scholarly journals Lipoprotein-associated phospholipase A2: A paradigm for allosteric regulation by membranes

2022 ◽  
Vol 119 (2) ◽  
pp. e2102953118
Author(s):  
Varnavas D. Mouchlis ◽  
Daiki Hayashi ◽  
Alexis M. Vasquez ◽  
Jian Cao ◽  
J. Andrew McCammon ◽  
...  
Keyword(s):  
Conformational Change ◽  
Acyl Chain ◽  
Allosteric Regulation ◽  
High Density Lipoproteins ◽  
Oxidized Phospholipids ◽  
Exchange Mass Spectrometry ◽  
Helical Peptide ◽  
Significant Movement ◽  
Large Conformational Change ◽  
Dynamics Simulations

Lipoprotein-associated phospholipase A2 (Lp-PLA2) associates with low- and high-density lipoproteins in human plasma and specifically hydrolyzes circulating oxidized phospholipids involved in oxidative stress. The association of this enzyme with the lipoprotein’s phospholipid monolayer to access its substrate is the most crucial first step in its catalytic cycle. The current study demonstrates unequivocally that a significant movement of a major helical peptide region occurs upon membrane binding, resulting in a large conformational change upon Lp-PLA2 binding to a phospholipid surface. This allosteric regulation of an enzyme’s activity by a large membrane-like interface inducing a conformational change in the catalytic site defines a unique dimension of allosterism. The mechanism by which this enzyme associates with phospholipid interfaces to select and extract a single phospholipid substrate molecule and carry out catalysis is key to understanding its physiological functioning. A lipidomics platform was employed to determine the precise substrate specificity of human recombinant Lp-PLA2 and mutants. This study uniquely elucidates the association mechanism of this enzyme with membranes and its resulting conformational change as well as the extraction and binding of specific oxidized and short acyl-chain phospholipid substrates. Deuterium exchange mass spectrometry coupled with molecular dynamics simulations was used to define the precise specificity of the subsite for the oxidized fatty acid at the sn-2 position of the phospholipid backbone. Despite the existence of several crystal structures of this enzyme cocrystallized with inhibitors, little was understood about Lp-PLA2‘s specificity toward oxidized phospholipids.

scholarly journals SARS-CoV-2 S protein:ACE2 interaction reveals novel allosteric targets

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Palur V Raghuvamsi ◽  
Nikhil Kumar Tulsian ◽  
Firdaus Samsudin ◽  
Xinlei Qian ◽  
Kiren Purushotorman ◽  
...  
Keyword(s):  
Cleavage Site ◽  
Proteolytic Processing ◽  
Host Cells ◽  
Heptad Repeat ◽  
S Protein ◽  
Exchange Mass Spectrometry ◽  
Central Helix ◽  
Interaction Interface ◽  
Therapeutic Development ◽  
Dynamics Simulations

The Spike (S) protein is the main handle for SARS-CoV-2 to enter host cells via surface ACE2 receptors. How ACE2 binding activates proteolysis of S protein is unknown. Here, using amide hydrogen-deuterium exchange mass spectrometry and molecular dynamics simulations, we have mapped the S:ACE2 interaction interface and uncovered long-range allosteric propagation of ACE2 binding to sites necessary for host-mediated proteolysis of S protein, critical for viral host entry. Unexpectedly, ACE2 binding enhances dynamics at a distal S1/S2 cleavage site and flanking protease docking site ~27 Å away while dampening dynamics of the stalk hinge (central helix and heptad repeat) regions ~130 Å away. This highlights that the stalk and proteolysis sites of the S protein are dynamic hotspots in the pre-fusion state. Our findings provide a dynamics map of the S:ACE2 interface in solution and also offer mechanistic insights into how ACE2 binding is allosterically coupled to distal proteolytic processing sites and viral-host membrane fusion. Our findings highlight protease docking sites flanking the S1/S2 cleavage site, fusion peptide and heptad repeat 1 (HR1) as alternate allosteric hotspot targets for potential therapeutic development.

scholarly journals Membranes serve as allosteric activators of phospholipase A2, enabling it to extract, bind, and hydrolyze phospholipid substrates

2015 ◽  
Vol 112 (6) ◽  
pp. E516-E525 ◽  
Author(s):  
Varnavas D. Mouchlis ◽  
Denis Bucher ◽  
J. Andrew McCammon ◽  
Edward A. Dennis
Keyword(s):  
Extraction Process ◽  
Water Soluble ◽  
Mass Spectrometry Data ◽  
Allosteric Site ◽  
Dynamic Simulations ◽  
Lipid Interactions ◽  
Exchange Mass Spectrometry ◽  
Ideal System ◽  
Group Iva ◽  
Dynamics Simulations

Defining the molecular details and consequences of the association of water-soluble proteins with membranes is fundamental to understanding protein–lipid interactions and membrane functioning. Phospholipase A2(PLA2) enzymes, which catalyze the hydrolysis of phospholipid substrates that compose the membrane bilayers, provide the ideal system for studying protein–lipid interactions. Our study focuses on understanding the catalytic cycle of two different human PLA2s: the cytosolic Group IVA cPLA2and calcium-independent Group VIA iPLA2. Computer-aided techniques guided by deuterium exchange mass spectrometry data, were used to create structural complexes of each enzyme with a single phospholipid substrate molecule, whereas the substrate extraction process was studied using steered molecular dynamics simulations. Molecular dynamic simulations of the enzyme–substrate–membrane systems revealed important information about the mechanisms by which these enzymes associate with the membrane and then extract and bind their phospholipid substrate. Our data support the hypothesis that the membrane acts as an allosteric ligand that binds at the allosteric site of the enzyme’s interfacial surface, shifting its conformation from a closed (inactive) state in water to an open (active) state at the membrane interface.

scholarly journals Light and heat control over secondary structure and amyloid-like fiber formation in an overcrowded-alkene-modified Trp zipper

2015 ◽  
Vol 6 (12) ◽  
pp. 7311-7318 ◽  
Author(s):  
Claudia Poloni ◽  
Marc C. A. Stuart ◽  
Pieter van der Meulen ◽  
Wiktor Szymanski ◽  
Ben L. Feringa
Keyword(s):  
Secondary Structure ◽  
Conformational Change ◽  
Fiber Formation ◽  
Major Influence ◽  
Heat Control ◽  
Large Conformational Change

The use of an overcrowded alkene photoswitch to control a model β-hairpin peptide is described. The light-induced, large conformational change has major influence on the secondary structure and the aggregation of the peptide, permitting the triggered formation of amyloid-like fibrils.

scholarly journals The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1

2018 ◽  
Vol 217 (9) ◽  
pp. 3109-3126 ◽  
Author(s):  
Harald F. Hofbauer ◽  
Michael Gecht ◽  
Sabine C. Fischer ◽  
Anja Seybert ◽  
Achilleas S. Frangakis ◽  
...  
Keyword(s):  
Phosphatidic Acid ◽  
Rational Design ◽  
Acyl Chain ◽  
Membrane Biogenesis ◽  
Amphipathic Helix ◽  
New Feature ◽  
Dynamics Simulations ◽  
Membrane Recognition ◽  
And Control

A key event in cellular physiology is the decision between membrane biogenesis and fat storage. Phosphatidic acid (PA) is an important intermediate at the branch point of these pathways and is continuously monitored by the transcriptional repressor Opi1 to orchestrate lipid metabolism. In this study, we report on the mechanism of membrane recognition by Opi1 and identify an amphipathic helix (AH) for selective binding of PA over phosphatidylserine (PS). The insertion of the AH into the membrane core renders Opi1 sensitive to the lipid acyl chain composition and provides a means to adjust membrane biogenesis. By rational design of the AH, we tune the membrane-binding properties of Opi1 and control its responsiveness in vivo. Using extensive molecular dynamics simulations, we identify two PA-selective three-finger grips that tightly bind the PA phosphate headgroup while interacting less intimately with PS. This work establishes lipid headgroup selectivity as a new feature in the family of AH-containing membrane property sensors.

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