Predicting weakly stable regions, oligomerization state, and protein–protein interfaces in transmembrane domains of outer membrane proteins

Abstract

Although the structures of many ␤-barrel membrane proteins are available, our knowledge of the principles that govern their energetics and oligomerization states is incomplete. Here we describe a computational method to study the transmembrane (TM) domains of ␤-barrel membrane proteins. Our method is based on a physical interaction model, a simplified conformational space for efficient enumeration, and an empirical potential function from a detailed combinatorial analysis. Using this method, we can identify weakly stable regions in the TM domain, which are found to be important structural determinants for ␤-barrel membrane proteins. By calculating the melting temperatures of the TM strands, our method can also assess the stability of ␤-barrel membrane proteins. Predictions on membrane enzyme PagP are consistent with recent experimental NMR and mutant studies. We have also discovered that out-clamps, in-plugs, and oligomerization are 3 general mechanisms for stabilizing weakly stable TM regions. In addition, we have found that extended and contiguous weakly stable regions often signal the existence of an oligomer and that strands located in the interfaces of protein-protein interactions are considerably less stable. Based on these observations, we can predict oligomerization states and can identify the interfaces of protein-protein interactions for ␤-barrel membrane proteins by using either structure or sequence information. In a set of 25 nonhomologous proteins with known structures, our method successfully predicted whether a protein forms a monomer or an oligomer with 91% accuracy; in addition, our method identified with 82% accuracy the protein-protein interaction interfaces by using sequence information only when correct strands are given.in-plug ͉ membrane protein oligomerization ͉ out-clamp ͉ protein-protein interaction ͉ weakly stable TM strand D eveloping a general understanding of how proteins behave in membranes is of fundamental importance. ␤-barrel membrane proteins, one of the 2 major structural classes of membrane proteins, have been studied extensively. Currently, structures of 70 ␤-barrel membrane proteins have been resolved, and much has been learned about their thermodynamic stability (1), folding kinetics (2-4), biogenesis (5), and biological functions (6). These membrane proteins are thought to have very regular structures, with the basic principles of their architectural organization well understood (7). An overwhelming structural feature is the existence of an extensive regular hydrogen bond network between the transmembrane (TM) ␤-strands, which is thought to confer extreme stability on the proteins (8).However, ␤-barrel membrane proteins have diverse structures and often deviate significantly from the standard barrel architecture. For example, there are often small ␣-helices and ␤-strands, called in-plugs, found inside the ␤-barrel (9). Nonbarrel-embedded helices are also found to pack against the TM ␤-strands (10). In addition, some ␤-barrel membrane proteins exist in monomeric form, whe...

Functional dynamics in the voltage-dependent anion channel

“…Thus, our results imply that dynamics in the N-terminal region are relevant for hexokinase binding. This interpretation is in line with recent findings showing destabilized regions of outer membrane proteins to be preferentially involved in proteinprotein interaction (46).…”

Structure-based Analysis of VDAC1 Protein

“…The residues that required relatively high empirical energy to insert into the lipid bilayer were termed as weakly stable residues. The empirical energy function (TmSIP) used is derived from bioinformatics analysis of ␤-barrel membrane proteins (32)(33)(34). Those strands with energy higher than the mean energy of all of the strands were regarded as weakly stable.…”

“…It was found that these weakly stable regions strongly indicate the existence of protein-protein interaction sites. Using 25 ␤-barrel membrane proteins, the oligomeric state of each protein was predicted correctly, and the protein-protein interaction interfaces were recovered at an accuracy of 78% (32).…”

“…Although the analysis presented in Ref. 32 was based on bacterial TM ␤-barrels, we assume that it is applicable to mitochondrial proteins. This is reasonable, because the outer membrane insertion recognition machineries of bacteria and mitochondrial ␤-barrel membrane proteins are interchangeable (33, 34), and they share a similar evolutionary pattern (35).…”

Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states

“…For example, it has been shown how lowaffinity cadherin dimers formed through β-strand swapping can mediate and control highly specific intercellular adhesion (10,27). In another study it was proposed that β-barrel membrane proteins can oligomerize through the weakly stable interfacial beta-strands (28), while the C-terminal helix in certain p53 proteins might be essential for stabilizing tetramers (29). Finally, the manual inspection of insertions and deletions of homologous proteins in different oligomeric states revealed that for about a quarter of them certain protein regions are responsible for enabling or disabling the oligomeric interfaces (30).…”