BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

Background Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser. Results BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin. Conclusions BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper webcite

Exploring the early stages of chemical unfolding of proteins at the proteome scale

After decades of using urea as denaturant, the kinetic role of this molecule in the unfolding process is still undefined: does urea actively induce protein unfolding or passively stabilize the unfolded state? By analyzing a set of 30 proteins (representative of all native folds) through extensive molecular dynamics simulations in denaturant (using a range of force-fields), we derived robust rules for urea unfolding that are valid at the proteome level. Irrespective of the protein fold, presence or absence of disulphide bridges, and secondary structure composition, urea concentrates in the first solvation shell of quasi-native proteins, but with a density lower than that of the fully unfolded state. The presence of urea does not alter the spontaneous vibration pattern of proteins. In fact, it reduces the magnitude of such vibrations, leading to a counterintuitive slow down of the atomic-motions that opposes unfolding. Urea stickiness and slow diffusion is, however, crucial for unfolding. Long residence urea molecules placed around the hydrophobic core are crucial to stabilize partially open structures generated by thermal fluctuations. Our simulations indicate that although urea does not favor the formation of partially open microstates, it is not a mere spectator of unfolding that simply displaces to the right of the folded←→unfolded equilibrium. On the contrary, urea actively favors unfolding: it selects and stabilizes partially unfolded microstates, slowly driving the protein conformational ensemble far from the native one and also from the conformations sampled during thermal unfolding

Orchis cazorlensis Lacaita en el Parque Natural de la Sierra de las Nieves (Málaga)

Orchis cazorlensis Lacaita in the Natural Park Sierra de las Nieves (Málaga) Palabras clave. Orchidaceae, Orchis cazorlensis, Serranía de Ronda, Sierra de las Nieves, Málaga.Key words. Orchidaceae, Orchis cazorlensis, Serranía de Ronda, Sierra de las Nieves, Málaga

Estudio teórico sobre la influencia del solvente en la estructura y dinámica del ADN

[spa] Esta tesis se centra en el estudio de la influencia del solvente en la estructura y dinámica del ADN mediante técnicas de simulación por ordenador. En la misma se han realizado dos bloques diferenciados, cuyos objetivos concretos serían: 1- El estudio de una secuencia de ADN en solución con diferentes fuerzas iónicas con el objetivo de racionalizar cómo los contraiones modulan las propiedades estructurales y dinámicas de la molécula. 2- El estudio de diversos ácidos nucleicos canónicos y no canónicos en ausencia de solvente, bajo condiciones similares a las que tienen lugar en los experimentos de espectrometría de masas por ionización con electrospray (ESI-MS). Este bloque, a su vez, está dividido en tres trabajos: i/-estudio de la doble hélice de ADN en condiciones de vacío propias de los experimentos de ESI-M, ii/-estudio de la naturaleza de complejos no covalentes entre minor groove binders (mG-binders) y ADN de doble cadena en condiciones de vacío, iii/-análisis del comportamiento de estructuras de ADN formadas por cuatro cadenas (G-cuadrúplex) en condiciones de vacío. La técnica utilizada para este propósito ha sido la Dinámica Molecular, la cual permite la descripción rigurosa a nivel atómico de las propiedades estructurales, energéticas y dinámicas de la molécula. Los resultados obtenidos en esta tesis complementan la información disponible en la actualidad sobre la estructura y conformación del ADN en dichas condiciones extremas.[eng] This thesis is centered in the theoretical study of the influence of the solvent in the structure and dynamics of the DNA. First, there is a study of 12-mer sequence of DNA under different ionic strengths with the objective of elucidate how the molecule is influenced by the ionic atmosphere. Later on, different nucleic acids are studied with the absence of solvent under similar conditions to the Electrospray Ionization Mass spectrometry technique with the objective of study the structural, energetic and dynamics properties of DNA in the gas phase. The systems studied are: -Double helix of DNA. -Non covalent complexes between minor-groove binders and double stranded DNA. -G-quadruplexes of DNA. The main computational approach used has been the Molecular Dynamics technique. This powerful method allows to study at atomistic level the Nucleic Acids under those extreme conditions mentioned. The results obtained in this thesis complement the experimental information available about the structure and conformation of DNA in vacuum

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

Background Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser. Results BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin. Conclusions BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper webcite