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1
Neuman, Keir C., i Attila Nagy. "Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy". Nature Methods 5, nr 6 (29.05.2008): 491–505. http://dx.doi.org/10.1038/nmeth.1218.
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Cheng, Chao, Jun-Li Jia i Shi-Yong Ran. "Polyethylene glycol and divalent salt-induced DNA reentrant condensation revealed by single molecule measurements". Soft Matter 11, nr 19 (2015): 3927–35. http://dx.doi.org/10.1039/c5sm00619h.
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In this study, we investigated the DNA condensation induced by polyethylene glycol (PEG) with different molecular weights (PEG 600 and PEG 6000) in the presence of NaCl or MgCl2 by using magnetic tweezers (MT) and atomic force microscopy (AFM).
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Banerjee, Souradeep, Soham Chakraborty, Abhijit Sreepada, Devshuvam Banerji, Shashwat Goyal, Yajushi Khurana i Shubhasis Haldar. "Cutting-Edge Single-Molecule Technologies Unveil New Mechanics in Cellular Biochemistry". Annual Review of Biophysics 50, nr 1 (6.05.2021): 419–45. http://dx.doi.org/10.1146/annurev-biophys-090420-083836.
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Single-molecule technologies have expanded our ability to detect biological events individually, in contrast to ensemble biophysical technologies, where the result provides averaged information. Recent developments in atomic force microscopy have not only enabled us to distinguish the heterogeneous phenomena of individual molecules, but also allowed us to view up to the resolution of a single covalent bond. Similarly, optical tweezers, due to their versatility and precision, have emerged as a potent technique to dissect a diverse range of complex biological processes, from the nanomechanics of ClpXP protease–dependent degradation to force-dependent processivity of motor proteins. Despite the advantages of optical tweezers, the time scales used in this technology were inconsistent with physiological scenarios, which led to the development of magnetic tweezers, where proteins are covalently linked with the glass surface, which in turn increases the observation window of a single biomolecule from minutes to weeks. Unlike optical tweezers, magnetic tweezers use magnetic fields to impose torque, which makes them convenient for studying DNA topology and topoisomerase functioning. Using modified magnetic tweezers, researchers were able to discover the mechanical role of chaperones, which support their substrate proteinsby pulling them during translocation and assist their native folding as a mechanical foldase. In this article, we provide a focused review of many of these new roles of single-molecule technologies, ranging from single bond breaking to complex chaperone machinery, along with the potential to design mechanomedicine, which would be a breakthrough in pharmacological interventions against many diseases.
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Cheng, Yuanlei, Yashuo Zhang i Huijuan You. "Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy". Biomolecules 11, nr 11 (25.10.2021): 1579. http://dx.doi.org/10.3390/biom11111579.
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G-quadruplexes (G4s) are stable secondary nucleic acid structures that play crucial roles in many fundamental biological processes. The folding/unfolding dynamics of G4 structures are associated with the replication and transcription regulation functions of G4s. However, many DNA G4 sequences can adopt a variety of topologies and have complex folding/unfolding dynamics. Determining the dynamics of G4s and their regulation by proteins remains challenging due to the coexistence of multiple structures in a heterogeneous sample. Here, in this mini-review, we introduce the application of single-molecule force-spectroscopy methods, such as magnetic tweezers, optical tweezers, and atomic force microscopy, to characterize the polymorphism and folding/unfolding dynamics of G4s. We also briefly introduce recent studies using single-molecule force spectroscopy to study the molecular mechanisms of G4-interacting proteins.
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van der Sleen, Lyan M., i Katarzyna M. Tych. "Bioconjugation Strategies for Connecting Proteins to DNA-Linkers for Single-Molecule Force-Based Experiments". Nanomaterials 11, nr 9 (17.09.2021): 2424. http://dx.doi.org/10.3390/nano11092424.
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The mechanical properties of proteins can be studied with single molecule force spectroscopy (SMFS) using optical tweezers, atomic force microscopy and magnetic tweezers. It is common to utilize a flexible linker between the protein and trapped probe to exclude short-range interactions in SMFS experiments. One of the most prevalent linkers is DNA due to its well-defined properties, although attachment strategies between the DNA linker and protein or probe may vary. We will therefore provide a general overview of the currently existing non-covalent and covalent bioconjugation strategies to site-specifically conjugate DNA-linkers to the protein of interest. In the search for a standardized conjugation strategy, considerations include their mechanical properties in the context of SMFS, feasibility of site-directed labeling, labeling efficiency, and costs.
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Velázquez-Carreras, Diana, Manuel Gavilan-Herrera, Ines Martinez-Martin, Carmen Suay-Corredera, Andra C. Dumitru, Elías Herrero Galán i Jorge Alegre-Cebollada. "Towards a new modular polyprotein system compatible with single-molecule force spectroscopy by atomic force microscopy and magnetic tweezers". Biophysical Journal 122, nr 3 (luty 2023): 304a. http://dx.doi.org/10.1016/j.bpj.2022.11.1710.
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Hall, Adam R. "Solid-State Nanopores: From Fabrication to Application". Microscopy Today 20, nr 5 (wrzesień 2012): 24–29. http://dx.doi.org/10.1017/s1551929512000703.
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There are relatively few technologies for measurement at the single-molecule scale. Fluorescent imaging, for example, can be used to directly visualize molecules and their interactions, but diffraction limitations and labeling requirements may push the system from its native state. Although recent advances in super-resolution imaging have been able to break this resolution barrier, important challenges remain. Atomic force microscopy (AFM) is capable of imaging molecules at high resolution and at high speed. However, AFM imaging is a surface technique, requiring sample preparation and some immobilization. Other technologies such as optical tweezers and magnetic tweezers are capable of molecular manipulation and spectroscopy to great effect but require a significant apparatus and have limited inherent analytical capabilities.
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Mularski, Anna, i Florence Niedergang. "Force Measurement of Living Professional Phagocytes of the Immune System". Australian Journal of Chemistry 73, nr 3 (2020): 104. http://dx.doi.org/10.1071/ch19409.
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In higher organisms, the professional phagocytes of the immune system (dendritic cells, neutrophils, monocytes, and macrophages) are responsible for pathogen clearance, the development of immune responses via cytokine secretion and presentation of antigens derived from internalized material, and the normal turnover and remodelling of tissues and disposal of dead cells. These functions rely on the ability of phagocytes to migrate and adhere to sites of infection, dynamically probe their environments to make contact with phagocytic targets, and perform phagocytosis, a mechanism of internalization of large particles, microorganisms, and cellular debris for intracellular degradation. The cell-generated forces that are necessary for the professional phagocytes to act in their roles as ‘first responders’ of the immune system have been the subject of mechanical studies in recent years. Methods of force measurement such as atomic force microscopy, traction force microscopy, micropipette aspiration, magnetic and optical tweezers, and exciting new variants of these have accompanied classical biological methods to perform mechanical investigations of these highly dynamic immune cells.
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Marin-Gonzalez, Alberto, Cesar L. Pastrana, Rebeca Bocanegra, Alejandro Martín-González, J. G. Vilhena, Rubén Pérez, Borja Ibarra, Clara Aicart-Ramos i Fernando Moreno-Herrero. "Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes". Nucleic Acids Research 48, nr 9 (13.04.2020): 5024–36. http://dx.doi.org/10.1093/nar/gkaa225.
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Abstract A-tracts are A:T rich DNA sequences that exhibit unique structural and mechanical properties associated with several functions in vivo. The crystallographic structure of A-tracts has been well characterized. However, the mechanical properties of these sequences is controversial and their response to force remains unexplored. Here, we rationalize the mechanical properties of in-phase A-tracts present in the Caenorhabditis elegans genome over a wide range of external forces, using single-molecule experiments and theoretical polymer models. Atomic Force Microscopy imaging shows that A-tracts induce long-range (∼200 nm) bending, which originates from an intrinsically bent structure rather than from larger bending flexibility. These data are well described with a theoretical model based on the worm-like chain model that includes intrinsic bending. Magnetic tweezers experiments show that the mechanical response of A-tracts and arbitrary DNA sequences have a similar dependence with monovalent salt supporting that the observed A-tract bend is intrinsic to the sequence. Optical tweezers experiments reveal a high stretch modulus of the A-tract sequences in the enthalpic regime. Our work rationalizes the complex multiscale flexibility of A-tracts, providing a physical basis for the versatile character of these sequences inside the cell.
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Kusaia, Viktoria S., Elena Yu Kozhunova, Darya A. Stepanova, Vladislava A. Pigareva, Andrey V. Sybachin, Sergey B. Zezin, Anastasiya V. Bolshakova i in. "Synthesis of Magneto-Controllable Polymer Nanocarrier Based on Poly(N-isopropylacrylamide-co-acrylic Acid) for Doxorubicin Immobilization". Polymers 14, nr 24 (12.12.2022): 5440. http://dx.doi.org/10.3390/polym14245440.
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In this work, the preparation procedure and properties of anionic magnetic microgels loaded with antitumor drug doxorubicin are described. The functional microgels were produced via the in situ formation of iron nanoparticles in an aqueous dispersion of polymer microgels based on poly(N-isopropylacrylamide-co-acrylic acid) (PNIPAM-PAA). The composition and morphology of the resulting composite microgels were studied by means of X-ray diffraction, Mössbauer spectroscopy, IR spectroscopy, scanning electron microscopy, atomic-force microscopy, laser microelectrophoresis, and static and dynamic light scattering. The forming nanoparticles were found to be β-FeO(OH). In physiological pH and ionic strength, the obtained composite microgels were shown to possess high colloid stability. The average size of the composites was 200 nm, while the zeta-potential was −27.5 mV. An optical tweezers study has demonstrated the possibility of manipulation with microgel using external magnetic fields. Loading of the composite microgel with doxorubicin did not lead to any change in particle size and colloidal stability. Magnetic-driven interaction of the drug-loaded microgel with model cell membranes was demonstrated by fluorescence microscopy. The described magnetic microgels demonstrate the potential for the controlled delivery of biologically active substances.
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Spakman, Dian, Julia A. M. Bakx, Andreas S. Biebricher, Erwin J. G. Peterman, Gijs J. L. Wuite i Graeme A. King. "Unravelling the mechanisms of Type 1A topoisomerases using single-molecule approaches". Nucleic Acids Research 49, nr 10 (8.05.2021): 5470–92. http://dx.doi.org/10.1093/nar/gkab239.
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Abstract Topoisomerases are essential enzymes that regulate DNA topology. Type 1A family topoisomerases are found in nearly all living organisms and are unique in that they require single-stranded (ss)DNA for activity. These enzymes are vital for maintaining supercoiling homeostasis and resolving DNA entanglements generated during DNA replication and repair. While the catalytic cycle of Type 1A topoisomerases has been long-known to involve an enzyme-bridged ssDNA gate that allows strand passage, a deeper mechanistic understanding of these enzymes has only recently begun to emerge. This knowledge has been greatly enhanced through the combination of biochemical studies and increasingly sophisticated single-molecule assays based on magnetic tweezers, optical tweezers, atomic force microscopy and Förster resonance energy transfer. In this review, we discuss how single-molecule assays have advanced our understanding of the gate opening dynamics and strand-passage mechanisms of Type 1A topoisomerases, as well as the interplay of Type 1A topoisomerases with partner proteins, such as RecQ-family helicases. We also highlight how these assays have shed new light on the likely functional roles of Type 1A topoisomerases in vivo and discuss recent developments in single-molecule technologies that could be applied to further enhance our understanding of these essential enzymes.
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Zhang, Rongyan, Yanwei Wang i Guangcan Yang. "DNA–Lysozyme Nanoarchitectonics: Quantitative Investigation on Charge Inversion and Compaction". Polymers 14, nr 7 (28.03.2022): 1377. http://dx.doi.org/10.3390/polym14071377.
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The interaction between DNA and proteins is fundamentally important not only for basic research in biology, but also for potential applications in nanotechnology. In the present study, the complexes formed by λ DNA and lysozyme in a dilute aqueous solution have been investigated using magnetic tweezers (MT), dynamic light scattering (DLS), and atomic force microscopy (AFM). We found that lysozyme induced DNA charge inversion by measuring its electrophoretic mobility by DLS. Lysozyme is very effective at neutralizing the positive charge of DNA, and its critical charge ration to induce charge inversion in solution is only 2.26. We infer that the high efficiency of charge neutralization is due to the highly positively charged (+8 e) and compact structure of lysozyme. When increasing the concentration of lysozymes from 6 ng·µL−1 to 70 ng·µL−1, DNA mobility (at fixed concentration of 2 ng·µL−1) increases from −2.8 to 1.5 (in unit of 10−4 cm2·V−1·S), implying that the effective charge of DNA switches its sign from negative to positive in the process. The corresponding condensing force increased from 0 pN to its maximal value of about 10.7 pN at concentrations of lysozyme at 25 ng·µL−1, then decreases gradually to 3.8 pN at 200 ng·µL−1. The maximal condensing force occurs at the complete DNA charge neutralization point. The corresponding morphology of DNA–lysozyme complex changes from loosely extensible chains to compact globule, and finally to less compact flower-like structure due to the change of attached lysozyme particles as observed by AFM.
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Whyte, Claire S., Irina N. Chernysh, Marco M. Domingues, Simon Connell, John W. Weisel, Robert A. S. Ariens i Nicola J. Mutch. "Polyphosphate delays fibrin polymerisation and alters the mechanical properties of the fibrin network". Thrombosis and Haemostasis 116, nr 11 (2016): 897–903. http://dx.doi.org/10.1160/th16-01-0062.
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SummaryPolyphosphate (polyP) binds to fibrin(ogen) and alters fibrin structure, generating a heterogeneous network composed of ‘knots’ interspersed by large pores. Here we show platelet-derived polyP elicits similar structural changes in fibrin and examine the mechanism by which polyP alters fibrin structure. Polymerisation of fibrinogen with thrombin and CaCl2 was studied using spinning disk confocal (SDC) microscopy. PolyP delayed fibrin polymerisation generating shorter protofibrils emanating from a nucleus-type structure. Consistent with this, cascade blue-polyP accumulated in fibrin ‘knots’. Protofibril formation was visualized by atomic force microscopy (AFM) ± polyP. In the presence of polyP abundant monomers of longer length were visualised by AFM, suggesting that polyP binds to monomeric fibrin. Shorter oligomers form in the presence of polyP, consistent with the stunted protofibrils visualised by SDC microscopy. We examined whether these structural changes induced by polyP alter fibrin’s viscoelastic properties by rheometry. PolyP reduced the stiffness (G’) and ability of the fibrin network to deform plastically G”, but to different extents. Consequently, the relative plastic component (loss tangent (G”/G’)) was 61 % higher implying that networks containing polyP are less stiff and more plastic. Local rheological measurements, performed using magnetic tweezers, indicate that the fibrin dense knots are stiffer and more plastic, reflecting the heterogeneity of the network. Our data show that polyP impedes fibrin polymerisation, stunting protofibril growth producing ‘knotted’ regions, which are rich in fibrin and polyP. Consequently, the mechanical properties of the fibrin network are altered resulting in clots with overall reduced stiffness and increased ability to deform plastically.Supplementary Material to this article is available online at www.thrombosis-online.com.
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Ma, Fangqin, Yanwei Wang i Guangcan Yang. "The Modulation of Chitosan-DNA Interaction by Concentration and pH in Solution". Polymers 11, nr 4 (9.04.2019): 646. http://dx.doi.org/10.3390/polym11040646.
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Chitosan has been widely used to prepare a DNA carrier for highly efficient and non-toxic gene therapy. In the present study, we investigated DNA charge neutralization and compaction by chitosan in solutions of various pH levels by dynamic light scattering (DLS), magnetic tweezers (MT), and atomic force microscopy (AFM). We found that when chitosan concentration is higher than a critical value (0.2 µM), corresponding the ratio of phosphate and NH2 in chitosan k = 1.9 , the electrophoretic mobility of DNA-chitosan complex maintains an almost constant value when pH of solution is less 6.5, the isoelectric point of chitosan. Then it decreases with increasing pH of solution. However, when chitosan concentration is lower than the critical value, the mobility of the complex increases with pH in the range of acidity and reaches the maximum when the pH of the solution approaches the isoelectric point of chitosan. It finally decreases with increasing pH in solutions. The corresponding condensing force of the DNA-chitosan complex measured by single molecular MT changes accordingly with its charge neutralization in the same solution concentration (20 µM) and is consistent with the DLS measurements. This phenomenon might be related to the weakening interaction between DNA and chitosan in low pH solutions, and is verified by measuring the ratio of free chitosan to DNA complex in solutions. We also observed the various morphologies of DNA-chitosan complexes, such as ring, rod, flower, braid, and other structures, under different degrees of deacetylation, molecular weight, solution concentration and pH in solutions by AFM.
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Ariens, Robert A. S. "Contribution of Red Blood Cells and Clot Structure to Thrombosis". Blood 126, nr 23 (3.12.2015): SCI—15—SCI—15. http://dx.doi.org/10.1182/blood.v126.23.sci-15.sci-15.
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Abstract The blood clot or thrombus is composed of red blood cells, platelets and white cells that interact with the fibrin meshwork produced by the coagulation system. The red blood cells form polyhedrocytes that seal the clot, platelets provide forces for clot contraction, and white cells contribute neutrophil extracellular traps, cytokines and complement activation. The fibrin network contributes clot elasticity and provides the proteinaceous backbone structure that stabilises the clot. Previous studies from our laboratory and others have shown that dense fibrin networks demonstrating small pores and increased resistance to fibrinolysis associate with thrombosis. However, the mechanisms underpinning this have not been fully understood. Recent studies using atomic force microscopy from our laboratory have shown that fibrinogen interacts with red cells with comparable affinity as that with platelets. A patient with mutations in the β3 integrin subunit showed no binding between red cells and fibrinogen, demonstrating that a β3-related integrin receptor is involved in the interaction. Mutations in the fibrinogen α-chain integrin binding sites (D97E and D574E) reduced frequency of red cell interactions with fibrinogen. Interestingly, a naturally occuring splice variant of the fibrinogen γ-chain that reduces binding to the platelets, fibrinogen γ', increased binding interactions between fibrinogen and red blood cells. Fibrinogen γ' is a naturally occurring splice variant of fibrinogen, in which the C-terminal AGDV residues of the more common γA-chain (85%) are replaced with a negatively charched VRPEHPAETEYDSLYPEDDL sequence of the γ' chain (15%). Fibrinogen γ' induced clustering of fibrin fibres into tightly interknit nuclei of fibrin fibres, interspersed by large pores that extend over more than 50 μm within the fibrin network structure. The effects of fibrinogen γ' on fibrin clot structure was independent of thrombin and FXIII as demonstrated using snake venom enzyme. Previously we showed impaired fibrin protofibril formation with fibrinogen γ' using atomic force microscopy. Using turbidimetric analysis of fibrin intrafibrillar structure, we show that fibrinogen γ' reduces protofibil packing per fibrin fiber. Furthermore, we find that reduced protofibril packing diminishes fibrin stiffness as analysed with magnetic tweezers both in purified systems as well as in plasma at (patho)physiological fibrinogen γ' levels that range from 3-40%, and in whole blood as analysed with thromboelastography. In conclusion, our data show that red blood cells and fibrinogen γ' play major roles in the regulation of clot structure and stability, and that these effects on clot structure are major determinants of the functional properties of the blood clot. Modulating fibrin clot structure and its interactions with blood cells may represent major new targets for the treatment of thrombosis. Disclosures No relevant conflicts of interest to declare.
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Litvinov, Rustem I., Karen Pei Yi Fong, Oleg V. Kim, Kathleen I. Molnar, Paul C. Billings, Alex Sternisha, James A. Wells, John W. Weisel, William F. DeGrado i Joel S. Bennett. "Active Calpain Promotes Fibrin Clot Contraction By Strengthening the Coupling of Fibrin-Bound αIIbβ3 to the Platelet Cytoskeleton". Blood 132, Supplement 1 (29.11.2018): 1128. http://dx.doi.org/10.1182/blood-2018-99-113063.
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Abstract Platelet-driven blood clot contraction reduces and compacts clot volume, promoting hemostasis while restoring blood flow past otherwise obstructive thrombi. Clot contraction is driven by traction forces in the range of tens of pN per platelet that are generated by platelet non-muscle myosin IIa and actin on αIIbβ3 bound to extracellular fibrin fibers. In an analysis of the kinetics of thrombin-induced clot formation and contraction in platelet-rich plasma, we found that clot contraction has two discernable phases: an exponential initiation phase and a second exponential contraction phase. It is noteworthy that Azam et al (Mol Cell Biol21:2213-20, 2001) observed that deleting the µ-calpain gene in mice impairs platelet-mediated clot contraction. In this context, we found that inhibiting calpain activity with ALLM (N-Acetyl-Leu-Leu-Methional), a cell-permeable calpain inhibitor, significantly prolonged the duration of the initiation phase and decreased the kinetic rate constants for both the initiation and contraction phases of thrombin-stimulated platelet-mediated clot contraction, but without affecting the overall extent of contraction. The calpain inhibitor ALLN (N-acetyl-Leu-Leu-Norleu) had the same effect. Thus, these studies imply that activation of platelet calpain facilitates the transmission of traction forces from the platelet cytoskeleton to the αIIbβ3 bound to fibrin fibers. μ-Calpain is calcium-dependent cytosolic neutral cysteine protease that is activated 30-60 seconds after the onset of platelet aggregation stimulated by platelet agonists such as thrombin. To identify the calpain-cleaved protein or proteins involved in clot contraction, we incubated washed human platelets with the thrombin activation peptide TRAP in the presence or absence of calpain inhibitors and identified calpain-cleaved proteins using subtiligase-mediated biotin-labeling of nascent N-termini followed by mass spectrometry. We identified 32 proteins in the platelet cytosol that undergo calpain-mediated cleavage after TRAP stimulation. Many of these are cytoskeletal proteins, most prominently talin which connects integrins to the cytoskeleton and vinculin which is required for myosin-contractility-dependent effects on traction force and adhesion strength. Accordingly, we focused our attention on these two proteins. Talin, a 250 kD protein, is composed of a 45 kD N-terminal head domain attached via a flexible linker to a 200 kD C-terminal rod domain. The rod domain consists of 62 amphipathic α-helices organized into a series of four- and five-helix bundles. Vinculin is a 116 kD protein composed of 5 domains and has an autoinhibited structure in which domains 1-3 bind to domain 5. We detected 8 calpain-mediated cleavages in talin, 2 previously identified cleavage sites in unstructured regions and 6 others in α-helical regions known to interact with other proteins. Four of the latter are located within the first 12 talin helices, a region that contains four vinculin binding sites (VBSs). Likewise, the remaining two cleavage sites are in proximity to a VBS. A VBS is a vinculin-binding α-helix that is buried in a helical bundle due to extensive hydrophobic interactions with other amphipathic helices. Because VBS are packed into the interior of a helical bundle, a structural rearrangement is required to initiate vinculin binding. Using magnetic tweezers and atomic force microscopy, del Rio et al demonstrated that force-induced stretching of single talin rod molecules activates VBSs (Science323:638-41, 2009)), implying that stretching causes the conformational change required to expose buried VBSs. Thus, based on the location of the calpain-mediated cleavages in talin, we hypothesize that by cleaving talin in proximity to a VBS, calpain facilitates vinculin to binding talin, thereby strengthening the coupling of fibrin-bound αIIbβ3 to the platelet cytoskeleton to promote fibrin clot contraction. Disclosures No relevant conflicts of interest to declare.
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Shi, Yan, Mingjun Cai i Hongda Wang. "Single-molecule Force Microscopy: A Powerful Tool for Studying the Mechanical Properties of Cell Membranes". Current Analytical Chemistry 17 (2.06.2021). http://dx.doi.org/10.2174/1573411017666210602144602.
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Background: Cell membrane is a physical barrier for cells, as well as an important structure with complex functions in cellular activities. The cell membrane can not only receive external mechanical signal stimulation and respond (e.g., cell migration, differentiation, tumorigenesis, growth), but it can also spontaneously exert force on the environment to regulate cellular activities (such as tissue repair, tumor metastasis, extracellular matrix regulation, etc.). Methods: This review introduces single-molecule force methods, such as atomic force microscopy, optical tweezers, magnetic tweezers, micropipette adhesion assay, tension gauge tethers, and traction force microscopy. Results: This review summarizes the principles, advantages, and disadvantages of single-molecule force methods developed in recent years, as well as their application in terms of force received and generated by cells. The study of cell mechanics enables us to understand the nature of mechanical signal transduction and the manifestation of the cell's movement. Conclusion: The study of the mechanical properties of the cell microenvironment leads to a gradual understanding of the important role of cell mechanics in development, physiology, and pathology. Recently developed combined methods are beneficial for further studying cell mechanics. The optimization of these methods and the invention of new methods enable the continuing research on cell mechanics.
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Hong, Haiyan, Zilong Guo, Hao Sun, Ping Yu, Huanhuan Su, Xuening Ma i Hu Chen. "Two energy barriers and a transient intermediate state determine the unfolding and folding dynamics of cold shock protein". Communications Chemistry 4, nr 1 (9.11.2021). http://dx.doi.org/10.1038/s42004-021-00592-1.
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AbstractCold shock protein (Csp) is a typical two-state folding model protein which has been widely studied by biochemistry and single molecule techniques. Recently two-state property of Csp was confirmed by atomic force microscopy (AFM) through direct pulling measurement, while several long-lifetime intermediate states were found by force-clamp AFM. We systematically studied force-dependent folding and unfolding dynamics of Csp using magnetic tweezers with intrinsic constant force capability. Here we report that Csp mostly folds and unfolds with a single step over force range from 5 pN to 50 pN, and the unfolding rates show different force sensitivities at forces below and above ~8 pN, which determines a free energy landscape with two barriers and a transient intermediate state between them along one transition pathway. Our results provide a new insight on protein folding mechanism of two-state proteins.
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Flormann, D. A. D., C. Anton, M. O. Pohland, Y. Bautz, K. Kaub, E. Terriac, T. E. Schäffer i in. "Oscillatory Microrheology, Creep Compliance and Stress Relaxation of Biological Cells Reveal Strong Correlations as Probed by Atomic Force Microscopy". Frontiers in Physics 9 (23.08.2021). http://dx.doi.org/10.3389/fphy.2021.711860.
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The mechanical properties of cells are important for many biological processes, including wound healing, cancers, and embryogenesis. Currently, our understanding of cell mechanical properties remains incomplete. Different techniques have been used to probe different aspects of the mechanical properties of cells, among them microplate rheology, optical tweezers, micropipette aspiration, and magnetic twisting cytometry. These techniques have given rise to different theoretical descriptions, reaching from simple Kelvin-Voigt or Maxwell models to fractional such as power law models, and their combinations. Atomic force microscopy (AFM) is a flexible technique that enables global and local probing of adherent cells. Here, using an AFM, we indented single retinal pigmented epithelium cells adhering to the bottom of a culture dish. The indentation was performed at two locations: above the nucleus, and towards the periphery of the cell. We applied creep compliance, stress relaxation, and oscillatory rheological tests to wild type and drug modified cells. Considering known fractional and semi-fractional descriptions, we found the extracted parameters to correlate. Moreover, the Young’s modulus as obtained from the initial indentation strongly correlated with all of the parameters from the applied power-law descriptions. Our study shows that the results from different rheological tests are directly comparable. This can be used in the future, for example, to reduce the number of measurements in planned experiments. Apparently, under these experimental conditions, the cells possess a limited number of degrees of freedom as their rheological properties change.
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Abraham, Zachary, Emma Hawley, Daniel Hayosh, Victoria A. Webster-Wood i Ozan Akkus. "Kinesin and Dynein Mechanics: Measurement Methods and Research Applications". Journal of Biomechanical Engineering 140, nr 2 (12.01.2018). http://dx.doi.org/10.1115/1.4037886.
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Motor proteins play critical roles in the normal function of cells and proper development of organisms. Among motor proteins, failings in the normal function of two types of proteins, kinesin and dynein, have been shown to lead many pathologies, including neurodegenerative diseases and cancers. As such, it is critical to researchers to understand the underlying mechanics and behaviors of these proteins, not only to shed light on how failures may lead to disease, but also to guide research toward novel treatment and nano-engineering solutions. To this end, many experimental techniques have been developed to measure the force and motility capabilities of these proteins. This review will (a) discuss such techniques, specifically microscopy, atomic force microscopy (AFM), optical trapping, and magnetic tweezers, and (b) the resulting nanomechanical properties of motor protein functions such as stalling force, velocity, and dependence on adenosine triphosophate (ATP) concentrations will be comparatively discussed. Additionally, this review will highlight the clinical importance of these proteins. Furthermore, as the understanding of the structure and function of motor proteins improves, novel applications are emerging in the field. Specifically, researchers have begun to modify the structure of existing proteins, thereby engineering novel elements to alter and improve native motor protein function, or even allow the motor proteins to perform entirely new tasks as parts of nanomachines. Kinesin and dynein are vital elements for the proper function of cells. While many exciting experiments have shed light on their function, mechanics, and applications, additional research is needed to completely understand their behavior.
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Zemljic Jokhadar, Spela, Jagoba Iturri, Jose Luis Toca-Herrera i Jure Derganc. "Cell Stiffness under Small and Large Deformations Measured by Optical Tweezers and Atomic Force Microscopy: Effects of Actin Disruptors CK-869 and Jasplakinolide". Journal of Physics D: Applied Physics, 4.12.2020. http://dx.doi.org/10.1088/1361-6463/abd0ae.
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Dorfman, Kevin D. "The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics". Journal of Biomechanical Engineering 140, nr 2 (12.01.2018). http://dx.doi.org/10.1115/1.4037790.
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The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.