bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of the L‐azetidine‐2‐carboxylic acid residue on protein conformation. I. Conformations of the residue and of dipeptides
Authors: Zagari Adriana , Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractThe L‐azetidine‐2‐carboxylic acid (Aze) residue can be incorporated into proteins in the place of L‐proline, of which it is the lower homologue. This substitution alters the properties of proteins, especially of collagen. Conformational constraints in N‐acetyl‐Aze‐N′‐methylamide and in several dipeptides containing Aze have been analyzed by means of energy computations. They have been compared with peptides containing Pro. The overall con‐formational preferences of Aze and Pro are similar, but several significant differences occur between them. In general, peptides containing Aze are somewhat more flexible than corresponding peptides containing Pro, because of a decrease in constraints caused by repulsive nonconvalent interactions of the atoms of the ring with neighboring residues. This results in an entropic effect that lessens the stability of ordered polypeptide conformations with respect to the disordered statistical coil. The collagen‐like near‐extended conformation is energetically less favorable for Aze than for Pro in the single residue and in dipeptides. This effect also contributes to a destabilization of the collagen triple helix. The influence of Aze on the conformation of polypeptides is discussed in the accompanying papers.
Evidential study of correlated events in biochemistry: Physicochemical mechanisms of nucleic acid hydration as revealed by factor analysis
Authors: Starikov E. B. , Semenov M. A. , Ya. Maleev V. , Gasan A. I. 
Published: December 2004

AbstractUsing a factor analysis technique, the experimental physicochemical data on the hydration of mononucleotides, several polynucleotides, their double‐helical complexes and natural DNAs were studied. The information about the factors determining the changes in physicochemical parameters vs the hydration was obtained. This work discusses a possible physical sense of the factors obtained and the expedience of using factor analysis to interpret the molecular‐biophysical experiments.
Toward the elucidation of the mechanism of attachment and entry of malaria sporozoites into cells: Synthetic polypeptides from the circumsporozoite protein of Plasmodium falciparumbind Ca2+ and interact with model phospholipid membranes
Authors: Verdini Antonio S. , Chiappinelli Lorella , Zanobi Antonio 
Published: December 2004

AbstractThrough the joint use of CD, Fourier transform ir (FTIR), and attenuated total reflectance FTIR we have found that synthetic polypeptide models of the Plasmodium falciparum circumsporozoite (CS) protein repeat domain bind calcium ions in helicogenic environments. Ca2+‐(NANP)n complexes (n ⩾ 20) interact vectorially with model phospholipid membranes orienting their polypeptide axes preferentially along those of the lipid acyl chains. It is proposed that the P. falciparum CS protein central region, rather than acting as a molecular lure helping the parasite to evade host immune control, plays, as a specific Ca2+ macroligand, a critical functional role during attachment, invasion, and development of the malaria parasite in the hepatic cell.
Conformational preferences and the role of the statine residue in the crystal state
Authors: Precigoux Gilles 
Published: December 2004

AbstractThe present paper is the result of an analysis of the available crystal structure data related to the statine amino acid so as to obtain information about bond lengths, bond angles, and preferential conformations. The number of configurations actually observed is small; nevertheless, some characteristic conformations should be pointed out for statine‐containing peptides. The presence of two additional carbon atoms in the statine main chain enhances the peptide conformational degree of freedom and the statine‐containing peptides are observed in a variety of different conformations including some usual secondary structure‐types as β‐turns and β‐strands.
Conformation‐based design of two cyclic physalaemin analogues
Authors: Hölzemann Günter , Jonczyk Alfred , Eiermann Volker , Pachler Klaus C. R. , Barnickel Gerhard , Regoli Domenico 
Published: December 2004

AbstractTwo new cyclic analogues of physalaemin were designed on the basis of the conformation found in DMSO solution. Glp‐Ala‐cyclo(‐Asp‐Pro‐Asn‐Lys‐)‐Phe‐Tyr‐Gly‐Leu‐Met‐NH2(1) was synthesized by cyclization of physalaemin. In 2 the Asp residue was replaced by Glu. The linear analogue of 2 was synthesized by the solid phase method and subsequently cyclized. Two‐dimensional nmr methods were employed to assign the proton and carbon resonances. Proton–proton distances were extracted from rotating frame nuclear Overhauser effect spectra and used as restraints in the molecular dynamics calculations. Analogue 1 was found to have a similar conformation as physalaemin, whereas 2 did not form intramolecular hydrogen bonds. The pharmacological evaluation revealed that both peptides have similar potencies as physalaemin in the dog carotid artery (NK‐1 receptor). Therefore, the charged side chains of physalaemin appear not essential for NK‐1 activation. However, the other tachykinin receptors show good sensitivity to the cyclic peptides. It is concluded that the replacement of a salt bridge by an amide bond connecting the side chains of natural residues might provide useful information about the biological significance of some charged side chains of neurokinins.
Prediction of fluorine chemical shifts in proteins
Authors: Gregory D. H. , Gerig J. T. 
Published: December 2004

AbstractMolecular dynamics calculations have been used in an effort to estimate the change in fluorine nmr shielding when a fluorine nucleus enters the tertiary structure of a protein. Considerations of the possible interactions that can define the shift parameter change suggest that van der Waals interactions are the leading determinant of fluorine shifts in proteins, although aromatic ring currents, other magnetic anisotropies, and electrostatic field effects could result in shift distinctions of 1 ppm or smaller. Results of our studies of a fluorine‐containing analogue of the ribonuclease A S‐protein/S‐peptide complex indicate that static structures such as those implied by crystallographic data lead to overestimates of the magnitude of the van der Waals shielding term; molecular dynamics simulations provide indications of the effects of conformational averaging in defining this term. The treatment used predicts the correct direction of the shift change when the fluorine enters this protein environment from aqueous solution and, with an experimentally supported choice of adjustable parameters, gives agreement with the magnitude of the shift.
An antigenic determinant common to human chorionic somatomammotropin and human growth hormone revealed by limited proteolysis of immune complexes
Authors: Santucci Annalisa , Rustici Mauro , Bracci Luisa , Neri Paolo 
Published: December 2004

AbstractAn epitope of human chorionic somatomammotropin for one of the monoclonal antibodies raised against the whole antigen has been identified. We compared the release of peptides from limited proteolysis of the antigen in the presence and absence of the related antibody. Using enzymes of different specificity, we could determine the amino acid sequence that can be considered at least inclusive of the epitope. The monoclonal antibody selected is 100% cross‐reactive with human growth hormone, so the antigenic determinant identified is shared by the two protein hormones.
Differential behavior of the two free sulfhydryl groups of human plasma fibronectin: Effects of environmental factors
Authors: Narasimhan C. , Lai Ching San 
Published: December 2004

AbstractWe report here a novel approach to label specifically one of the two cryptic, free sulfhydryl groups per subunit of human plasma fibronectin with either an 15N, 2H‐maleimide spin label or a coumarinylphenyl maleimide fluorescent label. This permits the use of electron spin resonance (ESR) or fluorescence techniques to study molecular dynamics of fibronectin with the label attached to a single site per chain on the protein molecule. The method is based on our observation that upon adsorption of fibronectin to a gelatin‐coated surface, the SH1 site, located between the DNA‐binding and the cell‐binding domains, is partially exposed, while the SH2 site, located within the carboxyl‐terminal fibrin‐binding domain, remains buried and unreactive. The procedures for the preparation of the selectively labeled fibronectins are described in detail. The physicochemical properties of these single‐site labeled fibronectins, particularly as affected by high salt, heparin, surface binding, and temperature, were characterized by ESR spin‐label and steady‐state fluorescence techniques. The steady‐state fluorescence measurement indicates that both local environments of SH1 and SH2 sites are relatively hydrophobic, and that the SH2 site is more hydrophobic than the SH1 site. The ESR results show that heparin or high salt induces an increase in the domainal flexibility in both SH1 and SH2 regions, perhaps through the disruption of domain–domain interactions in the fibronectin molecule, and that the former is more effective than the latter in producing such an effect. The observed heparin effect is reversible by addition of calcium ions in the SH2 regions but not in the SH1 regions. In addition, at temperatures above 44°C, both type III homologous regions containing the free sulfhydryl groups are shown to undergo denaturation and aggregation processes. The data presented here suggest that the newly developed method for differential labeling of the free sulfhydryl groups in fibronectin should be useful for mapping the spatial arrangement of structural domains in the protein molecule using spin‐label–spin‐probe and fluorescence energy transfer techniques.
Conformational studies on bombesin antagonists: CD and NMR characterization of [Thr6, Leu13ψ(CH2NH) Met14] bombesin (6–14)
Authors: Di Bello Carlo , Scatturin Angelo , Vertuani Gianni , D'Auria Gabriella , Gargiulo Mario , Paolillo Livio , Trivellone Enrico , Gozzini Luigia , De Castiglione Roberto 
Published: December 2004

AbstractThe conformational flexibility of the [Thr6, Leu13ψ(CH2NH) Met14]bombesin (6‐14) nonapeptide has been studied by CD and one‐ and two‐dimensional (1D and 2D) nmr techniques. The CD and nmr parameters in different solvents and in a micellar environment (SDS) are compared with the data collected for the parent bombesin (BN) and [D–Phe12, Leu14]BN. A preliminary investigation on spantide is also reported. In particular, the results obtained from CD measurements indicate that there is a shift from random coil structures, in aqueous solutions, toward folded structures in apolar media (2,2,2‐trifluoroethanol) and in a membrane–mimetic environment (40 mM SDS) for all three peptides, namely BN, [D‐Phe12, Leu14]BN, and [Thr6, Leu13ψ(CH2NH)Met14]BN (6‐14). Spantide, which also possesses some inhibitory activity against BN but very little sequence similarity, even in water, shows an ordered conformation. Nuclear magnetic resonance parameters such as backbone NH‐αCH coupling constant values, amidic temperature coefficients, and the presence of only sequential nuclear Overhauser effects have not provided, so far, any clear evidence for a preferential ordered structure in the peptides studied, and this may be due to rapid exchange among different conformers in the nmr time scale.
A general approach for determining scalar coupling constants in polypeptides and proteins
Authors: Montelione Gaetano T. , Emerson S. Donald , Lyons Barbara A. 
Published: December 2004

AbstractA general approach is described for measuring homo‐ and heteronuclear spin coupling constants in polypeptides and small proteins. This method uses selective magnetization transfer to generate cross peaks similar to exclusive correlated spectroscopy (E.COSY) and a large direct spin coupling (1J) in one dimension to “pull apart” cross‐peak components by frequencies much larger than the resonance line width. A general description of this method is presented, along with a brief discussion of spin topology and relaxation effects that must be considered in designing multidimensional nmr pulse sequences for measuring vicinal coupling constants. The principles are demonstrated in designs of several two‐dimensional nmr experiments for determining coupling constants in polypeptides and proteins. These include experiments for measuring 3J(HN‐Hα), 3J(H‐15Ni), 3J(15N‐Hβ), and 3J(Hα‐Hβ) coupling constants, which depend on the polypeptide dihedral angles ϕ, ψ and χ1. Multidimensional nmr experiments developed with this approach will allow measurements of many vicinal coupling constants in peptides, proteins, and other molecules. Coupling constants measured in these spectra can be used to determine backbone and side‐chain conformations, to obtain stereospecific resonance assignments of prochiral atoms, and to characterize conformational distributions of dihedral angles. Combined with information obtained from nuclear Overhauser effect measurements, these data will provide more precise determinations of protein solution structures by nmr spectroscopy.
Fixation of aldehydic dextrans onto human deoxyhemoglobin
Authors: Klett D. , Grandgeorge M. , Dellacherie E. 
Published: December 2004

AbstractA procedure commonly used to transform native adult human hemoglobin (Hb) into a physiological oxygen carrier consists of a pyridoxylation of the protein to lower its oxygen affinity, followed by its polymerization in the presence of glutaraldehyde, with or without further reduction, to increase its circulating half‐life. This series of reactions yields derivatives presenting a great molecular heterogeneity that have to be fractionated for use in vivo. Hemoglobin derivatives with low oxygen affinity and a narrow distribution of molecular weights were obtained by linking a dextran polyaldehydic derivative to deoxyhemoglobin at pH 8. From oxygen‐binding measurements carried out in the presence of inositolhexaphosphate, a strong effector of hemoglobin, it appeared that the allosteric site of hemoglobin was blocked, probably by crosslinking bonds, which stabilizes its deoxy structure. On the other hand, when the reaction was performed in the presence of inositolhexaphosphate, the resulting conjugates exhibited an oxygen affinity identical to that of unmodified hemoglobin. After treatment with NaBH4, the polymer–hemoglobin derivatives were stable and possessed a reversible oxygen‐carrying capacity similar to that of blood. The conjugates prepared from oxyhemoglobin all possessed a lower P50 than native hemoglobin whatever the reaction conditions.
Partial molar volumes of the amino acid side‐chains of proteins in aqueous solution: Some comments on their estimation using partial molar volumes of amino acids and small peptides
Authors: Hedwig Gavin R. 
Published: December 2004

AbstractThe partial molar volumes of some amino acid side‐chains were determined in two recent studies [Makhatadzes, G. I., et al. (1990) Biopolymers 30, 1001, and Reading, J. F. & Hedwig, G. R. (1990) J. Chem. Soc. Faraday Trans. 86, 3117] using partial molar volume data, V, in aqueous solution at 25°C for some peptides of sequence Gly‐X‐Gly, where X is an amino acid. These side‐chain partial molar volumes are critically compared with those obtained using V data for amino acids. It is concluded that side‐chain partial molar volumes calculated using V data for the tripeptides are better estimates of side‐chain partial molar volumes in proteins than are those determined using V data for amino acids.
Crystal and molecular structure of the doubly unsaturated dehydropeptide Ac‐ΔPhe‐Ala‐ΔPhe‐NH‐Me
Authors: Ciajolo M. Rosaria , Tuzi Angela , Pratesi Claudio R. , Fissi Adriano , Pieroni Osvaldo 
Published: December 2004

AbstractThe dehydropeptide Ac‐ΔPhe‐L‐Ala‐ΔPhe‐NH‐Me, containing two dehydro‐phenylalanine (ΔPhe) residues, crystallizes from methanol/water in space group P212121, with a = 12.508 (2), b = 12.746(1) and c = 15.465(9).In the crystalline state, the peptide chain assumes a right‐handed 310‐helical conformation stabilized by two intramolecular hydrogen bonds, between the N‐terminal acetyl group and the NH of ΔPhe3, and between the CO of ΔPhe1 and the NH of the C‐terminal methylamide group, respectively. The two consecutive 10‐membered rings formed by the hydrogen bonds have torsion angles quite close to the standard values for type III β‐bends. ΔPhe1 is located in the (i + 1) position of the first β‐bend, while ΔPhe2 is located in the (i + 2) position of the other β‐bend.In the crystal, the molecules are linked head to tail by intermolecular hydrogen bonds to form long helical chains. The axes of the helices are parallel to the c axis, but neighboring helices run in antiparallel directions. This crystal packing is similar to the packing motifs frequently observed in Aib‐containing peptides.
Studies of DNA dumbbells. III. Theoretical analysis of optical melting curves of dumbbells with a 16 base‐pair duplex stem and Tn end loops (n = 2, 3, 4, 6, 8, 10, 14)
Authors: Paner Teodoro M. , Amaratunga Mohan , Benight Albert S. 
Published: December 2004

AbstractOptical melting curves of seven DNA dumbbells with the 16 base‐pair duplex sequence 5′G‐C‐A‐T‐A‐G‐A‐T‐G‐A‐G‐A‐A‐T‐G‐C3′ linked on both ends by Tn (n = 2, 3, 4, 6, 8, 10, and 14) loops measured in 30, 70, and 120 mM Na+ are analyzed in terms of the numerically exact statistical thermodynamic model of DNA melting. The construction and characterization of these molecules were described in the previous paper (Amaratunga et al., 1992). As was recently reported for hairpins (T. M. Paner, M. Amaratunga, M. J. Doktycz, and A. S. Benight, 1990, Biopolymers, Vol. 29, pp. 1715‐1734) theoretically calculated melting curves were fitted to experimental curves by simultaneously adjusting the parameters representing loop and circle formation to optimize the fits. The systematically determined empirical parameters provide evaluations of the free energies of hairpin loop formation ΔGloop(n) and single‐strand circles ΔGcircle(N), as a function of end loop size, n = 2–14, and circle size, N = 32 + 2n. The dependence of these quantities on solvent ionic strength over the range from 30 to 120 mM Na+ was evaluated. An approximately analytical expression for the partition function Q(T) of the dumbbells was formulated that allowed a means for determining the transition enthalpy ΔH° and entropy ΔS° for every dumbbell, revealing the dependence of these quantities on loop size. In this multistate approach a manifold of partially melted intermediate microstates are considered and therefore no assumptions regarding the nature of the melting transitions (that they are two‐state) are required. The transition thermodynamic parameters were also determined from a van't Hoff analysis of the melting curves. Comparisons between the results of the multistate analysis and the two‐state van't Hoff analysis revealed significant differences for the dumbbells with larger end loops, indicating that the melting transitions of the larger looped dumbbells deviate considerably from two‐state behavior. Results are then compared with published melting studies of much larger DNA dumbbells (D. B. Naritsin and Y. L. Lyubchenko, 1990, Journal of Biomolecular Structure and Dynamics, Vol. 8, pp. 1–13), of small hairpins (Paner et al., 1990; M. J. Doktycz, T. M. Paner, M. Amaratunga and A. S. Benight, 1990, Biopolymers, Vol. 30, pp. 829–845) and another dumbbell (A. S. Benight, J. M. Schurr, P. F. Flynn, B. R. Reid, and D. E. Wemmer, 1988) Journal of Molecular Biology, Vol. 200, (pp. 377–399). ΔGloop (n = 4) and ΔGcircle (40) were also evaluated from analysis of the melting curves of the 15 DNA dumbbells with 16 base‐pair stems presented in the first paper (Doktycz et al., 1992). With the exception of the dumbbell with the central sequence 5′‐T‐T‐A‐A‐3′, these quantities were found to be virtually independent of the sequence identity of the central 4 base pairs of the stem.
Vibrational studies of the disulfide group in proteins. VI. General correlations of SS and CS stretch frequencies with disulfide bridge geometry
Authors: Qian Weili , Krimm Samuel 
Published: December 2004

AbstractNormal mode calculations have been done on a range of disulfide bridge conformations in order to determine how the SS stretch and CS stretch frequencies depend on structure. In addition to varying the CαCβSS and NCαCβS dihedral angles, we have varied the ϕ,Ψ of the adjoining peptide groups since we have shown that these also influence the above frequencies. In order to obtain structural information from the observed frequencies, we have done a study of the conformational states found in 92 disulfide bridges in 25 known protein structures. This permits making a statistically based correlation between CS stretch frequencies and the possible contributing conformers. © 1992 John Wiley & Sons, Inc.
Conformation of diastereomeric peptide sequences: Structural analysis of Z‐D‐Val‐Ac6c‐Gly‐L‐Phe‐OMe
Authors: Di Blasio B. , Lombardi A. , Nastri F. , Saviano M. , Pedone C. , Yamada T. , Nakao M. , Kuwata S. , Pavone V. 
Published: December 2004

AbstractWe have recently undertaken a systematic structural analysis of fully protected tetrapeptides containing at the N‐ and C‐terminus either homo‐ or heterochiral amino acids, spaced by an achiral dipeptide segment. The interest for this class of peptides derives from the observation that, on reverse‐phase (HPLC), the homo‐ and heterochiral sequences have a markedly different retention times. The diastereomeric sequences, namely Z‐(L/D)‐Val‐X‐Y‐L‐Phe‐OMe (X = Sar, Gly, Ac3c, Aib, Ac5c, Ac6c, Deg, Dpg, Dbu, Dip, Dph; Y = Sar, Gly, Ac3c, Aib, Ac6c, Ac6c) show different overall hydrophobicity attributed to a different three‐dimensional structure that also depends on the X‐Y segment. Therefore, following preliminary studies in solution, we report here the detailed x‐ray analysis of the tetrapeptide Z‐D‐Val‐Ac6c‐Gly‐L‐Phe‐OMe in order to understand the structural features governing the overall hydrophobicity of linear fully protected tetrapeptides. © 1992 John Wiley & Sons, Inc.
Determination of the aromatic lignin content in oak wood by quantitative solid state 13C‐NMR
Authors: Love G. D. , Snape C. E. , Jarvis M. C. 
Published: December 2004

AbstractThe problems concerning quantification with cross polarization (CP) and high‐field 13C‐nmr measurements has meant that, for ligno‐cellulosic plant materials, aromatic carbons in lignins are often discriminated against. In this study, the aromatic lignin content of an American red oak sample has been determined at the relatively low field strength of 25 MHz to obviate problems with spinning side bands using both CP and Bloch decay or single pulse excitation (SPE), a more time‐consuming acquisition technique but that is, in many cases, considerably more quantitative than CP. The value of 14 mole % carbon from SPE is in close agreement with that of 15% derived from elemental analysis and the Klason lignin content. Although virtually all of the carbon was observed by both SPE and CP, the latter significantly underestimated the aromatic content at contact times less than 1.5 ms and thus longer times should be used for reliable quantification. The quaternary carbon content was estimated as 11 mole % carbon by combining dipolar dephasing with SPE and CP. © 1992 John Wiley & Sons, Inc.