A team of researchers has developed an innovative method to design complicated all-α proteins, characterized by their non-uniformly arranged α-helices as seen in hemoglobin. Employing their novel approach, the team successfully created five unique all-α protein structures, each distinguished by their complicated arrangements of α-helices. This capability holds immense potential in designing functional proteins.
Proteins fold into unique three-dimensional structures based on their amino acid sequences, which then dictate their function. Although significant progress has been made in de novo protein design, the ability to design complicated all-α proteins, where α-helices are non-parallelly arranged within the three-dimensional structures, was lacking.
“Artificially designed proteins mostly show simple structures, but nature presents us with complicated ‘designs,'” said Prof. Nobuyasu Koga of Exploratory Research Center on Life and Living Systems (ExCELLS) at National Institutes of Natural Sciences (NINS). This gap drove the team to seek a method to design such complicated all-α proteins.
The team began by examining structures deposited in the Protein Data Bank (PDB) and identified 18 typical helix-loop-helix motifs. They then demonstrated that a broad spectrum of all-α protein tertiary structures, ranging from simple to complicated, can be computationally generated by combining these identified typical motifs and canonical α-helices.
“It is surprising that such a diverse set of all-α protein structures can be generated simply by combining typical or canonical components of naturally occurring proteins,” said Dr. Koya Sakuma, a former Ph.D. student in SOKENDAI (The Graduate University for Advanced Studies).
2024-01-04 07:00:03
Article from phys.org rnrn