Exploring the energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes

Energy landscapes of molecular recognition are explored by performing “semi-rigid” docking of FK-506 and rapamycin with the Fukisawa binding protein (FKBP-12), and flexible docking simulations of the Ro-31-8959 and AG-1284 inhibitors with HIV-1 protease by a genetic algorithm. The requirements of a molecular recognition model to meet thermodynamic and kinetic criteria of ligand-protein docking simultaneously are investigated using a family of simple molecular recognition energy functions. The critical factor that determines the success rate in predicting the structure of ligand-protein complexes is found to be the roughness of the binding energy landscape, in accordance with a minimal frustration principle. The results suggest that further progress in structure prediction of ligand-protein complexes can be achieved by designing molecular recognition energy functions that generate binding landscapes with reduced frustration. © 1996 Wiley-Liss, Inc.     

Fundamental measure theory of hydrated hydrocarbons

To calculate the solvation of hydrophobic solutes, we have developed a method based on the fundamental measure treatment of density functional theory. This method allows us to carry out calculations of density profiles and the solvation energy for various hydrophobic molecules with high accuracy. We have applied the method to the hydration of various hydrocarbons (linear, branched and cyclic). The calculations of the entropic and enthalpic parts are also carried out. We have examined the question of the temperature dependence of the entropy convergence. Finally, we have calculated the mean force potential between two large hydrophobic nanoparticles immersed in water. Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005.     

Aquatic phototrophs: efficient alternatives to land-based crops for biofuels

To mitigate some of the potentially deleterious environmental and agricultural consequences associated with current land-based-biofuel feedstocks, we propose the use of biofuels derived from aquatic microbial oxygenic photoautotrophs (AMOPs), more commonly known as cyanobacteria, algae, and diatoms. Herein we review their demonstrated productivity in mass culturing and aspects of their physiology that are particularly attractive for integration into renewable biofuel applications. Compared with terrestrial crops, AMOPs are inherently more efficient solar collectors, use less or no land, can be converted to liquid fuels using simpler technologies than cellulose, and offer secondary uses that fossil fuels do not provide. AMOPs pose a new set of technological challenges if they are to contribute as biofuel feedstocks.     

Metabolic and photosynthetic consequences of blocking starch biosynthesis in the green alga Chlamydomonas reinhardtii sta6 mutant

Upon nutrient deprivation, microalgae partition photosynthate into starch and lipids at the expense of protein synthesis and growth. We investigated the role of starch biosynthesis with respect to photosynthetic growth and carbon partitioning in the Chlamydomonas reinhardtii starchless mutant, sta6, which lacks ADP‐glucose pyrophosphorylase. This mutant is unable to convert glucose‐1–phosphate to ADP‐glucose, the precursor of starch biosynthesis. During nutrient‐replete culturing, sta6 does not re‐direct metabolism to make more proteins or lipids, and accumulates 20% less biomass. The underlying molecular basis for the decreased biomass phenotype was identified using LC–MS metabolomics studies and flux methods. Above a threshold light intensity, photosynthetic electron transport rates (water → CO₂) decrease in sta6 due to attenuated rates of NADPH re‐oxidation, without affecting photosystems I or II (no change in isolated photosynthetic electron transport). We observed large accumulations of carbon metabolites that are precursors for the biosynthesis of lipids, amino acids and sugars/starch, indicating system‐wide consequences of slower NADPH re‐oxidation. Attenuated carbon fixation resulted in imbalances in both redox and adenylate energy. The pool sizes of both pyridine and adenylate nucleotides in sta6 increased substantially to compensate for the slower rate of turnover. Mitochondrial respiration partially relieved the reductant stress; however, prolonged high‐light exposure caused accelerated photoinhibition. Thus, starch biosynthesis in Chlamydomonas plays a critical role as a principal carbon sink influencing cellular energy balance however, disrupting starch biosynthesis does not redirect resources to other bioproducts (lipids or proteins) during nutrient‐replete culturing, resulting in cells that are susceptible to photochemical damage caused by redox stress.     

Genetic diversity of tufted ducks (<Emphasis Type="Italic">Aythya fuligula</Emphasis>, Anatidae) in Eastern Europe

The tufted duck (Aythya fuligula, Anatidae) is widespread in the Palaearctic across Northern Eurasia. Birds breeding in Northern and Eastern Europe are highly migratory, while populations from Western Europe are partially migratory or resident. The aim of this study is to explore genetic variation within and between ducks breeding in Latvia and migrants sampled in North West Russia and Belarus. The technique of random amplified polymorphic DNA was applied using five random primers (ol-1, ol-9-12). Genetic variability was measured for all tufted ducks investigated and for different sub-populations from various regions. Individual genetic structure and genetic variability was higher in ducks collected from Latvia. Gene diversity of amplified DNA bands in birds of Latvian origin was 24% with 80% polymorphism. Means of gene diversity and polymorphism for tufted ducks sampled in other countries varied from 12 to 14% and from 27 to 40%, respectively. A high number of unique bands characterized ducks breeding in Latvia. The oligonucleotide primers used in this study were suitable to analyze differences among tufted ducks of different origin. Possible explanations for the variation observed among the studied ducks are discussed.     

Mycotoxin induction of somatic mosaicism in Drosophila and DNA repair in mammalian liver cell cultures

Thegenotoxic activity of four mycotoxins has been studied. A high level of somatic mutagenesis in imaginal disks of Drosophila melanogaster larvae and DNA repair synthesis in human embryo and adult rat liver cell cultures was induced only by the strong carcinogen aflatoxin B₁. Patulin somewhat elevated the level of somatic mutations in D. melanogaster, but did not elicit DNA repair synthesis. Citrinin and stachybotryotoxin were inactive in both systems.Abbreviations AFB₁ aflatoxin B₁ - DMSO dimethylsulfoxide - ³HTdR tritiated thymidine - SCE sisterchromatid exchange - UDS unscheduled DNA synthesis     

Molecular sub-classification of renal epithelial tumors using meta-analysis of gene expression microarrays

Purpose

To evaluate the accuracy of the sub-classification of renal cortical neoplasms using molecular signatures.

Experimental Design

A search of publicly available databases was performed to identify microarray datasets with multiple histologic sub-types of renal cortical neoplasms. Meta-analytic techniques were utilized to identify differentially expressed genes for each histologic subtype. The lists of genes obtained from the meta-analysis were used to create predictive signatures through the use of a pair-based method. These signatures were organized into an algorithm to sub-classify renal neoplasms. The use of these signatures according to our algorithm was validated on several independent datasets.

Results

We identified three Gene Expression Omnibus datasets that fit our criteria to develop a training set. All of the datasets in our study utilized the Affymetrix platform. The final training dataset included 149 samples represented by the four most common histologic subtypes of renal cortical neoplasms: 69 clear cell, 41 papillary, 16 chromophobe, and 23 oncocytomas. When validation of our signatures was performed on external datasets, we were able to correctly classify 68 of the 72 samples (94%). The correct classification by subtype was 19/20 (95%) for clear cell, 14/14 (100%) for papillary, 17/19 (89%) for chromophobe, 18/19 (95%) for oncocytomas.

Conclusions

Through the use of meta-analytic techniques, we were able to create an algorithm that sub-classified renal neoplasms on a molecular level with 94% accuracy across multiple independent datasets. This algorithm may aid in selecting molecular therapies and may improve the accuracy of subtyping of renal cortical tumors.     

Measuring photosynthetic parameters at a distance: laser induced fluorescence transient (LIFT) method for remote measurements of photosynthesis in terrestrial vegetation

We have developed a laser induced fluorescence transient (LIFT) technique and instrumentation to remotely measure photosynthetic properties in terrestrial vegetation at a distance of up to 50 m. The LIFT method uses a 665 nm laser to project a collimated, 100 mm diameter excitation beam onto leaves of the targeted plant. Fluorescence emission at 690 nm is collected by a 250 mm reflective telescope and processed in real time to calculate the efficiency of photosynthetic light utilization, quantum efficiency of PS II, and the kinetics of photosynthetic electron transport. Operating with peak excitation power of 125 W m⁻², and duty cycle of 10–50%, the instrument conforms to laser safety regulations. The LIFT instrument is controlled via an Internet connection, allowing it to operate from remote locations or platforms. Here we describe the theoretical basis of the LIFT methodology, and demonstrate its applications in remote measurements of photosynthetic properties in the canopy of cottonwood and oak trees, and in the rosette of Arabidopsis mutants.     

Identification of tumor promoters by their inhibitory effect on intercellular transfer of lucifer yellow

The effect of the tumor promoters 12-O-tetradecanoylphorbol-13-acetate (TPA), mezerein, teleocidin, anthralin, the Ca²⁺-ionophore A23187, butylated hydroxytoluene (BHT), dichlordiphenyltrichloroethane (DDT) and phenobarbital (PB) on lucifer yellow transfer in cultures of SV-40-transformed Djungarian hamster fibroblasts was studied. TPA, mezerein, teleocidin, A23187, DDT and BHT exerted a strong inhibitory effect on cell-to-cell dye transfer. Anthralin uncoupled cells in 3 experiments out of 6. PB appeared to enhance lucifer yellow transfer. Sodium nitrite, a substance with unknown promoting activity, effectively uncoupled cells. All the promoters investigated had a reversible effect on the dye transfer. The value of the dye transfer method for promoter screening is discussed.Abbreviations BHT butylated hydroxytoluene - DDT dichlordiphenyltrichloroethane - LY Lucifer Yellow - PB phenobarbital - TPA 12-O-tetradecanoylphorbol-13-acetate