scholarly journals Modeling Membrane-Protein Interactions

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.

scholarly journals Modeling Membrane Curvature Generation due to Membrane–Protein Interactions

Biomolecules ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 120 ◽  
Author(s):  
Haleh Alimohamadi ◽  
Padmini Rangamani
Keyword(s):  
Membrane Proteins ◽  
Protein Interactions ◽  
Current Model ◽  
Bilayer Membrane ◽  
Membrane Curvature ◽  
Elastic Membrane ◽  
Protein Distribution ◽  
Membrane Models ◽  
Generation Mechanisms ◽  
Mathematical And Computational Modeling

To alter and adjust the shape of the plasma 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. Mathematical and computational modeling of membrane curvature generation has provided great insights into the physics underlying these processes. However, one of the challenges in modeling these processes is identifying the suitable constitutive relationships that describe the membrane free energy including 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 to push the boundaries of current model applications.

scholarly journals Lipid-Protein Interactions of Integral Membrane Proteins: A Comparative Simulation Study

2004 ◽  
Vol 87 (6) ◽  
pp. 3737-3749 ◽  
Author(s):  
Sundeep S. Deol ◽  
Peter J. Bond ◽  
Carmen Domene ◽  
Mark S.P. Sansom
Keyword(s):  
Membrane Proteins ◽  
Protein Interactions ◽  
Simulation Study ◽  
Integral Membrane Proteins ◽  
Lipid Protein Interactions

scholarly journals Membrane models for molecular simulations of peripheral membrane proteins

2021 ◽  
Vol 6 (1) ◽  
pp. 1932589
Author(s):  
Mahmoud Moqadam ◽  
Thibault Tubiana ◽  
Emmanuel E. Moutoussamy ◽  
Nathalie Reuter
Keyword(s):  
Membrane Proteins ◽  
Molecular Simulations ◽  
Peripheral Membrane Proteins ◽  
Membrane Models

scholarly journals High-Throughput Identification of Nuclear Envelope Protein Interactions in Schizosaccharomyces pombe Using an Arrayed Membrane Yeast-Two Hybrid Library

2020 ◽  
Vol 10 (12) ◽  
pp. 4649-4663 ◽  
Author(s):  
Joseph M. Varberg ◽  
Jennifer M. Gardner ◽  
Scott McCroskey ◽  
Snehabala Saravanan ◽  
William D. Bradford ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Nuclear Envelope ◽  
Schizosaccharomyces Pombe ◽  
High Throughput ◽  
Protein Interactions ◽  
Transmembrane Protein ◽  
Integral Membrane Proteins ◽  
Model Organisms ◽  
Yeast Two Hybrid ◽  
Two Hybrid

The nuclear envelope (NE) contains a specialized set of integral membrane proteins that maintain nuclear shape and integrity and influence chromatin organization and gene expression. Advances in proteomics techniques and studies in model organisms have identified hundreds of proteins that localize to the NE. However, the function of many of these proteins at the NE remains unclear, in part due to a lack of understanding of the interactions that these proteins participate in at the NE membrane. To assist in the characterization of NE transmembrane protein interactions we developed an arrayed library of integral and peripheral membrane proteins from the fission yeast Schizosaccharomyces pombe for high-throughput screening using the split-ubiquitin based membrane yeast two -hybrid system. We used this approach to characterize protein interactions for three conserved proteins that localize to the inner nuclear membrane: Cut11/Ndc1, Lem2 and Ima1/Samp1/Net5. Additionally, we determined how the interaction network for Cut11 is altered in canonical temperature-sensitive cut11-ts mutants. This library and screening approach is readily applicable to characterizing the interactomes of integral membrane proteins localizing to various subcellular compartments.

scholarly journals An intrinsic compartmentalization code for peripheral membrane proteins in photoreceptor neurons

2019 ◽  
Vol 218 (11) ◽  
pp. 3753-3772 ◽  
Author(s):  
Nycole A. Maza ◽  
William E. Schiesser ◽  
Peter D. Calvert
Keyword(s):  
Membrane Proteins ◽  
Protein Interactions ◽  
Electrostatic Interactions ◽  
Transport Model ◽  
Fluorescent Proteins ◽  
Lipid Binding ◽  
Peripheral Membrane Proteins ◽  
Rhodopsin Kinase ◽  
Membrane Bound ◽  
Photoreceptor Neurons

In neurons, peripheral membrane proteins are enriched in subcellular compartments, where they play key roles, including transducing and transmitting information. However, little is known about the mechanisms underlying their compartmentalization. To explore the roles of hydrophobic and electrostatic interactions, we engineered probes consisting of lipidation motifs attached to fluorescent proteins by variously charged linkers and expressed them in Xenopus rod photoreceptors. Quantitative live cell imaging showed dramatic differences in distributions and dynamics of the probes, including presynapse and ciliary OS enrichment, depending on lipid moiety and protein surface charge. Opposing extant models of ciliary enrichment, most probes were weakly membrane bound and diffused through the connecting cilium without lipid binding chaperone protein interactions. A diffusion-binding-transport model showed that ciliary enrichment of a rhodopsin kinase probe occurs via recycling as it perpetually leaks out of the ciliary OS. The model accounts for weak membrane binding of peripheral membrane proteins and a leaky connecting cilium diffusion barrier.

scholarly journals High-throughput identification of nuclear envelope protein interactions in Schizosaccharomyces pombe using an arrayed membrane yeast-two hybrid library

2020 ◽  
Author(s):  
Joseph M. Varberg ◽  
Jennifer M. Gardner ◽  
Scott McCroskey ◽  
Snehabala Saravanan ◽  
William D. Bradford ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Nuclear Envelope ◽  
Schizosaccharomyces Pombe ◽  
High Throughput ◽  
Protein Interactions ◽  
Transmembrane Protein ◽  
Integral Membrane Proteins ◽  
Model Organisms ◽  
Yeast Two Hybrid ◽  
Two Hybrid

The nuclear envelope (NE) contains a specialized set of integral membrane proteins that maintain nuclear shape and integrity and influence chromatin organization and gene expression. Advances in proteomics techniques and studies in model organisms have identified hundreds of proteins that localize to the NE. However, the function of many of these proteins at the NE remains unclear, in part due to a lack of understanding of the interactions that these proteins participate in at the NE membrane. To assist in the characterization of NE transmembrane protein interactions we developed an arrayed library of integral and peripheral membrane proteins in the fission yeast Schizosaccharomyces pombe for high-throughput screening using the split-ubiquitin based membrane yeast two hybrid sys-tem. We used this approach to characterize protein interactions for three conserved proteins that localize to the inner nu-clear membrane: Cut11/Ndc1, Lem2, and Ima1/Samp1/NET5. Additionally, we determined how the interaction network for Cut11 is altered in canonical temperature-sensitive cut11 mutants. This library and screening approach is readily applicable to characterizing the interactomes of integral membrane proteins localizing to various subcellular compartments.

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

2019 ◽  
Vol 48 (1) ◽  
pp. 25-37 ◽  
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.

scholarly journals Prediction of amphipathic helix – membrane interactions with Rosetta

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.

Molecular cytochemistry of freeze-fractured cells

1986 ◽  
Vol 44 ◽  
pp. 894-897
Author(s):  
Pedro Pinto da Silva
Keyword(s):  
Membrane Proteins ◽  
Membrane Surface ◽  
Freeze Fracture ◽  
Biological Membranes ◽  
Bilayer Membrane ◽  
Integral Membrane Proteins ◽  
Distilled Water ◽  
Intramembrane Particles ◽  
Freeze Etching

I will describe four approaches that combine cytochemistry with freeze-fracture: 1) FREEZE-ETCHING; 2) FRACTURE-LABEL; 3) FRACTURE-PERMEATION; and 4) LABEL-FRACTURE. These techniques, in particular fracture-label, involve delicate points of interpretation and numerous validating controls. In the publications listed at the end, these issues have been addressed in detail.1. FREEZE-ETCHING. I developed freeze-etching as a cytochemical approach to prove that membranes were split by freeze-fracture and to show that biological membranes were comprised of a bilayer membrane continuum interrupted by integral membrane proteins.1 - 4 In freeze-etching, the distribution of the marker over the membrane surface exposed by sublimation is compared to that of the intramembrane particles exposed by fracture. It is often required to aggregate the particles into domains larger than the labeling molecules (Fig. 1). This, and the need for freezing in distilled water, severely limits the application of freeze-etching.

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