Sedimentation of generalized systems of interacting particles. I. Solution of systems of complete Lamm equations.

A very general approach to the chemical equilibria between many interacting molecules during sedimentation (boundary, band, or active enzyme) taking into account boundary conditions, cell geometry, equilibrium constants, diffusion, enzyme kinetics, etc., is presented. Through a Fortran program, the method has been applied to two very simple but typical cases. With only minor adjustments, the method presented here for sedimentation studies can be extended to all sorts of problems in which “pools” of various species are interacting with each other.     

The active site titration of proteinases by using alpha 2-macroglobulin and high-performance liquid chromatography.

The active site titration for various proteinases relies on the development of optimal enzyme titrants for each proteinase, but these titrants are only available for a limited number of proteinases. We have described a new active site titration method applicable to various kinds of endoproteinases using small quantities of the enzymes. This method was carried out by using alpha 2-macroglobulin (alpha 2M) as a titrant and a high-performance liquid chromatography (HPLC) system. When the proteinase solution was treated with alpha 2M, the active proteinase was trapped by alpha 2M. In this reaction alpha 2M does not usually complex with inactive proteinase. After the reaction of proteinase with an excess of alpha 2M, the reaction mixture is applied to an HPLC gel column to separate the uncomplexed enzyme from the one complexed with alpha 2M. The active proteinase is complexed and eluted with alpha 2M, but the inactive proteinase is eluted at the original elution volume. The same amount of the enzyme was also applied to the column. From the decrease of the peak height at the elution position of the uncomplexed proteinase, we can estimate the ratio between enzymatically active proteinases and total proteinases. To test the usefulness of this method, we applied this method to chymotrypsin and trypsin whose activities were predetermined by conventional active site titration, and there was good agreement between both results. With this new method, we can estimate a proteinase activity with as little as 200 ng of the enzyme, a very small amount compared with those required in conventional methods.(ABSTRACT TRUNCATED AT 250 WORDS)     

Active site mapping of yeast aspartyl-tRNA synthetase by in vivo selection of enzyme mutations lethal for cell growth.

The active site of yeast aspartyl-tRNA synthetase has been characterised by structural and functional approaches. However, residues or structural elements that indirectly contribute to the active site organisation have still to be described. They have not been assessed by simple analysis of structural data or site-directed mutagenesis analysis, since rational targetting has proven difficult. Here, we attempt to locate these functional features by using a genetic selection method to screen a randomly mutated yeast AspRS library for mutations lethal for cell growth. This approach is an efficient method to map the active site residues, since of the 23 different mutations isolated, 13 are in direct contact with the substrates. Most of the mutations are located in a 15 A radius sphere around the ATP molecule, where they affect the very conserved residues of the class-defining motifs. The results also showed the importance of the dimer interface for the enzyme activity: a single mutation of the invariant proline residue of motif 1 led to a structural defect inactivating the enzyme. From in vivo complementation studies it appeared that the enzyme activity can be recovered by reconstitution of an intact interface through the formation of heterodimers. We also show that a single mutation affecting an interaction with G34 of the tRNA can inactivate the enzyme by inducing a relaxation of the tRNA recognition specificity. Finally, several mutants whose functional importance could not be assessed from the structural data were selected, demonstrating the importance of this type of approach in the context of a structure-function relationship study.     

A novel approach to the recovery of biologically active oligosaccharides from milk using a combination of enzymatic treatment and nanofiltration

A new easily scalable approach to the recovery of biologically active oligosaccharides from milk has been developed which relies on the combination of enzymatic treatment of defatted milk using beta-galactosidase and nanofiltration. It was shown that enzymatic hydrolysis of lactose significantly improves the efficiency and selectivity of membrane-based separations. With the best membrane, as much as 6.7 g of oligosaccharides (containing very little contaminating lactose) could be obtained from one liter of defatted human milk in just four nanofiltration cycles. The human milk oligosaccharides recovered by this method were shown to inhibit binding of intimin, an adhesion molecule of enteropathogenic Escherichia coli, to epithelial cells in vitro. No significant difference in the oligosaccharide profile between samples prepared by this method and conventional gel-permeation chromatography was found. The developed approach is also suitable for the recovery of substantial quantities of tri- and tetra-saccharides from caprine milk.     

Studies on on-line bioreactor identification. I. Theory

An integrated approach is presented for the on-line estimation of the state of a biochemical reactor from presently attainable real-time measurements. Elemental and macroscopic balances are used for the determination of the total rate of growth and state-of-the-art estimation techniques are subsequently employed for the elimination of process and measurement noises and the estimation of state variables and unknown culture parameters. The proposed approach is very flexible in that as new sensors become available they can be easily incorporated within the present framework to estimate new variables or improve the accuray of the old ones. The method does not require any model for the growth kinetics and is very successful in accurately estimating the above variables in the presence of intense noise and under both steady-state and transient conditions. State estimates obtained by the presented method can be used for the development of adaptive optimal control schemes as well as for basic studies of the characteristic properties of microbial cultures.     

Conserved conformation of RecA protein after executing the DNA strand-exchange reaction. A site-specific linear dichroism structure study

RecA protein and its eukaryotic homologue Rad51 protein catalyzes the DNA strand exchange, which is a key reaction of homologous recombination. At the initial step of the reaction, RecA proteins form a helical filament on a single-stranded DNA (ssDNA). Binding of double-stranded DNA (dsDNA) to the filament triggers the homology search; as homology is found, the exchange of strands occurs, and the displaced DNA is released. These are the principal steps of genetic recombination; however, despite many years of extensive study of RecA activities, the details of the mechanism are still obscure. A high-resolution structure of the active nucleoprotein filament could provide information to help understand this process. Using a linear dichroism polarized-light spectroscopy technique, in combination with protein engineering (the site-specific linear dichroism method), we have previously studied the arrangement of RecA in complex with ssDNA. In the present study, we have used this approach to search for structural variations of RecA at the atomic level as the DNA in the complex is changed from ssDNA to dsDNA. The structural data of the RecA-dsDNA filament are found to be very similar to the data previously obtained for the RecA-ssDNA complex, indicating that the overall orientation and also the internal structure of RecA in the active filament are not markedly altered when the bound DNA changes from single- to double-stranded. The implications of the structural similarities as well as the significance of some conformational variations observed for a few amino acid residues that may be involved in interactions with DNA are discussed.     

The analysis of enzyme progress curves by numerical differentiation, including competitive product inhibition and enzyme reactivation

A new method for analyzing steady-state enzyme kinetic data is presented. The technique, which is based on the numerical differentiation of the complete reaction curve, has several advantages over initial velocity and integrated Michaelis-Menten equation methods. The differentiated data are fit to the differential equation describing the appropriate kinetic scheme. This approach is particularly valuable in cases of strong competitive product inhibition and of changing concentrations of active enzyme. The method assumes a reversible reaction and is applicable to a very wide variety of steady-state kinetic schemes. A particular advantage of this approach over integrated methods is that it is independent of [S0] and hence of errors in [S0]. The combination of complete progress curve and computer analysis makes this approach very efficient with respect to both time and materials. Running on an IBM PC XT or equivalent microcomputer with an 8087 coprocessor, the analyses are very fast, the complete process usually being complete in a minute or two. The utility of the technique is demonstrated by application to both simulated and real data. We show that the differentiation of the progress curve for the ribonuclease-catalyzed hydrolysis of 2',3'-cyclic cytidine monophosphate reveals strong product inhibition by 3'-CMP, and this product inhibition accounts for the large discrepancies reported in the literature for the value of Km for this substrate. The method was also applied to determine the rate of reactivation of beta-lactamase which had been reversibly inactivated by cloxacillin. Since large numbers of data points are required for the numerical differentiation the method has become practical only with the advent of computer-acquired data systems.     

Uncertainty/Safety Factors in Health Risk Assessment: Opportunities for Improvement

This paper presents the results of deliberations from participants who met on the second day of the Fourth Annual Workshop on the Evaluation of Uncertainty/Safety Factors in Health Risk Assessment. The group reviewed the previous day's presentations and implications for improvement in risk assessment. After much discussion, the group concluded that, in the short term, significant improvements could be made in the pharmacokinetic component of the inter-species uncertainty factor and developed a series of default options for this factor. These defaults consider route of exposure (oral or inhalation), and the form of the active compound (parent, metabolite, or very reactive metabolite). Several assumptions are key to this approach, such as a similar oral or inhalation bioavailability across species. We believe this method represents a useful default approach until more compound-specific information is available.     

Sequence-based enzyme catalytic domain prediction using clustering and aggregated mutual information content

Characterizing enzyme sequences and identifying their active sites is a very important task. The current experimental methods are too expensive and labor intensive to handle the rapidly accumulating protein sequences and structure data. Thus accurate, high-throughput in silico methods for identifying catalytic residues and enzyme function prediction are much needed. In this paper, we propose a novel sequence-based catalytic domain prediction method using a sequence clustering and an information-theoretic approaches. The first step is to perform the sequence clustering analysis of enzyme sequences from the same functional category (those with the same EC label). The clustering analysis is used to handle the problem of widely varying sequence similarity levels in enzyme sequences. The clustering analysis constructs a sequence graph where nodes are enzyme sequences and edges are a pair of sequences with a certain degree of sequence similarity, and uses graph properties, such as biconnected components and articulation points, to generate sequence segments common to the enzyme sequences. Then amino acid subsequences in the common shared regions are aligned and then an information theoretic approach called aggregated column related scoring scheme is performed to highlight potential active sites in enzyme sequences. The aggregated information content scoring scheme is shown to be effective to highlight residues of active sites effectively. The proposed method of combining the clustering and the aggregated information content scoring methods was successful in highlighting known catalytic sites in enzymes of Escherichia coli K12 in terms of the Catalytic Site Atlas database. Our method is shown to be not only accurate in predicting potential active sites in the enzyme sequences but also computationally efficient since the clustering approach utilizes two graph properties that can be computed in linear to the number of edges in the sequence graph and computation of mutual information does not require much time. We believe that the proposed method can be useful for identifying active sites of enzyme sequences from many genome projects.     

Robust Tract Skeleton Extraction of Cingulum Based on Active Contour Model from Diffusion Tensor MR Imaging

Cingulum is widely studied in healthy and psychiatric subjects. For cingulum analysis from diffusion tensor MR imaging, tractography and tract of interest method have been adopted for tract-based analysis. Because tractography performs fiber tracking according to local diffusion measures, they can be sensitive to noise and tracking errors can be accumulated along the fiber. For more accurate localization of cingulum, we attempt to define it by skeleton extraction using the tensors'' information throughout the tract of cingulum simultaneously, which is quite different from the idea of tractography. In this study, we introduce an approach to extract the skeleton of cingulum using active contour model, which allows us to optimize the location of cingulum in a global sense based on the diffusion measurements along the entire tract and contour regularity. Validation of this method on synthetic and experimental data proved that our approach is able to reduce the influence of noise and partial volume effect, and extract the skeleton of cingulum robustly and reliably. Our proposed method provides an approach to localize cingulum robustly, which is a very important feature for tract-based analysis and can be of important practical utility.     

Monitoring electropermeabilization in the plasma membrane of adherent mammalian cells.

When an electrical potential of order one volt is induced across a cell membrane for a fraction of a second, temporary breakdown of ordinary membrane functions may occur. One result of such a breakdown is that molecules normally excluded by the membrane can now enter the cells. This phenomenon, generally referred to as electropermeabilization, is known as electroporation when actual pores form in the membrane. This paper presents a unique approach to the measurement of pore formation and closure in anchored mammalian cells. The cells are cultured on small gold electrodes, and by constantly monitoring the impedance of the electrode with a low-amplitude AC signal, small changes in cell morphology, cell motion, and membrane resistance can be detected. Because the active electrode is small, the application of a few volts across the cell-covered electrode causes pore formation in the cell membrane. In addition, the heat transfer is very efficient, and the cells can be porated in their regular growth medium. By this method, the formation and resealing of pores due to applied electric fields can be followed in real time for anchorage-dependent cells.     

Docking of cyclohexanol-derivatives into the active site of liver alcohol dehydrogenase. Using computer graphics and energy minimization

Model building and energy minimization procedures have been used to determine a productive substrate binding mode in liver alcohol dehydrogenase for secondary alcohols. These docking results have been compared to some of the extensive amounts of kinetic data available for this enzyme. The indirect diamond lattice approach first suggested by Prelog (Prelog, V. (1964) Pure Appl. Chem. 9, 119-130) to describe the active site of an enzyme has been used to build a direct diamond lattice from the crystallographic model of the enzyme. This lattice was oriented and positioned into the active site using the productive binding mode of cyclohexanol derivatives obtained from model building. We then classified the positions as allowed, forbidden, or boundary depending on their distances to protein atoms. We found very good agreement between the classification of our direct diamond lattice points and those of the indirect lattice obtained by others from kinetic studies. Finally we have extended the lattice as an aid to predict the stereospecificity of the enzyme for molecules which cover other regions of the active site.     

Yeast ferrochelatase: expression in a baculovirus system and purification of the expression protein.

The terminal step of the heme biosynthetic pathway is catalyzed by the enzyme ferrochelatase (EC 4.99.1.1). In eukaryotes this enzyme is bound to the inner mitochondrial membrane with its active site facing the matrix side of the membrane. Previously this laboratory has characterized this enzyme via kinetic and protein chemical modification techniques, and with the recent cloning of the enzyme from yeast, mouse, and human sources it now becomes possible to approach structure-function questions by using site-directed mutagenesis. Of primary significance to this is the development of an efficient expression vector. This is of particular significance for ferrochelatase, as it is a low-abundance protein whose DNA coding sequence has a very low codon bias. In the current work we describe the production of yeast ferrochelatase in a baculovirus system. This system is shown to be an excellent one in which to produce large quantities of active ferrochelatase. The expressed enzyme is membrane associated and is not released into the growth medium either during or after virus development and cell lysis. The expressed protein can be purified in a procedure that requires only 1 day and makes use of a Pharmacia Hi Trap blue affinity column. The measured Km's for the substrates mesoporphyrin and iron are the same as those reported previously for the yeast enzyme. To our knowledge this is the first example of a mitochondrial membrane protein that has been expressed in a baculovirus system.     

The in situ localization of folic acid.

A histochemical azo-coupling method for localizing folic acid in situ is described. Cat and rat liver, kidney, bone marrow and brain were found to be rich in folic acid; stomach, intestine, salivary glands, and blood contained less. Folic acid was localized in the cytoplasm of tissues having a very active metabolism, but in the nucleus of highly specialized cells such as neurons.     

Probabilistic kinetic model of slow oxidation of low-density lipoprotein: I. Theory

The microscopic probabilistic model has been introduced to explain the kinetics of very slow oxidation of low-density lipoprotein (LDL) from human plasma. The LDL oxidation, carried out in very unfavorable conditions, is assumed to be initiated by the traces of the transition-metal ions associated with the lipoprotein. The substrates for the metal-ion attack are alpha-tocopherol and the pre-formed lipid hydroperoxide. The theory assumes oscillation of the metal ions and alpha-tocopherol from the oxidized to the reduced states. In this model alpha-tocopherol acts as a pro-oxidant. The entire oxidation process consists of rare bursts of events in individual LDL particles. The reactions within the particles are treated in terms of probabilities of individual active species to participate in a specified reaction. The circular flow of the radical reactions could be visualized as circular flow of microscopic probabilities. The empirical, macroscopic quantities are quantitatively related with the microscopic probabilities, determined by a set of five adjustable parameters. The differential equations describing the initial radical generation rate and the rates of change of concentration of oxygen, hydroperoxide, co-antioxidant and trapped radicals in an LDL system are numerically solved in a finite difference approach.     

Somatic hypermutagenesis in immunoglobulin genes. II. Influence of neighbouring base sequences on mutagenesis.

A new approach for the analysis of hotspots of mutations is described. It is based on the classification of hotspot site sequences. Using this approach, the consensuses RGYW and TAA of hotspot sites were revealed in the V gene. Correlation between somatic mutations and these consensuses is investigated by the statistical weight method in 323 somatic substitutions in 14 V genes. Assuming the absence of any correlation, the probability of observing such data in the sample would be very low (0.0003). These results support the idea that emergence of somatic mutation is significantly influenced by neighbouring base sequences. This idea was also supported by the analysis of 296 somatic mutations in flanking sequences of V genes. It is supposed that this influence is an important feature of somatic hypermutagenesis.     

Prediction of functionally important sites from protein sequences using sparse kernel least squares classifiers

Identification of functionally important sites (FIS) in proteins is a critical problem and can have profound importance where protein structural information is limited. Machine learning techniques have been very useful in successful classification of many important biological problems. In this paper, we adopt the sparse kernel least squares classifiers (SKLSC) approach for classification and/or prediction of FIS using protein sequence derived features. The SKLSC algorithm was applied to 5435 FIS that have been extracted from 312 reliable alignments for a wide range of protein families. We obtained 68.28% sensitivity and 68.66% specificity for training dataset and 65.34% sensitivity and 66.88% specificity for testing dataset. Further, large scale benchmarking study using alignments of 101 protein families containing 1899 FIS showed that our method achieved an average ∼70% sensitivity in predicting different types of FIS, such as active sites, metal, ligand or protein binding sites. Our findings also indicate that active sites and metal binding sites are comparably easier to predict compared to the ligand and protein binding sites. Despite moderate success, our results suggest the usefulness and potential of SKLSC approach in prediction of FIS using only protein sequence derived information.     

Rapid separation of tyrosine-specific tRNA from white lupin.

During isolation of total ribonucleic acids from white lupin (Lupinus albus) and their subsequent separation by 10% polyacrylamide gel electrophoresis, a fast migrating RNA band is very well separated. The nucleotide sequence analysis of 76 nucleotide long sequence with many modified nucleosides was found to be identical with that of tyrosine specific tRNA of yellow lupin seeds (Lupinus luteus) and wheat germ (Triticum aestivum). Also this tRNA(Tyr) is identical with plant amber suppressor tRNA. The presented approach offers a very rapid method of purification of plant tRNA with UAG suppressor activity.     

Increased production of active human beta(2)-adrenergic/G(alphas) fusion receptor in Sf-9 cells using nutrient limiting conditions

Using the baculovirus/insect-cell expression vector system, we succeeded in obtaining a high yield of active human beta(2)-adrenergic receptor/G(alphas) fusion protein. This was achieved following high cell density production under nutrient-limiting conditions using a very low multiplicity of infection (MOI). This approach was found to significantly reduce inactive protein accumulation that occurred when production was done using conventional high MOI procedures. The maximum specific and volumetric yields of active receptor using this strategy increased by factors of two- and sixfold, respectively. Our results suggest that the increase in the ratio of active/total protein produced results from production under nutrient limitation. Since low multiplicity of infection offers many advantages for large-scale applications, we suggest that this simple production method should be considered when optimizing expression of G-protein-coupled receptors and other complex proteins.