Cooperative allosteric ligand binding in calmodulin.
Degree: PhD, College of Arts and Sciences / Department of
Physics, 2017, Kent State University
Conformational dynamics is often essential for a
protein's function. For example, proteins are able to communicate
the effect of binding at one site to a distal region of the
molecule through changes in its conformational dynamics. This so
called allosteric coupling fine tunes the sensitivity of ligand
binding to changes in concentration. A conformational change
between a "closed" (apo) and an "open" (holo) conformation upon
ligation often produces this coupling between binding sites.
Enhanced sensitivity between the unbound and bound ensembles leads
to a sharper binding curve. There are two basic conceptual
frameworks that guide our visualization about ligand binding
mechanisms. First, a ligand can stabilize the unstable "open" state
from a dynamic ensemble of conformations within the unbound basin.
This binding mechanism is called conformational selection. Second,
a ligand can weakly bind to the low-affinity "closed" state
followed by a conformational transition to the "open" state. This
is called induced fit binding.In this dissertation, I focus on
molecular dynamics simulations to understand microscopic origins of
ligand binding cooperativity. A minimal model of allosteric binding
transitions must include ligand binding/unbinding events, while
capturing the transition mechanism between two distinct meta-stable
free energy basins. Due in part to computational timescales
limitations, work in this dissertation describes large-scale
conformational transitions through a simplified, coarse-grained
model based on the energy basins defined by the open and closed
conformations of the protein Calmodulin (CaM). CaM is a ubiquitous
calcium-binding protein consisting of two structurally similar
globular domains connected by a flexible linker. The two domains of
CaM, N-terminal domain (nCaM) and C-terminal domain (cCaM) consists
of two helix-loop-helix motifs (the EF-hands) connected by a
flexible linker. Each domain of CaM consists of two binding loops
and binds 2 calcium ions each. The intact domain binds up to 4
calcium ions. The simulations use a coupled molecular
dynamics/monte carlo scheme where the protein dynamics is simulated
explicitly, while ligand binding/unbinding are treated implicitly.
This helps us characterize complementary thermodynamic and kinetic
description of calcium binding mechanism to CaM.In the model,
ligand binding/unbinding events coupled with a conformational
change of the protein within the grand canonical ensemble. Here,
ligand concentration is controlled through the chemical potential
(µ). This allows us to use a simple thermodynamic model to analyze
the simulated data and quantify binding cooperativity. Simulated
binding titration curves are calculated through equilibrium
simulations at different values of µ.First, I study domain opening
transitions of isolated nCaM and cCaM in the absence of calcium.
This work is motivated by results from a recent analytic
variational model that predicts distinct domain opening transition
mechanism for the domains of CaM. This is a surprising result
Advisors/Committee Members: Portman, John (Advisor).
Subjects/Keywords: Physics; Biophysics; Protein; Ligand; Free Energy; Conformational Dynamics; Allostery; Cooperativity
to Zotero / EndNote / Reference
APA (6th Edition):
Nandigrami, P. (2017). Cooperative allosteric ligand binding in calmodulin. (Doctoral Dissertation). Kent State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=kent1507302866723977
Chicago Manual of Style (16th Edition):
Nandigrami, Prithviraj. “Cooperative allosteric ligand binding in calmodulin.” 2017. Doctoral Dissertation, Kent State University. Accessed March 20, 2018.
MLA Handbook (7th Edition):
Nandigrami, Prithviraj. “Cooperative allosteric ligand binding in calmodulin.” 2017. Web. 20 Mar 2018.
Nandigrami P. Cooperative allosteric ligand binding in calmodulin. [Internet] [Doctoral dissertation]. Kent State University; 2017. [cited 2018 Mar 20].
Available from: http://rave.ohiolink.edu/etdc/view?acc_num=kent1507302866723977.
Council of Science Editors:
Nandigrami P. Cooperative allosteric ligand binding in calmodulin. [Doctoral Dissertation]. Kent State University; 2017. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=kent1507302866723977