bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential scanning calorimetry studies of NaCl effect on the inverse temperature transition of some elastin‐based polytetra‐, polypenta‐, and polynonapeptides
Authors: Luan Chi‐Hao , Parker Timothy M. , Prasad Kari U. , Urry Dan W. 
Published: December 2004

AbstractDifferential scanning calorimetry studies of the effect of NaCl on protein‐based polymer self‐assembly has been carried out on six elastin‐based synthetic sequential polypeptides‐ i.e., the polypentapeptide (L‐Val1‐L‐Pro2‐Gly3‐L‐Val4‐Gly5)n and its more hydrophobic analogues (L‐Leu1‐L‐Pro2‐Gly3‐L‐Val4‐Gly5)n and (L‐Val1‐L‐Pro2‐L‐Ala3‐L‐Val4‐Gly5)n; the polytetrapeptide (L‐Val1‐L‐Pro2‐Gly3‐Gly4)n and its more hydrophobic analogue (L‐IIe1‐L‐Pro2‐Gly3‐Gly4)n; and the polynonapeptide (a pentatetra hybrid), (L‐Val1‐L‐Pro2‐Gly3‐L‐Val4‐Gly5‐L‐Val6‐L‐Pro7‐Gly8‐Gly9)n.Previous physical characterizations of the polypentapeptides have demonstrated the occurrence of an inverse temperature transition since increase in order of the polypentapeptide, as the temperature is raised from below to above that of the transition, has been repeatedly observed using different physical characterizations.In the present experiments, it is observed that the transition temperatures of the polypeptides studied are linearly dependent on NaCl concentration. The molar effectiveness of NaCl in shifting the transition temperature ΔTm/[N], is about 14°C/[N], with the dependence on peptide hydrophobicity being fairly small. Interestingly, however, the δΔQ/ [N] does depend on the hydrophobicity of a polypeptide.
Heat capacities of solid poly(amino acids). I. Polyglycine, poly(L‐alanine), and poly(L‐valine)
Authors: Roles K. A. , Wunderlich Bernhard 
Published: December 2004

AbstractHeat capacities of polyglycine, poly(L‐alanine), and poly(L‐valine) were analyzed using approximate group vibrations and fitting of the skeletal vibrations to a two‐parameter (Θ1, Θ3) Tarasov function. New experimental data were measured by differential scanning calorimetry in the temperature range of 230–390 K. Good agreement between our experimental data and the calculated data was observed for all three poly(amino acids). Previous investigations showed agreement between calculation and reported experimental data for only limited low temperature ranges. At higher temperatures, discrepancies of up to 55% existed between experiment and calculation. The cause of this discrepancy must be assumed to be experimental error. Recommended experimental data are revised on the basis of this investigation. Computed heat capacities are available for the three biopolymers in the solid state from 0 to 1000 K.
Effects of proline ring conformation on theoretical π‐π* absorption and CD spectra of helical poly(L‐proline) forms I and II
Authors: Thomasson Kathryn A. , Applequist Jon 
Published: December 2004

AbstractAbsorption and CD spectra of the π‐π* transition near 200 nm are calculated for helical (Pro)10 forms I and II with a variable proline ring conformation characterized by torsion angle χ2 in the range −60° to 60°. The spectra for poly (Pro) I are not sufficiently sensitive to χ2 to suggest a preferred ring conformation. The spectra for poly (Pro) II are more sensitive to χ2, and suggest preferred ring conformations near either or both of the χ2regions −50 ± 10° and 50 ± 10°.
Dynamic light scattering from weakly bending rods: Estimation of the dynamic bending rigidity of the M13 virus
Authors: Song Lu , Kim Ug‐Sung , Wilcoxon Jess , Schurr J. Michael 
Published: December 2004

AbstractA theory is presented for the dynamic structure factor [S(K, t)] of weakly bending rods. This treatment is based on a discrete bead model for the Brownian dynamics in which all bead motions associated with bending are constrained to occur in a plane perpendicular to the end‐to‐end vector, thus prohibiting extension or contraction along that axis. Preset hydrodynamic interactions are incorporated in a numerically exact manner. The predicted normalized dynamic structure factor S(K, t)/S(K, 0) should be valid for short times t such that the rms rotation of the end‐to‐end vector around any transverse axis is much less than 1.0 radian. With geometrical parameters appropriate for the M13 virus, the intensity autocorrelation function G(2)(K, t) = 1 + |S(K, t)/S(K, 0)|2 is calculated over a range of times and scattering vectors K for selected values of the persistence length P. The calculated G(2)(K, t) are fitted to a single exponential with unit baseline over the same range of times as the experimental photon correlation functions, and the apparent diffusion coefficients Dapp(K) are obtained from the best‐fit relaxation times. For the sake of completeness, an exact expression is derived for the apparent diffusion coefficient obtained from the initial slope of the dynamic structure factor. However, this does not reduce to the known correct result in the rigid rod limit. To obtain the correct result, the limit of infinite bending rigidity must be taken before the limit of zero time. For this and other reasons, the initial slope value of Dapp(K) is not useful for weakly bending rods.Photon correlation functions are measured for the M13 virus, which is virtually identical to the often‐studied fd virus. The experimental photon correlation functions are fitted over 8 relaxation times to a single‐exponential plus baseline, and the Dapp(K) are calculated from the best‐fit relaxation times. Theoretical curves of Dapp(K) vs K2 for selected values of P are compared with the experimental data, which are satisfactorily reproduced when P = 22000 ± 2000 Å. This dynamic value is close to the static value, P = 20000 ± 2000 Å, reported for the very similar fd virus. The most recent theories of Maeda and Fujime and their dynamic light scattering studies of fd virus are compared with the present results in some detail. Their optimum value of P is in surprisingly good agreement with the present value.
1H‐ and natural abundance 15N‐nmr studies of a derivative of a rabies glycoprotein fragment
Authors: Molinari Henriette , Consonni Roberto , Pegna Monica , Zetta Lucia , Neri Paolo , Niccolai Neri , Bonci Alessandra , Lozzi Luisa , Rustici Mauro , Scarselli Maria 
Published: December 2004

AbstractUsing a combination of one‐ and two‐dimensional methods, 1H‐ and 15N‐nmr spectroscopy has been employed to perform the complete assignment and the structural determination of the immunogenic undecapeptide CTTTNSRGTTT in DMSO solution. Nuclear Over‐hauser enhancement spectroscopy experiments indicated the presence of secondary structures, mainly turn‐like structures, which only represent a family, albeit a dominant one, of an ensemble of conformations available to the peptide. Since reverse turns may play an important role as intermediates in protein folding, the experimental observations described here may link the immunological and theoretical approaches to protein folding.
Backbone cyclization: A new method for conferring conformational constraint on peptides
Authors: Gilon Chaim , Halle David , Chorev Michael , Selincer Zvi , Byk Gerardo 
Published: December 2004

AbstractThis article describes a new concept of medium‐ and long‐range cyclization of peptides through “backbone cyclization.” In this approach, conformational constraints are conferred on a peptide by linking ω‐substituted alkylidene chains replacing Nα or Cα hydrogens in a peptidic backbone. Backbone cyclization, which is divided into N‐backbone and C‐backbone cyclizations, allow for new modes of cyclization in addition to the classical ones that are limited to cyclization through the side chains and/or the amino or carboxyl terminal groups. The article also describes the application of the N‐backbone cyclization to the active region of substance P. Conformational constraints of this peptide by the classical cyclization modes led to inactive analogues whereas N‐backbone cyclization provided an active, selective, and metabolically stable analogue.
X‐Ray conformational study of hydrazino peptide analogues
Authors: Aubry André , Bayeul Daniel , Mangeot Jean‐Paul , Vidal Joëlle , Sterin Sébastien , Collet André , Lecoq Alain , Marraud Michel 
Published: December 2004

AbstractWe have solved the crystal structures of nine pseudo‐peptide analogues deriving from the hydrazino analogue of glycine or valine (NβH2‐NαH‐CαHR‐CO2H, R = H or iPr) or proline (NβH2‐Nα‐CαH‐CO2H) and containing the hydrazide (CO‐NβH‐Nα) or Nβ‐Z‐aminoamide peptidomimetic link. This study gives access to the average geometry of these two links, to their inter‐ and intramolecular interaction modes, and to their influence on the conformational properties of the molecules.
Information concerning the mechanism of electrophoretic DNA separation provided by quantitative video‐epifluorescence microscopy
Authors: Rampino Nicholas J. 
Published: December 2004

AbstractChanges in conformation, length, and mobility of individual DNA molecules during agarose gel electrophbresis were measured using video micrographs obtained by epifluorescence microscopy. Globular, V‐shaped, and linear conformations of DNA are found. The mobility, upon transformation from the globular to the V‐shaped conformation, decreases, suggesting a collision with a gel fiber. The duration of interaction between DNA and gel fiber is proportional to the length of DNA. Hypothetically, this proportionality underlies the size separation of DNA by agarose gel electrophoresis.DNA release from the gel fiber appears to involve the movement of the arms of the V‐shaped molecule around the gel fiber. Concomitant with this movement is a length reduction the degree of which is constant for DNA of various lengths in a particular buffer milieu. The luminant densitometric profiles of DNA molecules in the V conformation show maxima at the ends and apex of the V. The unequal distribution of nucleotides along the DNA chain appears to provide the driving force for the molecular movement around the gel fiber.
The cystine‐stabilized α‐helix: A common structural motif of ion‐channel blocking neurotoxic peptides
Authors: Kobayashi Yuji , Takashima Hiroyuki , Tamaoki Haruhiko , Kyogoku Yoshimasa , Lambert Paul , Kuroda Hisaya , Chino Naoyoshi , Watanabe Takushi X. , Kimura Terutoshi , Sakakibara Shumpei , Moroder Luis 
Published: December 2004

AbstractNeurotoxic peptides from venoms of scorpions and honey bees exhibit a consensus pattern in the two disulfide bridgings related to the sequence portions Cys‐X‐Cys and Cys‐X‐X‐X‐Cys. A revised three‐dimensional structure of charybdotoxin, as determined by two‐dimensional nmr spectroscopy, confirms that the consensus cystine dislocation generates in all these toxins a common structural element, i.e., the cystine‐stabilized α‐helical (CSH) motif, which may be correlated with their common ion channel blocking activity.
Heat aggregation studies of phycobilisomes, ferritin, insulin, and immunoglobulin by dynamic light scattering
Authors: Singh Brahm Pal , Bohidar Himadri B. , Chopra S. 
Published: December 2004

AbstractDynamic laser light scattering studies on the heat aggregation behavior of phycobilisomes (PBS), ferritin, insulin, and immunoglobulin (IgG) in dilute aqueous solutions has been reported. Except for PBS, results are reported for heat aggregation trends in these proteins for three different pH environments (4.0, 7.5, 9.1). For PBS, studies were performed only in the neutral buffer medium (pH 7.5). The experiments were performed in the very dilute concentration regime (between 0.23 and 1.8 gL−1). For all these samples heat aggregation and dissociation trends were found to be linear with temperature. Upon temperature reversal (self‐cooling), hysteresis‐like behavior observed in insulin was found to be predominantly large at pH 7.5. PBS, ferritin, and IgG showed no such behavior at any of three pH values, and retraced their path of aggregation while dissociating on temperature reversal. Heat aggregation and dissociation processes in ferritin were found to be independent of pH. The IgG samples showed smooth aggregation tendency only up to 35°C in the buffer media pH 4.0 and 9.1, whereas for pH 7.0 the same could be observed until 60°C. Low polydispersity in the correlation spectra was observed in case of all these samples.
Conformational preferences of oligopeptides rich in α‐aminoisobutyric acid. II. A model for the 310/α‐helix transition with composition and sequence sensitivity
Authors: Basu Gautam , Kuki Atsuo 
Published: December 2004

AbstractThe analysis of the factors that control the helical folding of Aib‐rich peptides is extended to include sensitivity to sequence patterns, and in particular the presence of contiguous non‐Aib α‐mono‐alkylated residues. The distinct hydrogen‐bonding network of the 310−helix, as contrasted with that of the competing α‐helical structure, is explicitly incorporated into a theoretical model for the 310−helix/α‐helix equilibrium constant for a given peptide. Finite length effects and the “extra” intrahelical hydrogen bond of the 310 form are expressed naturally as a result of this loop analysis. This semiempirical model captures all the established features of existing empirical rules for helical conformational transitions in Aib‐rich sequences, as well as the recently detected helical transition induced solely by sequence permutation.
Molecular conformation of ascidiacyclamide, a cytotoxic cyclic peptide from Ascidian: X‐ray analyses of its free form and solvate crystals
Authors: Ishida Toshimasa , In Yasuko , Doi Mitsunobu , Inoue Masatoshi , Hamada Yasumasa , Shiori Takayuki 
Published: December 2004

AbstractIn order to investigate the conformational variation of ascidiacyclamide, a cytotoxic cyclic peptide from marine tunicate Ascidian, single crystals were prepared from ethanol and aqueous ethanol solutions as its free form (crystal I) and H2O/0.5 C2H5OH solvate (crystal II), respectively, and were determined by the x‐ray diffraction method. Crystal I showed a pseudo C2‐symmetric saddle‐shaped rectangular conformation. Similar conformations were also observed in crystal II, where there were two crystallographically independent C2‐symmetric molecules (named Mol‐A and ‐B) per asymmetric unit. Mol‐A and ‐B included H2O and H2O/C2H5OH solvents within their ring structures, respectively. These water and ethanol molecules were located on the crystallographic dyad axes, and were stabilized by the van der Waals contacts (including hydrogen bonds) with the polar‐ring N atoms and nonpolar D‐Val side‐chain atoms. The conformational characteristics of ascidiacyclamide and its fluctuation/variation were discussed based on the present and previously reported x‐ray results.
Bound water in the collagen‐like triple‐helical structure
Authors: Lazarev Yuri A. , Grishkovsky Boris A. , Khromova Tatyana B. , Lazareva Alisa A. , Grechishko Vera S. 
Published: December 2004

AbstractThe ir amide bands of the triple‐helical polytripeptides and collagens upon hydration of films are investigated. On the basis of our assignment of the amide I components, the formation of hydrogen bonds between the peptide backbone and structural water is studied. The C1O1—HOH hydrogen bonds are found more ordered than the C3O3—HOH hydrogen bonds. The specific incorporation of water in the triple helix is followed by multistep conformational changes and by increasing of the interpeptide hydrogen‐bond strength. The formation of the polypeptide hydrate structure depending on the amino acid composition and the chain length is examined.
Peptide models for the membrane destabilizing actions of viral fusion proteins
Authors: Epand Richard M. , Cheetham James J. , Epand Raquel F. , Yeagle Philip L. , Richardson Christopher D. , Rockwell Arlene , Degrado William F. 
Published: December 2004

AbstractThe fusion of enveloped viruses to target membranes is promoted by certain viral fusion proteins. However, many other proteins and peptides stabilize bilayer membranes and inhibit membrane fusion. We have evaluated some characteristics of the interaction of peptides that are models of segments of measles and influenza fusion proteins with membranes. Our results indicate that these models of the fusogenic domains of viral fusion proteins promote conversion of model membrane bilayers to nonbilayer phases. This is opposite to the effects of peptides and proteins that inhibit viral fusion. A peptide model for the fusion segment of the HA protein of influenza increased membrane leakage as well as promoted the formation of nonbilayer phases upon acidification from pH 7–5. We analyze the gross conformational features of the peptides, and speculate on how these conformational features relate to the structures of the intact proteins and to their role in promoting membrane fusion.
Conformation of uteroglobin fragments
Authors: Mammi Stefano , Foffani Maria Teresa , Improta Sabina , Tessari Marco , Schievano Elisabetta , Peggion Evaristo 
Published: December 2004

AbstractThe conformation of three fragments of uteroglobin in aqueous solution and in the presence of SDS micelles is described. Two of these fragments correspond to helix II and helix III of uteroglobin, the crystal structure of which is made of four helices. The third peptide comprises helices II and III, with the connecting β‐turn. While helix II does not interact strongly with the micelles, helix III adopts a rather clear α‐helix in this system. The elongation of helix III with the addition of helix II at the N‐terminus somewhat stabilizes the ordered structure. It is possible that the β‐turn found in the crystal is also present in solution.
Conformational analysis of an opioid peptide in solvent media that mimic cytoplasm viscosity
Authors: Temussi Piero Andrea , Picone Delia , Saviano Gabriella , Amodeo Piero , Motta Andrea , Tancredi Teodorico , Salvadori Severo , Tomatis Roberto 
Published: December 2004

AbstractMany neuropeptides exert their action between the presynaptic vesicles and postsynaptic transmembrane receptors, crossing different layers of specialized cytoplasm. Biomimetic media usually employed to study bioactive peptides do not reproduce the physico chemical environment of cytoplasm—in particular, the high viscosity of this biological fluid. Here we describe a Conformational study of a δ‐selective opioid peptide, deltorphin I, at variable temperatures in several biocompatible media characterized by varying values of viscosity and dielectric constant. It was found that only viscosity, among these parameters, induces ordered conformations; that is, it acts as a Conformational sieve. This finding suggests that the high viscosity of the intersynaptic fluid contributes, in addition to the membrane catalysis proposed by Schwyzer, in overcoming the so‐called entropic barrier to the transition state of peptide–receptor interaction by selecting ordered conformations prior to receptor interaction.The folded conformer found in the 80 : 20 (v : v) DMSOd6/H2O cryoprotective mixture at 265 K has a shape consistent with those of rigid nonpeptidic opiates.
Hydrophobicity‐induced pK shifts in elastin protein‐based polymers
Authors: Urry Dan W. , Peng Shao Qing , Parker Timothy M. 
Published: December 2004

AbstractThree polypentapeptides—poly[0.8(GVGVP), 0.2(GEGVP)], poly[0.8(GVGIP), 0.2‐(GEGIP)], and poly[0.75(GFGVP), 0.25(GEGVP)]—all analogues of the polypenta‐peptide of elastin—(Val1‐Pro2‐Gly3‐Val4‐Gly5)n or poly(VPGVG)—have been prepared to determine the effect of changing the hydrophobicity, i.e., Val1 → Ile1 (I) and Val4 → Phe4 (F), on the pKa and the temperature dependence of pKa of the Glu (E) residue. Shifts in pKa as large as 1.7 units are observed and the temperature dependence is much steeper for the structure‐dependent proximity of the more hydrophobic Ile1 residues to the Glu4 residue. Even though this system is dominated by the inverse temperature transition of hydrophobically driven folding on raising the temperature, the effect of adding 0.15 N NaCl is to suppress the hydrophobicity‐induced pKa shift.
NMR studies of structure and dynamics of isotope enriched proteins
Authors: Wagner Gerhard , Thanabal V. , Stockman Brian J. , Peng Jeffrey W. , Nirmala N. R. , Hyberts Sven G. , Goldberg Matthew S. , Detlefsen David J. , Clubb Robert T. , Adler Marc 
Published: December 2004

AbstractStructural studies of globular proteins by nmr can be enhanced by the use of isotope enrichment. We have been working with proteins enriched with 15N, and with both 15N and 13C. Due to the isotope enrichment we could assign several large proteins with up to 186 residues and could address structural questions. Furthermore, we can accurately measure heteronuclear and homonuclear vicinal coupling constants. This involves in part multidimensional multiple resonance experiments. This is important for characterization of minor conformational changes caused by mutations. We have also made use of isotope enrichment to study the internal mobility of proteins. We also have developed novel methods for measuring accurately 15N relaxation parameters, in particular transverse relaxation rates. This has led us toward a method for directly mapping spectral density functions of the rotational motions of N–H bond vectors in proteins. The protein systems that are discussed include the unlabeled proteins kistrin and cytochrome c551, and the labeled proteins eglin c, a flavodoxin, and human dihydrofolate reductase.
The two‐stranded α‐helical coiled‐coil is an ideal model for studying protein stability and subunit interactions
Authors: Zhou Nian E. , Zhu Bing‐Yan , Kay Cyril M. , Hodges Robert S. 
Published: December 2004

AbstractWe have designed de novo a two‐stranded α‐helical coiled‐coil which consists of two identical 35‐residue polypeptide chains arranged in a parallel and in‐register alignment. Their structure is stabilized by interchain hydrophobic interactions from hydrophobes at positions “a” and “d” of a repeating heptad sequence. The formation and stability of the coiled‐coil is dependent on peptide concentration due to the monomer‐dimer equilibrium. In contrast, the coiled‐coil containing an inter‐helical disulfide bond does not show any concentration dependence in the guanidine hydrochloride denaturation experiments as expected. Replacement of one large hydrophobic Leu residue in each chain with Ala significantly decreases coiled‐coil stability in both the reduced and oxidized coiled‐coils [decreases in transition midpoint of 1.6M (2.3 − 0.7) and 2.4M (5.3 − 2.9), respectively]. A large pH dependence on coiled‐coil stability is observed over the pH range 4 to 7 (transition midpoints at pH 4, 5, 5.5, 6 and 7 were 3.8, 3.2, 2.0, 1.2 and 0.7M, respectively). The increasing stability with decreasing pH correlates with the protonation of the Glu acid side‐chains and reduction of intrachain repulsions between Glu‐Glu side‐chains in positions i, i + 3 or i, i + 4 along each α‐helix of the coiled‐coil. In addition, coiled‐coil stability increases with increasing ionic strength.
Determination of the ϕ angle in a peptide backbone by NMR spectroscopy with a combination of homonuclear and heteronuclear coupling constants
Authors: Schmieder Peter , Kessler Horst 
Published: December 2004

AbstractThe ϕ angle in a cyclic peptide is determined by the combined use of homonuclear and heteronuclear coupling constants. Two of the four coupling constants that define the ϕ angle in a peptide are determined exactly, two qualitatively. Via Karplus‐type equations, they are transformed into dihedral angles and a good agreement is found, allowing for a determination of the ϕ angle with a certain range of degrees.