Author: Leili Zhang; David R. Bell; Binquan Luan; Ruhong Zhou
Title: Exploring the Binding Mechanism between Human Profilin (PFN1) and Polyproline-10 through Binding Mode Screening Document date: 2018_9_16
ID: 40pe21lm_36
Snippet: The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/418830 doi: bioRxiv preprint Next we examined how the binding process evolves when P10 approaches PFN1. A stepwise view of how hydrogen bonds form and break during umbrella sampling is shown in Figure 3 , which illustrates how P10 binds PFN1 through a "zipping" mechanism. Hydrogen bonds are first formed between the C-terminus of P1.....
Document: The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/418830 doi: bioRxiv preprint Next we examined how the binding process evolves when P10 approaches PFN1. A stepwise view of how hydrogen bonds form and break during umbrella sampling is shown in Figure 3 , which illustrates how P10 binds PFN1 through a "zipping" mechanism. Hydrogen bonds are first formed between the C-terminus of P10 (residue 9~10) and PFN1. Then the interactions gradually move along the chain to the N-terminal direction, up to the middle portion of the P10 (residue 5~6). The aromatic-proline stacking was also examined during the binding process. We defined an aromatic-proline stacking index (S) based on the minimal distances from any proline side chain on P10 to the side chains of W3, Y6, Y139 from PFN1
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