Recurring sequence-structure motifs in (βα)8-barrel proteins and experimental optimization of a chimeric protein designed based on such motifs.
An interesting way of generating novel artificial proteins is to combine sequence motifs from natural proteins, mimicking the evolutionary path suggested by natural proteins comprising recurring motifs. We analyzed the βα and αβ modules of TIM barrel proteins by structure alignment-based sequence clustering. A number of preferred motifs were identified. A chimeric TIM was designed by using recurring elements as mutually compatible interfaces. The foldability of the designed TIM protein was then significantly improved by six rounds of directed evolution. The melting temperature has been improved by more than 20°C. A variety of characteristics suggested that the resulting protein is well-folded. Our analysis provided a library of peptide motifs that is potentially useful for different protein engineering studies. The protein engineering strategy of using recurring motifs as interfaces to connect partial natural proteins may be applied to other protein folds.
School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
Jichao
J
Wang
School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
Tongchuan
T
Zhang
School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
Ruicun
R
Liu
School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
Meilin
M
Song
School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
Juncheng
J
Wang
School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
Jiong
J
Hong
School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
Quan
Q
Chen
School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China; Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230027, China; Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.
Haiyan
H
Liu
D000595:Amino Acid Sequence; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D000072417:Protein Domains; D015202:Protein Engineering / Q000379:methods; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D044366:Transition Temperature
D010455:Peptides; D011506:Proteins
Chimeric protein design; Common secondary structure unit; Directed evolution