Hasup Lee, Seungtaek Sun and Ye-Yeong Park ( Group 6 ) - - PowerPoint PPT Presentation

Hasup Lee, Seungtaek Sun and Ye-Yeong Park ( Group 6 )

• Protein-Protein interaction is important in biological process

such as antigen-antibody interaction and cell-signaling pathway.

• Protein-Protein Interaction is mediated by van der waals

force, electric force, Hydrophobic interaction, hydrogen bond and other interaction.

• Sometimes, interface bound water is playing a key role in

Protein-Protein Interaction, stabilizing electric force and making new hydrogen bond.

• Therefore, Prediction of interface bound water position is

important to understand Protein-Protein Interaction.

Prediction water position using 3D-RISM Determination bound water using MD-Simulation Calculating binding free energy using MM-PBSA Comparing with results of native crystal structure

• Target proteins
• Endonuclease colicin –

Immunity protein complexes

• E9-Im9 complex (1emv)
• E9-Im2 complex (2wpt)
• E2-Im2 complex

(unsolved structure )

E9-Im9 complex E9-Im2 complex

<Overall Procedure>

<Bound water> Native interaction Predicted interaction

Native Predicted

ΔGbind

(kcal/mol)

ΔΔGbind

(kcal/mol) Complex without water

• 60.33

0.00 Complex with native water

• 87.26
• 26.93

Complex with predicted water

• 96.24
• 35.91

2.898 3.384 3.596 2.761 2.748 2.842 2.812 2.856 2.864 3.334 3.634 2.770 3.855 2.586 2.695 2.772

<Bound water> Native interaction Predicted interaction

Native Predicted

ΔGbind

(kcal/mol)

ΔΔGbind

(kcal/mol) Complex without water

• 64.05

0.00 Complex with native water

• 87.40
• 23.35

Complex with predicted water

• 85.02
• 20.97

• It is known that colicin E2 interact with Immunity protein 2.
• Colicin E2 sequence was solved but its tertiary structure is

unknown

– MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFK NFDDFRKKFWEEVSKDPDLSKQFKGSNKTNIQKGKAPFARKKDQVGGR ERFELHHDKPISQDGGVYDMNNIRVTTPKRHIDIHRGK

• Colicin E2 sequence is similar with colicin E9 sequence

(Seq ID: 80%), supposing these tertiary structure is also similar.

• Therefore we studied E2-Im2 complex interaction following this

procedure

(1) Modeling tertiary structure of colicin E2 using GalaxyTBM (2) Modeling E2-Im2 complex structure using GalaxyPPDOCK (3) Predicting interface bound water position using 3D-RISM

2.692 3.471 2.844

Predicted

<Bound water> Predicted interaction

ΔGbind

(kcal/mol)

ΔΔGbind

(kcal/mol) Complex without water

• 49.35

0.00 Complex with predicted water

• 57.58
• 8.23

• We predicted Interface bound water position using 3D-RISM.
• Mostly, predicted bound water position is similar with native

bound water position.

• Bound water molecule stabilize electric force and make

hydrogen bound, lowering binding free energy compared with no-bound water complex.

• We applied 3D-RISM program for E2-Im2 complex having
• nly sequence information, so we searched bound water,

lowering binding free energy for stabilizing electric force.

(1) Mostafa H.Ahmed et al., Bound water at Protein-Protein Interfaces: Partners, Roles and Hydrophobic Bubbles as a Conserved Motif, Plos

• ne 2011; 6, e24712.

(2) Kuhlmann U., Pommer A., Moore G., James R. and Kleanthous C., Specificity in Protein-Protein Interaction: The structural Basis for Dual Recognition in Endonuclease Colicin-Immunity Protein Complexes, J. Mol.

• Biol. 2000; 301, pp. 1163-1178.

(3) Meenan A. et al., The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction, Prot. Natl. Acad. Sci. 2010; 107, pp.10080-10085. (4) Imai T., Hiraoka R., Kovalenko A. and Hirata F., Locating Missing Water Molecules in Protein cavities by the Three-Dimensional Reference Interaction Site Model Theory of Molecular Solvation, Proteins 2007; 66, pp.804-813. (5) Sindhikara D., Yoshida N. and Hirata F., Algorithm for accurate prediction

• f explicit solvent atom distribution: application to HIV-1 protease and F-

ATP synthase, In preparation.