Review
Biochemistry & Molecular Biology
Rafayel Petrosyan, Abhishek Narayan, Michael T. Woodside
Summary: Single-molecule force spectroscopy (SMFS) is a powerful tool for studying protein folding dynamics, uncovering energy landscapes of folding, complex folding pathways, mechanisms of chaperones in assisting folding, effects of ribosomes on co-translational folding, and monitoring membrane protein folding.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Nicholas R. Marzano, Bishnu P. Paudel, Antoine M. van Oijen, Heath Ecroyd
Summary: The study used total internal reflection fluorescence (TIRF) microscopy and single-molecule fluorescence resonance energy transfer (smFRET) to observe the folding process of firefly luciferase proteins mediated by the bacterial Hsp70 system. The researchers found that there are multiple cycles of chaperone binding and release to individual clients during refolding, and high rates of chaperone cycling improve refolding yield. Additionally, they discovered that DnaJ remodels misfolded proteins through a conformational selection mechanism, while DnaK resolves misfolded states through mechanical unfolding. This study elucidates important mechanistic details of chaperone-assisted folding that are inaccessible using other methods.
Article
Biology
Soham Chakraborty, Deep Chaudhuri, Souradeep Banerjee, Madhu Bhatt, Shubhasis Haldar
Summary: The role of chaperones in talin mechanics and stability is investigated. Chaperones were found to affect adhesion proteins' stability by changing their folding mechanics, with unfoldases reducing the unfolding force and foldases increasing it. Chaperones directly reshape the energy landscape of talin, influencing its force-dependent interactions and adhesion dynamics.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Lukas Rohland, Roman Kityk, Luka Smalinskaite, Matthias P. Mayer
Summary: The 70 kDa heat shock proteins (Hsp70s) are versatile molecular chaperones that assist in protein-folding processes. ATP and cochaperones induce structural rearrangements in Hsp70, with peptides causing larger changes and protein clients being more effective in stimulating ATP hydrolysis. The study provides insights into the mechanics, allostery, and dynamics of Hsp70 chaperones.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Philip To, Yingzi Xia, Sea On Lee, Taylor Devlin, Karen G. Fleming, Stephen D. Fried
Summary: The process of protein folding is complex and important, involving cellular factors and processes. Researchers have developed a new method to monitor the structural changes of Escherichia coli proteins in the cell cytosol and with chaperones. The results show that GroEL can assist in refolding the majority of proteins, while DnaK and GroEL have a similar set of proteins that they refold. Additionally, some proteins are not able to be refolded with any chaperones.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Il-Soo Park, Seongchan Kim, Yeajee Yim, Ginam Park, Jinahn Choi, Cheolhee Won, Dal-Hee Min
Summary: This study reports the creation of a synthetic chaperone to control the folding of therapeutic peptides and demonstrates its enhanced therapeutic potential in a tumor model. The synthetic chaperone, based on porous nanoparticles, provides an internal hydrophobic environment which stabilizes the secondary structure of the encapsulated peptides. Additionally, the modified nanoparticles serve as a nanoreactor and effectively deliver the stabilized peptides into cancer cells, resulting in inhibition of cancer growth.
NATURE COMMUNICATIONS
(2022)
Article
Optics
Rohit Chikkaraddy, Rakesh Arul, Lukas A. Jakob, Jeremy J. Baumberg
Summary: This study proposes a method for detecting molecular vibrations in the mid-infrared range at room temperature. By assembling molecules into a plasmonic nanocavity resonant at both mid-infrared and visible wavelengths, and optically pumping them below the electronic absorption band, successful conversion of mid-infrared light and observation of enhanced visible luminescence were achieved.
Article
Biochemical Research Methods
Erik Nordquist, Charles English, Eugenia Clerico, Woody Sherman, Lila Gierasch, Jianhan Chen
Summary: The researchers developed a physics-based molecular dynamics simulation model called Paladin to understand how DnaK binds to specific peptides, predicting the precise residues that bind at specific sites on DnaK and explaining features like binding orientations. The Paladin model provides a physical basis for designing therapeutic peptides and offers insights into how Hsp70s bind substrates with selectivity and promiscuity.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jonathan J. Knowlton, Daniel Gestaut, Boxue Ma, Gwen Taylor, Alpay Burak Seven, Alexander Leitner, Gregory J. Wilson, Sreejesh Shanker, Nathan A. Yates, B. V. Venkataram Prasad, Ruedi Aebersold, Wah Chiu, Judith Frydman, Terence S. Dermody
Summary: The TRiC chaperonin plays a crucial role in folding and assembly of the reovirus sigma 3 capsid protein, interacting with a network of chaperones including prefoldin. This study sheds light on the molecular dynamics of sigma 3 folding and establishes a biological function for TRiC in virus assembly, while also providing structural and functional insights into how TRiC and prefoldin participate in protein complex assembly.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
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
Chemistry, Analytical
Qian Wang, Hua He, Qian Zhang, Zhenzhen Feng, Jiqiang Li, Xiaoliang Chen, Lihua Liu, Xiaojuan Wang, Baosheng Ge, Daoyong Yu, Hao Ren, Fang Huang
Summary: The developed deep-learning assisted single-molecule imaging method can accurately distinguish between monomers and complexes, allowing for real-time tracking of protein interactions with a high accuracy rate.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Filipe E. P. Rodrigues, Antonio J. Figueira, Claudio M. Gomes, Miguel Machuqueiro
Summary: Computational analysis revealed that Aβ-Lys28 plays a key role in stabilizing interactions with S100B, involving residues such as Met79, Thr82, and Glu86. Coulombic interactions, potentially involving the Lys28(Aβ)/Glu86(S100B) pair, are crucial for the holdase-type chaperone activity of S100B, and high ionic strength can reduce the anti-aggregation activity of the Aβ-S100B interaction through electrostatic perturbation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Physics, Multidisciplinary
Yu-Hang Zhang, Zhen-Yong Xue, Hao Sun, Zhu-Wei Zhang, Hu Chen
Summary: There are significant differences in mechanical stability and unfolding dynamics among proteins with different structural compositions. Magnetic tweezers, which can precisely control forces on a pico-Newton scale, are suitable to measure force-induced conformation transitions of proteins. In this study, ACBP was stretched using magnetic tweezers and the unfolding forces at different loading rates were measured. The results showed that ACBP has an extraordinarily long unfolding distance and unfolding of α-helices is less cooperative than β-sheet structures.
ACTA PHYSICA SINICA
(2023)
Article
Biochemistry & Molecular Biology
Joseph Tibbs, Mohamed Ghoneim, Colleen C. Caldwell, Troy Buzynski, Wayne Bowie, Elizabeth M. Boehm, M. Todd Washington, S. M. Ali Tabei, Maria Spies
Summary: Molecular machines within cells exhibit dynamic assembly, disassembly, and reorganization, with molecular interactions between components being observed and quantified through single-molecule level studies and fluorescence microscopy techniques. Analyzing sequences of molecular interactions can reveal the structure and dynamic organization of complexes, providing important insights into complex biological systems.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Saisai Yuan, Yu Zhou, Tengyang Gao, Lichuan Chen, Wei Xu, Ping Duan, Juejun Wang, Zhichao Pan, Chun Tang, Yang Yang, Ruiyun Huang, Zongyuan Xiao, Wenjing Hong
Summary: The folding of molecules is an essential process in nature, and this study demonstrates the use of electric fields to drive and control the folding of molecular conformations. By utilizing the single-molecule break junction technique, the researchers were able to detect conformational changes through monitoring changes in single-molecule conductance, while also using electric fields to achieve in-situ control and detection of molecular folding at the single-molecule level.
CHINESE CHEMICAL LETTERS
(2024)
Article
Biochemistry & Molecular Biology
David C. Thorn, Elmira Bahraminejad, Aidan B. Grosas, Tomas Koudelka, Peter Hoffmann, Jitendra P. Mata, Glyn L. Devlin, Margaret Sunde, Heath Ecroyd, Carl Holt, John A. Carver
Summary: Bovine milk alpha(S2)-casein, an intrinsically disordered protein, readily forms amyloid fibrils in vitro. The disulfide-linked dimer of this protein has a greater propensity to form amyloid fibrils than its monomeric counterpart when incubated at 37 degrees Celsius. Experimental results suggest that the dimer structure of this protein exhibits amyloid-like characteristics.
BIOPHYSICAL CHEMISTRY
(2021)
Article
Genetics & Heredity
Sarah S. Henrikus, Antoine M. van Oijen, Andrew Robinson
Summary: The study demonstrates that the formation of pol IV foci in E. coli cells with DNA damage is recB-dependent, and UmuD and UmuDMODIFIER LETTER PRIME play important roles in modulating pol IV activity.
Article
Biochemistry & Molecular Biology
Caitlin L. Johnston, Nicholas R. Marzano, Bishnu P. Paudel, George Wright, Justin L. P. Benesch, Antoine M. van Oijen, Heath Ecroyd
Summary: Research on small heat shock proteins (sHsps) focuses on their molecular mechanisms and interactions with misfolded proteins, utilizing single-molecule fluorescence to determine the stoichiometries of complexes formed with client proteins like chloride intracellular channel 1. This approach reveals a two-step mechanism by which sHsps like alphaB-crystallin prevent protein aggregation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Michelle D. Wang, Mario Nicodemi, Nynke H. Dekker, Thomas Gregor, David Holcman, Antoine M. van Oijen, Suliana Manley
Article
Biochemistry & Molecular Biology
Richard R. Spinks, Lisanne M. Spenkelink, Sarah A. Stratmann, Zhi-Qiang Xu, N. Patrick J. Stamford, Susan E. Brown, Nicholas E. Dixon, Slobodan Jergic, Antoine M. van Oijen
Summary: In Escherichia coli, the helicase DnaB plays a crucial role in DNA replication by providing stability at the replication fork. Single-molecule experiments have shown that while DnaB is stable, it also has the ability to interact dynamically with other factors. This highlights the importance of DnaB as both a stable anchor and a dynamic player in the replication process.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Richard R. Spinks, Lisanne M. Spenkelink, Nicholas E. Dixon, Antoine M. van Oijen
Summary: Helicases are essential molecular motors that unwind DNA during replication. Recent advances in single-molecule methods have provided new insights into the mechanism of action of replicative helicases, revealing how they translocate and unwind DNA to facilitate DNA replication.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Kristian Claesson, Yee Lian Chew, Heath Ecroyd
Summary: This study describes a simple and rapid flow cytometry-based approach for quantifying fluorescently tagged inclusions in whole worm lysate. It is applicable to various models of aggregation and can monitor the dynamics of inclusion formation.
JOURNAL OF NEUROCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Bishnu P. Paudel, Zhi-Qiang Xu, Slobodan Jergic, Aaron J. Oakley, Nischal Sharma, Simon H. J. Brown, James C. Bouwer, Peter J. Lewis, Nicholas E. Dixon, Antoine M. van Oijen, Harshad Ghodke
Summary: Elongation by RNA polymerase can be dynamically modulated by accessory factors, and the transcription-repair coupling factor TRCF can choose to either rescue or terminate the paused/stalled RNAPs. The mechanism for TRCF's choice remains unclear. Using single-molecule assays with Escherichia coli as a model, it was found that nucleotide-bound Mfd, a bacterial TRCF, can convert the elongation complex (EC) into a catalytically poised state, allowing the EC to restart transcription. After a prolonged residence in this state, ATP hydrolysis by Mfd leads to a remodeling of the EC and loss of the RNA transcript. Biophysical studies also revealed that the motor domain of Mfd can bind and partially melt DNA with a template strand overhang.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Emily E. Selig, Roberta J. Lynn, Courtney O. Zlatic, Yee-Foong Mok, Heath Ecroyd, Paul R. Gooley, Michael D. W. Griffin
Summary: The crystallin domain of human sHSPs interacts with amyloid fibrils to inhibit their elongation and joining. This interaction is sensitive to fibril concentration, suggesting a regulatory role in fibril dynamics.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Brian D. Reed, Michael J. Meyer, Valentin Abramzon, Omer Ad, Pat Adcock, Faisal R. Ahmad, Gun Alppay, James A. Ball, James Beach, Dominique Belhachemi, Anthony Bellofiore, Michael Bellos, Juan Felipe Beltran, Andrew Betts, Mohammad Wadud Bhuiya, Kristin Blacklock, Robert Boer, David Boisvert, Norman D. Brault, Aaron Buxbaum, Steve Caprio, Changhoon Choi, Thomas D. Christian, Robert Clancy, Joseph Clark, Thomas Connolly, Kathren Fink Croce, Richard Cullen, Mel Davey, Jack Davidson, Mohamed M. Elshenawy, Michael Ferrigno, Daniel Frier, Saketh Gudipati, Stephanie Hamill, Zhaoyu He, Sharath Hosali, Haidong Huang, Le Huang, Ali Kabiri, Gennadiy Kriger, Brittany Lathrop, An Li, Peter Lim, Stephen Liu, Feixiang Luo, Caixia Lv, Xiaoxiao Ma, Evan McCormack, Michele Millham, Roger Nani, Manjula Pandey, John Parillo, Gayatri Patel, Douglas H. Pike, Kyle Preston, Adeline Pichard-Kostuch, Kyle Rearick, Todd Rearick, Marco Ribezzi-Crivellari, Gerard Schmid, Jonathan Schultz, Xinghua Shi, Badri Singh, Nikita Srivastava, Shannon F. Stewman, T. R. Thurston, Philip Trioli, Jennifer Tullman, Xin Wang, Yen-Chih Wang, Eric A. G. Webster, Zhizhuo Zhang, Jorge Zuniga, Smita S. Patel, Andrew D. Griffiths, Antoine M. Van Oijen, Michael McKenna, Matthew D. Dyer, Jonathan M. Rothberg
Summary: This study presents a dynamic approach for single-molecule protein sequencing, where single peptides are probed in real time using a mixture of dye-labeled amino acid recognizers and simultaneously cleaved by aminopeptidases. The peptide sequence is identified by measuring fluorescence intensity, lifetime, and binding kinetics. This method enables discrimination of single amino acid substitutions and posttranslational modifications.
Article
Multidisciplinary Sciences
Yichen Zhong, Hakimeh Moghaddas Sani, Bishnu P. Paudel, Jason K. K. Low, Ana P. G. Silva, Stefan Mueller, Chandrika Deshpande, Santosh Panjikar, Xavier J. Reid, Max J. Bedward, Antoine M. van Oijen, Joel P. Mackay
Summary: CHD4 is an essential ATP-dependent translocase that alters chromatin accessibility by repositioning histone octamers. The N-terminal intrinsically disordered region (IDR) promotes remodelling integrity, while the C-terminal region harbours an auto-inhibitory region that is relieved by binding to substrate DNA.
NATURE COMMUNICATIONS
(2022)
Article
Infectious Diseases
Caitlin Keighley, Antoine M. van Oijen, Stuart J. Brentnall, Martina Sanderson-Smith, Peter Newton, Spiros Miyakis
Summary: The study found similar trends in antimicrobial resistance (AMR) among urinary Escherichia coli isolates from a private community-based laboratory and a public hospital-based laboratory in an Australian local health district. AMR rates increased over time in both settings, with consistently higher rates in the public hospital-based laboratory. Interventions targeting the community-based laboratory setting are crucial for addressing AMR in the community.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2022)
Article
Multidisciplinary Sciences
Nicholas R. Marzano, Bishnu P. Paudel, Antoine M. van Oijen, Heath Ecroyd
Summary: The study used total internal reflection fluorescence (TIRF) microscopy and single-molecule fluorescence resonance energy transfer (smFRET) to observe the folding process of firefly luciferase proteins mediated by the bacterial Hsp70 system. The researchers found that there are multiple cycles of chaperone binding and release to individual clients during refolding, and high rates of chaperone cycling improve refolding yield. Additionally, they discovered that DnaJ remodels misfolded proteins through a conformational selection mechanism, while DnaK resolves misfolded states through mechanical unfolding. This study elucidates important mechanistic details of chaperone-assisted folding that are inaccessible using other methods.
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)