Title Page
ABSTRACT
Contents
Chapter 1. Introduction 12
Chapter 2. Site-Specific Backbone and Side-Chain Contributions to Thermodynamic Stabilizing Forces 17
2.1. Methods 18
2.1.1. Folded-State Simulations. 18
2.1.2. Unfolded-State Simulations. 18
2.1.3. Structural Analysis. 19
2.1.4. Thermodynamic Analysis. 20
2.1.5. Site-directed Thermodynamic Analysis 20
2.1.6. Error Analysis 21
2.2. Results and Discussions 22
2.2.1. Structural Differences between the Folded and Unfolded States of WW Domain 22
2.2.2. Folding Free Energy of Pin WW. 26
2.2.3. Site-specific Stabilizing Forces 29
Chapter 3. Comparing the Influence of Explicit and Implicit Solvation Models on Site-Specific Thermodynamic Stability of Two Model Proteins 36
3.1. Methods 37
3.1.1. GBSA Solvent MD Simulation of Folded and Unfolded States 37
3.1.2. Explicit Water MD Simulation of Folded and Unfolded States 38
3.1.3. Structural Analyses 39
3.1.4. Site-Specific Thermodynamic Analyses 40
3.2. Results and Discussions 41
3.2.1. Secondary Structure Preference 43
3.2.2. Hydrophobic Cluster Preference 47
3.2.3. Salt Bridge Preference 51
3.2.4. Generalization to Other Proteins 56
Chapter 4. Conclusion 59
SUPPLEMENTARY INFORMATION 61
BIBLIOGRAPHY 84
국문초록 91
Table 2.1. Native structural characteristics in the folded and unfolded states of Pin WW 25
Table 2.2. Non-native structural characteristics in the folded and unfolded states of Pin WW 26
Table 2.3. Tabulated data of folding free energy 28
Table 3.1. Tabulated Data of Thermodynamic Values for WW domain and HP-36 43
Table S2.1. Native contacts fraction in the folded and unfolded states of WW domain and HP-36 64
Table S2.2. Per-residue structural data of Pin WW upon folding 65
Table S2.3. Tabulated thermodynamic quantities summary table obtained for both folded and unfolded state trajectories 66
Table S2.4. Statistical analyses of the distribution function of effective energy 67
Table S2.5. Tabulated effective free energy by individual amino acid residue of Pin WW separated by the backbone atoms 68
Table S2.6. Tabulated effective free energy by individual amino acid residue of Pin WW separated by the side-chain atoms 69
Table S3.1. Native contacts fraction in the folded and unfolded states of WW domain and HP-36 75
Table S3.2. Native structural characteristics in the folded and unfolded states of WW domain and HP-36 76
Table S3.3. Non-native structural characteristics in the folded and unfolded states of Pin WW and HP-36 77
Table S3.4. Per-residue structural analysis data of Pin WW upon folding 78
Table S3.5. Per-residue structural analysis data of HP-36 upon folding 79
Table S3.6. Tabulated effective free energy by individual amino acid residue of WW domain separated by the backbone atoms 80
Table S3.7. Tabulated effective free energy by individual amino acid residue of Pin WW separated by the side-chain atoms. 81
Table S3.8. Tabulated effective free energy by individual amino acid residue of HP-36 separated by the backbone atoms 82
Table S3.9. Tabulated effective free energy by individual amino acid residue of HP-36 separated by the side-chain atoms. 83
Figure 2.1. Pin WW structure and sequence. The structural cartoon of Pin WW is colored with respect to the corresponding amino acid residue sequence. The... 17
Figure 2.2. Structural characteristics of Pin WW per amino acid residue averaged from the folded and unfolded states MD simulations at 300 K. (A) Root-mean-... 23
Figure 2.3. The MD simulation snapshot for the folded and the unfolded trajectories. Representative folded-state conformations selected using a k-means clustering... 24
Figure 2.4. The distribution of the effective free energy. (A) Probability distribution function W(f) of the effective energy f as a function of its deviation from the mean ƒ...[이미지참조] 27
Figure 2.5. Thermodynamic and structural analyses for each backbone and side-chain of the WW domain. (A) The folding effective energy contributions △ƒ=ƒ... 30
Figure 2.6. Thermodynamic and structural analyses for each backbone and sidechain of the HP-36. The folding effective energy contributions △ƒ=ƒ (folded) - ƒ... 33
Figure 3.1. Thermodynamic comparison of HP-36 and WW domain proteins in explicit and implicit solvents, regarding folding stability contributions from... 36
Figure 3.2. Comparative schematic of the protein-solvent systems in explicit and implicit solvents. The illustration juxtaposes the protein systems solvated in explicit... 38
Figure 3.3. Probability distribution plots of the WW domain and HP-36 in both explicit and implicit solvent models. Two-dimensional probability distribution plots... 42
Figure 3.4. Native and (B) non-native structural contents in the folded and unfolded states of the representative β-sheet (WW domain) and α-helix (HP-36) proteins from... 44
Figure 3.5. Thermodynamic and structural differences in solvation models upon folding of the WW domain. Between explicit (ex.) and implicit (im.) solvation... 46
Figure 3.6. Thermodynamic and structural differences in solvation models upon folding of the HP-36. Between explicit (ex.) and implicit (im.) solvation models, the... 50
Figure 3.7. Ion-pair distance distribution of a native salt-bridge, Arg9-Glu7, of the WW domain for the explicit (black) and implicit (red) solvent simulations obtained... 51
Figure 3.8. Correlation plots between the folding effective energy from explicit (ex.) and implicit (im.) solvent simulations, separated by backbones and side chains of (A,... 55
Figure 3.9. Thermodynamic analyses for each main and side chain residues of ubiquitin. The main and side chain contributions to the folding effective energy... 58
Figure S2.1. The number of hydrogen bonds (H-bonds) per residue. Three types of H-bonds are (A) between backbones, (B) between a backbone and a... 61
Figure S2.2. The running averages of configurational entropy TSconf over time in log scale. (A) Six independent folded-state trajectories based on protein...[이미지참조] 62
Figure S2.3. The running minimums of the adjusted effective energy △ƒ=ƒ − ƒ divided by trajectory standard deviation (σ) vs. time in each of (A) the...[이미지참조] 62
Figure S2.4. Thermodynamic analyses for each backbone and side-chain of the WW domain. (A, B) The intra-protein potential energy upon folding △Eu...[이미지참조] 63
Figure S3.1. Thermodynamic analyses for each main and side chain of the WW domain. The main and side chain contributions to (A, B) the folding... 70
Figure S3.2. Thermodynamic analyses for each main and side chain of the HP-36. The main and side chain contributions to (A, B) the folding intra-... 71
Figure S3.3. Per-residue analysis of salt-bridge contents of WW domain and HP-36. 72
Figure S3.4. Thermodynamic analyses for each main chain residues of ubiquitin. The main and side chain contributions to the folding intra-protein... 73
Figure S3.5. Thermodynamic analyses for each side chain residues of the ubiquitin. The main and side chain contributions to the folding intra-protein... 74