bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis and conformational analysis of N‐glycopeptides. II. CD, molecular dynamics, and nmr spectroscopic studies on linear N‐glycopeptides
Authors: Perczel András , Kollát Emma , Hollósi Miklós , Fasman Gerald D. 
Published: December 2004

AbstractThe comprehensive structural analysis reported herein of eight N‐glycopeptides, in three different solvents, is based on quantitative CD experiments, homonuclear nuclear Overhauser effect measurements, and molecular dynamics (MD) calculations. Although several orientations of the two amide planes attached to the carbohydrate pyranose ring are possible, according to NOE, CD data, and MD simulations, of all of the glycopeptide models, regardless of the type of the carrier peptide, only one dominant conformer population was found. This conformer is characterized by a nearly trans orientation of the CH and NH hydrogens of both acetamido groups. This finding is in perfect agreement with x‐ray crystallographic data on the solid state conformation of the 1‐N‐acetyl‐ and 1‐N‐(β‐aspartoyl)‐2‐acetamido‐2‐deoxy‐β‐D‐glucopyranosylamine. The precise identification of this dominant conformer of N‐glycopeptides in solution was the major question addressed herein by the structural analyses. A “CD additivity” experiment was carried out using an equimolar solution of Boc‐Pro‐Asp‐NHCH3 and l‐N‐acetyl‐3,4,6‐tri‐O‐acetyl‐2‐acetamido‐2‐deoxy‐β‐D‐gluco‐pyranosylamine at ambient temperature in acetonitrile. The CD spectrum obtained from the equimolar solution of the above two molecules (the “spectroscopic sum”) was identical with the CD curve obtained from the algebraic summation of the individually recorded CD spectra of the peptide and the carbohydrate moiety (“mathematical sum”).The global picture of the CD spectral analyses of the eight parent peptides with the eight N‐glycopeptides revealed that in trifluoroethanol and acetonitrile, the side‐chain modification of the Asn models (natural N‐glycopeptide analogues) by N‐glycosylation has a significant effect on the conformation of the carrier peptide, resulting in a decrease in the original type I β‐turn content. Simultaneously, the type II β‐turn conformational percentage increased to ≈ 20%. Such a conformational ratio change seems to be larger than the expected errors arising from the CD analyses, and agrees with the results of MD calculations. N‐glycosylation of Asn residues causes perturbations, not only through the covalent bond, but also through specific hydrogen bonds between the backbone and side chain atoms. CD spectroscopy, augmented by efficient CD curve deconvolution techniques, has proved to be a useful tool for studying multicomponent conformer mixtures of small linear peptides in solution and changes of conformational equilibria caused by N‐glycosylation. © 1993 John Wiley & Sons, Inc.
Sol–gel transition of alginate solution by the addition of various divalent cations: 13C‐nmr spectroscopic study
Authors: Wang Zheng‐Yu , Zhang Qinc‐Zhi , Konno Mikio , Saito Shozaburo 
Published: December 2004

Abstract13C‐NMR spectroscopic studies have been made on alginate solutions undergoing sol–gel transition induced by four different divalent cations: Ca, Cu, Co, and Mn. From the analysis of nmr spectra and relaxation times, we have found different interaction modes existing between the Ca–alginate systems and the transition metal (Cu, Co, and Mn)–alginate systems. In the Ca–alginate systems, there exists a specific interaction characterized by a strong autocooperative binding between guluronate residues and calcium ions, and all functional groups in guluronate residues are considered to involve the interaction with calcium ions. On the other hand, in transition metal (Cu, Co, and Mn)–alginate systems, sol–gel transition is characterized by a complex formation in which the carboxyl groups in both mannuronate and guluronate residues are coordinated to metal ions. The other functional groups, like hydroxyl groups, do not participate in the binding to metal ions. It is suggested by relaxation time measurements that from a microscopic point of view the sol–gel transition phenomena can be explained as a dynamic process in which the low frequency molecular motions are dominant and increase their proportions with the formation of three‐dimensional cross‐links. © 1993 John Wiley & Sons, Inc.
Unfolding of an α‐helix in peptide crystals by solvation: Conformational fragility in a heptapeptide
Authors: Karle Isabella L. , Flippen‐Anderson Judith L. , Uma K. , Balaram P. 
Published: December 2004

AbstractThe structure of the peptide Boc‐Val‐Ala‐Leu‐Aib‐Val‐Ala‐Leu‐OMe has been determined in crystals obtained from a dimethylsulfoxide–isopropanol mixture. Crystal parameters are as follows: C38H69N7O10 · H2O · 2C3H7OH, space group P21, a = 10.350 (2) Å, b = 26.084 (4) Å, c = 10.395(2) Å, β = 96.87(12), Z = 2, R = 8.7% for 2686 reflections observed > 3.0 σ (F). A single 5 → 1 hydrogen bond is observed at the N‐terminus, while two 4 → 1 hydrogen bonds characteristic of a 310‐helix are seen in the central segment. The C‐terminus residues, Ala(6) and Leu(7) are expended, while Val(5) is considerably distorted from a helical conformation. Two isopropanol molecules make hydrogen bonds to the C‐terminal segment, while a water molecule interacts with the N‐terminus. The structure is in contrast to that obtained for the same peptide in crystals from methanol‐water [ I. L. Karle, J. L. Flippen‐Anderson, K. Uma, and P. Balaram (1990) Proteins: Structure, Function and Genetics, Vol. 7, pp. 62–73] in which two independent molecules reveal an almost perfect α‐helix and a helix penetrated by a water molecule. A comparison of the three structures provides a snapshot of the progressive effects of solvation leading to helix unwinding. The fragility of the heptapeptide helix in solution is demonstrated by nmr studies in CDC13 and (CD3)2SO. A helical conformation is supported in the apolar solvent CDCl3, whereas almost complete unfolding is observed in the strongly solvating medium (CD3)2SO. © 1993 John Wiley & Sons, Inc.
Probing protein structure by solvent perturbation of nmr spectra. II. Determination of surface and buried residues in homologous proteins
Authors: Esposito Gennaro , Lesk Arthur M. , Molinari Henriette , Motta Andrea , Niccolai Neri , Pastore Annalisa 
Published: December 2004

AbstractThe experimental assignment of most residues in a protein to the surface or interior is in principle possible without prior solution of a complete three‐dimensional structure. The method described is based on nmr measurements that determine the amino acid composition of the surface of a protein [A. Petros, L. Mueller, and K. D. Kopple (1990) Biochemistry, Vol. 29, pp. 10041–10048; G. Esposito, A. M. Lesk, H. Molinari, A. Motta, N. Niccolai, and A. Pastore (1992) Journal of Molecular Biology, Vol. 224, pp. 659–670]. If these measurements are carried out on several homologous proteins of known sequence, it is possible to combine the results to determine, in most cases, which positions in the sequence contain exposed residues. © 1993 John Wiley & Sons, Inc.
Conformational requirements for molecular recognition of acetylcholine receptor main immunogenic region (MIR) analogues by monoclonal anti‐MIR antibody: A two‐dimensional nuclear magnetic resonance and molecular dynamics approach
Authors: Tsikaris Vassilios , Detsikas Evangelos , Sakarellos‐Daitsiotis Maria , Sakarellos Constantinos , Vatzaki Efstratia , Tzartos Socrates J. , Marraud Michel , Cung Manh Thong 
Published: December 2004

AbstractThe conformational properties of two [D‐A70, A76] and [Aib70, A76] analogues of the α67–76 Torpedo acetylcholine receptor fragment, with low binding capacity for the anti main immunogenic region (MIR) antibodies, were studied in DMSO by two‐dimensional nmr techniques and molecular dynamics simulations. The results were compared to the free and bound conformations of the [A76] analogue, which has twice more affinity for the anti‐MIR monoclonal antibody 6 (mAb6), than the natural Torpedo sequence. It appeared that a single substitution of the A70, at a crucial position, by the D‐A70 or Aib70, could modify completely the conformational behavior of the peptide and reduced its recognition by the anti‐MIR antibody. The WNPADY rigid structure at the N‐terminal part was essential for antibody recognition. The adjacent more flexible C‐terminal sequence (GGIK) gives additional stability to the monoclonal antibody–peptide complex probably due to an adequate orientation of the peptide side chains in the complex, by setting them in close contact with the antibody. © 1993 John Wiley & Sons, Inc.
Molecular dynamics simulation of the stability of a 22‐residue α‐helix in water and 30% trifluoroethanol
Authors: Van Buuren Aldert R. , Berendsen Herman J. C. 
Published: December 2004

AbstractA molecular dynamics (MD) simulation was performed on the α‐helix H8‐HC5, the C‐terminal part of myoglobin (residue 132–153), under periodic boundary conditions in two different solutions, water and water with 30% (v/v) 2,2,2‐trifluoroethanol (TFE), at 300 K to investigate the stability of the helix. In both simulations, the initial configuration was a canonical right‐handed α‐helix. In the course of the MD trajectory in water (200 ps), the helix clearly destabilized and began to unfold after 100 ps. In the TFE solution, two stable parts of helical regions were observed after 70 ps of a 200‐ps MD simulation, supporting the notion that TFE acts as a structure‐forming solvent. © 1993 John Wiley & Sons, Inc.
The solution conformation Ac‐Pen‐Arg‐Gly‐Asp‐Cys‐OH, a potent fibrinogen receptor antagonist
Authors: Bogusky Michael J. , Naylor Adel M. , Mertzman Michael E. , Pitzenberger Steven M. , Nutt Ruth F. , Brady Stephen F. , Colton Christiane D. , Veber Daniel F. 
Published: December 2004

AbstractThe solution conformation of , a potent fibrinogen receptor antagonist, was characterized in DMSO‐d6 by the combination of nmr and molecular modeling. The conformational space available to the peptide was explored using a distance geometry algorithm with distance constraints derived from 1H‐nmr spectra. The dynamics of the peptide were examined by relaxation time measurements and low temperature studies. The results from the low temperature studies suggest that the peptide backbone does not exist in a single, well‐defined conformation but undergoes exchange between multiple conformers. This result is consistent with the inability to find a single structure that satisfies all the nmr‐derived constraints. The constraints could only be satisfied by considering pairs of conformers to represent the experimental data. The low energy conformers comprise type II′ or type V β‐turns with distinct side‐chain directionality. The Arg‐Gly‐Asp portion of the ring is flexible and can be described by amide‐plane rotations of the Arg‐Gly and Gly‐Asp peptide bonds. Although some backbone flexibility is evident, the incorporation of β,β‐dimethyl cysteine imparted greater conformational rigidity as compared to the previously studied cyclic pentapeptide, . © 1993 John Wiley & Sons, Inc.
Molecular recognition of watson–crick base‐pair reversals in triple‐helix formation: Use of nonnatural oligonucleotide bases
Authors: Mohan V. , Cheng Y.‐K. , Marlow Gail E. , Pettitt B. Montgomery 
Published: December 2004

AbstractWe report the calculated characteristics of nonnatural triplex‐forming oligonucleotide (TFO) bases recognizing base‐pair reversals (TA → AT) in a double‐helical DNA sequence. Ab initio and molecular mechanics calculations have been carried out to characterize the geometric and energetic consequences at the base‐pair reversal sites. We have estimated the free energies of solvation of the natural and proposed bases by solving the linearized Poisson–Boltzmann equation. The calculations indicate that the proposed TFO bases should bind with some specificity to the duplex. Implications of the strategy used in the context of molecular biology is discussed. © 1993 John Wiley & Sons, Inc.
Individual‐site binding data and the energetics of protein–DNA interactions
Authors: Saroff Harry A. 
Published: December 2004

AbstractIndividual‐site isotherms for the binding of bacteriophage λ repressor to the left and right λ operators have been determined [D. F. Senear, M. Brenowitz, M. A. Shea, and G. K. Ackers (1986) Biochemistry, Vol. 25, pp. 7344–7354.] using the DNAse protection technique [ footprinting; D. J. Galas and A. Schmitz (1978) Nucleic Acids Research, Vol. 5, pp. 3157–3170]. These extensive data have been interpreted with a quantitative model that emphasized cooperative interactions between adjacently bound ligands [occupied ↔ occupied interactions; G. K. Ackers, A. D. Johnson, and M. A. Shea (1982) Proceedings of the National Academy of Science, USA, Vol. 79, pp. 1129–1133]. Overlooked in this model are the effects of cooperative interactions between a site containing a bound ligand and its neighboring unoccupied site (occupied ↔ unoccupied interactions). This paper reinterprets the existing data with a model that considers occupied ↔ unoccupied as well as occupied ↔ occupied interactions. The results yield parameters that differ substantially from those already reported. A discussion on the advisability of ignoring occupied ↔ unoccupied interactions is included. © 1993 John Wiley & Sons, Inc.
Chain length dependent transition of 310‐ to α‐helix of Boc‐(Ala‐Aib)n‐OMe
Authors: Otoda Kazuya , Kitagawa Yasuyuki , Kimura Shunsaku , Imanishi Yukio 
Published: December 2004

AbstractAn apolar synthetic octapeptide, Boc‐(Ala‐Aib)4‐OMe, was crystallized in the triclinic space group P1 with cell dimensions a = 11.558 Å, b = 11.643 Å, c = 9.650 Å, α = 120.220°, β = 107.000°, γ = 90.430°, V = 1055.889 Å3, Z = 1, C34H60O11N8·H2O. The calculated crystal density was 1.217 g/cm3 and the absorption coefficient ϕ was 6.1. All the intrahelical hydrogen bonds are of the 310 type, but the torsion angles, ϕ and ψ, of Ala(5) and Ala(7) deviate from the standard values. The distortion of the 310‐helix at the C‐terminal half is due to accommodation of the bulky Boc group of an adjacent peptide in the nacking. A water molecule is held between the N‐terminal of one peptide and the C‐terminal of the other. The oxygen atom of water forms hydrogen bonds with N (1) ‐H and N (2) ‐H, which are not involved in the intrahelical hydrogen bonds. The hydrogen atoms of water also formed hydrogen bonds with carbonyl oxygens of the adjacent peptide molecule. On the other hand, 1H‐nmr analysis revealed that the octapeptide took an α‐helical structure in a CD3CN solution. The longer peptides, Boc‐(Ala‐Aib)6‐OMe and Boc‐(Ala‐Aib)8‐OMe, were also shown to take an α‐helical structure in a CD3CN solution. An α‐helical conformation of the hexadecapeptide in the solid state was suggested by x‐ray analysis of the crystalline structure. Thus, the critical length for transition from the 310‐ to α‐helix of Boc‐(Ala‐Aib)n‐OMe is 8. © 1993 John Wiley & Sons, Inc.
An NMR and conformational investigation of the trans‐syn cyclobutane photodimers of dTpdU
Authors: Tabaczynski Walter A. , Lemaire Danielle G. E. , Ruzsicska Bŕla P. , Alderfer James L. 
Published: December 2004

AbstractTwo trans‐syn cyclobutane photodimers of thymidylyl (3′–5′) deoxyuridine were formed by deamination of the corresponding trans‐syn cyclobutane photodimers of thymidylyl(3′–5′) deoxycytidine and were examined by 1H−, 13C−, and 31P‐nmr spectroscopy. Correlation spectroscopy, nuclear Overhauser enhancement spectroscopy, and one‐dimensional heterodecoupling experiments allowed a more complete assignment of the 1H spectra, compared with previous reports by Koning et al. [ (1991) European Journal of Biochemistry, Vol. 195, pp. 29–40] and Liu and Yang [(1978) Biochemistry, Vol. 17, pp. 4865–4876]. Deoxyribose ring conformations were calculated from 1H coupling constants by pseudorotational analysis, and rotamer distributions of exocyclic bonds were calculated from the observed homonuclear and heteronuclear coupling constants. The cyclobutane ring configuration (CB) of each isomer was identified, using arguments based upon observed scalar and dipolar couplings. Glycosidic bond conformation was ascertained from nuclear Overhauser enhancements observed between base and deoxyribose protons. Isomer I (S‐type class; CB−; SYN‐ANTI) and isomer II (N‐type class; CB+; ANTI‐SYN) exhibit markedly different conformational features. 31P chemical shifts and exocyclic bond rotamer distributions indicate diminished backbone flexibility for both photoproducts relative to parent thymidylyl (3′–5′) deoxyuridine. Isomer I (SYN‐ANTI) is particularly rigid, while isomer II (ANTI‐S YN) maintains some flexibility. Also, 13C spectra were acquired and assigned unequivocally with the aid of short‐ and long‐range two‐dimensional heteronuclear shift correlation experiments. © 1993 John Wiley & Sons, Inc.
Formation of several stable complexes between the minor components of the cyclic tetrapeptide cyclo‐(‐Pro1‐Ala2‐D‐Phe3‐Leu4‐) and some specific Boc‐amino acids
Authors: McEwen I. , Ottosson K. 
Published: December 2004

AbstractThe cyclic tetrapeptide cyclo(‐Pro1‐Ala2‐D‐Phe3‐Leu4‐) was modeled and synthesized to be used for molecular interactions and chiral discrimination studies in CDCl3. Total correlation spectroscopy and nuclear Overhauser effect spectroscopy spectra of the cyclic tetrapeptide showed the presence of one dominant stereoisomer—1—and three minor ones— 2a, 2b, and 2c—in a relationship of 92:6:1:1. They formed three‐ to five‐hydrogen bond complexes with Boc‐D‐Ser, Boc‐L‐Ser and Boc‐L‐Thr (Boc: t‐butyloxylcarbonyl). These three Boc‐amino acids interact more strongly with 2a, 2b, and 2c than with 1, altering their relative concentrations to 48:40:6:6. In the complex between the cyclic tetrapeptide and Boc‐D‐Ser, the stereoisomer 2a exchanged chemically with 1, 2b, and 2c, while 1 did not exchange with either 2b or 2c. This chemical exchange is due to cis‐trans isomerization of the peptide bonds. The chiral discrimination of 2a, 2b, and 2c was stronger than that of 1. No complexation occurred with Boc‐L‐Ala or Boc‐L‐Trp. © 1993 John Wiley & Sons, Inc.
Quinacrine: Spectroscopic properties and interactions with polynucleotides
Authors: Doglia S. M. , Albinsson B. , Hiort C. , Nordén B. , Gräslund A. 
Published: December 2004

AbstractThe acridine dye quinacrine and its interactions with calf thymus DNA, poly(dA‐dT) · poly (dA‐dT), and poly (dG‐dC) · poly(dG‐dC) were studied by light absorption, linear dichroism, and fluorescence spectroscopy. The transition moments of quinacrine give rise to absorption bands polarized along the short axis (400–480‐nm band), and the long axis (345‐nm and 290‐nm bands) of the molecule, respectively. Linear dichroism studies show that quinacrine intercalates into calf thymus DNA as well as into the polynucleotides, displaying fairly homogeneous binding to poly (dA‐dT) · poly (dA‐dT), but more than one type of intercalation site for calf thymus DNA and poly (dG‐dC) · poly(dG‐dC). Fluorescence spectroscopy shows that for free quinacrine the pK = 8.1 between the mono‐ and diprotonated states also remains unchanged in the excited state. Quinacrine bound to calf thymus DNA and polynucleotides exhibits light absorption typical for the intercalated diprotonated form. The fluorescence enhancement of quinacrine bound to poly (dA‐dT) · poly(dA‐dT) may be due to shielding from water interactions involving transient H‐bond formation. The fluorescence quenching in poly(dG‐dC) · poly(dG‐dC) may be due to excited state electron transfer from guanine to quinacrine. © 1993 John Wiley & Sons, Inc.
Photoresponsive polypeptides: Photochromism and conformation of poly (L‐glutamic acid) containing spiropyran units
Authors: Fissi A. , Pieroni O. , Ciardelli F. , Fabbri D. , Ruggeri C. , Umezawa K. 
Published: December 2004

AbstractSpirobenzopyran units were bound to the side chains of poly (L‐glutamic acid) and partially methylated poly(L‐glutamate)s. The modified polymers were found to exhibit “reverse photochromism” in hexafluoro‐2‐propanol (HFP), so the samples kept in the dark were characterized by an intense absorption band in the visible range of the spectrum, which was completely erased upon exposure to sunlight or irradiation at 500–550 nm.The CD spectra showed that the macromolecules adopted a random coil conformation in the dark, whereas the bleached solutions after exposure to light displayed the typical CD pattern of the α‐helix. The back reaction in the dark was accompanied by the progressive decrease of the helix content and recovery of the original disordered conformation. The photoinduced conformational changes resulted in large and reversible viscosity variations.When spiropyran side chains were converted to “spiropyran salts” of trifluoroacetic acid, the system was still photochromic, but the macromolecules were disordered both in the dark and light conditions. However, when appropriate amounts of methanol were added as a cosolvent to the HFP solutions, the system responded to light, giving reversible variations of the α‐helix content. Irradiation at appropriate solvent compositions allowed modulation of the extent of the photoresponse. © 1993 John Wiley & Sons, Inc.
A and Z canonical conformations in d(CnGCGn) crystals characterized by microFTIR and microRaman spectroscopies
Authors: Sfihi H. , Liquier J. , Urpi L , Verdaguer N. , Subirana J. A. , Igolen J. , Taillandier E. 
Published: December 2004

AbstractTwo crystals d(C2GCG2) and d(C5GCG5) have been studied under microscope by Fourier transform ir spectroscopy and Raman spectroscopy. The x‐ray diffraction study of the latter crystal had shown that the d(C5GCG5) sequence is the first DNA dodecamer known to adopt a canonical A conformation [N. Verdaguer, J. Aymami, D. Fernandez‐Forner, I. Fita, M. Coll, T. Huynh‐Dinh, J. Igolen, and J. A. Subirana (1991) Journal of Molecular Biology, Vol. 221, pp. 623–635]. Characteristic ir marker bands and Raman marker peaks of the A conformation have thus been obtained and are compared with previously proposed assignments correlated to fiber diffraction x‐ray results obtained on polymers. The d(C2GCG2) sequence crystal had previously been studied in an intermediate form between B and Z [L. Urpi, J. P. Ridoux, J. Liquier, N. Verdagner, I. Fita, J. A. Subirana, F. Iglesias, T. Huynh‐Dinh, J. Igolen, and E. Taillandier (1989) Nucleic Acids Research, Vol. 17, pp. 6669–6679]. In this paper we present results obtained from a crystal with this oligonucleotide in Z conformation. The effect of the crystallization conditions on the geometry of the obtained oligomer helix is discussed. The influence of the addition, to the central tetramer CGCG, of dCn stretches (at the 5′ end) and dGn stretches (at the 3′ end) of different lengths, on the conformational flexibility of the nucleic acid, is considered. © 1993 John Wiley & Sons, Inc.