An alpha helix is a stretch of amino acids coiled in three-dimensional space, similar to a spring, which can serve a variety of functions in transmembrane proteins (proteins that span the membrane of a cell). For example, a protein may be anchored into the membrane by one or more alpha helices. Or, since alpha helices physically link the interior and exterior of the cell, they can stimulate the initiation of a signaling cascade inside the cell in response to an external binding event. In addition, multiple alpha helices bundled together can form a channel, enabling ions to move across the hydrophobic interior of the cell membrane where they are otherwise excluded. These are just a small sample of the large number of biological processes and pathways thought to involve alpha helices in transmembrane proteins; therefore, researchers like Dr. Roger Koeppe II and his students are studying alpha helices to fill in the gaps in our fundamental understanding of the dynamics of transmembrane proteins.
One such gap involves identifying the factors that stabilize tilted transmembrane alpha helices. Alpha helices display a variety of orientations within a membrane. Some may reside in the membrane vertical to its axis; others tilt across the membrane at different angles. In his lab in the Department of Chemistry and Biochemistry at the University of Arkansas, Fayetteville, Dr. Koeppe and his students established an experimental model and used a biophysical technique to determine the positions of amino acid residues inside tilted alpha helices in a membrane environment.
In a recent publication, the team described their efforts to design, synthesize, and purify a series of nearly-identical peptides (23 amino acid strands that only varied slightly in amino acid composition). At the ends of each peptide, the team placed deuterium (radioactive isotope) labels on two alanine amino acid residues (at positions 3 and 21). When the team exposed these peptides to lipids (fatty acids that compose the interior of a cell membrane), they formed tilted alpha helices. Using a technique called solid-state deuterium nuclear magnetic resonance (NMR), a series of spectra were gathered for each helix.
As the cover for the March 2016 issue of ChemBioChem depicts, the team detected a deviation between actual and expected orientations of the deuterium-labeled alanine residues at positions 3 and 21 – they actually appeared far from their expected orientations as part of the alpha helix (blue curve). In this way, Dr. Koeppe and his research team discovered that the first and last few amino acids at each end of the tilted alpha helix were unraveled from and no longer part of the alpha helix.
A driving force behind the formation of an alpha helix is the increased stability that results from numerous interactions between the amino acids in the helix, so unraveling these interactions at the ends of the helix may seem to disrupt stability. However, Dr. Koeppe and his team noted that unwinding the helix at both ends creates a larger surface area, enabling new interactions to occur between the amino acids in the helix and the surrounding membrane lipids – providing additional conformational stability in support of the tilt and limiting the helix’s motion. These research findings contribute to our understanding of fundamental biological processes including lipid-protein interactions, membrane protein stability, and membrane biophysics.
When asked about the broader impacts of his research, Dr. Koeppe responded:
“Notably, much of this research involved an undergraduate honors student, Armin Mortazavi. The opportunities for undergraduate students to conduct cutting-edge research alongside graduate students provide students with valuable hands on experience, exposure to new techniques, and mentoring at an early stage in their scientific careers. We have also increased the exposure of communities in Arkansas to science – establishing science cafés and statewide infrastructure projects such as a laboratory where you can explore proteins using virtual reality technology. These efforts broaden the participation of non-traditional or underrepresented groups in science.”
This work is partially funded by the Molecular Biophysics Cluster of the Division of Molecular and Cellular Biosciences, Award #MCB – 1327611.