Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding

Abstract

As a structural class, tight turns can control molecular recognition, enzymatic activity, and nucleation of folding. They have been extensively characterized in soluble proteins but have not been characterized in outer membrane proteins (OMPs), where they also support critical functions. We clustered the 4 to 6 residue tight turns of 110 OMPs to characterize the phi/psi angles, sequence, and hydrogen bonding of these structures. We find significant differences between reports of soluble protein tight turns and OMP tight turns. Since OMP strands are less twisted than soluble strands, they favor different turn structures types. Moreover, the membrane localization of OMPs yields different sequence hallmarks for their tight turns relative to soluble protein turns. We also characterize the differences in phi/psi angles, sequence, and hydrogen bonding between OMP extracellular loops and OMP periplasmic turns. As previously noted, the extracellular loops tend to be much longer than the periplasmic turns. We find that this difference in length is due to the broader distribution of lengths of the extracellular loops not a large difference in the median length. Extracellular loops also tend to have more charged residues as predicted by the charge-out rule. Finally, in all OMP tight turns, hydrogen bonding between the side chain and backbone 2 to 4 residues away from that side chain plays an important role. These bonds preferentially use an Asp, Asn, Ser, or Thr residue in a beta or pro phi/psi conformation. We anticipate that this study will be applicable to future design and structure prediction of OMPs.

Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

“…We compiled a data set of 138 OMBBs at <85% sequence similarity, 118 of which share <50% sequence similarity (Franklin et al, 2018a; Franklin and Slusky, 2018b). To determine evolutionary relationships, we selected homologues to the structurally solved proteins from a database of 279,715 nonredundant sequences and generated hidden Markov model (HMM) profile alignments.…”

Reticulon‐like properties of a plant virus‐encoded movement protein

“…On the other hand, the C‐terminal BMB2 hydrophobic fragment confidently predicted as a helix may form kinks as a result of internal glycine residues (Fig. S7), as glycines are known to confer a high degree of local flexibility on polypeptides and are frequently found in protein regions where the polypeptide chain makes a sharp turn (Franklin & Slusky, 2018). It should be also noted that neither hydrophilic nor membrane‐embedded regions of BMB2 or TGB2 have a sequence similarity to reticulons, suggesting a reticulon‐independent evolutionary origin of viral proteins with reticulon‐like properties.…”

Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria

“…As the OMP approaches and moves through the membrane, it begins folding on a 'typical' liquid-disordered bilayer leaflet where phospholipids are free to diffuse before entering a region of low lateral mobility and increased hydration in the outer leaflet. These gradients of lateral mobility, lipid packing, hydration, and lipid headgroup polarity as an OMP inserts across the membrane normal could help to stabilize the tertiary structure of OMPs, particularly the hydrophilic loop regions (which can be >20 residues in length) ( 301 ), and drive the folding of the β-barrel domain to completion. Overall, therefore, the above studies have shown that the physical properties of the OM are highly complex and can vary dependent on the underlying lipid phase and the elastic stress, as well as the presence of OMPs and lipoproteins, and the LPR ( 175 , 214 , 302 ).…”