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To get mechanistic insight into the DNA strand-exchange reaction of homologous recombination, we solved a filament structure of a human Rad51 protein, combining molecular modeling with experimental data. We build our structure on reported structures for central and N-terminal parts of pure (uncomplexed) Rad51 protein by aid of linear dichroism spectroscopy, providing angular orientations of substituted tyrosine residues of Rad51-dsDNA filaments in solution. The structure, validated by comparison with an electron microscopy density map and results from mutation analysis, is proposed to represent an active solution structure of the nucleo-protein complex. An inhomogeneously stretched double-stranded DNA fitted into the filament emphasizes the strategic positioning of 2 putative DNA-binding loops in a way that allows us speculate about their possibly distinct roles in nucleo-protein filament assembly and DNA strand-exchange reaction. The model suggests that the extension of a single-stranded DNA molecule upon binding of Rad51 is ensured by intercalation of Tyr-232 of the L1 loop, which might act as a docking tool, aligning protein monomers along the DNA strand upon filament assembly. Arg-235, also sitting on L1, is in the right position to make electrostatic contact with the phosphate backbone of the other DNA strand. The L2 loop position and its more ordered compact conformation makes us propose that this loop has another role, as a binding site for an incoming double-stranded DNA. Our filament structure and spectroscopic approach open the possibility of analyzing details along the multistep path of the strand-exchange reaction. homologous recombination | HsRad51

We describe studies in molecular profiling and biological pathway analysis that use sparse latent factor and regression models for microarray gene expression data. We discuss breast cancer applications and key aspects of the modeling and computational methodology. Our case studies aim to investigate and characterize heterogeneity of structure related to specific oncogenic pathways, as well as links between aggregate patterns in gene expression profiles and clinical biomarkers. Based on the metaphor of statistically derived 'factors' as representing biological 'subpathway' structure, we explore the decomposition of fitted sparse factor models into pathway subcomponents and investigate how these components overlay multiple aspects of known biological activity. Our methodology is based on sparsity modeling of multivariate regression. ANOVA. and latent factor models, as well as a class of models that combines all components. Hierarchical sparsity priors address questions of dimension reduction and multiple comparisons, as well as scalability of the methodology. The models include practically relevant non-Gaussian/nonparametric components for latent structure, underlying often quite complex non-Gaussianity in multivariate expression patterns. Model search and fitting are addressed through stochastic simulation and evolutionary stochastic search methods that are exemplified in the oncogenic pathway studies. Supplementary supporting material provides more details of the applications, as well as examples of the use of freely available software tools for implementing the methodology. KEY WORDS: Biological pathways: Breast cancer genomics: Decomposing gene expression patterns; Dirichlet process factor model; Evolutionary stochastic search: Factor regression: Gene expression analysis: Gene expression profiling: Gene networks: Non-Gaussian multivariate analysis: Sparse factor models: Sparsity priors.

One of the challenges faced in malarial control is the acquisition of insecticide resistance that has developed in mosquitoes that are vectors for this disease. Anopheles gambiae, which has been the major mosquito vector of the malaria parasite Plasmodium falciparum in Africa, has over the years developed resistance to insecticides including dieldrin, 1,1-bis(p-chlorophenyl)-2,2,2-trichloroethane (DDT), and pyrethroids. Previous microarray studies using fragments of 230 An. gambiae genes identified five P450 loci, including CYP4C27, CYP4H15, CYP6Z1, CYP6Z2, and CYP12F1, that showed significantly higher expression in the DDT-resistant ZAN/U strain compared with the DDT-susceptible Kisumu strain. To predict whether either of the CYP6Z1 and CYP6Z2 proteins might potentially metabolize DDT, we generated and compared molecular models of these two proteins with and without DDT docked in their catalytic sites. This comparison indicated that, although these two CYP6Z proteins share high sequence identity, their metabolic profiles were likely to differ dramatically from the larger catalytic site of CYP6Z1, potentially involved in DDT metabolism, and the more constrained catalytic site of CYP6Z2, not likely to metabolize DDT. Heterologous expressions of these proteins have corroborated these predictions: only CYP6Z1 is capable of metabolizing DDT. Overlays of these models indicate that slight differences in the backbone of SRS1 and variations of side chains in SRS2 and SRS4 account for the significant differences in their catalytic site volumes and DDT-metabolic capacities. These data identify CYP6Z1 as one important target for inhibitor design aimed at inactivating insecticide-metabolizing P450s in natural populations of this malarial mosquito. cytochrome P450 monooxygenases | insecticides | plant allelochemicals

The molecular modeling study of an human angiotensin-I converting enzyme (ACE)-peptide substrate complex with gonadotropin-releasing hormone (GnRH) which is cleaved releasing both the protected N[H.sub.2]- and COOH-terminal tripeptides is described.

A simple, novel and generally applicable method to demonstrate structure-activity associations of a group of biologically interesting compounds in relation to receptor binding is described. This method is useful for undergraduates and graduate students in medicinal chemistry and computer modeling programs.

G protein-coupled receptors (GPCRs) belonging to class A contain several highly conserved (>90%) amino acids in their transmembrane helices. Results of mutational studies of these highly conserved residues suggest a common mechanism for locking GPCRs in an inactive conformation and for their subsequent activation upon ligand binding. Recently, a second set of sites in the transmembrane helices has been identified in which amino acids with small side chains, such as Gly, Ala, Ser, Thr, and Cys, are highly conserved (>90%) when considered as a group. These group-conserved residues have not been recognized as having essential structural or functional roles. To determine the role of group-conserved residues in the [[beta].sub.2]-adrenergic receptor ([[beta].sub.2]-AR), amino acid replacements guided by molecular modeling were carried out at key positions in transmembrane helices H2-H4. The most significant changes in receptor expression and activity were observed upon replacement of the amino acids Ser-161 and Ser-165 in H4. Substitution at these sites by larger residues lowered the expression and activity of the receptor but did not affect specific binding to the antagonist ligand dihydroalprenolol. A second site mutation, V114A, rescued the low expression of the $165V mutant. Substitution of other group-conserved residues in H2-H4 by larger amino acids lowered receptor activity in the order Ala-128, Ala-76, Ser-120, and Ala-78. Together these data provide comprehensive analysis of group-conserved residues in a class A GPCR and allow insights into the roles of these residues in GPCR structure and function. rhodopsin | G protein-coupled receptors | helix packing | site-directed mutagenesis | molecular modeling

The rugged folding-energy landscapes of RNAs often display many competing minima. How do RNAs discriminate among competing conformations in their search for the native state? By using optical tweezers, we show that the folding-energy landscape can be manipulated to control the fate of an RNA: individual RNA molecules can be induced into either native or misfolding pathways by modulating the relaxation rate of applied force and even be redirected during the folding process to switch from misfolding to native folding pathways. Controlling folding pathways at the single-molecule level provides a way to survey the manifold of folding trajectories and intermediates, a capability that previously was available only to theoretical studies. mechanical force | misfolding | optical tweezers | RNA folding | single molecule

The intrinsic chemical reaction of adenosine triphosphate (ATP) hydrolysis catalyzed by myosin is modeled by using a combined quantum mechanics and molecular mechanics (QM/MM) methodology that achieves a near ab initio representation of the entire model. Starting with coordinates derived from the heavy atoms of the crystal structure (Protein Data Bank ID code 1VOM) in which myosin is bound to the ATP analog ADP x V[O.sub.4.sup.-], a minimum-energy path is found for the transformation ATP + [H.sub.2]O [right arrow] ADP + [P.sub.i] that is characterized by two distinct events: (i) a low activation-energy cleavage of the [P.sub.[gamma]]--[O.sub.[beta][gamma]] bond and separation of the [gamma]-phosphate from ADP and (ii) the formation of the inorganic phosphate as a consequence of proton transfers mediated by two water molecules and assisted by the Glu-459-Arg-238 salt bridge of the protein. The minimum-energy model of the enzyme-substrate complex features a stable hydrogen-bonding network in which the lytic water is positioned favorably for a nucleophilic attack of the ATP [gamma]-phosphate and for the transfer of a proton to stably bound second water. In addition, the [P.sub.[gamma]]--[O.sub.[beta][gamma]] bond has become significantly longer than in the unbound state of the ATP and thus is predisposed to cleavage. The modeled transformation is viewed as the part of the overall hydrolysis reaction occurring in the closed enzyme pocket after ATP is bound tightly to myosin and before conformational changes preceding release of inorganic phosphate. ATP hydrolysis | enzymatic catalysis | energy profile | quantum mechanics and molecular mechanics simulations

The De novo molecule building software, HostDesigner, is interfaced with molecular mechanics software, GMMX, providing a tool for generating and screening millions of potential structures, in a computational approach to the deliberate design of improved host structures. The efficacy of this method is illustrated with a search for bisurea podands that are structurally organized for complexion with tetrahedral oxoanions.

The torsional potential energy surface of a chemical compounds, the accessible conformations at a specified temperature and the transition states that connect these confirmations establishes many chemical properties such as dynamic behavior, reactivity and biological activity. A conformational search of n-pentane is presented using computational excrement designed for advance undergraduate students and beginning graduate students.

Byline: Francisco M. Fernandez (1), Eduardo A. Castro (1) Keywords: bond stretching; bond bending; molecular interactions; potential-energy functions; molecular mechanics; mathematical relationships Abstract: We analyse recently proposed connection formulas between potential-energy functions for bond stretching, bond bending and molecular interactions, and propose more convenient and practical expressions. For example, our mathematical relationships between Morse and Murrel--Mottram potential parameters yield much closer agreement between such potential-energy functions. Author Affiliation: (1) INIFTA (Conicet, UNL P), Diag. 113 y 64 (S/N), Sucursal 4, Casilla de Correo 16, 1900, La Plata, Argentina Article History: Registration Date: 07/10/2004

Large dendrimers are synthesized using a tripodal branching unit that multiplies the branch number by 3 at each generation up to a diameter of 13 nm. Thus, the feasibility of the synthesis of giant dendrimers, far beyond the dense-packing limit opens a new scope of supramolecular chemistry involving dendritic structures.

The unique properties of DNA make it a fundamental building block in the fields of supramolecular chemistry, nanotechnology, nano-circuits, molecular switches, molecular devices, and molecular computing. In our recently introduced autonomous molecular automaton, DNA molecules serve as input, output, and software, and the hardware consists of DNA restriction and ligation enzymes using ATP as fuel. In addition to information, DNA stores energy, available on hybridization of complementary strands or hydrolysis of its phosphodiester backbone. Here we show that a single DNA molecule can provide both the input data and all of the necessary fuel for a molecular automaton. Each computational step of the automaton consists of a reversible software molecule/input molecule hybridization followed by an irreversible software-directed cleavage of the input molecule, which drives the computation forward by increasing entropy and releasing heat. The cleavage uses a hitherto unknown capability of the restriction enzyme Fokl, which serves as the hardware, to operate on a noncovalent software/input hybrid. In the previous automaton, software/input ligation consumed one software molecule and two ATP molecules per step. As ligation is not performed in this automaton, a fixed amount of software and hardware molecules can, in principle, process any input molecule of any length without external energy supply. Our experiments demonstrate 3 x [10.sup.12] automata per [micro]l performing 6.6 x [10.sup.10] transitions per second per [micro]l with transition fidelity of 99.9%, dissipating about 5 x [10.sup.-9] W/ [micro]l as heat at ambient temperature.

New molecules can function as wires, switches and logic gates, as is discussed in this presentation of molecular electronics. Chemistry offers an entirely new, bottom-up approach to the problems of constantly increasing the number of electronic components that can be crammed onto a computer chip by making the components smaller. The processing power of the best available computer has doubled roughly every 18 months. That process might soon reach a physical limit. New approaches may be needed.

Shifts of absorption of azulene derivatives using molecular modeling and ZINDCO CI calculations of UV-Vis spectra are presented. This activity enables students to qualitatively predict whether a substituent will cause a blue or red shift of the absorption peaks of azulene and to verify their predictions using computational chemistry.

The effectiveness of using Darling or Maruzen molecular models in teaching biochemical structures is evaluated. Findings show that using these models and transparent ziplock plastic bags lead to students giving more sophisticated answers on their examination compared to the years when such activities were not implemented. Examples of active-learning strategies are also given.

The article explains the synthesis, as well as the supramolecular and molecular recognition properties of the various different melamine-bridged bis(porphyrin-[Zn.sup.II]) receptors. The steric impact of the bulky substituents at the periphery is shown to act as the major factor that affects the geometry of these compounds.

The ESI-MS, NMR, fluorescence, and molecular modeling techniques were used to study the binding between a pseudopeptidic macrocyclic naphthalenophane and different N-protected amino acid derivatives. The results obtained provide insight into the structure of the supramolecular complexes in which the interactions with the naphthyl ring of the receptor play a fundamental role in the strength and selectivity of the molecular recognition event.

An approach to the integration of molecular modeling into a curriculum for organic chemistry laboratory is described. The strategy highlights the use of molecular modeling as an efficient and readily available mechanism for exploring reactivity and structure and studying the outcome of organic reactions. Students who use this approach will have a better understanding of reactivity, bonding, and structure.

The application of photoaffinity labeling and molecular modeling to gain insight into the structural basis of binding a natural peptide ligand to a family A G protein-coupled receptor, the type 1 cholecystokinin receptor is demonstrated. The resultant agonist ligand-occupied receptor models fully accomodated all the existing experimental data and represent the best refined models of a peptide hormone receptor family.

The isothermal titration calorimetry is used to demonstrate the binding affinities of the nSH3 domain in the physiological range to all four sites containing PX[psi]PXR motifs, designated S1, S2, S3, and S4, and the cSH3 domain binding at the S1 site. The results obtained from site-directed mutagenesis suggested that the two additional arginine residues flanking the PX[psi]PXR motif at the S1 site contributed to free energy of binding via the formation of salt bridges with specific acidic residues in SH3 domains.

Single crystal X-ray diffraction, NMR and molecular modeling are used for examining the formation and high stability of the H-bond-driven supramolecular architectures of the syn and anti isomers of the dioxime of bicyclo[3.3.1]nonane-3,7-dione. The self-assembly of the achiral syn isomer into a cyclic trimer and of the chiral anti isomer into homochiral cyclic dimers is seen.

A combination of solid-state nuclear magnetic resonance (SSNMR) and X-ray fiber diffraction studies is employed to explain the molecular architectures of the fibrils that are formed by the amyloidogenic segment of a medin. The various constraints that are imposed on the distances between the atomic sites in these fibrils are also discussed.

The results from experimental and computational studies, which explain the nature of the hydrogen bonding between water and a series of organic liquids, are presented. The findings provide insight into the molecular processes at aqueous interfaces and also allow testing the validity of various molecular models commonly used to describe molecular structure and interactions at water-oil interfaces.

A forensic chemistry exercise in which model compounds are used to stimulate the behavior of various drugs in a series of chemical tests is described. The exercise involves the structural study of chlorpromazine with three V-like ring formations and deformation of approximately 50 degrees from planarity.

A combination of molecular modeling and site directed mutagenesis is employed for explaining the design of the drug-resistant alleles of type-III phosphatidylinositol 4-kinases (PI4Ks).

New pyrroloisoquinoline-based enantiopure tetrapeptides are synthesized and their conformational features are studied by using molecular-modeling methods. The results have shown the presence of a reverse turn in both structures and also that a type II' [beta]-turn is stabilized in tetrapeptide mimic.

The changes that have taken place in the organic chemistry laboratory course since 1980s are reviewed with reference to the quantity and diversity of discovery-based experiments available to date. The data illustrates that significant progress is towards accomplishing dramatic changes such as the almost universal adoption of microscale, the use of spectroscopy, and the incorporation of molecular modeling.

Experiments suited for the undergraduate instructional laboratory in which the heats of formation of several aliphatic and aromatic compounds are calculated, are described. The experiments could be used to introduce students to commercially available computational chemistry and its thermodynamics, while assess and compare the energy content of high explosives.

The effects of temperature and salt concentration on the structural stability of the human Lymphotactin (hLtn) are investigated using molecular dynamics simulations with explicit solvent molecules and salt ions. The distribution of ions near the protein surface and the stability of various structural patterns exhibit temperature dependence on the local sequence and structure, indicating an important role for solvent and salt screening in stabilizing the canonical chemokine fold of hLtn.

Computational advances together with the availability of user-friendly software have promoted the development of simple computer-assisted molecular-modeling experiments for bioactive molecules. The students draw biologically-active molecules, analyze their conformations, compare the conformations with different molecules, match the preferred conformations of the Ach with the proposed structure of the actylcholine receptor and compare the results with literature data. .

Cytotoxicity-guided fractionation of the crude methanol extract of a marine sponge Ircinia sp., yields tedanolide C, an 18-membered ring that exhibits potent cyclotoxicity against HCT-116 cells in vitro. The structure is solved by interpreting NMR and MS data, and the relative stereochemistry is determined from a combination of homo- and heteronuclear coupling constants in conjunction with molecular modeling.

A new stereoselective route to endo, exo-2,6-diarlyfurofuranones has been developed using Mn(III)-mediated intramolecular cyclopropanation and C-H insertation reactions as key C-C bond forming steps.

The crystal structure of Cu2[o-Br-C6H3(CO2)2]2(H2O)2.(DMF)8-(H2O)2 termed as MOF-101 is deliberately designed to have an NbO framework. Molecular building blocks can be directed by the geometry links to reticulate into target frameworks by design.

Researchers at Nanoscale Science Dept., Max Plank Institute for Solid State Research, Stuttgart, Germany, are using quantum point contact microscopy (QPCM), which uses single atoms at the contact between tip [...]

A specific disruption of DNA-protein or protein-protein interaction is required to inhibit the function of a transcription factor. Diversity-oriented synthesis (DOS) could be a source of candidate antagonist of these interactions. To test this possibility, a small molecule microarray-based screen aimed at identifying the DOS derived small molecules that directly bind and modulate the transcriptional activity of Hap3p was devised.

Signal processing is discussed in terms of combining mechanical, pneumatic and other devices, such as molecular-sized switches.