Ligand migration between internal docking sites in photodissociated carbonmonoxy neuroglobin.
Neuroglobin (Ngb) belongs to the large family of globular heme proteins capable of binding small gaseous ligands such as O(2), CO, or NO within their active site. In this work, we have analyzed CO migration pathways in photolyzed NgbCO using molecular dynamics (MD) simulations in combination with Fourier transform infrared temperature derivative spectroscopy (FTIR-TDS). A total of 55 ns of MD simulation was analyzed to explore the approximately 300 A(3) internal Ngb cavity. Overall, the simulations differentiated between eight possible docking sites, three of which were also identified experimentally. Low-temperature FTIR-TDS experiments on wild-type (wt) and F28W mutant NgbCO revealed that a small fraction of ligands migrates from site B to site C from which they rebound after slow cool illumination. For the F28L mutant, however, population of site C was not observed. In agreement with these findings, the simulations at 20 K showed ligand transfer between sites B and C for wt Ngb, but not for the F28L mutant. The ligand migration network could be mapped out and two key gate residues, Phe28 and Pro52, were identified. Ligand population analysis from the MD simulations revealed a direct relation between the size of the B10 side chain (Phe28 in wild-type Ngb) and the barrier against migration. Barriers for the transition of photodissociated CO from the distal pocket to the Xe4 site in Ngb are lower by up to 4 kcal/mol compared to myoglobin, suggesting that ligand migration between different docking sites is more facile in Ngb than in myoglobin.
Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland.
Stephan
S
Lutz
Karin
K
Nienhaus
G Ulrich
GU
Nienhaus
Markus
M
Meuwly
D019943:Amino Acid Substitution; D001665:Binding Sites; D002248:Carbon Monoxide / Q000737:chemistry; D005914:Globins / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D009419:Nerve Tissue Proteins / Q000737:chemistry* / Q000378:metabolism; D000078787:Neuroglobin; D010782:Photolysis; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D017550:Spectroscopy, Fourier Transform Infrared; D013696:Temperature; D013816:Thermodynamics
D008024:Ligands; D009419:Nerve Tissue Proteins; D000078787:Neuroglobin; D011994:Recombinant Proteins; D002248:Carbon Monoxide; D005914:Globins