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Title
CERTIFICATE 1
CERTIFICATE-2
DECLARATION
CONTENTS
ACKNOWLEDGEMENT
ABBREVIATIONS
1 On Conformational Investigations of Peptides
1.1 Nuclear Magnetic Resonance
1.2 Computational Studies of Peptides
2 Biological background
2.1 Bovine seminalplasmin: Background
2.2 Human Lactoferrin: Background
2.2.1 Sequence conservation among lactoferrins
3 Peptide Synthesis
3.1 Introduction
3.2 Solid Phase Peptide Synthesis
3.2.1 Solid-phase synthesis
3.2.2 Overview of peptide synthesis on solid phase
3.2.3 Protecting group strategies
3.2.4 The solid phase and the solvent
3.2.5 Attachment to the solid phase
3.2.6 Different synthesis techniques
3.2.7 Peptide bond forming methods and reagents
3.2.8 Monitoring the acylation reaction
3.2.9 Problems encountered during peptide coupling reactions
3.2.10 Release from the solid phase and deprotection of protected groups
3.2.11 Purification and characterization of the synthesized peptide
3.3 Synthesis of Peptides
3.3.1 Experimental
3.3.1.1 Purification of solvents and reagents
3.3.1.2 Preparation of 2% BDDMA cross-linked polystyrene (BDDMA-PS)
3.3.1.3 Functionalization of BDDMA-PS (Chloromethylation)
3.3.1.4 General Methods of Solid Phase Peptide Synthesis
3.3.2 Results and discussion
3.3.2.1 PELLETFL
3.3.2.2 LLETFL
3.3.2.3 FLSEWIG
3.3.2.4 FSASCVPG
3.3.2.5 AVGEQELRGCNQWSGL
3.3.3 Conclusion
4 Conformational analysis of peptides in solution
4.1 Introduction
4.2 Peptide conformation in solution
4.2.1 Definition of peptide and protein conformation
4.2.2 Peptide and protein structures
4.2.3 Linear peptides in solution
4.3 NMR spectroscopy
4.3.1 Conformational information from NMR spectroscopy
4.3.2 One dimensional (1D) NMR experiments
4.3.3 Two dimensional (2D) NMR spectroscopy
4.3.3.1 COSY: Correlated spectroscopy
4.3.3.2 DQF-COSY: Double Quantum Filtered-COSY
4.3.3.3 TOCSY: Total Correlation Spectroscopy
4.3.3.4 NOESY: Nuclear Overhauser Enhancement Spectroscopy
4.3.3.5 ROESY: Rotating frame Overhauser Effect Spectroscopy
4.4 NMR data for peptide and protein structure calculation
4.4.1 Nualear Overhauser Effects (NOEs)
4.4.2 Scalar coupling constants
4.4.3 Hydrogen bonds
4.4.4 Chemical shifts
4.5 Sequence Specific Resonance Assignment
4.6 Structure Calculation
4.7 Conformational analysis of target peptides derived from bovine seminalplasmin
4.7.1 NMR Analysis of PELLETFL
4.7.1.1 Sequence specific resonance assignments
4.7.1.2 JNHcoupling constants
4.7.1.3 3D structure calculation
4.7.1.4 Conclusion
4.7.2 NMR Analysis of LLETFL
4.7.2.1 Sequence specific resonance assignments
4.7.2.2 JNH Coupling constants
4.7.2.3 3D structure calculation
4.7.2.4 Conclusion
4.7.3 NMR Analysis of FLSEWIG
4.7.3.1 Sequence Specific Resonance Assignments
4.7.3.2 JNH coupling constants
4.7.3.3 3D structure calculation
4.7.3.4 Conclusion
4.8 Conformational analysis of target peptides derived fromhuman lactoferrin
4.8.1 NMR Analysis of FSASCVPG
4.8.1.1 Sequence Specific Resonance assignments
4.8.1.2 Temperature dependence of amide proton resonances
4.8.1.3 JNH coupling constants
4.8.1.4 3D structure calculation
4.8.1.5 Conclusion
4.8.2 NMR analysis of AVGEQELRGCNQWSGL
4.8.2.1 Sequence specific resonance assignments
4.8.2.2 3D structure calculation
4.8.2.3 Conclusion
4.9. Discussion on conformational analysis of target peptides
5 Summary and Observations
5.1 Summary
5.2 Observations
5.2.1 General (hypothetical) inference
References