Permanent URL to this publication: http://dx.doi.org/10.5167/uzh-9831
Interlandi, G (2009). Backbone conformations and side chain flexibility of two somatostatin mimics investigated by molecular dynamics simulations. Proteins, 75(3):659-670.
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Molecular dynamics simulations with two designed somatostatin mimics, SOM230 and SMS 201-995, were performed in explicit water for a total aggregated time of 208 ns. Analysis of the runs with SOM230 revealed the presence of two clusters of conformations. Strikingly, the two sampled conformers correspond to the two main X-ray structures in the asymmetric unit of SMS 201-995. Structural comparison between the residues of SOM230 and SMS 201-995 provides an explanation for the high binding affinity of SOM230 to four of five somatostatin receptors. Similarly, cluster analysis of the simulations with SMS 201-995 shows that the backbone of the peptide interconverts between its two main crystallographic conformers. The conformations of SMS 201-995 sampled in the two clusters violated two different sets of NOE distance constraints in agreement with a previous NMR study. Differences in side chain fluctuations between SOM230 and SMS 201-995 observed in the simulations may contribute to the relatively higher binding affinity of SOM230 to most somatostatin receptors. Proteins 2009. (c) 2008 Wiley-Liss, Inc.
|Item Type:||Journal Article, refereed, original work|
|Communities & Collections:||04 Faculty of Medicine > Institute of Biochemistry|
07 Faculty of Science > Institute of Biochemistry
|DDC:||570 Life sciences; biology|
|Date:||15 May 2009|
|Deposited On:||14 Jan 2009 11:27|
|Last Modified:||23 Nov 2012 14:01|
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