Related Experiment Video
Updated: Aug 4, 2026
07:08
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
PDB2CD visualises dynamics within protein structures
1School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK. r.w.janes@qmul.ac.uk.
European Biophysics Journal : EBJ
|April 5, 2017
Summary
This study introduces PDB2CD, a bioinformatics tool that visualizes protein conformational differences between solution nuclear magnetic resonance (NMR) and crystal structures using circular dichroism (CD) spectroscopy.
Area of Science:
- Biophysics
- Structural Biology
- Bioinformatics
Background:
- Proteins possess defined conformations crucial for their biological functions.
- Atomic resolution protein structures are typically determined using solution nuclear magnetic resonance (NMR) and X-ray crystallography.
- Discrepancies in protein conformations are often observed between NMR and crystal structures.
Purpose of the Study:
- To examine and visualize conformational differences between protein structures obtained from NMR and crystallography.
- To introduce a novel bioinformatics approach for comparing these structural ensembles.
Main Methods:
- Utilizing atomic resolution structural data from NMR and crystal structures.
- Employing circular dichroism (CD) spectroscopy to characterize protein structures in solution.
- Developing and applying the PDB2CD bioinformatics tool to generate CD spectra from protein structures.
Main Results:
- PDB2CD effectively visualizes conformational variations within NMR ensembles.
- The tool highlights differences between solution NMR and crystal structures.
- Observed differences suggest protein dynamics in solution versus ordered states in crystals.
Conclusions:
- The PDB2CD tool offers a novel method for visualizing and comparing protein conformations.
- This approach aids in understanding the dynamic range and conformational flexibility of proteins.
- Comparing NMR and crystal structures provides insights into protein behavior in different environments.
Related Concept Videos
02:18Intrinsically Disordered Proteins
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
01:24Protein Organization
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.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
02:15Protein and Protein Structures
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...
01:19Protein Dynamics in Living Cells
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...