Prediction of amphipathic helix—Membrane interactions with Rosetta

Amphipathic helices have hydrophobic and hydrophilic/charged residues situated on oppo site faces of the helix. They can anchor peripheral membrane proteins to the membrane, be attached to integral membrane proteins, or exist as independent peptides. Despite the widespread presence of membrane-interacting amphipathic helices, there is no computational tool within Rosetta to model their interactions with membranes. In order to address this need, we developed the AmphiScan protocol with PyRosetta, which runs a grid search to find the most favorable position of an amphipathic helix with respect to the membrane. The performance of the algorithm was tested in benchmarks with the RosettaMembrane, ref2015_memb, and franklin2019 score functions on six engineered and 44 naturally-occurring amphipathic helices using membrane coordinates from the OPM and PDBTM databases, OREMPRO server, and MD simulations for comparison. The AmphiScan protocol predicted the coordinates of amphipathic helices within less than 3Å of the reference structures and identified membrane-embedded residues with a Matthews Correlation Constant (MCC) of up to 0.57. Overall, AmphiScan stands as fast, accurate, and highly-customizable protocol that can be pipelined with other Rosetta and Python applications.

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Prediction of amphipathic helix – membrane interactions with Rosetta

10.1101/2020.06.15.152322 ◽

2020 ◽

Author(s):

Alican Gulsevin ◽

Jens Meiler

Keyword(s):

Membrane Proteins ◽

Md Simulations ◽

Integral Membrane Proteins ◽

Grid Search ◽

Amphipathic Helix ◽

Computational Tool ◽

Amphipathic Helices ◽

Peripheral Membrane Proteins ◽

Naturally Occurring ◽

Correlation Constant

AbstractAmphipathic helices have hydrophobic and hydrophilic/charged residues situated on opposite faces of the helix. They can anchor peripheral membrane proteins to the membrane, be attached to integral membrane proteins, or exist as independent peptides. Despite the widespread presence of membrane-interacting amphipathic helices, there is no computational tool within Rosetta to model their interactions with membranes. In order to address this need, we developed the AmphiScan protocol with PyRosetta, which runs a grid search to find the most favorable position of an amphipathic helix with respect to the membrane. The performance of the algorithm was tested in benchmarks with six engineered and 44 naturally occurring amphipathic helices using membrane coordinates from the OPM and PDBTM databases, OREMPRO server, and MD simulations as reference. The AmphiScan protocol predicted the coordinates of amphipathic helices within less than 3Å of the reference structures and identified membrane-embedded residues with a Matthews Correlation Constant (MCC) up to 0.61. Overall, AmphiScan stands as fast, accurate, and highly-customizable protocol that can be pipelined with other Rosetta and Python applications.

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Modeling Membrane-Protein Interactions

10.20944/preprints201809.0055.v1 ◽

2018 ◽

Author(s):

Haleh Alimohamadi ◽

Padmini Rangamani

Keyword(s):

Membrane Proteins ◽

Protein Interactions ◽

Current Model ◽

Bilayer Membrane ◽

Integral Membrane Proteins ◽

Elastic Membrane ◽

Protein Distribution ◽

Peripheral Membrane Proteins ◽

Membrane Models ◽

Generation Mechanisms

In order to alter and adjust the shape of the membrane, cells harness various mechanisms of curvature generation. Many of these curvature generation mechanisms rely on the interactions between peripheral membrane proteins, integral membrane proteins, and lipids in the bilayer membrane. One of the challenges in modeling these processes is identifying the suitable constitutive relationships that describe the membrane free energy that includes protein distribution and curvature generation capability. Here, we review some of the commonly used continuum elastic membrane models that have been developed for this purpose and discuss their applications. Finally, we address some fundamental challenges that future theoretical methods need to overcome in order to push the boundaries of current model applications.

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The energetics of protein–lipid interactions as viewed by molecular simulations

Biochemical Society Transactions ◽

10.1042/bst20190149 ◽

2019 ◽

Vol 48 (1) ◽

pp. 25-37 ◽

Cited By ~ 2

Author(s):

Robin A. Corey ◽

Phillip J. Stansfeld ◽

Mark S.P. Sansom

Keyword(s):

Membrane Proteins ◽

Biological Membrane ◽

Lipid Binding ◽

Integral Membrane Proteins ◽

Free Energies ◽

Computational Approaches ◽

Lipid Interactions ◽

Current State ◽

Peripheral Membrane Proteins ◽

Lipid Species

Membranes are formed from a bilayer containing diverse lipid species with which membrane proteins interact. Integral, membrane proteins are embedded in this bilayer, where they interact with lipids from their surroundings, whilst peripheral membrane proteins bind to lipids at the surface of membranes. Lipid interactions can influence the function of membrane proteins, either directly or allosterically. Both experimental (structural) and computational approaches can reveal lipid binding sites on membrane proteins. It is, therefore, important to understand the free energies of these interactions. This affords a more complete view of the engagement of a particular protein with the biological membrane surrounding it. Here, we describe many computational approaches currently in use for this purpose, including recent advances using both free energy and unbiased simulation methods. In particular, we focus on interactions of integral membrane proteins with cholesterol, and with anionic lipids such as phosphatidylinositol 4,5-bis-phosphate and cardiolipin. Peripheral membrane proteins are exemplified via interactions of PH domains with phosphoinositide-containing membranes. We summarise the current state of the field and provide an outlook on likely future directions of investigation.

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The surface of lipid droplets constitutes a barrier for endoplasmic reticulum residential integral membrane proteins

Journal of Cell Science ◽

10.1242/jcs.256206 ◽

2021 ◽

Author(s):

Rasha Khaddaj ◽

Muriel Mari ◽

Stéphanie Cottier ◽

Fulvio Reggiori ◽

Roger Schneiter

Keyword(s):

Endoplasmic Reticulum ◽

Membrane Proteins ◽

Fusion Proteins ◽

Mammalian Cells ◽

Lipid Droplets ◽

Neutral Lipids ◽

Integral Membrane Proteins ◽

Bimolecular Fluorescence Complementation ◽

Amphipathic Helix ◽

Mitochondrial Membrane Protein

Lipid droplets (LDs) are globular subcellular structures that store neutral lipids. LDs are closely associated with the endoplasmic reticulum (ER), and are limited by a phospholipid monolayer harboring a specific set of proteins. Most of these proteins associate with LDs through either an amphipathic helix or a membrane-embedded hairpin motif. Here we address the question whether integral membrane proteins could localize to the surface of LDs. To test this, we fused perilipin 3 (PLIN3), a mammalian LD-targeted protein, to ER residential proteins. The resulting fusion proteins localized to the periphery of LDs in both yeast and mammalian cells. This peripheral LD localization of the fusion proteins, however, was due to a redistribution of the ER around LDs, as revealed by bimolecular fluorescence complementation between ER- and LD-localized partners. A LD-tethering function of PLIN3-containing membrane proteins was confirmed by fusing PLIN3 to the cytoplasmic domain of an outer mitochondrial membrane protein, OM14. Expression of OM14-PLIN3 induced a close apposition between LDs and mitochondria. These data indicate that the ER-LD junction constitutes a barrier for ER-residential integral membrane proteins.

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Folding of Aquaporin 1: Multiple evidence that helix 3 can shift out of the membrane core

10.1101/014167 ◽

2015 ◽

Author(s):

Minttu T Virkki ◽

Nitin Agrawal ◽

Elin Edsbäcker ◽

Susana Cristobal ◽

Arne Elofsson ◽

...

Keyword(s):

Membrane Proteins ◽

Md Simulations ◽

Integral Membrane Proteins ◽

Second Step ◽

Transmembrane Helices ◽

Step Process ◽

Aquaporin 1 ◽

The Third ◽

Rearrangement Process ◽

Sec Translocon

The folding of most integral membrane proteins follows a two-step process: Initially, individual transmembrane helices are inserted into the membrane by the Sec translocon. Thereafter, these helices fold to shape the final conformation of the protein. However, for some proteins, including Aquaporin 1 (AQP1), the folding appears to follow a more complicated path. AQP1 has been reported to first insert as a four-helical intermediate, where helix 2 and 4 are not inserted into the membrane. In a second step this intermediate is folded into a six-helical topology. During this process, the orientation of the third helix is inverted. Here, we propose a mechanism for how this reorientation could be initiated: First, helix 3 slides out from the membrane core resulting in that the preceding loop enters the membrane. The final conformation could then be formed as helix 2, 3 and 4 are inserted into the membrane and the reentrant regions come together. We find support for the first step in this process by showing that the loop preceding helix 3 can insert into the membrane. Further, hydrophobicity curves, experimentally measured insertion efficiencies and MD-simulations suggest that the barrier between these two hydrophobic regions is relatively low, supporting the idea that helix 3 can slide out of the membrane core, initiating the rearrangement process

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Image Analysis of Intramembrane Particles in Freeze-Fractured Biomembranes Using Computer Simulation Techniques

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100114694 ◽

1975 ◽

Vol 33 ◽

pp. 214-215

Author(s):

D.J. Benefiel ◽

R.S. Weinstein

Keyword(s):

Membrane Proteins ◽

Freeze Fracture ◽

Integral Membrane Proteins ◽

Systematic Evaluation ◽

Intramembrane Particles ◽

Modeling Methods ◽

Simulation Techniques ◽

Freeze Fracture Electron Microscopy ◽

Fracture Electron ◽

Computer Simulation Techniques

Intramembrane particles (IMP or MAP) are components of most biomembranes. They are visualized by freeze-fracture electron microscopy, and they probably represent replicas of integral membrane proteins. The presence of MAP in biomembranes has been extensively investigated but their detailed ultrastructure has been largely ignored. In this study, we have attempted to lay groundwork for a systematic evaluation of MAP ultrastructure. Using mathematical modeling methods, we have simulated the electron optical appearances of idealized globular proteins as they might be expected to appear in replicas under defined conditions. By comparing these images with the apearances of MAPs in replicas, we have attempted to evaluate dimensional and shape distortions that may be introduced by the freeze-fracture technique and further to deduce the actual shapes of integral membrane proteins from their freezefracture images.

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Spotting Differences in Molecular Dynamic Simulations of Influenza A M2 Protein-Ligand Complexes by Varying M2 construct, Lipid Bilayer and Force Field

10.26434/chemrxiv.11365943.v1 ◽

2019 ◽

Author(s):

Dimitrios Kolokouris ◽

Iris Kalenderoglou ◽

Panagiotis Lagarias ◽

Antonios Kolocouris

Keyword(s):

Molecular Dynamic ◽

Lipid Bilayer ◽

Influenza A ◽

Md Simulations ◽

Membrane Curvature ◽

Buffer Size ◽

M2 Protein ◽

Dynamic Simulations ◽

Amphipathic Helices ◽

Drug Protein Binding

We studied by molecular dynamic (MD) simulations systems including the inwardclosed state of influenza A M2 protein in complex with aminoadamantane drugs in membrane bilayers. We varied the M2 construct and performed MD simulations in M2TM or M2TM with amphipathic helices (M2AH). We also varied the lipid bilayer by changing either the lipid, DMPC or POPC, POPE or POPC/cholesterol (chol), or the lipids buffer size, 10x10 Å2 or 20x20 Å2. We aimed to suggest optimal system conditions for the computational description of this ion channel and related systems. Measures performed include quantities that are available experimentally and include: (a) the position of ligand, waters and chlorine anion inside the M2 pore, (b) the passage of waters from the outward Val27 gate of M2 S31N in complex with an aminoadamantane-aryl head blocker, (c) M2 orientation, (d) the AHs conformation and structure which is affected from interactions with lipids and chol and is important for membrane curvature and virus budding. In several cases we tested OPLS2005, which is routinely applied to describe drug-protein binding, and CHARMM36 which describes reliably protein conformation. We found that for the description of the ligands position inside the M2 pore, a 10x10 Å2 lipids buffer in DMPC is needed when M2TM is used but 20x20 Å2 lipids buffer of the softer POPC; when M2AH is used all 10x10 Å2 lipid buffers with any of the tested lipids can be used. For the passage of waters at least M2AH with a 10x10 Å2 lipid buffer is needed. The folding conformation of AHs which is defined from hydrogen bonding interactions with the bilayer and the complex with chol is described well with a 10x10 Å2 lipids buffer and CHARMM36.

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