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Conserved lipid-binding sites in membrane proteins: a focus on cytochrome c oxidase.

ABSTRACT: Specific interactions between lipids and membrane proteins have been observed in recent high-resolution crystal structures of membrane proteins. A number of cytochrome oxidase structures were analyzed, along with many amino acid sequences of membrane-spanning regions aligned according to their location in the membrane. The results reveal conservation of lipid-binding sites and of the residues that form them. These studies imply that bound lipids have important roles that are crucial to the assembly, structure, or activity of the protein. Evidence for some of these roles in subunit interactions, membrane insertion, and protein-protein complex formation is reviewed.

SUBMITTER: Qin L

PROVIDER: S-EPMC2395296 | biostudies-literature | 2007 Aug

REPOSITORIES: biostudies-literature

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Conserved lipid-binding sites in membrane proteins: a focus on cytochrome c oxidase.

Qin Ling L Sharpe Martyn A MA Garavito R Michael RM Ferguson-Miller Shelagh S

Current opinion in structural biology 20070823 4

Specific interactions between lipids and membrane proteins have been observed in recent high-resolution crystal structures of membrane proteins. A number of cytochrome oxidase structures were analyzed, along with many amino acid sequences of membrane-spanning regions aligned according to their location in the membrane. The results reveal conservation of lipid-binding sites and of the residues that form them. These studies imply that bound lipids have important roles that are crucial to the assem ...[more]

PMID: 17719219

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Project description:BackgroundMany integral membrane proteins, like their non-membrane counterparts, form either transient or permanent multi-subunit complexes in order to carry out their biochemical function. Computational methods that provide structural details of these interactions are needed since, despite their importance, relatively few structures of membrane protein complexes are available.ResultsWe present a method for predicting which residues are in protein-protein binding sites within the transmembrane regions of membrane proteins. The method uses a Random Forest classifier trained on residue type distributions and evolutionary conservation for individual surface residues, followed by spatial averaging of the residue scores. The prediction accuracy achieved for membrane proteins is comparable to that for non-membrane proteins. Also, like previous results for non-membrane proteins, the accuracy is significantly higher for residues distant from the binding site boundary. Furthermore, a predictor trained on non-membrane proteins was found to yield poor accuracy on membrane proteins, as expected from the different distribution of surface residue types between the two classes of proteins. Thus, although the same procedure can be used to predict binding sites in membrane and non-membrane proteins, separate predictors trained on each class of proteins are required. Finally, the contribution of each residue property to the overall prediction accuracy is analyzed and prediction examples are discussed.ConclusionGiven a membrane protein structure and a multiple alignment of related sequences, the presented method gives a prioritized list of which surface residues participate in intramembrane protein-protein interactions. The method has potential applications in guiding the experimental verification of membrane protein interactions, structure-based drug discovery, and also in constraining the search space for computational methods, such as protein docking or threading, that predict membrane protein complex structures.

Dataset Information

Conserved lipid-binding sites in membrane proteins: a focus on cytochrome c oxidase.

Publications

Conserved lipid-binding sites in membrane proteins: a focus on cytochrome c oxidase.

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