tumble more rapidly than OmpX/A8-35 ones (Fernández et al. 2001; Catoire et al. 2010b). Several
causes may contribute to this apparent contradiction. It may be that some factors that contribute to
slowing down the tumbling of MP/APol complexes have not yet been identified. Such was the case, in
early experiments (Zoonens et al. 2005), of the presence of traces of Ca
2+ , which, presumably, bridged
some of the complexes – a problem later identified and eliminated by adding EDTA to NMR buffers
(Catoire et al. 2010b). A higher complement of bound water, for instance, could contribute to slowing
down the tumbling of MP/A8-35 complexes. Factors that affect the resolution of NMR data will be
discussed in Chap. 10. Note that it cannot be excluded either that the MD model of OmpX/diC 6 PC
complexes may just have too much diC 6 PC bound.
MD simulations have been exploited to examine the effects of transferring OmpX from a lipid
bilayer to a detergent or APol environment on its dynamics (Perlmutter et al. 2014). This issue will be
discussed in § 5.6, after we have considered the effects of APols on the stability and functionality of
APol-trapped MPs.
5.4
Functionality of Amphipol-Trapped Membrane Proteins
Functional studies have been carried out with close to 40 different APol-trapped MPs. These data are
compiled in Table 5.1, where the cells summarizing the evidence for the preservation of the native state
(last-but-one column) are salmon-colored when functional evidence is available. This evidence is
usually in the form of either enzymatic measurements or ligand-binding ones. Even though there are
some exceptions, which will be discussed below, the overwhelming evidence is that most proteins
remain functional after transfer to APols and that the binding of small ligands, toxins, and antibodies is
Fig. 5.24 Relative solvent protection of the backbone of OmpX in A8-35, diC 6 PC, or a bilayer of
dioleoylphosphatidylcholine (DOPC), as deduced from MD simulations. Each solid line represents an
independent simulation. The experimental accessibility of amide protons in OmpX/A8-35 complexes,
based on the rate of
1
H/
2
H exchange (Catoire et al. 2010b), is shown as blue diamonds (From Perlmutter
et al. 2014).
286
5 Formation and Properties of Membrane Protein/Amphipol Complexes
causes may contribute to this apparent contradiction. It may be that some factors that contribute to
slowing down the tumbling of MP/APol complexes have not yet been identified. Such was the case, in
early experiments (Zoonens et al. 2005), of the presence of traces of Ca
2+ , which, presumably, bridged
some of the complexes – a problem later identified and eliminated by adding EDTA to NMR buffers
(Catoire et al. 2010b). A higher complement of bound water, for instance, could contribute to slowing
down the tumbling of MP/A8-35 complexes. Factors that affect the resolution of NMR data will be
discussed in Chap. 10. Note that it cannot be excluded either that the MD model of OmpX/diC 6 PC
complexes may just have too much diC 6 PC bound.
MD simulations have been exploited to examine the effects of transferring OmpX from a lipid
bilayer to a detergent or APol environment on its dynamics (Perlmutter et al. 2014). This issue will be
discussed in § 5.6, after we have considered the effects of APols on the stability and functionality of
APol-trapped MPs.
5.4
Functionality of Amphipol-Trapped Membrane Proteins
Functional studies have been carried out with close to 40 different APol-trapped MPs. These data are
compiled in Table 5.1, where the cells summarizing the evidence for the preservation of the native state
(last-but-one column) are salmon-colored when functional evidence is available. This evidence is
usually in the form of either enzymatic measurements or ligand-binding ones. Even though there are
some exceptions, which will be discussed below, the overwhelming evidence is that most proteins
remain functional after transfer to APols and that the binding of small ligands, toxins, and antibodies is
Fig. 5.24 Relative solvent protection of the backbone of OmpX in A8-35, diC 6 PC, or a bilayer of
dioleoylphosphatidylcholine (DOPC), as deduced from MD simulations. Each solid line represents an
independent simulation. The experimental accessibility of amide protons in OmpX/A8-35 complexes,
based on the rate of
1
H/
2
H exchange (Catoire et al. 2010b), is shown as blue diamonds (From Perlmutter
et al. 2014).
286
5 Formation and Properties of Membrane Protein/Amphipol Complexes