Analysis of correlated mutations in HIV-1 protease using spectral clustering

Motivation: The ability of human immunodeficiency virus-1 (HIV-1) protease to develop mutations that confer multi-drug resistance (MDR) has been a major obstacle in designing rational therapies against HIV. Resistance is usually imparted by a cooperative mechanism that can be elucidated by a covariance analysis of sequence data. Identification of such correlated substitutions of amino acids may be obscured by evolutionary noise

Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

Concepts, perspectives and implications of a hybrid system made of nucleic acids biopolymers and hydroxyapatite mineral

The origin of building blocks of life and how life thrived on Earth remains a topic of high interest for researchers of the Origin of Life. In this thesis, we deal with concepts, perspectives and implications of the system termed hydroxyolite, a combination of outstanding biopolymers (nucleic acids such as DNA and RNA) and an exceptional mineral (hydroxyapatite). First we study, based on Revilla et al. (2013) and Bertran et al. (2014), how hydroxyapatite forms crystals able to encapsulate DNA or RNA when nucleic acids are used as a nucleating template. Later, in Bertran et al., (2016), we reported the mechanism of how the encapsulated nucleic acid is released to the surroundings when environmental conditions change, for instance becoming more acidic. As a consequence, we postulated that DNA existing in cells can be encapsulated and protected by hydroxyapatite against environmental attacks (i.e. poisonous gases, gamma radiation or enzymatic degradation) until they change, making feasible the reintroduction of nucleic acids in the mainstream of life. We hypothesized about the implications of such a system in the early history of life when mass extinction events occurred on Earth (Turon et al., 2015). Moreover, we extended the hydroxyolite concept, borrowed from the materials chemistry, to other disciplines such as paleontology, biology, biotechnology and medicine by considering hydroxyolites as equivalents to non-viral vectors that can introduce and release DNA into a cell (transfection). Such nucleic acid triggers the expression of foreign proteins if released in the cytosol or might be recombined with cell genome when DNA is released in the target cell nucleus. In the second part of the thesis, we studied the hydroxyolite system from a complementary perspective. We speculate about the consequences of being hydroxyapatite the first actor and not the nucleic acid. We propose that hydroxyapatite might act as an inorganic mold if considered as a catalytic substrate that facilitates the synthesis of simple organic molecules as the building blocks of life. Thus, we identified a prebiotic scenario, a volcanic eruption under lightning, where a phenomenon known as dirty storm usually occurs under certain conditions. Hydroxyapatite is known in nature to be part of igneous rocks and volcanic ash in small but significant concentrations. We replicated in the laboratory such extreme conditions by developing a thermally and electrically stimulated polarization. A process performed at 1000 ºC and under a difference of potential of 300 kV·m-1, to obtain permanently polarized hydroxyapatite (Turon et al., 2016; PCT/EP2017/069437) that turned out to be an enhanced catalyst compared to hydroxyapatite able to fix nitrogen and carbon from a gas mixture of N2, CO2 and CH4 (Rivas et al., 2018). The catalyst, under UV light, converts them into amino acids (Glycine and D/L-Alanine) and small organic molecules by means of a new inorganic photosynthetic process. In this work, we develop an integrative prebiotic model that describes how simple molecules might be synthesized from mildly reducing atmospheres by combining previous models such as volcanos as giant reactors, minerals as catalysts and photochemical reactions in the atmosphere under prebiotic sun light. All of them under the framework of a prebiotic inorganic photosynthesis, a process that might be considered the corner stone of the rise of the building blocks of life.L’origen de les molècules que van donar lloc a la vida i com la vida va prosperar a la Terra segueix essent un tema del màxim interès pels investigadors de l’origen de la vida. En aquesta tesi, discutim conceptes, perspectives de futur i implicacions del sistema que hem anomenat hidroxiolita (hydroxyolite), una combinació de biopolímers amb característiques molt especials (àcids nucleics com l’ADN i l’ARN) i un mineral excepcional (hidroxiapatita). En primer lloc, en els treballs Revilla et al., (2013) i Bertran et al., (2014) estudiem com els cristalls d’hidroxiapatita tenen la capacitat d’encapsular ADN o ARN quan l’àcid nucleic es comporta com agent nucleant. Reportem com l’àcid nucleic prèviament encapsulat pot ser alliberat si les condicions ambientals canvien, per exemple tornant-se lleugerament més àcides (Bertran et al., 2016). Com a conseqüència, postulem que l’ADN existent a les cèl·lules pot ser encapsulat per la hidroxiapatita protegint-lo contra atacs de l’entorn (per exemple, la influència de gasos tòxics, la radiació gamma o la degradació enzimàtica) fins que les condicions externes canvien i els àcids nucleics poder ser reintroduïts en el torrent principal de la vida. Discutim les implicacions d’aquest sistema híbrid a la història primitiva de la vida a la Terra, quan van ocórrer les grans catàstrofes que van donar lloc a extincions massives d’éssers vius. Tanmateix, estenem el concepte d’hidroxiolita a altres disciplines com la paleontologia, la biologia cel·lular, la biotecnologia i la medicina, considerant les hidroxiolites com a vectors no virals que poden introduir i alliberar ADN dins una cèl·lula (transfecció). Aquest àcid nucleic, si s’allibera en el citosol pot desencadenar l’expressió de proteïnes codificades en l’ADN introduït, o si s’allibera en el nucli podria recombinar-se amb el propi ADN de la cèl·lula diana de manera transitòria o permanent. A la segona part de la tesi, estudiem el sistema hidroxiolita des d’una perspectiva complementària. Especulem sobre les conseqüències de ser la hidroxiapatita l’actor principal del sistema i no l’àcid nucleic. Proposem que la hidroxiapatita pot actuar com un motlle inorgànic si es comporta com a substrat catalític que facilita la síntesi de molècules orgàniques, com les molècules que van donar lloc a la vida. A partir d’aquest concepte hem identificat un escenari prebiòtic, una erupció volcànica acompanyada de descàrregues elèctriques, fenomen que succeeix amb certa freqüència en funció de les característiques de l’erupció. La hidroxiapatita a la natura és coneguda per formar part de la composició de roques ígnies i de la cendra volcànica en petites però significatives quantitats. Al laboratori hem replicat aquestes condicions extremes i hem desenvolupat un procés de polarització mitjançant estimulació elèctrica i tèrmica, aplicant 1000 ºC i una diferència de potencial de 300 kV·m-1, que dóna com a resultat hidroxiapatita polaritzada permanentment que converteix el mineral en un catalitzador extraordinari comparat amb la hidroxiapatita i que té la capacitat de fixar nitrogen i carboni a partir d’una mescla de gasos composada per N2, CO2 i CH4 en presència d’aigua. El catalitzador, sota il·luminació de llum UV facilita la conversió d’aquests gasos en aminoàcids (Glicina i D/L-Alanina) i en molècules orgàniques simples a través d’un procés fotosintètic inorgànic. En aquest treball, desenvolupem un model prebiòtic que descriu com molècules senzilles van poder ser sintetitzades a partir d’atmosferes suaument reductores combinant models prebiòtics previs (volcans que es comporten com grans reactors, reaccions fotoquímiques que succeeixen a l’atmosfera sota el sol prebiòtic i minerals que actuen com a catalitzadors) sota el marc de la fotosíntesi inorgànica prebiòtica, un procés que podria ser considerat la pedra angular de l’aparició de les molècules que van donar lloc a la vida.El origen de las moléculas que dieron lugar a la vida y como la vida prosperó en la Tierra sigue siendo un tema del máximo interés para los investigadores del Origen de la Vida. En esta tesis discutimos conceptos, perspectivas de futuro e implicaciones del sistema que hemos denominado hidroxiolita (hydroxyolite), una combinación de biopolímeros con características muy especiales (ácidos nucleicos tales como el ADN y el ARN) y un mineral excepcional (hidroxiapatita). En primer lugar, en nuestros trabajos Revilla et al. (2013) y Bertrán et al. (2014) estudiamos como los cristales de hidroxiapatita tienen la capacidad de encapsular ADN o ARN cuando el ácido nucleico se comporta como un agente nucleante. A continuación, reportamos como el ácido nucleico previamente encapsulado puede ser liberado cuando las condiciones ambientales cambian, por ejemplo, cuando se vuelven ligeramente más ácidas (Bertrán et al., 2016). A consecuencia, postulamos que el ADN existente en las células puede ser encapsulado por la hidroxiapatita protegiéndolo contra ataques del entorno (por ejemplo, la influencia de gases tóxicos, la radiación gamma o la degradación enzimática) hasta que cambian las condiciones externas y los ácidos nucleicos pueden ser reintroducidos de nuevo en el torrente principal de la vida. A continuación, discutimos las implicaciones de este sistema híbrido en la historia primitiva de la vida en la Tierra, cuando ocurrieron las grandes catástrofes que dieron lugar a extinciones masivas de seres vivos (Turon et al., 2015). Asimismo, extendemos el concepto hidroxiolita, acuñado en la ciencia de materiales, a otras disciplinas como la paleontología, la biología celular, la biotecnología y la medicina, considerando las hidroxiolitas como vectores no virales que pueden introducir y liberar ADN dentro de una célula (transfección). Este ácido nucleico, si es liberado en el citosol puede desencadenar la expresión de proteínas codificadas en el ADN introducido, o si se libera en el núcleo podría recombinarse con el propio ADN de la célula diana de forma transitoria o permanente. En la segunda parte de la tesis, estudiamos el sistema hidroxiolita desde una perspectiva complementaria. Especulamos sobre las consecuencias de ser la hidroxiolita el actor principal y no el ácido nucleico. Proponemos que la hidroxiolita puede actuar como un molde inorgánico si se comporta como un sustrato catalítico que facilita la síntesis de moléculas orgánicas, como las moléculas que dieron lugar a la vida. Hemos identificado un escenario prebiótico basado en una erupción volcánica con descargas eléctricas, fenómeno que ocurre con cierta frecuencia en función de las características de la erupción. La hidroxiapatita es conocida en la naturaleza por formar parte de la composición de rocas ígneas y ceniza volcánica en bajas pero significativas concentraciones. Hemos replicado en el laboratorio estas condiciones extremas y hemos desarrollado un proceso de polarización mediante estimulación térmica y eléctrica, aplicando 1000ºC y una diferencia de potencial de 300 kV·m-1, que da como resultado hidroxiapatita permanentemente polarizada (Turón et al, 2016; PCT/EP2017/069437). Este proceso convierte el mineral en un catalizador extraordinario comparado con la hidroxiapatita y tiene la capacidad de fijar nitrógeno y carbono a partir de una mezcla de gases compuesta por N2, CO2 y CH4 (Rivas et al., 2018) en presencia de agua. El catalizador, bajo iluminación de luz UV, facilita la conversión de estos gases en aminoácidos (Glicina y D/L-Alanina) y en ácidos orgánicos simples a través de un proceso de fotosíntesis inorgánica. En este trabajo desarrollamos un modelo prebiótico que describe como moléculas sencillas pudieron ser sintetizadas a partir de atmósferas suavemente reductores combinando modelos prebióticos ya existentes (volcanes que se comportan grandes reactores, reacciones fotoquímicas que ocurren en la atmosfera bajo el sol prebiótico y minerales que actúan como catalizadores) bajo el marco de una fotosíntesis prebiótica inorgánica, un proceso que podría ser considerado la piedra angular en la que se basó la aparición de las moléculas que dieron lugar a la vida.Postprint (published version

Parallel and Distributed Computing

The 14 chapters presented in this book cover a wide variety of representative works ranging from hardware design to application development. Particularly, the topics that are addressed are programmable and reconfigurable devices and systems, dependability of GPUs (General Purpose Units), network topologies, cache coherence protocols, resource allocation, scheduling algorithms, peertopeer networks, largescale network simulation, and parallel routines and algorithms. In this way, the articles included in this book constitute an excellent reference for engineers and researchers who have particular interests in each of these topics in parallel and distributed computing

Combining Sequence and Structure Information to Model Biological Systems Dynamics

Biochemical activity and core stability are essential properties of proteins, maintained usually by conserved amino acids. Structural dynamics emerged in recent years as another essential aspect of protein functionality, which enables the adaptation of the protein to substrate binding. It also underlies its ability to undergo allosteric transitions, while maintaining its fold. Key residues that mediate structural dynamics would thus be expected to be conserved, or exhibit co-evolutionary patterns at least. Yet, the correlation between sequence evolution and structural dynamics is yet to be established. To this end, we have performed in-depth analyses of a number of representative proteins, using a combined approach of sequence analyses and coarse-grained physics-based models. For the Hsp70 family, we studied the interactions of Hsp70 ATPase domains with four different nucleotide exchange factors (NEFs) and revealed two classes of key residues: (i) those highly conserved residues involved in nucleotide binding, which mediate the ATPase domain opening via a global hinge-bending, and (ii) those co-evolving and highly mobile residues engaged in specific interactions with NEFs. The observed interplay between these respective intrinsic (pre-existing, structure-encoded) and specific (co-evolved, sequence-dependent) interactions provides us with insights into the allosteric dynamics and functional evolution of the modular Hsp70 ATPase domain, and inspired a follow-up study that identified a group of key residues mediating the Hsp70 allosteric pathways using perturbation analysis. Along the same lines, a systematic study has been performed on a set of 34 enzymes representing various folds and functional classes, which generalizes the previous findings and unravels a unique correlation between sequence evolutionary properties and conformational dynamics. Our findings suggest that there is a balance between physical adaptability (enabled by structure-encoded motions) and chemical specificity (conferred by correlated amino acid substitutions), and this balance underlies the selection of a relatively small set of versatile folds by proteins. In another study, HIV-1 protease was investigated as a special case in which short-term evolutionary pressure plays a significant role. With advanced clustering techniques, we differentiated multi-drug resistant mutations from those arising from phylogenetic variations; correspondingly, these mutations exhibit distinctive structural/dynamical features, underlying the role of protein dynamics in conferring drug resistance

Bioinorganic Chemistry

This book covers material that could be included in a one-quarter or one-semester course in bioinorganic chemistry for graduate students and advanced undergraduate students in chemistry or biochemistry. We believe that such a course should provide students with the background required to follow the research literature in the field. The topics were chosen to represent those areas of bioinorganic chemistry that are mature enough for textbook presentation. Although each chapter presents material at a more advanced level than that of bioinorganic textbooks published previously, the chapters are not specialized review articles. What we have attempted to do in each chapter is to teach the underlying principles of bioinorganic chemistry as well as outlining the state of knowledge in selected areas. We have chosen not to include abbreviated summaries of the inorganic chemistry, biochemistry, and spectroscopy that students may need as background in order to master the material presented. We instead assume that the instructor using this book will assign reading from relevant sources that is appropriate to the background of the students taking the course. For the convenience of the instructors, students, and other readers of this book, we have included an appendix that lists references to reviews of the research literature that we have found to be particularly useful in our courses on bioinorganic chemistry

Interaction of the HeLa cell protein EBP1 with viral and cellular enhancers

A cellular protein, EBP1, was identified, which bound to the "core" region of the SV40 enhancer. The DNA sequences requirements for specific EBP1 binding distinguished this protein from a number of previously reported enhancer binding proteins, Multiple copies of the EBP1 binding site could serve, in vivo, to enhance transcription. The in vivo transcriptional activity of wild type and mutant SV40 enhancers correlated with EBP1 binding. Mutations that abolish EBP1 binding also severely reduced transcription, indicating that this protein may be important for SV40 enhancer activity. Nuclease protection and chemical probing studies identified purine bases and backbone phosphate groups which participate in the formation of a specific EBP1/DNA complex. "Footprinting" with hydroxyl radicals revealed deoxyribose residues in the binding site which are protected from cleavage by EBP1. Computer graphics were used to display this information indicating that EBP1 made specific base and backbone contacts over one complete turn of the DNA double helix, supporting a model whereby the protein makes sequence-specific contacts in the major groove, although binding may also be influenced by interactions in the minor groove. Competition and contact point analyses revealed that EBP1 bound similarly to sites present in several other viral and cellular enhancers. Mutational analysis of EBP1 binding sites identified base pairs important for specific EBP1/DNA complex formation. All high affinity binding sites contained the sequence 5'-GG(N)6CC-3'. Although single base pair changes in the region between the conserved guanines and cytosines can generally be tolerated, it is clear that the central six base pairs contribute to binding affinity. Mutations in the recognition site which could lead to gross structural changes in the DNA abolish EPB1 binding

Women in Science 2015

Women in Science 2015 summarizes research done by Smith College’s Summer Research Fellowship (SURF) Program participants. Ever since its 1967 start, SURF has been a cornerstone of Smith’s science education. In 2015, 162 students participated in SURF (153 hosted on campus and nearby eld sites), supervised by 60 faculty mentor-advisors drawn from the Clark Science Center and connected to its eighteen science, mathematics, and engineering departments and programs and associated centers and units. At summer’s end, SURF participants were asked to summarize their research experiences for this publication.https://scholarworks.smith.edu/clark_womeninscience/1002/thumbnail.jp