Application of Computational Molecular Biophysics to Problems in Bacterial Chemotaxis

The combination of physics, biology, chemistry, and computer science constitutes the promising field of computational molecular biophysics. This field studies the molecular properties of DNA, protein lipids and biomolecules using computational methods. For this dissertation, I approached four problems involving the chemotaxis pathway, the set of proteins that function as the navigation system of bacteria and lower eukaryotes. In the first chapter, I used a special-purpose machine for molecular dynamics simulations, Anton, to simulate the signaling domain of the chemoreceptor in different signaling states for a total of 6 microseconds. Among other findings, this study provides enough evidence to propose a novel molecular mechanism for the kinase activation by the chemoreceptor and reconcile previously conflicting experimental data. In the second chapter, my molecular dynamics studies of the scaffold protein cheW reveals the existence and role of a conserved salt-bridge that stabilizes the relative position of the two binding sites in the chew surface: the chemoreceptor and the kinase. The results were further confirmed with NMR experiments performed with collaborators at the University of California in Santa Barbara, CA. In the third chapter, my colleagues and I investigate the quality of homology modeled structures with cheW protein as a benchmark. By subjecting the models to molecular dynamics and Monte Carlo simulations, we show that the homology models are snapshots of a larger ensemble of conformations very similar to the one generated by the experimental structures. In the fourth chapter, I use bioinformatics and basic mathematical modeling to predict the specific chemoreceptor(s) expressed in vivo and imaged with electron cryo tomography (ECT) by our collaborators at the California Institute of Technology. The study was essential to validate the argument that the hexagonal arrangement of transmembrane chemoreceptors is universal among bacteria, a major breakthrough in the field of chemotaxis. In summary, this thesis presents a collection of four works in the field of bacterial chemotaxis where either methods of physics or the quantitative approach of physicists were of fundamental importance for the success of the project

Computational Modeling of Protein Kinases: Molecular Basis for Inhibition and Catalysis

Protein kinases catalyze protein phosphorylation reactions, i.e. the transfer of the γ-phosphoryl group of ATP to tyrosine, serine and threonine residues of protein substrates. This phosphorylation plays an important role in regulating various cellular processes. Deregulation of many kinases is directly linked to cancer development and the protein kinase family is one of the most important targets in current cancer therapy regimens. This relevance to disease has stimulated intensive efforts in the biomedical research community to understand their catalytic mechanisms, discern their cellular functions, and discover inhibitors. With the advantage of being able to simultaneously define structural as well as dynamic properties for complex systems, computational studies at the atomic level has been recognized as a powerful complement to experimental studies. In this work, we employed a suite of computational and molecular simulation methods to (1) explore the catalytic mechanism of a particular protein kinase, namely, epidermal growth factor receptor (EGFR); (2) study the interaction between EGFR and one of its inhibitors, namely erlotinib (Tarceva); (3) discern the effects of molecular alterations (somatic mutations) of EGFR to differential downstream signaling response; and (4) model the interactions of a novel class of kinase inhibitors with a common ruthenium based organometallic scaffold with different protein kinases. Our simulations established some important molecular rules in operation in the contexts of inhibitor-binding, substrate-recognition, catalytic landscapes, and signaling in the EGFR tyrosine kinase. Our results also shed insights on the mechanisms of inhibition and phosphorylation commonly employed by many kinases

Alternative Strategies To Inhibit Lysine Methyltransferases And Deubiquitinases In Human Cancers

X-ray crystallography is the gold standard method for imagining macromolecules to atomic resolution. Three dimensional data is central to understanding the molecular mechanism how DNA, RNA and proteins function in biological events. Structural insights into these events provide a molecular window to visualize how biological molecules influence human health. Visualizing the architecture of these molecules set the stage for rational and selective drug design. The following dissertation utilizes biochemical and biophysical tools, including X-ray crystallography, to shed light on poorly understood mechanisms related to SMYD2 activity and regulation, USP10 architecture and function, and PDZ-RhoGEF dimerization. SMYD2 is one member of the SET and MYND domain-containing protein (SMYD) family known to play key roles in cardiac function and development, innate immunity and tumorigenesis. While the molecular pathways involved in these events have been fairly described, the molecular mechanism of substrate recognition and bilobal changes have not. In this dissertation, I review the structure and function of SMYD protein family. In addition, I demonstrate SMYD2 and SMYD3 can exist in open and closed conformations based on X-ray crystallography, small angle X-ray scattering, and molecular dynamic simulations data. Lastly, I revealed a novel binding site in SMYD2 that appears to be the first recognition site for SMYD methylation clients. USP10 is one member of the ubiquitin-specific protease family important for DNA repair and apoptosis by recycling cytosolic p53. However, in the mutant p53 environment, USP10 serves as an oncogene; thereby promoting mutant p53-dependent cancer cell growth. Additional studies found related USP10 oncogene roles in other cancers. Unfortunately the biochemistry and structure of USP10 hasn’t been thoroughly explored. My dissertation aims to understand the biochemistry and architecture of the catalytic domain of USP10 along with reported USP10 inhibitors which would be valuable for future studies to probe USP10 function and inhibition. PDZ-RhoGEF is one member of the Rho guanine exchange factors (RhoGEF) family important for modulating Rho activity and actin-based cytoskeleton remodeling. PDZ-RhoGEF possesses a PDZ domain known for complexing with the cytoplasmic tail of Plexin B serving as modulator for downstream signaling factors. In our study, we found PDZ-RhoGEF complexes with the Interleukin-8 chemokine receptor, CXCR2. This novel interaction hasn’t been reported before, and in my dissertation, I solved the crystal structure of PDZ-RhoGEF in complex with the PDZ motif of CXCR2. Unexpectedly, we identified a disulfide bond linking two PDZ-RhoGEF molecules. This disulfide bond was previously reported to be important for promoting PDZ-ligand binding between PDZ-RhoGEF and Plexin B2 peptides. Here, I describe the architecture of the disulfide-linked PDZ domain of PDZ-RhoGEF in complex with two CXCR2 PDZ-motifs

Novel mechanisms of G-protein-coupled receptors functions: AT1 angiotensin receptor acts as a signaling hub and focal point of receptor cross-talk

AT1 angiotensin receptor (AT1R), a prototypical G protein-coupled receptor (GPCR), is the main receptor, which mediates the effects of the renin-angiotensin system (RAS). AT1R plays a crucial role in the regulation of blood pressure and salt-water homeostasis, and in the development of pathological conditions, such as hypertension, heart failure, cardiovascular remodeling, renal fibrosis, inflammation, and metabolic disorders. Stimulation of AT1R leads to pleiotropic signal transduction pathways generating arrays of complex cellular responses. Growing amount of evidence shows that AT1R is a versatile GPCR, which has multiple unique faces with distinct conformations and signaling properties providing new opportunities for functionally selective pharmacological targeting of the receptor. Biased ligands of AT1R have been developed to selectively activate the β-arrestin pathway, which may have therapeutic benefits compared to the conventional angiotensin converting enzyme inhibitors and angiotensin receptor blockers. In this review, we provide a summary about the most recent findings and novel aspects of the AT1R function, signaling, regulation, dimerization or oligomerization and its cross-talk with other receptors, including epidermal growth factor (EGF) receptor, adrenergic receptors and CB1 cannabinoid receptor. Better understanding of the mechanisms and structural aspects of AT1R activation and cross-talk can lead to the development of novel type of drugs for the treatment of cardiovascular and other diseases. © 201

Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases

The emerging structural information about allosteric kinase complexes and the growing number of allosteric inhibitors call for a systematic strategy to delineate and classify mechanisms of allosteric regulation and long-range communication that control kinase activity. In this work, we have investigated mechanistic aspects of long-range communications in ABL and EGFR kinases based on the results of multiscale simulations of regulatory complexes and computational modeling of signal propagation in proteins. These approaches have been systematically employed to elucidate organizing molecular principles of allosteric signaling in the ABL and EGFR multi-domain regulatory complexes and analyze allosteric signatures of the gate-keeper cancer mutations. We have presented evidence that mechanisms of allosteric activation may have universally evolved in the ABL and EGFR regulatory complexes as a product of a functional cross-talk between the organizing αF-helix and conformationally adaptive αI-helix and αC-helix. These structural elements form a dynamic network of efficiently communicated clusters that may control the long-range interdomain coupling and allosteric activation. The results of this study have unveiled a unifying effect of the gate-keeper cancer mutations as catalysts of kinase activation, leading to the enhanced long-range communication among allosterically coupled segments and stabilization of the active kinase form. The results of this study can reconcile recent experimental studies of allosteric inhibition and long-range cooperativity between binding sites in protein kinases. The presented study offers a novel molecular insight into mechanistic aspects of allosteric kinase signaling and provides a quantitative picture of activation mechanisms in protein kinases at the atomic level.This work was partly supported by funding from The University of Kansas

The Structural and Functional Study of GIT1 Paxillin Binding Domain

The G protein coupled receptor (GPCR)-kinase (GRK) interacting protein 1 (GIT1) is a multidomain protein that plays an important role in cell adhesion, motility, cytoskeletal remodeling, and membrane trafficking. GIT1 mediates the localization of p21-activated kinase (PAK) and PAK-interactive exchange factor (PIX) to focal adhesions, and its activation is regulated by the interaction between its C terminal paxillin-binding domain (PBD) and the LD motifs of paxillin. In this dissertation, we determined the solution structure of rat GIT1 PBD by nuclear magnetic resonance (NMR) spectroscopy. The PBD folds into a four-helix bundle, which is structurally similar to the focal adhesion targeting (FAT) domain and the vinculin tail (Vt) domain. The PBD is more stable than the FAT domain and there is no evidence of helix 1 swapping. Previous studies showed that GIT1 interacts with paxillin through the LD4 motif. However, studies in this dissertation demonstrated that in addition to the LD4 motif, the GIT1 PBD can also bind to the paxillin LD2 motif; and both LD2 and LD4 motifs competitively target the same site on the PBD surface. This dissertation also probed the function of paxillin splice variants by comparing their interaction with GIT1 PBD. It seems the paxillin isoforms did not play an important role in determining the affinity to GIT1. We also revealed that paxillin S272 phosphorylation does not influence GIT1 PBD binding in vitro. These results are in agreement with the notion that phosphorylation of paxillin S272 plays an essential role in regulating focal adhesion turnover.This dissertation also computationally derived the complex structures of GIT1 PBD bound with either LD2 peptide or LD4 peptide, based on the experimental binding site information. The LD2 and LD4 peptides bound to GIT1 PBD in a manner similar to the crystal structure of FAT-LD2 complex. The complex structures visualized the reason why both LD2 and LD4 can bind to the same GIT1 binding site. It also addressed the specificity problem in determining paxillin binding to GIT1 versus FAK. Our finding reconciles the controversial observations of earlier studies and provides a clearer picture of focal adhesion regulation. The structural studies of GIT1 PBD presented in this dissertation shed more light on the understanding of GIT functions. The novel findings also allow us to propose a working model regarding FA disassembly

Role of a highly conserved region of the NF-kappaB essential modulator in its scaffolding function

Scaffold proteins facilitate many aspects of intracellular signaling. These proteins can regulate two or more proteins in the same pathway, or coordinate signaling from multiple pathways. Scaffold proteins are therefore key control points for the flux of signaling and play essential roles in biological systems. There are four possible mechanisms by which scaffold proteins achieve activation and propagate signaling: 1) rigid protein binding between two or more proteins to co-localize binding partners, 2) ligand-induced activation such as may result from a conformational change, 3) disorder-to-order transition where the scaffold protein folds as a result of a protein-protein interaction, and 4) dynamic processes such as phosphorylation. The scaffold protein NF-κB essential modulator (NEMO) functions via ligand-induced activation and serves as the key control point for canonical NF-κB signaling. The work described in this thesis investigates the role of a previously uncharacterized domain within NEMO that is required for function, which we term the Intervening Domain (IVD). Bioinformatic analysis reveals a high level of sequence conservation across species within this domain. Conformational changes following ligand binding are observed for NEMO and these changes require conserved sequences in the IVD. Additionally, a functional IVD is shown to increase the binding affinity of NEMO for IKKβ, enhance the thermal stability of NEMO, and is required to propagate NF-κB signaling in cells. A fluorescence-based assay is also developed to characterize the formation of a complex composed of NEMO, a zinc ion, and IκBα. A separate fluorescence-based assay is developed to measure IKK activity and is used to determine that NEMO alone or in the presence of linear tetraubiquitin does not enhance the rate of IKKβ phosphorylation of an IκBα-derived peptide. Furthermore, a number of organic small molecules and macrocycles are screened against the NEMO-IKKβ interaction. One small molecule was validated as an inhibitor and its biophysical properties and inhibition kinetics are described in this thesis. These analyses represent the first characterization of a highly conserved domain required for the function of the key control point in NF-κB signaling. The IVD domain of NEMO could be targeted for development of an allosteric effector for therapeutic discovery

Unveiling the Molecular Mechanisms Regulating the Activation of the ErbB Family Receptors at Atomic Resolution through Molecular Modeling and Simulations

The EGFR/ErbB/HER family of kinases contains four homologous receptor tyrosine kinases that are important regulatory elements in key signaling pathways. To elucidate the atomistic mechanisms of dimerization-dependent activation in the ErbB family, we have performed molecular dynamics simulations of the intracellular kinase domains of the four members of the ErbB family (those with known kinase activity), namely EGFR, ErbB2 (HER2) and ErbB4 (HER4) as well as ErbB3 (HER3), an assumed pseudokinase, in different molecular contexts: monomer vs. dimer, wildtype vs. mutant. Using bioinformatics and fluctuation analyses of the molecular dynamics trajectories, we relate sequence similarities to correspondence of specific bond-interaction networks and collective dynamical modes. We find that in the active conformation of the ErbB kinases (except ErbB3), key subdomain motions are coordinated through conserved hydrophilic interactions: activating bond-networks consisting of hydrogen bonds and salt bridges. The inactive conformations also demonstrate conserved bonding patterns (albeit less extensive) that sequester key residues and disrupt the activating bond network. Both conformational states have distinct hydrophobic advantages through context-specific hydrophobic interactions. The inactive ErbB3 kinase domain also shows coordinated motions similar to the active conformations, in line with recent evidence that ErbB3 is a weakly active kinase, though the coordination seems to arise from hydrophobic interactions rather than hydrophilic ones. We show that the functional (activating) asymmetric kinase dimer interface forces a corresponding change in the hydrophobic and hydrophilic interactions that characterize the inactivating interaction network, resulting in motion of the αC-helix through allostery. Several of the clinically identified activating kinase mutations of EGFR act in a similar fashion to disrupt the inactivating interaction network. Our molecular dynamics study reveals the asymmetric dimer interface helps progress the ErbB family through the activation pathway using both hydrophilic and hydrophobic interaction. There is a fundamental difference in the sequence of events in EGFR activation compared with that described for the Src kinase Hck

Structure-Functional Prediction and Analysis of Cancer Mutation Effects in Protein Kinases

A central goal of cancer research is to discover and characterize the functional effects of mutated genes that contribute to tumorigenesis. In this study, we provide a detailed structural classification and analysis of functional dynamics for members of protein kinase families that are known to harbor cancer mutations. We also present a systematic computational analysis that combines sequence and structure-based prediction models to characterize the effect of cancer mutations in protein kinases. We focus on the differential effects of activating point mutations that increase protein kinase activity and kinase-inactivating mutations that decrease activity. Mapping of cancer mutations onto the conformational mobility profiles of known crystal structures demonstrated that activating mutations could reduce a steric barrier for the movement from the basal low activity state to the active state. According to our analysis, the mechanism of activating mutations reflects a combined effect of partial destabilization of the kinase in its inactive state and a concomitant stabilization of its active-like form, which is likely to drive tumorigenesis at some level. Ultimately, the analysis of the evolutionary and structural features of the major cancer-causing mutational hotspot in kinases can also aid in the correlation of kinase mutation effects with clinical outcomes