New energy scales to study folding and assembly energetics of cell membrane proteins

25 Sep 2017

New energy scales to study folding and assembly energetics of cell membrane proteins


By Dr. R Mahalakshmi, Intermediate Fellow 2014

Indian Institute of Science Education and Research (IISER) Bhopal

Outer membrane of a cell is made up of ordered assembly of lipid molecules that possess a hydrophilic (water-loving) head group and a hydrophobic (water-repelling) diacyl tail. Proteins in these cell membrane are one of the most important biomolecules as they act as gatekeepers of the cell and regulate various cellular processes. To be able to perform its function, the three-dimensional structure of these membrane proteins is stabilized by energetic contributions of each amino acid that make up these macromolecules. These contributions also decide the extent of intra-protein and protein-lipid interactions which ultimately regulates key biological processes on the cell membrane such as transport of nutrients, drugs etc. through ion-channels, excreting toxic waste via diffusion and other signaling processes. Deducing these energetic contributions from amino acids that stabilize membrane proteins is a fundamental problem of immense biological importance as these thermodynamic parameters decide membrane protein folding, protein stability, turnover, and regulation in all biological systems. Amino acids of these membrane proteins that lie along the membrane interface of the cell membrane are also crucial for membrane protein folding, and serve as anchors to the membrane protein’s post-folding.


Intrinsic proteins penetrate and bind tightly to the lipid bilayer, which is made up largely of phospholipids and cholesterol and which typically is between 4 and 10 nanometers (nm; 1 nm = 10−9 metre) in thickness. Extrinsic proteins are loosely bound to the hydrophilic (polar) surfaces, which face the watery medium both inside and outside the cell. Some intrinsic proteins present sugar side chains on the cell’s outer surface.


In our study using the native transmembrane protein PagP (an 8-stranded β-barrel), we have experimentally measured the per-residue transfer free energy for all the 20 amino acids present at the membrane interface. We present novel interface free energy scales for the lipid- and protein-facing membrane interfaces, which would act as the missing link in our understanding of folding and assembly energetics of membrane proteins.  

Our results demonstrate how a balance exists between concerted folding and hydrophobic collapse of the membrane protein at the interface of the membrane. These careful assessment of residues most suited for the environment of the membrane interface will now allow for the successful de novo design and development of membrane proteins as nanopore channels, membrane penetrating and antimicrobial peptides, and nanodevices for biotechnological applications.

Energetics of side chain partitioning of ß-signal residues in unassisted folding of a transmembrane ß-barrel protein. Iyer, BR, Zadafiya, P, Vetal, PV and Mahalakshmi, R. J. Biol. Chem. 2017

Banner image: RCSB Protein Data Bank Crystal Structure of Outer Membrane Enzyme PagP