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Miguel Machuqueiro

Publications and source records attributed to Miguel Machuqueiro.

6 recordsLinked to original sources
PubMed2006

The pH-dependent conformational states of kyotorphin: a constant-pH molecular dynamics study.

An extensive conformational study of the analgesic dipeptide kyotorphin (L-Tyr-L-Arg) at different pH values was performed using a constant-pH molecular dynamics method. This dipeptide showed a remarkable pH-dependent conformational variety. The protonation of the N-terminal amine was identified as a key element in the transition between the more extended and the more packed conformational states, as monitored by the dihedral angle defined by the atoms 1Cbeta-1Calpha-2Calpha-2Cbeta. The principal-component analysis of kyotorphin identified two major conformational populations (the extended trans and the packed cis) together with conformations that occur exclusively at extreme pH values. Other, less stable conformations were also identified, which help us to understand the transitions between the predominant populations. The fitting of kyotorphin's conformational space to the structure of morphine resulted in a set of conformers that were able to fulfill most of the constraints for the mu-receptor. These results suggest that there may be strong similarities between the kyotorphin receptor and the structural family of opioid receptors.

Computer Simulation↗
PubMed2006

Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine.

A new implementation of the stochastic titration method for constant-pH molecular dynamics is presented, which introduces ionic strength effects in the simulations. In addition, the new implementation uses a faster molecular dynamics algorithm and an improved treatment of protonation events and of their effect on force field parameters. This new methodology is applied to a decalysine peptide, yielding very good quantitative agreement with experiments, both in terms of titration and helix-coil transition. The results show a significant dependence on ionic strength, illustrating the importance of including this parameter in constant-pH molecular dynamics simulations. Overall, the method seems to properly capture the protonation-conformation coupling and its dependence on ionic strength.

Algorithms↗
PubMed2005

On the use of different dielectric constants for computing individual and pairwise terms in poisson-boltzmann studies of protein ionization equilibrium.

Poisson-Boltzmann (PB) models are a fast and common tool for studying electrostatic processes in proteins, particularly their ionization equilibrium (protonation and/or reduction), often yielding quite good results when compared with more detailed models. Yet, they are conceptually very simple and necessarily approximate, their empirical character being most evident when it comes to the choice of the dielectric constant assigned to the protein region. The present study analyzes several factors affecting the ability of PB-based methods to model protein ionization equilibrium. We give particular attention to a suggestion made by Warshel and co-workers (e.g., Sham et al. J. Phys. Chem. B 1997, 101, 4458) of using different protein dielectric constants for computing the individual (site) and the pairwise (site-site) terms of the ionization free energies. Our prediction of pK(a) values for several proteins indicates that no advantage is obtained by such a procedure, even for sites that are buried and/or display large pK(a) shifts relative to the solution values. In particular, the present methodology gives the best predictions using a dielectric constant around 20, for shifted/buried and nonshifted/exposed sites alike. The similarities and differences between the PB model and Warshel's PDLD/S model are discussed, as well as the reasons behind their apparently discrepant results. The present PB model is shown to predict also good reduction potentials in redox proteins.

Animals↗
PubMed2003

Zn-proline catalyzed direct aldol reaction in aqueous media.

Zn complexes of proline, lysine and arginine are efficient catalysts for the aldol addition of p-nitrobenzaldehyde and acetone in aqueous medium, giving quantitative yields and enantiomeric excesses up to 56% with 5 mol% of the catalysts at room temperature.

Acetone↗
PubMed2003

Zinc mediated methyl transfer from trimethyl phosphate to chelating and non-chelating alkyl thiols. Model for Zn-dependent methyltransferases.

The methyl transfer from trimethyl phosphate to alkyl thiols was investigated in the presence of zinc ions and in the absence of strong base. The chelating thiol N-(2-mercaptoethyl)picolylamine (MEPAH) was methylated by trimethyl phosphate, in MeOH, in the presence of Zn salts whereas the reaction did not take place in the absence of Zn(2+). The pre-formed complex (MEPA)(2)Zn was methylated faster than the MEPAH in the presence of zinc ions The methyl transfer also took place in chloroform with similar yields at room temperature. When non-chelating hexanethiol was the methyl acceptor, a slower reaction took place in the presence of pyridine which was independent of Zn(2+). Kinetic studies of the methyl transfer from trimethyl phosphate to (MEPA)(2)Zn gave a second-order rate constant of 5.0 x 10(-5) M(-1) s(-1) as measured by 1H NMR spectroscopy in MeOH. The results obtained suggest that the methyl transfer to MEPA-Zn involves a zinc-bound thiolate.

Chelating Agents↗