Outer Membrane Protein Folding and Topology from a Computational Transfer Free Energy Scale

Abstract

Knowledge of the transfer free energy of amino acids from aqueous solution to a lipid bilayer is essential for understanding membrane protein folding and for predicting membrane protein structure. Here we report a computational approach that can calculate the folding free energy of the transmembrane region of outer membrane β-barrel proteins (OMPs) by combining an empirical energy function with a reduced discrete state space model. We quantitatively analyzed the transfer free energies of 20 amino acid residues at the center of the lipid bilayer of OmpLA. Our results are in excellent agreement with the experimentally derived hydrophobicity scales. We further exhaustively calculated the transfer free energies of 20 amino acids at all positions in the TM region of OmpLA. We found that the asymmetry of the gram-negative bacterial outer membrane as well as the TM residues of an OMP determine its functional fold in vivo. Our results suggest that the folding process of an OMP is driven by the lipid-facing residues in its hydrophobic core, and its NC-IN topology is determined by the differential stabilities of OMPs in the asymmetrical outer membrane. The folding free energy is further reduced by lipid A and assisted by general depth-dependent cooperativities that exist between polar and ionizable residues. Moreover, context-dependency of transfer free energies at specific positions in OmpLA predict regions important for protein function as well as structural anomalies. Our computational approach is fast, effcient and applicable to any OMP.

GeTFEP: A general transfer free energy profile of transmembrane proteins

“…Although it was previously shown that LFRs of the hydrophobic core is the main driving force for TMBs to be inserted into membrane [20], interestingly, we observed that the TFEs of hydrophobic core never reach their minimum when TMBs are fully inserted in all 52 cases, while TFEs of the whole TMBs reach their minimum at the fully inserted position (step 0). The "W" shape free energy curves of the two head group regions indicates that LFRs there act like "energetic latches" to lock TMBs in their fully…”

“…Particularly, GeTFEP-mid has a r = 0.87 correlation with MFscale, which was measured using a TMB, OmpLa, as the host system. GeTFEP-mid correlates with the computational OmpLa scale [20,21] as well with r = 0.90 (Fig. S3).…”

“…Using the methods we previously developed [20,21], we calculated the depth-dependent TFE profiles for TMBs in a non-redundant dataset of 58 TMBs. Although these TMBs are in different assembly states, have different size (strand numbers), and come from different organisms, their TFE profiles are remarkably similar (see Fig.…”

“…Experimentally measured thermodynamic parameters suggest that folding free energies ensure successful periplasm translocation [26]. Computational results identify TFE of lipid-facing residues (LFRs) of hydrophobic core regions of TMBs are the main driving force for TMBs to insert into membrane [20]. However, knowledge is still lacking about what happens thermodynamically during the membrane insertion process.…”

“…We have developed an ab initio method that conquers these obstacles by considering intra-and inter-strand interactions among residues in TMBs and calculates the TFE of a given TM residue in a TMB with 14 or less strands [20]. Our method calculates the free energy of a TMB by enumerating its conformations in a reduce state space.…”