The two sides of a lipid-protein story

Abstract

Protein-membrane interactions play essential roles in a variety of cell functions such as signaling, membrane trafficking, and transport. Membrane-recruited cytosolic proteins that interact transiently and interfacially with lipid bilayers perform several of those functions. Experimental techniques capable of probing changes on the structural dynamics of this weak association are surprisingly limited. Among such techniques, electron spin resonance (ESR) has the enormous advantage of providing valuable local information from both membrane and protein perspectives by using intrinsic paramagnetic probes in metalloproteins or by attaching nitroxide spin labels to proteins and lipids. In this review, we discuss the power of ESR to unravel relevant structural and functional details of lipid-peripheral membrane protein interactions with special emphasis on local changes of specific regions of the protein and/or the lipids. First, we show how ESR can be used to investigate the direct interaction between a protein and a particular lipid, illustrating the case of lipid binding into a hydrophobic pocket of chlorocatechol 1,2-dioxygenase, a non-heme iron enzyme responsible for catabolism of aromatic compounds that are industrially released in the environment. In the second case, we show the effects of GPI-anchored tissue-nonspecific alkaline phosphatase, a protein that plays a crucial role in skeletal mineralization, and on the ordering and dynamics of lipid acyl chains. Then, switching to the protein perspective, we analyze the interaction with model membranes of the brain fatty acid binding protein, the major actor in the reversible binding and transport of hydrophobic ligands such as long-chain, saturated, or unsaturated fatty acids. Finally, we conclude by discussing how both lipid and protein views can be associated to address a common question regarding the molecular mechanism by which dihydroorotate dehydrogenase, an essential enzyme for the de novo synthesis of pyrimidine nucleotides, and how it fishes out membrane-embedded quinones to perform its function.

SARS-CoV fusion peptides induce membrane surface ordering and curvature

“…S1), which monitor different regions of the lipid bilayers. DPPTC reports on the lipid/water interface, whereas 5-PCSL and 16-PCSL monitor the hydrophobic core of the membranes at different depths of penetration 33,[42][43][44] .…”

“…The more fusogenic SARS FP consistently increased the ordering of 5-PCSL and 16-PCSL more than SARS IFP . Particularly, since the 16-PCSL probe is more sensitive to molecular motions than DPPTC and 5-PCSL 43,48 , the structural dynamics of the gel-like and fluid-like lipid states could be resolved and characterized (Table S3). Although the peptides shifted the equilibrium between the two states towards the fluid-like one (the population of the fluid-like component increased from 10 to ~25%), the packing (S 0 ) of the center of the bilayer was also increased for both lipid states.…”

Lignocellulose binding of a Cel5A-RtCBM11 chimera with enhanced β-glucanase activity monitored by electron paramagnetic resonance

“…The use of EPR is well suited to study the binding of spin-labeled proteins to lignocellulosic biomass, and in contrast to Nuclear Magnetic Resonance (NMR) and X-ray crystallography, the technique can be applied under conditions found in natura [ 19 ] or under high solids loading. In SDSL, an extrinsic spin probe is covalently attached to the thiol side chain in a native or site-directed mutated Cys residue [ 16 ], and analyses of the EPR spectrum can provide information with respect to protein chain dynamics, solvent accessibility, local polarity, and protein interactions under the chosen experimental conditions [ 14 , 20 – 24 ]. Furthermore, when multiple probes are introduced into a protein, EPR-SDSL can be used to measure distances between the spin probes within the polypeptide chain [ 25 , 26 ].…”

A review and summary of the contents of biophysical reviews volume 8, 2016

“…It is a scholarly work that shines a light on the theory and practice of studying tyrosines rather than the more common spectroscopic investigations that examine tryptophans. Basso et al (2016): This paper reviewed the use of Electron Spin Resonance (ESR) for studying protein-membrane interactions. First the authors discussed how ESR can be used to study lipid as it binds to a hydrophobic pocket on diogenase enzyme.…”