bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Monomer Size Distribution on the fractal dimensionality of diffusion‐limited aggregates
Authors: Chou Charles C.‐K. , Lee Chung‐Te 
Published: May 2005

AbstractComputer simulations of diffusion‐limited aggregation (DLA) for monomers to investigate the effects of size and of lognormal distribution on the fractal dimensionality of the aggregates were conducted on a two‐dimensional lattice. The results show the DLA clusters posses multifractal characteristics. For clusters consisting of monodisperse monomers, the bifurcation point on the graph of the pair correlation function (PCF) for each cluster is located right at the monomers size under investigation The textural dimension (Df1) has a stable value of about 1.65, whereas the structural dimension (Df2) decreased with increase in monomer size. For the cases with monomers in log‐normal distributions, the textural dimension is around 1.67; however, the structural dimension decreases with increasing polydispersity of monomer size.
Characterising Semi‐Cohesive Powders using angle of repose
Authors: Wouters Ilse M. F. , Geldart Derek 
Published: May 2005

AbstractWhen properly measured and interpreted angle of repose (AOR) can be a useful method of characterising a powder. Unfortunately, a multitude of definitions and measuring equipment is used. A review of the inherent problems is presented in the first part of this paper.The second part of the paper describes the improvements made to a measuring device developed originally for measuring the angle of repose of soda ash, so that a wider range of powders can be tested. In the improved design, the tendency of cohesive and semi‐cohesive powders to block the device's funnel has been eliminated.A total of 73 powders consisting of four different materials, and covering Groups A, A/C and C of Geldart's classification, have been tested using the new equipment. The results show that AOR increases systematically with decrease in mean particle size. Combination of AOR measured in the new device with aerated bulk density provides a quick, sensitive and effective method for characterising a wide range of powders.
Particle shape characterization using morphological descriptors
Authors: Pons Marie‐Noëlle , Vivier Hervé , Dodds John 
Published: May 2005

AbstractTwo descriptors based on mathematical morphology are described which permit discrimination between convex and concave polygonal shapes which often characterize crystalline particles. Their computation is based on the comparison between the silhouette of the particle and a reference shape. Three reference shapes are discussed: the convex hull, the circle circumscribed to the particle and the equivalent circle.
A fourier optics method for the simulation of measurement‐volume‐effect by the slit constraint
Authors: Qiu Hui‐He , Hsu Chin‐Tsau 
Published: May 2005

AbstractA new method is introduced to analyze the accuracy of phase‐Doppler anemometry (PDA) for sizing large particles in two‐phase flows. The method is based on Fourier optics theory (FOT) and geometrical optics theory (GOT) to calculate the intensity ratio of refractive and reflective light scattered by a sphere under a slit constraint. To examine the accuracy in calculating the light intensity, the results from the GOT method were compared with those of the direct simulation based on the generalized Lorenz‐Mie theory (GLMT). This newly developed FOT/GOT method also predicts the results of phase jump due to the slit constraint. The performance of dual‐mode phase‐Doppler anemometry can also be simulated by this method.
Protein folding kinetics by combined use of rapid mixing techniques and NMR observation of individual amide protons
Authors: Roder Heinrich , Wüthrich Kurt 
Published: May 2005

AbstractA method to be used for experimental studies of protein folding introduced by Schmid and Baldwin (J. Mol. Biol. 135: 199–215, 1979), which is based on the competition between amide hydrogen exchange and protein refolding, was extended by using rapid mixing techniques and 1H NMR to provide site‐resolved kinetic information on the early phases of protein structure acquisition. In this method, a protonated solution of the unfolded protein is rapidly mixed with a deuterated buffer solution at conditions assuring protein refolding in the mixture. This simultaneously initates the exchange of unprotected amide protons with solvent deuterium and the refolding of protein segments which can protect amide groups from further exchange. After variable reaction times the amide proton exchange is quenched while folding to the native form continues to completion. By using 1H NMR, the extent of exchange at individual amide sites is then measured in the refolded protein. Competition experiments at variable reaction times or variable pH indicate the time at which each amide group is protected in the refolding process. This technique was applied to the basic pancreatic trypsin inhibitor, for which sequence‐specific assignments of the amide proton NMR lines had previously been obtained. For eight individual amide protons located in the β‐sheet and the C‐terminal α‐helix of this protein, apparent refolding rates in the range from 15s−1 to 60 s−1 were observed. These rates are on the time scale of the fast folding phase observed with optical probes.
Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification
Authors: Klapper Isaac , Hagstrom Ray , Fine Richard , Sharp Kim , Honig Barry 
Published: May 2005

AbstractIn this paper we report the implementation of a finite‐difference algorithm which solves the linearized Poisson‐Boltzmann equation for molecules of arbitrary shape and charge distribution and which includes the screening effects of electrolytes. The microcoding of the algorithm on an ST‐100 array processor allows us to obtain electrostatic potential maps in and around a protein, including the effects of ionic strength, in about 30 minutes. We have applied the algorithm to a dimer of the protein Cu‐Zn superoxide dismutase (SOD) and compared our results to those obtained from uniform dielectric models based on coulombic potentials. We find that both the shape of the protein‐solvent boundary and the ionic strength of the solvent have a profound effect on the potentials in the solvent. For the case of SOD, the cluster of positive charge at the bottom of the active site channel produces a strongly enhanced positive potential due to the focusing of field lines in the channel—a result that cannot be obtained with any uniform dielectric model. The remainder of the protein is surrounded by a weak negative potential. The electrostatic potential of the enzyme seems designed to provide a large cross‐sectional area for productive collisions. Based on the ionic strength dependence of the size of the positive potential region emanating from the active site and the repulsive negative potential barrier surrounding the protein, we are able to suggest an explanation for the ionic strength dependence of the activity of the native and chemically modified forms of the enzyme.
PseqIP: A nonredundant and exhaustive protein sequence data bank generated from 4 major existing collections
Authors: Claverie Jean Michel , Bricault Laurence 
Published: May 2005

AbstractFour major protein sequence data collections (NBRF‐PIR, PSD‐Kyoto, PGtrans, and NEWAT) have been merged into a single nonredundant data bank called PseqIP. The data bank entries were automatically matched by a heuristic computer program relying on the fast computation of the number of tetrapeptides shared by two sequences. PseqIP 1.0 includes 6,068 different protein sequences for a total of 1,357,067 residues, representing most of the available sequence information to date. During the course of this work, we found about 600 occurrences course of a protein sequence recorded with a one‐amino‐acid variation in at least two different data banks. A flat file (ASCII computer‐readable format) version of PseqIP 1.0, well‐suited for exhaustive homology searches and statistical sequence analysis, is available from our laboratory.
A domain of the klenow fragment of Escherichia coli DNA polymerase I has polymerase but no exonuclease activity
Authors: Freemont P. S. , Ollis D. L. , Steitz T. A. , Joyce C. M. 
Published: May 2005

AbstractThe Klenow fragment of DNA polymerase I from Escherichia coli has two enzymatic activities: DNA polymerase and 3′–5′ exonuclease. The crystal structure showed that the fragment is folded into two distinct domains. The smaller domain has a binding site for deoxynucleoside monophosphate and a divalent metal ion that is thought to identify the 3′‐5′ exonuclease active site. The larger C‐terminal domain contains a deep cleft that is believed to bind duplex DNA. Several lines of evidence suggested that the large domain also contains the polymerase active site. To test this hypothesis, we have cloned the DNA coding for the large domain into an expression system and purified the protein product. We find that the C‐terminal domain has polymerase activity (albeit at a lower specific activity than the native Klenow fragment) but no measurable 3′‐5′ exonuclease activity. These data are consistent with the hypothesis that each of the three enzymatic activities of DNA polymerase I from E. coli resides on a separate protein structural domain.
Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation
Authors: Shortle David , Meeker Alan K. 
Published: May 2005

AbstractEleven mutant forms of staphylococcal nuclease with one or more defined amino acid substitutions have been analyzed by solvent denaturation by using intrinsic fluorescence to follow the denaturation reaction. On the basis of patterns observed in the value of m–the rate of change of log Kapp (the apparent equilibrium constant between the native and denatured states) with denaturant concentration—these proteins can be grouped into two classes. For class I mutants, the value of m with guanidine hydrochloride is less than the wild‐type value and is either constant or increases slightly with increasing denaturant; the value of m with urea is also less than wild type but shows a marked increase with increasing denaturant concentration, often approaching but never exceeding the wild‐type value. For class II mutants, m is constant and is greater than wild type in both denaturants, with the increase being consistently larger in guanidine hydrochloride than in urea. When double or triple mutants are constructed from members of the same mutant class, the change in m is usually the sum of the changes produced by each mutation in isolation. One plausible explanation for these altered patterns of denaturation is that chain‐chain or chain‐solvent interactions in the denatured state have been modified—interactions which appear to involve hydrophobic groups.
Reciprocal control of retinal rod cyclic GMP phosphodiesterase by its γ subunit and transducin
Authors: Wensel Theodore G. , Stryer Lubert 
Published: May 2005

AbstractThe switching on of the cGMP phosphodiesterase (PDE) in retinal rod outer segments by activated transducin (Tα‐GTP) is a key step invisual excitation. The finding that trypsin activates PDE (αβγ) by degrading its γ subunit and the reversal of this activation by γ led to the proposal that Tα‐GTP activates PDE by relieving an inhibitory constraint imposed by γ (Hurley and Stryer: J. Biol. Chem. 257:11094–11099, 1982). We report here studies showing that the addition of γ subunit also reverses the activation of PDE by Tα‐GTP‐γS. A procedure for preparing γ in high yield (50–80%) is presented. Analyses of SDS polyacrylamide gel slices confirmed that inhibitorya activity resides in the γ subunit. Nanomolar γ blocks the activation of PDE by micromolar Tα‐GTPγS. The degree of activation of PDE depends reciprocally on the concentrations of γ and Tα‐GTPγS. γ remains bound to the disk membrane during the activation of PDE by transducin. The binding of γ to the αβ subunits of native PDE is very tight; the dissociation constant is less than 10 pM, indicating that fewer than 1 in 1,700 PDE molecules in rod outer segments are activated in the absence of Tα‐GTP.
Properties of a second sensory receptor protein inHalobacterium halobiumphototaxis
Authors: Spudich Elena N. , Sundberg Steven A. , Manor Danny , Spudich John L. 
Published: May 2005

AbstractA second slow‐cycling retinylidene protein, in addition to slow‐cycling (sensory) rhodopsin (SR), can be bleached with hydroxylamine and regenerated with all‐transretinal in photosensory signalingHalobacterium halobiummembranes. Flash photolysis shows this protein undergoes a photochemical reaction cycle characterized by photoconversion of its ground state (λmax480 nm) to a species with λmax⩽ 360 nm, which thermally regenerates the 480‐nm species with a t½of 260 msec at 25°C, under conditions in which SR photocycles at 650 msec in the same membranes. Mutants characterized with respect to their phototaxis behavior are identified which contain SR and the 480‐nm pigment, the latter ranging from undetectable to a concentration equal to that of SR. Receptor mutants lacking all phototaxis sensitivity lack both of the photochemically reactive proteins. The mutant properties contribute to an accumulation of behavioral and spectroscopic evidence that the 480‐nm pigment is a second sensory photoreceptor inH. halobium. NaDodSO4‐polyacrylamide gel electrophoresis of [3H]retinal‐labeled membrane proteins from the mutants indicates SR and the 480‐nm pigment contain distinct chromophoric polypeptides differing in their migration rates. The data implicate polypeptides of 25,000 Mrand 23,000 Mras retinal‐binding polypeptides of SR and the 480‐nm protein, respectively.
Isolation and analysis of arc repressor mutants: Evidence for an unusual mechanism of DNA binding
Authors: Vershon Andrew K. , Bowie James U. , Karplus Theresa M. , Sauer Robert T. 
Published: May 2005

AbstractWe have isolated 64 different missense mutations at 36 out of 53 residue positions in the Arc repressor of bacteriophage P22. Many of the mutant proteins with substitutions in the C‐terminal 40 residues of Arc have reduced intracellular levels and probably have altered structures or stabilities. Mutations in the N‐terminal ten residues of Arc cause large decreases in operator DNA binding affinity without affecting the ability of Arc to fold into a stable three‐dimensional structure. We argue that these N‐terminal residues are important for operator recognition but that they are not part of a conventional helix‐turn‐helix DNA binding structure. These results suggest that Arc may use a new mechanism for sequence specific DNA binding.
Primary structure of a precursor to the asprartic proteinase from Rhizomucor miehei shows that the enzyme is synthesized as a zymogen
Authors: Boel Esper , Bech Anne‐Marie , Randrup Karen , Draeger Bodil , Fiil Neils Peter , Foltmann Bent 
Published: May 2005

AbstractIn order to characterize the zymogen of the milk‐clotting enzyme from Rhizomucor miehei, we constructed a cDNA library on pBR327 in Escherichia coli. Aspartic proteinase‐specific recombinants were isolated by colony hybridization to a specific oligonucleotide mixture, and the cDNA sequence corresponding to a precursor form of the enzyme was determined.The decuced amino sequence shows that this secreted fungal proteinase is synthesized as a precursor. The first 22 amino acid residues in this precursor constitute a typical signal peptide. The amino acid sequence of the following 47‐amino‐acid‐long prosegment shows homology to the prosegments from both the extracellular and intracellular vertebrate aspartic proteinases, and to the prosegments from the yeast and Mucor pusillus aspartic proteinases as well. These observations suggest that all aspartic proteinases are synthesized with a prosegment and that this prosegment is essential for the correct folding of all the mature enzymes. The active Rhizomucor miehei enzyme consists of 361 amino acide residues with a total molecular weight of 38,701. Clusters of idendtities around the active site cleft support the assumption that these proteinasess have a common folding of their peptide chains. The disulphide bridges were localized in the fungal enzyme, and 2 N‐glycosylation sites were identified.
Multiple conformations of amino acid residues in ribonuclease A
Authors: Svensson L. Anders , Sjölin Lennart , Gilliland Gary L. , Finzel Barry C. , Wlodawer Alexander 
Published: May 2005

AbstractThe highly refined 1.26 Å structure (R = 0.15) of phosphate‐free bovine pancreatic ribonuclease A was modeled with 13 residues having discrete multiple conformations of side chains. These residues are widely distributed over the protein surface, but only one of them, Lys 61, is involved in crystal packing interactions. The discrete conformers have no unusual torsion angles, and their interactions with the solvent and with other atoms of the protein are similar to those residues modeled with a single conformation. For three of the residues–Val 43, Asp 83, and Arg 85–two correlated conformations are found. The observed multiple conformations on the protein surfaces will be of significance in analyzing structure‐function relationships and in performing protein engineering.
Predicted calmodulin‐binding sequence in the γ subunit of phosphorylase b kinase
Authors: Degrado William F. , Erickson‐Viitanen Susan , Wolfe Henry R. , O'Neil Karyn T. 
Published: May 2005

AbstractA basic, amphiphilic α helix is a structural feature common to a variety of inhibitors of calmodulin and to the calmodulin‐binding domains of myosin light chain kinases. To aid in recognizing this structural feature in sequences of peptides and proteins we have developed a computer algorithm which searches for sequences of appropriate length, hydrophobicity, helical hydrophobic moment, and charge to be considered as potential calmodulin‐binding sequences. Such sequences occurred infrequently in proteins of known crystal structure. This algorithm was used to find the most likely site in the catalytic (γ) subunit of phosphorylase b kinase for interaction with calmodulin (the δ subunit). A peptide corresponding to this site (residues 341–361 of the γ subunit) was synthesized and found to bind calmodulin with approximately an 11 nM dissociation constant. A variant of this peptide in which an aspartic acid at position 7 in its sequence (347 of the γ subunit) was replaced with an asparagin was found to bind calmodulin with approximately a 3 nM dissociation constant.
Characterization of a slow folding reaction for the α subunit of tryptophan synthase
Authors: Hurle Mark R. , Michelotti Greg A. , Crisanti Mark M. , Matthews C. Robert 
Published: May 2005

AbstractThe equilibria and kinetics of ureainduced unfolding and refolding of the α subunit of tryptophan synthase of E. coli have been examined for their dependences on viscosity, pH, and temperature in order to investigate the properties of one of the rate‐limiting steps, domain association. A viscosity enhancer, 0.58 M sucrose, was found to slow unfolding and accelerate refolding. This apparently anomolous results was shown to be due to the stabilizting effect of sucrose on the folding reaction. After accounting for this stabilization effect by using linear free‐energy plots, the unfolding and refolding kinetics were found to have a viscosity dependence. A decrease in pH was found to stabilize the domain association reaction by increasing the refolding rate and decreasing the unfolding rate. This effect was accounted for by protonation of a single residue with a pK value of 8.8 in the native state and 7.1 in the intermediate, in which the two domains are not yet associated. The activation energy of unfolding is 4.8 kcal/mol, close to the diffusion limit. The negative activation entropy of unfolding, −47 cal/deg‐mol, which controls this reaction, may result from ordering of solvent about the newly exposed domain interface of the transition state. These results may provide information on the types of noncovalent interactions involved in domain association and improve the ability to interpret the folding of mutants with single amino‐acid substitutions at the interface.
Contribution of arginine (HC3) 141α to the Bohr effect of the fourth binding step in the reaction of ligand with human hemoglobin
Authors: Kwiatkowski Laura D. , Noble Robert W. 
Published: May 2005

AbstractA few years ago we reported that histidine (HC3) 146β plays a major role in the pH‐dependent propeties of the R‐state of human hemoglobin, accounting for close to 50% of the R‐state Bohr effect. We have extended these studies by examining the role of arginine 141α, another group known to affect the overall Bohr effect. We have compared the pH dependencies of the rate constants for the dissociation and combination of the fourth carbon monoxide molecule, I4 and I′4, respectively, for native hemoglobin A (HbA) and a control reconstututed HbA, and des‐(Arg 141α) HbA, the hemoglobin molecule resulting from the enzymatic removal of the C–terminal arginine of the α‐chain of human Hb. From these kinetic contants the pH dependence of L4, by about 80% between pH 6 and 8, where the aldkaline Bohr effect normally occurs, The sum of the effects of the removal of His 146β and of Arg 141α is grater than 100%. This suggests that at least one of these modifications altrs the contrubutions of other residues of this Bohr effect.
Extension of the fragment method to calculate amino acid zwitterion and side chain partition coefficients
Authors: Abraham Donald J. , Leo Albert J. 
Published: May 2005

AbstractThe fragment method of calculation partition coefficients (P) has been extended to include the common amino acids (AAs). The results indicate that polar and charged side chains influence the hydrophobicity of atoms in the side chain in a predictable manner. Feild effects, as evidenced through polar proximity factors and bond factors, need to be considered for accurate estimation of transfer phenomena. The calculated log P and ΔG°′ values of the 20 AAs agree well with the observed values. Pro calculates to be more hydrophilic than the observed log P. Hydrophobicity scales for peptide side chain residues are compared and evaluated in terms of suitability. Calculated π values for nonpolar side chain residures agree well with the observed values; calculated values for uncharged polar side chain residues deviate by about 0.6 log units except for Gln and Cys; and polar side chain residues with charged side chains calculate as too hydorphilic. Reasons for the differences are explored. We also suggest that tightly bound water to polar moieties in amino acids and peptides may be transferred into the octanol phase during partitioning experiments. A quantitative methodology is persented which characterizes the thermodynamic partitioning of groups and individual atoms in amino acids and proteins.
Intron/exon structure of the human gene for the muscle isozyme of glycogen phosphorylase
Authors: Burke J. , Hwang P. , Anderson L. , Lebo R. , Gorin F. , Fletterick R. 
Published: May 2005

AbstractThe intron/exon organization of the human gene for glycogen phosphorylase has been determined. The segments of the polypeptide chain that corresponds to the 19 exons of the gene are examined for relationships between the three‐dimensional structure to the protein and gene structure. Only weak correlations are observed between domains of phosphorylase and exons. The nucleotide binding domains that are found in phosphorylase and other glycolytic enzymes are examined for relationships between exons of the genes and structures of the domains. When mapped to the three‐dimensional structures, the intron/exon boundaries are shown to be widely distributed in this family of protein domains.