Clustering and percolation in protein loop structures.
BACKGROUND
High precision protein loop modelling remains a challenge, both in template based and template independent approaches to protein structure prediction.


METHODS
We introduce the concepts of protein loop clustering and percolation, to develop a quantitative approach to systematically classify the modular building blocks of loops in crystallographic folded proteins. These fragments are all different parameterisations of a unique kink solution to a generalised discrete nonlinear Schrödinger (DNLS) equation. Accordingly, the fragments are also local energy minima of the ensuing energy function.


RESULTS
We show how the loop fragments cover practically all ultrahigh resolution crystallographic protein structures in Protein Data Bank (PDB), with a 0.2 Ångström root-mean-square (RMS) precision. We find that no more than 12 different loop fragments are needed, to describe around 38 % of ultrahigh resolution loops in PDB. But there is also a large number of loop fragments that are either unique, or very rare, and examples of unique fragments are found even in the structure of a myoglobin.


CONCLUSIONS
Protein loops are built in a modular fashion. The loops are composed of fragments that can be modelled by the kink of the DNLS equation. The majority of loop fragments are also common, which are shared by many proteins. These common fragments are probably important for supporting the overall protein conformation. But there are also several fragments that are either unique to a given protein, or very rare. Such fragments are probably related to the function of the protein. Furthermore, we have found that the amino acid sequence does not determine the structure in a unique fashion. There are many examples of loop fragments with an identical amino acid sequence, but with a very different structure.
Department of Physics and Astronomy, Uppsala University, P.O. Box 803, Uppsala, S-75108, Sweden. xubiaopeng@gmail.com.
Xubiao
X
Peng
School of Physics, Beijing Institute of Technology, Beijing, 100081, People's Republic of China. hjf@bit.edu.cn.
Jianfeng
J
He
Department of Physics and Astronomy, Uppsala University, P.O. Box 803, Uppsala, S-75108, Sweden. Antti.Niemi@physics.uu.se.|Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, Tours, F37200, France. Antti.Niemi@physics.uu.se.
Antti J
AJ
Niemi
D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D011506:Proteins