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Protein Organization01:24

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Quantitative Structural Interpretation of Protein Crosslinks.

Isaac Filella-Merce1, Benjamin Bardiaux2, Michael Nilges2

  • 1Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, C3BI, USR3756 Paris, France; Faculty of Health and Life Sciences, University Pompeu Fabra, Carrer del Doctor Aiguader 80, Barcelona 08003, Spain.

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|November 23, 2019
PubMed
Summary
This summary is machine-generated.

This study introduces NRGXL, a new method for protein crosslinking analysis that models crosslinker flexibility and protein dynamics for more accurate structural characterization. NRGXL improves 3D model validation using chemical crosslinking data.

Keywords:
NRGXLbinary classification studycrosslinksmodelingprotein complexesrestraintssampling

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Chemical crosslinking coupled with mass spectrometry is vital for protein assembly structure determination.
  • Current methods often oversimplify crosslinker flexibility and physico-chemical interactions, limiting accuracy in molecular modeling.

Purpose of the Study:

  • To develop a novel computational method, NRGXL, for enhanced analysis of chemical crosslinking data.
  • To incorporate crosslinker flexibility, side-chain dynamics, and protein dynamics into structural modeling.

Main Methods:

  • Developed NRGXL (new realistic grid for crosslinks), a method that explicitly samples conformations to model crosslinker and side-chain flexibility.
  • Integrated modeling of overall protein dynamics.
  • Created a physical model of the crosslinker with associated energy calculations.

Main Results:

  • The NRGXL classifier demonstrated superior performance compared to methods relying on Euclidean or solvent-accessible distances.
  • The method efficiently handles protein dynamics, enhancing its applicability.
  • NRGXL provides a robust framework for validating 3D models derived from crosslinking data.

Conclusions:

  • NRGXL offers a more realistic and accurate approach to interpreting chemical crosslinking data for protein structure analysis.
  • The method's efficiency and improved accuracy facilitate better validation of 3D protein assembly models.
  • NRGXL is available as a free web server for broader scientific use.