9. Panel N, Sun YJ, Fuentes EJ, Simonson T
(2017) A simple PB/LIE free energy function
accurately predicts the peptide binding specificity of the Tiam1 PDZ domain. Front Mol
Biosci 4:65
10. Panel N, Villa F, Fuentes EJ, Simonson T
(2018) Accurate PDZ/peptide binding specificity with additive and polarizable free energy
simulations. Biophys J 114:1091–1102
11. Liu X, Golden LC, Lopez JA, Shepherd TR,
Yu L, Fuentes EJ (2019) Conformational
dynamics and cooperativity drive the specificty
of a protein-ligand interaction. Biophys J 116
(12):2314–2330
12. Halabi N, Rivoire O, Leibler S, Ranganathan R
(2009) Protein sectors: evolutionary units of
three-dimensional
structure.
Cell
138:774–786
13. McLaughlin RN Jr, Poelwijk FJ, Raman A,
Gosal WS, Ranganathan R (2012) The spatial
architecture of protein function and adaptation. Nature 491:138–142
14. Salinas VH, Ranganathan R (2018)
Coevolution-based inference of amino acid
interactions underlying protein function. elife
7:e34300
15. Shepherd TR, Fuentes EJ (2011) Structural
and thermodynamic analysis of PDZ-ligand
interactions. Methods Enzymol 488:81–100
16. Harris BZ, Hillier BJ, Lim WA (2001) Energetic determinants of internal motif recognition by PDZ domains. Biochemistry
40:5921–5930
17. Harris BZ, Lau FW, Fujii N, Guy RK, Lim WA
(2003) Role of electrostatic interactions in
PDZ domain ligand recognition. Biochemistry
42:2797–2805
18. Awadia S, Huq F, Arnold TR, Goicoechea SM,
Sun YJ, Hou T et al (2019) SGEF forms a
complex with scribble and Dlg1 and regulates
epithelial junctions and contractility. J Cell Biol
218:2699–2725
19. Pace CN, Vajdos F, Fee L, Grimsley G, Gray T
(1995) How to measure and predict the molar
absorption coefficient of a protein. Protein Sci
4:2411–2423
20. Grimsley GR, Pace CN (2004) Spectrophotometric determination of protein concentration.
Curr Protoc Protein Sci Chapter 3:Unit 3.1
21. Chen RF (1968) Dansyl labeled proteins:
determination of extinction coefficient and
number of bound residues with radioactive
dansyl chloride. Anal Biochem 25:412–416
148
Young Joo Sun and Ernesto J. Fuentes
(2017) A simple PB/LIE free energy function
accurately predicts the peptide binding specificity of the Tiam1 PDZ domain. Front Mol
Biosci 4:65
10. Panel N, Villa F, Fuentes EJ, Simonson T
(2018) Accurate PDZ/peptide binding specificity with additive and polarizable free energy
simulations. Biophys J 114:1091–1102
11. Liu X, Golden LC, Lopez JA, Shepherd TR,
Yu L, Fuentes EJ (2019) Conformational
dynamics and cooperativity drive the specificty
of a protein-ligand interaction. Biophys J 116
(12):2314–2330
12. Halabi N, Rivoire O, Leibler S, Ranganathan R
(2009) Protein sectors: evolutionary units of
three-dimensional
structure.
Cell
138:774–786
13. McLaughlin RN Jr, Poelwijk FJ, Raman A,
Gosal WS, Ranganathan R (2012) The spatial
architecture of protein function and adaptation. Nature 491:138–142
14. Salinas VH, Ranganathan R (2018)
Coevolution-based inference of amino acid
interactions underlying protein function. elife
7:e34300
15. Shepherd TR, Fuentes EJ (2011) Structural
and thermodynamic analysis of PDZ-ligand
interactions. Methods Enzymol 488:81–100
16. Harris BZ, Hillier BJ, Lim WA (2001) Energetic determinants of internal motif recognition by PDZ domains. Biochemistry
40:5921–5930
17. Harris BZ, Lau FW, Fujii N, Guy RK, Lim WA
(2003) Role of electrostatic interactions in
PDZ domain ligand recognition. Biochemistry
42:2797–2805
18. Awadia S, Huq F, Arnold TR, Goicoechea SM,
Sun YJ, Hou T et al (2019) SGEF forms a
complex with scribble and Dlg1 and regulates
epithelial junctions and contractility. J Cell Biol
218:2699–2725
19. Pace CN, Vajdos F, Fee L, Grimsley G, Gray T
(1995) How to measure and predict the molar
absorption coefficient of a protein. Protein Sci
4:2411–2423
20. Grimsley GR, Pace CN (2004) Spectrophotometric determination of protein concentration.
Curr Protoc Protein Sci Chapter 3:Unit 3.1
21. Chen RF (1968) Dansyl labeled proteins:
determination of extinction coefficient and
number of bound residues with radioactive
dansyl chloride. Anal Biochem 25:412–416
148
Young Joo Sun and Ernesto J. Fuentes