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PubMed2001

Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule.

Ligand-protein docking has been developed and used in facilitating new drug discoveries. In this approach, docking single or multiple small molecules to a receptor site is attempted to find putative ligands. A number of studies have shown that docking algorithms are capable of finding ligands and binding conformations at a receptor site close to experimentally determined structures. These algorithms are expected to be equally applicable to the identification of multiple proteins to which a small molecule can bind or weakly bind. We introduce a ligand-protein inverse-docking approach for finding potential protein targets of a small molecule by the computer-automated docking search of a protein cavity database. This database is developed from protein structures in the Protein Data Bank (PDB). Docking is conducted with a procedure involving multiple-conformer shape-matching alignment of a molecule to a cavity followed by molecular-mechanics torsion optimization and energy minimization on both the molecule and the protein residues at the binding region. Scoring is conducted by the evaluation of molecular-mechanics energy and, when applicable, by the further analysis of binding competitiveness against other ligands that bind to the same receptor site in at least one PDB entry. Testing results on two therapeutic agents, 4H-tamoxifen and vitamin E, showed that 50% of the computer-identified potential protein targets were implicated or confirmed by experiments. The application of this approach may facilitate the prediction of unknown and secondary therapeutic target proteins and those related to the side effects and toxicity of a drug or drug candidate. Proteins 2001;43:217-226.

Computer Simulation↗

PubMed2001

Homonuclear (1)H-NMR assignment and structural characterization of human immunodeficiency virus type 1 Tat Mal protein.

The transacting transcriptional activator (Tat) is a viral protein essential for activation of the human immunodeficiency virus (HIV) genes, and it plays an important role in HIV induced immunodeficiency. We report the NMR structural characterization of the active Tat Mal variant that belongs to a highly virulent D-subtype HIV type-1 (HIV-1) strain (Mal) found mainly in Africa. A full Tat Mal protein (87 residues) is synthesized. This synthetic protein is active in a transactivation assay with HeLa cells infected with the HIV long terminal repeated noncoding sequences of the HIV-1 provirus (LTR) lac Z gene. Homonuclear (1)H-NMR spectra allows the sequential assignment of the Tat Mal spin systems. Simulating annealing generates 20 conformers with similar folding. The geometry of the mean structure is optimized with energy minimization to obtain a final structure. As the European variant (Tat Bru) the N-terminal region of Tat Mal constitutes the core, and there is a hydrophobic pocket composed of the conserved Trp 11 interacting with several aromatic residues. The two functional regions of Tat (basic and the cysteine-rich regions) are well exposed to the solvent. A short alpha-helix is observed in region V adjacent to the basic region. This alpha helix induces local structural variations compared to the NMR structure of Tat Bru, and it brings the cysteine-rich and basic regions closer. This study suggests that similar folding exists among Tat variants.

Africa↗

PubMed2006

Hydrogen atom and hydride anion addition to adenine: structures and energetics.

The radicals and anions derived from the 9H tautomer of adenine by adding a hydrogen atom to one of the four double bonds of the adenine framework have been studied. Computations were carried out using a carefully calibrated density functional (B3LYP) method and basis set (DZP++). Optimized geometries, energies, and vibrational frequencies are predicted for eight radicals and anions. The radicals are found to lie in a range of 22 kcal mol(-1), with the radical derived by addition to the C(8) carbon atom being the lowest lying energetically. The anions are predicted to be bound species in the gas phase with an energetic range of 43 kcal mol(-1). Anions produced by addition of a hydride ion to adenine carbon atoms are found to be the most favorable. Six of the anions are predicted to be stable species with respect to electron detachment. The adiabatic electron affinities, vertical electron affinities, and vertical detachment energies are computed for the first time. Electron affinities for these radicals range from 0.0 to 2.0 eV. Radicals produced by addition to a nitrogen atom have near-zero adiabatic electron affinities, while radicals produced by addition at carbon atoms have considerably higher electron affinities.

Adenine↗

PubMed2002

Analytical energy gradient evaluation in relativistic and nonrelativistic density functional calculations.

The expressions of analytical energy gradients in density functional theory and their implementation in programs are reported. The evaluation of analytical energy gradients can be carried out in the fully 4-component relativistic, approximate relativistic, and nonrelativistic density functional calculations under local density approximation or general gradient approximation with or without frozen core approximation using different basis sets in our programs. The translational invariance condition and the fact that the one-center terms do not contribute to the energy gradients are utilized to improve the calculation accuracy and to reduce the computational effort. The calculated results of energy gradients and optimized geometry as well as atomization energies of some molecules by the analytical gradient method are in very good agreement with results obtained by the numerical derivative method.

Journal Article↗

PubMed2004

Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: new energy gradients and molecular surface tessellation.

New equations are derived and implemented for efficient and accurate computation of solvation energy derivatives for the conductor-like polarizable continuum model (C-PCM) and the isotropic integral equation formalism polarizable continuum model (IEF-PCM). Two new molecular surface tessellation procedures GEPOL-RT and GEPOL-AS that generate near continuous potential energy surfaces are proposed for PCM geometry optimization. The combined use of these new techniques leads to efficient and convergent geometry optimizations with the PCMs.

Journal Article↗

PubMed1988

Robotized scanning laser handpiece for the treatment of port wine stains and other angiodysplasias.

Port wine stains are currently treated by the argon laser with the "point-by-point" technique, or the "painting technique." In both cases, the quality of the results depends greatly on the dermatologist's experience. Furthermore, the first technique is slow, and the second is painful and requires anesthesia. Therefore, we have decided to design a robotized system with the following specifications: easy, fast, non-painful treatment giving a homogeneous and reproducible blanching. The system is made of a handpiece with the scanning mechanism and a control box with the microprocessor. The system is independent of the laser (no electrical connection) and has its own power meter. The deposit of energy was optimized in function of heat diffusion in the skin. Over a 12-month period, 123 patients were treated with the robotized handpiece. The treatment modalities and the results conformed to the above-mentioned specifications. Hypertrophic scars were not reported. Therefore, we think that this system will be an interesting tool for the laser treatment of port wine stains and other cutaneous angiodysplasias.

Adolescent↗

PubMed2001

Computer simulations aimed at structure prediction of supersecondary motifs in proteins.

It is well established that protein structures are more conserved than protein sequences. One-third of all known protein structures can be classified into ten protein folds, which themselves are composed mainly of alpha-helical hairpin, beta hairpin, and betaalphabeta supersecondary structural elements. In this study, we explore the ability of a recent Monte Carlo-based procedure to generate the 3D structures of eight polypeptides that correspond to units of supersecondary structure and three-stranded antiparallel beta sheet. Starting from extended or misfolded compact conformations, all Monte Carlo simulations show significant success in predicting the native topology using a simplified chain representation and an energy model optimized on other structures. Preliminary results on model peptides from nucleotide binding proteins suggest that this simple protein folding model can help clarify the relation between sequence and topology.

Amino Acid Motifs↗

PubMed2005

Protein loop structure prediction with flexible stem geometries.

The structure prediction of loops with flexible stem residues is addressed in this article. While the secondary structure of the stem residues is assumed to be known, the geometry of the protein into which the loop must fit is considered to be unknown in our methodology. As a consequence, the compatibility of the loop with the remainder of the protein is not used as a criterion to reject loop decoys. The loop structure prediction with flexible stems is more difficult than fitting loops into a known protein structure in that a larger conformational space has to be covered. The main focus of the study is to assess the precision of loop structure prediction if no information on the protein geometry is available. The proposed approach is based on (1) dihedral angle sampling, (2) structure optimization by energy minimization with a physically based energy function, (3) clustering, and (4) a comparison of strategies for the selection of loops identified in (3). Steps (1) and (2) have similarities to previous approaches to loop structure prediction with fixed stems. Step (3) is based on a new iterative approach to clustering that is tailored for the loop structure prediction problem with flexible stems. In this new approach, clustering is not only used to identify conformers that are likely to be close to the native structure, but clustering is also employed to identify far-from-native decoys. By discarding these decoys iteratively, the overall quality of the ensemble and the loop structure prediction is improved. Step (4) provides a comparative study of criteria for loop selection based on energy, colony energy, cluster density, and a hybrid criterion introduced here. The proposed method is tested on a large set of 3215 loops from proteins in the Pdb-Select25 set and to 179 loops from proteins from the Casp6 experiment.

Cluster Analysis↗

PubMed2001

Automatic function switching and its usefulness in peptide and protein analysis using direct infusion microspray quadrupole time-of-flight mass spectrometry.

Automatic function switching has been investigated for high-throughput protein identification and sequencing of peptides using direct infusion of tryptic digests on a quadrupole time-of-flight instrument. The increase in speed and the high quality of data make it a favourable technique for tandem mass spectrometry when compared to manual selection of each precursor ion; these advantages are not restricted to combined LC/MS/MS analyses for which the automatic function-switching mode was originally developed. This mode was compared to analyses performed using a slow scan of the quadrupole analyzer with repeated recording of product ion spectra. For the specific purpose of generating product ion data for sequence determination (as opposed to surveying all precursors of a selected product ion), the automatic function-switching mode was, as expected, markedly superior with respect to speed of analysis and quality of data. Furthermore, the automatic function-switching mode provides greater versatility with respect to selection of optimal collision energies.

Alcohol Dehydrogenase↗

PubMedDate not supplied

Imaging of specimens at optimized low and very low energies in scanning electron microscopes.

The modern trend towards low electron energies in scanning electron microscopy (SEM), characterised by lowering the acceleration voltages in low-voltage SEM (LVSEM) or by utilising a retarding-field optical element in low-energy SEM (LESEM), makes the energy range where new contrasts appear accessible. This range is further extended by a scanning low-energy electron microscope (SLEEM) fitted with a cathode lens that achieves nearly constant spatial resolution throughout the energy scale. This enables one to optimise freely the electron beam energy according to the given task. At low energies, there exist classes of image contrast that make particular specimen data visible most effectively or even exclusively within certain energy intervals or at certain energy values. Some contrasts are well understood and can presently be utilised for practical surface examinations, but others have not yet been reliably explained and therefore supplementary experiments are needed.

Journal Article↗

PubMed1996

Structure and energetics of the glucoamylase-isomaltose transition-state complex probed by using modeling and deoxygenated substrates coupled with site-directed mutagenesis.

Molecular recognition, site-directed mutagenesis, and molecular modeling are combined to describe hydrogen bonds important for formation and catalysis of the Aspergillus niger glucomylase-isomaltose complex. This analysis of the energetics of the transition-state complex identified OH-4', -6', and -4 as critical for isomaltose hydrolysis. Side-chains hydrogen bonded to isomaltose OH-4 (reducing end unit, i.e. at glucoamylase binding subsite 2) induced substrate conformation adjustment to optimize binding energy contributed by charged hydrogen bonds to OH-4' and -6' at the non-reducing unit (i.e. at subsite 1). These interactions were evident in the modeled complex of glucoamylase and isomaltose in the preferred trans-gauche conformation. Kinetic analysis demonstrated reductions in kcat of 10(3) to 10(5)-fold for the corresponding deoxy- and O-methyl analogs of isomaltose. Analysis of two mutants at the level of subsite 2, Glu 180-->Gln and Asp 309-->Glu, showed the binding energy for the enzyme-transition state complex, delta delta G, contributed by OH-3 and -4 to be 6-7 kJ mol-1 weaker than with wild-type enzyme. Unexpectedly, however, substitution of isomaltose OH-4' and -6' (at subsite 1) resulted in 10 to 12 kJ mol-1 lower delta delta G++ for both the mutants. Mutation at subsite 2, therefore, strongly perturbed distant transition-state stabilizing interactions. This was confirmed with 4'- and 6'-deoxy analogs of the conformationally biased methyl 6-R-C-methyl-alpha-isomaltoside, readily adopting trans-gauche conformation, that exhibit full delta delta G++ 18 to 20 kJ mol-1 for both mutants and wild-typ-. Glucoamylase, during catalysis, thus seems to induce a change from the predominant solution gauche-gauche conformer to trans-gauche isomaltose. This leads to enhanced binding at subsite 1 in the enzyme transition-state complex.

Aspergillus niger↗

PubMed2000

Stabilization of GroEL minichaperones by core and surface mutations.

We report the crystal structures of two hexa-substituted mutants of a GroEL minichaperone that are more stable than wild-type by 7.0 and 6.1 kcal mol(-1). Their structures imply that the increased stability results from multiple factors including improved hydrophobic packing, optimised hydrogen bonding and favourable structural rearrangements. It is commonly believed that protein core residues are immutable and generally optimized for energy, while on the contrary, surface residues are variable and hence unimportant for stability. But, it is now becoming clear that mutations of both core and surface residues can increase protein stability, and that protein cores are more flexible and thus more tolerant to mutation than expected. Sequence comparison of homologous proteins has provided a way to pinpoint the residues that contribute constructively to stability and to guide the engineering of protein stability. Stabilizing mutations identified by this approach are most frequently located at protein surfaces but with a few found in protein cores. In the latter case, local flexibility in the hydrophobic core is the key factor that allows the energetically favourable burial of larger hydrophobic side-chains without undue energetic penalties from steric clashes.

Amino Acid Substitution↗

PubMed1990

Modeling of protease I collagenolytic enzyme from the fiddler crab Uca pugilator.

Collagenolytic protease I from the fiddler crab Uca pugilator belongs to the serine proteases of the trypsin family. A graphic molecular model was built using information from sequences and X-ray structures of four homologous proteins which were superimposed to define structurally conserved regions. Protease I sequence was aligned, with sequences of the model proteins, without permitting any deletion or insertion in these regions. Elastase alpha-carbon chain was selected as a template molecule. For the structurally variable regions, fragments of the four homologous proteins which were 'closet' in sequence were selected. Intramolecular steric hindrance, that resulted from the substitution of the residues of the templates by protease I residues, was corrected by adjustment of the side-chain conformational angles. The model was then optimized by energy minimization. The primary specificity pocket in the model of collagenolytic protease I predict a substrate preference for both P1 hydrophobic and positively charged residues which is in agreement with the biochemical observations. As soybean trypsin inhibitor (STI) is known to inhibit collagenolytic protease I, a tentative model of the complex was constructed and possibilities of interaction examined.

Amino Acid Sequence↗

PubMed1980

A simple reproducible cell-free system for measuring brain protein synthesis.

A simple, rapid, sensitive, and reproducible cell-free assay system for studying brain protein synthesis is described. This system uses small amounts of brain postmitochondrial supernatant, making it a convenient screening test when only small amounts of tissue are available. It showed over 95% dependence on Mg2+ and on an energy source. Optimal incorporation occurred under the following conditions: Mg2+ 3 mM; ATP, 0.6 mM; GTP, 0.6 mM; high K+, greater than or equal to 25 mM; Low Na+, less than or equal to 15 mM; pH 7.1-7.5. The rate of amino acid incorporation did not vary with leucine concentrations in vitro up to 1 mM, which obviated the need to measure endogenous leucine concentrations.

Adenosine Triphosphate↗

PubMed1999

Constructing the suitable initial configuration of the membrane-protein system in molecular dynamics simulations.

A method for constructing the suitable initial configuration of the membrane-protein system for molecular dynamics (MD) simulations is presented. This method could provide some hydrated initial configurations and help us to determine the best surface area of the system by contracting the surface area and comparing the optimized lowest energy of the system by energy minimization. The gramicidin A (GA) channel in;the fully hydrated dimyristoylphosphatidylcholine (DMPC) bilayer was used as our model. Three configurations with different surface areas were selected and applied for one 400 ps and two 300 ps MD simulations at constant pressure and temperature. All simulations were fairly stable without any constraints. Through analysis of the MD trajectories we found that the system with the best surface area was more stable than the other two systems, whose sizes were changed in the simulations. Further analysis of the bilayer normal length and the order parameters of the lipid alkyl tails indicates that the system with the best surface area shows some characteristics of the L(alpha) phase, while both the smaller and the larger size systems have distinct deviations from the L(alpha) phase that we expect. This illustrates that the correct surface area and the suitable initial configuration have an important influence on the phase of the membrane in the MD simulation. In addition, by comparing the root mean square differences of GA relative to the initial structure and interaction energy between different components of the system for all three systems, we find that the state of the DMPC bilayer has exerted a significant influence on the structure of GA. All these results demonstrate the validity of our method for constructing the initial configuration of the membrane-protein system for MD simulations.

Carbon↗

PubMed2000

Dietary lean red meat and human evolution.

Scientific evidence is accumulating that meat itself is not a risk factor for Western lifestyle diseases such as cardiovascular disease, but rather the risk stems from the excessive fat and particularly saturated fat associated with the meat of modern domesticated animals. In our own studies, we have shown evidence that diets high in lean red meat can actually lower plasma cholesterol, contribute significantly to tissue omega-3 fatty acid and provide a good source of iron, zinc and vitamin B12. A study of human and pre-human diet history shows that for a period of at least 2 million years the human ancestral line had been consuming increasing quantities of meat. During that time, evolutionary selection was in action, adapting our genetic make up and hence our physiological features to a diet high in lean meat. This meat was wild game meat, low in total and saturated fat and relatively rich in polyunsaturated fatty acids (PUFA). The evidence presented in this review looks at various lines of study which indicate the reliance on meat intake as a major energy source by pre-agricultural humans. The distinct fields briefly reviewed include: fossil isotope studies, human gut morphology, human encephalisation and energy requirements, optimal foraging theory, insulin resistance and studies on hunter-gatherer societies. In conclusion, lean meat is a healthy and beneficial component of any well-balanced diet as long as it is fat trimmed and consumed as part of a varied diet.

Adaptation, Biological↗

PubMed2006

Closure of skin incisions by 980-nm diode laser welding.

A 980-nm diode laser is proposed to be an alternative welding laser in dermatology due to its optimal penetration in tissue. An in vivo predosimetry study was done to estimate the optimal laser energy delivery conditions (6 W, 400 ms). Next, in vivo experiments were comparatively performed to examine healing of wounds closed either with suture or laser welding. One-centimeter-long, full-thickness incisions were done on the dorsal side of Wistar rats. Wounds were surgically removed at 1, 4, 7, 14, and 21 days postoperatively. Macroscopic examinations showed that welding had minimal scarring and a fine quality healing. According to histological (hematoxylin and eosin staining) results, change of epidermal thickness and granulation tissue formation through 21 days of healing period showed similarities in both methods. Epidermal thickness of welded wounds decreased from 62.46+/-6.87 microm (first day) to 36.49+/-0.92 microm (21st day) and that of sutured wounds decreased from 62.94+/-13.53 microm (first day) to 37.88+/-7.41 microm (21st day). At day 14, epidermal thickness of sutured wounds (61.20+/-6.60 microm) were higher than welded wounds (49.69+/-6.31 microm) (p<0.05). Besides, granulation values were greater for the sutured wounds but the difference was statistically significant (p<0.05) only for the seventh day (197,190.29+/-.89,554.96 microm(2) for sutured wounds, 138,433.1+/-51,077.17 microm(2) for welded wounds). Those differences indicate a faster recovery with laser welding. It is concluded that tissue welding with a 980-nm diode laser can be a good candidate for tissue welding applications with accelerated and improved healing, but further investigations are in progress for clinical use.

Animals↗

PubMed1995

Low levels of reactive oxygen species as modulators of cell function.

In this paper, we present various arguments supporting the hypothesis that reactive oxygen species (ROS) could be responsible for the modulation of various cellular functions, besides their well known toxic effects. We first review the recent evidence indicating that ROS are able to modulate genome expression through specific and precise mechanisms during cell activation. The role of the nitrogen reactive radicals such as nitric oxide is separately analyzed because of its specific role in the nervous and vascular systems. The action of the other ROS on gene activation will then be reviewed by first looking at their possible involvement in the activation of transcription factors like NF-kappa B. Arguments will then be developed in favor of the implication of the ROS in the cellular effects of PMA, TNF-alpha and other cytokines on the modulation of the genetic expression. Possible mechanisms will be presented for linking the production of the ROS with cell activation. In a general way we postulate that ROS can play a role of secondary messengers in several cell responses to external stimuli. In the second part of the paper, we will examine the long term influence of ROS and their possible roles in cellular aging. Different links exist between ROS and aging and the relationship between them is probably indirect. We propose to consider the effect of ROS as one of the multiple challenges that cells have to face, the cell being considered as a global system which must optimize its energy expenditure for carrying out its basic functions such as turnover, differentiated phenotype functions, multiplication, defense and repair processes. This thermodynamic point of view will help to understand the effect of low ROS stresses, among others, on accelerated aging.

Animals↗