5 Naturwissenschaften und Mathematik
Monte Carlo Simulation Methods for Studying the Thermodynamics of Ligand Binding & Transfer Processes in Biomolecules
R. Thomas Ullmann
- The binding and transfer of ligands is of central
importance for the function of many biomolecular
systems. The main topic of this thesis is the
development and application of Monte Carlo (MC)
simulation methods for studying complex ligand
binding equilibria which can also involve
conformational changes. The simulated systems
were described by microstates within a continuum
electrostatics/molecular mechanics (CE/MM) model
of the receptor-ligand system. The CE/MM modeling
methodology was improved. The improvements led to
more detailed molecular models that enable a more
realistic reproduction of system properties and
environmental conditions. The developed simulation
methods were applied to biomolecular systems whose
function involves aspects that are important for
the understanding of bioenergetic energy
transduction. The results of this thesis are
presented in five articles that are published in
peer reviewed scientific journals.
Manuscript A presents the Monte Carlo simulation
software GMCT which was largely developed in this
thesis. The software offers a variety of different
simulation methods that allow the user to harness
the full potential of CE/MM models in the simulation
of complex receptor systems.
Manuscript B presents a novel theoretical framework
for free energy calculations with the free energy
perturbation method. The novel framework is more
broadly applicable and can lead to more efficient
simulations than previous formulations. The
derivation of the formalism also led to interesting
insights into general statistical mechanics. The
formalism was implemented in GMCT and could already
be used fruitfully for the free energy calculations
presented in Manuscripts C and D.
Manuscript C demonstrates the application of free
energy measures of cooperativity to study the
coupling of protonation, reduction and conformational
change in azurin from Pseudomonas aeruginosa (PaAz).
Such a coupling is prototypic for bioenergetic systems
because it forms the thermodynamic basis of their
energy transducing function. PaAz is an experimentally
well characterized, small electron transport protein.
For this reason, PaAz was used here as model system
to demonstrate the usefulness of cooperativity free
energies in detecting and quantifying thermodynamic
coupling between events in complex biomolecular
systems. The results of this study led to new insight
that could help to determine the still enigmatic
physiological role of PaAz.
In Manuscript D, free energy calculations were
applied to study the thermodynamics of transport
through the ammonium transporter Amt-1 from
Archaeoglobus fulgidus (AfAmt-1). Ammonium is the most
directly utilizable nitrogen source for plants and
microorganisms. AfAmt-1 and its homologues facilitate
the transport of ammonia/ammonium across biological
membranes in living beings from all domains of life.
It is intensely debated how these proteins perform
their function and whether ammonia or its protonated
form ammonium is actually transported. The study
extended upon previous theoretical studies by
including the effects of substrate concentration,
electrochemical transmembrane gradients,
proton-coupled binding equilibria and competitive
binding of different ligand species. It was found
that the transported species is most likely the
ammonium ion. An ammonia/proton symport mechanism
that involves a pair of coplanar histidine residues
at the center of the transmembrane pore as transient
proton acceptor is made plausible by the high
genetic conservation of these residues.
Manuscript E presents a first application of the
microstate description within a CE/MM model to the
simulation of the non-equilibrium dynamics of a
molecular system. We simulated the re-reduction
kinetics of the primary electron donor in the
photocycle of the bacterial photosynthetic reaction
center from Blastochloris viridis. The simulation
results are in very good agreement with
experimentally measured data.
Etablierung von Methoden zur Bioevaluation antitumoraler Naturstoffe, Metabolite und Analoga
- Die Ziele, die ich mir vor Beginn meiner Arbeit gesteckt habe (siehe 1.3), wurden weitestgehend erreicht. Es wurde ein Verfahren entwickelt, mit dessen Hilfe Illudin M 11 zuverlässig gewonnen werden kann. Die Aufzucht von O. olearius im Medium HA- und die Extraktion nach Kutscher-Steudel erwiesen sich hierbei als Methoden der Wahl. Illudin S 11a konnte jedoch nicht isoliert werden.
Daneben konnte eine Reihe von Verfahren zur Evaluierung von Testsubstanzen etabliert werden. Die Untersuchungen der Substanzeigenschaften (siehe 2.5 bis 2.8) lieferten nützliche und verlässliche Ergebnisse, auch wenn man hinsichtlich des Einsatzbereiches manchmal Einschränkungen in Kauf nehmen musste. Die Stabilität von Esterbindungen wurde auf zwei Arten untersucht. Die getesteten Substanzen 16c, 18 und 19b erwiesen sich hierbei als weitestgehend stabil gegenüber Hydrolyse (siehe 3.2). Die Methode, die zur Untersuchung der Komplexbildung eingesetzt wurde, lässt sich nicht auf alle Verbindungen übertragen, sondern nur auf solche, deren Komplexe ein Absorptionsmaximum im sichtbaren Bereich besitzen (siehe 3.3). Bei den Eisenkomplexen war das Potential der getesteten Liganden, Komplexe zu bilden vergleichbar mit dem von EDTA. Bei den anderen getesteten Kationen war dieses schwächer ausgeprägt. Im Rahmen des Glutathion-Monitorings wurde festgestellt, dass – im Gegensatz zur Muttersubstanz 11 – keines der getesteten Illudinderivate 27 eine spontane Reaktion mit GSH eingeht (siehe 3.4). Der Alkylierungsassay mit Aceton liefert nur für farblose Verbindungen verlässliche Ergebnisse. Bei den getesteten Illudinderivaten 27 konnte zwar ein Alkylierungspotential gemessen werden, doch stellt deren vorhandene Eigenabsorption einen gewissen Unsicherheitsfaktor dar. Der Alkylierungsassay mit Acetophenon lieferte keine verwertbaren Ergebnisse (siehe 3.5).
Die zellbasierten Analysen (siehe 2.9 bis 2.11) sowie der CAM-Assay (siehe 2.12) sind für alle Stoffe durchführbar. Auch wenn die untersuchten Organismen (Zellen und Embryonen) nicht immer auf die gleiche Weise reagieren, kommen auch hierbei verlässliche Resultate zu Stande. Da die Zahl der durchführbaren Tests durch Kosten und Verfügbarkeit der Untersuchungsobjekte limitiert ist, wurde hinsichtlich der Testsubstanzen immer eine Vorauswahl getroffen. Beim TUNEL-Test zeigten die meisten Verbindungen ein proapoptotisches Verhalten, besonders gut wirkten die Illudinderivate 27 (siehe 3.6). Der Annexin-Test ist nur bedingt aussagekräftig. Er ließ sich zum einen nur mit Suspensionszellen durchführen, zum anderen war es manchmal kaum möglich, spätapoptotische von nekrotischen Zellen zu unterscheiden (siehe 3.7). Mit Hilfe von Immunoblots wollte man Rückschlüsse hinsichtlich des Mechanismus der Apoptoseinitiierung ziehen. Die schnelle Prozessierung der Caspase 9 legt den Schluß nahe, dass die Platinkomplexkonjugate 13 (HL 60), die Oxazole 26 (Kb-V1), die Illudinderivate 27 (HL 60 und 518 A2) und die Chalkone 20, 21a und 21c (HL 60) zu einer Aktivierung über den mitochondrialen Weg führen. Die anderen Testverbindungen bedürfen weiterer Untersuchungen in Bezug auf den Signalweg der Apoptoseinitiierung (siehe 3.8). Einige Derivate der antivaskulären Verbindung Combretastatin A-4 7a wurden mit Hilfe des CAM-Assays untersucht. Die meisten zeigten hierbei erwartungsgemäß ein vergleichbares Verhalten. Besonders interessant ist der Aktivitätsunterschied der Combretastatin-Analoga 26h und 26i. Dieser wurde sowohl beim TUNEL-Test als auch beim CAM-Assay beobachtet, obwohl sich beide Verbindungen strukturell kaum unterscheiden.
Effect of Dopants on the Local Atomic Structure and Sintering Behavior of Bismuth Sodium Titanate
- The most commonly used piezoceramic is lead zirconate titanate Pb(ZrxTi(1-x))O (PZT). It possesses outstanding piezoelectric properties which can be modified for numerous applications by the addition of dopants. However, because of environmental and health concerns regarding lead, lead-free alternatives are demanded by politics.
One of the two most promising lead-free replacement materials is the ferroelectric bismuth sodium titanate (Bi0.5Na0.5)TiO3 (BNT). Like PZT, it crystallizes in the perovskite structure.
Since the dielectric and piezoelectric properties of pure BNT ceramics are insufficient for application, BNT is often modified by the addition of dopants. These influence a great variety of material properties to different degrees, e.g. the sintering behavior, the dielectric and piezoelectric properties and their respective temperature stabilities. Doping of BNT aims to decrease the sintering temperature in order to avoid Bi vaporization, to increase the depolarization temperature and to enhance the piezoelectric coefficient.
The effects of numerous dopants on the resulting performance of BNT were studied extensively in the literature. However, so far little attention has been payed to the way in which dopants interact with the piezomaterial. Nevertheless, it is the understanding of these relationships that would make targeted modifications and improvements of BNT possible.
The primary goal of this study was to investigate and explain the effects of a model dopant -cobalt- on the phase formation, sintering behavior and microstructure of BNT as well as on the resulting dielectric and piezoelectric properties. In this regard, a core issue was to determine the preferred lattice site of Co in BNT.
BNT was synthesized from oxide powders using the classic solid-state route and sintered at temperatures ranging from 1000 °C to 1150 °C. Cobalt was added in concentrations between 0.1 mol% and 2.6 mol% Co prior to the calcination as Co3O4.
About one third of the total cobalt amount was incorporated into the BNT lattice on the perovskite B-site, that is, it substituted for Ti. The cobalt in BNT appeared to be in equilibrium with the secondary phase Co2TiO4, which invariably formed at cobalt concentrations greater than 0.1 mol% Co. For charge balancing reasons, oxygen vacancies were created in the lattice of cobalt-doped BNT. These markedly enhanced the diffusivity. As a result, the sintering temperature of doped BNT decreased with increasing cobalt concentrations, and high final densities were achieved. However, in highly doped BNT sample swelling occurred at elevated temperatures of the sintering cycle. This phenomenon was attributed to evaporating oxygen caused by the valence transition of Co3+ to Co2+.
Up to 950 °C, BNT was found to densify via solid state sintering mechanisms. Above this temperature, a small amount of liquid phase was present, which probably formed from decomposing BNT because of a slight Ti-deficiency due to doping. Increased Bi vaporization from the melt above 1000 °C appeared to have stabilized sodium cobalt titanate, an additional secondary phase.
The rotation of the iso-lines in the kinetic field diagram of doped BNT was interpreted such that the activation energy for grain growth was higher than the activation energy for densification. Possible reasons are the solute-drag effect and the pinning of domain walls by secondary phase particles.
Both the depolarization temperature and the piezoelectric coefficient d33 decreased with increasing cobalt concentrations. The dielectric properties deteriorated as well. This was attributed to the high electrical conductivity of the doped samples, which prevented full poling.
Direct Force Measurements on the Colloidal Scale: From Modified Electrodes to Particle Manipulation
- In this thesis the interfacial surface forces and mechanical properties of thin films have been studied by the colloidal probe technique. One central point is the combination of direct force measurements with an electrochemical setup in order to tune interfacial properties of an electrode modified with an organic layer. In particular the adhesion and ion adsorption have been studied, which are ubiquitous phenomena in the colloid science, electrochemistry, and biology. Moreover, a novel technique has been developed to fabricate chemically and mechanically stable colloidal probes for atomic force microscopy (AFM). Additionally, the elastic properties of polyelectrolyte multilayer films were locally resolved under controlled humidity.
The adhesive behaviour of colloidal particles on modified electrodes has been studied by direct force measurements with a micrometre-sized silica probe attached to an AFM-cantilever. By controlling the external potential applied to the modified electrode by means of a potentiostat, separate adhesion contributions at the modification layers in electrolyte solution were quantified. In particular, to determine the influence of the terminating functional groups, gold electrodes modified with self-assembled monolayers (SAMs) terminated in non-ionizable groups were used. It has been demonstrated that electrostatic double-layer forces dominate the adhesion of colloidal particles on hydrophobic and hydrophilic interfaces. In contrast to hydrophilic interface, for hydrophobic one forces due to the solvent exclusion play a significant role and leads to an offset in the adhesive force, which otherwise can be compensated by the external potential. However, the electrocapillarity is of minor importance and can be neglected.
To quantify the ion adsorption at organic interfaces a novel approach was followed, which is based on direct force measurements with silica colloidal probes on SAM-modified electrodes in electrolyte solutions. By variation of applied potential and concentration of specifically adsorbed ions, given by the solution’s pH, the charging behaviour of hydrophilic SAM-OH and hydrophobic SAM-CH3 has been determined. In difference to electrokinetic techniques, direct force measurements allow to probe the full range of the diffuse layer. The analysis of the diffuse layer potential as a function of externally applied potential provides important information. In particular, the shift of the potential of zero charge (pzc) indicates on the specific ion adsorption in the Stern layer as it alters the charging behaviour of the electrode’s interface. It has been demonstrated that hydronium and hydroxide ions adsorb on both the hydrophobic and hydrophilic interfaces. However, the presence of the background electrolyte (KCl) does not shift pzc and thus its ions have no specific affinity towards the interfacial adsorption. The adsorption of hydronium and hydroxide ions is stronger on hydrophobic, than on hydrophilic interface. This is in agreement with theoretical studies. The simple three-capacitor model based on a Langmuir-type adsorption isotherm provides semi-quantitative description of observed dependence of the diffuse double layer potential on applied potential.
A new technique for colloidal probe preparation was developed. A great challenge for the force measurements with the AFM is to ensure the cleanliness, chemical and mechanical stability of the used probes. The approach is based on high-temperature sintering of micrometer-sized silica particles to AFM cantilever with enhanced contact area. Due to a “neck” formed by nanometer-sized particles the increased mechanical stability of colloidal probes was achieved, which has been quantitatively determined by lateral force spectroscopy. The implementation of sintering procedure for silica colloids allowed the development of the highly stable colloidal probes, whose surface properties could be renewed by heating.
Finally, the mechanical properties of polyelectrolyte multilayer films have been determined by nanoindentation as a function of relative humidity. For these series of measurements again a colloidal probe has been used. It has been demonstrated that films containing polyglutamic acid have Young’s modulus, which depends on humidity. The change of stiffness with ambient humidity has reversible character.
Design of Robust Heterogeneous Catalysts for Sustainable Chemistry
- Robust heterogeneous catalysts based on polymer derived non-oxide ceramics (SiC/SiCN) with integrated late transition metal (Ni, Pd) nanoparticles (NPs) were designed, characterized and tested for their catalytic potential. For the decoration of SiCN support with metal NPs, a molecular approach was applied which makes the use of amido metal complexes for the chemical modification of the preceramic polymer (commercially known as HTT 1800, Clariant Advanced Materials GmbH, Sulzbach, Germany) by the transfer of metal to its nitrogen functions. The modified polymer was transformed to an amorphous SiCN material containing metal NPs by controlled pyrolysis under an inert atmosphere. By following aforementioned approach, Cu@SiCN materials (non-porous) have already been developed in our research group.
In present thesis, attempts were made to fabricate porous SiCN/SiC materials with good accessibility of metal (Ni and Pd) NPs. Firstly, the synthesis of palladium containg SiCN materials by the pyrolysis of palladium modified polysilazane was attempted. It was found that during polymer to ceramic transformation, palladium reacts with silicon to form intermetallic palladium silicide particles. The materials were characterized (TGA, FT-IR, NMR, PXRD and TEM) and applied in catalytic hydrogenation reactions. The activity of the catalysts was found low because of the silicidation of metal and non-porous SiCN support.
The issues of the low porosity of SiCN ceramics and the formation of metal silicides were addressed in the synthesis of Ni@SiCN materials. Controlled pyroylsis of Ni modified polysilazane at 600°C provided microporous Ni@SiCN materials, whereas at 1100°C the formation of nickel silicides in non-porous SiCN matrix was observed. Ni@SiCN materials were characterized by solid state NMR, FT-IR, PXRD, TGA, N2-physisorption and TEM. Hyperpolarized 129Xe NMR was used to study the effect of nickel loading and annealing time on pore structure. The microporous materials showed good thermal stability and activity in selective hydrogenation of aryl acetylenes but as polymer to ceramic conversion was not complete at 600°C, the materials possessed low hydrothermal stability at higher temperatures due to the hydrolysis of Si-N bonds.
In order to replace Si-N bonds with more stable Si-C bonds, a commercial polycarbosilane was used to fabricate SiC materials with integrated Ni NPs by the pyrolysis of nanostructured polycarbosilane-block-polyethylene (PCS-b-PE) polymer. PCS-b-PE was synthesized by the reaction of PCS with PE-OH catalyzed by an amido nickel complex followed by its nanostructuring via microphase separation technique. The length of PE block affected the type of pores generated in SiC material and the synthesis of highly porous materials with micro-, meso- and hierarchical porosity was achieved. Ni@SiC materials were characterized by TGA, PXRD, N2-physisorption and TEM. Hierarchically porous Ni@SiC selectively cleaves aromatic C-O bond of aryl ethers in water and was found a reusable catalyst.
Lastly, controlled pyrolysis of palladium modified polysilzane provided nanoporous SiCN materials with very small and highly accessible Pd NPs. This shows the role of SiCN support whose nitrogen atoms have a stabilizing effect on small metal nanoparticles. Moreover, SiCN support ineracts nicely with the NPs leading to the prevention of their leaching. In general, NPs have agglomeration tendencies with increasing metal loading but in the case of Pd@SiCN, size of metal NPs remained small even with a palladium loading of 14 wt%. Pulse titration with hydrogen showed high accessibility of Pd. Pd@SiCN materials showed better activity than commercial Pd/C catalyst in oxidation of alcohols in the absence of air or oxygen with the evolution of hydrogen.
M@SiCN/SiC materials may find applications in sustainable production of chemicals and fuels from renewable sources, for instance, from lignocellulosic biomass.
Crystalline-core micelles based on triblock terpolymers with polyethylene middle blocks
- This thesis is focused on the crystallization-induced structure formation of polyethylene containing triblock terpolymers in organic solvents to surface-compartmentalized worm-like crystalline-core micelles (wCCMs). Obtaining profound knowledge of the parameters controlling the self-assembly process allowed the production of a variety of complex one-dimensional micellar architectures with many potential applications, such as adaptive surfactants.
At first, the basic parameters that control the crystallization-induced self-assembly were explored using symmetric polystyrene-block-polyethylene-block-poly(methyl methacrylate) (PS-b-PE-b-PMMA) triblock terpolymers and a PS-b-PE-b-PS triblock copolymer. In good solvents for the PE block, e.g. THF and toluene, the selective formation of wCCMs was observed over a wide range of concentration, applied crystallization temperature and polymer composition. Whereas wCCMs produced by PS-b-PE-b-PS showed a homogeneous PS corona, a patch-like compartmentalization of the corona was observed if the micelles were formed by PS-b-PE-b-PMMA. As THF shows equal solvent quality for both corona blocks, wCCMs with almost alternating PS and PMMA compartments of about 15 nm were observed in this solvent. However, if structure formation was conducted in bad solvents for PE, such as dioxane or dimethylacetamide, spherical micelles with amorphous PE cores were formed already before crystallization. Hence, the subsequent crystallization of PE resulted in spherical CCMs with a patchy or a homogeneous corona depending on the used triblock. These findings allow the highly selective production of stable spherical or worm-like CCMs from the same polymer.
As the corona structure of the patchy micelles self-assembled from triblock terpolymers was mainly deduced from transmission electron microscopy (TEM) performed on dried samples, a small-angle neutron scattering (SANS) study was performed in order to elucidate the morphology in solution. Therefore a partly deuterated triblock terpolymer was synthesized and measured at different contrasts to allow the selective detection of the different corona compartments. The resulting SANS curves could be interpreted using a form factor model for core-shell cylinders with alternating PS and PMMA hemishells including interparticle interactions, thus validating the TEM observations. Notably, Janus-type and patchy cylinders can be clearly distinguished using the applied form factor model.
Moreover, the controlled formation of wCCMs with tunable corona composition and structure was achieved using the cocrystallization of different triblock copolymers. Via random cocrystallization of PS-b-PE-b-PMMA and PS-b-PE-b-PS the corona morphology could be tuned continuously from a mixed corona at low PMMA content over spherical PMMA patches of increasing number and size to alternating PS and PMMA patches. This approach allows to manufacture wCCMs with predefined corona structure omitting the need to synthesize a new tailor-made triblock terpolymer for every desired morphology.
By establishing the controlled crystallization-driven self-assembly of triblock terpolymers with PE middle blocks, it was further possible to prepare wCCMs with predefined average lengths up to 500 nm and length polydispersities as low as Lw/Ln = 1.1. Here, self-assembled spherical CCMs of PS-b-PE-b-PS were used as seeds for the controlled growth of PS-b-PE-b-PS unimers. Upon further addition of PS-b-PE-b-PMMA unimers these grew epitaxially onto the preexisting wCCMs, resulting in triblock co-micelles that consisted of middle blocks with a homogeneous PS corona and outer blocks with alternating PS/PMMA compartments. These structures represent not only the first block co-micelles including blocks with a patchy corona, but also the first ones produced from purely organic block copolymers.
In view of application, the ability of patchy wCCMs formed by PS-b-PE-b-PMMA to stabilize interfaces was investigated using pendant-drop tensiometry. The observed reduction of the interfacial tension at the toluene/water interface was significantly higher than that of comparable triblock terpolymer single chains and that of wCCMs with a homogeneous PS corona. Interestingly, the obtained equilibrium interfacial tension equaled that of Janus cylinders with similar dimensions. To explain this unexpected finding the corona chains were proposed to adapt to the interface via selective collapse and shielding of the incompatible part of the corona chains. Studying wCCMs formed by several triblock terpolymers with different compositions, the interfacial activity was found to increase with increasing overall length of the corona chains, and to a certain extent with the molar fraction of PS units in the corona.
Coarse-grained Modeling of Protein Dynamics using Elastic Network Models
- Dynamics is crucial for the functioning of biological macromolecules. Because of severe limitations in studying protein dynamics experimentally or with all-atom simulations, coarse-grained methods, especially elastic network models (ENMs), are frequently employed. In the last years, studies on various proteins showed that ENMs reliably reproduce experimental data, despite the simplified protein representation and the purely harmonic potential function. This work on two proteins with very different dynamical properties highlights the remarkable success of ENMs and shows which kind of questions can be answered using coarse-grained methods.
The allosteric enzyme aminoglycoside phosphotransferase(3')-IIIa (APH), which confers resistance against a broad range of aminoglycoside antibiotics to pathogenic bacteria, drastically changes its flexibility upon binding of substrates, but without changing its average conformation. In contrast, the homotrimeric vesicular stomatitis virus glycoprotein G (VSV-G), which triggers the pH-dependent fusion of viral and host membrane, undergoes a large structural rearrangement. A striking difference between the two proteins is their shape. VSV-G contains weakly constrained protein segments, the fusion loops, which can undergo large-scale motions at low energetic cost, whereas APH is not obviously arranged into different protein segments. Nevertheless, ENM calculations show that also APH consists of independently moving segments with correlated internal motion, so-called dynamic domains. The concept of dynamic domains can explain the differential effects of ligand binding on the dynamics of APH.
The first chapter of this thesis describes how experimental evidence for the importance of dynamics successively replaced the former idea of static proteins, and explains the dynamic basis of ligand binding, allostery and conformational changes. In the second chapter, theoretical methods for the analysis of protein dynamics are introduced, with emphasis on the ENM-based methods used in my studies. The studies are summarized in the third chapter. In the study on APH, I employ the Gaussian network model to analyze the ligand-dependent dynamics, the broad substrate specificity and the perturbation-sensitivity of the ligand binding sites. In a second study, ENM-based as well as all-atom molecular dynamics simulations are used to analyze the conformational change of VSV-G. Both approaches detect the fusion loops of VSV-G as most flexible parts of the protein, and thus as most likely starting point for the structural rearrangement, but only the all-atom model can generate deviations from the average structure at low pH. The last study describes the implementation and application of a dynamic domain assignment method, called CovarDom, which is based on covariances of residue fluctuations. Calculation of dynamic domains for a large protein set demonstrates the general applicability of CovarDom.