No description available.

Living cells are dependent upon protein synthesis for virtually all cellular functions. The cellular machine responsible for protein synthesis, called the ribosome, is formed through the association of two unequally sized subunits, each composed of RNA and proteins. Proper assembly of each subunit is essential to ribosome function and therefore essential to the cellular life cycle. Previous studies focused on dissecting the assembly of the small ribosomal subunit (30S subunit) from E. coli have shown that 21 proteins sequentially assemble on the 16S rRNA at multiple nucleation sites. For the first time, we are able to monitor changes in the secondary and tertiary structure of the 16S rRNA upon the addition of single proteins during assembly by using time-dependent chemical probing. Results from these studies suggest that protein S17 induces multiple structural changes in 16S rRNA by first binding to helix 11 and then helix 7. S20 also induces changes in the rRNA by interacting with helix 9, 11, 44 and 13 in that order. These structural formations and rearrangements then prepare the binding sites for additional proteins (S12 and S16, respectively). This study demonstrates that time-dependent chemical probing is able to monitor the assembly of the 30S subunit at a level of detail never before seen. These studies also suggest that many motifs in the 16S rRNA structure are formed as a result of the proteins binding, lending evidence to the hypothesis that the function of ribosomal proteins is to shape and/or hold the RNA structure in place.

No description available.

Thesis (Ph.D.) in Chemistry--University of Maine, 2007. / Includes vita. Includes bibliographical references (leaves 86-90).

Thesis (Ph.D.) in Physics--University of Maine, 2004. / Includes vita. Includes bibliographical references (leaves 100-104).

Nous avons présenté COMMA, une méthode pour décrire et comparer les architectures dynamiques de différentes protéines. Il extrait propriétés dynamiques de ensembles conformationnels pour identifier les voies de communication, des chaînes de résidus liés par des interactions stables qui se déplacent ensemble, et cliques indépendants, des groupes de résidus qui fluctuent de manière concertée. Il fournit une description de l'infostery d'un complexe de protéines qui va au-delà des mesures au-delà de classiques de la façon dont une protéine se déplace ou change de forme. Nous avons montré l'efficacité de notre approche pour fournir des idées mécanistiques sur les effets des mutations délétères en identifiant les résidus qui jouent un rôle clé dans la propagation de ces effets. En outre COMMA révèle un lien entre les clusters de coévoluant résidus et les réseaux de corrélations dynamiques. Il permet de comparer les différents types de communication se produisant entre les résidus et de hiérarchiser les différentes régions d'une protéine en fonction de l'efficacité de leur communication. En outre, nous avons présenté une approche pour exploiter les séquences et les dynamiques structurelles pour prédire un paysage mutationnel. La discussion des exemples, a révélé l'interprétation physique sur la façon dont l'étude de la conservation apporte des idées importantes sur la sensibilité des positions conservées à des mutations. Notre méthode proposée, peut détecter des régions de protéines qui sont sujettes à des troubles ou des réarrangements conformationnels substantiels. De plus, il nous a permis de proposer des mutations qui régulent la stabilité des bobines enroulées désordonnées. / We presented COMMA, a method to describe and compare the dynamical architectures of different proteins or different variants of the same protein. COMMA extracts dynamical properties from conformational ensembles to identify communication pathways, chains of residues linked by stable interactions that move together, and independent cliques, clusters of residues that fluctuate in a concerted way. It provides a description of the infostery of a protein or protein complex that goes beyond the notions of chain, domain and secondary structure element/motif, and beyond classical measures of how a protein moves and/or changes its shape. We showed the efficiency of our approach in providing mechanistic insights on the effects of deleterious mutations by pinpointing residues playing key roles in the propagation of these effects. In addition COMMA reveals a link between clusters of coevolving residues and networks of dynamical correlations. It enables to contrast the different types of communication occurring between residues and to hierarchise the different regions of a protein depending on their communication efficiency. Furthermore, we presented an approach to exploit both the sequences and structural dynamics to predict a mutational landscape. The discussion of examples, revealed physical interpretation on how the study of conservation brings significant insights on the sensitivity of conserved positions to mutations. Our proposed method, can detect protein regions that are prone to disorder or substantial conformational rearrangements. Moreover, it enabled us to suggest mutations that regulate the stability of the disordered coiled-coils.

L'étude de la dynamique intrinsèque de l'ADN-B permet de caractériser l'espace conformationnel exploré par cette macromolécule. Cette dynamique, qui dépend de la séquence, est un facteur clé dans les mécanismes d'interaction avec les protéines, l'ADN étant plus ou moins prédisposé à s'adapter à son partenaire. Lors de cette thèse, nous avons sondé la dynamique de l'ADN à deux échelles de temps, en nous basant sur l'étude de quatre dodécamères par Résonance Magnétique Nucléaire (RMN). Nous nous sommes d'abord intéressés à la dynamique des groupements phosphates, qui correspondent à des mouvements rapides (picoseconde-nanoseconde). Nous avons ainsi confirmé l'effet de la séquence dinucléotidique sur cette dynamique, qui peut être prédit et quantifié. Nous avons également mis en lumière pour la première fois l'étroite inter-dépendance qui existe entre déplacements chimiques du phosphore, distances internucléotides et constantes de couplage dipolaire résiduel. L'interprétation de ces observables RMN en termes de conformations des phosphates, de paramètres hélicoïdaux et de taille des sillons, montre qu'en fait ces couplages reflètent la mécanique intrinsèque de l'ADN en solution. En interfaçant ces résultats avec l'effet de séquence observé sur la dynamique des phosphates, il est aussi possible de saisir de quelle façon la conformation moyenne de la double hélice et l'espace conformationnel associé sont modulés par la séquence au niveau dinucléotidique. Enfin, des dynamiques moléculaires réalisées avec les très récents champs de force CHARMM36 et Parmbsc0ezOLI, confrontées aux données expérimentales, ont permis d'apprécier le réalisme croissant des ADN simulés et ont aidé à préciser des éléments de la dynamique qui échappent à l'expérience. Le deuxième volet de cette thèse a porté sur les mouvements de l'ADN se produisant à l'échelle de la milliseconde, encore très peu étudiés. Nous avons mis au point des expériences de dispersion-relaxation qui ont apporté la preuve de l’existence d’un échange conformationnel d'un type totalement nouveau. Cet échange ne semble apparaitre que sur un type particulier de séquence, riche en A:T. Certaines régions de l’ADN, probablement spécifiques, peuvent ainsi localement évoluer vers une forme très faiblement peuplée, dont la structure détaillée reste à caractériser. L'ensemble de ces résultats offre un panorama des capacités dynamiques de l'ADN, dépendantes de la séquence, et ouvre ainsi de nombreuses perspectives vers une meilleure compréhension des mécanismes qui guident la formation des complexes ADN-protéines. / The study of B-DNA intrinsic dynamics enables to characterize the conformational landscape explored by this macromolecule. Indeed, binding of DNA to proteins is modulated by subtle sequence-dependent variations inherent to the dynamics of free DNA, which facilitate or disfavor the structural fit with cognate partners.In this thesis, the DNA dynamics was investigated at two time-scales, on the basis of the Nuclear Magnetic Resonance (NMR) study of four dodecamers. First, we examined the fast dynamics (pico-nanosecond) of phosphate linkages. We confirmed that the dinucleotide sequence modulates the backbone dynamics, an effect that can be quantified and predicted. Then, our experimental data enabled to establish that phosphorus chemical shifts, internucleotide distances and residual dipolar couplings constants are closely correlated. The translation of the NMR observables in terms of phosphate conformations, helicoidal parameters and minor groove dimension, allowed the structural interpretation of the couplings and led to the first coherent description of the intrinsic DNA mechanics in solution. Owing our knowledge of the effect of the sequence on the backbone behavior, it is now possible to understand how the DNA shape and the associated conformational landscape are modulated at the dinucleotide level. Finally, the performance of molecular dynamics (MD) simulations with the recent force-fields Parmbsc0εζOLI and CHARMM36 was tested extensively against our NMR data. We found impressive progress towards a realistic representation of DNA, despite residual shortcomings. This advance allowed to reveal new aspects of the DNA dynamics, which cannot be assessed from experiments.The second part of this thesis focused on slow motions in B-DNA, which are still largely under-investigated. Using and developing sophisticated relaxation-dispersion NMR experiments, we demonstrated the existence of a new conformational exchange at the millisecond time-scale, which seems to only occur in a particular type of sequence, A:T rich. Thus, in addition to the familiar structural patterns that are the signature of the B double helix, some short DNA regions, likely specific, are able to explore another conformational state, weakly populated, whose detailed structure still needs to be characterized.Overall, these results provide original insights on the DNA dynamic repertoire, sequence-dependent, and open the way towards a better understanding of the mechanisms underlying the formation of DNA-protein complexes.

No description available.

<p>Adhesives  are  found  in  almost  every  aspect  of  the  modern  world.  They  are  found  in plywood used in buildings, electronics, shoes, plumbing and in almost every facet of your daily life. Nature also has an abundance of these adhesives that are used fora multitude of applications. Some  animals, like  the  blue  mussel, use  their  adhesive  for  protection  against  ocean  waves  and predators  while other animals, such  as  the  spider, use  it  to  trap  prey. Investigation  of  theses adhesives has led to the identification of several different proteins that allow for these animals to make  their  adhesive.  Some  of  them  are  composed of rare  amino  acids that  while  other  animals use  a combination  of  inorganic  and  organic  components.  Understanding  of  these  unique adhesives  can be  a  boon  for designof future  adhesives  that  do  not  have  the disadvantagesof current day commercialized glues.</p> <p>Increasing interest  in  the  restoration  of  natural  oyster  reefs  and  the  cement  that  holds them  together  has  resulted  in  the  identification  of  the  Shelk2  protein  that  is  found  both  in  the mantle  of  the  oyster’s  shell  as  well  as  the  cement  that  holds  the  reefs  together. Gaining  an understanding  of  how  this  protein  functions  and  its  part  in  the  oyster  reef  could  be  quite beneficial  for  projects  investing  in  reef  restorations  as  well  as  underwater  adhesion.  Gathering protein  from  the  animal  for  experimentation  and  characterization  can  be  labor  intensive  and extremely challenging. Luckily, cloning technology has become a useful tool for the expression of large quantities of proteins that can be difficult or impossible to gather from the native animal. Using <em>E. coli</em>, it  is  possible  to design  and express  this protein  in  hopes  of  gaining  a  better understanding of its impact on oyster settlement and adhesion.</p> <p>Sustainability is a major downside to current day adhesives that current technologies have not  been  able  to  solve. Most adhesives  that  are  on  the  market  today  are  primarily  derived  from petroleum. Current  research  has  begun  investigating  alternatives  to  the  large   epoxy   and formaldehyde  adhesive  market,  but  the  barrier  of  entry  is  hard  to  overcome.  To  replace  these glues  the  new  material  must  be  affordable,  non-petroleum  derived,  and  available  on  a  massive scale.  These  requirements  are  hard  to  meet  for  many  materials  and  due  to  that  the  current  bio-adhesive are generally very low strength.</p> <p>The work presented here will detail the characterization, and expression of some of these natural  adhesives that  have  been  found  in  the  Eastern  oyster. Another  aspect of  this  work includes the synthesis of a new bio-based adhesive system. Utilizing biomimetic chemistry along with  sustainably  sourced  materials  a  new  adhesive  has  been  formulated that  has  comparable adhesive strength to current day commercial adhesives.</p>

The UN predicts that by 2050 there will water shortages throughout the globe. Current sources for safe, clean drinking water are being over mined and exhausted. Seawater provides an alternative water source, but a high salt content makes it unsuitable for the majority of applications. However, reverse osmosis lowers the salt content producing water that is safe for human consumption. Reverse osmosis uses a semi-permeable membrane to prevent the transport of salt but allows for the transport of water. Currently these membranes are susceptible to fouling and contamination, which reduces their efficiency. Graphene-oxide membranes offer a new material for reserves osmosis membranes. Sheets of graphene-oxide are stacked in a layered structure. The separation between the sheets can be controlled using physical confinement, resulting in limited ion permeation of abundant cations in seawater, like Na+ and K+. This is believed to be due to the separation of 0.76 nm between the graphene sheets, forcing the ions to lose its surrounding water molecules, making it unfavourable for the ion to travel through the membrane. Molecular dynamics simulations can give an atomic level insight into the molecular processes within GO membranes. Recent simulations have shown that charged species are attracted to graphene surfaces due to polarisation of the pi-electron system. This work has managed to incorporate these ion-pi interactions into molecular dynamics simulations. Including ion-pi interactions caused some ions, like Na+ and K+, to prefer to lose water molecules and reside at a graphene surface. This work observed the same phenomena when ions were confined to graphene channel ranging from 1.3 nm - 0.7 nm. This observation could have a large impact on whether dehydration is limiting the permeation of these two ions, or if there are additional processes that limit their molecular transport.