In Silico Molecular Engineering for a Targeted Replacement in a Tumor-Homing Peptide
| Autor: | Carlos Cativiela, Erkki Ruoslahti, Ruth Nussinov, David Zanuy, Alejandra Flores-Ortega, M. Isabel Calaza, Ana I. Jiménez, Carlos Alemán |
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| Rok vydání: | 2009 |
| Předmět: |
Models
Molecular chemistry.chemical_classification Proteases Proline Arginine Protein Conformation Chemistry In silico Peptide Pentapeptide repeat Article Surfaces Coatings and Films Amino acid Protein structure Amino Acid Substitution Biochemistry Materials Chemistry Computer Simulation Amino Acid Sequence Physical and Theoretical Chemistry Oligopeptides Peptide sequence Guanidine |
| Zdroj: | The Journal of Physical Chemistry B. 113:7879-7889 |
| ISSN: | 1520-5207 1520-6106 |
| DOI: | 10.1021/jp9006119 |
| Popis: | A new amino acid has been designed as a replacement for arginine (Arg, R) to protect the tumor-homing pentapeptide CREKA (Cys-Arg-Glu-Lys-Ala) from proteases. This amino acid, denoted (Pro)hArg, is characterized by a proline skeleton bearing a specifically oriented guanidinium side chain. This residue combines the ability of Pro to induce turn-like conformations with the Arg side-chain functionality. The conformational profile of the CREKA analogue incorporating this Arg substitute has been investigated by a combination of simulated annealing and molecular dynamics. Comparison of the results with those previously obtained for the natural CREKA shows that (Pro)hArg significantly reduces the conformational flexibility of the peptide. Although some changes are observed in the backbone...backbone and side-chain...side-chain interactions, the modified peptide exhibits a strong tendency to accommodate turn conformations centered at the (Pro)hArg residue and the overall shape of the molecule in the lowest energy conformations characterized for the natural and the modified peptides exhibit a high degree of similarity. In particular, the turn orients the backbone such that the Arg, Glu, and Lys side chains face the same side of the molecule, which is considered important for bioactivity. These results suggest that replacement of Arg by (Pro)hArg in CREKA may be useful in providing resistance against proteolytic enzymes while retaining conformational features which are essential for tumor-homing activity. |
| Databáze: | OpenAIRE |
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