Native Cell Membrane Nanoparticles System for Membrane Protein-Protein Interaction Analysis

Kroeck, Kyle G.; Qiu, Weihua; Catalano, Claudio; Trinh, Thi Kim Hoang; Guo, Youzhong

doi:10.3791/61298

Cited by 8 publications

(4 citation statements)

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“…Membrane protein folding and the resulting activity require the presence of the native lipid environment, which is often corrupted by the detergents used for extraction( Guo, 2020 ). The recent developments of detergent-free systems ( Gulamhussein et al., 2020 ; Guo, 2021 ; Kroeck et al., 2020 ; Lee et al., 2016 ; Marconnet et al., 2020 ; Qiu et al., 2018 ; Simon et al., 2018 ; Yang et al., 2021 ) allows co-extraction and stabilization of membrane proteins and their associated lipids in their near-to-native conformation. This increases the environmental diversity of the lipid bilayer, enhancing our understanding of protein structure, and the critical roles of lipids as designed by Nature.…”

Section: Discussionmentioning

confidence: 99%

3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins

Catalano

Mughram

Guo

et al. 2021

Current Research in Structural Biology

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Atomic-resolution protein structural models are prerequisites for many downstream activities like structure-function studies or structure-based drug discovery. Unfortunately, this data is often unavailable for some of the most interesting and therapeutically important proteins. Thus, computational tools for building native-like structural models from less-than-ideal experimental data are needed. To this end, interaction homology exploits the character, strength and loci of the sets of interactions that define a structure. Each residue type has its own limited set of backbone angle-dependent interaction motifs, as defined by their environments. In this work, we characterize the interactions of serine, cysteine and S-bridged cysteine in terms of 3D hydropathic environment maps. As a result, we explore several intriguing questions. Are the environments different between the isosteric serine and cysteine residues? Do some environments promote the formation of cystine S–S bonds? With the increasing availability of structural data for water-insoluble membrane proteins, are there environmental differences for these residues between soluble and membrane proteins? The environments surrounding serine and cysteine residues are dramatically different: serine residues are about 50% solvent exposed, while cysteines are only 10% exposed; the latter are more involved in hydrophobic interactions although there are backbone angle-dependent differences. Our analysis suggests that one driving force for –S–S– bond formation is a rather substantial increase in burial and hydrophobic interactions in cystines. Serine and cysteine become less and more, respectively, solvent-exposed in membrane proteins. 3D hydropathic environment maps are an evolving structure analysis tool showing promise as elements in a new protein structure prediction paradigm.

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Section: Discussionmentioning

confidence: 99%

3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins

Catalano

Mughram

Guo

et al. 2021

Current Research in Structural Biology

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“…The expression and cell lysis of AcrB and BcTSPO membrane were carried out based on our previous protocol. 71,76 Following a typical solubilization procedure, 1 g membrane fraction was suspended in 10 mL NCMN Buffer A and then homogenized by using a Dounce homogenizer. Consequently, the suspended membrane was transferred to a 50 mL polypropylene tube and mixed with NCMNP2a-x for a nal concentration of 2.5% w/v.…”

Section: Expression Solubilization and Purication Of Acrb And Bctspomentioning

confidence: 99%

pH-tunable membrane-active polymers, NCMNP2a-x, and their potential membrane protein applications

et al. 2023

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“…MscS were over-expressed in the outer membrane of the E.coli, and their membrane fractions were prepared as described previously. 24,42,43 Following a general solubilization protocol, 1 g membrane fraction was suspended and homogenized in 10 mL NCMN Buffer A using a Dounce homogenizer. Afterward, the homogenized membrane was transferred to a 50 mL polypropylene tube and mixed with NCMN polymer for a final concentration of 2.5% w/v.…”

Section: Expression and Purification Of Acrb And Mscs Both 8 His-tagged Acrb And 10 His-taggedmentioning

confidence: 99%

Membrane-active Polymers: NCMNP13-x, NCMNP21-x and NCMNP21b-x for Membrane Protein Structural Biology

Trinh

Catalano

Guo

2022

Preprint

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Membrane proteins are a ubiquitous group of bio-macromolecules responsible for many crucial biological processes and serve as drug targets for a wide range of modern drugs. Detergent-free technologies such as styrene-maleic acid lipid particles (SMALP), diisobutylene-maleic acid lipid particles (DIBMALP), and native cell membrane nanoparticles (NCMN) systems have recently emerged as revolutionary alternatives to the traditional detergent-based approaches for membrane protein research. NCMN systems aim to create a membrane-active polymer library suitable for high-resolution structure determination. Herein, we report our design, synthesis, characterization and comparative application analyses of three novel classes of NCMN polymers, NCMNP13-x, NCMNP21-x and NCMNP21b-x. Although each NCMN polymer can solubilize various model membrane proteins and conserve native lipids into NCMN particles, only the NCMNP21b-x series reveals lipid-protein particles with good buffer compatibility and high homogeneity suitable for single-particle cryo-EM analysis. Consequently, the NCMNP21b-x polymers that bring out high-quality NCMN particles are particularly attractive for membrane protein structural biology.

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Native Cell Membrane Nanoparticles System for Membrane Protein-Protein Interaction Analysis

Cited by 8 publications

References 0 publications

3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins

3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins

pH-tunable membrane-active polymers, NCMNP2a-x, and their potential membrane protein applications

Membrane-active Polymers: NCMNP13-x, NCMNP21-x and NCMNP21b-x for Membrane Protein Structural Biology

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