1P092
Theoretical Studies on Effects of Protein--protein Interactions onAzurin Complex Stability by Coarse-grained Model(Kanazawa University*, Tokyo University of Pharmacy and Life Sciences**)○ Micke Rusmerryani*, Masako Takasu**, Kazutomo Kawaguchi*,Hiroaki Saito*, and Hidemi Nagao*
micke@wriron1.s.kanazawa-u.ac.jp[Introduction]
The formation of protein--protein complexes are essential in many biologicalfunctions. These complexes can be homocomplexes and heterocomplexes. In sucha complex system, protein--protein interactions will certainly play an importantrole on the dynamics and stability of protein complex. There are several
experimental methodologies and computational methods to investigate theprotein—protein interactions. All-atom molecular dynamics simulation has beencommonly used to observe the dynamics of protein complexes in microscopic level.
Nevertheless, the all-atom simulation needs high cost and long time range.
In this study, we develop a coarse-grained model that allows the simulationof larger systems at longer time scales. The off-lattice Gō model is implemented
to represent the intramolecular interactions [1,2]. Meanwhile, we consider the 612 Lennard-Jones potential to represent the intermolecular interactions. We
chose this potential because of its simplicity [3]. We also limit our focus on thehomocomplexes of Pseudomonas Aeruginosa azurin complex, a small cupredoxin(128 amino acids) that can bind to many intracellular molecules.
In order to study the effects of protein--protein interactions to the stabilityof azurin complex, we observe the static and dynamical properties such as thedisplacement, surface area, and conformational changes. In addition, crowding
effect will also be considered in our study.
[Method]
We simulated two to four apo-azurin taken from the X-ray crystal structureof wild type azurin (PDB ID: 4AZU) [4]. In our coarse-grained model, each aminoacid is treated as a single bead located at the C position. The potential energy forthe entire system includes Gō model (as the intramolecular interactions) and
Lennard-Jones potential (as the intermolecular interactions). The beads arecoupled to Langevin thermostat to mimic the effects of surrounding solvent andcontrol a constant temperature at 300 K. We work with the friction constant, γ=0.5 (τ-1) where τ, a time unit, is of order 3 ps.
For the analyses, we monitored some physical properties calculated fromthe simulated trajectories such as root mean square displacement, surface area,and conformational changes.

[Results]
We monitored the RMSD of each chain to obtain information about how
much the given conformation differs from the native structure. From the 300 ns
simulation time, the averages of RMSD are 1.79 Å and 1.74 Å for chain A and B,respectively. We also monitored the total surface area to investigate the binding
possibility between two azurin as shown in Fig. 1. At the first 50 ns the total
surface area decreases, and then it becomes stable during the rest of simulation
time. We can also confirm the binding possibility by looking at the conformationalchanges of azurin at Fig. 1. The more detailed observations show that theminimum distance between two chains becomes larger, while the average
distance on the buried area is getting closer. Besides, the number of contacts
between these two chains also increases. More detailed explanation and different
cases will be shown in poster session.

Fig 1. Time series of normalized total surface area is calculated at the residue level. Thestructures of azurin for every 100 ns are also shown, where the red spheres represent thecontacted monomers in the binding site.

Keyword : Protein complex, Azurin, Protein--protein interactions, Coarse-grainedmodel, Lennard-Jones potential
References:[1] Gō, N. Annu. Rev. of Biophys. and Bioengineering 12: 183–210, 1983.
[2] Clementi C, Nymeyer H, Onuchic JN. J. Mol. Biol. 298: 937–953, 2000.
[3] Jones, J.E. Proc. R. Soc. A 106: 463, 1924.
[4] Nar, H. Messerschmidt A., Huber R. J. Mol. Biol. 221: 765, 1991.