The protein-protein interactions (PPIs) occur when two or more proteins are bound together. Also, this protein-protein interactions (PPIs) cause the various biological processes in the body. Due to this reason, abilities of controlling or inhibiting PPIs can give us promising advantages like (1) better understanding of biological systems, (2) development of new diagnostic approaches for health or disease, and (3) establishment of novel molecular therapeutics. Many proteins adopt the secondary structures, where most of protein-protein interactions take place. -Helices and -sheets are the prevalent secondary conformations, but there are extended secondary structures such as -hairpins, -turns, 310 helix, and so on. As a result, construction of molecules mimicking these protein secondary structures is tractable target for drug design. Moreover, in drug discovery, designing peptidomimetics or non-peptidic mimetics is a popular strategy instead using peptides or truncated peptides because peptides or truncated peptides are prone to proteolysis and degraded in the body. Also, peptidomimetics and non-peptidic mimetics have not only the similar topology as peptides but also resistance to proteolysis. Due to these advantages, in this study, peptidomimetics or non-peptidic mimetics were synthesized and tested for different targets: (1) synthesis of non-peptidic -helical mimetics for p53-MDM2 inhibition, (2) solution-phase synthesis of -hairpin peptide for the inhibition of multiple myeloma cells (MM) adhesion, and (3) synthesis of -hairpin peptoid-peptide hybrids. The synthesis in all three different studies was succeeded, but they still need some improvements. For instance, non-peptidic -helical mimetics, terpyrimidyl derivatives, were synthesized successfully, but they did not show any bioactivity against p53-MDM2. Also, they have a solubility problem. Based on these results, it is necessary to improve the pharmacokinetic properties and bioactivity by changing the substituents on the rings or structures. The -hairpin peptide for the second case already showed good bioactivity against multiple myeloma (MM). For the next level of bio-study, the considerable amount of a -hairpin peptide was demanded. In order to make the substantial -hairpin peptide, the solution phase peptide synthesis was chosen instead of the solid phase peptide synthesis because of the cost-effect. Two methodology were tried for the solution-phase peptide synthesis: (1) segment ligation and (2) continuous synthesis. In the former case, the -hairpin peptide synthesis was successful, but, in the latter case, it is necessary to investigate the appropriate coupling reagents for each step. Peptoid-peptide hybrids has been one of the popular peptidomimetics in the last two decades. Also, mimicking the peptide secondary structure in peptoids has been studied extensively these days. The combination of these two factors was the goal for the third case. Because peptoid-peptide hybrids with a secondary structure can be recognizable by native proteins and resistant to proteolysis. So far, three sets of peptoid-peptide hybrids were synthesize and checked the secondary structure formation by using NMR. However, there was no indication of the secondary structure formation in the three sets of peptoid-peptide hybrids. This result suggests that it is necessary to introduce the more constrained components in peptoid-peptide hybrids. In the above three chapters, it has been tried to find the new drug candidates by synthesizing peptidomimetics or non-peptidic mimetics. Even though the synthesis was successful, some intended results such as the bioactivity or the secondary structure formation were not obtained. However, these results can give us the inspirations to improve properties of peptidomimetics or non-peptidic mimetics for a certain purpose, which leads to earn the intended results and eventually find new drug candidates.

The p53 protein promotes tumor eradication upon activation, making it an attractive target in cancer therapies. A reported 50% of all human cancers display aberrant activation of the MDM2 oncoprotein, which directly promotes tumorgenesis by inactivating the transcriptional activity of wild type p53, and is commonly associated with drug, chemo, and radio therapy resistance. Previously reported crystallographic analysis of the p53/MDM2 complex infers that the p53 protein forms a 2.5 turn amphipathic alpha helix whose hydrophobic face interacts within a deep hydrophobic cleft in the NH2-terminal domain of the globular MDM2. This suggests that the synthesis of small molecular antagonists of p53/MDM2 binding interactions, capable of reactivating wild type p53 function, show a promising therapeutic strategy in pharmaceutical discovery. The use of alpha helix mimics for the disruption of p53/MDM2 binding interactions has been amply documented in the literature; however, these compounds contain hydrophobic scaffolds that limit their usefulness as potential drug candidates. Presented is the design, synthesis, and biological evaluation of novel non-peptidic, drug-like, small molecule inhibitors to target p53/MDM2 binding interactions. The mimetics are designed to bind to the NH2-terminal domain of MDM2 protein leaving p53 unbound and capable of activation. The inhibitor design is based on an alpha helix mimetic scaffold derived from functionalized piperazines, diketopiperazines, and/or pyrimides. The mimetics are designed to have a comparably higher degree of solubility and notably facile synthesis yet still maintain the desired spacial arrangements of hydrophobic side chains in the ith, ith+4, and ith+7 positions of a natural alpha helix. The small molecules are designed to act as antagonists of protein/protein interactions, tumor inhibitors, and potent p53 activators.

Many currently relevant diseases such as cancer arise from altered biological pathways that rely on protein-protein interactions. The proteins involved in these interactions contain certain functional domains that are responsible for the protein's biological activities. These domains consist of secondary structural elements such as α-helices and Β-sheets which are at the heart of the protein's biological activity. Therefore, designing drugs that inhibit protein-protein interactions by binding to these key secondary structural elements should provide an effective treatment for many diseases. Presented in this dissertation are the designs, syntheses, and biological evaluations for both novel α-helix and novel Β-sheet mimics. The α-helix mimics were designed to inhibit the interactions between the tumor suppressor protein p53 and its inhibitor protein, MDM2. We also targeted the interactions between the Bak/Bcl-xL proteins. Using the knowledge gained from Hamilton's 1,4-terphenylene scaffold, we designed our inhibitors to be non-peptidic small molecule α-helix mimics. These molecules were designed to bind to the NH2-terminal domain of MDM2 protein thus preventing it from binding to the p53 protein thereby allowing p53 to induce apoptosis. The α-helix mimetic scaffold is designed around a central functionalized pyridazine ring while maintaining the appropriate distances between the ith, ith+4, and ith+7 positions of a natural alpha helix. The Β-sheet mimics were designed as inhibitors for the integrin mediated extracellular matrix cell adhesion found in Multiple Myeloma. We have designed, synthesized, and incorporated novel Β-turns to induce the formation of Β-hairpins as well as to cyclize the peptides in order to increase their binding affinities and reduce proteolytic cleavage. Given that many protein-protein interactions occur through hydrophobic interactions; our primary Β-turn promoter was designed with the ability to alter the Β-hairpin's hydrophobicity depending on the sulfonyl group used in the turn. The synthesis of several different sulfonyl chlorides for use in our Β-turn promoter is included in this section. We have also provided a detailed structural analysis and characterization of these new cyclic peptides via NMR and CD spectrometry. Using standard 2D NMR methods, we have elucidated the 3D conformation of several peptides in solution. We have also studied the structure activity relationships (SAR) for these cyclic peptides and then correlated these results with those obtained from the NMR studies.

The most common secondary structure of proteins is the alpha-helix. The alpha-helix can be involved in various protein-protein interactions (PPIs) through the recognition of three or more side chains along one face of the alpha-helix (Wells and McClendon, 2007). In recent years, there has been an increasing interest in the development of peptidic and non-peptidic compounds that bind to PPI surfaces. We focused on the design and synthesis of compounds that mimic the orientation of side chain residues of an alpha-helical protein domain. Although our scaffolds could potentially inhibit various PPIs, we focused mainly on the disruption of interactions among the Bcl-2-family of proteins and the Mdm-2-family of proteins to favor apoptosis in cancer cells. A summary of Bcl-2 and Mdm-2 structure and function relationships that focuses on the possibility of using peptidic and non-peptidic alpha-helical mimics as PPI inhibitors is described in Chapter One. Chapter Two discusses the design and synthesis of 3-substituted-2,6- and 2,5-piperazinedione oligomers as more hydrophilic scaffolds compared to previously reported alpha-helical mimetics (Yin, et al., 2005). A key feature of this design is the linkage of the units by a hydrazine bond. While we were able to prepare several monomers containing the hydrazine linkage, synthesis of the dimers and trimers is very challenging. Due to the difficulty of synthesizing oligomeric piperazine-diones in practical yields, we next focused on the design and synthesis of novel 2,5-terpyrimidinylene scaffolds as an alternative to obtain alpha-helical mimetics; this is discussed in Chapter Three. The main outcome of this project was the efficient preparation of a "first-generation" non-peptidic compound library via a facile iterative synthesis enabled by the key conversion of 5-cyanopyrimidine to 5-carboxamidine. Chapter Three also discusses our progress towards the synthesis of structurally similar substituted-2,5-terpyrimidinylenes, but with more drug-like properties as determined by QikProp calculations. Chapter Four describes an independent study on the synthesis of a guanidine derivative as an alkylating agent for the synthesis of cysteine peptide nucleic acids, CPNA, which is another current project in our lab.

Secondary structure dynamics of biopolymers play a vital role in many of the complex processes within a cell. However, due to the substantial number of atoms in the involved biopolymers along with the multitude of interactions that occur between the molecules, understanding these processes in detail is challenging and often involves computationally demanding simulations. In this thesis, the secondary structure dynamics of three different biopolymer systems were modeled using a single approach, which is based on intuitive principles that facilitate the interpretation. To this end, the kinetic behavior of each system was experimentally determined, and described by simplified reaction schemes, which were then connected to Markov chain models encompassing all principal secondary structural conformations. Firstly, we investigated the toehold-mediated strand displacement reaction, which is widely applied in nanotechnology to create DNA-based nano-devices and biochemical reaction networks. Our model correctly described the impact of base pair mismatches on the kinetics of these reactions, as measured by bulk fluorescence experiments. Additionally, it revealed that incumbent dissociation, base pair fraying, and internal loop formation are important processes during strand displacement. Furthermore, we established two dissipative elements to enhance temporal control over toehold-mediated strand displacement reactions. The first element allowed a reversible and repeatable incumbent strand release, whereas the second element provided the possibility to start the displacement reaction after a programmable temporal delay. Secondly, we studied the target recognition by the CRISPR-Cas effector complex Cascade, a highly promising protein for applications in genome engineering. Our model successfully reproduced all aspects of the torque- and mismatch-dependent R-loop formation time by Cascade obtained by single-molecule torque and bulk fluorescence measurements. Furthermore, we demonstrated that the seed effect observed for Cascade results from DNA supercoiling, rather than a structural property of the protein complex. Lastly, we explored the folding/unfolding of α-helices, which plays a critical role in the folding and function of proteins. Our model accurately described α-helix unfolding kinetics obtained by fast triplet-triplet energy transfer. Moreover, we showed that the complex α-helix unfolding does not follow a simple Einstein-type diffusion but is a combination of the sub-diffusive boundary diffusion and the rather peptide-length-independent coil nucleation. The presented models enabled access to the diverse timescales of the characterized processes, which are generally difficult to access experimentally, despite utilizing just a single approach. In particular, we obtained: tens of microseconds for the branch migration step time of the toehold-mediated strand displacement, hundreds of microseconds for the R-loop formation steps by Cascade, and tens of nanoseconds for folding or unfolding of an α-helix by a single residue. Given the simplicity and accessibility of the established models, we are confident that they will become useful tools for researchers to analyze the dynamics of biomolecules, and anticipate that similar modeling approaches can be applied to other biopolymer systems, being well-described by probabilistic models. / Die Sekundärstrukturdynamik von Biopolymeren spielt eine entscheidende Rolle bei vielen komplexen Prozessen innerhalb einer Zelle. Aufgrund der beträchtlichen Anzahl von Atomen in den beteiligten Biopolymeren und der Vielzahl an Wechselwirkungen zwischen den Molekülen ist es jedoch eine Herausforderung diese Prozesse im Detail zu verstehen, und erfordert oft rechenintensive Simulationen. In dieser Arbeit wurde die Sekundärstrukturdynamik von drei verschiedenen Biopolymersystemen mit einem einzigen Ansatz modelliert, welcher auf intuitiven Prinzipien beruht und somit eine erleichterte Interpretation der Ergebnisse ermöglicht. Hierzu wurde das kinetische Verhalten jedes Systems experimentell bestimmt und durch vereinfachte Reaktionsschemata beschrieben. Diese wurden anschließend mit Markov-Kettenmodellen verknüpft, welche alle wichtigen Konformationen der Sekundärstruktur abbilden. Als erstes System untersuchten wir die DNA Strangaustauschreaktion, welche in der Nanotechnologie häufig zur Herstellung von DNA-basierten Nanomaschinen und biochemischen Reaktionsnetzwerken eingesetzt wird. Unser Modell beschrieb die durch Ensemble-Fluoreszenz-Experimente gemessenen Auswirkungen von Basenfehlpaarungen auf die Kinetik dieser Reaktionen korrekt. Des Weiteren zeigte sich, dass die vorzeitige Strangablösung, das Ausfransen von Basenpaaren und die Bildung interner Schleifen wichtige Prozesse während des Strangaustausches sind. Darüber hinaus konnten wir zwei dissipative Elemente etablieren, um die zeitliche Kontrolle über die Strangaustauschreaktionen zu verbessern. Das erste Element ermöglicht eine reversible und wiederholbare Strangablösung, während das zweite Element die Möglichkeit bietet die Strangaustauschreaktionen nach einer programmierbaren zeitlichen Verzögerung zu starten. Zweitens untersuchten wir den Zielerkennungsprozess durch den CRISPR-Cas Komplex Cascade, ein vielversprechendes Protein für Anwendungen in der Genomtechnologie. Unser Modell reproduzierte erfolgreich alle Aspekte der torsions- und fehlpaarungs-abhängigen R-Schleifenbildung durch Cascade, welche durch Einzelmolekül-Torsions- und Ensemble-Fluoreszenz-Messungen ermittelt wurden. Zusätzlich konnten wir nachweisen, dass der für Cascade beobachtete „seed“-Effekt auf DNA-Verdrehung und nicht auf eine strukturelle Eigenschaft des Proteinkomplexes zurückzuführen ist. Schließlich untersuchten wir die Faltung/Entfaltung von α-Helices, welche eine entscheidende Rolle bei der Faltung und Funktion von Proteinen spielen. Unser Modell beschrieb die durch schnelle Triplett-Triplett-Energietransfer Experimente ermittelte α-Helix-Entfaltungskinetik exakt. Darüber hinaus konnten wir zeigen, dass die komplexe α-Helix-Entfaltung nicht einer einfachen Diffusion vom Einstein-Typ folgt, sondern eine Kombination aus subdiffusiver Grenzdiffusion und der eher peptidlängenunabhängigen Coil-Nukleation ist. Obwohl nur ein einziger Ansatz verwendet wurde, ermöglichten die vorgestellten Modelle den Zugang zu den vielschichtigen Zeitskalen der charakterisierten Prozesse, welche im Allgemeinen experimentell schwer zugänglich sind. Insbesondere konnten die folgenden zeitlichen Bereiche bestimmt werden: Dutzende von Mikrosekunden für die Schrittzeit der Strangaustauschreaktion, Hunderte von Mikrosekunden für die Schritte der R-Schleifenbildung durch Cascade, und Dutzende von Nanosekunden für die Faltung oder Entfaltung einer α-Helix um ein einzelnes Segment. Angesichts der Simplizität und Zugänglichkeit der etablierten Modelle sind wir zuversichtlich, dass sie zu nützlichen Werkzeugen für Forscher werden, um die Dynamik von Biomolekülen zu analysieren. Zusätzlich gehen wir davon aus, dass ähnliche Modellierungsansätze auf andere Biopolymersysteme angewendet werden können, sofern sie gut durch probabilistische Modelle beschrieben werden.

Coordination of transition metals to peptides, either through the incorporation of unnatural chelating groups or amino acid ligating side-chains, expands the utility of peptides for biological studies. The first part of this project describes induction of α-helical secondary structure in pentapeptides upon side-chain coordination of inert transition metal ions. The second part of this project describes the syntheses of biologically active peptide species that contain a macrobicyclic hexaamine ligand that can complex radioactive metal ions for diagnostic imaging purposes. / Short peptide sequences do not form thermodynamically stable α-helices in water. The capacity of two metal clips, cis-[Ru(NH3)4(solvent)2]2+ and cis [Pd(en)(solvent)2]2+ to induce α-helicity in peptides that are five amino acids long, Ac HARAH NH2 and Ac MARAM-NH2 has been explored. In all cases at pH < 5, the metal ions bind to the side-chains of amino acid residues at positions i, i+4 of the pentapeptides resulting in formation of bidentate macrocyclic species. Circular dichroism and 1H nuclear magnetic resonance data indicate that the metal complexes of Ac-MARAM-NH2 are highly α helical in water, and in the most spectacular case, coordination of Ac-MARAM-NH2 to cis-[Ru(NH3)4(solvent)2]2+ results in up to 80% α-helicity. In contrast, metal complexes of Ac-HARAH-NH2 exhibit significantly less α-helicity in water. / 64Cu-radiolabelled peptides have been investigated for their ability to target specific tissue or cell types. These peptides require a chelating group that binds copper ions strongly. Macrobicyclic hexaamine ligands, based on the compound commonly referred to as “sarcophagine”, have demonstrated extremely high stability under biological conditions. Here we describe the synthesis of diaminosarcophagine chelators with carboxylate groups for conjugation to peptides. These new chelators have been attached to the N-terminus or lysine side-chain of biologically-active peptides, including Tyr3 octreotate, Lys3-bombesin and an integrin targeting peptide. Spectroscopic and voltammetric studies of these species suggest that the conjugated sarcophagine group retains the high metal binding affinity and structural properties of the parent species, diaminosarcophagine. These are among the first sarcophagine-peptide compounds that have been properly characterised. The new sarcophagine-peptide conjugates can be easily radiolabelled with 64Cu2+ over a wide pH range at ambient temperature.

Proteins are large biomolecules consisting of one or more long chains of amino acid residues. They perform a vast array of functions within living organisms. In this thesis, we present analyses of different secondary structural elements (SSEs) in proteins and various methods developed for the same purpose. Using only the geometric parameters, a program for identification of SSEs has been developed, which is more sensitive to the local structural variations. An understanding of the factors that determine the length, geometry as well as location of a particular SSE in the protein is essential to fully appreciate their respective roles in protein structures. The comparative analysis of the geometry of α-helices identified by different programs showed that STRIDE assigned α-helices are more kinked. Conformation of Pro residues in α-helices has also been studied in detail. Several interesting conclusions are drawn from the comprehensive study of π-helices and PolyProline-II (PPII) helices. In the subsequent paragraphs, a brief summary of each chapter is provided. The Introduction (Chapter 1) summarizes the relevant literature, which includes both experimental as well as theoretical studies explaining the structural and functional importance of SSEs in proteins and lays down a suitable background for the subsequent chapters in the thesis. The major questions addressed and the main goals of this thesis are described to set a suitable stage for the detailed discussions. The methodologies involved are discussed in Chapter 2. These include protocol used for preparing non-redundant datasets of protein structures, various statistical methods used to test the significance of position-wise amino acid propensities and different programs used during the course of present investigations. SSEs play an important role in the folding of proteins. However, identification of these SSEs in proteins is a common yet important concern in structural biology. Chapter 3 details a new method ASSP (Assignment of Secondary Structure in Proteins), which uses only the path traversed by the Cα atoms of the consecutive residues. The algorithm is based on the premise that the protein structure can be divided into continuous or uniform stretches, which can be defined in terms of helical parameters and depending on their values, the stretches can be classified into different SSEs, viz. α, 310, π, extended β-strands and PPII and other left handed helices. The methodology was validated using an unbiased clustering of these parameters for a protein dataset containing 1008 protein chains, which advocate that there are seven well defined clusters associated with different SSEs. Apart from α-helices and extended β-strands, 310 and π-helices were also found to occur in considerable numbers. Various analyses demonstrated that the ASSP was able to discriminate the non α-helical segments from flanking α-helices, which were often identified as a part of α-helix by other algorithms. The standalone version of the program for the Linux as well as Windows operating systems is freely downloadable and the web server version is also available at http://nucleix.mbu.iisc.ernet.in/assp/index.html. Among all SSEs in proteins, α-helices are relatively well defined. However, a precise quantitative estimate of their geometrical features and identification of terminal residues is difficult. In Chapter 4, a set of major changes/ updates, implemented in the algorithm of in-house program for analysis of geometry of helices in proteins (HELANAL), has been discussed in detail. It defines the helix parameters based on the path traced by Cα atoms alone and classifies the geometry of the helices into linear, curved, kinked and unassigned type, by fitting the least square 3D line and sphere to the local helix origin points (LHOP). The geometry assigned using HELANAL-Plus is independent of the orientation of the helix in 3D space and also does not depend on the database from which it is taken. The program is made available as a webserver as well as standalone and the helices can be viewed in the JmolApplet along with the best fit helix axis, which makes HELANAL-Plus useful for analysing the inter helix interaction and packing. The utility of the webserver has been increased by incorporating the use of SSE assignment programs like ASSP, DSSP or STRIDE. Pro kinked helices and correlation with the UP and DOWN conformation of Pro were studied in more detail. HELANAL-Plus is available at http://nucleix.mbu.iisc.ernet.in/helanalplus/index.html. Linux/Unix and windows compatible executables are also available for download. The analyses of kinks in a dataset of helices indicated a correlation with the large radius of the cylinder encompassing the residue at which the kink has been observed and many a time ASSP identified that as a π-helix. The detailed analysis of π-helices was limited due to the low frequency of identification by different algorithms. ASSP identified 659 π-helices in 3582 protein chains, solved at resolution ≤ 2.5Å and validated by molprobity. Chapter 5 reports the detailed study of the functional and structural roles of π-helices along with the position-wise amino acid propensity within and around them. These helices were found to range from 5 to 18 residues in length with the average twist and rise being 85.2°±7.2° and 1.28ű0.31Å respectively. The investigation of π-helices illustrated that they occur mostly in conjunction with α-helices. The majority of π-helices, with flanking α-helices at both termini, were found to be conserved across a large number of structures within a protein family and induce local distortions in the neighbouring α-helices. The presence of a π-helical fragment leads to appropriate orientation as well as positioning of the constituent residues and hence facilitate favourable interactions and also help in proper folding of the protein chain. The comprehensive analyses of position-wise amino acid propensity within and around π-helices showed their unique preferences, which are different from those of α-helices. Additionally and most importantly, the study also brought to light the influence of π-helices on the residue preference in preceding or succeeding α-helices and vice-versa. Study of another important SSE in proteins (Chapter 6), PPII helices, was inspired by their large number of occurrence and initiated with the aim of understanding their structural and functional roles. These helices are defined as an extended, flexible left-handed helix without intra-helical H-bonds and found to occur very frequently. ASSP identifies 3597 PPII helices in 3582 protein chains. Though PPII helices occur on a much smaller scale than α-helices and β-strands, their sheer number is still more than that of π-helices. The analyses of PPII-helices revealed that almost 50% of the total helices do not contain Pro residues and show a preference for polar residues. PPII-helices were found in conjunction with major SSEs and they often connect them. These helices range from 3 to 13 residues in length with the average twist and rise being -121.2°±9.2° and 3.0ű0.1Å respectively. The analysis of various non-bonded interactions revealed the frequent presence of C-H…N and C-H…O non-bonded interactions. The analysis of the amino acid preference within and around PPII-helices showed the avoidance of aromatic residues within the helix, while preference of Gly, Asn and Asp residues in the flanking region. Detailed analyses of various functional and structural roles mediated by PPII-helices have also been carried out. Identification and analysis of non-bonded interactions within a molecule and with the surrounding molecules are an essential part of structural studies. Given the importance of these interactions, we have developed a new algorithm named MolBridge and Chapter 7 provides the detailed description about it. MolBridge is an easy to use algorithm based purely on geometric criteria that can identify all possible non-bonded interactions, such as hydrogen bond, halogen bond, cation…π, π…π and van der Waals, in small molecules as well as biomolecules. Various features available in the webserver make it more user-friendly and interactive. The Unix/Linux version of the program is freely downloadable and the web server version is available at http://nucleix.mbu.iisc.ernet.in/molbridge/index.php. The overall conclusion from the current investigation and the possible future directions are presented in Chapter 8. Our findings suggest that the path traversed by Cα atoms is enough for the identification of SSEs. We believe that the various algorithms (ASSP, HELANAL-Plus and MolBridge) developed can provide a better understanding of the finer nuances of protein secondary structures. ASSP can make an important contribution in the better understanding of comparatively less frequent structural motifs and identification of novel SSEs. The most comprehensive study of π-helices gives in-depth insight about it. The analysis of interspersed π-helices gives a comprehensive understanding of the local deformations and variations in the helical segments. Apart from studies embodied in the thesis, author has been involved in few other studies, which are provided as appendix: Appendix A describes a program RNAHelix, which can regenerate duplexes from the dinucleotide step and base pair parameters for a given double helical DNA or RNA sequence. It can be used to generate/ regenerate the duplexes with the non-canonical base pairing as well.

The sequence of a polypeptide chain determines its structure which in turns determines its function. A protein is stabilized by multiple forces; hydrophobic interaction, electrostatic interactions and hydrogen bond formation between residues. While the above forces are non-covalent in nature the protein structure is also stabilized by disulfide bonds. Structural features such as naturally occurring cavities in proteins also affect its stability. Studying factors which affect a protein’s structural stability helps us understand complex sequence-structure-function relationships, the knowledge of which can be applied in areas such as protein engineering. The work presented in this thesis deals with various and diverse aspects of protein structure. Chapter 1 gives an overall introduction on the topics studied in this thesis. Chapter 2 focuses on a unique, non-regular, structural feature of proteins, viz. protein cavities. Cavities directly affect the packing density of the protein. It has been shown that large to small cavity creating mutations destabilize the protein with the extent of destabilization being proportional to the size of cavity created. On the other hand, small to large cavity filling mutations have been shown to increase protein stability. Tools which analyze protein cavities are thus important in studies pertaining to protein structure and stability. The chapter presents two methods which detect and calculate cavity volumes in proteins. The first method, DEPTH 2.0, focuses on accurate detection and volume calculation of cavities. The second method, ROBUSTCAVITIES, focuses on detection of biologically relevant cavities in proteins. We then study another aspect of protein structure – the disulfide bond. Disulfide bonds confer stability to the protein by decreasing the entropy of the unfolded state. Previous studies which attempted to engineer disulfides in proteins have shown mixed results. Previously, disulfide bonds in individual secondary structures were characterized. Analysis of disulfides in α-helices and antiparallel β-strands yielded important common features of such bonds. In Chapter 3 we present a review of these studies. We then use MODIP; a tool that identifies amino acid pairs which when mutated to cysteines will most likely form a disulfide bond, to analyze disulfide bonds in parallel β-strands. A direct way to analyze sequence-structure relationships is via mutating individual residues, evaluating the effect on stability and activity of the protein and inferring its effect on protein structure. Saturation mutagenesis libraries, where all possible mutations are made at every position in the protein contain a huge amount of information pertaining to the effect of mutations on structure. Making such libraries and screening them has been an extremely resource intensive process. We combine a fast inverse PCR based method to rapidly generate saturation mutagenesis libraries with the power of deep sequencing to derive phenotypes of individual mutants without any large scale screening. In Chapter 4 we present an Illumina data analysis pipeline which analyzes sequencing data from a saturation mutagenesis library, and derives individual mutant phenotypes with high confidence. In Chapter 5 we apply the insights derived from structure-function studies and apply it to the problem of protein engineering, specifically immunogen design. The Human Immunodeficiency Virus adopts various strategies to evade the host immune system. Being able to display the conserved epitopes which elicit a broadly neutralizing response is the first step towards an effective vaccine. Grafting such an epitope onto a foreign scaffold will mitigate some of the key HIV defenses. We develop a computational protocol which grafts the broadly neutralizing antibody b12 epitope on scaffolds selected from the PDB. This chapter also describes the only experimental work presented in this thesis viz. cloning, expressing and screening the epitope-scaffolds using Yeast Surface Display. Our epitope-scaffolds show modest but specific binding. In a bid to improve binding, we make random mutant libraries of the epitope-scaffolds and screen them for better binders using FACS. This work is on-going and we aim to purify our epitope-scaffolds, characterize them biophysically and eventually test their efficacy as immunogens.

Le repliement des protéines est principalement gouverné par les interactions spécifiques des structures secondaires. 1, 2 Toutefois, il existe expérimentalement peu d’informations sur les propriétés mécaniques fondamentales des hélices α et des feuillets β isolées. Les recherches antérieures sur l'étude du déploiement des hélices sont peu concluantes 3-5 et à notre connaissance l'étude des propriétés mécaniques d'un feuillet β isolé, intramoléculaire est sans précédent. Les copolymères PEG114-b-poly(L-lysine)134-(2-pyridyl disulfure),PEG114-b-poly(L-lysine)-b-PEG114 et poly(L-acide glutamique)85-b-(2-pyridyldisulfure) été synthétisés et utilisés comme systèmes modèles pour tester les propriétés mécaniques des motifs secondaires de type hélice α et feuillet β. Les résultats obtenus se sont révélés être en bon accord avec les résultats théoriques obtenus en utilisant un modèle statistique basé sur AGAGIR 6. La différence de force de déroulement comparant les hélices de poly(L-Lysine) ≈ 30 pN et de poly(L-acide glutamique) ≈ 20 pN des copolymères diblocs a été attribuée à l'hydrophobicité différente des chaînes latérales. La plus grande hydrophobie dumotif lysine conduit à de plus grandes interactions entre les chaînes latérales qui empêchent les fluctuations aléatoires au sein de l’hélice, et conduisent à une stabilité supérieure de l'hélice α. Lorsque les expériences ont été conduites dans des conditions favorisant la solubilité des chaînes latérales de lysine, les interactions ont diminué à une force de ≈ 20 pN, similaire à la force des interactions observées pour le poly(L-acide glutamique). Nous supposons qu'un minimum de ≈ 20 pN est nécessaire pour rompre la liaison hydrogène en maintenant l'hélice α, car cette force a été obtenue dans des conditions où les interactions de la chaîne latérale étaient minimisées. La présence de plateaux de force constants et d'inflexions correspondantes démontre une force de dépliement indépendante de la longueur, qui supporte un mécanisme de déroulement tour-par-tour pour l'hélice. De plus, la plus grande hydrophobie des chaînes latérales a été suggérée non seulement pour stabiliser la structure en hélice, mais également pour inhiber la formation d'une structure de type β-turn métastable intermédiaire lorsque les forces entropiques dominent. Des études préliminaires ont été effectuées sur le système de PEG114-bpoly(L-Lysine)134-(2-pyridyl disulfure) après induction d’une transition - β par un traitement thermique dans des conditions basiques. Une inflexion à une force≈ 70 pN a été obtenue, ce qui suggère la formation d'une interaction de type feuillet β. Une stratégie bottom-up a ainsi été proposée avec succès, démontrant le potentiel d'utilisation de tels systèmes artificiels pour simplifier et modéliser des systèmes biologiques réels. La compréhension de ces modèles isolés plus simples aidera sans doute la compréhension de systèmes plus complexes. / Proteins fold by the initial, preferential folding of secondarystructures 1, 2, however surprisingly little is known about the basic mechanicalproperties of isolated α-helices and β-sheets from an experimental standpoint.Previous investigations into studying the generic unfolding behaviour of α-heliceshave proved inconclusive 3-5, and to our knowledge the study of an isolated,intramolecular β-sheet is unprecedented.Bioinspired PEG114-b-poly(L-glutamic acid)85-(2-pyridyl disulphide),PEG114-b-poly(L-lysine)134-(2-pyridyl disulphide) and PEG114-b-poly(Llysine)134–b-PEG114 were designed, synthesized and utilized as model systems toprobe the mechanical properties of α-helix and β-sheet secondary motifs. Theobtained results were shown to be in good agreement with theoretical resultsobtained by utilizing a AGAGIR-based statistical mechanical model 6. Thedifference in unravelling force comparing the helices of poly(L-Lysine) ≈30 pNand poly(L-glutamic acid) ≈20 pN diblock copolymers was attributed to thediffering hydrophobicity of the side chains. The greater hydrophobicity of thelysine allowed greater interactions between the side chains and sterically hinderedrandom helix-coil fluctuations, which lead to a superior α-helix stability. Whenexperiments were conducted in conditions promoting the solubility of the lysineside chains, the interactions decreased to a force of ≈20 pN, similar to the force ofinteractions observed for the poly(L-glutamic acid). We infer that a minimum of≈20 pN is needed to rupture the hydrogen bonding maintaining the α-helix as thisforce was obtained in conditions where the side chain interactions wereminimized.The presence of constant force plateaus and corresponding inflectionsdemonstrates a length independent unfolding force, which supports a turn-by-turnunfolding mechanism for the α-helix.In addition, the greater hydrophobicity of the side chains was suggestedto not only stabilize the α-helix structure, but also to inhibit the formation of anintermediate metastable β-hairpin-like structure when entropic forces dominate.Preliminary studies were also conducted on the PEG114-b-poly(LLysine)134-(2-pyridyl disulphide) system after a α-β transition had been inducedby heat in basic conditions, where an inflection at a much higher force of ≈ 70 pNwas obtained suggesting the formation of a β-sheet interaction.A bottom-up, investigative strategy has thus been successfully proposeddemonstrating the potential of utilizing such artificial systems to simplify andexemplify real biological systems. The comprehension of these simpler isolatedmodels will no doubt aid the understanding of more complex systems.