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Raul E Cachau

Publications and source records attributed to Raul E Cachau.

8 recordsLinked to original sources
PubMed2006

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.

Binding Sites↗
PubMed2005

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.

Catalysis↗
PubMed2005

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.

Binding Sites↗
PubMed2005

Molecular structure and internal rotation in 2,3,5,6-tetrafluoroanisole as studied by gas-phase electron diffraction and quantum chemical calculations.

The geometric structure of 2,3,5,6-tetrafluoroanisole and the potential function for internal rotation around the C(sp2)-O bond were determined by gas electron diffraction (GED) and quantum chemical calculations. Analysis of the GED intensities with a static model resulted in near-perpendicular orientation of the O-CH3 bond relative to the benzene plane with a torsional angle around the C(sp2)-O bond of tau(C-O) = 67(15) degrees. With a dynamic model, a wide single-minimum potential for internal rotation around the C(sp2)-O bond with perpendicular orientation of the methoxy group [tau(C-O) = 90 degrees] and a barrier of 2.7 +/- 1.6 kcal/mol at planar orientation [tau(C-O) = 0 degrees] was derived. Calculated potential functions depend strongly on the computational method (HF, MP2, or B3LYP) and converge adequately only if large basis sets are used. The electronic energy curves show internal structure, with local minima appearing because of the interplay between electron delocalization, changes in the hybridization around the oxygen atom, and the attraction between the positively polarized hydrogen atoms in the methyl group and the fluorine atom at the ortho position. The internal structure of the electronic energy curves mostly disappears if zero-point energies and thermal corrections are added. The calculated free energy barrier at 298 K is 2.0 +/- 1.0 kcal/mol, in good agreement with the experimental determination.

Anisoles↗
PubMed2004

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.

Crystallography, X-Ray↗
PubMed2003

Identification of critical residues of an immunodominant region of Echinococcus granulosus antigen B.

Immune evasion strategies often shape the immunogenicity of parasite components. We recently found that the N-terminal extension of the major subunit of Echinococcus granulosus antigen B (AgB), the causative agent of hydatid disease, concentrates the immunoreactive B cell epitopes of the native molecule. The nature of this immunodominance was analyzed using four monoclonal antibodies (mAbs) defining overlapping epitopes in this region of the AgB molecule. The minimal epitope requirements of these mAbs were determined using phage display peptide libraries. The consensus sequences isolated with the mAbs, and alanine replacement analysis with synthetic peptides mapped the relevant molecular contacts within a short stretch corresponding to residues 17-24 of the AgB major subunit. Substitution of two critical residues within this stretch produced a dramatic loss of antigenicity, as determined by using patient sera. The circular dichroism spectra of the antigen, together with the distribution of the contact residues, suggest that this region adopts an amphipathic alpha-helix structure that clusters the contact residues on its polar side. To provide further insight in the interpretation of the structure activity relationships for this immunoreactive region of E. granulosus AgB, we developed a model for the N-terminal extension of the AgB major subunit, which helps to rationalize our data.

Amino Acid Sequence↗
PubMedDate not supplied

Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools.

A B-cell epitope is the three-dimensional structure within an antigen that can be bound to the variable region of an antibody. The prediction of B-cell epitopes is highly desirable for various immunological applications, but has presented a set of unique challenges to the bioinformatics and immunology communities. Improving the accuracy of B-cell epitope prediction methods depends on a community consensus on the data and metrics utilized to develop and evaluate such tools. A workshop, sponsored by the National Institute of Allergy and Infectious Disease (NIAID), was recently held in Washington, DC to discuss the current state of the B-cell epitope prediction field. Many of the currently available tools were surveyed and a set of recommendations was devised to facilitate improvements in the currently existing tools and to expedite future tool development. An underlying theme of the recommendations put forth by the panel is increased collaboration among research groups. By developing common datasets, standardized data formats, and the means with which to consolidate information, we hope to greatly enhance the development of B-cell epitope prediction tools.

Animals↗