Resilience of the iron environment in heme proteins.
Conformational flexibility is essential to the functional behavior of proteins. We use an effective force constant introduced by Zaccai, the resilience, to quantify this flexibility. Site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. The vibrational density of states of the heme Fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the Fe environment, which we compare quantitatively with values derived from the temperature dependence of atomic mean-squared displacements in molecular dynamics simulations. Vibrational normal modes in the THz frequency range dominate the resilience. Both experimental and computational methods find a higher resilience for cytochrome c than for myoglobin, which we attribute to the increased number of covalent links to the peptide in the former protein. For myoglobin, the resilience of the iron environment is larger than the average resilience previously determined for hydrogen sites using neutron scattering. Experimental results suggest a slightly reduced resilience for cytochrome c upon oxidation, although the change is smaller than reported in previous Mössbauer investigations on a bacterial cytochrome c, and is not reproduced by the simulations. Oxidation state also has no significant influence on the compressibility calculated for cyt c, although a slightly larger compressibility is predicted for myoglobin.
Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts, USA.
Bogdan M
BM
Leu
Yong
Y
Zhang
Lintao
L
Bu
John E
JE
Straub
Jiyong
J
Zhao
Wolfgang
W
Sturhahn
E Ercan
EE
Alp
J Timothy
JT
Sage
D045304:Cytochromes c / Q000737:chemistry / Q000378:metabolism; D006420:Hemeproteins / Q000737:chemistry* / Q000378:metabolism*; D007501:Iron / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D013696:Temperature; D014732:Vibration
D006420:Hemeproteins; D009211:Myoglobin; C055547:deoxymyoglobin; D045304:Cytochromes c; D007501:Iron