NDLI: Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study

Content Provider	Springer Nature Link
Author	Kieseritzky, Gert Morra, Giulia Knapp, Ernst Walter
Copyright Year	2005
Abstract	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.
Starting Page	26
Ending Page	40
Page Count	15
File Format	PDF
ISSN	09498257
Journal	JBIC Journal of Biological Inorganic Chemistry
Volume Number	11
Issue Number	1
e-ISSN	14321327
Language	English
Publisher	Springer-Verlag
Publisher Date	2005-11-16
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Molecular dynamics Protein stability Hydrogen protection factor Protein unfolding Native protein structure Hydrogen exchange Microbiology Biochemistry
Content Type	Text
Resource Type	Article
Subject	Biochemistry Inorganic Chemistry

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