Browsing by Author "Cruzeiro, Leonor"
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- Are the native states of proteins kinetic traps?Publication . Cruzeiro, Leonor; Lopes, P. A.Four proteins were selected to represent each of the four different CATH classes and, for each protein, three decoys were constructed with structures totally alien to the native state. The decoys were scored against the native state with the help of the AMBER force field, using three measures: the average energy, the average fluctuation and the resistance to a heat pulse. Two sets of simulations were performed, one with explicit solvent and the other with implicit solvent. The overall conclusion is that, of these three measures, the most successful in picking out the native states was the last one, since the native structures take a consistently longer time to be destabilized in this manner. However, the general conclusion is also that none of the measures is completely effective in discriminating all the decoys, a result that supports other studies, according to which the native state is reached by a kinetic step.
- Electron pairing in one-dimensional anharmonic crystal latticesPublication . Velarde, M. G.; Brizhik, L.; Chetverikov, A. P.; Cruzeiro, Leonor; Ebeling, W.; Röpke, G.We show that when anharmonicity is added to the electron–phonon interaction it facilitates electron pairing in a localized state. Such localized state appears as singlet state of two electrons bound with the traveling local lattice soliton distortion, which survives when Coulomb repulsion is included.
- Erratum: Mixed quantum-classical dynamics of an amide-I vibrational excitation in a protein a-helix [Phys. Rev. B 82, 174308 (2010)]Publication . Freedman, Holly; Martel, Paulo; Cruzeiro, LeonorIn the GROMACS codemodifications, instead of the nanometer unit for the distance that is standard in GROMACS, a unit of 1 °A was previously assumed. This led to dipole-dipole interactions between amide I vibrations at different sites and the interaction energies of the amide I vibration with the protein hydrogen bonds being overestimated, respectively, by three orders and by one order of magnitude.
- Exploring the Levinthal limit in protein foldingPublication . Cruzeiro, Leonor; Degreve, LeoAccording to the thermodynamic hypothesis, the native state of proteins is uniquely defined by their amino acid sequence. On the other hand, according to Levinthal, the native state is just a local minimum of the free energy and a given amino acid sequence, in the same thermodynamic conditions, can assume many, very different structures that are as thermodynamically stable as the native state. This is the Levinthal limit explored in this work. Using computer simulations, we compare the interactions that stabilize the native state of four different proteins with those that stabilize three non-native states of each protein and find that the nature of the interactions is very similar for all such 16 conformers. Furthermore, an enhancement of the degree of fluctuation of the non-native conformers can be explained by an insufficient relaxation to their local free energy minimum. These results favor Levinthal's hypothesis that protein folding is a kinetic non-equilibrium process.
- Influence of the sign of the coupling on the temperature dependence of optical properties of one-dimensional exciton modelsPublication . Cruzeiro, LeonorA new physical cause for a temperature-dependent double peak in exciton systems is put forward within a thermal equilibrium approach for the calculation of optical properties of exciton systems. Indeed, it is found that one-dimensional exciton systems with only one molecule per unit cell can have an absorption spectrum characterized by a double peak provided that the coupling between excitations in different molecules is positive. The two peaks, whose relative intensities vary with temperature, are located around the exciton band edges, being separated by an energy of approximately 4V, where V is the average coupling between nearest neighbours. For small amounts of diagonal and off-diagonal disorder, the contributions from the intermediate states in the band are also visible as intermediate structure between the two peaks, this being enhanced for systems with periodic boundary conditions. At a qualitative level, these results correlate well with experimental observations in the molecular aggregates of the thiacarbocyanine dye THIATS and in the organic crystals of acetanilide and N-methylacetamide.
- Knowns and unknowns in the Davydov model for energy transfer in proteinsPublication . Cruzeiro, LeonorThe Davydov model for amide I propagation in hydrogen-bonded chains of proteins is revisited. The many similarities between the mixed quantum-classical dynamical equations and those that are derived from the full quantum Davydov model while applying the so-called D-2 ansatz are highlighted. The transition from a minimum energy localized amide I state to a fully delocalized state is shown to operate in four phases, one of which is abrupt and the last of which is a fast but smooth change from a very broad yet localized state to a completely delocalized one. Exploration of the dynamical phase space at zero temperature includes the well-known soliton propagation as well as double and triple discrete breathers, and dispersion of initially localized states. The uncertainties related to the question of the thermal stability of the Davydov soliton are illustrated. A solution to the seemingly endless problem of the short radiative lifetime of the amide I excitations is proposed.
- Mixed quantum-classical dynamics of an amide-I vibrational excitation in a protein a-helixPublication . Freedman, Holly; Martel, Paulo; Cruzeiro, LeonorAdenosine triphosphate sATPd is known to be the main energy currency of the living cell, and is used as a coenzyme to generate energy for many cellular processes through hydrolysis to adenosine diphosphate sADPd,although the mechanism of energy transfer is not well understood. It has been proposed that following hydrolysis of the ATP cofactor bound to a protein, up to two quanta of amide-I vibrational energy are excited and utilized to bring about important structural changes in the protein. To study whether, and how, amide-I vibrational excitations are capable of leading to protein structural changes, we have added components arising from quantum-mechanical amide-I vibrational excitations to the total energy and force terms within a moleculardynamics simulation. This model is applied to helical deca-alanine as a test case to investigate how its dynamics differs in the presence or absence of an amide-I excitation. We find that the presence of an amide-I excitation can bias the structure toward a more helical state.
- On the possibility of electric transport mediated by long living intrinsic localized solectron modesPublication . Cantu Ros, O. G.; Cruzeiro, Leonor; Velarde, M. G.; Ebeling, W.We consider a polaron Hamiltonian in which not only the lattice and the electron-lattice interactions, but also the electron hopping term is affected by anharmonicity. We find that the one-electron ground states of this system are localized in a wide range of the parameter space. Furthermore, low energy excited states, generated either by additional momenta in the lattice sites or by appropriate initial electron conditions, lead to states constituted by a localized electron density and an associated lattice distortion, which move together through the system, at subsonic or supersonic velocities. Thus we investigate here the localized states above the ground state which correspond to moving electrons. We show that besides the stationary localized electron states (proper polaron states) there exist moving localized solectron states which can be easily excited. The evolution of these localized states suggests their potential as new carriers for fast electric charge transport.
- Protein FoldingPublication . Cruzeiro, Leonor; Springborg, MichaelThe existing experimental data on protein folding is briefly reviewed. It is argued that the optimal fit is within a multi-funnel shaped free energy landscape and a kinetic mechanism for folding. The possibility that the transient forces responsible for such a kinetic mechanism come from vibrational excited states (the VES hypothesis) is introduced. Two applications of the VES hypothesis to the structural instability of the proteins associated with misfolding diseases are presented. Finally, in the last section, a detailed kinetic mechanism is put forward according to which, in cells, the structure that polypeptide chains adopt, as they come out of the ribosome, is a helix, and the proposed general pathway followed by all amino acid sequences from this initial structure to the final three dimensional structure is described. An analysis is made of how the proposed kinetic mechanism can account for many of the experimentally observed features of protein folding. It is pointed out how this new kinetic mechanism, which was arrived at by the application of physical principles, may also help to derive a method of determining the tertiary structure of a protein from its primary sequence.
- Protein folding in vivo is a non-equilibrium processPublication . Cruzeiro, LeonorProtein refolding experiments have led to the thermodynamics hypothesis according to which the native structures of proteins are uniquely defined by their primary sequences.