Spatio-temporal coordination among functional residues in protein.
Sutapa Dutta1, Mahua Ghosh1, J Chakrabarti1,2
1Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India.
Scientific Reports
|January 17, 2017
Summary
Researchers explored bio-macromolecule communication using temporal cross-correlation analysis. This study reveals insights into protein dynamics and function at a microscopic level.
Area of Science:
- Biophysics
- Computational Biology
- Protein Dynamics
Background:
- Understanding bio-macromolecule functional site communication is crucial for deciphering molecular mechanisms.
- Temporal cross-correlation analysis offers a method to study these interactions.
Purpose of the Study:
- To investigate communication pathways within bio-macromolecules at a microscopic level.
- To analyze temporal cross-correlations between binding sites in proteins.
Main Methods:
- Utilized Molecular Dynamics (MD) simulations.
- Analyzed temporal cross-correlations between dihedral angles of protein residues.
- Developed a general mathematical model to explain observed cross-correlations.
Main Results:
- Identified non-trivial temporal cross-correlations in ubiquitin's dihedral angles.
- Observed low-frequency peaks (nanosecond timescales) and a universal algebraic tail at high frequencies.
- Demonstrated the existence of communication pathways among functional residues.
Conclusions:
- Temporal cross-correlations reveal microscopic communication mechanisms in bio-macromolecules.
- This analytical framework can advance the understanding of protein functions.
- The findings suggest a general approach applicable to various bio-macromolecular systems.
Related Concept Videos
01:49Conserved Binding Sites
5.3K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.3K
02:26Conservation of Protein Domains Over Different Proteins
14.9K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
14.9K
01:19Protein Dynamics in Living Cells
2.8K
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...
2.8K
00:49Ligand Binding and Linkage
5.8K
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...
5.8K
02:26Conservation of Protein Domains
4.3K
4.3K
01:56Structural Protein Function
3.3K
3.3K