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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Published on: July 25, 2013

Clustering and percolation in protein loop structures.

Xubiao Peng¹, Jianfeng He², Antti J Niemi^3,4

¹Department of Physics and Astronomy, Uppsala University, P.O. Box 803, Uppsala, S-75108, Sweden. xubiaopeng@gmail.com.

BMC Structural Biology

|October 30, 2015

Summary

This summary is machine-generated.

Protein loops are modular, built from common fragments described by the nonlinear Schrödinger equation. Unique fragments may relate to protein function, and sequence doesn't uniquely determine loop structure.

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Combining Wet and Dry Lab Techniques to Guide the Crystallization of Large Coiled-coil Containing Proteins

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Published on: January 6, 2017

Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

Protein loop modeling is a persistent challenge in protein structure prediction.
Both template-based and template-independent methods face difficulties in achieving high precision.

Purpose of the Study:

To develop a quantitative method for classifying protein loop building blocks.
To systematically analyze the modular nature of loops in crystallographic protein structures.

Main Methods:

Introduced protein loop clustering and percolation concepts.
Developed a classification system for loop fragments based on a generalized discrete nonlinear Schrödinger (DNLS) equation.
Characterized fragments as local energy minima.

Main Results:

Loop fragments accurately represent ultrahigh resolution protein structures (0.2 Å RMS precision).
A limited set of 12 fragments describes approximately 38% of ultrahigh resolution loops in the Protein Data Bank (PDB).
Identified both common and rare/unique loop fragments, with unique ones found even in myoglobin.

Conclusions:

Protein loops exhibit modular construction using fragments derived from the DNLS equation's kink solution.
Common fragments likely stabilize protein conformation, while rare/unique fragments may be functionally relevant.
Amino acid sequence does not uniquely dictate loop structure; variations exist for identical sequences.