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Journal of the American Chemical Society, Volume 143; doi:10.1021/jav143i013_1468819

Journal of the American Chemical Society, Volume 143; doi:10.1021/jav143i013_1468757

Acs Contributing Correspondents
Journal of the American Chemical Society, Volume 143, pp 4857-4858; doi:10.1021/jacs.1c03271

Victor K. Outlaw, , Eric M. Jurgens, Francesca T. Bovier, Yun Zhu, Dale F. Kreitler, Olivia Harder, Stefan Niewiesk, Matteo Porotto, , et al.
Journal of the American Chemical Society; doi:10.1021/jacs.1c01565

The publisher has not yet granted permission to display this abstract.
Liying Kang, Albert Chao, Meng Zhang, Tianyi Yu, Jun Wang, Qi Wang, Huihui Yu, ,
Journal of the American Chemical Society; doi:10.1021/jacs.1c01088

Abstract:
Solution self-assembly of coil-crystalline diblock copolypeptoids has attracted increasing attention due to its capability to form hierarchical nanostructures with tailorable morphologies and functionalities. While the N-substituent (or side chain) structures are known to affect the crystallization of polypeptoids, their roles in dictating the hierarchical solution self-assembly of diblock copolypeptoids are not fully understood. Herein, we designed and synthesized two types of diblock copolypeptoids, i.e., poly(N-methylglycine)-b-poly(N-octylglycine) (PNMG-b-PNOG) and poly(N-methylglycine)-b-poly(N-2-ethyl-1-hexylglycine) (PNMG-b-PNEHG), to investigate the influence of N-substituent structure on the crystalline packing and hierarchical self-assembly of diblock copolypeptoids in methanol. With a linear aliphatic N-substituent, the PNOG blocks pack into a highly ordered crystalline structure with a board-like molecular geometry, resulting in the self-assembly of PNMG-b-PNOG molecules into a hierarchical microflower morphology composed of radially arranged nanoribbon subunits. By contrast, the PNEHG blocks bearing bulky branched aliphatic N-substituents are rod-like and prefer to stack into a columnar hexagonal liquid crystalline mesophase, which drives PNMG-b-PNEHG molecules to self-assemble into symmetrical hexagonal nanosheets in solution. A combination of time-dependent small/wide-angle X-ray scattering and microscopic imaging analysis further revealed the self-assembly mechanisms for the formation of these microflowers and hexagonal nanosheets. These results highlight the significant impact of the N-substituent architecture (i.e., linear versus branched) on the supramolecular self-assembly of diblock copolypeptoids in solution, which can serve as an effective strategy to tune the geometry and hierarchical structure of polypeptoid-based nanomaterials.
Sayaka Imanishi, , Yizhen Yin, Mituhiro Yamada, Marina Kawai,
Journal of the American Chemical Society; doi:10.1021/jacs.1c02593

Abstract:
D/l-Hybrid peptides are an attractive class of molecular modality because they are able to exhibit high proteolytic stability and unique structural diversity which cannot be accessed by those consisting of only proteinogenic l-amino acids. Despite such an expectation, it has not been possible to devise de novo d/l-hybrid peptides capable of disrupting the function of a protein target(s) due to the lack of an effective method that reliably constructs a highly diverse library and screens active species. Here we report for the first time construction of a library consisting of 1012 members of macrocyclic d/l-hybrid peptides containing five kinds of d-amino acids and performance of the RaPID selection against human EGFR as a showcase to uncover PPI (protein–protein interaction) inhibitors.
Madushani Dharmarwardana, , Raymond P. Welch, Carlos Caicedo-Narvaez, Michael A. Luzuriaga, Bhargav S. Arimilli, Gregory T. McCandless, Babak Fahimi, ,
Journal of the American Chemical Society; doi:10.1021/jacs.1c01549

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, Mohamed Fathi Sanad, Antonio Moreno-Vicente, , Maira R. Cerón, Yang-Rong Yao, , , ,
Journal of the American Chemical Society; doi:10.1021/jacs.0c13002

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Samuel N. Gockel, Travis L. Buchanan, Kami L. Hull
Journal of the American Chemical Society; doi:10.1021/jacs.1c03077

Acs Contributing Correspondents
Journal of the American Chemical Society; doi:10.1021/jacs.1c03484

, Jon G. C. Kragskow,
Journal of the American Chemical Society; doi:10.1021/jacs.1c01410

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Yuanyuan Si, Ashley M. Kretsch, Laura M. Daigh, Mark J. Burk,
Journal of the American Chemical Society; doi:10.1021/jacs.1c01452

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Yasuhiro Yamashita, Aika Noguchi, Seiya Fushimi, Miho Hatanaka,
Journal of the American Chemical Society; doi:10.1021/jacs.0c13317

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Yifeng Zhu, Simuck F. Yuk, , Manh-Thuong Nguyen, , , , , Mahalingam Balasubramanian, , et al.
Journal of the American Chemical Society; doi:10.1021/jacs.1c02276

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Maciej D. Korzyński, Zachariah J. Berkson, , ,
Journal of the American Chemical Society; doi:10.1021/jacs.1c00706

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Peng Xu, Priscila López-Rojas,
Journal of the American Chemical Society; doi:10.1021/jacs.1c02490

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Tomas Ricciardulli, Sahithi Gorthy, Jason S. Adams, Coogan Thompson, Ayman M. Karim, Matthew Neurock,
Journal of the American Chemical Society; doi:10.1021/jacs.1c00539

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En-Chih Liu,
Journal of the American Chemical Society; doi:10.1021/jacs.1c01354

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Bhavesh Premdjee, Asser S. Andersen, , ,
Journal of the American Chemical Society; doi:10.1021/jacs.1c02280

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Joshua L. Turnbull, Brittany R. Benlian, Ryan P. Golden,
Journal of the American Chemical Society; doi:10.1021/jacs.1c01139

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, Jesper R. Nilsson, Audrey Gallud, Emanuele Celauro, Cécile Gasse, Fabienne Levi-Acobas, Ivo Sarac, , Anders Dahlén, , et al.
Journal of the American Chemical Society; doi:10.1021/jacs.1c00014

Abstract:
Methods for tracking RNA inside living cells without perturbing their natural interactions and functions are critical within biology and, in particular, to facilitate studies of therapeutic RNA delivery. We present a stealth labeling approach that can efficiently, and with high fidelity, generate RNA transcripts, through enzymatic incorporation of the triphosphate of tCO, a fluorescent tricyclic cytosine analogue. We demonstrate this by incorporation of tCO in up to 100% of the natural cytosine positions of a 1.2 kb mRNA encoding for the histone H2B fused to GFP (H2B:GFP). Spectroscopic characterization of this mRNA shows that the incorporation rate of tCO is similar to cytosine, which allows for efficient labeling and controlled tuning of labeling ratios for different applications. Using live cell confocal microscopy and flow cytometry, we show that the tCO-labeled mRNA is efficiently translated into H2B:GFP inside human cells. Hence, we not only develop the use of fluorescent base analogue labeling of nucleic acids in live-cell microscopy but also, importantly, show that the resulting transcript is translated into the correct protein. Moreover, the spectral properties of our transcripts and their translation product allow for their straightforward, simultaneous visualization in live cells. Finally, we find that chemically transfected tCO-labeled RNA, unlike a state-of-the-art fluorescently labeled RNA, gives rise to expression of a similar amount of protein as its natural counterpart, hence representing a methodology for studying natural, unperturbed processing of mRNA used in RNA therapeutics and in vaccines, like the ones developed against SARS-CoV-2.
Dongsoo Yang, Woo Dae Jang,
Journal of the American Chemical Society; doi:10.1021/jacs.0c12406

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Jiefeng Zhu, Shuyou Chen,
Journal of the American Chemical Society; doi:10.1021/jacs.1c01106

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Ruibin Liang, Jimmy K. Yu, , Fang Liu,
Journal of the American Chemical Society; doi:10.1021/jacs.1c00058

Abstract:
Channelrhodopsin 2 (ChR2) is the most commonly used tool in optogenetics. Because of its faster photocycle compared to wild-type (WT) ChR2, the E123T mutant of ChR2 is a useful optogenetic tool when fast neuronal stimulation is needed. Interestingly, in spite of its faster photocycle, the initial step of the photocycle in E123T (photoisomerization of retinal protonated Schiff base or RPSB) was found experimentally to be much slower than that of WT ChR2. The E123T mutant replaces the negatively charged E123 residue with a neutral T123 residue, perturbing the electric field around the RPSB. Understanding the RPSB photoisomerization mechanism in ChR2 mutants will provide molecular-level insights into how ChR2 photochemical reactivity can be controlled, which will lay the foundation for improving the design of optogenetic tools. In this work, we combine ab initio nonadiabatic dynamics simulation, excited state free energy calculation, and reaction path search to comprehensively characterize the RPSB photoisomerization mechanism in the E123T mutant of ChR2. Our simulation agrees with previous experiments in predicting a red-shifted absorption spectrum and significant slowdown of photoisomerization in the E123T mutant. Interestingly, our simulations predict similar photoisomerization quantum yields for the mutant and WT despite the differences in excited-state lifetime and absorption maximum. Upon mutation, the neutralization of the negative charge on the E123 residue increases the isomerization barrier, alters the reaction pathway, and changes the relative stability of two fluorescent states. Our findings provide new insight into the intricate role of the electrostatic environment on the RPSB photoisomerization mechanism in microbial rhodopsins.
Qi Liu, Jun Yin, Bin-Bin Zhang, Jia-Kai Chen, Yang Zhou, Lu-Min Zhang, Lu-Ming Wang, Qing Zhao, , Jie Shu, et al.
Journal of the American Chemical Society; doi:10.1021/jacs.1c01049

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Yafei Gao, Veronica Carta, Maren Pink,
Journal of the American Chemical Society; doi:10.1021/jacs.1c02068

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Amanda Clifford, Jagotamoy Das, Hanie Yousefi, Alam Mahmud, Jenise B. Chen,
Journal of the American Chemical Society; doi:10.1021/jacs.0c13138

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Jing Zhao, Zehao Pan, Deborah Snyder, ,
Journal of the American Chemical Society; doi:10.1021/jacs.1c02576

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Jingzhen Du, David Hunger, , Jonathan D. Cryer, David M. King, , ,
Journal of the American Chemical Society; doi:10.1021/jacs.1c02482

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Clifton L. Wagner, Gabriel Herrera, Qiao Lin, Chunhua T. Hu,
Journal of the American Chemical Society; doi:10.1021/jacs.1c00440

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Journal of the American Chemical Society; doi:10.1021/jacs.1c00504

Abstract:
This work critically assesses the electrocatalytic activity, stability, and nature of the active phase of a two-dimensional molybdenum carbide (MXene) with single-atomic iron sites, Mo2CTx:Fe (Tx are surface terminating groups O, OH, and F), in the catalysis of the oxygen reduction reaction (ORR). X-ray absorption spectroscopy unequivocally confirmed that the iron single sites were incorporated into the Mo2CTx structure by substituting Mo atoms in the molybdenum carbide lattice with no other detectable Fe-containing phases. Mo2CTx:Fe, the first two-dimensional carbide with isolated iron sites, demonstrates a high catalytic activity and selectivity in the oxygen reduction to hydrogen peroxide. However, an analysis of the electrode material after the catalytic tests revealed that Mo2CTx:Fe transformed in situ into a graphitic carbon framework with dispersed iron oxyhydroxide (ferrihydrite, Fh) species (Fh/C), which are the actual active species. This experimental observation and the results obtained for the titanium and vanadium 2D carbides challenge previous studies that discuss the activity of the native MXene phases in oxygen electrocatalysis. Our work showcases the role of 2D metal carbides as precursors for active carbon-based (electro)catalysts and, more fundamentally, highlights the intrinsic evolution pathways of MXenes in electrocatalysis.
Journal of the American Chemical Society, Volume 143; doi:10.1021/jav143i012_1466851

Journal of the American Chemical Society, Volume 143; doi:10.1021/jav143i012_1466848

Amit Ghosh, Indrajit Paul,
Journal of the American Chemical Society; doi:10.1021/jacs.1c01948

The publisher has not yet granted permission to display this abstract.
Gang Zhou, Tinghui Li, Rong Huang, , Bin Hu, Hao Li, ,
Journal of the American Chemical Society; doi:10.1021/jacs.0c12458

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Chan Shu, Maren Pink, Tobias Junghoefer, Elke Nadler, Suchada Rajca, ,
Journal of the American Chemical Society; doi:10.1021/jacs.1c01305

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Tao Zhou, Yuichiro Hirayama, , Nanami Suzuki, Seiji Tanaka, Nahoko Uchiyama, Yukihiro Goda, Yuko Yoshikawa, Yuji Iwashita, Michio Sato, et al.
Journal of the American Chemical Society; doi:10.1021/jacs.1c01495

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, Vijayanath Elakkat, , , Eskedar Tessema, Ka Long Chan, Rong-Jun Wei, Tarek Trabelsi,
Journal of the American Chemical Society; doi:10.1021/jacs.1c02570

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, Shu Wang, Tatiana B. Kouznetsova, Haley K. Beech, , Michael Rubinstein,
Journal of the American Chemical Society; doi:10.1021/jacs.1c02149

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Sota Akiyama, Natsuki Oyama, Tsubura Endo, Koji Kubota,
Journal of the American Chemical Society, Volume 143, pp 5260-5268; doi:10.1021/jacs.1c02050

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Arunika I. Ekanayake, Lena Sobze, Payam Kelich, Jihea Youk, Nicholas J. Bennett, Raja Mukherjee, Atul Bhardwaj, , ,
Journal of the American Chemical Society; doi:10.1021/jacs.1c01186

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Pengcai Liu, Xing-Yu Chen, Jiawen Cao, Lukas Ruppenthal, , ,
Journal of the American Chemical Society; doi:10.1021/jacs.1c01826

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Journal of the American Chemical Society; doi:10.1021/jacs.1c01328

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Kristen A. Colwell, Megan N. Jackson, Rodolfo M. Torres-Gavosto, Sudi Jawahery, , Joseph M. Falkowski, , ,
Journal of the American Chemical Society; doi:10.1021/jacs.1c00136

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Jihyun Kim, Mihajlo Novakovic, Sundaresan Jayanthi, Adonis Lupulescu, Eriks Kupce, J. Tassilo Grün, Klara Mertinkus, Andreas Oxenfarth, Christian Richter, Robbin Schnieders, et al.
Journal of the American Chemical Society; doi:10.1021/jacs.1c01914

Abstract:
Multidimensional NOESY experiments targeting correlations between exchangeable imino and amino protons provide valuable information about base pairing in nucleic acids. It has been recently shown that the sensitivity of homonuclear correlations involving RNA’s labile imino protons can be significantly enhanced, by exploiting the repolarization brought about by solvent exchanges. Homonuclear correlations, however, are of limited spectral resolution, and usually incapable of tackling relatively large homopolymers with repeating structures like RNAs. This study presents a heteronuclear-resolved version of those NOESY experiments, in which magnetization transfers between the aqueous solvent and the nucleic acid protons are controlled by selecting specific chemical shift combinations of a coupled 1H–15N spin pair. This selective control effectively leads to a pseudo-3D version of HSQC-NOESY, but with cross-peaks enhanced by ∼2–5× as compared with conventional 2D NOESY counterparts. The enhanced signal sensitivity as well as access to both 15N–1H and 1H–1H NOESY dimensions can greatly facilitate RNA assignments and secondary structure determinations, as demonstrated here with the analysis of genome fragments derived from the SARS-CoV-2 virus.
Emdadul Hoque, Mirja Md Mahamudul Hassan,
Journal of the American Chemical Society; doi:10.1021/jacs.0c13415

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