Article
Multidisciplinary Sciences
Akihiro Otomo, Tatsuya Iida, Yasuko Okuni, Hiroshi Ueno, Takeshi Murata, Ryota Iino
Summary: V-ATPases are rotary motor proteins that convert ATP chemical energy into the electrochemical potential of ions, and the study of ATP-driven stepping rotation under different conditions provides insights into the effects of Na+ and ATP on rotation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Physics, Multidisciplinary
Xin Shi, Anna-Katharina Pumm, Jonas Isensee, Wenxuan Zhao, Daniel Verschueren, Alejandro Martin-Gonzalez, Ramin Golestanian, Hendrik Dietz, Cees Dekker
Summary: Researchers have demonstrated a self-assembled DNA nanostructure that exhibits flow-driven rotary motion when docked onto a nanopore. These artificial nanoengines operate autonomously under physiological conditions, providing a new approach to constructing energy-transducing motors at nanoscale interfaces.
Article
Pharmacology & Pharmacy
Yujing Wu, Bang Lou, Ning Zheng, Xuhui Zhou, Ying Gao, Weiyong Hong, Qingliang Yang, Gensheng Yang
Summary: This study presents chromatophore nanoparticles embedded with FOF1-ATPase motors to enhance mucus penetration and improve drug absorption in mucosal tissues. The results show that these motor-embedded nanoparticles successfully increase mucus permeation and exhibit promising potential for glioma therapy.
Article
Nanoscience & Nanotechnology
Stefano Corra, Marina Tranfic Bakic, Jessica Groppi, Massimo Baroncini, Serena Silvi, Emanuele Penocchio, Massimiliano Esposito, Alberto Credi
Summary: This study presents a theoretical model and experimental evidence for the operation of an out-of-equilibrium photoactivated artificial molecular pump. The relationship between light energy input and the deviation of the dissipative state from thermodynamic equilibrium in this artificial system is quantitatively analyzed.
NATURE NANOTECHNOLOGY
(2022)
Article
Physics, Fluids & Plasmas
Thomas Speck
Summary: This study investigates microscopic engines that utilize a single active particle as the working medium, demonstrating the recovery of energy for work during the directed motion of the particle at constant temperature. By considering the chemical degrees of freedom, a wide range of synthetic active particles can be studied without the need to determine the exact microscopic mechanism. Analytical results reveal that the quasistatic thermodynamic efficiency increases beyond the linear-response regime and reaches a maximum at high propulsion speeds, indicating the nontrivial consequences of driving in the active engine's efficiency.
Article
Nanoscience & Nanotechnology
Michael Kathan, Stefano Crespi, Niklas O. Thiel, Daniel L. Stares, Denis Morsa, John de Boer, Gianni Pacella, Tobias van den Enk, Piermichele Kobauri, Giuseppe Portale, Christoph A. Schalley, Ben L. Feringa
Summary: In this study, researchers reported a light-fuelled small-molecule ratchet capable of driving a coupled chemical equilibrium energetically uphill. By bridging imine macrocycles with a molecular motor, the machine can adopt different topologies, allowing for the coupling of continuous mechanical motion with a chemical transformation.
NATURE NANOTECHNOLOGY
(2022)
Article
Chemistry, Physical
Mykola Tasinkevych, Artem Ryabov
Summary: We studied the dynamics of a chemical nanoswimmer in a periodically rocked ratchet potential, and found that mechanochemical coupling can be utilized to control the motion of chemically active particles at the nanoscale.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Multidisciplinary
Nicolai N. Bach, Verena Josef, Harald Maid, Henry Dube
Summary: Researchers have developed a macrocyclic molecular motor structure that can convert a flexible chain into unidirectional linear motion through active mechanical threading. This offers a new approach for molecular knitting technology.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Mathematics, Applied
N. J. Lopez-Alamilla, R. U. L. Cachi
Summary: We present a methodology to approximate the entropy production for Brownian motion in a tilted periodic potential. The approximation is based on the well-known thermodynamic uncertainty relation and provides a tighter lower limit solely based on drift velocity and diffusion. The approach is systematically analyzed in the tight-binding regime, and a relatively simple rule is provided to validate using the tight-binding approach. The implications of the results outside the tight-binding regime are also discussed.
Article
Chemistry, Multidisciplinary
Sofie K. Jensen, Mathias S. Neumann, Rikke Frederiksen, Mathias L. Skavenborg, Mads C. Larsen, Stinne E. Wessel, Jan O. Jeppesen
Summary: Controlling the movement of CBPQT(4+) ring is essential for the full potential utilization of artificial molecular machines. In this study, two isomeric tri-stable [2]rotaxanes incorporating TTF and MPTTF units were synthesized to measure the energy barriers during the movement of CBPQT(4+) ring. By strategically exchanging thiomethyl barriers with thioethyl groups, the movement of CBPQT(4+) ring in the synthesized compounds can be controlled to occur in only one direction. Cyclic voltammetry and H-1 NMR spectroscopy were used to investigate the switching mechanism. The results demonstrate the first successful induction of directional movement of CBPQT(4+) ring in molecular machines using a combination of TTF and MPTTF units with 90% efficiency.
Article
Chemistry, Multidisciplinary
Anastasia Yu Gitlina, Farzaneh Fadaei-Tirani, Albert Ruggi, Carolina Plaice, Kay Severin
Summary: This study demonstrates that fac-Ir(C^N)(3) can be converted into the thermodynamically less stable mer form through a consecutive reaction with acid and base, which is fast, quantitative, and stereoselective and can be reversed by light. This new isomerization process opens up the possibility of using highly luminescent Ir(C^N)(3) complexes as molecular switches.
Review
Chemistry, Multidisciplinary
Anirban Mondal, Ryojun Toyoda, Romain Costil, Ben L. Feringa
Summary: This article summarizes the design, synthesis, and dynamic properties of molecular machines, and presents methods for controlled switching or rotation of different classes of atropisomers under chemical stimulus, categorizing them as molecular switches, rotors, motors, and autonomous motors. Future perspectives and challenges for building sophisticated molecular machines are also provided.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Fengfeng Niu, Yong Liu, Kang Sun, Shun Xu, Jiayuan Dong, Cong Yu, Kaige Yan, Zhiyi Wei
Summary: The study provides insights into the structural and functional regulation of myosin Va, revealing the molecular mechanisms of autoinhibition and activation as well as the specific activation mechanism dependent on multiple cargo adaptors.
Article
Chemistry, Multidisciplinary
Marta Urbanska, Annemarie Ludecke, Wilhelm J. Walter, Antoine M. van Oijen, Karl E. Duderstadt, Stefan Diez
Summary: This study introduces a highly-parallel, microfluidics-based method for rapid collection of force-dependent motility parameters of cytoskeletal motors, significantly improving throughput. DNA-tethered beads are used to apply tunable hydrodynamic forces to stepping kinesin-1 motors, allowing for simultaneous tracking of various motility parameters of hundreds of individual molecules. The approach, applicable to other molecular systems, represents a new methodology for parallelized single-molecule force studies on cytoskeletal motors.
Article
Multidisciplinary Sciences
Alex Albaugh, Geyao Gu, Todd R. Gingrich
Summary: Simulations can unravel the complex relationship between molecular structure and function. In this study, we demonstrate how slight changes in a molecular motor's structure can reverse its typical dynamic behavior using molecular simulations. These findings highlight the potential of molecular simulation in guiding the development of artificial molecular motors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Taekjip Ha, Christian Kaiser, Sua Myong, Bin Wu, Jie Xiao
Summary: Due to their unique abilities to manipulate, label, and image individual molecules, single-molecule techniques provide unprecedented access to elementary biological processes.
Article
Cell Biology
Jonathan J. Ipsaro, Leemor Joshua-Tor
Summary: Maintenance of germline genomic integrity is crucial for animal species survival, with Asterix/GTSF1 playing essential roles in healthy germline development and the piRNA-RNA interference pathway to repress harmful transposons and ensure faithful transmission of genetic information to the next generation.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2022)
Article
Multidisciplinary Sciences
Xiaoli S. Wu, Xue-Yan He, Jonathan J. Ipsaro, Yu-Han Huang, Jonathan B. Preall, David Ng, Yan Ting Shue, Julien Sage, Mikala Egeblad, Leemor Joshua-Tor, Christopher R. Vakoc
Summary: Tuft cells are rare chemosensory cells that play a role in coordinating immune and neural responses to foreign pathogens. Recent studies have shown their involvement in small-cell lung cancer. This study reveals the critical role of POU2F3-OCA-T complex in tuft cell identity and its potential as a molecular vulnerability in small-cell lung cancer.
Article
Chemistry, Multidisciplinary
Hossein Moghimianavval, Chintan Patel, Sonisilpa Mohapatra, Sung-Won Hwang, Tunc Kayikcioglu, Yashar Bashirzadeh, Allen P. Liu, Taekjip Ha
Summary: InterSpy is introduced as a synthetic biology tool for engineering membrane-membrane interfaces. It allows tracking and reconstitution of functional fluorescent protein between apposing synthetic or cell membranes, demonstrating the potential for designing non-native cellular communication pathways and creating synthetic tissues. The technology is tested using a mammalian cell-free expression system and shows promising results.
Article
Biology
Brianna Bibel, Elad Elkayam, Steve Silletti, Elizabeth A. Komives, Leemor Joshua-Tor
Summary: Argonaute (Ago) proteins play a crucial role in post-transcriptional gene regulation through RNA interference. Phosphorylation by CK1 alpha can alleviate miRNA-mediated repression by promoting target release, allowing Ago to target additional mRNAs.
Article
Biology
Claudia C. Carcamo, Matthew F. Poyton, Anand Ranjan, Giho Park, Robert K. Louder, Xinyu A. Feng, Jee Min Kim, Thuc Dzu, Carl Wu, Taekjip Ha
Summary: This study characterizes the 1D scanning properties of SWR1, a chromatin remodeler, and reveals the impacts of various factors on its scanning process. By directly observing SWR1 diffusion on DNA, the study demonstrates that ATP and a DNA-binding subunit play important roles in the overall diffusive behavior of the complex. The findings provide valuable insights into the role of SWR1 in chromatin remodeling.
Article
Cell Biology
Roger S. Zou, Alberto Marin-Gonzalez, Yang Liu, Hans B. Liu, Leo Shen, Rachel K. Dveirin, Jay X. J. Luo, Reza Kalhor, Taekjip Ha
Summary: Here, we propose an approach that combines CRISPR system with high-throughput sequencing to target hundreds of epigenetically diverse endogenous genomic sites simultaneously, measuring Cas9 dynamics and cellular responses. The use of multi-target guide RNAs (mgRNAs) enables massive multiplexing of CRISPR, providing insights into Cas9 binding, cleavage, and cellular response to DNA damage.
NATURE CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Momcilo Gavrilov, Joshua Y. C. Yang, Roger S. Zou, Wen Ma, Chun-Ying Lee, Sonisilpa Mohapatra, Jimin Kang, Ting-Wei Liao, Sua Myong, Taekjip Ha
Summary: Polymerase Chain Reaction (PCR) is a crucial method in molecular diagnostics and life sciences. This study introduces a new method, SHARP (SSB-Helicase Assisted Rapid PCR), which uses an engineered helicase and single-stranded DNA binding protein (SSB) to replace the heating step of PCR. The new method allows the isothermal amplification of DNA fragments up to 6000 base pairs.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Ikenna C. Okafor, Taekjip Ha
Summary: CRISPR Cas9 is an RNA-guided endonuclease that is a part of bacterial adaptive immune system. By developing a single molecule FRET assay, the study investigated the conformational changes of sgRNA and the binding of Cas9 to sgRNA, providing insights into the assembly dynamics of Cas9 RNA ribonucleoprotein complex. This research could contribute to the rational design of sgRNAs and improve the editing outcomes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Cell Biology
Yuan Gao, Xue-Yan He, Xiaoli S. Wu, Yu-Han Huang, Shushan Toneyan, Taehoon Ha, Jonathan J. Ipsaro, Peter K. Koo, Leemor Joshua-Tor, Kelly M. Bailey, Mikala Egeblad, Christopher R. Vakoc
Summary: The transcriptional repressor ETV6 competes with EWS-FLI1 for binding to DNA elements, leading to disrupted transcription regulation and accelerated Ewing sarcoma development. Inactivating ETV6 allows EWS-FLI1 to hyper-activate these cis-elements, promoting mesenchymal differentiation and growth of the tumor.
NATURE CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Aakash Basu, Dmitriy G. Bobrovnikov, Basilio Cieza, Juan Pablo Arcon, Zan Qureshi, Modesto Orozco, Taekjip Ha
Summary: In this study, we comprehensively characterized the mechanical code of DNA using high-throughput experimental methods and developed a physical model to describe the sequence and methylation dependence of DNA deformation. Our measurements and model validations demonstrated that sequence and epigenetic modifications can encode regulatory information in diverse contexts.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yanbo Wang, W. Taylor Cottle, Haobo Wang, Momcilo Gavrilov, Roger S. Zou, Minh-Tam Pham, Srinivasan Yegnasubramanian, Scott Bailey, Taekjip Ha
Summary: We describe a method called sgGOLDFISH for direct visualization of point mutations in situ, which can differentiate wild-type and mutant sequences with single-nucleotide sensitivity. This method has potential applications in studying genetic diseases and nuclear biology.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Katarina Meze, Armend Axhemi, Dennis R. Thomas, Ahmet Doymaz, Leemor Joshua-Tor
Summary: This study employs cryogenic electron microscopy and kinetic analysis to characterize the steps of how the Dis3L2 3'-5' exoribonuclease recognizes and degrades structured RNA targets. The authors discovered a conformational change triggered by dsRNA, repositioning cold shock domains and separating RNA strands. The findings reveal the conformational plasticity of Dis3L2 and detail a mechanism of structured RNA degradation.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Aman Y. Husbands, Antje Feller, Vasudha Aggarwal, Courtney E. Dresden, Ashton S. Holub, Taekjip Ha, Marja C. P. Timmermans
Summary: The START domain of the HD-ZIPIII transcription factors plays a crucial role in promoting homodimerization and increasing transcriptional potency, while also binding to phospholipids. This discovery resolves a long-standing mystery in plant development and highlights the regulatory potential of this evolutionary module.
Article
Cell Biology
Zhe Qian, Dongyan Song, Jonathan J. Ipsaro, Carmelita Bautista, Leemor Joshua-Tor, Johannes T. -H. Yeh, Nicholas K. Tonks
Summary: In this study, the researchers generated a novel monoclonal antibody, RD-43, which targeted the ectodomain of PTPRD to inhibit its function and promote its degradation. Treatment with RD-43 was found to suppress SRC signaling required for breast cancer cell invasion. These findings suggest that antibodies targeting extracellular segments of receptor protein tyrosine phosphatases may have therapeutic potential.
GENES & DEVELOPMENT
(2023)