Exploring the topology of cytoplasmic membrane proteins involved in lipopolysaccharide biosynthesis by in silico and biochemical analyses

Julia Monjarás Feria; Miguel A. Valvano

doi:10.1007/978-1-0716-2581-1_5

Exploring the topology of cytoplasmic membrane proteins involved in lipopolysaccharide biosynthesis by in silico and biochemical analyses

Julia Monjarás Feria, Miguel A. Valvano^*

^*Corresponding author for this work

Wellcome Wolfson Institute for Experimental Medicine

Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed) › peer-review

Abstract

In the absence of a tri-dimensional structure, revealing the topology of a membrane protein provides relevant information to identify the number and orientation of transmembrane helices and the localization of critical amino acid residues, contributing to a better understanding of function and intermolecular associations. Topology can be predicted in silico by bioinformatic analysis or solved by biochemical methods. In this chapter, we describe a pipeline employing bioinformatic approaches for the prediction of membrane protein topology, followed by experimental validation through the substituted-cysteine accessibility method and the analysis of the protein's oligomerization state.

Original language	English
Title of host publication	Lipopolysaccharide Transport. Methods and Protocols
Editors	Paola Sperandeo
Publisher	Springer
Pages	71-82
Number of pages	12
ISBN (Electronic)	9781071625811
ISBN (Print)	9781071625804
DOIs	https://doi.org/10.1007/978-1-0716-2581-1_5
Publication status	Published - 24 Sept 2022

Publication series

Name	Methods in molecular biology (Clifton, N.J.)
Publisher	Humana Press
Volume	2548
ISSN (Print)	1064-3745

Bibliographical note

Publisher Copyright:
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Keywords

Lipopolysaccharide
Membrane protein
Protein oligomerization
Protein topology
Substituted cysteine accessibility mutagenesis
Sulfhydryl labeling

ASJC Scopus subject areas

Molecular Biology
Genetics

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Cite this

Monjarás Feria, J., & Valvano, M. A. (2022). Exploring the topology of cytoplasmic membrane proteins involved in lipopolysaccharide biosynthesis by in silico and biochemical analyses. In P. Sperandeo (Ed.), Lipopolysaccharide Transport. Methods and Protocols (pp. 71-82). (Methods in molecular biology (Clifton, N.J.); Vol. 2548). Springer. https://doi.org/10.1007/978-1-0716-2581-1_5

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keywords = "Lipopolysaccharide, Membrane protein, Protein oligomerization, Protein topology, Substituted cysteine accessibility mutagenesis, Sulfhydryl labeling",

author = "{Monjar{\'a}s Feria}, Julia and Valvano, {Miguel A.}",

note = "Publisher Copyright: {\textcopyright} 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",

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Monjarás Feria, J & Valvano, MA 2022, Exploring the topology of cytoplasmic membrane proteins involved in lipopolysaccharide biosynthesis by in silico and biochemical analyses. in P Sperandeo (ed.), Lipopolysaccharide Transport. Methods and Protocols. Methods in molecular biology (Clifton, N.J.), vol. 2548, Springer, pp. 71-82. https://doi.org/10.1007/978-1-0716-2581-1_5

Exploring the topology of cytoplasmic membrane proteins involved in lipopolysaccharide biosynthesis by in silico and biochemical analyses. / Monjarás Feria, Julia ; Valvano, Miguel A.
Lipopolysaccharide Transport. Methods and Protocols. ed. / Paola Sperandeo. Springer, 2022. p. 71-82 (Methods in molecular biology (Clifton, N.J.); Vol. 2548).

Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed) › peer-review

TY - CHAP

T1 - Exploring the topology of cytoplasmic membrane proteins involved in lipopolysaccharide biosynthesis by in silico and biochemical analyses

AU - Monjarás Feria, Julia

AU - Valvano, Miguel A.

PY - 2022/9/24

Y1 - 2022/9/24

N2 - In the absence of a tri-dimensional structure, revealing the topology of a membrane protein provides relevant information to identify the number and orientation of transmembrane helices and the localization of critical amino acid residues, contributing to a better understanding of function and intermolecular associations. Topology can be predicted in silico by bioinformatic analysis or solved by biochemical methods. In this chapter, we describe a pipeline employing bioinformatic approaches for the prediction of membrane protein topology, followed by experimental validation through the substituted-cysteine accessibility method and the analysis of the protein's oligomerization state.

AB - In the absence of a tri-dimensional structure, revealing the topology of a membrane protein provides relevant information to identify the number and orientation of transmembrane helices and the localization of critical amino acid residues, contributing to a better understanding of function and intermolecular associations. Topology can be predicted in silico by bioinformatic analysis or solved by biochemical methods. In this chapter, we describe a pipeline employing bioinformatic approaches for the prediction of membrane protein topology, followed by experimental validation through the substituted-cysteine accessibility method and the analysis of the protein's oligomerization state.

KW - Lipopolysaccharide

KW - Membrane protein

KW - Protein oligomerization

KW - Protein topology

KW - Substituted cysteine accessibility mutagenesis

KW - Sulfhydryl labeling

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DO - 10.1007/978-1-0716-2581-1_5

M3 - Chapter (peer-reviewed)

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AN - SCOPUS:85138457902

SN - 9781071625804

T3 - Methods in molecular biology (Clifton, N.J.)

SP - 71

EP - 82

BT - Lipopolysaccharide Transport. Methods and Protocols

A2 - Sperandeo, Paola

PB - Springer

ER -

Exploring the topology of cytoplasmic membrane proteins involved in lipopolysaccharide biosynthesis by in silico and biochemical analyses

Abstract

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Bibliographical note

Keywords

ASJC Scopus subject areas

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