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Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

Protein Complexes with Interchangeable Parts

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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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Conservation of Protein Domains

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Conservation of Protein Domains Over Different Proteins

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Nucleic Acid Structure

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Related Experiment Video

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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KOSMOS: a universal morph server for nucleic acids, proteins and their complexes.

Sangjae Seo¹, Moon Ki Kim

¹Department of Nano Science and Technology and School of Mechanical Engineering, Sungkyunkwan University, 300, Cheoncheon-dong, Jangan-gu, Suwon 440-746, Korea.

Nucleic Acids Research

|June 7, 2012

Summary

KOSMOS is a novel online server for analyzing macromolecular structural dynamics. It uniquely combines harmonic and anharmonic analyses, offering versatile coarse-graining and elastic network models for comprehensive molecular motion insights.

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Published on: April 26, 2013

Area of Science:

Structural Biology
Computational Biophysics
Bioinformatics

Background:

Understanding macromolecular structural dynamics is crucial for deciphering biological functions.
Existing tools often lack the versatility to analyze diverse molecular complexes and dynamics comprehensively.

Purpose of the Study:

To introduce KOSMOS, the first online morph server designed for comprehensive structural dynamics analysis of DNA/RNA, proteins, and their complexes.
To provide advanced tools for both harmonic and anharmonic analyses of macromolecular motion.

Main Methods:

Utilizes normal mode analysis (NMA) with elastic network models (ENM) for harmonic analysis, calculating vibrational modes and B-factors.
Employs elastic network interpolation (ENI) for anharmonic analysis to generate transition pathways between conformations.
Offers versatile coarse-graining methods and various ENM connection rules (distance-cutoff, number-cutoff, chemical-cutoff) for flexible model building.

Main Results:

KOSMOS enables detailed insights into potential biological functions through structural dynamics.
It generates plausible, sterically clash-free transition pathways between molecular conformations.
The server allows analysis with maximum degrees of freedom by integrating diverse ENM approaches.

Conclusions:

KOSMOS provides a powerful and versatile platform for studying macromolecular structural dynamics.
Its unique features in coarse-graining and ENM enhance the analysis of molecular motion and conformational changes.
The server facilitates a deeper understanding of the relationship between structure, dynamics, and biological function.