bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational perturbation of the anticancer nucleoside arabinosylcytosine on Z‐DNA: Molecular structure of (araC‐dG)3 at 1.3 Å resolution
Authors: Zhang Hong , Van Der Marel Gijs A. , Van Boom Jacques H. , Wang Andrew H.‐J. 
Published: December 2004

AbstractThe left‐handed Z‐DNA structure of an araC‐containing (where araC stands for arabinosylcytosine) hexamer, (araC‐dG)3, has been solved by x‐ray diffraction analysis at 1.3 A resolution. This hexamer was crystallized in the hexagonal P6522 (a = b = 17.96 Å, c = 43.22 Å) space group in which the hexamers have statistically disordered packing arrangement along the 65 screw axis, yet the crystals diffract x‐rays to high resolution. Its structure has been refined by the constrained least square refinement to a final R factor of 0.287 using 737 [> 3.0 σ(F)] observed reflections. The asymmetric unit of the unit cell contains only a dinucleotide, 5′‐p(araC)p(dG). The overall conformation resembles that of the canonical Z‐DNA, but with some differences in details. The O2′ hydroxyl groups of the araC residues form intramolecular hydrogen bonds with N2 of the 5′‐guanine residues. In the deep groove of Z‐DNA, these hydroxy groups replace the bridging water molecules that stabilize the guanine in the syn conformation. The results reinforce the earlier observation made by the structural analysis of another hexamer, d(CG[araC]GCG), with a mono‐substitution of araC [M.‐K. Teng, Y.‐C. Liaw, G. A. van der Marel, J. H. van Boom, and A. H.‐J. Wang (1989) Biochemistry, vol. 28, pp. 4923–4928]. These two structures show that araC residue can be incorporated readily into the Z structure and probably facilitates the B to Z transition, as supported by uv absorption spectroscopic studies in a number of araC‐containing oligonucleotides. The potential biological roles of the araC‐modified Z‐DNA are discussed. © 1992 John Wiley & Sons, Inc.
Kinetics of folding and unfolding of ββ‐tropomyosin
Authors: Mo Jianming , Holtzer Marilyn Emerson , Holtzer Alfred 
Published: December 2004

AbstractThe kinetics of folding from random coils to two‐chain coiled coils of ββ‐tropomyosin was studied by stopped‐flow CD (SFCD) in the backbone region (222 nm). Two species were studied: the reduced form and the doubly disulfide cross‐linked form. The proteins were totally unfolded in 6M urea‐saline buffer, then refolded by tenfold dilution into benign k buffer. In the refolding medium, they spontaneously recover the two‐chain coiled‐coil structure. Reduced ββ refolds in at least two stages: one or more fast phases (<0.04 s), in which an intermediate with 71% of the equilibrium ellipticity forms, followed by a slower time‐resolvable phase that completes the folding. The slow phase is first order, signifying that dimerization occurs in the fast phase. The time constant of the slow phase is 2 s at 20°C and requires activation parameters of ΔS≠ = –7 ± 0.3 cal/mol · K, ΔH≠ = 15 ± 1 kcal/ mol. These results are very similar to those previously found for the reduced genetic variant αα‐tropomyosin. In contrast, refolding of doubly disulfide cross‐linked ββ is complete within the dead time (< 0.04 s), whereas the singly cross‐linked αα species also displays a slow phase. The opposite process, unfolding reduced ββ from the coiled‐coil state, is complete within the dead time, as in the αα variant.
Solution conformations of two flexible cyclic pentapeptides: cyclo(Gly‐Pro‐D‐Phe‐Gly‐Ala) and cyclo(Gly‐Pro‐D‐Phe‐Gly‐Val)
Authors: Stroup Adam N. , Rockwell Arlene L , Gierasch Lila M. 
Published: December 2004

AbstractIn an effort to explore the residue preferences in three‐residue reverse turns (so‐called ‐γ‐turns), two cyclic pentapeptides—cyclo(Gly1‐Pro2‐D‐Phe3‐Gly4‐Ala5) (I) and cyclo (Gly1‐Pro2‐D‐Phe3‐Gly4‐Val5) (II)—have been synthesized and analyzed by nmr. It was anticipated that the Gly‐Pro‐D‐Phe‐Gly portions of these molecules would favor a β‐turn conformation, leaving the remainder of the molecule to adopt a γ turn, as seen in several previously studied model cyclic pentapeptides. The nmr data for both peptides in CDCl3 (5% DMSO‐d6) and in neat DMSO‐d6 indicate that the most populated conformation contains a distorted β turn around Pro2‐D‐Phe3, which includes a γ turn around D‐Phe3. The distorsion in the β turn does not impede the formation of an inverse γ turn around residue 5, and indeed, this conformation is observed in both peptides. Both the alanine and the bulkier valine residues are therefore found to be compatible with an inverse γ turn. Molecular dynamics simulations on the title peptides are reported in the following paper. These simulations indicate that there is conformational flexibility around the D‐Phe3‐Gly4 peptide bond, which enables the formation of the γ turn around D‐Phe3. The third paper in this series explores the impact of a micellar environment on conformational equilibria in II. © 1992 John Wiley & Sons, Inc.
Hydrational and intrinsic compressibilities of globular proteins
Authors: Kharakoz D. P. , Sarvazyan A. P. 
Published: December 2004

AbstractPartial compressibilities of globular proteins in water are reviewed. Contribution of hydrational and of intrinsic compressibilities to experimental partial quantity have been evaluated from ultrasonic data using two independent methods: (a) additive calculation of the hydrational contributions of the surface atomic groups and (b) an analysis of correlation between partial compressibility and molecular surface area. The value (14 ± 3) × 10−6 bar −1 for the isothermal compressibility coefficient of the protein interior at 25°C was obtained as an average value for variety of globular proteins. This value is similar to that of solid organic polymers. Possible relaxation contribution to partial compressibility is roughly estimated from comparison of thermodynamic with x‐ray data on protein compressibility. The average compressibility of water in the hydration shell of proteins was found to be 35 × 10−6 bar −1, which is 20% less than that of pure water. © 1993 John Wiley & Sons, Inc.
Calcium‐dependence of laminin binding to phospholipid membranes
Authors: Ramsden Jeremy J. 
Published: December 2004

AbstractLaminin is the most abundant noncollagenous protein in basement membranes. Its selfassembly has been studied in solution, and it has been established that calcium ions induce partially reversible aggregation. The behavior at a lipid membrane surface is of greater biological significance, but it is difficult to study quantitatively binding kinetics at a surface. The present work uses a powerful new integrated optics technique to measure the absorption and aggregation of the laminin–nidogen at a bilayer lipid membrane surface. It is found that the binding of a single layer of laminin at the lipid membrane is independent of the presence of calcium, but that the building up of multilayer laminin membranes requires calcium, and that these may not be destroyed by a calcium‐complexing agent. © 1993 John Wiley & Sons, Inc.
1H, 13C, and 15N assignments and secondary structure of the FK506 binding protein when bound to ascomycin
Authors: Xu Robert X. , Nettesheim David , Olejniczak Edward T. , Meadows Robert , Gemmecker Gerd , Fesik Stephen W. 
Published: December 2004

AbstractThe 1H, 13C, and 15N resonances of FKBP when bound to the immunosuppressant, ascomycin, were assigned using a computer‐aided analysis of heteronuclear double and triple resonance three‐dimensional nmr spectra of [U‐15N] FKBP/ascomycin and [U‐15N, 13C] FKBP/ascomycin. In addition, from a preliminary analysis of two heteronuclear four‐dimensional data sets, 3J coupling constants, amide exchange data, and the differences between the Cα and Cβ chemical shifts of FKBP to random coil values, the secondary structure of FKBP when bound to ascomycin was determined. The secondary structure of FKBP when bound to ascomycin in solution closely resembled the x‐ray structure of the FKBP/FK506 complex but differed in some aspects from the structure of uncomplexed FKBP in solution. © 1993 John Wiley & Sons, Inc.
IR study of the proton acceptor ability of N‐t‐butoxycarbonylproline N′‐methylamide
Authors: Parmentier J. , De Wael K. , Samyn C. , Zeegers‐Huyskens Th. 
Published: December 2004

AbstractHydrogen bonding between N‐t‐butoxycarbonylproline N′‐methylamide and phenol derivatives (pKa = 10.20–7.75) are investigated by ir and Fourier transform ir spectrometry. The thermodynamic parameters determined in carbon tetrachloride solution show that the complexes are of medium strength, the stability constants at 298 K range from 80 to 1530 L mol−1, and the enthalpies of complex formation range from – 30 to –34 kJ mol−1. The study of the ir spectra in the νOH, νNH, and νco regions shows that complex formation occurs at the oxygen atom of the amide carbonyl. Hydrogen‐bond formation at this site strengthens the intramolecular hydrogen bond of the seven‐membered ring. © 1993 John Wiley & Sons, Inc.
Molecular dynamics of sickle and normal hemoglobins
Authors: Prabhakaran M. , Johnson Michael E. 
Published: December 2004

AbstractMolecular dynamics (MD) simulations have been carried out for 62.5 ps on crystal structures of deoxy sickle cell hemoglobin (HbS) and normal deoxy hemoglobin (HbA) using the CHARMM MD algorithm, with a time step of 0.001 ps. In the trajectory analysis of the 12.5–62.5 (50 ps) simulation, oscillations of the radius of gyration and solvent‐accessible surface area were calculated. HbS exhibited a general contraction during the simulation, while HbA exhibited a nearly constant size. The average deviations of simulated structures from the starting structures were found to be 1.8 Å for HbA and 2.3 Å for HbS. The average rms amplitudes of atomic motions (atomic flexibility) were about 0.7 Å for HbA and about 1.0 Å for HbS. The amplitudes of backbone motion correlate well with temperature factors derived from x‐ray crystallography. A comparison of flexibility between the α‐ and β‐chains in both HbA and HbS indicates that the β‐chains generally exhibited greater flexibility than the α‐chains, and that the HbS β‐chains exhibit greater flexibility in the N‐terminal and D‐ and F‐helix regions than do those of HbA. The average amplitude of backbone torsional oscillations was about 9°, a value comparable with that of other simulations, with enhanced torsional oscillation occurring primarily at the ends of helices or in loop regions between helices. Comparison of atomic flexibility and torsional oscillation results suggests that the increased β‐chain flexibility results from relatively concerted motions of secondary structure elements. The increased flexibility may play an important role in HbS polymerization. Time course analysis of conformational energy of association, hydrogen bonding and hydrophobic bonding (as calculated from solvent accessibility) shows that all three of these factors contribute to the stability of subunit association for both hemoglobins. © 1993 John Wiley & Sons, Inc.
Specific helix stabilization of poly(L‐glutamic acid) in mixed counterion systems
Authors: Satoh Mitsuru , Kato Fusaaki , Komiyama Jiro 
Published: December 2004

AbstractThe coil–helix transitions of poly (L‐glutamic acid) in aqueous alcohol solutions have been investigated for mixed counterion systems. It has been found that coexistence of two kinds of counterion species, i.e., two alkali metal counterions, alkali and alkaline earth metal, and two alkaline earth metals, specifically stabilizes or destabilizes the helix conformation depending upon the combination of the counterion species. The most striking enhancement of the helix content was observed for the combination of Li+ and K+ counterions. It has been suggested that the helix stabilization is attributed to the reduction of the free energy in the contact ion pair formation between the polymer charges and the counterions in the mixed counterion systems. © 1993 John Wiley & Sons, Inc.
Crystal state conformation of three azapeptides containing the Azaproline residue, a β‐turn regulator
Authors: Lecoq A. , Boussard G. , Marraud M. , Aubry A. 
Published: December 2004

AbstractThe molecular structure of three protected AzaPro‐containing peptides have been determined by x‐ray diffraction: Z‐AzaPro‐NHiPr (1; Z: benzyloxycarbonyl), Z‐AzaPro‐L‐Ala‐NHiPr (2), and Boc‐L‐Ala‐AzaPro‐NHiPr (3; Boc: tert‐butyloxycarbonyl). Starting from the key synthon benzyl‐azaprolinate, compounds 1, 2, and 3 have been prepared by combined use of liquid phase peptide synthesis method and adequate isocyanates. In all peptides, the following geometric characteristics are retained: (a) pyramidal character of the two nitrogen atoms of the pyrazolidine ring; (b) pseudo cis conformation of the urethane (1, 2) or tertiary amide (3) function preceding the AzaPro residue; (c) identical absolute values of the Azaproline residue torsion angles “ϕ, ψ” respectively 111° and 23°. In compound 2, the two nitrogen atoms of the pyrazolidine ring are R, R but the opposite S, S absolute configurations are observed in compound 3. In the crystal, compound 3 adopts a folded structure similar to a type VI β‐turn with a weak intramolecular i + 3 → i hydrogen bond, while an extended structure is observed in compound 2. In the light of our findings, in a peptide chain and contrary to the Pro residue, an AzaPro residue should prevent the formation of any type of any type of β‐turn with the residue following it but could accommodate a folded structure with a pseudo type VI βturn with the preceding residue. If confirmed, this would be of tremendous importance in the design of biologically active peptides and drugs. © 1993 John Wiley & Sons, Inc.
Structures of peptides from α‐amino acids methylated at the α‐carbon,
Authors: Toniolo C. , Crisma M. , Formaggio F. , Valle C. , Cavicchioni G. , Precigoux G. , Aubry A. , Kamphuis J. 
Published: December 2004

AbstractThe structural preferences of peptides (and depsipeptides) from the achiral MeAib and Hib residues, and the chiral Iva, (αMe) Val, (αMe) Leu, and (αMe) Phe residues, as determined by conformational energy computations, x‐ray diffraction analyses, and 1H‐nmr and spectroscopic studies, are reviewed and compared with literature data on Aib‐containing peptides. The results obtained indicate that helical structures are preferentially adopted by peptides rich in these α‐amino acids methylated at the α‐carbon. Intriguing experimental findings on the impact of the chirality of Iva, (αMe) Val, and (αMe) Phe residues on helix screw sense are illustrated. © 1993 John Wiley & Sons, Inc.
Conformational and topographical considerations in the design of biologically active peptides
Authors: Hruby Victor J. 
Published: December 2004

AbstractAn outline of the basic considerations that are under development for the rational design of biologically active peptides and peptidomimetics is given. The necessary interplay of biophysical, chemical, and biological considerations is emphasized. The importance of properly designed biological assays to provide chemical information analogous to that from biophysical studies is discussed. The development of asymmetric synthesis in conjunction with conformational considerations for the preparation of specialized amino acids and amino acid mimetics is a critical aspect of the approach. The overall approach is illustrated with three examples from our laboratory: (1) the redesign of somatostatin to a highly potent and selective μ‐opioid receptor antagonist using conformational and topographical considerations in design and for obtaining insights into the pharmacophor; (2) the use of topographical considerations for obtaining oxytocin antagonists; and (3) the application of designer amino acids prepared by asymmetric synthesis to obtain insight into the topographical requirements at δ‐opioid receptors. © 1993 John Wiley & Sons, Inc.
Conformational mobility in cyclic oligopeptides
Authors: Kopple Kenneth D. , Bean John W. , Bhandary Krishna K. , Briand Jacques , D'Ambrosio Cynthia A. , Peishoff Catherine E. 
Published: December 2004

AbstractAnalysis of two isomeric cyclic hexapeptides of composition (Asp, Arg, Gly2, Pro, D‐Pro) by a nuclear Overhauser effect constrained distance geometry conformation search yielded a narrowly defined backbone conformation for one and considerable ambiguity about the conformation in part of the other. Preliminary 13C relaxation studies of these peptides suggest that it is possible that this difference may correspond to a physical difference in internal mobility. In connection with this observation, other experimental evidence bearing on the backbone conformational mobility of cyclic oligopeptides with 4–10 residues, frequently considered to have well‐defined backbones, is reviewed. Conformational heterogeneity involving rotation of a peptide bond plane relative to the overall ring plane is identified as a common phenomenon. Nuclear magnetic resonance line‐shape studies at temperatures down to 200 K can detect backbone motions with activation free energy barriers down to about 10 kcal/mole, but conformational exchange with lower barriers, though detectable in other ways, will not be obvious from nmr spectra alone. © 1993 John Wiley & Sons, Inc.
Hydrophobicity and stability for a family of model proteins
Authors: Muller Norbert 
Published: December 2004

AbstractAccording to the conventional definition, the hydrophobic effect is a result of thermodynamic changes occurring when a nonpolar group dissolves in water and attributable to the fact that water in contact with such a group has special structural and energetic properties. Disagreement now exists as to whether this effect promotes or hinders protein denaturation. Taking the heat capacity change of unfolding as a measure of the hydrophobicity of the protein interior, others have shown that protein stabilities are systematically affected by changes in hydrophobicity. It has been suggested that the observed trends show that hydrophobic hydration is intrinsically a destabilizing factor. Model calculations using known equations for the stability curves and certain simplifying assumptions now show that such regularities provide no evidence for or against this conclusion. All available data can be rationalized if hydrophobic terms are evaluated from models that require a positive hydrophobic contribution to the Gibbs energy of unfolding. The calculations also confirm the recent finding that any set of proteins with denaturation temperatures between about 330 and 380 K that exhibits entropy convergence at about 386 K is thermodynamically required to show enthalpy convergence at approximately the same temperature. © 1993 John Wiley & Sons, Inc.
Effect of cationic drugs on suprahelical organization of DNA
Authors: Krishna K. Gopala , Kumar T. K. Suresh , Pandit M. W. 
Published: December 2004

AbstractInteraction of a minor groove‐binding drug Hoechst‐33258, and an intercalating drug, proflavin, with the PSI (+) form of DNA, was studied using CD spectroscopy. Both drugs are shown to relax the suprahelical organization of DNA, leading to the formation of a B‐like structure, above a certain drug to phosphate ratio. However, unlike proflavin, Hoechst‐33258 brings about further structural changes after formation of the B‐like structure whereas proflavin does not. A reversal of the CD signal in the 300–450‐nm spectral region is also observed with Hoechst‐33258, indicating a change in the handedness of the suprahelical organization of DNA. To the best of our knowledge, drug‐mediated changes as presented in this paper have not been reported so far. © 1993 John Wiley & Sons, Inc.
Intramolecular interference effects in dynamic light scattering from rigid rings
Authors: Gebe John A. , Schurr J. Michael 
Published: December 2004

AbstractA formula for the apparent diffusion coefficient [Dapp(κ)] of a rigid ring is derived from the exact first cumulant of its dynamic structure factor. Dapp(κ) is expressed in terms of the ring radius, the diffusion coefficients (Dzz and Dxx) for translation parallel and perpendicular, respectively, to the symmetry axis, and the diffusion coefficients (D and D) for rotation around the symmetry and transverse axes, respectively. Dapp(κ) exhibits oscillations as a function of the scattering vector k, which depend on D and the anisotropy of translational diffusion (Dzz − Dxx). The maxima in Dapp(κ) are associated with minima in the static structure factor S(κ, 0), which are due to destructive intramolecular interference. The oscillations in Dapp(κ) result from periodic variations in the relative intensities of scattered light from different orientations of the ring, which manifest the various motions to different extents. The orientations contributing most to the scattered intensity are those that exhibit the least destructive interference and consequently contribute most to the decay of the dynamic structure factor. © 1993 John Wiley & Sons, Inc.
Low oxygen affinity derivatives of human hemoglobin by fixation of polycarboxylic dextran to the oxyform
Authors: Prouchayret F. , Dellacherie E. 
Published: December 2004

AbstractSolutions of modified adult human hemoglobin (Hb) have potential applications as physiological oxygen carriers. The chemical modification that has been the most studied during the last few years is the cross‐linking of the protein between its two αβ dimers, in order, first, to hamper their diffusion through the kidney and therefore increase the plasma persistence of Hb, and second, to decrease its oxygen affinity. However, despite the cross‐linking, the vascular retention time is only increased by a factor of three, and a supplementary modification of cross‐linked Hb is needed in order to further improve its in vivo half‐life. The Hb derivatives described in this paper were obtained by the covalent fixation of benzene tetracarboxylate‐substituted dextran onto oxyHb. The resulting conjugates all exhibited a higher P50 than native Hb. The experiments carried out in the presence of inositolhexaphosphate showed that the allosteric sites of Hb molecules were occupied by the polymeric reagent. The important decrease in the Bohr effect and the lack of the Cl− effect on the oxygen‐binding properties proved that the Val 1α residue was also substituted. Finally, the ability of some conjugates to unload as much O2 as blood, together with their other properties, make them quite promising candidates as red cell substitutes. © 1993 John Wiley & Sons, Inc.
The influence of hydration on the conformation of bovine serum albumin studied by solid‐state 13C‐nmr spectroscopy
Authors: Gregory Roger B. , Gangoda Mahinda , Gilpin R. K. , Su Wen 
Published: December 2004

Abstract13C proton‐decoupled cross‐polarization magic‐angle spinning nmr spectra of bovine serum albumin are reported as a function of hydration. Increases in hydration level enhance the resolution of the peak centered at about 40 ppm but has little or no effect on the other spectral peaks. Hydration has little effect on either the rotating frame proton spin–lattice relaxation time or the cross‐relaxation time for any of the peaks, suggesting that the efficiency of dipolar coupling is largely preserved on hydration of the protein. Resolution enhancement of the peak at 40 ppm is not understood, but possible sources of the behavior include a decrease in the line width of contributing resonances from lysine ε carbons due to increased motional averaging on hydration, reordering of disulfide bridges, and titration shifts induced by hydration. Hydration of bovine serum albumin appears to have little effect on the distribution of conformations sampled by the protein so that the broad distribution of conformations observed in the dry state is also observed in the fully hydrated state. This is in contrast to lysozyme where significant ordering of the conformation is seen on hydration. © 1993 John Wiley & Sons, Inc.