bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self‐assembly of a bioelastomeric structure: Solution dynamics and the spinodal and coacervation lines
Authors: Sciortino F. , Urry D. W. , Palma M. U. , Prasad K. U. 
Published: December 2004

AbstractThe stability, metastability, and instability regions of aqueous solutions of a representative synthetic bioelastomeric polymer, poly (Val‐Pro‐Gly‐Val‐Gly), were determined by a combined used of elastic and quasi‐elastic light scattering experiments. The approach followed here offers the attractive advantage of singling out the relevant contributions to the total scattering even in the presence of traces of noninteracting larger sized impurities. Conclusions so reached were checked by means of independent experiments. The present results provide descriptions of the very early events in the physics of bioelastogenesis in terms of general polymer science and phase transitions, and in terms of an unexpected possible functional role of density fluctuations.
A 1.8 Å resolution potential function for protein folding
Authors: Crippen Gordon M. , Snow Mark E. 
Published: December 2004

AbstractA general method is presented for constructing a potential function for approximate conformational calculations on globular proteins. The method involves solving a nonlinear program that seeks to adjust the potential's parameters in such a way that a minimum near the native remains a minimum and does not move far away, while any alternative minima shift so as to remain local minima but eventually rise higher than the level of the near‐native minimum. Although the potential trades computational speed for detail by representing each amino acid residue as only a single point, correct secondary structural preferences and reasonable tertiary folding can be built into the potential in an entirely routine way. The potential has been parameterized to agree with the crystal structure of avian pancreatic polypeptide (having 36 residues) in the sense that the lowest minimum found (‐407 arbitrary units) is reasonably close to the native (1.8 Å rms interresidue distance deviation). In contrast, the lowest nonnative conformation found after extensive searches by a variety of methods was −399 units and 7.5 Å away. Such potentials may prove to be useful in predicting approximate tertiary structure from amino acid sequence, if they can be generalized to apply to more than one protein.
Theoretical studies on the conformation of saccharides. XIV. Structure and conformational properties of the glycosylamines
Authors: Kožár Tibor , Tvaroška Igor 
Published: December 2004

AbstractThe 2‐methylaminotetrahydropyran was used as a model to study conformational properties of the N‐glycosidic linkage in glycosylamines. Relaxed two‐dimensional conformational (Φ,Ψ) maps in 20 solvents were calculated by a method in which the total energy is divided into the energy of the isolated molecule and the solvation energy. Molecular geometry optimization has been carried out for each conformer using the quantum chemical method PCILO. The calculated variations of the geometry are consistent with the results obtained by the statistical analysis of available experimental data retrieved from the Cambridge Structural Database. The calculated abundances of conformers show that the polarity of the solvent has little effect on the anomeric ratio, and the form having the methylamino group equatorial is favored in all considered solvents.
Binding of cationic dyes to potassium alginate: A spectrophotometric and dichroic probe
Authors: Pal Medini Kanta , Mandal Nemai 
Published: December 2004

AbstractAcridine orange (AO) binds to potassium alginate (KAlg) stoichiometrically as is evidenced from conductometric and spectrofluorometric titrations. However, AO as well as methylene blue (MB) exhibits weak metachromasia and no induced dichroism at any sensible polymer to dye ratio (P / D). KAlg induces large blue shifts (by as much as 125 nm) of the λmax of the strongly aggregating dyes 1, 9‐dimethylmethyleneblue (DMMB) and pinacyanol at reasonable P / D values; KAlg also induces strong dichroism in these dyes. The signs of the induced CD spectra indicate KAlg to have a left‐handed helical conformation. This polymer also induces red‐shifted J band and dichroism in the dye N‐N′‐diethylpseudoisocyanine (PIC) at high P / D under which condition the signs of CD spectra in DMMB reverse with drastic reduction in [θ] values. This reversal of sign of CD or induction of J band in PIC at only high KAlg concentrations does not involve any conformational change in the polymer as indicated by the insensitivity of the UV‐CD spectrum of KAlg as a function of concentration.
On the dependence of molecular conformation on the type of solvent environment: A molecular dynamics study of cyclosporin A
Authors: Lautz J. , Kessler H. , van Gunsteren W. F. , Weber H.‐P. , Wenger R. M. 
Published: December 2004

AbstractThe dependence of the conformation of cyclosporin A (CPA), a cyclic undecapeptide with potent immunosuppressive activity, on the type of solvent environment is examined using the computer simulation method of molecular dynamics (MD). Conformational and dynamic properties of CPA in aqueous solution are obtained from MD simulations of a CPA molecule dissolved in a box with water molecules. Corresponding properties of CPA in apolar solution are obtained from MD simulation of CPA in a box with carbontetrachloride. The Results of these simulations in H2O and in CCl4 are compared to each other and to those of previous simulations of crystalline CPA and of an isolated CPA molecule.The conformation of the backbone of the cyclic polypeptide is basically independent of the type of solvent. In aqueous solution the β‐pleated sheet is slightly weaker and the γ‐turn is a bit less pronounced than in apolar solution. Side chains may adopt different conformations in different solvents. In apolar solution the hydrophobic side chain of the MeBmt residue is in an extended conformation with its hydroxyl group hydrogen bonded to the backbone carbonyl group. In aqueous solution this hydrophobic side chain folds over the core of the molecule and the mentioned hydrogen bond is broken in favor of hydrogen bonding to water molecules. The conformation obtained from the MD simulation in CCl4 nicely agrees with experimental atom‐atom distance data as obtained from nmr experiments in chloroform. In aqueous solution the relaxation of atomic motion tends to be slower than in apolar solution.
Differential scanning calorimetry studies of the inverse temperature transition of the polypentapeptide of elastin and its analogues
Authors: Luan Chi‐Hao , Harris R. Dean , Prasad Kari U. , Urry Dan W. 
Published: December 2004

AbstractDifferential scanning calorimetry studies have been carried out on the sequential polypeptide of elastin, (L‐Val1–L‐Pro2–Gly3–L‐Val4–Gly5)n, abrreviated as PPP, and its more hydrophobic analogues (L‐Val1–L‐Pro2–Gly3–L‐Val4–Gly5)n, referred to as Leu1‐PPP, and (L‐Ile1–L‐Pro2–Gly3–L‐Val4–Gly5)n, referred to as Ile1‐PPP. Consistent with inverse temperature transitions, the temperatures of the transitions for which maximum heat absorption occurs are inversely proportional to the hydrophobicities of the polypentapeptides (31°C for PPP, 16°C for Leu1‐PPP, and 12°C for Ile1‐PPP), and the endothermic heats of the transitions are small and increase with increasing hydrophobicity, i.e., 1.2, 2.9, and 3.0 kcal/mol pentamer for PPP, Leu1‐PPP, and Ile1‐PPP, respectively. Previous physical characterizations of the polypentapeptides have demonstrated the occurrence of an inverse temperature transition since increase in order, as the temperature is raised above that of the transition, has been repeatedly observed using different physical characterizations. Furthermore, the studies demonstrated indentical conformations for PPP and Ile1‐PPP above and below the transition. Both heats and temperature of the transitions vary with hydrophobicity, but not in simple proportionality.
Viscoelastic properties of alginate aqueous solutions in the presence of salts
Authors: Matsumoto Takayoshi , Mashiko Kimio 
Published: December 2004

AbstractThe influence of added salts on the dynamic viscoelastic properties are investigated for aqueous solutions of alginates that have various molecular weights and mannuronate/guluronate (M/G) ratios. The dynamic moduli of the systems increase with increasing concentration of the added salt in the low‐frequency region. The effect is notable in the order of KCl < NaCl < MgCl2 ≪ CaCl2. The values of the dynamic moduli in the rubbery plateau are independent of the addition of the salts, irrespective of the M/G ratio of the alginate. These facts strongly suggest that the structure that is formed by the interaction between the alginates and the metal ions does not work as cross‐linking points but as heterogeneous relaxation units having a relatively long relaxation time from a rheological viewpoint.
Normal mode theory for the Brownian dynamics of a weakly bending rod: Comparison with Brownian dynamics simulations
Authors: Song Lu , Allison Stuart A. , Schurr J. Michael 
Published: December 2004

AbstractA normal mode theory is developed for the Brownian dynamics of weakly bending rods with preset hydrodynamic interactions. The rod is replaced by a chain of contiguous spheres whose radius is chosen to yield the appropriate uniform translational and rotational diffusion coefficients. Despite the inclusion of preset hydrodynamic interactions in the dynamical operator, its normal modes are not coupled by the potential energy, so their amplitudes remain pairwise “orthogonal” under equilibrium averaging. The uniform translational and rotational diffusion coefficients obtained from Langevin theory are shown to be identical to those obtained from the Kirkwood algorithm, despite their rather different appearance. An expression is given for the mean squared angular displacement 〈Δxm(t)2〉 of the mth bond vector around the instantaneous x axis (perpendicular to the end‐to‐end vector z). Necessary algorithms are presented for the numerical evaluation of all quantities. The normal mode theory is compared with Brownian dynamics simulations for the same model by examining 3〈Δxm(t)2〉 for the central bond vector of rods comprising 10 and 30 subunits with various persistence lengths. The normal mode theory works very well for all times for L/P ≲ 0.6, where P = κ/kBT is the persistence length and κ is the bending rigidity. With increasing flexibility, the domain of validity of the normal mode theory is restricted to shorter times, where violations of the weak bending approximation are less severe. However, increasing the length of the rod from 10 to 30 subunits yields improved agreement with the simulations for the same and even longer times. This latter effect is tentatively attributed to the greater fluctuating tension in the longer chains, which acts to retard the rotational relaxation in the simulations, but is not taken into account in the present normal mode theory.
Application of the distance geometry algorithm to cyclic oligopeptide conformation searches
Authors: Peishoff Catherine E. , Dixon J. Scott , Kopple Kenneth D. 
Published: December 2004

AbstractThe distance geometry algorithm as embodied in the program DGEOM was examined as a method for searching cyclic peptide conformations. Conformations were randomly generated using covalent distance and chirality constraints, but torsion angle rather than distance sampling was used for 1, 4 relationships. Structures so generated were energy minimized by a fixed number of iterations using the molecular mechanics program AMBER 3.0; electrostatic terms were excluded in the minimization. The effectiveness of this procedure in sampling conformational space for cyclic peptides was measured by the ability to recover, from a set of 500 structures, conformations similar to those experimentally observed for six cyclic peptides containing from 8 to 20 rotatable backbone bonds. Structures similar to experimental structures were recovered in a 16‐bond case, but not for a 20‐bond example. The method was also applied, with constraints on the peptide bond angles ω, to an additional example containing 21 ring bonds.
Crystal structure and solution conformation of S,S′‐bis(Boc‐Cys‐Ala‐OMe): Intramolecular antiparallel β‐sheet conformation of an acyclic cystine peptide
Authors: Raj P. Antony , Soni S. D. , Ramasubbu N. , Bhandary K. K. , Levine M. J. 
Published: December 2004

AbstractThe conformation of the acyclic biscystine peptide S,S′‐bis(Boc‐Cys‐Ala‐OMe) has been studied in the solid state by x‐ray diffraction, and in solution by1H‐ and13C‐nmr, ir, and CD methods. The peptide molecule has a twofold rotation symmetry and adopts an intramolecular antiparallel β‐sheet structure in the solid state. The two antiparallel extended strands are stabilized by two hydrogen bonds between the Boc CO and Ala NH groups [N ⃛O 2.964 (3) Å, O ⃛HN 2.11 (3) Å, and NH ⃛O angle 162 (3)°]. The disulfide bridge has a right‐handed conformation with the torsion angle CβSSCβ = 95.8 (2)°. In solution the presence of a twofold rotation symmetry in the molecule is evident from the1H‐ and13C‐nmr spectra. 1H‐nmr studies, using solvent and temperature dependencies of NH chemical shifts, paramagnetic radical induced line broadening, and rate of deuterium‐hydrogen exchange effects on NH resonances, suggest that Ala NH is solvent shielded and intramolecularly hydrogen bonded in CDCl3 and in (CD3)2SO. Nuclear Overhauser effects observed between Cys CαH and Ala NH protons and ir studies provide evidence of the occurrence of antiparallel β‐sheet structure in these solvents. The CD spectra of the peptide in organic solvents are characteristic of those observed for cystine peptides that have been shown to adopt antiparallel β‐sheet structures.
A polarized and depolarized dynamic light scattering study of the tRNAphe conformation in solution
Authors: Patkowski A. , Eimer W. , Dorfmüller Th. 
Published: December 2004

AbstractThe dynamics of tRNAphe from brewer's yeast in solution was studied over a broad concentration and temperature range by polarized and depolarized dynamic light scattering. It is shown that measurements of the depolarized Rayleigh spectrum with a high‐resolution confocal Fabry‐Perot interferometer provide very accurate values for the rotational diffusion coefficient of the biopolymer. The translational diffusion coefficient was determined by polarized photon correlation spectroscopy. A combination of both transport coefficients allows one to calculate the hydrodynamic size of tRNAphe using the Perrin equations for an biaxial ellipsoid. Within a temperature range from 9 to 45°C, the tRNAphe molecule adopts a nearly spherical shape. The dimensions are similar to the previously proposed U‐shaped structure. In the melting region a second relaxation process was observed that is attributed to the collective reorientation of the bases. The concentration dependence of the rotational diffusion coefficient of tRNAphe in the concentration range of 2–75 mg/mL exhibits a slightly positive slope, in agreement with previous experimental findings and in contradiction to the theoretical predictions based on hydrodynamic interactions in solution.
Computer modeling studies of ribonuclease T1–guanosine monophosphate complexes
Authors: Balaji P. V. , Rao V. S. R. , Saenger W. 
Published: December 2004

AbstractThe three‐dimensional structures of ribonuclease (RNase) T1 complexes with the inhibitors 2′‐guanylic acid (2′‐GMP), 3′‐guanylic acid (3′‐GMP), and 5′‐guanylic acid (5′‐GMP) were predicted by energy minimization studies. It is shown that these inhibitors can bind to RNase T1 in either of the ribose puckered conformations (C2′‐endo and C3′‐endo) in solid state and exist in significant amounts in both forms in solution. These studies are in agreement with the x‐ray crystallographic studies of the 2′‐GMP–Lys25–RNase T1 complex, where the inhibitor binds in C2′‐endo puckered conformation. These results are also in good agreement with the available 1H‐nmr results of Inagaki et al. [(1985) Biochemistry 24, 1013–1020], but differ from their conclusions where the authors favor only the C3′‐endo ribose conformation for all the three inhibitors. The calculations explain the apparent discrepancies in the conclusions drawn by x‐ray crystallographic and spectroscopic studies. An extensive hydrogen‐bonding scheme was predicted in all the three complexes. The hydrogen‐bonding scheme predicted for the 2′‐GMP (C2′‐endo)–RNase T1 complex agrees well with those reported from x‐ray crystallographic studies. In all three complexes the base and the phosphate bind in nearly identical sites independent of the position of the phosphate or the ribose pucker. The glycosyl torsion angle favors a value in the +syn range in the 2′‐GMP(C2′‐endo)–RNase T1, 3′‐GMP(C2′‐endo)–RNase T1, and 3′‐GMP(C3′‐endo)–RNase T1 complexes; in the high‐synrange in the 2′‐GMP(C3′‐endo)–RNase T1 complex; and in the ‐syn range in the 5′‐GMP(C2′‐endo)–RNase T1, and 5′‐GMP(C3′‐endo)–RNase T1 complexes. These results are in agreement with experimental studies showing that the inhibitory power decreases in the order 2′‐GMP > 3′‐GMP > 5′‐GMP, and they also explain the high pKa value observed for Glu58 in the 2′‐GMP–RNase T1 complex.
Conformational studies on peptides with proline in the right‐handed α‐helical region
Authors: Sankararamakrishnan R. , Vishveshwara Saraswathi 
Published: December 2004

AbstractThe proline residues in proteins are known to play an important structural role. Recently, the role of a proline residue in the middle of right‐handed α‐helical segments of peptides has been the focus of attention. This role seems to be particularly important in the case of membrane proteins and in the tight packing of globular proteins. In the present study the right‐handed α‐helical region of the Ala‐Pro dipeptide and of polypeptides containing this group have been investigated. Crystal structures of proline‐containing α‐helices from some proteins have been analyzed and energy minimization studies on some model fragments containing Ala‐Pro in the right‐handed α‐helical conformation have been carried out using flexible geometry. The present calculations indicate that the right‐handed α‐helical region of conformational space is an energetically favored region that can also accommodate Ala‐Pro in longer segments of right‐handed α‐helix. This is achieved due to minor variations in some of the internal parameters. Deviations in the backbone parameters of proline in the right‐handed α‐helix lead to a kink of about 23° in the helix axis. These deviations have been characterized and a set of standard values has been suggested for producing such a kink. These values can be used for model building and as starting points for further minimization studies. Previous energy minimization studies have been done using rigid geometry. This may explain why the minimum for Ala‐Pro in the right‐handed α‐helical region has not been recognized thus far.
A hierarchical “nesting” approach to describe the stability of alpha helices with side‐chain interactions
Authors: Robert Charles H. 
Published: December 2004

AbstractA straightforward hierarchical statistical–mechanical approach is shown to enable one to describe the stability of the alpha helix in the presence of side‐chain interactions. The formulation can be used with even the simple nearest‐neighbor models and it is demonstrated explicitly with the popular 2 × 2 Zimm‐Bragg model [B. H. Zimm and J. K. Bragg (1959) J. Chem. Physics 31, 526–535]. It involves a conceptual dissection of the polypeptide chain into interacting blocks; the behavior of any block with side‐chain interactions is treated then with conventional binding polynomial techniques. This dissection is a manifestation of “nesting,” which is a hierarchical framework for the description of the behavior of complex macromoecules [C. H. Robert, H. Decker, B. Richey, S. J. Gill, and J. Wyman (1987) Proc. Natl. Acad. Sci. 84, 1891–1895]. The method is demonstrated through applications to existing detailed data for the pH and salt dependences of the helix–coil transition in the S peptide and in synthetic peptides.
Helix‐Coil transition in polypeptides: A microscopical approach
Authors: Ananikyan N. S. , Hajryan Sh. A. , Mamasakhlisov E. Sh. , Morozov V. F. 
Published: December 2004

AbstractAnalogous with the Potts model that describes the helix‐coil transition in the isolated polypeptide chain (a Hamiltonian model allowing for the energy U of hydrogen bond formation) the number Q of conformational states of a repeating unit of the chain and the topology of Δ = 3 hydrogen bond formation (the hydrogen bond fixing three pairs of φψ chain rotations) has been constructed and the corresponding transfer‐matrix has been obtained. In the thermodynamical limit, the partition function is expressed through the principal root of the cubic equation. The degree of helicity, the transition point and range, the correlation length, the number of junctions between the helical and coiling sections as well as the mean length of helical and coiling sections are calculated. Empirically introduced parameters of the Zimm–Bragg theory, constants of hydrogen bond formation s, and the cooperativity parameter σ as functions of microscopic parameters U, Q, and Δ are obtained by direct calculations. The behavior of this model was investigated at other topologies of the hydrogen‐bond closing Δ = 2 and Δ = 4, and it was suggested that the actual polypeptide chain (Δ = 3) provides the optimum correlation of helical structure of the order of globule dimensions. An expression was obtained for the maximum correlation length of the order ξ ∼ Q(Δ‐1)/2. For a System with solvent competing for the formation of hydrogen bonds with peptide groups a Hamiltonian model was constructed that took account of the energy E of the formation of hydrogen bond with the solvent and the number q of orientations of a solvent molecule about the peptide groups. It is shown that by the redefinition of the temperature parameter, the model with solvent reduces to the model of an isolated chain. Aside from the definition relationship that exists between the parameters of the theory U < 2E < Uq and the ordinary helix‐coil transitions (“melting”), the model also describes the transition from the coiling state to the helical one (“arrangement”) under heating. The change in temperature and transition range with solvent parameters was discussed and it was shown, that despite the difference in ΔT for the given polypeptide chain (Q = constant) with different solvent parameters, at “melting” and “arrangement,” the transition occurred at the same correlation length (the same cooperativity).
Bicyclic peptides: Solid state conformation of cyclo(Glu‐Leu‐Pro‐Gly‐Lys‐Leu‐Pro‐Gly)cyclo(1γ‐5ϵ)Gly
Authors: Di Blasio Benedetto , Benedetti Ettore , Pavone Vincenzo , Pedone Carlo , Saviano Michele , Zanotti Giancarlo , Blout Elkan R. 
Published: December 2004

AbstractThe solid state conformational analysis of the ionophoric homodetic bicyclic cyclo(Glu‐Leu‐Pro‐Gly‐Lys‐Leu‐Pro‐Gly)cyclo(1γ‐5ϵ)Gly (BCP3) has been carried out by x‐ray diffraction. It crystallizes with 4.5 molecules of water per peptide molecule in the monoclinic system, space group P21, with a = 11.425 Å, b = 16.616 Å, c = 13.931 Å, β = 109.24°, and Z = 2. The structure has been determined by direct methods and refined to an R factor of 0.061 for 2448 observed reflections. The structure characterized by all trans peptide bonds is stabilized by three intramolecular hydrogen bonds: a type II β‐turn, a mixed type I‐type III β‐turn, and a pseudo γ‐turn, which involves the side chain CO and the main‐chain NH groups of the Glu1 residue. The resulting globular molecule presents a rather hydrophilic surface with most of the CO groups available to hydration of the solvent molecules, which are linked through hydrogen bonds of the NH … O or OH … O types in a complicated H‐bonding scheme. The conformation observed in the solid state is rather different from the conformation proposed in solution for both the free and the Ca2+‐complexed BCP3 molecule.