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Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data

BACKGROUND: Protein-lipid interactions play essential roles in the conformational stability and biological functions of membrane proteins. However, few of the previous computational studies have taken into account the atomic details of protein-lipid interactions explicitly. RESULTS: To gain an insig...

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Autores principales: Morita, Mizuki, Katta, AVSK Mohan, Ahmad, Shandar, Mori, Takaharu, Sugita, Yuji, Mizuguchi, Kenji
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3747235/
https://www.ncbi.nlm.nih.gov/pubmed/22168953
http://dx.doi.org/10.1186/2046-1682-4-21
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author Morita, Mizuki
Katta, AVSK Mohan
Ahmad, Shandar
Mori, Takaharu
Sugita, Yuji
Mizuguchi, Kenji
author_facet Morita, Mizuki
Katta, AVSK Mohan
Ahmad, Shandar
Mori, Takaharu
Sugita, Yuji
Mizuguchi, Kenji
author_sort Morita, Mizuki
collection PubMed
description BACKGROUND: Protein-lipid interactions play essential roles in the conformational stability and biological functions of membrane proteins. However, few of the previous computational studies have taken into account the atomic details of protein-lipid interactions explicitly. RESULTS: To gain an insight into the molecular mechanisms of the recognition of lipid molecules by membrane proteins, we investigated amino acid propensities in membrane proteins for interacting with the head and tail groups of lipid molecules. We observed a common pattern of lipid tail-amino acid interactions in two different data sources, crystal structures and molecular dynamics simulations. These interactions are largely explained by general lipophilicity, whereas the preferences for lipid head groups vary among individual proteins. We also found that membrane and water-soluble proteins utilize essentially an identical set of amino acids for interacting with lipid head and tail groups. CONCLUSIONS: We showed that the lipophilicity of amino acid residues determines the amino acid preferences for lipid tail groups in both membrane and water-soluble proteins, suggesting that tightly-bound lipid molecules and lipids in the annular shell interact with membrane proteins in a similar manner. In contrast, interactions between lipid head groups and amino acids showed a more variable pattern, apparently constrained by each protein's specific molecular function.
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spelling pubmed-37472352013-08-20 Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data Morita, Mizuki Katta, AVSK Mohan Ahmad, Shandar Mori, Takaharu Sugita, Yuji Mizuguchi, Kenji BMC Biophys Research Article BACKGROUND: Protein-lipid interactions play essential roles in the conformational stability and biological functions of membrane proteins. However, few of the previous computational studies have taken into account the atomic details of protein-lipid interactions explicitly. RESULTS: To gain an insight into the molecular mechanisms of the recognition of lipid molecules by membrane proteins, we investigated amino acid propensities in membrane proteins for interacting with the head and tail groups of lipid molecules. We observed a common pattern of lipid tail-amino acid interactions in two different data sources, crystal structures and molecular dynamics simulations. These interactions are largely explained by general lipophilicity, whereas the preferences for lipid head groups vary among individual proteins. We also found that membrane and water-soluble proteins utilize essentially an identical set of amino acids for interacting with lipid head and tail groups. CONCLUSIONS: We showed that the lipophilicity of amino acid residues determines the amino acid preferences for lipid tail groups in both membrane and water-soluble proteins, suggesting that tightly-bound lipid molecules and lipids in the annular shell interact with membrane proteins in a similar manner. In contrast, interactions between lipid head groups and amino acids showed a more variable pattern, apparently constrained by each protein's specific molecular function. BioMed Central 2011-12-14 /pmc/articles/PMC3747235/ /pubmed/22168953 http://dx.doi.org/10.1186/2046-1682-4-21 Text en Copyright ©2011 Morita et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Morita, Mizuki
Katta, AVSK Mohan
Ahmad, Shandar
Mori, Takaharu
Sugita, Yuji
Mizuguchi, Kenji
Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data
title Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data
title_full Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data
title_fullStr Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data
title_full_unstemmed Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data
title_short Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data
title_sort lipid recognition propensities of amino acids in membrane proteins from atomic resolution data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3747235/
https://www.ncbi.nlm.nih.gov/pubmed/22168953
http://dx.doi.org/10.1186/2046-1682-4-21
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