Characterizing the denatured state ensemble of ubiquitin under native conditions using replica exchange molecular dynamics

Chang, Nai-yuan; Li, Yi-Ci; Jheng, Cheng-Ping; Kuo, Yu‐Ting; Lee, Cheng-I

doi:10.1039/c6ra23300g

Cited by 1 publication

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“…Molecular dynamics (MD) simulations offer an atomic-level description but are unsuitable for slower dynamical processes as a result of the computational cost and complexity (Figure ). − ,,,− Structurally heterogeneous proteins like IDPs and proteins with IDRs are dynamic at the same time which can intrinsically sample a multitude of diverse structures, thus providing a robust data set for testing structural refinement methodologies and kinetic pathway sampling using time-resolved techniques with molecular models.…”

Section: Introductionmentioning

confidence: 99%

“…Time scales for protein dynamics grouped by technique. − ,,,− Relevant protein time scales are plotted vs the number of residues for the system of interest for studies done using MD (purple), TRXSS (green), IR (blue), and trp-fluorescence (orange). MD studies are primarily located around smaller proteins and shorter time scales.…”

Section: Introductionmentioning

confidence: 99%

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Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures

et al. 2021

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Proteins have been found to inhabit a diverse set of threedimensional structures. The dynamics that govern protein interconversion between structures happen over a wide range of time scalespicoseconds to seconds. Our understanding of protein functions and dynamics is largely reliant upon our ability to elucidate physically populated structures. From an experimental structural characterization perspective, we are often limited to measuring the ensemble-averaged structure both in the steady-state and time-resolved regimes. Generating kinetic models and understanding protein structure−function relationships require atomistic knowledge of the populated states in the ensemble. In this Perspective, we present ensemble refinement methodologies that integrate time-resolved experimental signals with molecular dynamics models. We first discuss integration of experimental structural restraints to molecular models in disordered protein systems that adhere to the principle of maximum entropy for creating a complete set of ensemble structures. We then propose strategies to find kinetic pathways between the refined structures, using time-resolved inputs to guide molecular dynamics trajectories and the use of inference to generate tailored stimuli to prepare a desired ensemble of protein states.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures

et al. 2021

View full text Add to dashboard Cite

show abstract

Characterizing the denatured state ensemble of ubiquitin under native conditions using replica exchange molecular dynamics

Abstract: The representative structures of the denatured state ensemble of ubiquitin under a native condition and heat-denatured ubiquitin simulated from a fully extended conformation.

Cited by 1 publication

References 44 publications

Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures

Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures

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