inactive, active-like functional states, fully active state with
G-protein and intermediate states linking these states. Agonist
binding generally tends to shift the conformational ensemble that
closer resembles the active-like states [29, 35]. A key unresolved
mystery is how GPCRs transmit the allosteric signal across the TM
region leading to activation. In particular, how does binding of
certain ligands (agonists, partial agonist, positive allosteric modulators, etc.) trigger an allosteric transmission and the necessary
conformational change for activation at the intracellular part of
the receptor, while other ligands such as antagonists do not produce this effect. The mechanism that controls ligand binding and
GPCR activation is extremely complex, and this puzzle is a major
research interest with big implications to design of novel therapeutics [30, 34].
Adenosine receptor is a prototypical family A GPCR and probing how it functions and transmits allosteric signals across the TM
region is critical for deepening our overall understanding of GPCR
activation mechanism. The A 2A receptor plays an important role in
regulating myocardial oxygen consumption, coronary blood flow,
and is a drug target for multitude of disorders (inflammation,
insomnia, Parkinson’s disease, cancer, diabetes, infectious diseases,
and neuronal defect disorders) [31, 35, 36].
To provide insight into potential allosteric mechanism activation in GPCRs, we have applied the RTA algorithm on several
structures of human adenosine A 2A receptor (Fig. 5). We defined
site A as the orthosteric site (here taken to be all atoms and bonds
that are interacting with the agonist (or antagonist)) and site B
chosen as residues 230 and 291 at the intracellular side where the
receptor interacts with the G protein (Fig. 5b). Starting with four
crystal structures of A 2A receptor in the presence of different
ligands, RTA algorithm was performed for all hydrogen bond
energy cutoffs h (see Subheading 3.2) in increment steps of
0.01 kcal/mol and DOF transmission (DOF
AB ) is calculated for
each cutoff h. Results are shown in Fig. 5c.
The RTA algorithm predicts that in all three agonist-bound
(active-like) structures, perturbation of rigidity at the orthorsteric
site will transmit across the receptor, and in turn induce a change in
conformational DOF at a remote G protein binding region. The
addition of agonist allosterically restricts the overall available DOF
at the G-protein binding region, and in terms of conformational
selection, agonist binding will bias the receptor to more often
sample the conformational state(s) increasing the likelihood for
GPCR activation and interaction with G protein [29]. On the
other hand, in the inactive structure with a bound antagonist, no
DOF transmission occurs; equivalently no allosteric transmission is
induced. This analysis suggests that transmissions of rigidity and
DOF upon binding of agonist are important for facilitating structural and conformational changes at G-protein binding region, and
Probing Allosteric Mechanism with Rigidity Transmission
71
G-protein and intermediate states linking these states. Agonist
binding generally tends to shift the conformational ensemble that
closer resembles the active-like states [29, 35]. A key unresolved
mystery is how GPCRs transmit the allosteric signal across the TM
region leading to activation. In particular, how does binding of
certain ligands (agonists, partial agonist, positive allosteric modulators, etc.) trigger an allosteric transmission and the necessary
conformational change for activation at the intracellular part of
the receptor, while other ligands such as antagonists do not produce this effect. The mechanism that controls ligand binding and
GPCR activation is extremely complex, and this puzzle is a major
research interest with big implications to design of novel therapeutics [30, 34].
Adenosine receptor is a prototypical family A GPCR and probing how it functions and transmits allosteric signals across the TM
region is critical for deepening our overall understanding of GPCR
activation mechanism. The A 2A receptor plays an important role in
regulating myocardial oxygen consumption, coronary blood flow,
and is a drug target for multitude of disorders (inflammation,
insomnia, Parkinson’s disease, cancer, diabetes, infectious diseases,
and neuronal defect disorders) [31, 35, 36].
To provide insight into potential allosteric mechanism activation in GPCRs, we have applied the RTA algorithm on several
structures of human adenosine A 2A receptor (Fig. 5). We defined
site A as the orthosteric site (here taken to be all atoms and bonds
that are interacting with the agonist (or antagonist)) and site B
chosen as residues 230 and 291 at the intracellular side where the
receptor interacts with the G protein (Fig. 5b). Starting with four
crystal structures of A 2A receptor in the presence of different
ligands, RTA algorithm was performed for all hydrogen bond
energy cutoffs h (see Subheading 3.2) in increment steps of
0.01 kcal/mol and DOF transmission (DOF
AB ) is calculated for
each cutoff h. Results are shown in Fig. 5c.
The RTA algorithm predicts that in all three agonist-bound
(active-like) structures, perturbation of rigidity at the orthorsteric
site will transmit across the receptor, and in turn induce a change in
conformational DOF at a remote G protein binding region. The
addition of agonist allosterically restricts the overall available DOF
at the G-protein binding region, and in terms of conformational
selection, agonist binding will bias the receptor to more often
sample the conformational state(s) increasing the likelihood for
GPCR activation and interaction with G protein [29]. On the
other hand, in the inactive structure with a bound antagonist, no
DOF transmission occurs; equivalently no allosteric transmission is
induced. This analysis suggests that transmissions of rigidity and
DOF upon binding of agonist are important for facilitating structural and conformational changes at G-protein binding region, and
Probing Allosteric Mechanism with Rigidity Transmission
71