Energy landscape underlying spontaneous insertion and folding of an alpha-helical transmembrane protein into a bilayer

Lu, Wei; Schafer, Nicholas P.; Wolynes, Peter G.

doi:10.1038/s41467-018-07320-9

Cited by 28 publications

(19 citation statements)

References 35 publications

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“…A recent GlpG force-induced unfolding study concluded that the two-stage membrane folding model (44) is overly simplistic because isolated helices can coexist with a folded domain, and all the helices do not have to be in the bilayer before the initiation of folding (45). Although our study reproduces these two items, some technical differences between the two studies are worth noting.…”

Section: Discussionmentioning

confidence: 70%

On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations

Wang

Jumper

Freed

et al. 2019

Biophysical Journal

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Single-molecule force spectroscopy has proven extremely beneficial in elucidating folding pathways for membrane proteins. Here, we simulate these measurements, conducting hundreds of unfolding trajectories using our fast Upside algorithm for slow enough speeds to reproduce key experimental features that may be missed using all-atom methods. The speed also enables us to determine the logarithmic dependence of pulling velocities on the rupture levels to better compare to experimental values. For simulations of atomic force microscope measurements in which force is applied vertically to the C-terminus of bacteriorhodopsin, we reproduce the major experimental features including even the back-and-forth unfolding of single helical turns. When pulling laterally on GlpG to mimic the experiment, we observe quite different behavior depending on the stiffness of the spring. With a soft spring, as used in the experimental studies with magnetic tweezers, the force remains nearly constant after the initial unfolding event, and a few pathways and a high degree of cooperativity are observed in both the experiment and simulation. With a stiff spring, however, the force drops to near zero after each major unfolding event, and numerous intermediates are observed along a wide variety of pathways. Hence, the mode of force application significantly alters the perception of the folding landscape, including the number of intermediates and the degree of folding cooperativity, important issues that should be considered when designing experiments and interpreting unfolding data.

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Section: Discussionmentioning

confidence: 70%

On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations

Wang

Jumper

Freed

et al. 2019

Biophysical Journal

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“…Simulations can play a vital role in helping to rationalize the folding and assembly mechanism of membrane proteins. Some elegant examples include the use of coarse-grained models to study the mechanism of GlpG folding [13], or to predict the topology of multi-pass transmembrane helical proteins [14]. Studying the details of the helix assembly into the specific native structure, however, requires a higher-resolution model.…”

Section: Introductionmentioning

confidence: 99%

Atomistic mechanism of transmembrane helix association

et al. 2020

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Transmembrane helix association is a fundamental step in the folding of helical membrane proteins. The prototypical example of this association is formation of the glycophorin dimer. While its structure and stability have been well-characterized experimentally, the detailed assembly mechanism is harder to obtain. Here, we use all-atom simulations within phospholipid membrane to study glycophorin association. We find that initial association results in the formation of a non-native intermediate, separated by a significant free energy barrier from the dimer with a native binding interface. We have used transition-path sampling to determine the association mechanism. We find that the mechanism of the initial bimolecular association to form the intermediate state can be mediated by many possible contacts, but seems to be particularly favoured by formation of non-native contacts between the C-termini of the two helices. On the other hand, the contacts which are key to determining progression from the intermediate to the native state are those which define the native binding interface, reminiscent of the role played by native contacts in determining folding of globular proteins. As a check on the simulations, we have computed association and dissociation rates from the transition-path sampling. We obtain results in reasonable accord with available experimental data, after correcting for differences in native state stability. Our results yield an atomistic description of the mechanism for a simple prototype of helical membrane protein folding.

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“…Point mutations in an upstream TMH can affect the pulling force generated by downstream TMHs in a highly position-dependent manner, suggestive of residue-specific interactions between TMHs during the membrane-integration process. Complementing in vitro unfolding/folding studies (27,28), real-time FRET analyses (15), chemical crosslinking (29), structure determination (30), and computational modeling (31), high-resolution in vivo FPA can help identify the molecular interactions underlying cotranslational membrane protein biogenesis with single-residue precision. For constructs with N≥298, the C-terminal tail is 75 residues long.…”

mentioning

confidence: 99%

Residue-by-residue analysis of cotranslational membrane protein integrationin vivo

Nicolaus

Metola

Mermans

et al. 2020

Preprint

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We follow the cotranslational biosynthesis of three multi-spanning E. coli inner membrane proteins in vivo using high-resolution Force Profile Analysis. The force profiles show that the nascent chain is subjected to rapidly varying pulling forces during translation, and reveal unexpected complexities in the membrane integration process. We find that an N-terminal cytoplasmic domains can fold in the ribosome exit tunnel before membrane integration starts, that charged residues and membrane-interacting segments such as re-entrant loops and surface helices flanking a transmembrane helix (TMH) can advance or delay membrane integration, and that point mutations in an upstream TMH can affect the pulling forces generated by downstream TMHs in a highly position-dependent manner, suggestive of residue-specific interactions between TMHs during the integration process.

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Energy landscape underlying spontaneous insertion and folding of an alpha-helical transmembrane protein into a bilayer

Cited by 28 publications

References 35 publications

On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations

On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations

Atomistic mechanism of transmembrane helix association

Residue-by-residue analysis of cotranslational membrane protein integrationin vivo

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