2021
DOI: 10.1080/14789450.2021.1962302
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The phosphoinositide code is read by a plethora of protein domains

Abstract: Introduction:The proteins that decipher nucleic acid-and protein-based information are well known, however, those that read membrane-encoded information remain understudied. Here, we report 70 different human, microbial and viral protein folds that recognize phosphoinositides (PIs), comprising the readers of a vast membrane code. Areas covered: Membrane recognition is best understood for FYVE, PH and PX domains, which exemplify hundreds of PI code readers. Comparable lipid interaction mechanisms may be mediate… Show more

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Cited by 20 publications
(17 citation statements)
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References 209 publications
(168 reference statements)
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“…This progression iScience Article continues with variants of concern gaining additional membrane-binding propensity owing to favorable substitutions. The density of interactive aromatic, aliphatic, basic, and polar groups in the spike head contributes to a broad membrane docking surface (Figure 2C) that is larger than the lipid recognition sites of any eukaryotic membrane reader (Overduin and Kervin, 2021). The overall structure of this array of binding motifs is conserved across betacoronaviruses, supporting a common membrane docking mode that appears to be growing over time.…”
Section: Membrane Interactivity In Variants Of Concernmentioning
confidence: 88%
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“…This progression iScience Article continues with variants of concern gaining additional membrane-binding propensity owing to favorable substitutions. The density of interactive aromatic, aliphatic, basic, and polar groups in the spike head contributes to a broad membrane docking surface (Figure 2C) that is larger than the lipid recognition sites of any eukaryotic membrane reader (Overduin and Kervin, 2021). The overall structure of this array of binding motifs is conserved across betacoronaviruses, supporting a common membrane docking mode that appears to be growing over time.…”
Section: Membrane Interactivity In Variants Of Concernmentioning
confidence: 88%
“…This program assigns a membrane binding propensity to each residue in a structure based on the presence of features typically found in well-characterized protein structures known to bind lipid bilayers via exposed hydrophobic, aromatic and polar moieties as well as surface curvature and electrostatic properties (Kufareva et al, 2014). This approach has been previously used to discover lipid recognition surfaces on viral trafficking proteins (Bissig et al, 2013) as well as binding and regulatory features of many phosphoinositide recognition domains Overduin and Kervin, 2021). The spike structures were further analyzed with PyMol (DeLano, 2014) and the ICM Browser (Raush et al, 2009), which inputs ICB output files from the MODA program.…”
Section: Membrane Binding Propensities and Sitesmentioning
confidence: 99%
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“…Clusters of at least two residues having MODA scores above 20 in at least one structure were considered likely to participate in membrane interactions, while such clusters with residues scoring above 40 indicated a substantial likelihood. This is based on our original calibrations ( Kufareva et al, 2014 ) and on the observation that membrane recognition generally involves multivalent phospholipid binding and bilayer insertion by several proximal basic and apolar residues ( Overduin and Kervin, 2021 ). The confidence of such clusters can be increased by finding of recurrent MODA patterns from structures of the same state.…”
Section: Methodsmentioning
confidence: 99%
“…The MODA algorithm was developed in order to identify novel phospholipid bilayer recognition sites within protein structures ( Kufareva et al, 2014 ). This approach has since been used to resolve such binding surfaces on hundreds of eukaryotic membrane readers ( Overduin and Kervin, 2021 ), prions ( Overduin et al, 2021 ) and viral ( Bissig et al, 2013 ) and bacterial proteins ( Bryant et al, 2020a ) but has not yet been applied to coronavirus proteins to our knowledge.…”
Section: Introductionmentioning
confidence: 99%