Neural network prediction of the HIV-1 protease cleavage sites

A back propagation neural network method has been developed to study the pattern of polypeptides that can be cleaved by the HIV-1 protease. This method can incorporate many characteristics of the peptides, such as hydrophobicity, beta-sheet and alpha-helix propensities. Mutations can also be applied to probe the most important factors that influence the cleavage.

Effect of phorbol ester on cAMP-dependent protein kinase activity in cardiomyocytes

Cardiomyocytes isolated from neonatal rats were treated with phorbol-12-myristate-13-acetate (PMA) ranging from 10(-11) to 10(-7) mol/L for 20 min, causing cytosol protein kinase A (PKA) activity to decrease while particulate PKA activity increase in a concentration-dependent manner. The change of PKA activity induced by PMA was abolished completely by pretreatment of polymyxin B or depletion of protein kinase C (PKC). Type II PKA activity in particulate fraction was enhanced remarkably, while that of type I PKA was not altered when the cells were treated with 100 nmol/L PMA. The results suggested that subcellular distribution and activity of PKA in cardiomyocytes may be regulated by PKC.

[Evaluation of surgical treatment for patients with multiple aldosteronoma: analysis of 11 cases]

From 1957 to 1994, 332 patients underwent surgical treatment for aldosteronoma at Ruijin Hospital. Among them, 11 patients (3.9%) were diagnosed as having multiple aldosteronoma. We ususally used the same method to make the qualitative diagnosis for both single and multiple aldosteronoma. In our experience, however, it was difficult to distinguish the unilateral multiple aldosteronoma by rutine B-type ultrasonography, CT or gamma-scintigraphy before surgery. The correct diagnosis could be obtained only by carefully exploring during the adrenal operation and a satisfactory prognosis also can be acquired if multiple aldosteronoma could be removed completely.

Analysis of the loop-helix interaction in bundle motif protein structures

Molecular dynamics simulations and energy analysis have been carried out to study the structural mobility and stability of the four alpha-helix bundle motifs. The simulation results as well as the X-ray data show that the atomic RMS fluctuation is larger at the loop region for four representative proteins investigated: methemerythrin, cytochrome b-562, cytochrome c', and bovine somatotropin. The loop-loop, helix-helix, and loop-helix interactions are computed for the unfolded and folded proteins. In the folded and solvated protein structures the loop-helix interaction is stronger than the helix-helix interaction, especially in the electrostatic component. But the stabilization energies of both the loop-helix and the helix-helix interactions relative to those of an unfolded structure are of the same order of magnitude. The stabilization due to protein-solvent interaction is greater in the helix region than in the loop region. The percentage of hydrophilic solvent accessible area for the four proteins studied was calculated with the method of Eisenberg and McLachlan. The percentage of the hydrophilic area is greater in the loops than in the helices. A Poisson-Boltzmann calculation shows that the potential from the loops acting on a helix is generally more negative than that from other helices.

[Experimental studies of protective effects of ischemic myocardium preconditioning and its mechanism]

Recent research has shown that repeated brief myocardial ischemia (RBMI) can increase the tolerance of myocardium to a subsequent sustained ischemia and have protective effects on myocardial cells. With the isolated rat heart Langendorff model, we investigated the effects of RBMI on myocardial morphology, systolic function, coronary flow rates (CFR), myocardial membrane phospholipid (PL) content and its marker enzyme's activity (5'-AMPase). The results showed: After ischemia-reflow, the HR, LVP and CFR in control and experimental groups had no significant difference (P > 0.05). But the PL content and specific activity of 5'-AMPase were significantly higher in the experimental group than that in control group (P < 0.01, P < 0.05). And the observations of ultrastructure suggested that the myocardium of the experimental group was preserved better than that in control group. It was also shown that RBMI had protective effects on myocardial membrane structure, and however effective had no relation to CFR.

Detection of ECG characteristic points using wavelet transforms

An algorithm based on wavelet transforms (WT's) has been developed for detecting ECG characteristic points. With the multiscale feature of WT's, the QRS complex can be distinguished from high P or T waves, noise, baseline drift, and artifacts. The relation between the characteristic points of ECG signal and those of modulus maximum pairs of its WT's is illustrated. By using this method, the detection rate of QRS complexes is above 99.8% for the MIT/BIH database and the P and T waves can also be detected, even with serious baseline drift and noise.

Reduced Rho-dependent transcription termination permits NusA-independent growth of Escherichia coli

NusA and Rho are essential Escherichia coli proteins that influence transcription elongation and termination. We show that an E. coli derivative unable to express NusA, because its sole nusA gene contains a large deletion/substitution, is viable providing that the bacterium also carries a rho mutation that reduces transcription termination. This Rho-mediated suppression is not allele specific, since either a mutation changing amino acid 134 [rho(E134D)] or a mutation changing amino acid 352 (rho1) allows growth of a nusA-deleted E. coli. However, both rho mutations similarly decrease transcription termination 8- to 9-fold. We propose that the essential role of NusA is to enhance pausing of RNA polymerase at certain sites, permitting tight coupling of transcription and translation. This coupling interferes with Rho access to and/or movement on the nascent RNA and blocks premature termination of transcription. Thus, NusA-dependent coupling should be less important in a mutant with low Rho activity. The fact that E. coli grows without NusA argues that NusA should be considered an accessory factor rather than a subunit of RNA polymerase.

Escherichia coli-Salmonella typhimurium hybrid nusA genes: identification of a short motif required for action of the lambda N transcription antitermination protein

The Escherichia coli nusA gene, nusAEc, encodes an essential protein that influences transcription elongation. Derivatives of E. coli in which the Salmonella typhimurium nusA gene, nusASt, has replaced nusAEc are viable. Thus, NusASt can substitute for NusAEc in supporting essential bacterial activities. However, hybrid E. coli strains with the nusASt substitution do not effectively support transcription antitermination mediated by the N gene product of phage lambda. We report the DNA sequence of nusASt, showing that the derived amino acid sequence is 95% identical to the derived amino acid sequence of nusAEc. The alignment of the amino acid sequences reveals scattered single amino acid differences and one region of significant heterogeneity. In this region, called 449, NusAEc has four amino acids and NusASt has nine amino acids. Functional studies of hybrid nusA genes, constructed from nusAEc and nusASt, show that the 449 region of the NusAEc protein is important for lambda N-mediated transcription antitermination. A hybrid that has a substitution of the four E. coli codons for the nine S. typhimurium codons, but is otherwise nusASt, supports the action of the N antitermination protein. The 449 region and, presumably, adjacent sequences appear to compose a functional domain of NusAEc important for the action of the N transcription antitermination protein of phage lambda.

Molecular origin of the internal dipole potential in lipid bilayers: calculation of the electrostatic potential

The finite difference linearized Poisson-Boltzmann equation was solved for a segment of bilayer for two lipids (phosphatidylcholine dihydrate and phosphatidylethanolamine-acetic acid) in order to obtain the transbilayer electrostatic potential. Atomic coordinates derived from the crystal structures of these lipids were used, and partial changes were assigned to all atoms in the polar parts of the molecules. These calculations confirmed that a dipole potential exists in the uncharged hydrophobic interior of a bilayer. The phosphocholine and phosphoethanolamine groups make negative contributions to the internal potential, and the glycerol acyl esters make positive contributions, but the sum of these terms is negative. The water of hydration in phosphatidylcholine, and the acetic acid which is present in the phosphatidylethanolamine crystal structure, make positive contributions to the internal potential. It is concluded that the water of hydration in fully hydrated lipid bilayers is mainly responsible for the experimentally inferred positive sign of the internal potential.

Strong electrostatic loop-helix interactions in bundle motif protein structures

Based on CHARMM potential (Brooks et al., 1983) an energetic analysis has been carried out for four typical 4-alpha-helix bundle proteins, i.e., methemerythrin, cytochrome b-562, cytochrome c', and bovine somatotropin. The bovine somatotropin possesses long loops, but all the other three proteins have short loops. It was found that in all these four 4-alpha-helix bundle motif structures the interaction between loops and helices was much stronger than the interaction among the four helices themselves. Particularly for the electrostatic interaction energy, the loop-helix interaction is overwhelmingly stronger than the interhelix interaction although the latter involves the favorable helix dipole interaction due to the antiparallel arrangement of neighboring alpha-helices. The present study indicates that such a conclusion holds true regardless of what loops, long or short, are in the 4-alpha-helix bundle protein, and also regardless of which empirical potential, ECEPP or CHARMM, is used for calculations although in CHARMM the electrostatic energy is much more heavily emphasized than in ECEPP. Therefore, no appropriate conclusion can be drawn in arguing whether the dipole interaction among the four alpha-helices play a stabilizing role or destabilizing role for a 4-alpha-helix bundle protein without taking into consideration the effect of interaction between helices and loops. The calculated results reported here provide, from a different point of view, insights that might be useful for revealing the essence of the driving forces during the folding of proteins.

Time frequency distributions of TMJ sounds

For analysis of time-varying signals such as the TMJ sounds, it is often desirable to know how the frequency components change with time, using methods of time-frequency analysis. The aim of this study was to compare two of the most familiar methods for energy density representation with a newly developed technique. The sounds were recorded with a microphone fastened to the subject's forehead, transformed to the time-frequency domain and displayed as 3D- and contour plots using spectrogram, Wigner distribution (WD), and the reduced interference distribution (RID) to display their time-frequency energy distributions. The spectrogram resolved only the low-frequency components. The WD provided higher resolution but also exhibited strong interference between components. The RID gave a detailed representation of the TMJ signals' relative energy distribution in the time and frequency domains, with a great reduction in the interference or cross terms. The RID therefore appears to be most useful in the application of time-frequency distributions in classification of TMJ sounds.

Quantum simulation of ferrocytochrome c

The dramatic progress in the understanding of the dynamics of biomolecules has been largely fuelled by computer simulations based on the law of classical mechanics. However in some respects biomolecules are at the borders of the domain of applicability of classical mechanics. The role of quantum mechanical effects in biomolecular structure and function is therefore worth investigating. Here we present preliminary results from a quantum simulation of a protein and contrast them with results from full classical simulations. The most significant differences are found in motions of high frequency, such as bond stretching or the torsional oscillation of groups that bear hydrogen atoms. The amplitudes of such motions are significantly increased by the penetration of atoms into classically forbidden regions. These differences will directly influence the rates of such processes as proton and electron transfer.

Inhibitory effect of methacholine on drug-induced relaxation, cyclic AMP accumulation, and cyclic AMP-dependent protein kinase activation in canine tracheal smooth muscle

Functional antagonism between bronchoconstricting and bronchodilating pathways was examined in canine tracheal smooth muscle. Trachealis strips were contracted with either 0.3 microM (EC55) or 3.0 microM (EC80) methacholine before being relaxed by the cumulative addition of isoproterenol, prostaglandin E2, or forskolin. The EC50 for all three relaxants was increased 10-fold in tissues contracted with 3.0 microM methacholine vs. those contracted with 0.3 microM methacholine. Moreover, contracting tissues with the higher concentration of methacholine reduced the maximum relaxation induced by prostaglandin E2 and isoproterenol. Forskolin produced total relaxation regardless of the concentration of methacholine used and thus was a much more effective bronchodilator than either isoproterenol or prostaglandin E2. The inhibitory effect of methacholine on the relaxant response to these agents was paralleled by a reduction in drug-stimulated cyclic AMP-dependent protein kinase activity. Methacholine reduced the maximum activation of cyclic AMP-dependent protein kinase elicited by isoproterenol, prostaglandin E2 and submaximal concentrations of forskolin, which was a much more powerful enzyme activator than the other two agents. The ability of a maximum concentration of forskolin (30 microM) to activate cyclic AMP-dependent protein kinase was not inhibited by methacholine. Although methacholine also appeared to suppress drug-stimulated cyclic AMP accumulation, the inhibitory effect was only statistically significant in forskolin-treated tissues.(ABSTRACT TRUNCATED AT 250 WORDS)