Seipin transmembrane segments critically function in triglyceride nucleation and lipid droplet budding from the membrane
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Evaluation Summary:
Kim et al. investigate interactions between Seipin transmembrane domains and triacylglycerol using molecular dynamics simulations. They identify the leading steps in droplet formation and provide a physical basis for understanding the initial phases of this process, highlighting the importance of transmembrane helices in the function of seipin protein. This paper will be of interest to cell biologists and biophysicists aiming to unveil and understand how lipid droplets are formed inside cells. The topic is important given that lipid droplets are key organelles used for energy storage, and that the failure in their formation can result in various metabolic diseases.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)
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Abstract
Lipid droplets (LDs) are organelles formed in the endoplasmic reticulum (ER) to store triacylglycerol (TG) and sterol esters. The ER protein seipin is key for LD biogenesis. Seipin forms a cage-like structure, with each seipin monomer containing a conserved hydrophobic helix and two transmembrane (TM) segments. How the different parts of seipin function in TG nucleation and LD budding is poorly understood. Here, we utilized molecular dynamics simulations of human seipin, along with cell-based experiments, to study seipin’s functions in protein–lipid interactions, lipid diffusion, and LD maturation. An all-atom simulation indicates that seipin TM segment residues and hydrophobic helices residues located in the phospholipid tail region of the bilayer attract TG. Simulating larger, growing LDs with coarse-grained models, we find that the seipin TM segments form a constricted neck structure to facilitate conversion of a flat oil lens into a budding LD. Using cell experiments and simulations, we also show that conserved, positively charged residues at the end of seipin’s TM segments affect LD maturation. We propose a model in which seipin TM segments critically function in TG nucleation and LD growth.
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Evaluation Summary:
Kim et al. investigate interactions between Seipin transmembrane domains and triacylglycerol using molecular dynamics simulations. They identify the leading steps in droplet formation and provide a physical basis for understanding the initial phases of this process, highlighting the importance of transmembrane helices in the function of seipin protein. This paper will be of interest to cell biologists and biophysicists aiming to unveil and understand how lipid droplets are formed inside cells. The topic is important given that lipid droplets are key organelles used for energy storage, and that the failure in their formation can result in various metabolic diseases.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested …
Evaluation Summary:
Kim et al. investigate interactions between Seipin transmembrane domains and triacylglycerol using molecular dynamics simulations. They identify the leading steps in droplet formation and provide a physical basis for understanding the initial phases of this process, highlighting the importance of transmembrane helices in the function of seipin protein. This paper will be of interest to cell biologists and biophysicists aiming to unveil and understand how lipid droplets are formed inside cells. The topic is important given that lipid droplets are key organelles used for energy storage, and that the failure in their formation can result in various metabolic diseases.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)
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Reviewer #1 (Public Review):
This study interrogates the important topic of seipin droplet formation, and addresses a current lack of knowledge owing to limited information on the transmembrane (TM) domains of human seipin. In this study, the seipin TM domains, which are missing from the structure of the human system, are modelled in and evaluated using atomistic simulation. The authors discover a cage-like assembly, with a very high degree of dynamics. From the presented data however, it is unclear if these dynamics are a natural part of the seipin dynamical behaviour, or are a result of limitations in the input model.
Then, using coarse-grained simulations, the authors demonstrate that this cage-like assembly, as well as conserved basic residues at the ends of the TM helices, are necessary for the initial stages of lipid droplet …
Reviewer #1 (Public Review):
This study interrogates the important topic of seipin droplet formation, and addresses a current lack of knowledge owing to limited information on the transmembrane (TM) domains of human seipin. In this study, the seipin TM domains, which are missing from the structure of the human system, are modelled in and evaluated using atomistic simulation. The authors discover a cage-like assembly, with a very high degree of dynamics. From the presented data however, it is unclear if these dynamics are a natural part of the seipin dynamical behaviour, or are a result of limitations in the input model.
Then, using coarse-grained simulations, the authors demonstrate that this cage-like assembly, as well as conserved basic residues at the ends of the TM helices, are necessary for the initial stages of lipid droplet formation, i.e. the transition from a lens to a more bulged structure. They demonstrate that conserved basic residues are necessary for this process, which they back up with confocal imaging experiments. These findings are convincing, but rely on very coarse simulations.
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Reviewer #2 (Public Review):
In this manuscript, Kim et al. scrutinize the role of the Seipin transmembrane domains during lipid droplet biogenesis mainly by molecular dynamics simulations. The study primarily exploits a a new structural model of human Seipin that includes the transmembrane regions. The authors do an excellent job in introducing/explaining the parameters analysed from the MD simulations, and confirm previously observed roles for the transmembrane segments in LD biogenesis. The authors identify key charged residues flanking Seipin transmembrane regions and propose a model for how the they facilitate the budding of lipid droplets from the ER membrane.
The role of the Seipin TMs in the formation of LDs is of great interest to the field. However, much of the data in this manuscript confirms previous observations, and as …
Reviewer #2 (Public Review):
In this manuscript, Kim et al. scrutinize the role of the Seipin transmembrane domains during lipid droplet biogenesis mainly by molecular dynamics simulations. The study primarily exploits a a new structural model of human Seipin that includes the transmembrane regions. The authors do an excellent job in introducing/explaining the parameters analysed from the MD simulations, and confirm previously observed roles for the transmembrane segments in LD biogenesis. The authors identify key charged residues flanking Seipin transmembrane regions and propose a model for how the they facilitate the budding of lipid droplets from the ER membrane.
The role of the Seipin TMs in the formation of LDs is of great interest to the field. However, much of the data in this manuscript confirms previous observations, and as such the conceptual leap achieved is minor. On the other hand, the identification of conformational changes in the transmembrane region and flanking charged residues is novel and interesting. A drawback of the study is its complete dependence of incompletely described structural model of human Seipin. Given the importance of this model for the conclusions of the study, it is essential to describe the model in detail. The role of the charged residues flanking Seipin transmembrane segments should also be further characterized, in particular their potential impact in protein expression, membrane insertion and topology.
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Reviewer #3 (Public Review):
The paper uses atomistic molecular dynamics simulations and selected cryo-EM imaging data to develop a phenomenological coarse-grained simulation model for studies of seipin and its role in lipid droplet formation. These coarse-grained simulations are complemented with atomistic molecular dynamics simulations and cell-based experiments. The aim of the paper is to clarify the role of seipin's transmembrane helices in the clustering of triglycerides, to form a triglyceride-rich lipid phase bound to seipin, and the importance of the transmembrane helices in the initial stages of lipid droplet formation.
A major strength of the simulation approach is the coupling of atomistic simulation results and cryo-EM imaging data, which are used to develop a phenomenological coarse-grained model. In this manner, the …
Reviewer #3 (Public Review):
The paper uses atomistic molecular dynamics simulations and selected cryo-EM imaging data to develop a phenomenological coarse-grained simulation model for studies of seipin and its role in lipid droplet formation. These coarse-grained simulations are complemented with atomistic molecular dynamics simulations and cell-based experiments. The aim of the paper is to clarify the role of seipin's transmembrane helices in the clustering of triglycerides, to form a triglyceride-rich lipid phase bound to seipin, and the importance of the transmembrane helices in the initial stages of lipid droplet formation.
A major strength of the simulation approach is the coupling of atomistic simulation results and cryo-EM imaging data, which are used to develop a phenomenological coarse-grained model. In this manner, the quality of the coarse-grained model reaches a level where it is expected to have predictive power. Meanwhile, the conclusions of atomistic simulations are based on a single, quite short simulation, hence the results of this atomistic simulation reflect the initial structure used in the simulation and sampling of atomistic simulations is not fully adequate.
The value of the paper is mainly based on the view produced by the coarse-grained model of the early stages of lipid droplet formation. These results are very interesting. They emphasize the importance of the chemical details of seipin's transmembrane structure, the interactions of seipin residues with lipids, and the effect of the lipid phase formed by triglycerides on the local physical properties of the cell membrane. As a result, seipin forms a neck-like structure that is likely to favor the formation of lipid droplets.
The key goal is to understand how lipid droplets are formed under native conditions. This paper will help to address precisely this challenge, and at the same time lay the groundwork for future research to find out how the formation of lipid droplets can fail and lead to various diseases.
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