Understanding how small helical proteins fold: conformational dynamics of Im proteins relevant to their folding landscapes

Understanding the mechanism of folding of small proteins requires characterization of their starting unfolded states and any partially unfolded states populated during folding. Here, we review what is known from NMR about these states of Im7, a 4-helix bundle protein that folds via an on-pathway intermediate, and show that there is an alignment of non-native structure in urea-unfolded Im7 with the helices of native Im7 that is a consequence of hydrophobic helix-promoting residues also promoting cluster-formation in the unfolded protein. We suggest that this kind of alignment is present in other proteins and is relevant to how native state topology determines folding rates.

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Molecular Dynamics Simulations of Protein Unfolding and Limited Refolding: Characterization of Partially Unfolded States of Ubiquitin in 60% Methanol and in Water

Journal of Molecular Biology ◽

10.1006/jmbi.1994.0156 ◽

1995 ◽

Vol 247 (3) ◽

pp. 501-520 ◽

Cited By ~ 75

Author(s):

Darwin O.V. Alonso ◽

Valerie Daggett

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Protein Unfolding ◽

Partially Unfolded ◽

Dynamics Simulations ◽

Partially Unfolded States

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Mechanism of the small ATP-independent chaperone Spy is substrate specific

Nature Communications ◽

10.1038/s41467-021-21120-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Rishav Mitra ◽

Varun V. Gadkari ◽

Ben A. Meinen ◽

Carlo P. M. van Mierlo ◽

Brandon T. Ruotolo ◽

...

Keyword(s):

Relative Affinity ◽

Complex Protein ◽

Partially Unfolded ◽

Substrate Proteins ◽

Partially Unfolded States

AbstractATP-independent chaperones are usually considered to be holdases that rapidly bind to non-native states of substrate proteins and prevent their aggregation. These chaperones are thought to release their substrate proteins prior to their folding. Spy is an ATP-independent chaperone that acts as an aggregation inhibiting holdase but does so by allowing its substrate proteins to fold while they remain continuously chaperone bound, thus acting as a foldase as well. The attributes that allow such dual chaperoning behavior are unclear. Here, we used the topologically complex protein apoflavodoxin to show that the outcome of Spy’s action is substrate specific and depends on its relative affinity for different folding states. Tighter binding of Spy to partially unfolded states of apoflavodoxin limits the possibility of folding while bound, converting Spy to a holdase chaperone. Our results highlight the central role of the substrate in determining the mechanism of chaperone action.

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Characterization of partially-unfolded intermediates in the urea-induced unfolding of Ribonuclease A

10.31979/etd.2tjg-bsah ◽

1990 ◽

Author(s):

Sangita Seshadri

Keyword(s):

Ribonuclease A ◽

Partially Unfolded

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Two Crinivirus-Conserved Small Proteins, P5 and P9, Are Indispensable for Efficient Lettuce infectious yellows virus Infectivity in Plants

Viruses ◽

10.3390/v10090459 ◽

2018 ◽

Vol 10 (9) ◽

pp. 459 ◽

Cited By ~ 3

Author(s):

Wenjie Qiao ◽

Erin Helpio ◽

Bryce Falk

Keyword(s):

Transmembrane Protein ◽

Genomic Analysis ◽

Open Reading Frames ◽

Virus Infectivity ◽

Gene Block ◽

Unfolded Protein ◽

Small Proteins ◽

Lettuce Infectious Yellows Virus ◽

The Unfolded Protein Response ◽

Protein Response

Genomic analysis of Lettuce infectious yellows virus (LIYV) has revealed two short open reading frames (ORFs) on LIYV RNA2, that are predicted to encode a 5-kDa (P5) and a 9-kDa (P9) protein. The P5 ORF is part of the conserved quintuple gene block in the family Closteroviridae, while P9 orthologs are found in all Criniviruses. In this study, the expression of LIYV P5 and P9 proteins was confirmed; P5 is further characterized as an endoplasmic reticulum (ER)-localized integral transmembrane protein and P9 is a soluble protein. The knockout LIYV mutants presented reduced symptom severity and virus accumulation in Nicotiana benthamiana or lettuce plants, indicating their importance in efficient virus infection. The P5 mutant was successfully complemented by a dislocated P5 in the LIYV genome. The structural regions of P5 were tested and all were found to be required for the appropriate functions of P5. In addition, P5, as well as its ortholog P6, encoded by Citrus tristeza virus (CTV) and another ER-localized protein encoded by LIYV RNA1, were found to cause cell death when expressed in N. benthamiana plants from a TMV vector, and induce ER stress and the unfolded protein response (UPR).

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