Investigating Substate Transitions in Myoglobin using Molecular Dynamics Simulation
ثبت نشده
چکیده
منابع مشابه
A study of vibrational relaxation of B-state carbon monoxide in the heme pocket of photolyzed carboxymyoglobin.
The vibrational energy relaxation of dissociated carbon monoxide in the heme pocket of sperm whale myoglobin has been studied using equilibrium molecular dynamics simulation and normal mode analysis methods. Molecular dynamics trajectories of solvated myoglobin were run at 300 K for both the delta- and epsilon-tautomers of the distal histidine, His64. Vibrational population relaxation times wer...
متن کاملMyoglobin-CO substate structures and dynamics: multidimensional vibrational echoes and molecular dynamics simulations.
Spectrally resolved infrared stimulated vibrational echo data were obtained for sperm whale carbonmonoxymyoglobin (MbCO) at 300 K. The measured dephasing dynamics of the CO ligand are in agreement with dephasing dynamics calculated with molecular dynamics (MD) simulations for MbCO with the residue histidine-64 (His64) having its imidazole epsilon nitrogen protonated (N(epsilon)-H). The two conf...
متن کاملConformational switching between protein substates studied with 2D IR vibrational echo spectroscopy and molecular dynamics simulations.
Myoglobin is an important protein for the study of structure and dynamics. Three conformational substates have been identified for the carbonmonoxy form of myoglobin (MbCO). These are manifested as distinct peaks in the IR absorption spectrum of the CO stretching mode. Ultrafast 2D IR vibrational echo chemical exchange experiments are used to observed switching between two of these substates, A...
متن کاملMyoglobin-CO conformational substate dynamics: 2D vibrational echoes and MD simulations.
Two-dimensional (2D) infrared vibrational echoes were performed on horse heart carbonmonoxymyoglobin (MbCO) in water over a range of temperatures. The A(1) and A(3) conformational substates of MbCO are found to have different dephasing rates with different temperature dependences. A frequency-frequency correlation function derived from molecular dynamics simulations on MbCO at 298 K is used to ...
متن کاملNUMERICAL SIMULATIONS OF THE PHASE TRANSITIONS IN CLUSTERS
We have studied the phase transitions in atomic clusters by molecular dynamics simulation, assuming Lennard-Jones interatomic pair potential. Calculations are performed by DAP parallel computer. The results are analyzed by simulating their orientational distribution plots (dot-plot), and neutron diffraction patterns. It is shown that all the main features of the bulk phase transitions are e...
متن کامل