Ionic Hydrogen Bonds and Lipid Packing Defects Determine the Binding Orientation and Insertion Depth of RecA on Multicomponent Lipid Bilayers.
We describe a computational and experimental approach for probing the binding properties of the RecA protein at the surface of anionic membranes. Fluorescence measurements indicate that RecA behaves differently when bound to phosphatidylglycerol (PG)- and cardiolipin (CL)-containing liposomes. We use a multistage computational protocol that integrates an implicit membrane/solvent model, the highly mobile mimetic membrane model, and the full atomistic membrane model to study how different anionic lipids perturb RecA binding to the membrane. With anionic lipids studied here, the binding interface involves three key regions: the N-terminal helix, the DNA binding loop L2, and the M-M7 region. The nature of binding involves both electrostatic interactions between cationic protein residues and lipid polar/charged groups and insertion of hydrophobic residues. The L2 loop contributes more to membrane insertion than the N-terminal helix. More subtle aspects of RecA-membrane interaction are influenced by specific properties of anionic lipids. Ionic hydrogen bonds between the carboxylate group in phosphatidylserine and several lysine residues in the C-terminal region of RecA stabilize the parallel (∥) binding orientation, which is not locally stable on PG- and CL-containing membranes despite similarity in the overall charge density. Lipid packing defects, which are more prevalent in the presence of conical lipids, are observed to enhance the insertion depth of hydrophobic motifs. The computational finding that RecA binds in a similar orientation to PG- and CL-containing membranes is consistent with the fact that PG alone is sufficient to induce RecA polar localization, although CL might be more effective because of its tighter binding to RecA. The different fluorescence behaviors of RecA upon binding to PG- and CL-containing liposomes is likely due to the different structures and flexibility of the C-terminal region of RecA when it binds to different anionic phospholipids.
Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.
Leili
L
Zhang
Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States.
Manohary
M
Rajendram
Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.|Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States.|Department of Biomedical Engineering, University of Wisconsin-Madison , 1415 Engineering Drive, Madison, Wisconsin 53706, United States.
Douglas B
DB
Weibel
Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.
Arun
A
Yethiraj
Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.
Qiang
Q
Cui
D003198:Computer Simulation; D004075:Diglycerides / Q000737:chemistry; D004926:Escherichia coli; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008051:Lipid Bilayers / Q000737:chemistry*; D008958:Models, Molecular; D010713:Phosphatidylcholines / Q000737:chemistry; D010715:Phosphatidylglycerols / Q000737:chemistry; D011485:Protein Binding; D011938:Rec A Recombinases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity
D004075:Diglycerides; D008051:Lipid Bilayers; D010713:Phosphatidylcholines; D010715:Phosphatidylglycerols; D012997:Solvents; C051388:1,2-dioleoyl-sn-glycero-3-phosphoglycerol; D011938:Rec A Recombinases; C017251:1,2-oleoylphosphatidylcholine; C013965:diolein