is no change in the organization on the nanosecond time scale, even though there is a difference in
sampling between the resolutions.
The character of the particle interior is of particular interest because it is likely to resemble that
fraction of the APol belt that is directly in contact with the TM surface of MPs in MP/A8-35
complexes. As mentioned above, the available experimental data are limited: Stuhrmann plots of the
data for DAPol do suggest the existence of a hydrophobic core, but the data collected on unlabeled
A8-35 are inconclusive, possibly because of insufficient contrast (Gohon et al. 2006). The particles
observed in the AAMD and rCG simulations have very different particle cores (Perlmutter et al. 2011).
The AAMD simulations carried out in the first step of the MD work show a core that is to a surprising
degree permeable to water. In contrast, in the rCG simulations there is practically no water in the
particle center, which forms a hydrophobic, water-excluding domain (Fig. 4.20).
In summary, SANS and MD data are consistent in describing A8-35 particles as compact,
roughly spherical, micelle-like particles, with a nearly water-free hydrophobic core and a well-defined
hydrophilic surface providing a sharp interface with the solution. In the next section, we will examine
what is known of the dynamics of these objects.
4.3.1.2.4 Dynamics of A8-35 Particles
The dynamics of A8-35 particles has been investigated by neutron scattering (Tehei et al. 2014), MD
simulations (Perlmutter et al. 2011; Tehei et al. 2014), AUC (Gohon et al. 2006), and, indirectly, FRET
(Zoonens et al. 2007). It comprises three fairly different aspects, which we will examine successively:
(i) the internal dynamics of the particles, (ii) their diffusion in solution, and (iii) their interactions.
Internal Dynamics of A8-35 Particles
In the preceding two sections, we have dealt with coherent neutron scattering, which informs on
structure. Neutrons that exchange energy with the target, and therefore experience a change of
wavelength, provide precious experimental information on the dynamics of scattering nuclei on a
picosecond to nanosecond time scale and an ångström length scale. Because the incoherent scattering
cross section of
1 H is much larger than that of
2 H or any other nucleus present in A8-35, motions of
different regions in the polymer can be discriminated using selective deuteration. The thermal
dynamics of A8-35 particles has been examined by elastic incoherent neutron scattering (EINS) and
quasi-elastic neutron scattering (QENS) using either unlabeled A8-35 (HAPol) or DAPol, in which the
hydrogen atoms in the octyl and isopropyl side chains are replaced by deuterium (Fig. 4.12) (Tehei
et al. 2014). The HAPol sample yielded information on all backbone and side-chain group motions,
whereas the DAPol sample data were dominated by the backbone. Experiments were performed at
7
C, a temperature that provides good signal-to-noise ratios in both EINS and QENS experiments, on
the time scales of ~10 ps and ~18 ps (90 and 50 μeV resolution, respectively) and ~1 ns (0.9 μeV
resolution). All experiments were performed in D 2 O in order to minimize the incoherent scattering
contribution of the solvent.
The mean square displacements (MSDs) calculated from the EINS data include vibrational as
well as conformational sampling motions in the 10 and 18 ps time scales (Fig. 4.21). At 7
C, the MSD
measured for DAPol (~0.5 Å
2 ) is half that for HAPol (~1 Å
2 ) (Fig. 4.21, right), indicating that the side
chains contribute significantly larger conformational fluctuations than the backbone groups. MSDs
have been measured on different time scales for proteins, lipids, and polysaccharides (Daniel et al.
1999; Zaccai 2000, 2011, 2013; Natali et al. 2004). HAPol values are significantly larger than protein
MSDs and similar to those estimated for lipid MSDs under similar time scale, hydration, and
temperature conditions.
4.3 Self-Association Behavior of Amphipols in Aqueous Solutions
187
sampling between the resolutions.
The character of the particle interior is of particular interest because it is likely to resemble that
fraction of the APol belt that is directly in contact with the TM surface of MPs in MP/A8-35
complexes. As mentioned above, the available experimental data are limited: Stuhrmann plots of the
data for DAPol do suggest the existence of a hydrophobic core, but the data collected on unlabeled
A8-35 are inconclusive, possibly because of insufficient contrast (Gohon et al. 2006). The particles
observed in the AAMD and rCG simulations have very different particle cores (Perlmutter et al. 2011).
The AAMD simulations carried out in the first step of the MD work show a core that is to a surprising
degree permeable to water. In contrast, in the rCG simulations there is practically no water in the
particle center, which forms a hydrophobic, water-excluding domain (Fig. 4.20).
In summary, SANS and MD data are consistent in describing A8-35 particles as compact,
roughly spherical, micelle-like particles, with a nearly water-free hydrophobic core and a well-defined
hydrophilic surface providing a sharp interface with the solution. In the next section, we will examine
what is known of the dynamics of these objects.
4.3.1.2.4 Dynamics of A8-35 Particles
The dynamics of A8-35 particles has been investigated by neutron scattering (Tehei et al. 2014), MD
simulations (Perlmutter et al. 2011; Tehei et al. 2014), AUC (Gohon et al. 2006), and, indirectly, FRET
(Zoonens et al. 2007). It comprises three fairly different aspects, which we will examine successively:
(i) the internal dynamics of the particles, (ii) their diffusion in solution, and (iii) their interactions.
Internal Dynamics of A8-35 Particles
In the preceding two sections, we have dealt with coherent neutron scattering, which informs on
structure. Neutrons that exchange energy with the target, and therefore experience a change of
wavelength, provide precious experimental information on the dynamics of scattering nuclei on a
picosecond to nanosecond time scale and an ångström length scale. Because the incoherent scattering
cross section of
1 H is much larger than that of
2 H or any other nucleus present in A8-35, motions of
different regions in the polymer can be discriminated using selective deuteration. The thermal
dynamics of A8-35 particles has been examined by elastic incoherent neutron scattering (EINS) and
quasi-elastic neutron scattering (QENS) using either unlabeled A8-35 (HAPol) or DAPol, in which the
hydrogen atoms in the octyl and isopropyl side chains are replaced by deuterium (Fig. 4.12) (Tehei
et al. 2014). The HAPol sample yielded information on all backbone and side-chain group motions,
whereas the DAPol sample data were dominated by the backbone. Experiments were performed at
7
C, a temperature that provides good signal-to-noise ratios in both EINS and QENS experiments, on
the time scales of ~10 ps and ~18 ps (90 and 50 μeV resolution, respectively) and ~1 ns (0.9 μeV
resolution). All experiments were performed in D 2 O in order to minimize the incoherent scattering
contribution of the solvent.
The mean square displacements (MSDs) calculated from the EINS data include vibrational as
well as conformational sampling motions in the 10 and 18 ps time scales (Fig. 4.21). At 7
C, the MSD
measured for DAPol (~0.5 Å
2 ) is half that for HAPol (~1 Å
2 ) (Fig. 4.21, right), indicating that the side
chains contribute significantly larger conformational fluctuations than the backbone groups. MSDs
have been measured on different time scales for proteins, lipids, and polysaccharides (Daniel et al.
1999; Zaccai 2000, 2011, 2013; Natali et al. 2004). HAPol values are significantly larger than protein
MSDs and similar to those estimated for lipid MSDs under similar time scale, hydration, and
temperature conditions.
4.3 Self-Association Behavior of Amphipols in Aqueous Solutions
187