MSc.Thesis Defense:Büşra Tayhan
EXPLORING THE SHIFTS IN THE ENERGY LANDSCAPE OF
CALMODULIN UNDER DIFFERENT ENVIRONMENTAL CONDITIONS
Büşra Tayhan
Molecular Biology, Genetics and Bioengineering
MSc. Thesis, 2024
Thesis Jury
Prof. Dr. Canan Atılgan (Thesis Advisor),
Prof. Dr. Ali Rana Atılgan (Thesis Co-Advisor),
Assoc. Prof. Dr. Umut Şahin,
Assoc. Prof. Dr. Öznur Taştan,
Prof. Dr. Nihan Çelebi.
Date & Time: 20th of December, 2024 – 13:00
Place: FMAN G056
Keywords : molecular dynamics simulations, calmodulin,
metadynamics simulations, ionic strength, collective variables.
Abstract
Proteins are flexible structures, and their functions are closely tied to their ability to adopt multiple conformations. Their dynamic nature enables them to shift between different shapes or states, which is crucial for interacting with other biomolecules or catalyzing reactions. This behavior of proteins is strongly influenced by environmental conditions, such as temperature, pH, and ionic strength, which can significantly alter their structural states and functions.In this thesis, we investigate how the conformational landscape of proteins shifts under changing environmental conditions. Our model system is calmodulin (CaM), a calcium-binding protein involved in numerous cellular processes. Known for its adaptability, CaM exhibits a wide array of conformations under various experimental conditions, making it an ideal candidate for studying environmental effects on protein dynamics. Moreover, CaM serves as the sensing domain in genetically encoded fluorescent calcium biosensors, highlighting the importance of understanding its conformational changes for designing efficient and responsive sensors. The regions visited by CaM are well-represented by a pair of essential degrees of freedom (DoF) describing the relative positioning of its two lobes (cis/trans) and the compactness of the overall CaM structure. Since the time scale of classical molecular dynamics (MD) simulations do not allow for overcoming the high energy barriers that might separate various minima, we resort to well-tempered metadynamics simulations using the essential DoF as collective variables (CVs). We explore four different conditions representing Ca2+ bound/unbound CaM at physiological/low ionic strength. We find that CaM acts like a juggler, adjusting the position of its minima between four stable regions (cis-compact, trans-compact, cis-open, trans-open). After identifying the locations of the minima via metadynamics, we select representative structures from these minima and perform equilibration runs. Our work unveils the structural basis of the observed minima and validates the effectiveness of our chosen CVs. Our results reveal that, although the energy surface is much shallower under low ionic strength (IS) conditions, conformers get stuck in artificial minima due to strong transient salt bridges. It appears that ions act as lubricants, helping to release salt bridges that cause the conformers to become trapped. As a result, we find IS of the environment to be a major factor to be considered in protein design problems.