bluuebunny/crossref_metadata_2025_split huggingface dataset:
The influence of glycerol on hydrogen isotope exchange in lysozyme
Authors: Gregory Roger B. 
Published: December 2004

AbstractHydrogen isotope exchange rates for lysozyme in glycerol cosolvent mixtures [D. G. Knox and A. Rosenberg (1980) Biopolymers 19, 1049–1068] have been analyzed as functions of solvent viscosity and glycerol activity in an attempt to determine which solvent properties influence protein internal dynamics. The effect of glycerol on the fast‐ and slow‐exchanging protons is different. Slow‐exchanging protons [H(t) < 20] are slowed by ever‐increasing amounts as H(t) decreases. However, comparison with data for the effect of glycerol on the thermal unfolding of lysozyme [K. Gekko (1982) J. Biochem. 19, 1197–1204] indicates that the large decrease in exchange rates for the slow protons is not consistent with a local unfolding mechanism of exchange. These effects are also too large to be easily rationalized in terms of solvent viscosity. Instead, we suggest that the large effect of glycerol on exchange of the slow protons is due to a “compression” of the protein, as a result of thermodynamically unfavorable interactions of glycerol with the protein surface. This reduces the protein void volume, which in turn decreases the probability of conformational transitions required for exchange of the slowest protons. Present data do not allow a distinction to be made between thermodynamic (glycerol activity) and dynamic (solvent viscosity) influences on exchange rates for the fast‐exchanging protons, although the effect of glycerol on these protons is also probably too large to be consistent with a local unfolding mechanism. In this case, glycerol decreases the rate of catalyst diffusion within the protein matrix, either by decreasing the probabilities or amplitudes of “gating” reactions that allow passage of the catalyst from the solvent to the exchange site, or by increasing the relaxation times for these conformational rearrangements.
Cluster analysis of protein fourier transform infrared spectra
Authors: Lipkus Alan H. , Lenk Thomas J. , Chittur Krishnan K. , Gendreau R. Michael 
Published: December 2004

AbstractCluster analysis techniques were used to examine a set of Fourier transform infrared (FT‐IR) spectra of bovine serum albumin (BSA) in the adsorbed and nonadsorbed states. The region from 1480 to 1600 cm−1, comprising the amide II band, was used. Spectra were preprocessed to compensate for linear baseline variation, and the single linkage method of cluster analysis was applied. As expected, the spectra of adsorbed and nonadsorbed BSA fell into two distinct clusters. However, no further clustering was observed among the adsorbed BSA spectra on the basis of surface type, suggesting that surface specificity of the spectral changes induced in BSA by adsorption is not detectable above experimental variation. This work illustrates the value of using cluster analysis in the FT‐IR study of proteins as a complement to other data analysis methods.
Pseudopeptides and β folding: X‐ray structures compared with structures in solution
Authors: Aubry André , Marraud Michel 
Published: December 2004

AbstractIn order to restrain the flexibility of the peptide molecules and reduce their biodegradation, modifications of the main chain are now introduced in pseudopeptide analogues. Surprisingly, there is very little data on the conformational properties of these derivatives. We have examined pseudopeptide analogues of RCO‐X‐Y‐NHR′ model dipeptides in the depsi, N‐methylated, reduced, retro, α, β‐dehydro, β‐amino acid, and hydrazino series, in the solid state by x‐ray diffraction, and in solution by ir and 1H‐nmr spectroscopy. This study provides us with accurate dimensions of the peptide surrogates, and gives some information on the conformational tendencies induced by these substitutions, with reference to those of the related dipeptide sequences.
Structural versatility of peptides from Cα,αdialkylated glycines: Linear Ac3c homo‐oligopeptides
Authors: Benedetti E. , Di Blasio B. , Pavone V. , Pedone C. , Santini A. , Crisma M. , Valle G. , Toniolo C. 
Published: December 2004

AbstractThe crystal‐state molecular structures of five linear Ac3c homo‐oligopeptides to the tetramer were determined by x‐ray diffraction. The oligomers are H‐(Ac3c)2‐OMe, Fmoc‐(Ac3c)2‐OMe MeOH, Ac‐(Ac3c)2‐OMe, pBrBz‐(Ac3c)3‐OMe · H2O, and t‐Boc‐(Ac3c)4‐OMe · 2H2O. The results indicate the propensity of the tri‐ and tetrapeptides to fold into type I β‐bends and distorted 310‐helices, respectively, in partial contrast to Aib, Ac5c, and Ac6c homo‐peptides of comparable main‐chain length, where regular type III β‐bends and 310‐helical structures were found. When the influence of the constraints produced by the intramolecular H bonds of the C10‐type is absent, other less common structural features may be observed. The average geometry of the cyclopropyl group of the Ac3c residue is found to be asymmetric and the NCαC′ bond angle significantly expanded from the regular tetrahedral value.
1H‐nmr studies of synthetic polypeptide models of Plasmodium falciparum circumsporozoite protein tandemly repeated sequence
Authors: Esposito G. , Pessi A. , Verdini A. S. 
Published: December 2004

AbstractThe major immunodominant region of the coating protein of Plasmodium falciparum sporozoites contains multiple tandem copies of the sequence Asn‐Ala‐Asn‐Pro (NANP). Current efforts for the development of an antisporozoite vaccine are focused on the synthesis of polypeptides reproducing part of the circumsporozoite protein repeat sequence and, in an attempt to relate conformational properties and biological response, 1H‐nmr one‐ and two‐dimensional studies of the synthetic models (NANP)2NA and (NANP)6 were carried out in water and water/methanol mixtures, at 400 and 500 MHz. In water, (NANP)6 undergoes fast conformational averaging. At variance, in water/methanol, the molecule appears to adopt an extensive structure, but detailed analysis is impaired by high spectral degeneracy. Based on the results obtained with (NANP)2NA and from preliminary expermints in water/trifluoroethanol, an interpretation is suggested for the (NANP)6 data in water/methanol in terms of a mixed sequence of βI‐turns and half‐turns (or/and γI‐turns) around the positions Ni−1‐Pi‐Ni+1.
Conformation and ion binding properties of peptides related to calcium binding domain III of bovine brain calmodulin
Authors: Borin Gianfranco , Ruzza Paolo , Rossi Maura , Calderan Andrea , Marchiori Fernando , Peggion Evaristo 
Published: December 2004

AbstractThe conformational and ion binding properties of the sequences 93–104, 96–104, and 93–98 of domain III of bovine brain calmodulin (CaM) have been studied by CD and Tb3+‐mediated fluorescence. In aqueous solution the interaction of all fragments with Ca2+ and Mg2+ ions is very weak and without any effect on the peptide conformation, which remains always random. In trifluoroethanol the interaction is very strong and the different fragments exhibit very distinct binding properties. In particular, the dodecapeptide fragment 93–104, and its N‐terminal hexapeptide 98–104, bind calcium and magnesium with a very high binding constant (Kb > 105M−1), undergoing a substantial conformational change. The structural rearrangement is particularly evident in the hexapeptide fragment, which tend to form a β‐bend. The C‐terminal nonapeptide fragment 96–104 interacts with calcium and magnesium more weakly, and the binding process causes a decrease of ordered structure. These results suggest that, even in the entire dodecapeptide sequence corresponding to the loop of domain III of CaM, the calcium binding site is shifted toward the N‐terminal hexapeptide segment. This interpretation is consistent with the results of crystallographic studies of CaM, which show that the calcium ions are located toward the amino terminal portion of the loop.
The crystal and molecular structure of the α‐helical nonapeptide antibiotic leucinostatin A
Authors: Cerrini S. , Lamba D. , Scatturin A. , Rossi C. , Ughetto G. 
Published: December 2004

AbstractThe crystal and molecular structure of the nonapeptide antibiotic leucinostatin A, containing some uncommon amino acids and three Aib residues, has been determined by x‐ray diffraction analysis. The molecule crystallizes in the orthorhombic space group P212121, a = 10.924, b = 17.810, c = 40.50 Å, C62H111N11O13, HCl · H2O, Z = 4. The peptide backbone folds in a regular right‐handed α‐helix conformation, with six intramolecular i ← (i + 4) hydrogen bonds, forming C13 rings. The nonapeptide chain includes at the C end an unusual β‐Ala residue, which also adopts the helical structure of the other eight residues. In the crystal the helices are linked head to tail by electrostatic and hydrogen‐bond interactions, forming continuous helical rods. The crystal packing is formed by adjacent parallel and antiparallel helical rods. Between adjacent parallel helical columns there are only van der Waals contacts, while between adjacent antiparallel helical columns hydrogen‐bond interactions are formed.
Conformations of dehydrophenylalanine containing peptides: nmr studies of an acyclic hexapeptide with two Δz‐Phe residues
Authors: Chauhan V. S. , Uma K. , Kaur Paramjeet , Balaram P. 
Published: December 2004

AbstractThe conformation of an acyclic dehydrophenylalanine (Δz‐Phe) containing hexapeptide, Boc‐Phe‐Δz‐Phe‐Val‐Phe‐Δz‐Phe‐Val‐OMe, has been investigated in CDCl3 and (CD3)2SO by 270‐MHz 1H‐nmr. Studies of NH group solvent accessibility and observation of interresidue nuclear Overhauser effects (NOEs) suggest a significant solvent‐dependent conformational variability. In CDCl3, a population of folded helical conformations is supported by the inaccessibility to solvent of the NH groups of residues 3–6 and the detection of several NiH ⟷ Ni+1H NOEs. Evidence is also obtained for conformational heterogeneity from the detection of some CH ⟷ Ni+1H NOEs characteristic of extended strands. In (CD3)2SO, the peptide largely favors an extended conformation, characterized by five solvent‐exposed NH groups and successive CH ⟷ Ni+1 H NOEs for the L‐residues and CH ⟷ Ni+1H NOEs for the Δz‐Phe residues. The results suggest that Δz‐Phe residues do not provide compelling conformational constraints.
Effect of the mitogenic lectin concanavalin A on the thermotropic behavior of glycosyl‐free cationic lipids and their mixtures with zwitterionic lipids
Authors: Lüscher‐Mattli Madeleine 
Published: December 2004

AbstractThe effect of concanavalin A (Con A) on the thermotropic behavior of positively charged, glycosyl‐free lipids and their mixtures with zwitterionic lipids was investigated by differential scanning calorimetry.The gel to liquid‐crystal phase transition enthalpy of pure dipalmitoylcholine (DPC) was found to be significantly increased in the presence of Con A (ΔH = 31.2 and 42.5 KJ mol−1 lipid in the presence and in absence of Con A, respectively). Addition of the lectin to DPC liposomes, furthermore, induces the appearance of a new phase transition centered at 320 K. These results are interpretable by a partial hydrophobic interdigitation of the lectin molecule into the liposomal bilayer.The effect of Con A on the phase behavior of three 2:1 mixtures of zwitterionic and of positively charged lipids was also investigated. Phase diagrams of the systems dipalmitoylphosphatidylcholine‐dihydrosphingosine (DPPC‐DHS), sphingomyelin‐dipalmitoylcholine (SPM‐DPC), and dimyristoylphosphatidylcholine‐dipalmitoylcholine (DMPC‐DPC) are presented. In lipid mixtures of limited miscibility (DPPC‐DHS and SPM‐DPC), Con A induces pronounced phase‐separation effects. These effects are attributable to a direct hydrophobic interaction of the lectin with the liposomal bilayer and do not require the presence of specific receptor groups.The possible relationship between lectin‐induced phase separations in the lipid matrix of biomembranes, and the observed changes in membrane permeability, membranal enzymatic activities, etc., is briefly discussed.
Adduct‐induced base‐shifts: A mechanism by which the adducts of bulky carcinogens might induce mutations
Authors: Loechler Edward L. 
Published: December 2004

AbstractMost carcinogens have been shown to be mutagens, and DNA adducts are formed when mutagenic/carcinogenic substances react with DNA. It is generally believed these adduclts (or their derivatives) induce misreplication events that result in mutations. Many of the more potently mutagenic substances are bulky and three‐dimensionally complex, such as the polycyclic aromatic hydrocarbons, aromatic amines, and aflatoxins; little is known about the mechanisms by which they induce mutations. Several theories exist and herein an additional mechanism is proposed by which bulky adducts might induce mutations at GC base pairs. Molecular modeling in conjunction with molecular mechanical calculation is used to assess if the mutagen/carcinogen moiety of the adduct might be able to shift the position of the base moiety of the adduct in such a way that misreplication events might be facilitated. This mechanism is referred to as adduct‐induced base‐shift, and two classes appeared possible; adduct‐induced base‐wobble and adduct‐induced base‐rotation. The latter has been proposed previously. By addut‐induced, base‐wobble, the mutagen/carcinogen moiety of the adduct induces a shift in the position of the base moiety of the adduct with respect to the helix axis, which might facilitate mispairing events that are reminisent of non‐Watson/Crick pairing that occurs at the wobble base of tRNA during translation. For example, in some guanine adducts, the guanine appears more thymine‐like, which might facilitate G. A mispairing and thereby ultimately GC to TA transversion mutations. Adduct‐induced base‐rotation involves the rotation of the adducted base from the anti to the syn conformation and a variety of mispairing events might result.
The acceleration of linear DNA during pulsed‐field gel electrophoresis
Authors: Holzwarth G. , Platt Kevin J. , McKee Chad B. , Whitcomb Richard W. , Crater Glenn D. 
Published: December 2004

AbstractThe velocity and orientation of T4 and λ DNA have been measured for the first 20 s during pulsed‐field gel electrophoresis in order to clarify the DNA motions that occur. For a square pulse with field strength E = 10 V/cm, the velocity of λ DNA increases gradually to 10.5 μm/s in 1.0 s, declines to 8.6 μm/s, and then rises to a plateau value of 9.3 μm/s after 4 s. T4 DNA behaves similarly, but more slowly. Parallel measurements of fluorescence‐detected linear dichroism show that the DNA becomes substantially aligned with its chain axis parallel to the electrophoretic field E after the pulse is applied. The alignment also shows an overshoot, an undershoot, and a plateau comparable to those seen for velocity. When the field strength increases, both the velocity and the alignment reach their peaks more quickly. For all field strengths and both molecular weights, the velocity peak occurs when the molecular center of mass has moved 0.3 to 0.5 L, where L is the chain contour length. A qualitative model is provided.
Two‐dimensional 1H‐NMR study of the 1–34 fragment of human parathyroid hormone
Authors: Lee Susannie C. , Russell Anne F. 
Published: December 2004

AbstractThe complete assignment of resonances in the proton nmr spectrum of the 1–34 amino acid fragment of human parathyroid hormone [hPTH(1–34)], determined using a combination of one‐ and two‐dimensional nmr techniques at 500 MHz, is described. In particular, homonuclear Hartmann–Hahn experiments, recorded in H2O and D2O, are used to resolve ambiguities in the connectivities between the highly overlapped resonances in the aliphatic region of the spectrum. One‐dimensional multiple quantum filtering experiments are used to identify serine and phenylalanine spin systems. Analyses of the through‐bond and through‐space connectivities in the αH‐NH fingerprint regions of the correlated spectroscopy (COSY) and nuclear Overhauser effect spectroscopy (NOESY) spectra lead to the assignment of resonances to specific amino acid residues in the polypeptide. Examination of the observed NOE cross peaks indicates that hPTH(1–34) has no detectable secondary structural elements in aqueous solution.
Light scattering studies of bovine skin proteodermatan sulfate
Authors: Zangrando David , Gupta Rekha , Jamieson Alex M. , Blackwell John , Scott Paul G. 
Published: December 2004

AbstractThe proteodermatan sulfate (PDS) of bovine skin is a low molecular weight proteoglycan with a molecular structure consisting of a protein chain and a sulfated polysaccharide chain covalently linked at the 4‐serine of the protein. Static and dynamic laser light scattering methods have been used to determine the weight‐average molecular weight, Mw, z‐average radius of gyration, R′, and z‐average translational diffusion coefficient, Dt,z°, of bovine skin PDS. We have also characterized the two components of PDS, i.e., the protein core and the dermatan sulfate (DS) chain. (The latter contained an N‐terminal‐linked penta‐ or tetrapeptide.) Interpretation of the PDS data is complicated by the block copolymer nature of its structure. When appropriate corrections are made, our results indicate that Mw for PDS monomer is 62,000 when dissolved in 4M guanidine hydrochloride (GdnHCl), and increases to 610,000 in 0.15M NaCl. Mw for the core protein in 4M GdnHCl is 39,000, and this also increases substantially to 650,000 in 0.15M NaCl. In contrast, Mw for the DS chain is 24,000 in 0.15M NaCl, indicating that there is minimal self‐association of DS in 0.15M NaCl. Thus we conclude that the self‐association of PDS involves the protein core. Comparison of R and Rh, the average hydrodynamic radius, suggests that trace amounts of aggregation persist for the PDS and its core protein even in 4M GdnHCl. This conclusion is supported by evaluation of the second moments of the dynamic light scattering correlation function. Comparisons of the observed Dt,z° for PDS with predicted values using hydrodynamic theory are consistent with a “lollipop” conformation for the molecule.
The osmotic coefficients of the sodium form of some biopolymers
Authors: Jang Larry K. , Quintero Ernesto J. , Gordon Grisel , Röhricht Markus , Geesey Gill G. 
Published: December 2004

AbstractThe osmotic coefficients ϕp,Na of dilute solutions of the sodium form of some weakly acidic polymers are theoretically predicted in this work. Based on the measured value 0.73 of γNa, the activity coefficient of free Na+, of the completely ionized humic acid (sodium salt) in a salt‐free solution, the effective interligand distance b is calculated to be 11.34 Å by using Manning's counterion condensation theory [Manning, G. S. (1969) J. Chem. Phys. 51(3), 924]. The corresponding values of γNa (measured experimentally) and b for the completely ionized exopolymer of Pseudomonas atlantica are 0.624 and 7.57 Å when cultivated at a dilution rate D = 0.015 h−1, 0.647 and 8.19 Å at D = 0.025 h−1, and 0.613 and 7.29 Åat D = 0.06 h−1. For alginic acid (in the completely ionized sodium form), γNa = 0.40 and b = 4.71 Å. The osmotic coefficients ϕp,Na for the partially and the completely ionized polymers are then predicted with Manning's theory as well.
Time‐resolved synchrotron radiation x‐ray solution scattering study of DNA melting
Authors: Puigdomenech J. , Perez‐Grau L. , Porta J. , Vega M. C. , Sicre P. , Koch M. H. J. 
Published: December 2004

AbstractTime resolved x‐ray solution scattering measurements were made during thermal denaturation of DNA from various sources in the temperature range of 20–90°C. Preliminary results on the influence of fragement length, ionic strength, and origin of the DNA on the time course of the scattering are described. Interpretation is based on model calculations of the scattering patterns. The resluts indicate that, for long DNA fragments at very low ionic strength, the melting process is a continuous phenomenon over the whole temperature range. It is accompanied by a progressive decrease of the radius of gyration of the cross section and of the mass per unit length. For short fragments of 146 base pair nucleosomal core DNA, stiffening of the DNA appears to precede a sharp melting transition.
Glycosaminoglycan conformations and changes on periodate oxidation
Authors: Ueno Norio , Chakrabarti Bireswar 
Published: December 2004

AbstractThe progressive periodate oxidation of glycosaminoglycans (GAG), including hyaluronate (HA), chondroitins (CH) (chondroitin, chondroitin 4‐ and 6‐sulfate), dermatan sulfate (DS), and keratan sulfate (KS), were monitored by CD and high performance liquid chromatography (HPLC) using a size‐exclusion column. The rate of oxidation also was measured and calculated using first‐ and second‐order kinetics, and the data appear to fit better with first‐order kinetics. In both HA and CH, the n – π* amide band at 208 nm decreases in intensity upon oxidation, but in HA it becomes positive after 16 h of periodate treatment. In CH, the band disappears, and the π – π* amide band below 200 nm becomes optically active. Concomitantly, a second negative band near 290 nm appears for these two oxidized GAG. Oxidation causes a slight change in the CD of DS. It ordinarily displays a very weak n – π* band at 210 nm, but instead shows an intense π – π* amide band near 190 nm. CD of KS remains unaffected by periodate. Kinetic studies, however, show a higher oxidation rate for DS than HA and CH. With the exception of KS, all other oxidized polymers shown an apparent decrease in molecular weight (higher peak retention time) in HPLC analysis. Both CD and HPLC results have been attributed to a major conformational cahange of HA and CH, and a minor one for DS. The ease and extent of periodate oxidation as well as the changes in molecular properties following periodate treatmenat are critically dependent on the changes in molecular properties following periodate treatment are critically dependent on the configuration of the individual GAG rather than the oxidation rate. There is a distinct difference in the conformational change between HA and CH, as manifested by their dichroic behavior, that was attributed to the equatorial disposition of C‐4 hydroxyl group in HA and axial disposition CH.
Secondary structure of a core protein from pig skin proteodermatan sulfate: Cd and fourier transform ir spectroscopic studies in solution
Authors: Renugopalakrishnan V. , Damle Shridhar P. , Horowitz Paul M. , Moore Sheri , Hutson Timothy B. , Gregory John D. 
Published: December 2004

AbstractThe secondary structure of a 38 kDa core protein from pig skin proteodermatan sulfate (PDS), was investigated in solution using CD and Fourier transform (FT) ir spectroscopy. Both techniques generally have provided complementary data on the secondary structures of proteins. CD spectral analysis has shown that the core protein contains 60% β‐turn and α‐helical structures, the rest being “unordered” structure. FT ir data do not permit calculation of quantitative contributions of substructures, at the present time, to the overall secondary structure of the core protein. CD spectrum of the intact PDS is similar to the core protein CD spectrum.