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
Multidisciplinary Sciences
Eve E. Weatherill, Monifa A. Fahie, David P. Marshall, Rachel A. Andvig, Matthew R. Cheetham, Min Chen, Mark Wallace
Summary: Compared to globular proteins, the folding and insertion of beta-barrel membrane proteins are slow but rapid, occurring within seconds upon arrival at the membrane interface. This combination of infrequent yet fast folding events resolves the apparent contradiction between slow ensemble kinetics and typical biomolecular folding timescales.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Golam Mustafa, Prabesh Gyawali, Jacob A. Taylor, Parastoo Maleki, Marlon V. Nunez, Michael C. Guntrum, Sajad Shiekh, Hamza Balci
Summary: This paper presents a collection of single molecule studies on the i-motif structure formed by the human telomeric sequence. The i-motif structure has recently gained attention as a physiologically relevant structure and a pH sensor. The study establishes single molecule Forster resonance energy transfer (smFRET) as a tool to investigate the i-motif under different pH and ionic conditions, revealing the pH and salt dependence of i-motif formation and capturing the intermediate folding states in real time. Furthermore, the i-motif is demonstrated to be a potential in-situ pH sensor.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Virology
Sudip Nepal, Erik D. Holmstrom
Summary: The highly conserved hepatitis C virus core protein (HCVcp) plays a crucial role in nucleocapsid assembly. Single-molecule FRET spectroscopy reveals distinct binding mechanisms between HCVcp and antiviral therapeutics.
JOURNAL OF VIROLOGY
(2023)
Article
Multidisciplinary Sciences
Neharika Chamachi, Andreas Hartmann, Mai Quynh Ma, Anna Svirina, Georg Krainer, Michael Schlierf
Summary: This study investigates the essential role of periplasmic chaperones, 17-kilodalton protein (Skp) and survival factor A (SurA), in outer membrane protein (OMP) biogenesis. The researchers use single-molecule fluorescence spectroscopy to analyze the conformational dynamics and thermodynamics of Skp and SurA binding to unfolded OmpX and study their disaggre-gase activities. The findings provide insights into the multifaceted functionalities of Skp and SurA and shed light on the balance between conformational flexibility and underlying ener-getics in aiding chaperone action during OMP biogenesis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Ikenna C. Okafor, Taekjip Ha
Summary: CRISPR Cas9 is an RNA-guided endonuclease that is a part of bacterial adaptive immune system. By developing a single molecule FRET assay, the study investigated the conformational changes of sgRNA and the binding of Cas9 to sgRNA, providing insights into the assembly dynamics of Cas9 RNA ribonucleoprotein complex. This research could contribute to the rational design of sgRNAs and improve the editing outcomes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Andrew J. Lee, Masayuki Endo, Jamie K. Hobbs, A. Giles Davies, Christoph Walti
Summary: The study used DNA nanostructure-augmented high-speed AFM to directly observe the RecA-orchestrated alignment of homologous DNA strands, revealing transient sampling of micro-homology by RecA during the search for sequence alignment. These transient interactions are early steps in the search for sequence homology.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Analytical
Hong Sun, Chuan Yao, Kaibo You, Can Chen, Shuoshuo Liu, Zhihong Xu
Summary: In this study, a dynamic monitoring approach based on nanopore single-molecule biosensor was developed to detect the folding and unfolding transitions of proteins. By gradually increasing the concentration of denaturant guanidine hydrochloride (GdmCl), sensitive responses were observed with lysozyme unfolding. The existence of a stable intermediate was experimentally confirmed, providing insights into the conformation of the intermediate and the manner of denaturant towards lysozyme.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemistry & Molecular Biology
Chaoyou Xue, Lucia Molnarova, Justin B. Steinfeld, Weixing Zhao, Chujian Ma, Mario Spirek, Kyle Kaniecki, Youngho Kwon, Ondrej Belan, Katerina Krejci, Simon J. Boulton, Patrick Sung, Eric C. Greene, Lumir Krejci
Summary: RECQ5 is identified as an ATP-dependent single-stranded DNA motor protein that can translocate on various nucleoprotein complexes and dismantle RAD51-ssDNA filaments. Protein-protein interaction with RAD51 is crucial for RECQ5's functions, but its substrate specificity and ability to remove certain mutant RAD51 proteins suggest a complex regulatory role in genome maintenance.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Analytical
Xiaojia Jiang, Tiezheng Pan, Chao Lang, Chao Zeng, Jinxing Hou, Jiayun Xu, Quan Luo, Chunxi Hou, Junqiu Liu
Summary: In this study, a semisynthetic selenoenzyme nanoreactor was created to monitor and analyze intermediates in enzymatic reactions, revealing the mysteries of selenoenzyme catalysis at the single-molecule level.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Hsuan-Lei Sung, Abhigyan Sengupta, David Nesbitt
Summary: The crowded cellular environment has a significant impact on the stability and functionality of biomolecules, with smaller molecular weight crowders proving to be more effective in increasing the folding rate and decreasing the unfolding rate of RNA tertiary structures. Experimental verification of the entropic crowding effects can predict the stabilization of RNA tertiary structures in the cellular environment under the influence of small molecular weight crowders.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Multidisciplinary Sciences
Patrick Moessmer, Thomas Suren, Ulrike Majdic, Vinay Dahiya, Daniel Rutz, Johannes Buchner, Matthias Rief
Summary: In this study, the interaction between the glucocorticoid receptor and the molecular chaperone system was observed using single-molecule force spectroscopy. The results show that the molecular chaperones can unfold the receptor in a stepwise manner through ATP hydrolysis. These findings provide important insights into the regulation of the glucocorticoid receptor by molecular chaperones.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Fasil Ali, Usma Manzoor, Faez Iqbal Khan, Dakun Lai, Md Khurshid A. Khan, K. S. Chandrashekharaiah, Laishram Rajendrakumar Singh, Tanveer Ali Dar
Summary: This study investigated the ability of various polyols to modulate the structure, activity, and aggregation of catalase. The results showed that all polyols increased catalase activity and improved its stability, with glycerol being the most effective polyol. Simulation studies further supported the findings. Overall, glycerol has the potential to prevent aggregation of catalase and enhance its stability during industrial processing.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Multidisciplinary
Sung Hyun Kim, Hyunwoo Kim, Hawoong Jeong, Tae-Young Yoon
Summary: The study demonstrates the use of single-molecule FRET technology to encode virtual signals in DNA barcodes, allowing for precise measurement of FRET efficiency for each binding event and differentiation of six DNA barcodes.
Article
Multidisciplinary Sciences
Sahar Foroutannejad, Lydia L. L. Good, Changfan Lin, Zachariah I. I. Carter, Mahlet G. G. Tadesse, Aaron L. L. Lucius, Brian R. R. Crane, Rodrigo A. A. Maillard
Summary: Characterizing folding pathways of large proteins that bind complex cofactors is challenging. The authors use optical tweezers to study the folding mechanism of dCRY and identify the role of FAD moieties in folding. They show that FAD binds to unfolded intermediates and drives the folding process, but not all FAD moieties are necessary for complete folding.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Murat Sunbul, Jens Lackner, Annabell Martin, Daniel Englert, Benjamin Hacene, Franziska Grun, Karin Nienhaus, G. Ulrich Nienhaus, Andres Jaschke
Summary: A newly developed light-up RNA aptamer, RhoBAST, enables super-resolution imaging with single-molecule localization microscopy, surpassing the limitation of photobleaching. The intermittent fluorescence emission of RhoBAST allows for high-resolution imaging of RNA subcellular structures in live and fixed cells with precise localization and high signal-to-noise ratio.
NATURE BIOTECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Hendrik Sielaff, Frank Dienerowitz, Maria Dienerowitz
Summary: In this study, we combined smFRET and electrokinetic trapping to non-invasively hold single FOF1-ATP synthases. The observation time was extended by a factor of 10 compared to Brownian diffusion without surface attachment. Our method allows for monitoring complete reaction cycles and extracting kinetic rates, making it a versatile tool for studying protein dynamics, not limited to motor proteins.
Article
Biochemical Research Methods
Manuel Huepfel, Manuel Fernandez Merino, Johannes Bennemann, Masanari Takamiya, Sepand Rastegar, Anja Tursch, Thomas W. Holstein, G. Ulrich Nienhaus
Summary: This study proposes a fast approximation of three-dimensional multi-view deconvolution and demonstrates its advantages in image processing. The method is capable of handling large amounts of image data and performs well in time-critical applications.
BIOMEDICAL OPTICS EXPRESS
(2022)
Article
Biology
Giulia Ambrosi, Oksana Voloshanenko, Antonia F. Eckert, Dominique Kranz, G. Ulrich Nienhaus, Michael Boutros
Summary: Wnt signaling is important in various biological processes, and mutations in beta-catenin can activate this signaling pathway. In this study, fluorescently tagged alleles of wild-type and mutant beta-catenin were engineered and analyzed to understand their properties. The results revealed distinct biophysical properties between the two alleles, and the wild-type allele could be manipulated to mimic the properties of the mutant allele through specific treatments.
Review
Nanoscience & Nanotechnology
Karin Nienhaus, Yumeng Xue, Li Shang, Gerd Ulrich Nienhaus
Summary: This review summarizes the key role of biomolecule adsorption onto engineered nanomaterials in therapeutic and diagnostic applications. It discusses the recent shift towards gaining active control of nano-bio interactions to enhance the efficacy of nanomaterials in biomedical applications. The review provides an overview of fundamental knowledge about protein-nanomaterial interactions and explores ways to exploit these interactions in biomedical applications.
Article
Multidisciplinary Sciences
Nane C. Kuznik, Valeria Solozobova, Irene I. Lee, Nicole Jung, Linxiao Yang, Karin Nienhaus, Emmanuel A. Ntim, Jaice T. Rottenberg, Claudia Muhle-Goll, Amrish Rajendra Kumar, Ravindra Peravali, Simone Graessle, Victor Gourain, Celia Deville, Laura Cato, Antje Neeb, Marco Dilger, Christina A. Cramer von Clausbruch, Carsten Weiss, Bruno Kieffer, G. Ulrich Nienhaus, Myles Brown, Stefan Braese, Andrew C. B. Cato
Summary: BAG1 proteins, particularly the isoform BAG1L, play crucial roles in prostate cancer by regulating the androgen receptor (AR) and affecting gene expression related to oxidative stress and metabolism. A small molecule, A4B17, targeting the BAG domain, shows promising results in downregulating AR target genes and inhibiting prostate tumor development, outperforming the clinically approved antagonist enzalutamide. BAG1 inhibitors offer unique opportunities for antagonizing AR action and prostate cancer growth.
Article
Biochemistry & Molecular Biology
Karin Nienhaus, Vandna Sharma, Gerd Ulrich Nienhaus, Larissa M. Podust
Summary: This study investigated the interplay between enzyme activity and oligomerization state of CYP51 enzymes in Acanthamoeba castellanii and Naegleria fowleri. The results indicate that dimeric assembly is critical for stabilizing thiolate coordination to heme and sustaining enzyme activity.
Article
Chemistry, Multidisciplinary
Haixia Wang, Karin Nienhaus, Li Shang, Gerd Ulrich Nienhaus
Summary: In this study, we investigated the interactions between positively charged MUTAB-stabilized quantum dots (QDs) and proteins, serum, and live cells using various techniques. The results showed that MUTAB-QDs have affinity towards HSA and serum, and can bind to and perforate the cell membrane. Pre-adsorption of proteins on the QD surfaces can reduce this process.
CHINESE JOURNAL OF CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Woei Shyuan Ng, Hendrik Sielaff, Ziqing Winston Zhao
Summary: Phase separation is an effective strategy to compartmentalize cellular components, particularly those involving chromatin. Advanced imaging-based approaches have enabled the quantitative characterization of chromatin-based phase condensates. The complex interplay between chromatin and other molecular species mediated by phase separation regulates the genome within the dynamic nuclear space at multiple scales and modes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Chemistry, Analytical
Karin Nienhaus, Gerd Ulrich Nienhaus
Summary: Optical fluorescence microscopy is crucial for studying biological structure and dynamics, and genetically encodable fluorescent proteins are invaluable markers for live specimens. Protein engineering has enabled the development of FP variants with specific photophysical properties for advanced imaging techniques.
METHODS AND APPLICATIONS IN FLUORESCENCE
(2022)
Review
Chemistry, Multidisciplinary
Karin Nienhaus, Gerd Ulrich Nienhaus
Summary: Although a variety of nanoparticles have been developed for medical use, their application in clinical settings is limited. The lack of understanding of nanoparticle interactions in the bio-environment, particularly the protein corona, is a major obstacle. This article critically reviews research on the protein corona, including its structure, reversibility, time dependence, and role in nanoparticle agglomeration, highlighting the need for further mechanistic studies. The article concludes with a discussion of future research directions to enhance the understanding of the protein corona and improve the design of nanomedicines.
Article
Optics
Lan Yu, Yu Wang, Yang Wang, Kequn Zhuo, Min Liu, G. Ulrich Nienhaus, Peng Gao
Summary: We introduce a label-free technique called two-beam phase correlation spectroscopy (2B-ICS) to measure the dynamics of flowing particles, such as blood flow. This method combines phase imaging with correlation spectroscopy and uses the refractive index contrast of particles against the fluid background for analysis. 2B-ICS is a simple procedure that involves acquiring phase images of flowing particles and correlating the phase fluctuations to determine concentration and flow velocity.
PHOTONICS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Afaf Elkurdi, Gernot Guigas, Latifa Hourani-Alsharafat, Patrick Scheerer, Gerd Ulrich Nienhaus, Norbert Krauss, Tilman Lamparter
Summary: Phytochromes are photoreceptor proteins that can convert between two different forms, Pr and Pfr. The N-terminal photosensory chromophore module (PCM), composed of PAS, GAF, and PHY domains, and the C-terminus histidine kinase module play important roles in this process. By studying Agp1 mutants, researchers found a mechanical coupling between position 362 and the histidine kinase, and flexibility around position 308 in both Pr and Pfr forms.
PHOTOCHEMISTRY AND PHOTOBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Daniel Englert, Eva-Maria Burger, Franziska Gruen, Mrigank S. Verma, Jens Lackner, Marko Lampe, Bastian Buehler, Janin Schokolowski, G. Ulrich Nienhaus, Andres Jaeschke, Murat Sunbul
Summary: Spirocyclic rhodamine probes were designed for visualizing RNA in live or fixed cells using SMLM and STED microscopy modalities. A novel probe called SpyRho was developed, which tightly binds to the RhoBAST aptamer and exhibits high brightness and fluorogenicity. This system represents significant advances in live-cell RNA imaging.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Rui Ma, Martin Stefl, Gerd Ulrich Nienhaus
Summary: This study used super-resolution microscopy to analyze the development of Clathrin-coated pits and caveolae on the plasma membrane of cells, and found that they have remarkably similar temporal evolution, suggesting the involvement of shared key accessory proteins in this process.
NANOSCALE HORIZONS
(2022)