ArticleBMC structural biology2015
Clustering and percolation in protein loop structures.
Article in BMC structural biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Insights into Comparative Modeling of VInternational journal of molecular sciences · 2021Article
- Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example.PloS one · 2021Article
- Protein tertiary structure and the myoglobin phase diagram.Scientific reports · 2019Article
- Molecular docking studies of α-mangostin, γ-mangostin, and xanthone on peroxisome proliferator-activated receptor gamma diphenyl peptidase-4 enzyme, and aldose reductase enzyme as an antidiabetic drug candidate.Journal of advanced pharmaceutical technology & researchArticle
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3 authors.
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Abstract
backgroundHigh precision protein loop modelling remains a challenge, both in template based and template independent approaches to protein structure prediction.
methodWe 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.
resultsWe 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.
conclusionsProtein 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.
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