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RNA design rules from a massive open laboratory
Lee, Jeehyung,Kladwang, Wipapat,Lee, Minjae,Cantu, Daniel,Azizyan, Martin,Kim, Hanjoo,Limpaecher, Alex,Yoon, Sungroh,Treuille, Adrien,Das, Rhiju National Academy of Sciences 2014 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.111 No.6
<P>Self-assembling RNA molecules present compelling substrates for the rational interrogation and control of living systems. However, imperfect in silico models—even at the secondary structure level—hinder the design of new RNAs that function properly when synthesized. Here, we present a unique and potentially general approach to such empirical problems: the Massive Open Laboratory. The EteRNA project connects 37,000 enthusiasts to RNA design puzzles through an online interface. Uniquely, EteRNA participants not only manipulate simulated molecules but also control a remote experimental pipeline for high-throughput RNA synthesis and structure mapping. We show herein that the EteRNA community leveraged dozens of cycles of continuous wet laboratory feedback to learn strategies for solving in vitro RNA design problems on which automated methods fail. The top strategies—including several previously unrecognized negative design rules—were distilled by machine learning into an algorithm, EteRNABot. Over a rigorous 1-y testing phase, both the EteRNA community and EteRNABot significantly outperformed prior algorithms in a dozen RNA secondary structure design tests, including the creation of dendrimer-like structures and scaffolds for small molecule sensors. These results show that an online community can carry out large-scale experiments, hypothesis generation, and algorithm design to create practical advances in empirical science.</P>
Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
Brunk, Elizabeth,Chang, Roger L.,Xia, Jing,Hefzi, Hooman,Yurkovich, James T.,Kim, Donghyuk,Buckmiller, Evan,Wang, Harris H.,Cho, Byung-Kwan,Yang, Chen,Palsson, Bernhard O.,Church, George M.,Lewis, Nat National Academy of Sciences 2018 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.115 No.43
<P>Understanding the complex interactions of protein posttranslational modifications (PTMs) represents a major challenge in metabolic engineering, synthetic biology, and the biomedical sciences. Here, we present a workflow that integrates multiplex automated genome editing (MAGE), genome-scale metabolic modeling, and atomistic molecular dynamics to study the effects of PTMs on metabolic enzymes and microbial fitness. This workflow incorporates complementary approaches across scientific disciplines; provides molecular insight into how PTMs influence cellular fitness during nutrient shifts; and demonstrates how mechanistic details of PTMs can be explored at different biological scales. As a proof of concept, we present a global analysis of PTMs on enzymes in the metabolic network of Escherichia coll. Based on our workflow results, we conduct a more detailed, mechanistic analysis of the PTMs in three proteins: enolase, serine hydroxymethyltransferase, and transaldolase. Application of this workflow identified the roles of specific PTMs in observed experimental phenomena and demonstrated how individual PTMs regulate enzymes, pathways, and, ultimately, cell phenotypes.</P>
Self-aligned deterministic coupling of single quantum emitter to nanofocused plasmonic modes
Gong, Su-Hyun,Kim, Je-Hyung,Ko, Young-Ho,Rodriguez, Christophe,Shin, Jonghwa,Lee, Yong-Hee,Dang, Le Si,Zhang, Xiang,Cho, Yong-Hoon National Academy of Sciences 2015 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.112 No.17
<P><B>Significance</B></P><P>Control and optimization of interaction between light and single quantum emitters are a crucial issue for cavity quantum electrodynamics studies and quantum information science. Although considerable efforts have been made, reliable and reproducible coupling between quantum emitter and cavity mode still remains a grand challenge due to the uncertainty of the size, i.e., the emission wavelength, and position of the quantum emitter. Here, we demonstrate an unprecedented approach of the self-aligned deterministic coupling of single quantum dots (QDs) to nanofocused plasmonic modes on an entire wafer. Spatial precision is better than any nanopositioning techniques, and almost all processed QDs exhibit outstanding spontaneous emission rate enhancement. This reliable approach eliminates a major obstacle in the implementation of practical solid-state quantum emitters.</P><P>The quantum plasmonics field has emerged and been growing increasingly, including study of single emitter–light coupling using plasmonic system and scalable quantum plasmonic circuit. This offers opportunity for the quantum control of light with compact device footprint. However, coupling of a single emitter to highly localized plasmonic mode with nanoscale precision remains an important challenge. Today, the spatial overlap between metallic structure and single emitter mostly relies either on chance or on advanced nanopositioning control. Here, we demonstrate deterministic coupling between three-dimensionally nanofocused plasmonic modes and single quantum dots (QDs) without any positioning for single QDs. By depositing a thin silver layer on a site-controlled pyramid QD wafer, three-dimensional plasmonic nanofocusing on each QD at the pyramid apex is geometrically achieved through the silver-coated pyramid facets. Enhancement of the QD spontaneous emission rate as high as 22 ± 16 is measured for all processed QDs emitting over ∼150-meV spectral range. This approach could apply to high fabrication yield on-chip devices for wide application fields, e.g., high-efficiency light-emitting devices and quantum information processing.</P>
Jung, Du-Kyo,Lee, Youra,Park, Sung Goo,Park, Byoung Chul,Kim, Ghyung-Hwa,Rhee, Sangkee National Academy of Sciences 2006 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.103 No.26
<P>The ureide pathway, which produces ureides from uric acid, is an essential purine catabolic process for storing and transporting the nitrogen fixed in leguminous plants and some bacteria. PucM from Bacillus subtilis was recently characterized and found to catalyze the second reaction of the pathway, hydrolyzing 5-hydroxyisourate (HIU), a product of uricase in the first step. PucM has 121 amino acid residues and shows high sequence similarity to the functionally unrelated protein transthyretin (TTR), a thyroid hormone-binding protein. Therefore, PucM belongs to the TTR-related proteins (TRP) family. The crystal structures of PucM at 2.0 A and its complexes with the substrate analogs 8-azaxanthine and 5,6-diaminouracil reveal that even with their overall structure similarity, homotetrameric PucM and TTR are completely different, both in their electrostatic potential and in the size of the active sites located at the dimeric interface. Nevertheless, the absolutely conserved residues across the TRP family, including His-14, Arg-49, His-105, and the C-terminal Tyr-118-Arg-119-Gly-120-Ser-121, indeed form the active site of PucM. Based on the results of site-directed mutagenesis of these residues, we propose a possible mechanism for HIU hydrolysis. The PucM structure determined for the TRP family leads to the conclusion that diverse members of the TRP family would function similarly to PucM as HIU hydrolase.</P>
Park, Chiyoung,Lee, Im Hae,Lee, Sanghwa,Song, Yumi,Rhue, Mikyo,Kim, Chulhee National Academy of Sciences 2006 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.103 No.5
<P>The dendritic building blocks with a focal pyrene unit self-organize into vesicles in aqueous phase. The in situ inclusion of the focal pyrene units into the cavity of beta- or gamma-cyclodextrin (CD) induces self-assembled organic nanotubes with an average outer diameter of approximately 45 nm and inner diameter of 22 nm. The surface of the nanotube is covered with CD. Therefore, the functional group on the surface of the nanotube is controlled simply by modifying the functionality of CD. The removal of CD from the nanotube with poly(propylene glycol) reversibly generates vesicles. This work provides an efficient methodology not only to create an additional class of CD-covered organic nanotubes but also to exhibit reversible transformation of nanotubes and vesicles triggered by the motifs of dendron self-assembly, CD inclusion, and pseudorotaxane formation.</P>
Ishikawa, Haruto,Kim, Seongheun,Kwak, Kyungwon,Wakasugi, Keisuke,Fayer, Michael D National Academy of Sciences 2007 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.104 No.49
<P>Intramolecular disulfide bonds are understood to play a role in regulating protein stability and activity. Because disulfide bonds covalently link different components of a protein, they influence protein structure. However, the effects of disulfide bonds on fast (subpicosecond to approximately 100 ps) protein equilibrium structural fluctuations have not been characterized experimentally. Here, ultrafast 2D-IR vibrational echo spectroscopy is used to examine the constraints an intramolecular disulfide bond places on the structural fluctuations of the protein neuroglobin (Ngb). Ngb is a globin family protein found in vertebrate brains that binds oxygen reversibly. Like myoglobin (Mb), Ngb has the classical globin fold and key residues around the heme are conserved. Furthermore, the heme-ligated CO vibrational spectra of Mb (Mb-CO) and Ngb (Ngb-CO) are virtually identical. However, in contrast to Mb, human Ngb has an intramolecular disulfide bond that affects its oxygen affinity and protein stability. By using 2D-IR vibrational echo spectroscopy, we investigated the equilibrium protein dynamics of Ngb-CO by observing the CO spectral diffusion (time dependence of the 2D-IR line shapes) with and without the disulfide bond. Despite the similarity of the linear FTIR spectra of Ngb-CO with and without the disulfide bond, 2D-IR measurements reveal that the equilibrium sampling of different protein configurations is accelerated by disruption of the disulfide bond. The observations indicate that the intramolecular disulfide bond in Ngb acts as an inhibitor of fast protein dynamics even though eliminating it does not produce significant conformational change in the protein's structure.</P>
Graphene transistor based on tunable Dirac fermion optics
Wang, Ke,Elahi, Mirza M.,Wang, Lei,Habib, K. M. Masum,Taniguchi, Takashi,Watanabe, Kenji,Hone, James,Ghosh, Avik W.,Lee, Gil-Ho,Kim, Philip National Academy of Sciences 2019 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.116 No.14
<P><B>Significance</B></P><P>We report an electrically tunable graphene quantum switch based on Dirac fermion optics (DFO), with electrostatically defined analogies of mirror and collimators utilizing angle-dependent Klein tunneling. The device design allows a previously unreported quantitative characterization of the net DFO contribution and leads to improved device performance resilient to abrupt change in temperature, bias, doping, and electrostatic environment. The electrically tunable collimator and reflector demonstrated in this work, and the capability of accurate in situ characterization of their performance, provide the building blocks toward more complicated functional quantum device architecture such as highly integrated electron-optical circuits.</P><P>We present a quantum switch based on analogous Dirac fermion optics (DFO), in which the angle dependence of Klein tunneling is explicitly utilized to build tunable collimators and reflectors for the quantum wave function of Dirac fermions. We employ a dual-source design with a single flat reflector, which minimizes diffusive edge scattering and suppresses the background incoherent transmission. Our gate-tunable collimator–reflector device design enables the quantitative measurement of the net DFO contribution in the switching device operation. We obtain a full set of transmission coefficients between multiple leads of the device, separating the classical contribution from the coherent transport contribution. The DFO behavior demonstrated in this work requires no explicit energy gap. We demonstrate its robustness against thermal fluctuations up to 230 K and large bias current density up to 10<SUP>2</SUP> A/m, over a wide range of carrier densities. The characterizable and tunable optical components (collimator–reflector) coupled with the conjugated source electrodes developed in this work provide essential building blocks toward more advanced DFO circuits such as quantum interferometers. The capability of building optical circuit analogies at a microscopic scale with highly tunable electron wavelength paves a path toward highly integrated and electrically tunable electron-optical components and circuits.</P>