Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study.
Molecular dynamics (MD) simulations on a bacterial cytochrome c were performed to investigate the lifetime and fluctuations of backbone hydrogen bonds and to correlate these data with protection factors for hydrogen exchange measured by NMR spectroscopy (Bartalesi et al. in Biochemistry, 42:10923-10930, 2003). The MD simulations provide a consistent pattern in that long lifetimes of hydrogen bonds go along with small amplitude fluctuations. In agreement with experiments, differences in stability were found with a rather flexible N-terminal segment as compared with a more rigid C-terminal part. Protection factors of backbone hydrogen exchange correlate strongly with the number of contacts but also with hydrogen-bond occupancy, hydrogen-bond survival times, as well as the inverse of fluctuations of backbone atoms and hydrogen-bond lengths derived from MD simulation data. We observed a conformational transition in the C-terminal loop, and significant motion in the N-terminal loop, which can be interpreted as being the structural units involved in the onset of the protein unfolding process in agreement with experimental evidence on mitochondrial cytochrome c.
Kieseritzky
Gernot
G
Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Free University of Berlin, Takustrasse 6, 14195 Berlin, Germany.
Morra
Giulia
G
Knapp
Ernst-Walter
EW
D000577:Amides / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D003198:Computer Simulation; D045304:Cytochromes c / Q000737:chemistry* / Q000378:metabolism; D006859:Hydrogen / Q000737:chemistry; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D024101:Mitochondrial Proteins / Q000737:chemistry / Q000378:metabolism; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D017433:Protein Structure, Secondary
D000577:Amides; D001426:Bacterial Proteins; D024101:Mitochondrial Proteins; D010446:Peptide Fragments; D006859:Hydrogen; D045304:Cytochromes c