Connecting conformational stiffness of the protein with energy landscape by a single experiment

Chakraborty, Soham; Chaudhuri, Deep; Chaudhuri, Dyuti; Singh, Vihan; Banerjee, Souradeep; Chowdhury, Debojyoti; Haldar, Shubhasis

doi:10.1039/d1nr07582a

Cited by 9 publications

(23 citation statements)

References 100 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Similarly, during quenching, the total time required to refold all the polyprotein domains is defined as refolding FPT. Averaging such numerous trajectories, we can determine mean-FPT (MFPT), describing both unfolding and refolding kinetics 16,17,21–23 . Following the complete refolding, the polyprotein hops between folded and unfolded states under force-induced equilibrium condition, which are observed as ascending unfolding steps and descending refolding steps.…”

Section: Resultsmentioning

confidence: 99%

“…The N terminus of the polyprotein is tethered to a glass surface via HaloTag covalent chemistry, while the C terminus is attached with streptavidin-coated paramagnetic bead. Force is applied by introducing a pair of permanent magnets that can exert a magnetic field vertically towards the tethered protein 13,14,17 (Fig. 1A).…”

Section: Folding Dynamics Of Protein L Measured By Single-molecule Ma...mentioning

confidence: 99%

Section: Folding Dynamics Of Protein L Measured By Single-molecule Ma...mentioning

confidence: 99%

“…Here, we have investigated the TMAO effect on protein L as a model substrate, which has previously been used in force spectroscopic studies [14][15][16][17] . Since protein L is not biologically relevant to function under mechanical tension, we selected another substrate talin, which is well-known to work under physiological force and extensively used in force spectroscopy studies 13,[18][19][20] .…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Trimethylamine N-oxide (TMAO) enhances substrate mechanical stability probed by single molecule magnetic tweezers

Chaudhuri

Chowdhury

Chakraborty

et al. 2022

Preprint

View full text Add to dashboard Cite

Trimethylamine N-oxide (TMAO) is a well-known osmolyte to stabilize the folded proteins through a variety of mechanisms. Since mechanical strength of proteins is a critical determinant of its stabilization, TMAO might play a relevant role by favoring its folding dynamics or by enhancing its mechanical stability. To address this question, we have performed the single-molecule magnetic tweezers experiment to explore the TMAO effect on two structurally distinct substrates-protein L and talin. We observed that TMAO increases the mechanical stability of these proteins through increasing their unfolding force. Additionally, we are able to demonstrate that TMAO retards the unfolding kinetics, while accelerating the refolding kinetics under force; which eventually tilts the energy landscape towards the folded state. Interestingly, this TMAO-enhanced protein folding generates mechanical work output upto ∼67 zJ, allowing the protein folding under higher force regime. Overall this TMAO-enhanced mechanical stability provides a significant implication to folding-induced structural stability of proteins.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Folding Dynamics Of Protein L Measured By Single-molecule Ma...mentioning

confidence: 99%

Section: Folding Dynamics Of Protein L Measured By Single-molecule Ma...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Trimethylamine N-oxide (TMAO) enhances substrate mechanical stability probed by single molecule magnetic tweezers

Chaudhuri

Chowdhury

Chakraborty

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…The copyright holder for this preprint this version posted March 16, 2023. ; https://doi.org/10.1101/2023.03. 16.532907 doi: bioRxiv preprint behaviour using strain theory, suggesting that the mechanical behaviour of chaperones arises from their intrinsic strain energy: DnaK and DnaJ have higher strain energy difference during their interaction with the unfolded protein L and thereby stabilizing the unfolded state; while BiP and ERdj3 exhibit higher energy difference during binding to folded protein L conformation, signifying favored folded state of protein L in their presence. Overall, these data suggest that chaperones, by modifying the mechanical folding landscape of substrate protein, modulate the mechanical energy; providing a distinct mechanistic view of mechanical chaperone behaviour during protein folding under force.…”

Section: Introductionmentioning

confidence: 99%

Force-regulated chaperone activity of BiP/ERdj3 is opposite to their homologs DnaK/DnaJ: explained by strain energy

Haldar

Banerjee

Chowdhury

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Polypeptide chains experiences mechanical tension while translocating through cellular tunnel. In this scenario, interaction of tunnel-associated chaperones with the emerging polypeptide occurs under force; however, this force-regulated chaperone behaviour is not fully understood. We studied the mechanical chaperone activity of two tunnel-associated chaperones BiP and ERdj3 both in the absence and presence of force; and compared to their respective cytoplasmic homologs DnaK and DnaJ. We found that BiP/ERdj3 shows strong foldase activity under force; whereas their cytoplasmic homolog DnaK/DnaJ behave as holdase. Importantly, these tunnel-associated chaperones (BiP/ERdj3) revert to holdase in the absence of force, suggesting that mechanical chaperone activity differs depending on the presence or absence of force. This tunnel-associated chaperone-driven folding event generates additional mechanical energy of up to 54 zJ that could help protein translocation. The mechanical-chaperone behaviour can be explained by strain theory: chaperones with higher intrinsic deformability function as mechanical foldase (BiP, ERdj3), while chaperones with lower intrinsic deformability act as holdase (DnaK and DnaJ). Our study thus unveils the underlying mechanism of mechanically regulated chaperoning activity and provides a novel mechanism of co-translocational protein folding.

show abstract

Integrin αIIbβ3 intermediates: From molecular dynamics to adhesion assembly

Tong¹,

Soley²,

Kolasangiani³

et al. 2023

Biophysical Journal

View full text Add to dashboard Cite

Connecting conformational stiffness of the protein with energy landscape by a single experiment

Abstract: Structure-function dynamics of protein, as a flexible polymer, is essential to describe their biological functions. Here, using a single-molecule magnetic tweezers, we have studied the effect of ionic strength on...

Cited by 9 publications

References 100 publications

Trimethylamine N-oxide (TMAO) enhances substrate mechanical stability probed by single molecule magnetic tweezers

Trimethylamine N-oxide (TMAO) enhances substrate mechanical stability probed by single molecule magnetic tweezers

Force-regulated chaperone activity of BiP/ERdj3 is opposite to their homologs DnaK/DnaJ: explained by strain energy

Integrin αIIbβ3 intermediates: From molecular dynamics to adhesion assembly

Contact Info

Product

Resources

About