Exploring the boundaries of molecular modeling : a study of nanochannels and transmembrane proteins

Many interesting physical and biological phenomena can be investigated using molecular modeling techniques, either theoretically or by using computer simulation methods, such as molecular dynamics and Monte Carlo simulations. Due to the increasing power of computer processing units, these simulation methods allowed over the last decades for the dramatic increase in knowledge of the behavior of systems at the molecular level. In the first part of this thesis the foundations of molecular modeling techniques are revisited. Empirical force fields and the physical background between thermodynamics and individual particles are discussed. The applicability of molecular modeling techniques is shown by two representative cases. First, the molecular dynamics simulation method is used to understand the dynamics of specific proteins at the molecular level. This is important, because drug design efforts are increasingly laborious, especially with the paucity of available structural information. Therefore, computational methods are helpful in predicting the structure of proteins, and, more importantly, to predict conformational dynamics leading to protein activation. To that end a specific asthma-related protein, the beta2-adrenergic receptor, is investigated in atomistic detail together with the molecules that can bind to the protein to cause activation or inhibition. Clearly, molecular dynamics simulations are an important tool to provide further knowledge on the activation pathway of this protein. Although these all-atom simulations give some insight on the dynamics, the computational demand does not allow for systems much larger than several nanometers or time scales exceeding several nanoseconds. An attempt to overcome these problems is presented by the development of a coarse grained description of the transmembrane proteins. Because coarse graining reduces the number of degrees of freedom, the computational demands decrease, and larger systems can be investigated. However, to maintain the specific characteristics of transmembrane proteins, the general force field used in molecular modeling techniques needs to be extended with hydrogen bonding capabilities and helical backbone stabilization. This new coarse grained model is applicable to transmembrane proteins, and is used to investigate two independent cases: WALP-peptides and antimicrobial peptides. The first serve as a model system for both experiments and theory to investigate the interaction between transmembrane peptides and lipid membranes, whereas the latter are antibiotics whose pore-forming capacities are of great interest to act as target-specific drug candidates. From the molecular dynamics simulations of the WALP-peptides it is shown that the apparent hydrophobic mismatch between peptide and membrane can be resolved by two mechanisms (membrane thickness adaptation and peptide tilting) and that these two mechanisms occur sequential and not in parallel. In the case of the antimicrobial peptides it is shown that many of the orientations found with the molecular simulation techniques are in agreement with experimental observations. The second case to show the applicability of the molecular modeling techniques is that of the heat transfer characteristics of gas flows in nanochannels. Understanding these characteristics is important, because these very small channels are considered to be promising devices to locally cool systems (such as computer processing units) or to be used in lab-on-chip devices for at home medical diagnostics. Thus, understanding the interactions between the channel walls and the gas flow is of great importance. Unfortunately, the computational cost involved in simulating the solid wall, currently restrains the size of the systems that can be investigated using molecular dynamics simulations. Therefore, instead of the explicit modeling of the solid wall, appropriate boundary conditions are used, such as wall potentials or stochastic models. Both of these boundary conditions are examined in great detail and a new wall potential is presented. Also the investigations of a specific case of a channel with platinum walls with a noble gas (argon or xenon) in between allows to introduce a new method to compute an important heat transfer determining parameter. Furthermore, it is shown that both boundary conditions have their benefits and drawbacks, and that the use of either one depends heavily on the application under consideration. Both cases used to show the applicability of molecular modeling techniques, although very different from each other, indicate the importance of particle simulation methods. Investigating the interactions at the molecular level, and the development of new models allows for an even better understanding of underlying molecular processes

Network measures for protein folding state discrimination

Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there is not a first-principle model to explain this different behavior. We exploit the network properties of protein structures by introducing novel observables to address the problem of classifying the different types of folding kinetics. These observables display a plain physical meaning, in terms of vibrational modes, possible configurations compatible with the native protein structure, and folding cooperativity. The relevance of these observables is supported by a classification performance up to 90%, even with simple classifiers such as discriminant analysis

Simulations of Chemical Catalysis

This dissertation contains simulations of chemical catalysis in both biological and heterogeneous contexts. A mixture of classical, quantum, and hybrid techniques are applied to explore the energy profiles and compare possible chemical mechanisms both within the context of human and bacterial enzymes, as well as exploring surface reactions on a metal catalyst. A brief summary of each project follows. Project 1 — Bacterial Enzyme SpvC The newly discovered SpvC effector protein from Salmonella typhimurium interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (MAPKs) with a -elimination mechanism. The dynamics of the enzyme substrate complex of the SpvC effector is investigated with a 3.2 ns molecular dynamics simulation, which reveals that the phosphorylated peptide substrate is tightly held in the active site by a hydrogen bond network and the lysine general base is positioned for the abstraction of the alpha hydrogen. The catalysis is further modeled with density functional theory (DFT) in a truncated active-site model at the B3LYP/6-31 G(d,p) level of theory. The truncated model suggested the reaction proceeds via a single transition state. After including the enzyme environment in ab initio QM/MM studies, it was found to proceed via an E1cB-like pathway, in which the carbanion intermediate is stabilized by an enzyme oxyanion hole provided by Lys104 and Tyr158 of SpvC. Project 2 — Human Enzyme CDK2 Phosphorylation reactions catalyzed by kinases and phosphatases play an indispensable role in cellular signaling, and their malfunctioning is implicated in many diseases. Ab initio quantum mechanical/molecular mechanical studies are reported for the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase, CDK2. Our results suggest that an active-site Asp residue, rather than ATP as previously proposed, serves as the general base to activate the Ser nucleophile. The corresponding transition state features a dissociative, metaphosphate-like structure, stabilized by the Mg(II) ion and several hydrogen bonds. The calculated free-energy barrier is consistent with experimental values. Project 3 — Bacterial Enzyme Anthrax Lethal Factor In this dissertation, we report a hybrid quantum mechanical and molecular mechanical study of the catalysis of anthrax lethal factor, an important first step in designing inhibitors to help treat this powerful bacterial toxin. The calculations suggest that the zinc peptidase uses the same general base-general acid mechanism as in thermolysin and carboxypeptidase A, in which a zinc-bound water is activated by Glu687 to nucleophilically attack the scissile carbonyl carbon in the substrate. The catalysis is aided by an oxyanion hole formed by the zinc ion and the side chain of Tyr728, which provide stabilization for the fractionally charged carbonyl oxygen. Project 4 — Methanol Steam Reforming on PdZn alloy Recent experiments suggested that PdZn alloy on ZnO support is a very active and selective catalyst for methanol steam reforming (MSR). Plane-wave density functional theory calculations were carried out on the initial steps of MSR on both PdZn and ZnO surfaces. Our calculations indicate that the dissociation of both methanol and water is highly activated on \ufb02at surfaces of PdZn such as (111) and (100), while the dissociation barriers can be lowered significantly by surface defects, represented here by the (221), (110), and (321) faces of PdZn. The corresponding processes on the polar Zn-terminated ZnO(0001) surfaces are found to have low or null barriers. Implications of these results for both MSR and low temperature mechanisms are discussed

Scoring predictive models using a reduced representation of proteins: model and energy definition

BACKGROUND: Reduced representations of proteins have been playing a keyrole in the study of protein folding. Many such models are available, with different representation detail. Although the usefulness of many such models for structural bioinformatics applications has been demonstrated in recent years, there are few intermediate resolution models endowed with an energy model capable, for instance, of detecting native or native-like structures among decoy sets. The aim of the present work is to provide a discrete empirical potential for a reduced protein model termed here PC2CA, because it employs a PseudoCovalent structure with only 2 Centers of interactions per Amino acid, suitable for protein model quality assessment. RESULTS: All protein structures in the set top500H have been converted in reduced form. The distribution of pseudobonds, pseudoangle, pseudodihedrals and distances between centers of interactions have been converted into potentials of mean force. A suitable reference distribution has been defined for non-bonded interactions which takes into account excluded volume effects and protein finite size. The correlation between adjacent main chain pseudodihedrals has been converted in an additional energetic term which is able to account for cooperative effects in secondary structure elements. Local energy surface exploration is performed in order to increase the robustness of the energy function. CONCLUSION: The model and the energy definition proposed have been tested on all the multiple decoys' sets in the Decoys'R'us database. The energetic model is able to recognize, for almost all sets, native-like structures (RMSD less than 2.0 Å). These results and those obtained in the blind CASP7 quality assessment experiment suggest that the model compares well with scoring potentials with finer granularity and could be useful for fast exploration of conformational space. Parameters are available at the url:

Aspects of biomacromolecular dynamics at different scales

Biological functions of biomacromolecules are often indispensably linked to their internal dynamics. To investigate the dynamic nature of biomolecules, molecular dynamics (MD) simulation offers unique advantages by providing high spatial and temporal resolution over orders of magnitude in time- and length scales. Here, simulations at two different scales are used to investigate different aspects of biomolecular dynamics. At the atomistic scale, the first study investigates the relationship between the axial methyl group order parameter and the corresponding entropy in protein side chains. Three classes of methyl group are characterized based on the methyl group’s “topological distance” from the backbone (that is the number of bonds between the methyl group axis and the closest backbone atom) even when direct effects of the topological distance are removed. This distinction implies that methyl groups at the same topological position share similar nonbonded environments. Furthermore, consideration of these classes of methyl group improves the accuracy of entropy-estimates based upon changes in order parameter. The second study investigates the deconstruction of crystalline cellulose, a problem relevant to bioenergy research. The large size of crystalline cellulose together with the associated long-time dynamics exceeds the capabilities of atomistic simulation. Thus, a residue-scale, coarse-grained model of cellulose is calculated using the REACH (Realistic Extension Algorithm via Covariance Hessian) method. The model is successfully validated against experiment using Young’s moduli and the velocity of sound. The coarse-grained analysis of the cellulose fibril suggests that the intrinsic dynamics facilitates deconstruction of the crystalline cellulose fibril from the hydrophobic surface. Both applications share the same concept of approach (that is, computational modeling and simulation at an appropriate scale), which reveals key insights into biomolecules by investigating their dynamic behavior

Multiscale Molecular Dynamics Simulations of Histidine Kinase Activity

Zweikomponentensysteme (TCS), bestehend aus einer Sensorhistidinkinase (HK) und einem Antwortregulationsprotein, sind Schlüsselbausteine in bakteriellen Signaluebertragungsmechanismen. Die Fähigkeit von Bakterien auf eine breite Vielfalt von chemischen und physikalischen Stimuli angemessen zu reagieren ist ausschlaggebend für ihr Überleben. Es ist daher nicht überraschend, dass TCS zu den meistuntersuchten bakteriellen Proteinsystemen gehört. Sensorhistidinkinasen sind typischerweise in die Zellmembran integrierte, homodimere Proteine bestehend aus mehreren Domänen. Reizwahrnehmung an der Sensordomäne von HK löst eine Reihe von großskaligen Konformationsübergangen entlang der Domänen aus. Während sich die strukturellen Eigenschaften von verschiedenen HKs unterscheiden können, erhalten sie alle einen katalytischen ATP-bindenden Kern (CA) und dimerisierende Histidinphosphotransferdomänen (DHp). Während der Signalkaskade nimmt der Kern eine asymmetrische Konformation an, sodass die Kinase an einem der Protomere aktiv ist und die der anderen inaktiv. Das ermöglicht es dem ATP in einer der CA-Domänen seine $\gamma$-Phosphatgruppe an das Histidin der DHp abzugeben. Diese Phosphorylgrouppe wird anschließend an das Antwortregulationsprotein weitergegeben, die eine angemessene Reaktion der Zelle veranlasst. In der vorliegenden Arbeit untersuche ich die Konformationsdynamik des Kinasekerns mithilfe von Molekulardynamiksimulationen (MD). Der Fokus der Arbeit liegt auf zwei verschiedenen HKs: WalK und CpxA. Wegen der Größe der Systeme und den erforderlichen biologischen Zeitskalen, ist es nicht möglich die relevanten Konformationsübergänge in klassischen MD-Simulationen zu berechnen. Um dieses Problem zu umgehen, verwende ich ein strukturbasiertes Modell mit paarweisen harmonischen Potentialen. Diese Näherung erlaubt es, den Übergang zwischen dem inaktiven und den aktiven Zustand mit wesentlich geringerem rechnerischen Aufwand zu untersuchen. Nachdem ich das System mithilfe dieses vereinfachten Modells erkundet habe, benutze ich angereicherte Stichprobenverfahren mit atomistischen Modellen um detailliertere Einsichten in die Dynamik zu gewinnen. Die Ergebnisse in dieser Arbeit legen nahe, dass das Verhalten der einzelnen Unterdomänen des Kinasekerns eng miteinander gekoppelt ist

Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide