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Alejandro D Nadra

Publications and source records attributed to Alejandro D Nadra.

6 recordsLinked to original sources
PubMed2006

Modeling heme proteins using atomistic simulations.

Heme proteins are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, to the oxidation of organic compounds, to the sensing and transport of small molecules. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of several relevant issues in heme proteins chemistry: (i) conformational analysis, ligand migration, and solvation effects studied using classical molecular dynamics simulations; (ii) electronic structure and spin state energetics of the active sites explored using quantum-mechanics (QM) methods; (iii) the interaction of heme proteins with small ligands studied through hybrid quantum mechanics-molecular mechanics (QM-MM) techniques; (iv) and finally chemical reactivity and catalysis tackled by a combination of quantum and classical tools.

Computer Simulation↗
PubMed2006

Structural and thermodynamic basis for the enhanced transcriptional control by the human papillomavirus strain-16 E2 protein.

Strain 16 of the human papillomavirus is responsible for the largest number of cases of cervical cancers linked to this virus, and the E2 protein is the transcriptional regulator of all viral genes. We present the first structure for the DNA binding domain of HPV16 E2 bound to DNA, and in particular, to a natural cognate sequence. The NMR structure of the protein backbone reveals that the overall conformation remains virtually unchanged, and chemical shift analysis of the protein bound to a shorter DNA duplex uncovered a contact out of the minimal E2 DNA binding site, made by lysine 349. This contact was confirmed by titration calorimetry and mutagenesis, with a contribution of 1.0 kcal mol(-)(1) to binding energy. HPV16 E2 has the highest DNA binding affinity and exerts a strict transcriptional control, translated into the repression of the E6 and E7 oncogenes. These novel features provide the structural and thermodynamic basis for this tight transcriptional control, the loss of which correlates with carcinogenesis.

Amino Acid Sequence↗
PubMed2005

The folding mechanism of a dimeric beta-barrel domain.

The dimeric beta-barrel domain is an unusual topology, shared only by two viral origin binding proteins, where secondary, tertiary and quaternary structure are coupled, and where the dimerization interface is composed of two four-stranded half-beta-barrels. The folding of the DNA binding domain of the E2 transcriptional regulator from human papillomavirus, strain-16, takes place through a stable and compact monomeric intermediate, with 31% the stability of the folded dimeric domain. Double jump multiple wavelength experiments allowed the reconstruction of the fluorescence spectrum of the monomeric intermediate at 100 milliseconds, indicating that tryptophan residues, otherwise buried in the folded state, are accessible to the solvent. Burial of surface area as well as differential behavior to ionic strength and pH with respect to the native ground state, plus the impossibility of having over 2500 A2 of surface area of the half-barrel exposed to the solvent, indicates that the formation of a non-native compact tertiary structure precedes the assembly of native quaternary structure. The monomeric intermediate can dimerize, albeit with a weaker affinity (approximately 1 microM), to yield a non-native dimeric intermediate, which rearranges to the native dimer through a parallel folding channel, with a unimolecular rate-limiting step. Folding pathways from either acid or urea unfolded states are identical, making the folding model robust. Unfolding takes place through a major phase accounting for apparently all the secondary structure change, with identical rate constant to that of the fluorescence unfolding experiment. In contrast to the folding direction, no unfolding intermediate was found.

Dimerization↗
PubMed2005

Free energy contributions to direct readout of a DNA sequence.

The energetic contributions of individual DNA-contacting side chains to specific DNA recognition in the human papillomavirus 16 E2C-DNA complex is small (less than 1.0 kcal mol(-1)), independent of the physical and chemical nature of the interaction, and is strictly additive. The sum of the individual contributions differs 1.0 kcal mol(-1) from the binding energy of the wild-type protein. This difference corresponds to the contribution from the deformability of the DNA, known as "indirect readout." Thus, we can dissect the energetic contribution to DNA binding into 90% direct and 10% indirect readout components. The lack of high energy interactions indicates the absence of "hot spots," such as those found in protein-protein interfaces. These results are compatible with a highly dynamic and "wet" protein-DNA interface, yet highly specific and tight, where individual interactions are constantly being formed and broken.

Amino Acid Sequence↗
PubMed2002

High-risk (HPV16) human papillomavirus E7 oncoprotein is highly stable and extended, with conformational transitions that could explain its multiple cellular binding partners.

High-risk papillomaviruses are known to exert their transforming activity mainly through E7, one of their two oncoproteins. Despite its relevance, no structural information has been obtained that could explain the apparent broad binding specificity of E7. Recombinant E7 from HPV-16 purified to near homogeneity showed two species in gel filtration chromatography, one of these corresponding to a dimer with a molecular weight of 22 kDa, determined by multiangle light scattering. The E7 dimer was isolated for characterization and was shown to undergo a substantial conformational transition when changing from pH 7.0 to 5.0, with an increase in helical structure and increased solvent accessibility to hydrophobic surfaces. The protein was resistant to thermal denaturation even in the presence of SDS, and we show that persistent residual structure in the monomer is responsible for its reported anomalous electrophoretic behavior. The dimer also displays a nonglobular hydrodynamic volume based on gel filtration experiments and becomes more globular in the presence of 0.3 M guanidinium chloride, with hydrophobic surfaces becoming accessible to the solvent, as indicated by the large increase in ANS binding. At low protein concentration, dissociation of the globular E7 dimer was observed, preceding the cooperative unfolding of the structured and extended monomer. Although E7 bears properties that resemble natively unfolded polypeptides, its far-UV circular dichroism spectrum, cooperative unfolding, and exposure of ANS binding sites support a folded and extended, as opposed to disordered and fluctuating, conformation. The large increase in solvent accessibility to hydrophobic surfaces upon small pH decrease within physiological range and in mild denaturant concentrations suggests conformational properties that could have evolved to enable protein-protein recognition of the large number of cellular binding partners reported.

Anilino Naphthalenesulfonates↗