scholarly journals Bak Conformational Changes Induced by Ligand Binding: Insight into BH3 Domain Binding and Bak Homo-Oligomerization

2012 ◽  
Vol 2 (1) ◽  
Author(s):  
Yuan-Ping Pang ◽  
Haiming Dai ◽  
Alyson Smith ◽  
X. Wei Meng ◽  
Paula A. Schneider ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Conformational Changes ◽  
Bh3 Domain ◽  
Insight Into

CarR, a MarR-family regulator from Corynebacterium glutamicum, modulated antibiotic and aromatic compound resistance

2019 ◽  
Vol 476 (21) ◽  
pp. 3141-3159 ◽  
Author(s):  
Meiru Si ◽  
Can Chen ◽  
Zengfan Wei ◽  
Zhijin Gong ◽  
GuiZhi Li ◽  
...  
Keyword(s):  
Stress Response ◽  
Ligand Binding ◽  
Corynebacterium Glutamicum ◽  
Conformational Changes ◽  
Cysteine Oxidation ◽  
Transcriptional Regulatory ◽  
Ligand Free ◽  
Redox Sensing

Abstract MarR (multiple antibiotic resistance regulator) proteins are a family of transcriptional regulators that is prevalent in Corynebacterium glutamicum. Understanding the physiological and biochemical function of MarR homologs in C. glutamicum has focused on cysteine oxidation-based redox-sensing and substrate metabolism-involving regulators. In this study, we characterized the stress-related ligand-binding functions of the C. glutamicum MarR-type regulator CarR (C. glutamicum antibiotic-responding regulator). We demonstrate that CarR negatively regulates the expression of the carR (ncgl2886)–uspA (ncgl2887) operon and the adjacent, oppositely oriented gene ncgl2885, encoding the hypothetical deacylase DecE. We also show that CarR directly activates transcription of the ncgl2882–ncgl2884 operon, encoding the peptidoglycan synthesis operon (PSO) located upstream of carR in the opposite orientation. The addition of stress-associated ligands such as penicillin and streptomycin induced carR, uspA, decE, and PSO expression in vivo, as well as attenuated binding of CarR to operator DNA in vitro. Importantly, stress response-induced up-regulation of carR, uspA, and PSO gene expression correlated with cell resistance to β-lactam antibiotics and aromatic compounds. Six highly conserved residues in CarR were found to strongly influence its ligand binding and transcriptional regulatory properties. Collectively, the results indicate that the ligand binding of CarR induces its dissociation from the carR–uspA promoter to derepress carR and uspA transcription. Ligand-free CarR also activates PSO expression, which in turn contributes to C. glutamicum stress resistance. The outcomes indicate that the stress response mechanism of CarR in C. glutamicum occurs via ligand-induced conformational changes to the protein, not via cysteine oxidation-based thiol modifications.

scholarly journals Putative ligand binding sites of two functionally characterized bark beetle odorant receptors

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Jothi K. Yuvaraj ◽  
Rebecca E. Roberts ◽  
Yonathan Sonntag ◽  
Xiao-Qing Hou ◽  
Ewald Grosse-Wilde ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Bark Beetle ◽  
Pest Control ◽  
Binding Sites ◽  
Functional Characterization ◽  
Site Directed Mutagenesis ◽  
Odorant Receptors ◽  
Functional Evolution ◽  
General Importance ◽  
Insight Into

Abstract Background Bark beetles are major pests of conifer forests, and their behavior is primarily mediated via olfaction. Targeting the odorant receptors (ORs) may thus provide avenues towards improved pest control. Such an approach requires information on the function of ORs and their interactions with ligands, which is also essential for understanding the functional evolution of these receptors. Hence, we aimed to identify a high-quality complement of ORs from the destructive spruce bark beetle Ips typographus (Coleoptera, Curculionidae, Scolytinae) and analyze their antennal expression and phylogenetic relationships with ORs from other beetles. Using 68 biologically relevant test compounds, we next aimed to functionally characterize ecologically important ORs, using two systems for heterologous expression. Our final aim was to gain insight into the ligand-OR interaction of the functionally characterized ORs, using a combination of computational and experimental methods. Results We annotated 73 ORs from an antennal transcriptome of I. typographus and report the functional characterization of two ORs (ItypOR46 and ItypOR49), which are responsive to single enantiomers of the common bark beetle pheromone compounds ipsenol and ipsdienol, respectively. Their responses and antennal expression correlate with the specificities, localizations, and/or abundances of olfactory sensory neurons detecting these enantiomers. We use homology modeling and molecular docking to predict their binding sites. Our models reveal a likely binding cleft lined with residues that previously have been shown to affect the responses of insect ORs. Within this cleft, the active ligands are predicted to specifically interact with residues Tyr84 and Thr205 in ItypOR46. The suggested importance of these residues in the activation by ipsenol is experimentally supported through site-directed mutagenesis and functional testing, and hydrogen bonding appears key in pheromone binding. Conclusions The emerging insight into ligand binding in the two characterized ItypORs has a general importance for our understanding of the molecular and functional evolution of the insect OR gene family. Due to the ecological importance of the characterized receptors and widespread use of ipsenol and ipsdienol in bark beetle chemical communication, these ORs should be evaluated for their potential use in pest control and biosensors to detect bark beetle infestations.

scholarly journals Conformational Changes in IpaD fromShigella flexneriupon Binding Bile Salts Provide Insight into the Second Step of Type III Secretion

Biochemistry ◽  
2011 ◽  
Vol 50 (2) ◽  
pp. 172-180 ◽  
Author(s):  
Nicholas E. Dickenson ◽  
Lingling Zhang ◽  
Chelsea R. Epler ◽  
Philip R. Adam ◽  
Wendy L. Picking ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Type Iii Secretion ◽  
Bile Salts ◽  
Second Step ◽  
Type Iii ◽  
Insight Into

scholarly journals Using Fourier Transform Infrared Spectroscopy to Study Effects of Magnetic Field Treatment on Wheat (Triticum aestivumL.) Seedlings

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Zhenlin Wei ◽  
Dejie Jiao ◽  
Junxiao Xu
Keyword(s):  
Magnetic Field ◽  
Fourier Transform ◽  
Conformational Changes ◽  
Structural Variation ◽  
Fourier Transform Infrared ◽  
Biological Mechanisms ◽  
Wheat Seedlings ◽  
Wheat Leaves ◽  
Germination And Growth ◽  
Insight Into

Magnetic field treatments have been utilized to promote germination and growth of a variety of species of plants; however the mechanism of concern has not been fully elucidated. In this research, wheat seedlings were treated with 500 mT and 1500 mT static magnetic field (SMF) for 10 and 20 min, respectively. Analyzing Fourier transform infrared spectra collected from leaves of seedlings showed that SMF treatments decreased the contents of lipids and proteins, shifted bands to higher wavenumbers in 3000–2800 cm−1regions, and increased the ratio of CH2/CH3which likely indicates a structural variation of lipids. For bands assigned to different second structures of proteins, slight bands shifting and changing the ratio of different second structures of proteins were observed due to SMF treatments. To summarize, the results revealed that lipids rather than proteins were sensitive to SMF treatments. The results provided insight into the SMF induced conformational changes of lipids and proteins in wheat leaves, which will help elucidate the biological mechanisms of SMF on plant growth and development.

scholarly journals Cell adaptive response to extracellular matrix density is controlled by ICAP-1–dependent β1-integrin affinity

2008 ◽  
Vol 180 (2) ◽  
pp. 427-441 ◽  
Author(s):  
Angélique Millon-Frémillon ◽  
Daniel Bouvard ◽  
Alexei Grichine ◽  
Sandra Manet-Dupé ◽  
Marc R. Block ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Β1 Integrin ◽  
Embryonic Fibroblasts ◽  
Matrix Surface ◽  
Extracellular Microenvironment ◽  
And Migration ◽  
Integrated Response ◽  
Insight Into

Cell migration is an integrated process requiring the continuous coordinated assembly and disassembly of adhesion structures. How cells orchestrate adhesion turnover is only partially understood. We provide evidence for a novel mechanistic insight into focal adhesion (FA) dynamics by demonstrating that integrin cytoplasmic domain–associated protein 1 (ICAP-1) slows down FA assembly. Live cell imaging, which was performed in both Icap-1–deficient mouse embryonic fibroblasts and cells expressing active β1 integrin, shows that the integrin high affinity state favored by talin is antagonistically controlled by ICAP-1. This affinity switch results in modulation in the speed of FA assembly and, consequently, of cell spreading and migration. Unexpectedly, the ICAP-1–dependent decrease in integrin affinity allows cell sensing of matrix surface density, suggesting that integrin conformational changes are important in mechanotransduction. Our results clarify the function of ICAP-1 in cell adhesion and highlight the central role it plays in the cell's integrated response to the extracellular microenvironment.

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