Yuan-Chi Huang

All Publications

• Cytoplasmic organization promotes protein diffusion in Xenopus extracts. Nature communications Huang, W. Y., Cheng, X., Ferrell, J. E. 2022; 13 (1): 5599

  Abstract

  The cytoplasm is highly organized. However, the extent to which this organization influences the dynamics of cytoplasmic proteins is not well understood. Here, we use Xenopus laevis egg extracts as a model system to study diffusion dynamics in organized versus disorganized cytoplasm. Such extracts are initially homogenized and disorganized, and self-organize into cell-like units over the course of tens of minutes. Using fluorescence correlation spectroscopy, we observe that as the cytoplasm organizes, protein diffusion speeds up by about a factor of two over a length scale of a few hundred nanometers, eventually approaching the diffusion time measured in organelle-depleted cytosol. Even though the ordered cytoplasm contained organelles and cytoskeletal elements that might interfere with diffusion, the convergence of protein diffusion in the cytoplasm toward that in organelle-depleted cytosol suggests that subcellular organization maximizes protein diffusivity. The effect of organization on diffusion varies with molecular size, with the effects being largest for protein-sized molecules, and with the time scale of the measurement. These results show that cytoplasmic organization promotes the efficient diffusion of protein molecules in a densely packed environment.

  View details for DOI 10.1038/s41467-022-33339-0

  View details for PubMedID 36151204

• Stochasticity and positive feedback enable enzyme kinetics at the membrane to sense reaction size. Proceedings of the National Academy of Sciences of the United States of America Lee, A. A., Huang, W. Y., Hansen, S. D., Kim, N. H., Alvarez, S., Groves, J. T. 2021; 118 (47)

  Abstract

  Here, we present detailed kinetic analyses of a panel of soluble lipid kinases and phosphatases, as well as Ras activating proteins, acting on their respective membrane surface substrates. The results reveal that the mean catalytic rate of such interfacial enzymes can exhibit a strong dependence on the size of the reaction system-in this case membrane area. Experimental measurements and kinetic modeling reveal how stochastic effects stemming from low molecular copy numbers of the enzymes alter reaction kinetics based on mechanistic characteristics of the enzyme, such as positive feedback. For the competitive enzymatic cycles studied here, the final product-consisting of a specific lipid composition or Ras activity state-depends on the size of the reaction system. Furthermore, we demonstrate how these reaction size dependencies can be controlled by engineering feedback mechanisms into the enzymes.

  View details for DOI 10.1073/pnas.2103626118

  View details for PubMedID 34789575

• Relating cellular signaling timescales to single-molecule kinetics: A first-passage time analysis of Ras activation by SOS. Proceedings of the National Academy of Sciences of the United States of America Huang, W. Y., Alvarez, S., Kondo, Y., Kuriyan, J., Groves, J. T. 2021; 118 (45)

  Abstract

  Son of Sevenless (SOS) is a Ras guanine nucleotide exchange factor (GEF) that plays a central role in numerous cellular signaling pathways. Like many other signaling molecules, SOS is autoinhibited in the cytosol and activates only after recruitment to the membrane. The mean activation time of individual SOS molecules has recently been measured to be 60 s, which is unexpectedly long and seemingly contradictory with cellular signaling timescales, which have been measured to be as fast as several seconds. Here, we rectify this discrepancy using a first-passage time analysis to reconstruct the effective signaling timescale of multiple SOS molecules from their single-molecule activation kinetics. Along with corresponding experimental measurements, this analysis reveals how the functional response time, comprised of many slowly activating molecules, can become substantially faster than the average molecular kinetics. This consequence stems from the enzymatic processivity of SOS in a highly out-of-equilibrium reaction cycle during receptor triggering. Ultimately, rare, early activation events dominate the macroscopic reaction dynamics.

  View details for DOI 10.1073/pnas.2103598118

  View details for PubMedID 34740968

• Coupled Membrane Lipid Miscibility and Phosphotyrosine-Driven Protein Condensation Phase Transitions. Biophysical journal Chung, J. K., Huang, W. Y., Carbone, C. B., Nocka, L. M., Parikh, A. N., Vale, R. D., Groves, J. T. 2020

  Abstract

  Lipid miscibility phase separation has long been considered to be a central element of cell membrane organization. More recently, protein condensation phase transitions, into three-dimensional droplets or in two-dimensional lattices on membrane surfaces, have emerged as another important organizational principle within cells. Here, we reconstitute the linker for activation of Tcells (LAT):growth-factor-receptor-bound protein 2 (Grb2):son of sevenless (SOS) protein condensation on the surface of giant unilamellar vesicles capable of undergoing lipid phase separations. Our results indicate that the assembly of the protein condensate on the membrane surface can drive lipid phase separation. This phase transition occurs isothermally and is governed by tyrosine phosphorylation on LAT. Furthermore, we observe that the induced lipid phase separation drives localization of the SOS substrate, K-Ras, into the LAT:Grb2:SOS protein condensate.

  View details for DOI 10.1016/j.bpj.2020.09.017

  View details for PubMedID 33080222

• Stochastic geometry sensing and polarization in a lipid kinase-phosphatase competitive reaction. Proceedings of the National Academy of Sciences of the United States of America Hansen, S. D., Huang, W. Y., Lee, Y. K., Bieling, P., Christensen, S. M., Groves, J. T. 2019

  Abstract

  Phosphorylation reactions, driven by competing kinases and phosphatases, are central elements of cellular signal transduction. We reconstituted a native eukaryotic lipid kinase-phosphatase reaction that drives the interconversion of phosphatidylinositol-4-phosphate [PI(4)P] and phosphatidylinositol-4,5-phosphate [PI(4,5)P2] on membrane surfaces. This system exhibited bistability and formed spatial composition patterns on supported membranes. In smaller confined regions of membrane, rapid diffusion ensures the system remains spatially homogeneous, but the final outcome-a predominantly PI(4)P or PI(4,5)P2 membrane composition-was governed by the size of the reaction environment. In larger confined regions, interplay between the reactions, diffusion, and confinement created a variety of differentially patterned states, including polarization. Experiments and kinetic modeling reveal how these geometric confinement effects arise from a mechanism based on stochastic fluctuations in the copy number of membrane-bound kinases and phosphatases. The underlying requirements for such behavior are unexpectedly simple and likely to occur in natural biological signaling systems.

  View details for DOI 10.1073/pnas.1901744116

  View details for PubMedID 31278151

• A molecular assembly phase transition and kinetic proofreading modulate Ras activation by SOS. Science (New York, N.Y.) Huang, W. Y., Alvarez, S. n., Kondo, Y. n., Lee, Y. K., Chung, J. K., Lam, H. Y., Biswas, K. H., Kuriyan, J. n., Groves, J. T. 2019; 363 (6431): 1098–1103

  Abstract

  The guanine nucleotide exchange factor (GEF) Son of Sevenless (SOS) is a key Ras activator that is autoinhibited in the cytosol and activates upon membrane recruitment. Autoinhibition release involves structural rearrangements of the protein at the membrane and thus introduces a delay between initial recruitment and activation. In this study, we designed a single-molecule assay to resolve the time between initial receptor-mediated membrane recruitment and the initiation of GEF activity of individual SOS molecules on microarrays of Ras-functionalized supported membranes. The rise-and-fall shape of the measured SOS activation time distribution and the long mean time scale to activation (~50 seconds) establish a basis for kinetic proofreading in the receptor-mediated activation of Ras. We further demonstrate that this kinetic proofreading is modulated by the LAT (linker for activation of T cells)-Grb2-SOS phosphotyrosine-driven phase transition at the membrane.

  View details for DOI 10.1126/science.aau5721

  View details for PubMedID 30846600

• Proceedings of the fifth international RASopathies symposium: When development and cancer intersect. American journal of medical genetics. Part A Rauen, K. A., Schoyer, L., Schill, L., Stronach, B., Albeck, J., Andresen, B. S., Cave, H., Ellis, M., Fruchtman, S. M., Gelb, B. D., Gibson, C. C., Gripp, K., Hefner, E., Huang, W. Y., Itkin, M., Kerr, B., Linardic, C. M., McMahon, M., Oberlander, B., Perlstein, E., Ratner, N., Rogers, L., Schenck, A., Shankar, S., Shvartsman, S., Stevenson, D. A., Stites, E. C., Stork, P. J., Sun, C., Therrien, M., Ullian, E. M., Widemann, B. C., Yeh, E., Zampino, G., Zenker, M., Timmer, W., McCormick, F. 2018: e40632

  Abstract

  This report summarizes and highlights the fifth International RASopathies Symposium: When Development and Cancer Intersect, held in Orlando, Florida in July 2017. The RASopathies comprise a recognizable pattern of malformation syndromes that are caused by germ line mutations in genes that encode components of the RAS/mitogen-activated protein kinase (MAPK) pathway. Because of their common underlying pathogenetic etiology, there is significant overlap in their phenotypic features, which includes craniofacial dysmorphology, cardiac, cutaneous, musculoskeletal, gastrointestinal and ocular abnormalities, neurological and neurocognitive issues, and a predisposition to cancer. The RAS pathway is a well-known oncogenic pathway that is commonly found to be activated in somatic malignancies. As in somatic cancers, the RASopathies can be caused by various pathogenetic mechanisms that ultimately impact or alter the normal function and regulation of the MAPK pathway. As such, the RASopathies represent an excellent model of study to explore the intersection of the effects of dysregulation and its consequence in both development and oncogenesis.

  View details for PubMedID 30302932

• Allosteric Modulation of Grb2 Recruitment to the Intrinsically Disordered Scaffold Protein, LAT, by Remote Site Phosphorylation JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Huang, W. C., Ditlev, J. A., Chiang, H., Rosen, M. K., Groves, J. T. 2017; 139 (49): 18009–15

  Abstract

  Tyrosine phosphorylation of membrane receptors and scaffold proteins followed by recruitment of SH2 domain-containing adaptor proteins constitutes a central mechanism of intracellular signal transduction. During early T-cell receptor (TCR) activation, phosphorylation of linker for activation of T cells (LAT) leading to recruitment of adaptor proteins, including Grb2, is one prototypical example. LAT contains multiple modifiable sites, and this multivalency may provide additional layers of regulation, although this is not well understood. Here, we quantitatively analyze the effects of multivalent phosphorylation of LAT by reconstituting the initial reactions of the TCR signaling pathway on supported membranes. Results from a series of LAT constructs with combinatorial mutations of tyrosine residues reveal a previously unidentified allosteric mechanism in which the binding affinity of LAT:Grb2 depends on the phosphorylation at remote tyrosine sites. Additionally, we find that LAT:Grb2 binding affinity is altered by membrane localization. This allostery mainly regulates the kinetic on-rate, not off-rate, of LAT:Grb2 interactions. LAT is an intrinsically disordered protein, and these data suggest that phosphorylation changes the overall ensemble of configurations to modulate the accessibility of other phosphorylated sites to Grb2. Using Grb2 as a phosphorylation reporter, we further monitored LAT phosphorylation by TCR ζ chain-recruited ZAP-70, which suggests a weakly processive catalysis on membranes. Taken together, these results suggest that signal transmission through LAT is strongly gated and requires multiple phosphorylation events before efficient signal transmission is achieved.

  View details for PubMedID 29182244

• Dynamic Scaling Analysis of Molecular Motion within the LAT:Grb2:SOS Protein Network on Membranes BIOPHYSICAL JOURNAL Huang, W. C., Chiang, H., Groves, J. T. 2017; 113 (8): 1807–13

  Abstract

  Biochemical signaling pathways often involve proteins with multiple, modular interaction domains. Signaling activates binding sites, such as by tyrosine phosphorylation, which enables protein recruitment and growth of networked protein assemblies. Although widely observed, the physical properties of the assemblies, as well as the mechanisms by which they function, remain largely unknown. Here we examine molecular mobility within LAT:Grb2:SOS assemblies on supported membranes by single-molecule tracking. Trajectory analysis reveals a discrete temporal transition to subdiffusive motion below a characteristic timescale, indicating that the LAT:Grb2:SOS assembly has the dynamical structure of a loosely entangled polymer. Such dynamical analysis is also applicable in living cells, where it offers another dimension on the characteristics of cellular signaling assemblies.

  View details for DOI 10.1016/j.bpj.2017.08.024

  View details for Web of Science ID 000413835500016

  View details for PubMedID 29045874

  View details for PubMedCentralID PMC5647511

• Two-step membrane binding by the bacterial SRP receptor enable efficient and accurate Co-translational protein targeting ELIFE Fu, Y., Huang, W. C., Shen, K., Groves, J. T., Miller, T., Shan, S. 2017; 6

  Abstract

  The signal recognition particle (SRP) delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum, or the bacterial plasma membrane. The precise mechanism by which the bacterial SRP receptor, FtsY, interacts with and is regulated at the target membrane remain unclear. Here, quantitative analysis of FtsY-lipid interactions at single-molecule resolution revealed a two-step mechanism in which FtsY initially contacts membrane via a Dynamic mode, followed by an SRP-induced conformational transition to a Stable mode that activates FtsY for downstream steps. Importantly, mutational analyses revealed extensive auto-inhibitory mechanisms that prevent free FtsY from engaging membrane in the Stable mode; an engineered FtsY pre-organized into the Stable mode led to indiscriminate targeting in vitro and disrupted FtsY function in vivo. Our results show that the two-step lipid-binding mechanism uncouples the membrane association of FtsY from its conformational activation, thus optimizing the balance between the efficiency and fidelity of co-translational protein targeting.

  View details for DOI 10.7554/eLife.25885

  View details for Web of Science ID 000406475500001

  View details for PubMedID 28753124

  View details for PubMedCentralID PMC5533587

• Phosphotyrosine-mediated LAT assembly on membranes drives kinetic bifurcation in recruitment dynamics of the Ras activator SOS PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Huang, W. C., Yan, Q., Lin, W., Chung, J. K., Hansen, S. D., Christensen, S. M., Tu, H., Kuriyan, J., Groves, J. T. 2016; 113 (29): 8218–23

  Abstract

  The assembly of cell surface receptors with downstream signaling molecules is a commonly occurring theme in multiple signaling systems. However, little is known about how these assemblies modulate reaction kinetics and the ultimate propagation of signals. Here, we reconstitute phosphotyrosine-mediated assembly of extended linker for the activation of T cells (LAT):growth factor receptor-bound protein 2 (Grb2):Son of Sevenless (SOS) networks, derived from the T-cell receptor signaling system, on supported membranes. Single-molecule dwell time distributions reveal two, well-differentiated kinetic species for both Grb2 and SOS on the LAT assemblies. The majority fraction of membrane-recruited Grb2 and SOS both exhibit fast kinetics and single exponential dwell time distributions, with average dwell times of hundreds of milliseconds. The minor fraction exhibits much slower kinetics, extending the dwell times to tens of seconds. Considering this result in the context of the multistep process by which the Ras GEF (guanine nucleotide exchange factor) activity of SOS is activated indicates that kinetic stabilization from the LAT assembly may be important. This kinetic proofreading effect would additionally serve as a stochastic noise filter by reducing the relative probability of spontaneous SOS activation in the absence of receptor triggering. The generality of receptor-mediated assembly suggests that such effects may play a role in multiple receptor proximal signaling processes.

  View details for DOI 10.1073/pnas.1602602113

  View details for Web of Science ID 000380224500068

  View details for PubMedID 27370798

  View details for PubMedCentralID PMC4961118

• E-cadherin junction formation involves an active kinetic nucleation process PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Biswas, K. H., Hartman, K. L., Yu, C., Harrison, O. J., Song, H., Smith, A. W., Huang, W. C., Lin, W., Guo, Z., Padmanabhan, A., Troyanovsky, S. M., Dustin, M. L., Shapiro, L., Honig, B., Zaidel-Bar, R., Groves, J. T. 2015; 112 (35): 10932–37

  Abstract

  Epithelial (E)-cadherin-mediated cell-cell junctions play important roles in the development and maintenance of tissue structure in multicellular organisms. E-cadherin adhesion is thus a key element of the cellular microenvironment that provides both mechanical and biochemical signaling inputs. Here, we report in vitro reconstitution of junction-like structures between native E-cadherin in living cells and the extracellular domain of E-cadherin (E-cad-ECD) in a supported membrane. Junction formation in this hybrid live cell-supported membrane configuration requires both active processes within the living cell and a supported membrane with low E-cad-ECD mobility. The hybrid junctions recruit α-catenin and exhibit remodeled cortical actin. Observations suggest that the initial stages of junction formation in this hybrid system depend on the trans but not the cis interactions between E-cadherin molecules, and proceed via a nucleation process in which protrusion and retraction of filopodia play a key role.

  View details for DOI 10.1073/pnas.1513775112

  View details for Web of Science ID 000360383200046

  View details for PubMedID 26290581

  View details for PubMedCentralID PMC4568248

• Importin-beta modulates the permeability of the nuclear pore complex in a Ran-dependent manner ELIFE Lowe, A. R., Tang, J. H., Yassif, J., Graf, M., Huang, W. Y., Groves, J. T., Weis, K., Liphardt, J. T. 2015; 4

  Abstract

  Soluble karyopherins of the importin-β (impβ) family use RanGTP to transport cargos directionally through the nuclear pore complex (NPC). Whether impβ or RanGTP regulate the permeability of the NPC itself has been unknown. In this study, we identify a stable pool of impβ at the NPC. A subpopulation of this pool is rapidly turned-over by RanGTP, likely at Nup153. Impβ, but not transportin-1 (TRN1), alters the pore's permeability in a Ran-dependent manner, suggesting that impβ is a functional component of the NPC. Upon reduction of Nup153 levels, inert cargos more readily equilibrate across the NPC yet active transport is impaired. When purified impβ or TRN1 are mixed with Nup153 in vitro, higher-order, multivalent complexes form. RanGTP dissolves the impβ•Nup153 complexes but not those of TRN1•Nup153. We propose that impβ and Nup153 interact at the NPC's nuclear face to form a Ran-regulated mesh that modulates NPC permeability.

  View details for DOI 10.7554/eLife.04052

  View details for Web of Science ID 000351864100002

  View details for PubMedID 25748139

  View details for PubMedCentralID PMC4375889

• H-Ras forms dimers on membrane surfaces via a protein-protein interface PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lin, W., Iversen, L., Tu, H., Rhodes, C., Christensen, S. M., Iwig, J. S., Hansen, S. D., Huang, W. C., Groves, J. T. 2014; 111 (8): 2996–3001

  Abstract

  The lipid-anchored small GTPase Ras is an important signaling node in mammalian cells. A number of observations suggest that Ras is laterally organized within the cell membrane, and this may play a regulatory role in its activation. Lipid anchors composed of palmitoyl and farnesyl moieties in H-, N-, and K-Ras are widely suspected to be responsible for guiding protein organization in membranes. Here, we report that H-Ras forms a dimer on membrane surfaces through a protein-protein binding interface. A Y64A point mutation in the switch II region, known to prevent Son of sevenless and PI3K effector interactions, abolishes dimer formation. This suggests that the switch II region, near the nucleotide binding cleft, is either part of, or allosterically coupled to, the dimer interface. By tethering H-Ras to bilayers via a membrane-miscible lipid tail, we show that dimer formation is mediated by protein interactions and does not require lipid anchor clustering. We quantitatively characterize H-Ras dimerization in supported membranes using a combination of fluorescence correlation spectroscopy, photon counting histogram analysis, time-resolved fluorescence anisotropy, single-molecule tracking, and step photobleaching analysis. The 2D dimerization Kd is measured to be ∼1 × 10(3) molecules/µm(2), and no higher-order oligomers were observed. Dimerization only occurs on the membrane surface; H-Ras is strictly monomeric at comparable densities in solution. Analysis of a number of H-Ras constructs, including key changes to the lipidation pattern of the hypervariable region, suggest that dimerization is a general property of native H-Ras on membrane surfaces.

  View details for DOI 10.1073/pnas.1321155111

  View details for Web of Science ID 000332180900033

  View details for PubMedID 24516166

  View details for PubMedCentralID PMC3939930

• Depletion of Water Molecules Near the End Stage of Steric Zipper Formation JOURNAL OF THE CHINESE CHEMICAL SOCIETY Cheng, H., Huang, W. C., Tsai, T. T., Mou, Y., Chao, J., Chan, J. C. 2013; 60 (7): 794–800

  View details for DOI 10.1002/jccs.201300073

  View details for Web of Science ID 000327695600016

• Steric Zipper Formed by Hydrophobic Peptide Fragment of Syrian Hamster Prion Protein BIOCHEMISTRY Cheng, H., Tsai, T. T., Huang, W. C., Lee, H., Lian, H., Chou, F., Mou, Y., Chan, J. C. 2011; 50 (32): 6815–23

  Abstract

  Steric zippers, where the residues of two neighboring β-sheet layers are tightly interdigitated, have been proposed as fundamental structural units of amyloid fibrils by Eisenberg and co-workers. The steric zipper formed by polypeptides containing the palindromic sequence AGAAAAGA has a distinctive feature that the distance between two interdigitated β-sheet layers is comparable to the interstrand distance of the individual β-sheet. This structural motif is of great interest in the study of prion disease because the AGAAAAGA sequence is highly conserved in prion proteins of different species. In this work, the amyloid fibrils formed by the polypeptides of PrP(113-127), viz. Ac-AGAAAAGAVVGGLGG-NH(2), are taken as the model compound to investigate the biophysical principles governing the steric zipper formation. The target fibrils adopt the structural motif of class 7 steric zipper, which is formed by stacking of antiparallel β-sheet layers with residue 117 + k forming backbone hydrogen bonds to residue 120 - k. Implication of our results in the infectivity of scrapie prion is briefly discussed.

  View details for PubMedID 21749158