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S Faggiano,
S Abbruzzetti,
F Spyrakis,
E Grandi,
C Viappiani,
S Bruno,
A Mozzarelli,
P Cozzini,
A Astegno,
P Dominici,
S Brogioni,
A Feis,
G Smulevich,
O Carrillo,
P Schmidtke,
A Bidon-Chanal, F J Luque
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ABSTRACT: The increasing number of nonsymbiotic plant hemoglobins discovered in genomic studies in the past decade raises intriguing questions about their physiological role. Among them, the nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana deserves particular attention, as it combines an extremely high oxygen affinity with an internal hexacoordination of the distal histidine HisE7 to the heme iron in the absence of exogenous ligands. In order to gain insight into the structure−function relationships of the protein, the ligand binding properties of mutants of two conserved residues of the distal cavity, HisE7 → Leu and PheB10 → Leu, were investigated by experimental and computational studies and compared to results determined for the wild type (wt) protein. The Fe2+-deoxy HisE7 → Leu mutant exists, as expected, in the pentacoordinated form, while a mixture of penta- and hexacoordinated forms is found for the PheB10 → Leu mutant, with an equilibrium shifted toward the pentacoordinated form with respect to the wt protein. Spectroscopic studies of the complexes of CO and CN− with AHb1 and its mutants show a subtle interplay of steric and electrostatic effects by distal residues on the ligand binding to the heme. Moreover, stopped-flow and flash photolysis experiments reveal substantial kinetic differences triggered by those mutations, which are particularly manifested in the enhanced geminate rebinding and bimolecular association rate. These findings are discussed in light of the drastic alterations found by molecular dynamics simulations in the nature and distribution of internal cavities in the protein matrix of the mutants, revealing an extremely large sensitivity of the protein structure to changes in distal HisE7 and PheB10 residues. Overall, data are consistent with the putative NO-dioxygenase activity attributed to AHb1.
The Journal of Physical Chemistry B. 11/2009;
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ABSTRACT: Mycobacterium tuberculosis, the causative agent of human tuberculosis, encodes a haemoprotein named Truncated Haemoglobin
N (trHbN), which in its active site transforms nitric oxide (NO) to nitrate anion.
( \textNO3- )\left( {{\text{NO}}_3^ - } \right). The NO-dioxygenase activity of trHbN seems to be crucial for the bacillus, which can survive under the nitrosative stress
conditions that occur upon infection of the host. As a defense mechanism against the copious amounts of NO produced by macrophages
upon infection, the protein must achieve a high level of NO-dioxygenase activity to eliminate NO, but this is modulated by
its efficiency in capturing O2 and NO. Migration of small diatomic ligands through the protein matrix is related to the presence of a doubly branched tunnel
system connecting the surface and the haem cavity site. In this work, we have studied the mechanism that controls ligand diffusion
and product egression with state-of-the-art molecular dynamics simulations. The results support a dual path mechanism for
migration of O2 and NO through distinct branches of the tunnel, where migration of NO is facilitated upon binding of O2 to the haem group. Finally, egression of
( \textNO3- )\left( {{\text{NO}}_3^ - } \right) is preceded by the entrance of water to the haem cavity and occurs through a different pathway. Overall, the results highlight
the intimate relationship between structure, dynamical behavior and biological function of trHbN.
05/2009: pages 33-47;
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ABSTRACT: The influence of pressure on the equilibrium between five-(5c) and six-coordination (6c) forms in neuroglobin (Ngb) and myoglobin (Mb) has been examined by means of molecular dynamics (MD) simulations at normal and high pressure. The results show that the main effect of high pressure is to reduce the protein mobility without altering the structure in a significant manner. Moreover, our data suggest that the equilibrium between 5c and 6c states in globins is largely controlled by the structure and dynamics of the C-D region. Finally, in agreement with the available experimental data, the free energy profiles obtained from steered MD for both proteins indicate that high pressure enhances hexacoordination. In Ngb, the shift in equilibrium is mainly related to an increase in the 6c-->5c transition barrier, whereas in Mb such a shift is primarily due to a destabilization of the 5c state.
Proteins Structure Function and Bioinformatics 10/2008; 75(4):885-94. · 3.39 Impact Factor
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D Alonso,
I Dorronsoro,
L Rubio,
P Muñoz,
E García-Palomero,
M Del Monte,
A Bidon-Chanal,
M Orozco, F J Luque,
A Castro,
M Medina,
A Martínez
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ABSTRACT: A new series of donepezil-tacrine hybrid related derivatives have been synthesised as dual acetylcholinesterase inhibitors that could bind simultaneously to the peripheral and catalytic sites of the enzyme. These new hybrids combined a tacrine, 6-chlorotacrine or acridine unit as catalytic binding site and indanone (the heterocycle present in donepezil) or phthalimide moiety as peripheral binding site of the enzyme, connected through a different linker tether length. One of the synthesised compounds emerged as a potent and selective AChE inhibitor, which is able to displace propidium in a competition assay. These results seem to confirm the ability of this inhibitor to bind simultaneously to both sites of the enzyme and make it a promising lead for developing disease-modifying drugs for the future treatment of Alzheimer's disease. To gain insight into the molecular determinants that modulate the inhibitory activity of these compounds, a molecular modelling study was performed to explore their binding to the enzyme.
Bioorganic & Medicinal Chemistry 01/2006; 13(24):6588-97. · 2.92 Impact Factor
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D Alonso,
I Dorronsoro,
L Rubio,
P Muñ,
E García-Palomero,
M Del,
A Bidon-Chanal,
M Orozco, F J Luque,
A Castro,
M Medina,
A Martínez
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ABSTRACT: A new series of donepezil–tacrine hybrid related derivatives have been synthesised as dual acetylcholinesterase inhibitors that could bind simultaneously to the peripheral and catalytic sites of the enzyme. These new hybrids combined a tacrine, 6-chlo-rotacrine or acridine unit as catalytic binding site and indanone (the heterocycle present in donepezil) or phthalimide moiety as peripheral binding site of the enzyme, connected through a different linker tether length. One of the synthesised compounds emerged as a potent and selective AChE inhibitor, which is able to displace propidium in a competition assay. These results seem to confirm the ability of this inhibitor to bind simultaneously to both sites of the enzyme and make it a promising lead for developing disease-modifying drugs for the future treatment of AlzheimerÕs disease. To gain insight into the molecular determinants that modulate the inhibitory activity of these compounds, a molecular modelling study was performed to explore their binding to the enzyme.
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ABSTRACT: A systematic analysis of the molecular electrostatic potential (MEP) is presented. This study has been performed with a twofold purpose: first, to study the MEP dependence with regard to the quality of the basis set used to compute the ab initio SCF wavefunction and second, to develop and to assess a new strategy for computing isoelectrostatic potential maps using the semiempirical MNDO wavefunction. The only differences between this procedure and the ab initio SCF MEP computation lie in the freezing of the inner electrons and in the origin of the first-order density matrix. The statistical analysis of MEPs computed for a large number of molecules from MNDO wavefunction and ab initio SCF wavefunctions obtained using STO-3G, 4-31G, 6-31G, 4-31G*, 6-31G*, and 6-31G** basis sets points out the ability of any wavefunction to reproduce the general topological characteristics of the MEP surfaces. Nevertheless, split-valence basis sets including polarization functions are necessary to obtain accurate MEP minimum energy values. MNDO wavefunction tends to overestimate the MEP minima depth by a constant factor and shows an excellent ability to reflect the relative variation of MEP minima energies derived from a rather sophisticated (6-31G*) basis set, lacking of the shortcomings detected in the semiempirical CNDO approximation.
Journal of Computational Chemistry 09/2004; 11(4):416 - 430. · 4.58 Impact Factor
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ABSTRACT: A new methodology to compute molecular interaction potentials (MIPs) is developed and tested. The calculation of the MIP is based upon the generalization of the rigorous quantum mechanical molecular electrostatic potential (MEP) and further addition of a classical repulsion-dispersion term. As a result, the MIP is able to represent not only with high accuracy electrostatic interactions but also represent in a suitable way steric effects. The analysis of the results obtained for different molecules demonstrates the superiority of the MIP with regard to the standard MEP to describe nonbonded interactions, in particular hydrogen bonds. The comparison of results calculated at the ab initio I 6-31G* and semiempirical AM1 levels points out the suitability of semiempirical calculations to qualitatively reproduce the most relevant reactive features of the molecules. Finally, possible applications of the MIP in different fields are discussed. © 1993 John Wiley & Sons, Inc.
Journal of Computational Chemistry 09/2004; 14(5):587 - 602. · 4.58 Impact Factor
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ABSTRACT: A comparison between Miertus–Scrocco–Tomasi (MST) SCRF and free energy perturbation (FEP) estimates of the free energy of hydration of eight small neutral molecules is presented. In both cases, the 6-31G* molecular electrostatic potential is used to describe the electrostatic properties of the molecules. The results demonstrate the ability of both methodologies to provide useful theoretical estimates of the total free energy of hydration; the average errors are only 1.5 kcal/mol (FEP) and 0.8 kcal/mol (MST/SCRF). The largest errors in the FEP and MST/SCRF results are less than 1.5 kcal/mol for all molecules except acetic acid, where the FEP method overestimates the free energy of hydration by 3.3 kcal/mol. © John Wiley & Sons, Inc.
Journal of Computational Chemistry 09/2004; 14(12):1498 - 1503. · 4.58 Impact Factor
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ABSTRACT: The suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi-ab initio method. Results demonstrate that the quasi-ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi-ab initio methods. In these two cases, the quality of the results is fully comparable with 6-31G* values. © 1994 by John Wiley & Sons, Inc.
Journal of Computational Chemistry 09/2004; 15(1):12 - 22. · 4.58 Impact Factor
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ABSTRACT: The AM1/MST strategy for the computation of hydrated neutral molecules has been optimized. For this purpose, we have systematically explored the best cavity definition, the most suitable strategy to compute the molecular electrostatic potential (MEP), and the use of MEP scaling factors to correct the semiempirical MEPs. As a result, we have developed an optimized version of the AM1/MST method, which allows us to reproduce well the experimental free energies of hydration (root mean square, rms, deviation in the range of 1 kcal/mol) as well as the water-induced dipoles computed at the 6-31G*/MST level (rms deviations in the range of 0.3 D). © 1994 by John Wiley & Sons, Inc.
Journal of Computational Chemistry 09/2004; 15(8):847 - 857. · 4.58 Impact Factor
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ABSTRACT: We report a theoretical study of the stretching of chemical bonds and its implications on the force-field parametrization. Computations were performed at the SCF and MCSCF levels by using minimal, split-valence, and large extended and polarized basis sets. The stretching energy profiles were determined considering up to 25 perturbed geometries of 11 different bonds (6 singles, 2 doubles, and 3 triples). The energy profiles and stretching parameters are compared with the experimental data compiled in the most popular force fields. MCSCF stretching energy profiles are mainly anharmonic and can be only roughly reproduced by quadratic equations. The use of Allinger's MM2 quasiharmonic expression appears as the best choice because it fits with reasonable accuracy a large percentage of the stretching profile without increasing the complexity of the formalism and of the parametrization procedure. MCSCF computations are needed to obtain reliable stretching force parameters. In this respect, MCSCF calculations considering as active space only the bonded and nonbonded orbitals of the perturbed bond seems to be the best strategy to obtain good results at a minimum computational cost, especially if small split-valence basis sets like the 3-21G are used. Results obtained at this level of sophistication are completely comparable to stretching parameters compiled on empirical force fields. © 1993 John Wiley & Sons, Inc.
Journal of Computational Chemistry 09/2004; 14(8):881 - 894. · 4.58 Impact Factor
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ABSTRACT: A new strategy to evaluate accurate electrostatic charges from semiempirical wave functions is reported. The rigorous quantum mechanical molecular electrostatic potentials computed from both MNDO and AM1 wave functions are fitted to the point-charge molecular electrostatic potential to obtain the electrostatic charges. The reliability of this strategy is tested by comparing the semiempirical electrostatic charges for 21 molecules with the semiempirical Mulliken charges and with the ab initio STO-3G and 6-31G* electrostatic charges. The ability of the dipoles derived from the semiempirical electrostatic and Mulliken charges as well as from the SCF charge distributions to reproduce the ab initio 6-31G* electrostatic dipoles and the gas phase experimental values is determined. The statistical analysis clearly point out the goodness of the semiempirical electrostatic charges, specially when the MNDO method is used. The excellent relationships found between the MNDO and 6-31G* electrostatic charges permit to define a scaling factor which allows to accurately reproduce the 6-31G* electrostatic charge distribution as well as the experimental dipoles from the semiempirical electrostatic charges.
Journal of Computational Chemistry 09/2004; 11(8):909 - 923. · 4.58 Impact Factor
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ABSTRACT: The effect of the solvent in the molecular properties of DNA bases has been explored by using a self-consistent reaction field (SCRF) method based on the AM1 (Austin Model 1) Hamiltonian and a modified version of the high level Miertus–Scrocco–Tomasi (MST) algorithm. MST/AM1 estimates of free energies of hydration compare qualitatively well with the available experimental data, as well as with the results obtained from molecular dynamic simulations. Furthermore, the changes in the dipole predicted by the MST/AM1 method are in good agreement with Monte Carlo/quantum mechanical data, as well as with AM1-SM2 (Soluation Model 2) estimates. AM1/MST calculations of Mulliken, and electrostatic charges, dipoles, molecular electrostatic potentials and molecular interaction potentials in both vacuum and solution allowed us to quantify the effect of the water on the reactive characteristics of the DNA bases. This effect is large and complex, and cannot be neglected in theoretical calculations where an accurate representation of the DNA bases is needed. The possibility of including the polarization effect of the water into force-field simulations of DNA structures is discussed. © 1993 John Wiley & Sons, Inc.
Biopolymers 01/2004; 33(12):1851 - 1869. · 2.87 Impact Factor
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ABSTRACT: Classical molecular interaction potentials, in conjunction with other theoretical techniques, are used to analyze the dependence of the binding sites of representative proteins on the bound ligand. It is found that the ligand bound introduces in general small structural perturbations at the binding site of the protein. However, such small structural changes can lead to important alterations in the recognition pattern of the protein. The impact of these findings in docking procedures is discussed.
Bioinformatics 08/2002; 18(7):939-48. · 5.47 Impact Factor
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