bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrational Raman optical activity of alanyl peptide oligomers: A new perspective on aqueous solution conformation
Authors: Ford Steven J. , Wen Zai Q. , Hecht Lutz , Barron Laurence D. 
Published: December 2004

AbstractThe vibrational Raman optical activity (ROA) spectra of di‐ and tri‐L‐alanine in the range 650–1750 cm−1 have been measured in H2O and D2O solution at high, neutral, and low pH and pD. Corresponding ROA spectra for tetra‐ and penta‐L‐alanine have also been obtained, but over a more restricted set of pH and pD conditions. There are similarities with the ROA spectrum of L‐alanine below ∼ 1200 cm−1, but the spectra are very different above this wavenumber due to the influence of the vibrational coordinates of the peptide group. The similar overall appearance of the di‐, tri‐, and tetrapeptide ROA under selected conditions of pH and pD, and of all four peptide ROA spectra in DCl and HCl solutions, in the backbone skeletal stretch region ∼ 1050–1200 cm−1 and the extended amide III region ∼ 1250–1350 cm−1, suggests that the backbone conformation is approximately the same in all four structures. One difference, however, is a shift of a large positive ROA band in H2O at ∼ 1341 cm−1 in the dipeptide, assigned to Cα–H and in‐plane N–H deformations, down to ∼ 1331 cm −1 in the tripeptide and to ∼ 1315 cm−1 in the tetrapeptide and pentapeptide (the last in HCl due to insufficient solubility in H2O), which indicates increasing delocalization of the corresponding normal mode with increasing chain length. Our results do not support the suggestion that stabilizing interactions of the zwitterionic end groups in tri‐L‐alanine at neutral pH leads to a different solution structure to that at high pH. © 1994 John Wiley & Sons, Inc.
Analyzing the normal mode dynamics of macromolecules by the component synthesis method: Residue clustering and multiple‐component approach
Authors: Hao Ming‐Hong , Scheraga Harold A. 
Published: December 2004

AbstractA study of the component synthesis method (CSM) for analyzing the normal mode dynamics of macromolecules is reported. The procedure involves a reduction of the dimensions of the normal mode problems for large molecular systems and the accurate extraction of the low‐frequency modes. A macromolecule is divided into small components based on a hierarchical clustering of the residues in the structure. Interactions between coupled components are treated by the method of static correlation. The normal modes of the components are obtained first, and a fraction of the low‐frequency normal modes of the components under mutual correlations are then used as a reduced basis for solving for the normal modes of the whole molecule. Multiple components are introduced for large macromolecules so that the dimensions of the eigenvalue problems at the component level are small. The method is applied to the protein crambin. In test calculations in which the dimensions of the eigenvalue equations are reduced to 1/6 of their natural size, the errors in the normal mode frequencies calculated by the CSM procedure are only about 1–2% when compared with the exact values. The rms fluctuations of all atoms in crambin calculated by the CSM procedure are basically identical to the exact results. The CSM procedure is shown to be accurate for calculating the normal modes of large macromolecules with a significant reduction of the size of the problem. © 1994 John Wiley & Sons, Inc.
Lagrangian molecular dynamics using selected conformational degrees of freedom, with application to the pseudorotation dynamics of furanose rings
Authors: Rudnicki Witold R. , Lesyng Bogdan , Harvey Stephen C. 
Published: December 2004

AbstractUsing internal conformational degrees of freedom for biopolymers as natural variables, and introducing a Lagrangian dynamics approach, one can simulate time‐dependent processes over a much longer time scale than in classical Newtonian molecular dynamics (MD) techniques. Two factors contribute to this: a substantial reduction in the number of degrees of freedom and a very large increase in the size of the time step. We present the Lagrangian equations of motion for repuckering transitions in model furanose (F), ribose (R), and 2′‐deoxyribose (dR) ring systems using the pseudorotation phase angle as the single dynamic variable. As in most Lagrangian analyses, the effective masses for the R and dRmodels are dependent on conformation, and we test the behavior of this variable mass (VM) model. Since the variation in effective mass is small, the VM model is compared with a simplified constant mass (CM) model, which is shown to be an excellent approximation. The equations of motion for the CM and VM models are integrated with the leapfrog and the iterative leapfrog algorithms, respectively. The Lagrangian dynamics approach reduces the number of degrees of freedom from about 40 to 1, and allows the use of time steps on the order of 20 fs, about an order of magnitude greater than is used in conventional MD simulations. © 1994 John Wiley & Sons, Inc.
Crystal structure and nmr conformation of a cyclic pseudotetrapeptide containing urethane backbone linkages
Authors: Parkinson Gary N. , Wu Youling , Fan Pei , Kohn Joachim , Baum Jean , Berman Helen M. 
Published: December 2004

AbstractUrethane bonds, derived from the hydroxyl group of the tyrosine side chain, have been investigated as a new type of amide bond mimetic in the design of pseudopeptides. The structure of a representative cyclic pseudotetrapeptide that consists of an — Ala — Tyr(urethane) Ala — Tyr (urethane) sequence fused into a rigid ring has been studied in the solid state by x‐ray crystallography and in solution by two‐dimensional nmr techniques. The cyclic pseudotetrapeptide has an oblong shape. The backbone urethane bonds assume a trans–trans conformation. The carbonyl groups in the ring have an alternating pattern of down, up, down, up with respect to the average ring plane. Solution nmr studies give observed nuclear Overhauser effects and coupling constants largely in agreement with the crystal structure. However, in solution the observed structure is likely to be conformationally averaged, and in the averaged structure, the urethane bond is perpendicular to the plane of the aromatic ring of the tyrosine, while in the crystal it is close to this plane. These differences may be explained by intermolecular hydrogen‐bonding interactions. Four aspects of the conformation of the cyclic pseudotetrapeptide were investigated in detail: the tyrosine residue with the attached side‐chain urethane bond (the tyrosine‐urethane unit), the conformation of the two urethane backbone linkages, the conformation of the two conventional peptide bonds within this unusual ring structure, and the tight turns within the cyclic pseudotetrapeptide. The conformation of the tight turns present in the cyclic pseudotetrapeptide is very similar to that of a β‐bend of type II. Intermolecular hydrogen bonding, joining adjacent layers of the cyclic pseudotetrapeptide in the solid state, resemble a parallel β‐pleated sheet. The presence of these structural motifs in the cyclic pseudotetrapeptide indicates that the tyrosine urethane unit may find applications in peptide and protein engineering. © 1994 John Wiley & Sons, Inc.
Kinetics of DNA supercoiling studied by Brownian dynamics simulation
Authors: Chirico Giuseppe , Langowski Jörg 
Published: December 2004

AbstractWe have developed a model for the simulation of the structure and dynamics of covalently closed circular DNA. It is based on the generalization of the original Brownian dynamics algorithm [D. L. Ermak & J. A. McCammon (1978) Journal of Chemical Physics, Vol. 69, pp. 1352–1359; M. Fixman (1978) Journal of Chemical Physics, Vol. 69, pp. 1527–1537] developed for bead‐chain models of linear DNA to a second order numerical integration [ A. Iniesta & J. Garcia de la Torre (1990) Journal of Chemical Physics.Vol. 92, pp. 2015–2018], which we extended here to accommodate the torsional potential. The topological constraints and torsional‐bending coupling in superhelical DNA are explicitly taken into account in this work by adapting a model for torsional‐bending motion of linear DNA developed by Allison et al. [S. A. Allison, R. Austin, & M. Hogan (1989) Journal of Chemical Physics, Vol. 90, pp. 3843–3854].The dynamics of closed DNAs of 1124 base pairs (380 nm in length) were simulated up to ≅ 40 μs for linking number differences ΔLk between 0 and −6. Each bead in the model corresponded to 37 base pairs.For −2 ≅ ΔLk −6, the writhing number appears to decay to a limiting negative value with a single exponential law, and the relaxation time of this decay, starting from a planar closed molecule, is 3–6 μs. For the trajectories studied here, the formation of the superhelix proceeds through an initial phase of 1–2 μs where a toroidal‐like structure is formed, which then converts into an interwound structure starting from a random nucleation site. For one simulation at ΔLk = −6, a branched structure was observed that did not convert into the linear interwound form for the time course of the simulation (31 μs).A verification of the simulation was performed by computing the diffusion coefficient of the 1124 base pair circle through known hydrodynamic formulas or through the center of mass displacement, and comparing these theoretical values with diffusion coefficients previously measured by dynamic light scattering. © 1994 John Wiley & Sons, Inc.
Evidence of hemoglobin dissociation
Authors: Lunelli Lorenzo , Zuliani Paola , Baldini Giancarlo 
Published: December 2004

AbstractBovine carbonmonoxy hemoglobin investigated with light scattering studies is found to dissociate from its native tetramer structure into dimers and monomers. The values of the hydrated tetramer radius, RT = 32.1 Å, and the fractional dissociation vs pH, have been obtained at different ionic strengths from the autocorrelation function of the scattered light.The results suggest that a relevant contribution to Hb dissociation is due to electrostatic effects and, by means of a model derived by Tanford, it has been possible to predict the behavior of dissociation. Among the findings of this approach, we recall the estimates of the electrostatic energy contributions to Hb dissociation, up to ≃ GRT, and the predicted charge of tetrameric Hb vs pH, which agrees very well with the experimental data. © 1994 John Wiley & Sons, Inc.
Physicochemical properties of aqueous xanthan solutions: Static light scattering
Authors: Gamini Amelia , Mandel Michel 
Published: December 2004

AbstractThe secondary structure of xanthan in solutions of relatively low salt concentration and at room temperature has been investigated using static light scattering experiments. Additional evidence has been found for a dimeric structure at 25°C in 0.01M NaCl. From the experimental z‐average mean square (ms) radius of gyration, a value for the persistence length p has been estimated, taking explicitly into account the polydispersity of the three samples used, which has been established by gel permeation chromatography (GPC) measurements. The experimental particle scattering functions of the three samples are consistent with theoretical estimates for polydisperse systems with the same value of p = 65 ± 10 nm and the molar mass per unit length for a dimeric structure.This secondary structure remains unaffected by the ionic strength in the 0.005–0.0lM range. Partial aggregation seems to occur at higher NaCl concentrations.Light scattering and GPC data show that heating the xanthan 0.01M NaCl solutions to about 70°C considerably reduces the Mw of the low molar mass sample (2.3 × 105‐g·mol−1), contrary to what is observed for the high molar mass sample (1.8 × 106‐g·mol−1). These experimental findings can be accounted for by a partial temperature‐induced dissociation of the xanthan dimers according to an all‐or‐none mechanism. © 1994 John Wiley & Sons, Inc.
Circularization of small DNAs in the presence of ethidium: A theoretical analysis
Authors: Clendenning James B. , Schurr J. Michael 
Published: December 2004

AbstractA rigorous theory is developed for ethidium binding to linear and circular DNAs and for the ratios of topoisomers produced upon ligation of an equilibrium population of noncovalently closed circles in the presence of ethidium. Assuming an unwinding angle ϕE = 26° for intercalated ethidium, optimum values of the intrinsic binding constant, KE = 7.16 × 104 M−1, the intrinsic twist, l0 = 23.746 turns, and twist energy parameter, Et = 5250, are obtained by fitting the present theory to the data of Shore and Baldwin [(1993) Journal of Molecular Biology, Vol. 170, pp. 983–1007] for a 247 base pair DNA. A very good fit is achieved with these optimum values, but a poor fit results when the parameters estimated by Shore and Baldwin are employed in the same theory. Three assumptions employed in the analysis of Shore and Baldwin are found to be not strictly valid. Adoption of the present substantially larger Et value as representative of their short DNAs would allow the Et vs N data of Shore and Baldwin to conform to the shape predicted by Shimada Yamakawa [(1985) Journal of Molecular Biology, Vol. 184, pp. 319–329] and Frank‐Kamenetskii et al. [(1985) Journal of Biomolecular Structure and Dynamics, Vol. 2, pp. 1005–1012], and would imply that all of their DNAs exist in a substantially stiffer than normal state. © 1994 John Wiley & Sons, Inc.
Nanometric design of extraordinary hydrophobic‐induced pKa shifts for aspartic acid: Relevance to protein mechanisms
Authors: Urry Dan W. , Gowda D. Channe , Peng Shaoqing , Parker Timothy M. , Jing Naijie , Harris R. Dean 
Published: December 2004

AbstractCommonly a key element enabling proteins to function is an amino acid residue or residues with functional side chains having shifted pKa values. This article reports the results on a set of protein‐based polymers (model proteins) that exhibit hydrophobic folding and assembly transitions, and that have been designed for the purpose of achieving large hydrophobic‐induced pKa shifts by selectively replacing Val residues by Phe residues. The high molecular weight polypentapeptides, actually poly (tricosapeptides) with six varied pentamers in fixed sequence, were designed and synthesized to have the same amino acid compositions but different proximities between a single aspartic acid residue and 5 Phe residues per 30 residues. With the 5 Phe residues distal from the Asp residue, the observed pKa shift was 2.9 when compared to the Val‐containing reference. With the 5 Phe residues within 1 nm of the Asp residue, the pKa shift was 6.2. This represents a free energy of interaction of 8 kcal/moles. To our knowledge, this is the largest pKa shift documented for an Asp residue in a polypeptide– or protein–water system.Data are reviewed that do not support the usual electrostatic arguments for pKa shifts of charge–charge repulsion and/or unfavorable ion self‐energies arising from displacement of water by hydrophobic moieties, but rather the data are interpreted to indicate the presence of an apolar–polar repulsive free energy of hydration, which results from a potentially highly cooperative competition between apolar and polar species for hydration. © 1994 John Wiley & Sons, Inc.
Mechanochemical study of conformational transitions and melting of Li‐, Na‐, K‐, and CsDNA fibers in ethanol–water solutions
Authors: Rupprecht Allan , Piškur Jure , Schultz Johan , Nordenskiöld Lars , Song Zhiyan , Lahajnar Gojmir 
Published: December 2004

AbstractHighly oriented fibers of Li‐, Na‐, K‐, and CsDNA were prepared with a previously developed wet spinning method. The procedure gave a large number of equivalent fiber bundle samples (reference length, L0, typically = 12–15 cm) for systematic measurements of the fiber length L in ethanol–water solutions, using a simple mechanochemical set up. The decrease in relative length L/L0 with increasing ethanol concentration at room temperature gave evidence for the B‐A transition centered at 76% (v/v) ethanol for NaDNA fibers and at 80 and 84% ethanol for K‐ and CsDNA fibers. A smaller decrease in L/L0 of LiDNA fibers was attributed to the B‐C transition centered at 80% ethanol. In a second type of experiment with DNA fibers in ethanol–water solutions, the heat‐induced helix–coil transition, or melting, revealed itself in a marked contraction of the DNA fibers. The melting temperature Tm, decreased linearly with increasing ethanol concentration for fibers in the B‐DNA ethanol concentration region. In the B‐A transition region, Na‐ and KDNA fibers showed a local maximum in Tm. On further increase of the ethanol concentration, the A‐DXA region followed with an even steeper linear decrease in Tm. The dependence on the identity of the counterion is discussed with reference to the model for groove binding of cations in B‐DNA developed by Skuratovskii and co‐workers and to the results from Raman studies of the interhelical bonds in A‐DNA performed by Lindsay and co‐workers. An attempt to apply the theory of Chogovadze and Frank‐Kamenetskii on DNA melting in the B‐A transition region to the curves failed. However, for Na‐ and KDNA the Tm dependence in and around the A‐B transition region could be expressed as a weighted mean value of Tm of A‐ and B‐DNA. On further increase of the ethanol concentration, above 84% ethanol for LiDNA and above about 90% ethanol for Na‐, K‐, and CsDNA, a drastic change occurred. Tm increased and a few percentages higher ethanol concentrations were found to stabilize the DNA fibers so that they did not melt at all, not even at the upper temperature limit of the experiments (∼ 80°C). This is interpreted as being due to the strong aggregation induced by these high ethanol concentrations and to the formation of P‐DNA. Many features of the results are compatible with the counterion–water affinity model. In another series of measurements, Tm of DNA fibers in 75% ethanol was measured at various salt concentrations. No salt effect was observed (with the exception of LiDNA at low salt concentrations). This result is supported by calculations within the Poisson–Boltzmann cylindrical cell model. © 1994 John Wiley & Sons, Inc.
The thermodynamics of solvent exchange
Authors: Schellman John A. 
Published: December 2004

AbstractA model for solvation in mixed solvents, which was developed for the free energy and preferential interaction [J. A. Schellman (1987), Biopolymers, Vol. 26, pp. 549–559; (1990), Biophysical Chemistry, Vol. 37, pp. 121–140; (1993), Biophysical Chemistry, Vol. 45, pp. 273–279], is extended in this paper to cover the thermal properties: enthalpy, entropy, and heat capacity. An important result is that the enthalpy of solvation H̄ responds directly to the fraction of site occupation. This differs from the free energy Ḡ and preferential interaction Γ32, which are measures of the excess binding above a random distribution of solvent molecules. In other words, the enthalpy is governed by K while Ḡ and Γ32 are governed by (K − 1) where K is the equilibrium constant on a mole fraction scale [Schellman (1987)].The solvation heat capacity C̄p consists of two term: (1) the intrinsic heat capacity of species in solution with no change in composition, and (2) a term that accounts for the change in composition that accompanies solvent exchange.Binding to biological macromolecules is heterogeneous but experiementalists must use binding isotherms that assume the homogeneity of sites. Equations are developed for the interpretation of the experimental parameters (number of sites nexp, equilibrium constant Kexp, and enthalpy, Δhexp), when homogeneous formulas are applied to the heterogeneous case. It is shown that the experimental parameters for the occupation and enthalpy are simple functions of the moments of the distribution of equilibrium constants over the sites. In general, nexp is greater than the true number of sites and Kexp is greater than the average of the equilibrium constants. The free energy and preferential interaction can be fit to a homogenious formula, but the parameters of the curve are not easily represented in terms of the moments of distributions over the sites.The strengths and deficiencies of this type of thermodynamic model are discussed. © 1994 John Wiley & Sons, Inc.
Morphology and primary crystal structure of a silk‐like protein polymer synthesized by genetically engineered Escherichia coli bacteria
Authors: Anderson J. Philip , Cappello Joseph , Martin David C. 
Published: December 2004

AbstractThe morphology and primary crystal structure of SLPF, a protein polymer produced by genetically engineered Escherichia coli bacteria, were characterized. SLPF is a segmented copolymer consisting of amino acid sequence blocks modeled on the crystalline segments of silk fibroin and the cell attachment domain of human fibronectin. Wide angle x‐ray scattering (WAXS), transmission electron microscopy (TEM), selected area electron diffraction (SAED), and molecular simulations were used to analyze the primary crystal structure of SLPF. TEM experiments conducted on SLPF droplets cast from formic acid on amorphous carbon film demonstrated that these protein films have a microstructure formed of woven sheaves. The sheaves are composed of well‐defined whisker crystallites. The width of the whiskers, 11.8 ± 2.2 nm, may be correlated to the length of the silk‐like segment in SLPF as predicted by molecular simulations. WAXS data, TEM images, SAED, patterns, molecular simulations, and theoretical diffraction patterns all were consistent with the crankshaft model proposed for Silk I by Lotz and Keith. © 1994 John Wiley & Sons, Inc.
Conformational study of sequential Lys and Leu based polymers and oligomers using vibrational and electronic CD spectra
Authors: Baumruk Vladimir , Huo Dongfang , Dukor Rina K. , Keiderling Timothy A. , Lelievre Dominique , Brack André 
Published: December 2004

AbstractVibrational CD (VCD) and electronic CD (ECD) spectra of some sequential Lys and Leu based oligo‐ and polypeptides were studied as a function of added salt and (for ECD) as a function of concentration in aqueous solution. For these samples, the VCD spectra can only be measured at relatively high concentrations under which the well‐known salt‐induced transition to a β‐sheet form can be observed for the KL based species, but only the end‐state α‐helical conformation is obvious for the LKKL based samples. ECD concentration dependence demonstrates that, at high concentration with no added or with added salt, LKKL based oligomers and polymers give α‐helical spectra. These data provide evidence of aggregation induced secondary structure formation in an exceptionally simple peptide system. Similarly, the KL based oligomers and polymers give β‐sheet like spectra at high concentration or at high salt. These systems further provide model systems under “normal” aqueous conditions that yield VCD band shapes that correlate to the major secondary structural types of polypeptides. They are in substantial agreement with those spectra obtained on homopolypeptides and on proteins, confirming the relative independence of the VCD technique from side‐chain and solvent effects. © 1994 John Wiley & Sons, Inc.