STUDY OF MECHANICAL PROPERTY OF UBIQUITIN-LIKE PROTEIN WITH STEERED MOLECULAR DYNAMICS AND ONIOM

• Main Author: ADITYA WIBAWA SAKTI (NIM: 20511018); Pembimbing 1 : Dr. Muhamad Abdulkadir Martoprawiro ; Pemb, RADEN
• Format: Theses
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/16878
• Institution: Institut Teknologi Bandung

Presently, mechanical property of a protein can be studied experimentally by using force mode of atomic force microscope (AFM). The experimental force-extension <br /> <br /> <br /> <br /> <br /> curve from AFM reveal the tensile force magnitude required to break interactions stabilized the protein when it is stretched from its ends up to its full extension. From this <br /> <br /> <br /> <br /> <br /> experiment, therefore, we can detect the presence of the flexible and rigid substructures of a protein. The former substructures require lower tensile force compare to the later one. Although AFM force extension curve can reveal mechanical property of a protein but it cannot directly pinpoint the location of the flexible and rigid substructure in the protein. Steered molecular dynamics (SMD) simulations is the simulation method devised to mimic the force mode of AFM hence by using this simulation the location of flexible and rigid substructures of a protein can readily be located. In this work, we are interested to study the mechanical property of ubiquitin-like protein. The aim of this work is to probe the existence of rigid substructures in this protein and to evaluate the interactions stabilize them. The correlation between the mechanical property of this small protein and its folding mechanism was also discussed. <br /> <br /> <br /> <br /> <br /> The initial stage of the simulation was preparing initial structures. This was accomplished by using a Monte-Carlo and replica exchange method (REM) method. From both procedures, 23 samples of initial structures have been successfully generated for SMD simulations. The simulations were performed using two different methods, namely constant velocity and force constant. The analysis for hydrogen bonds interactions on each b-strands were performed using n-layered integrated molecular orbital and molecular mechanics (ONIOM). <br /> <br /> <br /> <br /> <br /> The result of both velocity and force constant SMD simulations revealed the presence of a single rigid substructure in ubiquitin-like protein. Detail molecular analysis found that the substructure was stabilized by clustered hydrogen bonds among b-strands within the structure. Further molecular analysis to the event of hydrogen bond breaking inside the substructure accounted for the role of water molecules and K+ ions. Water molecules penetration to the rigid substructure perturbed the clustered hydrogen bonds between b-strand and eventually weakening the substructure. The presence of K+ ion reduced the number of free water molecules due to the hydration of the ions making the clustered hydrogen bonds become less perturbed, thereby increasing the stability of the substructure. In the presence of K+ ions, the amount of <br /> <br /> <br /> <br /> <br /> energy required to break the hydrogen bond in b-strand A was about 8 kJ/mol, which is smaller than those to break b-strand B (10 kJ/mol). Our calculation was close to the experimental range of hydrogen bonds in ubiquitin molecule, which is about 4-13 kJ/mol. In addition, the presence of the single substructure may account for the folding <br /> <br /> <br /> <br /> <br /> mechanism of the protein, which is agree with the nucleation-condensation model. Our simulation thus can reveal the mechanical property and its correlation with the <br /> <br /> <br /> <br /> <br /> folding mechanism of ubiquitin-like protein.