bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fourier transform ir spectroscopy of collagen and gelatin solutions: Deconvolution of the amide I band for conformational studies
Authors: Payne K. J. , Veis A. 
Published: December 2004

AbstractThe ir spectra of lathyritic rat skin collagen and calf skin gelatin solutions at a variety of temperatures were obtained using Fourier transform ir spectroscopy and a 9‐reflection, 2‐pass ZnSe prism sample cell. The spectra were then deconvolved (based on Kauppinnen's method) and the behavior of the amide I band at ∼ 1650 cm−1 observed in detail. Throughout the temperature range studied (4–50°C), three component absorption peaks within the amide I band (at 1633, 1643, and 1660 cm−1) are common to the spectra irrespective of the degree of triple helix content of the sample. Changes in the relative intensities of these component peaks are, however, conformationally dependent. During denaturation of the triple helix, the dominant 1660‐cm−1 component in the native collagen spectrum diminishes and the 1633‐cm−1 peak becomes relatively intensified. The inherently strong basicity of the carbonyl group of the proline residues together with the frequent occurrence of this imino acid in the X position of the Gly‐X‐Y triplet of collagen largely accounts for the −30‐cm−1 shift of the amide I band during denaturation. Temperature and conformationally dependent changes in the fine structure of the amide I band from dilute solutions of collagen can be monitored in a reproducible and quantitative fashion.
Thermodynamics of cyclophilin catalyzed peptidyl‐prolyl isomerization by nmr spectroscopy
Authors: Videen John S. , Stamnes Mark A. , Hsu Victor L. , Goodman Murray 
Published: December 2004

AbstractOne‐dimensional nmr exchange spectroscopy was carried out to determine thermodynamic parameters of cyclophilin‐induced cis‐trans isomerization of succinyl‐Ala‐Phe‐Pro‐Phe‐p‐nitroanilide. Rate measurements were possible at physiological temperatures. The kc/Km of rat cyclophilin was found to he 12.8 (±0.5) s−1 μM−1 at 37°C, intermediate to previously reported values that used a coupled enzyme assay extrapolated to this temperature. Activation energies (ΔG≠) for the uncatalyzed and catalyzed reaction at 37°C were found to be 19.7 and 17.1 kcal/mol, respectively, and were primarily due to an enthalpic barrier. © 1994 John Wiley & Sons, Inc.
Monte Carlo and Poisson–Boltzmann calculations of the fraction of counterions bound to DNA
Authors: Lamm Gene , Wong Linda , Pack George R. 
Published: December 2004

AbstractThe counterion density and the condensation region around DNA have been examined as functions of both ion size and added‐salt concentration using Metropolis Monte Carlo (MC) and Poisson–Boltzmann (PB) methods. Two different definitions of the “bound” and “free” components of the electrolyte ion atmosphere were used to compare these approaches. First, calculation of the ion density in different spatial regions around the polyelectrolyte molecule indicates, in agreement with previous work, that the PB equation does not predict an invariance of the surface concentration of counterions as electrolyte is added to the system. Further, the PB equation underestimates the counterion concentration at the DNA surface, compared to the MC results, the difference being greatest in the grooves, where ionic concentrations are highest. If counterions within a fixed radius of the helical axis are considered to be bound, then the fraction of polyelectrolyte charge neutralized by counterions would be predicted to increase as the bulk electrolyte concentration increases.A second categorization—one in which monovalent cations in regions where the average electrostatic potential is ledd than −kT are considered to be bound—provides an informative basis for comparison of MC and PB with each other and with counterion‐condensation theory. By this criterion, PB calculations on the B from of DNA indicate that the amount of bound counterion charge per phosphate group is about .67 and is independent of salt concentration. A particularly provocative observatiob is that when this binding criterion is used, MC calculations quantitatively reproduce the bound fraction predicated by counterion‐condensation theory for all‐atom models of B‐DNA and A‐DNA as well as for charged cylindera of varying lineat charge densities. For example, for B‐DNA and A‐DNA, the fractions of phosphate groups neutralized by 2 Å hard sphere counterions are 0.768 and .817, respectively. For theoretical studies, the rediys enclosing the region in which the electrostatic potential is calculated studies, the radius enclosing the region in which the electrostatic potential is calculated to be less than −kT is advocated s a more suitable binding or condensation radius that enclosing the fraction of counterions given by (1 – ξ−1). A comparsion of radii calculated using both of these definitions is presented. © 1994 John Wiley & Sons, Inc.
Does Flory–Huggins theory help in interpreting solute partitioning experiments?
Authors: Holtzer Alfred 
Published: December 2004

AbstractThe development of Flory–Huggins (FH) theory is reviewed, particularly with regard to the molecular significance of the interaction parameter that scales the contact interaction of solute and solvent. The chemical potential given by FH theory for an “idealute” solute is then compared with that provided by a more general, statistical thermodynamic approach. It is found that the FH contact term does not directly correspond to the solvation free energy. The significance of this result for the interpretation of free energies of transfer of a solute from one solvent to another is examined. It is shown that neither the earlier recommended standard free energy change for the process (using the infinitely dilute reference state, mole fraction units) nor the recently recommended FH‐corrected standard free energy change provides the solvation energy desired. Instead, the standard free energy using the infinitely dilute reference state and molarity units, as long advocated by Ben‐Naim, provides the desired solvation free energy. Correction of extant values, based on mole fraction units, is easily made. However, application of such results to problems of protein folding is not straightforward. © 1994 John Wiley & Sons, Inc.
Microcalorimetric investigations of the interactions of small ions with arterial elastin
Authors: Winlove C. Peter , Parker Kim H. 
Published: December 2004

AbstractThe enthalpies of interactions of porcine arterial elastin with alkali metal and alkali earth halides and sulphates were investigated by means of flow microcalorimetry and the stoichiometry measured using radiotracer techniques. In aqueous solutions, all alkali earth halides interacted exothermically at concentrations ranging from 0.01 to 2.5M. All the alkali metal halides, particularly NaCl, exhibited complex concentration‐dependent interactions, exothermic at low concentrations and endothermic at high concentrations. Both the anion and cation contributed to the response, although the anion seemed to dominate. SO interacted most strongly of the anions tested. All interactions were reversible in the sense that repeat experiments gave identical results, but the enthalpy of “adsorption” was generally different from that of “desorption.” The enthalpy of interaction depended on the conformation of the elastin in a salt‐specific manner. For example, CaCl2 and MgCl2 interacted similarly in water but very differently in 1 : 1 water : methanol. © 1994 John Wiley & Sons, Inc.
Phosphophoryn, a biomineralization template protein: pH‐dependent protein folding experiments
Authors: Evans John Spencer , Chan Sunney I. 
Published: December 2004

AbstractThe protein folding behavior of a polyelectrolyte protein, bovine dentine phosphophoryn (BDPP), in the pH range of 1.82–11.0 has been investigated. One‐ and two‐dimensional nmr spectroscopy has been utilized to obtain proton spin assignments for amino acid residues in D2O and in H2O. One‐dimensional 31P‐nmr experiments verify the existence of three separate classes of O‐phosphoserine (PSer) resonances in BDPP (α, β, χ), representing three distinct PSer residue populations at pH 6.94. By means of pH titration and 1H‐nmr, five populations of Asp residues can be identified. Three of these populations exhibit secondary inflection points on their pH titration curves that correspond to an observed pKa of 6.17–6.95. The presence or absence of secondary inflection points for Asp populations and the 31P‐nmr chemical shift dispersion for the three PSer residue populations indicate that BDPP may be comprised of homologous (Asp‐Asp)n. (PSer‐PSer)n, and heterologous (PSer‐Asp)n sequences arranged into polyelectrolyte cluster regions.The pH titration also revealed that certain populations of Ser, Gly, and Pro residues in BDPP exhibit pH‐dependent resonance frequency shifts. The “apparent” pK, for the transition points of these frequency shifts corresponds to either the pK of Pser monophosphatc ester and/or the pKa of Asp COOH group of BDPP polyelectrolyte regions. On the basis of these transition points, we can assign four types of Ser, Gly, or Pro‐containing “intervening” regions in BDPP, based on their sensitivity to protonation and deprotonation events occurring at (Asp)n, (PSer)n, or (PSer‐Asp)n anionic cluster regions that flank the intervening regions.Our 1H‐ninr experiments also reveal that BDPP assumes a folded conformation at low pH. As the pH increases, this conformation undergoes several unfolding transitions as the BDPP molecule assumes more open conformations in response to increased electrostatic repulsion between polyelectrolyte anionic regions in the protein. These folding‐unfolding transitions are mediated by the intervening regions, which act as “hinges” to allow the polyelectrolyte regions to fold relative to one another. © 1994 John Wiley & Sons, Inc.
Dependence on the dielectric model and pH in a synthetic helical peptide studied by Monte Carlo simulated annealing
Authors: Okamoto Yuko 
Published: December 2004

AbstractMonte Carlo simulated annealing is applied to the tertiary structure prediction of a 17‐residue synthetic peptide, which is known by experiment to exhibit high helical content at low pH. Two dielectric models are considered: sigmoidal distance‐dependent dielectric function and a constant dielectric function (ϵ = 2). Starting from completely random initial conformations, our simulations for both dielectric models at low pH gave many helical conformations. The obtained low‐energy conformations are compared with the nuclear Overhauser effect spectroscopy cross‐peak data for both main chain and side chains, and it is shown that the results for the sigmoidal dielectric function are in remarkable agreement with the experimental data. The results predict the existence of two disjoint helices around residues 5–9 and 11–16, while nmr experiments imply significant α‐helix content between residues 5 and 14. Simulations with high pH, on the other hand, hardly gave a helical conformation, which is also in accord with the experiment. These findings indicate that when side chains are charged, electrostatic interactions due to these charges play a major role in the helix stability. Our results are compared with the previous 500 ps molecular dynamics simulations of the same peptide. It is argued that simulated annealing is superior to molecular dynamics in two respects: (1) direct folding of α‐helix from completely random initial conformations is possible for the former, whereas only unfolding of an α‐helix can be studied by the latter; (2) while both methods predict high helix content for low pH, the results for high pH agree with experiment (low helix content) only for the former method. © 1994 John Wiley & Sons, Inc.
Partial molar volumes, expansibilities, and compressibilities of oligoglycines in aqueous solutions at 18–55°C
Authors: Chalikian Tigran V. , Sarvazyan Armen P. , Funck Theodor , Breslauer Kenneth J. 
Published: December 2004

AbstractWe have determined the partial molar volumes, expansibilities, and adiabatic compressibilities of glycine, diglycine, triglycine, tetraglycine, and pentaglycine over the temperature range 18–55°C. These data were analyzed and interpreted in terms of the hydration of these short oligoglycines and their constituent groups. From our results, we have estimated the contributions of the peptide group to the partial molar volume and the partial molar adiabatic compressibility of these oligoglycines. Based on these data, we propose that each of the polar atomic groups of the peptide bond forms approximately two hydrogen bonds with adjacent water molecules. Furthermore, the temperature dependence of the partial molar volume suggests that water that solvates the polar groups of a peptide linkage behaves more like a “normal” liquid than does bulk water, which exhibits its well‐known anomalous liquid properties. © 1994 John Wiley & Sons, Inc.
Nmr and molecular modeling investigations of the neuropeptide bradykinin in three different solvent systems: DMSO, 9 : 1 dioxane/water, and in the presence of 7.4 mM lyso phosphatidylcholine micelles
Authors: Young John K. , Hicks Rickey P. 
Published: December 2004

AbstractThe linear nonapeptide hormone bradykinin (Arg1‐Pro2‐Pro3‐Gly4‐Phe5‐Ser6‐Pro7‐Phe8‐Arg9) is involved, either directly or indirectly, in a wide variety of physiological processes, particularly pain and hyperanalgesia. Additional evidence suggests that bradykinin also plays a major role in inflammatory response, asthma, sepsis, and symptoms associated with the rhinoviral infection. It has long been speculated that a β‐turn at the C‐terminus of bradykinin plays a major role in the biological activity of the neuropeptide. The β‐turn forming potential of bradykinin in three vastly different local chemical environments, DMSO, 9 : 1 dioxane/water, and in the presence of 7.4 mM lyso phosphatidylcholine micelles, was investigated using two‐dimensional homonuclear nmr experiments coupled with simulated annealing calculations. The results of these investigations show that in all three systems residues 6–9 of the C‐terminus adopt very similar β‐turn like structures. These results suggest that the β‐turn at the C‐terminus of bradykinin is an important secondary structural feature for receptor recognition and binding. © 1994 John Wiley & Sons, Inc.
Helix formation by the phospholipase A2 38–59 fragment: Influence of chain shortening and dimerization monitored by nmr chemical shifts
Authors: Jiménez M. Angeles , Carreño Cristina , Andreu David , Blanco Francisco J. , Herranz José , Rico Manuel , Nieto José L. 
Published: December 2004

AbstractThe solution structure of a peptide fragment corresponding to the 38–59 region of porcine phospholipase A2 has been investigated using CD, nmr chemical shifts, and nuclear over‐hauser effects (NOEs). This isolated fragment of phospholipase forms an α‐helix spanning residues 38–55, very similar to the one found in the native protein, except for residues 56–58, which were helical in the crystal but found random in solution. Addition of triflouro‐ethanol (TFE) merely increased helix population but it did not redefine helix limits. To investigate how the folding information, in particular that concerning eventual helix start and stop signals, was coded in this particular amino acid sequence, the helices formed by synthetic peptides reproducing sections of this phospholipase 38–59 fragment, namely 40–59, 42–59, 38–50, and 45–57, were characterized using NOEs and helix populations quantitatively evaluated on different peptide chain segments using nmr chemical shifts in two solvents (H2O and 30% TFE/H2O). A set of nmr spectra was also recorded and assigned under denaturing conditions (6Murea) to obtain reliable values for the chemical shifts of each peptide in the random state. Based on chemical shift data, it was concluded that the helix formed by the phospholipase 38–59 fragment was not abruptly, but progressively, destabilized all along its length by successive elimination of residues at the N end, while the removal of residues at the C end affected helix stability more locally and to a lesser extent. These results are consistent with the idea that there are not single residues responsible for helix initiation or helix stability, and they also evidence an asymmetry for contributions to helix stability by residues located at the two chain ends. The restriction of molecular mobility caused by linking with a disulphide bridge at Cys 51 two identical 38–59 peptide chains did not increase helix stability. The helix formed by the covalently formed homodimer was very similar in length and population to that formed by the monomer. © 1994 John Wiley & Sons, Inc.
Site‐Specific thermodynamics of ising networks: A theorem for linearly connected subsystems
Authors: Di Cera Enrico , Keating Sean 
Published: December 2004

AbstractAn Ising network consists of a set of N units existing in two possible states, 0 and 1. If two units contact each other in the network, there is a nearest neighbor interaction that depends only on the states of the units. If an Ising network can be split into two independent subsystems by deleting the contact between two units, then these units specify each other's site‐specific properties and the state of either unit uniquely specifies the state of the other. This theorem holds regardless of (a) the dimensional embedding of the network as a whole, (b) the precise interaction geometry among the units within either subsystem, and (c) the intrinsic energy for the 0 → 1 switching of any given unit. Either subsystem in the network can be considered as a probe for the state of the unit in the other subsystem to which the probe is connected. Application of the theorem to the analysis of the site‐specific properties of the biologically relevant case of a linear network, or heteropolymer, yields a rather counterintuitive result. Knowledge of the state of the end unit in the network, as a function of the change in the thermodynamic driving force for the 0 → 1 transition, is sufficient to completely resolve the energetics of the network. © 1994 John Wiley & Sons, Inc.
Copper ion complex formation of polypeptide containing side‐chain pyridyl groups
Authors: Nagata Yoshitomo , Kanuka Satoru , Kinoshita Takatoshi , Takizawa Akira , Tsujita Yoshiharu , Yoshimizu Hiroaki 
Published: December 2004

AbstractThe complex formation behaviors of an α‐helical polypeptide containing pyridyl ligands in the side chains, poly (Nω‐2‐pyridylmethyl L‐glutamine) (P2PG), were investigated by absorption and CD spectroscopy using Cu2+ ion as a guest molecule in 2,2,2‐trifiuoroethanol solution. In the low Cu2+ ion concentration, P2PG exhibited the predominant formation of Cu2+ and two pyridyl side‐chain complexes, involving a regular arrangement of the pyridyl side chains. On the other hand, the complexes were converted to Cu2+ and one pyridyl side‐chain species with increasing Cu2+ ion concentration. The conversion was accompanied by the disappearance of the side‐chain ordered structure without any changes in the backbone conformation. Moreover, the still remaining coordination sites of Cu2+ were capable of complexing monomer pyridine (Py) added as a second guest to form ternary complexes, P2PG‐Cu2+‐Py, following the reconstitution of the ordered structure on the periphery of the α‐helix backbone. The unique characteristics of P2PG can be explained in terms of the restriction of the pyridyl side chains to form intramolecular chelate complexes, depending on the rigid α‐helix conformation. © 1994 John Wiley & Sons, Inc.
Sol–Gel transition of alginate solution by the addition of various divalent cations: A rheological study
Authors: Wang Zheng‐Yu , Zhang Qing‐Zhi , Konno Mikio , Saito Shozaburo 
Published: December 2004

AbstractSeveral rheological properties of aqueous alginate solution have been investigated in the absence and presence of four divalent cations: Ca, Cu, Mn, and Co. The concentration dependence of viscosity in alginate solution without addition of divalent cations shows a similar behavior to that found for other polysaccharides and synthetic polymers. We have found that for Ca(II) ‐added systems, sol‐gel transition curves for different alginate concentrations can be superimposed over the concentration range of this study by using a normalized parameter. Shear‐thinning behavior has been observed for all the alginate solutions by addition of four divalent cations over sol‐gel transition process. The values of exponent b in the power‐law relation \documentclass{article}\pagestyle{empty}\begin{document}$ {\eta \propto \dot \gamma }$\end{document} were found in the range of −0.3 ∼ −0.6. It is suggested that a considerable portion of divalent cations remains in a cross‐linking state even under shear flow. The results obtained from thixotropy measurements indicate the existence of a major framework formed in the gel‐like and well‐gelled samples, which can be maintained until shear rate (or shear stress) reaches a threshold value. © 1994 John Wiley & Sons, Inc.
A quantum mechanical study of the intrinsic helix‐forming tendency of α‐aminoisobutyric acid and dehydroalanine residues
Authors: Alemán Carlos 
Published: December 2004

AbstractA quantum mechanical study to compare the ability of α‐aminoisobutyric acid (Aib), de‐hydroalanine (ΔAla), and alanine (Ala) residues to stabilize helical conformations has been performed. To address the study, the oligopeptides Xn (X = Aib, ΔAla and Ala), where n varies from 1 to 6, were computed with the AM1 semiempirical method. The results show that the residues modified at the Cα carbon atom, Aib and ΔAla, are better helical formers than Ala. Thus, a cooperative energy effect was found for both residues, and especially for ΔAla. These terms permit the understanding the different conformational behaviors between Ala and its Cα‐modified residues Aib and ΔAla. This trend is important for de novo protein design, where Aib and ΔAla must be considered useful residues in the design of synthetic helical motifs. © 1994 John Wiley & Sons, Inc.
Conformational and binding properties of chicken liver basic fatty acid binding protein in solution
Authors: Schievano Elisabetta , Quarzago Daniela , Spadon Paola , Monaco Hugo Luis , Zanotti Giuseppe , Peggion Evaristo 
Published: December 2004

AbstractThe conformation of basic fatty acid binding protein from chicken liver and the binding properties of the apo protein toward 11‐dansylamino‐undecanoic acid were investigated by CD and fluorescence spectroscopy. In one set of experiments the binding process was followed by the appearance of induced optical activity in the absorption region of the dansyl chromophore. In a second set of experiments the binding process was followed by the large enhancement of emission fluorescence of the dansyl fluorophore. From the saturation curves, the stoichiometry of the complex and the binding constant of the fatty acid to the protein were precisely determined. The values of the dissociation constant determined with the two methods were in excellent agreement: we obtained KD = (1.0 ± 0.1) · 10−6M in a 0.9 : 1 stoichiometry. The native conformation of the protein is remarkably stable in a variety of solvent systems, including acetonitrile–water, ethylene glycol–water, and dicxane–water of various compositions. The CD results also showed that the binding of the fatty acid does not induce any appreciable change in the protein conformation. In a mixture of water and 2,2,2‐trifluoroethanol 1 : 9 (v/v), the native conformation collapses and a new ordered structure is formed, characterized by a high amount of α‐helix. © 1994 John Wiley & Sons, Inc.