Related Experiment Video
Updated: Apr 7, 2026

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
Published on: November 29, 2013
Energy exchange network of inter-residue interactions within a thermally fluctuating protein molecule: A
Takakazu Ishikura1, Yuki Iwata1, Tatsuro Hatano1
1Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, 464-8602, Japan.
Abstract:
Protein function is regulated not only by the structure but also by physical dynamics and thermal fluctuations. We have developed the computer program, CURrent calculation for proteins (CURP), for the flow analysis of physical quantities within thermally fluctuating protein media. The CURP program was used to calculate the energy flow within the third PDZ domain of the neuronal protein PSD-95, and the results were used to illustrate the energy exchange network of inter-residue interactions based on atomistic molecular dynamics simulations. The removal of the α3 helix is known to decrease ligand affinity by 21-fold without changing the overall protein structure; nevertheless, we demonstrated that the helix constitutes an essential part of the network graph.
Related Concept Videos
Noncovalent Attractions in Biomolecules
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Noncovalent Attractions in Biomolecules
Protein-protein Interfaces
Protein-Protein Interfaces
Protein Diffusion in the Membrane
Protein Folding
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

