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  Department of Brain Sciences Theses Ph.D.

Study of the importance of broad sampling through NMR chemical-shift-based reweighting of intrinsically disordered proteins

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dc.contributor.advisor 유우경 -
dc.contributor.author Juhyeong Jeon -
dc.date.accessioned 2026-09-01T19:29:28Z -
dc.date.available 2026-09-01T19:29:28Z -
dc.date.issued 2026 -
dc.identifier.uri https://scholar.dgist.ac.kr/handle/20.500.11750/60722 -
dc.identifier.uri http://dgist.dcollection.net/common/orgView/200001006733 -
dc.description intrinsically disordered protein, conformational ensemble, NMR chemical shift, reweighting -
dc.description.tableofcontents Ⅰ.Introduction 1
1.1 Intrinsically Disordered Proteins and Protein Regions 1
1.2 Experimental and Computational Challenges in IDP Ensemble Characterization 1
1.3 Integration Algorithms 3
1.4 Multi-Prior Reweighting for Heterogeneous IDP Landscapes 4
1.5 NMR Chemical Shifts as a Reweighting Observable 4
1.6 Aim and Objectives 5
Ⅱ.Materials and Methods 6
2.1 Data Preprocessing 6
2.2 Ensemble Generation 7
2.3 Forward Model for Chemical Shift 8
2.4 Constrained Multiple Linear Regression 9
2.5 Maximum Entropy Reweighting Approach 10
2.6 Metrics 11
2.7 Offset Correction 12
2.8 Structural Analysis 14
Ⅲ.Results 16
3.1 Overall Workflow 16
3.1.1 Alignment and Filtering 17
3.1.2 Ensemble Generation and All-Atom Reconstruction 21
3.1.3 Chemical Shift Prediction 25
3.1.4 Parameter Selection and Metrics for Reweighting 28
3.1.5 Offset Correction 33
3.1.6 Outlier Removal and Final Reweighting 34
3.2 Effect of Ensemble Input 35
3.2.1 Atom Score Improvement 35
3.2.2 Dependence on the Number of Conformers 39
3.2.3 Relation between Score Improvement and Structural Features 42
3.3 Classification and Structural Analysis Based on Weights 48
3.3.1 Classification Criteria 48
3.3.2 Predictor Consistency of Classification 49
3.3.3 Information Content from Chemical Shift 52
3.3.4 Global Structural Features 56
3.3.5 AlphaFold Metrics across Classes 61
3.3.6 Model-Dependent Structural Biases 63
3.3.7 Model-Dependent Contributions to Statistical Weights 67
3.4 Case Studies of Reweighting 71
3.4.1 TDP-43: Mutation-Dependent Ensemble Redistribution 71
3.4.2 PHOX2B: Temperature-Dependent Ensemble Remodeling 75
Ⅳ.Discussion 81
Ⅴ.References 85
Appendix 94
Abstract in Korean 100		 -
dc.format.extent 100 -
dc.language eng -
dc.publisher DGIST -
dc.title Study of the importance of broad sampling through NMR chemical-shift-based reweighting of intrinsically disordered proteins -
dc.title.alternative NMR chemical shift 기반 재가중을 통한 무정형 단백질의 광범위한 구조 탐색 중요성 연구 -
dc.type Thesis -
dc.identifier.doi 10.22677/THESIS.200001006733 -
dc.description.degree Doctor -
dc.contributor.department Department of Brain Sciences -
dc.contributor.coadvisor Jin Hae Kim -
dc.date.awarded 2026-08-01 -
dc.publisher.location Daegu -
dc.description.database dCollection -
dc.citation XT.BD 전76 202608 -
dc.date.accepted 2026-07-21 -
dc.contributor.alternativeDepartment 뇌과학과 -
dc.subject.keyword intrinsically disordered protein, conformational ensemble, NMR chemical shift, reweighting -
dc.contributor.affiliatedAuthor Juhyeong Jeon -
dc.contributor.affiliatedAuthor Wookyung Yu -
dc.contributor.affiliatedAuthor Jin Hae Kim -
dc.contributor.alternativeName 전주형 -
dc.contributor.alternativeName Wookyung Yu -
dc.contributor.alternativeName 김진해 -
dc.rights.embargoReleaseDate 2028-08-31 -
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