scholarly journals Too packed to change: side-chain packing and site-specific substitution rates in protein evolution

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e911 ◽  
Author(s):  
María Laura Marcos ◽  
Julian Echave
Keyword(s):  
Protein Evolution ◽  
Side Chain ◽  
Chain Packing ◽  
Substitution Rates ◽  
Site Specific ◽  
Side Chain Packing

scholarly journals Too packed to change: site-specific substitution rates and side-chain packing in protein evolution

2014 ◽  
Author(s):  
María Laura Marcos ◽  
Julian Echave
Keyword(s):  
Protein Evolution ◽  
Packing Density ◽  
Main Chain ◽  
Side Chain ◽  
Side Chains ◽  
Contact Density ◽  
Chain Packing ◽  
Site Specific ◽  
Stress Theory ◽  
Side Chain Packing

In protein evolution, due to functional and biophysical constraints, the rates of amino acid substitution differ from site to site. Among the best predictors of site-specific rates is packing density. The packing density measure that best correlates with rates is the weighted contact number (WCN), the sum of inverse square distances between the site’s Cαand the other Cαs . According to a mechanistic stress model proposed recently, rates are determined by packing because mutating packed sites stresses and destabilizes the protein’s active conformation. While WCN is a measure of Cαpacking, mutations replace side chains, which prompted us to consider whether a site’s evolutionary divergence is constrained by main-chain packing or side-chain packing. To address this issue, we extended the stress theory to model side chains explicitly. The theory predicts that rates should depend solely on side-chain packing. We tested these predictions on a data set of structurally and functionally diverse monomeric enzymes. We found that, on average, side-chain contact density (WCNρ) explains 39.1% of among-sites rate variation, larger than main-chain contact density (WCNα) which explains 32.1%. More importantly, the independent contribution of WCNαis only 0.7%. Thus, as predicted by the stress theory, site-specific evolutionary rates are determined by side-chain packing.

Side Chain Packing of the N- and C-Terminal Helices Plays a Critical Role in the Kinetics of CytochromecFolding†

Biochemistry ◽  
1996 ◽  
Vol 35 (17) ◽  
pp. 5538-5549 ◽  
Author(s):  
Wilfredo Colón ◽  
Gülnur A. Elöve ◽  
L. Paul Wakem ◽  
Fred Sherman ◽  
Heinrich Roder
Keyword(s):  
Critical Role ◽  
Side Chain ◽  
Chain Packing ◽  
Kinetics Of ◽  
Side Chain Packing

scholarly journals Side-chain Packing Using SE(3)-Transformer

2021 ◽  
Author(s):  
Akhil Jindal ◽  
Sergei Kotelnikov ◽  
Dzmitry Padhorny ◽  
Dima Kozakov ◽  
Yimin Zhu ◽  
...  
Keyword(s):  
Side Chain ◽  
Chain Packing ◽  
Side Chain Packing
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