Ligand screening by exoproteolysis and mass spectrometry in combination with computer modelling

Here, we present a new approach for protein ligand screening based on the use of limited exoproteolysis coupled to MALDI-TOF mass spectrometry, combined with computational modelling and prediction of binding energies. As a test for this combined approach, we have screened a combinatorial library containing 8000 peptides (organized in 60 peptide samples) based on positional scanning format. This library is attached to a poly-Pro framework, and screened against the Abl-SH3 domain. The results obtained demonstrated the validity of the experimental and theoretical approaches in identifying better ligands and in rationalizing the changes in affinity. Exoproteolysis coupled to MALDI-TOF mass spectrometry could be used to screen complex libraries in a fast and efficient way.     

On Parametric Stability of Gene Networks Controlling Ontogenetic Processes

The problem of evaluation of parametric stability of three models of pro- and eukaryotic gene networks controlling ontogenetic processes has been defined and solved. Experimental schemes of testing gene networks for parametric stability based on the method of generalized threshold models were developed and realized as a software application. We studied the sensitivity of the functioning modes to random variations of the parameters in three model systems: phage development control system, Arabidopsis thaliana flower morphogenesis control subsystem, and gene subnetwork controlling early ontogeny of Drosophila melanogaster. The parametric stability was quantitatively assessed for these models.     

Computer simulation studies of the fidelity of DNA polymerases

Computer simulations can provide in principle quantitative correlation between the structures of DNA polymerases and the replication fidelity. This paper describes our progress in this direction. Using several theoretical approaches, including the free energy perturbation (FEP), linear response approximation (LRA), and the empirical valence bond (EVB) methods, we examined the stability of several mismatched base pairs in DNA duplex in aqueous solution, the contribution of binding energy to the fidelity of DNA polymerases beta and T7, and the mechanism and energetics of the polymerization reaction catalyzed by T7 DNA polymerase.     

Mutagenesis and computer modelling approach to study determinants for recognition of signal peptides by the mitochondrial processing peptidase

Determinants for the recognition of a mitochondrial presequence by the mitochondrial processing peptidase (MPP) have been investigated using mutagenesis and bioinformatics approaches. All plant mitochondrial presequences with a cleavage site that was confirmed by experimental studies can be grouped into three classes. Two major classes contain an arginine residue at position -2 or -3, and the third class does not have any conserved arginines. Sequence logos revealed loosely conserved cleavage motifs for the first two classes but no significant amino acid conservation for the third class. Investigation of processing determinants for a class III precursor, Nicotiana plumbaginifolia F1beta precursor of ATP synthase (pF1beta), was performed using a series of pF1beta presequence mutants and mutant presequence peptides derived from the C-terminal portion of the presequence. Replacement of -2 Gln by Arg inhibited processing, whereas replacement of either the most proximally located -5 Arg or -15 Arg by Leu had only a low inhibitory effect. The C-terminal portion of the pF1beta presequence forms a helix-turn-helix structure. Mutations disturbing or prolonging the helical element upstream of the cleavage site inhibited processing significantly. Structural models of potato MPP and the C-terminal pF1beta presequence peptide were built by homology modelling and empirical conformational energy search methods, respectively. Molecular docking of the pF1beta presequence peptide to the MPP model suggested binding of the peptide to the negatively charged binding cleft formed by the alpha-MPP and beta-MPP subunits in close proximity to the H111XXE114H115X(116-190)E191 proteolytic active site on beta-MPP. Our results show for the first time that the amino acid at the -2 position, even if not an arginine, as well as structural properties of the C-terminal portion of the presequence are important determinants for the processing of a class III precursor by MPP.     

Specific mode of interaction between components of model pulmonary surfactants using computer simulations

Atomistic molecular dynamics simulations and structural bioinformatics tools enable the identification of the exact mode of interaction between model pulmonary surfactant components. Two nanosecond long simulations of the N-terminal region of human surfactant protein-B (SP-B(1-25)) in dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylglycerol (DPPG) monolayers of different lipid surface densities reveal the preferential affinity of SP-B(1-25) for anionic phospholipids. In particular, arginine 12 and lysine 24 interact strongly and with high specificity with the phosphate group of the DPPG lipids, stabilizing the position, the orientation, and the secondary structure of the peptide in the monolayer. The peptide lies at an oblique angle to the interfacial plane, ranging between 47 degrees and 62 degrees, increasing with decreasing lipid surface density. In DPPC monolayers the interaction is largely determined by hydrophobic interactions. The non-specific nature of DPPC-SP-B(1-25) interactions allows for significant flexibility in the topology of the peptide in the lipid matrix. Bioinformatics tools are employed to generalize the simulation results to the sequences of SP-B(1-25) in other organisms. The importance of specific residues, and the role of the largely helical and amphiphilic nature of the peptide in the functionality of SP-B(1-25) are established. The synergy of classical mechanics tools with bioinformatics methods greatly enhances the molecular-level interpretation of pulmonary surfactant action and facilitates the development of design rules for synthetic surfactant analogues.     

Program MULDER -- a tool for extracting torsion angles from NMR data

MULDER (Mostly UniversaL Dihedral angle ExtractoR) is a program for extraction of torsion angle information from NMR data. Currently, it can analyze two types of input data: The torsion angle data, where several ³J-coupling constants and/or interatomic distances are combined in order to reduce the torsion angle ambiguity arising from solving the isolated Karplus (or distance) equation, and the sugar pucker data, where the dynamics of five-membered sugar rings is evaluated by postprocessing the results calculated from ³J_(HH) coupling constants by program PSEUROT. Program MULDER can be used either as an alternative to r-MD programs in situations where only specific structural features are studied, or as a preparatory tool in connection with full r-MD structure calculation for extraction of unambiguous torsion angle restraints.     

EEG-based communication and control: speed-accuracy relationships

People can learn to control mu (8–12 Hz) or beta (18–25 Hz) rhythm amplitude in the EEG recorded over sensorimotor cortex and use it to move a cursor to a target on a video screen. In our current EEG-based brain–computer interface (BCI) system, cursor movement is a linear function of mu or beta rhythm amplitude. In order to maximize the participant's control over the direction of cursor movement, the intercept in this equation is kept equal to the mean amplitude of recent performance. Selection of the optimal slope, or gain, which determines the magnitude of the individual cursor movements, is a more difficult problem. This study examined the relationship between gain and accuracy in a 1-dimensional EEG-based cursor movement task in which individuals select among 2 or more choices by holding the cursor at the desired choice for a fixed period of time (i.e., the dwell time). With 4 targets arranged in a vertical column on the screen, large gains favored the end targets whereas smaller gains favored the central targets. In addition, manipulating gain and dwell time within participants produces results that are in agreement with simulations based on a simple theoretical model of performance. Optimal performance occurs when correct selection of targets is uniform across position. Thus, it is desirable to remove any trend in the function relating accuracy to target position. We evaluated a controller that is designed to minimize the linear and quadratic trends in the accuracy with which participants hit the 4 targets. These results indicate that gain should be adjusted to the individual participants, and suggest that continual online gain adaptation could increase the speed and accuracy of EEG-based cursor control.     

Dynamics of evolutionary patterns of clades in a food web system model

The evolutionary patterns of animal species clades in an evolving food web system were examined by computer simulation. In this system, each animal species fed on other species according to feeding preference. The food web system evolved via the appearance and extinction of species. The model succeeded in reproducing evolutionary patterns of diversity similar to those seen in the fossil record. This result indicates that the model reproduced the temporal changes of the rates of colonization and extinction of species in the system, which have been decided a priori in the previous stochastic models. In the food web system, the numbers of both predatory and prey species influenced the temporal diversity patterns in each clade in the system. The number of prey species fluctuated strongly, whereas the number of predatory species gradually increased with time. Therefore, temporal diversity patterns were influenced mainly by the number of predatory species. As a result of the gradual increase of the number of predatory species, it was difficult for each clade to maintain its species diversity for a long time. Slight changes of interspecific interaction can sometimes decide the destiny of a clade. When a clade is faced with extinction, if one predatory species of the clade becomes extinct and one or two prey species of the clade appear, the species diversity in the clade increases again. This result indicates that slight changes of interspecific interaction sometimes decide the destiny of a clade.     

Calculation of electric fields induced in the human knee by a coil applicator

Calculations are presented of the induced electric fields and current densities in the cartilage of the knee produced by a coil applicator developed for applying pulsed magnetic fields to osteoarthritic knees. This applicator produces a sawtooth-like magnetic field waveform composed of a series of 260-micros pulses with a peak to peak magnitude of approximately 0.12 mT in the cartilage region. The simulations were performed using a recently developed 3 dimensional finite difference frequency domain technique for solving Maxwell's equations with an equivalent circuit model. The tissue model was obtained from the anatomically segmented human body model of Gandhi. The temporal peak electric field magnitude was found to be -153 mV/m, averaged within the medial cartilage of the knee for the typical dB/dt excitation levels of this coil. The technique can be extended to analyze other excitation waveforms and applicator designs.     

Evidence for a Distinct Light-Induced Calcium-Dependent Potassium Current in Hermissenda Crassicornis

A model of phototransduction is developed as a first step toward a model for investigating the critical interaction of light and turbulence stimuli within the type B photoreceptor of Hermissenda crassicronis. The model includes equations describing phototransduction, release of calcium from intracellular stores, and other calcium regulatory mechanisms, as well as equations describing ligand-gating of a rhabdomeric sodium current. The model is used to determine the sources of calcium in the soma, whether calcium or IP₃ is a plausible ligand of the light-induced sodium current, and whether the light-induced potassium current is equivalent to the calcium-dependent potassium current activated by light-induced calcium release. Simulations show that the early light-induced calcium elevation is due to influx through voltage-dependent channels, whereas the later calcium elevation is due to release from intracellular stores. Simulations suggest that the ligand of the fast, light-induced sodium current is IP₃ but that there is a smaller, prolonged component of the light-induced sodium current that is activated by calcium. In the model, the calcium-dependent potassium current, located in the soma, is activated only slightly by light-induced calcium elevation, leading to the prediction that a calcium-dependent potassium current, active at resting potential, is located in the rhabdomere and is responsible for the light-induced potassium current.