Author ORCID Identifier

https://orcid.org/0000-0001-6912-507X

Document Type

Thesis

Date of Award

Spring 5-10-2022

Keywords

Calmodulin, protein, photocontrol, azobenzene, biochemistry, isomerization, binding, calcium, affinity, peptide

Degree Name

Biochemistry (BS)

Department

BIOCHEMISTRY

First Advisor

Dr. Puja Goyal

Second Advisor

Dr. Christof Grewer

Third Advisor

Dr. Jennifer Hirschi

Series

Science and Mathematics

Subject Heading(s)

Calmodulin; Photosensitizing compounds; Molecular dynamics

Abstract

The ability to control the activity and binding capability of enzymes in a reversible manner offers tremendous control over biological processes. Photocontrol, in particular, is promising in that electromagnetic radiation can be fine-tuned in terms of its strength, location, and duration. Photosensitive compounds, such as the azobenzene family, experience an isomerization at certain wavelengths, and attaching these compounds to enzymes has the potential to alter their structure and activity. Calmodulin (CaM) is a Ca2+ -sensitive signaling protein that has the ability to affect several downstream processes in eukaryotes and is an excellent target for photocontrol due to its small size and biological ubiquity. Each of CaM’s globular domains contain two EF-binding loops with the ability to bind Ca2+ ions. CaM primarily functions by receiving Ca2+ -ion signals and transducing these signals by binding to target proteins, including myosin light chain kinase, calcitonin, and several phosphatases. Computational methods such as molecular dynamics (MD) are a practical approach that allow the simulation of large biochemical systems. In this study, classical MD (cMD) simulations were used with the intention of determining the binding free energy of Ca2+ to CaM, and accelerated MD (aMD) trajectories were used to simulate the attachment of two conformations of PAM to different residue locations on CaM. The cMD simulations showed the ability of CaM to bind monovalent solvent ions, while the aMD simulations displayed different behavior between the cis- and trans- conformations of PAM.

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