ArticleTheoretical biology & medical modelling2006
Protein-lipid interactions: correlation of a predictive algorithm for lipid-binding sites with three-dimensional structural data.
Article in Theoretical biology & medical modelling, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design.Bioinformatics (Oxford, England) · 2022Article
- Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning.Briefings in bioinformatics · 2022Article
- Vinculin in cell-cell and cell-matrix adhesions.Cellular and molecular life sciences : CMLS · 2017Review
- Multiple membrane interactions and versatile vesicle deformations elicited by melittin.Toxins · 2013Article
- New user-friendly approach to obtain an Eisenberg plot and its use as a practical tool in protein sequence analysis.International journal of molecular sciences · 2011Article
- Prediction of lipid-binding sites based on support vector machine and position specific scoring matrix.The protein journal · 2010Article
- An experimentally based computer search identifies unstructured membrane-binding sites in proteins: application to class I myosins, PAKS, and CARMIL.The Journal of biological chemistry · 2010Article
- Neutrophil recruitment under shear flow: it's all about endothelial cell rings and gaps.Microcirculation (New York, N.Y. : 1994) · 2009Review
- Acanthamoeba myosin IC colocalizes with phosphatidylinositol 4,5-bisphosphate at the plasma membrane due to the high concentration of negative charge.The Journal of biological chemistry · 2008Article
- MAPAS: a tool for predicting membrane-contacting protein surfaces.Nature methods · 2008Article
- CapZ-lipid membrane interactions: a computer analysis.Theoretical biology & medical modelling · 2006Article
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3 authors.
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Abstract
backgroundOver the past decade our laboratory has focused on understanding how soluble cytoskeleton-associated proteins interact with membranes and other lipid aggregates. Many protein domains mediating specific cell membrane interactions appear by fluorescence microscopy and other precision techniques to be partially inserted into the lipid bilayer. It is unclear whether these protein-lipid-interactions are dependent on shared protein motifs or unique regional physiochemistry, or are due to more global characteristics of the protein.
resultsWe have developed a novel computational program that predicts a protein's lipid-binding site(s) from primary sequence data. Hydrophobic labeling, Fourier transform infrared spectroscopy (FTIR), film balance, T-jump, CD spectroscopy and calorimetry experiments confirm that the interfaces predicted for several key cytoskeletal proteins (alpha-actinin, Arp2, CapZ, talin and vinculin) partially insert into lipid aggregates. The validity of these predictions is supported by an analysis of the available three-dimensional structural data. The lipid interfaces predicted by our algorithm generally contain energetically favorable secondary structures (e.g., an amphipathic alpha-helix flanked by a flexible hinge or loop region), are solvent-exposed in the intact protein, and possess favorable local or global electrostatic properties.
conclusionAt present, there are few reliable methods to determine the region of a protein that mediates biologically important interactions with lipids or lipid aggregates. Our matrix-based algorithm predicts lipid interaction sites that are consistent with the available biochemical and structural data. To determine whether these sites are indeed correctly identified, and whether use of the algorithm can be safely extended to other classes of proteins, will require further mapping of these sites, including genetic manipulation and/or targeted crystallography.
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