Search PubMed⌕ Search

Biomedical subjects

Peng Yu

Publications and source records attributed to Peng Yu.

22 records · Page 2Linked to original sources

Linkage between fructose 1,6-bisphosphate binding and the dimer-tetramer equilibrium of Escherichia coli glycerol kinase: critical behavior arising from change of ligand stoichiometry.

Escherichia coli glycerol kinase (EC 2.7.1.30; ATP-glycerol 3-phosphotransferase) is inhibited allosterically by fructose 1,6-bisphosphate (FBP), and this inhibition is a primary mechanism by which glucose controls glycerol utilization in vivo. Earlier work indicates that glycerol kinase displays a dimer-tetramer equilibrium in solution, FBP shifts the equilibrium toward the tetramer, and tetramer formation is required for FBP inhibition. However, equilibrium constants for FBP binding and dimer-tetramer assembly that describe the linkage between these processes are unknown. Here, decreased fluorescence anisotropy of extrinsic fluorophores fluorescein and 2',7'-difluorofluorescein due to homo fluorescence resonance energy transfer (homo-FRET) is used to quantitate tetramer assembly and FBP binding. Glycerol kinase is labeled with extrinsic fluorophores covalently attached to an engineered surface cysteine residue under conditions that prevent labeling of native cysteine residues. Tryptic peptide mapping and MALDI-MS verify labeling at the engineered site only. Initial velocity studies show the labeling does not alter the catalytic properties or FBP inhibition. The steady-state fluorescence anisotropy of enzyme with a labeling stoichiometry of approximately 0.1 mol of fluorophore/mol of subunit is not sensitive to increased protein concentration or binding of FBP, indicating the absence of homo-FRET. However, steady-state fluorescence anisotropy of enzyme with a labeling stoichiometry of approximately 0.4 mol of fluorophore/mol of subunit decreases with increasing protein concentration, which is consistent with depolarization due to homo-FRET. The protein concentration dependence of the decreased fluorescence anisotropy is described by a dimer-tetramer equilibrium with an apparent dissociation constant of 61 +/- 7 nM (subunits) at pH 7.0 and 25 degrees C. FBP binds to both the dimer and tetramer of glycerol kinase, and the FBP concentration dependence of the apparent dissociation constant for the dimer-tetramer equilibrium shows critical behavior. The apparent dissociation constant decreases and then increases with increasing FBP concentration, reaching a minimum at about 20 mM FBP. Critical behavior is seen also in the FBP dependence of the inhibition. The critical behavior arises because tetramer dissociation increases FBP stoichiometry from two sites per tetramer to four half-sites per two dimers. The phenomenological description of the coupling between tetramer assembly and FBP binding shows antagonistic binding of FBP to the two sites on the tetramer, indicating that the strong positive cooperativity observed for FBP inhibition of catalytic activity (Hill coefficient approximately 1.5) is due to the approximately 4000-fold higher affinity of the tetramer for FBP rather than to positive coupling between the two FBP sites.

Biopolymers↗

Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT.

To increase the coverage of secreted protein prediction, we describe a combination strategy. Instead of using a single method, we combine Hidden Markov Model (HMM)-based methods CJ-SPHMM and TMHMM with PSORT in secreted protein prediction. CJ-SPHMM is an HMM-based signal peptide prediction method, while TMHMM is an HMM-based transmembrane (TM) protein prediction algorithm. With CJ-SPHMM and TMHMM, proteins with predicted signal peptide and without predicted TM regions are taken as putative secreted proteins. This HMM-based approach predicts secreted protein with Ac (Accuracy) at 0.82 and Cc (Correlation coefficient) at 0.75, which are similar to PSORT with Ac at 0.82 and Cc at 0.76. When we further complement the HMM-based method, i.e., CJ-SPHMM + TMHMM with PSORT in secreted protein prediction, the Ac value is increased to 0.86 and the Cc value is increased to 0.81. Taking this combination strategy to search putative secreted proteins from the International Protein Index (IPI) maintained at the European Bioinformatics Institute (EBI), we constructed a putative human secretome with 5235 proteins. The prediction system described here can also be applied to predicting secreted proteins from other vertebrate proteomes.

Computational Biology↗

Clinical study on therapeutic effect of acupuncture on Behcet's disease.

Forty-six cases of Behcet's disease were randomly divided into two groups. The 26 cases in the treatment group were treated by acupuncture and the 20 cases in the control group with the drugs. The level of L-chain (kappa) of IgM and the level of the trace element Zn were determined before and after treatment in the treatment group. The results showed that the recurrence rate in the treatment group was significantly lower than that in the control group (P < 0.01), and the differences in the level of L-chain (kappa) of IgM and level of Zn in the treatment group before and after treatment were very significant (P < 0.01). These two indexes tended to become normal after treatment.

Acupuncture Therapy↗

Enantiospecific Formation of Trans 1,3-Disubstituted Tetrahydro-beta-carbolines by the Pictet-Spengler Reaction and Conversion of Cis Diastereomers into Their Trans Counterparts by Scission of the C-1/N-2 Bond.

The factors which effect the stereoselective formation of trans-1-alkyl-2-benzyl-3-(alkoxycarbonyl)-1,2,3,4-tetrahydro-beta-carbolines and trans-3-(alkoxycarbonyl)-1-alkyl-2-(diphenylmethyl)-1,2,3,4-tetrahydro-beta-carbolines by the Pictet-Spengler cyclization were examined by heating tryptophan derivatives with aldehydes of varied steric bulk under aprotic and acidic conditions, followed by determination of the ratio of cis to trans diastereomers so formed. The presence of a benzyl group at the N(b)-nitrogen atom alters the diastereochemical outcome of this condensation to provide 100% trans stereoselectivity when the cyclization is carried out with cyclohexanecarboxaldehyde. Furthermore, when N(b)-(diphenylmethyl)tryptophan isopropyl ester was condensed with aldehydes of any size, trans diastereomers are formed with 100% stereoselectively. The trans N(b)-substituted diastereomers are thermodynamically more stable than their cis congeners as shown by equilibration experiments in TFA. Conversion of the cis diastereomers into the more stable trans diastereomers is believed to occur under acidic conditions by cleavage of the carbon (C-1)-nitrogen (N-2) bond with complete retention of configuration at the C-3 stereocenter. Evidence from deuterium exchange experiments as well as optical rotations support this model for epimerization. In addition, when cis diastereomer 66a was allowed to stir in CF(3)COOD, the trans isomer 66b was isolated in 90% yield, while treatment of cis 66a with CF(3)COOH/NaBH(4) provided a mixture of the ring cleaved [scission across C(1)-N(2) bond] product 67 and the trans isomer 66b. Treatment of 66b (control experiment) with NaBH(4)/CF(3)COOH under the same conditions returned only starting trans 66b in excellent yield. The Pictet-Spengler reaction of substrates with sufficiently large substituents, followed by treatment with acid, permits the 100% enantiospecific formation of trans-1,3-disubstituted-1,2,3,4-tetrahydro-beta-carbolines for alkaloid total synthesis.

Journal Article↗