Backbone conformational flexibility of the lipid modified membrane anchor of the human N-Ras protein investigated by solid-state NMR and molecular dynamics simulation.
The lipid modified human N-Ras protein, implicated in human cancer development, is of particular interest due to its membrane anchor that determines the activity and subcellular location of the protein. Previous solid-state NMR investigations indicated that this membrane anchor is highly dynamic, which may be indicative of backbone conformational flexibility. This article aims to address if a dynamic exchange between three structural models exist that had been determined previously. We applied a combination of solid-state nuclear magnetic resonance (NMR) methods and replica exchange molecular dynamics (MD) simulations using a Ras peptide that represents the terminal seven amino acids of the human N-Ras protein. Analysis of correlations between the conformations of individual amino acids revealed that Cys 181 and Met 182 undergo collective conformational exchange. Two major structures constituting about 60% of all conformations could be identified. The two conformations found in the simulation are in rapid exchange, which gives rise to low backbone order parameters and nuclear spin relaxation as measured by experimental NMR methods. These parameters were also determined from two 300 ns conventional MD simulations, providing very good agreement with the experimental data.
Vogel
Alexander
A
Junior Research Group Structural Biology of Membrane Proteins, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle, Germany. alexander.vogel@biochemtech.uni-halle.de
Reuther
Guido
G
Roark
Matthew B
MB
Tan
Kui-Thong
KT
Waldmann
Herbert
H
Feller
Scott E
SE
Huster
Daniel
D
D003198:Computer Simulation; D006801:Humans; D008055:Lipids / Q000737:chemistry*; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D017433:Protein Structure, Secondary / Q000502:physiology; D017434:Protein Structure, Tertiary / Q000502:physiology; D016283:Proto-Oncogene Proteins p21(ras) / Q000737:chemistry* / Q000378:metabolism; D013329:Structure-Activity Relationship
D008055:Lipids; D010455:Peptides; D016283:Proto-Oncogene Proteins p21(ras)