Theoretical study of the intermolecular recognition mechanism between Survivin and substrate based on conserved binding mode analysis

2018 ◽  
Vol 83 ◽  
pp. 53-63 ◽  
Author(s):  
Chao Wu ◽  
Liguang Mao ◽  
Xie Huang ◽  
Weitao Fu ◽  
Xiong Cai ◽  
...  
Keyword(s):  
Theoretical Study ◽  
Binding Mode ◽  
Mode Analysis ◽  
Recognition Mechanism ◽  
Intermolecular Recognition

Application of the ESMACS Binding Free Energy Protocol to a Highly Varied Ligand Dataset: Lactate Dehydogenase A

2019 ◽  
Author(s):  
David Wright ◽  
Fouad Husseini ◽  
Shunzhou Wan ◽  
Christophe Meyer ◽  
Herman Van Vlijmen ◽  
...  
Keyword(s):  
Free Energy ◽  
Surface Area ◽  
Binding Free Energy ◽  
Normal Mode Analysis ◽  
Binding Mode ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Mode Analysis ◽  
Energy Calculation ◽  
Accessible Surface

<div>Here, we evaluate the performance of our range of ensemble simulation based binding free energy calculation protocols, called ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) for use in fragment based drug design scenarios. ESMACS is designed to generate reproducible binding affinity predictions from the widely used molecular mechanics Poisson-Boltzmann surface area (MMPBSA) approach. We study ligands designed to target two binding pockets in the lactate dehydogenase A target protein, which vary in size, charge and binding mode. When comparing to experimental results, we obtain excellent statistical rankings across this highly diverse set of ligands. In addition, we investigate three approaches to account for entropic contributions not captured by standard MMPBSA calculations: (1) normal mode analysis, (2) weighted solvent accessible surface area (WSAS) and (3) variational entropy. </div>

scholarly journals Crystal structure and functional implication of bacterial STING

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Tzu-Ping Ko ◽  
Yu-Chuan Wang ◽  
Chia-Shin Yang ◽  
Mei-Hui Hou ◽  
Chao-Jung Chen ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Driving Force ◽  
Binding Mode ◽  
Innate Immune ◽  
Ligand Specificity ◽  
Protein Protein Interactions ◽  
Recognition Mechanism ◽  
Cyclic Dinucleotides ◽  
Phage Propagation ◽  
Complex Crystal

AbstractMammalian innate immune sensor STING (STimulator of INterferon Gene) was recently found to originate from bacteria. During phage infection, bacterial STING sense c-di-GMP generated by the CD-NTase (cGAS/DncV-like nucleotidyltransferase) encoded in the same operon and signal suicide commitment as a defense strategy that restricts phage propagation. However, the precise binding mode of c-di-GMP to bacterial STING and the specific recognition mechanism are still elusive. Here, we determine two complex crystal structures of bacterial STING/c-di-GMP, which provide a clear picture of how c-di-GMP is distinguished from other cyclic dinucleotides. The protein-protein interactions further reveal the driving force behind filament formation of bacterial STING. Finally, we group the bacterial STING into two classes based on the conserved motif in β-strand lid, which dictate their ligand specificity and oligomerization mechanism, and propose an evolution-based model that describes the transition from c-di-GMP-dependent signaling in bacteria to 2’3’-cGAMP-dependent signaling in eukaryotes.

Structural Evaluation and Binding Mode Analysis of CCL19 and CCR7 Proteins—Identification of Novel Leads for Rheumatic and Autoimmune Diseases: An Insilico study

2017 ◽  
Vol 10 (2) ◽  
pp. 346-366 ◽  
Author(s):  
Santhi Prada Vellanki ◽  
Ramasree Dulapalli ◽  
Bhargavi Kondagari ◽  
Navaneetha Nambigari ◽  
Rajender Vadija ◽  
...  
Keyword(s):  
Autoimmune Diseases ◽  
Binding Mode ◽  
Mode Analysis ◽  
Structural Evaluation

Pyrrolidine Derivatives as Plasmepsin Inhibitors: Binding Mode Analysis Assisted by Molecular Dynamics Simulations of a Highly Flexible Protein

ChemMedChem ◽  
2010 ◽  
Vol 5 (3) ◽  
pp. 443-454 ◽  
Author(s):  
Torsten Luksch ◽  
Andreas Blum ◽  
Nina Klee ◽  
Wibke E. Diederich ◽  
Christoph A. Sotriffer ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Mode ◽  
Mode Analysis ◽  
Flexible Protein ◽  
Dynamics Simulations

Amide analogues of TSA: synthesis, binding mode analysis and HDAC inhibition

2003 ◽  
Vol 13 (11) ◽  
pp. 1861-1864 ◽  
Author(s):  
K Van Ommeslaeghe ◽  
G Elaut ◽  
V Brecx ◽  
P Papeleu ◽  
K Iterbeke ◽  
...  
Keyword(s):  
Binding Mode ◽  
Mode Analysis ◽  
Hdac Inhibition

scholarly journals Finding biologically relevant protein domain interactions: Conserved binding mode analysis

2006 ◽  
Vol 15 (2) ◽  
pp. 352-361 ◽  
Author(s):  
Benjamin A. Shoemaker ◽  
Anna R. Panchenko ◽  
Stephen H. Bryant
Keyword(s):  
Binding Mode ◽  
Protein Domain ◽  
Mode Analysis ◽  
Biologically Relevant ◽  
Domain Interactions
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