Bellucci, Luca Felline, Angelo Fanelli, Francesca
Published in
Biochimica et biophysica acta. Biomembranes
G protein-coupled receptors (GPCRs) are critically regulated by arrestins, which not only desensitize G-protein signaling but also initiate a G protein-independent wave of signaling. The information from structure determination was herein exploited to build a structural model of the ternary complex, comprising fully phosphorylated V2 vasopressin re...
Shao, Qi Gong, Weikang Li, Chunhua
Published in
Biophysical chemistry
The allosteric regulation during the binding interactions between small nuclear RNAs (snRNAs) and the associated protein factors is critical to the function of spliceosomes in alternative RNA splicing. Although network models combined with molecular dynamics simulations have shown to be powerful tools for the analysis of protein allostery, the atom...
Kürkçüoğlu, Özge
Published in
Turkish journal of biology = Turk biyoloji dergisi
Antibiotic resistance is one of the most important problems of our era and hence the discovery of new effective therapeutics is urgent. At this point, studying the allosteric communication pathways in the bacterial ribosome and revealing allosteric sites/residues is critical for designing new inhibitors or repurposing readily approved drugs for thi...
Liang, Zhongjie Hu, Junchi Yan, Wenying Jiang, Hualiang Hu, Guang Luo, Cheng
Published in
Biochimica et biophysica acta. General subjects
DNMT3A, as de novo DNA methyltransferase, is essential for regulating gene expression through cellular development and differentiation. The functions of DNMT3A rely on its oligomeric states and allosteric regulations between its catalytic domain and binding partners. Despite recent resolution of autoinhibitory and active DNMT3A/3L crystal structure...
Karami, Yasaman
We presented COMMA, a method to describe and compare the dynamical architectures of different proteins or different variants of the same protein. COMMA extracts dynamical properties from conformational ensembles to identify communication pathways, chains of residues linked by stable interactions that move together, and independent cliques, clusters...
Fanelli, Francesca Felline, Angelo Raimondi, Francesco
Published in
Methods in Cell Biology
Protein structure network (PSN) analysis is one of the graph theory-based approaches currently used to investigate the structural communication in biomolecular systems. Information on system dynamics can be provided by atomistic molecular dynamics simulations or coarse-grained Elastic Network Models paired with Normal Mode Analysis (ENM–NMA).This c...
Preller, M. Manstein, D.J.
Published in
Comprehensive Biophysics
In this chapter, the authors present an overview of the myosin family of actin-based motors. Properties of the members of individual myosin subfamilies are described and the diversity of myosin-domain structures and cellular functions is outlined. The myosin motor is described as an intrinsic allosterically regulated protein providing ample opportu...
Lu, Jianyun Chen, Minghe Stanley, Susan E. Li, Ellen
Published in
Biochemical and Biophysical Research Communications
The structural mechanism of allosteric communication between retinoid X receptor (RXR) and its heterodimer partners remains controversial. As a first step towards addressing this question, we report a nuclear magnetic resonance (NMR) study on the GW1929-bound peroxisome proliferator-activated receptor gamma (PPARγ) ligand-binding domain (LBD) with ...
