The Relaxed Complex Method: Accommodating Receptor Flexibility for Drug Design with an Improved Scoring SchemeJung-Hsin Lin, Alexander L. Perryman, Julie R. Schames and J. Andrew McCammonBiopolymers, Vol. 68, Issue 1, pp. 47-62 (2003, Kollman memorial issue) [PubMed 12579579]An extension of the new computational methodology for drug design, the
"relaxed complex" method (http://dx.doi.org/10.1021/ja0260162"
target="_blank" class="ref">J.-H. Lin, A.L. Perryman, J. Schames, J.A.
McCammon, J. Amer. Chem. Soc. 124, 2002, 5632-5633), that accommodates
receptor flexibility is described. This "relaxed complex" method
recognizes that ligand may bind to conformations that occur only rarely
in the dynamics of the receptor. We have shown that the ligand-enzyme
binding modes are very sensitive to the enzyme conformations, and our
approach is capable of finding the best ligand enzyme complexes. Rapid
docking serves as an efficient initial filtering method to screen a
myraid of docking modes to a limited set, and it is then followed by
more accurate scoring with the MM/PBSA approach to find the best
ligand-receptor complexes. The MM/PBSA scorings consistently indicate
that the calculated binding modes which are most similar to those
observed in the X-ray crystallographic complexes are the ones with the
lowest free energies.
Modeling HIV-1 Integrase Complexes Based on their Hydrodynamic PropertiesAlexei A. Podtelezhnikov, Kui Gao, Frederic D. Bushman and J. Andrew McCammonBiopolymers, Vol. 68, Issue 1, pp. 110-120 (2003, Kollman memorial issue) [PubMed 12579583]We present a model structure of a candidate tetramer for HIV-1
integrase. The model was built in 3 steps using data from fluorescence
anisotropy, structures of the individual integrase domains,
cross-linking data, and other biochemical data. First, the structure of
the full-length integrase monomer was modeled using the individual
domain structures and the hydrodynamic properties of the full-length
protein that was recently measured by fluorescence depolarization. We
calculated the rotational correlation times for different arrangements
of three integrase domains, revealing that only structures with close
proximity among the domains satisfied the experimental data. The
orientations of the domains were constrained by iterative tests against
the data on cross-linking and fooprinting in integrase-DNA complexes.
Second, the structure of an integrase dimer was obtained by joining the
model monomers in accordance with the available dimeric crystal
structures of the catalytic core. The hydrodynamic properties of the
dimer were in agreement with the experimental values. Third, the active
sites of the two model dimers were placed in agreement with the spacing
between the sites of integration on target DNA as well as the
integrase-DNA cross-linking data, resulting in 2-fold symmetry of a
tetrameric complex. The model is consistent with the experimental data
indicating that the F185K substitution, which is found in the model at
tetramerization interface, selectively disrupts correct complex
formation
in vitro and HIV replication
in vivo. Our model
of the integrase tetramer bound to DNA may help to design anti-integrase
inhibitors.
Electrostatic InteractionsNathan A. Baker and J. Andrew McCammonIn "Structural Bioinformatics," H. Weissig and P.E. Bourne, Eds., John Wiley & Sons, New York, pp. 427-440 (2003) [PubMed 12647398]An understanding of electrostatic interactions is essential for the full
development of structural bioinformatics. The structures of proteins and
other biopolymers are being determined at an increasing rate through
structural genomics and other efforts. Specific linkages of these
biopolymers in cellular pathways or supramolecular assemblages are being
detected by genetic and other experimental efforts. To integrate this
information in physical models for drug discovery and other applications
requires the ability to evaluate the energetic interactions within and
among biopolymers. Among the various components of molecular energetics,
the electrostatic interactions are of special importance due to the long
range of these interactions and the substantial charges of typical
components of biopolymers. Indeed, electrostatics can be used to help
assign biopolymers such as proteins to functional families, since
particular kinds of ligand binding sites may be indicated by the spatial
distribution of the charges in the proteins. In what follows, we provide
a brief overview of the roles of electrostatics in biopolymers and
supramolecular assemblages, and then outline some of the methods that
have been developed for analyzing electrostatic interactions.
Protein Flexibility and Computer-aided Drug DesignChung F. Wong and J. Andrew McCammonAnnual Review of Pharmacology and Toxicology, Vol. 43, No. 1, pp. 31-45 (2003) [PubMed 12142469]Although computational techniques are increasingly being used in
computer-aided drug design, the effects due to protein flexibility are
still ignored in many applications. This review revisits rigorous
statistical mechanical methods for predicting binding affinity,
discusses some recent developments for improving their speed and
reliability, and examines faster approximate models for facilitating
virtual screening and lead optimization.
On the Evaluation and Optimisation of Protein X-ray Structures for pKa CalculationsJens Erik Nielsen and J. Andrew McCammonProtein Science, Vol. 12, Issue 2, pp. 313-326 (2003) [PubMed 12538895]The calculation of the physical properties of a protein from its X-ray
structure is of importance in virtually every aspect of modern biology.
Although computational algorithms have been developed for calculating
everything from the dynamics of a protein to its binding specificity,
only limited information is available on the ability of these methods to
give accurate results when used with a particular X-ray structure. We
examine the ability of a pKa calculation algorithm to predict the
proton-donating residue in the catalytic mechanism of Hen Egg White
Lysozyme. We examine the correlation between the ability of the pKa
calculation method to get the correct result and the overall
characteristics of 41 X-ray structures such as crystallisation
conditions, resolution and the output of structure validation software.
We furthermore examine the ability of Energy Minimisations, Molecular
Dynamics simulations and structure-perturbation methods to optimise the
X-ray structures such that these give correct results with the pKa
calculation algorithm. We propose a set of criteria for identifying the
proton donor in a catalytic mechanism, and demonstrate that the
application of these criteria give highly accurate prediction results
when using unmodified X-ray structures. More specifically we are able to
successfully identify the proton donor in 85% of the X-ray structures
when excluding structures with crystal contacts near the active site.
Neither the use of the overall chacteristics of the X-ray structures nor
the optimisation of the structure by EM, MDL or other methods improves
the results of the pKa calculation algorithm. We discuss these results
and their implications for the design of structure-based energy
calculation algorithms in general.
Studying the Affinity and Kinetics of Molecular Association with Molecular Dynamics SimulationYingkai Zhang and J.A. McCammonJournal of Chemical Physics, Vol. 118, pp. 1821-1827 (2003)
Given a long molecular dynamics trajectory which consists of hundreds of
association and dissociation events, the theoretical formulas to
calculate the affinity and dissociation rate constant are presented. The
derivation is based on the survival function of the associated complex,
and it emphasizes the nearest neighbor distribution function. The
applicability of this brute-force approach is demonstrated by the
simulation of methane association in water.
Protein Simulation and Drug DesignChung F. Wong and J. Andrew McCammonAdvances in Protein Chemistry, Vol. 66, pp. 87-121 (2003)
The rapid advance of computer technology, force-field developments, and
simulation methods and algorithms has gradually made force-field-based
methods more easily and reliably useful in computer-aided drug design.
In some applications, simple molecular mechanics geometry optimization
and energy calculations can already suggest compounds that are
worthwhile to make and/or screen. Such calculations can be improved by
using modern continuum solvent models in improving the description of
solvation effects. Proper account of protein flexibility, via molecular
dynamics simulations, for example, can further enhance the predictive
reliability of simulation models. Combined with rigorous statistical
mechanical theories, these simulations can help predict binding free
energy (Tembe and McCammon, 1984; Wong and McCammon, 1986b; Wong and
McCammon, 1986a; Mezei and Beveridge, 1986; Bash et al., 1987;
Jorgenson, 1989; Beveridge and DiCapua, 1989). While these simulations
were limited to several tens of picoseconds in the early stages, they
had moved a step forward beyond the fixed-conformation picture that
dominated many scientists' thinking at the time. Recent developments in
simulation methods and computer hardware have made it possible to extend
the time scale of these simulations so that more reliable predictions
can be made, and that results can be obtained more quickly. Methods that
improve conformational sampling should further faciliate these
simulations. Various approximate methods with different degrees of
sophistication have also been introduced to faciliate the modeling of
molecular recognition. In practice drug design, it should be beneficial
to use a hierarchical approach in which simple but fast methods are
first used for preliminary screening of real and virtual compound
libraries and for suggesting potentially useful drug candidates to
make/screen, followed by further evaluations by models with increasing
levels of sophistication. In this article, we will review various
approximate and rigorous force-field-based methods that can fit into
such a hierarchical approach.
The pH Dependence of Stability of the Activation Helix and the Catalytic site of GARTDimitrios Morikis, Adrian H. Elcock, Patricia A. Jennings and J. Andrew McCammonBiophysical Chemistry, Vol. 105, Issues 2-3, pp. 279-291 (2003) [PubMed 14499900]We have predicted the free energy of unfolding for the pH-dependent
helix-coil transition of the activtion helix of GART using continuum
electrostatic calculations and structural modeling. We have assigned the
contributions of each element of secondary structure and of each
ionizable residue, within and in the vicinity of the activation helix,
to the stability of several fragments of GART that participate in the
formation of the catalytic site. We demonstrate that the interaction of
His121-His132 contributes 2.2 kcal/mole to the ionization free energy
between pH 0 and ~6. We also show that the ionization state of a network
of five histidines, His108, His119, His121, His132, and His137, and two
aspartic acids Asp141 and Asp144, contributes ~12 kcal/mol to the
stability of the catalytic site of GART, out of a total stability of 16
kcal/mole of the whole enzyme. These interactions are important for the
formation of the catalytic site of GART.
Brownian Dynamics Simulation of Helix-Capping MotifsTongye Shen, Chung F. Wong and J. Andrew McCammonBiopolymers, Vol. 70, Issue 2, pp. 252-259 (2003) [PubMed 14517913]Helix-capping motifs are believed to play an important role in
stabalizing α-helices and defining helix start and stop signals.
We performed microsecond scale Brownian dynamics simulations to study
ten XAAD sequences with x=(A,E,I,L,N,Q,S,T,V,Y), to examine their
propensity to form helix capping motifs and correlate these reulsts with
those obtained from analyzing a structural database of proteins. For the
widely studied capping box motif S**D, where * can be any amino acid
residue, the simulations suggested that one of the two hydrogen bonds
proposed earlier as a stabilizing factor might not be as important. On
the other hand, side chain interactions between the capping residue and
the third residue downstream on the polypeptide chain might also play a
role in stabilizing this motif. These results are consistent with the
explicit-solvent molecular dynamics simulations of two capping box
motifs found in the proteins BPTI and α-dendrotoxin. Principal
component analysis of the SAAD trajectory showed that the first three
principal components, after those corresponding to
translational-rotational motion were removed, accounted for more than
half of the conformational fluctuations. The first component separated
the conformational space into two parts with the all-helical
conformation and the capping box motif lying largely in one part. the
second component, on the other hand, could be used to describe
conformational transitions between the all-helical form and the capping
box motif.
Computational Analysis of the Interactions between the Angiogenesis Inhibitor PD173074 and Fibroblast Growth Factor Receptor 1Kristin Tøndel, Chung F. Wong and J.A. McCammonJournal of Theoretical and Computational Chemistry, Vol. 2, No. 1, pp. 43-56 (2003)
We have carried out computational sensitivity analysis to analyze the
interactions between the inhibitor PD173074 and FGFR1 in order to
identify the determinants of their recognition and generate insights
into further refining the inhibitor. The analysis has identified the
parts of the inhibitor that are already useful for binding, e.g., the
part that recognizes the linker connecting the N-terminal and C-terminal
lobes of the kinase domain. These parts are profitably kept during a
lead optimization process. The analysis has also pointed out regions of
the inhibitors that may be useful to modify to improve its binding
affinity, e.g., the dimethoxyphenyl ring. Comparative structural
analysis of the binding pocket of almost 400 protein kinases also
suggests that modifying the dimethoxyphenyl moiety might improve
selective binding. Selectivity may be achieved not only by introducing
groups to the 3 and 5 positions but also to the 1 and 6 positions.
Replacing the tertiary amines by hydrocarbon might also improve binding
affinity.
Finite Element Simulations of Acetylcholine Diffusion in Neuromuscular JunctionsKaihsu Tai, Stephen D. Bond, Hugh R. MacMillan, Nathan Andrew Baker, Michael Jay Holst and J. Andrew McCammonBiophysical Journal, Vol. 84, No. 4, pp. 2234-2241 (2003) [PubMed 12668432]A robust infrastructure for solving time-dependent diffusion using the
finite element package FEtk has been developed to simulate synaptic
transmission in a neuromuscular junction with realistic postsynaptic
folds. Simplified rectilinear synapse models serve as benchmarks in
initial numerical studies of how variations in geometry and kinetics
relate to endplate currents associated with fast-twitch, slow-twitch,
and dystrophic muscles. The flexibility and scalability of FEtk affords
increasingly realistic and complex models that can be formed in concert
with expanding experimental understanding from electron microscopy.
Ultimately, such models may provide useful insight on the functional
implications of controlled changes in processes, suggesting therapies
for neuromuscular diseases.
Influence of Structural Fluctuation on Enzyme Reaction Energy Barriers in Combined Quantum Mechanical/Molecular Mechanical StudiesYingkai Zhang, Jeremy Kua and J. Andrew McCammonJournal of Physical Chemistry B, Vol. 107, No. 18, pp. 4459-4463 (2003)
To account for protein dynamics and to investigate the effect of
different conformations on the enzyme reaction energy barrier, we have
studied the initial step of the acylation reaction catalyzed by
acetylcholinesterase (AChE) with a multiple QM/MM reaction path
approach. The approach consists of two main components: generating
enzyme-substrate conformations with classical molecular dynamics
simulation, and mapping out the minimum reaction energy path for each
conformational snapshot with combined quantum mechanical/molecular
mechanical (QM/MM) calculations. It is found that enzyme-substrate
conformation fluctuations lead to significant differences in the
calculated reaction energy barrier; however, the qualitative picture of
the role of the catalytic triad and oxyanion hole in AChE catalysis is
very consistent. Our results emphasize the importance of employing
multiple starting structures in the QM/MM study of enzyme reactions, and
indicate that structural fluctuation is an integral part of the enzyme
reaction process.
A Computational Model of Binding Thermodynamics: The Design of Cyclin-dependent Kinase 2 InhibitorsPeter A. Sims, Chung F. Wong and J. Andrew McCammonJournal of Medicinal Chemistry, Vol. 46, No. 15, pp. 3314-3325 (2003) [PubMed 12852762]The cyclin-dependent protein kinases are important targets in drug
discovery because of their role in cell cycle regulation. In this
computational study, we have applied a continuum solvent model to study
the interactions between cyclin-dependent kinases 2 (CDK2) and analogs
of the clinically tested anticancer agent, flavopiridol. The continuum
solvent model uses Coulomb's law to account for direct electrostatic
interactions, solves the Poisson equation to obtain the electrostatic
contributions to solvation energy, and calculates scaled solvent
accessible surface area to account for hydrophobic interactions. The
computed free energy of binding gauges the strength of protein-ligand
interactions. Our model was first validated through a binding study on a
number of flavopiridol derivatives to CKD2, and its ability to identify
potent inhibitors was observed. The model was then used to aid in the
design of novel CDK2 inhibitors with the aid of a computational
sensitivity analysis. Some of these hypothetical structures could be
significantly more potent than the lead compound, flavopiridol. We
applied two approaches to gaining insights into designing selective
inhibitors. One relied on the comparative analysis of the binding pocket
for several hundred protein kinases to identify the parts of a lead
compound whose modifications might lead to selective compounds. The
other was based on building and using homology for energy calculations.
The homology models appear to be able to classify ligand potency into
groups but cannot yet give reliable quantitative results.
Nanosecond Dynamics of the Mouse Acetylcholinesterase Cys69-Cys96 Omega LoopJianxin Shi, Kaihsu Tai, J. Andrew McCammon, Palmer Taylor and David A. JohnsonJournal of Biological Chemistry, Vol. 278, Issue 33, pp. 30905-30911 (2003) [PubMed 12759360]The paradox of high substrate turnover occurring within the confines of
a deep, narrow gorge through which acetylcholine must traverse to reach
the catalytic site of acetylcholinesterase has suggested the existence
of transient gorge enlargements that would enhance substrate
accessibility. To establish a foundation for the experimental study of
transient fluctuations in structure, site-directed labeling in
conjunction with time-resolved fluorescence anisotropy were utilized to
assess the possible involvement of the omega loop, a segment that forms
the outer wall of the gorge. Specifically, the flexibility of three
residues (L76C, E81C, and E84C) in the Cys
69-Cys
96
omega loop and one residue (Y124C) across the gorge from the omega loop
were studied in the absence and presence of two inhibitors of different
size, fasciculin and huperzine. Additionally, to validate the approach
molecular dynamics was employed to simulate anisotropy decay of the side
chains. The results show that the omega loop residues are significantly
more mobile than the non-loop residue facing the interior of the gorge.
Moreover, fasciculin, which binds at the mouth of the gorge, well
removed from the active site, decreases the mobility of IAEDANS reporter
groups attached to L76C and Y124C, but increases the mobility of the
reporter groups attached to E81C and E84C. Huperzine, which binds at the
base of active site gorge, has no effect on the mobility of reporter
groups attached to L76C and Y124C, but increases the mobility of
reporter groups attached to E81C and E84C. Besides showing that
fluctuations of the omega-loop residues are not tightly coupled, the
results indicate that residues in the omega loop exhibit distinctive
conformational fluctuations and therefore are likely to contribute to
transient gorge enlargements in the non-liganded enzyme.
From Model Complexes to Metalloprotein Inhibition: A Synergistic Approach to Structure-based Drug DiscoveryDavid T. Puerta, Julie R. Schames, Richard H. Henchman, J. Andrew McCammon and Seth M. CohenAngewandte Chemie International Edition, Vol. 42, Issue 32, pp. 3772-3774 (2003) [PubMed 12923840]Matrix metalloproteinases (MMPs) are zinc-containing hydrolytic enzymes
that are involved in restructuring the connective tissue. The design of
effective inhibitors of matrix metalloproteinases is a significant goal
in chemotherapeutic development, due to the correlation of MMP activity
with a variety of illnesses including cancer, arthritis, and
inflammatory disease. However, the design of inhibitors for MMPs and
other metalloproteins is limited by the ability to predict the
interaction of a given inhibitor with the active site metal ion. In most
cases, the elucidation of a protein structure with the bound inhibitor,
by using X-ray diffraction or NMR spectroscopic methods, is necessary
for revealing the metal-inhibitor interactions. Innovative approaches to
increasing the efficiency and speed of the drug discovery process may
provide attractive, alternative routes to identifying new drug
candidates. For example, the structure-activity-relationship by nuclear
magnetic resonance (SAR by NMR) approach has been used to reveal
probable binding modes of metal chelators in order to facilitate the
development of improved MMP inhibitors. Despite being a very effective
approach, the use of SAR by NMR still requires substantial amounts of
15N-labeled metalloprotein to determine the interactions of
potential inhibitor fragments with the macromolecule. In addition, it is
likely that SAR by NMR, in terms of metalloprotein drug design, would be
limited to metalloenzymes that contain diamagnetic metal centers.
Another approach for metalloprotein drug design is to reproduce the
drug-metalloenzyme interactions using small molecule models that can be
readily characterized. Recently we have shown that synthetic inorganic
model complexes can be used to determine metal-ligand interactions
relevant to MMP inhibitors.
Calculating pKa Values in Enzyme Active SitesJens Erik Nielsen and J. Andrew McCammonProtein Science, Vol. 12, Issue 9, pp. 1894-1901 (2003) [PubMed 12930989]The ionization properties of the active-site residues in enzymes are of
considerable interest in the study of the catalytic mechanisms of
enzymes. Knowledge of these ionization constants (pKa values) often
allows the researcher to identify the proton donor and the catalytic
nucleophile in the reaction mechanism of the enzyme. Estimates of
protein residue pKa values can be obtained by applying pKa calculation
algorithms to protein X-ray structures. We show that pKa values accurate
enough for identifying the proton donor in an enzyme active site can be
calculated by considering in detail only the active-site residues and
their immediate electrostatic interaction partners, thus allowing for a
large decrease in calculation time. More specifically we omit the
calculation of site-site interaction energies, and the calculation of
desolvation and background interaction energies for a large number of
pairs of titratable groups. The method presented here is well suited to
be applied on a genomic scale, and can be implemented in most pKa
calculation algorithms to give significant reductions in calculation
time with little or no impact on the accuracy of the results. The work
presented here has implications for understanding of enzymes in general
and for the design of novel biocatalysts.
Brownian Dynamics Simulations of Ion Atmospheres around Polyalanine and B-DNA: Effects of Biomolecular DielectricDavid S. Cerutti, Chung F. Wong and J. Andrew McCammonBiopolymers, Vol. 70, Issue 3, pp. 391-402 (2003) [PubMed 14579311]We have extended an earlier Brownian dynamics simulation algorithm for
simulating the structural dynamics of ions around biomolecules to
accommodate dielectric inhomogeneity. The electrostatic environment of a
biomolecule immersed in water was obtained by numerically solving the
Poisson equation with the biomolecule treated as a low dielectric region
and the solvent treated as a high dielectric region. Instead of using
the mean-field type approximations of ion interactions as in the
Poisson-Boltzmann model, the ions were treated explicitly by allowing
them to evolve dynamically under the electrostatic field of the
biomolecule. This model thus accounts for ion-ion correlations and the
finite-size effects of the ions. For a 13-residue α-helical
polyalanine and a 12-bp B-form DNA, we found that the choice of the
dielectric constant of the biomolecule has much larger effects on the
mean ionic structure around the biomolecule than on the fluctuational
and dynamical properties of the ions surrounding the biomolecule.
The Physical Basis of Microtubule Structure and StabilityDavid Sept, Nathan A. Baker and J. Andrew McCammonProtein Science, Vol. 12, Issue 10, pp. 2257-2261 (2003) [PubMed 14500883]Microtubules are cylindrical polymers found in every eukaryotic cell.
They have a unique helical structure that has implications at both the
cellular level, in terms of the functions they perform, and
multi-cellular level, such as determining the left-right asymmetry in
plants. Through the combination of an atomically-detailed model for a
microtubule and new large scale computational techniques for computing
electrostatic interactions, we are able to explain the observed
microtubule structure. Based on the lateral interactions between
protofilaments, we have determined that a helix with a subunit rise of
8-9 Å is the most favourable configuration. Further, we find that
these lateral bonds are significantly weaker than the longitudinal bonds
along protofilaments. This explains observations of microtubule
disassembly and may serve as another step toward understanding the basis
for dynamic instability.
The Dynamics of Ligand Barrier Crossing inside the Acetylcholinesterase GorgeJennifer M. Bui, Richard H. Henchman and J. Andrew McCammonBiophysical Journal, Vol. 85, No. 4, pp. 2267-2272 (2003) [PubMed 14507691]The dynamics of ligand movement through the constricted region of the
acetylcholinesterase gorge is important in understanding how the ligand
gains access to and is released from the active site of the enzyme.
Molecular dynamics simulations of the simple ligand,
tetramethylammonium, crossing this bottleneck region are conducted using
umbrella potential sampling and activated flux techniques. The low
potential of mean force obtained is consistent with the fast reaction
rate of acetylcholinesterase observed experimentally. From the results
of the activated dynamics simulations, local conformational fluctuations
of the gorge residues and larger scale collective motions of the protein
are found to correlate highly with the ligand crossing.
Asymmetric Structural Motions of the Homomeric α7 Nicotinic Receptor Ligand Binding Domain Revealed by Molecular Dynamics SimulationRichard H. Henchman, Hai-Long Wang, Steven M. Sine, Palmer Taylor and J. Andrew McCammonBiophysical Journal, Vol. 85, No. 5, pp. 3007-3018 (2003) [PubMed 14581202]A homology model of the ligand binding domain of the α7 nicotinic
receptor is constructed based on the AChBP crystal structure. This
structure is refined in a 10 ns molecular dynamics simulation. The model
structure proves fairly resilient, with no significant changes at the
secondary or tertiary structural levels. The hypothesis that the AChBP
template is in the activated or desensitized state and the absence of a
bound agonist in the simulation suggests that the structure may also be
relaxing from this state to the activatable state. Candidate motions
that take place involve not only the side chains of residues lining the
binding sites, but also the subunit positions that determine the overall
shape of the receptor. In particular, two non-adjacent subunits move
outward while their partners counter-clockwise to them move inward,
leading to a marginally wider interface between themselves and an
overall asymmetric structure. This in turn affects the binding sites,
producing two that are more open and characterized by distinct side
chain conformations of W54 and L118, although motions of the side chains
of all residues in every binding site still contribute to a reduction in
binding site size, especially the outward motion of W148, which hinders
ACh binding. The Cys loop at the membrane interface also displays some
flexibility. While the short simulation time scale is unlikely to sample
adequately all the conformational states, the pattern of observed
motions suggests how ligand binding may correlate with larger scale
subunit motions that would connect with the transmembrane region that
controls the passage of ions. Further, the shape of the asymmetry with
binding sites of differing affinity for ACh, characteristic of other
nicotinic receptors, may be a natural property of the relaxed,
activatable state of α7.
Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approachJeremy Kua, Yingkai Zhang, Angelique C. Eslami, John R. Butler and J. Andrew McCammonProtein Science, Vol. 12, Issue 12, pp. 2675-2684 (2003) [PubMed 14627729]A combined molecular dynamics simulation and multiple ligand docking
approach is applied to study the roles of the anionic subsite residues
(W86, E202, Y337) in the binding of acetylcholine (ACh) to
acetylcholinesterase (AChE). We find that E202 stabilizes docking of ACh
via electrostatic interactions. However, we find no significant
electrostatic contribution from the aromatic residues. Docking energies
of ACh to mutant AChE show a more pronounced effect due to size/shape
complementarity. Mutating to smaller residues results in poorer binding,
both in terms of docking energy and statistical docking probability.
Besides separating out electrostatics by turning off the partial charges
from each residue and comparing to the native, the mutations in this
study are W86F, W86A, E202D, E202Q, E202A, Y337F, and Y337A. We also
find that all perturbations result in a significant reduction in binding
of extended ACh in the catalytically productive orientation. This effect
is primarily due to a small shift in preferred position of the
quaternary tail.