20 research outputs found
Equipartition Principle for Internal Coordinate Molecular Dynamics
The <i>principle of equipartition of (kinetic) energy</i> for all-atom Cartesian molecular dynamics states that each momentum
phase space coordinate on the average has <i>kT</i>/2 of
kinetic energy in a canonical ensemble. This principle is used in
molecular dynamics simulations to initialize velocities, and to calculate
statistical properties such as entropy. Internal coordinate molecular
dynamics (ICMD) models differ from Cartesian models in that the overall
kinetic energy depends on the generalized coordinates and includes
cross-terms. Due to this coupled structure, no such equipartition
principle holds for ICMD models. In this paper, we introduce noncanonical <i>modal coordinates</i> to recover some of the structural simplicity
of Cartesian models and develop a new equipartition principle for
ICMD models. We derive low-order recursive computational algorithms
for transforming between the modal and physical coordinates. The equipartition
principle in modal coordinates provides a rigorous method for initializing
velocities in ICMD simulations, thus replacing the <i>ad hoc</i> methods used until now. It also sets the basis for calculating conformational
entropy using internal coordinates
Conserved Mechanism of Conformational Stability and Dynamics in GāProtein-Coupled Receptors
G-protein-coupled
receptors (GPCRs) are transmembrane receptors
involved in diverse biological functions. Despite the diversity in
their amino acid sequences, class A GPCRs exhibit a conserved structural
topology and possibly a common mechanism of receptor activation. To
understand how this high sequence diversity translates to a conserved
functional mechanism, we have compared the dynamic behavior of eight
class A GPCRs comprised of six biogenic amine receptors, adenosine
A<sub>2A</sub>, and the peptide receptor protease-activated receptor
1. Starting from the crystal structures of the inactive state of these
receptors bound to inverse agonists or antagonists, we have performed
multiple all-atom MD simulations adding up to several microseconds
of simulation. We elucidated the similarities and differences in the
dynamic behavior and the conformational ensembles sampled by these
eight class A GPCRs. Among the six biogenic amine receptors studied
here, Ī²<sub>2</sub>-adrenergic receptor shows the highest level
of fluctuation in the sixth and seventh transmembrane helices, possibly
explaining its high basal activity. In contrast, the muscarinic acetylcholine
receptors show the lowest fluctuations as well as tight packing and
low hydration of the transmembrane domain. All eight GPCRs show several
conserved allosteric communication pipelines from the residues in
the agonist binding site with the G-protein interface. Positions of
the residues along these pipelines that serve as major hubs of allosteric
communication are conserved in their respective structures. These
findings have important implications in understanding the dynamics
and allosteric mechanism of communication in class A GPCRs and hence
are useful for designing conformation-specific drugs
Structural Dynamics and Thermostabilization of Neurotensin Receptor 1
The neurotensin receptor NTSR1 binds
the peptide agonist neurotensin
(NTS) and signals preferentially via the G<sub>q</sub> protein. Recently,
Grisshammer and co-workers reported the crystal structure of a thermostable
mutant NTSR1-GW5 with NTS bound. Understanding how the mutations thermostabilize
the structure would allow efficient design of thermostable mutant
GPCRs for protein purification, and subsequent biophysical studies.
Using microsecond scale molecular dynamics simulations (4 Ī¼s)
of the thermostable mutant NTSR1-GW5 and wild type NTSR1, we have
elucidated the structural and energetic factors that affect the thermostability
and dynamics of NTSR1. The thermostable mutant NTSR1-GW5 is found
to be less flexible and less dynamic than the wild type NTSR1. The
point mutations confer thermostability by improving the interhelical
hydrogen bonds, hydrophobic packing, and receptor interactions with
the lipid bilayer, especially in the intracellular regions. During
MD, NTSR1-GW5 becomes more hydrated compared to wild type NTSR1, with
tight hydrogen bonded water clusters within the transmembrane core
of the receptor, thus providing evidence that water plays an important
role in improving helical packing in the thermostable mutant. Our
studies provide valuable insights into the stability and functioning
of NTSR1 that will be useful in future design of thermostable mutants
of other peptide GPCRs
Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures
DNA three-way junctions (TWJs) are important intermediates
in various
cellular processes and are the simplest of a family of branched nucleic
acids being considered as scaffolds for biomolecular nanotechnology.
Branched nucleic acids are stabilized by divalent cations such as
Mg<sup>2+</sup>, presumably due to condensation and neutralization
of the negatively charged DNA backbone. However, electrostatic screening
effects point to more complex solvation dynamics and a large role
of interfacial waters in thermodynamic stability. Here, we report
extensive computer simulations in explicit water and salt on a model
TWJ and use free energy calculations to quantify the role of ionic
character and strength on stability. We find that enthalpic stabilization
of the first and second hydration shells by Mg<sup>2+</sup> accounts
for 1/3 and all of the free energy gain in 50% and pure MgCl<sub>2</sub> solutions, respectively. The more distorted DNA molecule is actually
destabilized in pure MgCl<sub>2</sub> compared to pure NaCl. Notably,
the first shell, interfacial waters have very low translational and
rotational entropy (i.e., mobility) compared to the bulk, an entropic
loss that is overcompensated by increased enthalpy from additional
electrostatic interactions with Mg<sup>2+</sup>. In contrast, the
second hydration shell has anomalously high entropy as it is trapped
between an immobile and bulklike layer. The nonmonotonic entropic
signature and long-range perturbations of the hydration shells to
Mg<sup>2+</sup> may have implications in the molecular recognition
of these motifs. For example, we find that low salt stabilizes the
parallel configuration of the three-way junction, whereas at normal
salt we find antiparallel configurations deduced from the NMR. We
use the 2PT analysis to follow the thermodynamics of this transition
and find that the free energy barrier is dominated by entropic effects
that result from the decreased surface area of the antiparallel form
which has a smaller number of low entropy waters in the first monolayer
Protein Structure Refinement of CASP Target Proteins Using GNEIMO Torsional Dynamics Method
A longstanding
challenge in using computational methods for protein
structure prediction is the refinement of low-resolution structural
models derived from comparative modeling methods into highly accurate
atomistic models useful for detailed structural studies. Previously,
we have developed and demonstrated the utility of the internal coordinate
molecular dynamics (MD) technique, generalized NewtonāEuler
inverse mass operator (GNEIMO), for refinement of small proteins.
Using GNEIMO, the high-frequency degrees of freedom are frozen and
the protein is modeled as a collection of rigid clusters connected
by torsional hinges. This physical model allows larger integration
time steps and focuses the conformational search in the low frequency
torsional degrees of freedom. Here, we have applied GNEIMO with temperature
replica exchange to refine low-resolution protein models of 30 proteins
taken from the continuous assessment of structure prediction (CASP)
competition. We have shown that GNEIMO torsional MD method leads to
refinement of up to 1.3 Ć
in the root-mean-square deviation in
coordinates for 30 CASP target proteins without using any experimental
data as restraints in performing the GNEIMO simulations. This is in
contrast with the unconstrained all-atom Cartesian MD method performed
under the same conditions, where refinement requires the use of restraints
during the simulations
Dynamic Behavior of the Active and Inactive States of the Adenosine A<sub>2A</sub> Receptor
The adenosine A<sub>2A</sub> receptor
(A<sub>2A</sub>R) belongs
to the superfamily of membrane proteins called the G-protein-coupled
receptors (GPCRs) that form one of the largest superfamilies of drug
targets. Deriving thermostable mutants has been one of the strategies
used for crystallization of A<sub>2A</sub>R in both the agonist and
antagonist bound conformational states. The crystal structures do
not reveal differences in the activation mechanism of the mutant receptors
compared to the wild type receptor, that have been observed experimentally.
These differences stem from the dynamic behavior of the mutant receptors.
Furthermore, it is not understood how the mutations confer thermostability.
Since these details are difficult to obtain from experiments, we have
used atomic level simulations to elucidate the dynamic behavior of
the agonist and antagonist bound mutants as well the wild type A<sub>2A</sub>R. We found that significant enthalpic contribution leads
to stabilization of both the inactive state (StaR2) and active-like
state (GL31) thermostable mutants of A<sub>2A</sub>R. Stabilization
resulting from mutations of bulky residues to alanine is due to the
formation of interhelical hydrogen bonds and van der Waals packing
that improves the transmembrane domain packing. The thermostable mutant
GL31 shows less movement of the transmembrane helix TM6 with respect
to TM3 than the wild type receptor. While restricted dynamics of GL31
is advantageous in its purification and crystallization, it could
also be the reason why these mutants are not efficient in activating
the G proteins. We observed that the calculated stress on each residue
is higher in the wild type receptor compared to the thermostable mutants,
and this stress is required for activation to occur. Thus, reduced
dynamic behavior of the thermostable mutants leading to lowered activation
of these receptors originates from reduced stress on each residue.
Finally, accurate calculation of the change in free energy for single
mutations shows good correlation with the change in the measured thermostability.
These results provide insights into the effect of mutations that can
be incorporated in deriving thermostable mutants for other GPCRs
Structure Refinement of Protein Low Resolution Models Using the GNEIMO Constrained Dynamics Method
The challenge in protein structure prediction using homology
modeling
is the lack of reliable methods to refine the low resolution homology
models. Unconstrained all-atom molecular dynamics (MD) does not serve
well for structure refinement due to its limited conformational search.
We have developed and tested the constrained MD method, based on the
generalized NewtonāEuler inverse mass operator (GNEIMO) algorithm
for protein structure refinement. In this method, the high-frequency
degrees of freedom are replaced with hard holonomic constraints and
a protein is modeled as a collection of rigid body clusters connected
by flexible torsional hinges. This allows larger integration time
steps and enhances the conformational search space. In this work,
we have demonstrated the use of torsional GNEIMO method without using
any experimental data as constraints, for protein structure refinement
starting from low-resolution decoy sets derived from homology methods.
In the eight proteins with three decoys for each, we observed an improvement
of ā¼2 Ć
in the rmsd in coordinates to the known experimental
structures of these proteins. The GNEIMO trajectories also showed
enrichment in the population density of native-like conformations.
In addition, we demonstrated structural refinement using a āfreeze
and thawā clustering scheme with the GNEIMO framework as a
viable tool for enhancing localized conformational search. We have
derived a robust protocol based on the GNEIMO replica exchange method
for protein structure refinement that can be readily extended to other
proteins and possibly applicable for high throughput protein structure
refinement
Computational Method To Identify Druggable Binding Sites That Target ProteināProtein Interactions
Proteināprotein
interactions are implicated in the pathogenesis
of many diseases and are therefore attractive but challenging targets
for drug design. One of the challenges in development is the identification
of potential druggable binding sites in protein interacting interfaces.
Identification of interface surfaces can greatly aid rational drug
design of small molecules inhibiting proteināprotein interactions.
In this work, starting from the structure of a free monomer, we have
developed a ligand docking based method, called ā<i>FindBindSite</i>ā (FBS), to locate proteināprotein interacting interface
regions and potential druggable sites in this interface. <i>FindBindSite</i> utilizes the results from docking a small and diverse library of
small molecules to the entire protein structure. By clustering regions
with the highest docked ligand density from FBS, we have shown that
these high ligand density regions strongly correlate with the known
proteināprotein interacting surfaces. We have further predicted
potential druggable binding sites on the protein surface using FBS,
with druggability being defined as the site with high density of ligands
docked. FBS shows a hit rate of 71% with high confidence and 93% with
lower confidence for the 41 proteins used for predicting druggable
binding sites on the proteināprotein interface. Mining the
regions of lower ligand density that are contiguous with the high
scoring high ligand density regions from FBS, we were able to map
70% of the proteināprotein interacting surface in 24 out of
41 structures tested. We also observed that FBS has limited sensitivity
to the size and nature of the small molecule library used for docking.
The experimentally determined hotspot residues for each proteināprotein
complex cluster near the best scoring druggable binding sites identified
by FBS. These results validate the ability of our technique to identify
druggable sites within proteināprotein interface regions that
have the maximal possibility of interface disruption
Thermostabilization of the Ī²<sub>1</sub>āAdrenergic Receptor Correlates with Increased Entropy of the Inactive State
The
dynamic nature of GPCRs is a major hurdle in their purification
and crystallization. Thermostabilization can facilitate GPCR structure
determination, as has been shown by the structure of the thermostabilized
Ī²<sub>1</sub>-adrenergic receptor (Ī²<sub>1</sub>AR) mutant,
m23-Ī²<sub>1</sub>AR, which has been thermostabilized in the
inactive state. However, it is unclear from the structure how the
six thermostabilizing mutations in m23-Ī²<sub>1</sub>AR affect
receptor dynamics. We have used molecular dynamics simulations in
explicit solvent to compare the conformational ensembles for both
wild type Ī²<sub>1</sub>AR (wt-Ī²<sub>1</sub>AR) and m23-Ī²<sub>1</sub>AR. Thermostabilization results in an increase in the number
of accessible microscopic conformational states within the inactive
state ensemble, effectively increasing the side chain entropy of the
inactive state at room temperature, while suppressing large-scale
main chain conformational changes that lead to activation. We identified
several diverse mechanisms of thermostabilization upon mutation. These
include decrease of long-range correlated movement between residues
in the G-protein coupling site to the extracellular region (Y227A<sup>5.58</sup>, F338M<sup>7.48</sup>), formation of new hydrogen bonds
(R68S), and reduction of local stress (Y227<sup>5.58</sup>, F327<sup>7.37</sup>, and F338<sup>7.48</sup>). This study provides insights
into microscopic mechanisms underlying thermostability that leads
to an understanding of the effect of these mutations on the structure
of the receptor
How Do Short Chain Nonionic Detergents Destabilize GāProtein-Coupled Receptors?
Stability
of detergent-solubilized G-protein-coupled receptors (GPCRs) is crucial
for their purification in a biologically relevant state, and it is
well-known that short chain detergents such as octylglucoside are
more denaturing than long chain detergents such as dodecylmaltoside.
However, the molecular basis for this phenomenon is poorly understood.
To gain insights into the mechanism of detergent destabilization of
GPCRs, we used atomistic molecular dynamics simulations of thermostabilized
adenosine receptor (A<sub>2A</sub>R) mutants embedded in either a
lipid bilayer or detergent micelles of alkylmaltosides and alkylglucosides.
A<sub>2A</sub>R mutants in dodecylmaltoside or phospholipid showed
low flexibility and good interhelical packing. In contrast, A<sub>2A</sub>R mutants in either octylglucoside or nonylglucoside showed
decreased Ī±-helicity in transmembrane regions, decreased Ī±-helical
packing, and the interpenetration of detergent molecules between transmembrane
Ī±-helices. This was not observed in octylglucoside containing
phospholipid. Cholesteryl hemisuccinate in dodecylmaltoside increased
the energetic stability of the receptor by wedging into crevices on
the hydrophobic surface of A<sub>2A</sub>R, increasing packing interactions
within the receptor and stiffening the detergent micelle. The data
suggest a three-stage process for the initial events in the destabilization
of GPCRs by octylglucoside: (i) highly mobile detergent molecules
form small micelles around the receptor; (ii) loss of Ī±-helicity
and decreased interhelical packing interactions in transmembrane regions
are promoted by increased receptor thermal motion; (iii) transient
separation of transmembrane helices allowed penetration of detergent
molecules into the core of the receptor. The relative hydration of
the headgroup and alkyl chain correlates with detergent harshness
and suggests new avenues to develop milder versions of octylglucoside
for receptor crystallization