bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrophobic interaction between globin helices
Authors: Weaver David L. 
Published: December 2004

AbstractThe interhelical interfaces have been examined in seven high‐resolution globin chains. The profiles of hydrophobic contact, as measured by the residue solvent‐accessible area loss upon folding, have been calculated. The seven globins studied differ in their overall loss of solvent‐accessible area upon packing of their helices, the order being 1MBD > 1LH1 > 1ECD > 2MHBB > 2HHBB > 2HHBA > 2MHBA, which gives a measure of the difference in stability due to the hydrophobic interaction. The five helix‐pair packings (AH, BE, BG, FH and GH) examined in detail have qualitative similarities. There are, however, substantial quantitative differences both at the equivalent residue level and at the level of overall helix–helix contact, which has significance in some models of folding. The AH pair has the most uniform area loss over the seven globins and the largest variation in accessible area loss on packing among the five helix pairs is the GH pair. The set of residues required to produce the globin fold has been deduced from the residue area losses.
Crystal and molecular structure of the depsipeptide ionophore Hexadecaisoleucinomycin, cyclo‐[‐(D‐Ile‐L‐Lac‐L‐Ile‐D‐Hyi)4‐] (C80H136N8O24)
Authors: Pletnev V. Z. , Ivanov V. T. , Langs D. A. , Strong P. , Duax W. L 
Published: December 2004

AbstractThe crystal structure of a synthetic depsipeptide ionophore hexadecaisoleucinomycin, cyclo[‐(D‐Ile‐L‐Lac‐L‐Ile‐D‐Hyi)4‐] (C80H136N8O24), has been determined by single crystal x‐ray diffraction techniques. The crystals are orthorhombic, space group P212121, number of molecules per unit cell z = 4, and cell parameters a = 11.195, b = 17.853, c = 54.835 Å. The values of the standard ( R) and weighted ( Rw ) discrepancy factors after refinement are 0.122 and 0.135, respectively. The structure is characterized by an elongated bracelet form with a twofold axis of pseudosymmetry. It is stabilized by eight intramolecular 4 → 1 hydrogen bonds between the amide CO and NH groups. The ester carbonyls are directed toward the inside of the molecule, their oxygen atoms forming an ellipsoidal internal cavity. The side chains are located on the molecular periphery. The conformational states of hexadecaisoleucinomycin in solution are discussed in the light of the data obtained.
Presence of a thermostable domain in the helical part of the type I collagen molecule and its role in the mechanism of triple helix folding
Authors: Burjanadze Tengiz V. , Bezhitadze Manama O. 
Published: December 2004

AbstractA study has been done of the effect of neutral salts (NaCl and CaCl2) on the mechanism of type I collagen triple helix folding and unfolding in concentrated acetic acid solutions (2–8.8M). It is shown that in these conditions, thermoabsorption and secondary structure change in heated solutions proceed in two consecutive stages. Salts exert a different destabilizing effect on different sites of the macromolecule, promoting the detection of a thermostable domain. The presence of a thermostable domain permits one to carry out reversible denaturation of collagen and to study the mechanism of the triple helix folding. Proceeding from the mechanism of the triple helix folding, an assumption has been made on the localization of the thermostable domain and its biological role.
Aggregates and other particles as the origin of the “extraordinary” diffusional phase in polyelectrolyte solutions
Authors: Ghosh Snehasish , Peitzsch Robert M. , Reed Wayne F. 
Published: December 2004

AbstractThe “extraordinary” diffusional phase (EP) at low ionic strength, and the conditions for 1 its removability by filtration were investigated for dilute solutions of the following linear polyelectrolytes: poly(L‐lysine), heparin, chondroitin‐6‐sulfate, hyaluronate, polystyrene sulfonate, and variably ionized polyacrylamide. The EP was not present for all the different types studied, and for heparin, for example, the phase was present only for samples from certain sources. In all cases the phase was removable by filtration through sufficiently small pore‐size membranes. Once filtered, the EP remained absent for over one week. It is concluded that the extraordinary diffusional phase consists of fairly stable polyelectrolyte aggregates, and sometimes also includes other very small particulate impurities. These aggregates and other small particles are thought to be present, or at least nascent, in the dry polyelectrolyte material, so that their properties may depend critically on the manner in which such dry material is produced. Tests for “reversibility” of the EP by cycling between high and low Cs by dialysis further confirm these conclusions. The evidence is thus against the EP representing any type of temporal aggregates or local ordering, at least for the linear polyelectrolytes studied in this work Rather, due to the extremely feeble scattering of ordinary polyelectrolytes at low ionic strength, the weak scattering from residual aggregates and other particles, not removed by ordinary filtration and centrifugation procedures, give autocorrelable scattering signals with long decay times. The “loss” of the extraordinary phase as ionic strength increases appears to be due simply to the weak EP scattering signal getting buried in the sharply increasing scattering from the ordinary polyelectrolyte phase. Model calculations based on experimental data support this latter conclusion. © 1992 John Wiley & Sons, Inc.
The electrostatic potential for the phosphodiester group determined from X‐ray diffraction
Authors: Klooster W. T. , Craven B. M. 
Published: December 2004

AbstractThe charge density distribution in the crystal structure of ammonium dimethylphosphate at 123 K has been determined from x‐ray diffraction data (MoKα) using 8437 reflections with sin θ/λ < 1.33.Å−1 [NH · (CH3)2PO, Mr = 143.08, monoclinic, P21/c, a = 10.007(1), b = 6.926(1), c = 9.599(2) Å, β = 105.40(1) °, V = 641.4(3) Å3, Z = 4, F000 = 304, Dx = 1.4815 g· cm−3, µ = 3.726 cm−1]. Least‐squares structure refinement assuming Stewart's rigid pseudoatom model (variables including Slater‐type radial exponents and electron populations for multipole terms extending to octapoles for C, N, O, and P, and dipoles for H) gave R(F2) = 0.039 for all reflections. The dimethylphosphate anion is in the gauche‐gauche conformation and has approximate twofold symmetry. One phosphoryl O atom forms three hydrogen bonds and the other forms one. Neither of the ester O atoms is hydrogen bonded. For the dimethylphosphate anion isolated from the crystal structure, a map of the electrostatic potential obtained using the pseudoatom charge parameters shows that the phosphoryl O atoms are considerably more electronegative than the ester O atoms. The electrostatic potential distribution obtained in this way has been fitted by least squares to a system of atom‐centered point charges. The potential calculated from these point charges agrees with the experimental result. It also agrees reasonably well with potentials obtained from three other systems of point charges that are widely used as part of the semiempirical force field for molecular mechanics and molecular dynamics calculations involving nucleic acids. © 1992 John Wiley & Sons, Inc.
α‐Elastin coacervate as a protein liquid membrane: Effect of pH on transmembrane potential responses
Authors: Kaibara K. , Sakai K. , Okamoto K. , Uemura Y. , Miyakawa K. , Kondo M. 
Published: December 2004

AbstractA protein liquid membrane composed of coacervated α‐elastin, a chemical fragmentation product of the biological elastic fiber protein, functioned as an amphoteric liquid ion‐exchange membrane. Ionic permselectivities of the α‐elastin coacervate membrane to a series of metal chlorides were investigated for the concentration‐cell systems by the ordinary electrochemical measurements. Effects of pH on the transmembrane potential responses for NaCl, CaCl2, and MgCl2 systems were examined. Only in the Ca2+ ‐containing system did potential responses stay at constant levels against the pH changes, whereas in the other systems, increasing pH caused potential changes, indicating a improvement of cationic permselectivity across the α‐elastin coacervate membrane. It was suggested that the characteristic Ca2+ transport mechanisms across the α‐elastin coacervate membrane are related in some way to the polypeptide backbone interactions specific and selective to Ca2+ ions. © 1992 John Wiley & Sons, Inc.
Salt bridge induced changes in the secondary structure of ionic polypeptides
Authors: Ismail Ashraf A. , Mantsch Henry H. 
Published: December 2004

AbstractThe carboxylate‐containing homopolypeptides poly(L‐glutamate) [poly(Glu)] and poly(L‐aspartate) [poly(Asp)] were found to form different types of ordered structures in the presence of poly(L‐lysine) [poly(Lys)]. Mixing poly(Glu) with poly(Lys) in aqueous solution at neutral pH results in the instantaneous formation of a gel‐like precipitate. The secondary structure of the gel precipitate can be best described as intermolecular antiparallel β‐strands, involving the backbone amide groups, as evidenced by the presence of characteristic amide I bands in the ir spectrum at 1684 and 1612 cm−1. Mixing poly (Asp) with poly(Lys) under identical conditions results in the formation of a fine precipitate with a different morphology. Examination of the ir spectrum of the precipitate revealed that unlike poly(Glu), poly (Asp) did not yield any discrete secondary structure upon precipitation with poly(Lys). Addition of solutions containing Ca2+ or Mg2+ to the poly (Glu)/poly (Lys) aggregates resulted in complete dissolution of the gel, with the disappearance of the ir bands characteristic of the intermolecular hydrogen‐bonded network. The results demonstrate the importance of salt bridges in establishing strong hydrogen bonds between the backbone amide groups. Reaggregation occurred upon heating the poly (Glu)/poly (Lys) mixture in the presence of Ca2+, but not in the presence of Mg2+ ions. In the presence of Ca2+ ions, aggregation and formation of an extended hydrogen‐bonded network occurred upon heating. The aggregates formed upon heating poly (Glu)/poly (Lys) in the presence of Ca2+ were attributed solely to complexation of Ca2+ to the carboxylate groups of poly (Glu) with poly (Lys) remaining free in solution. Dissolution of the aggregate could be accomplished through addition of Mg2+ at room temperature. © 1992 John Wiley & Sons, Inc.
Facilitated synthesis of peptaibols: Alamethicin via enzymatic segment condensation
Authors: Slomczynska Urszula , Zabrocki Janusz , Kaczmarek Krzysztof , Leplawy Miroslaw T. , Beusen Demise D. , Marshall Garland R. 
Published: December 2004

AbstractWe have used a combined chemical‐enzymatic approach to facilitate the total synthesis of the 20‐residue peptaibol, alamethicin. The 1–11 segment of alamethicin, having a C‐terminal Gly, and the 12–20 segment, having an N‐terminal Leu, were prepared by well‐established chemical methods, and then coupled using papain to afford a 54% yield of alamethicin in straightforward fashion. In contrast to the reported chemical syntheses of alamethicin requiring side‐chain protection at Glu, 18 the papain‐catalyzed coupling proceeded readily and selectively using a C‐terminal segment having a free γ‐carboxyl group at this position. Several alamethicin partial sequences were obtained via enzymatic formation of the Gly 11−Leu12 bond. The high efficiency of this route is illustrated by the enzymatic assembly of the 1–17 alamethicin fragment on a 400–mg scale in 62% yield. An alternative route to alamethicin through enzymatic formation of the Ala6−Gln7 bond was less successful because of a low yield in the final coupling. © 1992 John Wiley & Sons, Inc.
Conformational properties of oxytocin in dimethyl sulfoxide solution: NMR and restrained molecular dynamics studies
Authors: Bhaskaran R. , Chuang Li‐Chin , Yu Chin 
Published: December 2004

AbstractThe conformation of oxytocin, the neurohypophyseal nonapeptide hormone, in solution in deuterated dimethyl sulfoxide has been determined by 1H‐nmr. The structural determination is based on the experimental data set of nuclear Overhauser effect restraints. Obtained after the restrained molecular dynamics simulation on an initial structure of extended conformation, five resultant structures satisfy the experimental restraints well. These structures resemble that of the crystal structure of deamino‐oxytocin, an analogue of oxytocin, in terms of a close correlation observed both at two β‐turn regions of the 20‐membered tocin ring and at the tripeptide tail end. Based on this comparison and analysis of restrained molecular dynamics trajectories, we found that, although the turns are stabilized by the formation of hydrogen bonds, the oxytocin molecule possesses a slight twist in DMSO solution relative to the orientation of deamino‐oxytocin in the crystalline state. Analyses of oxytocin conformation indicate that the tripeptide tail is more flexible than the tocin ring. © 1992 John Wiley & Sons, Inc.
Volume changes correlate with entropies and enthalpies in the formation of nucleic acid homoduplexes: Differential hydration of A and B conformations
Authors: Rentzeperis Dionisios , Kupke Donald W. , Marky Luis A. 
Published: December 2004

AbstractWe have used a combination of densimetric, calorimetric, and uv absorption techniques to obtain a complete thermodynamic characterization for the formation of nucleic acid homoduplexes of known sequence and conformation. The volume change ΔV accompanying the formation of four duplexes was interpreted to reflect changes in hydration based on the electrostriction phenomenon. In 10 mM sodium phosphate buffer at pH 7, the magnitude of the measured ΔV's ranged from −2.0 to +7.2 ml/mol base pair and followed the order of poly(rA) · poly(dT) ∼ poly(dA) · poly(dT) < poly(rA) · poly(dU) ∼ poly(rA) · poly(rU). Inclusion of 100 mM NaCl in the same buffer gave the range of −17.4 to −2.3 mL/mol base pair and the following order: poly(dA) · poly(dT) < poly(rA) · poly(dT) < poly(rA) · poly(rU) ∼ poly(rA) ∼ polyr(dU). Standard thermodynamic profiles of forming these duplexes from their corresponding complementary single strands indicated similar free energies that resulted from the compensation of favorable enthalpies with unfavorable entropies along with a similar counterion uptake at both ionic strengths. The differences in these compensating effects of entropy and enthalpy correlated very well with the volume change measurements in a manner suggesting that the homoduplexes in the B conformation are more hydrated than are those in the A conformation. Moreover, the increased thermal stability of these homoduplexes resulted from an increase in the salt concentration corresponding to larger hydration levels as reflected by the ΔV results. © 1993 John Wiley & Sons, Inc.
Temperature‐Induced conformational transition in xanthans with partially hydrolyzed side chains
Authors: Christensen Bjørn E. , Knudsen Kenneth D. , Smidsrød Olav , Kitamura Shinichi , Takeo Kenichi 
Published: December 2004

AbstractThe conformational properties of xanthans with partially hydrolyzed side chains were in vestigated by optical rotation, CD, and differential scanning calorimetry (DSC). All variants displayed the well‐known temperature‐driven, cooperative order–disorder transition, and both optical rotation and DSC showed that the transition temperature was essentially independent of the content of terminal β‐mannose. It was found that up to 80% of the changes in the specific optical rotation accompanying the transition reflects conformational changes linked to the terminal β‐mannose in the side chains. Modification of the sidechains also affected the CD when xanthan was in the ordered state, but in this case the data suggest that the glucuronic acid is the major component determining the magnitude of the CD signal. DSC measurements showed that the transition enthalpy (ΔHcal) increased linearly with the fraction of β‐mannose, again indicating that a significant part (up to 80%) of ΔHcal reflects conformational changes in the side chains. The conformational transition of the xanthan variants generally showed a higher degree of cooperativity (sharper transition) than unmodified, pyruvated xanthan. Calculation of the cooperativity parameter σ by means of the Zimm–Bragg theory (OR data) or from the ratio between ΔHcal and the van't Hoff enthalpy (ΔHvH) using DSC data showed a correlation between σ and the content of β‐mannose, but the two methods gave different results when the content of β‐mannose approached 100%. The ionic strength dependence of the transition temperature, expressed as d (log I)/d(T−1m), was nearly identical for intact xanthan and a sample containing only 6% of the terminal β‐mannose. Application of the Manning polyelectrolyte theory does not readily account for the observed ΔHcal values, neither does it provide new information on the nature of the ordered and disordered conformations in xanthan. © 1993 John Wiley & Sons, Inc.
Photodynamic induction of DNA–protein cross‐linking in solution by several sensitizers and visible light
Authors: Villanueva A. , Cañete M. , Trigueros C. , Rodriguez‐Borlado L. , Juarranz A. 
Published: December 2004

AbstractThe combined effect of several sensitizers and light on H 2O or D2O solutions of DNA‐histone complexes, as well as the significance of singlet oxygen (1O2), in this photosensitizing reaction has been studied. On H2O solutions, the production of 1O2, as well as the formation of DNA‐protein cross‐links (DPCs), were found to be dependent on light dose for all the sensitizers. Mesotetra (4N‐methylpyridyl) porphine (T4 MPyP), methylene blue (MB), and toluidine blue (TB) were the best photosensitizers with regard to tryptophan photolysis, followed by hematoporphyrin (HP), thioflavine T (TT), and pyronin G (PG). The formation of DPCs showed high initial rates, reaching a plateau at dose over 90 J/cm 2. Under these irradiation conditions, the percentage of DPCs induced by the sensitizers decreases in the order T4 MPyP > MB > TB ≫ HP ≈ TT ≫ PG (≈0). These DPCs were totally destroyed with proteinase K (15μg/ml). The irradiation of the DNA‐histone‐sensitizer solutions in the presence of L‐carnosine (5 × 10‐4 M) produced approximately a 50% of DPCs inhibition for T4 MPyP, MB, and TB, and a total inhibition for HP, TT, and PG. The substitution of H2O by D2O as solvent significantly increased the photodegradation of tryptophan, as well as the photoinduction of DPCs by the sensitizers. The results obtained indicate that singlet oxygen is the main agent responsible in the DNA–protein cross‐linking formation. © 1993 John Wiley & Sons, Inc.
Conformational preference functions for predicting helices in membrane proteins
Authors: Juretić Davor , Lee Byungkook , Trinajstić Nenad , Williams Robert W. 
Published: December 2004

AbstractA suite of FORTRAN programs, PREF, is described for calculating preference functions from the data base of known protein structures and for comparing smoothed profiles of sequence‐dependent preferences in proteins of unknown structure. Amino acid preferences for a secondary structure are considered as functions of a sequence environment. Sequence environment of amino acid residue in a protein is defined as an average over some physical, chemical, or statistical property of its primary structure neighbors. The frequency distribution of sequence environments in the data base of soluble protein structures is approximately normal for each amino acid type of known secondary conformation. An analytical expression for the dependence of preferences on sequence environment is obtained after each frequency distribution is replaced by corresponding Gaussian function. The preference for the α‐helical conformation increases for each amino acid type with the increase of sequence environment of buried solvent‐accessible surface areas. We show that a set of preference functions based on buried surface area is useful for predicting folding motifs in α‐class proteins and in integral membrane proteins. The prediction accuracy for helical residues is 79% for 5 integral membrane proteins and 74% for 11 α‐class soluble proteins. Most residues found in transmembrane segments of membrane proteins with known α‐helical structure are predicted to be indeed in the helical conformation because of very high middle helix preferences. Both extramembrane and transmembrane helices in the photosynthetic reaction center M and L subunits are correctly predicted. We point out in the discussion that our method of conformational preference functions can identify what physical properties of the amino acids are important in the formation of particular secondary structure elements. © 1993 John Wiley & Sons, Inc.
Predicting polypeptide and protein structures from amino acid sequence: Antlion method applied to melittin
Authors: Head‐Gordon Teresa , Stillinger Frank H. 
Published: December 2004

AbstractThis report continues to explore the use of a strategy known as the antlion method for predicting polypeptide and protein structure. The method involves deformation of a biopolymer's potential energy hypersurface in order to retain only a single minimum, near to the native structure. The vexing multiple minimum problem thus is relieved, and the deformed hypersurface constitutes a key element in three‐dimensional structure predictions with atomic resolution. In this more demanding pilot study, we provide evidence that the antlion method is capable of dramatically simplifying the surface of polypeptides by successfully predicting the native form of the naturally occurring 26‐residue polypeptide melittin. The systematic hypersurface modifications employed in our previous work have been used again for this case, but have been supplemented by the output of a suitable neural network. This neural network involves a new feature: the use of amino acid biophysical scales for improving the secondary structure prediction accuracy of simple perceptrons. © 1993 John Wiley & Sons, Inc.
Synthetic peptide and template‐assembled synthetic protein models of the hen egg white lysozyme 87–97 helix: Importance of a protein‐like framework for conformational stability in a short peptide sequence
Authors: Vuilleumier Stéphane , Mutter Manfred 
Published: December 2004

AbstractIn the native structure of hen egg white lysozyme (HEL), the amino acid sequence 87–97 (HEL 87–97) forms an amphiphilic helix, with hydrophilic residues in the sequence directed toward the solvent. A synthetic version of the HEL 87–97 sequence (with the cysteine corresponding to position 94 of HEL replaced by alanine) displays conformational features in solution typical of an unordered structure as judged by CD. However, various modifications in the sequence result in increased helix‐forming potential of the HEL 87–97 analogues. Further stabilization of the helical conformation in the most helical analogue of the HEL 87–97 sequence is obtained when 4 copies of this peptide sequence are coupled on a peptide carrier molecule following the template‐assembled synthetic protein (TASP) approach M. Mutter and S. Vuilleumier (1989) Angew. Chem. Int. Ed. Engl., Vol. 28, pp. 535–554 “A Chemical Approach to Protein Design–Template‐Assembled Synthetic Proteins (TASP).” This suggests that long‐range interactions of the peptide with its environment contribute to conformational stability in short peptide sequences. TASP molecules may prove useful for the study of the factors that determine secondary structure formation in short peptides by providing a protein‐like framework. © 1993 John Wiley & Sons, Inc.