Global relativistic folding optical potential and the relativistic Green's function model

Optical potentials provide critical input for calculations on a wide variety of nuclear reactions, in particular, for neutrino-nucleus reactions, which are of great interest in the light of the new neutrino oscillation experiments. We present the global relativistic folding optical potential (GRFOP) fits to elastic proton scattering data from C-12 nucleus at energies between 20 and 1040 MeV. We estimate observables, such as the differential cross section, the analyzing power, and the spin rotation parameter, in elastic proton scattering within the relativistic impulse approximation. The new GRFOP potential is employed within the relativistic Green's function model for inclusive quasielastic electron scattering and for (anti) neutrino-nucleus scattering at MiniBooNE kinematics.

Fracture patterns and petrophysical properties of carbonates undergoing regional folding : A case study from Kurdistan, N Iraq

Acknowledgements The authors thank the Ministry of Natural Resources in Iraqi Kurdistan Region for permission to publish this paper. Gulf Keystone Petroleum Ltd. and HKN Energy Ltd. are acknowledged for providing the subsurface datasets. Great thanks to Colin Taylor at the University of Aberdeen for his assistance in the laboratory work. Thoughtful reviews by two anonymous referees improved the clarity of the paper. Graham Banks is thanked for his helpful and constructive review on a late version of the manuscript, which has significantly improved this paper.

Development and Application of Covalent-Labeling Strategies for the Large-Scale Thermodynamic Analysis of Protein Folding and Ligand Binding

Thermodynamic stability measurements on proteins and protein-ligand complexes can offer insights not only into the fundamental properties of protein folding reactions and protein functions, but also into the development of protein-directed therapeutic agents to combat disease. Conventional calorimetric or spectroscopic approaches for measuring protein stability typically require large amounts of purified protein. This requirement has precluded their use in proteomic applications. Stability of Proteins from Rates of Oxidation (SPROX) is a recently developed mass spectrometry-based approach for proteome-wide thermodynamic stability analysis. Since the proteomic coverage of SPROX is fundamentally limited by the detection of methionine-containing peptides, the use of tryptophan-containing peptides was investigated in this dissertation. A new SPROX-like protocol was developed that measured protein folding free energies using the denaturant dependence of the rate at which globally protected tryptophan and methionine residues are modified with dimethyl (2-hydroxyl-5-nitrobenzyl) sulfonium bromide and hydrogen peroxide, respectively. This so-called Hybrid protocol was applied to proteins in yeast and MCF-7 cell lysates and achieved a ~50% increase in proteomic coverage compared to probing only methionine-containing peptides. Subsequently, the Hybrid protocol was successfully utilized to identify and quantify both known and novel protein-ligand interactions in cell lysates. The ligands under study included the well-known Hsp90 inhibitor geldanamycin and the less well-understood omeprazole sulfide that inhibits liver-stage malaria. In addition to protein-small molecule interactions, protein-protein interactions involving Puf6 were investigated using the SPROX technique in comparative thermodynamic analyses performed on wild-type and Puf6-deletion yeast strains. A total of 39 proteins were detected as Puf6 targets and 36 of these targets were previously unknown to interact with Puf6. Finally, to facilitate the SPROX/Hybrid data analysis process and minimize human errors, a Bayesian algorithm was developed for transition midpoint assignment. In summary, the work in this dissertation expanded the scope of SPROX and evaluated the use of SPROX/Hybrid protocols for characterizing protein-ligand interactions in complex biological mixtures.

Electrostatic Contributions to the Thermodynamics of Ribonuclease P Protein Folding

Electrostatic interactions are of fundamental importance in determining the structure and stability of macromolecules. For example, charge-charge interactions modulate the folding and binding of proteins and influence protein solubility. Electrostatic interactions are highly variable and can be both favorable and unfavorable. The ability to quantify these interactions is challenging but vital to understanding the detailed balance and major roles that they have in different proteins and biological processes. Measuring pKa values of ionizable groups provides a sensitive method for experimentally probing the electrostatic properties of a protein.

pKa values report the free energy of site-specific proton binding and provide a direct means of studying protein folding and pH-dependent stability. Using a combination of NMR, circular dichroism, and fluorescence spectroscopy along with singular value decomposition, we investigated the contributions of electrostatic interactions to the thermodynamic stability and folding of the protein subunit of Bacillus subtilis ribonuclease P, P protein. Taken together, the results suggest that unfavorable electrostatics alone do not account for the fact that P protein is intrinsically unfolded in the absence of ligand because the pKa differences observed between the folded and unfolded state are small. Presumably, multiple factors encoded in the P protein sequence account for its IUP property, which may play an important role in its function.

The (Un)Folding of Multidomain Proteins Through the Lens of Single-molecule Force-spectroscopy and Computer Simulation

Proteins are specialized molecules that catalyze most of the reactions that can sustain life, and they become functional by folding into a specific 3D structure. Despite their importance, the question, "how do proteins fold?" - first pondered in in the 1930's - is still listed as one of the top unanswered scientific questions as of 2005, according to the journal Science. Answering this question would provide a foundation for understanding protein function and would enable improved drug targeting, efficient biofuel production, and stronger biomaterials. Much of what we currently know about protein folding comes from studies on small, single-domain proteins, which may be quite different from the folding of large, multidomain proteins that predominate the proteomes of all organisms.

In this thesis I will discuss my work to fill this gap in understanding by studying the unfolding and refolding of large, multidomain proteins using the powerful combination of single-molecule force-spectroscopy experiments and molecular dynamic simulations.

The three model proteins studied - Luciferase, Protein S, and Streptavidin - lend insight into the inter-domain dependence for unfolding and the subdomain stabilization of binding ligands, and ultimately provide new insight into atomistic details of the intermediate states along the folding pathway.

Enhancing the Manufacturing Knowledge of Undergraduate Engineering Students: A Case Study of a Design-Build-Test Challenge Involving Folding Bicycles

Many engineers currently in professional practice will have gained a degree level qualification which involved studying a curriculum heavy with mathematics and engineering science. While this knowledge is vital to the engineering design process so also is manufacturing knowledge, if the resulting designs are to be both technically and commercially viable.
The methodology advanced by the CDIO Initiative aims to improve engineering education by teaching in the context of Conceiving, Designing, Implementing and Operating products, processes or systems. A key element of this approach is the use of Design-Built-Test (DBT) projects as the core of an integrated curriculum. This approach facilitates the development of professional skills as well as the application of technical knowledge and skills developed in other parts of the degree programme. This approach also changes the role of lecturer to that of facilitator / coach in an active learning environment in which students gain concrete experiences that support their development.
The case study herein describes Mechanical Engineering undergraduate student involvement in the manufacture and assembly of concept and functional prototypes of a folding bicycle.

Composites and foams based on polylactic acid (PLA)

Cette étude est destinée à la production et à la caractérisation des composites d’acide polylactique (PLA) et des fibres naturelles (lin, poudre de bois). Le moussage du PLA et ses composites ont également été étudiés afin d’évaluer les effets des conditions de moulage par injection et du renfort sur les propriétés finales de ces matériaux. Dans la première partie, les composites constitués de PLA et des fibres de lin ont été produits par extrusion suivit par un moulage en injection. L’effet de la variation du taux de charge (15, 25 et 40% en poids) sur les caractéristiques morphologique, mécanique, thermique et rhéologique des composites a été évalué. Dans la deuxième étape, la poudre de bois (WF) a été choisie pour renforcer le PLA. La préparation des composites de PLA et WF a été effectuée comme dans la première partie et une série complète de caractérisations morphologique, mécanique, thermique et l’analyse mécanique dynamique ont été effectués afin d’obtenir une évaluation complète de l’effet du taux de charge (15, 25 et 40% en poids) sur les propriétés du PLA. Finalement, la troisième partie de cette étude porte sur les composites de PLA et de renfort naturel afin de produire des composites moussés. Ces mousses ont été réalisées à l’aide d’un agent moussant exothermique (azodicarbonamide) via le moulage par injection, suite à un mélange du PLA et de fibres naturelles. Dans ce cas, la charge d’injection (quantité de matière injectée dans le moule: 31, 33, 36, 38 et 43% de la capacité de la presse à injection) et la concentration en poudre de bois (15, 25 et 40% en poids) ont été variées. La caractérisation des propriétés mécanique et thermique a été effectuée et les résultats ont démontré que les renforts naturels étudiés (lin et poudre de bois) permettaient d’améliorer les propriétés mécaniques des composites, notamment le module de flexion et la résistance au choc du polymère (PLA). En outre, la formation de la mousse était également efficace pour le PLA vierge et ses composites car les masses volumiques ont été significativement réduites.

Effet du greffage de TiO2 à la surface de fibres de lin sur les propriétés mécaniques d'un composite PLA/fibre de lin longues unidirectionnelles

Les matériaux composites sont utilisés dans beaucoup de domaines pour leurs propriétés mécaniques spécifiques, leur mise en forme facile et leur bas coût. Cependant, lorsque les composites pétro-sourcées sont en fin de vie, le traitement des déchets a un fort impact environnemental. C’est pour cette raison que les industriels se tournent vers des matériaux bio-sourcés. Ils souhaitent ainsi abaisser le coût des matières premières mais aussi se donner une image plus « verte » grâce à l’utilisation de matériaux renouvelables et/ou compostables. Le projet présenté s’inscrit dans dans cette optique où il est question d’élaborer de nouveaux composites à renfort et matrices bio-sourcés et tout particulièrement des composites fibre de lin/acide polylactique (PLA). Ces derniers sont généralement appelés bio-composites. L’originalité de cette étude réside dans le traitement des fibres de lin afin de les compatibilité avec la matrice PLA. Le traitement consiste au greffage de dioxyde de titane sur la surface de fibres de lin fonctionnalisée par oxydation au TEMPO. Ces fibres longues sont ensuite utilisées comme renfort sous forme de tissu unidirectionnel dans la matrice PLA. Le comportement mécanique en traction, flexion et la résistance à l’impact de ces biocomposites sont étudiés afin d’analyser l’influence du traitement des fibres sur leur performances.

Analysis of Molecular Dynamics Simulations of Protein Folding

Microsecond long Molecular Dynamics (MD) trajectories of biomolecular processes are now possible due to advances in computer technology. Soon, trajectories long enough to probe dynamics over many milliseconds will become available. Since these timescales match the physiological timescales over which many small proteins fold, all atom MD simulations of protein folding are now becoming popular. To distill features of such large folding trajectories, we must develop methods that can both compress trajectory data to enable visualization, and that can yield themselves to further analysis, such as the finding of collective coordinates and reduction of the dynamics. Conventionally, clustering has been the most popular MD trajectory analysis technique, followed by principal component analysis (PCA). Simple clustering used in MD trajectory analysis suffers from various serious drawbacks, namely, (i) it is not data driven, (ii) it is unstable to noise and change in cutoff parameters, and (iii) since it does not take into account interrelationships amongst data points, the separation of data into clusters can often be artificial. Usually, partitions generated by clustering techniques are validated visually, but such validation is not possible for MD trajectories of protein folding, as the underlying structural transitions are not well understood. Rigorous cluster validation techniques may be adapted, but it is more crucial to reduce the dimensions in which MD trajectories reside, while still preserving their salient features. PCA has often been used for dimension reduction and while it is computationally inexpensive, being a linear method, it does not achieve good data compression. In this thesis, I propose a different method, a nonmetric multidimensional scaling (nMDS) technique, which achieves superior data compression by virtue of being nonlinear, and also provides a clear insight into the structural processes underlying MD trajectories. I illustrate the capabilities of nMDS by analyzing three complete villin headpiece folding and six norleucine mutant (NLE) folding trajectories simulated by Freddolino and Schulten [1]. Using these trajectories, I make comparisons between nMDS, PCA and clustering to demonstrate the superiority of nMDS. The three villin headpiece trajectories showed great structural heterogeneity. Apart from a few trivial features like early formation of secondary structure, no commonalities between trajectories were found. There were no units of residues or atoms found moving in concert across the trajectories. A flipping transition, corresponding to the flipping of helix 1 relative to the plane formed by helices 2 and 3 was observed towards the end of the folding process in all trajectories, when nearly all native contacts had been formed. However, the transition occurred through a different series of steps in all trajectories, indicating that it may not be a common transition in villin folding. The trajectories showed competition between local structure formation/hydrophobic collapse and global structure formation in all trajectories. Our analysis on the NLE trajectories confirms the notion that a tight hydrophobic core inhibits correct 3-D rearrangement. Only one of the six NLE trajectories folded, and it showed no flipping transition. All the other trajectories get trapped in hydrophobically collapsed states. The NLE residues were found to be buried deeply into the core, compared to the corresponding lysines in the villin headpiece, thereby making the core tighter and harder to undo for 3-D rearrangement. Our results suggest that the NLE may not be a fast folder as experiments suggest. The tightness of the hydrophobic core may be a very important factor in the folding of larger proteins. It is likely that chaperones like GroEL act to undo the tight hydrophobic core of proteins, after most secondary structure elements have been formed, so that global rearrangement is easier. I conclude by presenting facts about chaperone-protein complexes and propose further directions for the study of protein folding.

Unas «cartas de Francia» de Josep Pla en Destino : Aproximación a la IV República francesa en los inicios de la Guerra de Argelia

This article means a first approach to the information given to its readers by the magazine Destino about the France of the IV French Republic, exactly during Pierre Mendès-France´s term in 1954, and having its origin in four articles published by the journalist and writer Josep Pla just when the Algeria conflict started. That information was determined by the obsessive anti-communist editorial policy of the aforementioned charismatic publication of the francoist Spain.

A biochemical analysis into the co-translational folding of a G protein-coupled receptor; GPR35

The folding and targeting of membrane proteins poses a major challenge to the cell, as they must remain insertion competent while their highly hydrophobic transmembrane (TM) domains are transferred from the ribosome, through the aqueous cytosol and into the lipid bilayer. The biogenesis of a mature membrane protein takes place through the insertion and integration into the lipid bilayer. A number of TM proteins have been shown to gain some degree of secondary structure within the ribosome tunnel and to retain this conformation throughout maturation. Although studies into the folding and targeting of a number of membrane proteins have been carried out to date, there is little information on one of the largest class of eukaryotic membrane proteins; the G-protein-coupled receptors (GPCRs). This project studies the early folding events of the human ortholog of GPR35. To analyse the structure of the 1st TM domain, intermediates were generated and assessed by the biochemical method of pegylation (PEG-MAL). A structurally-similar microbial opsin (Bacterioopsin) was also used to investigate the differences in the early protein folding within eukaryotic and prokaryotic translation systems. Results showed that neither the 1st TM domain of GPR35 nor Bacterioopsin were capable of compacting in the ribosome tunnel before their N-terminus reached the ribosome exit point. The results for this assay remained consistent whether the proteins were translated in a eukaryotic or prokaryotic translation system. To examine the communication mechanism between the ribosome, the nascent chain and the protein targeting pathway, crosslinking experiments were carried out using the homobifunctional lysine cross-linker BS3. Specifically, the data generated here show that the nascent chain of GPR35 reaches the ribosomal protein uL23 in an extended conformation and interacts with the SRP protein as it exits the ribosome tunnel. This confirms the role of SRP in the co-translational targeting of GPR35. Using these methods insights into the early folding of GPCRs has been obtained. Further experiments using site-directed mutagenesis to reduce hydrophobicity in the 1st TM domain of GPR35, highlighted the mechanisms by which GPCRs are targeted to the endoplasmic reticulum. Confirming that hydrophobicity within the signal anchor sequence is essential of SRP-dependent targeting. Following the successful interaction of the nascent GPR35 and SRP, GPR35 is successfully targeted to ER membranes, shown here as dog pancreas microsomes (DPMs). Glycosylation of the GPR35 N-terminus was used to determine nascent chain structure as it is inserted into the ER membrane. These glycosylation experiments confirm that TM1 has obtained its compacted state whilst residing in the translocon. Finally, a site-specific cross-linking approach using the homobifunctional cysteine cross-linker, BMH, was used to study the lateral integration of GPR35 into the ER. Cross-linking of GPR35 TM1 and TM2 could be detected adjacent to a protein of ~45kDa, believed to be Sec61α. The loss of this adduct, as the nascent chain extends, showed the lateral movement of GPR35 TM1 from the translocon was dependent on the subsequent synthesis of TM2.

An investigation into the folding and assembly of engineered antibodies and novel antibody formats

Monoclonal antibodies and novel antibody formats are currently one of the principal therapeutic in the biopharmaceutical industry worldwide and are widely used in the treatment of autoimmune diseases and cancer. It is for this reason that the productivity and quality of antibody production requires improvement; specifically investigations into the engineering of antibodies and any issues that may arise from the production of these therapeutics. The work presented in this thesis describes an investigation into the folding and assembly of seven antibodies plus the novel antibody format FabFv. IgG is comprised of two identical HCs and two identical LCs. The folding process of immunoglobulin is controlled by the CH1 domain within the HC. The CH1 domain remains in a disordered state and is sequestered by BiP in the endoplasmic reticulum. Upon the addition of a folded CL domain, BiP is displaced, the CH1 domain is able to fold and the complete IgG protein can then be secreted from the cell. The results presented in this thesis however, have outlined an additional mechanism for the folding of the CH1 domain. We have shown that the CH1 domain is able to fold in the absence of LC resulting in the secretion of HC dimers in a VH dependent manner. The proposed mechanism for the secretion of HC dimers suggests that some VH domains can interact with each other in order to bring the CH1 domains in close proximity to enable folding to occur. As HC dimer secretion is a hindrance in antibody production, this result has highlighted an engineering target to improve antibody yield. Examination of the folding of IgG4 with the variable region A33 has revealed the inability to secrete LC dimers, cleavage of the HC during expression and secretion of HC dimers in the Fab, FabFv and full length forms. The attributes described have also been shown to be variable region dependent. This has introduced a new concept that the variable domain is important in determining the expression and secretion of antibodies and their individual chains. Pulse chase and 2D gel electrophoresis analysis of the novel antibody format FabFv has revealed that the folding and expression of the LC and HC causes multimeric species of FabFv to be secreted, as opposed to the monomeric form which is the desired therapeutic. Our hypothesis is that this process occurs via a LC dependent mechanism. The proposed hypothesis suggests that further engineering to the LC could diminish the formation and secretion of FabFv multimers. The results from these investigations can be applied to increase the productivity of therapeutics and increase the biological understanding of the domain interactions of IgG during folding, assembly and secretion.

Música de câmara de Rodil, Pla e Avondano: a flauta na 2ª metade do séc. XVIII e o estilo galante ibérico

O presente trabalho é uma abordagem teórica e interpretativa à música para traverso de António Rodil (c.1730-1787), Pedro Avondano (1714-1782) e dos irmãos Pla. A interação entre as duas componentes do discurso são fundamentos essenciais para uma global compreensão das obras, sendo por sua vez, foco central no tratamento do estilo galante ibérico. A dissertação esta dividida em 5 capítulos; 1. contextualização da prática musical em Portugal na segunda metade do séc. XVIII; 2. o percurso artístico do flautista António Rodil (c.1730-1787); 3. a música de câmara de Pedro Avondano (1714-1782) e a primeira obra conhecida para o traverso em Portugal A Collection ofLisbon Minuets for two Violins or two German flutes and bass (1766); 4. o traverso na obra dos irmãos PLA; 5. reflexões em torno das questões interpretativas.

STRUCTURE AND FUNCTION OF THE GROUP III CHAPERONINS, A UNIQUE CLADE OF PROTEIN FOLDING NANOMACHINES

The survival and descent of cells is universally dependent on maintaining their proteins in a properly folded condition. It is widely accepted that the information for the folding of the nascent polypeptide chain into a native protein is encrypted in the amino acid sequence, and the Nobel Laureate Christian Anfinsen was the first to demonstrate that a protein could spontaneously refold after complete unfolding. However, it became clear that the observed folding rates for many proteins were much slower than rates estimated in vivo. This led to the recognition of required protein-protein interactions that promote proper folding. A unique group of proteins, the molecular chaperones, are responsible for maintaining protein homeostasis during normal growth as well as stress conditions. Chaperonins (CPNs) are ubiquitous and essential chaperones. They form ATP-dependent, hollow complexes that encapsulate polypeptides in two back-to-back stacked multisubunit rings, facilitating protein folding through highly cooperative allosteric articulation. CPNs are usually classified into Group I and Group II. Here, I report the characterization of a novel CPN belonging to a third Group, recently discovered in bacteria. Group III CPNs have close phylogenetic association to the Group II CPNs found in Archaea and Eukarya, and may be a relic of the Last Common Ancestor of the CPN family. The gene encoding the Group III CPN from Carboxydothermus hydrogenoformans and Candidatus Desulforudis audaxviator was cloned in E. coli and overexpressed in order to both characterize the protein and to demonstrate its ability to function as an ATPase chaperone. The opening and closing cycle of the Chy chaperonin was examined via site-directed mutations affecting the ATP binding site at R155. To relate the mutational analysis to the structure of the CPN, the crystal structure of both the AMP-PNP (an ATP analogue) and ADP bound forms were obtained in collaboration with Sun-Shin Cha in Seoul, South Korea. The ADP and ATP binding site substitutions resulted in frozen forms of the structures in open and closed conformations. From this, mutants were designed to validate hypotheses regarding key ATP interacting sites as well as important stabilizing interactions, and to observe the physical properties of the resulting complexes by calorimetry.

Effects of morin on snake venom phospholipase A(2) (PLA(2))

Flavonoids are potent anti-inflammatory compounds isolated from several plant extracts, and have been used experimentally against inflammatory processes. In this work, a PLA(2) isolated from the Crotalus durissus cascavella venom and rat paw oedema were used as a model to. study the effect of flavonoids on PLA(2). We observed that a treatment of PLA(2) with morin induces several modifications in the aromatic amino acids, with accompanying changes in its amino acid composition. In addition, results from circular dichroism spectroscopy and UV scanning revealed important structural modifications. Concomitantly, a considerable decrease in the enzymatic and antibacterial activities was observed, even though anti-inflammatory and neurotoxic activities were not affected. These apparent controversial results may be an indication that PLA(2) possess a second pharmacological site which does not affect or depend on the enzymatic activity. (c) 2005 Elsevier Ltd. All rights reserved.