Secondary structures transition of tau protein with intrinsically disordered proteins specific force field

2018 ◽  
Vol 93 (3) ◽  
pp. 242-253
Author(s):  
Aohuan Dan ◽  
Hai-Feng Chen
Keyword(s):  
Force Field ◽  
Tau Protein ◽  
Intrinsically Disordered Proteins ◽  
Secondary Structures ◽  
Disordered Proteins ◽  
Specific Force ◽  
Intrinsically Disordered

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 Transient Secondary Structures as General Target-Binding Motifs in Intrinsically Disordered Proteins

2018 ◽  
Vol 19 (11) ◽  
pp. 3614 ◽  
Author(s):  
Do-Hyoung Kim ◽  
Kyou-Hoon Han
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Disordered Proteins ◽  
Ample Evidence ◽  
Binding Motifs ◽  
Intrinsically Disordered ◽  
Long Time ◽  
Science Community ◽  
Target Binding

Intrinsically disordered proteins (IDPs) are unorthodox proteins that do not form three-dimensional structures under non-denaturing conditions, but perform important biological functions. In addition, IDPs are associated with many critical diseases including cancers, neurodegenerative diseases, and viral diseases. Due to the generic name of “unstructured” proteins used for IDPs in the early days, the notion that IDPs would be completely unstructured down to the level of secondary structures has prevailed for a long time. During the last two decades, ample evidence has been accumulated showing that IDPs in their target-free state are pre-populated with transient secondary structures critical for target binding. Nevertheless, such a message did not seem to have reached with sufficient clarity to the IDP or protein science community largely because similar but different expressions were used to denote the fundamentally same phenomenon of presence of such transient secondary structures, which is not surprising for a quickly evolving field. Here, we summarize the critical roles that these transient secondary structures play for diverse functions of IDPs by describing how various expressions referring to transient secondary structures have been used in different contexts.

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 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

scholarly journals Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field

2014 ◽  
Vol 106 (2) ◽  
pp. 271a ◽  
Author(s):  
Sarah Rauscher ◽  
Vytautas Gapsys ◽  
Andreas Volkhardt ◽  
Christian Blau ◽  
Bert L. de Groot ◽  
...  
Keyword(s):  
Force Field ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Structural Ensembles

scholarly journals Bayesian inference of protein ensembles from SAXS data

2016 ◽  
Vol 18 (8) ◽  
pp. 5832-5838 ◽  
Author(s):  
L. D. Antonov ◽  
S. Olsson ◽  
W. Boomsma ◽  
T. Hamelryck
Keyword(s):  
Bayesian Inference ◽  
Force Field ◽  
Intrinsically Disordered Proteins ◽  
Probabilistic Method ◽  
Disordered Proteins ◽  
Saxs Data ◽  
Intrinsically Disordered ◽  
Protein Ensembles

A probabilistic method infers ensembles of intrinsically disordered proteins (IDPs) by combining SAXS data with a force field.

scholarly journals Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations

2021 ◽  
Author(s):  
Lunna Li ◽  
Tommaso Casalini ◽  
Paolo Arosio ◽  
Matteo Salvalaglio
Keyword(s):  
Force Field ◽  
Sampling Method ◽  
Intrinsically Disordered Proteins ◽  
Thermodynamic Characteristics ◽  
Building Blocks ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Self Association ◽  
Disordered Peptides

Intrinsically disordered proteins (IDPs) play a key role in many biological processes, including the formation of biomolecular condensates within cells. A detailed characterization of their configurational ensemble and structure-function paradigm is crucial for understanding their biological activity and for exploiting them as building blocks in material sciences. In this work, we incorporate bias-exchange metadynamics and parallel-tempering well-tempered metadynamics with CHARMM36m and CHARMM22* to explore the structural and thermodynamic characteristics of a short archetypal disordered sequence derived from a DEAD-box protein. The conformational landscapes emerging from our simulations are largely congruent across methods and forcefields. Nevertheless, differences in fine details emerge from varying forcefield/sampling method combinations. For this protein, our analysis identifies features that help to explain the low propensity of this sequence to undergo self-association in vitro, which can be common to all force-field/sampling method combinations. Overall, our work demonstrates the importance of using multiple force-field/enhanced sampling method combinations for accurate structural and thermodynamic information in the study of general disordered proteins.

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