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Title: X-ray Crystallographic Studies Of Designed Peptides, Self Assembling Pseudopeptides And Molecular Modeling
Authors: Hegde, Raghurama P
Advisors: Shamala, N
Keywords: Peptides - X-ray Crystallography
Proteins
Peptides - Crystal Structures
Cholecystokinin Type 1 Receptor (CCKIR) - Molecular Model
Designed Peptides
Self Assembling Pseudopeptides
Tetrapeptide
Submitted Date: Jun-2006
Series/Report no.: G20312
Abstract: Structural studies of peptides has relevance for various applications, like, in de novo design of proteins, in designing better catalysts for organic synthesis, in structure based drug design, in the design and construction of synthetic protein mimics and in building novel materials via supramolecular self assembly. Crystal structure determination of peptides is expected to provide information about their static structure, mode of aggregation, solvation and hydrogen bond interactions of the sequences in the solid state. Comparison and analysis of the related structures from the database analysis could provide information about sequence dependent conformational features, which eventually would act as precursor for de novo protein design. Self assembling processes are common throughout nature and technology. Living cells self assemble, and understanding life will therefore require an understanding of self assembly. Supramolecular chemistry has become an area of intense research, partly inspired by biological ensembles in nature, such as collagen and enzymes or protein assemblies in general. Understanding, inducing, and directing such self assembling processes are key to unraveling the progressive emergence of complex matter. Most of the drugs available today have a broad spectrum of action in that they can act on more than one receptor and the mechanism of action of these drugs are poorly understood. Homology modeling of receptors and docking studies with drug molecules (both peptides and non-peptides) would result in a better understanding of the mechanism of drug-receptor binding thus resulting in the design of more specific and effective drugs. This thesis reports the results of X-ray crystallographic studies of ten molecules listed below (Ter: terephthalic acid) and the molecular model of cholecystokinin type 1 receptor (CCK1R). The abbreviations used for the sequences are given in parenthesis. Boc-Gly-Dpg-Gly-Leu-OMe (GDGL), C24H44N4O7 Boc-Val-Ala-Leu-Dpg-Val-Ala-Leu-Val-Ala-Leu-Dpg-Val-Ala-Leu-OMe (VAL14), C78H14 2N14O17 MeO-Leu-Ter-Leu-OMe (LTeL), C22H32N2O6 MeO-DLeu-Ter-DLeu-OMe (DLTeDL), C22H32N2O6 MeO-Ile-Ter-Ile-OMe (ITeI), C22H32N2O6 MeO-Aib-Ter-Aib-OMe (UTeU), C18H24N2O6 Tyr-Aib-Tyr-Val (YUYV), C27H36N4O7 Tyr-Aib-Ala (YUA), C16H23N3O5 Z-Gly-Gly-Val (ZGGV), C17 H23 N3 O6 DL-4-benzamido-N, N-dipropylglutaramic acid (proglumide), C18 H26 N2 O4 Results from the Dpg containing peptide sequences helped to further the understanding of conformational preferences of this residue. The crystallographic studies on the peptide sequence, which forms a supramolecular triple helix and four pseudopeptide sequences, which adopt supramolecular ladder conformations has provided substantial information on the role of non covalent interactions in supramolecular self assembly. Crystal structure of a Gly-Gly containing tripeptide and database analysis has provided insights into the conformations adopted by this segment in peptides and proteins. The docking of the crystal structure of proglumide, an antagonist of CCK1R has led to the understanding of the mechanism of its interaction with CCK1R.
URI: http://hdl.handle.net/2005/402
Appears in Collections:Physics (physics)

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