Intracellular transport provides a mechanism by which cellular material, such as organelles, vesicles, and protein, can be actively transported throughout the cell. This process relies on the activity of the cytoskeletal filament, microtubules, and their associated motor proteins. These motors are able to walk along microtubule tracks while carrying cellular cargos to enable the fast, regulated transport of these cargos. In cells, these microtubule filaments act as a binding platform for numerous different motor species as well as microtubule-associated proteins. In addition, these filaments often form higher order structures, such as microtubule bundles. How motors navigate such complex, crowded tracks to ensure the efficient transport of cargos is unclear. While motor transport can be studied in vivo, such studies are complicated to interpret as there are many unknowns, such as which motors are driving transport, which MAPs are bound to specific regions of microtubule tracks, and what types of microtubule architectures are present. Here I use in vitro studies to reconstitute motor transport and systematically study how motors navigate complex microtubule tracks. With this system, I can control the motor type, the relative number of motors per cargo, and the types of tracks I study transport on. To understand how kinesin motors navigate complex microtubule tracks, I studied how motor traffic and microtubule architecture affect kinesin motor transport. In addition, I also studied how motor domain mutations affect the transport properties of kinesin motors. The studies presented here shed light on how motor transport is altered on complex microtubule tracks, as well as mechanisms utilized by kinesin motors to efficiently navigate these complex tracks.^

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Localized cytosolic Ca2+ elevations known as puffs and sparks are important regulators of cellular function that arise due to the cooperative activity of Ca2+-regulated inositol 1,4,5-trisphosphate receptors (IP3Rs) or ryanodine receptors (RyRs) co-localized at Ca2+ release sites on the surface of the endoplasmic reticulum or sarcoplasmic reticulum. Theoretical studies have demonstrated that the cooperative gating of a cluster of Ca2+-regulated Ca 2+ channels modeled as a continuous-time discrete-state Markov chain may result in dynamics reminiscent of Ca2+ puffs and sparks. In such simulations, individual Ca2+-release channels are coupled via a mathematical representation of the local [Ca2+] and exhibit "stochastic Ca2+ excitability" where channels open and close in a concerted fashion. This dissertation uses Markov chain models of Ca 2+ release sites to advance our understanding of the biophysics connecting the microscopic parameters of IP3R and RyR gating to the collective phenomenon of puffs and sparks.;The dynamics of puffs and sparks exhibited by release site models that include both Ca2+ coupling and nearest-neighbor allosteric coupling are studied. Allosteric interactions are included in a manner that promotes the synchronous gating of channels by stabilizing neighboring closed-closed and/or open-open channel pairs. When the strength of Ca2+-mediated channel coupling is systematically varied, simulations that include allosteric interactions often exhibit more robust Ca2+ puffs and sparks. Interestingly, the changes in puff/spark duration, inter-event interval, and frequency observed upon the random removal of allosteric couplings that stabilize closed-closed channel pairs are qualitatively different than the changes observed when open-open channel pairs, or both open-open and closed-closed channel pairs are stabilized. The validity of a computationally efficient mean-field reduction applicable to the dynamics of a cluster of Ca2+-release Ca2+ channels coupled via the local [Ca2+] and allosteric interactions is also investigated.;Markov chain models of Ca2+ release sites composed of channels that are both activated and inactivated by Ca2+ are used to clarify the role of Ca2+ inactivation in the generation and termination of puffs and sparks. It is found that when the average fraction of inactivated channels is significant, puffs and sparks are often less sensitive to variations in the number of channels at release sites and the strength of Ca2+ coupling. While excessively fast Ca2+ inactivation can preclude puffs and sparks moderately fast Ca2+ inactivation often leads to time-irreversible puff/sparks whose termination is facilitated by the recruitment of inactivated channels throughout the duration of the puff/spark event. On the other hand, Ca2+ inactivation may be an important negative feedback mechanism even when its time constant is much greater than the duration of puffs and sparks. In fact, slow Ca 2+ inactivation can lead to release sites with a substantial fraction of inactivated channels that exhibit nearly time-reversible puffs and sparks that terminate without additional recruitment of inactivated channels.

Localized calcium elevations known as calcium puffs or sparks are cellular signals arising from cooperative activity of clusters of inositol 1,4,5-trisphosphate receptors (IP3Rs) or ryanodine receptors (RyRs) located at calcium release sites on the endoplasmic or sarcoplasmic reticulum membrane. When Markov chain models of these intracellular calcium-regulated calcium channels are coupled via a mathematical representation of the calcium microdomain, simulated calcium release sites may exhibit the phenomenon of "stochastic calcium excitability" where the IP3Rs or RyRs open and close in a concerted fashion. Although the biophysical theory relating the kinetics of single channels to the collective phenomena of puffs and sparks is only beginning to be developed, Markov chain models of coupled intracellular channels give insight into the dynamics of calcium puffs and sparks.;Interestingly, under some conditions simulated puffs and sparks can be observed even when the single channel model used does not include slow calcium inactivation or any long-lived closed state. In this case termination of the localized calcium elevation occurs when all of the intracellular channels at a release site simultaneously close through a process called stochastic attrition. This dissertation investigates the statistical properties of stochastic attrition viewed as an absorption time on a terminating Markov chain that represents a calcium release site composed of two-state channels that are activated by calcium. Assuming that the local calcium concentration experienced by a channel depends only on the number of open channels at the calcium release site, the probability distribution function for the time until stochastic attrition occurs is derived and an analytical formula for the expectation of this random variable is presented. Also explored is how the contribution of stochastic attrition to the termination of calcium puffs and sparks depends on the number of channels at a release site, the source amplitude of the channels, the background calcium concentration, channel kinetics, and the cooperativity of calcium binding.;This dissertation also studies whether single channel models with calcium inactivation are less sensitive to the details of release site ultrastructure than models that lack a slow calcium-inactivation process. Release site dynamics obtained from simulated calcium release sites composed of instantaneously coupled calcium-regulated calcium channels whose random spatial locations were chosen from a uniform distribution on a disc of specified radius are compared to simulations with channels arranged on hexagonal lattices. Analysis of puff/spark statistics confirms that puffs and sparks are less sensitive to the spatial organization of release sites when the single channel model includes a slow inactivation process. The validity of several different mean-field reductions that do not explicitly account for the details of release site ultrastructure is also investigated.;Calcium release site models are stochastic automata networks that involve many functional transitions, that is, the transition probabilities of each channel depend on the local calcium concentration and thus the state of the other channels. A Kronecker structured representation for calcium release site models is presented and benchmark stationary distribution calculations using both exact and approximate iterative numerical solution techniques that leverage this structure are performed. When it is possible to obtain an exact solution, response measures such as the number of channels in a particular state converge more quickly using the iterative numerical methods than occupation measures calculated via Monte Carlo simulation. When an exact solution is not feasible, iterative approximate methods based on the Power method may be used, with performance similar to Monte Carlo estimates.

Considerable insight into intracellular calcium (Ca) responses has been obtained through the development of whole cell models that are based on molecular mechanisms, e.g., the kinetics of intracellular Ca channels and the feedback of Ca upon these channels. However, a limitation of most deterministic whole cell models to date is the assumption that channels are globally coupled by a single [Ca], when in fact channels experience localized "domain" Ca concentrations. More realistic stochastic Monte Carlo simulations are capable of representing individual domain Ca concentrations but suffer from increased computational demand. This dissertation introduces a novel probability approach which captures important aspects of local Ca signaling while improving computational efficiency.;In many cell types calcium release is mediated by diffusely distributed 1,4,5-trisphosphate receptors (IP3Rs). In Chapter 2 a Monte Carlo whole cell model is presented where each IP3R has a local cytosolic and luminal domain [Ca]. The Monte Carlo model is used to validate a probability density approach where local cytosolic and luminal domains Ca concentrations are represented as bivariate probability densities jointly distributed with IP3R state. Using this probability density approach, analysis shows that the time scale of Ca domain formation and collapse (both cytosolic and luminal) influences global Ca oscillations. Additionally, two reduced models of Ca signaling are derived that are valid when there is a separation of time scales between the stochastic gating of IP3Rs and the dynamics of domain Ca. These reduced whole cell models account for the influence of local Ca signaling on global Ca dynamics and are therefore more realistic than other conventional deterministic whole cell models.;In cardiac myocytes, Ca influx through voltage gated channels causes the release of intracellular Ca, a process known as Ca-induced Ca release (CICR). In Chapter 3 a probability density approach to CICR is derived from advection-reaction equations relating the time-dependent probability density of subsarcolemmal subspace and junctional sarcoplasmic reticulum [Ca] conditioned on "Ca release unit" state. When these equations are coupled to ordinary differential equations for the bulk myoplasmic and sarcoplasmic reticulum [Ca], a realistic but minimal whole cell model is produced. Modeling Ca release unit activity using this probability density approach avoids the computationally demanding task of resolving spatial aspects of global Ca signaling, while accurately representing heterogeneous local Ca signals in a population of diadic subspaces and junctional sarcoplasmic reticulum domains. The probability density approach is validated and benchmarked for computational efficiency by comparison to traditional Monte Carlo simulations. However, a probability density calculation can be significantly faster than the corresponding Monte Carlo simulation, especially when cellular parameters are such that univariate rather than multivariate probability densities may be employed.;Expanding upon the computational advantages of the probability density approach, a moment closure technique is introduced in Chapter 4 which facilitates whole cell modeling of cardiac myocytes when the dynamics of subspace [Ca] are much faster than those of junctional SR [Ca]. The method begins with the derivation of a system of ODEs describing the time-evolution of the moments of the univariate probability density functions for junctional SR [Ca] jointly distributed with CaRU state. This open system of ODEs is then closed using an algebraic relationship that expresses the third moment of junctional SR [Ca] in terms of the first and second moments. Benchmark simulations indicate that the moment closure approach is nearly 10,000-times more computationally efficient than corresponding Monte Carlo simulations while leading to nearly identical results.

The orthogonal space tempering (OST) scheme is a robust and high-order generalized ensemble sampling method that can make sampling in MD simulation much more efficiently and recover the desired thermodynamic properties of interest in complex biophysical protein behaviors. The OST technique provides a powerful tool to study the protein dynamics and mechanistic details of biophysical and biochemical processes that are difficult to be realized by experimental techniques. Here the orthogonal space tempering technique is applied to explore protein dynamics and interactions of actin monomer and TrmD methyltransferase. The first system studied is nucleotide dependent dynamics of actin monomer. Nucleotide-dependent dynamics transition of actin has been studied for a decade. However, those models proposed were based on crystal structures of monomer actin that are typically modified with mutation or complexed with blocking agents to prevent polymerization, and thus subject to alteration. Additionally, typically experimental techniques cannot observe the mechanistic transition in a time-dependent manner. Here dynamics of monomer actin with different states of bound nucleotide—ATP, ADP, and apo form of actin—are investigated. Corresponding conformations and nucleotide binding cleft width-dependent free-energy profiles are calculated via all-atom simulations based on OST scheme. Current results suggest G-actin-ATP prefers flat and closed conformation, while G-actin-ADP and G-actin-APO prefers open conformation. Folding and unfolding motion of D-loop in subdomain 2 is observed in both G-actin with ADP and ATP bound simulations. The dynamic conformations of G-actin-ATP are consistent with previous experimental results. Our simulations will provide insights for the nucleotide-dependent mechanistic transitions and native structure of G-actin with ADP bound after the free energy profiles converge. The second system of interest is the dynamics of TrmD tRNA (m1G37) methyltransferase. m1G37 methylation prevent frameshift errors in translation and is important for bacteria growth. TrmD methyltransferase has been considered as an important drug target. Asymmetric features have been reported in TrmD catalysis and in the TrmD structure with sinefungin and tRNA bound. Yet mechanistic details of TrmD catalysis remains elusive since TrmD with AdoMet and tRNA bound ternary structure has not been resolved. Here free energy calculations based on OST scheme are performed on corresponding conformational changes with perturbation of defined AdoMet dihedral angle on both active and inactive side of TrmD dimer. The conformation of AdoMet ligands and how both sides of TrmD dimer coordinate with each other are investigated. Current results suggest the cooperativity of TrmD dimer is not through AdoMet ligands on both sides but through the positioning of catalytic residues instead. Another Mg[superscript 2+] dependent TrmD methylation simulation perturbing the distance between the target guanosine G37 and Mg[superscript 2+] is performed to study the function of Mg[superscript 2+] in the catalysis. It is found that G37 base moves out the catalytic binding pocket while Mg[superscript 2+] approaches the carbonyl group of G37, which suggests Mg[superscript 2+] is not involved in the transition state during methylation. Further, conserved Mg[superscript 2+] binding motif (residue 162-179) is found in the disorder linker loop. In the simulation, Mg[superscript 2+] binding motif interacts with G37 via Mg[superscript 2+] and water hydrogen bonding network while G37 is moving into the binding site. Those results formulate a new hypothesis that Mg[superscript 2+] and Mg[superscript 2+] binding motif helps with flipping and positioning of G37 into the catalytic binding pocket. After simulations complete, converged free energy profiles will test this new hypothesis and disclose the actual mechanism of TrmD methylation catalysis. / A Thesis submitted to the Department of Chemistry & Biochemistry in partial fulfillment of the Master of Science. / Fall Semester 2016. / September 27, 2016. / G-actin, orthogonal space tempering, simulation, TrmD methyltransferase / Includes bibliographical references. / Wei Yang, Professor Directing Thesis; James Frederich, Committee Member; Timothy Logan, Committee Member.

A major focus of scientific research is to understand biological phenomena and to explain our basic observations of life, however these phenomena have an underlying basis and are the result of many biophysical processes. The study of biophysical processes provides a more detailed examination of the components and actions involved, however many of these processes are not adequately understood and need further exploration. Experimental studies of biophysical processes such biomolecular dynamics, protein folding, molecular transport and enzymatic reactions provide a wealth of knowledge, however all these techniques have their limitations. To be able to adequately understand a biophysical process both spatial and temporal resolution is required and computational biophysical techniques such as molecular dynamics provides the atomic and temporal resolution to further understand these processes. Additionally, computational techniques allow us to be able to not see and observe the motions of biomolecules but to better define these states and motions through the systems free energy surfaces. As stated previously, all techniques have their limitations, including molecular dynamics, with limitations in atomic interaction descriptors or force fields as well as reaching timescales that are relevant to the target biophysical processes. The development of enhanced sampling techniques and more specifically the Orthogonal Space Sampling Scheme have been used to address this timescale issue. In this study of work, we aim to use this enhanced sampling technique to explore several biophysical processes of biomolecules. The first study investigates the reaction site dynamics and how long timescale protein dynamics are involved. By using the High Order Orthogonal Space Tempering technique, we explored a novel tRNA Methyltranferase TrmD which has an unusual fold that is used to bind a cofactor and the conformation of the cofactor when bound is unusual as well. Differences in the tRNA bound ternary complex and binary complex show differences in protein backbone collective motions as well as differing degree of coupling to the reaction site dynamics. The dynamics of binary complex reveal distant protein collective motions that are coupled to the cofactor internal dynamics, whereas the ternary complex shows coupling of methyl transfer distance and protein ligand stabilizing interactions which suggest when tRNA is bound motions are focused on those that are enzymatically productive. The second study investigates the long timescale protein dynamics and its involvement protein misfolding as well as how known perturbations that induce misfolding might change these dynamics. Murine prion protein or PrP is a protein that can undergo a misfolding event that leads to neurodegenerative diseases and has been established as an infectious agent which interactions with the misfolded protein can induce misfolding as well. Misfolding events have been observed in vivo and in vitro under low pH conditions, however the misfolded structure is still yet to be atomically resolved and the experimental data does not provide a defined process for the misfolding event. Simulations using the neutral and charged states of the PrP system and the perturbation of the β-sheet motif that has been suggested is involved in the misfolding process, we observe differences in dynamics of the β-sheet motif as well as overall protein collective motion. The protein in charged state where histidine 187 is protonated destabilizes the protein structure due to the buried charged making β-sheet dynamics easier where in the neutral state we see stronger hydrogen bonding interactions. Additionally, sites that have been implicated through experimental studies have shown correlated motions with the perturbed β-sheet motif. The final study investigates long timescale intrinsic DNA dynamics as well as the effects of 6mA methylation on DNA dynamics. DNA undergoes dynamics that span several levels from local base pair dynamics to global conformational changes. These levels of dynamics play a critical role for processes such as DNA transcription, repair, regulation and replication. Epigenetic regulation, typically, occurs through chemical modifications of the individual bases and methylation has been observed to control several processes. A shift in focus for an understudied methylation modification, 6mA, has found that it plays a more significant role in regulation of eukaryotes but the biophysical nature of the modification is unknown. Simulations of an 33 base pair fragment of DNA in the unmodified and 6mA methylated modification find significant differences in the dynamics across all levels. The unmodified DNA is considerably more flexible and is able to undergo base flipping events whereas the methylated DNA is more rigid and does not undergo any base flipping events in the simulated time. Further analysis shows coupling of the base flipping events and global DNA bending and coupling is loss in the methylated DNA. This loss in coupling is proposed to be caused by two sources: steric clashing of the added methyl groups and neighbor base steps as seen by the reduction in roll fluctuation and changes in water density distributions showing a loss of high water density in the major groove at the modification site and the formation of high water density across a stretch of associated DNA backbone. The results are consistent with previous and recent biophysical evidence which suggests that this fragment becomes more rigid and base pair lifetimes increase across the whole fragment. It is also consistent with biochemical data suggesting that the introduced rigidity prevents nucleosome wrapping. / A Dissertation submitted to the Institute of Molecular Biophysics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester 2019. / April 19, 2019. / Enhanced Sampling, Free Energy Simulations, Molecular Dynamics / Includes bibliographical references. / Wei Yang, Professor Directing Dissertation; Biwu Ma, University Representative; Hong Li, Committee Member; Branko Stefanovic, Committee Member; M. Elizabeth Stroupe, Committee Member.

Eukaryotic ribosome is maturated through a complicated process orchestrated by a large network of biogenesis factors. Small nucleolar ribonucleoprotein particles (snoRNPs) contribute to ribosome biogenesis by processing and chemically modifying ribosomal RNA (rRNA). Several snoRNP proteins are found to be unstable and require the chaperone activities of two AAA+ ATPase complexes, R2TP and R2BRH, in collaboration with the heat shock protein, Hsp90. There is currently is no structural information of R2TP and R2BRH and their interactions with snoRNP proteins or Hsp90 (CHAPTER 1). We obtained a structural model of the Saccharomyces cerevisiae (Sc) R2TP complex made up of two AAA+ ATPases, Rvb1/2p, and two Hsp90 co-chaperone proteins, Tah1p and Pih1p, by a combination of analytical ultracentrifugation, chemical cross-linking, and electron cryomicroscopy methods (CHAPTER 2). These studies showed that that the Pih1p-Tah1p heterodimer caps the Rvb1/2p heterohexameric ring through its association with the nucleotide-sensitive insertion domain of Rvb1/2p. Here I characterized how the assembled ScR2TP interacts with a client protein, Nop58p and with Hsp90 and how these interactions depend on nucleotide binding/hydrolysis (CHAPTER 2 and CHAPTER 3). I show that Nop58p binds primarily to Pih1p and upon ATP or ADP binding, dissociates along with Pih1p-Tah1p from R2TP. I also showed that Hsp90 forms a ternary complex with isolated Pih1p-Tah1p but not with R2TP, suggesting two separate chaperone activities for snoRNP proteins. On the basis that Hsp90 is localized to cytosol and R2TP is to nucleus, I propose that snoRNP proteins are separately stabilized by both activities in cytosol and nucleus, respectively. I have begun characterizing Sc R2BRH that comprises Rvb1/2p and three additional proteins, Bcd1p, Rsa1p, and Hit1p. I show that Bcd1p interacts with Rvb1/2p in the presence of ADP and that the Rsa1p-Hit1p heterodimer interacts with another snoRNP protein, Snu13p (CHAPTER 4). The nucleotide-dependent assembly of R2BRH contrasts the nucleotide-independent assembly of R2TP, suggesting that nucleotide binding can coordinate assembly of different snoRNP proteins, thereby ensuring a proper order of snoRNP assembly (CHAPTER 5). / A Dissertation submitted to the Department of Chemistry & Biochemistry in partial fulfillment of the Doctor of Philosophy. / Spring Semester 2017. / March 29, 2017. / Includes bibliographical references. / Hong Li, Professor Directing Dissertation; Piotr G. Fajer, University Representative; Susan E. Latturner, Committee Member; Scott M. Stagg, Committee Member.

Molecular interactions form the basis for all cellular functions ranging from nutrient sequestration to signal transduction. While specific interactions have been extensively studied in the biomolecular context, the importance of non-specific and weak interactions between proteins have also become apparent. In this dissertation I study two phenomena that are emergent from non-specific and weak interactions: the effect of macromolecular crowding on protein-ligand equilibria and the regulatory effects of macromolecules on liquid-liquid phase separation of proteins. In the first project, I have shown that macromolecular crowders can compete with ligands for ligand binding proteins and are just as sensitive to conformational changes in the protein as ligands are. More specifically I showed, the polymeric crowder Ficoll70 competes against maltose for maltose binding protein (MBP) for the same binding site. I also showed the protein crowder BSA shows similar competitive effects. In the second project, I have experimentally verified the existence of three archetypical classes of regulators that can affect the liquid-liquid phase boundary of proteins that form membraneless organelles inside the cell. The three classes were passive promotors, active suppressors and active promotors, exemplified by the polymeric crowder Ficoll70, a positively charged folded protein lysozyme and a mimic of RNA, heparin. The third project continued from this and shows that intrinsically disordered proteins can dramatically alter liquid phase behavior of structured proteins. From these three studies I was able to show that bystander molecules in the cellular environment play a role in governing functional aspects of the cell. Two types of macromolecules, Ficoll70 and BSA, were shown to modulate MBP-maltose interactions. Three classes of macromolecules were shown to have disparate regulatory effects on the formation of membraneless organelles and some even form such organelles with distinct viscoelastic properties. / A Dissertation submitted to the Department of Molecular Biophysics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / 2019 / June 12, 2019. / Liquid-liquid phase separation, Macromolecular crowding, Membraneless organelles, Protein droplets / Includes bibliographical references. / Hong Li, Professor Co-Directing Dissertation; Huan-Xiang Zhou, Professor Co-Directing Dissertation; Jose Renato Dias Oliveira Pinto, University Representative; Prescott Bryant Chase, Committee Member; Michael Blaber, Committee Member.

Microenvironmental stimuli are important in maintenance of homeostasis, development, and tumor progression. For example, in tumor tissues the collagen becomes abnormal when tumor advances, and this remodeling may potentially in turn impact cell fates and even malignancy. However, little has been investigated into how this matrix reorganization occurs and regulates cellular behaviors through intracellular signaling transduction. This also poses a challenging but important question regarding how cells dynamically integrate cell-cell and cell-matrix interactions to respond to this mechanical remodeling. Tumor microenvironment is multi-faceted and dynamic, and quantitative understanding of the feedback between the tumor and the microenvironment requires a high-dimensional quantitative analysis. To pursue these goals, we first developed a toolkit to precisely and reliably quantify matrix-based microenvironmental features during tumor progression. A collagen network dynamic model was also built to further study and predict the mechanical property changes during collagen remodeling in tumor expansion. The transcriptional regulators Yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ) have been found as the most robust mechanosensors that tightly regulate malignant phenotypes and chemo-resistance in many cancers, however we have little knowledge of how they are regulated by multiplexed microenvironmental stimuli simultaneously. Here, we combined computational modeling with experimental evidence to examine how changes in matrix mechanical property regulate YAP/TAZ and related phenotypes integrating varying local cell densities and the integration signaling mechanism. The kinetic parameter estimation of our model suggests that the key mechanism in driving YAP/TAZ activation in the triple negative breast cancer MDA-MB-231 cell lines is the endogenous high contractility. Therefore, the matrix feature quantification, the collagen network mechanical predictions and integration mechanism of YAP/TAZ upstream signaling present a comprehensive knowledge of the role of collagen remodeling in cancer at different scales and time points. This study of platform enables potential treatment strategy exploration based on mechanical inhibition in cancer cells, and more importantly, the role of multiplexed microenvironment in tumor progression with the big data analysis. / 2020-07-02T00:00:00Z