An Efficient Null Model for Conformational Fluctuations in Proteins

Harder, Tim (author)

Borg, Mikael (author)

Bottaro, Sandro (author)

Boomsma, Wouter (author): Lund University,Lunds universitet,Beräkningsbiologi och biologisk fysik - Genomgår omorganisation,Institutionen för astronomi och teoretisk fysik - Genomgår omorganisation,Naturvetenskapliga fakulteten,Computational Biology and Biological Physics - Undergoing reorganization,Department of Astronomy and Theoretical Physics - Undergoing reorganization,Faculty of Science

Olsson, Simon (author)

Ferkinghoff-Borg, Jesper (author)

Hamelryck, Thomas (author)

(creator_code:org_t)

Related links:: https://portal.resea... (primary) (free); show more...; http://dx.doi.org/10...; http://www.cell.com/...; https://lup.lub.lu.s...; https://doi.org/10.1...; show less...

Abstract Subject headings

Protein dynamics play a crucial role in function, catalytic activity, and pathogenesis. Consequently, there is great interest in computational methods that probe the conformational fluctuations of a protein. However, molecular dynamics simulations are computationally costly and therefore are often limited to comparatively short timescales. TYPHON is a probabilistic method to explore the conformational space of proteins under the guidance of a sophisticated probabilistic model of local structure and a given set of restraints that represent nonlocal interactions, such as hydrogen bonds or disulfide bridges. The choice of the restraints themselves is heuristic, but the resulting probabilistic model is well-defined and rigorous. Conceptually, TYPHON constitutes a null model of conformational fluctuations under a given set of restraints. We demonstrate that TYPHON can provide information on conformational fluctuations that is in correspondence with experimental measurements. TYPHON provides a flexible, yet computationally efficient, method to explore possible conformational fluctuations in proteins.

By the author/editor: Harder, Tim; Borg, Mikael; Bottaro, Sandro; Boomsma, Wouter; Olsson, Simon; Ferkinghoff-Borg ...; show more...; Hamelryck, Thoma ...; show less...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Biophysics

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