Properties of contact matrices induced by pairwise interactions in proteins

The total conformational energy is assumed to consist of pairwise interaction energies between atoms or residues, each of which is expressed as a product of a conformation-dependent function (an element of a contact matrix, C-matrix) and a sequence-dependent energy parameter (an element of a contact energy matrix, E-matrix). Such pairwise interactions in proteins force native C-matrices to be in a relationship as if the interactions are a Go-like potential [N. Go, Annu. Rev. Biophys. Bioeng. 12. 183 (1983)] for the native C-matrix, because the lowest bound of the total energy function is equal to the total energy of the native conformation interacting in a Go-like pairwise potential. This relationship between C- and E-matrices corresponds to (a) a parallel relationship between the eigenvectors of the C- and E-matrices and a linear relationship between their eigenvalues, and (b) a parallel relationship between a contact number vector and the principal eigenvectors of the C- and E-matrices; the E-matrix is expanded in a series of eigenspaces with an additional constant term, which corresponds to a threshold of contact energy that approximately separates native contacts from non-native ones. These relationships are confirmed in 182 representatives from each family of the SCOP database by examining inner products between the principal eigenvector of the C-matrix, that of the E-matrix evaluated with a statistical contact potential, and a contact number vector. In addition, the spectral representation of C- and E-matrices reveals that pairwise residue-residue interactions, which depends only on the types of interacting amino acids but not on other residues in a protein, are insufficient and other interactions including residue connectivities and steric hindrance are needed to make native structures the unique lowest energy conformations.Comment: Errata in DOI:10.1103/PhysRevE.77.051910 has been corrected in the present versio

Self-Assembly of Polyhedral Hybrid Colloidal Particles

We have developed a new method to produce hybrid particles with polyhedral shapes in very high yield (liter quantities at up to 70% purity) using a combination of emulsion polymerization and inorganic surface chemistry. The procedure has been generalized to create complex geometries, including hybrid line segments, triangles, tetrahedra, octahedra, and more. The optical properties of these particles are tailored for studying their dynamics and self-assembly. For example, we produce systems that consist of index-matched spheres allowing us to define the position of each elementary particle in three-dimensional space. We present some preliminary studies on the self-assembly of these complex shaped systems based on electron and optical microscopy.Engineering and Applied SciencesPhysic

Descrit el possible mecanisme d'activació del receptor cannabinoide 1

Un estudi, publicat a la revista Journal of Medicinal Chemistry pels investigadors Óscar Díaz, James Dalton i Jesús Giraldo de l'Institut de Neurociències, descriu el possible mecanisme d'activació del receptor cannabinoide 1 (CB1). Aquest receptor és activat pel principal component psicoactiu del cànnabis; així doncs, conèixer i comprendre el seu mecanisme d'activació afavorirà el desenvolupament de fàrmacs que modulen el seu funcionament de manera més econòmica i eficient.Un estudio, publicado en la revista Journal of Medicinal Chemistry por los investigadores Óscar Díaz, James Dalton y Jesús Giraldo del Instituto de Neurociencias, describe el posible mecanismo de activación del receptor cannabinoide 1 (CB1). Este receptor es activado por el principal componente psicoactivo del cannabis; así pues, conocer y comprender su mecanismo de activación favorecerá el desarrollo de fármacos que modulen su funcionamiento, de manera más económica y eficiente.A study published in the Journal of Medicinal Chemistry by the Neuroscience Institute researchers Óscar Díaz, James Dalton and Jesús Giraldo, describes the potential activation mechanism of cannabinoid receptor 1 (CB1). This receptor is activated by the main psychoactive component of cannabis; thus, knowing and understanding its mechanism of activation will favor the development of drugs that modulate their functioning, in a more economic and efficacious way

Regulatory T-cells in chronic lymphocytic leukemia: actor or innocent bystander?

Abstract: Regulatory T (Treg) cells are now under extensive investigation in chronic lymphocytic leukemia (CLL). This small subset of T-cells has been, in fact, considered to be involved in the pathogenesis and progression of CLL. However, whether Treg dysregulation in CLL plays a key role or it rather represents a simple epiphenomenon is still matter of debate. In the former case, Treg cells could be appealing for targeting therapies. Finally, Treg cells have also been proposed as a prognostic indicator of the disease clinical course

Genetic Variants of the Renin-Angiotensin-Aldosterone System and Reverse Remodeling After Cardiac Resynchronization Therapy

Background: Reverse remodeling (RR) after cardiac resynchronization therapy (CRT) is associated with favorable clinical outcomes in heart failure (HF). The renin-angiotensin-aldosterone system (RAAS) is involved in the remodeling process. Methods and Results: We assessed the association between RR and 8 common RAAS gene variants, which were determined by TaqMan assays, in 156 outpatients with chronic HF. RR was defined as a O15% decrease in left ventricular end systolic volume (LVESV) at 9 (interquartile range 7e12) months after CRT. We matched 76 patients who did not show RR (RR) to 80 RR? control subjects by age, sex, HF etiology, New York Heart Association (NYHA) functional class and left ventricular ejection fraction (LVEF). The frequency of the minor allele of the NR3C2 gene (rs5522 C/T), encoding the mineralocorticoid receptor, was higher in RR than in RR (24/126 vs 10/150; P value after false discovery rate correction: <.0193). Conversely, LVESV decreased significantly less after CRT in carriers of the NR3C2 minor C allele (P 5 .02). After adjustment for age, sex, NYHA functional class, previous myocardial infarction, atrial fibrillation, and LVEF, RR remained independently associated with NR3C2 C allele carriage (odds ratio 3.093, 95% confidence interval 1.253e7.632). Conclusions: The association of RR after CRT with a common polymorphism in the mineralocorticoid receptor gene involved in aldosterone signaling suggests a possible role for variants in RAAS genes in progressive LV function decline, despite apparently effective CRT

Redox-dependent and redox-independent functions of Caenorhabditis elegans thioredoxin 1

Thioredoxins (TRX) are traditionally considered as enzymes catalyzing redox reactions. However, redox-independent functions of thioredoxins have been described in different organisms, although the underlying molecular mechanisms are yet unknown. We report here the characterization of the first generated endogenous redox-inactive thioredoxin in an animal model, the TRX-1 in the nematode Caenorhabditis elegans. We find that TRX-1 dually regulates the formation of an endurance larval stage (dauer) by interacting with the insulin pathway in a redox-independent manner and the cGMP pathway in a redox-dependent manner. Moreover, the requirement of TRX-1 for the extended longevity of worms with compromised insulin signalling or under calorie restriction relies on TRX-1 redox activity. In contrast, the nuclear translocation of the SKN-1 transcription factor and increased LIPS-6 protein levels in the intestine upon trx-1 deficiency are strictly redox-independent. Finally, we identify a novel function of C. elegans TRX-1 in male food-leaving behaviour that is redox-dependent. Taken together, our results position C. elegans as an ideal model to gain mechanistic insight into the redox-independent functions of metazoan thioredoxins, overcoming the limitations imposed by the embryonic lethal phenotypes of thioredoxin mutants in higher organisms

Selective Constraints on Amino Acids Estimated by a Mechanistic Codon Substitution Model with Multiple Nucleotide Changes

Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code, and the strength of selective constraints against amino acid replacements can be tailored to a given gene. First, selective constraints averaged over proteins are estimated by maximizing the likelihood of each 1-PAM matrix of empirical amino acid (JTT, WAG, and LG) and codon (KHG) substitution matrices. Then, selective constraints specific to given proteins are approximated as a linear function of those estimated from the empirical substitution matrices. Akaike information criterion (AIC) values indicate that a model allowing multiple nucleotide changes fits the empirical substitution matrices significantly better. Also, the ML estimates of transition-transversion bias obtained from these empirical matrices are not so large as previously estimated. The selective constraints are characteristic of proteins rather than species. However, their relative strengths among amino acid pairs can be approximated not to depend very much on protein families but amino acid pairs, because the present model, in which selective constraints are approximated to be a linear function of those estimated from the JTT/WAG/LG/KHG matrices, can provide a good fit to other empirical substitution matrices including cpREV for chloroplast proteins and mtREV for vertebrate mitochondrial proteins. The present codon-based model with the ML estimates of selective constraints and with adjustable mutation rates of nucleotide would be useful as a simple substitution model in ML and Bayesian inferences of molecular phylogenetic trees, and enables us to obtain biologically meaningful information at both nucleotide and amino acid levels from codon and protein sequences.Comment: Table 9 in this article includes corrections for errata in the Table 9 published in 10.1371/journal.pone.0017244. Supporting information is attached at the end of the article, and a computer-readable dataset of the ML estimates of selective constraints is available from 10.1371/journal.pone.001724