In Silico Calculation of Interhelical Angles in NCS1
Abstract
Proteins are important macromolecules responsible for a variety of processes in living organisms. One of the most important features of proteins is their ability to respond to environmental stimuli, such as changes in intracellular metal concentration by binding metal ions, which in turns triggers structural changes within the protein that can modify its function or allow the protein to participate in a signaling pathway. One such signaling protein is the so-called neuronal calcium sensor 1 protein or NCS1, which binds Ca2+ along with other abiogenic metals such as Li+, and the metal binding regulates NCS1 interactions with other intracellular partners. NCS1 binds Ca2+ ions through the EF-hands, consisting of a helix-loop-helix motif. The exact nature of the structural changes triggered by Ca2+ binding to the EF-hands in NCS1 is currently unknown. In an attempt to elucidate the nature of these structural changes, we performed a variety of molecular dynamics simulations on NCS1 in the calcium bound, lithium bound, and metal unbound states. We then calculated the angles between helices in EF-hands to determine if these angles change upon metal ion binding. Using the outputs of the molecular dynamics simulations, we developed a python script in house using MDAnalysis and Numpy libraries to select and calculate the angle between each alpha helix pair as a function of simulation time. Based on our calculations, the EF-hand interhelical angles change significantly upon metal…
How strong is the evidence?
Evidence Hub reads this as a report, done in computer models (in silico), not in people. Its evidence level is 5 of 5 (Very low · case / narrative / animal / in vitro / in silico). Case reports, narrative reviews, and animal, cell or computer-model studies give the weakest evidence for human health.
Read the paper
Related studies
- Quantum dots: synthesis, bioapplications, and toxicity
- A Guide to In Silico Drug Design
- Quantum Computing for Healthcare: A Review
- Automated in Silico Design of Homogeneous Catalysts
- Identification of Novel 3-Hydroxy-pyran-4-One Derivatives as Potent HIV-1 Integrase Inhibitors Using in silico Structure-Based Combinatorial Library Design Approach
- In silico structural elucidation of RNA-dependent RNA polymerase towards the identification of potential Crimean-Congo Hemorrhagic Fever Virus inhibitors
Go deeper in Evidence Hub
Evidence Hub adds a study data sheet (design, sample size, evidence level, key numbers), an AI summary and a chat grounded in the paper's text.