Characterization of Protein Conformational Changes with Sparse Spin-Label Distance Constraints

2012 ◽  
Vol 8 (10) ◽  
pp. 3854-3863 ◽  
Author(s):  
G. Jeschke
Keyword(s):  
Conformational Changes ◽  
Spin Label ◽  
Distance Constraints ◽  
Protein Conformational Changes

scholarly journals Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER Distance Restraints

2021 ◽  
Vol 17 (6) ◽  
pp. e1009107
Author(s):  
Diego del Alamo ◽  
Kevin L. Jagessar ◽  
Jens Meiler ◽  
Hassane S. Mchaourab
Keyword(s):  
Conformational Changes ◽  
Spin Label ◽  
Protein Conformational Changes ◽  
Alternative Protein ◽  
Distance Distributions ◽  
Distance Restraints ◽  
Double Electron ◽  
The Time Domain ◽  
Double Electron Electron Resonance ◽  
Experimental Structure

We describe an approach for integrating distance restraints from Double Electron-Electron Resonance (DEER) spectroscopy into Rosetta with the purpose of modeling alternative protein conformations from an initial experimental structure. Fundamental to this approach is a multilateration algorithm that harnesses sets of interconnected spin label pairs to identify optimal rotamer ensembles at each residue that fit the DEER decay in the time domain. Benchmarked relative to data analysis packages, the algorithm yields comparable distance distributions with the advantage that fitting the DEER decay and rotamer ensemble optimization are coupled. We demonstrate this approach by modeling the protonation-dependent transition of the multidrug transporter PfMATE to an inward facing conformation with a deviation to the experimental structure of less than 2Å Cα RMSD. By decreasing spin label rotamer entropy, this approach engenders more accurate Rosetta models that are also more closely clustered, thus setting the stage for more robust modeling of protein conformational changes.

scholarly journals Protein conformational changes and myelin solubilization by anion-detergent solutions

FEBS Letters ◽  
1992 ◽  
Vol 309 (3) ◽  
pp. 376-380 ◽  
Author(s):  
Jaime Monreal ◽  
Pedro Carmona ◽  
Pilar Regueiro ◽  
Ricardo S. Diaz
Keyword(s):  
Conformational Changes ◽  
Protein Conformational Changes ◽  
Detergent Solutions
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