Article
Biochemistry & Molecular Biology
Eva Griesser, Venukumar Vemula, Andreia Monico, Dolores Perez-Sala, Maria Fedorova
Summary: The cytoskeleton is a supramolecular structure made up of interacting protein networks that play crucial roles in cell dynamics, including migration, division, and stress responses. Redox-related posttranslational modifications (PTMs) are emerging as key players in cytoskeletal regulation, as shown by a study on mild nitroxidative stress inducing changes in cytoskeletal protein organization and PTM profiles. High-resolution mass spectrometry identified 62 different PTMs in vimentin, actin, and tubulin, revealing a chain reaction with formation of numerous reactive species and activation of multiple signaling pathways.
Article
Biology
Marko Usaj, Luisa Moretto, Venukumar Vemula, Aseem Salhotra, Alf Mansson
Summary: The benefits of single molecule studies of biomolecules include the need for minimal amounts of material and the potential to reveal phenomena hidden in ensembles. However, recent single molecule studies of fluorescent ATP turnover by myosin are difficult to reconcile with ensemble studies, with key reasons being complexities due to dye photophysics and fluorescent contaminants. After eliminating these complexities, the distributions of ATP binding dwell times on myosin are best described by 2 to 3 exponential processes, providing new insights into ATP turnover mechanisms.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Galina V. V. Kopylova, Anastasia M. M. Kochurova, Daria S. S. Yampolskaya, Victoria V. V. Nefedova, Andrey K. K. Tsaturyan, Natalia A. A. Koubassova, Sergey Y. Y. Kleymenov, Dmitrii I. I. Levitsky, Sergey Y. Y. Bershitsky, Alexander M. M. Matyushenko, Daniil V. V. Shchepkin
Summary: The TPM1 gene expresses two isoforms of tropomyosin (Tpm) in the myocardium, alpha (aTpm; Tpm 1.1) and kappa (?Tpm; Tpm 1.2), with ?Tpm being the result of alternative splicing. In this study, the structural features and regulatory function of ?Tpm in the atrial and ventricular myocardium were investigated using an in vitro motility assay. The formation of a?Tpm heterodimer was found to be thermodynamically favorable, indicating that ?Tpm most likely exists as a?Tpm heterodimer in the myocardium.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Vlad Costache, Serena Prigent Garcia, Camille N. Plancke, Jing Li, Simon Begnaud, Shashi Kumar Suman, Anne-Cecile Reymann, Taeyoon Kim, Francois B. Robin
Summary: The architecture and dynamics of the actin network are crucial for cell contractility and tissue morphogenesis. This study reveals how formins assemble a polar actin network during pulsed contractions, leading to efficient network contraction.
Article
Multidisciplinary Sciences
Chiao-Peng Hsu, Alfredo Sciortino, Yu Alice de la Trobe, Andreas R. Bausch
Summary: Active matter systems exhibit collective behaviors and this study introduces an experimental setup where active filaments are confined to the surface of a lipid vesicle. The results show the formation of off-equator polar vortices and jammed patterns, demonstrating that spherical confinement and topology can shape activity-induced complex patterns.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Katarzyna Robaszkiewicz, Julia Wrobel, Joanna Moraczewska
Summary: Defects in maintaining the length of actin filaments may contribute to skeletal muscle diseases associated with mutations in tropomyosin genes. The p.R91C variant in Tpm3.12, a tropomyosin isoform expressed in slow-twitch muscle fibers, impairs the regulation of actin severing and depolymerization by cofilin-2, leading to abnormal actin filament turnover. Additionally, troponin also inhibits actin severing and depolymerization to some extent.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Barbara Wawro, Hanna Nieznanska, Krzysztof Nieznanski, Joanna Gruszczynska-Biegala, Dariusz Stepkowski, Hanna Strzelecka-Golaszewska
Summary: This study found that the N-terminal extension of myosin A1 essential light chain interacts with actin and regulates myosin motor activity by changing actin filament conformation. These findings suggest that modifying the sequence of N-terminal ELC peptides may enhance their therapeutic effects.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2022)
Article
Chemistry, Physical
Gloria Lee, Gregor Leech, Pancy Lwin, Jonathan Michel, Christopher Currie, Michael J. Rust, Jennifer L. Ross, Ryan J. McGorty, Moumita Das, Rae M. Robertson-Anderson
Summary: This study combines microscale experiments with mechanistic modeling to investigate how connectivity, rigidity, and force-generation affect emergent material properties in composite networks of actin, tubulin, and myosin in the cytoskeleton. The research reveals that percolated actomyosin networks are essential for contraction, and a critical fraction of microtubules is necessary to sustain controlled dynamics. The comprehensive phase map presented not only provides important insight into different routes the cytoskeleton can use to alter its dynamics and structure, but also serves as a blueprint for designing cytoskeleton-inspired materials with tunability, resilience, and adaptability for diverse applications.
Article
Biophysics
Xi Li, Bin Chen
Summary: By investigating different torque relaxation methods, this study demonstrates that the way torque is relaxed in a formin strongly affects cellular swirling, providing an efficient approach to regulate cellular swirling.
BIOPHYSICAL JOURNAL
(2022)
Article
Virology
Steven J. Moran, Shelby Puckett, David A. Ornelles, Jed C. Macosko, George Holzwarth, Douglas S. Lyles
Summary: A recent study using pattern recognition and machine learning analyzed the movement of single viral ribonucleoprotein particles in living cells and provided a quantitative molecular explanation for active diffusion. The study found that these particles are temporarily confined to traps or pores formed by cytoskeletal elements, and active diffusion occurs when they escape from one trap to another. This research has important implications for understanding the motion of other viral and cellular elements.
JOURNAL OF VIROLOGY
(2022)
Article
Physics, Fluids & Plasmas
Laeschkir Wuerthner, Andriy Goychuk, Erwin Frey
Summary: Intracellular protein patterns play a crucial role in regulating important cellular processes and their dynamics are influenced by changes in cell shape. To understand the underlying mechanisms, a conceptual model for cell polarity on a dynamic one-dimensional manifold is explored. The dynamics of the membrane shape induce pattern-forming instabilities and can also suppress pattern formation and shift existing patterns.
Article
Cell Biology
Brandon Slater, Wonyeong Jung, Taeyoon Kim
Summary: Actomyosin contractility generated by interactions between F-actin and myosin motors in the actin cytoskeleton drives various cellular processes. A computational model was used to study the effects of filaments' length, rigidity, concentration, and repulsive strength on collective movements and pattern formation. The study found four distinct types of structures formed by gliding filaments due to collisions. The study provides better insights into the origin and properties of patterns formed by gliding filaments.
Article
Biochemistry & Molecular Biology
Sotaro Fuchigami, Shoji Takada
Summary: High-speed atomic force microscopy (HS-AFM) is a powerful technique for imaging the structural dynamics of biomolecules. In this study, the authors developed a flexible fitting molecular dynamics (MD) simulation method to infer the conformational and chemical states of a molecular motor, myosin V, from AFM images.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Elias T. Spiliotis, Konstantinos Nakos
Summary: Septins are key components of the cytoskeleton, interacting with actin filaments, microtubules, and membranes to regulate the organization and dynamics of the cytoskeletal networks essential for cellular morphogenesis. They play roles in cytokinesis, cell migration, and host defense against pathogens, with emerging functions at the interface of microtubules and membranes. Additionally, septins are involved in mitosis and meiosis, making them a unique module of cytoskeletal regulators with properties of actin-binding and microtubule-associated proteins.
Article
Biochemistry & Molecular Biology
Cristina Risi, Luisa U. Schaefer, Betty Belknap, Ian Pepper, Howard D. White, Gunnar F. Schroeder, Vitold E. Galkin
Summary: Heart contraction relies on complex interactions between sarcomeric proteins, and missense mutations can lead to cardiovascular diseases. Structural studies have revealed the molecular basis of cardiac diseases caused by missense mutations in myosin and actin proteins, providing insights into the detailed structural description of the cardiac actomyosin interface.
Article
Cell Biology
Alf Mansson
Summary: The study tested models of muscle contraction and found that they performed well in explaining certain aspects of muscle contraction but varied in their capacity to account for maximum power output. The models were able to explain the relationship between phosphate concentration and isometric force, but showed anomalies at high phosphate concentrations.
JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY
(2021)
Article
Biology
Marko Usaj, Luisa Moretto, Venukumar Vemula, Aseem Salhotra, Alf Mansson
Summary: The benefits of single molecule studies of biomolecules include the need for minimal amounts of material and the potential to reveal phenomena hidden in ensembles. However, recent single molecule studies of fluorescent ATP turnover by myosin are difficult to reconcile with ensemble studies, with key reasons being complexities due to dye photophysics and fluorescent contaminants. After eliminating these complexities, the distributions of ATP binding dwell times on myosin are best described by 2 to 3 exponential processes, providing new insights into ATP turnover mechanisms.
COMMUNICATIONS BIOLOGY
(2021)
Review
Pathology
Rajesh Ahirwar, Nabab Khan, Saroj Kumar
Summary: Accurate determination of breast cancer biomarkers such as HER2, CEA, PDGF, MUC1, and VEGF(165) is essential in clinical management. Aptamer-based diagnostic tools show promise as substitutes for conventional methods, with the potential for future clinical adoption. The analytical merits of aptasensors for detecting these biomarkers have been highlighted, showing potential for detection within the pathophysiological range.
EXPERT REVIEW OF MOLECULAR DIAGNOSTICS
(2021)
Review
Biochemistry & Molecular Biology
Rajeshy Ahirwar, Sonu Gandhi, Komal Komal, Geeta Dhaniya, Prem Prakash Tripathi, Vyas Madhavrao Shingatgeri, Krishan Kumar, Jai Gopal Sharma, Saroj Kumar
Summary: COVID-19, caused by SARS-CoV-2, is a life-threatening respiratory infection declared a pandemic in March 2020 due to its rapid global spread. Despite various technological advancements in testing and diagnosis, effective antiretroviral drugs and widespread vaccination are necessary to curb the escalating pandemic.
BIOSCIENCE REPORTS
(2021)
Article
Physics, Multidisciplinary
Aseem Salhotra, Jingyuan Zhu, Pradheebha Surendiran, Christoph Robert Meinecke, Roman Lyttleton, Marko Usaj, Frida W. Lindberg, Marlene Norrby, Heiner Linke, Alf Mansson
Summary: Significant progress has been made in utilizing naturally available molecular motors and cytoskeletal filaments for nanotechnological applications, specifically in biosensing and network-based biocomputation. To prolong the function of the biological system, critical factors such as biocompatibility of flow cell components, air exposure, assay solution composition, and nanofabrication methods need to be systematically investigated and optimized. By optimizing these factors, the function of actin and myosin in nanodevices for biocomputation was prolonged from 60 minutes to > 20 hours, demonstrating the importance of using pyranose oxidase and non-fluorescent actin filaments to increase motility run times. Using commercially available microfluidic channel slides, the viability of these approaches in the in vitro motility assay was demonstrated. Additionally, it was shown that myosin motor fragments can be stored at -80 degrees C for over 10 years, indicating the potential for long-term sustainability in network-based biocomputation.
NEW JOURNAL OF PHYSICS
(2021)
Article
Physics, Multidisciplinary
Cordula Reuther, Rachele Catalano, Aseem Salhotra, Venukumar Vemula, Till Korten, Stefan Diez, Alf Mansson
Summary: Over the past 25 years, significant progress has been made in developing nanotechnological applications involving cytoskeletal filaments and molecular motors. Actin-based and microtubule-based systems have different advantages and face distinct challenges when used for tasks such as biosensing and biocomputation. Understanding these differences can facilitate the design of new devices and optimize future developments.
NEW JOURNAL OF PHYSICS
(2021)
Review
Biochemistry & Molecular Biology
Marko Usaj, Luisa Moretto, Alf Mansson
Summary: Hereditary hypertrophic cardiomyopathy (HCM), caused by mutations in sarcomere proteins, is a common and potentially life-threatening condition. The mechanisms underlying the development of the disease are not well understood, but recent research suggests that hypercontractility and inefficient energy usage may play a central role. Further studies are needed to fully understand the pathogenesis of HCM and identify potential therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Biographical-Item
Physiology
Alf Mansson, Fang Lou, Nancy Curtin, Carlo Reggiani
Review
Engineering, Environmental
Lakhan Kumar, Mohita Chugh, Saroj Kumar, Krishna Kumar, Jaigopal Sharma, Navneeta Bharadvaja
Summary: The wastewater generated in the petrorefinery industry contains various toxic components and can contaminate the environment if not properly treated. Prolonged exposure to these hazardous compounds can have adverse effects on living beings, including pulmonary diseases and neurological toxicity. Petrorefinery wastewater can be treated through physical, chemical, and biological processes, with biological methods being cost-effective and environmentally friendly.
PROCESS SAFETY AND ENVIRONMENTAL PROTECTION
(2022)
Article
Multidisciplinary Sciences
Luisa Moretto, Marko Usaj, Oleg Matusovsky, Dilson E. Rassier, Ran Friedman, Alf Mansson
Summary: Release of Pi from the myosin active site is essential for force generation, but the mechanism behind it is not well understood. This study presents evidence for a multistep Pi-release model that reconciles conflicting views and reveals potential functional complexities.
NATURE COMMUNICATIONS
(2022)
Review
Nanoscience & Nanotechnology
Falco C. M. J. M. van Delft, Alf Mansson, Hillel Kugler, Till Korten, Cordula Reuther, Jingyuan Zhu, Roman Lyttleton, Thomas Blaudeck, Christoph Robert Meinecke, Danny Reuter, Stefan Diez, Heiner Linke
Summary: Network-based biocomputation is an alternative parallel computing approach that can potentially solve combinatorial problems with lower energy consumption. Although there have been advancements in proof-of-principle experiments, there are still challenges in scaling up NBC to an industrial level. A roadmap identifying key scientific and technological needs can provide guidance for this expansion.
Article
Biochemistry & Molecular Biology
Alf Mansson, Dilson E. Rassier
Summary: Bottom-up mechanokinetic models predict ensemble function of actin and myosin based on parameter values derived from studies using isolated proteins. This study tests the prediction capability of a model for different drugs and concentrations, and finds that it qualitatively predicts the effects of most drugs but quantitatively fails to account for the effects of one specific drug. By adjusting key model parameters, the modified model not only improves the prediction of the effects of the specific drug, but also maintains good prediction accuracy for normal physiological ensemble function.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Christoph R. Meinecke, Georg Heldt, Thomas Blaudeck, Frida W. Lindberg, Falco C. M. J. M. van Delft, Mohammad Ashikur Rahman, Aseem Salhotra, Alf Mansson, Heiner Linke, Till Korten, Stefan Diez, Danny Reuter, Stefan E. Schulz
Summary: Network-based biocomputation (NBC) relies on nanofabricated channels to guide biological agents accurately. In this study, we present the large-scale fabrication of optimized microfluidic channel networks (NBC networks) using electron-beam lithography. To confirm their functionality, we solve a classical NP-complete problem, the subset-sum problem, on these NBC networks. By optimizing the material stack, nanolithographic fabrication processes, and motor-protein expression and purification, we improve the attachment of functional motor proteins, the smoothness of channel walls and floors, and the motility of filaments. These optimizations increase the reliability of NBC devices and enable the production of larger NBC networks for solving complex combinatorial problems.
Article
Biochemistry & Molecular Biology
Alf Mansson, Marko Usaj, Luisa Moretto, Oleg Matusovsky, Lok Priya Velayuthan, Ran Friedman, Dilson E. Rassier
Summary: The release of Pi from myosin is crucial for energy transduction and the power-stroke. The timing of Pi-release and the power-stroke is poorly understood. Traditional models propose either pre- or post-power-stroke Pi-release, while alternative models suggest a branched kinetic scheme or partial uncoupling. More research is needed to unify these models and enhance our understanding.
Review
Pathology
Rajesh Ahirwar, Akanksha Bhattacharya, Saroj Kumar
Summary: The article reviews non-conventional ELISA formats such as microfluidic-ELISA, paper-ELISA, aptamer-ELISA, and those based on novel incubation methods such as heat-ELISA, pressure-ELISA, microwave-ELISA, and sound-ELISA. The potential of these formats in clinical diagnostics is discussed, highlighting their advantages in terms of speed, low reagent volumes, multiplexing, and affordability.
EXPERT REVIEW OF MOLECULAR DIAGNOSTICS
(2022)
