Structural stability of proteins

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Table of contents

1 Introduction 
2 Background 
2.1 Molecular dynamics
2.1.1 Force eld
2.1.2 Leap-frog algorithm
2.2 Ubiquitin
2.3 Electric eld composition
2.4 Dipole orientation
2.5 Structural stability of proteins
2.5.1 Root Mean Square Deviation, RMSD
2.5.2 Root Mean Square Fluctuation, RMSF
2.6 Simulations
3 Method 
3.1 Electric eld implementation
3.2 Degree of orientation D
3.3 Simulation setup
4 Results 
4.1 Alignment of protein
4.1.1 Average nal degree of orientation, Df
4.1.2 Time of orientation
4.2 Unfolding and structural damage
4.2.1 RMSD
4.2.2 RMSF
4.2.3 Temperature
5 Discussion 
6 Recommendations 
7 Conclusions