Article
Biophysics
Alia dos Santos, Natalia Fili, David S. Pearson, Yukti Hari-Gupta, Christopher P. Toseland
Summary: Mechanobiology focuses on how physical forces and mechanical properties affect physiology and disease, with tools often restricted to single-molecule manipulations. However, a novel method has been developed to perform ensemble biochemical and cell-based assays in high-throughput format, greatly increasing availability of mechanobiology measurements.
BIOPHYSICAL JOURNAL
(2021)
Article
Multidisciplinary Sciences
Daniel Ramirez Montero, Humberto Sanchez, Edo van Veen, Theo van Laar, Belen Solano, John F. X. Diffley, Nynke H. Dekker
Summary: In this study, the authors examined the single-molecule motion of fully reconstituted and activated CMG helicases. They found that CMG can move on DNA through both unidirectional translocation and diffusion, with a preference for the former in the presence of ATP and the latter in the absence of ATP. They also demonstrated that nucleotide binding can halt the diffusive motion of CMG. These findings support a mechanism in which nucleotide binding allows newly assembled CMG to engage with the DNA, halting diffusion and facilitating DNA melting for replication initiation.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Barbara Stekas, Steve Yeo, Alice Troitskaia, Masayoshi Honda, Sei Sho, Maria Spies, Yann R. Chemla
Summary: Helicases use NTP hydrolysis to move along and unwind single-stranded nucleic acids in cells, often working in conjunction with other nucleic acid-associated proteins. By studying the interaction between XPD helicase and RPA2, it has been discovered that helicases can switch between different processive states, with transient RPA2 interactions stabilizing the more processive state. This finding sheds light on how accessory proteins regulate helicase activity.
Article
Biology
Martin Rieu, Jessica Valle-Orero, Bertrand Ducos, Jean-Francois Allemand, Vincent Croquette
Summary: The researchers introduced a single-molecule manipulation method called kinetic locking based on magnetic tweezers, which enables direct detection of biomolecular binding without the use of fluorescent probes. By measuring the dynamic interactions of E. coli RecQ helicase with its DNA substrate, they demonstrated the potential of this method for studying DNA-DNA and DNA-protein interactions while avoiding the need for labeling. This fluorescence-free micro-manipulation technique allows functional characterization of DNA/RNA processing proteins, without interference from labels.
COMMUNICATIONS BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Itaru Yanagi, Rena Akahori, Ken-ichi Takeda
Summary: The study investigated the ionic current blockades when poly-(dT)(60) or dNTPs passed through SiN nanopores in an aqueous solution containing (NH4)(2)SO4. The dwell time of poly-(dT)(60) and dCTP in the nanopores was significantly longer in the aqueous solution containing (NH4)(2)SO4 compared to the solution without it. The prolonged dwell time effect was also observed when the nanopores were fabricated via dielectric breakdown in the aqueous solution containing (NH4)(2)SO4 and remained even after replacing the solution with one without (NH4)(2)SO4. Furthermore, the four types of dNTPs could be statistically identified based on their current blockade values when passed through the same nanopore.
Article
Polymer Science
Li-Zhen Sun, Jun-Lin Qian, Pinggen Cai, Han-Xian Hu, Xiaojun Xu, Meng-Bo Luo
Summary: The influence of Mg2+ ion concentration and ssDNA length on the conformation and transcription dynamics is studied, revealing similar behaviors of radius of gyration and translocation time with changes in ion concentration and length. Half-empirical functions are used to predict the effects, and changes in conformation and scaling exponent are observed under different ion concentrations.
Article
Chemistry, Multidisciplinary
Chaoming Gu, Zhoubin Yu, Xiaojie Li, Xin Zhu, Chuanhong Jin, Zhen Cao, Shurong Dong, Jikui Luo, Zhi Ye, Yang Liu
Summary: Solid-state nanopores are crucial in sensing single-biomolecules, but their ultra-short translocation time limits the acquisition of detailed information and further applications. Combining MoS2 and graphene, we fabricated sub-10 nm ultra-thin MoS2-graphene heterostructure nanopores that slowed down the passage of biomolecules. By testing dsDNA and BSA at the single-molecule level, we observed special signals indicating the shape change of BSA during the slow translocation process. These findings suggest the potential of MoS2-graphene heterostructure nanopores in slowing down translocation and acquiring more detailed information about biomolecules.
Article
Multidisciplinary Sciences
Masahiro Naganuma, Hisashi Tadakuma, Yukihide Tomari
Summary: By utilizing single-molecule imaging, this study found that the terminal structures of long dsRNAs and the presence or absence of Loqs-PD do not fundamentally alter Dcr-2's cleavage mode between processive and distributive, but simply impact the likelihood of Dcr-2 undergoing the cleavage reaction. These results provide a refined model for the regulation of the dicing reaction by Dcr-2.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Julia A. M. Bakx, Andreas S. Biebricher, Graeme A. King, Panagiotis Christodoulis, Kata Sarlos, Anna H. Bizard, Ian D. Hickson, Gijs J. L. Wuite, Erwin J. G. Peterman
Summary: Topoisomerase IIIa is a type 1A topoisomerase that forms a complex with RMI1 and RMI2 called TRR in human cells. In this study, the authors used optical tweezers and fluorescence microscopy to investigate the catalytic steps of TRR. They found that TRR forms an open gate in single-stranded DNA and can bind a second single-stranded or double-stranded DNA molecule, leading to catenation. Interestingly, double-stranded DNA binding increases the gate size and the helicase BLM affects the flexibility of the gate. These findings suggest that TRR-mediated transfer of double-stranded DNA may be more important than previously believed.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Matthew Jessop, Jan Felix, Irina Gutsche
Summary: AAA+ ATPases are a diverse protein superfamily that drive various cellular processes. Advances in cryo-EM have provided more detailed insights into their structures, leading to a better understanding of their functional relationships and revealing discrepancies in their classification.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Mihaela-Carmen Unciuleac, Aviv Meir, Chaoyou Xue, Garrett M. Warren, Eric C. Greene, Stewart Shuman
Summary: Mycobacterial AdnAB is a pivotal enzyme involved in DNA repair, particularly in the recombination process of double-strand breaks (DSBs). The study highlights the crucial role of AdnB Trp325 as the key active component of the enzyme, showing that its interaction with the DNA tracking strand is essential for ATP hydrolysis and DNA translocation, without which the enzyme's activity during DSB resection is significantly impaired.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Jonathan M. Craig, Maria Mills, Hwanhee C. Kim, Jesse R. Huang, Sarah J. Abell, Jonathan W. Mount, Jens H. Gundlach, Keir C. Neuman, Andrew H. Laszlo
Summary: Nanopore Tweezers are used to observe the translocation and unwinding processes of Escherichia coli RecQ helicases on DNA at ultra-high spatiotemporal resolution, revealing the mechanochemical coupling and asymmetric energy landscape that drive helicase motion.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jinghua Li, Jianbing Ma, Vikash Kumar, Hang Fu, Chunhua Xu, Shuang Wang, Qi Jia, Qinkai Fan, Xuguang Xi, Ming Li, Haiguang Liu, Ying Lu
Summary: In this study, the authors used single-molecule techniques and computational modeling to investigate the dynamic conformations and their impact on structure-function relationships in two Pif1 helicases. They found that solvent-exposed nucleotides interact dynamically with the helicase surfaces and these interactions play a crucial role in the enzymatic activities of the helicases.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Jiangchuan Shen, Yiling Zhao, Nhung Tuyet Pham, Yuxi Li, Yixiang Zhang, Jonathan Trinidad, Grzegorz Ira, Zhi Qi, Hengyao Niu
Summary: The key nuclease Dna2 interacts with the ssDNA binding protein RPA in two ways to protect the integrity of single stranded DNA and facilitate double strand break repair.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Joshua A. Sommers, Lorin N. Loftus, Martin P. Jones III, Rebecca A. Lee, Caitlin E. Haren, Adaira J. Dumm, Robert M. Brosh Jr
Summary: This study characterized the catalytic functions and properties of the helicase protein Nsp13 of SARS-CoV-2. It was found that Nsp13 exhibits functional cooperativity and has a preference for single-stranded DNA. The study also revealed the regulatory role of Mg2+ concentration in the catalytic functions of Nsp13.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Mate Gyimesi, Adam Horvath, Demeter Turos, Sharad Kumar Suthar, Mate Penzes, Csilla Kurdi, Louise Canon, Carlos Kikuti, Kathleen M. Ruppel, Darshan Trivedi, James A. Spudich, Istvan Lorincz, Anna A. Rauscher, Mihaly Kovacs, Endre Pal, Samuel Komoly, Anne Houdusse, Andras Malnasi-Csizmadia
Article
Pharmacology & Pharmacy
Mate Gyimesi, Anna A. Rauscher, Sharad Kumar Suthar, Kamiran A. Hamow, Kinga Oravecz, Istvan Lorincz, Zsolt Borhegyi, Mate T. Deri, Adam F. Kiss, Katalin Monostory, Pal Tamas Szabo, Suman Nag, Ivan Tomasic, Jacob Krans, Patrick J. Tierney, Mihaly Kovacs, Laszlo Kornya, Andras Malnasi-Csizmadia
Summary: The study demonstrates the potential of small substitutions on the blebbistatin scaffold in drug development targeting myosin-2 family proteins, with implications for isoform-specific inhibition and pharmacokinetic properties. The inhibitory properties of NBleb and AmBleb on various myosin-2 isoforms highlight the importance of fine-tuning compound specificity.
JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS
(2021)
Meeting Abstract
Clinical Neurology
Mate Gyimesi, Adam Horvath, Demeter Turos, Mate Penzes, Csilla Kurdi, Mihaly Kovacs, Andras Malnasi-Csizmadia
Meeting Abstract
Clinical Neurology
Mate Penzes, Demeter Turos, Domokos Mathe, Anna Rauscher, Peter Toth, Ivan Ivic, Mate Gyimesi, Arpad Doboi, Andras Malnasi-Csizmadia
Article
Biochemistry & Molecular Biology
Zoltan Szeltner, Adam Poti, Gabor M. Harami, Mihaly Kovacs, David Szuts
Summary: This study demonstrated the applicability of an SV40 large T antigen-based replication system for studying DNA damage removal and DNA replicative bypass processes. While effective for examining NER and TLS, especially its one-polymerase branch, it is less suited for investigations of homology-related repair processes such as TSw.
Article
Chemistry, Analytical
Sharad Kumar Suthar, Anna A. Rauscher, Mate Winternitz, Mate Gyimesi, Andras Malnasi-Csizmadia
Summary: The study developed simple and consistent chiral HPLC methods for efficient separation of enantiomeric blebbistatin derivatives, showing different derivatives have varied separation outcomes under different column and solvent conditions.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2021)
Article
Multidisciplinary Sciences
Gabor M. Harami, Janos Palinkas, Yeonee SeoI, Zoltan J. Kovacs, Mate Gyimesi, Hajnalka Harami-Papp, Keir C. Neuman, Mihaly Kovacs
Summary: In this study, the researchers found that human Bloom's syndrome helicase plays a role in the processing of displacement loops during DNA repair, depending on cellular regulatory mechanisms. In the presence of interaction partners Topoisomerase III alpha-RMI1-RMI2, the helicase's activity shifts towards efficient disruption of displacement loops, aiding genome stability and faithful inheritance.
NATURE COMMUNICATIONS
(2022)
Meeting Abstract
Biophysics
Mate Gyimesi, Adam I. Horvath, Demeter Turos, Sharad Kumar Suthar, Mate Penzes, Louise Canon, Carlos Kikuti, Kathleen Ruppel, Darshan V. Trivedi, James A. Spudich, Anna A. Rauscher, Mihaly Kovacs, Samuel Komoly, Anne M. Houdusse, Andras Malnasi-Csizmadia
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Mate Gyimesi, Mate Winternitz, Andras Malnasi-Csizmadia
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Adam I. Horvath, Mate Gyimesi, Miklos Kepiro, Boglarka Varkuti, Andras Malnasi-Csizmadia
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Anna A. Rauscher, Mate Gyimesi, Andras Malnasi-Csizmadia
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Mate Winternitz, Mate Gyimesi, Adam I. Horvath, Mate Penzes, Andras Malnasi-Csizmadia
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Clinical Neurology
M. Penzes, D. Turos, D. Mathe, A. Rauscher, P. Toth, I. Ivic, A. Dobolyi, M. Gyimesi, A. Malnasi Csizmadia
INTERNATIONAL JOURNAL OF STROKE
(2020)
Meeting Abstract
Clinical Neurology
M. Gyimesi, A. Horvath, D. Turos, M. Penzes, C. Kurdi, A. Szabo, M. Kovacs, A. Malnasi Csizmadia
INTERNATIONAL JOURNAL OF STROKE
(2020)