Energetic Selection of Topology in Ferredoxins

Models of early protein evolution posit the existence of short peptides that bound metals and ions and served as transporters, membranes or catalysts. The Cys-X-X-Cys-X-X-Cys heptapeptide located within bacterial ferredoxins, enclosing an Fe4S4 metal center, is an attractive candidate for such an early peptide. Ferredoxins are ancient proteins and the simple α+β fold is found alone or as a domain in larger proteins throughout all three kingdoms of life. Previous analyses of the heptapeptide conformation in experimentally determined ferredoxin structures revealed a pervasive right-handed topology, despite the fact that the Fe4S4 cluster is achiral. Conformational enumeration of a model CGGCGGC heptapeptide bound to a cubane iron-sulfur cluster indicates both left-handed and right-handed folds could exist and have comparable stabilities. However, only the natural ferredoxin topology provides a significant network of backbone-to-cluster hydrogen bonds that would stabilize the metal-peptide complex. The optimal peptide configuration (alternating αL,αR) is that of an α-sheet, providing an additional mechanism where oligomerization could stabilize the peptide and facilitate iron-sulfur cluster binding

Effect of doxycycline on atherosclerosis: From bench to bedside

Matrix metalloproteinases (MMPs) have a pivotal role in the natural history of atherosclerosis and its cardiovascular consequences. Non-selective MMP inhibition with doxycycline appears as a potential strategy to reduce the residual risk observed in patients already at intensive lipid lowering strategies. However, specific MMPs have different and even contradicting roles in the natural history of atherosclerosis, rendering broad spectrum MMP inhibition an important yet somewhat simplistic approach towards residual risk reduction in coronary atherosclerosis. Overall, the balance of non-selective MMP inhibition might shift to the favorable side in particular settings such as in acute coronary syndromes, where in addition to its potential plaque stabilization properties, doxycycline shows promise in preventing ischemia-reperfusion injury and left ventricular remodeling. Nevertheless, to date, most animal models used do not represent advanced coronary atherosclerosis seen in humans, and large and well-designed clinical studies are lacking. We discuss the available evidence and recent patents supporting the role of doxycycline in atherosclerosis.Fil: Rodriguez Granillo, Gaston Alfredo. Universidad de Buenos Aires. Facultad de Medicina; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Rodriguez Granillo, Agustina. Universidad de Buenos Aires. Facultad de Medicina; ArgentinaFil: Milei, Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Cardiológicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Cardiológicas; Argentin

Advantages and disadvantages of biodegradable platforms in drug eluting stents

Coronary angioplasty with drug-eluting stent (DES) implantation is currently the most common stent procedure worldwide. Since the introduction of DES, coronary restenosis as well as the incidence of target vessel and target lesion revascularization have been significantly reduced. However, the incidence of very late stent thrombosis beyond the first year after stent deployment has more commonly been linked to DES than to bare-metal stent (BMS) implantation. Several factors have been associated with very late stent thrombosis after DES implantation, such as delayed healing, inflammation, stent mal-apposition and endothelial dysfunction. Some of these adverse events were associated with the presence of durable polymers, which were essential to allow the elution of the immunosuppressive drug in the first DES designs. The introduction of erodable polymers in DES technology has provided the potential to complete the degradation of the polymer simultaneously or immediately after the release of the immunosuppressive drug, after which a BMS remains in place. Several DES designs with biodegradable (BIO) polymers have been introduced in preclinical and clinical studies, including randomized trials. In this review, we analyze the clinical results from 6 observational and randomized studies with BIO polymers and discuss advantages and disadvantages of this new technology

Copper-transfer mechanism from the human chaperone Atox1 to a metal-binding domain of wilson disease protein

The molecular details of how copper (Cu) is transferred from the human Cu chaperone Atox1 to metalbinding domains (MBDs) of P1B-type ATPases are still unclear. Here, we use a computational approach, employing quantum mechanics/molecular mechanics (QM/MM) methods, to shed light on the reaction mechanism [probable intermediates, Cu(I) coordination geometries, activation barriers, and energetics] of Cu(I) transfer from Atox1 to the fourth MBD of Wilson disease protein (WD4). Both Atox1 and WD4 have solvent-exposed metal-binding motifs with two Cys residues that coordinate Cu(I). After assessing the existence of all possible 2-, 3- and 4-coordinate Cu-intermediate species, one dominant reaction path emerged. First, without activation barrier, WD4's Cys1 binds Cu(I) in Atox1 to form a 3-coordinated intermediate. Next, with an activation barrier of about 9.5 kcal/mol, a second 3-coordinated intermediate forms that involves both of the Cys residues in WD4 and Cys1 of Atox1. This species can then form the product by decoordination of Atox1's Cys1 (barrier of about 8 kcal/mol). Overall, the Cu-transfer reaction from Atox1 to WD4 appears to be kinetically accessible but less energetically favorable (△E = 7.7 kcal/mol). Our results provide unique insights into the molecular mechanism of protein-mediated Cu(I) transfer in the secretory pathway and are in agreement with existing experimental data. © 2010 American Chemical Society.Fil: Rodriguez-Granillo, Agustina. Rice Universite; Estados UnidosFil: Crespo, Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Rice Universite; Estados Unidos. Merck Research Laboratories; Estados UnidosFil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Wittung-Stafshede, Pernilla. Rice University; Estados Unidos. Universidad de Umea; Sueci

STAT5 transcriptional activity is impaired by LIF in a mammary epithelial cell line

Gene regulation mediated by STAT factors has been implicated in cellular functions with relevance to a variety of processes. Particularly, STAT5 and STAT3 play a crucial role in mammary epithelium displaying reciprocal activation kinetics during pregnancy, lactation and involution. Here, we show that LIF treatment of mammary epithelial HC11 cells reduces the phosphorylation levels and transcriptional activity of p-STAT5 in correlation with STAT3 phosphorylation. We have also found that STAT5 activity is negatively modulated by this cytokine, both on a gene whose expression is induced, as well as on a promoter repressed by STAT5. Besides, our results show that lactogenic hormones increase LIF effect on gene induction without modifying STAT3 phosphorylation state. Our findings strongly suggest that there is crosstalk between STAT5 and STAT3 pathways that could modulate their ability to regulate gene expression.Fil: Rodriguez Granillo, Agustina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Boffi, Juan Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Barañao, Jose Lino Salvador. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Kordon, Edith Claudia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Pecci, Adali. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Guberman, Alejandra Sonia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentin

Protein ensemble generated by modifying psi, phi and chi dihedral angles.

<p>For a model heptapeptide-cluster complex, CGGCGGC fused to an iron-sulfur cluster, there are total 6 ψ angles, 6 Φ angles, 3 χ₁ angles, and one each for χ₂ and χ₃ angles. The permutations are carried out by 60 degrees step size for Φ and ψ and 120 degrees step size for χ angles.</p

Cys-Gly-Gly-Clu-Gly-Gly-Cys peptide created with protCAD.

<p>All possible structures are explored by permuting 17 rotatable dihedral angles of the peptide from −180 to 180 with a step size of 60 degrees.</p

Hydrogen bonding environment of the 232 left- and right-handed heptapeptide-cluster conformations.

<p>(A) Interaction energy vs. average H-S distance of left (red), right-handed (blue) complexes. Experimentally determined ferredoxin structures (green) and non-ferredoxin redox active proteins (purple) show nearly identical bond geometries and calculated interaction energies. (B). The same dataset presented as the number of hydrogen bonds versus interaction energy. Only one simulated peptide in the ensemble contributes six hydrogen bonds, corresponding to the best interaction energy. This is equivalent to the natural right-handed fold.</p

The energy distributions of right (blue) and left-handed (red) structures.

<p>The gaussian fits are very similar, which suggests that the natural selection was not influenced by the energetic stability alone. The energy corresponding to the ensemble that has the lowest RMSD to the experimentally determined ferredoxin structure (PDB: 2FDN)- green circle.</p

Topology angle in a ferredoxin fold for database analysis.

<p>An arbitrary plane was defined with three cysteine carbon alpha coordinates. Three dimensional vector calculations were done to determine the topology angle of the protein fold.</p