Abstract:Membrane proteins are essential for many cell processes yet are more difficult to investigate than soluble proteins. Charged residues often contribute significantly to membrane protein function. Model peptides such as GWALP23 (acetyl‐GGALW5LAL8LALALAL16ALW19LAGA‐amide) can be used to characterize the influence of specific residues on transmembrane protein domains. We have substituted R8 and R16 in GWALP23 in place of L8 and L16, equidistant from the peptide center, and incorporated specific 2H‐labeled alanine … Show more
“…At the next step of verification, we compared FMAP 2.0 predictions of TM and non-TM peptide arrangements in lipid bilayers with published experimental data. The test set 6 included synthetic pH-triggered membrane peptides with ionizable residues within hydrophobic α-helices studied by solid-state NMR, − ATR-FTIR spectroscopy, and OCD ,− at different pH values (50 data points for 32 peptides). These peptides were designed to examine the pH-dependent equilibrium between membrane-spanning TM α-helices and surface-bound non-TM states in model PC bilayers .…”
The Folding of Membrane-Associated
Peptides (FMAP) method was developed
for modeling α-helix formation by linear peptides in micelles
and lipid bilayers. FMAP 2.0 identifies locations of α-helices
in the amino acid sequence, generates their three-dimensional models
in planar bilayers or spherical micelles, and estimates their thermodynamic
stabilities and tilt angles, depending on temperature and pH. The
method was tested for 723 peptides (926 data points) experimentally
studied in different environments and for 170 single-pass transmembrane
(TM) proteins with available crystal structures. FMAP 2.0 detected
more than 95% of experimentally observed α-helices with an average
error in helix end determination of around 2, 3, 4, and 5 residues
per helix for peptides in water, micelles, bilayers, and TM proteins,
respectively. Helical and nonhelical residue states were predicted
with an accuracy from 0.86 to 0.96, and the Matthews correlation coefficient
was
from 0.64 to 0.88 depending on the environment. Experimental micelle-
and membrane-binding energies and tilt angles of peptides were reproduced
with a root-mean-square deviation of around 2 kcal/mol and 7°,
respectively. The TM and non-TM states of hydrophobic and pH-triggered
α-helical peptides in various lipid bilayers were reproduced
in more than 95% of cases. The FMAP 2.0 web server () is publicly available to explore the structural polymorphism of
antimicrobial, cell-penetrating, fusion, and other membrane-binding
peptides, which is important for understanding the mechanisms of their
biological activities.
“…At the next step of verification, we compared FMAP 2.0 predictions of TM and non-TM peptide arrangements in lipid bilayers with published experimental data. The test set 6 included synthetic pH-triggered membrane peptides with ionizable residues within hydrophobic α-helices studied by solid-state NMR, − ATR-FTIR spectroscopy, and OCD ,− at different pH values (50 data points for 32 peptides). These peptides were designed to examine the pH-dependent equilibrium between membrane-spanning TM α-helices and surface-bound non-TM states in model PC bilayers .…”
The Folding of Membrane-Associated
Peptides (FMAP) method was developed
for modeling α-helix formation by linear peptides in micelles
and lipid bilayers. FMAP 2.0 identifies locations of α-helices
in the amino acid sequence, generates their three-dimensional models
in planar bilayers or spherical micelles, and estimates their thermodynamic
stabilities and tilt angles, depending on temperature and pH. The
method was tested for 723 peptides (926 data points) experimentally
studied in different environments and for 170 single-pass transmembrane
(TM) proteins with available crystal structures. FMAP 2.0 detected
more than 95% of experimentally observed α-helices with an average
error in helix end determination of around 2, 3, 4, and 5 residues
per helix for peptides in water, micelles, bilayers, and TM proteins,
respectively. Helical and nonhelical residue states were predicted
with an accuracy from 0.86 to 0.96, and the Matthews correlation coefficient
was
from 0.64 to 0.88 depending on the environment. Experimental micelle-
and membrane-binding energies and tilt angles of peptides were reproduced
with a root-mean-square deviation of around 2 kcal/mol and 7°,
respectively. The TM and non-TM states of hydrophobic and pH-triggered
α-helical peptides in various lipid bilayers were reproduced
in more than 95% of cases. The FMAP 2.0 web server () is publicly available to explore the structural polymorphism of
antimicrobial, cell-penetrating, fusion, and other membrane-binding
peptides, which is important for understanding the mechanisms of their
biological activities.
“…Because gel-phase conditions were not investigated, the lipid phase is not a factor for the Glu titrations reported here. Acyl chain unsaturation also is unlikely to be a significant factor for the titration behavior, as related experiments have shown that chain unsaturation is relatively unimportant for the lipid interactions or orientations of helices with charged residues . By contrast, bilayer thickness is highly important for regulating the orientations of Arg-containing helices …”
Section: Discussionmentioning
confidence: 99%
“…Acyl chain unsaturation also is unlikely to be a significant factor for the titration behavior, as related experiments have shown that chain unsaturation is relatively unimportant for the lipid interactions or orientations of helices with charged residues. 26 By contrast, bilayer thickness is highly important for regulating the orientations of Arg-containing helices. 26 The results for titrating glutamic acid E4 reveal a pK a (4.8) close to the aqueous value at the DLPC membrane interface (Figure 4) and higher values of 6.3 and 11, respectively, in DMPC and DOPC.…”
The ionization properties of protein side chains in lipid-bilayer membranes will differ from the canonical values of side chains exposed to an aqueous solution. While the propensities of positively charged side chains of His, Lys, and Arg to release a proton in lipid membranes have been rather well characterized, the propensity for a negatively charged Glu side chain to receive a proton and achieve the neutral state in a bilayer membrane has been less well characterized. Indeed, the ionization of the glutamic acid side chain has been predicted to depend on its depth of burial in a lipid membrane but has been difficult to verify experimentally. To address the issue, we incorporated an interfacial Glu residue at position 4 of a distinct 23-residue transmembrane helix and used 2 H NMR to examine the helix properties as a function of pH. We observe that the helix tilt and azimuthal rotation vary little with pH, but the extent of helix unraveling near residues 3 and 4 changes as the Glu residue E4 titrates. Remarkably, the 2 H quadrupolar splitting for the side chain of alanine A3 responds to pH with an apparent pK a of 4.8 in 1,2-dilauroyl-snglycero-3-phosphocholine (DLPC) and 6.3 in 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC), but is unchanged up to pH 8.0 in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) in the presence of residue E4. With bilayers composed of alkali-stable ether-linked lipids, the side chain of A3 responds to pH with an apparent pK a of 11.0 in the ether analogue of DOPC. These results suggest that the depth dependence of Glu ionization in lipid-bilayer membranes may be steeper than previously predicted or envisioned.
“…These features will be important for understanding the plasticity of protein functional domains for which, notably, the cholesterol content also is a significant regulatory factor. 23,34,35 While induced by E16, the disorder in the R 14 E 16 GWALP23 population can be attributed to both residues E16 and R14 and their possible interactions and influence upon the core helix orientations and terminal fraying. When E16 is present without R14, the 2 H resonances are broad 20 yet the number of states remains few.…”
Section: ■ Discussionmentioning
confidence: 99%
“…Partial unwinding of the helix terminals is anticipated, even for the parent R14 helix, with the extent of fraying notably depending on the identities and ionization states of particular residues near the membrane interface. ,− While small changes in the local fraying are detected easily by the highly sensitive 2 H NMR methods, such changes involving helix terminal disorder may not necessarily be reflected in the circular dichroism spectra. , Notably, the helix disorder, whether arising from changes in end fraying or orientations of the core helix, is lipid-dependent as well as pH-dependent as the detailed behavior varies among bilayers of DLPC, DMPC, and DOPC. These features will be important for understanding the plasticity of protein functional domains for which, notably, the cholesterol content also is a significant regulatory factor. ,, …”
Membrane proteins
are vital for biological function and are complex
to study. Even in model peptide-lipid systems, the combined influence
or interaction of pairs of chemical groups still is not well understood.
Disordered proteins, whether in solution or near lipid membranes,
are an emerging paradigm for the initiation and control of biological
function. The disorder can involve molecular orientation as well as
molecular folding. This paper reports an astonishing induction of
disorder when one Glu residue is introduced into a highly stable 23-residue
transmembrane helix. The parent helix is anchored by a single Arg
residue, tilted at a well-defined angle with respect to the DOPC bilayer
normal and undergoes rapid cone precession. When Glu is introduced
two residues away from Arg, with 200° (or 160°) radial separation,
the helix properties change radically to exhibit a multiplicity of
three or more disordered states. The helix characteristics have been
monitored by deuterium (2H) NMR spectroscopy as functions
of the pH and lipid bilayer composition. The disordered multistate
behavior of the (Glu, Arg)-containing helix varies with the lipid
bilayer thickness and pH. The results highlight a fundamental induction
of protein multistate properties by a single Glu residue in a lipid
membrane environment.
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