Significance of Knotted Structures for Function of Proteins and Nucleic Acids
Thursday Abstracts
Knots and Slipknots in Proteins
Kenneth Millett
.
University of California, Santa Barbara, Santa Barbara, USA.
The strict conservation of knotted and slipknotted features within protein families despite large
sequence divergence suggests the possibility of an important physiological role and the utility of
a deeper understanding of their spatial character vis-à-vis the entire structure in order to identify
contributing evidence that can clarify their role. The “knotting fingerprint” has provided a
foundational method by which to encode and assess these structures. Its generation and
application to protein structures provide the principal foci of the presentation.
What Forces Drive Conformational Changes?
Robert L. Jernigan
, Jie Liu, Yuan Wang, Kejue Jia, Kannan Sankar.
Iowa State University, Ames, USA.
There are now many conformational transitions known for proteins. In many cases the transition
directions appear to be an intrinsic property of the structure itself, and this has been observed in
many cases by the use of elastic network models. This approach is successful for transitions from
open to closed forms in enzymes. However, the elastic models cannot describe the opposite
transitions from closed to open forms. In such cases forces may be required to open a protein
structure. If the protein is an enzyme and its chemical reaction is exothermic, then this could be
the origin of the forces. Wherever ATP hydrolysis is involved, this seems likely.
Meaningful dynamics information can be extracted from multiple experimental structures of the
same, or closely related, proteins or RNAs. Usually only a few principal components dominate
the motions of the structures, and these usually relate to the functional dynamics. This dynamics
information provides strong evidence for the plasticity of protein and RNA structures, and also
suggests that these structures almost always have a highly limited repertoire of motions. The
variabilities of the internal distances among such a set of structures can be used to construct
elastic models that represent well these variabilities.
We are computing pathways for transitions from closed to open forms, by applying forces to
elastic models, by generating structures with a Metropolis Monte Carlo method, using free
energies for structural intermediates computed using our 4-body potentials and entropies from
elastic network models.
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