References:
1. Chakrabartty A, Kortemme T, Baldwin RL. Helix propensities of the
amino acids measured in alanine-based peptides without helix-stabilizing
side-chain interactions. Protein Sci. 1994;3(5):843-852.
2. Heinz DW, Baase WA, Matthews BW. Folding and function of a T4
lysozyme containing 10 consecutive alanines illustrate the redundancy of
information in an amino acid sequence. Proc Natl Acad Sci U S A.1992;89(9):3751-3755.
3. Davies MN, Secker A, Freitas AA, Mendao M, Timmis J, Flower DR. On
the hierarchical classification of G protein-coupled receptors.Bioinformatics. 2007;23(23):3113-3118.
4. Isberg V, de Graaf C, Bortolato A, et al. Generic GPCR residue
numbers - aligning topology maps while minding the gaps. Trends
Pharmacol Sci. 2015;36(1):22-31.
5. Zhou Q, Yang D, Wu M, et al. Common activation mechanism of class A
GPCRs. Elife. 2019;8.
6. Cymer F, von Heijne G, White SH. Mechanisms of integral membrane
protein insertion and folding. J Mol Biol. 2015;427(5):999-1022.
7. Skach WR. Cellular mechanisms of membrane protein folding. Nat
Struct Mol Biol. 2009;16(6):606-612.
8. Popot JL, Engelman DM. Membrane protein folding and oligomerization:
the two-stage model. Biochemistry. 1990;29(17):4031-4037.
9. Yamane K, Akiyama Y, Ito K, Mizushima S. A positively charged region
is a determinant of the orientation of cytoplasmic membrane proteins in
Escherichia coli. J Biol Chem. 1990;265(34):21166-21171.
10. White SH, Wimley WC. Membrane protein folding and stability:
physical principles. Annu Rev Biophys Biomol Struct.1999;28:319-365.
11. Wimley WC, White SH. Experimentally determined hydrophobicity scale
for proteins at membrane interfaces. Nat Struct Biol.1996;3(10):842-848.
12. Pándy-Szekeres G, Munk C, Tsonkov TM, et al. GPCRdb in 2018: adding
GPCR structure models and ligands. Nucleic Acids Res.2018;46(D1):D440-D446.
13. The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.
In.
14. Fraczkiewicz R, Braun W. Exact and efficient analytical calculation
of the accessible surface areas and their gradients for macromolecules.
In. Vol 19. J Comp Chem1998:319-333.
15. Team RC. R: A language and environment for statistical computing. R
Foundation for Statistical Computing, Vienna, Austria. URL
https://www.R-project.org/. In:2020.
16. Team R. RStudio: Integrated Development Environment for R. RStudio,
PBC, Boston, MA URL http://www.rstudio.com/. In:2021.
17. Grant BJ, Rodrigues AP, ElSawy KM, McCammon JA, Caves LS. Bio3d: an
R package for the comparative analysis of protein structures.Bioinformatics. 2006;22(21):2695-2696.
18. Wickham H. stringr: Simple, Consistent Wrappers for Common String
Operations. R package version 1.4.0.
https://CRAN.R-project.org/package=stringr. In:2019.
19. Ahn D, Ham D, Chung KY. The conformational transition during G
protein-coupled receptor (GPCR) and G protein interaction. Curr
Opin Struct Biol. 2021;69:117-123.
20. Wang J, Hua T, Liu ZJ. Structural features of activated GPCR
signaling complexes. Curr Opin Struct Biol. 2020;63:82-89.
21. Congreve M, de Graaf C, Swain NA, Tate CG. Impact of GPCR Structures
on Drug Discovery. Cell. 2020;181(1):81-91.
22. Haney P, Konisky J, Koretke KK, Luthey-Schulten Z, Wolynes PG.
Structural basis for thermostability and identification of potential
active site residues for adenylate kinases from the archaeal genus
Methanococcus. Proteins. 1997;28(1):117-130.
23. Lu B, Wang G, Huang P. [A comparison of amino acid composition of
proteins from thermophiles and mesophiles]. Wei Sheng Wu Xue
Bao. 1998;38(1):20-25.
24. Ikai A. Thermostability and aliphatic index of globular proteins.J Biochem. 1980;88(6):1895-1898.
25. Maeda S, Schertler GF. Production of GPCR and GPCR complexes for
structure determination. Curr Opin Struct Biol.2013;23(3):381-392.
26. Li SC, Deber CM. A measure of helical propensity for amino acids in
membrane environments. Nat Struct Biol. 1994;1(8):558.