Characterizations of human odorant receptor classes by physicochemical conservations of residues in human odorant receptors
- Title
- Characterizations of human odorant receptor classes by physicochemical conservations of residues in human odorant receptors
- Author(s)
- Won-Cheol Kim
- DGIST Authors
- Won-Cheol Kim ; Cheil Moon ; Kyuhyung Kim
- Advisor
- 문제일
- Co-Advisor(s)
- Kyuhyung Kim
- Issued Date
- 2022
- Awarded Date
- 2022/08
- Type
- Thesis
- Description
- Human odorant receptors, Conservation analysis, Physicochemical features of amino acids
- Abstract
- Table Of Contents
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Ⅰ. Introduction 1
1.1 Human odorant receptors and their phylogenetic division into two classes 1
1.2 Differences in functions of ORs between two OR classes 1
1.3 Differences in conservations of residues between two OR classes and approaches to find the differences 1
1.4 Purpose of this study 2
Ⅱ. Materials and Methods 3
2.1 Physicochemical conservation analysis on amino acid sequences of human ORs 3
2.1.1 Preparation of human OR sequences and their alignment 3
2.1.2 Defining physicochemically conserved amino acid residues in ORs 3
2.1.3 Classification of the physicochemically conserved amino acid residues of ORs 4
2.2 Molecular dynamics simulation of human ORs 6
2.2.1 Preparation of human OR systems 6
2.2.2 Production of trajectories of the OR systems by MD simulation 6
2.2.3 Analysis of the trajectories 6
2.2.3.1 Calculation of standard deviations of RMSD in the trajectories 6
2.2.3.2 Dimension reduction of OR coordinates using PCA 6
2.3 Overexpression of ORs on a heterologous system 9
2.3.1 Preparation of DNA and vectors 9
2.3.2 Cell culture 9
2.3.3 Transfection of OR genes 9
2.4 Measurement of functional expressions of ORs in HEK293T cells 9
2.5 cAMP assay in OR expressing HEK293T cells 9
2.5.1 Measurement of basal activities of ORs 9
2.5.2 Measurement of agonist-induced responses of ORs 10
Ⅲ. Results 13
3.1 Physicochemical conservation analysis on amino acid sequences of human ORs 13
3.1.1 Identification of class-specifically physicochemically conserved amino acid residues of ORs 13
3.1.2 Identification of PDCCs in human ORs 13
3.2 Validation of functional roles of PDCCs in each human OR class 16
3.2.1 Backgrounds 16
3.2.2 Experimental designs for the validation 16
3.3 Functional roles of residue 1.46 in ORs in each OR class as a PDCC 17
3.3.1 Roles of residue 1.46 on structures of ORs 17
3.3.2 Roles of residue 1.46 on functional expressions of ORs 20
3.3.3 Roles of residue 1.46 on activations of ORs 22
3.4 Functional roles of residue 2.53 in ORs in each OR class as a PDCC 24
3.4.1 Roles of residue 2.53 on structures of ORs 24
3.4.2 Roles of residue 2.53 on functional expressions of ORs 26
3.4.3 Roles of residue 2.53 on activations of ORs 28
3.5. Functional roles of PDCCs in ORs as conserved sets 30
3.5.1 Backgrounds 30
3.5.2 Roles of PDCCs as conserved sets in structures of ORs 30
3.5.3 Roles of PDCCs as conserved sets in functional expressions of ORs 33
3.5.4 Roles of PDCCs as conserved sets in activations in ORs 35
Ⅳ. Discussion 38
4.1 Understanding of differences in functions of ORs between two human OR classes 38
4.2 Identification of class-specific physicochemical features on conserved residues in human ORs 38
4.3 Roles of individual PDCCs on functions of ORs in each human OR class 41
4.4 Functional roles of PDCCs as conserved sets in each human OR class 42
4.5. Limitations of this study 42
4.5.1 Mutation models of ORs in each human OR class 42
4.5.2 Examination of roles of PDCCs only in one case of OR in each OR class 43
Ⅴ. Conclusion 44
References 45
- URI
-
http://dgist.dcollection.net/common/orgView/200000629238
http://hdl.handle.net/20.500.11750/16789
- Degree
- Master
- Department
- Department of Brain Sciences
- Publisher
- DGIST
- Related Researcher
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Moon, Cheil
- Research Interests Brain convergent science based on chemical senses; olfaction; 감각신경계 기반 뇌융합과학; 후각 신경계
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- Appears in Collections:
- Department of Brain Sciences Theses Master
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