Different 3D domain-swapped oligomeric cyanovirin-N structures suggest trapped folding intermediates

Abstract

Although it has long been established that the amino acid sequence encodes the fold of a protein, how individual proteins arrive at their final conformation is still difficult to predict, especially for oligomeric structures. Here, we present a comprehensive characterization of oligomeric species of cyanovirin-N that all are formed by a polypeptide chain with the identical amino acid sequence. Structures of the oligomers were determined by X-ray crystallography, and each one exhibits 3D domain swapping. One unique 3D domainswapped structure is observed for the trimer, while for both dimer and tetramer, two different 3D domain-swapped structures were obtained. In addition to the previously identified hinge-loop region of the 3D domain-swapped dimer, which resides between strands β5 and β6 in the middle of the polypeptide sequence, another hinge-loop region is observed between strands β7 and β8 in the structures. Plasticity in these two regions allows for variability in dihedral angles and concomitant differences in chain conformation that results in the differently 3D domain-swapped multimers. Based on all of the different structures, we propose possible folding pathways for this protein. Altogether, our results illuminate the amazing ability of cyanovirin-N to proceed down different folding paths and provide general insights into oligomer formation via 3D domain swapping.CV-N | NMR spectroscopy | protein folding | X-ray structures

Cyanobacterial lectins characteristics and their role as antiviral agents

“…Crystal structure analysis of two different dimeric structures of P51GCV-N reveals difference in their overall domain orientation along with variation in relative positioning of the two pseudomonomers [110]. The trimer structure of P51G CV-N variant contains both monomer and domain-swapped dimer folds.…”

“…Koharudin et al [110] depicted structural data for five different species of P51GCV-N variant (monomer, dimmers, trimer and tetramer) and their different ways of 3D domain swapping. Crystal structure analysis of two different dimeric structures of P51GCV-N reveals difference in their overall domain orientation along with variation in relative positioning of the two pseudomonomers [110].…”

“…In third chain, double 3D domain swapping occurs along with both these hinges. Thus, three different pseudomonomers are formed in the trimer owing to three different chain swaps [110]. The tetramer structure of P51G CV-N variant is composed of four chains which swap structural elements in two varied ways [110].…”

“…Thus, three different pseudomonomers are formed in the trimer owing to three different chain swaps [110]. The tetramer structure of P51G CV-N variant is composed of four chains which swap structural elements in two varied ways [110]. In this, two of the chains use hinge between two SRs and undergo single swapping event whereas, other two chains have hinges at junction between two SRs and at turn (between strands ␤7 and ␤8) and undergo double swapping [110].…”

A review on protein oligomerization process

“…101 RNase A was thought to be unique in its capability to swap more than one domain, but BS-RNase, 102 cyanovirin-N and the mammalian DUF59-Fam96a protein were also found to display a similar multiple DS behavior. 103,104 In particular, the natively N-swapped dimeric BS-RNase, known to be able to self-associate since 1969, 105 was found to form both N-and C-swapped tetramers and higher DP oligomers. 102,106 In addition, it has recently been reported that a monomerized BSRNase 107 can be induced to form a C-swapped dimer similar to the one of RNase A.…”