Elucidating the molecular basis of spontaneous activation in an engineered mechanosensitive channel

Immadisetty, Kalyan; Polasa, Adithya; Shelton, Reid; Moradi, Mahmoud

doi:10.1016/j.csbj.2022.05.022

Cited by 6 publications

(15 citation statements)

References 87 publications

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“…The interhelical angles were calculated as the angle between the third principal axes of the corresponding helices. [52][53][54] The TM helices and other sub-domains were defined for analysis as follows: TM1a respectively. The angle between the two vectors was calculated as 180…”

Section: Methodsmentioning

confidence: 99%

“…The interhelical angles were calculated as the angle between the third principal axes of the corresponding helices. 52–54 The TM helices and other sub-domains were defined for analysis as follows: TM1a (58 − 78), TM1b (79 − 104), TM2 (134 − 155), TM3 (175 − 190), TM4 (219 − 233), TM5 (233 − 258), C1 region (84 − 133), C2 loop (195 − 216), and modified C-terminal region (256 − 272) respectively. The number of contacts within 3 Å of selection was measured for contact analysis.…”

Section: Methodsmentioning

confidence: 99%

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An Investigation of the YidC-Mediated Membrane Insertion of Pf3 Coat Protein Using Molecular Dynamics Simulations

Polasa

Hettige

Immadisetty

et al. 2022

Preprint

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YidC is a membrane protein that facilitates the insertion of newly synthesized proteins into lipid membranes. Through YidC, proteins are inserted into the lipid bilayer via the SecYEG-dependent complex. Additionally, YidC functions as a chaperone in protein folding processes. Several studies have provided evidence of its independent insertion mechanism. However, the mechanistic details of the YidC independent protein insertion mechanism remain elusive at the molecular level. This study elucidates the insertion mechanism of YidC at an atomic level through a combination of equilibrium and non-equilibrium molecular dynamics (MD) simulations. Different docking models of YidC-Pf3 in the lipid bilayer were built in this study to better understand the insertion mechanism. To conduct a complete investigation of the conformational difference between the two docking models developed, we used classical molecular dynamics simulations supplemented with a non-equilibrium technique. Our findings indicate that the YidC transmembrane (TM) groove is essential for this high-affinity interaction and that the hydrophilic nature of the YidC groove plays an important role in protein transport across the cytoplasmic membrane bilayer to the periplasmic side. At different stages of the insertion process, conformational changes in YidC’s TM domain and membrane core have a mechanistic effect on the Pf3 coat. Furthermore, during the insertion phase, the hydration and dehydration of the YidC’s hydrophilic groove are critical. These demonstrate that Pf3 interactions with the membrane and YidC vary in different conformational states during the insertion process. Finally, this extensive study directly confirms that YidC functions as an independent insertase.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

An Investigation of the YidC-Mediated Membrane Insertion of Pf3 Coat Protein Using Molecular Dynamics Simulations

Polasa

Hettige

Immadisetty

et al. 2022

Preprint

Self Cite

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“…In the NPT ensemble at 310 K, 1 µ s of equilibrium MD simulations were performed under periodic boundary conditions for each system. In the simulations, a Langevin integrator with a damping coefficient of γ =0.5 ps − 1 and 1 atm pressure was maintained using the Nose-Hoover Langevin piston method 56,57 18,58–67 .…”

Section: Methodsmentioning

confidence: 99%

Deciphering the Inter-domain Decoupling in the Gram-negative Bacterial Membrane Insertase

Polasa

Moradi

2022

Preprint

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YidC is a protein found in membranes that plays an important role in the process of inserting newly generated proteins into lipid membranes. The SecYEG-dependent complex is responsible for inserting proteins into the lipid bilayer, and this process is facilitated by YidC. In addition, YidC acts as a chaperone during the folding processes of proteins. Multiple investigations have conclusively shown that the gram-positive bacterium YidC has SecY-independent insertion mechanisms. Through the use of microsecond level all-atom molecular dynamics simulations, we have carried out the first in-depth investigation of the YidC protein originating from gram-negative bacteria. This research sheds light on the significance of several structural areas related to YidC at an atomic level by utilizing equilibrium molecular dynamics (MD) simulations. In this research, multiple models of YidC inside the lipid bilayer were constructed in order to achieve a deeper understanding of the critical role of the C2 loop and the extra periplasmic domain present in gram-negative YidC. According to the results of our research, the C2 loop is responsible for the overall stabilization of the protein, most notably in the transmembrane region, and it also has an allosteric influence on the periplasmic domain. We have found critical interactions that contribute to the stability of the protein as well as its functional aspect. Finally, our study provides a hypothetical SecY-independent insertion mechanism for gram-negative bacterial YidC.

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“…We have previously shown how designing system-specific collective variables can be used to more efficiently and flexibly sample the relevant conformational space of various proteins. − Combined with microsecond-level unbiased MD, these simulations can shed light on conformational stability and flexibility of proteins. − Here, using a combination of biased and unbiased MD simulations, we have studied the conformational dynamics of cpSRP43 in its monomeric form in comparison to the more well-characterized cpSRP54-bound form of this protein. Our simulations have revealed that cpSRP43 adopts a stable globular conformation in the absence of cpSRP54 that is substantially different from the “linear” crystal structures reported previously. , The results of these microsecond-level MD simulations clearly suggest that cpSRP43 has a stable structure containing regions that exhibit significant backbone dynamics.…”

Section: Introductionmentioning

confidence: 99%

cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational Approach

Benton

Furr

Kumar

et al. 2023

J. Chem. Inf. Model.

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The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of lightharvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 has demonstrated significant flexibility and interdomain dynamics. In this study, we explore the structural stability and flexibility of cpSRP43 using a combination of computational and experimental techniques and find that this protein is concurrently highly stable and flexible. In addition to microsecond-level unbiased molecular dynamics (MD), biased MD simulations based on system-specific collective variables are used along with biophysical experimentation to explain the basis of the flexibility and stability of cpSRP43, showing that the free and cpSRP54-bound cpSRP43 has substantially different conformations and conformational dynamics.

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Elucidating the molecular basis of spontaneous activation in an engineered mechanosensitive channel

Cited by 6 publications

References 87 publications

An Investigation of the YidC-Mediated Membrane Insertion of Pf3 Coat Protein Using Molecular Dynamics Simulations

An Investigation of the YidC-Mediated Membrane Insertion of Pf3 Coat Protein Using Molecular Dynamics Simulations

Deciphering the Inter-domain Decoupling in the Gram-negative Bacterial Membrane Insertase

cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational Approach

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