Dry bean protein functionality

Dry beans are an important source of proteins, carbohydrates, dietary fiber, and certain minerals and vitamins in the human food supply. Among dry beans, Phaseolus beans are cultivated and consumed in the greatest quantity on a worldwide basis. Typically, most dry beans contain 15 to 25% protein on a dry weight basis (dwb). Water-soluble albumins and salt-soluble globulins, respectively, account for up to 10 to 30% and 45 to 70% of the total proteins (dwb). Dry bean albumins are typically composed of several different proteins, including lectins and enzyme inhibitors. A single 7S globulin dominates dry bean salt soluble fraction (globulins) and may account for up to 50 to 55% of the total proteins in the dry beans (dwb). Most dry bean proteins are deficient in sulfur amino acids, methionine, and cysteine, and therefore are of lower nutritional quality when compared with the animal proteins. Despite this limitation, dry beans make a significant contribution to the human dietary protein intake. In bean-based foods, dry bean proteins also serve additional functions that may include surface activity, hydration, and hydration-related properties, structure, and certain organoleptic properties. This article is intended to provide an overview of dry bean protein functionality with emphases on nutritional quality and hydration-related properties.     

Computational aspects of systematic biology

We review the resources available to systematic biologists who wish to use computers to build classifications. Algorithm development is in an early stage, and only a few examples of integrated applications for systematic biology are available. The availability of data is crucial if systematic biology is to enter the computer age.     

MCSS functionality maps for a flexible protein

The Multiple Copy Simultaneous Search (MCSS) methodology for finding energetically favorable positions and orientations of small functional groups in a binding site is extended to include flexibility of the target. This makes possible the finding of novel minima not present in a fixed structure and so extends the diversity of inhibitors that can be constructed starting with the MCSS procedure. Quenched molecular dynamics is used to generate energetically favorable positions and orientations of the functional groups in the field of a flexible protein. The method is applied to the viral protein HIV-1 protease with methanol and methyl ammonium as a test case. If the protein is quenched with many copies of functional groups randomly distributed in the binding site, the resulting minima have ligand-protein interaction energies that are, on average, less favorable than those obtained with standard MCSS. This is a consequence of the renormalized potential function employed in the Locally Enhanced Sampling (LES) approximation. However, local optimizations of existing MCSS minima with a flexible protein results in lower energy minima in regions of the protein that are of particular interest. Their use in constructing a consensus protein model for ligand design is discussed.     

Computational design of protein self-assembly

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Thermodynamic aspects of biopolymer functionality in biological systems,foods, and beverages

Molecular mimicry and molecular symbiosis are proposed to be the main factors controlling thermodynamic activity and phase behavior of macromolecular compounds in foods, beverages, and chyme. Molecular mimicry implies a chemical resemblance of hydrophilic surfaces of globular proteins with their chemical information hidden in the hydrophobic interior and low excluded volume of the globules. The molecular mimicry contributes to the efficiency of enzymes. Molecular symbiosis means that interactions attraction or repulsion) between biopolymer molecules greatly differing in conformation (globular and rod-like) favor the biological efficiency of one of them at least. The symbiosis is based on excluded volume effects of macromolecules in mixed solutions. Association-dissociation of rod-like macromolecules can dictate thermodynamic activity of an enzyme in the mixed solution. Thermodynamic incompatibility is typical of food macromolecules, whose denaturation, association, complexing, and chemical modification reduce their mimicry and co-solubility. Foods are normally phase-separated systems with highly volume-occupied phases. The phase-separated nature of the gel-like chyme is important to the efficiency of digestion of mixed diets. Phase separation of biopolymer mixtures, presumably, underlies mechanisms of nonspecific immune defense. The phase behavior-functionality relationships is presented through concrete examples of some foods (such as milk products, low-fat spreads, ice cream, wheat and rye doughs, thermoplastic extrudates, etc.), beverages (tea and coffee), and chyme.     

Computational analysis of human protein interaction networks

Large amounts of human protein interaction data have been produced by experiments and prediction methods. However, the experimental coverage of the human interactome is still low in contrast to predicted data. To gain insight into the value of publicly available human protein network data, we compared predicted datasets, high-throughput results from yeast two-hybrid screens, and literature-curated protein-protein interactions. This evaluation is not only important for further methodological improvements, but also for increasing the confidence in functional hypotheses derived from predictions. Therefore, we assessed the quality and the potential bias of the different datasets using functional similarity based on the Gene Ontology, structural iPfam domain-domain interactions, likelihood ratios, and topological network parameters. This analysis revealed major differences between predicted datasets, but some of them also scored at least as high as the experimental ones regarding multiple quality measures. Therefore, since only small pair wise overlap between most datasets is observed, they may be combined to enlarge the available human interactome data. For this purpose, we additionally studied the influence of protein length on data quality and the number of disease proteins covered by each dataset. We could further demonstrate that protein interactions predicted by more than one method achieve an elevated reliability.     

Functional aspects of protein mono-ADP-ribosylation

Mono-ADP-ribosylation is the enzymatic transfer of ADP-ribose from NAD(+) to acceptor proteins. It is catalysed by cellular ADP-ribosyltransferases and certain bacterial toxins. There are two subclasses of cellular enzymes: the ectoenzymes that modify targets such as integrins, defensin and other cell surface molecules; and the intracellular enzymes that act on proteins involved in cell signalling and metabolism, such as the beta-subunit of heterotrimeric G proteins, GRP78/BiP and elongation factor 2. The genes that encode the ectoenzymes have been cloned and their protein products are well characterized, yet little is known about the intracellular ADP-ribosyltransferases, which may be part of a novel protein family with an important role in regulating cell function. ADP-ribosylation usually leads to protein inactivation, providing a mechanism to inhibit protein functions in both physiological and pathological conditions.     

Computational analyses of TBC protein family in eukaryotes

Tre-2/Bub2/Cdc16 domain-containing proteins (TBC proteins) participate in wide range cellular processes. With computational approaches, 137 non-redundant TBC proteins from five model organisms were identified and classified into 13 subfamilies base on molecular evolutionary tree. This phylogenetic analysis provides useful functional annotation of newly-identified TBC proteins and guides for further experimentation.     

Computational study of ligand binding to protein receptors

We have determined, for the first time, the enthalpic contributions to the energy change associated with ligand reorganization (LR) upon the binding of the same ligand to multiple sites within human serum albumine (HSA). Quantum mechanics based density functional theory (DFT) has been used for the LR calculations, which provides much better accuracy than previously used molecular mechanics methods (MM). Our findings show that for some ligands these enthalpic contributions can be attributed to specific structural and conformational changes.     

Effect of calcium on the morphology and functionality of whey protein nanofibrils

Self-assembly of amyloid-like nanofibrils during heating of bovine whey proteins at 80 °C and pH 2 is accelerated by the presence of NaCl and/or CaCl(2), but the rheological consequences of accelerated self-assembly are largely unknown. This investigation focused on the impact of CaCl(2) on the evolution of rheological properties and fibril morphology of heated whey protein isolate (WPI), both during self-assembly at high temperature and after cooling. Continuous rotational rheometry of heated 2% w/w WPI showed a nonlinear effect of CaCl(2) on the viscosity of fibril dispersions, which we attributed to effects on fibril flexibility and thus the balance between intrafibril and interfibril entanglements. Small-amplitude oscillatory measurements made in situ during heating of 10% w/w WPI at 80 °C suggest that CaCl(2) is not involved in either fibril structure or gel structure, and this was confirmed with dialysis experiments.     

Potent and selective disruption of protein kinase D functionality by a benzoxoloazepinolone

Protein kinase D (PKD) is a novel family of serine/threonine kinases targeted by the second messenger diacylglycerol. It has been implicated in many important cellular processes and pathological conditions. However, further analysis of PKD in these processes is severely hampered by the lack of a PKD-specific inhibitor that can be readily applied to cells and in animal models. We now report the discovery of the first potent and selective cell-active small molecule inhibitor for PKD, benzoxoloazepinolone (CID755673). This inhibitor was identified from the National Institutes of Health small molecule repository library of 196,173 compounds using a human PKD1 (PKCmu)-based fluorescence polarization high throughput screening assay. CID755673 suppressed half of the PKD1 enzyme activity at 182 nm and exhibited selective PKD1 inhibition when compared with AKT, polo-like kinase 1 (PLK1), CDK activating kinase (CAK), CAMKIIalpha, and three different PKC isoforms. Moreover, it was not competitive with ATP for enzyme inhibition. In cell-based assays, CID755673 blocked phorbol ester-induced endogenous PKD1 activation in LNCaP cells in a concentration-dependent manner. Functionally, CID755673 inhibited the known biological actions of PKD1 including phorbol ester-induced class IIa histone deacetylase 5 nuclear exclusion, vesicular stomatitis virus glycoprotein transport from the Golgi to the plasma membrane, and the ilimaquinone-induced Golgi fragmentation. Moreover, CID755673 inhibited prostate cancer cell proliferation, cell migration, and invasion. In summary, our findings indicate that CID755673 is a potent and selective PKD1 inhibitor with valuable pharmacological and cell biological potential.     

Computational aspects of motion perception in natural and artificial vision systems.

In this paper a computational scheme for motion perception in artificial and natural vision systems is described. The scheme is motivated by a mathematical analysis in which first-order spatial properties of optical flow, such as singular points and elementary components of optical flow, are shown to be salient features for the computation and analysis of visual motion. The fact that different methods for the computation of optical flow produce similar results is explained in terms of the simple spatial structure of the image motion of rigid bodies. Singular points and elementary flow components are used to compute motion parameters, such as time-to-collision and angular velocity, and also to segment the visual field into areas which correspond to different motions. Then a number of biological implications are discussed. Electrophysiological findings suggest that the brain perceives visual motion by detecting and analysing optical flow components. However, the cortical neurons, which seem to detect elementary flow components, are not able to extract these components from more complex flows. A simple model for the organization of the receptive field of these cells, which is consistent with anatomical and electrophysiological data, is described at the end of the paper.     

Studies on membrane topology, N-glycosylation and functionality of SARS-CoV membrane protein

Background

Dengue is the most important arbovirus disease in tropical and subtropical countries. The viral envelope (E) protein is responsible for cell receptor binding and is the main target of neutralizing antibodies. The aim of this study was to analyze the diversity of the E protein gene of DENV-3. E protein gene sequences of 20 new viruses isolated in Ribeirao Preto, Brazil, and 427 sequences retrieved from GenBank were aligned for diversity and phylogenetic analysis.

Results

Comparison of the E protein gene sequences revealed the presence of 47 variable sites distributed in the protein; most of those amino acids changes are located on the viral surface. The phylogenetic analysis showed the distribution of DENV-3 in four genotypes. Genotypes I, II and III revealed internal groups that we have called lineages and sub-lineages. All amino acids that characterize a group (genotype, lineage, or sub-lineage) are located in the 47 variable sites of the E protein.

Conclusion

Our results provide information about the most frequent amino acid changes and diversity of the E protein of DENV-3.     

Analysis of aluminum-yeast hexokinase interaction: modifications on protein structure and functionality

The aluminum and yeast hexokinase interaction was studied. Structural changes were correlated with variations in protein functionality. Results show two different behaviors: At low metal concentrations preferential adsorption of metal (and water exclusion) induces aggregate formation. No significant changes in the protein structure occur, but there is a continuous loss of activity (from the first concentration). At large salt concentrations a monomerization process and a conformational change in the secondary structure as well as in the three-dimensional structure take place. This change reduces the percentage of -helix conformation, gives thermal stability to the protein, and allows the exposure of some tryptophan residue and hydrophobic regions. The protein inhibition increases. Conformational change and monomerization may allow access of the metal to the substrate site, mainly the ATP site. The inhibition in any case is of mixed type with a competitive component.