Article
Multidisciplinary Sciences
Wenzhe Liu, Limin Chen, Dongbao Yin, Zhiheng Yang, Jianfei Feng, Qi Sun, Luhua Lai, Xuefeng Guo
Summary: This article introduces a single-molecule electrical nanocircuit based on silicon nanowire field-effect transistors (SiNW-FETs), which enables label-free and long-term measurements of intrinsically disordered proteins (IDPs) at the single-molecule level. By studying the interaction of c-Myc with Max and small molecule inhibitors, the self-folding/unfolding process of c-Myc and its interaction mechanism are observed and analyzed in real time. These findings provide a better understanding of the IDP-binding/folding mechanism and offer a promising nanotechnology platform for IDP conformation/interaction studies and drug discovery.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Samuel Naudi-Fabra, Maud Tengo, Malene Ringkjobing Jensen, Martin Blackledge, Sigrid Milles
Summary: Studying the conformational landscape of intrinsically disordered and partially folded proteins is challenging and requires an integrated approach using multiple techniques to accurately describe the conformational ensembles of these proteins. This integrated approach has been successfully tested and validated, providing new insights into the conformational landscape of viral proteins and demonstrating its potential for integrative dynamic structural biology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Liqun He, Daniel R. Tessier, Kyle Briggs, Matthaios Tsangaris, Martin Charron, Erin M. McConnell, Dmytro Lomovtsev, Vincent Tabard-Cossa
Summary: The research presents a digital immunoassay scheme utilizing solid-state nanopores to reliably quantify the concentration of a target protein in complex biofluids, overcoming challenges in specificity, sensitivity, and consistency associated with protein sensing in solid-state nanopores. The study demonstrates the quantification of thyroid-stimulating hormone from human serum samples, achieving high femtomolar range detection, with further optimization promising increased sensitivity and dynamic range for the development of precision diagnostic tools compatible with point-of-care format.
NATURE COMMUNICATIONS
(2021)
Article
Materials Science, Multidisciplinary
Rui Hu, Wenlong Lu, Guanghao Wei, Hexin Nan, Juan Li, Qing Zhao
Summary: This study demonstrates label-free detection and detailed translocation dynamics study of Herceptin using solid-state nanopores, improving detection sensitivity and temporal resolution for probing structural information of single-molecule Herceptin.
ADVANCED MATERIALS TECHNOLOGIES
(2022)
Review
Biochemistry & Molecular Biology
Samuel Naudi-Fabra, Martin Blackledge, Sigrid Milles
Summary: Single molecule fluorescence and nuclear magnetic resonance spectroscopy are powerful techniques for analyzing intrinsically disordered proteins. They provide complementary views to decipher the complex properties and interactions of IDPs, and have made significant contributions to our understanding of their molecular characteristics.
Article
Chemistry, Multidisciplinary
Jing Yang, Juan Wang, Xuan Liu, Yiming Chen, Yuan Liang, Qi Wang, Shuoxing Jiang, Cheng Zhang
Summary: The solid-state nanopore (SS nanopore) is a sensitive tool for detecting single molecules. By using a DNA polyhedral carrier coating strategy to assist protein translocation through SS nanopores, the current signal-to-noise ratios are significantly improved, which aids the detection of proteins. This coating-assisted method offers a wide range of applications for SS nanopore detection and promotes the development of single-molecule detection.
Article
Biology
Raghavendar R. Sanganna Gari, Grigory Tagiltsev, Ruth A. Pumroy, Yining Jiang, Martin Blackledge, Vera Y. Moiseenkova-Bell, Simon Scheuring
Summary: This study used high-speed atomic force microscopy to image TRPV2 channels in membranes and found that the N-terminal intrinsically disordered regions (IDRs) were involved in intermolecular interactions. The results provide evidence about the 'structure' of TRPV2 IDRs and suggest their potential role in mediating protein-protein interactions.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Jhullian J. Alston, Andrea Soranno, Alex S. Holehouse
Summary: Over the past two decades, intrinsically disordered proteins and protein regions have been recognized as essential drivers of cellular function, with singlemolecule fluorescence spectroscopy and molecular simulations providing insight into their behavior. When combined, these techniques offer complementary information that can help uncover complex molecular details.
Article
Biophysics
Derya Vural, Utsab R. Shrestha, Loukas Petridis, Jeremy C. Smith
Summary: The local structure of water molecules hydrating a globular protein and an intrinsically disordered protein (IDP) was compared using molecular dynamics simulation. The results showed that both proteins experienced perturbations in the first hydration shell, but the perturbation was more significant for the folded protein. This difference was attributed to an increase in the fraction of hydration water molecules interacting with oxygen in the IDP's first hydration shell.
BIOPHYSICAL JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Rakesh Trivedi, Hampapathalu Adimurthy Nagarajaram
Summary: This review discusses different aspects of disordered proteins and protein regions, as well as the experimental and computational methods used to characterize them. Additionally, the role of disordered proteins in diseases and their potential as drug targets are explored.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Nanoscience & Nanotechnology
Ji Wu, Liyuan Liang, Mingkun Zhang, Rui Zhu, Zhong Wang, Yajie Yin, Bohua Yin, Ting Weng, Shaoxi Fang, Wanyi Xie, Liang Wang, Deqiang Wang
Summary: This study utilized a nanopore-based approach to analyze the conformation and translocation behavior of CRP under different conditions. The results showed that the voltage polarity and pH value significantly influenced the translocation speed of CRP, and CRP-aptamer complexes exhibited distinct translocation behavior compared to CRP alone.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Multidisciplinary
Guy Jacoby, Merav Segal Asher, Tamara Ehm, Inbal Abutbul Ionita, Hila Shinar, Salome Azoulay-Ginsburg, Ido Zemach, Gil Koren, Dganit Danino, Michael M. Kozlov, Roey J. Amir, Roy Beck
Summary: This study introduces a new type of peptide amphiphiles, intrinsically disordered peptide amphiphiles (IDPA), that exhibit a sharp pH-induced micellar phase-transition. The shape transition can serve as a mechanism for the design of cargo hold-and-release applications, demonstrating the potential of tailoring interactions between disordered peptides for various stimuli-responsive biomedical applications.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Review
Biophysics
Aritra Chowdhury, Daniel Nettels, Benjamin Schuler
Summary: Many proteins have structurally disordered regions or are entirely disordered under physiological conditions. Understanding the mechanisms of interactions for these intrinsically disordered proteins (IDPs) is important, and single-molecule fluorescence spectroscopy is a versatile tool to investigate their conformational heterogeneity and dynamics. Through this technique, we can observe the diverse structural and dynamic properties of bound IDPs and the kinetic mechanisms facilitated by disorder. This review also discusses emerging links to aggregation, liquid-liquid phase separation, and cellular processes.
ANNUAL REVIEW OF BIOPHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Neeraj Soni, Noam Freundlich, Shilo Ohayon, Diana Huttner, Amit Meller
Summary: Utilizing heat denaturation and sodium dodecyl sulfate (SDS) as aids, nanopore sensing can detect and distinguish unfolded proteins, aiding in single-cell proteomics research.
Article
Nanoscience & Nanotechnology
Yingqi Zhao, Marzia Iarossi, Angela Federica De Fazio, Jian-An Huang, Francesco De Angelis
Summary: Sequence identification of peptides and proteins is crucial for proteomics, but current methods face challenges in discriminating amino acids, unfolding proteins, and controlling motion of proteins with nonuniformly charged sequences. Label-free optical analysis techniques, such as localized surface plasmon resonance detection and surface-enhanced Raman spectroscopy on plasmonic nanopores, show promise for addressing these challenges and enabling single-molecule protein sequencing.
Article
Biochemical Research Methods
Jugal Saharia, Y. M. Nuwan D. Y. Bandara, Min Jun Kim
Summary: Electrolyte chemistry plays a crucial role in the transport properties of analytes through nanopores. In this study, the translocation properties of human serum transferrin (hSTf) protein were investigated under different salt concentrations with positive or negative chemical gradients. The experiments showed that translocations occurred in all configurations under positive gradient conditions, while no translocations were observed under negative gradient conditions.
Article
Chemistry, Multidisciplinary
Y. M. Nuwan D. Y. Bandara, Nasim Farajpour, Kevin J. Freedman
Summary: This study presents a thorough investigation of protein sensing under low electrolyte conditions. The unfolding of proteins was found to be correlated with their isoelectric point and sensitive to the applied voltage and pH. The different forces acting on the protein movement also play a critical role.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Vinay Sharma, Nasim Farajpour, Lauren S. Lastra, Kevin J. Freedman
Summary: Nanopores are widely used in genome sequencing and DNA data storage, and the impact of hydrodynamic forces on DNA sensing in nanopores is still not well understood. In this study, the researchers conducted experiments and developed a computational model to analyze the effects of hydrodynamic flow on DNA transit time, capture rate, current blockade depth, and DNA folding in nanopores. The findings have important implications for DNA sensing technologies.
Article
Biochemical Research Methods
Matthew O'Donohue, Jugal Saharia, Nuwan Bandara, Georgios Alexandrakis, Min Jun Kim
Summary: A silicon nitride-based nanopore was used to characterize the human serum transferrin receptor protein (TfR). The study showed that the presence of dimeric forms of TfR decreased exponentially with increasing applied electric field, while the unfolding behaviors of monomeric TfR were positively dependent on the applied voltage. Comparison with the ligand protein hSTf demonstrated the ability to distinguish between these two protein populations using a solid-state nanopore (SSN). The excluded volumes of TfR were experimentally determined and found to be within error of their theoretical values.
Article
Chemistry, Multidisciplinary
K. K. Sarigamala, T. Albrecht, S. Shukla, S. Saxena
Summary: The article presents a synthesis strategy involving dynamic growth of Ag fractals to achieve in situ interfacial manipulation of imidazole-bridged one-dimensional single-crystalline nanoribbons. It successfully demonstrates the structural and morphological changes of silver vanadate nanoribbons and their ability to harness and store photogenerated auxiliary charge carriers. The synthesis methodology overcomes the major bottleneck in nanoengineering of solid-solid interfacial hetero-structures by using real-time feedback of the imaging e-beam to precisely fabricate these hetero-structures and study the interface transition.
MATERIALS TODAY CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Wesley Flavell, Andreas Neophytou, Angela Demetriadou, Tim Albrecht, Dwaipayan Chakrabarti
Summary: This article presents a method for programmed self-assembly of single colloidal gyroid crystals using rationally designed patchy spheres. The single colloidal gyroid has a wide photonic bandgap and rich chiroptical properties, making it an attractive chiral photonic crystal.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Physical
Joseph M. Hamill, Ali Ismael, Alaa Al-Jobory, Troy L. R. Bennett, Maryam Alshahrani, Xintai Wang, Maxwell Akers-Douglas, Luke A. Wilkinson, Benjamin J. Robinson, Nicholas J. Long, Colin Lambert, Tim Albrecht
Summary: We study the properties of anthracene-based molecules with anchor groups capable of binding to noble metal substrates. The effect of different anchor groups and quantum interference on the electronic and thermoelectric properties of single-molecule junctions is investigated. The results show good agreement between theory and experiments, and suggest that the choice of anchor group and electrode material can significantly influence the thermoelectric behavior of the molecular junction. This finding has important implications for the design of thermoelectric generator devices.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Multidisciplinary
Jugal Saharia, Yapa Mudiyanselage Nuwan Dhananjaya Yapa Bandara, Buddini Iroshika Karawdeniya, Jason Rodger Dwyer, Min Jun Kim
Summary: Stability, long lifetime, resilience against clogging, low noise, and low cost are the key features of solid-state nanopore technology. This study presents a fabrication protocol that allows for obtaining more than 1 million events from a single solid-state nanopore. Additionally, approximately 8.1 million events were reported in this work, encompassing both DNA and protein analytes. The collected data represents a significant advancement in solid-state pore performance and has potential applications in machine learning and other fields.
Article
Chemistry, Analytical
Gokhan Kararsiz, Yasin Cagatay Duygu, Zhengguang Wang, Louis William Rogowski, Sung Jea Park, Min Jun Kim
Summary: This study investigates the motion characteristics of soft alginate microrobots in complex fluidic environments utilizing wireless magnetic fields for actuation. The aim is to explore the diverse motion modes that arise due to shear forces in viscoelastic fluids by employing snowman-shaped microrobots. Microrobots are fabricated via an extrusion-based microcentrifugal droplet method, successfully demonstrating the feasibility of both wiggling and tumbling motions. Through velocity analysis, valuable insights into the relationship between applied magnetic fields and motion characteristics are obtained, facilitating a more realistic understanding of surface locomotion for targeted drug delivery purposes while accounting for swarm dynamics and non-uniform behavior.
Article
Robotics
Yitong Lu, Anuruddha Bhattacharjee, Conlan C. Taylor, Julien Leclerc, Jason M. O'Kane, MinJun Kim, Aaron T. Becker
Summary: Reconfigurable modular robots can dynamically assemble/disassemble using magnetic fields. In this study, magnetic modular cubes with embedded permanent magnets are used to self-assemble into desired 2D polyomino shapes. A closed-loop control method is presented, using computer vision feedback and re-planning, which improves the success rate of forming user-specified polyominoes. The validity of the approach is demonstrated with different cube sizes.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Christopher Weaver, Adrian C. Fortuin, Anton Vladyka, Tim Albrecht
Summary: This study evaluates different approaches for unsupervised classification of cyclic voltammetric data and finds that t-SNE performs the best in both noise-free and noisy cases, followed by UMAP and then PCA.
CHEMICAL COMMUNICATIONS
(2022)
Proceedings Paper
Engineering, Biomedical
Scott Renkes, Minjun Kim, George Alexandrakis
Summary: This study demonstrates the feasibility of using AC modulation of command voltage applied across a Self-induced Back Action Actuated Nanopore Electrophoresis (SANE) sensor to enhance the characterization of nanoparticles (NPs) and single molecules. By analyzing frequency response and electrical behavior, this method provides valuable insights into the charge and dielectric constant of analytes. The results show that different types of NPs exhibit distinctly different electrical responses.
PLASMONICS IN BIOLOGY AND MEDICINE XIX
(2022)
Proceedings Paper
Engineering, Biomedical
Homayoun Asadzadeh, Scott Renkes, MinJun Kim, George Alexandrakis
Summary: This work presents Multiphysics COMSOL simulations to analyze the contributions of optical and electrical forces acting on a 20 nm silica nanoparticle trapped by a plasmonic nanopore sensor. The simulations aim to understand the underlying forces and their impact on the optical-electric measurements.
PLASMONICS IN BIOLOGY AND MEDICINE XIX
(2022)
Article
Chemistry, Multidisciplinary
Luke A. Wilkinson, Troy L. R. Bennett, Iain M. Grace, Joseph Hamill, Xintai Wang, Sophie Au-Yong, Ali Ismael, Samuel P. Jarvis, Songjun Hou, Tim Albrecht, Lesley F. Cohen, Colin Lambert, Benjamin J. Robinson, Nicholas J. Long
Summary: This study investigates the geometric and electronic structure of 1,1'-dialkynylferrocene molecules using various techniques. It reveals that these molecules prefer a 'hairpin' conformation and that the presence and nature of the second alkyne affect their thermoelectric properties. The study also shows that modulating the position of molecular orbitals and the relative position of the secondary alkyne with the metal surface can control the thermoelectric properties of these systems.
Article
Chemistry, Multidisciplinary
Troy L. R. Bennett, Majed Alshammari, Sophie Au-Yong, Ahmad Almutlg, Xintai Wang, Luke A. Wilkinson, Tim Albrecht, Samuel P. Jarvis, Lesley F. Cohen, Ali Ismael, Colin J. Lambert, Benjamin J. Robinson, Nicholas J. Long
Summary: The thermoelectric properties of self-assembled monolayers (SAMs) can be enhanced by incorporating extra molecular layers, providing a new strategy for the design of thin-film thermoelectric materials.