ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of BiomoleculesAndreas Vitalis, Nathan A. Baker and J. Andrew McCammonMolecular Simulation, Vol. 30, Issue 1, pp. 45-61 (2004)
In this work we present a new software package (ISIM), which represents
a flexible, computational tool for simulations of electrolyte solutions
via a grand canonical Monte Carlo procedure (GCMC) with a specific
capability of treating biomolecules in solution. The GCMC method
provides a powerful tool for studying the ionic environments of highly
charged macromolecules with attention to the atomic detail of both the
solute and the mobile counterions. The ISIM software differs from
previous schemes mainly by treating different ion types independently
and offering a new parameterization procedure for calibrating excess
chemical potentials and bulk ion concentrations. Additionally, ISIM
leverages the APBS software package to provide accurate descriptions of
the biomolecular electrostatic potential through the efficient solution
of Poisson's equations. ISIM has been validated on a variety of test
systems; we successfully reproduce elementary properties of electrolyte
solutions as well as theoretical and experimental results for
challenging test systems like Calmodulin and DNA.
Mechanism of Acetylcholinesterase Inhibition by Fasciculin: A 5 ns Molecular Dynamics SimulationKaihsu Tai, Tongye Shen, Richard H. Henchman, Yves Bourne, Pascale Marchot and J. Andrew McCammonIn "Cholinergic Mechanisms," I. Silman, H. Soreq, L. Anglister, D.M. Michaelson, A. Fisher, Eds., Taylor & Francis, Ch. 141, pp. 727-728 (2004)
In our previous molecular dynamics simulation of mouse
acetylcholinesterase (EC 3.1.1.7), the enzyme revealed complex gorge
fluctuation. Now we report another 5 ns simulation, with
acetylcholinesterase complexed with fasciculin 2. Fasciculin 2 binds to
the gorge entrance of acetylcholinesterase with excellent
complementarity and many polar interactions. In this simulation of the
protein-protein complex,we continue to observe a two-peaked probability
distribution of the gorge width, though fasciculin 2 appears to block
access of ligands to the gorge. The gorge width distribution is altered
when fasciculin is present: the gorge is more likely to be narrow.
Though the gorge is sterically blocked by fasciculin 2, there are large
increases in the opening of alternative passages, namely the side door
and the back door. The catalytic triad arrangement in the
acetylcholinesterase active site is disrupted with fasciculin bound.
These data suggest that, in addition to the steric obstruction,
fasciculin may inhibit acetylcholinesterase by allosteric and dynamical
means. Additional information from these simulations can be found in
reference 1 and at http://mccammon.ucsd.edu/" target="_blank"
class="ref">http://mccammon.ucsd.edu/.
Influence of Water on the Function of AcetylcholinesteraseRichard Henchman, Kaihsu Tai, Tongye Shen and J. Andrew McCammonIn "Cholinergic Mechanisms," I. Silman, H. Soreq, L. Anglister, D.M. Michaelson, A. Fisher, Eds., Taylor & Francis, Ch. 98, pp. 589-590 (2004)
A 10 ns trajectory from a molecular dynamics simulation is used to
examine the structure and dynamics of water around acetylcholinesterase
to determine what influence water may have on its function. Particular
emphasis is placed on water in the active site gorge to understand how
water may affect ligand entry and binding. Despite the confining nature
of the deep active site gorge ligand entry appears to be aided by a
number of water properties -- fluctuations in the population of gorge
waters, moderate mobility of water in the entrance to the gorge, reduced
water hydrogen bonding ability, and transient cavities in the gorge.
While a ligand is signifcantly slowed down by the less mobile water,
this effect does not appear to be large enough to be rate limiting for
enzyme catalysis of acetycholine. Images and further information are
available at the website http://mccammon.ucsd.edu/" target="_blank"
class="ref">http://mccammon.ucsd.edu/.
The Displacement of Ligand through the Bottleneck Region of the Acetylcholinesterase GorgeJ. Bui and J.A. McCammonIn "Cholinesterases in the Second Millennium: Biomolecular and Pathological Aspects," N.C. Inestrosa and E.O. Campos, Eds., pp. 207-211 (2004)
Molecular dynamics simulations are applied to understand how
acetylcholine can pass through the constricted region of the 20 Å
deep gorge of acetylcholinesterase and gain access to the active site.
The molecular dynamics (MD) simulations of the simpler ligand
tetramethylammonium (TMA+) in this bottleneck were conducted using
umbrella potential sampling and activated flux techniques. Potential of
mean force (pmf) and barrier crossing rate constants in this
constriction region were calculated. From the results of activated
dynamics simulations, local conformational fluctuations of the gorge
residues that were coupled to the motion of the ligand crossing were
observed.
Drug DesignChung F. Wong and J. Andrew McCammonIn "Encyclopedia of Supramolecular Chemistry," J. Atwood and J. Steed, Eds., Marcel Dekker, NY, pp. 490-496 (2004)
Computer-aided drug design is playing an increasing role in the
development of pharmaceuticals. Computers can now be used in many ways
to aid the design of therapeutic drugs. Molecular graphics software
running on powerful workstations can draw useful qualitative insights
from the experimental structure of a receptor and/or its complex with
ligands. Rapid advances in computing technology and computational
chemistry have facilitated the generation of quantitative data to help
sort out promising drug leads from real and virtual chemistry libraries
and to aid rational drug design. These methods range from rigid
structural models employing simple but easy-to-compute scoring functions
to flexible structural models with sophisticated description of intra
and intermolecular interactions. Structural prediction programs have
been developed to provide structural models of receptors when
experimental structure is not yet available. Alternatively, useful
insights into drug design can be obtained by comparative analysis of a
number of inhibitors that are known to bind to a receptor. This
ligand-based approach can be used without a knowledge of the three
dimensional structure of the receptor. Each approach has its pros and
cons and effective computer-aided drug design usually utilizes a number
of methods. Here, we give a glimpse of some of these approaches with a
short selected list of references that aids interested readers to
further explore the subject.
Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free EnergyJessica M.J. Swanson, Richard H. Henchman and J. Andrew McCammonBiophysical Journal, Vol. 86, No. 1, pp. 67-74 (2004) [PubMed 14695250]The prediction of absolute ligand-receptor binding affinities is
essential in a wide range of biophysical queries, from the study of
protein-protein interactions to structure based drug design. End-point
free energy methods, such as the Molecular Mechanics Poisson Boltzmann
Surface Area (MM/PBSA) model, have received much attention and
widespread application in recent literature. These methods benefit from
computational efficiency as only the initial and final states of the
system are evaluated, yet there remains a need for strengthening their
theoretical foundation. Here a clear connection between statistical
thermodynamics and end-point free energy models is presented. The
importance of the association free energy, arising from one molecule's
loss of translational and rotational freedom from the standard state
concentration, is addressed. A novel method for calculating this
quantity directly from a molecular dynamics simulation is described. The
challenges of accounting for changes in the protein conformation and its
fluctuations from separate simulations are discussed. A simple first
order approximation of the configuration integral is presented to lay
the groundwork for future efforts. This model has been applied to
FKBP12, a small immunophilin that has been widely studied in the drug
industry for its potential immunosuppressive and neuroregenerative
effects.
The Role of Hydrogen Bonding in the Enzymatic Reaction Catalyzed by HIV-1 ProteaseJoanna Trylska, Pawe&Protein Science, Vol. 13, No. 2, pp. 513-528 (2004) [PubMed 14739332]The hydrogen bond network in various stages of the enzymatic reaction
catalyzed by HIV-1 protease was studied through quantum-classical
molecular dynamics simulations. The approximate valence bond method was
applied to the active site atoms participating directly in the
rearrangement of chemical bonds. The rest of the protein with explicit
solvent was treated with a classical molecular mechanics model. Two
possible mechanisms were studied, general-acid/general-base (GA/GB) with
Asp25 protonated at the inner oxygen, and a direct nucleophilic attack
by Asp25. Strong hydrogen bonds leading to spontaneous proton transfers
were observed in both reaction paths. A single-well hydrogen bond was
formed between the peptide nitrogen and outer oxygen of Asp125. The
proton was diffusely distributed with an average central position and
transferred back and forth on a picosecond scale. In both mechanisms
this interaction helped change the peptide bond hybridization, increased
the partial charge on peptidyl carbon, and in the GA/GB mechanism helped
deprotonate the water molecule. The inner oxygens of the aspartic dyad
formed a low-barrier but asymmetric hydrogen bond; the proton was not
positioned midway and made a slightly elongated covalent bond
transferring from one to the other aspartate. In the GA/GB mechanism
both aspartates may help deprotonate the water molecule. We observed the
breakage of the peptide bond and found that the protonation of the
peptidyl amine group was essential for the peptide bond cleavage. In
studies of the direct nucleophilic mechanism the peptide carbon of the
substrate and oxygen of Asp25 approached as close as 2.3Å.
Finite Element Solution of the Steady-state Smoluchowski Equation for Rate Constant CalculationsYuhua Song, Yongjie Zhang, Tongye Shen, Chandrajit L. Bajaj, J. Andrew McCammon and Nathan A. BakerBiophysical Journal, Vol. 86, No. 4, pp. 2017-2029 (2004) [PubMed 15041644]This article describes the development and implementation of algorithms
to study diffusion in biomolecular systems using continuum mechanics
equations. Specifically, finite element methods have been developed to
solve the steady-state Smoluchowski equation to calculate ligand binding
rate constants for large biomolecules. The resulting software has been
validated and applied to mouse acetylcholinesterase. Rates for inhibitor
binding to mAChE were calculated at various ionic strengths with several
different reaction criteria. The calculated rates were compared with
experimental data and show very good agreement when the correct reaction
criterion is used. Additionally, these finite element methods require
significantly less computational resources than existing particle-based
Brownian dynamics methods.
HIV-1 Protease Molecular Dynamics of a Wild-Type and of the V82F/I84V Mutant: Possible Contributions to Drug Resistance and a Potential New Target Site for DrugsAlexander L. Perryman, Jung-Hsin Lin and J. Andrew McCammonProtein Science, Vol. 13, Issue 4, pp. 1108-1123 (2004) [PubMed 15044738]The protease from type 1 human immunodeficiency virus (HIV-1) is a
critical drug target against which many therapeutically useful
inhibitors have been developed. Because of selective pressures applied
on the viral strains by the different protease inhibitors in the Highly
Active Anti-Retroviral Therapies (HAART), the set of viral strains in
the population has been shifting to become more drug-resistant. Because
indirect effects are contributing to drug resistance, an examination of
the dynamic structures of a wild type and a mutant could be insightful.
Consequently, this study examined structural properties sampled during
22 nanosecond, all atom molecular dynamics (MD) simulations (in explicit
water) of both a wild type and the drug-resistant V82F/I84V mutant of
HIV-1 protease. The V82F/I84V mutation significantly decreases the
binding affinity of all HIV-1 protease inhibitors currently used
clinically. Simulations
(http://dx.doi.org/10.1016/S0969-2126(00)00537-2" target="_blank"
class="ref">Scott, W.R.P. & Schiffer, C.A., 2000, Structure 8,
1259-1265) have shown that the curling of the tips of the active site
flaps immediately results in flap opening. In the 22ns MD simulations
presented here, more frequent and more rapid curling of the mutant's
active site flap tips was observed. The mutant protease's flaps opened
farther than the wild type's flaps did and displayed more flexibility.
This suggests that the effect of the mutations on the equilibrium
between the semi-open and closed conformations could be one aspect of
the mechanism of drug resistance for this mutant. In addition,
correlated fluctuations in the active site and periphery were noted that
point to a possible binding site for allosteric inhibitors.
Discovery of a Novel Binding Trench in HIV IntegraseJulie R. Schames, Richard H. Henchman, Jay S. Siegel, Christoph A. Sotriffer, Haihong Ni and J. Andrew McCammonJournal of Medicinal Chemistry, Vol. 47, No. 8, pp. 1879-1881 (2004) [PubMed 15055986]Docking of the 5CITEP inhibitor to snapshots of a 2 ns HIV-1 integrase
MD trajectory indicated a previously uncharacterized trench adjacent to
the active site that intermittently opens. Further docking studies of
novel ligands with the potential to bind to both regions showed greater
selective affinity when able to bind to the trench. Our ranking of
ligands is open to experimental testing, and our approach suggests a new
target for HIV-1 therapeutics.
Ribosome Motions Modulate Electrostatic PropertiesJoanna Trylska, Robert Konecny, Florence Tama, Charles L. Brooks III and J. Andrew McCammonBiopolymers, Vol. 74, No. 6, pp. 423-431 (2004) [PubMed 15274086]The electrostatic properties of the 70S ribosome of Thermus thermophilus
were studied qualitatively by solving the Poisson-Boltzmann (PB)
equation in aqueous solution and with physiological ionic strength. The
electrostatic potential was calculated for conformations of the ribosome
derived by recent normal mode analysis
(http://dx.doi.org/10.1073/pnas.1632476100" target="_blank"
class="ref">Tama, F. et al.
Proc. Natl. Acad. Sci. USA 2003,
100, 9319--9323) of the ratchet-like reorganization that occurs
during translocation (http://dx.doi.org/10.1038/35018597"
target="_blank" class="ref">Frank, J.; Agrawal, R.K.
Nature
2000,
406, 318--322). To solve the PB equation, effective
parameters (charges and radii), applicable to a highly charged backbone
model of the ribosome, were developed. Regions of positive potential
were found at the binding site of the elongation factors G and Tu, as
well as where the release factors bind. Large positive potential areas
are especially pronounced around the L11 and L6 proteins. The region
around the L1 protein is also positively charged, supporting the idea
that L1 may interact with the E-site tRNA during its release from the
ribosome after translocation. Functional rearrangement of the ribosome
leads to electrostatic changes which may help the translocation of the
tRNAs during the elongation stage.
PDB2PQR: An Automated Pipeline for the Setup, Execution and Analysis of Poisson-Boltzmann Electrostatics CalculationsTodd J. Dolinsky, Jens E. Nielsen, J. Andrew McCammon and Nathan A. BakerNucleic Acids Research, Vol. 32, pp. W665-W667 (2004) [PubMed 15215472]Continuum solvation models, such as Poisson-Boltzmann and Generalized
Born methods, have become increasingly popular tools for investigating
the influence of electrostatics on biomolecular structure, energetics
and dynamics. However, the use of such methods requires accurate and
complete structural data as well as force field parameters such as
atomic charges and radii. Unfortunately, the limiting step in continuum
electrostatics calculations is often addition of missing atomic
coordinates to molecular structures from the Protein Data Bank and the
assignment of parameters to biomolecular structures. To address this
problem, we have developed the PDB2PQR web service
(http://www.poissonboltzmann.org/pdb2pqr" target="_blank"
class="ref">http://www.poissonboltzmann.org/pdb2pqr). This server
automates many of the common tasks of preparing structures for continuum
electrostatics calculations, including: adding a limited number of
missing heavy atoms to biomolecular structures, estimating titration
states and protonating biomolecules in a manner consistent with
favorable hydrogen-bonding, assigning charge and radius parameters from
a variety of force fields, and finally generating "PQR" output
compatible with several popular computational biology packages. This
service is intended to facilitate the setup and execution of
electrostatics calculations for both experts and non-experts and thereby
broaden the accessibility of the biological community to continuum
electrostatics analyses of biomolecular systems.
Accelerated Molecular Dynamics: A Promising and Efficient Simulation Method for BiomoleculesDonald Hamelberg, John Mongan and J. Andrew McCammonJournal of Chemical Physics, Vol. 120, Issue 24, pp. 11919-11929 (2004) [PubMed 15268227]Many interesting dynamic properties of biological molecules cannot be
simulated directly using molecular dynamics because of nanosecond
timescale limitations. These systems are trapped in potential energy
minima with high free energy barriers for large numbers of computational
steps. The dynamic evolution of many molecular systems occurs through a
series of rare events as the system moves from one potential energy
basin to another. Therefore, we have proposed a robust bias potential
function that can be used in an efficient accelerated molecular dynamics
approach to simulate the transition of high energy barriers without any
advance knowledge of the location of either the potential energy wells
or saddle points. In this method, the potential energy landscape is
altered by adding a bias potential to the true potential such that the
escape rates from potential wells are enhanced, which accelerates and
extends the time scale in molecular dynamics simulations. Our definition
of the bias potential echoes the underlying shape of the potential
energy landscape on the modified surface, thus allowing for the
potential energy minima to be well defined, and hence properly sampled
during the simulation. We have shown that our approach, which can be
extended to biomolecules, samples the conformational space more
efficiently than normal molecular dynamics simulations, and converges to
the correct canonical distribution.
Acetylcholinesterase: Enhanced Fluctuations and Alternative Routes to the Active Site in the Complex with Fasciculin-2Jennifer M. Bui, Kaihsu Tai and J. Andrew McCammonJournal of the American Chemical Society, Vol. 126, No. 23, pp. 7198-7205 (2004) [PubMed 15186156]A 15ns molecular dynamics simulation is reported for the complex of
mouse acetylcholinesterase (mAChE) and the protein neurotoxin
fasciculin-2. Compared to a 15ns simulation of apo-mAChE, the structural
fluctuations of the enzyme are substantially increased in magnitude for
the enzyme in the complex. Fluctuations of part of the long omega loop
(residues 69-96) are particularly enhanced. This loop forms one wall of
the active site, and the enhanced fluctuations lead to additional routes
of access to the active site.
Charge Optimization of the Interface between Protein Kinases and their LigandsPeter A. Sims, Chung F. Wong and J. Andrew McCammonJournal of Computational Chemistry, Vol. 25, No. 11, pp. 1416-1429 (2004) [PubMed 15185335]Examining the potential for electrostatic complementarity between a
ligand and a receptor is a useful technique for rational drug design and
can demonstrate how a system prioritizes interactions when allowed to
optimize its charge distribution. In this computational study, we
implemented the previously developed, continuum solvent-based charge
optimization theory with a simple, quadratic programming algorithm and
the UHBD Poisson-Boltzmann solver. This method allows one to compute the
best set of point charges for a ligand or ligand region based on the
ligand and receptor shape, and the receptor partial charges, by
optimizing the binding free energy obtained from a continuum-solvent
model. We applied charge optimization to a fragment of the heat-stable
protein kinase inhibitor (PKI) of protein kinase A (PKA), to three
flavopiridol inhibitors of CDK2, and to cyclin A which interacts with
CDK2 to regulate the cell cycle. We found that a combination of global
(involving every charge) and local (involving only charges in a local
region) optimization can give useful hints for designing better
inhibitors. Although some parts of an inhibitor may already contribute
significantly to binding, we found that they could still be the most
important targets for modifications to obtain stronger binders. In
studying the binding of flavopiridol inhibitors to CDK2, comparable
binding affinity could be obtained regardless of whether the net charges
of the inhibitors were constrained to -2, -1, 0, 1, or 2 during the
optimization. This provides flexibility in inhibitor design when a
certain net charge of the inhibitor is desired in addition to strong
binding affinity. For the study of the PKA-PKI and CDK2-cylin A
interfaces, we identified residues whose charge distributions are
already close to optimal and those whose charge distributions could be
refined to further improve binding.
Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins: Double-Decoupling MethodDonald Hamelberg and J. Andrew McCammonJournal of the American Chemical Society, Vol. 126, No. 24, pp. 7683-7689 (2004) [PubMed 15198616]Localized water molecules in the binding pockets of proteins play an
important role in non-covalent association of proteins and small drug
compounds. At times the dominant contribution to the binding free energy
comes from the release of localized water molecules in the binding
pockets of biomolecules. Therefore, in order to quantify the energetic
importance of these water molecules for drug design purposes, we have
used the double-decoupling approach to calculate the standard free
energy of tying up a water molecule in the binding pockets of two
protein complexes. The double-decoupling approach is based on the
underlying principle of statistical thermodynamics. We have calculated
the standard free energies of tying up the water molecule in the binding
pockets of these complexes to be favorable. These water molecules
stabilize the protein-drug complexes by interacting with the ligands and
binding pockets of the protein complexes. Our results offer ideas that
could be used in optimizing protein-drug interactions, by designing
ligands that are capable of targeting localized water molecules in the
binding pockets of proteins. The resulting free energy of ligand binding
could benefit from the potential free energy gain accompanying the
release of these water molecules. Furthermore, we have examined the
theoretical background of the double-decoupling method and its
connection to the molecular dynamics thermodynamic integration
techniques.
Electrostatic Interaction between RNA and Protein Capsid in CCMV Simulated by a Coarse-grain RNA model and a Monte Carlo ApproachDeqiang Zhang, Robert Konecny, Nathan A. Baker and J. Andrew McCammonBiopolymers, Vol. 75, No. 4, pp. 325-337 (2004) [PubMed 15386271]Although many viruses have been crystallized and the protein capsid
structures have been determined by x-ray crystallography, the nucleic
acids often cannot be resolved. This is especially true for RNA viruses.
The lack of information about the conformation of DNA/RNA greatly
hinders our understanding of the assembly mechanism of various viruses.
Here we combine a coarse-grain model and a Monte Carlo method to
simulate the distribution of viral RNA inside the capsid of cowpea
chlorotic mottle virus. Our results show that there is very strong
interaction between the N-terminal residues of the capsid proteins,
which are highly positive charged, and the viral RNA. Without these
residues, the binding energy disfavors the binding of RNA by the capsid.
The RNA forms a shell close to the capsid with the highest densities
associated with the capsid dimers. These high-density regions are
connected to each other in the shape of a continuous net of triangles.
The overall icosahedral shape of the net overlaps with the capsid
subunit icosahedral organization. Medium density of RNA is found under
the pentamers of the capsid. These findings are consistent with
experimental observations.
Finite concentration effects on diffusion-controlled reactionsSanjib Senapati, Chung F. Wong and J. Andrew McCammonJournal of Chemical Physics, Vol. 121, Issue 16, pp. 7896-7900 (2004) [PubMed 15485251]The algorithm by Northrup, Allison, and McCammon
http://dx.doi.org/10.1063/1.446900" target="_blank" class="ref">J. Chem.
Phys. 80, 1517 (1984) has been used for two decades for calculating the
diffusion-influenced rate-constants of enzymatic reactions. Although
many interesting results have been obtained, the algorithm is based on
the assumption that substrate/substrate interactions can be neglected.
This approximation may not be valid when the concentration of the ligand
is high. In this work, we constructed a simulation model that can take
substrate/substrate interactions into account. We first validated the
model by carrying out simulations in ways that could be compared to
analytical theories. We then carried out simulations to examine the
possible effects of substrate/substrate interactions on
diffusion-controlled reaction rates. For a substrate concentration of
0.1 mM, we found that the diffusion-controlled reaction rates were not
sensitive to whether substrate/substrate interactions were included. On
the other hand, we observed significant influence of substrate/substrate
interactions on calculated reaction rates at a substrate concentation of
0.1M. Therefore, a simulation model that takes substrate/substrate
interactions into account is essential for reliably predicting
diffusion-controlled reaction rates at high substrate concentrations,
and one such simulation model is presented here.
Constant pH Molecular Dynamics in Generalized Born Implicit SolventJohn Mongan, David A. Case and J. Andrew McCammonJournal of Computational Chemistry, Vol. 25, Issue 16, pp. 2038-2048 (2004) [PubMed 15481090]A new method is proposed for constant pH molecular dynamics (MD),
employing generalized Born (GB) electrostatics. Protonation states are
modeled with different charge sets, and titrating residues sample a
Boltzmann distribution of protonation states as the simulation
progresses, using Monte Carlo sampling based on GB-derived energies. The
method is applied to four different crystal structures of hen egg-white
lysozyme (HEWL). pKa predictions derived from the simulations have
root-mean-square (RMS) error of 0.82 relative to experimental values.
Similarity of results between the four crystal structures shows the
method to be independent of starting crystal structure; this is in
contrast to most electrostatics-only models. A strong correlation
between conformation and protonation state is noted and quantitatively
analyzed, emphasizing the importance of sampling protonation states in
conjunction with dynamics.