R-3 Repository :: Browsing by Author "Onuchic, José Nelson"

Browsing by Author "Onuchic, José Nelson"

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A magnesium-induced triplex pre-organizes the SAM-II riboswitch
(Public Library of Science, 2017) Roy, Susmita; Lammert, Heiko; Hayes, Ryan L.; Chen, Bin; LeBlanc, Regan; Dayie, T.Kwaku; Onuchic, José Nelson; Sanbonmatsu, Karissa Y.; Center for Theoretical Biological Physics
Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state. Our CEST and SAXS experiments, at different magnesium ion concentrations, quantitatively confirm our simulation results, demonstrating that magnesium ions induce collapse and pre-organization. Agreement between theory and experiment bolsters microscopic interpretation of our simulations, which shows that triplex formation between helix P2b and loop L1 is highly sensitive to magnesium and plays a key role in pre-organization. Pre-organization of the SAM-II riboswitch allows rapid detection of ligand with high selectivity, which is important for biological function.
A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells and Notch-Jagged signaling
(Oncotarget, 2018) Bocci, Federico; Jolly, Mohit Kumar; George, Jason Thomas; Levine, Herbert; Onuchic, José Nelson; Center for Theoretical Biological Physics
Epithelial-mesenchymal transition (EMT) and cancer stem cell (CSCs) formation are two fundamental and well-studied processes contributing to cancer metastasis and tumor relapse. Cells can undergo a partial EMT to attain a hybrid epithelial/mesenchymal (E/M) phenotype or a complete EMT to attain a mesenchymal one. Similarly, cells can reversibly gain or lose 'stemness'. This plasticity in cell states is modulated by signaling pathways such as Notch. However, the interconnections among the cell states enabled by EMT, CSCs and Notch signaling remain elusive. Here, we devise a computational model to investigate the coupling among the core decision-making circuits for EMT, CSCs and Notch. Our model predicts that hybrid E/M cells are most likely to associate with stem-like traits and enhanced Notch-Jagged signaling – a pathway implicated in therapeutic resistance. Further, we show that the position of the 'stemness window' on the 'EMT axis' is varied by altering the coupling strength between EMT and CSC circuits, and/or modulating Notch signaling. Finally, we analyze the gene expression profile of CSCs from several cancer types and observe a heterogeneous distribution along the 'EMT axis', suggesting that different subsets of CSCs may exist with varying phenotypes along the epithelial-mesenchymal axis. We further investigate therapeutic perturbations such as treatment with metformin, a drug associated with decreased cancer incidence and increased lifespan of patients. Our mechanism-based model explains how metformin can both inhibit EMT and blunt the aggressive potential of CSCs simultaneously, by driving the cells out of a hybrid E/M stem-like state with enhanced Notch-Jagged signaling.
A Transferable Model for Chromosome Architecture
(National Academy of Sciences, 2016) Di Pierro, M.; Zhang, Boyu; Aiden, Erez Lieberman; Wolynes, P.G.; Onuchic, José Nelson
In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. We report a theoretical model for chromatin (Minimal Chromatin Model) that explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops. First, we trained our energy function using the Hi-C contact map of chromosome 10 from human GM12878 lymphoblastoid cells. Then, we used the model to perform molecular dynamics simulations producing an ensemble of 3D structures for all GM12878 autosomes. Finally, we used these 3D structures to generate contact maps. We found that simulated contact maps closely agree with experimental results for all GM12878 autosomes. The ensemble of structures resulting from these simulations exhibited unknotted chromosomes, phase separation of chromatin types, and a tendency for open chromatin to lie at the periphery of chromosome territories.
Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes
(National Academy of Sciences of the United States of America, 2018) Di Pierro, Michele; Potoyan, Davit A.; Wolynes, Peter G.; Onuchic, José Nelson
The nucleus of a eukaryotic cell is a nonequilibrium system where chromatin is subjected to active processes that continuously rearrange it over the cell's life cycle. Tracking the motion of chromosomal loci provides information about the organization of the genome and the physical processes shaping that organization. Optical experiments report that loci move with subdiffusive dynamics and that there is spatially coherent motion of the chromatin. We recently showed that it is possible to predict the 3D architecture of genomes through a physical model for chromosomes that accounts for the biochemical interactions mediated by proteins and regulated by epigenetic markers through a transferable energy landscape. Here, we study the temporal dynamics generated by this quasi-equilibrium energy landscape assuming Langevin dynamics at an effective temperature. Using molecular dynamics simulations of two interacting human chromosomes, we show that the very same interactions that account for genome architecture naturally reproduce the spatial coherence, viscoelasticity, and the subdiffusive behavior of the motion in interphase chromosomes as observed in numerous experiments. The agreement between theory and experiments suggests that even if active processes are involved, an effective quasi-equilibrium landscape model can largely mimic their dynamical effects.
Coevolutionary signals across protein lineages help capture multiple protein conformations
(National Academy of Sciences, 2013) Morcos, Faruck; Jana, Biman; Hwa, Terence; Onuchic, José Nelson
A long-standing problem in molecular biology is the determination of a complete functional conformational landscape of proteins. This includes not only proteins’ native structures, but also all their respective functional states, including functionally important intermediates. Here, we reveal a signature of functionally important states in several protein families, using direct coupling analysis, which detects residue pair coevolution of protein sequence composition. This signature is exploited in a protein structure-based model to uncover conformational diversity, including hidden functional configurations. We uncovered, with high resolution (mean ∼1.9 Å rmsd for nonapo structures), different functional structural states for medium to large proteins (200–450 aa) belonging to several distinct families. The combination of direct coupling analysis and the structure-based model also predicts several intermediates or hidden states that are of functional importance. This enhanced sampling is broadly applicable and has direct implications in protein structure determination and the design of ligands or drugs to trap intermediate states.
Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes
(Oxford University Press, 2016) Cheng, R.R.; Nordesjӧ, O.; Hayes, R.L.; Levine, H.; Flores, S.C.; Onuchic, José Nelson; Morcos, F.; Center for Theoretical Biological Physics
Two-component signaling (TCS) is the primary means by which bacteria sense and respond to the environment. TCS involves two partner proteins working in tandem, which interact to perform cellular functions whereas limiting interactions with non-partners (i.e., cross-talk). We construct a Potts model for TCS that can quantitatively predict how mutating amino acid identities affect the interaction between TCS partners and non-partners. The parameters of this model are inferred directly from protein sequence data. This approach drastically reduces the computational complexity of exploring the sequence-space of TCS proteins. As a stringent test, we compare its predictions to a recent comprehensive mutational study, which characterized the functionality of 204 mutational variants of the PhoQ kinase in Escherichia coli. We find that our best predictions accurately reproduce the amino acid combinations found in experiment, which enable functional signaling with its partner PhoP. These predictions demonstrate the evolutionary pressure to preserve the interaction between TCS partners as well as prevent unwanted cross-talk. Further, we calculate the mutational change in the binding affinity between PhoQ and PhoP, providing an estimate to the amount of destabilization needed to disrupt TCS.
Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain
(National Academy of Sciences, 2021) Staquicini, Daniela I.; Tang, Fenny H.F.; Markosian, Christopher; Yao, Virginia J.; Staquicini, Fernanda I.; Dodero-Rojas, Esteban; Contessoto, Vinícius G.; Davis, Deodate; O’Brien, Paul; Habib, Nazia; Smith, Tracey L.; Bruiners, Natalie; Sidman, Richard L.; Gennaro, Maria L.; Lattime, Edmund C.; Libutti, Steven K.; Whitford, Paul C.; Burley, Stephen K.; Onuchic, José Nelson; Arap, Wadih; Pasqualini, Renata; Center for Theoretical Biological Physics
Development of effective vaccines against coronavirus disease 2019 (COVID-19) is a global imperative. Rapid immunization of the entire human population against a widespread, continually evolving, and highly pathogenic virus is an unprecedented challenge, and different vaccine approaches are being pursued. Engineered filamentous bacteriophage (phage) particles have unique potential in vaccine development due to their inherent immunogenicity, genetic plasticity, stability, cost-effectiveness for large-scale production, and proven safety profile in humans. Herein we report the development and initial evaluation of two targeted phage-based vaccination approaches against SARS-CoV-2: dual ligand peptide-targeted phage and adeno-associated virus/phage (AAVP) particles. For peptide-targeted phage, we performed structure-guided antigen design to select six solvent-exposed epitopes of the SARS-CoV-2 spike (S) protein. One of these epitopes displayed on the major capsid protein pVIII of phage induced a specific and sustained humoral response when injected in mice. These phage were further engineered to simultaneously display the peptide CAKSMGDIVC on the minor capsid protein pIII to enable their transport from the lung epithelium into the systemic circulation. Aerosolization of these “dual-display” phage into the lungs of mice generated a systemic and specific antibody response. In the second approach, targeted AAVP particles were engineered to deliver the entire S protein gene under the control of a constitutive CMV promoter. This induced tissue-specific transgene expression, stimulating a systemic S protein-specific antibody response in mice. With these proof-of-concept preclinical experiments, we show that both targeted phage- and AAVP-based particles serve as robust yet versatile platforms that can promptly yield COVID-19 vaccine prototypes for translational development.
Distinguishing mechanisms underlying EMT tristability
(Springer International Publishing, 2017) Jia, Dongya; Jolly, Mohit K.; Tripathi, Satyendra C.; Den Hollander, Petra; Huang, Bin; Lu, Mingyang; Celiktas, Muge; Ramirez-Peña, Esmeralda; Ben-Jacob, Eshel; Onuchic, José Nelson; Hanash, Samir M.; Mani, Sendurai A.; Levine, Herbert
Abstract Background The Epithelial-Mesenchymal Transition (EMT) endows epithelial-looking cells with enhanced migratory ability during embryonic development and tissue repair. EMT can also be co-opted by cancer cells to acquire metastatic potential and drug-resistance. Recent research has argued that epithelial (E) cells can undergo either a partial EMT to attain a hybrid epithelial/mesenchymal (E/M) phenotype that typically displays collective migration, or a complete EMT to adopt a mesenchymal (M) phenotype that shows individual migration. The core EMT regulatory network - miR-34/SNAIL/miR-200/ZEB1 - has been identified by various studies, but how this network regulates the transitions among the E, E/M, and M phenotypes remains controversial. Two major mathematical models – ternary chimera switch (TCS) and cascading bistable switches (CBS) - that both focus on the miR-34/SNAIL/miR-200/ZEB1 network, have been proposed to elucidate the EMT dynamics, but a detailed analysis of how well either or both of these two models can capture recent experimental observations about EMT dynamics remains to be done. Results Here, via an integrated experimental and theoretical approach, we first show that both these two models can be used to understand the two-step transition of EMT - E→E/M→M, the different responses of SNAIL and ZEB1 to exogenous TGF-β and the irreversibility of complete EMT. Next, we present new experimental results that tend to discriminate between these two models. We show that ZEB1 is present at intermediate levels in the hybrid E/M H1975 cells, and that in HMLE cells, overexpression of SNAIL is not sufficient to initiate EMT in the absence of ZEB1 and FOXC2. Conclusions These experimental results argue in favor of the TCS model proposing that miR-200/ZEB1 behaves as a three-way decision-making switch enabling transitions among the E, hybrid E/M and M phenotypes.
Exploring chromosomal structural heterogeneity across multiple cell lines
(eLife, 2020) Cheng, Ryan R.; Contessoto, Vinícius G.; Aiden, Erez Lieberman; Wolynes, Peter G.; Di Pierro, Michele; Onuchic, José Nelson; Center for Theoretical Biological Physics
Using computer simulations, we generate cell-specific 3D chromosomal structures and compare them to recently published chromatin structures obtained through microscopy. We demonstrate using machine learning and polymer physics simulations that epigenetic information can be used to predict the structural ensembles of multiple human cell lines. Theory predicts that chromosome structures are fluid and can only be described by an ensemble, which is consistent with the observation that chromosomes exhibit no unique fold. Nevertheless, our analysis of both structures from simulation and microscopy reveals that short segments of chromatin make two-state transitions between closed conformations and open dumbbell conformations. Finally, we study the conformational changes associated with the switching of genomic compartments observed in human cell lines. The formation of genomic compartments resembles hydrophobic collapse in protein folding, with the aggregation of denser and predominantly inactive chromatin driving the positioning of active chromatin toward the surface of individual chromosomal territories.
Exploring the structure-function relationship of biomacromolecules: simulation and prediction of structural behavior of viral proteins and chromatin
(2024-07-01) Dodero Rojas, Esteban; Onuchic, José Nelson; Hazzard, Kaden; Kolomeisky, Anatoly
Biomacromolecules are the main functional constituents in living systems. They exhibit a great diversity of tasks depending on the composition of their monomers. Most protein and chromatin functions emerge from the interactions with other biomacromolecules. This dissertation focuses on viral proteins and chromatin systems, describing the relationship between their structure, composition and function using computational and theoretical models. Chapter 1 presents the motivation and describes the two main studied systems: the SARS-CoV-2 Spike protein and the eukaryote interphase genome. Chapter 2 focuses on the implementation of Structure Based Models to simulate the conformational change of the S2 subunit of the SARS-CoV-2 Spike protein associated with the membrane fusion process. We determined the transition states of the Spike protein, and predicted relevant intermediate states readily available to serve as druggable or vaccine targets. The simulated transitions highlight the role of post-translational modification (branched glycans) during viral entry. This model was further expanded to explore how the neutralizing CV3-25 antibody blocks viral entry by inhibiting the full transition of the Spike protein. Chapter 3 describes a pipeline to infer the efficiency of SARS-CoV-2 epitopes in scaffold vaccine strategies. Using explicit solvent simulations, we observed the dynamics of the target epitopes on exposed environments, similar to their context in scaffold-driven vaccines. When compared with experiments, we noticed that the most experimentally efficient epitope (S1Ep4) correlates with high thermal stability around the Wuhan-1 Spike protein conformation. To assess whether the S1Ep4 epitope would trigger immune response for SARS-CoV-2 variants, we performed explicit solvent simulations of the variant local environment of the epitope. The target epitope showed high conformational stability for all the variants around the Wuhan-1 strain structure. We determined that there is high likelihood the S1Ep4 epitope to incite immunoreponse on all the SARS-CoV-2 variants. Lastly, using the aforementioned simulated transitions of Spike during the membrane fusion, we identify new epitopes in the S2 subunit and the conformational study pipeline was implemented. Two new epitopes on the S2 subunit were proposed in highly conserved regions of the Spike protein, stepping towards pan-coronavirus vaccine strategies. Chapter 4 delves into the correlation between the biochemical composition of the DNA and its structural behavior. We expanded upon previous models to predict the subcompartment annotations of the chromatin based on biomarker enrichment along the genomes; including Histone Modification frequencies, transcriptor factor binding profiles and transcription activities. The prediction method, called PyMEGABASE (PYMB), is based on a graph model with a trainable Potts model. Within the model one node corresponds to the locus subcompartment and the remaining nodes are associated with the biomarker enrichment profiles. Using PYMB, we inferred the subcompartment annotations for hundreds of cell lines in multiple eukaryotes, which allow us to determine the cell identity from the subcompartment profile. In Chapter 5 we aim to increase the accuracy at predicting subcompartments by training a transformer architecture, called TECSAS. The new model is able to outperform PYMB's accuracy by more than 20%. From the new predictions, we determined that the transition region in sequence between subcompartments is approximately 150kbp. Finally, we expanded the model to predict the likelihood of genome loci to bind to nuclear bodies (Lamina, Nucleoli, and Speckles). We demonstrated based on the projection of the predicted likelihoods upon 3D chromatin data on the cell IMR-90 that both Lamina and Speckles create a stronger structural bias than the nucleoli. In summary, we explored the relationship between structure and function in the Spike protein's refolding pathway and demonstrated the significance of the conformational stability of epitopes around the target protein structure for vaccine efficiency. Further, the biochemical composition to structural behavior was examined for chromatin systems by the prediction of subcompartments from biochemical data, as well as the impact of the nuclear bodies, such as the lamina, in the overall ensemble behavior of chromatin systems. Overall, we determined that the mechanisms driving function of biomacromolecules are tightly correlated with their composition and structure.
Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble
(Public Library of Science, 2015) Fisher, Kaitlin M.; Haglund, Ellinor; Noel, Jeffrey K.; Hailey, Kendra L.; Onuchic, José Nelson; Jennings, Patricia A.; Center for Theoretical Biological Physics
Interleukin-33 (IL-33) is currently the focus of multiple investigations into targeting pernicious inflammatory disorders. This mediator of inflammation plays a prevalent role in chronic disorders such as asthma, rheumatoid arthritis, and progressive heart disease. In order to better understand the possible link between the folding free energy landscape and functional regions in IL-33, a combined experimental and theoretical approach was applied. IL-33 is a pseudo- symmetrical protein composed of three distinct structural elements that complicate the folding mechanism due to competition for nucleation on the dominant folding route. Trefoil 1 constitutes the majority of the binding interface with the receptor whereas Trefoils 2 and 3 provide the stable scaffold to anchor Trefoil 1. We identified that IL-33 folds with a three-state mechanism, leading to a rollover in the refolding arm of its chevron plots in strongly native conditions. In addition, there is a second slower refolding phase that exhibits the same rollover suggesting similar limitations in folding along parallel routes. Characterization of the intermediate state and the rate limiting steps required for folding suggests that the rollover is attributable to a moving transition state, shifting from a post- to pre-intermediate transition state as you move from strongly native conditions to the midpoint of the transition. On a structural level, we found that initially, all independent Trefoil units fold equally well until a QCA of 0.35 when Trefoil 1 will backtrack in order to allow Trefoils 2 and 3 to fold in the intermediate state, creating a stable scaffold for Trefoil 1 to fold onto during the final folding transition. The formation of this intermediate state and subsequent moving transition state is a result of balancing the difficulty in folding the functionally important Trefoil 1 onto the remainder of the protein. Taken together our results indicate that the functional element of the protein is geometrically frustrated, requiring the more stable elements to fold first, acting as a scaffold for docking of the functional element to allow productive folding to the native state.
Implications of the hybrid epithelial/mesenchymal phenotype in metastasis
(Frontiers Media S.A., 2015) Jolly, Mohit Kumar; Boareto, Marcelo; Huang, Bin; Jia, Dongya; Lu, Mingyang; Ben-Jacob, Eshel; Onuchic, José Nelson; Levine, Herbert; Center for Theoretical Biological Physics; Systems, Synthetic, and Physical Biology Program
Transitions between epithelial and mesenchymal phenotypes - the epithelial to -mesenchymal transition (EMT) and its reverse the mesenchymal to epithelial transition (MET) - are hallmarks of cancer metastasis. While transitioning between the epithelial and mesenchymal phenotypes, cells can also attain a hybrid epithelial/mesenchymal (E/M) (i.e., partial or intermediate EMT) phenotype. Cells in this phenotype have mixed epithelial (e.g., adhesion) and mesenchymal (e.g., migration) properties, thereby allowing them to move collectively as clusters. If these clusters reach the bloodstream intact, they can give rise to clusters of circulating tumor cells (CTCs), as have often been seen experimentally. Here, we review the operating principles of the core regulatory network for EMT/MET that acts as a "three-way" switch giving rise to three distinct phenotypes - E, M and hybrid E/M - and present a theoretical framework that can elucidate the role of many other players in regulating epithelial plasticity. Furthermore, we highlight recent studies on partial EMT and its association with drug resistance and tumor-initiating potential; and discuss how cell-cell communication between cells in a partial EMT phenotype can enable the formation of clusters of CTCs. These clusters can be more apoptosis-resistant and have more tumor-initiating potential than singly moving CTCs with a wholly mesenchymal (complete EMT) phenotype. Also, more such clusters can be formed under inflammatory conditions that are often generated by various therapies. Finally, we discuss the multiple advantages that the partial EMT or hybrid E/M phenotype have as compared to a complete EMT phenotype and argue that these collectively migrating cells are the primary "bad actors" of metastasis.
Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1
(PNAS, 2014) Tamir, Sagi; Rotem-Bamberger, Shahar; Katz, Chen; Morcos, Faruck; Hailey, Kendra L.; Zuris, John A.; Wang, Charles; Conlan, Andrea R.; Lipper, Colin H.; Paddock, Mark L.; Mittler, Ron; Onuchic, José Nelson; Jennings, Patricia A.; Friedler, Assaf; Nechushtai, Rachel; Center for Theoretical Biological Physics
Life requires orchestrated control of cell proliferation, cell maintenance, and cell death. Involved in these decisions are protein complexes that assimilate a variety of inputs that report on the status of the cell and lead to an output response. Among the proteins involved in this response are nutrient-deprivation autophagy factor-1 (NAF-1)- and Bcl-2. NAF-1 is a homodimeric member of the novel Fe-S protein NEET family, which binds two 2Fe-2S clusters. NAF-1 is an important partner for Bcl-2 at the endoplasmic reticulum to functionally antagonize Beclin 1-dependent autophagy [Chang NC, Nguyen M, Germain M, Shore GC (2010) EMBO J 29 (3):606–618]. We used an integrated approach involving peptide array, deuterium exchange mass spectrometry (DXMS), and functional studies aided by the power of sufficient constraints from direct coupling analysis (DCA) to determine the dominant docked conformation of the NAF-1–Bcl-2 complex. NAF-1 binds to both the pro- and antiapoptotic regions (BH3 and BH4) of Bcl-2, as demonstrated by a nested protein fragment analysis in a peptide array and DXMS analysis. A combination of the solution studies together with a new application of DCA to the eukaryotic proteins NAF-1 and Bcl-2 provided sufficient constraints at amino acid resolution to predict the interaction surfaces and orientation of the protein–protein interactions involved in the docked structure. The specific integrated approach described in this paper provides the first structural information, to our knowledge, for future targeting of the NAF-1–Bcl-2 complex in the regulation of apoptosis/autophagy in cancer biology.
Interactions between mitoNEET and NAF-1 in cells
(Public Library of Science, 2017) Karmi, Ola; Holt, Sarah H.; Song, Luhua; Tamir, Sagi; Luo, Yuting; Bai, Fang; Adenwalla, Ammar; Darash-Yahana, Merav; Sohn, Yang-Sung; Jennings, Patricia A.; Azad, Rajeev K.; Onuchic, José Nelson; Morcos, Faruck; Nechushtai, Rachel; Mittler, Ron; Center for Theoretical Biological Physics
The NEET proteins mitoNEET (mNT) and nutrient-deprivation autophagy factor-1 (NAF-1) are required for cancer cell proliferation and resistance to oxidative stress. NAF-1 and mNT are also implicated in a number of other human pathologies including diabetes, neurodegeneration and cardiovascular disease, as well as in development, differentiation and aging. Previous studies suggested that mNT and NAF-1 could function in the same pathway in mammalian cells, preventing the over-accumulation of iron and reactive oxygen species (ROS) in mitochondria. Nevertheless, it is unknown whether these two proteins directly interact in cells, and how they mediate their function. Here we demonstrate, using yeast two-hybrid, in vivo bimolecular fluorescence complementation (BiFC), direct coupling analysis (DCA), RNA-sequencing, ROS and iron imaging, and single and double shRNA lines with suppressed mNT, NAF-1 and mNT/NAF-1 expression, that mNT and NAF-1 directly interact in mammalian cells and could function in the same cellular pathway. We further show using an in vitro cluster transfer assay that mNT can transfer its clusters to NAF-1. Our study highlights the possibility that mNT and NAF-1 function as part of an iron-sulfur (2Fe-2S) cluster relay to maintain the levels of iron and Fe-S clusters under control in the mitochondria of mammalian cells, thereby preventing the activation of apoptosis and/or autophagy and supporting cellular proliferation.
Interrogating the topological robustness of gene regulatory circuits by randomization
(Public Library of Science, 2017) Huang, Bin; Lu, Mingyang; Jia, Dongya; Ben-Jacob, Eshel; Levine, Herbert; Onuchic, José Nelson; Center for Theoretical Biological Physics
One of the most important roles of cells is performing their cellular tasks properly for survival. Cells usually achieve robust functionality, for example, cell-fate decision-making and signal transduction, through multiple layers of regulation involving many genes. Despite the combinatorial complexity of gene regulation, its quantitative behavior has been typically studied on the basis of experimentally verified core gene regulatory circuitry, composed of a small set of important elements. It is still unclear how such a core circuit operates in the presence of many other regulatory molecules and in a crowded and noisy cellular environment. Here we report a new computational method, named random circuit perturbation (RACIPE), for interrogating the robust dynamical behavior of a gene regulatory circuit even without accurate measurements of circuit kinetic parameters. RACIPE generates an ensemble of random kinetic models corresponding to a fixed circuit topology, and utilizes statistical tools to identify generic properties of the circuit. By applying RACIPE to simple toggle-switch-like motifs, we observed that the stable states of all models converge to experimentally observed gene state clusters even when the parameters are strongly perturbed. RACIPE was further applied to a proposed 22-gene network of the Epithelial-to-Mesenchymal Transition (EMT), from which we identified four experimentally observed gene states, including the states that are associated with two different types of hybrid Epithelial/Mesenchymal phenotypes. Our results suggest that dynamics of a gene circuit is mainly determined by its topology, not by detailed circuit parameters. Our work provides a theoretical foundation for circuit-based systems biology modeling. We anticipate RACIPE to be a powerful tool to predict and decode circuit design principles in an unbiased manner, and to quantitatively evaluate the robustness and heterogeneity of gene expression.
Lowered pH Leads to Fusion Peptide Release and a Highly Dynamic Intermediate of Influenza Hemagglutinin
(American Chemical Society, 2016) Lin, Xingcheng; Noel, Jeffrey K.; Wang, Qinghua; Ma, Jianpeng; Onuchic, José Nelson; Center for Theoretical Biological Physics
Hemagglutinin (HA), the membrane-bound fusion protein of the influenza virus, enables the entry of virus into host cells via a structural rearrangement. There is strong evidence that the primary trigger for this rearrangement is the low pH environment of a late endosome. To understand the structural basis and the dynamic consequences of the pH trigger, we employed explicit-solvent molecular dynamics simulations to investigate the initial stages of the HA transition. Our results indicate that lowered pH destabilizes HA and speeds up the dissociation of the fusion peptides (FPs). A buried salt bridge between the N-terminus and Asp1122 of HA stem domain locks the FPs and may act as one of the pH sensors. In line with recent observations from simplified protein models, we find that, after the dissociation of FPs, a structural order–disorder transition in a loop connecting the central coiled-coil to the C-terminal domains produces a highly mobile HA. This motion suggests the existence of a long-lived asymmetric or “symmetry-broken” intermediate during the HA conformational change. This intermediate conformation is consistent with models of hemifusion, and its early formation during the conformational change has implications for the aggregation seen in HA activity.
Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch
(Oxford University Press, 2019) Roy, Susmita; Hennelly, Scott P.; Lammert, Heiko; Onuchic, José Nelson; Sanbonmatsu, Karissa Y.
Investigations of most riboswitches remain confined to the ligand-binding aptamer domain. However, during the riboswitch mediated transcription regulation process, the aptamer domain and the expression platform compete for a shared strand. If the expression platform dominates, an anti-terminator helix is formed, and the transcription process is active (ON state). When the aptamer dominates, transcription is terminated (OFF state). Here, we use an expression platform switching experimental assay and structure-based electrostatic simulations to investigate this ON-OFF transition of the full length SAM-I riboswitch and its magnesium concentration dependence. Interestingly, we find the ratio of the OFF population to the ON population to vary non-monotonically as magnesium concentration increases. Upon addition of magnesium, the aptamer domain pre-organizes, populating the OFF state, but only up to an intermediate magnesium concentration level. Higher magnesium concentration preferentially stabilizes the anti-terminator helix, populating the ON state, relatively destabilizing the OFF state. Magnesium mediated aptamer-expression platform domain closure explains this relative destabilization of the OFF state at higher magnesium concentration. Our study reveals the functional potential of magnesium in controlling transcription of its downstream genes and underscores the importance of a narrow concentration regime near the physiological magnesium concentration ranges, striking a balance between the OFF and ON states in bacterial gene regulation.
Modeling the Transitions between Collective and Solitary Migration Phenotypes in Cancer Metastasis
(Macmillan Publishers Limited, 2015) Huang, Bin; Jolly, Mohit Kumar; Lu, Mingyang; Tsarfaty, Ilan; Ben-Jacob, Eshel; Onuchic, José Nelson; Center for Theoretical Biological Physics
Cellular plasticity during cancer metastasis is a major clinical challenge. Two key cellular plasticity mechanisms —Epithelial-to-Mesenchymal Transition (EMT) and Mesenchymal-to-Amoeboid Transition (MAT) – have been carefully investigated individually, yet a comprehensive understanding of their interconnections remains elusive. Previously, we have modeled the dynamics of the core regulatory circuits for both EMT (miR-200/ZEB/miR-34/SNAIL) and MAT (Rac1/RhoA). We now extend our previous work to study the coupling between these two core circuits by considering the two microRNAs (miR-200 and miR-34) as external signals to the core MAT circuit. We show that this coupled circuit enables four different stable steady states (phenotypes) that correspond to hybrid epithelial/mesenchymal (E/M), mesenchymal (M), amoeboid (A) and hybrid amoeboid/mesenchymal (A/M) phenotypes. Our model recapitulates the metastasis-suppressing role of the microRNAs even in the presence of EMT-inducing signals like Hepatocyte Growth Factor (HGF). It also enables mapping the microRNA levels to the transitions among various cell migration phenotypes. Finally, it offers a mechanistic understanding for the observed phenotypic transitions among different cell migration phenotypes, specifically the Collective-to-Amoeboid Transition (CAT).
Molecular mechanisms of the interhead coordination by interhead tension in cytoplasmic dyneins
(National Academy of Sciences of the United States of America, 2018) Wang, Qian; Jana, Biman; Diehl, Michael R.; Cheung, Margaret S.; Kolomeisky, Anatoly B.; Onuchic, José Nelson
Cytoplasmic dyneins play a major role in retrograde cellular transport by moving vesicles and organelles along microtubule filaments. Dyneins are multidomain motor proteins with two heads that coordinate their motion via their interhead tension. Compared with the leading head, the trailing head has a higher detachment rate from microtubules, facilitating the movement. However, the molecular mechanism of such coordination is unknown. To elucidate this mechanism, we performed molecular dynamics simulations on a cytoplasmic dynein with a structure-based coarse-grained model that probes the effect of the interhead tension on the structure. The tension creates a torque that influences the head rotating about its stalk. The conformation of the stalk switches from the α registry to the β registry during the rotation, weakening the binding affinity to microtubules. The directions of the tension and the torque of the leading head are opposite to those of the trailing head, breaking the structural symmetry between the heads. The leading head transitions less often to the β registry than the trailing head. The former thus has a greater binding affinity to the microtubule than the latter. We measured the moment arm of the torque from a dynein structure in the simulations to develop a phenomenological model that captures the influence of the head rotating about its stalk on the differential detachment rates of the two heads. Our study provides a consistent molecular picture for interhead coordination via interhead tension.
Molecular origin of the weak susceptibility of kinesin velocity to loads and its relation to the collective behavior of kinesins
(National Academy of Sciences, 2017) Wang, Qian; Diehl, Michael R.; Jana, Biman; Cheung, Margaret S.; Kolomeisky, Anatoly B.; Onuchic, José Nelson
Motor proteins are active enzymatic molecules that support important cellular processes by transforming chemical energy into mechanical work. Although the structures and chemomechanical cycles of motor proteins have been extensively investigated, the sensitivity of a motor’s velocity in response to a force is not well-understood. For kinesin, velocity is weakly influenced by a small to midrange external force (weak susceptibility) but is steeply reduced by a large force. Here, we utilize a structure-based molecular dynamic simulation to study the molecular origin of the weak susceptibility for a single kinesin. We show that the key step in controlling the velocity of a single kinesin under an external force is the ATP release from the microtubule-bound head. Only under large loading forces can the motor head release ATP at a fast rate, which significantly reduces the velocity of kinesin. It underpins the weak susceptibility that the velocity will not change at small to midrange forces. The molecular origin of this velocity reduction is that the neck linker of a kinesin only detaches from the motor head when pulled by a large force. This prompts the ATP binding site to adopt an open state, favoring ATP release and reducing the velocity. Furthermore, we show that two load-bearing kinesins are incapable of equally sharing the load unless they are very close to each other. As a consequence of the weak susceptibility, the trailing kinesin faces the challenge of catching up to the leading one, which accounts for experimentally observed weak cooperativity of kinesins motors.

Browsing by Author "Onuchic, José Nelson"

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