Extensive Evaluation of Environment-specific Force Field for Ordered and Disordered Proteins

2021 ◽  
Author(s):  
Xiaocheng Cui ◽  
Hao Liu ◽  
Ashfaq Ur Rehman ◽  
Haifeng Chen
Keyword(s):  
Force Field ◽  
Intrinsically Disordered Proteins ◽  
Tertiary Structure ◽  
Experimental Methods ◽  
Human Diseases ◽  
Disordered Proteins ◽  
Specific Force ◽  
Intrinsically Disordered ◽  
Extensive Evaluation

Intrinsically disordered proteins (IDPs) have not fixed tertiary structure under physiology condition and associate with many human diseases. Because IDPs have the characters of diverse conformation, current experimental methods can...

scholarly journals Reinforcement Learning to Boost Molecular Docking upon Protein Conformational Ensemble

2021 ◽  
Author(s):  
Bin Chong ◽  
Yingguang Yang ◽  
Zi-Le Wang ◽  
Han Xing ◽  
Zhirong Liu
Keyword(s):  
Molecular Docking ◽  
Reinforcement Learning ◽  
Intrinsically Disordered Proteins ◽  
Therapeutic Targets ◽  
Human Diseases ◽  
Disordered Proteins ◽  
Conformational Ensemble ◽  
Intrinsically Disordered

Intrinsically disordered proteins (IDPs) widely involve in human diseases and are thus attractive therapeutic targets. In practice, however, it is computationally prohibitive to dock large ligand libraries to thousands and...

scholarly journals Rescuing the Over-Collapse of Intrinsically Disordered Proteins using a Force Field Derived by a New Paradigm

2016 ◽  
Vol 110 (3) ◽  
pp. 556a
Author(s):  
Davide Mercadante ◽  
Sigrid Milles ◽  
Gustavo Fuertes ◽  
Dmitri Svergun ◽  
Edward A. Lemke ◽  
...  
Keyword(s):  
Force Field ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
New Paradigm ◽  
Intrinsically Disordered

scholarly journals Genetically tunable frustration controls allostery in an intrinsically disordered transcription factor

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Jing Li ◽  
Jordan T White ◽  
Harry Saavedra ◽  
James O Wrabl ◽  
Hesam N Motlagh ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Structural Changes ◽  
Intrinsically Disordered Proteins ◽  
Tertiary Structure ◽  
Control Function ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Novel Strategy ◽  
Structured Proteins

Intrinsically disordered proteins (IDPs) present a functional paradox because they lack stable tertiary structure, but nonetheless play a central role in signaling, utilizing a process known as allostery. Historically, allostery in structured proteins has been interpreted in terms of propagated structural changes that are induced by effector binding. Thus, it is not clear how IDPs, lacking such well-defined structures, can allosterically affect function. Here, we show a mechanism by which an IDP can allosterically control function by simultaneously tuning transcriptional activation and repression, using a novel strategy that relies on the principle of ‘energetic frustration’. We demonstrate that human glucocorticoid receptor tunes this signaling in vivo by producing translational isoforms differing only in the length of the disordered region, which modulates the degree of frustration. We expect this frustration-based model of allostery will prove to be generally important in explaining signaling in other IDPs.

scholarly journals CHARMM36: An Improved Force Field for Folded and Intrinsically Disordered Proteins

2017 ◽  
Vol 112 (3) ◽  
pp. 175a-176a ◽  
Author(s):  
Jing Huang ◽  
Sarah Rauscher ◽  
Grzegorz Nawrocki ◽  
Ting Ran ◽  
Michael Feig ◽  
...  
Keyword(s):  
Force Field ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Intrinsically Disordered
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