Comparison of residue motion correlation in BPTI using vacuum and solvent molecular dynamics simulations

Dissertant

al-Ajarmah, Basim

Comitee Members

Awad, Hani
Qarain, Wail
Hamid, Mazin Y.

University

Birzeit University

Faculty

Faculty of Engineering and Technology

Department

Department of Computer Science

University Country

Palestine (West Bank)

Degree

Master

Degree Date

2005

English Abstract

Correlated motions in protein molecules play a very important role in the function of the protein.

The method of essential dynamics was used in this work to study these correlated motions in the protein Bovine Pancreatic Trypsin Inhibitor (BPTI).

Molecular dynamics trajectories were simulated using the program NAMD both in solution and in vacuum for 20 ns.

Several diagnostic tests were performed on the trajectories: RMSD, temperature factor, correlation maps, and essential dynamics (PCA) analysis as well.

The results were compared for the two environments, and inspected for their behavior versus time.

The main contribution of this work is that this is the longest reported simulation for this protein and ores new insights into how the atoms of the protein behave versus time for "long" simulations.

Main Subjects

Information Technology and Computer Science

Topics

• Molecules

No. of Pages

168

Table of Contents

• APA
• MLA
• AMA

Language

English

Data Type

Arab Theses

Record ID

BIM-303443