Od stabala (dendograma i stabala usaglašavanja) do topologije

We describe a methodology to endow a set of chemical interest with a topology. This procedure starts with the definition of the chemical set as a group of elements plus their neighborhood relationships. A graphical representation of these two conditions is a dendrogram (tree). Next, we show a mathematical procedure to build up a basis for a topology with which we can calculate several topological properties, such as: closures and boundaries of sets of chemical interest. We show four practical examples of this methodology: 72 chemical elements, 31 steroids, 250 benzimidazoles and 20 amino acids.Opisana je metodologija koja topologiju pridružuje kemijski zanimljivim skupovima, i to tako da se definiciji takvih skupova kao grupe elemenata doda još relacija susjedstva, što se grafički opisuje dendogramom (stablom). Dalje je prikazan topološki postupak koji omogućava računanje niza topoloških svojstava, uključivo zatvorenost i granice kemijskih skupova, a koji postupak je onda primjenjen na 72 kemijska elementa, 31 steroida, 250 benzimidazola i 20 amino kiselina

Variations in the Electrostatic Landscape of Class II Human Leukocyte Antigen Molecule Induced by Modifications in the Myelin Basic Protein Peptide: A Theoretical Approach

The receptor-ligand interactions involved in the formation of the complex between Class II Major Histocompatibility Complex molecules and antigenic peptides, which are essential for establishing an adaptive immunological response, were analyzed in the Class II Human Leukocyte Antigen (HLA) - Myelin Basic Protein (MBP) peptide complex (HLA-DRβ1*1501-MBP) using a multipolar molecular electrostatic potential approach. The Human Leukocyte Antigen - peptide complex system was divided into four pockets together with their respective peptide fragment and the corresponding occupying amino acid was replaced by each of the remaining 19 amino acids. Partial atomic charges were calculated by a quantum chemistry approach at the Hatree Fock/3-21*G level, to study the behavior of monopole, dipole and quadrupole electrostatic multipolar moments. Two types of electrostatic behavior were distinguished in the pockets' amino acids: “anchoring” located in Pocket 1 and 4, and “recognition” located in Pocket 4 and 7. According to variations in the electrostatic landscape, pockets were ordered as: Pocket 1>Pocket 9≫Pocket 4≈Pocket 7 which is in agreement with the binding ability reported for Class II Major Histocompatibility Complex pockets. In the same way, amino acids occupying the polymorphic positions β13R, β26F, β28D, β9W, β74A, β47F and β57D were shown to be key for this Receptor-Ligand interaction. The results show that the multipolar molecular electrostatic potential approach is appropriate for characterizing receptor-ligand interactions in the MHC–antigenic peptide complex, which could have potential implications for synthetic vaccine design

Influencia del solvente en el espectro ultravioleta del 4-nitrobifenilo

Se estudiaron los efectos de solvente en la banda del 4-nitrobifenilo en los alcoholes metanol, etanol, I propanol, 2 propanol, 1-butanol, 2-metilpropanol, que fueron purificados cuidadosamente, determinándose luego el grado de pureza que resultó satisfactorio en casi todos los casos. Por ser el agua la impureza persistente en todos ellos, fue necesario estudiar su efecto con cierto detalle

3D Pocket representations.

<p>Maximal Speed Molecular Surface representations (<a href="http://www.scripps.edu/~sanner/html/msms_home.html" target="_blank">www.scripps.edu/̃sanner/html/msms_home.html</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004164#pone.0004164-Sanner1" target="_blank">[37]</a> of each of the four pockets showing the position of primary anchoring amino acids within pocket 1 and 9, while amino acids indicated in pocket 4 and 7 correspond to amino acids being assign a recognition electrostatic effect (A,B). The antigenic fragment fitting into the pocket is shown in yellow sticks with the occupying amino acid highlighted in purple. (A) Empty pockets. (B) Occupied pocket. (C) Stick representation showing the disposition of anchoring amino acids (in red), recognition amino acids (in green) and amino acids having a dual effect are shown (in blue) inside pockets buried inside the PBR formed by residues lying in the α-chain (shown in pink) and the β-chain (light blue). It can clearly seen that the α55E and β81H primary anchoring amino acids of P1 are located towards the outermost portion of the binding groove (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004164#pone-0004164-g001" target="_blank">Fig. 1</a>) and that α24F lies in the farthest portion of the pocket near to P1.</p

Amino acids in each pocket being critical for peptide-HLA groove interaction according to their electrostatic behavior.

*<p>Polymorphic positions are shown in bold-types.</p

Box plot analysis applied to distinguish amino acids according to their particular electrostatic behavior.

<p>The box plot analysis allows separating data into high and low values in a quantitative-manner. High values were those lying above the third quartile and were further differentiated into outliers and upper-whisker values. (A) Summary of the <i>S_aa</i> mean values of amino acids defining the four pockets allowing to differentiate amino acids having <i>S_aa</i> outliers values, denoted as <i>primary anchoring</i> amino acids and those having upper-whisker values, named <i>secondary anchoring</i> amino acids. The higher anchoring effect occurred in α81H and β55E of pocket 1 (B) Summary of IQR values obtained from the box plot analysis of <i>S_aa</i> allowing differentiating amino acids having IQR outliers values, denoted as <i>fine differentiation</i> amino acids and those having upper-whisker values, named <i>coarse differentiation</i> amino acids. The higher differentiation effect was seen in α26F, α13R and α28D residues.</p

Rethinking research management in Colombia

Purpose - This paper seeks to present a proposal to change the form in which knowledge is produced in Colombia. Design/methodology/approach - Discusses the key issue - to transform the way in which the production of knowledge is currently taking place at the university level. Findings - To be able to increase the production of knowledge in this country there is a need to create bonds among industrial, governmental, and academic institutions. It is believed that this can be done by the development of a system capable of continuously forming researchers at a doctoral level. Originality/value - The paper puts forward a proposal for the construction of such a system based on the developments of organizational cybernetics. The proposal is based on the concept of autonomy which is crucial to solve this problem. © Emerald Group Publishing Limited