Biomedical subjects

Christopher A Reynolds

Publications and source records attributed to Christopher A Reynolds.

6 recordsLinked to original sources

PubMed2006

Classical polarization in hybrid QM/MM methods.

We have presented a method for modeling polarization in hybrid QM/MM calculations. The method, which expresses the induced dipoles as a set of "induced" charges, is based on the induced dipole approach and methodology for calculating potential-derived point charges from distributed multipole series. The method has the advantage that the same methodology can be used to determine the induced charges and the potential derived charges and so both sets of charges are rigorously defined within the same framework. This underlying link with the wave function makes the method particularly suitable for use in hybrid QM/MM calculations. Here we assess the importance of explicit polarization in the classical part of a QM/MM system with regard to improving the classical description and the consequent effects on the quantum description. The main advantages of the induced charge approach are that the method is readily interfaced with quantum mechanical methods and that induced charges are more readily interpreted than induced dipoles. The ease of interpretation is illustrated by analysis of the charges involved in dimeric and trimeric hydrogen bonded systems. The method for treating the MM polarization has been validated by a regression analysis of the charges induced in both the QM and MM systems against those derived from full quantum mechanical calculations. The method has also been validated using two energy decomposition approaches, which show that MM polarization makes a significant and reliable contribution to the QM - MM interaction energy in a hybrid system. The distance dependency of the induced charges is investigated in calculations on methylsuccinyl-Ala-Ala-Pro-Ala chlormethyl ketone interacting with human neutrophil elastase and propranolol interacting with asparagine residues in a model of the beta(2)-adrenergic receptor.

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PubMed2005

Entropy and oligomerization in GPCRs.

Evolutionary trace (ET) and entropy are two related methods for analyzing a multiple sequence alignment to determine functionally important residues in proteins. In this article, these methods have been enhanced with a view to reinvestigate the issue ofGPCR dimerization and oligomerization. In particular, cluster analysis has replaced the subjective visual analysis element of the original ET method. Previous applications of the ET method predicted two dimerization interfaces on the external transmembrane lipid-facing region of GPCRs; these were discussed in terms of dimerization and linear oligomers. Removing the subjective element of the ET method gives rise to the prediction of functionally important residues on the external face of each transmembrane helix for a large number of class A GPCRs. These results are consistent with a growing body of experimental information that, taken over many receptor subtypes, has implicated each transmembrane helix in dimeric interactions. In this application, entropy gave superior results to those obtained from the ET method in that its use gives rise to higher z-scores and fewer instances of z-scores below 3.

Animals↗

PubMed2004

Toward the active conformations of rhodopsin and the beta2-adrenergic receptor.

Using sets of experimental distance restraints, which characterize active or inactive receptor conformations, and the X-ray crystal structure of the inactive form of bovine rhodopsin as a starting point, we have constructed models of both the active and inactive forms of rhodopsin and the beta2-adrenergic G-protein coupled receptors (GPCRs). The distance restraints were obtained from published data for site-directed crosslinking, engineered zinc binding, site-directed spin-labeling, IR spectroscopy, and cysteine accessibility studies conducted on class A GPCRs. Molecular dynamics simulations in the presence of either "active" or "inactive" restraints were used to generate two distinguishable receptor models. The process for generating the inactive and active models was validated by the hit rates, yields, and enrichment factors determined for the selection of antagonists in the inactive model and for the selection of agonists in the active model from a set of nonadrenergic GPCR drug-like ligands in a virtual screen using ligand docking software. The simulation results provide new insights into the relationships observed between selected biochemical data, the crystal structure of rhodopsin, and the structural rearrangements that occur during activation.

Animals↗

PubMed2004

A multilayered approach to approximating solute polarization.

A hybrid multilayered "ONIOM"-type approach to solvation is presented in which the basic free energy of hydration is taken from the Poisson Boltzmann method and the contribution to the solute polarization is taken from a quantum mechanical implementation of the Born method. The method has been tested on the 52 neutral molecules used in the AM1-SM2 parameterization, and the polarized continuum method is taken as the standard by which the results are assessed. Regression analysis shows that the method gives a small improvement over the standard Poisson Boltzmann method or a dramatic improvement over the Born method. The system presented here represents one of the more straightforward applications of the multilayered approach to solvation, but other more sophisticated approaches are discussed.

Journal Article↗

PubMed2003

Hypoxia-targeting copper bis(selenosemicarbazone) complexes: comparison with their sulfur analogues.

The first copper bis(selenosemicarbazone) complexes have been synthesized, using the ligands glyoxal bis(selenosemicarbazone), pyruvaldehyde bis(selenosemicarbazone), and 2,3-butanedione bis(selenosemicarbazone). Their spectroscopic properties indicate that they are structurally analogous to their well-known square-planar sulfur-containing counterparts, the copper bis(thiosemicarbazone) complexes. Spectroscopic comparison of the sulfur- and selenium-containing complexes provides insight into their electronic structure. The effects on spectroscopic and redox properties of replacing sulfur with selenium, and of successive addition of methyl groups to the ligand backbone, are rationalized in terms of their electronic structure using spin-unrestricted density functional calculations. These suggest that, like the sulfur analogues, the complexes have a very low-lying empty ligand-based pi-orbital immediately above the LUMO, while the LUMO itself has d(x2)-(y2) character (i.e., is the spin partner of the HOMO). Replacement of S by Se shifts the oxidation potentials much more than the reduction potentials, whereas alkylation of the ligand backbone shifts the reduction potentials more than the oxidation potentials. This suggests that oxidation and reduction involve spatially different orbitals, with the additional electron in the reduced species occupying the ligand-based pi-orbital rather than d(x2)-(y2). Density functional calculations on the putative singlet Cu(I)-reduced species suggest that this ligand pi-character could be brought about by distortion away from planarity during reduction, allowing the low-lying ligand pi-LUMO to mix into the d(x2)-(y2)-based HOMO. The analogy in the structure and reduction behavior between the sulfur- and selenium-containing complexes suggests that labeled with positron emitting isotopes of copper (Cu-60, Cu-62, Cu-64), the complexes warrant biological evaluation as radiopharmaceuticals for imaging of tissue perfusion and hypoxia.

Copper↗

PubMed2002

Studies on the mechanism of hypoxic selectivity in copper bis(thiosemicarbazone) radiopharmaceuticals.

Copper diacetyl-bis(N4-methylthiosemicarbazone), Cu(II)ATSM, is a promising agent for imaging hypoxic tissue. Here we present results that provide insight into the chemical and electronic properties underlying previously observed structure-activity relationships. Density functional theory (DFT) calculations on the electronic structures and molecular orbitals of a series of 13 Cu(II)bis(thiosemicarbazone) analogues with different alkylation patterns and with fixed geometries based on the known structure of Cu(II)PTSM showed that the LUMO and the next lowest orbital were very close in energy, and their energy order was strikingly dependent on the ligand alkylation pattern in a way that correlated with hypoxia-selectivity and redox potentials. The LUMOs of Cu(II)ATSM and other hypoxia-selective analogues were predominantly metal-based (leading to a singlet reduced species) while the LUMOs of Cu(II)PTSM and other nonselective analogues were predominantly ligand-based (leading to a triplet reduced species). Upon relaxation of the geometric constraint and full optimization in both Cu(II)ATSM and Cu(II)GTS, the metal-based orbital became the LUMO, and the singlet was the thermodynamically preferred form of the reduced species. Chemical and electrochemical investigation showed that all Cu(II) complexes were reducible, but Cu(I)PTSM and other nonselective analogues dissociated immediately upon reduction with release of ligand (detected by UV-vis) while Cu(I)ATSM and other hypoxia-selective analogues did not. Instead they were rapidly re-oxidized to the Cu(II) complex by molecular oxygen. The reversible electrochemical reduction of nonselective complexes Cu(II)PTSM and Cu(II)GTS became irreversible in the presence of weak acid, whereas that of Cu(II)ATSM was unaffected. In light of these results we present a model to explain the structure-activity relationships on the basis of electronic structure and molecular vibrations.

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