Dissecting the critical factors for thermodynamic stability of modular proteins using molecular modeling approach.
Repeat proteins have recently attracted much attention as alternative scaffolds to immunoglobulin antibodies due to their unique structural and biophysical features. In particular, repeat proteins show high stability against temperature and chaotic agents. Despite many studies, structural features for the stability of repeat proteins remain poorly understood. Here we present an interesting result from in silico analyses pursuing the factors which affect the stability of repeat proteins. Previously developed repebody structure based on variable lymphocytes receptors (VLRs) which consists of leucine-rich repeat (LRR) modules was used as initial structure for the present study. We constructed extra six repebody structures with varying numbers of repeat modules and those structures were used for molecular dynamics simulations. For the structures, the intramolecular interactions including backbone H-bonds, van der Waals energy, and hydrophobicity were investigated and then the radius of gyration, solvent-accessible surface area, ratio of secondary structure, and hydration free energy were also calculated to find out the relationship between the number of LRR modules and stability of the protein. Our results show that the intramolecular interactions lead to more compact structure and smaller surface area of the repebodies, which are critical for the stability of repeat proteins. The other features were also well compatible with the experimental results. Based on our observations, the repebody-5 was proposed as the best structure from the all repebodies in structure optimization process. The present study successfully demonstrated that our computer-based molecular modeling approach can significantly contribute to the experiment-based protein engineering challenge.
Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, Korea.
Yuno
Y
Lee
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejon, Korea.
Joong-jae
JJ
Lee
Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, Korea.
Songmi
S
Kim
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejon, Korea.
Sang-Chul
SC
Lee
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejon, Korea.
Jieun
J
Han
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejon, Korea.
Woosung
W
Heu
Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
Keunwan
K
Park
Division of Magnetic Resonance Research, Korea Basic Science Institute, Cheongwon, Chungbuk, Korea.
Hyun Jung
HJ
Kim
Division of Magnetic Resonance Research, Korea Basic Science Institute, Cheongwon, Chungbuk, Korea.
Hae-Kap
HK
Cheong
Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
Dongsup
D
Kim
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejon, Korea.
Hak-Sung
HS
Kim
Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, Korea.
Keun Woo
KW
Lee
D000595:Amino Acid Sequence; D002942:Circular Dichroism; D019295:Computational Biology / Q000379:methods; D004926:Escherichia coli / Q000378:metabolism; D057927:Hydrophobic and Hydrophilic Interactions; D007930:Leucine / Q000737:chemistry; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D015202:Protein Engineering / Q000379:methods; D055550:Protein Stability; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
D011506:Proteins; D012997:Solvents; D007930:Leucine