@phdthesis{Lee2013,
  author    = {Lee, Wook},
  title     = {Computational study on the catalytic mechanism of mtKasA},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-83989},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2013},
  abstract  = {Das Enzym KasA spielt eine entscheidende Rolle in der Biosynthese von Mykols{\"a}uren, den Bausteinen der Zellw{\"a}nde von Mycobacteriumtuberculosis. Dessen essentielle Notwendigkeit zeigt sich bei Abwesenheit von KasA in einer Zelllyse (Aufl{\"o}sung von Zellen) bei Mycobacteriumtuberculosis. Durch seine Bedeutung f{\"u}r Mycobacteriumtuberculosis, dem Erreger von Tuberkulose und damit der zweith{\"a}ufigsten Todesursache durch Infektionskrankheiten, stellt KasA ein vielversprechendes Ziel f{\"u}r die Entwicklung neuer Medikamente gegen Tuberkulose dar. Durch das Auftreten von extensiv resistenten St{\"a}mmen welche die meisten bekannten Antibiotika zur Bek{\"a}mpfung von Tuberkulose inaktivieren wird es dringend notwendig neue Medikamente gegen Tuberkulose zu entwickeln. In Kapitel 3.1 wird der Protonierungszustand der katalytischen Reste im Ruhezustand untersucht. F{\"u}r diese Untersuchungen wurden Free Energy Perturbation (FEP) Rechnungen und MD Simulationen verwendet. Die Ergebnisse zeigten, dass der zwitterionische Zustand am wahrscheinlichsten ist. Um diese Aussage mit weiteren handfesten Daten zu untermauern wurden Potential(hyper)fl{\"a}chen (PES) f{\"u}r den Protonentransfer zwischen neutralen und zwitterionischen Zustand mit Hilfe von QM/MM Methoden berechnet. Durch die starke Abh{\"a}ngigkeit der QM/MM Optimierung von der Ausgangsstruktur war es nicht m{\"o}glich konsistente Ergebnisse f{\"u}r diese Berechnungen zu bekommen. Um dieses Problem zu umgehen wurde ein auf QM/MM basierendes Umbrella Sampling mit Semiempirischen Methoden (RM1) durchgef{\"u}hrt. Die sich daraus ergebende PMF Fl{\"a}che zeigt das der zwitterionische Zustand stabiler ist als der neutrale Zustand. In Kapitel 3.2 wurde der Protonierungszustand der entsprechenden Reste im Acyl-Enzym Zustand untersucht. Im Unterschied zu anderen katalytischen Resten ist der Protonierungszustand von His311 ist nicht eindeutig im Acyl-Enzym Zustand und es ergeben sich aus den verschiedenen Protonierungszust{\"a}nden verschiedene Decarboxylierungsmechanismen. Um den wahrscheinlichsten Protonierungszustand bez{\"u}glich der freien Energie zu bestimmen wurden FEP Rechnungen durchgef{\"u}hrt. Die Ergebnisse zeigen, dass der pKa Wert an Nδ betr{\"a}chtlich durch die Enzymumgebung verringert wird, w{\"a}hrend dies f{\"u}r Nε nicht der Fall ist. Zus{\"a}tzlich dazu wurden die PMF Profile f{\"u}r den Protonentransfer zwischen Lys340 und Glu354 mit der QM/MM basierten Umbrella Sampling Methode berechnet. Die Ergebnisse zeigen, dass das Lys340/Glu354 Paar eher neutral als ionisch ist, wenn His311 an Nε protoniert ist. Ein relativ hoher ionischer Charakter des Lys340/Glu354 Paares, wenn His311 doppelt protoniert ist, gibt einen wertvollen Einblick in die Rolle welche das Lys340/Glu354 Paar beim verschieben des Protonierungszustandes von Nδ zu Nε im His311 nach dem Acyltransferschritt spielt. Die Ergebnisse zeigen, dass His311 neutral und an Nε protoniert ist. Ebenso ist das Lys340/Glu354 Paar neutral im Acyl-Enzym Zustand. Diese berechneten Ergebnisse f{\"u}hren zu dem Schluss, dass die Decarboxylierung durch ein Oxyanion Loch erleichtert wird welches aus zwei katalytischen Histidin Resten besteht. In Kapitel 3.3 wurde der Protonierungszustand der katalytischen Reste im Ruhezustand erneut untersucht da eine aktuelle Benchmarkstudie zeigte, dass die verwendete Semiempirische Methode (RM1) in Kapitel 3.1 dazu tendiert die Stabilisation des zwitterionischen Zustandes zu {\"u}bersch{\"a}tzen. Auch wurde in Kapitel 3.1 das Lys340/Glu354 Paar als rein ionisch angesehen, w{\"a}hrend sich in Kapitel 3.2 herausstellte, dass es sich um eine Mischung aus neutralen und ionischen Charakter handelt. Die neuen Untersuchungen beinhalten eine gr{\"o}ßere QM Region inklusive des Lys340/Glu354 Paares. Der daf{\"u}r verwendete BLYP/6-31G** Ansatz ist ausreichend akkurat f{\"u}r die aktuelle Fragestellung, was durch Vergleichsrechnungen bewiesen wurde. Die neuen Ergebnisse der QM/MM MD und FEP Rechnungen deuten an, dass die katalytischen Reste im Ruhezustand h{\"o}chst wahrscheinlich neutral vorliegen. Dies wiederum f{\"u}hrt zu der Frage wie KasA aktiviert werden kann um die katalytische Reaktion zu initiieren. Auf der Basis der Ergebnisse der MD Simulationen und FEP Rechnungen f{\"u}r den His311Ala Mutanten in Kapitel 3.1 stellten wir die Hypothese auf, dass die offene Konformation von Phe404 die Aktivierung der katalytischen Reste durch die (Aus)bildung einer starken Wasserstoffbindung einleitet. Die QM/MM MD Simulation best{\"a}tigt dass diese Aktivierung der katalytischen Reste durch die offene Konformation des Phe404 bewerkstelligt werden kann. Das entsprechende auf Kraftfeld basierende PMF Profil zeigt auch, dass dieser Konformationswechsel energetisch realisierbar ist. Die Verteilung der hydrophilen und hydrophoben Reste in der Malonyl Bindungstasche in Verbindung mit unseren berechneten Ergebnissen geben einen Einblick in den detaillierten},
  subject      = {Tuberkelbakterium},
  language  = {en}
}
@phdthesis{Becker2015,
  author    = {Becker, Johannes},
  title     = {Development and implementation of new simulation possibilities in the CAST program package},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-132032},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2015},
  abstract  = {The aim of the present work is the development and implementation of new simulation possibilities for the CAST program package. Development included, among other things, the partial parallelization of the already existing force fields, extension of the treatment of electrostatic interactions and implementation of molecular dynamics and free energy algorithms. The most time consuming part of force field calculations is the evaluation of the nonbonded interactions. The calculation of these interactions has been parallelized and it could be shown to yield a significant speed up for multi-core calculations compared to the serial execution on only one CPU. For both, simple energy/gradient as well as molecular dynamics simulations the computational time could be significantly reduced. To further increase the performance of calculations employing a cutoff radius, a linkedcell algorithm was implemented which is able to build up the non-bonded interaction list up to 7 times faster than the original algorithm. To provide access to dynamic properties based on the natural time evolution of a system, a molecular dynamics code has been implemented. The MD implementation features two integration schemes for the equations of motion which are able to generate stable trajectories. The basic MD algorithm as described in Section 1.2 leads to the sampling in the microcanonical (NVE) ensemble. The practical use of NVE simulations is limited though because it does not correspond to any experimentally realistic situation. More realistic simulation conditions are found in the isothermal (NVT) and isothermalisobaric (NPT) ensembles. To generate those ensembles, temperature and pressure control has been implemented. The temperature can be controlled in two ways: by direct velocity scaling and by a Nose-Hoover thermostat which produces a real canonical ensemble. The pressure coupling is realized by implementation of a Berendsen barostat. The pressure coupling can be used for isotropic or anisotropic box dimensions with the restriction that the angles of the box need to be 90� . A crucial simulation parameter in MD simulations is the length of the timestep. The timestep is usually in the rang of 1fs. Increasing the timestep beyond 1fs can lead to unstable trajectories since the fastest motion in the system, usually the H-X stretch vibration can not be sampled anymore. A way to allow for bigger timesteps is the use of a constraint algorithm which constrains the H-X bonds to the equilibrium distance. For this the RATTLE algorithm has been implemented in the CAST program. The velocity Verlet algorithm in combination with the RATTLE algorithm has been shown to yield stable trajectories for an arbitrary length of simulation time. In a first application the MD implementation is used in conjunction with the MOPAC interface for the investigation of PBI sidechains and their rigidity. The theoretical investigations show a nice agreement with experimentally obtained results. Based on the MD techniques two algorithms for the determination of free energy differences have been implemented. The umbrella sampling algorithm can be used to determine the free energy change along a reaction coordinate based on distances or dihedral angles. The implementation was tested on the stretching of a deca-L-alanine and the rotation barrier of butane in vacuum. The results are in nearly perfect agreement with literature values. For the FEP implementation calculations were performed for a zero-sum transformation of ethane in explicit solvent, the charging of a sodium ion in explicit solvent and the transformations of a tripeptide in explicit solvent. All results are in agreement with benchmark calculations of the NAMD program as well as literature values. The FEP formalism was then applied to determine the relative binding free energies between two inhibitors in an inhibitor-protein complex. Next to force fields, ab-initio methods can be used for simulations and global optimizations. Since the performance of such methods is usually significantly poorer than force field applications, the use for global optimizations is limited. Nevertheless significant progress has been made by porting these codes to GPUs. In order to make use of these developments a MPI interface has been implemented into CAST for communication with the DFT code TeraChem. The CAST/TeraChem combination has been tested on the \$H_2 O_{10}\$ cluster as well as the polypeptide met-Enkephalin. The pure ab-initio calculations showed a superior behavior compared to the standard procedure where the force field results are usually refined using quantum chemical methods.},
  subject      = {Molekulardynamik},
  language  = {en}
}
@phdthesis{Mladenovic2008,
  author    = {Mladenovic, Milena},
  title     = {Theoretical Investigation into the Inhibition of Cystein Proteases},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-25763},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2008},
  abstract  = {Although known about and investigated since the late 1970's, the picture of the basic principles governing inhibitor strengths and the structure-activity relationships of the cysteine protease inhibition mechanism is still very incomplete. Computational approaches can be a very useful tool for investigating such questions, as they allow the inspection of single, specific effects in isolation from all others, in a manner very difficult to achieve experimentally. The ab initio treatments of such large systems like proteins are still not feasible. However, there is a vast number of computational approaches capable of dealing with protein structures with reasonable accuracy. This work presents a summary of theoretical investigations into cysteine protease cathepsin B using a range of methods. We have concentrated on the investigation of cysteine protease inhibition by epoxide- and aziridine-based inhibitors in order to obtain better insight into these important topics. Various model systems are simulated by means of pure quantum mechanical methods and by hybrid (QM/MM) methods. Both approaches provide a static picture. Dynamical effects are then accounted for by additional molecular dynamics (MD) simulations, using both classical and QM/MM MD approaches. The quantum mechanical approach was used to study very small model systems consisting only of the electrophilic warhead of the inhibitor (both substitituted and not) and molecular moieties simulating a very simplified protein active site (methylthiolate instead of Cys29 and methylimidazolium instead of His199 residue) and solvent surroundings (two waters or two ammonium ions, in combination with a continuum solvent model). Although simple, such a system provides a good description of the most important interactions involved in the inhibition reaction. It also allows investigation of the influence of the properties of the electrophilic warhead on the reaction rate. Beside the properties of the electrophilic warhead, the protein and solvent environment is also an important factor in the irreversible deactivation of the enzyme active site by the inhibitor. The non-covalent interactions of the inhibitor with the oxyanion hole and other subsites of the enzyme, as well as its interaction with the solvent molecules, need to be explicitly taken into account in the calculations, because of their possible impact on the reaction profile. As molecular modeling methods allow the treatment of such large systems, but lack the possibility of describing covalent interactions, our method of choice was the combined quantum mechanics/molecular modeling approach. By splitting the system into a smaller part that undergoes the bond cleavage/formation process and must be treated quantum mechanically, and a larger part, comprised of the rest of the protein, which could be treated using force fields, we managed to simulate the system at the desired precision. Our investigations concentrated on the role of His199 in the inhibition mechanism as well as on the structure-reactivity relationships between cysteine protease and various inhibitors, yielding new insight into the kinetics, regio- and stereospecificity of the inhibition. In particular, our calculations provide the following insights: i.) an explanation for the regioselectivity of the reaction, and original insight into which interactions affect the stereoselectivity; ii.) a clear model which explains the known structure-activity relationships and connects these effects with the pH-dependency of the inhibition; iii.) our computations question the generally accepted two-step model by showing that substituent effects accelerate the irreversible step to such an extent that the achievement of an equilibrium in the first step is doubtful; iv.) by way of theoretical characterizations of aziridine models, the reasons for similarities and differences in the mode of action of epoxide- and aziridine-based inhibitors are elucidated; and finally, v.) combining our results with experimental knowledge will allow rational design of new inhibitors. To account for dynamical effects as well, molecular dynamics (MD) computations were also performed. In these calculations the potential energy was computed at the force field level. The results not only supported and clarified the QM/MM results, but comparison with previous X-ray structures helped correct existing errors in the available geometrical models and resolved inconsistencies in the weighting of various factors governing the inhibition. In the work the first QM/MM MD calculations on the active site of the cysteine proteases are presented. In contrast to the MD simulations, these calculations used potential energies computed at the QM/MM-level. With the help of these computations we sought to address strongly disputed questions about the reasons for the existence of the active site ion pair and its role in the high activity of the enzyme.},
  subject      = {Quantenchemie},
  language  = {en}
}