Rational Design of Heterodimeric Protein using Domain Swapping for Myoglobin

Lin, Ying‐Wu; Nagao, Shigeaki; Zhang, Mohan; Shomura, Yasuhito; Higuchi, Yoshiki; Hirota, Shun

doi:10.1002/ange.201409267

Cited by 9 publications

(7 citation statements)

References 73 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Many proteins with domain‐swapped structures have been reported, including class I cyts c and cyt cb 562 . AVCP is the first example of the domain swapping oligomerization of a class II cyt c .…”

Section: Discussionmentioning

confidence: 99%

“…Domain swapping has also been used to construct various protein oligomers. We have constructed an artificial Mb heterodimer, which possessed two different heme coordination sites: His/H 2 O and bis‐His coordinated hemes . A protein nanoring has been constructed by domain swapping a hinge loop‐elongated HT cyt c 552 mutant, whereas a protein nanocage has been constructed with three domain‐swapped cyt cb 562 dimers …”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Formation and carbon monoxide‐dependent dissociation of Allochromatium vinosum cytochrome c′ oligomers using domain‐swapped dimers

et al. 2017

Self Cite

View full text Add to dashboard Cite

The number of artificial protein supramolecules has been increasing; however, control of protein oligomer formation remains challenging. Cytochrome c' from Allochromatium vinosum (AVCP) is a homodimeric protein in its native form, where its protomer exhibits a four-helix bundle structure containing a covalently bound five-coordinate heme as a gas binding site. AVCP exhibits a unique reversible dimer-monomer transition according to the absence and presence of CO. Herein, domain-swapped dimeric AVCP was constructed and utilized to form a tetramer and high-order oligomers. The X-ray crystal structure of oxidized tetrameric AVCP consisted of two monomer subunits and one domain-swapped dimer subunit, which exchanged the region containing helices αA and αB between protomers. The active site structures of the domain-swapped dimer subunit and monomer subunits in the tetramer were similar to those of the monomer subunits in the native dimer. The subunit-subunit interactions at the interfaces of the domain-swapped dimer and monomer subunits in the tetramer were also similar to the subunit-subunit interaction in the native dimer. Reduced tetrameric AVCP dissociated to a domain-swapped dimer and two monomers upon CO binding. Without monomers, the domain-swapped dimers formed tetramers, hexamers, and higher-order oligomers in the absence of CO, whereas the oligomers dissociated to domain-swapped dimers in the presence of CO, demonstrating that the domain-swapped dimer maintains the CO-induced subunit dissociation behavior of native ACVP. These results suggest that protein oligomer formation may be controlled by utilizing domain swapping for a dimer-monomer transition protein.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Formation and carbon monoxide‐dependent dissociation of Allochromatium vinosum cytochrome c′ oligomers using domain‐swapped dimers

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…This mechanism is attractive for constructing de novo designed domain‐swapped dimers because it requires minimal modification at the loop, whereas interface engineering requires the design of a large number of residues to achieve di‐/oligomer formation. Thus, the protein design approach for domain swapping has focused on engineering the putative hinge loop . The engineering strategy varies from a domain insertion to a hydrophobic shortsequence insertion .…”

Section: Figurementioning

confidence: 99%

Domain‐Swapping Design by Polyproline Rod Insertion

et al. 2019

Self Cite

View full text Add to dashboard Cite

During domain swapping, proteins mutually interconvert structural elements to form a di‐/oligomer. Engineering this process by design is important for creating a higher order protein assembly with minimal modification. Herein, a simple design strategy is shown for domain‐swapping formation by loop deletion and insertion of a polyproline rod. Crystal structures revealed the formation of the domain‐swapped dimers and polyproline portion formed a polyproline II (PPII) structure. Small‐angle X‐ray scattering demonstrated that an extended orientation of domain‐swapped dimer was retained in solution. It is found that a multiple of three of inserting proline residue is favored for domain swapping because of the helical nature of PPII. The rigid nature of the polyproline rod enables precise control of the interdomain distance and orientation.

show abstract

“…The two active sites in the domainswapped dimers (homodimers) of heme proteins have the same structures and functions . To obtain a protein with two different active sites, we previously constructed a heterodimeric heme protein based on domain swapping by using two myoglobin (Mb) surface mutants with opposite charges at the protomer interfaces and mutating an amino acid at the active site of one of the two protomers . The Mb heterodimer contained two different active sites, His/H 2 O and bis‐His coordinate hemes, but the method was limited to Mb.…”

Section: Figurementioning

confidence: 99%

Rational Design of Domain‐Swapping‐Based c‐Type Cytochrome Heterodimers by Using Chimeric Proteins

et al. 2017

Self Cite

View full text Add to dashboard Cite

The design of protein oligomers with multiple active sites has been gaining interest, owing to their potential use for biomaterials, which has encouraged researchers to develop a new design method. Three-dimensional domain swapping is the unique phenomenon in which protein molecules exchange the same structural region between each other. Herein, to construct oligomeric heme proteins with different active sites by utilizing domain swapping, two c-type cytochrome-based chimeric proteins have been constructed and the domains swapped. According to X-ray crystallographic analysis, the two chimeric proteins formed a domain-swapped dimer with two His/Met coordinated hemes. By mutating the heme coordination structure of one of the two chimeric proteins, a domainswapped heterodimer with His/Met and His/H O coordinated hemes was formed. Binding of an oxygen molecule to the His/H O site of the heterodimer was confirmed by resonance Raman spectroscopy, in which the Fe-O stretching band was observed at 580 cm for the reduced/oxygenated heterodimer (at 554 cm under an O atmosphere). These results show that domain swapping is a useful method to design multiheme proteins.

show abstract

Rational Design of Heterodimeric Protein using Domain Swapping for Myoglobin

Cited by 9 publications

References 73 publications

Formation and carbon monoxide‐dependent dissociation of Allochromatium vinosum cytochrome c′ oligomers using domain‐swapped dimers

Formation and carbon monoxide‐dependent dissociation of Allochromatium vinosum cytochrome c′ oligomers using domain‐swapped dimers

Domain‐Swapping Design by Polyproline Rod Insertion

Rational Design of Domain‐Swapping‐Based c‐Type Cytochrome Heterodimers by Using Chimeric Proteins

Contact Info

Product

Resources

About