The secondary structure of peptides is of pivotal importance for their biological function. The introduction of photoswitchable moieties into the backbones of peptides provides a unique way of regulating their conformation using an external stimulus, i.e., light. This thesis addresses the design, synthesis, and conformational analysis of photoswitchable peptidomimetics (PSPM). Examples of photomodulation of their functional properties are given. PSPM were prepared by incorporation of stilbene and thioaurone chromophores (switches) into dipeptides. Synthetic schemes for preparing these chromophores have been developed. Their suitability for incorporation into peptidomimetics has been demonstrated, and the resulting PSPM have been subjected to photoisomerization as well as computational and spectroscopic conformational analysis. The chromophore’s potential as a β-hairpin inducer was particularly interesting. To investigate the factors that govern the formation of β-hairpins, a series of decapeptides were prepared. Turn regions consisting of amino acids or chromophores were combined with antiparallel peptide strands with hydrophobic side chains. Linear tryptophan zipper peptidomimetics and cyclic peptidomimetics with a second, hairpin-inducing turn region were particularly promising. Comparison between switches revealed that the more flexible stilbene is a better choice for upholding the β-hairpin conformation than the thioaurone. The catalytic properties of an artificial hydrolase with a helix-loop-helix structure can be improved by introducing a stilbene photoswitch into the loop region. Photoisomerization regulates the catalytic activity of this peptidomimetic, and provides a means to control its aggregation state. The activity of the enzyme Mycobacterium tuberculosis ribonucleotide reductase was realized by incorporating a stilbene moiety into a linear peptide. Here, one photoisomer proved to be an inhibitor at nM concentrations. A significantly lower effect was observed for the other isomer. Finally, the decomposition of thioaurones, mainly to thioflavonols and thiaindenes, under conditions used for solid-phase peptide synthesis has been mapped. These findings are expected to have implications for future use of this chromophore.

The study of synthetic peptides aid in improving our current understanding of the fundamental principles for the de novo design of functional proteins. The investigation of designed peptides has been instrumental in providing answers to many questions ranging from the conformational preferences of amino acids to the compact folded structures and also in developing tools for understanding the growth and formation of the protein secondary structures (helices, sheets and turns). In addition, the self-assembly of peptides through non-covalent interactions is also an emerging area of growing interest. The design of peptides which can mimic the protein secondary structures relies on the use of stereochemically constrained amino acid residues at select positions in the linear peptide sequences, leading to the construction of protein secondary structural modules like helices, hairpins and turns. The use of non-coded amino acid residues with strict preferences for adopting particular conformations in the conformational space becomes the most crucial step in peptide design strategies. In addition the crystallographic characterization and analysis of the sequences provides the necessary optimization of the design strategies. The crystallographic characterization of designed peptides provides a definitive and conclusive proof of the success of a design strategy. Furthermore, the X-ray structures provide an atomic view of the interactions, both strong and weak, which govern the growth of the crystal. The information on the geometric parameters and stereochemical properties of a series of peptides, through a systematic study, provides the necessary basis for further scientific investigation, like the molecular dynamics and can also aid in improving the force field parameters meant for carrying out molecular simulations. This can be further complemented by constructing biologically active peptide sequences. The focus of this thesis is to characterize crystallographically the conformational and structural aspects of peptide nanotubes and encapsulated water wires and the β-hairpin peptide models of β-sheets. The systematic study of a series of pentapeptide and octapeptide sequences, containing Aib and D-amino acid residues incorporated at strategic positions, establish the conformation and structural properties of designed peptides as mimics of protein secondary structures and hydrophobic tubular peptide channels and close-packed forms. The structures reported in this thesis are given below: 1 Boc-DPro-Aib-Leu-Aib-Val-OMe (DPUL5) C30H53N5O8 2 Boc-DPro-Aib-Val-Aib-Val-OMe (DPUV5a) C29H51N5O8 .(0.5) H2O 3 Boc-DPro-Aib-Val-Aib-Val-OMe (DPUV5b) C27H51N5O8 .(0.17) H2O 4 Boc-DPro-Aib-Ala-Aib-Val-OMe (DPUA5) C27H47N5O8 5 Boc-DPro-Aib-Phe-Aib-Val-OMe (DPUF5) C33H48N5O8 6 Boc-Pro-Aib-DLeu-Aib-DVal-OMe (PUDL5) C30H53N5O8 7 Boc-Pro-Aib-DVal-Aib-DVal-OMe (PUDV5a) C27H51N5O8 .(0.17) H2O 8 Boc-Pro-Aib-DVal-Aib-DVal-OMe (PUDV5b) C27H51N5O8 . 2H2O 9 Boc-Pro-Aib-DAla-Aib-DVal-OMe (PUDA5) C27H47N5O8 10 Boc-Pro-Aib-DPhe-Aib-DVal-OMe (PUDF5) C33H48N5O8 11 Ac-Phe-Pro-Trp-OMe (FPW) C28H32N4O5.(0.33)H2O 12 Boc-Leu-Phe-Val-DPro-Pro-Leu-Phe-Val-OMe (DPLP8) C56H84N8O1 1 .(0.5) H2O 13 Boc-Leu-Phe-Val-DPro-Pro-Leu-Phe-Val-OMe (YDPP8) C56H83N8O12 .(1.5) H2O 14 Boc-Leu-Val-Val-DPro-ψPro-Leu-Val-Val-OMe (PSIP8) C56H84N8O11S1 .(1.5) H2O 15 Boc-Leu-Phe-Val-DPro-Pro-Leu-Phe-Val-OMe (DPPV8) C48H84N8O11 16 Boc-Leu-Phe-Val-DPro-Aib-Leu-Phe-Val-OMe (DPUF8) C57H88N8O11.(1.5) H2O 17 Piv-Pro-ψH,CH3Pro-NHMe (PSPL3) C22H37N3O5S1 18 Boc-Leu-Val-Val-Aib-DPro-Leu-Val-Val-OMe (UDPV8) C47H84N8O11.2(C3H7NO) 19 Boc-Leu-Phe-Val-DPro-Ala-Leu-Phe-Val-OMe (BH1P8) C54H78N8O11.H2O 20 Boc-Leu-Phe-Val-DPro-Aib-Leu-Phe-Val-OMe (DPUFP8) C55H84N8O11. (0.5) H2O 21 Boc-Leu-Phe-Val-DPro-Pro-Leu-Phe-Val-OMe (YDPPP8) C56H83N8O12. (1.5) H2O The crystal structure determination of the peptides presented in this thesis provides a wealth of information on the folding patterns of the sequences, in addition to the characterization of many structural and geometric properties. In particular, the study sheds light on the growth and formation of peptide nanotubes and the structure of encapsulated water wires, and also the structural details of Type I′ and Type II′β-turn nucleated hairpins. The study provides the backbone and side chain conformational parameters of the sequences, highlighting the varied conformational excursions possible in the peptide molecules. The thesis is divided into 6 chapters and one appendix. Chapter 1 gives a general introduction to the stereochemistry of the polypeptide chain, description of backbone torsion angles of α-amino acid residues and the major secondary structures of α-peptides, namely α-helix, β-sheet and β-turns. The basic structural features of helices and sheets are given. A brief introduction to polymorphism and weak interactions is also presented, followed by a discussion on X-ray diffraction and solution to the phase problem. Chapter 2 is divided into two parts. PART 1 describes the crystal structures of a series of eight related enantiomeric peptide sequences (Raghavender et al., 2009; Raghavender et al., 2010). The crystal structures of four sequences with the general formula Boc-DPro-Aib-Xxx-Aib-Val-OMe (Xxx = Ala/Val/Leu/Phe) and the enantiomeric sequences provided a set of crystal structures withdifferent packing arrangements. The structure of the peptide with Xxx = Leu revealed a nanotube formation with the Leu lining the inner walls of channel. The channels were found to be empty. The sequence with Xxx = Val revealed a solvent-filled water channel.Investigation of the water wire structures on the diffraction data collected on the same crystal over a period of time revealed the existence of two different kinds of water wires in thechannels. Comparison with the peptide tubular structures available in the literature and the water structure inside the aquaporin channels are contrasted. Close-packed structures are observed in the case of Xxx=Ala and Phe. The backbone conformations are essentially identical. Enantiomeric sequences also revealed similar structures. Polymorphic forms were observed in the case of DVal(3) containing sequence. One form is observed to have water-filled channels forming a nanotube, as opposed to the close-packed structure in the polymorphic form. Crystal parameters DPUL5: C30H53N5O8; P65; a = b = 24.3673 (9) Å, c = 10.6844 (13) Å; α = β = 90°, γ = 120°; Z = 6; R = 0.0671, wR2 = 0.1446. DPUV5a: C29H51N5O8 .(0.5) H2O; P65; a = b = 24.2920 (13) Å, c = 10.4838 (11) Å; α = β = 90°, γ = 120°; Z = 6; R = 0.0554, wR2 = 0.1546. DPUV5b: C29H51N5O8 .(0.17) H2O; P65; a = b = 24.3161 (3) Å, c = 10.1805 (1) Å; α = β = 90°, γ = 120°; Z = 6; R = 0.0617, wR2 = 0.1844. DPUA5: C27H47N5O8; P212121; a = 12.2403 (8), b = 15.7531 (11) Å, c = 16.6894 (11) Å; Z =4; R = 0.0439, wR2 = 0.1249. DPUF5: C33H48N5O8; P212121; a = 10.3268 (8), b = 18.7549 (15) Å, c = 18.9682 (16) Å; Z = 4; R = 0.0472, wR2 = 0.1325. PUDL5: C30H53N5O8; P61; a = b = 24.4102 (8) Å, c = 10.6627 (7) Å; α = β = 90°, γ = 120°; Z = 6; R = 0.0543, wR2 = 0.1495. PUDV5a: C29H51N5O8 .(0.17)H2O; P61; a = b = 24.3645 (14) Å, c = 10.4875 (14) Å; α = β = 90°, γ = 120°; Z = 6; R = 0.0745, wR2 = 0.1810. PUDV5b: C29H51N5O8. 2H2O; C2; a = 20.7278 (35), b = 9.1079 (15) Å, c = 19.5728 (33) Å; α = γ = 90°, β = 94.207°; Z = 6; R = 0.0659, wR2 = 0.1755. PUDA5: C27H47N5O8; P212121; a = 12.2528 (12), b = 15.7498 (16) Å, c = 16.6866 (16) Å; Z = 4; R = 0.0473, wR2 = 0.1278. PUDF5: C33H48N5O8; P212121; a = 10.3354 (8), b = 18.7733 (10) Å, c = 18.9820 (10) Å; Z = 4; R = 0.0510, wR2 = 0.1526. PART 2 describes the crystallographic characterization of the tubular structure in a tripeptide Ac-Phe-Pro-Trp-OMe (FPW) sequence. The arrangement of the single-file water moleculesin the peptide nanotubes of FPW could be established by X-ray diffraction. In addition, the energetically favoured arrangement of the water wire inside the peptide channels could be modeled by understanding the construction of the peptide nanotube. In particular, the helicalmacrodipole of the peptide nanotube and the water wire dipoles prefer an antiparallel arrangement inside the peptide channels as opposed to parallel arrangements, is established by the classical dipole-dipole interaction energy calculation. In addition, the growth of thenanotubes and the arrangement of the water wires inside the channels could be correlated to the macroscopic dimensions of the crystal by the indexing of the crystal faces and contrasted with the structure of DPUV5. Crystal parameters FPW: C28H32N4O5.(0.33)H2O; P65; a = b = 21.5674 (3) Å, c = 10.1035 (2) Å; α = β = 90°, γ = 120 °; Z = 6; R = 0.0786, wR2 = 0.1771 Chapter 3 provides the crystal structures of five octapeptide β-hairpin forming sequences and a tripeptide containing a modified amino acid, with modification in the side chain (pseudo-proline, ψH,CH3Pro). The parent peptide, Boc-Leu-Phe-Val-DPro-Pro-Leu-Phe-Val-OMe (DPLP8), was observed to form a strong Type II′β-turn at the DPro-Pro segment, and the strand segments adopting a β-sheet conformation. Two molecules were observed in the asymmetric unit, inclined to each other at approximately 70°. Modification in the strand sequence Phe(2) to Tyr(2) also resulted in a hairpin with identical conformation and similar packing arrangement. The difference was in the solvent content. In both the cases the molecules were packed orthogonal with respect to each other, resulting in the formation of ribbon-like structures in three dimensions. The replacement of Phe(2) and Phe(7) with Valine residues, with the retention of DPro-Pro β-turn segment, results in an entiely different packing arrangement (parallel). Modification of Pro(5) residue of the turn segment to Aib(5) and ψPro, also results in the molecules packing orthogonally to each other. The tripeptide with a modified form of ψPro, namely ψH,CH3Pro, resulted in a folded structure with a Type VIa β-turn, with the amide bond between the Pro-ψH,CH3Pro segment adopting a cis configuration (Kantharaju et al., 2009). Crystal parameters DPLP8: C56H84N8O11 .(0.5) H2O; P21; a = 14.4028 (8), b = 18.9623 (11) Å, c = 25.4903 (17) Å, β = 105.674 ° (4); Z = 4; R = 0.0959, wR2 = 0.2251. YDPP8: C56H84N8O12 .(1.5) H2O; P212121; a = 14.4028 (8), b = 18.9623 (11) Å, c = 25.4903 (17) Å, Z = 8; R = 0.0989, wR2 = 0.2064. PSIP8: C57H86N8O11S1.(1.5) H2O; C2; a = 34.6080 (2), b = 15.3179 (10) Å, c = 25.6025 (15) Å, β = 103.593 ° (3); Z = 4; R = 0.0931, wR2 = 0.2259. DPPV8: C48H84N8O11; P1; a = 9.922 (3), b = 11.229 (4) Å, c = 26.423 (9) Å, α = 87.146 (6), β = 89.440° (6), γ = 73.282 (7); Z = 2; R = 0.1058, wR2 = 0.2354. DPUF8: C57H88N8O11 .(1.5) H2O; P21; a = 18.410 (2), b = 23.220 (3) Å, c = 19.240 (3) Å, β = 118.036 ° (4); Z = 4; R = 0.1012, wR2 = 0.2061. PSPL3: C22H37N3O5S1; P31; a = b = 14.6323 (22), c = 10.4359 (22) Å, α = β = 90°, γ = 120°; Z = 3; R = 0.0597, wR2 = 0.1590. Chapter 4 describes the crystal structure and molecular conformation of Type I′β-turn nucleated hairpin. The incorporation of Aib-DPro segment in the middle of Leu-Val-Val strands in the peptide sequence Boc-Leu-Val-Val-Aib-DPro-Leu-Val-Val-OMe results in an obligatory Type I′ turn containing hairpin. The molecular conformation and the packing arrangement of the molecules in the crystal are contrasted with the only Type I′β-hairpin reported in the literature and with a sequence where the turn residues are flipped and strand residues replaced with Phe(2) and Phe(7). Crystal parameters UDPV8: C47H84N8O11.2(C3H7NO); P21; a = 11.0623 (53), b = 18.7635 (89) Å, c = 16.6426 (80) Å, β = 102.369 (8); Z = 2; R = 0.0947, wR2 = 0.1730. Chapter 5 provides the crystal structures of three polymorphic forms of β-hairpins. The structure of BH1P8 provides new insights into the packing of hairpins inclined orthogonally to each other. The two polymorphic forms differ not only in their modes of packing in crystals but also in the strong and weak interactions stabilizing the packing arrangements. The polymorphic forms of DPUFP8 differ only in the content of the solvent in the asymmetric unit and the role it plays in bridging the symmetry related pairs of molecules. The polymorphic form YDPPP8 crystallized in a completely different space group, revealing a completely different mode of packing and also the cocrystallized solvent participating in a different set of interactions. Crystal parameters BH1P8: C54H78N8O11.H2O; P212121; a = 18.7511 (9), b = 23.3396 (11) Å, c = 28.1926 (13)Å; Z = 8; R = 0.1208, wR2 = 0.2898. DPUFP8: C55H84N8O11. (0.5) H2O; P21; a = 18.0950 (4), b = 23.0316 (5) Å, c = 18.6368 (5) Å, β = 117.471 (2); Z = 4; R = 0.0915, wR2 = 0.2096. YDPPP8: C56H83N8O12. (1.5) H2O; P21; a = 14.3184 (8), b = 18.9924 (9) Å, c = 25.1569 (14) Å, β = 105.590 (4); Z = 4; R = 0.1249, wR2 = 0.2929. Chapter 6 provides a comprehensive overview of the β-hairpin peptide crystal structures published in the literature as well as those included in the thesis. The hairpins are classified based on the residues composing the β-strands and the mode of their packing in the crystals. In the crystal structures the hairpins are observed to adopt either a Type II′ or Type I′β-turns. The indexing of the crystal faces of a few representative hairpin peptides crystallographically characterized in this thesis, provides a rational explanation for the preferential growth of the crystals in certain directions, when correlated with the strong directional forces (hydrogen bonding) and weak interactions (van der Waals, aromatic-aromatic) observed in the crystal packing. The insights gained by these studies would be highly valuable in understanding the nucleation and growth of β-hairpin peptides and the formation of β-sheet structures. Appendix I describes the Cambridge Structural Database (CSD) analysis of the conformational preferences of the proline residues found in the peptide crystal structures. The frequency distributions of the backbone φ, ψ and ω and side chain χ1, χ2, χ3, χ4 and θ torsion angles of the proline residues are calculated, tabulated and represented as graphical plots. The correlation between the backbone and endocyclic torsion angles provides for a clear evidence of the role of a particular torsion variable χ2 in deciding the state of puckering. In addition, the endocyclic bond angles also appear to be correlated, relatively strongly, with the χ2 torsion. This provides a geometrical explanation of the factors governing the puckering of the proline ring.

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.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第18316号 / 農博第2041号 / 新制||農||1020(附属図書館) / 学位論文||H26||N4823(農学部図書室) / 31174 / 京都大学大学院農学研究科食品生物科学専攻 / (主査)教授 保川 清, 教授 安達 修二, 教授 伏木 亨 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

<p>Peptide secondary structure mimetics are important tools in medicinal chemistry, as they provide analogues of endogeneous peptides with new physicochemical and pharmacological properties. The <i>β</i>-hairpin motif has been shown to be involved in numerous physiological processes, among others in regulation of eucariotic gene transcription. This thesis addresses the design, synthesis and conformational analysis of photoswitchable <i>β</i>-hairpin mimetics.</p><p>The developmental work included the establishment of an improved procedure for cross coupling of aryl halides with terminal alkynes. Microwave mediated Sonogashira couplings in closed vessels were optimized under homogeneous and solid-phase conditions furnishing excellent yields for a large variety of substrates within 5 – 25 minutes. In addition, microwave heating was shown not to have any non-conventional effect on the reaction rate.</p><p>Furthermore, the most important factors affecting <i>β</i>-hairpin stability were evaluated. Studies of tetrapeptide and decapeptide analogues revealed the essential role of the <i>β</i>-turn in initiation of hairpin folding. Moreover, hydrogen bonding was shown to be the main interchain stabilizing force, whereas hydrophobic interactions were found to be relatively weak. Nevertheless, hydrophobic packing appears to provide an important contribution to the thermodynamic stability of <i>β</i>-hairpins.</p><p>Photoswitchable peptidomimetics were prepared by incorporation of various stilbene moieties into tetra- and decapeptides. Synthesis, photochemical isomerisation and spectroscopic conformational analysis of the compounds were performed.</p>

Peptide secondary structure mimetics are important tools in medicinal chemistry, as they provide analogues of endogeneous peptides with new physicochemical and pharmacological properties. The β-hairpin motif has been shown to be involved in numerous physiological processes, among others in regulation of eucariotic gene transcription. This thesis addresses the design, synthesis and conformational analysis of photoswitchable β-hairpin mimetics. The developmental work included the establishment of an improved procedure for cross coupling of aryl halides with terminal alkynes. Microwave mediated Sonogashira couplings in closed vessels were optimized under homogeneous and solid-phase conditions furnishing excellent yields for a large variety of substrates within 5 – 25 minutes. In addition, microwave heating was shown not to have any non-conventional effect on the reaction rate. Furthermore, the most important factors affecting β-hairpin stability were evaluated. Studies of tetrapeptide and decapeptide analogues revealed the essential role of the β-turn in initiation of hairpin folding. Moreover, hydrogen bonding was shown to be the main interchain stabilizing force, whereas hydrophobic interactions were found to be relatively weak. Nevertheless, hydrophobic packing appears to provide an important contribution to the thermodynamic stability of β-hairpins. Photoswitchable peptidomimetics were prepared by incorporation of various stilbene moieties into tetra- and decapeptides. Synthesis, photochemical isomerisation and spectroscopic conformational analysis of the compounds were performed.

DNA polymerase epsilon (Pol ε) is a multi-subunit B-family DNA polymerase that is involved in leading strand DNA replication in eukaryotes. DNA Pol ε in yeast consists of four subunits, Pol2, Dpb2, Dpb3, and Dpb4. Pol2 is the catalytic subunit and Dpb2, Dpb3, and Dpb4 are the accessory subunits. Pol2 can be further divided into an N-terminal catalytic core (Pol2core) containing both the polymerase and exonuclease active sites and a C-terminus domain. We determined the X-ray crystal structure of Pol2core at 2.2 Å bound to DNA and with an incoming dATP. Pol ε has typical fingers, palm, thumb, exonuclease, and N-terminal domains in common with all other B-family DNA polymerases. However, we also identified a seemingly novel domain we named the P-domain that only appears to be present in Pol ε. This domain partially encircles the nascent duplex DNA as it leaves the active site and contributes to the high intrinsic processivity of Pol ε. To ask if the crystal structure of Pol2core can serve as a model for catalysis by Pol ε, we investigated how the C-terminus of Pol2 and the accessory subunits of Pol ε influence the enzymatic mechanism by which Pol ε builds new DNA efficiently and with high fidelity. Pre-steady state kinetics revealed that the exonuclease and polymerization rates were comparable between Pol2core and Pol ε. However, a global fit of the data over five nucleotide-incorporation events revealed that Pol ε is slightly more processive than Pol2 core. The largest differences were observed when measuring the time for loading the polymerase onto a 3' primer-terminus and the subsequent incorporation of one nucleotide. We found that Pol ε needed less than a second to incorporate the first nucleotide, but it took several seconds for Pol2core to incorporate similar amounts of the first nucleotide. B-family polymerases have evolved an extended β-hairpin loop that is important for switching the primer terminus between the polymerase and exonuclease active sites. The high-resolution structure of Pol2core revealed that Pol ε does not possess an extended β-hairpin loop. Here, we show that Pol ε can processively transfer a mismatched 3' primer-terminus between the polymerase and exonuclease active sites despite the absence of a β-hairpin loop. Additionally we have characterized a series of amino acid substitutions in Pol ε that lead to altered partitioning of the 3'primer-terminus between the two active sites. In a final set of experiments, we investigated the ability of Pol ε to displace the downstream double-stranded DNA while carrying out DNA synthesis. Pol ε displaced only one base pair when encountering double-stranded DNA after filling a gap or a nick. However, exonuclease deficient Pol ε carries out robust strand displacement synthesis and can reach the end of the templates tested here. Similarly, an abasic site or a ribonucleotide on the 5'-end of the downstream primer was efficiently displaced but still only by one nucleotide. However, a flap on the 5'-end of the blocking primer resembling a D-loop inhibited Pol ε before it could reach the double-stranded junction. Our results are in agreement with the possible involvement of Pol ε in short-patch base excision repair and ribonucleotide excision repair but not in D-loop extension or long-patch base excision repair.

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This thesis describes NMR studies which probe weak interactions between amino acid side chains in folded peptide structures. Aromatic/aromatic interactions between facing phenylalanine residues have been probed in antiparallel β-sheets, while aromatic/proline interactions have been examined using cyclic peptide disulfides that occur in the venom of marine cone snails. Novel intramolecular hydrogen bonded structures in hybrid peptides containing backbone homologated residues, specifically γ-amino acids, are also described. Chapter 1 provides a brief background to the principles involved in the design of antiparallel β-sheet structures and an introduction to previous studies on aromatic/aromatic and aromatic/proline interactions in influencing peptide conformations. A summary of the NMR methods used is also presented. Chapter 2 discusses the structural characterisation of a designed 14 residue, three stranded β-sheet peptide, Boc-LFVDP-PLFVADP-PLFV-OMe (LFV14). The results described in this Chapter support the presence of multiple conformational states about the χ1 (Cα-Cβ) torsional degree of freedom for the interacting aromatic pairs in solution. Chapter 3 presents the structural characterisation of a designed 19 residue three stranded hybrid β-sheet peptide, Boc-LVβFVDPGLβFVVLDPGLVLβFVV-OMe (BBH19). β-amino acid residues (β-phenylalanine, βPhe) were incorporated at facing positions on antiparallel β-sheets. The BBH19 structure provides an example of interaction between the N and C-terminal strands in a three stranded structure with an α/β hybrid backbone. Chapter 4 focuses on studies of the conformations of the contryphan In936 (GCVDLYPWC*) from Conus inscriptus and the related peptide Lo959 (GCPDWDPWC*) from Conus loroissi. Both peptides possess a macrocyclic 23 membered ring, with multiple accessible conformational states. Chapter 5 describes conformational analysis of a novel 20 membered cyclic peptide disulfide, CIWPWC (Vi804), from Conus virgo. NMR structures were calculated for Vi804 and an analog peptide, CIDWPWC, DW3-Vi804. Chapter 6 explores the solution conformation of hybrid sequences containing α and γ residues. Oligopeptides of the type (αγ)n and (αγγ)n have been studied in solution by NMR methods. Chapter 7 provides a summary of the results described in this thesis and highlights the major conclusions.