Gee, Clifford T Arntson, Keith E Urick, Andrew K Mishra, Neeraj K Hawk, Laura M L Wisniewski, Andrea J Pomerantz, William C K
Published in
Nature protocols
NMR spectroscopy can be used to quantify the binding affinity between proteins and low-complexity molecules, termed 'fragments'; this versatile screening approach allows researchers to assess the druggability of new protein targets. Protein-observed (19)F-NMR (PrOF NMR) using (19)F-labeled amino acids generates relatively simple spectra that are ab...
Ly, Alice Buck, Achim Balluff, Benjamin Sun, Na Gorzolka, Karin Feuchtinger, Annette Janssen, Klaus-Peter Kuppen, Peter J K van de Velde, Cornelis J H Weirich, Gregor
...
Published in
Nature protocols
Formalin-fixed and paraffin-embedded (FFPE) tissue specimens are the gold standard for histological examination, and they provide valuable molecular information in tissue-based research. Metabolite assessment from archived tissue samples has not been extensively conducted because of a lack of appropriate protocols and concerns about changes in meta...
Magnani, Francesca Serrano-Vega, Maria J Shibata, Yoko Abdul-Hussein, Saba Lebon, Guillaume Miller-Gallacher, Jennifer Singhal, Ankita Strege, Annette Thomas, Jennifer A Tate, Christopher G
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Published in
Nature protocols
The thermostability of an integral membrane protein (MP) in detergent solution is a key parameter that dictates the likelihood of obtaining well-diffracting crystals that are suitable for structure determination. However, many mammalian MPs are too unstable for crystallization. We developed a thermostabilization strategy based on systematic mutagen...
Grootjans, Sasker Hassannia, Behrouz Delrue, Iris Goossens, Vera Wiernicki, Bartosz Dondelinger, Yves Bertrand, Mathieu J M Krysko, Dmitri V Vuylsteke, Marnik Vandenabeele, Peter
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Published in
Nature protocols
Several cell death assays have been developed based on a single biochemical parameter such as caspase activation or plasma membrane permeabilization. Our fluorescent apoptosis/necrosis (FAN) assay directly measures cell death and distinguishes between caspase-dependent apoptosis and caspase-independent necrosis of cells grown in any multiwell plate...
Chen, Xiaoqiang Lee, Kyung-Ah Ren, Xintong Ryu, Jae-Chan Kim, Gyungmi Ryu, Ji-Hwan Lee, Won-Jae Yoon, Juyoung
Published in
Nature protocols
During infection, nicotinamide adenine dinucleotide phosphate-oxidase of innate immune cells generates important microbicidal reactive oxygen species (ROS) such as hypochlorous acid (HOCl) to kill the invading pathogens. However, excess amounts of HOCl induce oxidative damage of functional biomolecules such as DNA and proteins, which may cause chro...
Wang, Hailong Li, Zhen Jia, Ruonan Hou, Yu Yin, Jia Bian, Xiaoying Li, Aiying Müller, Rolf Stewart, A Francis Fu, Jun
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Published in
Nature protocols
Full-length RecE and RecT from Rac prophage mediate highly efficient linear-linear homologous recombination that can be used to clone large DNA regions directly from genomic DNA into expression vectors, bypassing library construction and screening. Homologous recombination mediated by Redαβ from lambda phage has been widely used for recombinant DNA...
Lin, Meihua Song, Ping Zhou, Guobao Zuo, Xiaolei Aldalbahi, Ali Lou, Xiaoding Shi, Jiye Fan, Chunhai
Published in
Nature protocols
The occurrence and prognosis of many complex diseases, such as cancers, is associated with the variation of various molecules, including DNA at the genetic level, RNA at the regulatory level, proteins at the functional level and small molecules at the metabolic level (defined collectively as multilevel molecules). Thus it is highly desirable to dev...
Lee, Sarah C Knowles, Tim J Postis, Vincent L G Jamshad, Mohammed Parslow, Rosemary A Lin, Yu-Pin Goldman, Adrian Sridhar, Pooja Overduin, Michael Muench, Stephen P
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Published in
Nature protocols
Despite the great importance of membrane proteins, structural and functional studies of these proteins present major challenges. A significant hurdle is the extraction of the functional protein from its natural lipid membrane. Traditionally achieved with detergents, purification procedures can be costly and time consuming. A critical flaw with dete...
Mundinano, Inaki-Carril Flecknell, Paul A Bourne, James A
Published in
Nature protocols
In the past decade, the New World common marmoset (Callithrix jacchus) has taken a seminal position in neurobiological research, fueled in part by its smooth cortical sheet, which allows cortical areas to be easily accessed by current technologies on the dorsal surface of the brain. In this protocol, we describe a method for the precision placement...
Li, Lei Woodward, Robert L Han, Weiqing Qu, Jingyao Song, Jing Ma, Cheng Wang, Peng G
Published in
Nature protocols
Polysaccharides are essential and immunologically relevant components of bacterial cell walls. These biomolecules can be found covalently attached to lipids (e.g., O-polysaccharide (PS) contains undecaprenyl and lipopolysaccharide (LPS) contains lipid A) or noncovalently associated with cell wells (e.g., capsular PS (CPS)). Although extensive genet...