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排序方式: 共有112条查询结果,搜索用时 31 毫秒
31.
The nature of protein dipole moments: experimental and calculated permanent dipole of alpha-chymotrypsin 总被引:5,自引:0,他引:5
The electric dichroism of alpha-chymotrypsin has been measured in buffers of various pH values and ion compositions. The stationary dichroism obtained as a function of the electric field strength is not compatible with an induced dipole mechanism and clearly shows that alpha-chymotrypsin is associated with a substantial permanent dipole moment. After correction for the internal directing electric field according to a sphere model, the dipole moment is 1.6 X 10(-27) C m at pH 8.3 (corresponding to 480 D). This value decreases with decreasing pH (to 1.2 X 10(-27) C m at pH 4.2), but is almost independent of the monovalent salt concentration in the range from 2 to 12 mM and of Mg2+ addition up to 1 mM. The assignment of the permanent dipole moment is confirmed by analysis of the dichroism rise curves. The dichroism decay time constants of (31 +/- 1) ns at 2 degrees C can be represented by a spherical model with a radius of 25-26 A, which is consistent with the known X-ray structure. The limiting linear dichroism is slightly dependent on the buffer composition and demonstrates subtle variations of the protein structure. As a complement to the experimental results, electric and hydrodynamic parameters of alpha-chymotrypsin have been calculated according to the known X-ray structure. Bead model simulations provide the center of diffusion, which is used to calculate dipole moments according to the equilibrium charge distribution evaluated from standard pK values.(ABSTRACT TRUNCATED AT 250 WORDS) 相似文献
32.
Variations among cell lines in the synthesis of sphingolipids in de novo and recycling pathways 总被引:1,自引:0,他引:1
There are several pathways for the incorporation of sugars into
glycosphingolipids (GSL). Sugars can be added to ceramide that contains
sphinganine (dihydrosphingosine) synthesized de novo (pathway 1), to
ceramide synthesized from sphingoid bases produced by hydrolysis of
sphingolipids (pathway 2), and into GSL recycling from the endosomal
pathway through the Golgi (pathway 3). We reported previously the
surprising observation that SW13 cells, a human adrenal carcinoma cell
line, synthesize most of their GSL in pathway 2. We now present data on the
synthesis of GSL in four additional cell lines. Approximately 90% of sugar
incorporation took place in pathway 2, and 10% or less in pathway 1, in
human foreskin fibroblasts and NB41A3 neuroblastoma cells. In contrast,
approximately 50-90% of sugar incorporation took place in pathway 1 in
C2C12 myoblasts. The C2C12 cells divide more rapidly and synthesize 10-14
times as much GSL as the other three cell lines. In C6 glioma cells,
approximately 30% of sugar incorporation occurred in pathway 1 and 60% in
pathway 2. There was no relation between the utilization of pathways for
GSL and sphingomyelin synthesis in foreskin fibroblasts and C2C12 cells. In
both cells pathways 1 and 2 each accounted for 50% of incorporation of
choline into sphingomyelin. In five of the six cell lines that we have
studied, most GSL synthesis takes place in pathway 2. We suggest that when
the need for synthesis is relatively low, as in slowly dividing cells, GSL
are synthesized predominantly from sphingoid bases salvaged from the
hydrolytic pathway. When cells are dividing more rapidly, the need for
increased synthesis is met by upregulating the de novo pathway.
相似文献
33.
Antosiewicz J Wielgus-Kutrowska B Długosz M Holy A Bzowska A 《Nucleosides, nucleotides & nucleic acids》2007,26(8-9):969-974
Complex formation of multisubstrate analogue inhibitor--2-amino-9-[2-(phosphonomethoxy)ethyl]-6-sulfanylpurine (PME-6-thio-Gua) with trimeric purine nucleoside phosphorylase from Cellulomonas sp. was investigated using a stopped-flow spectrofluorimetric approach. Results obtained indicate that, in contrast to binding of guanine, i.e., the transition-state conformation trapping ligand, for which binding at each active site is followed by the enzyme conformational change, association of the ground-state analogue PME-6-thio-Gua is a one-step process. 相似文献
34.
35.
Patr��cia F N Fa��sca Ana Nunes Rui DM Travasso Eugene I Shakhnovich 《Protein science : a publication of the Protein Society》2010,19(11):2196-2209
Systematic Monte Carlo simulations of simple lattice models show that the final stage of protein folding is an ordered process where native contacts get locked (i.e., the residues come into contact and remain in contact for the duration of the folding process) in a well‐defined order. The detailed study of the folding dynamics of protein‐like sequences designed as to exhibit different contact energy distributions, as well as different degrees of sequence optimization (i.e., participation of non‐native interactions in the folding process), reveals significant differences in the corresponding locking scenarios—the collection of native contacts and their average locking times, which are largely ascribable to the dynamics of non‐native contacts. Furthermore, strong evidence for a positive role played by non‐native contacts at an early folding stage was also found. Interestingly, for topologically simple target structures, a positive interplay between native and non‐native contacts is observed also toward the end of the folding process, suggesting that non‐native contacts may indeed affect the overall folding process. For target models exhibiting clear two‐state kinetics, the relation between the nucleation mechanism of folding and the locking scenario is investigated. Our results suggest that the stabilization of the folding transition state can be achieved through the establishment of a very small network of native contacts that are the first to lock during the folding process. 相似文献
36.
37.
Background
The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caenorhabditis Genetic Center (CGC) Bibliography using techniques from statistical information retrieval. Items in the CGC biomedical text corpus were modeled using the Latent Dirichlet Allocation (LDA) model. LDA is a hierarchical Bayesian model which represents a document as a random mixture over latent topics; each topic is characterized by a distribution over words. 相似文献38.
Background
The shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process. Previous studies have focused on speciation events, but gene duplication is another lineage splitting event, analogous to speciation, and gene loss or deletion is analogous to extinction. Measures of the shape of gene family phylogenies can thus be used to investigate the processes of gene duplication and loss. We make the first systematic attempt to use tree shape to study gene duplication using human gene phylogenies. 相似文献39.
Długosz M Bojarska E Antosiewicz JM 《Journal of biochemical and biophysical methods》2002,51(2):179-193
A method for extracting kinetic and optical parameters from progress curves for protein-ligand association, obtained by stopped-flow experiments, is described. The method is limited to one-step and two-step association kinetics, but it allows concentration of protein and offset of the signals to be adjustable parameters during an interactive non-linear least-squares fitting procedure. The method is tested on simulated pseudo-experimental data and applied to progress curves obtained in a stopped-flow spectrofluorimeter, for association of the translation initiation factor eIF4E with 7-methyl-GDP, an analog of 5'-end of mRNA. 相似文献
40.
Jan Antosiewicz Mitchell D. Miller Kurt L. Krause J. Andrew McCammon 《Biopolymers》1997,41(4):443-450
We analyze the electrostatic and hydrodynamic properties of a nuclease from the pathogenic gram-negative bacterium Serratia marcescens using finite-difference Poisson-Boltzmann methods for electrostatic calculations and a bead-model approach for diffusion coefficient calculations. Electrostatic properties are analyzed for the enzyme in monomeric and dimeric forms and also in the context of DNA binding by the nuclease. Our preliminary results show that binding of a double-stranded DNA dodecamer by nuclease causes an overall shift in the charge of the protein by approximately three units of elementary charge per monomer, resulting in a positively charged protein at physiologic pH. In these calculations, the free enzyme was found to have a negative (−1 e) charge per monomer at pH 7. The most dramatic shift in pKa involves His 89 whose pKa increases by three pH units upon DNA binding. This shift leads to a protonated residue at pH 7, in contrast to the unprotonated form in the free enzyme. DNA binding also leads to a decrease in the energetic distances between the most stable protonation states of the enzyme. Dimerization has no significant effect on the electrostatic properties of each of the monomers for both free enzyme and that bound to DNA. Results of hydrodynamic calculations are consistent with the dimeric form of the enzyme in solution. The computed translational diffusion coefficient for the dimer model of the enzyme is in very good agreement with measurements from light scattering experiments. Preliminary electrooptical calculations indicate that the dimer should possess a large dipole moment (approximately 600 Debye units) as well as substantial optical anisotropy (limiting reduced linear electric dichroism of about 0.3). Therefore, this system may serve as a good model for investigation of electric and hydrodynamic properties by relaxation electrooptical experiments. © 1997 John Wiley & Sons, Inc. 相似文献