Congruency between Biophysical Data from Multiple Platforms and Molecular Dynamics Simulation of the Double-Super Helix Model of Nascent High-Density Lipoprotein

Abstract

The predicted structure and molecular trajectories from over 80 ns molecular dynamics simulation of the solvated double super helix (DSH) model of nascent-high density lipoprotein (HDL) was determined and compared with experimental data on reconstituted nascent HDL obtained from multiple biophysical platforms including small angle neutron scattering (SANS) with contrast variation, hydrogen-deuterium exchange tandem mass spectrometry (H/D-MS/MS), nuclear magnetic resonance spectroscopy (NMR), cross-linking tandem mass spectrometry (MS/MS), fluorescent resonance energy transfer (FRET), electron spin resonance spectroscopy (ESR), and electron microscopy. In general, biophysical constraints experimentally derived from the multiple platforms agree with the same quantities evaluated using the simulation trajectory. Notably, key structural features postulated for the recent DSH model of nascent HDL are retained during the simulation including: 1) the super helical conformation of the anti-parallel apolipoprotein A1 (apoA1) chains; 2) the lipid micellar-pseudolamellar organization; and 3) the solvent exposed Solar Flare loops, proposed sites of interaction with LCAT (lecithin cholesteryl acyltransferase). Analysis of salt bridge persistence during simulation provides insights into structural features of apoA1 that form the backbone of the lipoprotein. The combination of molecular dynamics simulation and experimental data from a broad range of biophysical platforms serves as a powerful approach to study large macromolecular assemblies such as lipoproteins. The present application to nascent HDL validates the DSH model proposed earlier, and suggests new structural details of nascent HDL. 4 To whom correspondence should be addressed: Cleveland State University, 2121 Euclid Avenue, SI 422, Cleveland, OH 44115, or Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, v.gogonea@csuohio.edu or hazens@ccf.org,. SUPPORTING INFORMATION AVAILABLE. The supporting information contains Suplemmental Figures 1 and 2 that depict small angle neutron scattering intensities (I(q)) versus the scattering vector (q), and distance distribution functions (p(r)) versus the distance between scattering centers (r), and low-resolution structures of nascent rHDL in 12% and 42% D 2 O. The Supplemental Table 1 lists experimental and calculated per residue deuterium incorporation factors, H/D exchange rate constants, and residue unfolding constants. This material is available free of charge via the Internet at http://pubs.acs.org. Additionally, the following information is available for download from http://www.lerner.ccf.org/cellbio/hazen/data/ -neutron scattering intensities for HDL samples analyzed in 12% and 42% D 2 O (text files), low resolution structures of nascent HDL (pdb files), and calculated H/D exchange deuterium incorporation factors for all residues in apoA1 dimer (Excel file). NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2011 August 31. NIH-PA Author ManuscriptNIH-PA Author Manuscri...

Assessment of the Validity of the Double Superhelix Model for Reconstituted High Density Lipoproteins

“…To confirm this for HDL, we subjected the 60-ns MD simulation of the DSH particle (26) to the same conditions that we did the starting DSH particle (11). The central cavity shown in Fig.…”

“…3A), 107 Å in the final CGMD model (Fig. 3B), and 83 Å in the 60-ns MD simulation of the DSH particle performed by Hazen and co-workers (26).…”

“…Each system was solvated with CG water (the solvent was extended to at least 20 Å on each side) and ionized and charge-neutralized to 0.15 M with CG Na ϩ and Cl Ϫ ions. The partial atom model (without hydrogens) of the DSH particle that was simulated for 60 ns by Hazen and co-workers (26) was obtained from the Hazen data web page of Lerner Research Institute, Department of Cell Biology, Cleveland Clinic. This model was converted to an all-atom model using psfgen within VMD.…”

Structure of HDL: Particle Subclasses and Molecular Components

“…The viability of this model remains under debate as molecular dynamics studies suggest that this model rapidly collapses to a disc-shaped structure (Jones et al 2010). Even simulations done by the group that proposed the model seem to indicate that the elongated structure collapses to an oblate spheroid, though they argue it remains micellar (Gogonea et al 2010). Going forward, this model must be squared with observations of disclike shapes by electron microscopy (Zhang et al 2011), EPR data (Jones et al 2010), and the quantised changes in particle size that can be readily demonstrated by reconstituting different lipid to protein ratios (Wald et al 1990).…”

Structure of Apolipoprotein A-I N Terminus on Nascent High Density Lipoproteins

“…Of these, the "double-belt" model is the most widely supported by the literature (10 -18) wherein two apoA-I molecules circumscribe a circular lipid bilayer in an antiparallel alignment. Recently, Wu et al (19,20) have proposed the double superhelix model, based on small angle neutron scattering data, wherein apoA-I assumes a left-handed double helix, spiraling around an elliptical/rod-like lipid particle. Although compelling, this model remains to be validated by other methods.…”