Studies of biologically active peptides by NMR and molecular dynamics simulations: From structure and dynamics to design and synthesis

Persistent Link:
http://hdl.handle.net/10150/280667
Title:
Studies of biologically active peptides by NMR and molecular dynamics simulations: From structure and dynamics to design and synthesis
Author:
Ying, Jinfa
Issue Date:
2004
Publisher:
The University of Arizona.
Rights:
Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
Abstract:
Nuclear magnetic resonance spectroscopy and molecular dynamics simulation have been used to study the structure and dynamics of biologically active peptide ligands for glucagon and melanocortin receptors, providing valuable insights into the receptor ligand interactions and useful information for the further design of more potent and selective ligands for these receptors. The NMR structure of the potent glucagon antagonist [desHis¹, desPhe⁶, Glu⁹]glucagon amide consists of an unstructured N-terminal segment (2-5), an irregular helix (7-14), a hinge region (15-18), and a well-defined α-helix (19-29). The two helices form an L-shaped structure with an angle of about 90° between the helix axes. There is an extended hydrophobic cluster, which runs along the inner surface of the L-structure and incorporates the side chains of the hydrophobic residues of each of the amphipathic helices. The outer surface contains the hydrophilic side chains. This result is the first clear indication of an overall tertiary fold for a glucagon analogue in the micelle-bound state. In addition to the structural difference, molecular dynamics simulations showed both N- and C-terminal residues in the glucagon antagonist are more highly ordered than those in glucagon. The single helix obtained for glucagon in the crystal state was found to unravel in the simulation around the region approximately corresponding to the hinge region in the antagonist. These results may have important implications for the biological activities of both peptides. The conformational study of cyclic alpha-melanocyte stimulating hormone analogues by NMR showed that their overall backbone structures are similar around the message sequence (His⁶-D-Phe⁷/D-Nal(2')⁷-Arg⁸-Trp⁹). beta-Turns spanning His⁶ and D-Phe⁷/D-Nal(2')⁷ were identified in all analogues. However, a stacking between the aromatic rings of His⁶ and D-Phe⁷/D-Nal⁷ was observed for the melanocortin agonists, but not for the antagonists. Based on the NMR structure of MTII, a library of new alpha-MSH analogues was designed and synthesized with a disulfide or lactam bridge used as a conformational constraint and the pharmacophore group in Arg⁸ mimicked by Nᵅ-alkylation via the Mitsunobu reaction. These new analogues exhibited high binding affinity and selectivity for the human melanocortin-4 receptor, thus suggesting the usefulness of the NMR structural model of α-MSH peptides.
Type:
text; Dissertation-Reproduction (electronic)
Keywords:
Chemistry, Physical.
Degree Name:
Ph.D.
Degree Level:
doctoral
Degree Program:
Graduate College; Chemistry
Degree Grantor:
University of Arizona
Advisor:
Hruby, Victor J.

Full metadata record

DC FieldValue Language
dc.language.isoen_USen_US
dc.titleStudies of biologically active peptides by NMR and molecular dynamics simulations: From structure and dynamics to design and synthesisen_US
dc.creatorYing, Jinfaen_US
dc.contributor.authorYing, Jinfaen_US
dc.date.issued2004en_US
dc.publisherThe University of Arizona.en_US
dc.rightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.en_US
dc.description.abstractNuclear magnetic resonance spectroscopy and molecular dynamics simulation have been used to study the structure and dynamics of biologically active peptide ligands for glucagon and melanocortin receptors, providing valuable insights into the receptor ligand interactions and useful information for the further design of more potent and selective ligands for these receptors. The NMR structure of the potent glucagon antagonist [desHis¹, desPhe⁶, Glu⁹]glucagon amide consists of an unstructured N-terminal segment (2-5), an irregular helix (7-14), a hinge region (15-18), and a well-defined α-helix (19-29). The two helices form an L-shaped structure with an angle of about 90° between the helix axes. There is an extended hydrophobic cluster, which runs along the inner surface of the L-structure and incorporates the side chains of the hydrophobic residues of each of the amphipathic helices. The outer surface contains the hydrophilic side chains. This result is the first clear indication of an overall tertiary fold for a glucagon analogue in the micelle-bound state. In addition to the structural difference, molecular dynamics simulations showed both N- and C-terminal residues in the glucagon antagonist are more highly ordered than those in glucagon. The single helix obtained for glucagon in the crystal state was found to unravel in the simulation around the region approximately corresponding to the hinge region in the antagonist. These results may have important implications for the biological activities of both peptides. The conformational study of cyclic alpha-melanocyte stimulating hormone analogues by NMR showed that their overall backbone structures are similar around the message sequence (His⁶-D-Phe⁷/D-Nal(2')⁷-Arg⁸-Trp⁹). beta-Turns spanning His⁶ and D-Phe⁷/D-Nal(2')⁷ were identified in all analogues. However, a stacking between the aromatic rings of His⁶ and D-Phe⁷/D-Nal⁷ was observed for the melanocortin agonists, but not for the antagonists. Based on the NMR structure of MTII, a library of new alpha-MSH analogues was designed and synthesized with a disulfide or lactam bridge used as a conformational constraint and the pharmacophore group in Arg⁸ mimicked by Nᵅ-alkylation via the Mitsunobu reaction. These new analogues exhibited high binding affinity and selectivity for the human melanocortin-4 receptor, thus suggesting the usefulness of the NMR structural model of α-MSH peptides.en_US
dc.typetexten_US
dc.typeDissertation-Reproduction (electronic)en_US
dc.subjectChemistry, Physical.en_US
thesis.degree.namePh.D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.disciplineChemistryen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorHruby, Victor J.en_US
dc.identifier.proquest3145149en_US
dc.identifier.bibrecord.b47218319en_US
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