bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probe diffusion in solutions of filamentous actin formed in the presence of gelsolin
Authors: Newman Jay , Gukelberger Gerlinde , Schick Kenneth L. , Zaner Ken S. 
Published: December 2004

AbstractDynamic light scattering was used to characterize the diffusion of monodisperse polystyrene latex spheres (PLS) of different sizes (55‐, 105‐, and 265‐nm radii) in column‐purified 0.65 mg/mL actin solutions polymerized with 100 mM KCl in the absence and presence of various amounts of the actin‐binding protein gelsolin. The gelsolin and its interaction with actin was initially studied to ensure that the gelsolin could be used to produce filament populations with well‐defined mean lengths. Measurements with PLS diffusion probes present showed, in the absence of gelsolin, that the effective local microviscosity in the actin solutions was 5–20 times that of water and that a large fraction of the PLS are trapped within the pores of the actin filament network, as found previously [J. Newman, K. L. Schick, & K. S. Zaner, (1989) Biopolymers 28, 1969–1980]. As the molar ratio of gelsolin to actin was increased, the diffusion coefficients of the PLS approached those in pure water while the degree of PLS trapping went to zero. Measurements of the dependence of the PLS diffusion coefficients on the ratio of actin concentration to the semidilute overlap concentration showed, for the smaller PLS, a transition occurring near the mean global overlap concentration. These results reflect the dissolution of the actin network as the gelsolin concentration is increased and illustrate the role of gelsolin/actin interactions in the control of macromolecular transport within the periphery of cells.
Birefringence of actin
Authors: Kakar Sharwan K. , Bettelheim Frederick A. 
Published: December 2004

AbstractThe total strain birefringence of F‐actin isolated from chicken gizzards was measured as a function of elongation in thin transparent films. Each film held at a certain elongation in a jig was allowed to swell in a penetrating but nondissolving liquid. Seven liquids with different refractive indices were employed. The thickness of the film in each swelling liquid was obtained once equilibrium was established. At each elongation, from 0 to 16%, a Wiener curve was obtained. The minima of the Wiener curves yielded the intrinsic birefringence of F‐actin as a function of elongation. The intrinsic birefringence increases with elongation up to 16%, above which the thin films break. The form birefringence at a set refractive index also increases with elongation. The implication of the strain birefringence of F‐actin is discussed as it affects the optical properties, mainly light scattering, of tissues such as the fiber cells of lens of the eye.
Unfolding of an α‐helix in water
Authors: Soman Kizhake V. , Karimi Afshin , Case David A. 
Published: December 2004

AbstractWe describe a 1 ns molecular dynamics simulation of an 18‐residue peptide (corresponding to a portion pf the H helix of myoglobin) in water. The initial helical conformation progressively frays to a more disordered structure, with the loss of internal secondary structure generally proceeding from the C‐terminus toward the N‐terminus. Although a variety of mechanisms are involved in the breaking of helical hydrogen bonds, the formation of transient turn structures, with i → i + 3 hydrogen bonds, and bifurcated hydrogen‐bond structures intermediate between α and turn or 310 structures is a common motif. In some cases a single water molecule is inserted into an internal hydrogen bond, but it is also common to have several water molecules involved in transient intermediates. Overall, the results provide new information about the detailed mechanisms by which helices are made and broken in aqueous solution.
Solution conformation of laminaribioside and (1 → 3)‐β‐D‐glucan from optical rotation
Authors: Duda Christopher A. , Stevens Eugene S. 
Published: December 2004

AbstractA chiroptical method of conformational analysis is applied to linear (1 → 3)‐β‐D‐glucans and the dimeric analogues β‐ and α‐laminaribioside. The method is based on a recently developed semiempirical calculational model for saccharide optical activity. We conclude that disaccharide conformational energy maps in the literature represent the effective potential energy surface in aqueous solution well. The positive optical rotation observed with long chains in dilute alkaline solution is not characteristic of any single–chain conformation, and must reflect chain association.
Vibrational CD of the amide II band in some model polypeptides and proteins
Authors: Gupta Vijai P. , Keiderling Timothy A. 
Published: December 2004

AbstractThe amide II vibrational CD (VCD) spectra of poly(L‐glutamic acid) and poly(L‐lysine) in various conformational forms and those of several proteins in H2O have been measured. Characteristic VCD patterns have been observed in the amide II region due to helix, β‐sheet, and coil conformations in polypeptides. Based on their x‐ray crystal structures, the proteins studied have been assigned to six categories. Proteins in the same category give rise to similar amide II VCD. While the protein conformational type is indicated using the amide II VCD, discrimination between types is less characteristic than with the previously studied amide I' VCD in D2O.
Multivalent ions are necessary for poly[d(AC) · d(GT)] to assume the Z form: A CD study
Authors: Riazance‐Lawrences Jeannine H. , Johnson W. Curtis 
Published: December 2004

AbstractIn previous work, it was shown that poly [d(AC) · d(GT)] could be forced into the Z form by strong dehydrating conditions, provided EDTA was not present. Presumably multivalent impurities were also necessary for the transition. In order to gain control over the B to Z transition for this DNA, we carefully removed all divalent contaminants from the sample and asked the obvious question: What ions are necessary for the transition under dehydrating conditions? We systematically investigated the effect of various multivalent ions. The common contaminants Ca2+, Mg2+, and Fe3+ will not cause the transition, but Co2+ and Ni2+ facilitate the transition, undoubtedly because of their well‐known propensity to bind to purine N7. Since the transition also depends on the synergistic dehydrating action of sodium perchlorate and ethanol, we include CD spectra for the independent variations of these two factors. In addition, vacuum‐uv CD spectra for the A form and various B forms of poly [d (AC) · d (GT)] are presented for the first time.
Stoichiometry of calcium binding to a synthetic heterodimeric troponin‐C domain
Authors: Shaw Gary S. , Hodges Robert S. , Sykes Brian D. 
Published: December 2004

AbstractIn this work we describe calcium binding to two synthetic 34‐residue peptides, determined by 1H‐nmr spectroscopy. The peptides investigated, SCIII and SCIV, encompass the calcium‐binding sites III and IV, respectively, of troponin‐C. In the absence of calcium it has previously been shown that each of these peptides possesses little regular secondary structure. Further, the 1H‐nmr spectra of an equimolar mixture of both of these apo‐peptides (apo‐SCIII/SCIV) shows that little interaction occurs between peptides. Upon calcium binding the spectral changes that occur to SCIII/SCIV are consistent with global conformational changes in both peptides. We have shown previously that these conformational changes are a product of calcium binding to SCIII and SCIV to form a two‐site heterodimer Ca2‐SCIII/SCIV. It is proposed that this calcium‐induced folding proceeds via calcium binding to SCIII to form Ca‐SCIII, peptide association with apo‐SCIV to form the heterodimer Ca‐SCIII/SCIV, and calcium binding to form Ca2‐SCIII/SCIV. The dissociation constants involved in this pathway, K1, Kd, and K2, respectively, have been determined by stoichiometric calcium titration of SCIII/SCIV, monitored by 1H‐nmr spectroscopy. Using this procedure it has been determined that K1 = 3 μM, Kd = 10 μM, and K2 = 2 μM.
A molecular mechanical study of the structure of poly(α‐aminoisobutyric acid)
Authors: Alemán Carlos , Subirana Juan A. , Perez Juan J. 
Published: December 2004

AbstractA molecular mechanical study has been carried out to determine the most favorable conformation of poly(Aib) both in solution and in the solid state. An energetic approach to the packing has been carried out by studying the stability of pairs of poly(Aib) chains. The study reveals a higher stability of a 310‐helix when forming part of a dimer whereas in isolated molecules the α‐helix structure seems to be more stable depending on the length of the chain and dielectric constant of the environment.
Crystal structure of a helical oligopeptide model of polyglycine II and of other polyamides: Acetyl‐(glycyl‐β‐alanyl)2‐NH propyl
Authors: Tormo José , Puiggali Jordi , Vives Joan , Fita Ignasi , Lloveras Joaquim , Bella Jordi , Aymamí Joan , Subirana Juan A. 
Published: December 2004

AbstractWe synthesized and solved the crystalline structure of the oligopeptide acetyl‐ (glycyl‐β‐alanyl)2‐NH propyl. The crystal is formed by layers of helical molecules with the same chirality; however, right‐handed layers alternate with left‐handed ones. Inside every layer, the packing of helices is pseudohexagonal with hydrogen bonds between neighbor molecules. The structure found affords direct support for the model proposed by Crick and Rich for polyglycine II and also provides an interpretation for the structure of a newly found family of polyamides that do not form sheets as observed in most nylon structures.
Kinetics of folding of αα‐tropomyosin subsequences
Authors: Mo Jianming , Holtzer Marilyn Emerson , Holtzer Alfred 
Published: December 2004

AbstractThe kinetics of folding random coils of αα‐tropomyosin (Tm) subsequences to two‐chain coiled coils was studied by stopped‐flow CD. Subsequences studied were those comprising residues 11–127 (11Tm127), 142–281 (142Tm281), 1–189 (1Tm189), and 190–284 (190Tm284) of the parent 284‐residue α‐tropomyosin chain. Unlike the parent, subsequences 1Tm189 and 11Tm127 fold within the dead time of the instrument (< 0.04 s). Like the parent, subsequences 142Tm281 and 19Tm284 fold in two phases. In the fast phase, 45% and 32%, respectively, of the equilibrium helical content form. In the time‐resolvable, first‐order slow phase (k−l = 2.7 s at 20°C for 142Tm281 and k−l = 2.0 s at 15°C for 190Tm284), the remaining structure forms. Neither reduced 142Tm281 nor 190Tm284 show any dependence of the rate on concentration, so chain association occurs in the fast phase. Like the parent, 142Tm281 forms more helical content in the fast phase when cross‐linked at C‐190, and the remaining structure forms slowly with rate parameters similar to those of the reduced species. Comparison of the folding behavior of C‐ and N‐terminal subsequences with that of the parent protein suggests that the slow phase in the parent is caused by a folding bottleneck somewhere nearer the C‐terminus. However, rapid association and partial folding near the N‐terminus is not necessary for prompt folding, since even 190Tm284 chains associate and partially fold very rapidly (<0.04 s), and then complete the folding in seconds.
Spectroscopic study of the interaction between poly‐(9‐vinyladenine) and single or multistrand RNA
Authors: Yashima Eiji , Tajima Teruyo , Miyauchi Noriyuki , Akashi Mitsuru 
Published: December 2004

AbstractThe interaction between poly(9‐vinyladenine) (PVAd) and poly[r (U)] was investigated by means of uv, CD, 1H‐, and 31P‐nmr spectroscopies. The interaction was dependent on the molecular weight of PVAd determined by uv and CD spectroscopies. Based on imino proton nmr, it was clearly found that PVAd formed the complex with poly [r(U)] by complementary hydrogen bonding. The interaction of PVAd with double‐ and triple‐stranded helices of RNA was also investigated by uv melting behavior and 31P‐nmr spectroscopy. The results suggested that PVAd could not interact with the double‐stranded poly [r (A)] · poly[r(U)] but did with the triple‐stranded RNA.
Conformational and ion binding properties of a cyclic octapeptide, cyclo(Ala‐Leu‐Pro‐Gly)2
Authors: Jois D. S. Seetharama , Easwaran K. R. K. , Bednarek Maria , Blout E. R. 
Published: December 2004

AbstractThe conformation and ion‐binding characteristics of a cyclic octapeptide, cyclo(Ala‐Leu‐Pro‐Gly)2, in a liphophilic solvent, acetonitrile, have been studied using CD and nmr spectroscopy. The peptide binds preferentially to divalent cations such as calcium, magnesium, and barium. The conformations of the free cyclic peptide and its calcium complex are very similar with well‐defined β‐ and γ‐turns. The cyclic peptide readily forms equimolar and possibly 2 : 1 (peptide:cation) complexes with divalent cations.
Hydrophobicity scale for proteins based on inverse temperature transitions
Authors: Urry Dan W. , Gowda D. Channe , Parker Timothy M. , Luan Chi‐Hao , Reid Michael C. , Harris Cynthia M. , Pattanaik Asima , Harris R. Dean 
Published: December 2004

AbstractIn general, proteins fold with hydrophobia residues buried, away from water. Reversible protein folding due to hydrophobia interactions results from inverse temperature transitions where folding occurs on raising the temperature. Because homoiothermic animals constitute an infinite heat reservoir, it is the transition temperature, Tt, not the endothermic heat of the transition, that determines the hydrophobically folded state of polypeptides at body temperature. Reported here is a new hydrophobicity scale based on the values of Tt for each amino acid residue as a guest in a natural repeating peptide sequence, the high polymers of which exhibit reversible inverse temperature transitions. Significantly, a number of ways have been demonstrated for changing Tt such that reversibly lowering Tt, from above to below physiological temperature becomes a means of isothermally and reversibly driving hydrophobic folding. Accordingly, controlling Tt, becomes a mechanism whereby proteins can be induced to carry out isothermal free energy transduction. © 1992 John Wiley & Sons, Inc.
The spectroscopic properties of the lipodepsipeptide, syringomycin E
Authors: Vaillo Eva , Ballo Alessandro , Luisi Pier‐Luigi , Thomas Richard M. 
Published: December 2004

AbstractThe Spectroscopic properties of syringomycin E, an antibiotic lipodepsinonapeptide associated with pathological states in plants, have been investigated by uv absorbance and CD spectroscopies, and by the synthesis of relevant model compounds. Initial studies [E. Vaillo, A. Ballio, P. L. Luisi, and R. M. Thomas (1990) in Peptides 1990, Giralt, E. & Andreu, D., Eds., Escom Scientific, Leiden, Netherlands] suggested that a significant contribution to the spectra was due to the presence of a zdehydroaminobutyric acid residue in the amino acid sequence. The model peptides N‐Boc‐L‐Phe‐ΔZAbu‐OMe and its analogue, N‐Boc‐L‐Phe‐L‐Thr‐OMe, lacking the unsaturated bond, were synthesized using standard solution chemistry, and a detailed investigation was made in which the spectra of the models and that of syringotoxin (an antibiotic closely related to syringomycin E but without a Phe residue) were compared with those of syringomycin E under a variety of solvent conditions. The uv absorbance spectra of both N‐Boc‐L‐Phe‐ΔZAbu‐OMe and syringomycin E clearly showed the presence of the unsaturated residue while the CD spectra were complex, environmentally sensitive, and contained contributions from both the ΔzAbu and Phe residues. In the course of these studies extinction coefficients were obtained for syringomycin E and its dipeptide model. The origins of the uv and CD spectra are discussed in detail, and a comparison is made with the spectra of other, similar lipopeptide antibiotics. Finally, a structural model for syringomycin is proposed in which the changes induced in the spectrum by alterations in the solvent environment are accommodated. © 1992 John Wiley & Sons, Inc.
Interpretation of 25Mg spin relaxation in Mg‐DNA solutions: Temperature variation and chemical exchange effects
Authors: Berggren Elisabet , Nordenskiöld Lars , Braunlin William H. 
Published: December 2004

AbstractThe temperature dependencies of line shapes and spin lattice relaxation times Tl have been measured for 25Mg in dilute solutions of Na‐DNA/NaCl containing varying amounts of added magnesium(II) ions. The 25Mg spectrum is clearly non‐Lorentzian, due to the presence of motions modulating the quadrupolar interaction that are slow compared to the inverse of the Larmor frequency. The weakly temperature dependent line shapes and relaxation rates appear to be influenced by the relatively slow exchange of the Mg2+ ions between the DNA surface and the aqueous bulk phase. The observed temperature dependencies depend on the ratio of total magnesium to DNA phosphate, Mg/P. The line shape as well as the temperature dependence of the line width at half height can be qualitatively reproduced with a two‐site discrete exchange model for the quadrupolar relaxation of a spin \documentclass{article}\pagestyle{empty}\begin{document}$ \frac{5}{2} $\end{document} nucleus in isotropic solution. The calculations give a value of the lifetime for magnesium bound to DNA of 4 ms at room temperature. Previously reported temperature dependent 43Ca relaxation measurements in DNA solution can be reproduced under the assumption of a mean lifetime of bound calcium that is not, larger than 2 ms but not smaller than 50 μs at room temperature. The temperature variation of T1 for 25Mg has been calculated, giving some qualitative agreement with the data. The correlation time for bound 25Mg has been found to be about 40 ns at room temperature. © 1992 John Wiley & Sons, Inc.
Excluded volume effects on the partition of single‐ and double‐stranded oligodeoxynucleotides between two liquid phases
Authors: Zimmerman Steven B. , Murphy Lizabeth D. 
Published: December 2004

AbstractThe distribution coefficients of single‐ and double‐stranded Oligodeoxynucleotides in a PEG 8000/phosphate two‐phase system are a function of their chain length. Values of the distribution coefficients are in general agreement with a simple extension of a model for excluded volume effects (the “available volume model”) which was applied previously to the distribution of proteins in this system. The current results therefore provide a second set of examples for molecules of very different geometry where the distribution of added molecules is controlled by excluded volume interactions between those molecules and the PEG 8000 of the two‐phase system. © 1992 John Wiley & Sons, Inc.
Fourier transform IR study of enzymatically isolated tomato fruit cuticular membrane
Authors: Ramirez F. J. , Luque P. , Heredia A. , Bukovac M. J. 
Published: December 2004

AbstractFourier transform ir study on enzymatically isolated tomato fruit cuticle has been performed. Assignments of the observed frequencies to functional groups present in the cuticular membrane yield information on the polyester cross‐links and the interactions among the different components that form this plant protective barrier. © 1992 John Wiley & Sons, Inc.
Quasielastic light scattering study of thermal excitations of F‐actin solutions and of growth kinetics of actin filaments
Authors: Piekenbrock Th. , Sackmann E. 
Published: December 2004

AbstractIn the first part of this work we report quasielastic light scattering (QELS) studies of the internal dynamics of transient actin networks over a time range of 10−6–10−2 s, scattering angles between ζ = 20° and 150°, and a concentration range of 0.015 (0.3) to 0.7 mg/mL (15 μM). We confirm our previous result that (1) the dynamic structure factor g(q, t) is determined by the thermally excited undulations of the actin filaments and (2) that the initial decay of g(q, t) scales as g(q, t)∝ exp(qαt) while the long time decay scales as g(q, t) ∝ exp[‐(Aqαt)2/3] with α = 2.75. The deviation of α from the theoretical value of α = 3 predicted for Rouse‐Zimm chains is similar to that found for high molecular weight macromolecular solutions by QELS. A refined analysis of the dynamic structure factor showed that it can be interpreted in terms of three relaxation processes (besides the contribution of the residual monomer diffusion): (1) the dominant Rouse‐Zimm dynamics, which comprises between 65 (at high concentrations) and 85% of the signal; (2) a fast relaxation process with a decay constant of Γ = 9 × 103 s−1, which contributes at all concentrations with the same amplitude; and (3) a nonexponential ultraslow contribution of the form gus ∝ exp[(– Γust)] 1/4. The third contribution appears only at high concen‐trations and increases strongly with decreasing scattering angles. It is thus attributed to fluctuations of the mesh size of the transient actin network.In the second part we show that high sensitivity QELS may be applied to follow the actin polymerization process at low temperatures (10°C). The apparent diffusion coefficient and the static scattering intensity of the actin filaments were determined as functions of polymerization time tpol. We show that the process consists of the rapid growth of a few filaments that become very long (≈10 μm; even at actin concentrations of 0.04 μg/mL) near the critical growth concentration of 0.012 μg/mL, as is expected for a growth process determined by nucleation.Finally, we studied actin networks polymerized in the presence of complexes of gelsolin with actin. By application of the CONTIN program we could determine the length distribution of the filaments. The very broad length distribution is nearly exponential, quite analogous to the distribution predicted for polymers grown by the polycondensation process; that is the association of monomers and oligomers. © 1992 John Wiley & Sons, Inc.
Monte carlo calculations of ion distributions surrounding the oligonucleotide d(ATATATATAT)2 in the B, A, and wrinkled D conformations
Authors: Mills Pamela A. , Rashid Ali , James Thomas L. 
Published: December 2004

AbstractWe calculated the uni‐univalent ion distributions around‐ the oligonucleotide d(AT)5 · d(AT)5 in the A, B and wrinkled D conformation using the Metropolis Monte Carlo method. All atoms were included in the oligonucleotide model with partial charges and hard sphere radii assigned to each atom. The univalent counter‐ and coions were modeled as hard spheres with radius 0.3 nm. The solvent was assigned a dielectric constant of 80, corresponding to a temperature of 298K. The counterion distribution surrounding each of the conformers and the distribution surrounding an impenetrable cylinder, were calculated for four salt concentrations. We found significant counterion density in the major groove of the A DNA while fewer counterions occupied the grooves of B DNA. In the wrinkled D DNA, where groove occupancy is sterically hindered, the ion distributions were identical to the distributions surrounding the impenetrable, cylindrical model. This suggests that excluded volume effects significantly influence the details of the ion distributions near the oligomer, while the detailed charge distributions of the oligomer affects the ion distributions only minimally. Although substantial variation in counterion density was observed near the oligomers of differing conformations, the total number of counterions located within a cylinder surrounding the oligomer bounded radially by 2.4 nm was independent of the conformation of the oligomer. Therefore, for this model system, the local univalent counterion distributions are extremely sensitive to the geometry of the oligonucleotide whereas the extent of neutralization of the oligoanion is insensitive to the conformation of the oligomer. © 1992 John Wiley & Sons, Inc.