Activity and functional interaction of alternative oxidase and uncoupling protein in mitochondria from tomato fruit

Cyanide-resistant alternative oxidase (AOX) is not limited to plant mitochondria and is widespread among several types of protists. The uncoupling protein (UCP) is much more widespread than previously believed, not only in tissues of higher animals but also in plants and in an amoeboid protozoan. The redox energy-dissipating pathway (AOX) and the proton electrochemical gradient energy-dissipating pathway (UCP) lead to the same final effect, i.e., a decrease in ATP synthesis and an increase in heat production. Studies with green tomato fruit mitochondria show that both proteins are present simultaneously in the membrane. This raises the question of a specific physiological role for each energy-dissipating system and of a possible functional connection between them (shared regulation). Linoleic acid, an abundant free fatty acid in plants which activates UCP, strongly inhibits cyanide-resistant respiration mediated by AOX. Moreover, studies of the evolution of AOX and UCP protein expression and of their activities during post-harvest ripening of tomato fruit show that AOX and plant UCP work sequentially: AOX activity decreases in early post-growing stages and UCP activity is decreased in late ripening stages. Electron partitioning between the alternative oxidase and the cytochrome pathway as well as H+ gradient partitioning between ATP synthase and UCP can be evaluated by the ADP/O method. This method facilitates description of the kinetics of energy-dissipating pathways and of ATP synthase when state 3 respiration is decreased by limitation of oxidizable substrate.

Protein folding: a perspective for biology, medicine and biotechnology

At the present time, protein folding is an extremely active field of research including aspects of biology, chemistry, biochemistry, computer science and physics. The fundamental principles have practical applications in the exploitation of the advances in genome research, in the understanding of different pathologies and in the design of novel proteins with special functions. Although the detailed mechanisms of folding are not completely known, significant advances have been made in the understanding of this complex process through both experimental and theoretical approaches. In this review, the evolution of concepts from Anfinsen's postulate to the "new view" emphasizing the concept of the energy landscape of folding is presented. The main rules of protein folding have been established from in vitro experiments. It has been long accepted that the in vitro refolding process is a good model for understanding the mechanisms by which a nascent polypeptide chain reaches its native conformation in the cellular environment. Indeed, many denatured proteins, even those whose disulfide bridges have been disrupted, are able to refold spontaneously. Although this assumption was challenged by the discovery of molecular chaperones, from the amount of both structural and functional information now available, it has been clearly established that the main rules of protein folding deduced from in vitro experiments are also valid in the cellular environment. This modern view of protein folding permits a better understanding of the aggregation processes that play a role in several pathologies, including those induced by prions and Alzheimer's disease. Drug design and de novo protein design with the aim of creating proteins with novel functions by application of protein folding rules are making significant progress and offer perspectives for practical applications in the development of pharmaceuticals and medical diagnostics.

From Unspecific Quenching to Specific Signaling: Functional GTPase Assays Utilizing Quenching Resonance Energy Transfer (QRET) Technology

The aim of the work presented in this study was to demonstrate the wide applicability of a single-label quenching resonance energy transfer (QRET) assay based on time-resolved lanthanide luminescence. QRET technology is proximity dependent method utilizing weak and unspecific interaction between soluble quencher molecule and lanthanide chelate. The interaction between quencher and chelate is lost when the ligand binds to its target molecule. The properties of QRET technology are especially useful in high throughput screening (HTS) assays. At the beginning of this study, only end-point type QRET technology was available. To enable efficient study of enzymatic reactions, the QRET technology was further developed to enable measurement of reaction kinetics. This was performed using proteindeoxyribonuclei acid (DNA) interaction as a first tool to monitor reaction kinetics. Later, the QRET was used to study nucleotide exchange reaction kinetics and mutation induced effects to the small GTPase activity. Small GTPases act as a molecular switch shifting between active GTP bound and inactive GDP bound conformation. The possibility of monitoring reaction kinetics using the QRET technology was evaluated using two homogeneous assays: a direct growth factor detection assay and a nucleotide exchange monitoring assay with small GTPases. To complete the list, a heterogeneous assay for monitoring GTP hydrolysis using small GTPases, was developed. All these small GTPase assays could be performed using nanomolar protein concentrations without GTPase pretreatment. The results from these studies demonstrated that QRET technology can be used to monitor reaction kinetics and further enable the possibility to use the same method for screening.

Streptococcus mutans GlnK protein: an unusual PII family member

Streptococcus mutans is a Gram-positive bacterium present in the oral cavity, and is considered to be one of the leading causes of dental caries. S. mutans has a glnK gene, which codes for a PII-like protein that is possibly involved in the integration of carbon, nitrogen and energy metabolism in several organisms. To characterize the GlnK protein of S. mutans, the glnK gene was amplified by PCR, and cloned into the expression vectors pET29a(+) and pET28b(+). The native GlnK-Sm was purified by anion exchange (Q-Sepharose) and affinity (Hi-Trap Heparin) chromatography. The GlnK-His-Sm protein was purified using a Hi-Trap Chelating-Ni2+ column. The molecular mass of the GlnK-His-Sm proteins was 85 kDa as determined by gel filtration, indicating that this protein is a hexamer in solution. The GlnK-His-Sm protein is not uridylylated by the Escherichia coli GlnD protein. The activities of the GlnK-Sm and GlnK-His-Sm proteins were assayed in E. coli constitutively expressing the Klebsiella pneumoniae nifLA operon. In K. pneumoniae, NifL inhibits NifA activity in the presence of high ammonium levels and the GlnK protein is required to reduce the inhibition of NifL in the presence of low ammonium levels. The GlnK-Sm protein was unable to reduce NifL inhibition of NifA protein. Surprisingly, the GlnK-His-Sm protein was able to partially reduce NifL inhibition of the NifA protein under nitrogen-limiting conditions, in a manner similar to the GlnK protein of E. coli. These results suggested that S. mutans GlnK is functionally different from E. coli PII proteins.

Investigation of the mechanism of transfer of a-tocopherol by the human a-tocopherol transfer protein (H-a-TTP) /

The human a-tocopherol transfer protein (h-a-TTP) is understood to be the entity responsible for the specific retention of a-tocopherol (a-toc) in human tissues over all other forms of vitamin E obtained from the diet. a-Tocopherol is the most biologically active form of vitamin E, and to date has been studied extensively with regard to its antioxidant properties and its role of terminating membrane lipid peroxidation chain reactions. However, information surrounding the distribution of a-tocopherol, specifically its delivery to intracellular membranes by a-TTP, is still unclear and the molecular factors influencing transfer remain elusive. To investigate the mechanism of ligand transfer by the h-a-TTP, a fluorescent analogue of a-toc has been used in the development of a fluorescence resonance energy transfer (FRET) assay. (/?)-2,5,7,8-tetramethyl-2-[9-(7-nitro-benzo[l,2,5]oxdiazol-4-ylamino)-nonyl]- chroman-6-ol (NBD-toc) has allowed for the development of the FRET-based ligand transfer assay. This ligand has been utilized in a series of experiments where changes were made to acceptor lipid membrane concentration and composition, as well as to the ionic strength and viscosity of the buffer medium. Such changes have yielded evidence supporting a collisional mechanism of ligand transfer by a-TTP, and have brought to light a new line of inquiry pertaining to the nature of the forces governing the collisional transfer interaction. Through elucidation of the transfer mechanism type, a deeper understanding of the transfer event and the in vivo fate of a-tocopherol have been obtained. Furthermore, the results presented here allow for a deeper investigation of the forces controlling the collisional protein-membrane interaction and their effect on the transfer of a-toc to membranes. Future investigation in this direction will raise the possibility of a complete understanding of the molecular events surrounding the distribution of a-toc within the cell and to the body's tissues.

Synthesis of fluorescent analogues of a-tocopherol as ligands for the human a-tocopherol transfer protein (a-TTP) /

To further understand in vivo localization and trafficking of a-tocopherol (a-Toe), the most biologically active form of vitamin E, between lipid environments, tocopherols are required that can be followed by teclu1iques such as confocal microscopy and fluorescence resonance energy transfer (FRET) assays. To this end, sixteen fluorescent analogues of a-tocopherol (la-d [(1)anthroy loxy -a-tocopherols, A O-a-Toes], 2a-d [w-nitro benzoxadiazole-a-tocopherols, NBD-aToes], 3a-d [w-dansyl-a-tocopherols, DAN-a-Toes], and 4a-d [w-N-methylanthranilamide-atocopherols, NMA-a-TocsD were prepared by substituting fluorescent labels at the terminus of w-functionalized alkyl chains extending from C-2 of the chroman ring while retaining key binding features of the natural ligand. These compounds were prepared starting from (S)-Trolox® acid VIa esterification, protection, and reduction producing the silyl-protected (S)-Trolox aldehyde that was coupled using Wittig chemistry to different w-hydroxyalkylphosphonium bromides. Reduction of the alkene generated the w-hydroxy functionalized 2-n-alkyl intermediates 9a-d having the necessary 2R stereochemistry. A series of functional group manipulations including mesylation, substitution with azide, and hydride reduction provided w-amino functionalized intermediates 12a-d as well. Coupling intermediates 9a-d and 12a-d with the selected fluorophores (9- anthracene carboxylic acid, 4-chloro-7-nitrobenz-2-oxa-l,3-diazole, 5- dimethylaminonapthalene-l-sulfonyl chloride, and I-methyl-2H-3,1-benzoxazine-2,4(1H)dione), followed by deprotection of the phenolic silyl group, gave the desired fluorescent ligands la-d, 2a-d, 3a-d and 4a-d in good yield. Assessment of their binding affinities with recombinant human a-tocopherol transfer protein (ha-TTP) utilizing fluorescent titration binding assays identified competent ligands for further use in protein studies. Compounds Id (C9-AO-a-Toc) and 2d (C9-NBD-a-Toc) both having nonyl alkyl chain extensions between the chromanol and fluorophore were shown to bind specifically to ha-TTP with dissociation constants (KdS) of approximately 280 nM and 55 nM respectively, as compared to 25 nM for the natural ligand 2R,4'R,^'R-a-tocophQxoL.

Mechanism of tocopherol transfer by human α-tocopherol transfer protein (α-hTTP)

Vitamin E is a well known fat soluble chain breaking antioxidant. It is a general tenn used to describe a family of eight stereoisomers of tocopherols. Selective retention of a-tocopherol in the human circulation system is regulated by the a -Tocopherol Transfer Protein (a-TIP). Using a fluorescently labelled a-tocopherol (NBD-a-Toc) synthesized in our laboratory, a fluorescence resonance energy transfer (FRET) assay was developed to monitor the kinetics of ligand transfer by a-hTTP in lipid vesicles. Preliminary results implied that NBD-a-Toe simply diffused from 6-His-a-hTTP to acceptor membranes since the kinetics of transfer were not responsive to a variety of conditions tested. After a series of trouble shooting experiments, we identified a minor contaminant, E coli. outer membrane porin F (OmpF) that co-purified with 6-His-a-hTTP from the metal affinity column as the source of the problem. In order to completely avoid OmpF contamination, a GST -a-hTTP fusion protein was purified from a glutathione agarose column followed by an on-column thrombin digestion to remove the GST tag. We then demonstrated that a-hTTP utilizes a collisional mechanism to deliver its ligand. Furthennore, a higher rate of a-tocopherol transfer to small unilamellar vesicles (SUV s) versus large unilamellar vesicles (LUV s) indicated that transfer is sensitive to membrane curvature. These findings suggest that ahTTP mediated a-Toc transfer is dominated by the hydrophobic nature of a-hTTP and the packing density of phospholipid head groups within acceptor membranes. Based on the calculated free energy change (dG) when a protein is transferred from water to the lipid bilayer, a model was generated to predict the orientation of a-hTTP when it interacts with lipid membranes. Guided by this model, several hydrophobic residues expected to penetrate deeply into the bilayer hydrophobic core, were mutated to either aspartate or alanine. Utilizing dual polarization interferometry and size exclusion vesicle binding assays, we identified the key residues for membrane binding to be F 165, F 169 and 1202. In addition, the rates of ligand transfer of the u-TTP mutants were directly correlated to their membrane binding capabilities, indicating that membrane binding was likely the rate limiting step in u-TTP mediated transfer of u-Toc. The propensity of u-TTP for highly curved membrane provides a connection to its colocalization with u-Toc in late endosomes.

Optimizing Computational Frameworks to Study the Influence of the Protein Environment on the Individual Site Energies of Chromophores in Photosystem II of Photosynthesis

Photosynthesis is a process in which electromagnetic radiation is converted into chemical energy. Photosystems capture photons with chromophores and transfer their energy to reaction centers using chromophores as a medium. In the reaction center, the excitation energy is used to perform chemical reactions. Knowledge of chromophore site energies is crucial to the understanding of excitation energy transfer pathways in photosystems and the ability to compute the site energies in a fast and accurate manner is mandatory for investigating how protein dynamics ef-fect the site energies and ultimately energy pathways with time. In this work we developed two software frameworks designed to optimize the calculations of chro-mophore site energies within a protein environment. The first is for performing quantum mechanical energy optimizations on molecules and the second is for com-puting site energies of chromophores in a fast and accurate manner using the polar-izability embedding method. The two frameworks allow for the fast and accurate calculation of chromophore site energies within proteins, ultimately allowing for the effect of protein dynamics on energy pathways to be studied. We use these frame-works to compute the site energies of the eight chromophores in the reaction center of photosystem II (PSII) using a 1.9 Å resolution x-ray structure of photosystem II. We compare our results to conflicting experimental data obtained from both isolat-ed intact PSII core preparations and the minimal reaction center preparation of PSII, and find our work more supportive of the former.

Impact d’un épisode asphyxique périnatal associé à des convulsions sur le développement des interneurones corticaux : rôle de l’adenosine monophosphate-activated protein kinase (AMPK)

L’encéphalopathie hypoxique-­‐ischémique cause des milliers de victimes à travers le monde chaque année. Les enfants survivants à un épisode hypoxique-­‐ischémique sont à risque de développer des problèmes neurologiques incapacitants comme une paralysie cérébrale, un retard mental, une épilepsie ou des troubles d’ordre comportemental. Les modèles animaux ont amélioré nos connaissances sur les mécanismes sous-­‐jacents aux dommages cérébraux, mais elles sont encore trop incomplètes pour être capables de prévenir les problèmes neurologiques. Ce projet vise à comprendre l’impact d’un épisode asphyxique périnatale associé à des convulsions ainsi que l’activation de l’adenosine monophosphate-­‐activated protein kinase (AMPK) sur les circuits GABAergiques inhibiteurs en développement chez la souris. Dans le but d’investiguer le sort des neurones inhibiteurs, appelés interneurones, suite à un épisode asphyxique périnatal associé à des convulsions avec des animaux transgéniques, nous avons pris avantage d’un nouveau modèle d’hypoxie permettant d’induire des convulsions chez la souris. Deux populations d’interneurones représentant ensemble environ 60% de tous les interneurones corticaux ont été étudiées, soit les cellules exprimant la parvalbumine (PV) et les cellules exprimant la somatostatine (SOM). L’étude stéréologique n’a montré aucune mort neuronale de ces deux populations d’interneurones dans l’hippocampe chez les souris hypoxique d’âge adulte. Par contre, le cortex des souris hypoxiques présentait des zones complètement ou fortement dépourvues de cellules PV alors que les cellules SOM n’étaient pas affectées. L’utilisation d’une lignée de souris transgénique exprimant une protéine verte fluorescente (GFP) dans les cellules PV nous a permis de comprendre que les trous PV sont le reflet de deux choses : 1) une diminution des cellules PV et 2) une immaturité des cellules PV restantes. Puisque les cellules PV sont spécifiquement affectées dans la première partie de notre étude, nous avons voulu étudier les mécanismes moléculaires sous-­‐jacents à cette vulnérabilité. L’AMPK est un senseur d’énergie qui orchestre le rétablissement des i niveaux d’énergie cellulaire dans le cas d’une déplétion énergétique en modulant des voies de signalisation impliquant la synthèse de protéines et l’excitabilité membranaire. Il est possible que l’activation d’AMPK suite à un épisode asphyxique périnatal associé à des convulsions soit néfaste à long-­‐terme pour le circuit GABAergique en développement et modifie l’établissement de l’innervation périsomatique d’une cellule PV sur les cellules pyramidales. Nous avons étudié cette hypothèse dans un modèle de culture organotypique en surexprimant la forme wild-­‐type (WT) de la sous-­‐unité α2 d’AMPK, ainsi qu’une forme mutée dominante négative (DN), dans des cellules PV individuelles. Nous avons montré que pendant la phase de formation synaptique (jours post-­‐natals équivalents EP 10-­‐18), la surexpression de la forme WT désorganise la stabilisation des synapses. De plus, l’abolition de l’activité d’AMPK semble augmenter le nombre de synapses périsomatiques faits par la cellule PV sur les cellules pyramidales pendant la phase de formation et semble avoir l’effet inverse pendant la phase de maturation (EP 16-­‐24). La neurotransmission GABAergique joue plusieurs rôles dans le cerveau, depuis la naissance jusqu’à l’âge adulte des interneurones, et une dysfonction des interneurones a été associée à plusieurs troubles neurologiques, comme la schizophrénie, l’autisme et l’épilepsie. La maturation des circuits GABAergiques se fait majoritairement pendant la période post-­‐natale et est hautement dépendante de l’activité neuronale et de l’expérience sensorielle. Nos résultats révèlent que le lourd fardeau en demande énergétique d’un épisode asphyxique périnatal peut causer une mort neuronale sélective des cellules PV et compromettre l’intégrité de leur maturation. Un des mécanismes sous-­‐ jacents possible à cette immaturité des cellules PV suite à l’épisode hypoxique est l’activation d’AMPK, en désorganisant leur profil d’innervation sur les cellules pyramidales. Nous pensons que ces changements dans le réseau GABAergique pourrait contribuer aux problèmes neurologiques associés à une insulte hypoxique.

Monoacylglycerol, alpha/beta-hydrolase domain-6, and the regulation of insulin secretion and energy metabolism

Le cycle glycérolipides/acides gras libres (GL/FFA) est une voie métabolique clé qui relie le métabolisme du glucose et des acides gras et il est composé de deux processus métaboliques appelés lipogenèse et lipolyse. Le cycle GL/FFA, en particulier la lipolyse des triglycérides, génère diverses molécules de signalisation pour réguler la sécrétion d'insuline dans les cellules bêta pancréatiques et la thermogenèse non-frissonnante dans les adipocytes. Actuellement, les lipides provenant spécifiquement de la lipolyse impliqués dans ce processus sont mal connus. L’hydrolyse des triglycérides dans les cellules β est réalisée par les actions successives de la triglycéride lipase adipocytaire pour produire le diacylglycérol, ensuite par la lipase hormono-sensible pour produire le monoacylglycérol (MAG) et enfin par la MAG lipase (MAGL) qui relâche du glycerol et des acides gras. Dans les cellules bêta, la MAGL classique est très peu exprimée et cette étude a démontré que l’hydrolyse de MAG dans les cellules β est principalement réalisée par l'α/β-Hydrolase Domain-6 (ABHD6) nouvellement identifiée. L’inhibition d’ABHD6 par son inhibiteur spécifique WWL70, conduit à une accumulation des 1-MAG à longues chaines saturées à l'intérieur des cellules, accompagnée d’une augmentation de la sécrétion d'insuline stimulée par le glucose (GSIS). Baisser les niveaux de MAG en surexprimant ABHD6 dans la lignée cellulaire bêta INS832/13 réduit la GSIS, tandis qu’une augmentation des niveaux de MAG par le « knockdown » d’ABHD6 améliore la GSIS. L'exposition aiguë des monoacylglycérols exogènes stimule la sécrétion d'insuline de manière dose-dépendante et restaure la GSIS supprimée par un inhibiteur de lipases appelé orlistat. En outre, les souris avec une inactivation du gène ABHD6 dans tous les tissus (ABHD6-KO) et celles avec une inactivation du gène ABHD6 spécifiquement dans la cellule β présentent une GSIS stimulée, et leurs îlots montrent une augmentation de la production de monoacylglycérol et de la sécrétion d'insuline en réponse au glucose. L’inhibition d’ABHD6 chez les souris diabétiques (modèle induit par de faibles doses de streptozotocine) restaure la GSIS et améliore la tolérance au glucose. De plus, les résultats montrent que les MAGs non seulement améliorent la GSIS, mais potentialisent également la sécrétion d’insuline induite par les acides gras libres ainsi que la sécrétion d’insuline induite par divers agents et hormones, sans altération de l'oxydation et l'utilisation du glucose ainsi que l'oxydation des acides gras. Nous avons démontré que le MAG se lie à la protéine d’amorçage des vésicules appelée Munc13-1 et l’active, induisant ainsi l’exocytose de l'insuline. Sur la base de ces observations, nous proposons que le 1-MAG à chaines saturées agit comme facteur de couplage métabolique pour réguler la sécrétion d'insuline et que ABHD6 est un modulateur négatif de la sécrétion d'insuline. En plus de son rôle dans les cellules bêta, ABHD6 est également fortement exprimé dans les adipocytes et son niveau est augmenté avec l'obésité. Les souris dépourvues globalement d’ABHD6 et nourris avec une diète riche en gras (HFD) montrent une faible diminution de la prise alimentaire, une diminution du gain de poids corporel et de la glycémie à jeun et une amélioration de la tolérance au glucose et de la sensibilité à l'insuline et ont une activité locomotrice accrue. En outre, les souris ABHD6-KO affichent une augmentation de la dépense énergétique et de la thermogenèse induite par le froid. En conformité avec ceci, ces souris présentent des niveaux élevés d’UCP1 dans les adipocytes blancs et bruns, indiquant le brunissement des adipocytes blancs. Le phénotype de brunissement est reproduit dans les souris soit en les traitant de manière chronique avec WWL70 (inhibiteur d’ABHD6) ou des oligonucléotides anti-sense ciblant l’ABHD6. Les tissus adipeux blanc et brun isolés de souris ABHD6-KO montrent des niveaux très élevés de 1-MAG, mais pas de 2-MAG. L'augmentation des niveaux de MAG soit par administration exogène in vitro de 1-MAG ou par inhibition ou délétion génétique d’ABHD6 provoque le brunissement des adipocytes blancs. Une autre évidence indique que les 1-MAGs sont capables de transactiver PPARα et PPARγ et que l'effet de brunissement induit par WWL70 ou le MAG exogène est aboli par les antagonistes de PPARα et PPARγ. L’administration in vivo de l’antagoniste de PPARα GW6471 à des souris ABHD6-KO inverse partiellement les effets causés par l’inactivation du gène ABHD6 sur le gain de poids corporel, et abolit l’augmentation de la thermogenèse, le brunissement du tissu adipeux blanc et l'oxydation des acides gras dans le tissu adipeux brun. L’ensemble de ces observations indique que ABHD6 régule non seulement l’homéostasie de l'insuline et du glucose, mais aussi l'homéostasie énergétique et la fonction des tissus adipeux. Ainsi, 1-MAG agit non seulement comme un facteur de couplage métabolique pour réguler la sécrétion d'insuline en activant Munc13-1 dans les cellules bêta, mais régule aussi le brunissement des adipocytes blancs et améliore la fonction de la graisse brune par l'activation de PPARα et PPARγ. Ces résultats indiquent que ABHD6 est une cible prometteuse pour le développement de thérapies contre l'obésité, le diabète de type 2 et le syndrome métabolique.

Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

Determination of yield and quality parameters of energy crops applying laboratory and field spectroscopy

A real-time analysis of renewable energy sources, such as arable crops, is of great importance with regard to an optimised process management, since aspects of ecology and biodiversity are considered in crop production in order to provide a sustainable energy supply by biomass. This study was undertaken to explore the potential of spectroscopic measurement procedures for the prediction of potassium (K), chloride (Cl), and phosphate (P), of dry matter (DM) yield, metabolisable energy (ME), ash and crude fibre contents (ash, CF), crude lipid (EE), nitrate free extracts (NfE) as well as of crude protein (CP) and nitrogen (N), respectively in pretreated samples and undisturbed crops. Three experiments were conducted, one in a laboratory using near infrared reflectance spectroscopy (NIRS) and two field spectroscopic experiments. Laboratory NIRS measurements were conducted to evaluate to what extent a prediction of quality parameters is possible examining press cakes characterised by a wide heterogeneity of their parent material. 210 samples were analysed subsequent to a mechanical dehydration using a screw press. Press cakes serve as solid fuel for thermal conversion. Field spectroscopic measurements were carried out with regard to further technical development using different field grown crops. A one year lasting experiment over a binary mixture of grass and red clover examined the impact of different degrees of sky cover on prediction accuracies of distinct plant parameters. Furthermore, an artificial light source was used in order to evaluate to what extent such a light source is able to minimise cloud effects on prediction accuracies. A three years lasting experiment with maize was conducted in order to evaluate the potential of off-nadir measurements inside a canopy to predict different quality parameters in total biomass and DM yield using one sensor for a potential on-the-go application. This approach implements a measurement of the plants in 50 cm segments, since a sensor adjusted sideways is not able to record the entire plant height. Calibration results obtained by nadir top-of-canopy reflectance measurements were compared to calibration results obtained by off-nadir measurements. Results of all experiments approve the applicability of spectroscopic measurements for the prediction of distinct biophysical and biochemical parameters in the laboratory and under field conditions, respectively. The estimation of parameters could be conducted to a great extent with high accuracy. An enhanced basis of calibration for the laboratory study and the first field experiment (grass/clover-mixture) yields in improved robustness of calibration models and allows for an extended application of spectroscopic measurement techniques, even under varying conditions. Furthermore, off-nadir measurements inside a canopy yield in higher prediction accuracies, particularly for crops characterised by distinct height increment as observed for maize.

Impact of sward type, cutting date and conditioning temperature on mass and energy flows in the integrated generation of solid fuel and biogas from semi-natural grassland

Energy production from biomass and the conservation of ecologically valuable grassland habitats are two important issues of agriculture today. The combination of a bioenergy production, which minimises environmental impacts and competition with food production for land with a conversion of semi-natural grasslands through new utilization alternatives for the biomass, led to the development of the IFBB process. Its basic principle is the separation of biomass into a liquid fraction (press fluid, PF) for the production of electric and thermal energy after anaerobic digestion to biogas and a solid fraction (press cake, PC) for the production of thermal energy through combustion. This study was undertaken to explore mass and energy flows as well as quality aspects of energy carriers within the IFBB process and determine their dependency on biomass-related and technical parameters. Two experiments were conducted, in which biomass from semi-natural grassland was conserved as silage and subjected to a hydrothermal conditioning and a subsequent mechanical dehydration with a screw press. Methane yield of the PF and the untreated silage was determined in anaerobic digestion experiments in batch fermenters at 37°C with a fermentation time of 13-15 and 27-35 days for the PF and the silage, respectively. Concentrations of dry matter (DM), ash, crude protein (CP), crude fibre (CF), ether extract (EE), neutral detergent fibre (NDF), acid detergent fibre (ADF), acid detergent ligning (ADL) and elements (K, Mg, Ca, Cl, N, S, P, C, H, N) were determined in the untreated biomass and the PC. Higher heating value (HHV) and ash softening temperature (AST) were calculated based on elemental concentration. Chemical composition of the PF and mass flows of all plant compounds into the PF were calculated. In the first experiment, biomass from five different semi-natural grassland swards (Arrhenaterion I and II, Caricion fuscae, Filipendulion ulmariae, Polygono-Trisetion) was harvested at one late sampling (19 July or 31 August) and ensiled. Each silage was subjected to three different temperature treatments (5°C, 60°C, 80°C) during hydrothermal conditioning. Based on observed methane yields and HHV as energy output parameters as well as literature-based and observed energy input parameters, energy and green house gas (GHG) balances were calculated for IFBB and two reference conversion processes, whole-crop digestion of untreated silage (WCD) and combustion of hay (CH). In the second experiment, biomass from one single semi-natural grassland sward (Arrhenaterion) was harvested at eight consecutive dates (27/04, 02/05, 09/05, 16/05, 24/05, 31/05, 11/06, 21/06) and ensiled. Each silage was subjected to six different treatments (no hydrothermal conditioning and hydrothermal conditioning at 10°C, 30°C, 50°C, 70°C, 90°C). Energy balance was calculated for IFBB and WCD. Multiple regression models were developed to predict mass flows, concentrations of elements in the PC, concentration of organic compounds in the PF and energy conversion efficiency of the IFBB process from temperature of hydrothermal conditioning as well as NDF and DM concentration in the silage. Results showed a relative reduction of ash and all elements detrimental for combustion in the PC compared to the untreated biomass of 20-90%. Reduction was highest for K and Cl and lowest for N. HHV of PC and untreated biomass were in a comparable range (17.8-19.5 MJ kg-1 DM), but AST of PC was higher (1156-1254°C). Methane yields of PF were higher compared to those of WCD when the biomass was harvested late (end of May and later) and in a comparable range when the biomass was harvested early and ranged from 332 to 458 LN kg-1 VS. Regarding energy and GHG balances, IFBB, with a net energy yield of 11.9-14.1 MWh ha-1, a conversion efficiency of 0.43-0.51, and GHG mitigation of 3.6-4.4 t CO2eq ha-1, performed better than WCD, but worse than CH. WCD produces thermal and electric energy with low efficiency, CH produces only thermal energy with a low quality solid fuel with high efficiency, IFBB produces thermal and electric energy with a solid fuel of high quality with medium efficiency. Regression models were able to predict target parameters with high accuracy (R2=0.70-0.99). The influence of increasing temperature of hydrothermal conditioning was an increase of mass flows, a decrease of element concentrations in the PC and a differing effect on energy conversion efficiency. The influence of increasing NDF concentration of the silage was a differing effect on mass flows, a decrease of element concentrations in the PC and an increase of energy conversion efficiency. The influence of increasing DM concentration of the silage was a decrease of mass flows, an increase of element concentrations in the PC and an increase of energy conversion efficiency. Based on the models an optimised IFBB process would be obtained with a medium temperature of hydrothermal conditioning (50°C), high NDF concentrations in the silage and medium DM concentrations of the silage.

Cassava root peel as a replacement for maize in diets for growing pigs: effects on energy and nutrient digestibility, performance and carcass characteristics

Two experiments were conducted to evaluate cassava root peel (CRP) as diet component for fattening pigs. In the first experiment, ten male pigs were used to investigate the nutrient digestibility and the nutritive value of CRP as replacement for maize in the diet at 0 %, 30 %, 40 %, 50 % and 60 %, while supplementing free amino acids (fAA). During two experimental periods, faeces were quantitatively collected and analysed for chemical composition. In the second experiment, 40 pigs received the same diets as in Experiment 1, and daily feed intake and weekly weight changes were recorded. Four pigs per diet were slaughtered at 70 kg body weight to evaluate carcass traits. Digestibility of dry and organic matter, crude protein, acid detergent fibre and gross energy were depressed (p<0.05) at 60 % CRP; digestible energy content (MJ kg^(−1) DM) was 15.4 at 0 % CRP and 12.7 at 60 % CRP. In the second experiment, CRP inclusion had only a small impact on feed intake, weight gain and feed conversion ratio (p>0.05) as well as on the length of the small intestine and the Longissimus dorsi muscle area. The missing correlation of daily weight gain and feed-to-gain ratio up to a CRP inclusion of 40 % indicates that negative effects of CRP on pig growth can be avoided by respecting upper feeding limits. Hence, a combined use of CRP and fAA can reduce feeding costs for small-scale pig farmers in countries where this crop-by product is available in large amounts.

Whole crop cereals 2. Prediction of apparent digestibility and energy value from in vitro digestion techniques and near infrared reflectance spectroscopy and of chemical composition by near infrared reflectance spectroscopy

Samples of whole crop wheat (WCW, n = 134) and whole crop barley (WCB, n = 16) were collected from commercial farms in the UK over a 2-year period (2003/2004 and 2004/2005). Near infrared reflectance spectroscopy (NIRS) was compared with laboratory and in vitro digestibility measures to predict digestible organic matter in the dry matter (DOMD) and metabolisable energy (ME) contents measured in vivo using sheep. Spectral models using the mean spectra of two scans were compared with those using individual spectra (duplicate spectra). Overall NIRS accurately predicted the concentration of chemical components in whole crop cereals apart from crude protein. ammonia-nitrogen, water-soluble carbohydrates, fermentation acids and solubility values. In addition. the spectral models had higher prediction power for in vivo DOMD and ME than chemical components or in vitro digestion methods. Overall there Was a benefit from the use of duplicate spectra rather than mean spectra and this was especially so for predicting in vivo DOMD and ME where the sample population size was smaller. The spectral models derived deal equally well with WCW and WCB and Would he of considerable practical value allowing rapid determination of nutritive value of these forages before their use in diets of productive animals. (C) 2008 Elsevier B.V. All rights reserved.