Computer simulations provide a potentially powerful complement to conventional experimental techniques in elucidating the structures, dynamics and interactions of macromolecules. In this thesis, I present three applications of computer simulations to investigate important biomolecules with sizes ranging from two-residue peptides, to proteins, and to whole chromosome structures. First, I describe the results of 441 independent explicit-solvent molecular dynamics (MD) simulations of all possible two-residue peptides that contain the 20 standard amino acids with neutral and protonated histidine. 3JHNHα coupling constants and δHα chemical shifts calculated from the MD simulations correlated quite well with recently published experimental measurements for a corresponding set of two-residue peptides. Neighboring residue effects (NREs) on the average 3JHNHα and δHα values of adjacent residues were also reasonably well reproduced. The intrinsic conformational preferences of each residue, and their NREs on the conformational preferences of adjacent residues, were analyzed. Finally, these NREs were compared with corresponding effects observed in a coil library and the average β-turn preferences of all residue types were determined. Second, I compare the abilities of three derivatives of the Amber ff99SB force field to reproduce a recent report of 3JHNHα scalar coupling constants for hundreds of two-residue peptides. All-atom MD simulations of 256 two-residue peptides were performed and the results showed that a recently-developed force field (RSFF2) produced a dramatic improvement in the agreement with experimental 3JHNHα coupling constants. I further show that RSFF2 also improved modestly agreement with experimental 3JHNHα coupling constants of five model proteins. However, an analysis of NREs on the 3JHNHα coupling constants of the two-residue peptides indicated little difference between the force fields’ abilities to reproduce experimental NREs. I speculate that this might indicate limitations in the force fields’ descriptions of nonbonded interactions between adjacent side chains or with terminal capping groups. Finally, coarse-grained (CG) models and multi-scale modeling methods are used to develop structural models of entire E. coli chromosomes confined within the experimentally-determined volume of the nucleoid. The final resolution of the chromosome structures built here was one-nucleotide-per-bead (1 NTB), which represents a significant increase in resolution relative to previously published CG chromosome models, in which one bead corresponds to hundreds or even thousands of basepairs. Based on the high-resolution final 1 NTB structures, important physical properties such as major and minor groove widths, distributions of local DNA bending angles, and topological parameters (Linking Number (Lk), Twist (Tw) and Writhe (Wr)) were accurately computed and compared with experimental measurements or predictions from a worm-like chain (WLC) model. All these analyses indicated that the chromosome models built in this study are reasonable at a microscopic level. This chromosome model provides a significant step toward the goal of building a whole-cell model of a bacterial cell.

<p>Binding proteins are present both in gram-negative and gram-positive bacteria. They are the recognition components of the ABC transport systems that transport different nutrients into the cell, and are in some cases also involved in chemotaxis. In gram-negative bacteria, they are present in the periplasm between the inner and the porous outer membrane. Here, these highly specific proteins can bind to a certain ligand such as ions, sugars and amino acids. The protein-ligand complex can then interact with permeases bound to the inner membrane that transport the nutrient into the cell. Gram-positive bacteria lack an outer membrane and the binding protein must therefore be anchored to the cell membrane.</p><p>In this thesis different aspects of three members of the super-family of the periplasmic binding proteins have been studied. In the case of the allose-binding protein (ALBP) from <i>E. coli</i> we focused on the movement of the protein when ligand is bound and released. This protein was also compared with the ribose-binding protein (RBP) which belongs to the same structural cluster and from which both open and closed structures are available. The leucine-binding protein (LBP) from <i>E. coli</i> was studied with regards to the structural basis of its specificity for different ligands as well as its conformational changes. The leucine-isoleucine-valine protein has 80% sequence identity with LBP but still exhibits a different preference for ligands. The structure of the maltose-binding protein (MBP) was obtained from a gram-positive thermoacidophile, <i>A. acidocaldarius. </i>Here, our goal was to study acid-stability of proteins. Since little is known about this and structures of the mesophilic counterpart in <i>E. coli</i> are available, as well as structures from two hyperthermophiles, we had an opportunity to study differences in their structural properties that could explain their differing stabilities.</p>

<p>Molecular recognition via noncovalent interactions plays a key role in many biological processes such as antigen-antibody interactions, protein folding, the bonding and catalytic transformation of substrates by enzymes, etc. Amongst these noncovalent interactions, electrostatic interactions, hydrogen bonding, π-π interactions, and metal-to-ligand bonding are the most prominent. Exploring noncovalent interactions in host-guest systems that range from small hydrocarbon systems to more complex systems is the main motivation of this thesis. The present study involves the design, synthesis and characterization of clip-shaped molecules as host structures, and an examination of their binding properties with a variety of guests using NMR spectroscopy. </p><p>Several clips with a hydrocarbon or glycoluril backbone were synthesized. The binding of cations to small, hydrocarbon-based clips suggests that binding is enhanced by the rigidity and cooperativity between the two sidewalls of the clip. Binding is also very much dependant on the solvent properties. </p><p>Glycoluril-based clips built with aromatic sidewalls provide a deep cavity for binding guest molecules. The binding properties of these hosts were studied with several guests such as cations, Lewis acids and Lewis bases. Lewis basic binding sites in the acenaphthene-terminated clip were dominating in guest binding. Complexation-induced conformational changes in the wall-to-wall distance were observed for this clip.</p><p>In contrast, for a porphyrin-terminated clip with metal centers, very strong binding to a series of Lewis basic guests of various sizes into the clip cavity was observed. Conformational locking of guests with long alkyl chains was achieved, suggesting that, this clip could be useful as a potential molecular tool for the structural characterization of acyclic molecules with several stereogenic centers. This porphyrin clip was also shown to bind substituted fullerenes in the cavity.</p>

This thesis deals with the design of ligands for efficientasymmetric catalysis and studies of the conformation of theligands in the catalytically active complexes. All ligandsdeveloped contain chiral oxazoline heterocycles. The conformations of hydroxy- and methoxy-substitutedpyridinooxazolines and bis(oxazolines) during Pd-catalysedallylic alkylations were investigated using crystallography,2D-NMR techniques and DFT calculations. A stabilising OH-Pdinteraction was discovered which might explain the differencein reactivity between the hydroxy- and methoxy-containingligands. The conformational change in the ligands due to thisinteraction may explain the different selectivities observed inthe catalytic reaction. Polymer-bound pyridinooxazolines and bis(oxazolines) weresynthesised and employed in Pd-catalysed allylic alkylationswith results similar to those of monomeric analogues;enantioselectivities up to 95% were obtained. One polymer-boundligand could be re-used several times after removal of Pd(0).The polymer-bound bis(oxazoline) was also used in Zn-catalysedDiels-Alder reactions, but the heterogenised catalyst gavelower selectivities than a monomeric analogue. A series of chiral dendron-containing pyridinooxazolines andbis(oxazolines) were synthesised and evaluated in Pd-catalysedallylic alkylations. The dendrons did not seem to have anyinfluence on the selectivity and little influence on the yieldwhen introduced in the pyridinooxazoline ligands. In thebis(oxazoline) series lower generation dendrimers had a postiveon the selectivity, but the selectivity and the activitydecreased with increasing generation. Crown ether-containing ligands were investigated inpalladium-catalysed alkylations. No evidence of a possibleinteraction between the metal in the crown ether and thenucleophile was discovered. A new type of catalyst, an oxazoline-containing palladacyclewas found to be very active in oxidations of secondary alcoholsto the corresponding aldehydes or ketones. The reactions wereperformed with air as the re-oxidant. Therefore, this is anenviromentally friendly oxidation method. <b>Keywords:</b>asymmetric catalysis, chiral ligand,oxazolines, conformational study, allylic substitution,polymer-bound ligands, dendritic ligands, crown ether,oxidations, palladacycle.

Binding proteins are present both in gram-negative and gram-positive bacteria. They are the recognition components of the ABC transport systems that transport different nutrients into the cell, and are in some cases also involved in chemotaxis. In gram-negative bacteria, they are present in the periplasm between the inner and the porous outer membrane. Here, these highly specific proteins can bind to a certain ligand such as ions, sugars and amino acids. The protein-ligand complex can then interact with permeases bound to the inner membrane that transport the nutrient into the cell. Gram-positive bacteria lack an outer membrane and the binding protein must therefore be anchored to the cell membrane. In this thesis different aspects of three members of the super-family of the periplasmic binding proteins have been studied. In the case of the allose-binding protein (ALBP) from E. coli we focused on the movement of the protein when ligand is bound and released. This protein was also compared with the ribose-binding protein (RBP) which belongs to the same structural cluster and from which both open and closed structures are available. The leucine-binding protein (LBP) from E. coli was studied with regards to the structural basis of its specificity for different ligands as well as its conformational changes. The leucine-isoleucine-valine protein has 80% sequence identity with LBP but still exhibits a different preference for ligands. The structure of the maltose-binding protein (MBP) was obtained from a gram-positive thermoacidophile, A. acidocaldarius. Here, our goal was to study acid-stability of proteins. Since little is known about this and structures of the mesophilic counterpart in E. coli are available, as well as structures from two hyperthermophiles, we had an opportunity to study differences in their structural properties that could explain their differing stabilities.

AcrA is the periplasmic component of an efflux system AcrA-AcrB-TolC, which can expel different classes of antibiotics. AcrB is the inner membrane (IM) pump that utilizes proton-motive force for the active transport, TolC is the outer membrane (OM) channel, and AcrA coordinates the actions of AcrB and TolC, so that substrates are expelled across the two membranes, bypassing the periplasm. It has been proposed that AcrA either provides a static seamless link between AcrB and TolC, or acts like its analogous viral membrane fusion protein (MFP) and actively brings the IM and OM closer for substrate transfer. To better understand the role of AcrA in the efflux mechanism, site-directed spin labeling (SDSL)/EPR (electron paramagnetic resonance) spectroscopy is used to investigate the structure and dynamics of AcrA in solution. My results demonstrated that AcrA is a dynamic protein that undergoes pH-dependent and reversible conformational changes. AcrA contains an interrupted alpha-helical, coiled-coil domain flanked by a pair of beta-stranded lipoyl motifs, and my SDSL/EPR analysis revealed that the pH-induced conformation change mainly involves the coiled-coil and the lipoyl domains. In addition, I found that each AcrA monomer folds into an intra-molecular hairpin and AcrA monomers oligomerize with their coiled-coil hairpins aligned in parallel. Unlike the pH-induced conformational rearrangement of a viral MFP, change in pH alters both intra- and inter-molecular interaction along the coiled-coil of AcrA without rearranging the hairpin fold. The organization of AcrA protomers and its pH-induced conformational switching are, however, congruent with the TolC coiled-coil hairpins in the iris-like opening of the TolC channel. Together, my studies suggest that rather than being a passive structural linkage between AcrB and TolC, AcrA plays an active role mediating the drug efflux. The reported AcrA dynamics provides new insights into the AcrA-TolC interactions for the channel opening during the efflux process.

AcrA is the periplasmic component of an efflux system AcrA-AcrB-TolC, which can expel different classes of antibiotics. AcrB is the inner membrane (IM) pump that utilizes proton-motive force for the active transport, TolC is the outer membrane (OM) channel, and AcrA coordinates the actions of AcrB and TolC, so that substrates are expelled across the two membranes, bypassing the periplasm. It has been proposed that AcrA either provides a static seamless link between AcrB and TolC, or acts like its analogous viral membrane fusion protein (MFP) and actively brings the IM and OM closer for substrate transfer. To better understand the role of AcrA in the efflux mechanism, site-directed spin labeling (SDSL)/EPR (electron paramagnetic resonance) spectroscopy is used to investigate the structure and dynamics of AcrA in solution. My results demonstrated that AcrA is a dynamic protein that undergoes pH-dependent and reversible conformational changes. AcrA contains an interrupted alpha-helical, coiled-coil domain flanked by a pair of beta-stranded lipoyl motifs, and my SDSL/EPR analysis revealed that the pH-induced conformation change mainly involves the coiled-coil and the lipoyl domains. In addition, I found that each AcrA monomer folds into an intra-molecular hairpin and AcrA monomers oligomerize with their coiled-coil hairpins aligned in parallel. Unlike the pH-induced conformational rearrangement of a viral MFP, change in pH alters both intra- and inter-molecular interaction along the coiled-coil of AcrA without rearranging the hairpin fold. The organization of AcrA protomers and its pH-induced conformational switching are, however, congruent with the TolC coiled-coil hairpins in the iris-like opening of the TolC channel. Together, my studies suggest that rather than being a passive structural linkage between AcrB and TolC, AcrA plays an active role mediating the drug efflux. The reported AcrA dynamics provides new insights into the AcrA-TolC interactions for the channel opening during the efflux process.

En aquesta Tesi: 1) S’ha estudiat la reacció de metàtesi creuada (CM) de diferents derivats metilenciclopentànics utilitzant el catalitzador d’Hoveyda-Grubbs de segona generació, observant la formació dels alquens tetrasubstituïts corresponents amb bons rendiments. En el cas d’un derivat bis(metilenciclopentànic) s’ha observat la formació de productes de doble i triple CM amb elevada estereoselectivitat anti, fet que en el cas del producte de doble CM s’ha establert per difracció de raigs X. 2) S’ha preparat un nou ciclopentadiè 1,1-disubstituit funcionalitzat, i s’han estudiat les reaccions de Diels-Alder amb diferents dienòfils [anhídrid maleic, cis-1,2-bis(fenilsulfonil)etilè i triflat de fenil(2-iodoetinil)iodoni]. L’adducte amb l’últim dienòfil s’ha transformat en un derivat 2,3-diiodat 7,7-disubstituït del norbornadiè. 3) S’ha estudiat la reacció del triflat de (2-iodoetinil)feniliodoni amb 1,3-difenilisobenzofuran que depenen de les condicions dóna l’adducte Diels-Alder corresponent o un triflat naftalènic format per reducció de l’adducte inicial per part del 1,3.difenilisobenzofuran emprat en excés. 4) S’ha desenvolupat una seqüència sintètica per a l’obtenció de derivats del 2,8-etanonoradamantà molt funcionalitzats, que té com a etapa clau una reacció Diels-Alder intramolecular. Durant la reducció d’una enona a alcohol al•lílic amb NaBH4 / CeCl3•7H2O (mètode de Luche), es va haver de protegir una funció maleimida transformant-la en una barreja diastereomèrica d’adductes amb furà, regenerant la maleimida després de la reducció de l’enona, per escalfament en el sí de toluè a reflux durant 4 dies (reacció retro-Diels-Alder). També s’ha posat a punt un procediment alternatiu per preparar un intermediari clau en la seqüència sintètica anterior, 5-{[(t-butildimetilsilil)oxi]metil}-2-metil-5,6-dihidrociclopenta[c]pirrol-1,3(2H,4H)-diona, a partir de la N-metilmaleimida amb un rendiment cinc vegades superior al desenvolupat inicialment. 5) L’estructura dels diferents compostos obtinguts en aquesta Tesi s’ha establert per mètodes espectroscòpics [1H-RMN, 13C-RMN, correlacions 1H/1H (COSY, NOESY), correlacions 1H/13C (gHSQC, gHMBC), MS, IR] i en diversos casos, també per difracció de raigs X. / "Synthesis and reactivity of polycyclic compounds: Applications of the olefin metathesis reaction to their synthesis" In this PhD Thesis: 1) The cross metathesis (CM) reaction of different methylenecyclopentane derivatives using Hoveyda-Grubbs second generation catalyst has been studied. In these reactions, tetrasubstituted alkenes have been formed in good yields. In the case of a bis(methylenecyclopentane) derivative, the formation of products from double and triple CM has been observed. In general, high anti-stereoselectivity has been observed. The assignment of the stereochemistry of the single CM products has been performed through the analysis of the NMR data for the epoxide derivatives and in the case of the double CM product by X-ray diffraction analysis. 2) A new 1,1-disubstituted cyclopentadiene has been prepared. Its reactions with different dienophiles [maleic anhydride, cis-1,2-bis(phenylsulfonyl)ethylene and phenyl(2-iodoethynyl)iodonium triflate] has been studied. The adduct with the last dienophile has been transformed into a 2,3-diiodo-7,7-disubstituted norbornadiene. 3) The reaction of phenyl(2-iodoethynyl)iodonium triflate with 1,3-diphenylisobenzofuran has been studied. Depending on the reaction conditions, the corresponding Diels-Alder adduct or a naphthalenic triflate, formed by reduction of the initial adduct with 1,3-diphenylisobenzofuran used in excess, has been observed. 4) A synthetic sequence for the preparation of highly functionalized 2,8-ethanonoradamantane derivatives has been developed. The key step consists of an intramolecular Diels-Alder reaction. On reduction of an enone function to an allylic alcohol using NaBH4 / CeCl3•7H2O (Luche procedure), a maleimide function should be protected by transformation into a stereoisomeric mixture of Diels-Alder adducts with furan. The maleimide function was recovered, after reduction of the enone, through a thermal retro-Diels-Alder reaction. Also, an alternative procedure to prepare a key intermediate of the above synthetic sequence, 5-{[(t-butyldimethylsilyl)oxy]methyl}-2-methyl-5,6-dihydrocyclopenta[c]pyrrole-1,3(2H,4H)-dione, from N-methylmaleimide with a yield five times higher, have been developed. 5) The structure of the different compounds prepared in this PhD Thesis has been established by spectroscopic methods [1H NMR, 13C NMR, 1H/1H correlations (COSY, NOESY), 1H/13C correlations (gHSQC, gHMBC), MS, IR] and, in several cases, also by X-ray diffraction analysis.

Molecular recognition via noncovalent interactions plays a key role in many biological processes such as antigen-antibody interactions, protein folding, the bonding and catalytic transformation of substrates by enzymes, etc. Amongst these noncovalent interactions, electrostatic interactions, hydrogen bonding, π-π interactions, and metal-to-ligand bonding are the most prominent. Exploring noncovalent interactions in host-guest systems that range from small hydrocarbon systems to more complex systems is the main motivation of this thesis. The present study involves the design, synthesis and characterization of clip-shaped molecules as host structures, and an examination of their binding properties with a variety of guests using NMR spectroscopy. Several clips with a hydrocarbon or glycoluril backbone were synthesized. The binding of cations to small, hydrocarbon-based clips suggests that binding is enhanced by the rigidity and cooperativity between the two sidewalls of the clip. Binding is also very much dependant on the solvent properties. Glycoluril-based clips built with aromatic sidewalls provide a deep cavity for binding guest molecules. The binding properties of these hosts were studied with several guests such as cations, Lewis acids and Lewis bases. Lewis basic binding sites in the acenaphthene-terminated clip were dominating in guest binding. Complexation-induced conformational changes in the wall-to-wall distance were observed for this clip. In contrast, for a porphyrin-terminated clip with metal centers, very strong binding to a series of Lewis basic guests of various sizes into the clip cavity was observed. Conformational locking of guests with long alkyl chains was achieved, suggesting that, this clip could be useful as a potential molecular tool for the structural characterization of acyclic molecules with several stereogenic centers. This porphyrin clip was also shown to bind substituted fullerenes in the cavity.

<p>This thesis deals with the design of ligands for efficientasymmetric catalysis and studies of the conformation of theligands in the catalytically active complexes. All ligandsdeveloped contain chiral oxazoline heterocycles.</p><p>The conformations of hydroxy- and methoxy-substitutedpyridinooxazolines and bis(oxazolines) during Pd-catalysedallylic alkylations were investigated using crystallography,2D-NMR techniques and DFT calculations. A stabilising OH-Pdinteraction was discovered which might explain the differencein reactivity between the hydroxy- and methoxy-containingligands. The conformational change in the ligands due to thisinteraction may explain the different selectivities observed inthe catalytic reaction.</p><p>Polymer-bound pyridinooxazolines and bis(oxazolines) weresynthesised and employed in Pd-catalysed allylic alkylationswith results similar to those of monomeric analogues;enantioselectivities up to 95% were obtained. One polymer-boundligand could be re-used several times after removal of Pd(0).The polymer-bound bis(oxazoline) was also used in Zn-catalysedDiels-Alder reactions, but the heterogenised catalyst gavelower selectivities than a monomeric analogue.</p><p>A series of chiral dendron-containing pyridinooxazolines andbis(oxazolines) were synthesised and evaluated in Pd-catalysedallylic alkylations. The dendrons did not seem to have anyinfluence on the selectivity and little influence on the yieldwhen introduced in the pyridinooxazoline ligands. In thebis(oxazoline) series lower generation dendrimers had a postiveon the selectivity, but the selectivity and the activitydecreased with increasing generation.</p><p>Crown ether-containing ligands were investigated inpalladium-catalysed alkylations. No evidence of a possibleinteraction between the metal in the crown ether and thenucleophile was discovered.</p><p>A new type of catalyst, an oxazoline-containing palladacyclewas found to be very active in oxidations of secondary alcoholsto the corresponding aldehydes or ketones. The reactions wereperformed with air as the re-oxidant. Therefore, this is anenviromentally friendly oxidation method.</p><p><b>Keywords:</b>asymmetric catalysis, chiral ligand,oxazolines, conformational study, allylic substitution,polymer-bound ligands, dendritic ligands, crown ether,oxidations, palladacycle.</p>