Low-Resolution Molecular Models Reveal the Oligomeric State of the PPAR and the Conformational Organization of Its Domains in Solution

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

Characterization and oxygen binding properties of des-Arg human hemoglobin

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Calculating the Best Dual Bound for Problems with Multiple Lagrangian Relaxations

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1)

The 1.7 angstrom resolution crystal structure of recombinant family G/11 beta-1,4-xylanase (rXynA) from Bacillus subtilis 1A1 shows a jellyroll fold in which two curved P-sheets form the active-site and substrate-binding cleft. The onset of thermal denaturation of rXynA occurs at 328 K, in excellent agreement with the optimum catalytic temperature. Molecular dynamics simulations at temperatures of 298-328 K demonstrate that below the optimum temperature the thumb loop and palm domain adopt a closed conformation. However, at 328 K these two domains separate facilitating substrate access to the active-site pocket, thereby accounting for the optimum catalytic temperature of the rXynA. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

A micelle nucleation model for the interaction of dodecyl sulphate with Lys49-phospholipases A(2)

Bothropstoxin-I (BthTx-I) is a Lys49-PLA(2) from the venom of Bothrops jararacussu that lacks detectable catalytic activity, yet causes rapid Ca2+-independent membrane damage. With the aim of understanding the interaction between BthTx-I and amphiphilic molecules, we have studied the interaction of sodium dodecyl sulphate (SDS) with the protein. Circular dichroism and attenuated total reflection Fourier-transform infrared spectra of BthTx-I reveal changes in the alpha-helical organization of the protein at an SDS/BthTx-I molar ratio of 20-25. At SDS/BthTx-I ratios of 40-45 the alpha-helices return to a native-like conformation, although fluorescence emission anisotropy measurements of 2-amino-N-hexadecyl-benzamide (AHBA) demonstrate that the total SDS is below the critical micelle concentration when this transition occurs. These results may be interpreted as the result of SDS accumulation by the BthTx-I homodimer and the formation of a pre-micelle SDS/BthTx-I complex, which may subsequently be released from the protein surface as a free micelle. Similar changes in the alpha-helical organization of BthTx-I were observed in the presence of dipalmitoylphosphatidylcholine liposomes, suggesting that protein structure transitions coupled to organization changes of bound amphiphiles may play a role in the Ca2+-independent membrane damage by Lys49-PLA(2)s. (c) 2006 Elsevier B.V. All rights reserved.

Triple helix conformation of botryosphaeran, a (1 -> 3;1 -> 6)-beta-D-glucan produced by Botryosphaeria rhodina MAMB-05

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Integrable aspects of the scaling q-state Potts models I: bound states and bootstrap closure

We discuss the q-state Potts models for q less than or equal to 4, in the scaling regimes close to their critical or tricritical points. Starting from the kink S-matrix elements proposed by Chim and Zamolodchikov, the bootstrap is closed for the scaling regions of all critical points, and for the tricritical points when 4 > q greater than or equal to 2. We also note a curious appearance of the extended last line of Freudenthal's magic square in connection with the Potts models. (C) 2003 Elsevier B.V. B.V. All rights reserved.

Radii in weakly-bound light halo nuclei

A systematic study of the root-mean-square distance between the constituents of weakly-bound nuclei consisting of two halo neutrons and a core is performed using a renormalized zero-range model. The radii are obtained from a universal scaling function that depends on the mass ratio of the neutron and the core, as well as on the nature of the subsystems, bound or virtual. Our calculations are qualitatively consistent with recent data for the neutron-neutron root-mean-square distance in the halo of Li-11 and Be-14 nuclei. (C) 2004 Published by Elsevier B.V.

Quantization rules for bound states in quantum wells

An algebraic reformulation of the Bohr-Sommerfeld (BS) quantization rule is suggested and applied to the study of bound states in one-dimensional quantum wells. The energies obtained with the present quantization rule are compared to those obtained with the usual BS and WKB quantization rules and with the exact solution of the Schrodinger equation. We find that, in diverse cases of physical interest in molecular physics, the present quantization rule not only yields a good approximation to the exact solution of the Schrodinger equation, but yields more precise energies than those obtained with the usual BS and/or WKB quantization rules. Among the examples considered numerically are the Poeschl-Teller potential and several anharmonic oscillator potentials. which simulate molecular vibrational spectra and the problem of an isolated quantum well structure subject to an external electric field.

Bound states of attractive Bose-Einstein condensates in shallow traps in two and three dimensions

Using variational and numerical solutions of the mean-field Gross-Pitaevskii equation for attractive interaction (with cubic or Kerr nonlinearity), we show that a stable bound state can appear in a Bose-Einstein condensate (BEC) in a localized exponentially screened radially symmetric harmonic potential well in two and three dimensions. We also consider an axially symmetric configuration with zero axial trap and a exponentially screened radial trap so that the resulting bound state can freely move along the axial direction like a soliton. The binding of the present states in shallow wells is mostly due to the nonlinear interaction with the trap playing a minor role. Hence, these BEC states are more suitable to study the effect of the nonlinear force on the dynamics. We illustrate the highly nonlinear nature of breathing oscillations of these states. Such bound states could be created in BECs and studied in the laboratory with present knowhow.

Scaling limit of weakly bound triatomic states

The usefulness of a scale-independent approach to identify Efimov states in three-body systems is shown by comparing such an approach with a realistic calculation in the case of three helium atoms. We show that the scaling limit is realized in practice in this case, and suggest its application to study other similar systems, including the case where two kinds of atoms are mixed. We also consider the observed large scattering length of the Rb-87 dimer to estimate the critical value of the ground-state energy of the corresponding trimer (greater than or equal to 1.5 mK), in order to allow for one Efimov state above the ground state.

Reply to comment on 'Quantization rules for bound states in quantum wells'

In this reply to the comment on 'Quantization rules for bound states in quantum wells' we point out some interesting differences between the supersymmetric Wentzel-Kramers-Brillouin (WKB) quantization rule and a matrix generalization of usual WKB (mWKB) and Bohr-Sommerfeld (mBS) quantization rules suggested by us. There are certain advantages in each of the supersymmetric WKB (SWKB), mWKB and mBS quantization rules. Depending on the quantum well, one of these could be more useful than the other and it is premature to claim unconditional superiority of SWKB over mWKB and mBS quantization rules.

Effect of bound nucleon internal structure change on nuclear structure functions

Effect of bound nucleon internal structure change on nuclear structure functions is investigated based on local quark-hadron duality. The bound nucleon structure functions calculated for charged-lepton and (anti)neutrino scattering are all enhanced in symmetric nuclear matter at large Bjorken-x (x greater than or similar to 0.85) relative to those in a free nucleon. This implies that a part of the enhancement observed in the nuclear structure function F-2 (in the resonance region) at large Bjorken-x (the EMC effect) is due to the effect of the bound nucleon internal structure change. However, the x dependence for the charged-lepton and (anti)neutrino scattering is different. The former (latter) is enhanced (quenched) in the region 0.8 less than or similar to x less than or similar to 0.9 (0.7 less than or similar to x less than or similar to 0.85) due to the difference of the contribution from axial vector forrn factor. Because of these differences charge symmetry breaking in parton distributions will be enhanced in nuclei. (c) 2005 Elsevier B.V. All rights reserved.

Tightly bound gap solitons in a Fermi gas

Within the framework of the mean-field hydrodynamic model of a degenerate Fermi gas ( DFG), we study, by means of numerical methods and variational approximation ( VA), the formation of fundamental gap solitons ( FGSs) in a DFG ( or in a BCS superfluid generated by weak interaction between spin- up and spin- down fermions), which is trapped in a periodic optical- lattice ( OL) potential. An effectively one- dimensional ( 1D) con. guration is considered, assuming strong transverse confinement; in parallel, a proper 1D model of the DFG ( which amounts to the known quintic equation for the Tonks- Girardeau gas in the OL) is considered too. The FGSs found in the first two bandgaps of the OL- induced spectrum ( unless they are very close to edges of the gaps) feature a ( tightly bound) shape, being essentially confined to a single cell of the OL. In the second bandgap, we also find antisymmetric tightly bound subfundamental solitons ( SFSs), with zero at the midpoint. The SFSs are also confined to a single cell of the OL, but, unlike the FGSs, they are unstable. The predicted solitons, consisting of similar to 10(4) - 10(5) atoms, can be created by available experimental techniques in the DFG of Li-6 atoms.

Prediction of a weakly bound excited state in the He-4(2)-Li-7 molecule

A scale-independent approach, valid for weakly bound three-body systems, is used to analyze the existence of excited Thomas-Efimov states in molecular systems with three atoms: a helium dimer together with isotopes of lithium (Li-6 and Li-7) and sodium (Na-23). With the present study and the available data, we can clearly predict that the He-4(2)-Li-7 system supports an excited state with binding energy close to 2.31 mK. (C) 2000 American Institute of Physics. [S0021-9606(00)30442-1].