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A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single-molecule force spectroscopy

A. Marsico, D. Labudde, T. Sapra, D. J. Muller, M. Schroeder
2007 Bioinformatics  
Singlemolecule force spectroscopy is a novel technique, which measures the force necessary to pull a protein out of a membrane.  ...  High-throughput force spectroscopy experiments generate hundreds of force curves including spurious ones and good curves, which correspond to different unfolding pathways.  ...  ACKNOWLEDGEMENTS Thanks to Andreas Henschel for conservation colouring in PyMol, Christof Winter and Harald Janovjak for interesting discussions, Gihan Dawelbait, Andreas Doms and Thomas Wächter for critical  ... 
doi:10.1093/bioinformatics/btl293 pmid:17237097 fatcat:hvxju4dspvawzhppw4p75igpxy

13th EBSA congress, July 24–28, 2021, Vienna, Austria

2021 European Biophysics Journal  
celebrated in Dresden (2015), Edinburgh (2017) and Madrid (2019), with a very dynamic organization, ready to adapt to any conceivable possible situation.  ...  Biophysics is contributing significantly, in close collaboration with so many other disciplines, to a solution of the Covid-19 problem, and we will have in Vienna a good selection of biophysical studies  ...  Single molecule force spectroscopy (SMFS) based on the atomic force microscope (AFM) is capable of measuring minute forces of protein-receptor bonds and has been applied by Alsteens et al. to investigate  ... 
doi:10.1007/s00249-021-01558-w pmid:34245338 pmcid:PMC8272448 fatcat:z2svytd4kbamrmvarle4lxwtxm

No time to lose—high throughput screening to assess nanomaterial safety

R. Damoiseaux, S. George, M. Li, S. Pokhrel, Z. Ji, B. France, T. Xia, E. Suarez, R. Rallo, L. Mädler, Y. Cohen, E. M. V. Hoek (+1 others)
2011 Nanoscale  
Animal based systems lack the needed capacity to cope with the abundance of novel nanomaterials being produced, and thus we have to employ in vitro methods with high throughput to manage the rush logistically  ...  Towards this end, high throughput screening (HTS) and high content screening (HCS) approaches can be used to speed up the safety analysis on a scale that commensurate with the rate of expansion of new  ...  with the release of toxic metal ions 72 , cationic surface charge 73 , protein damage or triggering of the protein unfolding response 74 , membrane leakage, generation of inflammation (including chronic  ... 
doi:10.1039/c0nr00618a pmid:21301704 pmcid:PMC3980675 fatcat:aueozlboc5aanichx76ml3ftrq

Award Winners and Abstracts of the 30th Anniversary Symposium of The Protein Society, Baltimore, MD, July 16-19, 2016

2016 Protein Science  
New labware for high throughput screening of crystallization conditions and chemical libraries Ella Teplitsky 1 , Karan Joshi 2 , Lauren Zipper 3 , Anthony Borelli 4 , Alexander Scalia 5 , Daniel Ericson  ...  Isolated hE3-D444V generates ROS at a significantly higher rate than does the isolated hE3, which may contribute to the severity of the pathologies.  ...  Interestingly, two distributions of unfolding forces were observed with a force similar to and greater than the unfolding forces observed for apo R.  ... 
doi:10.1002/pro.3026 pmid:27783432 pmcid:PMC5081090 fatcat:c4k7luvl4vczfpol76ycqo4nji

Time, space, and disorder in the expanding proteome universe

David-Paul Minde, A. Keith Dunker, Kathryn S. Lilley
2017 Proteomics  
Their myriad functions require specific structures, but proteins' dynamic nature ranges all the way from the local mobility of their amino acid constituents to mobility within and well beyond single cells  ...  Computational tools that integrate and expand on multiple orthogonal data types promise to enable the transition from a disjointed list of static snapshots to a structurally explicit understanding of the  ...  Membrane enrichment is crucial for membrane-intrinsic transporters and helps to orchestrate a variety of metabolic pathways [96] .  ... 
doi:10.1002/pmic.201600399 pmid:28145059 pmcid:PMC5573936 fatcat:aapoxkehrzdapghneqqwp442fe

Nanoimaging, Molecular Interaction, and Nanotemplating of Human Rhinovirus [chapter]

Markus Kastner, Christian Rankl, Andreas Ebner, Philipp D. Pollheimer, Stefan Howorka, Hermann J. Gruber, Dieter Blaas, Peter Hinterdorfer
2010 Scanning Probe Microscopy in Nanoscience and Nanotechnology 2  
The atomic force microscope (AFM) offers not only tremendously high spatial and topographic resolution, but also allows localizing single molecules and determining their interaction on a molecular level  ...  A section of this chapter describes, for instance, the measurement of kinetic parameters governing the first step of viral infection -the attachment of a human rhinovirus to a cell -at the single-molecule  ...  A recent study by Puntheeranurak et al. [85] demonstrated the potential of molecule recognition force spectroscopy.  ... 
doi:10.1007/978-3-642-10497-8_21 fatcat:wovfmyzcgjg5hpygfm5lmvprjy

Award Winners and Abstracts of the 31st Annual Symposium of The Protein Society, Montreal, Canada, July 24-27, 2017

2017 Protein Science  
by imaging of the ACTN4 protein expression pattern with conventional light microscopy.  ...  limited to a 250nm resolution).  ...  We explored the effects of species-related sequence differences using force spectroscopy to observe the folding dynamics of single PrP molecules held by optical tweezers.  ... 
doi:10.1002/pro.3349 pmid:29280217 fatcat:jrxtwzblare37gxsvc5szbwuhu

NanoEHS beyond toxicity – focusing on biocorona

Sijie Lin, Monika Mortimer, Ran Chen, Aleksandr Kakinen, Jim E. Riviere, Thomas P. Davis, Feng Ding, Pu Chun Ke
2017 Environmental Science: Nano  
We believe continued development of the field of environmental health and safety of nanomaterials (nanoEHS) hinges on a critical extension from reporting macroscopic and microscopic phenomena to understanding  ...  [37] [38] [39] [40] High-throughput screening and the big data era In order to provide discovery platforms with the ability to consider a wide range of nano-bio interactions, streamlining experimental  ...  One of the most widely used classification algorithms, Support Vector Machine (SVM), adopts a classifier and adjusts its flexibility to reach an optimized point based on the training data, to ensure that  ... 
doi:10.1039/c6en00579a pmid:29123668 pmcid:PMC5673284 fatcat:47pifnwhbfhalfjfqz23pdbkia

The 2018 correlative microscopy techniques roadmap

Toshio Ando, Satya Prathyusha Bhamidimarri, Niklas Brending, H Colin-York, Lucy Collinson, Niels De Jonge, P J de Pablo, Elke Debroye, Christian Eggeling, Christian Franck, Marco Fritzsche, Hans Gerritsen (+24 others)
2018 Journal of Physics D: Applied Physics  
With this in mind, the Journal of Physics D: Applied Physics presents a special roadmap on the correlative microscopy techniques, giving a comprehensive overview from various leading scientists in this  ...  and forces involved in cell-cell interactions.  ...  J P H has a financial interest in Delmic BV, a company producing integrated microscopes.  ... 
doi:10.1088/1361-6463/aad055 pmid:30799880 pmcid:PMC6372154 fatcat:sg76jitzs5es7ksufvc76kawdi

Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis

Justin T. Marinko, Hui Huang, Wesley D. Penn, John A. Capra, Jonathan P. Schlebach, Charles R. Sanders
2019 Chemical Reviews  
Advances over the past 25 years have revealed much about how the structural properties of membranes and associated proteins are linked to the thermodynamics and kinetics of membrane protein (MP) folding  ...  This emerging framework has paved the way for the development of a new class of small molecule "pharmacological chaperones" that bind to and stabilize misfolded MP variants, some of which are now in clinical  ...  Figure 10 . 10 Single-molecule forced unfolding of a MP, GlpG. (A) Schematic of the single-molecule magnetic tweezers experiment for studying the unfolding and refolding of GlpG in a bicelle.  ... 
doi:10.1021/acs.chemrev.8b00532 pmid:30608666 pmcid:PMC6506414 fatcat:6u7o747gbnavlgon6rk5orq5ca

Abstracts of the 29th Annual Symposium of The Protein Society

2015 Protein Science  
useful reagent for importing fluorine into proteins via nucleophilic substitution such as with a cysteinyl-thiol [4].  ...  Nonetheless, our approach clearly demonstrates the ability of biological systems to produce advanced, functional nanomaterials, and provides a template for engineering biological systems to high-value  ...  the horizontal transfer of single stranded DNA from one cell to another.  ... 
doi:10.1002/pro.2823 pmid:26452528 pmcid:PMC4632850 fatcat:ejmksoqj3zbsrkabl4jyp7emgi

Computational modeling of membrane proteins

Julia Koehler Leman, Martin B. Ulmschneider, Jeffrey J. Gray
2014 Proteins: Structure, Function, and Bioinformatics  
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure  ...  The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade.  ...  Acknowledgments The authors would like to acknowledge the F. Stuart Hodgson Faculty Scholar Fund (to JJG) and NIH R01-GM078221 to JJG.  ... 
doi:10.1002/prot.24703 pmid:25355688 pmcid:PMC4270820 fatcat:lk7ku2koqnfi5axp7luxq6e44e


2016 Seibutsu Butsuri  
In order to identify the minority cells, high throughput single cell analysis is required.  ...  A novel motor complex developed from an F-type ATPase generates a force, which transmits across the membrane and a 512 kDa "crank" protein to a 314 kDa "leg" protein.  ...  3Pos313 Ohashi, Kaoru (大橋 郁) 3Pos279 3Pos284 Ohba, Yasunori (大庭 裕範) 3Pos065 Ohba, Yusuke (大場 雄介) 3SAA-03 Ohgita, Takashi (扇田 隆司) 3Pos072 Ohira, Ayaka (大平 彩花) 1Pos257 Ohki, Mio (大木 規央) 3Pos076 Ohkoshi, A.  ... 
doi:10.2142/biophys.56.s1 fatcat:jxxuc3tfpbhc5isjcmprzec2gi

Understanding protein non-folding

Vladimir N. Uversky, A. Keith Dunker
2010 Biochimica et Biophysica Acta - Proteins and Proteomics  
This shift in the paradigm represents a major breakthrough for biochemistry, biophysics and molecular biology, as it opens new levels of understanding with regard to the complex life of proteins.  ...  The existence of such proteins does not fit the prevailing structure-function paradigm, which states that unique 3-D structure is a prerequisite to function.  ...  Acknowledgments We thank Zoran Obradovic, Chris Oldfield, Bin Xue, Pedro Romero, Marc Cortese, and Ya-Yue Van for their continuing support and collaborations in the field of the ID proteins studies.  ... 
doi:10.1016/j.bbapap.2010.01.017 pmid:20117254 pmcid:PMC2882790 fatcat:h3tmwu2tirhillnt2pvunglday

A Review of Single-Cell Adhesion Force Kinetics and Applications

Ashwini Shinde, Kavitha Illath, Pallavi Gupta, Pallavi Shinde, Ki-Taek Lim, Moeto Nagai, Tuhin Subhra Santra
2021 Cells  
The adhesive force measurement for single-cell microorganisms and single-molecules is emphasized as well.  ...  This is used to functionalize from the measurement of cellular deformability to the quantification of the interaction forces generated by a cell and exerted on its surroundings at single-cell with attachment  ...  Data sharing is not applicable to this article. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cells10030577 pmid:33808043 pmcid:PMC8000588 fatcat:ku34ygdfkjhnvonjwxe3je4day
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