Abstract:
:Dynamic properties of class A beta-lactamase TEM-1 are investigated from molecular dynamics (MD) simulations. Comparison of MD-derived order parameters with those obtained from model-free analysis of nuclear magnetic resonance (NMR) relaxation data shows high agreement for N-H moieties within alpha- and beta-secondary structures, but significant deviation for those in loops. This was expected, because motions slower than the protein global tumbling often take place in loop regions. As previously shown using NMR, TEM-1 is a highly ordered protein. Motions are observed within the Omega loop that could, upon substrate binding, stabilize E166 in a catalytically efficient position as the cavity between the protein core and the Omega loop is partially filled. The rigidity of active site residues is consistent with the enzyme high turnover number. MD data are also shown to be useful during the model selection step of model-free analysis: local N-H motions observed over the course of the trajectories help assess whether a peptide plan undergoes low or high amplitude motions on one or more timescales. This joint use of MD and NMR provides a better description of protein dynamics than would be possible using either technique alone.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Fisette O,Morin S,Savard PY,Lagüe P,Gagné SMdoi
10.1016/j.bpj.2009.08.061subject
Has Abstractpub_date
2010-02-17 00:00:00pages
637-45issue
4eissn
0006-3495issn
1542-0086pii
S0006-3495(09)01561-6journal_volume
98pub_type
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