| Autor: |
Elizabeth Wood, Andrea Bordoni, Henrik Bohr, Per Amstrup Pedersen, Mathias F. Gruber, Claus Hélix-Nielsen |
| Rok vydání: |
2014 |
| Předmět: |
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| Zdroj: |
Biophysical Journal. 106(2) |
| ISSN: |
0006-3495 |
| DOI: |
10.1016/j.bpj.2013.11.611 |
| Popis: |
Binding of anions by proteins is a topic of great interest, the binding being due to interactions either with the protein's positively charged side chains and/or with the main chain. In particular the phosphate anion is essential for a large number of functions and pathways within cells, and the specific binding of phosphate anion has been widely studied. However, investigation of the structural features in phosphate binding sites and the mechanisms for phosphate binding is still a field that warrants more research.One of the most common ways in which proteins bind to phosphate is via a highly conserved consensus sequence that folds into what is known as a P-loop. Here, we use molecular mechanics and quantum mechanical calculations to characterize interactions of the phosphate anion with 1) a native P-loop whose structure available in the PDB database (1MAB), and 2) a synthetic peptide designed to bind phosphate by mimicking the P-loop function. Whereas the structure of the native P-loop is fairly well characterized and restricted within the 1MAB structure, the synthetic peptide explores a larger conformational space - yet the synthetic peptide is able to bind phosphate.Specifically we investigate the structural properties and the conformational space of both the peptides, we characterize how they interact with phosphate, and we examine the mechanism by which the peptides fold into the P-loop structure and bind phosphate. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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