the peptide and the dynamics and mechanism of the structural transitions. Our results correlate fairly well with the available experimental data and previous simulations aimed at addressing α‐helix dynamics. The peptide spends the bulk of its time fluctuating between different conformations with intermediate helix contents. Transitions between highly ordered and highly disordered structures were rare, but they occurred rapidly. Our distribution of conformations favored collapsed states. Hence, our transitions to structures with high helical content were from fluctuating compact structures. The conversion between helix and coil occurred sequentially on a residue‐by‐residue basis. However, there was local cooperativity; the transition of a residue to the coil state was facilitated after a neighboring group became non‐helical. The relevance of our results to protein folding is also discussed.
On the mechanism of dielectric relaxation in aqueous DNA solutions
Authors: Saif B. , Mohr R. K. , Montrose C. J. , Litovitz T. A. 
Published: December 2004

AbstractThe complex dielectric response of calf thymus DNA in aqueous saline solutions has been measured from 1 MHz to 1 GHz. The results are presented in terms of the relaxation of the incremental contributions to the permittivity and conductivity from the condensed counterions surrounding the DNA molecules. Measurements of the low‐frequency conductivity of the samples also lends support to the condensed counterion interpretation.