@article {2106,
	title = {Structural insights into actin filament recognition by commonly used cellular actin markers.},
	journal = {EMBO J},
	volume = {39},
	year = {2020},
	month = {2020 Jul 15},
	pages = {e104006},
	abstract = {<p>Cellular studies of filamentous actin (F-actin) processes commonly utilize fluorescent versions of toxins, peptides, and proteins that bind actin. While the choice of these markers has been largely based on availability and ease, there is a severe dearth of structural data for an informed judgment in employing suitable F-actin markers for a particular requirement. Here, we describe the electron cryomicroscopy structures of phalloidin, lifeAct, and utrophin bound to F-actin, providing a comprehensive high-resolution structural comparison of widely used actin markers and their influence towards F-actin. Our results show that phalloidin binding does not induce specific conformational change and lifeAct specifically recognizes closed D-loop conformation, i.e., ADP-Pi or ADP states of F-actin. The structural models aided designing of minimal utrophin and a shorter lifeAct, which can be utilized as F-actin marker. Together, our study provides a structural perspective, where the binding sites of utrophin and lifeAct overlap with majority of actin-binding proteins and thus offering an invaluable resource for researchers in choosing appropriate actin markers and generating new marker variants.</p>
},
	issn = {1460-2075},
	doi = {10.15252/embj.2019104006},
	author = {Kumari, Archana and Kesarwani, Shubham and Javoor, Manjunath G and Vinothkumar, Kutti R and Sirajuddin, Minhajuddin}
}
@article {1203,
	title = {Structural and functional studies of ferredoxin and oxygenase components of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2.},
	journal = {PLoS One},
	volume = {12},
	year = {2017},
	month = {2017},
	pages = {e0176398},
	abstract = {<p>3-nitrotoluene dioxygenase (3NTDO) from Diaphorobacter sp. strain DS2 catalyses the conversion of 3-nitrotoluene (3NT) into a mixture of 3- and 4-methylcatechols with release of nitrite. We report here, X-ray crystal structures of oxygenase and ferredoxin components of 3NTDO at 2.9 {\r A} and 2.4 {\r A}, respectively. The residues responsible for nitrite release in 3NTDO were further probed by four single and two double mutations in the catalytic site of α-subunit of the dioxygenase. Modification of Val 350 to Phe, Ile 204 to Ala, and Asn258 to Val by site directed mutagenesis resulted in inactive enzymes revealing the importance of these residues in catalysis. Docking studies of meta nitrotoluene to the active site of 3NTDO suggested possible orientations of binding that favor the formation of 3-methylcatechol (3MC) over 4-methylcatechol energetically. The electron transfer pathway from ferredoxin subunit to the active site of the oxygenase subunit is also proposed.</p>
},
	keywords = {Catalytic Domain, Comamonadaceae, Crystallography, X-Ray, Ferredoxins, Molecular Docking Simulation, Mutation, Oxygenases, Substrate Specificity, Toluene},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0176398},
	author = {Kumari, Archana and Singh, Deepak and Ramaswamy, S and Ramanathan, Gurunath}
}
