scholarly journals Use of enhancer trapping to identify pathogen-induced regulatory events spatially restricted to plant-microbe interaction sites

2015 ◽  
Vol 17 (3) ◽  
pp. 388-397 ◽  
Author(s):  
Mercedes Schroeder ◽  
Tokuji Tsuchiya ◽  
Shuilin He ◽  
Thomas Eulgem
Keyword(s):  
Plant Microbe Interaction ◽  
Interaction Sites ◽  
Enhancer Trapping

Decoding Protein-protein Interactions: An Overview

2020 ◽  
Vol 20 (10) ◽  
pp. 855-882
Author(s):  
Olivia Slater ◽  
Bethany Miller ◽  
Maria Kontoyianni
Keyword(s):  
Drug Discovery ◽  
Protein Interactions ◽  
Drug Repurposing ◽  
Protein Docking ◽  
Target Space ◽  
Protein Protein Interactions ◽  
X Ray Crystallography ◽  
Protein Protein Interaction ◽  
Interaction Sites ◽  
Long Time

Drug discovery has focused on the paradigm “one drug, one target” for a long time. However, small molecules can act at multiple macromolecular targets, which serves as the basis for drug repurposing. In an effort to expand the target space, and given advances in X-ray crystallography, protein-protein interactions have become an emerging focus area of drug discovery enterprises. Proteins interact with other biomolecules and it is this intricate network of interactions that determines the behavior of the system and its biological processes. In this review, we briefly discuss networks in disease, followed by computational methods for protein-protein complex prediction. Computational methodologies and techniques employed towards objectives such as protein-protein docking, protein-protein interactions, and interface predictions are described extensively. Docking aims at producing a complex between proteins, while interface predictions identify a subset of residues on one protein that could interact with a partner, and protein-protein interaction sites address whether two proteins interact. In addition, approaches to predict hot spots and binding sites are presented along with a representative example of our internal project on the chemokine CXC receptor 3 B-isoform and predictive modeling with IP10 and PF4.

PPIs Meta: A Meta-predictor of Protein-Protein Interaction Sites with Weighted Voting Strategy

2017 ◽  
Vol 14 (3) ◽  
Author(s):  
Xiaowei Zhao ◽  
Lingling Bao ◽  
Xiaosa Zhao ◽  
Minghao Yin
Keyword(s):  
Protein Interaction ◽  
Weighted Voting ◽  
Protein Protein Interaction ◽  
Interaction Sites ◽  
Voting Strategy ◽  
Protein Interaction Sites

scholarly journals Structural studies of phosphorylation-dependent interactions between the V2R receptor and arrestin-2

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qing-Tao He ◽  
Peng Xiao ◽  
Shen-Ming Huang ◽  
Ying-Li Jia ◽  
Zhong-Liang Zhu ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Nmr Spectrum ◽  
H Nmr ◽  
Interaction Sites ◽  
Receptor Interactions ◽  
Remote Sites ◽  
Genetic Code Expansion ◽  
G Protein Coupled ◽  
Interaction Change

AbstractArrestins recognize different receptor phosphorylation patterns and convert this information to selective arrestin functions to expand the functional diversity of the G protein-coupled receptor (GPCR) superfamilies. However, the principles governing arrestin-phospho-receptor interactions, as well as the contribution of each single phospho-interaction to selective arrestin structural and functional states, are undefined. Here, we determined the crystal structures of arrestin2 in complex with four different phosphopeptides derived from the vasopressin receptor-2 (V2R) C-tail. A comparison of these four crystal structures with previously solved Arrestin2 structures demonstrated that a single phospho-interaction change results in measurable conformational changes at remote sites in the complex. This conformational bias introduced by specific phosphorylation patterns was further inspected by FRET and 1H NMR spectrum analysis facilitated via genetic code expansion. Moreover, an interdependent phospho-binding mechanism of phospho-receptor-arrestin interactions between different phospho-interaction sites was unexpectedly revealed. Taken together, our results provide evidence showing that phospho-interaction changes at different arrestin sites can elicit changes in affinity and structural states at remote sites, which correlate with selective arrestin functions.

scholarly journals Identification of the retinal cyclic GMP phosphodiesterase inhibitory gamma-subunit interaction sites on the catalytic alpha-subunit.

1991 ◽  
Vol 266 (25) ◽  
pp. 16607-16613
Author(s):  
B. Oppert ◽  
J.M. Cunnick ◽  
D. Hurt ◽  
D.J. Takemoto
Keyword(s):  
Cyclic Gmp ◽  
Alpha Subunit ◽  
Subunit Interaction ◽  
Gamma Subunit ◽  
Interaction Sites

scholarly journals hobo enhancer trapping mutagenesis in Drosophila reveals an insertion specificity different from P elements.

Genetics ◽  
1993 ◽  
Vol 135 (4) ◽  
pp. 1063-1076 ◽  
Author(s):  
D Smith ◽  
J Wohlgemuth ◽  
B R Calvi ◽  
I Franklin ◽  
W M Gelbart
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Enhancer Trap ◽  
P Element ◽  
Present Evidence ◽  
P Elements ◽  
Element Insertion ◽  
Enhancer Trapping ◽  
Indispensable Tool

Abstract P element enhancer trapping has become an indispensable tool in the analysis of the Drosophila melanogaster genome. However, there is great variation in the mutability of loci by these elements such that some loci are relatively refractory to insertion. We have developed the hobo transposable element for use in enhancer trapping and we describe the results of a hobo enhancer trap screen. In addition, we present evidence that a hobo enhancer trap element has a pattern of insertion into the genome that is different from the distribution of P elements in the available database. Hence, hobo insertion may facilitate access to genes resistant to P element insertion.

Free H‐Bonding Interaction Sites in Rigid‐Chain Polymers and Their Filling Approach: A Molecular Dynamics Simulation Study

2021 ◽  
pp. 2100016
Author(s):  
Cheng Yang ◽  
Ruopei Xu ◽  
Siyi Tang ◽  
Yongbing Zhuang ◽  
Longbo Luo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Interaction Sites ◽  
Rigid Chain ◽  
Bonding Interaction

scholarly journals Enhancer Trapping Reveals Widespread Circadian Clock Transcriptional Control in Arabidopsis

2003 ◽  
Vol 132 (2) ◽  
pp. 629-639 ◽  
Author(s):  
Todd P. Michael ◽  
C. Robertson McClung
Keyword(s):  
Circadian Clock ◽  
Transcriptional Control ◽  
Enhancer Trapping

scholarly journals Binding of bisphenol A, bisphenol AF, and bisphenol S on the androgen receptor: Coregulator recruitment and stimulation of potential interaction sites

2017 ◽  
Vol 44 ◽  
pp. 287-302 ◽  
Author(s):  
Lalith Perera ◽  
Yin Li ◽  
Laurel A. Coons ◽  
Rene Houtman ◽  
Rinie van Beuningen ◽  
...  
Keyword(s):  
Androgen Receptor ◽  
Bisphenol A ◽  
Potential Interaction ◽  
Bisphenol S ◽  
Interaction Sites ◽  
Bisphenol Af ◽  
Stimulation Of
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