The third leg: Molecular dynamics simulations of lipid binding proteins

Molecular dynamics computer simulations can provide a third leg which balances the contributions of both structural biology and binding studies performed on the lipid binding protein family. In this context, these calculations help to establish a dialogue between all three communities, by relating experimental observables with details of structure. Working towards this connection is important, since experience has shown the difficulty of inferring thermodynamic properties from a single static conformation. The challenge is exemplified by ongoing attempts to interpret the impact of mutagenesis on structure and function (i.e. binding). A detailed atomic-level understanding of this system could be achieved with the support of all three legs, paving the way towards rational design of proteins with novel specificities. This paper provides an outline of the connections possible between experiment and theory concerning lipid binding proteins.     

An interactive toxicological data handling system for a PDP-12 computer.

This paper describes a program developed for the cataloguing, storage and retrieval of toxicological data. The user can, through dialogue with the program, enter and update data, and request reports with statistical analyses. The system is written in the FOCAL-12 language for a PDP-12 laboratory computer, and is suitable for a larger number of moderately-sized experiments.     

A computer experiment model to investigate the effects of drug dosage in animals, for use in pharmacological education and research

The ACD-IDEA database, which was originally developed by the authors in 2004, is an ongoing compilation of existing data on the in vivo doses of compounds at which various responses in certain animal species have been observed. It can provide an infrastructure for various research/educational efforts, and creates a synergy for new applications. In this paper, some of these applications are described. Specific interfaces within the database are designed for users who are not computer specialists. Users can search the database to find the answer to a query, or they can design a simple virtual animal experiment. In the second case, the interface is used to undertake a dialogue with the system, in order to test the user's knowledge regarding an experiment under consideration, and to allow the user to glean additional information on better experimental planning. The use of this virtual experimental tool should lead to savings in time, animals, materials, and monetary costs, while the effective learning outcomes of pharmacological experiments are maintained or enhanced.     

alpha-Helical solenoid model for the human involucrin

Involucrin is a key component of the cross-linked envelope of terminally differentiated keratinocytes. The human molecule largely consists of 10 residue repeats and forms a thin 460 A long rod. Summarized experimental data and a detailed stereochemical analysis made with computer modeling resulted in a structural model for the involucrin molecule. The suggested structure is a left-handed alpha-helical solenoid built of a tandem array of helix-turn-helix folds. The structure enables us to explain the whole set of experimental data and residue conservations within the repeats. It is ideally suited to serve as a scaffold for cell envelope assembly and proposes a possible mode of the intermolecular interactions of involucrin during cell cornification.     

Systematic simulation of a tubular recycle reactor on the basis of pilot plant experiments

Systematic simulation may decisively help in development and optimization of bioprocesses. By applying simulation techniques, optimal use can be made of experimental data, decreasing development costs and increasing the accuracy in predicting the behavior of an industrial scale plant.The procedure of the dialogue between simulation and experimental efforts will be exemplified in a case study. Alcoholic fermentation of glucose by zymomonas mobilis bacteria in a gasified tubular recycle reactor was studied first by systematic simulation, using a computer model based solely on literature data. On the base of the results of this simulation, a 0.013 m³ pilot plant reactor was constructed. The pilot plant experiments, too, were based on the results of the systematic simulation.Simulated and experimental data were well in agreement. The pilot plant experiments reiterated the trends and limits of the process as shown by the simulation results. Data from the pilot plant runs were then used to improve the simulation model. This improved model was subsequently used to simulate the performances of an industrial scale plant. The results of this simulation are presented. They show that the alcohol fermentation in a tubular recycle reactor is potentially advantageous to other reactor configurations, especially to continuous stirred tanks.List of Symbols CPFR Continous plug flow reactor - CST R Continous stirred tank reactor - CTR Continous tubular reactor - FMC Fermentation micro computer - P kg/m³ Product concentration - S kg/m³ Glucose concentration - S _o kg/m³ Glucose concentration in the feed - X kg/m³ Biomass concentration - z Cell damage     

Prediction of the structure of proteins using related structures,energy minimization and computer graphics

Insight into the functions and interactions of proteins may be gained by correlating a variety of types of experimental data (including kinetics, spectroscopy, biophysical measurements, among others) with three-dimensional structural models displayed and manipulated using interactive computer graphics. Although tertiary structures have been determined for a large number of proteins, one limiting factor in structure-function studies is the lack of availability of the structural coordinates of specific proteins for which other types of detailed experimental data are known. However, as the data base of known structures grows, it becomes more and more likely that the structure of a closely related protein will be available. Here we present a method for predicting structures by ( 1 ) careful alteration of a known structure of a homologous, functionally analogous protein followed by (2) energy minimization to optimize the predicted structure. This method provides a rapid and effective solution to the initial problem of obtaining a working structure for modeling studies.     

The computer simulation of RNA folding involving pseudoknot formation.

The algorithm and the program for the prediction of RNA secondary structure with pseudoknot formation have been proposed. The algorithm simulates stepwise folding by generating random structures using Monte Carlo method, followed by the selection of helices to final structure on the basis of both their probabilities of occurrence in a random structure and free energy parameters. The program versions have been tested on ribosomal RNA structures and on RNAs with pseudoknots evidenced by experimental data. It is shown that the simulation of folding during RNA synthesis improves the results. The introduction of pseudoknot formation permits to predict the pseudoknotted structures and to improve the prediction of long-range interactions. The computer program is rather fast and allows to predict the structures for long RNAs without using large memory volumes in usual personal computer.     

Demonstration of a highly-sensitive portable double-flash kinetic spectrophotometer for measurement of electron transfer reactions in intact plants

A highly sensitive, portable spectrophotometer for use in measuring flash-induced absorbance changes in intact leaves is demonstrated. The design of the instrument is modified for whole plant use from that suggested by Joliot and Joliot (Biochim. Biophys. Acta 765, 210–218). The spectrophotometer uses trifurcated light guides to deliver measuring and actinic beams to two comparable areas of the leaf. The measuring beam is provided by a series of short, relatively intense light pulses from a xenon flashlamp in place of the constant weak measuring beam used in conventional machines. The use of a flash measuring beam and differential detection allows for a high signal-to-noise ratio (noise levels of 10^-5A) without significant actinic effects. The time resolution of the instrument is 2 sec and the noise level is independent of the experimental time range. The instrument is battery or mains powered, computer operated, and has a liquid crystal display for computer-user interface and dialogue, and to show the kinetic traces graphically. Wavelength selection is provided by interchangeable interference filters. The instrument can communicate with a laboratory-based computer, receiving programming information and sending experimental data to be processed and plotted. The instrument is demonstrated by following the kinetics of the electrochromic shift, the change in redox states of cytochrome f and the b cytochromes in an intact cucumber leaf, and in the same leaf after infiltration with DCMU.     

All 16 centromere DNAs from Saccharomyces cerevisiae show DNA curvature

All 16 centromere DNA regions of Saccharomyces cerevisiae including 90 bp framing sequences on either side were cloned. These 300 bp long centromere regions were analysed by native polyacrylamide gel electrophoresis and found to display a reduced mobility indicative of DNA curvature. The degree of curvature is centromere dependent. The experimental data were confirmed by computer analysis of the 3-dimensional structure of the CEN DNAs. Altogether these data provide further evidence for a model for budding yeast centromeres in which CEN DNA structure could be important for the assembly, activity and/or regulation of the centromere protein-DNA complex.     

Automated information-diagnostic system for hereditary diseases in childhood]

This article describes computer-based information-and-diagnostic system dealing with child hereditary diseases which makes in possible to organize automated consultative service on a wide range of monogene and chromosome syndromes. The system is oriented for sorting out a narrow differential-and-diagnostic row from 1200 of genetically determined diseases at the stage of pre-laboratory child examination. The choice of diagnoses in the system is based on the analysis of the likeness of phenotypical manifestation of the syndromes described in literature with the case under analysis. The system envisages information exchange with a physician in a dialogue using the natural language. The system is based on IBM-370 computer and can be operated from remote video device in the data TV transmitting mode.     

Modeling of basolateral ATP release induced by hypotonic treatment in A6 cells

ATP is released from the basolateral membrane of A6 epithelia in response to hypotonic treatment. This study addresses the problem of ATP diffusion through the permeable supports used to culture the cells. A theoretical analysis of a recently introduced experimental protocol is presented and a model of ATP diffusion through the compartments of the measuring system is proposed. The model provides the ATP profiles near the cell layer and in the measurement chamber. Comparison of results from computer simulations and experimental data showed that the permeable support introduces a marked delay for ATP diffusion, supporting the correlation of apparently time-separated events: the mobilization of Ca²⁺ from internal stores and release of ATP from the cell. The model is consistent with experimental data obtained with the luciferin–luciferase pulse protocol and provides an indirect proof of related processes like the closure and opening of the lateral interspace that occur after imposing the hyposmotic shock. The influence of the pore structure of the permeable support in modulating the measured release rates revealed by computer simulation is experimentally validated for two types of Anopore filters.     

Sequence-dependent DNA structure

The three-dimensional structure of DNA depends subtly on its sequence, and this property is used by the proteins that regulate gene expression to locate their target sequences. Despite the large body of experimental data that has been accumulated on the relationship between sequence and DNA structure, we still do not fully understand the molecular basis for these properties, nor can we predict a three-dimensional structure from a given sequence. We have been using computer modelling to tackle these problems. Some of our results and the implications for understanding the biological role of key sequences are discussed here.     

X-ray and Fe Mössbauer study on a Fe(III) complex of 2-acetyl-1,3-indandione

Single-crystal X-ray structure of an iron(III) complex of 2-acetyl-1,3-indandione is resolved which reveals that a racemic mixture, composed of Δ-fac and Λ-fac stereoisomers, is formed. Both species have octahedral geometry, but slightly distinguishable. Detailed Mössbauer data indicate a high-spin electronic structure of the Fe(III) centres Fe1 and Fe2 with spin-spin magnetic relaxation process. Two different approaches for computer processing of the experimental Mössbauer spectra are considered.     

Prediction of RNA secondary structure by free energy minimization

RNA secondary structure is often predicted from sequence by free energy minimization. Over the past two years, advances have been made in the estimation of folding free energy change, the mapping of secondary structure and the implementation of computer programs for structure prediction. The trends in computer program development are: efficient use of experimental mapping of structures to constrain structure prediction; use of statistical mechanics to improve the fidelity of structure prediction; inclusion of pseudoknots in secondary structure prediction; and use of two or more homologous sequences to find a common structure.     

Proposed secondary structure of eukaryote specific expansion segment 15 in 28S rRNA from mice, rats, and rabbits

The expansion segments in eukaryotic ribosomal RNAs are additional RNA sequences not found in the RNA core common to both prokaryotes and eukaryotes. These regions show large species-dependent variations in sequence and size. This makes it difficult to create secondary structure models for the expansion segments exclusively based on phylogenetic sequence comparison. Here we have used a combination of experimental data and computational methods to generate secondary structure models for expansion segment 15 in 28S rRNA in mice, rats, and rabbits. The experimental data were collected using the structure sensitive reagents DMS, CMCT, kethoxal, micrococcal nuclease, RNase T(1), RNase CL3, RNase V(1), and lead(II) acetate. ES15 was folded with the computer program RNAStructure 3.5 using modification data and phylogenetic similarities between different ES15 sequences. This program uses energy minimization to find the most stable secondary structure of an RNA sequence. The presented secondary structure models include several common structural motifs, but they also have characteristics unique to each organism. Overall, the secondary structure models showed indications of an energetically stable but dynamic structure, easily accessible from the solution by the modification reagents, suggesting that the expansion segment is located on the ribosomal surface.     

The role of mRNA structure in the regulation of protein synthesis: Implications for studies of development

A method is described for the experimental determination of the secondary structure of RNA using enzymatic cleavage data coupled with computer analysis. The structure-specific enzymes S1 nuclease and cobra venom ribonuclease are used to locate nonpaired and basepaired nucleotides, respectively. Computer techniques that utilize the enzymatic susceptibility information to generate a minimum free-energy structure are used to obtain secondary structure models. A second method, using acrylamide-agarose gel electrophoresis, is described for the determination of the relative protein synthesis initiation rates of endlabeled eukaryotic mRNAs. These methods are applied to the rabbit globin mRNAs as an example of a general approach for relating mRNA structure and function. A discussion of the role of messenger RNA structure in the regulation of translation is included with an emphasis on studies of development.     

Tertiary structure of bacterial murein: the scaffold model

Although the chemical structure and physical properties of peptidoglycan have been elucidated for some time, the precise three-dimensional organization of murein has remained elusive. Earlier published computer simulations of the bacterial murein architecture modeled peptidoglycan strands in either a regular (D. Pink, J. Moeller, B. Quinn, M. Jericho, and T. Beveridge, J. Bacteriol. 182: 5925-5930, 2000) or an irregular (A. Koch, J. Theor. Biol. 204: 533-541, 2000) parallel orientation with respect to the plasma membrane. However, after integrating published experimental data on glycan chain length distribution and the degree of peptide side chain cross-linking into this computer simulation, we now report that the proposed planar network of murein appears largely dysfunctional. In contrast, a scaffold model of murein architecture, which assumes that glycan strands extend perpendicularly to the plasma membrane, was found to accommodate published experimental evidence and yield a viable stress-bearing matrix. Moreover, this model is in accordance with the well-established principle of murein assembly in vivo, i.e., sequential attachment of strands to the preexisting structure. For the first time, the phenomenon of division plane alternation in dividing bacteria can be reconciled with a computer model of the molecular architecture of murein.     

Spectroscopic measurements and numerical simulations of the electrode plasma of an electrode microwave discharge in hydrogen

The structure of an electrode microwave discharge in hydrogen at pressures of 1–8 torr and incident powers of 20–100 W is studied using optical spectroscopy. A two-dimensional computer code is developed for self-consistently simulating a self-sustained steady-sate electrode microwave discharge ignited at the end of the inner conductor of a coaxial line. The model is based on simultaneously solving time-dependent Maxwell’s equations, the balance equations for charged particles, and a homogeneous Boltzmann equation. The numerical results referring to the electrode region of the discharge are in fair agreement with the experimental data. This confirms the early suggestion (inferred from experimental data) of the combined “self-sustained-non-self-sustained” character of the electrode discharge. It is shown that the self-sustained discharge domain is located in the electrode region of the discharge.     

Calculation of boron neutron capture cell inactivation in vitro based on particle track structure and x-ray sensitivity

The Monte-Carlo technique was used to perform quantitative microdosimetric model calculations of cell survival after boron neutron capture irradiations in vitro. The high energy ⁷Li and alpha-particles resulting from the neutron capture reaction ¹⁰B (n,α)⁷Li are of short range and are highly damaging to cells. The biophysical model of the Monte-Carlo calculations is based on the track structure of these α-particles and ⁷Li-ions and the x-ray sensitivity of the irradiated cells. The biological effect of these particles can be determined if the lethal effect of local doses deposited in very small fractional volumes of the cell nucleus is known. This lethal effect can be deduced from experimental data of cell survival after x-ray irradiation assuming a Poisson distribution for lethal events. The input data used in a PC-based computer program are the radial dose distribution inside the track of the released particles, cell survival after x-ray irradiation, geometry of the tumor cells, subcellular ¹⁰B concentration, and thermal neutron fluence. The basic concept of this Monte-Carlo computer model is demonstrated. Validations of computer calculations are presented by comparing them with experimental data on cell survival.