Molecular modeling study of the binding and signaling properties of the TCRpMHC complex

The activation of the specific immune response against tumor cells is based on the recognition by the CD8+ Cytotoxic Τ Lymphocytes (CTL), of antigenic peptides (p) presented at the surface of the cell by the class I major histocompatibility complex (MHC). The ability of the so-called T-Cell Receptors (TCR) to discriminate between self and non-self peptides constitutes the most important specific control mechanism against infected cells. The TCR/pMHC interaction has been the subject of much attention in cancer therapy since the design of the adoptive transfer approach, in which Τ lymphocytes presenting an interesting response against tumor cells are extracted from the patient, expanded in vitro, and reinfused after immunodepletion, possibly leading to cancer regression. In the last decade, major progress has been achieved by the introduction of engineered lypmhocytes. In the meantime, the understanding of the molecular aspects of the TCRpMHC interaction has become essential to guide in vitro and in vivo studies. In 1996, the determination of the first structure of a TCRpMHC complex by X-ray crystallography revealed the molecular basis of the interaction. Since then, molecular modeling techniques have taken advantage of crystal structures to study the conformational space of the complex, and understand the specificity of the recognition of the pMHC by the TCR. In the meantime, experimental techniques used to determine the sequences of TCR that bind to a pMHC complex have been used intensively, leading to the collection of large repertoires of TCR sequences that are specific for a given pMHC. There is a growing need for computational approaches capable of predicting the molecular interactions that occur upon TCR/pMHC binding without relying on the time consuming resolution of a crystal structure. This work presents new approaches to analyze the molecular principles that govern the recognition of the pMHC by the TCR and the subsequent activation of the T-cell. We first introduce TCRep 3D, a new method to model and study the structural properties of TCR repertoires, based on homology and ab initio modeling. We discuss the methodology in details, and demonstrate that it outperforms state of the art modeling methods in predicting relevant TCR conformations. Two successful applications of TCRep 3D that supported experimental studies on TCR repertoires are presented. Second, we present a rigid body study of TCRpMHC complexes that gives a fair insight on the TCR approach towards pMHC. We show that the binding mode of the TCR is correctly described by long-distance interactions. Finally, the last section is dedicated to a detailed analysis of an experimental hydrogen exchange study, which suggests that some regions of the constant domain of the TCR are subject to conformational changes upon binding to the pMHC. We propose a hypothesis of the structural signaling of TCR molecules leading to the activation of the T-cell. It is based on the analysis of correlated motions in the TCRpMHC structure. - L'activation de la réponse immunitaire spécifique dirigée contre les cellules tumorales est basée sur la reconnaissance par les Lymphocytes Τ Cytotoxiques (CTL), d'un peptide antigénique (p) présenté à la suface de la cellule par le complexe majeur d'histocompatibilité de classe I (MHC). La capacité des récepteurs des lymphocytes (TCR) à distinguer les peptides endogènes des peptides étrangers constitue le mécanisme de contrôle le plus important dirigé contre les cellules infectées. L'interaction entre le TCR et le pMHC est le sujet de beaucoup d'attention dans la thérapie du cancer, depuis la conception de la méthode de transfer adoptif: les lymphocytes capables d'une réponse importante contre les cellules tumorales sont extraits du patient, amplifiés in vitro, et réintroduits après immunosuppression. Il peut en résulter une régression du cancer. Ces dix dernières années, d'importants progrès ont été réalisés grâce à l'introduction de lymphocytes modifiés par génie génétique. En parallèle, la compréhension du TCRpMHC au niveau moléculaire est donc devenue essentielle pour soutenir les études in vitro et in vivo. En 1996, l'obtention de la première structure du complexe TCRpMHC à l'aide de la cristallographie par rayons X a révélé les bases moléculaires de l'interaction. Depuis lors, les techniques de modélisation moléculaire ont exploité les structures expérimentales pour comprendre la spécificité de la reconnaissance du pMHC par le TCR. Dans le même temps, de nouvelles techniques expérimentales permettant de déterminer la séquence de TCR spécifiques envers un pMHC donné, ont été largement exploitées. Ainsi, d'importants répertoires de TCR sont devenus disponibles, et il est plus que jamais nécessaire de développer des approches informatiques capables de prédire les interactions moléculaires qui ont lieu lors de la liaison du TCR au pMHC, et ce sans dépendre systématiquement de la résolution d'une structure cristalline. Ce mémoire présente une nouvelle approche pour analyser les principes moléculaires régissant la reconnaissance du pMHC par le TCR, et l'activation du lymphocyte qui en résulte. Dans un premier temps, nous présentons TCRep 3D, une nouvelle méthode basée sur les modélisations par homologie et ab initio, pour l'étude de propriétés structurales des répertoires de TCR. Le procédé est discuté en détails et comparé à des approches standard. Nous démontrons ainsi que TCRep 3D est le plus performant pour prédire des conformations pertinentes du TCR. Deux applications à des études expérimentales des répertoires TCR sont ensuite présentées. Dans la seconde partie de ce travail nous présentons une étude de complexes TCRpMHC qui donne un aperçu intéressant du mécanisme d'approche du pMHC par le TCR. Finalement, la dernière section se concentre sur l'analyse détaillée d'une étude expérimentale basée sur les échanges deuterium/hydrogène, dont les résultats révèlent que certaines régions clés du domaine constant du TCR sont sujettes à un changement conformationnel lors de la liaison au pMHC. Nous proposons une hypothèse pour la signalisation structurelle des TCR, menant à l'activation du lymphocyte. Celle-ci est basée sur l'analyse des mouvements corrélés observés dans la structure du TCRpMHC.

Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine.

Nowadays, genome-wide association studies (GWAS) and genomic selection (GS) methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these methods for structured traits when using training populations with high levels of genetic diversity. Such an example of a highly heterozygous, perennial species is grapevine. The present study compares the accuracy of models based on GWAS or GS alone, or in combination, for predicting simple or complex traits, linked or not with population structure. In order to explore the relevance of these methods in this context, we performed simulations using approx 90,000 SNPs on a population of 3,000 individuals structured into three groups and corresponding to published diversity grapevine data. To estimate the parameters of the prediction models, we defined four training populations of 1,000 individuals, corresponding to these three groups and a core collection. Finally, to estimate the accuracy of the models, we also simulated four breeding populations of 200 individuals. Although prediction accuracy was low when breeding populations were too distant from the training populations, high accuracy levels were obtained using the sole core-collection as training population. The highest prediction accuracy was obtained (up to 0.9) using the combined GWAS-GS model. We thus recommend using the combined prediction model and a core-collection as training population for grapevine breeding or for other important economic crops with the same characteristics.

TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.

TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling.

Extent and limitations of density functional theory in describing magnetic systems

The performance of density-functional theory to solve the exact, nonrelativistic, many-electron problem for magnetic systems has been explored in a new implementation imposing space and spin symmetry constraints, as in ab initio wave function theory. Calculations on selected systems representative of organic diradicals, molecular magnets and antiferromagnetic solids carried out with and without these constraints lead to contradictory results, which provide numerical illustration on this usually obviated problem. It is concluded that the present exchange-correlation functionals provide reasonable numerical results although for the wrong physical reasons, thus evidencing the need for continued search for more accurate expressions.

Extent and limitations of density functional theory in describing magnetic systems

The performance of density-functional theory to solve the exact, nonrelativistic, many-electron problem for magnetic systems has been explored in a new implementation imposing space and spin symmetry constraints, as in ab initio wave function theory. Calculations on selected systems representative of organic diradicals, molecular magnets and antiferromagnetic solids carried out with and without these constraints lead to contradictory results, which provide numerical illustration on this usually obviated problem. It is concluded that the present exchange-correlation functionals provide reasonable numerical results although for the wrong physical reasons, thus evidencing the need for continued search for more accurate expressions.

Prediction of cross-recognition of peptide-HLA A2 by Melan-A-specific cytotoxic T lymphocytes using three-dimensional quantitative structure-activity relationships.

The cross-recognition of peptides by cytotoxic T lymphocytes is a key element in immunology and in particular in peptide based immunotherapy. Here we develop three-dimensional (3D) quantitative structure-activity relationships (QSARs) to predict cross-recognition by Melan-A-specific cytotoxic T lymphocytes of peptides bound to HLA A*0201 (hereafter referred to as HLA A2). First, we predict the structure of a set of self- and pathogen-derived peptides bound to HLA A2 using a previously developed ab initio structure prediction approach [Fagerberg et al., J. Mol. Biol., 521-46 (2006)]. Second, shape and electrostatic energy calculations are performed on a 3D grid to produce similarity matrices which are combined with a genetic neural network method [So et al., J. Med. Chem., 4347-59 (1997)] to generate 3D-QSAR models. The models are extensively validated using several different approaches. During the model generation, the leave-one-out cross-validated correlation coefficient (q (2)) is used as the fitness criterion and all obtained models are evaluated based on their q (2) values. Moreover, the best model obtained for a partitioned data set is evaluated by its correlation coefficient (r = 0.92 for the external test set). The physical relevance of all models is tested using a functional dependence analysis and the robustness of the models obtained for the entire data set is confirmed using y-randomization. Finally, the validated models are tested for their utility in the setting of rational peptide design: their ability to discriminate between peptides that only contain side chain substitutions in a single secondary anchor position is evaluated. In addition, the predicted cross-recognition of the mono-substituted peptides is confirmed experimentally in chromium-release assays. These results underline the utility of 3D-QSARs in peptide mimetic design and suggest that the properties of the unbound epitope are sufficient to capture most of the information to determine the cross-recognition.

Reliability of the density functional approximation to describe the charge transfer and electrostatic complexes involved in the modeling of organic conducting polymers

Both the intermolecular interaction energies and the geometries for M ̄ thiophene, M ̄ pyrrole, M n+ ̄ thiophene, and M n+ ̄ pyrrole ͑with M = Li, Na, K, Ca, and Mg; and M n+ = Li+ , Na+ , K+ , Ca2+, and Mg2+͒ have been estimated using four commonly used density functional theory ͑DFT͒ methods: B3LYP, B3PW91, PBE, and MPW1PW91. Results have been compared to those provided by HF, MP2, and MP4 conventional ab initio methods. The PBE and MPW1PW91 are the only DFT methods able to provide a reasonable description of the M ̄ complexes. Regarding M n+ ̄ ␲ complexes, the four DFT methods have been proven to be adequate in the prediction of these electrostatically stabilized systems, even though they tend to overestimate the interaction energies.

Effect of pressure on La2(WO4)3 with a modulated scheelite-type structure

We have studied the effect of pressure on the structural and vibrational properties of lanthanum tritungstate La2(WO4)3. This compound crystallizes under ambient conditions in the modulated scheelite-type structure known as the α phase. We have performed x-ray diffraction and Raman scattering measurements up to a pressure of 20 GPa, as well as ab initio calculations within the framework of the density functional theory. Up to 5 GPa, the three methods provide a similar picture of the evolution under pressure of α-La2(WO4)3. At 5 GPa, we begin to observe some structural changes, and above 6 GPa we find that the x-ray patterns cannot be indexed as a single phase. However, we find that a mixture of two phases with C2/c symmetry accounts for all diffraction peaks. Our ab initio study confirms the existence of several C2/c structures, which are very close in energy in this compression range. According to our measurements, a state with medium-range order appears at pressures above 9 and 11 GPa, from x-ray diffraction and Raman experiments, respectively. Based upon our theoretical calculations we propose several high-pressure candidates with high cationic coordinations at these pressures. The compound evolves into a partially amorphous phase at pressures above 20 GPa.

MgO/Ag(001) interface structure and STM images from first principles

The interface of MgO/Ag(001) has been studied with density functional theory applied to slabs. We have found that regular MgO films show a small adhesion to the silver substrate, the binding can be increased in off-stoichiometric regimes, either by the presence of O vacancies at the oxide film or by a small excess of O atoms at the interface between the ceramic to the metal. By means of theoretical methods, the scanning tunneling microscopy signatures of these films is also analyzed in some detail. For defect free deposits containing 1 or 2 ML and at low voltages, tunnelling takes place from the surface Ag substrate, and at large positive voltages Mg atoms are imaged. If defects, oxygen vacancies, are present on the surface of the oxide they introduce much easier channels for tunnelling resulting in big protrusions and controlling the shape of the image, the extra O stored at the interface can also be detected for very thin films.

Estrutura e propriedades de elipticinas

The ellipticines constitute a broad class of molecules with antitumor activity. In the present work we analyzed the structure and properties of a series of ellipticine derivatives in the gas phase and in solution using quantum mechanical and Monte Carlo methods. The results showed a good correlation between the solvation energies in water obtained with the continuum model and the Monte Carlo simulation. Molecular descriptors were considered in the development of QSAR models using the DNA association constant (log Kapp) as biological data. The results showed that the DNA binding is dominated by electronic parameters, with small contributions from the molecular volume and area.

NMR in Crystals and Powders of Topazes with Different Colours

The present work is a part of the large project with purpose to investigate microstructure and electronic structure of natural topazes using NMR method. To reach this task we determined the relative contents of fluorine and hydrogen in crystals blue, colorless, wine and wine irradiated topazes. Then we determined the electric field gradients in site of aluminium atoms by NMR method, calculated EFG using ab initio method, and measured relaxation time dependence on heating temperature for blue, colorless, Swiss blue and sky blue topazes. Nuclear magnetic resonance (NMR) is an effective method to investigate the local structure in the crystal. The NMR study of the single crystal gives detailed information especially about the local crystal structure. As a result of this work we have received practical data, which is possible to use in future for making personal dosimetry and for preparation of mullite, which is widely used in traditional and advanced ceramic materials.

Vibrational contribution to dipole polarizability and first hyperpolarizability of LiH

The role played by electron correlation and vibrational correction on the polarizability of the LiH molecule is demonstrated. We present results for the dipole moment, polarizability and first hyperpolarizability of the LiH molecule obtained through many-body perturbation-theory, coupled-cluster and quadratic configuration interaction methods. Our best result for the dipole polarizability, obtained using the QCISD(T) scheme, indicates that the vibrational contribution is appreciable, amounting to ca. 10% of the total polarizability. Regarding the first hyperpolarizability, the vibrational contribution is even more important and has opposite sign in comparison with the electronic contribution.

Estudo teórico de propriedades ópticas não-lineares de nanotubos de carbono de parede única quimicamente modificados

Structure and first hyperpolarizability for a series of armchair a(5,5) chemically modified carbon nanotubes (CNT) were calculated at semiempirical and density functional levels of theory. The 4,4´-substituted stilbenes were selected as chromophore with substituents at position 4´ set to X=NO2, H, Cl, OH and NH2. The calculated values for static first hyperpolarizability (β) were almost linearly dependent on the electronic effect of the group X, increasing from NO2 to NH2. At DFT level the effect of inserting the chromophore in the CNT surface was to enhance the β value up to 70% relative to the free 4,4´-substituted stilbene.

Analysis of the structural and electronic properties of 1-(5-Hydroxymethyl - 4 -[ 5 - (5-oxo-5-piperidin-1-yl-penta-1,3dienyl)-benzo[1,3]dioxol-2-yl] -tetrahydro-furan-2-yl)-5-methyl-1H-pyrimidine-2,4dione molecule

The structural and electronic properties of 1-(5-Hydroxymethyl - 4 -[ 5 - (5-oxo-5-piperidin- 1 -yl-penta- 1,3 -dienyl)-benzo [1,3] dioxol- 2 -yl]-tetrahydro -furan-2 -yl)-5-methy l-1Hpyrimidine-2,4dione (AHE) molecule have been investigated theoretically by performing density functional theory (DFT), and semi empirical molecular orbital calculations. The geometry of the molecule is optimized at the level of Austin Model 1 (AM1), and the electronic properties and relative energies of the molecules have been calculated by density functional theory in the ground state. The resultant dipole moment of the AHE molecule is about 2.6 and 2.3 Debyes by AM1 and DFT methods respectively, This property of AHE makes it an active molecule with its environment, that is AHE molecule may interacts with its environment strongly in solution.

Research and development of III-V semiconductor surfaces for improved device interfaces

This thesis is devoted to understanding and improving technologically important III-V compound semiconductor (e.g. GaAs, InAs, and InSb) surfaces and interfaces for devices. The surfaces and interfaces of crystalline III-V materials have a crucial role in the operation of field-effect-transistors (FET) and highefficiency solar-cells, for instance. However, the surfaces are also the most defective part of the semiconductor material and it is essential to decrease the amount of harmful surface or interface defects for the next-generation III-V semiconductor device applications. Any improvement in the crystal ordering at the semiconductor surface reduces the amount of defects and increases the material homogeneity. This is becoming more and more important when the semiconductor device structures decrease to atomic-scale dimensions. Toward that target, the effects of different adsorbates (i.e., Sn, In, and O) on the III-V surface structures and properties have been investigated in this work. Furthermore, novel thin-films have been synthesized, which show beneficial properties regarding the passivation of the reactive III-V surfaces. The work comprises ultra-high-vacuum (UHV) environment for the controlled fabrication of atomically ordered III-V(100) surfaces. The surface sensitive experimental methods [low energy electron diffraction (LEED), scanning tunneling microscopy/spectroscopy (STM/STS), and synchrotron radiation photoelectron spectroscopy (SRPES)] and computational density-functionaltheory (DFT) calculations are utilized for elucidating the atomic and electronic properties of the crucial III-V surfaces. The basic research results are also transferred to actual device tests by fabricating metal-oxide-semiconductor capacitors and utilizing the interface sensitive measurement techniques [capacitance voltage (CV) profiling, and photoluminescence (PL) spectroscopy] for the characterization. This part of the thesis includes the instrumentation of home-made UHV-compatible atomic-layer-deposition (ALD) reactor for growing good quality insulator layers. The results of this thesis elucidate the atomic structures of technologically promising Sn- and In-stabilized III-V compound semiconductor surfaces. It is shown that the Sn adsorbate induces an atomic structure with (1×2)/(1×4) surface symmetry which is characterized by Sn-group III dimers. Furthermore, the stability of peculiar ζa structure is demonstrated for the GaAs(100)-In surface. The beneficial effects of these surface structures regarding the crucial III-V oxide interface are demonstrated. Namely, it is found that it is possible to passivate the III-V surface by a careful atomic-scale engineering of the III-V surface prior to the gate-dielectric deposition. The thin (1×2)/(1×4)-Sn layer is found to catalyze the removal of harmful amorphous III-V oxides. Also, novel crystalline III-V-oxide structures are synthesized and it is shown that these structures improve the device characteristics. The finding of crystalline oxide structures is exploited by solving the atomic structure of InSb(100)(1×2) and elucidating the electronic structure of oxidized InSb(100) for the first time.