Les ARNt sont des molécules adaptatrices reliant l'information génétique de l’ARN messagers à la séquence d'acides aminés primaire des protéines. Les ARNt ont une structure typique, appelée "feuille de trèfle". Certains ARNt mitochondriaux montrent une forte dérivation de cette structure. Un cas extrême peut être observé dans les mitochondries du nématode R. culicivorax. Cette étude vise la caractérisation fonctionnelle de ces ARNt «bizarres» et de définir leurs propriétés structurales et leur fonctionnalité avec des protéines partenaires telles que les CCAses et les aminoacyl-ARNt synthetases. Ce travail révèle que les ARNt sans bras forment une structure secondaire en forme d'épingle à cheveux et que leurs structures 3D présentent une grande flexibilité intrinsèque. Les tests initiaux n’ont pas démontré l'activité d'aminoacylation. Cependant, les ARNt sans bras représentent des molécules fonctionnelles pour le CCAse, indiquant des adaptations de l’enzyme aux ARNt sans bras. / TRNAs are adapter molecules linking the genetic information of messenger RNAs with the primary amino acid sequence of proteins. tRNAs have a typical cloverleaf-like secondary structure. Some mitochondrial tRNAs show a high derivation from this canonical tRNA structure. An extreme case of structural truncations can be observed in mitochondria of the nematode R. culicivorax. This study aims the functional characterization of such “bizarre” tRNAs in defining their structural properties and their functionality with interacting partner proteins such as CCA-adding enzymes and aminoacyl-tRNA synthetases. This work reveals that armless tRNAs form a hairpin-shaped secondary structure. 3D structures exhibit a high intrinsic flexibility. Initial tests could not demonstrate aminoacylation activity. However, armless tRNAs represent functional molecules for CCA-incorporation, indicating adaptations of CCA-adding enzymes to armless tRNAs.

No description available.

No description available.

No description available.

Protein synthesis is a process by which organisms manufacture their proteins that perform various cellular activities either alone or in combination with other similar or different molecules. In eubacteria, protein synthesis proceeds at a rate of around 15 amino acids per second. The ribosomes, charged tRNAs and mRNAs can be considered as the core components of protein synthesis system which, in addition, involves a panel of non-ribosomal proteins that regulate the speed, specificity and accuracy of the process. Peptidyl-tRNA hydrolase (Pth) and ribosome recycling factor (RRF) are two such non-ribosomal proteins involved in protein synthesis. These two proteins are essential for eubacterial survival and the work reported in this thesis involves structural characterization of these two proteins from the bacterial pathogen, Mycobacterium tuberculosis. The protein structures were solved using established techniques of protein crystallography. Hanging drop vapour diffusion method and crystallization under oil using microbatch plates were the methods employed for protein crystallization. X-ray intensity data were collected on a MAR Research imaging plate mounted on a Rigaku RU200 X-ray generator in all the cases. The data were processed using DENZO and MOSFLM. The structures were solved by molecular replacement method using the program PHASER. Structure refinements were carried out using programs CNS and REFMAC. Model building was carried out using COOT. PROCHECK, ALIGN, CHIMERA, and PYMOL were used for structure validation and analysis of the refined structures. Peptidyl-tRNA hydrolase cleaves the ester bond between tRNA and the attached peptide in peptidyl-tRNA that has dropped off from ribosome before reaching the stop codon, in order to avoid the toxicity resulting from peptidyl-tRNA accumulation and to free the tRNA to make it available for further rounds in protein synthesis. To begin with, the structure of the enzyme from M. tuberculosis (MtPth) was determined in three crystal forms. This structure and the structure of the same enzyme from Escherichia coli (EcPth) in its crystal differ substantially on account of the binding of the C-terminus of the E.coli enzyme to the peptide binding site of a neighboring molecule in the crystal. A detailed examination of this difference led to an elucidation of the plasticity of the binding site of the enzyme. The peptide-binding site of the enzyme is a cleft between the body of the molecule and a polypeptide stretch involving a loop and a helix. This stretch is in open conformation when the enzyme is in the free state as in the crystals of MtPth. Furthermore, there is no physical continuity between the tRNA and the peptide-binding sites. The molecule in the EcPth crystal mimics the peptide-bound conformation of the enzyme. The peptide stretch involving a loop and a helix, referred to earlier, now closes on the bound peptide. Concurrently, a gate connecting the tRNA and the peptide-binding site opens primarily through the concerted movement of the two residues. Thus, the crystal structure of MtPth when compared with that of EcPth, leads to a model of structural changes associated with enzyme action on the basis of the plasticity of the molecule. A discrepancy between the X-ray results and NMR results, which subsequently became available, led to X-ray studies on new crystal forms of the enzyme. The results of these studies and those of the enzyme from different sources that became available, confirmed the connection deduced previously between the closure of the lid at the peptide-binding site and the opening of the gate that separates the peptide-binding site and tRNA binding site. The plasticity of the molecule indicated by X-ray structures is in general agreement with that deduced from the available solution NMR results. The correlation between the lid and the gate movement is not, however, observed in the NMR structure of MtPth. The discrepancy between the X-ray and NMR structures of MtPth in relation to the functionally important plasticity of the molecule, referred to earlier, also led to molecular dynamics simulations. The X-ray and the NMR studies along with the simulations indicated an inverse correlation between crowding and molecular volume. A detailed comparison of proteins for which X-ray and the NMR structures are available appears to confirm this correlation. In consonance with the reported results of the investigation in cellular components and aqueous solutions, the comparison indicates that the crowding results in compaction of the molecule as well as change in its shape, which could specifically involve regions of the molecule important for function. Crowding could thus influence the action of proteins through modulation of the functionally important plasticity of the molecule. After termination of protein synthesis at the stop codon, the ribosome remains as a post-termination complex (PoTC), consisting of the 30S and the 50S subunits, mRNA and a deacylated tRNA. This complex has to be disassembled so that the ribosome is available for the next round of translation initiation. Ribosome recycling factor (RRF) binds to ribosome and in concert with elongation factor G (EF.G), performs the recycling of ribosome that results in disassembly of PoTC. The structure of this L-shaped protein with two domains connected by a hinge, from Mycobacterium tuberculosis (MtRRF) was solved previously in our laboratory. The relative movement of domains lies at the heart of RRF function. Three salt bridges were hypothesized to reduce the flexibility of MtRRF when compared to the protein from E.coli (EcRRF), which has only one such salt bridge. Out of these three bridges, two are between domain 1 and domain 2, whereas the third is between the hinge region and the C-terminus of the molecule. These salt bridges were disrupted with appropriate mutations and the structure and activity of the mutants and their ability to complement EcRRF were explored. An inactive C-terminal deletion mutant of MtRRF was also studied. Major, but different, structural changes were observed in the C-terminal deletion mutant and the mutant involving the hinge region. Unlike the wild type protein and the other mutants, the hinge mutant complements EcRRF. This appears to result from the increased mobility of the domains in the mutant, as evidenced by the results of librational analysis. In addition to the work on PTH and RRF, the author was involved during the period of studentship in carrying out X-ray studies of crystalline complexes involving amino acids and carboxylic acids, which is described in the Appendix of the thesis. The complexes studied are that of tartaric acid with arginine and lysine.

Biological processes are so complicated that to understand the mechanisms underlying the functioning of biomolecules it is inevitable to study them from various perspectives and with a wide range of tools. Understanding the function at the molecular level obviously requires the knowledge of the three dimensional structure of the biomolecules. Experimentally this can be obtained by techniques such as X‐ray crystallography and NMR studies. Computational biology has also played an important role in elucidating the structure function relationship in biomolecules. Computationally one can obtain the temporal as well as ensemble behavior of biomolecules at atomic level under conditions that are experimentally not accessible. Molecular dynamics(MD) study is a technique that can be used to obtain information of the dynamic behavior of the biomolecules. Dynamics of large systems like proteins can be investigated by classical force fields. However, the changes at the level of covalent bond involve the reorganization of electron density distribution which can be addressed only at Quantum mechanical level. In the present thesis, some of the biological systems have been characterized both at the classical and quantum mechanical level. The systems investigated by MD simulations and the insights brought from these studies are presented in Chapters 3 and 4. The unusual bonds such as pyrophosphate linkage in ATP and short strong hydrogen bonds in proteins, investigated through high level quantum chemical methods, are presented in Chapters 5, 6 and 7. Part of this thesis is aimed to address some important issues related to the dynamics of Tryptophanyl tRNA synthetase (TrpRS) which belongs to classic of aminoacyl‐tRNA synthetases (aaRS). aaRSs are extremely important class of enzymes involved in the translation of genetic code. These enzymes catalyze the aminoacylation of tRNAs to relate the cognate amino acids to the anticodon trinucleotide sequences. aaRSs are modular enzymes with distinct domains on which extensive kinetic and mutational experiments as well as structural analyses have been carried out, highlighting the role of inter‐domain communication (Alexander and Schimmel, 2001). The overall architecture of tRNA synthetases consists of primarily two domains. The active site domain is responsible for the activation of an amino acid with ATP in synthesizing an enzyme‐bound aminoacyl‐adenylate, and transfer of the aminoacyl‐adenylate intermediate to the 3’end of tRNA. The second domain is responsible for selection and binding of the cognate tRNA. aaRSs are allosteric proteins in which the binding of tRNA at the anticodon domain influences the activity at the catalytic region. These two binding sites are separated by a large distance. One of the aims of this thesis is to characterize such long distance communication (allosteric communication) at atomic level in Tryptophanyl tRNA synthetase. This is achieved by generating ensembles of conformations by MD simulations and analyzing the trajectories by novel graph theoretic approach. Graph and network based approaches are well established in the field of protein structure analysis for analyzing protein structure, stability and function (Kannan and Vishveshwara, 1999; Brinda and Vishveshwara, 2005). The parameters such as clusters, hubs and shortest paths provide valuable information on the structure and dynamics of the proteins. In this thesis, network parameters are used for the analysis of molecular dynamics MD) simulation data, to represent the global dynamic behavior of protein in a more elegant way. MD simulations are performed on some available (and modeled) structures of TrpRS bound to a variety of ligands, and the protein structure networks( PSN) of non‐covalent interactions are characterized in dynamical equilibrium. The ligand induced conformational changes are investigated through structure networks. These networks are used to understand the mode of communication between the anticodon domain and the active site. The interface dynamics is crucial for the function of TrpRS (since it is a functional dimer) and it is investigated through interface clusters. The matter embodied in the thesis is presented as 9 chapters. Chapter 1 lays the suitable background and foundation for the study, surveying relevant literature from different fields .Chapter 2 describes in detail the various materials, methods and techniques employed in the different analyses and studies presented in this thesis. A brief description of well‐known methods of molecular dynamics simulations, essential dynamics calculations, cross correlation maps, conformational clustering etc.is presented. The methods for constructing protein structure graphs and networks, developed in our lab, are described in detail. The use of network parameters for the analysis of MD simulation data to address the problem of communication between the two distal sites is also presented. Some descriptions of the ab initio quantum mechanical methods, which are used to investigate the unusual bonds in biomolecules, are also presented in this chapter. Chapter 3 is devoted in discussing the results from several normal as well as high temperature MD simulations of ligand‐free and ligand bound Bacillus stearothermophilus Tryptophanyl‐tRNA synthetase (bsTrpRS). The essential modes of the protein in the presence of different ligands are captured by essential dynamics calculations. Different conformations of the protein associated with the catalysis process of TrpRS, as captured through experiments, are discussed in the context of conformational sampling. High temperature simulations are carried out to explore the larger conformational space. Chapter 4 is focused on the results obtained from the MD simulation of human Tryptophanyl‐tRNA synthetase (hTrpRS). The structure of human TrpRS bound to the activated ligand (TrpAMP) and the cognate tRNA(tRNATRP) is modeled since no structure in the presence of both TrpAMP and tRNATRP is available. MD simulations on these modeled as well as other complexes of hTrpRS are performed to capture the dynamical process of ligand induced conformational changes (Hansiaetal., communicated). Both the local and the global changes in the protein conformation from the protein structure network (PSN) of MD snapshots are analyzed. Several important information such as the ligand induced correlation between different residues of the protein, asymmetric binding of the ligands to the two subunits of the protein, and the path of communication between the anticodon region and the aminoacylation site are obtained. Also, the role of the dimmer interface, from a dynamic perspective, is obtained for the first time. The interface dynamics which stabilize different quaternary structures of lectins (with high sequence and structure similarity) were investigated in a collaborative work (Hansiaetal.,2007). The lectin peanut agglutinin (PNA) is a tetramer with three different types of interfaces. The interface dynamics of this protein in the presence and in the absence of metal ions was investigated and the paper reporting the results from this study is included as appendix in this thesis. Chapter 5 deals with high level ab initio quantum chemical calculations on tri‐ and diphosphate fragments of adenosine triphosphate (ATP). Pyrophosphate prototypes such as methyl triphosphate and methyl diphosphate molecules in their different protonation states have been investigated at high levels of calculations (Hansiaetal., 2006a). The optimized geometries, the thermochemistry of the hydrolysis and the molecular orbitals contributing to the high energy of these compounds have been analyzed. These investigations provide insights into the‘‘highenergy’’character of ATP molecule. Further, the dependence of vibrational frequencies on the number of phosphate groups and the charged states has also been presented. These results aid in the interpretation of spectra obtained by experiments on complexes containing pyrophosphate prototypes. Hydrogen bonding is fundamental in understanding the structure and properties of molecules of biological interest including proteins. A recent analysis carried out in our lab showed that a significant number of short hydrogen bonds (SHB) are present in proteins (Rajagopal and Vishveshwara, 2005). Chapters 6 and 7 elucidate the results obtained from ab initio quantum chemical calculations on some of these SHBs to get aquantitative estimation of their geometry and strength. In chapter 6, asystematic analysis of the geometries and the energetics of possible SHB systems, which are frequently encountered in proteins, are presented at different levels of theory (HF,DFTandMP2). It is found that the SHBs involving both charged residues in the proteins are intrinsic in nature. However, two neutral residues form a SHB in the protein crystal structures either due to geometric constraints or due to the environment of these residues. This analysis enables one to distinguish SHBs which are formed because of geometric constraints from those which are formed because of the inherent property of the chemical groups involved in the hydrogen bonding. These results are useful in refining protein structures determined by crystallographic or NMR methods. In addition, sulfur atom of methionine and cysteinein proteins also participate in SHBs, which are not so well characterized. Chapter 7 presents the similar analysis carried out on short hydrogen bonds in proteins involving sulfur atom. A detailed analysis of SHBs of sulfur containing groups in a data set of proteins has been carried out. Some of the residue pairs from this analysis were considered for ab initio calculations. However, the optimization of these examples resulted in breaking of the hydrogen bonds involving sulfur atoms and formation of new hydrogen bonds with oxygen and/or nitrogen atoms. Hence model systems, which mimic the real examples, were designed to carry out ab initio studies and to investigate the short hydrogen bonds involving sulfur atoms. Another study on the protein‐water interaction, which does not fall under the realm of the main objective of the thesis, is discussed in Chapter 8. Protein–water interaction is crucial for accomplishing many biological functions of proteins. In the recent past, natural probe tryptophan, located at the protein surfaces, has been extensively investigated using femtosecond spectroscopy experiments to understand salvation dynamics (Peonetal.,2002). In this chapter a method is described to follow up the molecular events of the protein–water interactions in detail. Tryptophan–water interaction in the protein Monellin is investigated in order to get the atomic level insights into the hydration dynamics, by carrying out MD simulations on Monellin (Hansiaetal.,2006b). The results are compared with those obtained from femtosecond resolved fluorescence spectroscopy. The time constants of the survival correlation function match well with the reported experimental values.This validates the procedure, adapted here for Monellin, to investigate the hydration dynamics in general. The last chapter (Chapter9) summarizes the results obtained from various studies and discusses the future directions. First part of this thesis aims to present the analysis by carrying out MD simulations on monomeric and dimeric TrpRS protein in order to understand the two steps of the aminoacylation reaction: activation of the aminoacid Trp in the first step and the transfer of the activated amino acid in the next step. In the second part, quantitative estimation of the geometry and the strength of pyrophosphate bond and short hydrogen bonds in proteins are reported in detail by subjecting the systems to high levels of quantum mechanical calculations(QM). The use of ab initio QM/MM calculations by combining the quantum mechanics(QM) with the molecular mechanics(MM) in order to study the enzymatic reactions is discussed as the future