Three-dimensional structure of ribonuclease T-1 complexed with an isosteric phosphonate substrate analogue of GpU: Alternate substrate binding modes and catalysis

The X-ray crystal structure of a complex between ribonuclease T-1 and guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2.0 Angstrom resolution. This Ligand is an isosteric analogue of the minimal RNA substrate, guanylyl(3'-5')uridine (GpU), where a methylene is substituted for the uridine 5'-oxygen atom. Two protein molecules are part of the asymmetric unit and both have a GpcU bound at the active site in the same manner. The protein-protein interface reveals an extended aromatic stack involving both guanines and three enzyme phenolic groups. A third GpcU has its guanine moiety stacked on His92 at the active site on enzyme molecule A and interacts with GpcU on molecule B in a neighboring unit via hydrogen bonding between uridine ribose 2'- and 3'-OH groups. None of the uridine moieties of the three GpcU molecules in the asymmetric unit interacts directly with the protein. GpcU-active-site interactions involve extensive hydrogen bonding of the guanine moiety at the primary recognition site and of the guanosine 2'-hydroxyl group with His40 and Glu58. on the other hand, the phosphonate group is weakly bound only by a single hydrogen bond with Tyr38, unlike ligand phosphate groups of other substrate analogues and 3'-GMP, which hydrogen-bonded with three additional active-site residues. Hydrogen bonding of the guanylyl 2'-OH group and the phosphonate moiety is essentially the same as that recently observed for a novel structure of a RNase T-1-3'-GMP complex obtained immediately after in situ hydrolysis of exo-(S-p)-guanosine 2',3'-cyclophosphorothioate [Zegers et al. (1998) Nature Struct. Biol. 5, 280-283]. It is likely that GpcU at the active site represents a nonproductive binding mode for GpU [:Steyaert, J., and Engleborghs (1995) fur. J. Biochem. 233, 140-144]. The results suggest that the active site of ribonuclease T-1 is adapted for optimal tight binding of both the guanylyl 2'-OH and phosphate groups (of GpU) only in the transition state for catalytic transesterification, which is stabilized by adjacent binding of the leaving nucleoside (U) group.

Three-Dimensional Modelling of Honeybee Venom Allergenic Proteases: Relation to Allergenicity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Can one cure the nommitarity of three-dimensional quadratic gravity using a topological Chern-Simons term?

Quadratic gravity in (2+1)D is nonunitarity at the tree level. When a topological Chern-Simons term is added to this theory, the harmless massive scalar mode of the former gives rise to a troublesome massive spin-0 ghost, while the massive spin-2 ghost is replaced by two massive physical particles both of spin-2. Therefore, unlike what it is claimed in the literature, quadratic Chern-Simons gravity in (2+1)D is nonunitary at the tree level.

Propagator, tree-level unitarity and effective nonrelativistic potential for three-dimensional higher-derivative gravity augmented by a gravitational Chern-Simons term

An algorithm for computing the propagator for three-dimensional quadratic gravity with a gravitational Chern-Simons term, based on an extension of the three-dimensional Barnes-Rivers operators, is proposed. A systematic study of the tree-level unitarity of this theory is developed and its agreement with Newton's law is investigated by computing the effective nonrelativistic potential. (C) 2000 Elsevier B.V. B.V. All rights reserved.

Is it physically sound to add a topologically massive term to three-dimensional massive electromagnetic or gravitational models?

The addition of a topologically massive term to an admittedly nonunitary three-dimensional massive model, be it an electromagnetic system or a gravitational one, does not cure its nonunitarity. What about the enlargement of avowedly unitary massive models by way of a topologically massive term? the electromagnetic models remain unitary after the topological augmentation but, surprisingly enough, the gravitational ones have their unitarity spoiled. Here we analyze these issues and present the explanation why unitary massive gravitational models, unlike unitary massive electromagnetic ones, cannot coexist from the viewpoint of unitarity with topologically massive terms. We also discuss the novel features of the three-term effective field models that are gauge-invariant.

Mean-field model for the interference of matter-waves from a three-dimensional optical trap

Using the mean-field time-dependent Gross-Pitaevskii equation we study the formation of a repulsive Bose-Einstein condensate on a combined optical and harmonic traps in two and three dimensions and subsequent generation of the interference pattern upon the removal of the combined traps as in the experiment by, Greiner et al. [Nature (London 415 (2002) 39]. For optical traps of moderate strength, interference pattern of 27 (9) prominent bright spots is found to be formed in three. (two) dimensions on a cubic (square) lattice in agreement with experiment. Similar interference pattern can also be formed upon removal of the optical lattice trap only. The pattern so formed can oscillate for a long time in the harmonic trap which can be observed experimentally. (C) 2003 Elsevier B.V. B.V. All rights reserved.

Stabilization of bright solitons and vortex solitons in a trapless three-dimensional Bose-Einstein condensate by temporal modulation of the scattering length

Using variational and numerical solutions of the mean-field Gross-Pitaevskii equation we show that a bright soliton can be stabilized in a trapless three-dimensional attractive Bose-Einstein condensate (BEC) by a rapid periodic temporal modulation of scattering length alone by using a Feshbach resonance. This scheme also stabilizes a rotating vortex soliton in two dimensions. Apart from possible experimental application in BEC, the present study suggests that the spatiotemporal solitons of nonlinear optics in three dimensions can also be stabilized in a layered Kerr medium with sign-changing nonlinearity along the propagation direction.

Three-dimensional solitons in cross-combined linear and nonlinear optical lattices

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Low dimensional behavior in three-dimensional coupled map lattices

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Gap solitons in a dipolar Bose-Einstein condensate on a three-dimensional optical lattice

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Toward the Application of Three-Dimensional Approach to Few-body Atomic Bound States

The first step toward the application of an effective non partial wave (PW) numerical approach to few-body atomic bound states has been taken. The two-body transition amplitude which appears in the kernel of three-dimensional Faddeev-Yakubovsky integral equations is calculated as function of two-body Jacobi momentum vectors, i.e. as a function of the magnitude of initial and final momentum vectors and the angle between them. For numerical calculation the realistic interatomic interactions HFDHE2, HFD-B, LM2M2 and TTY are used. The angular and momentum dependence of the fully off-shell transition amplitude is studied at negative energies. It has been numerically shown that, similar to the nuclear case, the transition amplitude exhibits a characteristic angular behavior in the vicinity of He-4 dimer pole.

Lower bounds on blow up solutions of the three-dimensional Navier-Stokes equations in homogeneous Sobolev spaces

Suppose that u(t) is a solution of the three-dimensional Navier-Stokes equations, either on the whole space or with periodic boundary conditions, that has a singularity at time T. In this paper we show that the norm of u(T - t) in the homogeneous Sobolev space (H)over dot(s) must be bounded below by c(s)t(-(2s-1)/4) for 1/2 < s < 5/2 (s not equal 3/2), where c(s) is an absolute constant depending only on s; and by c(s)parallel to u(0)parallel to((5-2s)/5)(L2)t(-2s/5) for s > 5/2. (The result for 1/2 < s < 3/2 follows from well-known lower bounds on blowup in Lp spaces.) We show in particular that the local existence time in (H)over dot(s)(R-3) depends only on the (H)over dot(s)-norm for 1/2 < s < 5/2, s not equal 3/2. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4762841]

Three-dimensional magnetic resonance reconstruction images before and after surgical therapy of spontaneous canine brain tumors

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Development and applications of three-dimensional gamma ray tomography system using ray casting volume rendering techniques

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)