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Creators/Authors contains: "Yang, Weitao"

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  1. Free, publicly-accessible full text available September 21, 2024
  2. Abstract

    Chaperones are a large family of proteins crucial for maintaining cellular protein homeostasis. One such chaperone is the 70 kDa heat shock protein (Hsp70), which plays a crucial role in protein (re)folding, stability, functionality, and translocation. While the key events in the Hsp70 chaperone cycle are well established, a relatively small number of distinct substrates were repetitively investigated. This is despite Hsp70 engaging with a plethora of cellular proteins of various structural properties and folding pathways. Here we analyzed novel Hsp70 substrates, based on tandem repeats of NanoLuc (Nluc), a small and highly bioluminescent protein with unique structural characteristics. In previous mechanical unfolding and refolding studies, we have identified interesting misfolding propensities of these Nluc‐based tandem repeats. In this study, we further investigate these properties through in vitro bulk experiments. Similar to monomeric Nluc, engineered Nluc dyads and triads proved to be highly bioluminescent. Using the bioluminescence signal as the proxy for their structural integrity, we determined that heat‐denatured Nluc dyads and triads can be efficiently refolded by theE. coliHsp70 chaperone system, which comprises DnaK, DnaJ, and GrpE. In contrast to previous studies with other substrates, we observed that Nluc repeats can be efficiently refolded by DnaK and DnaJ, even in the absence of GrpE co‐chaperone. Taken together, our study offers a new powerful substrate for chaperone research and raises intriguing questions about the Hsp70 mechanisms, particularly in the context of structurally diverse proteins.

     
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  3. We reformulate the thermally assisted-occupation density functional theory (TAO-DFT) into the Kohn–Sham single-determinant framework and construct two new post-self-consistent field (post-SCF) static correlation correction schemes, named rTAO and rTAO-1. In contrast to the original TAO-DFT with the density in an ensemble form, in which each orbital density is weighted with a fractional occupation number, the ground-state density is given by a single-determinant wavefunction, a regular Kohn–Sham (KS) density, and total ground state energy is expressed in the normal KS form with a static correlation energy formulated in terms of the KS orbitals. In post-SCF calculations with rTAO functionals, an efficient energy scanning to quantitatively determine θ is also proposed. The rTAOs provide a promising method to simulate systems with strong static correlation as original TAO, but simpler and more efficient. We show that both rTAO and rTAO-1 is capable of reproducing most results from TAO-DFT without the additional functional Eθ used in TAO-DFT. Furthermore, our numerical results support that, without the functional Eθ, both rTAO and rTAO-1 can capture correct static correlation profiles in various systems. 
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