Abstract：
:Proteins are not rigid molecules, but exhibit internal motions on timescales ranging from femto- to milliseconds and beyond. In solution, proteins also experience global translational and rotational motions, sometimes on timescales comparable to those of the internal fluctuations. The possibility that internal and global motions may be directly coupled has intriguing implications, given that enzymes and cell signaling proteins typically associate with binding partners and cellular scaffolds. Such processes alter their global motion and may affect protein function. Here, we present molecular dynamics simulations of extreme case scenarios to examine whether a possible relationship exists. In our model protein, a ubiquitin-like RhoGTPase binding domain of plexin-B1, we removed either internal or global motions. Comparisons with unrestrained simulations show that internal and global motions are not appreciably coupled in this single-domain protein. This lack of coupling is consistent with the observation that the dynamics of water around the protein, which is thought to permit, if not stimulate, internal dynamics, is also largely independent of global motion. We discuss implications of these results for the structure and function of proteins.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Hamaneh MB,Zhang L,Buck Mdoi
10.1016/j.bpj.2011.05.041subject
Has Abstractpub_date
2011-07-06 00:00:00pages
196-204issue
1eissn
0006-3495issn
1542-0086pii
S0006-3495(11)00611-4journal_volume
101pub_type
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