Computational study of the capability of the side chains of amino acids for setting up cation···π interactions relevant in protein stability and structure

Within every living organism, proteins carry out specific essential functions, so much that without them life would be non-viable. These molecular machines are the responsible of obtaining chemical energy and also of fabricating useful compounds for the organism itself. The interaction between cations and aromatic species in the side chains of some amino acids is one of the key factors that control the stability of proteins. Different studies suggest that this type of interaction is present in a variety of systems, pointing to its relevance in many processes of chemical and biological recognition, such as nerve transmission or transport through the membrane. Even though the interaction between cations and aromatic species is strong in the gas phase, everything seems to indicate that the environment of the interacting species may affect its characteristics, either causing changes in intensity or changes in the geometrical disposition of the interacting fragments. Considering the relevance of these interactions, the main objective of this thesis is to gain a deeper comprehension of the characteristics of systems that establish interactions between aromatic and cationic species by applying computational chemistry methods. A thorough study of this kind of interactions is performed in systems of interest, trying to clarify which are their main features. Therefore, it also aims to quantify the role played by the environment on these interactions and whether it can act as a modulator of them. Since the study of cation···π interactions is a wide field for study, this thesis is focused on interactions involving aromatic and charged species that can be on the side chain of amino acids. The results indicate that a small number of water molecules has a deep impact on the structural arrangement of the cation···π contact. The first water molecule close to the cation establishes specific interactions with the aromatic units so it is more strongly bound to the cation···π complex. Also, it has been determined that complexes of cations with aromatic amino acids tend to favour parallel arrangements of the cation over the aromatic rings, as a consequence of larger contributions of dispersion and induction which are capable of overcoming the cost of folding the amino acid

Computational Study on the effect of microhydration on amonium···phenol and methylammonium···phenol complexes

Interactions between cations and aromatic molecules can be often find on a large number of biomolecular systems, such as proteins and receptor-ligand complexes. In addition, its important role in biological processes such as molecular recognition, drug action, and protein folding has been revealed by extensive experimental and theoretical investigations. Most previous theoretical investigations of cation···p interactions, have been focused on their characteristics in the gas phase, with less attention to their behavior in aqueous environment. In this latter case, most of the work has been focused on the whole effect of water solution as a medium on the cation···p interactions. Hence, it is important studying the influence of individual water molecules on the interaction as the cation···p complex is sequentially hydrated. The ammonium···phenol and methylammonium···phenol cation···p complex was selected as a model system to explore how water molecules affect the cation···p interaction. To mimic the process of water molecules binding to a cation···p complex, water molecules were introduced into the complex one by one. The purpose of this study is studying the geometrical characteristic of cation···p complexes with different numbers of water molecules and to investigate how the binding of water molecules to an existing cation···p complex affects the cation···p interactio

A computational study of phenylalanine interaction with guanidinium cation

Despite being intense in the gas phase, the strength of the interaction between a cation and an aromatic cloud decreases significantly when solvated. This effect has an important impact on a variety of systems where the cation•••pi interaction is known to play a key role. In the case of cation•••pi contacts involving aromatic amino acid residues, the degree of exposure to the solvent can be widely variable, so the interaction can be modulated by the environment in an almost continuous way. Most theoretical studies regarding cation•••amino acid interactions have been performed by considering simple alkaline cations in the gas phase. However, interactions can also be established with more complex cations from other amino acids, such as it is the case with arginine cationic side chain and the aromatic units in phenylalanine, tyrosine and tryptophan. In the present work ab initio and DFT methods were employed to study complexes formed by phenylalanine and a guanidinium cation representing the cationic chain of arginine. The results help understanding the impact of the interaction on the structure of phenylalanine, and constitute a first step towards the study of the effects caused by water molecules in the characteristics of these system

A computational study of the role of water molecules on cation···p interactions

The 15th International Electronic Conference on Synthetic Organic Chemistry session Computational ChemistryAmong the different forces observed in biological complexes, the cation···p interaction is a strong, non-covalent binding force which participates in a wide variety of processes such as molecular recognition in biological receptors, enzymatic catalysis, etc. The nature and characteristics of this kind of interaction has been mainly theoretically studied in the gas phase, despite being known that the presence of water molecules modulates the strength of the interaction between metal ions and aromatic species. Besides, most studies have employed benzene as a prototype of aromatic unit. On the other hand, an also simple aromatic system as phenol presents two coordination sites for cations: the aromatic ring and the hydroxyl oxygen, thus allowing a greater variety of structures to be formed than in benzene. The hydroxyl group can also be hydrated and participate in the formation of the hydrogen bond network. In the present work, a study of the interaction between cations and phenol has been carried out to shed light on the effect of successive hydration on the interaction. So, ab initio and DFT methods were employed for studying the stepwise microhydration of phenol···cation complexes, locating the most stable structures and obtaining the corresponding complexation energies. The results suggest that the participation of the hydroxyl group is already relevant in clusters containing a small number of water molecule

Formation of secondary aerosols from the ozonolysis of styrene: effect of SO2 and H2O.

In this work we report the study of the ozonolysis of styrene and the reaction conditions leading to the formation of secondary aerosols. The reactions have been carried out in a Teflon chamber filled with synthetic air mixtures at atmospheric pressure and room temperature. We have found that the ozonolysis of styrene in the presence of low concentrations of SO2 readily produces new particles under concentrations of reactants lower than those required in experiments in the absence of SO2. Thus, nucleation events occur at concentrations around (5.6 ± 1.7) × 108molecule cm−3 (errors are 2σ±20%) and SO2 is consumed during the experiments. The reaction of the Criegee intermediates with SO2 to produce SO3 and then H2SO4 may explain (together with OH reactions’ contribution) the high capacity of styrene to produce particulate matter in polluted atmospheres. The formation of secondary aerosols in the smog chamber is inhibited under high H2O concentrations. So, the potential formation of secondary aerosols under atmospheric conditions depends on the concentration of SO2 and relative humidity, with a water to SO2 rate constants ratio kH2O/kSO2 = (2.8 ± 0.7) × 10−5 (errors are 2σ±20%)

Reformulating Pro-Oxidant Microglia in Neurodegeneration

In neurodegenerative diseases, microglia-mediated neuroinflammation and oxidative stress are central events. Recent genome-wide transcriptomic analyses of microglial cells under different disease conditions have uncovered a new subpopulation named disease-associated microglia (DAM). These studies have challenged the classical view of the microglia polarization state's proinflammatory M1 (classical activation) and immunosuppressive M2 (alternative activation). Molecular signatures of DAM and proinflammatory microglia (highly pro-oxidant) have shown clear differences, yet a partial overlapping gene profile is evident between both phenotypes. The switch activation of homeostatic microglia into reactive microglia relies on the selective activation of key surface receptors involved in the maintenance of brain homeostasis (a.k.a. pattern recognition receptors, PRRs). Two relevant PRRs are toll-like receptors (TLRs) and triggering receptors expressed on myeloid cells-2 (TREM2), whose selective activation is believed to generate either a proinflammatory or a DAM phenotype, respectively. However, the recent identification of endogenous disease-related ligands, which bind to and activate both TLRs and TREM2, anticipates the existence of rather complex microglia responses. Examples of potential endogenous dual ligands include amyloid β, galectin-3, and apolipoprotein E. These pleiotropic ligands induce a microglia polarization that is more complicated than initially expected, suggesting the possibility that different microglia subtypes may coexist. This review highlights the main microglia polarization states under disease conditions and their leading role orchestrating oxidative stress

Galectin-3 Deletion Reduces LPS and Acute Colitis-Induced Pro-Inflammatory Microglial Activation in the Ventral Mesencephalon

Parkinson’s disease is a highly prevalent neurological disorder for which there is currently no cure. Therefore, the knowledge of risk factors as well as the development of new putative molecular targets is mandatory. In this sense, peripheral inflammation, especially the originated in the colon, is emerging as a predisposing factor for suffering this disease. We have largely studied the pleiotropic roles of galectin-3 in driving microglia-associated immune responses. However, studies aimed at elucidating the role of galectin-3 in peripheral inflammation in terms of microglia polarization are lacking. To achieve this, we have evaluated the effect of galectin-3 deletion in two different models of acute peripheral inflammation: intraperitoneal injection of lipopolysaccharide or gut inflammation induced by oral administration of dextran sodium sulfate. We found that under peripheral inflammation the number of microglial cells and the expression levels of pro-inflammatory mediators take place specifically in the dopaminergic system, thus supporting causative links between Parkinson’s disease and peripheral inflammation. Absence of galectin-3 highly reduced neuroinflammation in both models, suggesting an important central regulatory role of galectin-3 in driving microglial activation provoked by the peripheral inflammation. Thus, modulation of galectin-3 function emerges as a promising strategy to minimize undesired microglia polarization states.This work was supported by grants from the Spanish Ministerio de Ciencia, Innovación y Universidades (RTI 2018-098830-B-I00), from the Consejería de Economía y Conocimiento of Junta de Andalucía (P18-RT-1372 and US-1264806). MJP, MDVC and PGM were supported by a grant from the Junta de Andalucía (CTS 5884) and AEC by an associated post-doctoral grant

Protagonismo del mentor en una actividad tutorial de carácter multidisciplinar en Ingeniería

XIX Congreso Universitario de Innovación Educativa en las Enseñanzas Técnicas : Barcelona, 6 a 8 de julio de 2011En la Escuela Politécnica Superior (EPS) de la Universidad de Sevilla se ha trabajado, por tercer curso consecutivo, en un Plan de Acción Tutorial desarrollado por 16 profesores tutores y 20 alumnos mentores de 5 titulaciones de Ingeniería Técnica. El objetivo perseguido en este curso ha sido potenciar actividades que han surgido del propio albedrío de los alumnos mentores, lo que ha dado como resultado la realización de una serie de actividades de mentoría motivadas y dirigidas desde el principio por los alumnos mentores. La actividad conjunta de todos ellos ha llevado a organizar unos subgrupos de mentorías en función de determinadas características del alumnado de primer curso (deportistas, trabajadores, becarios de otras universidades…), a realizar reuniones presenciales de mentores para puesta a punto de estas actividades así como de puesta al día de los resultados que se iban consiguiendo, además de organizar una segunda captación de mentorizados tras las notas del primer cuatrimestre, y la protagonización de una Jornada de Mentoría al final del curso.A third edition with 16 tutorial lecturers and 20 tutorial students from five different degrees (Technical Engineering of the Polytechnical School, EPS, at University of Seville) in a Tutorial Plan development, has been prepared. During the present year, the main characteristic has been a serial of mentoring actions motivated and directed by these mentors. This activity has been organized considering several subgroups of mentoring depending on special characteristics in first year students (sportsplayers, workers, grant holders from other universities…), moreover the organization of a second recruiting of new students after the first term marks, updating meetings for mentors only, and to be main figures in a Congress on Mentoring at the end of the academic year

La mentoría en la Escuela Universitaria Politécnica de la Universidad de Sevilla

XVIII Congreso Universitario de Innovación Educativa en las Enseñanzas Técnicas. Escuela Técnica Superior de Ingenieros Industriales y de Telecomunicación. Universidad de Cantabria : Santander, 6 a 9 de julio de 2010Con el fin de integrar a los alumnos de nuevo ingreso, la Escuela Universitaria Politécnica de la Universidad de Sevilla ha puesto en marcha en el curso 2008-09 un Plan de Acción Tutorial (EUPAT) basado en una red en la que participan el profesorado tutor, alumnado mentor y alumnado tutorizado. En el presente trabajo se resumirá el proceso de formación del alumnado mentor y el trabajo desarrollado por el mismo dentro del Plan de Acción Tutorial. Así mismo, se analizarán las dificultades encontradas durante el transcurso de su formación y realización de la labor de mentoría y el nivel de satisfacción alcanzado. Finalmente, se hará una reflexión sobre las debilidades y los puntos de mejora que se pueden deducir del desarrollo hasta el momento de esta acción tutorialIn order to integrate new students, the Polytechnic School of the University of Seville has launched in the year 2008-09 an Tutorial Action Plan (EUPAT) based on a network involving teachers, mentor students and tutored students. In this paper we resume the formation of mentor students and work developed by the same within the Tutorial Action Plan. Also, analyzing the difficulties encountered during the course of their training and carrying out the work of mentoring and the satisfaction level achieved. Finally, we will reflect on the weaknesses and areas for improvement that can be deducted from the development until the time of this action tutorial

Evolution of Quality of Life and Treatment Adherence after One Year of Intermittent Bladder Catheterisation in Functional Urology Unit Patients

Objective: To determine patient difficulties and concerns when performing IBC (Intermittent Bladder Catheterisation), as well as the evolution of adherence, quality of life, and emotional state of patients one year after starting IBC. Method: A prospective, observational, multicentre study conducted in 20 Spanish hospitals with a one-year follow-up. Data sources were patient records and the King's Health Questionnaire on quality of life, the Mini-Mental State Examination (MMSE), and the Hospital Anxiety and Depression Scale (HADS). Perceived adherence was measured using the ICAS (Intermittent Catheterization Adherence Scale) and perceived difficulties with IBC were assessed using the ICDQ (Intermittent Catheterization Difficulty Questionnaire). For data analysis, descriptive and bivariate statistics were performed for paired data at three points in time (T1: one month, T2: three months, T3: one year). Results: A total of 134 subjects initially participated in the study (T0), becoming 104 subjects at T1, 91 at T2, and 88 at T3, with a mean age of 39 years (standard deviation = 22.16 years). Actual IBC adherence ranged from 84.8% at T1 to 84.1% at T3. After one year of follow-up, a statistically significant improvement in quality of life (p <= 0.05) was observed in all dimensions with the exception of personal relationships. However, there were no changes in the levels of anxiety (p = 0.190) or depression (p = 0.682) at T3 compared to T0. Conclusions: Patients requiring IBC exhibit good treatment adherence, with a significant proportion of them performing self-catheterisation. After one year of IBC, a significant improvement in quality of life was noted, albeit with a significant impact on their daily lives and their personal and social relationships. Patient support programmes could be implemented to improve their ability to cope with difficulties and thus enhance both their quality of life and the maintenance of their adherence