<p>Proteins are among the most complex molecules in the cell and they play a major role in life itself. The complexity is not restricted to just structure and function, but also embraces the protein folding reaction. Within the field of protein folding, the focus of this thesis is on the features of the folding transition state in terms of growing contacts, common nucleation motifs and the contribution of charged residues to stability and folding kinetics. </p><p>During the resent decade, the importance of a certain residue in structure formation has been deduced from Φ-value analysis. As a complement to Φ-value analysis, I present how scatter in a Hammond plot is related to site-specific information of contact formation, Φ´(β^TS), and this new formalism was experimentally tested on the protein L23. The results show that the contacts with highest Φ growth at the barrier top were distributed like a second layer outside the folding nucleus. This contact layer is the critical interactions needed to be formed to overcome the entropic barrier. </p><p>Furthermore, the nature of the folding nucleus has been shown to be very similar among proteins with homologous structures and, in the split β-α-β family the proteins favour a two-strand-helix motif. Here I show that the two-strand-helix motif is also present in the ribosomal protein S6 from<i> A. aeolicus</i> even though the nucleation and core composition of this protein differ from other related structure-homologues. </p><p>In contrast to nucleation and contact growth, which are events driven by the hydrophobic effect, my most recent work is focused on electrostatic effects. By pH titration and protein engineering the charge content of S6 from <i>T. thermophilus</i> was altered and the results show that the charged groups at the protein surface might not be crucial for protein stability but, indeed, have impact on folding kinetics. Furthermore, by site-specific removal of all acidic groups the entire pH dependence of protein stability was depleted.</p>

Proteins are among the most complex molecules in the cell and they play a major role in life itself. The complexity is not restricted to just structure and function, but also embraces the protein folding reaction. Within the field of protein folding, the focus of this thesis is on the features of the folding transition state in terms of growing contacts, common nucleation motifs and the contribution of charged residues to stability and folding kinetics. During the resent decade, the importance of a certain residue in structure formation has been deduced from Φ-value analysis. As a complement to Φ-value analysis, I present how scatter in a Hammond plot is related to site-specific information of contact formation, Φ´(βTS), and this new formalism was experimentally tested on the protein L23. The results show that the contacts with highest Φ growth at the barrier top were distributed like a second layer outside the folding nucleus. This contact layer is the critical interactions needed to be formed to overcome the entropic barrier. Furthermore, the nature of the folding nucleus has been shown to be very similar among proteins with homologous structures and, in the split β-α-β family the proteins favour a two-strand-helix motif. Here I show that the two-strand-helix motif is also present in the ribosomal protein S6 from A. aeolicus even though the nucleation and core composition of this protein differ from other related structure-homologues. In contrast to nucleation and contact growth, which are events driven by the hydrophobic effect, my most recent work is focused on electrostatic effects. By pH titration and protein engineering the charge content of S6 from T. thermophilus was altered and the results show that the charged groups at the protein surface might not be crucial for protein stability but, indeed, have impact on folding kinetics. Furthermore, by site-specific removal of all acidic groups the entire pH dependence of protein stability was depleted.

In the thesis work we investigate four problems connected with dynamical processes in condensed medium, using different techniques of equilibrium and non-equilibrium statistical mechanics. Biology is rich in dynamical events ranging from processes involving single molecule [1] to collective phenomena [2]. In cell biology, translocation and transport processes of biological molecules constitute an important class of dynamical phenomena occurring in condensed phase. Examples include protein transport through membrane channels, gene transfer between bacteria, injection of DNA from virus head to the host cell, protein transport thorough the nuclear pores etc. We present a theoretical description of the problem of protein transport across the nuclear pore complex [3]. These nuclear pore complexes (NPCs) [4] are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. The first suggests that the plug is a reversible hydrogel while the other suggests that it is a polymer brush. In the thesis, we propose a model for the transport of a protein through the plug, which is treated as elastic continuum, which is general enough to cover both the models. The protein stretches the plug and creates a local deformation, which together with the protein is referred to as the bubble. The relevant coordinate describing the transport is the center of the bubble. We write down an expression for the energy of the system, which is used to analyze the motion. It shows that the bubble executes a random walk, within the gel. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. Further, on adopting the same kind of free energy for the brush too, one finds that though the energy cost for the entry of the particle is small but the diffusion coefficient is much lower and hence, explanation of the rapid diffusion of the particle across the nuclear pore complex is easier within the gel model. In chemical physics, processes occurring in condensed phases like liquid or solid often involve barrier crossing. Simplest possible description of rate for such barrier crossing phenomena is given by the transition state theory [5]. One can go one step further by introducing the effect of the environment by incorporating phenomenological friction as is done in Kramer’s theory [6]. The “method of reactive flux” [7, 8] in chemical physics allows one to calculate the time dependent rate constant for a process involving large barrier by expressing the rate as an ensemble average of an infinite number of trajectories starting at the barrier top and ending on the product side at a specified later time. We compute the time dependent transmission coefficient using this method for a structureless particle surmounting a one dimensional inverted parabolic barrier. The work shows an elegant way of combining the traditional system plus reservoir model [9] and the method of reactive flux [7] and the normal mode analysis approach by Pollak [10] to calculate the time dependent transmission coefficient [11]. As expected our formula for the time dependent rate constant becomes equal to the transition state rate constant when one takes the zero time limit. Similarly Kramers rate constant is obtained by taking infinite time limit. Finally we conclude by noting that the method of analyzing the coupled Hamiltonian, introduced by Pollak is very powerful and it enables us to obtain analytical expressions for the time dependent reaction rate in case of Ohmic dissipation, even in underdamped case. The theory of first passage time [12] is one of the most important topics of research in chemical physics. As a model problem we consider a particle executing Brownian motion in full phase space with an absorbing boundary condition at a point in the position space we derive a very general expression of the survival probability and the first passage time distribution, irrespective of the statistical nature of the dynamics. Also using the prescription adopted elsewhere [13] we define a bound to the actual survival probability and an approximate first passage time distribution which are expressed in terms of the position-position, velocity-velocity and position-velocity variances. Knowledge of these variances enables one to compute the survival probability and consequently the first passage distribution function. We compute both the quantities for gaussian Markovian process and also for non-Markovian dynamics. Our analysis shows that the survival probability decays exponentially at the long time, irrespective of the nature of the dynamics with an exponent equal to the transition state rate constant [14]. Although the field of equilibrium thermodynamics and equilibrium statistical mechanics are well explored, there existed almost no theory for systems arbitrarily far from equilibrium until the advent of fluctuation theorems (FTs)[15] in mid 90�s. In general, these fluctuation theorems have provided a general prescription on energy exchanges that take place between a system and its surroundings under general nonequilibrium conditions and explain how macroscopic irreversibility appears naturally in systems that obey time reversible microscopic dynamics. Based on a Hamiltonian description we present a rigorous derivation [16] of the transient state work fluctuation theorem and the Jarzynski equality [17] for a classical harmonic oscillator linearly coupled to a harmonic heat bath, which is dragged by an external agent. Coupling with the bath makes the dynamics dissipative. Since we do not assume anything about the spectral nature of the harmonic bath the derivation is valid for a general non-Ohmic bath.

To investigate how protein folding is affected by sequence connectivity five topological variants of the ribosomal protein S6 were constructed through circular permutation.  In these constructs, the chain connectivity (i.e. the order of secondary-structure elements) is changed without changing the native-state topology.  The effects of the permutations on the folding process were then characterised by φ-value analysis, which estimates the extent of contact formations in the transition-state ensemble.  The results show that the folding nuclei of the wild-type and permutant proteins comprises a common motif of one α-helix docking against two β-sheets, i.e. the minimal structure for folding.  However, this motif is recruited in different parts of the S6 structure depending on the permutation, either in the α1 or α2 half of the protein.  This minimal structure is not unique for S6 but can also be seen in other proteins.  As an effect of the dual nucleation possibilities, the transition-state changes describe a competition between two parallel pathways, which both include the central β-stand 1.  This strand constitutes thus a structural overlap between the two competing nuclei.  As similar overlap between competing nuclei is also seen in other proteins, I hypothesise that the coupling of several small nuclei into extended ‘super nuclei’ represents a general principle for propagating folding cooperativity across large structural distances.  Moreover, I demonstrate by NMR analysis that the existence of multiple folding nuclei renders the H/D-exchange kinetics independent of the folding pathway. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper IV: Manuscript

Despite numerous advances in experimental methodologies capable of addressing the various phenomenon occurring on metal surfaces, atomic scale resolution of the microscopic dynamics remains elusive for most systems. Computational models of the processes may serve as an alternative tool to fill this void. To this end, parallel molecular dynamics simulations of self-diffusion on metal surfaces have been developed and employed to address microscopic details of the system. However these simulations are not without their limitations and prove to be computationally impractical for a variety of chemically relevant systems, particularly for diffusive events occurring in the low temperature regime. To circumvent this difficulty, a corresponding coarse-grained representation of the surface is also developed resulting in a reduction of the required computational effort by several orders of magnitude, and this description becomes all the more advantageous with increasing system size and complexity. This representation provides a convenient framework to address fundamental aspects of diffusion in nonequilibrium environments and an interesting mechanism for directing diffusive motion along the surface is explored. In the ensuing discussion, additional topics including transition state theory in noisy systems and the construction of a checking function for protein structure validation are outlined. For decades the former has served as a cornerstone for estimates of chemical reaction rates. However, in complex environments transition state theory most always provides only an upper bound for the true rate. An alternative approach is described that may alleviate some of the difficulties associated with this problem. Finally, one of the grand challenges facing the computational sciences is to develop methods capable of reconstructing protein structure based solely on readily-available sequence information. Herein a checking function is developed that may prove useful for addressing whether a particular proposed structure is a viable possibility.

This thesis describes work done to design and synthesize protease inhibitors, with the intention of developing therapeutic agents for Alzheimer’s disease (AD) and the chronic liver condition caused by infection of the hepatitis C virus (HCV). AD is the most common form of dementia, and HCV infection is the primary reason for liver transplantation in industrialized countries. Today, these two illnesses affect 24 and 170 million people, respectively. It has been shown that the human aspartic protease BACE-1 plays an important role in the development of AD, and thus inhibition of BACE-1 may offer a way to improve the quality of life of individuals afflicted with the disease. Furthermore, it is known that the serine protease NS3 is a vital component in the replication of HCV. Several novel potent BACE-1 inhibitors encompassing different transition state mimics were prepared. First, a hydroxyethylene moiety encompassing a secondary hydroxyl group was evaluated as a transition state analogue, producing inhibitors in the low nanomolar range. Various tertiary hydroxyl isosteres were also investigated as the central core, with the aim of shielding the pivotal hydroxyl group. These transition state isosteres consisted of tertiary hydroxyl analogues of previously used secondary hydroxyl containing norstatine, statine, and hydroxyethylamine isosteres. Several tertiary hydroxyl-containing inhibitors were found to be active in the low micromolar range. In addition, two inhibitors were co-crystallized with the BACE-1 enzyme to provide X-ray crystal structures, which furnished valuable binding information for further design of improved BACE-1 inhibitors. The goal in the HCV NS3 protease inhibitor project was to design, synthesize and evaluate a novel hydroxycyclopentene bioisostere to the previously used acyl-hydroxyproline moiety. The investigation revealed that it was possible to synthesize inhibitors containing this new bioisostere that were potent in the low nanomolar range. Further optimization by rigidification of the most active inhibitor resulted in equipotent macrocyclic compounds.

No description available.

Die kovalente Bindung von elektrophilen körperfremden Stoffen an nukleophile Zentren in Peptiden und Proteinen ist der initiierende molekulare Schritt einer Vielzahl von Erkrankungen und toxischen Prozessen. Für a,b-ungesättigte Aldehyde, Ketone und Ester, die sogenannten Michael-Akzeptoren, spielt dabei die Reaktion mit endogenen Thiolen eine entscheidende Rolle. Für diese Stoffklasse ermöglicht die Quantifizierung der Thiolreaktivität (als logaritmische Geschwindigkeitskonstante zweiter Ordnung der Reaktion des Michael-Akzeptors mit dem Tripeptid Glutathion (GSH), log kGSH) eine Vorhersage der akuten aquatischen Toxizität gegenüber den Ciliaten Tetrahymena Pyriformis (quantifiziert als logaritmische 50%-Effekt-Konzentration (effect-concentration, EC) der Wachstumsinhibition, log EC50). Zum besseren Verständnis der an diesen Prozessen beteiligten Reaktionen wurden in dieser Arbeit mehrere mögliche Mechanismen der Addition von Methylthiol an a,b-ungesättigte Carbonylverbindungen quantenchemisch anhand ihrer Übergangszustände untersucht. Dabei lag der Fokus unter anderem auf der Identifikation einer Modellreaktion, deren Barriere eine quantitative Vorhersage der Thiolreaktivität ermöglicht. Entsprechende Regressionsmodelle wurde an experimentelle Daten angepasst. Auf der Basis der berechneten elektrophilen Reaktivität log kGSH und der Hydrophobie (quantifiziert als logarithmischer Oktanol/Wasser-Verteilungskoeffizient, log Kow) wurden Stoffklassenspezifische Regressionsmodelle zur Toxizitätsvorhersage entwickelt und für die Untergruppe der Ester eine Modell-Suite etabliert.

Thermodynamic stabilities of eighteen cyclic C5H6 isomers were explored computationally both on singlet and triplet state potential energy surfaces (PES). All isomers have singlet ground states except for bicyclo[2.1.0]pent-5-ylidene (B5) having no stable geometry on the singlet C5H6 PES. Cyclopenta-1,3-diene (M1) is the most stable cyclic C5H6 isomer while cyclopent-1,4-diylidene is the least stable one among all. Cyclopenta-1,2-diene (M2) and cyclopentyne (M3) have biradical characters of 46.9 and 21.5%, respectively. Seven unimolecular isomerization reactions occurring among several of these molecules were investigated by DFT and ab initio methods. The conversion of bicyclo[2.1.0]pent-2-ene (B1) and tricyclo[2.1.0.02,5]-pentane (T1) into 1,3-cyclopentadiene (M1) are shown to be concerted processes whose reaction paths pass through TSs with a high degree of biradical character. The reaction enthalpies (DH0) are predicted to be -47.7 kcal/mol for B1 and -63.8 kcal/mol for T1 at UB3LYP/6-31G(d) level. The activation enthalpy (DH0&sup1 / ) for the ring opening of B1 was calculated by the CR-CCSD(T) method to be 25.2 kcal/mol, in good agreement with experiment. Furthermore, the DH0&sup1 / for the ring opening of T1 was obtained by the CR-CCSD(T) method to be 48.2 kcal/mol. The self-conversion of M1 via 1,5-hydrogen shift is a facile and concerted reaction with aromatic TS. The DH0&sup1 / estimations of B3LYP and CC methods are 25.24 and 28.78 kcal/mol, respectively. For 1,2-hydrogen shift reactions of cyclopent-3-enylidene (M4) and cyclopenten-2-ylidene (M5), the single point CC calculations predicted the DH0&sup1 / values of 3.13 and 10.12 kcal/mol, as well as, the DH0 values of -71.28 and -64.05 kcal/mol, respectively. The reason of M5 being more stable than M4 is due to the conjugation of the carbene carbon and the double bond in M5. The reaction path of cyclobutylidene methylene to cyclopentyne rearrangement is found to be rather shallow. The DH0&sup1 / and DH0 values predicted by the RCCSD(T) method to be 3.65 and -5.72 kcal/mol, respectively. Finally, triplet state isomerization of bicyclo[2.1.0]pent-5-ylidene to cyclopenta-1,2-diene, as well as, its parent reaction, cyclopropylidene to 1,2-propadiene were investigated at several levels of theory including DFT, CASSCF and CC methods. The UCCSD(T) method estimated a moderate barrier whose value is 8.12 kcal/mol for the isomerization of 3B5 with the reaction enthalpy of -44.63 kcal/mol.

Orientador: Luiz Guimarães Ferreira / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin / Made available in DSpace on 2018-08-10T00:36:47Z (GMT). No. of bitstreams: 1 Pinho_MariaGloriadeOliveira_M.pdf: 832379 bytes, checksum: 05244cdafb054c3e2fffdc0bd34cdc3a (MD5) Previous issue date: 2007 / Resumo: Apresentamos neste trabalho o estudo da fotoionização, incluindo os efeitos relativísticos, de elétrons das camadas-s mais externas dos átomos de Sódio, Potássio, Rubídio e Césio. Tratamos do processo onde um átomo não polarizado é fotoionizado por luz incidente linearmente polarizada, utilizando o Estado de Transição de meia ocupação, sob a ótica da aproximação de dipolo elétrico e da Aproximação da Densidade Local (LDA). Em nosso procedimento fazemos uso das equações de Dirac para o cálculo das funções de onda relativísticas, utilizadas para a obtenção das seções de choque totais de fotoionização e dos parâmetros de assimetria. Mostramos as vantagens da utilização do Estado de Transção de meia ocupação e sua precisão numérica nos cálculos de grandezas físicas como o Potencial de Ionização dos átomos. Através dos resultados obtidos, observamos a influência que os mínimos das seções de choque, chamados Mínimos de Cooper, exercem sobre os parâmetros de assimetria. Estes dados sâo comparados com cálculos efetuados através de outras formulações por outros autores e também com resultados experimentais encontrados na literatura / Abstract: In this work we present photoionization results for the valence s-electrons of Sodium, Potassium, Rubidium and Cesium atoms including relativistic effects. In our calculations we consider the photoionization of a non-polarized atom by linearly polarized light, using half occupation transition states, within the electric dipole approximation and the Local Density Approximation. Our total photoionization cross sections and asymmetry parameters were calculated using relativistic wave functions obtained from Dirac¿s equations. We show that the use of half occupation transition states improves the results, producing many advantages, such as numeric precision in the evaluation of the Ionization Potentials. We have also studied the in uence of the cross section minimum (Cooper Minimum) on the asymmetry parameters. We compare our results with experimental data and with other calculations from the literature / Mestrado / Física Atômica e Molecular / Mestre em Física