bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational energy calculations on glycosylated turns in glycoproteins
Authors: Bush C. Allen 
Published: December 2004

AbstractAnalysis of the amino acid sequence of glycoproteins has suggested the β‐turn as a likely site of glycosylation in glycoproteins. According to this model, the peptide chain traverses the interior of a globular protein, reversing its direction at the protein surface, a likely point for the attachment of hydrophilic carbohydrate residues. In order to search for plausible conformations of glycosylated β‐turns in asparagine‐linked glycoproteins, we have adapted the conformational energy calculation method of Scheraga and coworkers for use in carbohydrates. The parameters for nonbonded and hydrogen‐bonded interactions have been published, and electrostatic parameters are derived from a CNDO calculation on a model glycopeptide. Our results indicate that the orientation of the glycosyl amide bond having the amide proton nearly trans to the anomeric proton of the sugar has the lowest energy. Although CD and nmr experiments in our laboratory have consistently found this conformation, our calculations show the conformation having these two protons in a cis relationship to lie very close in energy. Calculations on the glycopeptide linkage model, α‐N‐acetyl, δ‐N(2‐acetamido‐1,2‐dideoxy‐β‐D‐glucopyranosyl)‐N′‐methyl‐L‐asparaginyl amide show that several distinct geometries are allowed for glycosylated β‐turns. For a type I β‐turn, three conformations of the glycosylated side chain are found within 4 kcal of the minimum, while two conformations of the glycosylated side chain are allowed for a type II turn. The hydrogen‐bonded C7 conformation is also allowed. Stereoviews of the low‐energy conformations reveal no major hydrogen‐bonding interaction between the peptide and sugar.
Lipid‐induced conformational changes in glucagon, secretin, and vasoactive intestinal peptide
Authors: Robinson Randall M. , Blakeney Ernest W. , Mattice Wayne L. 
Published: December 2004

AbstractThe CD of glucagon, secretin, and vasoactive intestinal peptide has been studied as a function of temperature in water and in aqueous solutions of dodecyl sulfate, phosphatidyl glycerol, and L‐α‐phosphatidic acid (dipalmitoyl). The anionic detergent and lipids induce helix formation in all three peptides, with the amount of induced helical content increasing in the order glucagon < secretin < vasoactive intestinal peptide. These observations are subject to quantitative rationalization using a matrix formulation for the configuration partition function. In this formulation the major conformational consequences of the interaction with anionic lipids or detergents is an increase in the probability for helix formation by arginyl, histidyl, and lysyl residues. The region in which helix formation is maximal is found to be at amino acid residues 13–20 in all three peptides. Other studies have implicated this portion of the polypeptide chain in receptor binding. Thus, the helical segment induced by interaction with anionic lipids may play an important physiological role.
Type II β‐turn conformation of pivaloyl‐L‐prolyl‐α‐aminoisobutyryl‐N‐methylamide: Theoretical, spectroscopic, and X‐ray studies
Authors: Prasad B. V. Venkataram , Balaram Hemalatha , Balaram P. 
Published: December 2004

AbstractPivaloyl‐L‐Pro‐Aib‐N‐methylamide has been shown to possess one intramolecular hydrogen bond in (CD3)2SO solution, by 1H‐nmr methods, suggesting the existence of β‐turns, with Pro‐Aib as the corner residues. Theoretical conformational analysis suggests that Type II β‐turn conformations are about 2 kcal mol−1 more stable than Type III structures. A crystallographic study has established the Type II β‐turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, β = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II β‐turn conformation is stabilized by an intramolecular 4 → 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are ϕPro = −57.8°, ψPro = 139.3°, ϕAib = 61.4°, and ψAib = 25.1°. The Type II β‐turn conformation for Pro‐Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.
Ionization behavior of proteins. I. Spectral titration of the tyrosyl groups of chymotrypsinogen and nitrated‐chymotrypsinogen
Authors: Martin Charles J. , Marini Mario A. 
Published: December 2004

AbstractThe ionization constants of the tyrosyl groups of chymotrypsinogen and of nitrated‐chymotrypsinogen (two tyrosyl residues nitrated) have been determined by difference spectrophotometry. In chymotrypsinogen, two of the four tyrosyl groups ionize without any time dependence. Above pH greater than ca. 12.5, time‐dependent spectral changes are seen for 0.7 group equivalent. The data can be fitted to the values of pK′1 9.75 ± 0.07, pK′2 11.55 ± 0.05, pK′3 13.30 ± 0.05. In nitrated‐chymotrypsinogen, the two nitrated tyrosyl residues have pK′1 6.44 and pK′2 8.30. For both proteins, these pK′ values are in agreement with those evaluated from potentiometric titration and calorimetric data using computer‐assisted curve‐fitting analysis.
Theoretical studies on the conformation of saccharides. IV. Solvent effect on the stability of β‐maltose conformers
Authors: Tvaroška Igor 
Published: December 2004

AbstractThe conformational equilibria of four β‐maltose conformers have been studied theoretically in 12 solvents. The stability of the conformers in dilute solution has been compared by using the continuum reaction field method. The solvation energy consists of electrostatic, dispersion, and cavity terms, which have been determined from the calculated properties of β‐maltose and physicochemical properties of solvents. The calculated population of four conformers significantly depends on the solvent (e.g., in dioxane, M1:M2:M3:M4 = 53.3: 20.3:17.7:8.7; in dimethyl sulfoxide, 40.1:21.8:22.8:15.3; and in water, 25.7:17.5:26.3:30.5) and was found to correlate with experimentally observed data. The results obtained indicate that the conformation adopted by β‐maltose in the crystalline form is not the one preferred in solution. The roles of the individual contributions to the solvation energy have been analyzed. Based on the determined abundance of conformers, averaged residual optical activity and vicinal carbon–proton coupling constants have been calculated and discussed from the point of view of the solution behavior of β‐maltose.
Recent progress in the theoretical treatment of protein folding
Authors: Scheraga Harold A. 
Published: December 2004

AbstractThe multiple‐minima problem encountered in computations of the conformational energy of a globular protein can be approached by extending, in part, the methodology used heretofore to treat small oligopeptides and fibrous proteins, and by incorporating procedures to treat short‐, medium, and long‐range interactions. The latter consist primarily of energy minimization and application of distance constraints. Initial tests with the 20‐residue membrane‐bound portion of melittin and with the 58‐residue bovine pancreatic trypsin inhibitor are sufficiently encouraging to suggest that the potential functions and computational algorithms are reasonable and extendable to globular proteins containing as many as 200 amino acid residues.
An empirical approach to protein conformation stability and flexibility
Authors: Creighton Thomas E. 
Published: December 2004

AbstractExperimental measurements of disulfide bond stability at various stages of protein folding are considered in terms of the effective concentrations of the thiol groups relative to each other; values of up to 107M are observed, so that intramolecular interactions within the interior of a protein are much more stable, and provide greater stability to the folded conformation, than those on the surface or in a flexible segment. Intramolecular interactions can have substantially lower free energies than intermolecular, for solely entropic reasons; this implies that polar interactions, such as hydrogen bonds and salt bridges, can provide net stabilization to a folded conformation, in spite of the unfolded protein having intermolecular interactions with the solvent. These considerations can account for the lower free energy and enthalpy of the folded state and are useful for considering protein flexibility.
Folding of protein fragments: Conformational and biological studies on thioredoxin and its fragments
Authors: Reutimann Herbert , Luisi Pier Luigi , Holmgren Arne 
Published: December 2004

AbstractThioredoxin can be cleaved enzymatically into the two fragments (1–73) and (74–108) and chemically into two different ones (1–37) and (38–108). In this paper, the conformational properties of the short fragment (1–37) are reported and compared with those of the larger fragment (1–73). Using mainly circular dichroism (CD), it is shown that the (1–37) fragment, which contains the active disulfide unit center, is present as an unordered structure in the neutral pH range, but assumes a rigid folding at pH values below 6. The form of the CD spectrum is very similar to that of the complete native protein, and to that of the folded (1–73) fragment. The possible mechanisms for refolding of the short fragment are discussed.
Vibrational analysis of conformation in peptides, polypeptides, and proteins
Authors: Krimm S. 
Published: December 2004

AbstractA vibrational force field for the polypeptide chain has been developed for normal‐mode analysis of such molecules. It can reproduce observed frequencies of known structures to within about 5 cm−1. We review the application of this technique to conformational problems in peptides (β‐turns and their model compounds), polypeptides [the αII‐helix and crystalline poly(glycine II)], and proteins (bacteriorhodopsin and glucagon).
Spectroscopic studies of a hydrophobic peptide in membranelike environments
Authors: Gierasch Lila M. , Lacy Jeffrey E. , Anderle Gloria , Lalancette Roger , Mendelsohn Richard 
Published: December 2004

AbstractA hydrophobic linear peptide has been synthesized and studied over a range of environments using several complementary spectroscopic approaches, including nmr, CD, and vibrational spectroscopies. The sequence of this model peptide, carbobenzoxy‐L‐Pro‐D‐Phe‐D‐Ala‐L‐Pro‐NHCH3, was designed such that a small number of “folded” conformations, stabilized by intramolecular hydrogen bonding, would be accessible to it. Additionally, the extremely hydrophobic character of the peptide favors its interactions with hydrophobic regions of a membrane. The conformational impact of the membrane environment on the peptide, and the effect of the peptide on lipid organization have been explored both in micellar media and in vesicles. To facilitate nmr analysis, the peptide has been synthesized with one of the prolines perdeuterated. Results of these studies reveal that the peptide experiences a microenvironment of moderate polarity in micellar media and causes changes in lipid structure in a vesicle that are indicative of a hydrophobic peptide–lipid interaction.
Exploitation and exploration of ceruletide and eledoisin, two peptides of nonmammalian origin
Authors: De Castiglione R. 
Published: December 2004

AbstractEledoisin and ceruletide, two nonmammalian hormonelike peptides, have been explored for possible pharmaceutical application. At present, only a few of the potentialities of the two drugs have been exploited. Eledoisin is used in ophthalmology as a lachrymal secretagogue; ceruletide is applied in the radiological diagnosis of gallbladder, biliary system, and digestive tract disorders, in the study of exocrine pancreatic function, and in the treatment of postoperative paralytic ileus and intestinal hypotony and atony. Possible analgesic and antipsychotic applications of ceruletide are under study. Developments of synthetic and analytical methods for both peptides are briefly reviewed. Technical devices or alternative routes of administration are envisaged in order to enlarge both the present market and the field of application.
Salt‐ and sequence‐dependence of the secondary structure of DNA in Solution by 31P‐nmr spectroscopy
Authors: Chen Chi‐wan , Cohen Jack S. 
Published: December 2004

AbstractWe examined three sonicated, specific‐seqiemce polydeoxynucleotides in solution over a wide range of concentrations of several salts by 13P‐nmr spectroscopy, and we found that the alternating copolymer poly(dAdT)·poly(dAdT) exhibits a dinucleotide repeat unit in all five salts and at all concentrations studied, as indicated by the presence of a doubled in its 31P‐nmr spectra. The two components of the doublet show selective shift effects. The upfield component is assigned to dApdT in the gauche−‐gauche− conformation and shifts upfield in all four monovalent salts used, relative to a single‐stranded oligonucleotide control. The downfield component is assigned to dTpdA in the trans‐gauche− conformation and shifts downfield with increasing CsF concentration but remains essentially constant in LiCl, NaCl, and CsCl. These changes indicate a fast noncooperative transition for poly(dAdT)·poly‐(dAdT) from a presumed right‐handed dinucleotide‐repeat B‐form to another conformation with a dinucleotide‐repeat structure, via a continuum of structures that may differ in the extent of the winding of the double helix. Ethanol causes the upfield component to collapse into the other component, indicating conversion to a structure with a mononucleotide repeat unit and a trans‐gauche− conformation. Up to 1M Mg2+ appears to have no significant effect on the phosphodiester conformations of poly(dAdT)·poly(dAdT). By contrast, poly‐(dGdC)·poly(dGdC) gives a slow cooperative transition from what is considered to be a right‐handed regular B‐form to a left‐handed Z‐form on increasing MgCl2 and NaCl concentrations, although we observed no changes in chemical shifts below the transition points. The homopolymer poly(dA)·poly(dT) exhibits no unusual shift effects or transitions upon the addition of salts when compared to the oligonucleotide control and is considered to be a regular B‐form with a gauche−‐gauche− phosphodiester backbone conformation. These differences emphasize the distinct secondary structures of DNAs of different sequences and their selective responses to changes in solution conditions.
Structure of amphotericin B aggregates based on calculations of optical spectra
Authors: Hemenger R. P. , Kaplan Theodore , Gray L. J. 
Published: December 2004

AbstractThe Degenerate ground state approximation was used to calculate the optical absorption and CD spectra for helical polymer models of amphotericin B aggregates in aqueous solution. Comparisons with experimental spectra indicate that a two‐molecule/unit cell helical polymer model is a possible structure for aggregates of amphotericin B.
Temperature‐jump kinetics of the dC‐G‐T‐G‐A‐A‐T‐T‐C‐G‐C‐G double helix containing a G·T base pair and the dC‐G‐C‐A‐G‐A‐A‐T‐T‐C‐G‐C‐G double helix containing an extra adenine
Authors: Chu Y. Gloria , Tinoco Ignacio 
Published: December 2004

AbstractThe kinetics of helix formation were investigated using the temperature‐jump technique for the following two molecules: dC‐G‐T‐G‐A‐A‐T‐T‐C‐G‐C‐G, which forms a double helix containing a G·T base pair(the G·T 12‐mer), and dC‐G‐C‐A‐G‐A‐A‐T‐T‐C‐G‐C‐G, which forms a double helix containing an extra adenine (the 13‐mer). When data were analyzed in an all‐or‐none model, the activation energy for the helix association process was 22 ± 4 kcal/mol for the G·T 12‐mer and 16 ± 7 kcal/mol for the 13‐mer. The activation energy for the helix‐dissociation process was 68 ± 2 kcal/mol for the G·T 12‐mer and 74 ± 3 kcal/mol for the 13‐mer. Rate constants for recombination were near 105s−1M−1 in the temperature range from 32 to 47°C; for the dissociation process, the rate constants varied from 1s−1 near 32°C to 130s−1 near 47°C. Possible effects of hairpin loops and fraying ends on the above data are discussed.
Boundaries of the universal K3 region and plateau region of the dynamic structure factor for DNA
Authors: Schurr J. Michael 
Published: December 2004

AbstractA sufficiently long semiflexible filamentous macromolecule is theroretically expected to exhibit three different domains of behavior of its apparent diffusion coefficient Dapp(K) as a function of scattering vector K: (1) the small wave vector limit, where Dapp(K) = D0 is the translational diffusion coefficient of the center‐of‐mass; (2) the universal K3 region, where Dapp(K) = (kBT/6πη)K is a universal function of K independent of any property of the molecule itself; (c) the plateau region at large K2, where Dapp(K) approaches either a plateau, or gradually sloping quasiplateau, characteristic of local (elastic) rigid‐body motions of the filament. The existence of each of these different domains has now been established experimentally for at least some polymers. The boundaries of the universal K3 region and the plateau region are determined theoretically here using precise quantitative criteria for universal or plateau behavior of Dapp(K) for a Rouse‐Zimm model containing N + 1 subchains with rms subchain extension b. Allowing a maximum of 13% nonuniversal behavior, the domain of the universal K3 region is given by K2R2G = K2Nb2/6 ≥ 7 and K2b2 ⩽ 0.54. Allowing as much as 10% nonplateau behavior, the boundary for onset of plateau behavior is K2b2 = 18.3. Dapp(K) is at least 50% nonuniversal when K2b2/6 = 6 ln 3. Extension of these results to DNA is examined theoretically, and good agreement of the pertinent predictions with published experimental data is demonstrated.It is concluded that no truly universal K3 region exists for DNA with Mr ⩽ 107 and persistence length a ≥ 450 Å, although marginally (⩽17% nonuniversal) universal behavior, is exhibited in a very narrow domain 0.64 × 1010 ⩽ K2 ⩽ 0.84 × 1010 cm−2 for ϕ29 DNA (Mr = 11.5 × 106). More than 50% of Dapp(K) is governed by local (elastic) rigid‐body motions when K2 = 5.23 × 1010 cm−2. The existence of a very wide region of nonuniversal apparent K3 behavior extending up to very large K2, far into the plateau region, is demonstrated in a plot of Dapp(K)/K vs K2 for the Rouse‐Zimm model. This is shown to stem in part from visual artifacts of plotting Dapp(K)/K vs K2, even for rigid species.
Conformation of sequential polypeptides of (Lysi‐Leuj), (Lysi‐Serj), and (Lys‐Gly) in sodium dodecyl sulfate solution
Authors: Kubota Shigeo , Ikeda Kiyoshi , Yang Jen Tsi 
Published: December 2004

AbstractA series of sequential polypeptides (LysiRj)n (R is Leu, Ser, or Gly) and random copolypeptides, (Lysx, Leuy)n, were synthesized. Their conformation in NaDodSO4 solution was determined by CD. Only (Lys‐Leu)n, (Lys‐Ser)n, and (Lys3‐Ser)n adopt a stable β‐form in the surfactant solution; (Lys‐Ser2)n, (Lys‐Ser3)n, (Lys2‐Ser2)n, and (Lys2‐Ser)n have an unstable β‐form, which reverts to an unordered form in high NaDodSO4 concentrations, even though both Ser and DodSO‐bound Lys+ are β‐formers. In contrast, (Lys‐Gly)n remains unordered in NaDodSO4 solution. On the other hand, Lys‐rich (Lys2‐Leu)n forms an unstable helix and (Lys2‐Leu2)n a stable helix in NaDodSO4 solution. In 25 mM NaDodSO4 (Lysx, Leuy)n also forms a helix up to x = 75 and reverts to the β‐form at x = 90. This compares with the helical conformation of (Lysx, Alay)n up to x = 65 and its β‐form at x = 90, suggesting that Leu is an even stronger helix‐former than Ala. Our results may provide a plausible explanation for the increase in helicity and disruption of the β‐form for many proteins in NaDodSO4 solution, that is, the polypeptide chain of a protein usually favors a helical conformation over a β‐form in the presence of excess surfactant.
Cooperative ligand binding on multidimensional lattices: Bethe approximation
Authors: Miyazawa Sanzo 
Published: December 2004

AbstractA binding isotherm for ligands on multidimensional lattices has been calculated in the Bethe approximation. In this lattice model, a single bound ligand is assumed to occupy a contiguous sequence of lattice sites in all possible configurations; interactions between neighboring bound ligands are included. This lattice model is equivalent to one used for treating polymer solutions; a configurational entropy of athermal polymer solutions has been utilized directly to represent bound ligands. Binding isotherms are examined for their dependences on lattice coordination numbers and the number of sites occupied by a single bound ligand. Critical conditions for phase transitions in single‐ligand‐species systems are also presented. The binding isotherm reported here can be applied to a wide variety of binding phenomena; it is exact for one‐dimensional cases, i.e., it reduces to the binding isotherm of McGhee and von Hippel [(1974) J. Mol. Biol. 86, 469–489] and should serve as a good approximation for higher‐dimensional binding phenomena.
Extended retro‐inverso analogs of somatostatin
Authors: Pallai Peter , Struthers Scott , Goodman Murray , Rivier Jean , Vale Wylie 
Published: December 2004

AbstractAn extended retro‐inverso modification was introduced at the central six residues of the somatostatin molecule, the region of internal enzymatic degradations. The synthesis of the analog [Ala4,g‐Phe6‐r‐D‐Phe7‐r‐D‐Trp8‐r‐D‐Lys9‐r‐D‐Thr10‐m‐R,S‐Phe11]‐somatostatin required a unique strategy accommodating the unusual structure. Side‐chain protection based on the t‐butyl group in combination with Fmoc and Nps α‐amino protection was employed. The key component containing the gem‐diaminoalkyl residue was generated by an iodobenzene bistrifluoroacetate‐mediated reaction. The separation of diastereomers of the cyclic tetradecapeptide in highly pure form was accomplished by high‐performance liguid chromatography on a semipreparative scale. The analogs exhibited very low potency in the growth hormone inhibition test in vitro. This is interpreted as the consequence of the complex structural changes created by the extended retro‐inverso modification.
The C‐terminal extrahelical peptide of type I collagen and its role in fibrillogenesis in vitro: Effects of Ethylurea
Authors: Capaldi Michael J. , Chapman John A. 
Published: December 2004

AbstractEthylurea was used to weaken hydrophobic interactions during collagen fibrillogenesis in vitro. Intact and enzyme‐digested type I collagen was studied. In all preparations, ethylurea decreased the extent and rate of fibril formation, inhibition being greatest in the enzyme‐digested collagens. With intact collagen (and probably also with carboxypeptidasedigested collagen), there was no evidence the ethylurea altered the mechanism of fibril growth; in pepsin‐digested collagen, however, the growth mechanism was altered by ethylurea, possibly reflecting a conformational change of the “hydrophobic cluster” in the C‐terminal peptide. Such a structural change could occur in a hydrophobic environment once the distal portion of the C‐terminal peptide (presumed to be essential for its structural stability) is removed by pepsin. The results further emphasize the importance of hydrophobic interactions in collagen fibril nucleation and growth in vitro.