Dynamics and Regulation of Cytoskeletal Proteins

In this dissertation, I apply molecular dynamics (MD) simulations to improve our understanding of the dynamics, and hence, function and regulation of cytoskeletal proteins. Microtubules and kinesin motor proteins play a critical role in the cytoskeleton of the cell. They provide structural support, facilitate cellular transport, and are involved in beating of cilia and flagella, and in separation of chromosomes during the cell cycle. The importance of tubulin as a vital therapeutic target is exemplified by the widely prescribed paclitaxel (Taxol), an anti-cancer drug that prevents cancer cells from undergoing cell division by arresting tubulin dynamics. Furthermore, the importance of understanding the structural, dynamical, and functional aspects of kinesin motor domains and their modifications is demonstrated by efforts in developing small-molecule inhibitors as antimitotic therapeutic agents in various cancers. However, despite strong conservation of the motor domain across the kinesin superfamily, how various kinesins have tailored their motility characteristics to best meet their functional needs in cells remains unclear. Detailed comparison of structures from large heterogeneous protein families, such as kinesin motors, can inform on structural dynamic mechanisms critical for protein function including ligand binding, enzymatic catalysis, allosteric regulation and bimolecular recognition. However, existing tools for quantitative analyses of their sequence, structure and dynamics often require significant computational expertise and typically remain accessible only to expert users with relevant programming skills. In the first section of my dissertation, I describe the development of Bio3D-web, a free and open-source online application for interactive investigation of protein sequence-structure-dynamic relationships. Bio3D-web requires no programming knowledge and thus decreases the entry barrier to performing advanced comparative structural bioinformatics analyses. In the second part, I discuss a method for analyzing experimental structures and dynamical data generated with MD simulations. The ensemble distance difference matrix method (eDDM) analyzes changes in residue-residue distances in protein structures and dynamical data to identify residues critical for protein regulation and function. I apply eDDM to three families of kinesin motor proteins in the following case studies: First, I elucidate the effect of a posttranslational modification in kinesin 5 mitotic motor Eg5. I show that acetylation of residue K146 in Eg5 alters its mechanochemical properties, wherein it acts as a “brake” during spindle separation in cells during mitosis. Second, I identify residues critical for force generation in kinesin 1 transport motor KIF5C. Mutating these residues in two important structural elements—A5G and S8G in the cover strand and N334A in the neck linker—severely cripple the ability of motors in ensemble to generate force during intracellular transport. Third, I characterize the allosteric effects of disease-associated variants in kinesin 3 neuronal transport motor KIF1A. KIF1A-associated neurological disorder (KAND) is associated with cognitive disability, spasticity, and cerebellar atrophy, typically with a progressive course. In the third part, I highlight the divergent mechanism of tubulin polymerization in C. elegans. Through comparative analysis of MD simulations of C. elegans and B. taurus tubulin dimers, I found that sequence changes in the C. elegans tubulin lead to additional secondary structure formation in the lateral contact loops, and this changes the polymerization behavior as well as the structure of the microtubule. Finally, I also map the inter-conformer relationships of experimentally determined structures of tubulin through principal component analysis (PCA), enabling comparison of the intrinsic dynamics of tubulin heterodimers, such as different isoforms, nucleotide states, and disease-associated mutations.PHDBioinformaticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/153354/1/jari_1.pd

Altered chemomechanical coupling causes impaired motility of the kinesin-4 motors KIF27 and KIF7.

Kinesin-4 motors play important roles in cell division, microtubule organization, and signaling. Understanding how motors perform their functions requires an understanding of their mechanochemical and motility properties. We demonstrate that KIF27 can influence microtubule dynamics, suggesting a conserved function in microtubule organization across the kinesin-4 family. However, kinesin-4 motors display dramatically different motility characteristics: KIF4 and KIF21 motors are fast and processive, KIF7 and its Drosophila melanogaster homologue Costal2 (Cos2) are immotile, and KIF27 is slow and processive. Neither KIF7 nor KIF27 can cooperate for fast processive transport when working in teams. The mechanistic basis of immotile KIF7 behavior arises from an inability to release adenosine diphosphate in response to microtubule binding, whereas slow processive KIF27 behavior arises from a slow adenosine triphosphatase rate and a high affinity for both adenosine triphosphate and microtubules. We suggest that evolutionarily selected sequence differences enable immotile KIF7 and Cos2 motors to function not as transporters but as microtubule-based tethers of signaling complexes

Neck linker docking is critical for Kinesin-1 force generation in cells but at a cost to motor speed and processivity.

Kinesin force generation involves ATP-induced docking of the neck linker (NL) along the motor core. However, the roles of the proposed steps of NL docking, cover-neck bundle (CNB) and asparagine latch (N-latch) formation, during force generation are unclear. Furthermore, the necessity of NL docking for transport of membrane-bound cargo in cells has not been tested. We generated kinesin-1 motors impaired in CNB and/or N-latch formation based on molecular dynamics simulations. The mutant motors displayed reduced force output and inability to stall in optical trap assays but exhibited increased speeds, run lengths, and landing rates under unloaded conditions. NL docking thus enhances force production but at a cost to speed and processivity. In cells, teams of mutant motors were hindered in their ability to drive transport of Golgi elements (high-load cargo) but not peroxisomes (low-load cargo). These results demonstrate that the NL serves as a mechanical element for kinesin-1 transport under physiological conditions

Online interactive analysis of protein structure ensembles with Bio3D-web

Bio3D-web is an online application for analyzing the sequence, structure and conformational heterogeneity of protein families. Major functionality is provided for identifying protein structure sets for analysis, their alignment and refined structure superposition, sequence and structure conservation analysis, mapping and clustering of conformations and the quantitative comparison of their predicted structural dynamics

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web.

We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality for: (1) The identification of related protein structure sets to user specified thresholds of similarity; (2) Their multiple alignment and structure superposition; (3) Sequence and structure conservation analysis; (4) Inter-conformer relationship mapping with principal component analysis, and (5) comparison of predicted internal dynamics via ensemble normal mode analysis. This integrated functionality provides a complete online workflow for investigating sequence-structure-dynamic relationships within protein families and superfamilies

Adapting a Database of Text Messages to a Mobile-Based Weight Loss Program: The Case of the Middle East

Obesity has become a worldwide epidemic. Qatar, a rapidly developing country in the Middle East, has seen a sharp increase in the prevalence of obesity. The increase can be attributed to several reasons, including sedentary lifestyles imposed by a harsh climate and the introduction of Western fast food. Mobile technologies have been used and studied as a technology to support individuals’ weight loss. The authors have developed a mobile application that implements three strategies drawn from proven theories of behavioral change. The application is localized to the cultural context of its proposed users. The objective of this paper is to present a method through which we adapted the messaging content of a weight loss application to the context of its users while retaining an effective degree of automation. The adaptation addressed body image, eating and physical exercise habits, and regional/cultural needs. The paper discusses how surveying potential users can be used to build a profile of a target population, find common patterns, and then develop a database of text messages. The text messages are automated and sent to the users at specific times of day, as suggested by the survey results

Neck linker docking is critical for Kinesin-1 force generation in cells but at a cost to motor speed and processivity.

Kinesin force generation involves ATP-induced docking of the neck linker (NL) along the motor core. However, the roles of the proposed steps of NL docking, cover-neck bundle (CNB) and asparagine latch (N-latch) formation, during force generation are unclear. Furthermore, the necessity of NL docking for transport of membrane-bound cargo in cells has not been tested. We generated kinesin-1 motors impaired in CNB and/or N-latch formation based on molecular dynamics simulations. The mutant motors displayed reduced force output and inability to stall in optical trap assays but exhibited increased speeds, run lengths, and landing rates under unloaded conditions. NL docking thus enhances force production but at a cost to speed and processivity. In cells, teams of mutant motors were hindered in their ability to drive transport of Golgi elements (high-load cargo) but not peroxisomes (low-load cargo). These results demonstrate that the NL serves as a mechanical element for kinesin-1 transport under physiological conditions