This article is available online at http://www.jlr.org Phosphoinositides (PIPs) are phosphorylated derivatives of phosphatidylinositol (PtdIns), and the metabolism of these lipids constitutes a major membrane-associated signaling system in eukaryotic cells (1)(2)(3)(4)(5). The chemical heterogeneity that distinguishes individual PIP species forms one basis for functionally compartmentalizing signaling platform identities on membrane surfaces ( 6, 7 ). Yet while the chemical heterogeneity of PIP species is simple, it translates to an enormous diversity of biological outcomes that derive from PIP signaling. In that regard, recent studies demonstrate additional layers of functional specifi cation for PIP signaling that are of such resolution that production of an individual PIP species by a specifi c PtdIns kinase yields multiple biological outcomes in the same cell ( 8 ). We now appreciate that PtdIns transfer proteins (PITPs) play critical roles in functional compartmentalization of PIP signaling reactions by channeling PtdIns to PtdIns kinases and, subsequently, to distinct sets of effector proteins ( 9-11 ). The Sec14-like PITPs are best studied in this regard, and the multiplicity of Sec14-like PITPs expressed in even simple unicellular eukaryotes highlights the high degree of functional specifi cation for these proteins ( 12,13 ).Emerging evidence that PITPs instruct the biological outcomes of PtdIns kinase activities recommends these proteins as novel targets for chemical intervention with PIP signaling pathways in cells ( 11,14 ). The advantages of targeting PITPs for this purpose are that such interventions can be imposed with selectivities superior to those possible by popular strategies that either target individual PtdIns-kinase isoforms or individual PIP species ( 15,16 ). Proof of concept is exemplifi ed by the identifi cation and validation of several classes of small molecule inhibitors (SMIs) that target Sec14, the major PITP of yeast. Abbreviations: MM-GBSA, molecular mechanics with generalized born and surface area; NPPM, nitrophenyl(4-(2-methoxyphenyl)piperazin-1-yl)methanone; PDB, Protein Data Bank; PIP, phosphoinositide; PITP, phosphatidylinositol transfer protein; PtdCho, phosphatidylcholine; PtdIns, phosphatidylinositol; SMI, small molecule inhibitor .
Understanding how membrane proteins interact with their environment is fundamental to the understanding how the fold and interact with each other. We report coarse grain molecular dynamics simulations on a series of membrane proteins in a membrane environment and describe how the lipids are perturbed by the presence of proteins. We analyze these perturbations in terms of elastic membrane deformations and local lipid protein interactions. However these two factors are insufficient to describe the variety of effects that we observe and the changes caused by membranes proteins to the structure and dynamics of their lipid environment. Other factors that change the conformation available to lipid molecules are evident and are able to modify lipid structure far from the protein surface, and thus mediate long-range interactions between membrane proteins. We suggest that these multiple modifications to lipid behaviour are responsible, at the molecular level, for the lipophobic effect we have proposed to account for our observations of membrane protein organization.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.