Development and Application of Novel ... - Jacobs University

2.4.2. Phytase ......................................................................................................................................... 57
2.4.3. N-acetylneuraminic acid aldolase ..................................................................................... 61
2.5. Conclusions ......................................................................................................................................... 65
2.6. References ........................................................................................................................................... 66
Chapter 3 .............................................................................................................................................................. 71
3.1. Background ......................................................................................................................................... 71
3.2. Setup of the simulated systems ................................................................................................... 75
3.3. Equilibration procedure ................................................................................................................ 76
3.4. Structural and dynamical analysis ............................................................................................. 77
3.5. Cluster analysis ................................................................................................................................. 77
3.6. Principal component analysis ...................................................................................................... 78
3.7. References ........................................................................................................................................... 79
Chapter 4 .............................................................................................................................................................. 81
4.1. Abstract ................................................................................................................................................ 81
4.1. Introduction ........................................................................................................................................ 82
4.2. Methods ................................................................................................................................................ 84
4.2.1. Starting coordinates ............................................................................................................... 84
4.2.2. Molecular dynamics simulation ......................................................................................... 84
4.2.3. FMN binding site analysis ..................................................................................................... 86
4.2.4. Multiple structural alignment of FMN domain ............................................................. 86
4.3. Results ................................................................................................................................................... 87
4.3.1. FMN domain: structural and dynamical properties ................................................... 87
4.3.2. Cluster analysis of FMN domain......................................................................................... 89
4.3.3. FMN binding site ...................................................................................................................... 90
4.3.4. Conservation profile of FMN binding site ...................................................................... 94
4.3.5. Principal component analysis of FMN domain ............................................................. 96
4.3.6. FMN cofactor: structural and dynamical properties .................................................. 99
4.3.7. Cluster analysis of FMN cofactor ..................................................................................... 102
4.3.8. Principal component analysis of FMN cofactor.......................................................... 102
4.4. Discussions and conclusions ...................................................................................................... 103
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