Abstract
The response of the calmodulin (CaM) protein as a function of calcium ion removal, ionic strength, and temperature at physiological pH condition was investigated using classical molecular dynamics simulations. Changing the ionic strength and temperature came out to be two of the possible routes for observing a conformation change in the protein. This behavior is similar to the conformation change observed in our previous study where a change in the pH was observed to trigger a conformation change in this protein. In the present study, as the calcium ions are removed from the protein, the protein is observed to acquire more flexibility. This flexibility is observed to be more prominent at a higher ionic strength. At a lower ionic strength of 150 mM with all the four calcium ions intact, the N- and C-lobes are observed to come close to a distance of 30 Å starting from an initial separation distance of 48 Å. This conformation change is observed to take place around 50 ns in a simulation of 100 ns. As a second parameter, temperature is observed to play a key role in the conformation change of the protein. With an increase in the temperature, the protein is observed to acquire a more compact form with the formation of different salt bridges between the residues of the N- and the C-lobes. The salt bridge formation leads to an overall lowering of the energy of the protein thus favoring the bending of the two lobes towards each other. The improper and dihedral terms show a significant shift thus leading to a more compact form on increasing the temperature. Another set of simulations is also performed at an increased temperature of 500 K to verify the reproducibility of the results. Thus a set of three possible alterations in the environmental conditions of the protein CaM are studied, with two of them giving rise to a conformation change and one adding flexibility to the protein.
Highlights
Proteins are one of the most important parts present inside the eukaryotic cells
We discuss the results of all our molecular dynamics (MD) simulation sets: (1) calcium ion removal, (2) ionic strength change, and (3) temperature variation case
Root mean square deviation (RMSD) and distance distribution of residues 34–110 are used as a measure to study these conformations of the protein
Summary
Proteins are one of the most important parts present inside the eukaryotic cells One such protein named calmodulin is well known for its key role as a calcium ion carrier inside these cells [1]. This protein helps in various physiological processes inside these cells by activating different enzymes of various types [2]. Because of its various available forms, this protein is capable of sustaining large conformation changes which depend upon the partner to which it is interacting [1, 3, 4] These conformation changes would greatly be affected by the various environmental conditions of the protein. The environmental conditions would include a vast number of parameters though these sets of conditions are chosen as a first step in this work
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callMore From: Journal of biophysics (Hindawi Publishing Corporation : Online)
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
