Article
Chemistry, Multidisciplinary
Qigang Zhong, Alexander Ihle, Sebastian Ahles, Hermann A. Wegner, Andre Schirmeisen, Daniel Ebeling
Summary: Constructing low-dimensional covalent assemblies with tailored size and connectivity is challenging but important in molecular electronics for tuning the properties of quantum materials. A versatile approach has been developed for building such structures block by block on a surface through highly selective tip-induced intermolecular reactions.
Article
Chemistry, Multidisciplinary
Nicolas Neel, Joerg Kroeger
Summary: The study revealed that the formation of a chemical bond between a CO molecule and a Cu(111) surface is accompanied by bending of the molecular probe due to van der Waals attraction and Pauli repulsion, resulting in characteristic changes in the vertical force between CO and Cu(111) as a function of molecule-surface distance. Experimental data were successfully reproduced by model calculations, shedding new light on vertical-force extrema in scanning probe experiments.
Article
Chemistry, Multidisciplinary
Hiroyuki Tanaka, Akiharu Satake, Masateru Taniguchi
Summary: Utilizing STM and STS techniques, this study investigated the mechanical and electronic properties of ferrocene-bridged trisporphyrin (Fc2P3) adsorbed onto Au(111). The ferrocene moiety acts as a molecular ball bearing in the molecule, and distinct electronic states originating from the ferrocene group were observed, while absent in the porphyrin moieties.
Review
Biochemistry & Molecular Biology
Chiara Schirripa Spagnolo, Stefano Luin
Summary: The choice of probe in single-molecule microscopy requires careful evaluation due to the potential impact of fluorophore characteristics on subtle phenomena observable at the single-molecule level. Factors such as aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra should be considered in fluorophore selection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biophysics
Sarah R. Clippinger Schulte, Brent Scott, Samantha K. Barrick, W. Tom Stump, Thomas Blackwell, Michael J. Greenberg
Summary: The cardiac cycle is tightly regulated and disruption of this process can lead to various diseases. Cardiac contraction is driven by myosin, but it is unclear how thin-filament regulatory proteins affect the mechanics of the cardiac myosin motor. This study found that thin-filament regulatory proteins gate the calcium-dependent interactions between myosin and the thin filament, but do not affect the mechanics or load-dependent kinetics of cardiac myosin at physiologically relevant ATP concentrations.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Physical
Chaya Weeraratna, Chandika Amarasinghe, Wenchao Lu, Musahid Ahmed
Summary: Through techniques such as X-ray photoelectron spectroscopy and terahertz spectroscopy, it is found that aerosols generated from aqueous solutions of glycerol and water have a complex hydrogen bond network that is influenced by the mixing ratio. As the glycerol content increases, different configurations of the hydrogen bond network appear, eventually forming an aerosol resembling pure glycerol.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Instruments & Instrumentation
Bowei Cheng, Da Wu, Ke Bian, Ye Tian, Chaoyu Guo, Kaihui Liu, Ying Jiang
Summary: This article presents a scanning probe microscope (SPM) system based on the qPlus sensor for atomic-scale optical experiments. The system is designed to operate under ultrahigh vacuum and low temperature conditions, and includes front lenses with high numerical apertures to optimize light excitation and collection. The system achieves high mechanical and thermal stability, and enables atomic-resolution imaging, inelastic electron tunneling spectroscopy, and resolution of hydrogen-bonding structures.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2022)
Article
Multidisciplinary Sciences
Yuma Morimitsu, Hisao Matsuno, Yukari Oda, Satoru Yamamoto, Keiji Tanaka
Summary: This study visualizes the adsorption mechanism of polymer chains onto solid surfaces using atomic force microscopy and molecular dynamics simulations. The dependence of adsorption on the chain affects the formation of the interfacial layer and the mechanical properties of DNA/filler bulk composites.
Article
Chemistry, Multidisciplinary
Wonhee Ko, Jose L. Lado, Petro Maksymovych
Summary: Researchers present a new method to probe Andreev reflection in tunnel junctions, using tunneling spectroscopy and junction tunability for quantitative detection of superconductivity. This method allows for unambiguous identification of the origin of superconducting excitations and the detection of higher order Andreev processes in atomic-scale junctions.
Article
Chemistry, Multidisciplinary
Mong-Wen Gu, Chih-Ta Lai, I-Chih Ni, Chih- Wu, Chun-hsien Chen
Summary: Fermi's golden rule, a remarkable concept for transition probability, has not been reported in single-molecule junctions with gold electrodes. To increase electron-transport efficiency, gold electrodes were modified with a monolayer of platinum or palladium, which have partially filled d-shells and significant surface density of states at the Fermi energy. The improved junction conductance is attributed to a stronger electrode-molecule coupling and larger participation of d-electrons in the surface density of states.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Materials Science, Multidisciplinary
Felicity F. Dear, Paraskevas Kontis, Baptiste Gault, Jan Ilavsky, David Rugg, David Dye
Summary: The nucleation and growth of Ti3Al alpha(2) ordered domains in alpha-Ti-Al-X alloys were characterized using various techniques, showing that the addition of solutes such as Mo can increase nucleation density and decrease precipitate size and coarsening rate. The study also found that solutionizing temperature affects nucleation number density, supporting the hypothesis that vacancy concentration affects alpha(2) nucleation. Observation that all solutes increase nucleation number density is consistent with a vacancy-controlled nucleation mechanism.
Article
Multidisciplinary Sciences
David R. Jacobson, Thomas T. Perkins
Summary: By using an atomic-force-microscope assay optimized for mechanical force to reversibly unfold local regions of an individual protein, researchers overcame limitations of chemical denaturation assays in understanding the energetics of membrane proteins. This approach provided quantitative insight into the Delta Delta G of single amino acid mutations in membrane proteins and highlighted the contribution of membrane protein-lipid contacts to folding energetics. The platform established allows for determining Delta Delta G for fully folded membrane proteins embedded in their native bilayers.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Hyun-Kyu Choi, Hyun Gyu Kim, Min Ju Shon, Tae-Young Yoon
Summary: Single-molecule magnetic tweezers provide magnetic force and torque to single target molecules, allowing the study of dynamic changes in biomolecular structures and interactions. Using smaller magnetic beads and shorter tethers improves dynamic response times and measurement precision. High-resolution single-molecule magnetic tweezers can track nanometer changes in target molecules on a millisecond time scale.
ANNUAL REVIEW OF BIOCHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Mohammad Reza Safari, Frank Matthes, Claus M. Schneider, Karl-Heinz Ernst, Daniel E. Buergler
Summary: The interaction between chirality and magnetism has fascinated scientists for many years. Recently, chirality-induced spin selectivity has regained attention. Experimental observations have shown significant spin polarization when electron travels through layers of chiral molecules. However, the exact mechanism behind this phenomenon remains unclear.
Article
Biology
Mert Colpan, Jessika Iwanski, Carol C. Gregorio
Summary: CAP2 is a unique component of thin filament pointed ends in cardiac muscle, depolymerizing and inhibiting actin incorporation into thin filaments, while also playing a critical role in cardiomyocyte maturation. Its function is distinct from other pointed-end proteins, being inhibited by tropomyosin and not controlling thin filament lengths directly. Identification of CAP2's multifunctional roles provides key insights into thin filament architecture regulation in striated muscle.
COMMUNICATIONS BIOLOGY
(2021)
Article
Chemistry, Physical
Souvik Dey, Matthew MacAinsh, Huan-Xiang Zhou
Summary: For intrinsically disordered proteins (IDPs), the dynamics of the backbone play a key role in encoding their function. The dynamics are regulated by local interactions, secondary structures, and glycines. These sequence-dependent changes in backbone dynamics allow IDPs to respond to binding partners in a versatile manner.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Konstantinos Mazarakos, Ramesh Prasad, Huan-Xiang Zhou
Summary: Phase separation of intrinsically disordered proteins (IDPs) is a phenomenon associated with many essential cellular processes. However, there is still a difficulty in computing the binodal from molecular dynamics simulations of IDPs. In this study, a new method called SpiDec is proposed, which allows for the accurate determination of the phase equilibrium of IDPs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Matthew MacAinsh, Huan-Xiang Zhou
Summary: Tau, an intrinsically disordered protein, binds to both microtubules and acidic membranes. This study used molecular dynamics simulations to investigate the dynamic binding of Tau to an acidic membrane. The simulations validated the interaction between amphipathic helices in Tau and the membrane, and showed similarities and differences in residue contacts between Tau and microtubules. This mimicry facilitates both the anchoring of microtubules to membranes and the transfer of Tau from membranes to microtubules.
Article
Physiology
Kirsten R. R. Dunlap, Jennifer L. L. Steiner, Robert C. C. Hickner, P. Bryant Chase, Bradley S. S. Gordon
Summary: Glucocorticoids induce muscle myopathy, but resistance exercise can reverse muscle loss by promoting muscle protein synthesis. However, it is unclear whether resistance exercise can induce an anabolic response in glucocorticoid myopathic muscle, which may be due to altered gene expression caused by long-term glucocorticoid exposure. This study aimed to assess whether high-force contractions can initiate an anabolic response in glucocorticoid myopathic muscle.
JOURNAL OF APPLIED PHYSIOLOGY
(2023)
Article
Chemistry, Physical
Huan-Xiang Zhou
Summary: This article introduces an approach for estimating the lower and upper bounds of sample data using O(N) operations. The approach calculates the mean values of the smallest and largest x values in N-point samples and fits them as functions of N to obtain the estimates for the bounds. Application to synthetic data demonstrates the accuracy and reliability of this approach.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Souvik Dey, Huan-Xiang Zhou
Summary: This study used molecular dynamics simulations to investigate the regulation of the IDP N-WASP, finding that intramolecular interactions keep N-WASP in an autoinhibited state and PIP2 binding can activate it by freeing the acidic motif, which interacts with Arp2/3 to initiate actin polymerization. Competition exists between PIP2 and the acidic motif for binding to the basic region. Even at a 30% PIP2 level in the membrane, the acidic motif only contacts the basic region in 8.5% of the population.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Johansen B. Amin, Miaomiao He, Ramesh Prasad, Xiaoling Leng, Huan-Xiang Zhou, Lonnie P. Wollmuth
Summary: NMDA receptors have two gates that are regulated by distinct subunits, with one gate mainly regulating single channel events and the other gate mainly regulating entry and exit from clusters. The unique kinetics of NMDARs contribute to their role in synaptic signaling, with clusters of rapid opening and closing separated by long silent periods.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Sean T. Smrt, Cristian A. Escobar, Souvik Dey, Timothy A. Cross, Huan-Xiang Zhou
Summary: Mtb infects a quarter of the worldwide population and the rising drug resistance makes it urgent to better understand Mtb cell division. The study reveals that the transmembrane protein FtsQ may serve as a membrane anchor of the Mtb Z-ring, and its disordered cytoplasmic region interacts with multiple partners, indicating its potential role in cell division and as a drug target.
COMMUNICATIONS BIOLOGY
(2023)
Editorial Material
Physiology
P. Bryant Chase, Arianna N. Coons
Review
Biochemistry & Molecular Biology
Isabella Leite Coscarella, Maicon Landim-Vieira, Hosna Rastegarpouyani, Prescott Bryant Chase, Jerome Irianto, Jose Renato Pinto
Summary: Cardiac muscle contraction is different from other muscle types, with the heart continuously undergoing contraction-relaxation cycles. Mechanotransduction in the cardiomyocyte involves the transmission of mechanical signals to the nucleus, leading to changes in gene expression and nucleus morphology. Understanding the correlation between nucleus sensing and dysfunction of sarcomeric proteins may help in studying cardiomyopathic diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Michelle Rodriguez Garcia, Jeffrey Schmeckpeper, Maicon Landim-Vieira, Isabella Leite Coscarella, Xuan Fang, Weikang Ma, Payton A. Spran, Shengyao Yuan, Lin Qi, Aida Rahimi Kahmini, M. Benjamin Shoemaker, James B. Atkinson, Peter M. Kekenes-Huskey, Thomas C. Irving, Prescott Bryant Chase, Bjoern C. Knollmann, Jose Renato Pinto
Summary: In this study, the effects of an ACTN2 missense variant (p.A868T) on cardiac muscle structure and function were investigated. The results showed small structural changes in cardiomyocytes at the ultrastructural level, as well as increased myofilament Ca-2+ sensitivity and faster rates of tension redevelopment in the ACTN2 A868T variant cardiac tissue. Molecular dynamics simulations suggested that the mutation may alter the conformation associated with titin binding. This study establishes the role of alpha-actinin 2 in modulating cross-bridge kinetics and force development in the human myocardium, and provides insights into its involvement in the development of cardiac disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Guodong Hu, Huan-Xiang Zhou
Summary: The SAM/SAH riboswitch binds SAM and SAH with similar affinities. Molecular dynamics simulations reveal the role of Mg2+ ions in stabilizing the RNA structure, widening the groove for ligand entry, and facilitating ribosome binding. Mg2+ plays vital roles in the function of the SAM/SAH riboswitch.
COMMUNICATIONS BIOLOGY
(2023)
Meeting Abstract
Biophysics
Maicon Landim-Vieira, Weikang Ma, Taejeong Song, Coen A. Ottenheijm, Hyun S. Hwang, Henry M. Gong, Maria Papadaki, Bjorn C. Knollmann, Sakthivel Sadayappan, Thomas C. Irving, Prescott B. Chase, J. Renato Pinto
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Isabella Leite Coscarella, Lili Wang, Jerome Irianto, Bjorn C. Knollmann, Prescott B. Chase, J. Renato Pinto
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Michelle C. Rodriguez Garcia, Maicon Landim-Vieira, Jeffrey Schmeckpeper, Lili Wang, Moore B. Shoemaker, Prescott B. Chase, Bjorn C. Knollmann, J. Renato Pinto
BIOPHYSICAL JOURNAL
(2022)