The numerous toxic peptides, called conotoxins (Olivera et al 1990, 1991), that marine cone snails produce and use for capturing prey, deterring predators and presumably for other biotic interactions, are known to target several classes of mammalian voltage and ligand gated receptors with excellent specificity and good receptor-subtype discrimination (Terlau and Olivera 2004). This fine specificity has placed upon the conotoxins a great deal of scientific and medical interest, and cone snail venom is currently considered a vast natural resource of peptides that have the potential of eventually benefiting the prognosis of many human afflictions, either directly as therapeutics or indirectly as research tools. In this regard, the characterization of conotoxins and the identification of the specific receptors they target remains an actively pursued area of study in several countries. There has been an active effort to characterize peptides from Indian populations of cone snails that has resulted in several reports describing novel peptides from them. This thesis is part of these ongoing efforts and largely relates to the isolation and identification of cDNA sequences of precursor conotoxins from cone snails prospected in India. One final section of the thesis is concerned with the assessment of secondary structure predictions of conotoxin genes and discusses how such formations may determine the regions where variations and conservations are taking place among the conotoxins. Structure and Outline of the thesis Chapter 1 is an overview of the cone snails and the conotoxins that they produce. There is some emphasis on the variability and diversity that are found among conotoxins since these are some of the aspects that are discussed in subsequent chapters. Chapter 2 describes the identification of new cDNA sequences isolated from the relatively rare Indian population of the piscivorous cone snail, Conus achatinus. This species was chosen for the study since it is one of the few piscivorous cone species that have been reported from the coastlines of India. However, the limited availability of specimens belonging to this species precluded a direct study of individual venom peptides from it. To overcome this bottleneck of specimen availability, a molecular biological route to obtain cDNA sequences of superfamily specific conotoxins was considered. The steps of PCR mediated amplification and cloning that are incorporated within the procedures of preparing cDNA for sequencing, to some extent overcome the limitations of large sample requirements and in this respect have been used to investigate conotoxin sequences from this species. Using the cDNA route and comparative sequence analysis, it has been possible to identify 5 novel O-superfamily conotoxin sequences from C.achatinus. The precursor sequences have been classified as delta, omega and omega-like conotoxins that potentially target voltage gated sodium and calcium channels. A parallel study trying to detect the specific cDNA related conotoxins using mass spectrometry (MALDI-MS) as a screening tool is also discussed. In this search it has been possible to detect 3 of the 5 cDNA related peptides using small amounts of unpurified venom. The cDNA and mass spectrometric results show that precursor sequences of conotoxins from a relatively rare population of Conus species can be successfully identified and the existence of the peptides that they specify verified through the combined approach of obtaining cDNA sequences and MALDI-MS screening of total unpurified venom. Chapter 3 similarly relates to the isolation of cDNA sequences from a single specimen of the vermivorous cone snail, Conus monile. Three precursor sequences, Mo3.1, Mo15.1 and Mo16.1, of M-superfamily conotoxins have been isolated from this species out of which two precursors (Mo15.1 and Mo16.1) show unexpected cysteine distribution patterns within their putative mature toxin regions. In addition, several other features of these precursors do not fit into the description of known M-superfamily conotoxins. The sequence analyses and the deviations that have been noted among these sequences are described. Chapter 4 describes the efforts that have gone in towards detecting one of these deviant conotoxins (Mo16.1) in the venom of Conus monile using MALD-MS as a means for screening the venom. A peptide having the Mo16.1 predicted mass (1512 Da) has been detected as a minor component of the venom. The chapter describes additional mass-spectrometric experiments that strongly support the assignment of this detected peak being the specific Mo16.1 peptide. A speculative discussion on the role of minor peptide deviants such as the Mo16.1 peptide concludes the chapter. Chapter 5 is concerned with the assessment of secondary structure predictions of conotoxin genes and discusses how such formations may determine the regions where variations and conservations are taking place among the conotoxins. The comparative analysis of DNA sequences corresponding to the variable mature conotoxins reveal that it is possible to differentiate mature conotoxin sequences into variable and conserved regions. Using the prediction program mFold (Markham and Zuker 2005) it has been noted that regions of the DNA encompassing the conserved codons (including the highly conserved cysteine codons) correspond to predicted secondary structures of higher stabilities. In contrast the regions of the conotoxin that have a higher degree of variation correlate to regions of lower stability. These correlations have been observed quite consistently across several classes of conotoxins that show different patterns of variability and conservation in their sequence and representing different categories of conotoxins i.e intra species, inter species, and hyperconserved conotoxins. The observation on these co-relations allows for a simple model of inaccessibility of a mutator to these relatively structured regions of the conotoxin gene (including the cysteine codons) allowing them a relative degree of resistance towards change. Chapter 6 summarizes the findings of the thesis, briefly recapitulating the discussion of the individual chapters from a broader perspective.

No description available.

No description available.

The development of peptides as therapeutic agents has been hampered by their poor enzymatic stability and bioavailability. Many strategies, such as chemical modification, synthesis of peptidomimetics and formulation, have been employed to overcome these issues. For central nervous system (CNS) active peptides, the blood brain barrier is an added hurdle. Nasal delivery is believed to provide a direct access to the brain via the olfactory nerve, which would bypass the blood brain barrier. This route of administration, however, is dependant on the size and physico-chemical properties of the administered drug. For these reasons, three CNS active peptides were chosen as models. Leu-enkephalin, endomorphin-1 and a-conotoxin MII are three peptides that differ in their size, amino acid sequence and conformation. Using chemical modifications to improve their stability and ability to cross biological membranes, in vitro assessments of derivatives of these peptides were performed and in vivo nasal delivery was attempted on the most promising candidates. The chemical modifications consisted in the addition of lipids and/or sugars to the N- or C-terminus of the peptides. Assessment of the in vivo bioavailability after nasal administration, however, proved to be challenging. The initial method chosen for this purpose was the use of tritiated acetic anhydride which would radiolabel the peptide via acetylation at the N-terminus of the peptide derivatives. Consequently, in vitro stability and permeability of each acetylated derivatives was also studied. Acetylation of the lipidic derivatives, which formed an amide bond, proved to be beneficial for the stability of the lipidic peptides. In contrast, acetylation of the Nterminus sugar derivatives, which formed an ester bond at one or several positions of the sugar, was an unstable modification. Thus, an extraction method for the tested peptides from rat tissues was developed, and LC-MS/MS analyses were conducted to measure the level of peptide in the olfactory bulbs, brain and blood. Leu-enkephalin derivatives were all amide derivatives at the C-terminus of the peptide. The most successful Leu-enkephalinamide derivatives were C8-LeuEnk (2), C12- LeuEnk (3) and Lac-LeuEnk (8), which are the Leu-enphelinamide peptide modified with a C8 lipoamino acid, a C12 lipoamino acid and a lactose moiety respectively. They all exhibited improved permeability across Caco-2 monolayers and stability in Caco-2 cell homogenate and/or plasma. Problems of solubility encountered with C12-LeuEnk (3), however, hampered its testing in vivo after nasal administration. C8-LeuEnk (2) and Lac-LeuEnk (8) were administered intranasally to male Sprague-Dawley rats. Both peptides were found in the olfactory bulbs after 10 minutes administration (2: 49.2 ± 15.6 nM; 8: 40.6 ± 14.6 nM) while blood concentration remained low, showing that the peptide reached the olfactory bulbs directly from the nasal cavity via the olfactory nerve. Brain concentrations were 13.5 ± 10.1 nM for C8-LeuEnk (2) and 13.6 ± 6.9 nM for Lac-LeuEnk (8). These two peptides brain concentrations seemed to be high enough to exhibit analgesic effect when compared to their binding affinity in vitro. This was not statistically significant, however, due to the high standard deviations observed (Kiμ C8-LeuEnk (2) = 7.74 ± 1.15 nM; Kiμ Lac-LeuEnk (8) = 6.69 ± 1.81 nM). Endomorphin-1 was only modified at the N-terminus as previous results have shown that the activity of the peptide is strongly decreased by C-terminus modifications. The most successful modification, regarding permeability across Caco-2 monolayers and water solubility, was shown to be the addition of a lactose moiety to the N-terminus of the peptide. Lac-Endo1 (16) exhibited a permeability of 1.91 ± 0.76 x 10-6 cm/s and was soluble at the concentration used for in vivo nasal administration (2 mg/Kg, 50 μL administration). After 10 minutes administration, Lac-Endo1 (16) was found in the olfactory bulbs (418 ± 410 nM), in the brain (4.01 ± 4.61 nM) and in the blood (1.58 ± 1.85 nM). The large standard deviations observed reflect the difficulties encountered with the extraction process of this peptide. A direct transport for the nasal cavity to the olfactory bulb was observed as illustrated by the low blood concentrations. Brain concentrations, however, were too low to expect a strong analgesic effect from this compound after nasal administration (Kiμ Lac-Endo1 (16) = 11.3 ± 1.2 nM). a-Conotoxin MII is a 16 amino acid long peptide containing two disulfide bonds. The formation of these two disulfide bonds leads to low yields in the synthesis of the derivatives of this peptide. Addition of a lipidic moiety to the peptide did not seem to improve its permeability through biological membranes. This modification resulted in highly lipophilic peptides with dissolution issues in water based media such as those used in the permeability experiments. The most successful a-conotoxin MII derivative was GS-Ctx (25) which exhibited a permeability of 4.22 ± 0.53 x 10-7 cm/s across Caco-2 monolayers. This permeability, however, was too low to consider in vivo administration. In conclusion, we successfully synthesised a series of derivatives of Leu-enkephalin, endomorphin-1 and a-conotoxin MII and screened them through Caco-2 monolayers for permeability and Caco-2 cell homogenates and human plasma for stability. Three derivatives (C8-LeuEnk (2), Lac-LeuEnk (8) and Lac-Endo1 (16)) were intranasally administered and found in the olfactory bulbs 10 minutes after administration. The low blood concentrations observed show that a direct transport from the nasal cavity to the brain occurs. Thus, nasal administration could be an option for delivering to the brain low molecular weight peptides exhibiting increased stability and permeability in vitro.

The development of peptides as therapeutic agents has been hampered by their poor enzymatic stability and bioavailability. Many strategies, such as chemical modification, synthesis of peptidomimetics and formulation, have been employed to overcome these issues. For central nervous system (CNS) active peptides, the blood brain barrier is an added hurdle. Nasal delivery is believed to provide a direct access to the brain via the olfactory nerve, which would bypass the blood brain barrier. This route of administration, however, is dependant on the size and physico-chemical properties of the administered drug. For these reasons, three CNS active peptides were chosen as models. Leu-enkephalin, endomorphin-1 and a-conotoxin MII are three peptides that differ in their size, amino acid sequence and conformation. Using chemical modifications to improve their stability and ability to cross biological membranes, in vitro assessments of derivatives of these peptides were performed and in vivo nasal delivery was attempted on the most promising candidates. The chemical modifications consisted in the addition of lipids and/or sugars to the N- or C-terminus of the peptides. Assessment of the in vivo bioavailability after nasal administration, however, proved to be challenging. The initial method chosen for this purpose was the use of tritiated acetic anhydride which would radiolabel the peptide via acetylation at the N-terminus of the peptide derivatives. Consequently, in vitro stability and permeability of each acetylated derivatives was also studied. Acetylation of the lipidic derivatives, which formed an amide bond, proved to be beneficial for the stability of the lipidic peptides. In contrast, acetylation of the Nterminus sugar derivatives, which formed an ester bond at one or several positions of the sugar, was an unstable modification. Thus, an extraction method for the tested peptides from rat tissues was developed, and LC-MS/MS analyses were conducted to measure the level of peptide in the olfactory bulbs, brain and blood. Leu-enkephalin derivatives were all amide derivatives at the C-terminus of the peptide. The most successful Leu-enkephalinamide derivatives were C8-LeuEnk (2), C12- LeuEnk (3) and Lac-LeuEnk (8), which are the Leu-enphelinamide peptide modified with a C8 lipoamino acid, a C12 lipoamino acid and a lactose moiety respectively. They all exhibited improved permeability across Caco-2 monolayers and stability in Caco-2 cell homogenate and/or plasma. Problems of solubility encountered with C12-LeuEnk (3), however, hampered its testing in vivo after nasal administration. C8-LeuEnk (2) and Lac-LeuEnk (8) were administered intranasally to male Sprague-Dawley rats. Both peptides were found in the olfactory bulbs after 10 minutes administration (2: 49.2 ± 15.6 nM; 8: 40.6 ± 14.6 nM) while blood concentration remained low, showing that the peptide reached the olfactory bulbs directly from the nasal cavity via the olfactory nerve. Brain concentrations were 13.5 ± 10.1 nM for C8-LeuEnk (2) and 13.6 ± 6.9 nM for Lac-LeuEnk (8). These two peptides brain concentrations seemed to be high enough to exhibit analgesic effect when compared to their binding affinity in vitro. This was not statistically significant, however, due to the high standard deviations observed (Kiμ C8-LeuEnk (2) = 7.74 ± 1.15 nM; Kiμ Lac-LeuEnk (8) = 6.69 ± 1.81 nM). Endomorphin-1 was only modified at the N-terminus as previous results have shown that the activity of the peptide is strongly decreased by C-terminus modifications. The most successful modification, regarding permeability across Caco-2 monolayers and water solubility, was shown to be the addition of a lactose moiety to the N-terminus of the peptide. Lac-Endo1 (16) exhibited a permeability of 1.91 ± 0.76 x 10-6 cm/s and was soluble at the concentration used for in vivo nasal administration (2 mg/Kg, 50 μL administration). After 10 minutes administration, Lac-Endo1 (16) was found in the olfactory bulbs (418 ± 410 nM), in the brain (4.01 ± 4.61 nM) and in the blood (1.58 ± 1.85 nM). The large standard deviations observed reflect the difficulties encountered with the extraction process of this peptide. A direct transport for the nasal cavity to the olfactory bulb was observed as illustrated by the low blood concentrations. Brain concentrations, however, were too low to expect a strong analgesic effect from this compound after nasal administration (Kiμ Lac-Endo1 (16) = 11.3 ± 1.2 nM). a-Conotoxin MII is a 16 amino acid long peptide containing two disulfide bonds. The formation of these two disulfide bonds leads to low yields in the synthesis of the derivatives of this peptide. Addition of a lipidic moiety to the peptide did not seem to improve its permeability through biological membranes. This modification resulted in highly lipophilic peptides with dissolution issues in water based media such as those used in the permeability experiments. The most successful a-conotoxin MII derivative was GS-Ctx (25) which exhibited a permeability of 4.22 ± 0.53 x 10-7 cm/s across Caco-2 monolayers. This permeability, however, was too low to consider in vivo administration. In conclusion, we successfully synthesised a series of derivatives of Leu-enkephalin, endomorphin-1 and a-conotoxin MII and screened them through Caco-2 monolayers for permeability and Caco-2 cell homogenates and human plasma for stability. Three derivatives (C8-LeuEnk (2), Lac-LeuEnk (8) and Lac-Endo1 (16)) were intranasally administered and found in the olfactory bulbs 10 minutes after administration. The low blood concentrations observed show that a direct transport from the nasal cavity to the brain occurs. Thus, nasal administration could be an option for delivering to the brain low molecular weight peptides exhibiting increased stability and permeability in vitro.

The work presented in this thesis describes the determination of structures of peptides and proteins at atomic resolution. Nuclear Magnetic Resonance (NMR) spectroscopy was used as the principal method of investigation. The thesis is divided into three parts. Part I of the thesis consists of chapters 1 to 4, and deals with structural studies of two novel conotoxins. Part II of the thesis consists of chapter 5 and deals with structural studies of Small MutS Related (Smr) domain from Helicobacter pylori MutS2. Part III of the thesis consists of Appendices A to D. Appendix A describes implementation of a novel pulse sequence for determination of disulfide connectivity using long-range 13 C–13 C scalar couplings across disulfide bonds. Appendices B, C and D contain supplementary infor- mation (acquisition parameters and chemical shifts) for the structural studies presented in parts I and II of the thesis. Part I: Structural studies of novel conotoxins from Conus monile Chapter 1 gives a brief overview of the conotoxins and their structural studies. The first half of the chapter describes biosynthesis, classification schemes, nomenclature, com- monly observed post-translational modifications and applications of conotoxins. The latter half of this chapter summarizes the challenges involved in the structural studies of conotoxins in light of the recent developments in integrated transcriptomic and venomic studies of conotoxins. The key homonuclear and heteronuclear NMR experiments that are employed for structural studies of conotoxins are summarized. Emphasis was laid on describing the spectral features and the structural information that can be gleaned from these experiments. Finally, the current mass spectrometric and NMR methods available for determination of disulfide connectivity are discussed Chapter 2 describes sample preparation and preliminary biophysical characteriza- tion of a conotoxin Mo3964 that contains a hitherto uncharacterized cysteine framework (C–CC–C–C–C). The sequence of Mo3964 was identified at the nucleic acid level as a cDNA clone. Analysis of the signal sequence revealed that the toxin belongs to the M-superfamily, while the cysteine framework bears more resemblance to O- and K- super- family of conotoxins. Structural studies were initiated to determine the disulfide connec- tivity, tertiary structure and biological activity. The gene corresponding to the mature toxin sequence was cloned in a bacterial expression vector pET21a(+) as a C-terminal tag to the cytochrome b5 fusion protein host system. The fusion protein was obtained by recombinant expression using the bacterial expression host E. coli BL21(DE3) and the mature toxin was obtained by either enzymatic or chemical cleavage of the fusion protein followed by size exclusion chromatography and reverse phase HPLC. Proton 1D NMR spectra of the purified peptide exhibited sharp lines and good spec- tral dispersion indicating that molecule was well folded. Formation of disulfide bonds in the mature toxin was ascertained by high resolution mass spectra of intact and chemically modified Mo3964. The peptide toxin exhibited remarkable stability to chemical denatu- ration and proteolytic digestion. Spectroscopic studies clearly showed that Mo3964 pos- sesses a very stable and well defined structure as long as its disulfide bonds are intact. Analytical size exclusion chromatography and Multi Angle Light Scattering (MALS) studies showed that Mo3964 exists in solution as monomer albeit with a non-globular structure. Electrophysiological studies showed that Mo3964 inhibits outward potassium currents in rat Dorsal Root Ganglion (DRG) neurons and increases the reversal potential of rat voltage gated sodium channel rNav 1.2 stably expressed on Chinese Hamster Ovary (CHO) cells at peptide concentrations as low as 10 nM. Chapter 3 describes the determination of disulfide connectivity and tertiary stricture of Mo3964. Initial attempts to determine disulfide connectivity using direct fragmenta- tion of the intact peptide in the mass spectrometer failed due to the relatively large size of the molecule and its resistance to endoproteases. Partial reduction alkylation based methods failed as the first stage of partial reduction gave rise to a mixture of various single disulfide bond reduced species which could not be separated from each other. Subsequently, information about the disulfide connectivity was obtained using a method that does not necessitate separation of such a mixture of single disulfide bond reduced species. This method involves partial reduction, cyanylation of the reduced cysteines and alkali mediated cleavage of the peptide backbone on the N-terminus of cyanylated cysteines. Structural studies were carried out using homonuclear and heteronuclear NMR meth- ods. The hydrogen bond network and hence topology of the molecule was determined with high accuracy using the long-range HNCO-COSY experiment that correlates hydrogen- bond donor-acceptor pairs. This experiment utilizes the three bond heteronuclear scalar coupling, i.e., the h3JN C O′ coupling across the hydrogen bonds. All these restraints proved crucial to the assignment of the disulfide connectivity in Mo3964, given its novel cysteine framework. The structure of Mo3964 was calculated using a total of 549 NOE distance restraints, 84 dihedral angle restraints and 28 hydrogen bond distance restraints. The tertiary structure was constructed from the disulfide connectivity pattern 1–3, 2–5 and 4–6, that is hitherto undescribed for the M–superfamily conotoxins. The ensemble of structures showed a backbone Root Mean Square Deviation of 0.68 ± 0.18 Å, with 87% and 13% of the backbone dihedral (φ, ψ) angles lying in the most favored and additional allowed regions of the Ramachandran map. The remarkable stability and anomalous spectral properties exhibited by Mo3964 could be rationalized using the disulfide connectivity and the tertiary structure. The tertiary structural fold has not been described for any of the known Conus peptides. Further, a search for structures similar to that of Mo3964 using the web server DALI returned no hits indicating that the peptide scaffold of Mo3964 has no structural homologues. Hence, the conotoxin Mo3964 represents a new bioactive peptide fold that is stabilized by disulfide bonds and adds to the existing repertoire of scaffolds that can be used to design stable bioactive peptide molecules. The structure of Mo3964 was submitted to the Protein Data Bank (PDB ID: 2MW7)[1]. Chapter 4 describes the structural studies of a 17 residue, single disulfide containing conopeptide Mo1853. The samples for structural studies were obtained either by chemical synthesis or by recombinant expression methods. Structural studies using homonuclear solution NMR methods revealed that Mo1853 exists as two equally populated cis and trans X–Pro conformers which are in slow exchange regime, compared to the chemical shift timescale. Sequence specific assignments were obtained for both the conformers by analysis of homonuclear 2D 1 H,1H–DQF–COSY,1H,1 H–TOCSY, 1H,1 H–NOESY and 1H,1 H–ROESY spectra. Temperature dependence of chemical shifts was measured and coalescence was observed for two amide protons at 318 K. At this temperature, the rate of exchange and the free energy of activation were determined to be 59 Hz and ≈ 67.2 kJ mol−1 respectively. The evidence for this conformational equilibrium was also observed as exchange correlation peaks in the 2D- NOESY and ROESY spectra. Tertiary structures of both the cis and trans conformers were determined using distance restraints, backbone dihedral angle restraints, the disulfide bond restraint and the cis or trans conformation of the X–Pro peptide bond. Tertiary structures of both the conformers consist of a 29-membered macro-cyclic ring formed by 9 amino acid residues which are cyclized by side chain to side chain disulfide bond. The conformation of the X–Pro peptide bond which is located within this macro-cyclic ring causes the cis structure to be compact and the trans structure to be in an extended form. Analysis of the tertiary structures indicated that the trans conformer is stabilized by hydrogen bonds while the cis conformer is likely to be stabilized by hydrophobic interactions. This was further corroborated by the fact that at lower temperatures, the hydrophobic interactions became weaker reducing the population of the cis conformer with respect to that of the trans conformer. Preliminary electrophysiological studies carried out on rat DRG neurons indicate that Mo1853 transiently reduces late outward potassium currents. Part II: Structural studies of Small MutS Related (Smr) domain from Helicobacter pylori MutS2 Chapter 5 presents the solution NMR studies of the Smr domain from MutS2 of H. pylori , henceforth called as HpSmr. In H. pylori , MutS2 is involved in suppression of homologous recombination and its Smr domain was shown to be necessary for this activity. As of date, in spite of the availability of structural information for the Smr domain, unambiguous identification of the residues involved in metal binding, DNA binding and catalysis remains elusive. Structural studies were carried out on two different constructs of HpSmr viz., HpSmr– (His)6 and GSHM–HpSmr, with and without the hexahistidine tag respectively. Se- quence specific assignments of HpSmr–(His)6 were obtained at two different sample pH conditions viz., pH 8.0 and pH 5.35 using the standard suite of triple resonance NMR experiments. Since, valines and leucines constitute about 25% of the total number of amino acid residues in HpSmr–(His)6 , stereospecific assignments were obtained for di- astereotopic methyl groups of these residues by preparing a fractionally 13C labeled sample of HpSmr–(His)6 . Solution structure of HpSmr–(His)6 at pH 8.0 was determined using 766 NOE restraints, 170 backbone dihedral angle restraints and 70 hydrogen bond distance restraints. The tertiary structure exhibits the canonical α/β sandwich fold ex- hibited by all the other known structures of Smr domains. Further, NMR studies and analytical gel filtration studies indicated the presence of pH dependent conformational exchange in HpSmr that involves strand to coil transition in the C-terminal β-strand. In order ascertain that the conformational equilibrium is not at an artifact caused by the C-terminal hexa-histidine-tag, HpSmr protein construct GSHM–HpSmr, which does not have the hexa-histidine-tag, was prepared. Conformational exchange was observed in this construct as well. The preliminary NMR evidence suggests that the conformational exchange is caused by pH dependent cis–trans isomerization of a semi-conserved Proline residue Pro66 . We have hypothesized that the pH dependent modulation of the activity of Smr domain of MutS2 can be advantageous to H. pylori . Such a regulation could help the bacteria to achieve optimal rate of homologous recombination in response to changes in pH, which is necessary for maintaining homeostasis and tiding over stress conditions. Part III: Appendix Appendix A describes an NMR pulse program LRCC_CH2 that was designed with the aim of determining disulfide connectivity using long-range 13C–13 C (C β –C β ′ ) couplings across the disulfide bond. This experiment is a modification of an earlier experiment pub- lished by Bax and co-workers designed to measure the side-chain χ3 dihedral angle in me- thionines. The experiment described here is optimized for the detection of 3 bond scalar coupled methylene carbons. The details of modifications introduced in LRCC_CH2, its product operator analysis, a representative spectrum acquired on [U-13C,15 N]–Mo3964, short-comings and future directions are described. The C programming code that was used to implement the pulse program is also included in the appendix. Appendices B, C and D contain the supplementary information (acquisition pa- rameters for the NMR experiments and chemical shifts) for the structural studies carried out on Mo3964, Mo1853 and HpSmr.

α-conotoxins are 13–19 amino acid toxin peptides that bind various nicotinic acetylcholine receptor (nAChR) subtypes. α-conotoxin Mr1.7c (MrIC) is a 17 amino acid peptide that targets α7 nAChR. Although MrIC has no activating effect on α7 nAChR when applied by itself, it evokes a large response when co-applied with the type II positive allosteric modulator PNU-120596, which potentiates the α7 nAChR response by recovering it from a desensitized state. A lack of standalone activity, despite activation upon co-application with a positive allosteric modulator, was previously observed for molecules that bind to an extracellular domain allosteric activation (AA) site at the vestibule of the receptor. We hypothesized that MrIC may activate α7 nAChR allosterically through this site. We ran voltage-clamp electrophysiology experiments and in silico peptide docking calculations in order to gather evidence in support of α7 nAChR activation by MrIC through the AA site. The experiments with the wild-type α7 nAChR supported an allosteric mode of action, which was confirmed by the significantly increased MrIC + PNU-120596 responses of three α7 nAChR AA site mutants that were designed in silico to improve MrIC binding. Overall, our results shed light on the allosteric activation of α7 nAChR by MrIC and suggest the involvement of the AA site.

Major constituents of the venom of various animals are peptidogenic in nature. Marine snails belonging to the species Conus are venomous predators that use small, structurally constrained peptides present in their venom for prey capture and defense. It is known that ~500 Conus species are present in nature and the venom of each of these Conus species is a complex mixture of nearly 100 peptides accounting for > 50,000 peptides with little overlap among the different species. The peptides isolated from the venom of Conus species are commonly known as conotoxins or conopeptides. Some of the common targets of these peptides include the different ion channels like Na+, K+, and Ca2+, and receptor subtypes such as nicotinic acetylcholine and NMDA receptors. The ion channels and receptor subtypes were targeted by conopeptides with high degree of specificity and selectivity. The structural information on the peptides from cone snails can prove to be a valuable starting tool for the understanding of the function of different ion channels and hence in the design of neuropharmacologically active drugs. Conotoxins are disulfide-rich peptides and the number of disulfide generally ranges from two to five. Based on the arrangement of cysteines in their primary sequence, they are classified into different superfamilies. The signal sequences of the precursors belonging to a particular superfamily are highly conserved and hence the members within the same family have, in common, the unique disulfide arrangement and pharmacological activity. Conotoxins are classified into eleven superfamilies till date. In order to understand the underlying the principles involved in the action of these peptides on different ion channels, one needs to know the three-dimensional structures which, in potential, will help in the identification of the pharmacophores responsible for the observed pharmacological activity. With the aim of studying the structure-activity relationships found among the conotoxins, we have initiated a study on the peptides isolated from the marine snails found in the Indian coastal waters. This thesis is focused in the structural studies of the peptide toxins from marine cone snails and a terrestrial scorpion. The tool used for the structural studies of these peptide toxins is Nuclear Magnetic Resonance Spectroscopy. Chapter 1 provides an overview of the peptide toxins found among various animal species with more emphasis on conotoxins and scorpion toxins. In addition, the rationale behind the present study has also been explained. Chapter 2 describes the structure determination of two conopeptides isolated from Conus amadis, δ-Am2766 and Am2735, which are active on mammalian sodium channels. The structural aspects and comparison with other known conopeptides belonging to the same superfamily as that of these two peptides have also been described. Solution NMR studies of Ar1446 and Ar1248, two conopeptides isolated from the species Conus araneosus have also been studied using Homonuclear NMR methods. Ar1446 is a three disulfide-bonded peptide. Our studies have revealed that this peptide has a novel disulfide connectivity not previously observed in the M superfamily or any other superfamily of conotoxins. The structural features of Ar1446 will be described along with the NMR studies on two-disulfide bonded peptide, Ar1248, belonging to the A-superfamily of conotoxins. The main problem faced in the kind of study of peptides isolated from natural sources is the amount that can be isolated and purified to homogeneity. In order to obtain large quantities of peptides, we have successfully used Cytochrome b5 as fusion host to clone, over express and purify these peptides using recombinant methods. The use of recombinant methods has aided in the preparation of isotopically enriched peptides. The use of cyt b5 as fusion host for the large scale production of some of the peptides from Indian marine snails is described in Chapter 4. A novel pharmacologically active linear peptide, Mo1659 isolated from Conus monile, have been studied using Heteronuclear NMR methods. This peptide was cloned, over expressed and purified using Cytochrome b5 as a fusion host. Another linear peptide, Mo1692 (also from Conus monile), has been prepared using the same method and was studied using Homonuclear NMR methods. Both these peptides were liberated from the fusion host using cyanogen bromide cleavage and were subsequently purified using RP-HPLC. The results of the biosynthetic preparation and NMR studies of these two peptides have been described in Chapter 5. Chapter 6 describes the solution structure determination of a novel scorpion toxin characterized in the venom of the Indian red scorpion Buthus tamulus. The cloning, over expression, folding and purification of BTK-2 is described here. The structure and the function of this recombinantly produced BTK-2 will also be described.

The subcellular mechanism and site of action of linopirdine or DuP 996 (3,3‐bis(4‐pyridinylmethyl)‐1‐phenylindolin‐2‐one) was investigated at the frog neuromuscular junction, using miniature endplate potential (m.e.p.p.) counts and a new method for obtaining unbiased estimates of n (number of functional release sites), p (probability of release), and varsp (spatial variance in p). DuP 996 produced an increase in m (no. of quanta released), which was due to an increase in n and p. The increase in m was concentration‐dependent over a range of 0.1–100 μm and completely reversible with 15 min of wash. There was a saturation in the increase in p, but not in the increase in m and n, for [DuP 996] >10 μm. By contrast, there was no major change in varsp. Block of presynaptic Na+‐ and Ca2+‐channels with 3 μm tetrodotoxin and 1.8 mm Co2+prevented the m.e.p.p. frequency increase to DuP 996, and this effect was completely reversed by washing. Application of the neuronal Ca2+‐channel blocker, ω‐conotoxin GVIA (1 μm) brought about a rapid and profound decrease in the m.e.p.p. frequency increase produced by DuP 996. The effect of the toxin was not reversed by prolonged washing. Block of voltage‐gated K+‐channels with 100 μm 4‐aminopyridine (4‐AP) resulted in only a small (28%) increase in m. The combination of 4‐AP (100 μm) and DuP 996 (10 μm) produced an increase in m (189%) which was much greater than the sum of the responses to each agent alone. This increase in m was due solely to an increase in n, as p and varsp were unchanged. For [DuP 996] up to 100 μm, there was no apparent change in the mean size, amplitude distribution, or time course of m.e.p.ps, signifying that it had no anticholinesterase activity. It is concluded that DuP 996 increases the release of quantal transmitter but not the postsynaptic response to the quanta. This appears to involve an effect at the nerve terminal membrane, most likely an increase in Ca2+‐conductance, and not an action to block K+‐conductance or to release Ca2+from intraterminal organelles. 1994 British Pharmacological Society

Venomous animals have evolved a vast array of peptide toxins for prey capture and defense. Nature has evolved the venoms into a huge library of active molecules with high selectivity and affinity, which could be explored as therapeutics or serve as a template for drug design. The individual components of venom i.e. toxins are used in ion channel and receptor studies, drug discovery, and formulation of insecticides. ‘Venominformatics is a systematic bioinformatics approach in which classified, consolidated and cleaned venom data are stored into repositories and integrated with advanced bioinformatics tools and computational biology for the analysis of structure and function of toxins.’ Conus peptides (conopeptides), the main components of Conus venom, represent a unique arsenal of neuropharmacologically active molecules that have been evolutionarily tailored to afford unprecedented and exquisite selectivity for a wide variety of ion-channel subtypes and neuronal receptors. Ziconotide (ω-conotoxin MVIIa from Conus magus (Magician's cone snail)), is proven as an intrathecally administered N-type calcium channel antagonist for the treatment of chronic pain (U.S. Food and Drug Administration. Center for Drug Evaluation and Research) attesting to the pharmaceutical importance of Conus peptides. From the point of view of protein sequence and structure analysis, conopeptides can serve as attractive systems for the studies in sequence comparison, pattern extraction, structure–function correlations, protein–protein interactions and evolutionary analysis. Despite their importance and extensive experimental investigations on them, they have been hardly explored through in silico methods. The present thesis is perhaps the first attempt at deploying a multi-pronged bioinformatics approaches for studies in the burgeoning field of conopeptides. In the process of sequence-structure-function studies of conopeptides, we have created several sequence patterns of different conopeptide families and these have been accepted for inclusion in international databases such as PROSITE, the first pattern database to have been developed (http://www.expasy.org/prosite) and INTERPRO (http://www.ebi.ac.uk/interpro). More importantly, we have carried out extensive literature survey on the peptides for which we have defined the patterns to create PROSITE compatible documentation files (PDOC6004, PDOC60025 and PDOC60027). We have also created a series of sequence patterns and associated documentation filesof pharmaceutically promising peptides from plants and venomous animals (including O-conotoxin and P-conotoxin superfamily members) with knottin scaffold. Knottins provide appealing scaffolds for protein engineering and drug design due to their small size, high structural stability, strong sequence tolerance and easy access to chemical synthesis. The sequence patterns and associated documentation files created by us should be useful in protein family classification and functional annotation. Even though patterns might be useful at the family level, they may not always be adequate at the superfamily level due to hypervariability of mature toxins. In order to overcome this problem, we have demonstrated the applicationos of multi-class support vector machines (MC-SVMs) for the successful in silico classification of the mature conotoxins into their superfamilies. TheI- and J-conotoxin-superfamily members were analyzed in greater detail. On the basis of in silico analysis, we have divided the 28 entries previously grouped as I-conotoxin superfamily in UniProtKB/Swiss-Prot (release 49.0) into I1 and I2 superfamilies inview of their having two different types of signal peptides and exhibiting distinct functions. A comparative study of the theoretically modeled structure of ViTx from Conus virgo, a typical member of I2-conotoxin superfamily, reveals the crucial role of C-terminal region of ViTx in blocking therapeutically important voltage-gated potassium channels. Putative complexes created by us of very recently characterized J-superfamily conotoxin p11-4a with Kv1.6 suggest that the peptide interacts with negatively charged extracellular loops and pore-mouth of the potassium channel and blocks the channel by covering the pore as a lid, akin to previously proposed blocking mechanism of kM-conotoxin RIIIK from Conus radiatus to Tsha1 potassium channel. This finding provides a pointer to experimental work to validate the observations made here. Based on differences in the number and distribution of the positively charged residues in other conopeptides from the J-superfamily, we hypothesize different selectivity profile against subtypes of the potassium channels for these conopeptides. Furthermore, the present thesis reports the application of order-statistic filters and hydrophobicity profiles for predicting the location of membrane-spanning helices. The Proposed method is in particular effective for the class of helical membrane proteins, namely the therapeutically important voltage-gated ion channels, which are natural targets of several conotoxins. Our suggested ab initio approach is comparatively better than other spatial filters, confirming to the efficacy of including the concept of order or ranking information for prediction of TM helicdes. Such approaches should be of value for improved prediction performance including in large-scale applications. In addition, anlaysis has been carried out of the role of context in the relationship between form and function for the true PDB hits of some nonCys-rich PROSITE patterns. We have found specific examples of true hits of some PROSITE patterns displaying structural plasticity by assuming significantly different local conformation, depending upon the context. The work was carried out as a part of the research interest in our group in studying structural and other features of protein sequence patterns. The Contributions of the candidate to venominormatics include, creation of protein sequence patterns and information highlighting the importance of the patterns as gleaned from the lteratures for family classification: profile HMM and MC-SVMs for conotoxin superfamily classification; in silico characterization of I1 and I2 conotoxin superfamilies; studies of interaction with Kv1 channels of typical members of I2 and 3 conotoxin superfamilies and development of improved methods for detecting membrane-spanning helices. Chapter I starts with a brief account of venominformatics; bioinformatics for venoms and toxins. Chapter 2 presents a regular expression based classification of Conus peptides. Chapter 3 revisits the 28 entries previously grouped as I-conotoxin superfamily in UniProt Swiss-Prot knowledgebase (release 49.0) having four disulfide bonds with Cys arrangement C-C-CC-CC-C-C and they inhibit or modify ion channels of nerve cells. Chapter 4 describes pseudo-amino acid composition and MC-SVMs approach for conotoxin superfamily classification. Chapter 5 describes in silico detection of binding mode with Kv1.6 channel of J-superfamily conotoxin p114a from bermivorouos cone snail, Conus planorbis. Chapter 6 presents a comparative sequence-structure-function analysis of naturally occurring Cys-rich peptides having the Knottin or inhibitor cystine knot(ICK) scaffold, from different plants and venomous animals based on information available in the knottin database(http://knottin.cbs.cnrs.fr/). Chapter 7 describes the application of order-statistic filters and hydrophobicity profiles for detecting membrane-spanning helices. Chapter 8 describes the role of context in the relationship between form and function for the true PDB hits of some non Cys-rich PROSITE patterns. Chapter 9 summaries the important findings of the present studies on naturally occurring bioactive Cys-rich peptides with emphasis on Conus peptides and their interactions with respective target such as voltage-gated ion channels.