Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling.

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.VO(4)(-), a minimum-energy path is found for the transformation ATP + H(2)O --> ADP + P(i) that is characterized by two distinct events: (i) a low activation-energy cleavage of the P(gamma) O(betagamma) 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(gamma) O(betagamma) 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.

Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations.

The hydrolysis reaction of guanosine triphosphate (GTP) by p21(ras) (Ras) has been modeled by using the ab initio type quantum mechanical-molecular mechanical simulations. Initial geometry configurations have been prompted by atomic coordinates of the crystal structure (PDBID: 1QRA) corresponding to the prehydrolysis state of Ras in complex with GTP. Multiple searches of minimum energy geometry configurations consistent with the hydrogen bond networks have been performed, resulting in a series of stationary points on the potential energy surface for reaction intermediates and transition states. It is shown that the minimum energy reaction path is consistent with an assumption of a two-step mechanism of GTP hydrolysis. At the first stage, a unified action of the nearest residues of Ras and the nearest water molecules results in a substantial spatial separation of the gamma-phosphate group of GTP from the rest of the molecule (GDP). This phase of hydrolysis process proceeds through the low barrier (16.7 kcal/mol) transition state TS1. At the second stage, the inorganic phosphate is formed in consequence of proton transfers mediated by two water molecules and assisted by the Gln61 residue from Ras. The highest transition state at this segment, TS3, is estimated to have an energy 7.5 kcal/mol above the enzyme-substrate complex. The results of simulations are compared to the previous findings for the GTP hydrolysis in the Ras-GAP (p21(ras)-p120(GAP)) protein complex. Conclusions of the modeling lead to a better understanding of the anticatalytic effect of cancer causing mutation of Gln61 from Ras, which has been debated in recent years.

Increased serum levels of complement C3a anaphylatoxin indicate the presence of colorectal tumors.

BACKGROUND & AIMS: Late diagnosis of colorectal carcinoma results in a significant reduction of average survival times. Yet despite screening programs, about 70% of tumors are detected at advanced stages (International Union Against Cancer stages III/IV). We explored whether detection of malignant disease would be possible through identification of tumor-specific protein biomarkers in serum samples. METHODS: A discovery set of sera from patients with colorectal malignancy (n = 58) and healthy control individuals (n = 32) were screened for potential differences using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry. Candidate proteins were identified and their expression levels were validated in independent sample sets using a specific immunoassay (enzyme-linked immunosorbent assay). RESULTS: By using class comparison and custom-developed algorithms we identified several m/z values that were expressed differentially between the malignant samples and the healthy controls of the discovery set. Characterization of the most prominent m/z values revealed a member of the complement system, the stable form of C3a anaphylatoxin (ie, C3a-desArg). Based on a specific enzyme-linked immunosorbent assay, serum levels of complement C3a-desArg predicted the presence of colorectal malignancy in a blinded validation set (n = 59) with a sensitivity of 96.8% and a specificity of 96.2%. Increased serum levels were also detected in 86.1% of independently collected sera from patients with colorectal adenomas (n = 36), whereas only 5.6% were classified as normal. CONCLUSIONS: Complement C3a-desArg is present at significantly higher levels in serum from patients with colorectal adenomas (P < .0001) and carcinomas (P < .0001) than in healthy individuals. This suggests that quantification of C3a-desArg levels could ameliorate existing screening tests for colorectal cancer.

Quantum chemical modeling of reaction mechanism for 2-oxoglutarate dependent enzymes: effect of substitution of iron by nickel and cobalt.

Enzymatic hydroxylation reactions carried out by 2-oxoglutarate (2OG) dependent iron-containing oxygenases were recently implicated in oxygen sensing. In addition to oxygen depletion, two metals, cobalt and nickel, are capable of inducing hypoxic stress in cells by inhibiting oxygenase activity. Two possible scenarios have been proposed for the explanation of the hypoxic effects of cobalt and nickel: oxidation of enzyme-bound iron following cobalt or nickel exposure, and substitution of iron by cobalt or nickel. Here, by using density functional theory calculations, we modeled the reaction route from the reaction components to the high-spin metal-oxide intermediate in the activation of oxygen molecule by 2OG-dependent enzymes for three metal ions Fe(II), Ni(II), and Co(II) in the active site. An initial molecular model was constructed based on the crystal structure of iron-containing asparaginyl hydroxylase (FIH-1). Nickel- and cobalt-containing enzymes were modeled by a consequent replacement of the iron in the active center. The energy profiles connecting stationary points on the potential surfaces were computed by using the intrinsic reaction coordinate (IRC) technique from the located transition states. The results of calculations show that the substitution of iron by nickel or cobalt modifies the reaction energy profile; however, qualitatively, the reaction mechanism remains essentially the same. Thus, we would postulate that if the iron ion in the active site were substitutable by nickel and/or cobalt ions enzyme activity would be considerably altered due to high activation barriers.

Electronic Excitations of the Chromophore from the Fluorescent Protein asFP595 in Solutions.

We present the results of modeling spectral properties of the chromophore, 2-acetyl-4-(p-hydroxybenzylidene)-1-methyl-5-imidazolone (AHBMI), from the newly discovered fluorescent protein asFP595 in different solvents and compare computational and recent experimental data. The time-dependent density functional theory (TDDFT) method is used to estimate positions of spectral bands with large oscillator strengths for vertical transitions to excited states following geometry optimizations of chromophore coordinates in vacuo and in solutions. The performance of different TDDFT functionals in computing excitations for a simpler chromophore from the green fluorescent protein was tested at the preliminary stage. Properties of various protonation states (neutral, anionic, zwitterionic) for the cis and trans conformations of AHBMI are compared. By using the polarizable continuum model, the following solvents have been considered for AHBMI: water, ethanol, acetonitrile, and dimethyl sulfoxide. It is shown that the bands found experimentally in aqueous solution refer to the cis neutral and cis anionic (or trans zwitterionic) conformations. The computed band positions deviate from experimental ones in water by no more than 35 nm (0.23 eV). In accord with experimental studies, the band shifts in different solvents do not show correlation with the dielectric constant or dipole moment; however, the computed values of the shifts are much smaller than those measured experimentally for the ionic species.

Computational study of a transition state analog of phosphoryl transfer in the Ras-RasGAP complex: AlF(x) versus MgF3-.

The structures of the complexes between Ras*GDP bound to RasGAP in the presence of three probable gamma-phosphate analogs (AlF3, AlF4- and MgF3-) for the transition state (TS) of the hydrolysis of guanosine triphosphate (GTP) by the Ras-RasGAP enzymes have been modeled by quantum mechanical-molecular mechanical (QM/MM) calculations. These simulations contribute to the dispute on the nature of the TS in the hydrolysis reaction, since medium resolution X-ray crystallography cannot discern among stereochemically similar isoelectronic species (e.g., AlF3 or MgF3-). The optimized geometry for each structure has been found starting from experimental coordinates of one of them (PDBID: 1WQ1). Direct comparison of the experimental and computed geometry configurations in the immediate vicinity of the active site suggests that MgF3- is the most likely candidate for the phosphate analog in the experimental structure.

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID).

BACKGROUND: We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. The original version of GoMiner was oriented toward visualization and interpretation of the results from a single microarray (or other high-throughput experimental platform), using a graphical user interface. Although that version can be used to examine the results from a number of microarrays one at a time, that is a rather tedious task, and original GoMiner includes no apparatus for obtaining a global picture of results from an experiment that consists of multiple microarrays. We wanted to provide a computational resource that automates the analysis of multiple microarrays and then integrates the results across all of them in useful exportable output files and visualizations. RESULTS: We now introduce a new tool, High-Throughput GoMiner, that has those capabilities and a number of others: It (i) efficiently performs the computationally-intensive task of automated batch processing of an arbitrary number of microarrays, (ii) produces a human-or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories, (iii) integrates the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories, (iv) provides a fast form of 'false discovery rate' multiple comparisons calculation, and (v) provides annotations and visualizations for relating transcription factor binding sites to genes and GO categories. CONCLUSION: High-Throughput GoMiner achieves the desired goal of providing a computational resource that automates the analysis of multiple microarrays and integrates results across all of the microarrays. For illustration, we show an application of this new tool to the interpretation of altered gene expression patterns in Common Variable Immune Deficiency (CVID). High-Throughput GoMiner will be useful in a wide range of applications, including the study of time-courses, evaluation of multiple drug treatments, comparison of multiple gene knock-outs or knock-downs, and screening of large numbers of chemical derivatives generated from a promising lead compound.

QM/MM modeling the Ras-GAP catalyzed hydrolysis of guanosine triphosphate.

The mechanism of the hydrolysis reaction of guanosine triphosphate (GTP) by the protein complex Ras-GAP (p21(ras) - p120(GAP)) has been modeled by the quantum mechanical-molecular mechanical (QM/MM) and ab initio quantum calculations. Initial geometry configurations have been prompted by atomic coordinates of a structural analog (PDBID:1WQ1). It is shown that the minimum energy reaction path is consistent with an assumption of two-step chemical transformations. At the first stage, a unified motion of Arg789 of GAP, Gln61, Thr35 of Ras, and the lytic water molecule results in a substantial spatial separation of the gamma-phosphate group of GTP from the rest of the molecule (GDP). This phase of hydrolysis process proceeds through the low-barrier transition state TS1. At the second stage, Gln61 abstracts and releases protons within the subsystem including Gln61, the lytic water molecule and the gamma-phosphate group of GTP through the corresponding transition state TS2. Direct quantum calculations show that, in this particular environment, the reaction GTP + H(2)O --> GDP + H(2)PO(4) (-) can proceed with reasonable activation barriers of less than 15 kcal/mol at every stage. This conclusion leads to a better understanding of the anticatalytic effect of cancer-causing mutations of Ras, which has been debated in recent years.

(salen)MnIII compounds as nonpeptidyl mimics of catalase. Mechanism-based tuning of catalase activity: a theoretical study.

We present the results of the first theoretical investigation of salen-manganese complexes as synthetic catalytic scavengers of hydrogen peroxide molecules that mimic catalase enzymes. Catalase mimics can be used as therapeutic agents against oxidative stress in treatment of many diseases, including Alzheimer's disease, stroke, heart disease, aging, and cancer. A ping-pong mechanism approach has been considered to describe the H2O2 dismutation reaction. The real compounds reacting with a peroxide molecule were utilized in our BP density functional calculations to avoid uncertainties connected with using incomplete models. Part I of the dismutation reaction-converting a peroxide molecule into a water molecule with simultaneous oxidation of the metal atom of the catalyst-can be done quite effectively at the Mn catalytic center. To act as catalytic scavengers of hydrogen peroxide, the oxomanganese salen complexes have to be deoxidized during part II of the dismutation reaction. It has been shown that there are two possible reaction routes for the second part of the dismutation reaction: the top and the side substrate approach routes. Our results suggest that the catalyst could be at least temporarily deactivated (poisoned) in the side approach reaction route due to the formation of a kinetically stable intermediate. Overall, the side approach reaction route for the catalyst recovery is the bottleneck for the whole dismutation process. On the basis of the detailed knowledge of the mode of action of the (salen)MnIII catalase mimics, we suggest and rationalize structural changes of the catalyst that should lead to better therapeutic properties. The available experimental data support our conclusions. Our findings on the reaction dismutation mechanism could be the starting point for further improvement of salen-manganese complexes as synthetic catalytic scavengers of reactive oxygen species.

Quantum chemical modeling of the GTP hydrolysis by the RAS-GAP protein complex.

We present results of the modeling for the hydrolysis reaction of guanosine triphosphate (GTP) in the RAS-GAP protein complex using essentially ab initio quantum chemistry methods. One of the approaches considers a supermolecular cluster composed of 150 atoms at a consistent quantum level. Another is a hybrid QM/MM method based on the effective fragment potential technique, which describes interactions between quantum and molecular mechanical subsystems at the ab initio level of the theory. Our results show that the GTP hydrolysis in the RAS-GAP protein complex can be modeled by a substrate-assisted catalytic mechanism. We can locate a configuration on the top of the barrier corresponding to the transition state of the hydrolysis reaction such that the straightforward descents from this point lead either to reactants GTP+H(2)O or to products guanosine diphosphate (GDP)+H(2)PO(4)(-). However, in all calculations such a single-step process is characterized by an activation barrier that is too high. Another possibility is a two-step reaction consistent with formation of an intermediate. Here the Pgamma-O(Pbeta) bond is already broken, but the lytic water molecule is still in the pre-reactive state. We present arguments favoring the assumption that the first step of the GTP hydrolysis reaction in the RAS-GAP protein complex may be assigned to the breaking of the Pgamma-O(Pbeta) bond prior to the creation of the inorganic phosphate.

(Salen)Mn-catalyzed epoxidation of alkenes: a two-zone process with different spin-state channels as suggested by DFT study.

[structure: see text] A novel (two-zone process with different spin-state channels) mechanistic picture for the Jacobsen-Katsuki reaction is presented that provides insight into the still elusive understanding of the epoxidation mechanism. For the first time, we show that the salen moiety of the catalyst can be explicitly involved in the epoxidation process.

Theoretical studies on the hydrolysis of mono-phosphate and tri-phosphate in gas phase and aqueous solution.

Phosphate hydrolysis by GTPases plays an important role as a molecular switch in signal transduction and as an initiator of many other biological processes. Despite the centrality of this ubiquitous reaction, the mechanism is still poorly understood. As a first step to understand the mechanisms of this process, the nonenzymatic hydrolysis of mono-phosphate and tri-phosphate esters were systematically studied in gas phase and aqueous solution using hybrid density functional methods. The dielectric effect of the environment on the energetics of these processes was also explored. Theoretical results show that for mono-phosphate ester, the dissociative pathway is much more favorable than the associative pathway. However, the reaction barriers for the dissociative and associative pathways of tri-phosphate hydrolysis are very close in aqueous solution, though the dissociative pathway is more favorable in the gas phase. High dielectric solvents, such as water, significantly lower the activation barrier of the associative pathway due to the greater solvation energy of the associative transition states than that of the reactant complex. By contrast, the barrier of the dissociative pathway, with respect to the gas phase, is less sensitive to the surrounding dielectric. In the associative hydrolysis pathway of the tri-phosphate ester, negative charge is transferred from the gamma-phosphate to beta-phosphate through the bridging ester oxygen and results in Pgamma-O bond dissociation. No analogous charge transfer was observed in the dissociative pathway, where Pgamma-O bond dissociation resulted from proton transfer from the gamma-phosphate to the bridge oxygen. Finally, the active participation of local water molecules can significantly lower the activation energy of the dissociative pathway for both mono-phosphate and tri-phosphate.

An exhaustive DNA micro-satellite map of the human genome using high performance computing.

The current pace of the generation of sequence data requires the development of software tools that can rapidly provide full annotation of the data. We have developed a new method for rapid sequence comparison using the exact match algorithm without repeat masking. As a demonstration, we have identified all perfect simple tandem repeats (STR) within the draft sequence of the human genome. The STR elements (chromosome, position, length and repeat subunit) have been placed into a relational database. Repeat flanking sequence is also publicly accessible at http://grid.abcc.ncifcrf.gov. To illustrate the utility of this complete set of STR elements, we documented the increased density of potentially polymorphic markers throughout the genome. The new STR markers may be useful in disease association studies because so many STR elements manifest multiallelic polymorphism. Also, because triplet repeat expansions are important for human disease etiology, we identified trinucleotide repeats that exist within exons of known genes. This resulted in a list that includes all 14 genes known to undergo polynucleotide expansion, and 48 additional candidates. Several of these are non-polyglutamine triplet repeats. Other examinations of the STR database demonstrated repeats spanning splice junctions and identified SNPs within repeat elements.

The use of urine proteomic and metabonomic patterns for the diagnosis of interstitial cystitis and bacterial cystitis.

The advent of systems biology approaches that have stemmed from the sequencing of the human genome has led to the search for new methods to diagnose diseases. While much effort has been focused on the identification of disease-specific biomarkers, recent efforts are underway toward the use of proteomic and metabonomic patterns to indicate disease. We have developed and contrasted the use of both proteomic and metabonomic patterns in urine for the detection of interstitial cystitis (IC). The methodology relies on advanced bioinformatics to scrutinize information contained within mass spectrometry (MS) and high-resolution proton nuclear magnetic resonance (1H-NMR) spectral patterns to distinguish IC-affected from non-affected individuals as well as those suffering from bacterial cystitis (BC). We have applied a novel pattern recognition tool that employs an unsupervised system (self-organizing-type cluster mapping) as a fitness test for a supervised system (a genetic algorithm). With this approach, a training set comprised of mass spectra and 1H-NMR spectra from urine derived from either unaffected individuals or patients with IC is employed so that the most fit combination of relative, normalized intensity features defined at precise m/z or chemical shift values plotted in n-space can reliably distinguish the cohorts used in training. Using this bioinformatic approach, we were able to discriminate spectral patterns associated with IC-affected, BC-affected, and unaffected patients with a success rate of approximately 84%.

De novo structural prediction of transition metal complexes: application to technetium.

De novo structural prediction of transition metal complexes is investigated. Technetium complexes are chosen given their importance in medical imaging and nuclear waste remediation and for the chemical diversity they display. A new conformational searching algorithm (LIGB) for transition metals is described that allows one to search for different conformational and geometric isomers within a single simulation. In the preponderance of cases, both conformational searching techniques (LIGB and high-temperature molecular dynamics/simulated annealing) provide comparable results, while LIGB is superior for macrocyclic complexes. A genetic algorithm-optimized PM3(tm) parametrization for Tc is compared with the standard implementation and found to yield a significant improvement in predictive ability for the most prevalent Tc structural motifs. The utility of a coupled molecular mechanics-semiempirical quantum mechanics protocol is demonstrated for very rapid, efficient, and effective de novo prediction of transition metal complex geometries.