Simultaneous structure and dynamics of a membrane protein using REDCRAFT: membrane-bound form of Pf1 coat protein.
A strategy for simultaneous study of the structure and internal dynamics of a membrane protein is described using the REDCRAFT algorithm. The membrane-bound form of the Pf1 major coat protein (mbPf1) was used as an example. First, synthetic data is utilized to validate the simultaneous study of structure and dynamics with REDCRAFT using dihedral restraints and backbone N-H RDCs from two different alignments. Subsequently, the validated analysis is applied to experimental data and confirms that REDCRAFT produces meaningful structures from sparse RDC data. Furthermore, simulated data from a two-state jump motion is used to illustrate the necessity for simultaneous consideration of structure and dynamics. Disregarding internal dynamics during the course of structure determination is shown to produce an average-state that is not related to the two intermediate states. During the analysis of RDC data from the dynamic model, REDCRAFT appropriately identifies the region separating the static and dynamic domains of the protein. Finally, analysis of experimental data strongly suggests the existence of internal motion between the amphipathic and the transmembrane helices of the membrane-bound form of the protein. The ability to perform fragmented structure determination of each domain without a priori assumption of the order tensors allows an independent determination of the order tensors, which yields a more comprehensive description of protein structure and dynamics and is particularly relevant to the study of membrane proteins.
Shealy
Paul
P
Department of Computer Science & Engineering, University of South Carolina, 315 Main Street, Columbia, SC 29208, United States.
Simin
Mikhail
M
Park
Sang Ho
SH
Opella
Stanley J
SJ
Valafar
Homayoun
H
D000465:Algorithms; D036022:Capsid Proteins / Q000737:chemistry*; D003198:Computer Simulation; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation
D036022:Capsid Proteins; D008565:Membrane Proteins; C071283:coat protein, Pseudomonas phage Pf1