In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

En aquest treball, es presenta l'estudi de les propietats de fractura de films de polipropilè (PP) i copolímers etilè-propilè en blocs (EPBC) per mitjà de la tècnica del Treball Essencial de Fractura (EWF). Aquesta tècnica es mostra com una alternativa molt adapatada per a l'aplicació de la Mecànica de la Fractura a films dúctils, i permet separar l'energia total de fractura en un terme essencial, que fa referència al treball real de fractura, i un terme no essencial, relatiu a la dissipació d'energia de deformació plàstica al voltant del camí de fractura.En una primera part, s'estudien les condicions òptimes d'assaig de la técnica EWF per aplicar-la a films de polímers dúctils, analitzant la influència de variables d'assaig com són les dimensions de la proveta, la velocitat d'assaig o el mode de fractura.En una segona part, s'ha estudiat la relació entre els paràmetres de fractura obtinguts mitjançant la tècnica EWF i diferents propietats referents a l'estructura del material. Entre aquestes, s'ha analitzat la influència de les característiques cristal·lines, modificades per un procés de recuit previ als assajos, i del contingut d'etilè a diferents temperatures d'assaig. S'han aplicat nombroses tècniques de caracterització tant mecàniques i de fractura com físico-químiques.Els resultats mostren que el mètode EWF s'adapta bé a la necessitat de caracteritzar la fractura de films polimèrics, i permet estudiar la relació entre la seva estructura i les propietats de fractura que presenten. Alhora, es plantegen diferents modificacions del mètode que permeten potenciar les seves possibilitats. S'observa que al millorar la perfecció cristalina dels materials estudiats, el terme essencial augmenta en detriment del terme no essencial. També es demostra que la presència d'etilè en els EPBC minimitza la gran dependència que presenten les propietats de fractura del PP homopolímer en variar la temperatura, i es relaciona aquest comportament amb els canvis dels mecanismes de deformació predominants en el material. / En este trabajo, se presenta el estudio de las propiedades de fractura de films de polipropileno (PP) y copolímeros etileno-propileno (EPBC) por medio de la técnica del Trabajo Esencial de Fractura (EWF). Esta técnica se muestra como una alternativa muy adaptada para la aplicación de la Mecánica de la Fractura en films dúctiles, y permite separar la energía total de fractura en un término esencial, que hace referencia al trabajo real de fractura, y un término no esencial, relativo a la disipación de energía de deformación plástica alrededor del camino de fractura.En una primera parte, se estudian las condiciones óptimas de ensayo de la técnica WF para aplicarla a films de polímeros dúctiles, estudiando la influencia de variables de ensayo como son las dimensiones de probeta, la velocidad de ensayo o el modo de fractura.En una segunda parte, se ha estudiado la relación entre los parámetros de fractura obtenidos mediante la técnica EWF y distintas propiedades referentes a la estructura del material. Entre éstas, se ha analizado la influencia de las características cristalinas, modificadas por un proceso de recocido previo a los ensayos, y del contenido de etileno a diferentes temperaturas de ensayo. Se han aplicado numerosas técnicas de caracterización, tanto mecánicas y de fractura como físico-químicas.Los resultados muestran que el método EWF se adapta bien a la necesidad de caracterizar la fractura de films poliméricos, y permite estudiar la relación entre su estructura y las propiedades de fractura que presentan. También se plantean diferentes modificaciones del método que permiten potenciar sus posibilidades. Se observa que al mejorar la perfección cristalina de los materiales estudiados, el término esencial aumenta en detrimento del término no esencial. También se demuestra que la presencia de etileno en los EPBC minimiza la gran dependencia que presentan las propiedades de fractura del PP homopolímero al variar la temperatura, y se relaciona este comportamiento con los cambios de los mecanismos de deformación predominantes en el material. / In this work, the study of the fracture properties of polypropylene (PP) and ethylene-propylene block copolymers (EPBC) films by means of the Essential Work of Fracture (EWF) method is presented. This method is considered as a suitable alternative for applying Fracture Mechanics to ductile films, allowing the separation of the total fracture energy into two different items: an essential term, related to the actual fracture work, and a non essential term, related to the plastic deformation energy dissipation occurring in the region surrounding the fracture path.In a first part, the optimal EWF method test conditions for ductile plastic films are studied, by analysing the influence of such test variables as the specimen dimensions, the test rate or the fracture mode.In a second part, the relationship between the fracture parameters obtained by applying the EWF method and different materials structural properties are studied. Among these properties, the influence of the crystalline characteristics, modified by an annealing process before the tests, and that of the ethylene content at different test temperatures have been analysed.Various mechanical, fracture and physico-chemical characterisation techniques have been applied.The results show that the EWF method is very suitable to assess the fracture of polymeric films, and therefore to study the relationship between their structure and the fracture properties that they present. In addition, various modifications of the method are proposed in order to improve its possibilities.It is observed that as the crystalline perfection grows, the essential term increases but the non-essential term decreases. It is also shown that the ethylene presence in the EPBC minimises the strong temperature dependence shown by the fracture properties of the PP homopolymer. This behaviour is related to the predominant deformation mechanisms in the material. / Cet ouvrage présente l'étude des propriétés de rupture de films de polypropylène (PP) et de copolymères éthylène-propylène en blocs (EPBC) par moyen de la methode du Travail Essentiel de Rupture (EWF). Cette technique se révèle comme une alternative très adaptée à l'application de la Mécanique de la Rupture aux films ductiles, et permet la séparation de l'énergie totale de rupture en un terme essentiel, qui fait référence au travail réel de rupture, et en un terme non essentiel, relatif à la dissipation d'énergie de déformation plastique autour du chemin de rupture.Dans une première partie, les conditions optimales d'essai de la technique EWF pour l'application aux polymères ductiles sont étudiées, tout en analysant l'influence de variables d'essai telles que les dimensions de l'éprouvette, la vitesse de l'essai, ou le mode de rupture. La deuxième partie est consacrée à l'étude de la relation entre les paramètres de rupture obtenus par la méthode EWF et différentes propriétés de la structure du matériau. Parmis celles-ci, nous avons analysé l'influence des caractéristiques cristallines, modifiées par un processus de recuit préalable aux essais, et de l'effet du contenu en éthylène à différentes températures d'essai. Plusieurs techniques de caractérisation, aussi bien mécaniques, que de rupture, que physico-chimiques ont été utilisées.Les résultats montrent que la méthode EWF est très adaptée à la caractérisation de la rupture de films de polymères, et permet d'étudier la relation entre leur structure et leurs propriétés de rupture. Nous présentons, aussi, différentes approches modifiées de la technique EWF qui permettent d'accroître son potentiel. Il est observé que, quand la perfection cristalline des matériaux étudiés augmente, le terme essentiel augmente lui aussi, mais le terme non essentiel présente une tendance opposée. De même, il est démontré que la présence d'ethylène dans les EPBC a un effet de minimisation de l'importante dépendence que le PP homopolymère présente vis-à-vis de la température, et ce comportement est relié aux changements des mécanismes de déformation prédominants dans le matériau.

The present work focuses on the exploration of the conformational space of biological active peptides in different conditions with the aim of characterizing their conformational profile. Different techniques have been used within the molecular mechanics framework. A first hurdle is encountered in the exploration as the exhaustiveness of the exploration and the definition of a criterion for stopping the procedure were not well defined at the beginning of the present work. A solution to this problem is presented in the second chapter for the iterative simulated annealing.Determining the bioactive conformation is a requirement for the design of peptidomimetics in computer-aided drug design. The bioactive conformation can be simplified by the moieties that are known to interact with the receptor and the relative distances between these moieties, and this schematic entity is termed pharmacophore. The pharmacophore can be used to screen three-dimensional databases of molecules for the search of peptidomimetics. The compounds obtained in the search can be subsequently tested for activity and a new group of lead compounds can be thus identified. In chapter 3 an example of this procedure is described with the aim of obtaining a new group of bradykinin antagonists.Peptides have been traditionally considered as flexible molecules especially in polar solvents like water. This flexibility is difficult to measure by experimental techniques and as a consequence peptides have been regarded as molecules lacking of structure under such conditions. On the other hand, biological active peptides are known to interact with their receptors in a preferred conformation, often termed as the bioactive conformation. The most accepted hypothesis for explaining the interaction of peptides and their receptors is the induced fit. Thus, the peptide will exhibit in solution conformational motives that are part of the conformation adopted in the receptor. Subsequent to the binding of the peptide to the receptor, the conformation in solution will be modified in order to optimize the interaction of the peptide to the receptor. Therefore, a contradiction appears to exist between the need for certain degree of structure in the peptide prior to the receptor binding and the inherent lack of structure of peptides in solution. It has been argued in some instances that the binding of the peptide to the biological membrane is a prerequisite for the adoption of the bioactive conformation and the subsequent binding to the receptor. In chapters 4 and 5 this hypothesis will be criticized and an alternative hypothesis will be presented.Recently, it has been reported several instances were the folding of peptides has been simulated by means of long molecular dynamics trajectories. A problem arises when the wealth of conformations obtained has to be classified in terms of their respective degree of folding. In chapter 4 a novel methodology is described for the classification and grouping of the peptide structures based on the presence of structural motifs and the similarities among them. This methodology can prove very useful as it almost automated and it does not present any limitation regarding the size of the peptide or protein of study.In order to follow what are the problems arising when the size and the flexibility of peptides are increased, the sequence of chapters of the present study is presented with increasing size. Thus, in chapter 2 the conformational profile of 4-residue long farnesyltransferase inhibitors is studied by means of the iterative simulated annealing procedure. The first part of chapter 3 deals with a bradykinin antagonist, Hoe 140. Although Hoe 140 with 10 residues is larger than the 4-residue farnesyltransferase inhibitors, the conformational diversity of the peptide is only considered for the last 5 residues. This simplification of the peptide is carried out in order to compare the conformational profiles of Hoe 140 and the group of bradykinin analogs presented in the second part of the chapter: 5-residue long peptides containing 1-amino-2-phenylclyclopropanecarboxylic acid, a conformationally restricted residue. Finally, chapters 4 and 5 are dedicated to an 11-residue neuropeptide: substance P. The increase in size provoked a change in the methodology. Indeed, the conformational profile of the peptide has been studied by means of iterative simulated annealing and extensive molecular dynamics trajectories. This has permitted the comparison between both methodologies and to derive conclusions to the kind of information that can be obtained through these different methodologies for the exploration of the conformational space of peptides.The present work has been partially published through two papers:F.J Corcho, M. Filizola, J.J. Pérez. Evaluation of the iterative simulated annealing technique in conformational search of peptides. Chemical Physics Letters. 2000, 319: 65-70.F.J. Corcho, M. Filizola y J.J. Pérez. Assessment of the bioactive conformation of the farnesyltransferase protein binding recognition motif by computational methods.Journal of Biomolecular Structure and Dynamics. 1999, 16(5): 1043-1052. / El present treball està dedicat a l'exploració de l'espai conformacional de pèptids biològicament actius, sota diferent condicions, amb l'objectiu de caracteritzar el seu perfil conformacional. S'han usat diferents tècniques dins del marc de la mecànica molecular. Un primer obstacle a l'inici d'aquest treball va ser la definició d'un criteri per mesurar com d'exhaustiu havia estat i quan s'havia d'aturar la cerca. Al segon capítol es presenta una solució a aquest problema per al recuit simulat iteratiu.La determinació de la conformació bioactiva és un requeriment per al disseny de peptidomimetics assistit per ordinador. La conformació bioactiva pot ser simplificada prenent els grups funcionals que se sap que interactuen amb el receptor i la distància relativa entre aquests grups. Aquesta entitat esquemàtica és anomenada farmacòfor. El farmacòfor pot ésser utilitzat per cribar bases de dades tridimensionals de molècules per a la cerca de peptidomimètics. A continuació, per als compostos obtinguts en la cerca es pot testar la seva activitat i identificar així un nou grup de caps de sèrie. Al capítol 3 es descriu un exemple d'aquest procediment que té com a objectiu l'obtenció d'un nou grup d'antagonistes de la bradiquinina.Els pèptids han sigut tradicionalment considerats molècules flexibles especialment en solvents polars com l'aigua. La flexibilitat és difícil de mesurar mitjançant tècniques experimentals i com a conseqüència els pèptids han sigut considerats molècules que no presentaven estructura sota aquestes condicions. Per una altra banda els pèptids biològicament actius se sap que interactuen amb els seus receptors a través d'una conformació preferida, sovint anomenada conformació bioactiva. La hipòtesi més acceptada per explicar la interacció dels pèptids i els seus receptors és l'ajustament induït o "induced fit". Així, el pèptid mostrarà en solució motius conformacionals que són part de la conformació adoptada al receptor. Posteriorment a la unió del pèptid al receptor, la conformació en solució serà modificada de manera que s'optimitzi la interacció del pèptid i el receptor. Per tant, sembla existir una contradicció entre la necessitat de que hi hagi un cert grau d'estructura en el pèptid prèviament a la unió al receptor i la manca d'estructura del pèptid en solució. En alguns casos s'ha argumentat que la unió del pèptid a la membrana biològica és un prerequisit per a l'adopció de la conformació bioactiva i la subsegüent unió al receptor. Als capítols 4 i 5 aquesta hipòtesi és criticada i es presenta una hipòtesi alternativa.Recentment, s'han presentat diferent exemples de plegament de pèptids que han sigut simulats mitjançant llargues trajectòries de dinàmica molecular. Sorgeix un problema quan la gran diversitat de conformacions obtingudes ha de ser classificada en termes del seu grau de plegament respectiu. Al capítol 4 es descriu una nova metodologia per a la classificació i l'agrupament d'estructures peptídiques basades en la presència de motius estructurals i les similituds entre elles. Aquesta metodologia pot resultar molt útil ja que és gairebé automàtica i no presenta cap tipus de limitació respecte al tamany del pèptid o la proteïna en estudi.Per tal de seguir els problemes que apareixen quan la mida i la flexibilitat dels pèptids s'incrementen, la seqüència dels capítols d'aquest estudi es presenta amb mida dels pèptids creixent. Així, al capítol 2 el perfil conformacional dels inhibidors de la farnesiltransferasa que tenen una llargària de 4 residus és estudiat mitjançant el procés de recuit simulat iteratiu. La primera part del capítol 3 tracta amb un antagonista de la bradiquinina, Hoe 140. Malgrat que Hoe 140 amb 10 residus és més gran que els inhibidors de la farnesiltransferasa, que tenen 4 residus, la diversitat conformacional del pèptid només s'ha considerat pels darrers 5 residus. Aquesta simplificació del pèptid es realitza per tal de comparar el perfils conformationals de Hoe 140 i d'un grup d'anàlegs de la bradiquinina, que es presenten a la segona part del capítol, de 5 residus de llargària i que contenen l'àcid 1-amino-2-fenilciclopropacarboxílic que és un residu conformacionalment restringit. Finalment, els capítols 4 i 5 estan dedicats a un neuropèptid d'onze residus: substància P. L'increment de la mida va provocar un canvi en la metodologia emprada. Així, el perfil conformacional del pèptid ha sigut estudiat mitjançant el recuit simulat iteratiu i mitjançant trajectòries extenses de dinàmica molecular. Això ha permès la comparació entre ambdues metodologies i l'extracció de conclusions sobre el tipus d'informació que pot obtenir-se a través de les diferents metodologies per a l'exploració de l'espai conformacional de pèptids.El present treball s'ha publicat parcialment a dos articles:F.J Corcho, M. Filizola, J.J. Pérez. Evaluation of the iterative simulated annealing technique in conformational search of peptides. Chemical Physics Letters. 2000, 319: 65-70.F.J. Corcho, M. Filizola y J.J. Pérez. Assessment of the bioactive conformation of the farnesyltransferase protein binding recognition motif by computational methods.Journal of Biomolecular Structure and Dynamics. 1999, 16(5): 1043-1052. / de la Tesis DoctoralEl presente trabajo está dedicado a la exploración del espacio conformacional de pèptids biológicamente activos, bajo diferentes condiciones, i con el objetivo de caracterizar su perfil conformacional. Se han usado diferentes técnicas dentro del marco de la mecánica molecular. Un primer obstáculo al inicio de este trabajo fue la definición de un criterio para medir como de exhaustivo había sido y cuando se debía detener la búsqueda. En el segundo capítulo se presenta una solución a este problema para al recocido simulado iterativo.La determinación de la conformación bioactiva es un requerimiento para al diseño de peptidomiméticos asistido por ordenador. La conformación bioactiva puede ser simplificada tomando los grupos funcionales que se sabe que interactúan con el receptor y la distancia relativa entre estos grupos. Esta entidad esquemática es llamada farmacóforo. El farmacóforo puede ser utilizado para cribar bases de datos tridimensionales de moléculas para la búsqueda de peptidomiméticos. A continuación, para los compuestos obtenidos en la búsqueda se puede testar la actividad e identificar así un nuevo grupo de cabezas de serie. En el capítulo 3 se describe un ejemplo de este procedimiento que tiene como objetivo la obtención de un nuevo grupo de antagonistas de la bradiquinina.Los péptidos han sido tradicionalmente considerados moléculas flexibles especialmente en solventes polares como el agua. La flexibilidad es difícil de medir mediante técnicas experimentales y como consecuencia los péptidos han sido considerados moléculas que no presentaban estructura bajo estas condiciones. Por otra parte los péptidos biológicamente activos se sabe que interactúan con sus receptores a través de una conformación preferida, a menudo llamada conformación bioactiva. La hipótesis más aceptada para explicar la interacción de los péptidos y sus receptores es el ajuste inducido o "induced fit". Así, el péptid mostrará en solución motivos conformacionales que son parte de la conformación adoptada en el receptor. Posteriormente a la unión del péptido al receptor, la conformación en solución será modificada de manera que se optimice la interacción del péptido y el receptor. Por tanto, parece existir una contradicción entre la necesidad de que haya un cierto grado de estructura en el péptido previamente a la unión al receptor y la ausencia de estructura del péptido en solución. En algunos casos se ha argumentado que la unión del péptido a la membrana biológica es un prerrequisito para la adopción de la conformación bioactiva y la subsiguiente unión al receptor. En los capítulos 4 i 5 esta hipótesis es criticada y se presenta una hipótesis alternativa.Recientemente, se han presentado diferentes ejemplos de plegamiento de péptidos que han sido simulados mediante largas trayectorias de dinámica molecular. Surge un problema cuando la gran diversidad de conformaciones obtenidas ha de ser clasificada en términos de su grado de plegamiento respectivo. En el capítulo 4 se describe una nueva metodología para la clasificación y el agrupamiento de estructuras peptídicas basadas en la presencia de motivos estructurales y las similitudes entre ellas. Esta metodología puede resultar muy útil ya que está casi automatizada y no presenta ningún tipo de limitación respecto al tamaño del péptido o la proteína en estudio.Con el objetivo de seguir los problemas que aparecen cuando la medida y la flexibilidad de los péptidos se incrementan, la secuencia de los capítulos de este estudio se presenta con la medida de los péptidos creciente. Así, en el capítulo 2 el perfil conformacional de los inhibidores de la farnesiltransferasa que tienen una longitud de 4 residuos es estudiado mediante el proceso del recocido simulado iterativo. La primera parte del capítulo 3 trata con un antagonista de la bradiquinina, Hoe 140. Aunque Hoe 140 con 10 residuos es más grande que los inhibidores de la farnesiltransferasa, que tienen 4 residuos, la diversidad conformacional del péptido solo se ha considerado para los últimos 5 residuos. Esta simplificación del péptido se realiza por tal de comparar los perfiles conformationales de Hoe 140 y de un grupo de análogos de la bradiquinina, que se presentan en la segunda parte del capítulo, de 5 residuos de longitud y que contienen el ácido 1-amino-2-fenilciclopropacarboxílico que es un residuo conformacionalmente restringido. Finalmente, los capítulos 4 y 5 están dedicados a un neuropéptido de once residuos: sustancia P. El incremento de la medida provocó un cambio en la metodología utilizada. Así, el perfil conformacional del péptido ha sido estudiado mediante el recocido simulado iterativo y mediante trayectorias extensas de dinámica molecular. Esto ha permitido la comparación entre ambas metodologías y la extracción de conclusiones sobre el tipo de información que se puede obtener a través de las diferentes metodologías para la exploración del espacio conformacional de péptidos.El presente trabajo se ha publicado parcialmente en dos artículos:F.J Corcho, M. Filizola, J.J. Pérez. Evaluation of the iterative simulated annealing technique in conformational search of peptides. Chemical Physics Letters. 2000, 319: 65-70.F.J. Corcho, M. Filizola y J.J. Pérez. Assessment of the bioactive conformation of the farnesyltransferase protein binding recognition motif by computational methods.Journal of Biomolecular Structure and Dynamics. 1999, 16(5): 1043-1052.

Die RAFT-Polymerisation ("Reversible Addition-Fragmentation Chain Transfer") ist eine radikalische Polymerisation, die auf dem Prinzip des degenerativen Kettentransfers basiert. Es können Polymere hergestellt werden, die eine niedrige Dispersität aufweisen und komplexe makromolekulare Strukturen ausbilden. Für die Funktionalisierung von Polymerketten bietet sich die RAFT-Polymerisation ebenfalls an, da idealerweise jede auf diese Art hergestellte Polymerkette eine RAFT-Einheit trägt und so eine vollständige Funktionalisierung gewährleistet ist. Im Fokus dieser Arbeit stand die Funktionalisierung von Polybutadien und 1,3-Butadien enthaltenden Copolymeren mit gezielt eingebauten schwefelhaltigen Gruppen. Dabei wurden zwei verschiedene Ansätze verfolgt: Die α,ω-Funktionalisierung der Polymerketten mittels modifizierter RAFT-Agenzien sowie eine Funktionalisierung entlang der Polymerkette mit Hilfe von speziellen Monomeren. Da diese Polymere in technischen Anwendungen Verwendung finden sollen, standen einfache Synthesen, die sich gut auf den Technikums- und Industriemaßstab übertragen lassen, im Vordergrund. Da es sich bei der RAFT-Einheit auch um eine schwefelhaltige Gruppe handelt, wurden Strategien zur Funktionalisierung der Abgangsgruppe erarbeitet und experimentell untersucht, um so ein α,ω-funktionalisiertes Polymer zu erhalten. Neben klassischen RAFT-Agenzien wurden auch neuartige Makro-RAFT-Agenzien verwendet, bei denen die schwefelhaltige Gruppe während einer Polymerisation in situ angebunden wird. Darüber hinaus konnten erfolgreich Monomere synthetisiert werden, die wegen ihrer styrolähnlichen Struktur und der Ähnlichkeit der Monomere Styrol und 1,3-Butadien in ihrem Polymerisationsverhalten gut mit 1,3-Butadien copolymerisieren und dabei die schwefelhaltige Gruppe entlang der Polymerkette einbauen. Das Hauptaugenmerk weiterer Untersuchungen lag auf den Copolymerisationseigenschaften der Monomere. Dazu wurden umfangreiche Untersuchungen mit Styrol als Modellsystem für 1,3-Butadien durchgeführt und die gewonnenen Erkenntnisse in einer Copolymerisation der funktionalisierten Monomere mit 1,3-Butadien verifiziert. Es konnte weiterhin gezeigt werden, dass sich schaltbare RAFT-Agenzien für die Synthese von Poly(butadien)-block-poly(vinylacetat) eignen, obwohl es sich um zwei Monomere mit stark unterschiedlichen elektronischen Eigenschaften handelt, die in einer konventionellen radikalischen Polymerisation kein Copolymer bilden würden. Aufgrund der Ähnlichkeit der Monomere Vinylacetat und Ethylen eröffnet dies neue Wege in der kontrollierten radikalischen Polymerisation von Polybutadien-block-polyethylen und erweitert so das Spektrum der unpolaren Monomere in der RAFT-Polymerisation zur Herstellung von Blockcopolymeren.