Campus Units

Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Baker Center for Bioinformatics and Biological Statistics

Document Type


Publication Version

Accepted Manuscript

Publication Date


Journal or Book Title

Physical Biology





First Page





Loops in proteins connect secondary structures such as alpha-helix and beta-sheet, are often on the surface, and may play a critical role in some functions of a protein. The mobility of loops is central for the motional freedom and flexibility requirements of active-site loops and may play a critical role for some functions. The structures and behaviors of loops have not been much studied in the context of the whole structure and its overall motions, and especially how these might be coupled. Here we investigate loop motions by using coarse-grained structures ( atoms only) to solve for the motions of the system by applying Lagrange equations with elastic network models to learn about which loops move in an independent fashion and which move in coordination with domain motions, faster and slower, respectively. The normal modes of the system are calculated using eigen-decomposition of the stiffness matrix. The contribution of individual modes and groups of modes are investigated for their effects on all residues in each loop by using Fourier analyses. Our results indicate overall that the motions of functional sets of loops behave in similar ways as the whole structure. But, overall only a relatively few loops move in coordination with the dominant slow modes of motion, and that these are often closely related to function.


This is a manuscript of an article published as Skliros, Aris, Michael T. Zimmermann, Debkanta Chakraborty, Saras Saraswathi, Ataur R. Katebi, Sumudu P. Leelananda, Andrzej Kloczkowski, and Robert L. Jernigan. "The importance of slow motions for protein functional loops." Physical biology 9, no. 1 (2012): 014001. doi: 10.1088/1478-3975/9/1/014001. Posted with permission.

Copyright Owner

IOP Publishing Ltd



File Format


Published Version