Review
Biotechnology & Applied Microbiology
Ipek Simay Gokulu, Scott Banta
Summary: The functionalization of proteins with DNA through covalent bond formation enables various biotechnology advancements. DNA labeling of proteins allows for easy identification, organization, and control within DNA-protein networks. Bioconjugation reactions can target different amino acids within proteins, and further protein engineering methods can be used for conjugation reactions. The choice of technique depends on factors such as yield, selectivity, conjugation position, cost, and potential impact on protein function.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Hai Lei, Junsheng Zhang, Ying Li, Xin Wang, Meng Qin, Wei Wang, Yi Cao
Summary: In this study, a histidine-specific phosphorylation strategy was developed to covalently anchor proteins to an atomic force microscopy. This method improved the data quality of single-molecule force spectroscopy experiments and was successfully applied to investigate the mechanical stability and unfolding process of proteins.
Article
Multidisciplinary Sciences
Takanori Harashima, Shintaro Fujii, Yuki Jono, Tsuyoshi Terakawa, Noriyuki Kurita, Satoshi Kaneko, Manabu Kiguchi, Tomoaki Nishino
Summary: The electrical properties of DNA in the field of molecular electronics have been extensively studied, with a focus on the higher-order structures and design changes associated with single-molecule electronic devices. Researchers have developed a DNA zipper configuration to form a single-molecule junction, which exhibits high conductivity and an attractive self-restoring capability. This strategy provides a basis for novel designs of single-molecule junctions.
NATURE COMMUNICATIONS
(2021)
Article
Polymer Science
Xiaoye Zhang, Dandan Li, Yu Song, Wenke Zhang
Summary: In this study, the mechanical stability and melting pathway of highly stereoregular syndiotactic polypropylene (s-PP) were investigated using atomic force microscopy (AFM)-based single molecule force spectroscopy (SMFS). It was found that crystal thickness and structure have significant impacts on mechanical stability and melting pathway.
Review
Biochemistry & Molecular Biology
Rebeca Bocanegra, Ismael G. A. Plaza, Carlos R. Pulido, Borja Ibarra
Summary: The study reveals that the replisome machinery is stochastic, versatile, and highly dynamic, with transient protein-protein and protein-DNA interactions playing a key role in robust DNA replication.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Polymer Science
Lu Qian, Kai Zhang, Xin Guo, Junyu Zhou, Miao Yu
Summary: The study found that there was almost no difference in the single-chain elasticity of gelatin in nonane and DI water. When a single gelatin chain is pulled into loose nonane, dehydration does not occur due to strong binding water interactions. Gelatin chains can only interact with water molecules at high temperatures.
Article
Chemistry, Multidisciplinary
Haipei Liu, Zhaowei Liu, Mariana Sa Santos, Michael A. A. Nash
Summary: Single-molecule force spectroscopy (SMFS) is a powerful tool for studying protein folding and mechanical properties. However, the traditional method of immobilization using lysine residues results in a heterogeneous distribution of tether positions. In this study, we compared lysine-based immobilization to site-specific immobilization using genetically encoded peptide tags (ybbR). Our results showed that lysine-based immobilization led to signal deterioration and incorrect classification of unfolding pathways. We also developed a mixed immobilization approach that partially recovered specific signals.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Manish Bajaj, Mohd Muddassir, Bumjoon Choi, Priyanka Singh, Jong Bum Park, Surjeet Singh, Manisha Yadav, Rajesh Kumar, Kilho Eom, Deepak Sharma
Summary: This study investigates the effect of osmolytes on the mechanical unfolding properties of protein domain using atomic force microscopy. The results show that amines and methylamines enhance the mechanical stability of the protein, while polyols have no effect. Glycine betaine and trimethylamine-N-oxide increase the average unfolding force of the protein domain. These findings have potential applications in modulating the mechanical stability of proteins for nano-biotechnological purposes.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Polymer Science
Junpeng Wang, Tatiana B. Kouznetsova, Jianshe Xia, Felipe Jimenez Angeles, Monica Olvera de la Cruz, Stephen L. Craig
Summary: Single-molecule force spectroscopy is a powerful tool for studying the properties of individual polymer strands. However, the weak attachment between the atomic force microscope tip and the analyte limits its efficiency. In this study, we developed a polyelectrolyte handle that provides strong attachment, high success rate, non-fouling detachment, and specific attachment locations along the polymer strand.
JOURNAL OF POLYMER SCIENCE
(2023)
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
Chemistry, Multidisciplinary
Marta Urbanska, Annemarie Ludecke, Wilhelm J. Walter, Antoine M. van Oijen, Karl E. Duderstadt, Stefan Diez
Summary: This study introduces a highly-parallel, microfluidics-based method for rapid collection of force-dependent motility parameters of cytoskeletal motors, significantly improving throughput. DNA-tethered beads are used to apply tunable hydrodynamic forces to stepping kinesin-1 motors, allowing for simultaneous tracking of various motility parameters of hundreds of individual molecules. The approach, applicable to other molecular systems, represents a new methodology for parallelized single-molecule force studies on cytoskeletal motors.
Review
Chemistry, Multidisciplinary
Lyan M. van der Sleen, Katarzyna M. Tych
Summary: Research on the mechanical properties of proteins often involves the use of various connectors and techniques, with DNA being a common choice. When site-specifically conjugating DNA-linkers to proteins of interest, considerations include mechanical properties, labeling efficiency, and costs associated with different conjugation strategies.
Review
Nanoscience & Nanotechnology
Benjamin Brenner, Cheng Sun, Francisco M. Raymo, Hao F. F. Zhang
Summary: Single-molecule localization microscopy (SMLM) achieves super-resolution imaging by numerically localizing sparse fluorescence emitters beyond the optical diffraction limit. Spectroscopic SMLM (sSMLM) enables simultaneous spectroscopy and super-resolution imaging, extracting spectral features with single-molecule sensitivity, higher precision, and multiplexity. Despite reduced spatial precision compared to conventional SMLM, innovative optical design and image processing techniques have been developed to mitigate these weaknesses. This review summarizes the recent progress in sSMLM, its applications, and future perspectives.
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)
Article
Biochemical Research Methods
Beatrice W. W. Soh, Zi-En Ooi, Eleonore Vissol-Gaudin, Chang Jie Leong, Kedar Hippalgaonkar
Summary: In this work, an automated platform is introduced for trapping and stretching micro- and nanoscale objects in solution using electrokinetic forces. The platform demonstrates the capability to trap objects at the stagnation point of an elongational electrokinetic field for long periods of time, as evidenced by the trapping of <100 nm polystyrene beads and DNA molecules for minutes with minimal displacement. This platform allows for the high-throughput stretching of deformable nanoscale objects, as exemplified by stretching more than 400 DNA molecules within approximately 4 hours. Furthermore, the flexibility of the electrokinetic stretcher enables complex manipulation, such as sequential stretching at different voltages and multiple stretch-relaxation cycles of the same molecule. Overall, this platform provides an automated and high-throughput method for tracking and manipulating objects in real-time studies of micro- and nanoscale systems.
Editorial Material
Cell Biology
Harald Janovjak, Sonja Kleinlogel
NEURAL REGENERATION RESEARCH
(2022)
Article
Neurosciences
Prabhjot Dhami, Lena C. Quilty, Benjamin Schwartzmann, Rudolf Uher, Timothy A. Allen, Stefan Kloiber, Raymond W. Lam, Glenda MacQueen, Benicio N. Frey, Roumen Milev, Daniel J. Mueller, Stephen C. Strother, Pierre Blier, Claudio N. Soares, Sagar V. Parikh, Gustavo Turecki, Jane A. Foster, Susan Rotzinger, Sidney H. Kennedy, Faranak Farzan
Summary: The neurobiological correlates of response inhibition can predict the response of patients with major depressive disorder (MDD) to pharmacological and cognitive behavioral therapy treatment. The integrity of response inhibition may be crucial for the success of treatment for MDD. Electrophysiological correlates of response inhibition may serve as a general prognostic marker for treatment response in MDD.
BIOLOGICAL PSYCHIATRY-COGNITIVE NEUROSCIENCE AND NEUROIMAGING
(2023)
Article
Pharmacology & Pharmacy
Samuel H. Crossman, Harald Janovjak
Summary: Receptor tyrosine kinases (RTKs) are a crucial membrane receptor family that can be activated through various molecular mechanisms, resulting in diverse physiological consequences. The development of genetically-encoded light-activated RTKs (Opto-RTKs) has provided researchers with a valuable tool to study and manipulate RTK signaling and physiology with high precision and control, offering insights into subcellular, tissue, and animal models.
CURRENT OPINION IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Alexandra-Madelaine Tichy, Wang Lok So, Elliot J. Gerrard, Harald Janovjak
Summary: GPCRs are the largest human receptor family involved in various physiological processes. Researchers have optimized light-activated OptoXRs using structure-guided methods to improve signal coupling.
Article
Biochemistry & Molecular Biology
Tetiana Serdiuk, Moutusi Manna, Cheng Zhang, Stefania A. Mari, Waldemar Kulig, Kristyna Pluhackova, Brian K. Kobilka, Ilpo Vattulainen, Daniel J. Muller
Summary: Cholesterol interacts with G protein-coupled receptors in cell membranes, modulating their assembly, stability, and conformation. This study shows that the cholesterol analog CHS can nonlinearly stabilize different structural regions of GPCRs and affect their functionality, with the strongest effects observed at physiological temperature.
Article
Multidisciplinary Sciences
Andreas P. Cuny, K. Tanuj Sapra, David Martinez-Martin, Gotthold Flaschner, Jonathan D. Adams, Sascha Martin, Christoph Gerber, Fabian Rudolf, Daniel J. Mueller
Summary: The regulation of cell growth is of great significance in physiology, biotechnology, and medicine. However, monitoring the mass and growth of individual cells with high resolution is challenging. In this study, the authors modified a cell balance technique to monitor the proliferation of single yeast cells in real-time. They found that the mass of single yeast cells increases in linear segments of constant growth rates. This technology has the potential to directly and accurately monitor the growth of single cells throughout their cycle.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Selen Manioglu, Seyed Majed Modaresi, Noah Ritzmann, Johannes Thoma, Sarah A. Overall, Alexander Harms, Gregory Upert, Anatol Luther, Alexander B. Barnes, Daniel Obrecht, Daniel J. Muller, Sebastian Hiller
Summary: The study uses high-resolution atomic force microscopy to investigate the interaction mechanism between Polymyxins and bacterial membranes. The results show that Polymyxins can arrange bacterial lipids into regular hexagonal structures, making the membrane stiffer and leading to rupture.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Ilaria Incaviglia, Sophie Herzog, Gotthold Flaeschner, Nico Strohmeyer, Enrico Tosoratti, Daniel J. Mueller
Summary: Researchers design photothermally actuated microcantilevers to optimize the accuracy of cell mass measurements. By reducing the inertial mass of the microcantilever using a focused ion beam, they considerably increase its mass sensitivity. The improved microcantilevers allow for more accurate monitoring of cell mass and restrict cell migration, reducing measurement errors.
Article
Biochemistry & Molecular Biology
Nina Blaimschein, Parameswaran Hariharan, Selen Manioglu, Lan Guan, Daniel J. Muller
Summary: In this study, single-molecule force spectroscopy was used to investigate the substrate-induced structural changes of MelB from Salmonella typhimurium. The results showed that in the absence of substrate, MelB equally populated two different states, with one state showing higher mechanical structural stability. However, in the presence of melibiose or a coupling Na+-cation, MelB increasingly populated a mechanically less stable state. In the presence of both substrate and co-substrate, this mechanically less stable state of MelB was predominant. These findings provide mechanistic insights into the symport action of galactosides and cations catalyzed by MelB.
Article
Biochemistry & Molecular Biology
Christina G. Gangemi, Rahkesh T. T. Sabapathy, Harald Janovjak
Summary: In humans, more than 500 kinases phosphorylate approximately 15% of all proteins, forming a growing phosphorylation network. A comprehensive computational analysis revealed the existence of convergent kinase-substrate relationships (cKSRs), which are common and involve a large number of kinases and substrates. This study also demonstrated experimentally the convergence of CDK4/6 kinases in phosphorylating the tumor suppressor RB, and proposed a methodology to dissect these convergent interactions.
Article
Biochemistry & Molecular Biology
Hella Baumann, Melanie Schwingel, Marcello Sestu, Anna Burcza, Susanna Marg, Wolfgang Ziegler, Anna V. V. Taubenberger, Daniel J. J. Muller, Martin Bastmeyer, Clemens M. M. Franz
Summary: This study investigated the role of vinculin in the reinforcement of nascent adhesions between cells and fibronectin or vitronectin. The researchers found that vinculin is dispensable for adhesion initiation but is crucial for adhesion strength and traction after 60 to 120 seconds. Re-expression of full-length vinculin or a constitutively active vinculin mutant restored adhesion and traction, while vinculin with specific mutations was ineffective.
JOURNAL OF MOLECULAR RECOGNITION
(2023)
Article
Multidisciplinary Sciences
Morris Degen, Jose Carlos Santos, Kristyna Pluhackova, Gonzalo Cebrero, Saray Ramos, Gytis Jankevicius, Ella Hartenian, Undina Guillerm, Stefania A. Mari, Bastian Kohl, Daniel J. Mueller, Paul Schanda, Timm Maier, Camilo Perez, Christian Sieben, Petr Broz, Sebastian Hiller
Summary: Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture. The protein ninjurin-1 (NINJ1) mediates the active process of membrane rupture in dying cells. NINJ1 clusters into structurally diverse assemblies in dying cell membranes, particularly large filamentous assemblies with branched morphology. Molecular dynamics simulations show that NINJ1 can stably cap membrane edges. Therefore, NINJ1 is an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death.
Article
Multidisciplinary Sciences
Maximilian Huber, Javier Casares-Arias, Reinhard Faessler, Daniel J. Mueller, Nico Strohmeyer
Summary: Adopting a round cell morphology before mitosis is crucial. The authors found that, unlike interphase cells, mitotic cells cannot reinforce cell-ECM adhesion by engaging newly bound integrins via talin or vinculin. However, beta 1 integrins strengthen cell-cell adhesion in mitosis. This dual role of integrins weakens cell-ECM adhesion and strengthens cell-cell adhesion to prevent cell delamination during rounding and dividing.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Anna Stier, Samuel Gilberto, Weaam Mohamed, Lars N. Royall, Jonne Helenius, Ivan Mikicic, Tatjana Sajic, Petra Beli, Daniel J. Mueller, Sebastian Jessberger, Matthias Peter
Summary: CUL4A and CUL4B are paralogs that assemble cullin-RING E3 ubiquitin ligase (CRL) complexes regulating chromatin-associated cellular functions. The unique N-terminal extension of CUL4B is heavily phosphorylated during mitosis, and this phosphorylation is disrupted in the CUL4B-P50L mutation causing X-linked intellectual disability (XLID). Phenotypic characterization and mutational analysis showed that CUL4B phosphorylation is essential for mitosis progression and controls spindle positioning and cortical tension.
Article
Chemistry, Multidisciplinary
Seungkuk Ahn, Upnishad Sharma, Krishna Chaitanya Kasuba, Nico Strohmeyer, Daniel J. J. Muller
Summary: This study introduces a simple and scalable method to engineer biomimetic 3D fibrillar fibronectin matrices and characterizes how fibroblasts sense and adhere to these matrices. The findings demonstrate that fibroblasts accelerate adhesion initiation and strengthening to fibrillar fibronectin matrices compared to globular fibronectin. This immediate sensing and adhesion to fibrillar fibronectin also guide migration speed, persistency, and proliferation range in fibroblasts.
