Flap opening dynamics in HIV-1 protease explored with a coarse-grained modelValentina Tozzini, Joanna Trylska, Chia-en Chang and J. Andrew McCammonJournal of Structural Biology, Vol. 157, Issue 3, pp. 606-615 (2007) [PubMed 17029846]We present a one-bead coarse-grained model that enables dynamical
simulations of proteins on the time scale of tens of microseconds. The
parameterization of the force field includes accurate conformational
terms that allow for fast and reliable exploration of the
configurational space. The model is applied to the dynamics of flap
opening in HIV-1 protease. The experimental structure of the recently
crystallized semi-open conformation of HIV-1 protease is well reproduced
in the simulation, which supports the accuracy of our model. Thanks to
very long simulations and extensive sampling of opening and closing
events, we also investigate the thermodynamics and kinetics of the
opening process. We have shown that the effect of the solvent slows down
the dynamics to the experimentally observed time scales. The model is
found to be reliable for application to substrate docking simulations,
which are currently in progress.
Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies: Lessons Learned with Atom-Centered Dielectric FunctionsJessica M.J. Swanson, Jason A. Wagoner, Nathan A. Baker and J.A. McCammonJournal of Chemical Theory and Computation, Vol. 3, No. 1, pp. 170-183 (2007)
Accurate implicit solvent models require parameters that have been
optimized in a system- and/or atom-specific manner based on experimental
data or more rigorous explicit solvent simulations. Models based on the
Poisson or Poisson-Boltzmann equation are particularly sensitive to the
nature and location of the boundary which separates the low dielectric
solute from the high dielectric solvent. Here we present a novel method
for optimizing the solute radii, which define the dielectric boundary,
based on forces and energies from explicit solvent simulations. We use
this method to optimize radii for protein systems defined by AMBER
/ff/99 partial charges and a spline-smoothed solute surface. The
spline-smoothed surface is an atom-centered dielectric function that
enables stable and efficient force calculations. We explore the relative
performance of radii optimized with forces alone and those optimized
with forces and energies. We show that our radii reproduce the explicit
solvent forces and energies more accurately than four other parameter
sets commonly used in conjunction with the AMBER force field, each of
which has been appropriately scaled for spline-smoothed surfaces.
Finally, we demonstrate that spline-smoothed surfaces show surprising
accuracy for small, compact systems, but may have limitations for
highly-solvated protein systems. The optimization method presented here
is efficient and applicable to any system with explicit solvent
parameters. It can be used to determine the optimal continuum parameters
when experimental solvation energies are unavailable and the
computational costs of explicit solvent charging free energies are
prohibitive.
Generalized Born model with a simple, robust molecular volume correctionJohn Mongan, Carlos Simmerling, J. Andrew McCammon, David A. Case and Alexey OnufrievJournal of Chemical Theory and Computation, Vol. 3, No. 1, pp. 156-169 (2007) [PubMed 21072141]Generalized Born (GB) models provide a computationally efficient means
of representing the electrostatic effects of solvent and are widely
used, especially in molecular dynamics (MD). A class of particularly
fast GB models is based on integration over an interior volume
approximated as a pairwise union of atom spheres -- effectively, the
interior is defined by a van der Waals rather than Lee-Richards
molecular surface. The approximation is computationally efficient, but
if uncorrected, allows for high dielectric (water) regions smaller than
a water molecule between atoms, leading to decreased accuracy. Here, an
earlier pairwise GB model is extended by a simple analytic correction
term that largely alleviates the problem by correctly describing the
solvent-excluded volume of each pair of atoms. The correction term
introduces a free energy barrier to the separation of non-bonded atoms.
This free energy barrier is seen in explicit solvent and Lee-Richards
molecular surface implicit solvent calculations, but has been absent
from earlier pairwise GB models. When used in MD, the correction term
yields protein hydrogen bond length distributions and polypeptide
conformational ensembles that are in better agreement with explicit
solvent results than earlier pairwise models. The robustness and
simplicity of the correction preserves the efficiency of the pairwise GB
models while making them a better approximation to reality.
Unraveling the Three-Metal-Ion Catalytic Mechanism of the DNA Repair Enzyme Endonuclease IVIvaylo Ivanov, John A. Tainer and J. Andrew McCammonProceedings of the National Academy of Sciences of the USA, Vol. 104, No. 5, pp. 1465-1470 (2007) [PubMed 17242363]Endonuclease IV belongs to a class of important apurinic/apyrimidinic
(AP) endonucleases involved in DNA repair. Although a structure-based
mechanistic hypothesis has been put forth for this enzyme, the detailed
catalytic mechanism has remained unknown. Using thermodynamic
integration in the context of ab initio QM/MM molecular dynamics (AIMD),
we examined certain aspects of the phosphodiester cleavage step in the
mechanism. We found the reaction proceeded through a synchronous
bimolecular (ANDN) mechanism with reaction free energy and barrier of
-3.5 and 20.6 kcal/mol, in agreement with experimental estimates. In the
course of the reaction the tri-nuclear active site of endonuclease IV
underwent dramatic local conformational changes -- shifts in the mode of
coordination of both substrate and first-shell ligands. This qualitative
finding supports the notion that structural rearrangements in the active
sites of multinuclear enzymes are integral to biological function.
Towards an in vivo biologically inspired nanofactoryPhilip R. LeDuc, Michael S. Wong, Placid M. Ferreira, Richard E. Groff, Kiryn Haslinger, Michael P. Koonce, Woo Y. Lee, J. Christopher Love, J. Andrew McCammon, Nancy A. Monteiro-Riviere, Vincent M. Rotello, Gary W. Rubloff, Robert Westervelt and Minami YodaNature Nanotechnology, Vol. 2, No. 1, pp. 3-7 (2007) [PubMed 18654192]Nanotechnology is having a major impact on medicine and the treatment of
disease, notably in imaging and targeted drug delivery. It may, however,
be possible to go even further and design 'pseudo-cell' nanofactories
that work with molecules already in the body to fight disease.
SR protein kinase 1 is resilient to inactivationJacky Chi Ki Ngo, Justin Gullingsrud, Kayla Giang, Melinda Jean Yeh, Xiang-Dong Fu, Joseph A. Adams, J. Andrew McCammon and Gourisankar GhoshStructure, Vol. 15, Issue 1, pp. 123-133 (2007) [PubMed 17223538]SR protein kinase 1 (SRPK1) is a constitutively active kinase, which
processively phosphorylates multiple serines within its substrates,
ASF/SF2. We describe crystallographic, molecular dynamics, and
biochemical results that shed light on how SRPK1 preserves its
constitutive active conformation. Our structure reveals that unlike
other known active kinase structures, the activation loop remains in an
active state without any specific intraprotein interactions. Moreover,
SRPK1 remains active despite extensive mutation to the activation
segment. Molecular dynamics simulations reveal that SRPK1 partially
absorbs the effect of mutations by forming compensatory interactions
that maintain a catalytically competent chemical environment.
Furthermore, SRPK1 is similarly resistant to deletion of its spacer loop
region. Based upon a model of SRPK1 bound to a segment encompassing the
docking motif and active-site peptide of ASF/SF2, we suggest a mechanism
for processive phosphorylation and propose that the atypical resiliency
we observed is critical for SRPK1's processive activity.
Binding Pathways of Ligands to HIV-1 Protease: Coarse-grained and Atomistic SimulationsChia-en A. Chang, Joanna Trylska, Valentina Tozzini and J. Andrew McCammonChemical Biology & Drug Design, Vol. 69, Issue 1, pp. 5-13 (2007) [PubMed 17313452]Multiscale simulations (coarse-grained Brownian dynamics simulations and
all-atom molecular dynamics simulations in implicit solvent) were
applied to reveal the binding processes of ligands as they enter the
binding site of the HIV-1 protease. The initial structures used for the
molecular dynamics simulations were generated based on the Brownian
dynamics trajectories, and this is the first molecular dynamics
simulation of modeling the association of a ligand with the protease. We
found that a protease substrate successfully binds to the protein when
the flaps are fully open. Surprisingly, a smaller cyclic urea inhibitor
(XK263) can reach the binding site when the flaps are not fully open.
However, if the flaps are nearly closed, the inhibitor must rearrange or
binding can fail because the inhibitor cannot attain proper
conformations to enter the binding site. Both the peptide substrate and
XK263 can also affect the protein's internal motion, which may help the
flaps to open. Simulations allows us to efficiently study the ligand
binding processes and may help those who study drug discovery to find
optimal association pathways and to design those ligands with the best
binding kinetics.
HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamicsJoanna Trylska, Valentina Tozzini, Chia-en A. Chang and J. Andrew McCammonBiophysical Journal, Vol. 92, Issue 12, pp. 4179-4187 (2007) [PubMed 17384072]We analyze the encounter of a peptide substrate with the native HIV-1 protease, the mechanism of substrate incorporation in the binding cleft, and the dissociation of products after substrate hydrolysis. To account for the substrate, we extend a coarse-grained model force field which we previously developed to study the flap opening dynamics of HIV-1 protease on a microsecond time scale. Molecular and Langevin dynamics simulations show that the flaps need to open for the peptide to bind and that the protease interaction with the substrate influences the flap opening frequency and interval. On the other hand, release of the products does not require flap opening because they can slide out from the binding cleft to the sides of the enzyme. Our data show that in the protease-substrate complex the highest fluctuations correspond to the 17- and 39-turns and the substrate motion is anti-correlated with the 39-turn. Moreover, the active site residues and the flap tips move in phase with the peptide. We suggest some mechanistic principles for how the flexibility of the protein may be involved in ligand binding and release.
Structure and Dynamics of the Full-Length Lipid-Modified H-Ras Protein in a 1,2-dimyristoylglycero-3-phosphocholine BilayerAlemayehu A. Gorfe, Michael Hanzal-Bayer, Daniel Abankwa, John F. Hancock and J. Andrew McCammonJournal of Medicinal Chemistry, Vol. 50, No. 4, pp. 674-684 (2007) [PubMed 17263520]Ras proteins regulate signal transduction processes that control cell
growth and proliferation. Their dysregulation is a common cause of human
tumors. Atomic level structural and dynamical information in a membrane
environment is crucial for understanding signaling specificity among Ras
isoforms and for the design of selective anti-cancer agents. Here, the
structure of the full-length H-Ras protein in complex with a
1,2-dimyristoylglycero- 3-phosphocholine (DMPC) bilayer obtained from
modeling and all-atom explicit solvent molecular dynamics simulations,
as well as experimental validation of the main results, are presented.
We find that, in addition to the lipid anchor, H-Ras membrane binding
involves direct interaction of residues in the catalytic domain with
DMPC phosphates. Two modes of binding (possibly modulated by GTP/GDP
exchange) differing in the orientation and bilayer contact of the
soluble domain as well as in the participation of the flexible linker in
membrane binding are proposed. These results are supported by our
initial in vivo experiments. The overall structure of the protein and
the bilayer remain similar to that of the isolated components, with few
localized structural and dynamical changes. The implications of the
results to membrane lateral segregation and other aspects of Ras
signaling are discussed.
Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction modelsYuhui Cheng, Jason K. Suen, Zoran Radi&Biophysical Chemistry, Vol. 127, Issue 3, pp. 129-139 (2007) [PubMed 17307283]The reaction-diffusion system of the neuromuscular junction has been
modeled in 3D using the finite element package FEtk. The numerical
solution of the dynamics of acetylcholine with the detailed reaction
processes of acetylcholinesterases and nicotinic acetylcholine receptors
has been discussed with the reaction-determined boundary conditions. The
simulation results describe the detailed acetylcholine hydrolysis
process, and reveal the timedependent interconversion of the closed and
open states of the acetylcholine receptors as well as the percentages of
unliganded/monoliganded/diliganded states during the neurotransmission.
The finite element method has demonstrated its flexibility and
robustness in modeling large biological systems.
Finite Element Analysis of the Time-Dependent Smoluchowski Equation for Acetylcholinesterase Reaction Rate CalculationsYuhui Cheng, Jason K. Suen, Deqiang Zhang, Stephen D. Bond, Yongjie Zhang, Yuhua Song, Nathan A. Baker, Chandrajit L. Bajaj, Michael J. Holst and J. Andrew McCammonBiophysical Journal, Vol. 92, Issue 10, pp. 3397-3406 (2007) [PubMed 17307827]This article describes the numerical solution of the time-dependent
Smoluchowski equation to study diffusion in biomolecular systems.
Specifically, finite element methods have been developed to calculate
ligand binding rate constants for large biomolecules. The resulting
software has been validated and applied to the mouse
acetylcholinesterase monomer and several tetramers. Rates for inhibitor
binding to mAChE were calculated at various ionic strengths with several
different time steps. Calculated rates show very good agreement with
experimental and theoretical steady-state studies. Furthermore, these
finite element methods require significantly fewer computational
resources than existing particle-based Brownian dynamics methods and are
robust for complicated geometries. The key finding of biological
importance is that the rate accelerations of the monomeric and
tetrameric mAChE that result from electrostatic steering are preserved
under the non-steadystate conditions that are expected to occur in
physiological circumstances.
Peptide insertion, positioning, and stabilization in a membrane: Insight from an all-atom molecular dynamics simulationArneh Babakhani, Alemayehu A. Gorfe, Justin Gullingsrud, Judy E. Kim and J. Andrew McCammonBiopolymers, Vol. 85, Issue 5-6, pp. 490-497 (2007)
Peptide insertion, positioning, and stabilization in a model membrane
are probed via an all-atom molecular dynamics simulation. One peptide
(WL5) is simulated in each leaflet of a solvated
dimyristoylglycero-3-phosphate (DMPC) membrane. Within the first 5 ns,
the peptides spontaneously insert into the membrane and then stabilize
during the remaining 70 ns of simulation time. In both leaflets, the
peptides localize to the membrane interface, and this localization is
attributed to the formation of peptide-lipid hydrogen bonds. We show
that the single tryptophan residue in each peptide contributes
significantly to these hydrogen bonds; specifically, the nitrogen
heteroatom of the indole ring plays a critical role. The tilt angles of
the indole rings relative to the membrane normal in the upper and lower
leaflets are approximately 26° and 54°, respectively. The tilt
angles of the entire peptide chain are 62° and 74°. The membrane
induces conformations of the peptide that are characteristic of
β-sheets, and the peptide enhances the lipid ordering in the
membrane. Finally, the diffusion rate of the peptides in the membrane
plane is calculated (based on experimental peptide concentrations) to be
approximately 6 Å2/ns, thus suggesting a 500 ns time
scale for intermolecular interactions.
Comparative MD analysis of the stability of Transthyretin providing insight into the fibrillation mechanismJesper Sørensen, Donald Hamelberg, Birgit Schiøtt and J. Andrew McCammonBiopolymers, Vol. 86, Issue 1, pp. 73-82 (2007) [PubMed 17315201]Proteins can misfold and aggregate, which is believed to be the cause of
a variety of diseases, affecting very diverse organs in the body. Many
questions about the nature of aggregation and the proteins that are
involved in these events are still left unanswered. One of the proteins
that is known to form amyloids is transthyretin (TTR), the secondary
transporter of thyroxine, and transporter of retinol-binding protein.
Several experimental results have helped to explain this aberrant
behavior of TTR; however, structural insights of the amyloidgenic
process are still lacking. Therefore, we have used all-atom MD
simulation and free energy calculations to study the initial phase of
this process. We have calculated the free energy changes of the initial
tetramer dissociation under different conditions and in the presence of
thyroxine. We show that tetramer formation is indeed only
thermodynamically favorable in neutral pH conditions. We find that
binding of two thyroxine molecules stabilizes the complex, and that this
occurs with negative cooperativity. In addition to the energetic
calculations, we have also investigated the dominant motions of the TTR
and found that only the dimeric form of the protein could undergo the
initial fibril formation.
Multivariate analysis of conserved sequence-structure relationships in kinesins: Coupling of the active site and a tubulin-binding domainBarry J. Grant, J. Andrew McCammon, Leo S.D. Caves and Robert A. CrossJournal of Molecular Biology, Vol. 368, Issue 5, pp. 1231-1248 (2007) [PubMed 17399740]An extensive computational analysis of available sequence and crystal
structure data was used to identify functionally important residue
interactions within the motor domain of the kinesin molecular motor.
Principal component analysis revealed that all current kinesin crystal
structures reside in one of two main conformations, which differ at the
active site, and in the position of a microtubule-binding sub-domain
relative to a rigid central core. This sub-domain consists of secondary
structure elements α4-loop12-α5-loop13 and contains a
conserved hydrophilic surface patch that may be involved in strong
binding to microtubules. A hinge point for the sub-domain motion lies
near a conserved glycine at position 292. Statistical coupling analysis
revealed a network of co-evolving positions that link this region to the
nucleotide-binding site, via a highly conserved histidine in the switch
I loop. The data are consistent with a model in which the nucleotide
status of the active site shifts kinesin between weak and strong binding
conformations via reconfiguration of the identified sub-domain. Our data
provide a statistically supported framework for further examination of
this and other structure-function relationships in the kinesin family.
Molecular Dynamics Simulations of Metalloproteinases types 2 and 3 Reveal Differences in the Dynamic Behavior of the S1' Binding PocketCésar Augusto F. de Oliveira, Maurice Zissen, John Mongan and J. Andrew McCammonCurrent Pharmaceutical Design, Vol. 13, No. 34, pp. 3471-3475 (2007) [PubMed 18220784]Matrix Metalloproteinases (MMPs) are zinc-containing proteinases that
are responsible for the metabolism of extracellular matrix proteins.
Overexpression of MMPs has been associated with a wide range of
pathological diseases such as arthritis, cancer, multiple sclerosis and
Alzheimer's disease. The excessive and unregulated activity of Matrix
Metalloproteinases type 2 (MMP-2), also known as gelantinase A, has been
identified in a number of cancer metastases. Several MMP inhibitors
(MMPi) have been proposed in the literature aiming to interfere in the
MMPs activity. In this work we performed long MD simulations in order to
study the dynamical behavior of the binding pocket S1' in the
apo forms of MMP type 2 and 3, and identify, at the molecular
level, the structural properties relevant for the designing of specific
inhibitor MMP-2.
Improved Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force CalculationsBenzhuo Lu and J. Andrew McCammonJournal of Chemical Theory and Computation, Vol. 3, Issue 3, pp. 1134-1142 (2007)
A patch representation differing from the traditional treatments in the
boundary element method (BEM) is presented, which we call the constant
"node patch" method. Its application to solving the Poisson-Boltzmann
equation (PBE) demonstrates considerable improvement in speed compared
with the constant element and linear element methods. In addition, for
the node-based BEMs, we propose an efficient interpolation method for
the calculation of the electrostatic stress tensor and PB force on the
solvated molecular surface. This force calculation is simply an O(N)
algorithm (N is the number of elements). Moreover, our calculations also
show that the geometric factor correction in the boundary integral
equations (BIEs) significantly increases the accuracy of the potential
solution on the boundary, and thereby the PB force calculation.
Acetylcholinesterase: Mechanisms of Covalent Inhibition of Wild-Type and H447I Mutant Determined by Computational AnalysesYuhui Cheng, Xiaolin Cheng, Zoran Radi&Journal of the American Chemical Society, Vol. 129, Issue 20, pp. 6562-6570 (2007) [PubMed 17461584]The reaction mechanisms of two inhibitors
TFK+ and
TFK0 binding to both the wild-type and H447I mutant
mouse acetylcholinesterase (mAChE) have been investigated by using a
combined
ab initio quantum mechanical/molecular mechanical
(QM/MM) approach and classical molecular dynamics (MD) simulations. In
the wild-type mAChE, the binding reactions of
TFK+
and
TFK0 are both spontaneous processes, which
proceed through the nucleophilic addition of the
Ser203-
Oγ to the carbonyl-C of
TFK+ or
TFK0, accompanied with a
simultaneous proton transfer from Ser203 to His447. No barrier is found
along the reaction paths, consistent with the experimental reaction
rates approaching the diffusion-controlled limit. By contrast,
TFK+ binding to the H447I mutant may proceed with a
different reaction mechanism. A water molecule takes over the role of
His447 and participates in the bond breaking and forming as a "charge
relayer". Unlike in the wild-type mAChE case, Glu334, a conserved
residue from the catalytic triad, acts as a catalytic base in the
reaction. The calculated energy barrier for this reaction is about 8
kcal/mol. These predictions await experimental verification. In the case
of the neutral ligand
TFK0, however, multiple MD
simulations on the
TFK0/H447I complex reveal that
none of the water molecules can be retained in the active site as a
"catalytic" water. Furthermore, our alchemical free energy calculation
also suggests that the binding of
TFK0 to H447I is
much weaker than that of
TFK+. Taken together, our
computational studies confirm that
TFK0 is almost
inactive in the H447I mutant and also provide detailed mechanistic
insights into the experimental observations.
Barriers to Ion Translocation in Cationic and Anionic Receptors from the Cys-Loop FamilyIvaylo Ivanov, Xiaolin Cheng, Steven M. Sine and J. Andrew McCammonJournal of the American Chemical Society, Vol. 129, Issue 26, pp. 8217-8224 (2007) [PubMed 17552523]Understanding the mechanisms of gating and ion permeation in biological
channels and receptors has been a long-standing challenge in biophysics.
Recent advances in structural biology have revealed the architecture of
a number of transmembrane channels and allowed detailed, molecular-level
insight into these systems. Herein, we have examined the barriers to ion
conductance and origins of ion selectivity in models of the cationic
human α7 nicotinic acetylcholine receptor (nAChR) and the anionic
α1 glycine receptor (GlyR), based on the structure of Torpedo
nAChR. Molecular dynamics simulations were used to determine water
density profiles along the channel length and established that both
receptor pores were fully hydrated. The very low water density in the
middle of the nAChR pore indicated the existence of a hydrophobic
constriction. By contrast, the pore of GlyR was lined with hydrophilic
residues and remained well hydrated throughout. Adaptive biasing force
simulations allowed us to reconstruct potentials of mean force (PMFs)
for chloride and sodium ions in the two receptors. For the nicotinic
receptor we observed barriers to ion translocation associated with rings
of hydrophobic residues - Val13' and Leu9' - in the middle of the
transmembrane domain. This finding further substantiates the hydrophobic
gating hypothesis for nAChR. The PMF revealed no significant hydrophobic
barrier for chloride translocation in GlyR. For both receptors non-
permeant ions displayed considerable barriers. Thus, the overall
electrostatics and the presence of rings of charged residues at the
entrance and exit of the channels were sufficient to explain the
experimentally observed anion and cation selectivity.
Dealing with bound waters in a site: Do they leave or stay?Donald Hamelberg and J. Andrew McCammonIn "Computational and Structural Approaches to Drug Discovery," R.M. Stroud, Ed., Royal Society of Chemistry, Ch. 5, pp. 95-110 (2007)
Water molecules are ubiquitous to biomolecules. They play a very important
role in the function and structure of proteins. They also make up an integral
part of protein structures and contribute to their stability. Localized water
molecules can be found in the crevices on protein surfaces, in deeper channels
or ligand binding sites, and within buried hydrophilic cavities of protein
molecules. There is also evidence that water molecules could sometimes bind
to cavities that are mostly hydrophobic. Also, water molecules are
characteristically present in the interfaces found in protein-ligand,
protein-protein, protein-carbohydrate, protein-nucleic acid, and nucleic
acid-ligand complexes. These water molecules can now be routinely detected by
X-ray crytallographic and nuclear magnetic resonance (NMR) experiments.
Interfacial water molecules typically act as bridges between two solute
molecules, playing a role in recognition and specificity, and at the same
time stabilizing the complex by accepting and donating hydrogen bonds.
However, in some cases water molecules have been shown to direct the function
of an enzyme protein, for example the catalytic abilities of protein kinases.
The highly conserved protein kinase CK2, which utilizes ATP, could also
efficiently make use of GTP by localizing a water molecule at the interface
between GTP and the binding pocket.
Remarkable Loop Flexibility in Avian Influenza N1 and its Implications for Antiviral Drug DesignRommie E. Amaro, David D.L. Minh, Lily S. Cheng, William M. Lindstrom, Jr., Arthur J. Olson, Jung-Hsin Lin, Wilfred W. Li and J. Andrew McCammonJournal of the American Chemical Society, Vol. 129, Issue 25, pp. 7764-7765 (2007) [PubMed 17539643]The emergence and continuing global spread of the highly virulent avian
influenza H5N1 has raised concerns of a possible human pandemic. Several
approved anti-influenza drugs effectively target the neuraminidase (NA),
a surface glycoprotein that cleaves terminal sialic acid residues and
facilitates the release of viral progeny from infected cells. The first
crystal structures of group-1 NAs revealed that although the binding
pose of oseltamivir was similar to that seen in previous
crystallographic complexes, the 150-loop adopted a distinct
conformation, opening a new cavity adjacent to the active site. Here we
show that the 150-loop is able to open into significantly wider
conformations than seen in the crystal structures, through explicitly
solvated MD simulations of the apo and oseltamivir-bound forms of
tetrameric N1. We find that motion in the 150-loop is coupled to motion
in the neighboring 430-loop, which expands the active site cavity even
further. Furthermore, in simulations of the oseltamivir-bound system,
the 150-loop approaches the closed conformation, suggesting that the
loop switching motion may be more rapid than previously observed.
“New-version-fast-multipole-method” accelerated electrostatic calculations in biomolecular systemsBenzhuo Lu, Xiaolin Cheng and J. Andrew McCammonJournal of Computational Physics, Vol. 226, Issue 2, pp. 1348-1366 (2007) [PubMed 18379638]In this paper, we present an efficient and accurate numerical algorithm
for calculating the electrostatic interactions in biomolecular systems.
In our scheme, a boundary integral equation (BIE) approach is applied to
discretize the linearized Poisson-Boltzmann (PB) equation. The resulting
integral formulas are well conditioned for single molecule cases as well
as for systems with more than one macromolecule, and are solved
efficiently using Krylov subspace based iterative methods such as
generalized minimal residual (GMRES) or biconjugate gradients stabilized
(BiCGStab) methods. In each iteration, the convolution type
matrix-vector multiplications are accelerated by a new version of the
fast multipole method (FMM). The implemented algorithm is asymptotically
optimal $O(N)$ both in CPU time and memory usage with optimized
prefactors. Our approach enhances the present computational ability to
treat electrostatics of large scale systems in protein-protein
interactions and nano particle assembly processes. Applications
including calculating the electrostatics of the nicotinic acetylcholine
receptor (nAChR) and interactions between protein Sso7d and DNA are
presented.
Application of the level-set method to the implicit solvation of nonpolar moleculesLi-Tien Cheng, Joachim Dzubiella, J. Andrew McCammon and Bo LiJournal of Chemical Physics, Vol. 127, article 084503, 10 pages (2007) [PubMed 17764265]A level-set method is developed for numerically capturing the
equilibrium solute-solvent interface that is defined by the recently
proposed variational implicit solvent model
(http://dx.doi.org/10.1103/PhysRevLett.96.087802" target="_blank"
class="ref">Dzubiella, Swanson, and McCammon,
Phys. Rev. Lett.
96, 087802 (2006) and http://dx.doi.org/10.1063/1.2171192"
target="_blank" class="ref">
J. Chem. Phys. 124, 084905 (2006)).
In the level-set method, a possible solute-solvent interface is
represented by the zero level-set (i.e., the zero level surface) of a
level-set function and is eventually evolved into the equilibrium
solute-solvent interface. The evolution law is determined by
minimization of a solvation free energy
functional that couples
both the interfacial energy and the van der Waals type solute-solvent
interaction energy. The surface evolution is thus an energy minimizing
process, and the equilibrium solute-solvent interface is an output of
this process. The method is implemented and applied to the solvation of
nonpolar molecules such as two xenon atoms, two parallel paraffin
plates, helical alkane chains, and a single fullerene C60. The level-set
solutions show good agreement for the solvation energy when compared to
available molecular dynamics simulations. In particular, the method
captures solvent dewetting (nanobubble formation) and quantitatively
describes the interaction in the strongly hydrophobic plate system.
Nanosecond-Timescale Conformational Dynamics of the Human α7 Nicotinic Acetylcholine ReceptorXiaolin Cheng, Ivaylo Ivanov, Hailong Wang, Steven M. Sine and J. Andrew McCammonBiophysical Journal, Vol. 93, Issue 8, pp. 2622-2634 (2007) [PubMed 17573436]We explore the conformational dynamics of a homology model of the human
alpha7 nicotinic acetylcholine receptor (nAChR) using molecular dynamics
(MD) simulation and analyses of root-mean-square fluctuations (RMSF),
block partitioning of segmental motion and principal component analysis
(PCA). The results reveal flexible regions and concerted global motions
of the subunits encompassing extracellular and transmembrane domains of
the subunits. The most relevant motions comprise a bending, hinged at
the beta10-M1 region, accompanied by concerted tilting of the M2 helices
that widens the intracellular end of the channel. Despite the nanosecond
timescale, the observations suggest that tilting of the M2 helices may
initiate opening of the pore. The results also reveal direct coupling
between a twisting motion of the extracellular domain and dynamic
changes of M2. Covariance analysis of inter-residue motions shows that
this coupling arises through a network of residues within the Cys- and
M2-M3 loops where Phe135 is stabilized within a hydrophobic pocket
formed by Leu270 and Ile271. The resulting concerted motion causes a
downward shift of the M2 helices that disrupts a hydrophobic girdle
formed by 9' and 13' residues.
Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma bruceiRommie E. Amaro, Robert V. Swift and J. Andrew McCammonPLoS Neglected Tropical Diseases, Vol. 1, No. 2, article e68, 10 pages (2007) [PubMed 18060084]RNA editing ligase 1 (TbREL1) is required for the survival of both the
insect and bloodstream forms of Trypanosoma brucei, the parasite
responsible for the devastating tropical disease, African sleeping
sickness. The type of RNA editing that TbREL1 is involved in is unique
to the trypanosomes, and no close human homolog is known to exist. In
addition, the high-resolution crystal structure revealed several unique
features of the active site, making this enzyme a promising target for
structure-based drug design. In this work, two 20 ns atomistic molecular
dynamics (MD) simulations are employed to investigate the dynamics of
TbREL1, both with and without the ATP substrate present. The flexibility
of the active site, dynamics of conserved residues and crystallized
water molecules, and the interactions between TbREL1 and the ATP
substrate are investigated and discussed in the context of TbREL1's
function. Differences in local and global motion upon ATP binding
suggest that two peripheral loops, unique to the trypanosomes, may be
involved in interdomain signaling events. Notably, a significant
structural rearrangement of the enzyme's active site occurs during the
apo simulations, opening an additional cavity adjacent to the ATP
binding site that could be exploited in the development of effective
inhibitors directed against this protozoan parasite. Finally, ensemble
averaged electrostatics calculations over the MD simulations reveal a
novel putative RNA binding site, a discovery that has previously eluded
scientists. Ultimately, we use the insights gained through the MD
simulations to make several predictions and recommendations, which we
anticipate will help direct future experimental studies and
structure-based drug discovery efforts against this vital enzyme.
Free Energy Profile of H-ras Membrane Anchor upon Membrane InsertionAlemayehu A. Gorfe, Arneh Babakhani and J. Andrew McCammonAngewandte Chemie International Edition, Vol. 46, Issue 43, pp. 8234-8237 (2007) [PubMed 17886310]Ras GTPases mediatr signaling pathways in cell proliferation,
development, and apoptosis. They undergo isoprenylation at a C-terminal
CaaX signal (
a usually represents aliphatic and
X any amino acid) followed by proteolysis of aaX and
carboxymethylation. In the case of H-ras, a subsequent dual
palmitoylation of cysteines adjacent to the site of farnesylation
produces a mature anchor for plasma membrane targeting.
http://dx.doi.org/10.1038/nchembio834" target="_blank" class="ref">M.D.
Resh,
Nat. Chem. Biol. 2, 584 (2006);
http://www.pubmedcentral.nih.gov/articlerender.fcgi?pubmedid=2663468"
target="_blank" class="ref">L. Gutierrez, A.I. Magee, C.J. Marshall,
J.F. Hancock,
EMBO J. 8, 1093 (1989) Atomistic information,
such as the structure of membrane-bound ras and the free energy of
complex formation, are vital in research efforts geared towards
designing ras-isoform-selective anticancer agents. The most common
experimental techniques are not yet able to provide such information.
Here we present computational results on the free energy profile for the
transfer of the H-ras membrane anchor from water to a bilayer of
1,2-dimyristoyl-
sn-glycero-3-phosphocholine (1,2-DMPC) lipids.
We find that there is no significant barrier for insertion, and that
once a few carbon atoms of the ras lipid chains cross the membrane-water
interface, the free energy displays a steeply downhill profile.
Insertion into the hydrocarbon core of the ras lipids and the
interfacial localization of the backbone together produce a gain in free
energy of up to 30 kcal/mol. Additionally, using the recently reported
computationally derived structures of full-length H-ras in a DMPC
bilayer, http://dx.doi.org/10.1021/jm061053f" target="_blank"
class="ref">A.A. Gorfe, M. Hanzal-Bayer, D. Abankwa, J.F. Hancock, J.A.
McCammon,
J. Med. Chem. 50, 674 (2007) we explain how a small
difference in free energy would enable modulation of H-ras membrane
binding by the linker and the catalytic domain.
Generalized gradient-augmented harmonic Fourier beads method with multiple atomic and/or center-of-mass positional restraintsIlja V. Khavrutskii and J. Andrew McCammonJournal of Chemical Physics, Vol. 127, article 124901, 12 pages (2007) [PubMed 17902931]We describe a generalization of the gradient-augmented Harmonic Fourier
Beads method for finding minimum free energy transition path ensembles
and similarly minimum potential energy paths to allow positional
restraints on the centers of mass of selected atoms. The generalized
method (ggaHFB) further extends the scope of the HFB methodology to
studying molecule transport across various mobile phases such as lipid
membranes. Furthermore, the new implementation improves the
applicability of the HFB method to studies of ligand binding, protein
folding and enzyme catalysis as well as modeling equilibrium pulling
experiments. Like its predecessor, the ggaHFB method provides accurate
energy profiles along the specified paths and in certain simple cases
avoids the need for path optimization. The utility of the ggaHFB method
is demonstrated with an application to the water permeation through a
single-wall (5,5) carbon nanotube with a diameter of 6.78 A and length
of 16.0 A. We provide a simple rationale as to why water enters the
hydrophobic nanotube and why it does so in pulses and in wire assembly.
Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?David S. Cerutti, Nathan A. Baker and J. Andrew McCammonJournal of Chemical Physics, Vol. 127, article 155101, 12 pages (2007) [PubMed 17949217]The solvent reaction field potential of an uncharged protein immersed in
Simple Point Charge / Extended (SPC/E) explicit solvent was computed
over a series of molecular dynamics trajectories, in total 1560 ns of
simulation time. A finite, positive potential of 13 to 24 kT/e (where T
= 300K), dependent on the geometry of the solvent-accessible surface,
was observed inside the biomolecule. The primary contribution to this
potential arose from a layer of positive charge density 1.0 Angstroms
from the solute surface, on average 0.008 e per cubic Angstrom, which we
found to be the product of a highly ordered first solvation shell.
Significant second solvation shell effects, including additional layers
of charge density and a slight decrease in the short-range
solvent-solvent interaction strength, were also observed. The impact of
these findings on implicit solvent models was assessed by running
similar explicit-solvent simulations on the fully charged protein
system. When the energy due to the solvent reaction field in the
uncharged system is accounted for, correlation between per-atom
electrostatic energies for the explicit solvent model and a simple
implicit (Poisson) calculation is 0.97, and correlation between per-atom
energies for the explicit solvent model and a previously published,
optimized Poisson model is 0.99.
H-ras Protein in a Bilayer: Interaction and Structure PerturbationAlemayehu A. Gorfe, Arneh Babakhani and J. Andrew McCammonJournal of the American Chemical Society, Vol. 129, No. 40, pp. 12280-12286 (2007) [PubMed 17880077]Ras GTPases become functionally active when anchored to membranes by
inserting their lipid modified side chains. Their role in cell division,
development and cancer has made them targets of extensive research
efforts, yet the mechanism of membrane insertion and the structure of
the resulting complex remain elusive. Recently, the structure of the
full-length H-ras protein in a DMPC bilayer has been computationally
characterized. Here, the atomic interactions between the H-ras membrane
anchor and the DMPC bilayer are investigated in detail. We find that the
palmitoylated cysteines and Met182 have dual contributions to membrane
affinity: hydrogen bonding by their amides and vdW interaction by their
hydrophobic side chains. The polar side chains help maintain the
orientation of the anchor. Although the overall structure of the bilayer
is similar to that of a pure DMPC, there are localized perturbations.
These perturbations depend on the insertion depth and backbone
localization of the anchor, which in turn is modulated by the catalytic
domain and the linker. The pattern of anchor amide-DMPC
phosphate/carbonyl hydrogen bonds and the flexibility of Palm184 are
important in discriminating between different modes of ras-DMPC
interactions. The results provide structural arguments in support of the
proposed participation of ras in the organization of membrane
nanoclusters.
A proposed signaling motif for nuclear import in mRNA processing via the formation of Arginine ClawDonald Hamelberg, Tongye Shen and J. Andrew McCammonProceedings of the National Academy of Sciences of the USA, Vol. 104, No. 38, pp. 14947-14951 (2007) [PubMed 17823247]Phosphorylation of proteins by kinases is the most commonly studied
class of posttranslational modification, yet its structural consequences
are not well understood. The human SR (serine-arginine) protein ASF/SF2
relies on the processive phosphorylation of the serine residues of eight
consecutive arginine-serine (RS) dipeptide repeats at the C terminus by
SRPK1 before it can be transported into the nucleus. This SR protein
plays critical roles in spliceosome assembly, pre-mRNA splicing, and
mRNA export, and the phosphorylation process of the RS repeats has been
extensively studied experimentally. However, knowledge of the
conformational changes associated with the phosphorylation of this
simple sequence and how it triggers the importation of the SR protein is
lacking. Here, we have carried out extensive molecular dynamics
simulations to show that phosphorylation of the eight RS repeats
significantly alters the peptide's conformation and leads to the
formation of very stable structures that are likely to be involved in
the recognition, binding, and transport of the SR protein. Specifically,
we found an unusual symmetry-broken phase of conformations of the
repetitive and quasi-symmetric phosphorylated peptide sequence. One of
the main characteristics of these conformations is the exposed phosphate
groups on the periphery, which possibly could serve as the recognition
platform for the transport protein transportin-SR2.
Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolutionBenzhuo Lu, Y.C. Zhou, Gary A. Huber, Stephen D. Bond, Michael J. Holst and J. Andrew McCammonJournal of Chemical Physics, Vol. 127, article 135102, 17 pages (2007) [PubMed 17919055]A computational framework is presented for the continuum modeling of
cellular biomolecular diffusion influenced by electrostatic driving
forces. This framework is developed from a combination of
state-of-the-art numerical methods, geometric meshing and computer
visualization tools. In particular, a hybrid of (adaptive) finite
element and boundary element methods is adopted to solve the
Smoluchowski equation (SE), the Poisson equation (PE), and the
Poisson-Nernst-Planck equation (PNPE) in order to describe
electrodiffusion processes. The finite element method is used because of
its flexibility in modeling irregular geometries and complex boundary
conditions. The boundary element method is used due to the convenience
of treating the singularities in the source charge distribution and its
accurate solution to electrostatic problems on molecular boundaries.
Nonsteady-state diffusion can be studied using this framework, with the
electric field computed using the densities of charged small molecules
and mobile ions in the solvent. A solution for mesh generation for
biomolecular systems is supplied, which is an essential component for
the finite element and boundary element computations. The uncoupled
Smoluchowski equation and Poisson-Boltzmann equation (PBE) are
considered as special cases of the PNPE in numerical algorithm, and
therefore can be solved in this framework as well. Two types of
computations are reported in the results: stationary PNPE and
time-dependent SE or Nernst-Planck equations (PN) solutions. A
biological application of the first type is the ionic density
distribution around a fragment of DNA determined by the equilibrium
PNPE. The stationary PNPE with non-zero flux is also discussed for a
simple model system. The second is a time-dependent diffusion process:
the consumption of the neurotransmitter acetylcholine (ACh) by
acetylcholinesterase (AChE), determined by the SE and a single uncoupled
solution of the Poisson-Boltzmann equation. The electrostatic effects,
counterion compensation, spatiotemporal distribution, and
diffusion-controlled reaction kinetics are analyzed and different
methods are compared.
Dynamics, Hydration, and Motional Averaging of a Loop-Gated Artificial Protein Cavity: The W191G Mutant of Cytochrome c Peroxidase in Water as Revealed by Molecular Dynamics SimulationsRiccardo Baron and J. Andrew McCammonBiochemistry, Vol. 46, Issue 37, pp. 10629-10642 (2007) [PubMed 17718514]Five molecular dynamics simulations of the W191G cavity mutant of
cytochrome c peroxidase in explicit water reveal distinct dynamic and
hydration behavior depending on the closed or open state of the flexible
loop gating the cavity, the binding of (K
+ or small molecule)
cations, and the system temperature. The conformational spaces sampled
by the loop region and by the cavity significantly reduce upon binding.
The largest ordering factor on water dynamics is the presence of the
K
+ ion occupying the gated cavity. Considerable water
exchange occurs for the open-gate cavity when no ligand or cation is
bound. In all cases, good correspondence is found between the calculated
(ensemble-averaged) location of water molecules and the water sites
determined by X-ray crystallography experiments. However, our
simulations suggest that these sites do not necessarily correspond to
the presence of bound water molecules. In fact, individual water
molecules may repeatedly exchange within the cavity volume yet occupy on
average these water sites. Four major conclusions emerge. First, it
seems misleading to interpret the conformation of protein loop regions
in terms of single dominant structures. Second, our simulations support
the general picture of Pro 190
cis-trans isomerization as a
determinant of the loop-opening mechanism. Third, receptor flexibility
is fundamental for ligand binding and molecular recognition, and our
results suggest its importance for the docking of small compounds to the
artificial cavity. Fourth, after validation against the available
experimental data, molecular dynamics simulations can be used to
characterize the dynamics and exchange of water molecules and ions,
providing atomic level and time- dependent information otherwise
inaccessible to experiments.
Sampling of slow diffusive conformational transitions with accelerated molecular dynamicsDonald Hamelberg, César Augusto F. de Oliveira and J. Andrew McCammonJournal of Chemical Physics, Vol. 127, article 155102, 9 pages (2007) [PubMed 17949218]Slow diffusive conformational transitions play key functional roles in
biomolecular systems. Our ability to sample these motions with molecular
dynamics simulation in explicit solvent is limited by the slow diffusion
of the solvent molecules around the biomolecules. Previously, we
proposed an accelerated molecular dynamics method that has been shown to
efficiently sample the torsional degrees of freedom of biomolecules
beyond the millisecond timescale. However, in our previous approach,
large-amplitude displacements of biomolecules are still slowed by the
diffusion of the solvent. Here we present a unified approach of
efficiently sampling both the torsional degrees of freedom and the
diffusive motions concurrently. We show that this approach samples the
configuration space more efficiently than normal molecular dynamics and
that ensemble averages converge faster to the correct values.
Estimating Kinetic Rates from Accelerated Molecular Dynamics Simulations: Alanine Dipeptide in Explicit Solvent as a Case StudyCésar Augusto F. de Oliveira, Donald Hamelberg and J. Andrew McCammonJournal of Chemical Physics, Vol. 127, article 175105, 8 pages (2007) [PubMed 17994855]Molecular dynamics (MD) simulation is the standard computational
technique used to obtain information on the time evolution of the
conformations of proteins and many other molecular systems. However, for
most biological systems of interest, the time scale for slow
conformational transitions is still inaccessible to standard MD
simulations. Several sampling methods have been proposed to address this
issue, including the accelerated molecular dynamics method. In this
work, we study the extent of sampling of the phi/psi space of alanine
dipeptide in explicit water using accelerated molecular dynamics and
present a framework to recover the correct kinetic rate constant for the
helix to beta-strand transition. We show that the accelerated MD can
drastically enhance the sampling of the phi/psi conformational phase
space when compared to normal MD. In addition, the free energy density
plots of the phi/psi space show that all minima regions are accurately
sampled and the canonical distribution is recovered. Moreover, the
kinetic rate constant for the helix to beta-strand transition is
accurately estimated from these simulations by relating the diffusion
coefficient to the local energetic roughness of the energy landscape.
Surprisingly, even for such a low barrier transition, it is difficult to
obtain enough transitions to accurately estimate the rate constant when
one uses normal MD.
Accelerated entropy estimates with accelerated dynamicsDavid D.L. Minh, Donald Hamelberg and J. Andrew McCammonJournal of Chemical Physics, Vol. 127, article 154105, 5 pages (2007) [PubMed 17949130]Evaluating the entropy of a classical ensemble, requires integrating
over the probability density, p(r), as a function of configurational
space position, r. In practice, the actual probability is rarely known
and the entropy is calculated using a density estimate based on
statistical sampling. In complex systems such as biological
macromolecules, sampling all significant configurations is notoriously
difficult. Although technological progress has enabled molecular
dynamics simulations, which integrate Newton's equations of motion to
observe time-dependent system behaviors, to reach the nano- to
microsecond regime, some biologically relevant conformational changes
are known to occur on the order of seconds, hours, or even days. Even
the longest trajectories can be kinetically trapped in local energy
minima and fall far short of ergodicity. Monte Carlo algorithms, in
which random moves are proposed and stochastically accepted according to
their energetic properties, encounter a similar problem: it is difficult
to design large moves in phase space with reasonable acceptance
probabilities.