Dynamic binding of PKA regulatory subunit RIαJustin Gullingsrud, Choel Kim, Susan S. Taylor and J. Andrew McCammonStructure, Vol. 14, Issue 1, pp. 141-149 (2006) [PubMed 16407073]Recent crystal structures have revealed that regulatory subunit
RIα of PKA undergoes a dramatic conformational change upon complex
formation with the catalytic subunit. Molecular dynamics studies were
initiated to elucidate the contributions of intrinsic conformational
flexibility and interactions with the catalytic subunit in formation and
stabilization of the complex. Simulations of a single RIα
nucleotide-binding domain (NBD), missing cAMP, showed that its C helix
spontaneously occupies two distinct conformations: either packed against
the nucleotide binding domain as in its cAMP-bound structure, or
extended into an intermediate form resembling that of the holoenzyme
structure. C helix extension was not seen in a simulation of both
RIα NBDs. In a model complex containing both NBDs and the
catalytic subunit, well-conserved residues at the interface between the
NBDs in the cAMP-bound form were found to stabilize the complex through
contacts with the catalytic subunit. The model structure is consistent
with available experimental data.
Molecular Dynamics: A Survey of Methods for Simulating the Activity of ProteinsStewart A. Adcock and J. Andrew McCammonChemical Reviews, Vol. 106, No. 5, pp. 1589-1615 (2006) [PubMed 16683746]This review offers an outline of the origin of molecular dynamics
simulation for protein systems and how it has developed into a robust
and trusted tool. This review then covers more recent advances in theory
and an illustrative selection of practical studies in which it played a
central role. The range of studies in which MD has played a considerable
or pivotal role is immense, and this review cannot do justice to them.
Particular emphasis will be placed on the study of dynamic aspects of
protein recognition, an area where molecular dynamics has scope to
provide broad and far-ranging insights. This review concludes with a
brief discussion of the future potential offered to advancement of the
biological and biochemical sciences and the remaining issues that must
be overcome to allow the full extent of this potential to be realized.
Channel Opening Motion of α7 Nicotinic Acetylcholine Receptor as Suggested by Normal Mode AnalysisXiaolin Cheng, Benzhuo Lu, Barry Grant, Richard J. Law and J. Andrew McCammonJournal of Molecular Biology, Vol. 355, Issue 2, pp. 310-324 (2006) [PubMed 16307758]The gating motion of the human nicotinic acetylcholine receptor (nAChR)
α7 was investigated with normal mode analysis (NMA) of two
homology models. The first model, referred to as model I, was built from
both the Lymnaea stagnalis acetylcholine binding protein (AChBP) and the
transmembrane (TM) domain of the Torpedo marmorata nAChR. The second
model, referred to as model C, was based solely on the recent electron
microscopy structure of the T. marmorata nAChR. Despite structural
differences, both models exhibit nearly identical patterns of
flexibility and correlated motions. In addition, both models show a
similar global twisting motion that may represent channel gating. The
similar results obtained for the two models indicate that NMA is most
sensitive to the contact topology of the structure rather than its finer
detail. The major difference between the low-frequency motions sampled
for the two models is that a symmetrical pore-breathing motion, favoring
channel opening, is present as the second most dominant motion in model
I, whilst largely absent from model C. The absence of this mode in model
C can be attributed to its less symmetrical architecture. Finally, as a
further goal of the present study, an approximate open channel model,
consistent with many experimental findings, has been produced.
Restrained Molecular Dynamics Simulations of HIV-1 Protease: Validating a New Target for Drug DesignAlexander L. Perryman, Jung-Hsin Lin and J. Andrew McCammonBiopolymers, Vol. 82, Issue 3, pp. 272-284 (2006) [PubMed 16508951]To test the anti-correlated relationship that was recently displayed in
conventional Molecular Dynamics (MD) simulations, several different
restrained MD simulations on a wild type and on the V82F/I84V
drug-resistant mutant of HIV-1 protease were performed. This
anticorrelated relationship refers to the observation that compression
of the peripheral ear-to-cheek region of HIV protease (i.e., the elbow
of the flap to the fulcrum and the cantilever) occurred as the active
site flaps were opening, and, conversely, expansion of that ear-to-cheek
region occurred as both flaps were closing. An additional examination of
this anti-correlated relationship was necessary to determine whether it
can be harnessed in a useful manner. Consequently, six different MD
experiments were performed that incorporated pair-wise distance
restraints in that ear-to-cheek region (i.e., the distance between the
α-carbons of Gly40 and Gln61 was restrained to either 7.7 or 10.5
Angstroms, in both monomers). Pushing the backbones of the ear and the
cheek regions away from each other slightly did force the flaps that
guard the active site to remain closed in both the wild type and the
mutant systems--even though there were no ligands in the active sites.
Thus, these restrained MD simulations provided evidence that the
anti-correlated relationship can be exploited to affect the dynamic
behavior of the flaps that guard the active site of HIV-1 protease.
These simulations supported our hypothesis of the mechanism governing
flap motion, and they are the first step towards validating that
peripheral surface as a new target for drug design.
Increased Membrane Affinity of the C1 Domain of Protein Kinase Cδ Compensates for the Lack of Involvement of its C2 Domain in Membrane RecruitmentJennifer R. Giorgione, Jung-Hsin Lin, J. Andrew McCammon and Alexandra C. NewtonJournal of Biological Chemistry, Vol. 281, No. 3, pp. 1660-1669 (2006) [PubMed 16293612]Protein kinase C (PKC) family members are allosterically activated
following membrane recruitment by specific membrane-targeting modules.
Conventional PKC isozymes are recruited to membranes by two such
modules: a C1 domain, which binds diacylglycerol (DAG), and a C2 domain,
which is a Ca
2+-triggered phospholipid-binding module. In
contrast, novel PKC isozymes respond only to DAG, despite the presence
of a C2 domain. Here, we address the molecular mechanism of membrane
recruitment of the novel isozyme PKCδ. We show that PKCδ and
a conventional isozyme, PKCβII, bind membranes with comparable
affinities. However, dissection of the contribution of individual
domains to this binding revealed that, although the C2 domain is a major
determinant in driving the interaction of PKCβII with membranes,
the C2 domain of PKCδ does not bind membranes. Instead, the C1B
domain is the determinant that drives the interaction of PKCδ with
membranes. The C2 domain also does not play any detectable role in the
activity or subcellular location of PKCδ in cells;
in
vivo imaging studies revealed that deletion of the C2 domain does
not affect the stimulus-dependent translocation or activity of
PKCδ. Thus, the increased affinity of the C1 domain of PKCδ
allows this isozyme to respond to DAG alone, whereas conventional PKC
isozymes require the coordinated action of Ca
2+ binding to
the C2 domain and DAG binding to the C1 domain for activation.
Electrostatic Properties of Cowpea Chlorotic Mottle Virus and Cucumber Mosaic Virus CapsidsRobert Konecny, Joanna Trylska, Florence Tama, Deqiang Zhang, Nathan A. Baker, Charles L. Brooks III and J.A. McCammonBiopolymers, Vol. 82, Issue 2, pp. 106-120 (2006) [PubMed 16278831]Electrostatic properties of cowpea chlorotic mottle virus (CCMV) and
cucumber mosaic virus (CMV) were investigated using numerical solutions
to the Poisson-Boltzmann equation. Experimentally, it has been shown
that CCMV particles swell in the absence of divalent cations when the pH
is raised from 5 to 7. CMV, although structurally homologous, does not
undergo this transition. An analysis of the calculated electrostatic
potential confirms that a strong electrostatic repulsion at the calcium
binding sites in the CCMV capsid is most likely the driving force for
the capsid swelling process during the release of calcium. The binding
interaction between the encapsulated genome material (RNA) inside of the
capsid and the inner capsid shell is weakened during the swelling
transition. This probably aids in the RNA release process, but it is
unlikely that the RNA is released through capsid openings due to
unfavorable electrostatic interaction between the RNA and capsid inner
shell residues at these openings. Calculations of the calcium binding
energies show that Ca
2+ can bind both to the native and
swollen forms of the CCMV virion. Favorable binding to the swollen form
suggests that Ca
2+ ions can induce the capsid contraction and
stabilize the native form.
Conformational Transitions in Protein-Protein Association: Binding of Fasciculin-2 to AcetylcholinesteraseJennifer M. Bui, Zoran Radi&Biophysical Journal, Vol. 90, No. 9, pp. 3280-3287 (2006) [PubMed 16473897]The neurotoxin fasciculin-2 (FAS2) is a picomolar inhibitor of synaptic
acetylcholinesterase (AChE). The dynamics of binding between FAS2 and
AChE is influenced by conformational fluctuations both before and after
protein encounter. Submicrosecond molecular dynamics trajectories of apo
forms of fasciculin, corresponding to different conformational
substates, are reported here with reference to the conformational
changes of loop I of this three-fingered toxin. This highly flexible
loop exhibits an ensemble of conformations within each substate
corresponding to its functions. The high energy barrier found between
the two major substates leads to transitions that are slow on the
timescale of the diffusional encounter of noninteracting FAS2 and AChE.
The more stable of the two apo substates may not be the one observed in
the complex with AChE. It seems likely that the more stable apo form
binds rapidly to AChE and conformational readjustments then occur in the
resulting encounter complex.
E230Q Mutation of the Catalytic Subunit of cAMP-dependent Protein Kinase Affects Local Structure and the Binding of Peptide InhibitorMan-Un Ung, Benzhuo Lu and J.A. McCammonBiopolymers, Vol. 81, Issue 6, pp. 428-439 (2006) [PubMed 16365849]The active site of the mammalian cAMP-dependent protein kinase catalytic
subunit (C-subunit) has a cluster of non-conserved acidic residues --
Glu127, Glu170, Glu203, Glu230 and Asp241 -- that are crucial for
substrate recognition and binding. Studies showed that the Glu230 to Gln
mutant (E230Q) of the enzyme had physical properties similar to the
wild-type enzyme and had decreased affinity for a short peptide
substrate, Kemptide. However, recent experiments intended to crystallize
ternary complex of the E230Q mutant with MgATP and protein kinase
inhibitor (PKI) could only obtain crystals of the apo-enzyme of E230Q
mutant. To deduce the possible mechanism that prevented ternary complex
formation, we used the relaxed-complex method
http://dx.doi.org/10.1021/ja0260162" target="_blank" class="ref">J.-H.
Lin, A.L. Perryman, J.R. Schames, and J.A. McCammon, J. Amer. Chem.
Soc., 2002, vol. 24, pp. 5632-5633 to study PKI binding to the E230Q
mutant C-subunit. In the E230Q mutant, we observed local structural
changes of the peptide binding site that correlated closely to the
reduced PKI affinity. The structural changes occurred in the F-to-G
helix loop and appeared to hinder PKI binding. Reduced electrostatic
potential repulsion among Asp241 from the helix loop section and the
other acidic residues in the peptide binding site appear to be
responsible for the structural change.
A Simple Electrostatic Switch Important in the Activation of Type I Protein Kinase A By Cyclic AMPDominico Vigil, Jung-Hsin Lin, Christoph A. Sotriffer, Juniper K. Pennypacker, J. Andrew McCammon, Susan S. TaylorProtein Science, Vol. 15, No. 1, pp. 113-121 (2006) [PubMed 16322564]Cyclic AMP activates protein kinase A by binding to an inhibitory
regulatory (R) subunit and releasing inhibition of the catalytic (C)
subunit. Even though crystal structures of regulatory and catalytic
subunits have been solved, the precise molecular mechanism by which
cyclic AMP activates the kinase remains unknown. The dynamic properties
of the cAMP binding domain in the absence of cAMP or C-subunit are also
unknown. Here we report molecular-dynamics simulations and mutational
studies of the RIα R-subunit that identify the C-helix as a highly
dynamic switch which relays cAMP binding to the helical C-subunit
binding regions. Furthermore, we identify an important salt bridge which
links cAMP binding directly to the C-helix that is necessary for normal
activation. Additional mutations show that a hydrophobic "hinge" region
is not as critical for the cross-talk in PKA as it is in the homologous
EPAC protein, illustrating how cAMP can control diverse functions using
the evolutionarily conserved cAMP-binding domains.
Dependency Map of Proteins in the Small Ribosomal SubunitKay Hamacher, Joanna Trylska and J. Andrew McCammonPLoS Computational Biology, Vol. 2, Issue 2, pp. 80-87 (2006) [PubMed 16485038]The assembly of the ribosome has recently become an interesting target
for antibiotics in several bacteria. In this work, we extended an
analytical procedure to determine native state fluctuations and contact
breaking to investigate the protein stability dependence in the 30S
small ribosomal subunit of
Thermus thermophilus. We determined
the causal influence of the presence and absence of proteins in the 30S
complex on the binding free energies of other proteins. The predicted
dependencies are in overall agreement with the experimentally determined
assembly map for another organism,
Escherichia coli. We found
that the causal influences result from two distinct mechanisms, one is
pure internal energy change, the other originates from the entropy
change. We discuss the implications on how to target the ribosomal
assembly most effectively by suggesting six proteins as targets for
mutations or other hindering of their binding. Our results show that by
blocking one out of this set of proteins, the association of other
proteins is eventually reduced, thus reducing the translation efficiency
even more. We could additionally determine the binding dependency of THX
-- a peptide not present in the ribosome of E. coli -- and suggest its
assembly path.
Coupling hydrophobic, dispersion, and electrostatic contributions in continuum solvent modelsJ. Dzubiella, J.M.J. Swanson and J.A. McCammonPhysical Review Letters, Vol. 96, article 087802, 4 pages (2006) [PubMed 16606226]An implicit solvent model is presented that couples hydrophobic,
dispersion, and electrostatic solvation energies by minimizing the
system Gibbs free energy with respect to the solvent volume exclusion
function. The solvent accessible surface is output of the theory. The
method is illustrated with the solvation of simple solutes on different
length scales and captures the sensitivity of hydration to the
particular form of solute-solvent interactions in agreement with recent
computer simulations.
How does Activation Loop Phosphorylation Modulate Catalytic Activity in the cAMP-dependent Protein Kinase: A Theoretical StudyYuhui Cheng, Yingkai Zhang and J. Andrew McCammonProtein Science, Vol. 15, No. 4, pp. 672-683 (2006) [PubMed 16522793]Phosphorylation mediates the function of many proteins and enzymes. In
the catalytic subunit of cAMP-dependent protein kinase, phosphorylation
of Thr 197 in the activation loop strongly influences its catalytic
activity. In order to provide theoretical understanding about this
important regulatory process, classical molecular dynamics simulations
and ab initio QM/MM calculations have been carried out on the wild-type
PKA-Mg2 ATP-substrate complex and its dephosphorylated mutant, T197A. It
was found that pThr 197 not only facilitates the phosphoryl transfer
reaction by stabilizing the transition state through electrostatic
interactions but also strongly affects its essential protein dynamics as
well as the active site conformation.
Characterization of Nonbiological Antimicrobial Polymers in Aqueous Solution and at Water-Lipid Interfaces from All-Atom Molecular DynamicsIvaylo Ivanov, Satyavani Vemparala, Vojislava Pophristic, Kenichi Kuroda, William F. DeGrado, J. Andrew McCammon and Michael L. KleinJournal of the American Chemical Society, Vol. 128, No. 6, pp. 1778-1779 (2006) [PubMed 16464062]We have applied molecular dynamics to investigate the structural
properties and activity of recently synthesized amphiphilic
polymethacrylate derivatives, designed to mimic the antimicrobial
activity of natural peptides. The composition, molecular weight, and
hydrophobicity (ratio of hydrophobic and cationic units) of these short
copolymers can be modulated to achieve structural diversity, which is
crucial in controlling the antimicrobial activity. We have carried out
all-atom molecular dynamics to systematically investigate the
conformations adopted by these copolymers in water and at the water-
lipid interface as a function of sequence and the chemical nature of the
monomers. For two sequences, we observe partial insertion into the
bilayer. Formation of strong interactions between the lipid headgroups
and the amine groups of the polymers assists in the initial association
with the lipids. However, the primary driving force for the observed
partial insertion appears to be the hydrophobic effect. Our results
indicate sensitive dependence of the overall shape on the sequence,
suggesting that experimentally observed changes in activity can be
correlated with particular sequences, providing an avenue for rational
design.
Coupling nonpolar and polar solvation free energies in implicit solvent modelsJ. Dzubiella, J.M.J. Swanson and J.A. McCammonJournal of Chemical Physics, Vol. 124, article 084905, 12 pages (2006) [PubMed 16512740]Recent studies on the solvation of atomistic and nanoscale solutes
indicate that a strong coupling exists between the hydrophobic,
dispersion, and electrostatic contributions to the solvation free
energy, a facet not considered in current implicit solvent models. We
suggest a theoretical formalism which accounts for coupling by
minimizing the Gibbs free energy of the solvent with respect to a
solvent volume exclusion function. The resulting differential equation
is similar to the Laplace-Young equation for the geometrical description
of capillary interfaces, but is extended to microscopic scales by
explicitly considering curvature corrections as well as dispersion and
electrostatic contributions. Unlike existing implicit solvent
approaches, the solvent accessible surface is an output of our model.
The presented formalism is illustrated on spherically or cylindrically
symmetrical systems of neutral or charged solutes on different length
scales. The results are in agreement with computer simulations and, most
importantly, demonstrate that our method captures the strong sensitivity
of solvent expulsion and dewetting to the particular form of the
solvent-solute interactions.
Potentials of Mean Force for Acetylcholine Unbinding from the α7 Nicotinic Acetylcholine Receptor Ligand-Binding DomainDeqiang Zhang, Justin Gullingsrud and J. Andrew McCammonJournal of the American Chemical Society, Vol. 128, No. 9, pp. 3019-3026 (2006) [PubMed 16506783]The nicotinic acetylcholine receptor is a prototype ligand-gated ion
channel that mediates signal transduction in the neuromuscular junctions
and other cholinergic synapses. The molecular basis for the energetics
of ligand binding and unbinding is critical to our understanding of the
pharmacology of this class of receptors. Here, we used steered molecular
dynamics to investigate the unbinding of acetylcholine from the
ligand-binding domain of human α7 nicotinic acetylcholine receptor
along four different predetermined pathways. Pulling forces were found
to correlate well with interactions between acetylcholine and residues
in the binding site during the unbinding process. From multiple
trajectories along these unbinding pathways, we calculated the
potentials of mean force for acetylcholine unbinding. Four available
methods based on Jarzynski's equality were used and compared for their
efficiencies. The most probable pathway was identified to be along a
direction approximately parallel to the membrane. The derived binding
energy for acetylcholine was in good agreement with that derived from
the experimental binding constant for acetylcholine binding protein, but
significantly higher than that for the complete human α7 nicotinic
acetylcholine receptor. In addition, it is likely that several
intermediate states exist along the unbinding pathways.
Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Course-Grained ModelChia-En Chang, Tongye Shen, Joanna Trylska, Valentina Tozzini and J. Andrew McCammonBiophysical Journal, Vol. 90, No. 11, pp. 3880-3885 (2006) [PubMed 16533835]The internal motions of proteins may serve as a "gate" in some systems,
which controls ligand-protein association. This study applies Brownian
dynamics simulations in a coarse-grained model to study the gated
association rate constants of HIV-1 proteases and drugs. The computed
gated association rate constants of three protease mutants,
G48V/V82A/I84V/L90M, G48V and L90M with three drugs, amprenavir,
indinavir and saquinavir, yield good agreements with experiments. The
work shows that the flap dynamics leads to "slow gating". The
simulations suggest that the flap flexibility and the opening frequency
of the wild-type, the G48V and L90M mutants are similar, but the flaps
of the variant G48V/V82A/I84V/L90M open less frequently, resulting in a
lower gated rate constant. The developed methodology is fast and
provides an efficient way to predict the gated association rate
constants for various protease mutants and ligands.
A Minimal Model for Stabilization of Biomolecules by Hydrocarbon Cross-linkingK. Hamacher, A. Hübsch and J.A. McCammonJournal of Chemical Physics, Vol. 124, article 164907, 8 pages (2006) [PubMed 16674170]Programmed cell death regulating protein motifs play an essential role
in the development of an organism, its immune response and
disease-related cellular mechanisms. Among those motifs the BH3-domain
of the BCL-2 family is found to be of crucial importance. Recent
experiments showed how the isolated, otherwise unstructured BH3-peptide
can be modified by a hydrocarbon linkage to regain function. We
parametrized a reduced, dynamic model for the stability effects of such
covalent cross-linking and confirmed that the model reproduces the
reinforcement of the structural stability of the BH3 motif by
cross-linking. We show that an analytically solvable model for
thermostability around the native state is not capable of reproducing
the stabilization effect. This points to the crucial importance of the
peptide dynamics and the fluctuaions neglected in the analytic model for
the cross-linking system to function properly. This conclusion is
supported by a through analysis of a simulated Go-model. The resulting
model is suitable for rational design of generic cross-linking systems
in silicio.
Mapping All-Atom Models onto One-Bead Coarse-Grained Models: General Properties and Applications to a Minimal Polypeptide ModelValentina Tozzini, Walter Rocchia and J. Andrew McCammonJournal of Chemical Theory and Computation, Vol. 2, No. 3, pp. 667-673 (2006) [PubMed 19461947]In the one- and two-bead coarse-grained (CG) models for proteins, the
two conformational dihedrals φ and ψ that describe the backbone
geometry are no longer present as explicit internal coordinates; thus,
the information contained in the Ramachandran plot cannot be used
directly. We derive an analytical mapping between these dihedrals and
the internal variable describing the backbone conformation in the one-
(two-) bead CG models, namely, the pseudo-bond angle and pseudo-dihedral
between subsequent Cα's. This is used to derive a new density plot
that contains the same information as the Ramachandran plot and can be
used with the one- (two-) bead CG models. The use of this mapping is
then illustrated with a new one-bead polypeptide model that accounts for
transitions between α helices and β sheets.
Elasticity of peptide omega bondsTongye Shen, Donald Hamelberg and J. Andrew McCammonPhysical Review E, Vol. 73, article 041908, 6 pages (2006) [PubMed 16711837]We calculated the changes of the free energy profile of the
peptidyl-prolyl torsional angle of the dipeptide valine-proline under
pulling forces by simulations. Using a dynamic model built on the
equilibrium properties of this system and previously studied dynamic
properties of cis-trans isomerization of other dipeptides, we calculated
the dynamic viscoelasticity of this degree of freedom. The results show
significant differences between how thermal and mechanical forces alter
the equilibrium and the dynamics of the isomerization transition. The
former does not change the barrier heights but changes the prefactor of
the kinetics owing to temperature effects, while the latter changes
minima and thus the population. The force that is required to "excite"
this degree of freedom is small. Compared to other systems, we found
that this degree of freedom becomes already quite rigid at several
Hertz, which is a much lower value due to the high barrier of the
cis-trans isomerization. We also found that the tensile elastic modulus
of densely packed omega bonds is at the order of GPa, which is
comparable to that of polymer materials. These results give mechanical
properties of polyproline elasticity of a local nature and provide
guidance for future experimental designs.
Computing the amino acid specificity of fluctuations in biomolecular systemsK. Hamacher and J.A. McCammonJournal of Chemical Theory and Computation, Vol. 2, No. 3, pp. 873-878 (2006)
We developed a new amino acid specific method for the computation of
spatial fluctuations of proteins around their native structures. We show
the consistency with experimental values and the increased performance
in comparison to an established model, based on statistical estimates
for a set of test proteins. We apply the new method to HIV-1 protease in
its wild-type-form and to a V82F-I84V-mutant that shows resistance to
protease-inhibitors. We further show how the method can be successfully
used to explain the molecular biophysics of drug resistance of the
mutant.
Accelerating Conformational Transitions in Biomolecular SystemsDonald Hamelberg and J. Andrew McCammonAnnual Reports in Computational Chemistry, Vol. 2, Ch. 12, pp. 221-232 (2006)
Molecular dynamics simulation is one of the most extensively used
biophysical tools available to computational biologists and chemists due
to its ability to accurately sample the conformational space of
molecular systems. By integrating Newton's equations of motion, this
technique evaluates the time-dependent behavior and evolution of a
molecular system as it samples its conformational space. Therefore, with
an accurate representation of the system's potential energy landscape,
the thermodynamic and kinetic properties can be calculated while
studying a host of other structural and dynamic phenomena.
The Influence of Macromolecular Crowding on HIV-1 Protease Internal DynamicsDavid D.L. Minh, Chia-En Chang, Joanna Trylska, Valentina Tozzini and J. Andrew McCammonJournal of the American Chemical Society, Vol. 128, No. 18, pp. 6006-6007 (2006) [PubMed 16669648]High macromolecular concentrations, or crowded conditions, have been
shown to affect a wide variety of molecular processes, including
diffusion, association and dissociation, and protein folding and
stability. Here, we model the effect of macromolecular crowding on the
internal dynamics of a protein, HIV-1 protease, using Brownian dynamics
simulations. HIV-1 protease possesses a pair of flaps which are
postulated to open in the early stages of its catalytic mechanism.
Compared to low concentrations, close-packed concentrations of repulsive
crowding agents are found to significantly reduce the fraction of time
that the protease flaps are open. Macromolecular crowding is likely to
have a major effect on in vivo enzyme activity, and may play an
important regulatory role in the viral life cycle.
CIRSE: A solvation energy estimator compatible with flexible protein docking and design applicationsDavid S. Cerutti, Tushar Jain and J. Andrew McCammonProtein Science, Vol. 15, No. 7, pp. 1579-1596 (2006) [PubMed 16815913]We present the Coordinate Internal Representation of Solvation Energy
(CIRSE) for computing the solvation energy of protein configurations in
terms of pairwise interactions between their atoms with analytic
derivatives. Currently, CIRSE is trained to a Poisson / Surface-Area
benchmark, but CIRSE is not meant to fit this benchmark specifically.
CIRSE predicts the overall solvation energy of protein structures from
331 NMR ensembles with 0.951 +/- 0.047 correlation and predicts relative
solvation energy changes between members of individual ensembles with an
accuracy of 15.8 +/- 9.6 kcal/mol. The energy of individual atoms in any
of CIRSEs 17 types is predicted with at least 0.98 correlation. We apply
the model in energy minimization, rotamer optimization, protein design,
and protein docking applications. The CIRSE model shows some propensity
to accumulate errors in energy minimization as well as rotamer
optimization, but these errors are consistent enough that CIRSE
correctly identifies the relative solvation energies of designed
sequences as well as putative docked complexes. We analyze the errors
accumulated by the CIRSE model during each type of simulation and
suggest means of improving the model to be generally useful for all-atom
simulations.
Optimization and Computational Evaluation of a Series of Potential Active Site Inhibitors of the V82F/I84V Drug-resistant Mutant of HIV-1 Protease: an Application of the Relaxed Complex Method of Structure-based Drug DesignAlexander L. Perryman, Jung-Hsin Lin and J. Andrew McCammonChemical Biology & Drug Design, Vol. 67, Issue 5, pp. 336-345 (2006)
The Relaxed Complex method, an approach to structure-based drug design
that incorporates the flexibilities of both the ligand and target
protein, was applied to the HIV protease system. The control cases used
AutoDock3.0.5 to dock a fully-flexible version of the prospective drug
JE-2147 (aka SM-319777 or KNI-764) to large ensembles of conformations
extracted from conventional, all atom, explicitly-solvated Molecular
Dynamics simulations of the wild type and the V82F/I84V drug-resistant
mutant of HIV-1 protease. The best set of run parameters from the
control cases produced robust results when used against 2,200 different
conformations of the wild type HIV-1 protease or against 2,200
conformations of the mutant. The results of the control cases, the
published advice from experts, and structural intuition were used to
design a new series of 23 potential active site inhibitors. The
compounds were evaluated by docking them against 700 different
conformations of the V82F/I84V mutant. The results of this first round
of lead optimization were quite promising. Approximately one-third of
that series performed at least slightly better than the parent compound,
and four of those compounds displayed significantly better binding
affinities against that drug-resistant mutant (within our computational
model).
Computational investigation of pressure profiles in lipid bilayers with embedded proteinsJ. Gullingsrud, A. Babakhani and J.A. McCammonMolecular Simulation, Vol. 32, No. 10-11, pp. 831-838 (2006)
The distribution of surface tension within a lipid bilayer, also
referred to as the lateral pressure profile, has been the subject of
theoretical scrutiny recently due to its potential to radically alter
the function of biomedically important membrane proteins. Experimental
measurements of the pressure profile are still hard to come by, leaving
first-principles all-atom calculations of the profile as an important
investigative tool. We describe and validate an efficient implementation
of pressure profile calculations in the molecular dynamics package NAMD,
capable of distinguishing between internal, bonded, and nonbonded
contributions as well as those of selected atom groups. The new
implementation can also be used in conjunction with Ewald summation for
long-range electrostatics, improving the accuracy and reproducibility of
the calculated profiles. We then describe results of the calculation of
a pressure profile for a simple protein-lipid system consisting of
melittin embedded in a DMPC bilayer. While the lateral pressure in the
protein-lipid system is nearly the same as that of the bilayer alone,
partitioning of the lateral pressure by atom type revealed substantial
perturbation of the pressure profile and surface tension in an
asymmetric manner.
Evaluation and Binding Mode Prediction of Thiopyrone-Based Inhibitors of Anthrax Lethal FactorJana A. Lewis, John Mongan, J. Andrew McCammon and Seth M. CohenChemMedChem, Vol. 1, Issue 7, pp. 694-697 (2006) [PubMed 16902919]Anthrax lethal factor (LF) is one of three proteins involved in anthrax
pathogenesis and lethality. Inactivation of the LF gene in B. anthracis
leads to a decrease in virulence by 1000-fold or greater, which suggests
that anthrax pathology is highly dependent on LF. Herein, we report an
effective inhibitor of anthrax lethal factor based on a heterocyclic
chelator scaffold. We also present computational predictions of the
binding mode for this inhibitor and evidence that accurate prediction of
binding modes requires use of a molecular surface-like boundary between
solute and solvent.
Configurational-bias sampling technique for predicting side-chain conformations in proteinsTushar Jain, David S. Cerutti and J. Andrew McCammonProtein Science, Vol. 15, No. 9, pp. 2029-2039 (2006) [PubMed 16943441]Prediction of side-chain conformations is an important component of
several biological modeling applications. In this work, we have
developed and tested an advanced Monte-Carlo sampling strategy for
predicting side-chain conformations. Our method is based on a
cooperative rearrangement of atoms that belong to a group of neighboring
side-chains. This rearrangement is accomplished by deleting groups of
atoms from the side-chains in a particular region, and regrowing them
with the generation of trial positions that depends both on a rotamer
library and a molecular mechanics potential function. This method allows
us to incorporate flexibility about the rotamers in the library and
explore phase space in a continuous fashion about the primary rotamers.
We have tested our algorithm on a set of 76 proteins using the all-atom
AMBER99 force-field and electrostatics that are governed by a
distance-dependent dielectric function. When the tolerance for correct
prediction of the dihedral angles is less than a 20 degree deviation
from the native state, our prediction accuracies for χ
1
are 83.3%, and for χ
1 and χ
2 are 65.4%.
The accuracies of our predictions are comparable to the best results in
the literature that often used Hamiltonians that have been specifically
optimized for side-chain packing. We believe that the continuous
exploration of phase space enables our method to overcome limitations
inherent with using discrete rotamers as trials.
Insight into the role of hydration on protein dynamicsDonald Hamelberg, Tongye Shen and J. Andrew McCammonJournal of Chemical Physics, Vol. 125, article 094905, 7 pages (2006) [PubMed 16965117]The potential energy surface of a protein is rough. This intrinsic
energetic roughness affects diffusion, and hence the kinetics. The
dynamics of a system undergoing Brownian motion on this surface in an
implicit continuum solvent simulation can be tuned via the frictional
drag or collision frequency to be comparable to that of experiments or
explicit solvent simulations. We show that the kinetic rate constant for
a local rotational isomerization in stochastic simulations with
continuum solvent and a collision frequency of 2 ps
-1 is
about 10
4 times faster than that in explicit water and
experiments. A further increase in the collision frequency to 60
ps
-1 slows down the dynamics, but does not fully compensate
for the lack of explicit water. We also show that the addition of
explicit water does not only slow down the dynamics by increasing the
frictional drag, but also increases the local energetic roughness of the
energy landscape by as much as 1.0 kcal/mol.
Binding of Aminoglycosidic Antibiotics to the Oligonucleotide A-Site Model and 30S Ribosomal Subunit: Poisson-Boltzmann Model, Thermal Denaturation, and Fluorescence StudiesGrace Yang, Joanna Trylska, Yitzhak Tor and J. Andrew McCammonJournal of Medicinal Chemistry, Vol. 49, No. 18, pp. 5478-5490 (2006) [PubMed 16942021]The binding of paromomycin and similar antibiotics to the
oligonucleotide A-site model and the small (30S) ribosomal subunit has
been studied using continuum electrostatics methods. Crystallographic
information from complexes of paromomycin, tobramycin and geneticin
bound to an A-site oligonucleotide, and paromomycin and streptomycin
complexed to the 30S subunit was used as a foundation to develop
structures of similar antibiotics in the same ribosomal binding site.
Relative binding free energies were calculated by combining the
electrostatic contribution, which was obtained by solving the
Poisson-Boltzmann equation, with a surface area-dependent apolar term,
and contributions from conformational changes. These computed results
showed good correlation with the experimental data resulting from
fluorescence binding assays and thermal denaturation studies,
demonstrating the ability of the Poisson-Boltzmann model to provide
insight into the electrostatic mechanisms for aminoglycoside binding and
direction for designing more effective antibiotics.
Bio3d: An R package for the comparative analysis of protein structuresBarry J. Grant, Ana P.C. Rodrigues, Karim M. ElSawy, J. Andrew McCammon and Leo S.D. CavesBioinformatics, Vol. 22, No. 21, pp. 2695-2696 (2006) [PubMed 16940322]Summary: An automated procedure for the analysis of homologous protein
structures has been developed. The method facilitates the
characterization of internal conformational differences and inter-
conformer relationships and provides a framework for the analysis of
protein structural evolution. The method is implemented in bio3d, an R
package for the exploratory analysis of structure and sequence data.
Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic ReceptorsXiaolin Cheng, Hailong Wang, Barry Grant, Steven M. Sine and J. Andrew McCammonPLoS Computational Biology, Vol. 2, Issue 9, pp. 1173-1184 (2006) [PubMed 17009865]The initial coupling between ligand binding and channel gating in the
human α7 nicotinic acetylcholine receptor (nAChR) has been
investigated with targeted molecular dynamics (TMD) simulation. During
the simulation, 8 residues at the tip of the C-loop in two alternating
subunits were forced to move towards a ligand-bound conformation as
captured in the crystallographic structure of acetylcholine binding
protein (AChBP) in complex with carbamoylcholine. Comparison of apo- and
ligand-bound AChBP structures shows only minor rearrangements distal
from the ligand-binding site. In contrast, comparison of apo and TMD
simulation structures of the nAChR reveals significant changes towards
the bottom of the ligand-binding domain. These structural rearrangements
are subsequently translated to the pore domain, leading to a partly open
channel within 4 ns of TMD simulation. Furthermore, we confirmed that
two highly conserved residue pairs, one located near the ligand-binding
pocket (Lys145 and Tyr188), and the other located towards the bottom of
the ligand-binding domain (Arg206 and Glu45), are likely to play
important roles in coupling agonist binding to channel gating. Overall,
our simulations suggest that gating movements of the α7 receptor
may involve relatively small structural changes within the
ligand-binding domain implying that the gating transition is
energy-efficient, and can be easily modulated by agonist
binding/unbinding.
In-situ synthesis of an inhibitor of acetylcholinesterase: Configurational selection imposed by steric interactionsSanjib Senapati, Yuhui Cheng and J. Andrew McCammonJournal of Medicinal Chemistry, Vol. 49, No. 21, pp. 6222-6230 (2006) [PubMed 17034128]Recently researchers have used acetylcholinesterase (AChE) as a reaction
vessel to synthesize its own inhibitors. Thus 1 (syn-TZ2PA6), a
femtomolar AChE inhibitor, which is formed in 1:1 mixture with its anti
isomer by solution phase reaction from 3 (TZ2) and 4 (PA6), can be
synthesized exclusively inside the AChE gorge. Our computational
approach based on quantum mechanical/molecular mechanical (QM/MM)
calculations, molecular dynamics (MD), and targeted molecular dynamics
(TMD) studies answers why 1 is the sole product in the AChE environment.
Ab initio QM/MM results show that the reaction in the AChE gorge occurs
when 3: azide and 4: acetylene are extended in a parallel orientation.
An MD simulation started from the final structure of QM/MM calculations
keeps the azide and acetylene's parallel orientation intact for 10 ns
simulation time. A TMD simulation applied on an antiparallel
azide-acetylene conformation flips the acetylene easily to bring it to
parallel to azide. A second set of QM/MM calculations performed on this
flipped structure generates a similar minimum-energy path as obtained
previously. Even a TMD simulation carried out on a parallel
azide-acetylene conformation could not deform their parallel
arrangement. All these results thus imply that inside the AChE gorge the
azide group of 3 and the acetylene group of 4 always remain parallel,
with the consequence that 1 is the only product. The architecture of the
gorge plays an important role in this selective formation of 1.
Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanismJennifer M. Bui and J. Andrew McCammonProceedings of the National Academy of Sciences of the USA, Vol. 103, No. 42, pp. 15451-15456 (2006) [PubMed 17021015]Specific, rapid association of protein complexes is essential for all
forms of cellular existence. The initial association of two molecules in
diffusion-controlled reactions is often influenced by the electrostatic
potential. Yet, the detailed binding mechanisms of proteins are highly
dependent on the particular system. For the first time, a complete
protein complex formation pathway has been delineated using structural
information sampled over the course of the transformation reaction. The
pathway begins at an encounter complex that is formed by one of the apo
forms of neurotoxin fasciculin-2 and its high affinity binding protein,
acetylcholinesterase. This is followed by rapid conformational
rearrangements into an intermediate complex that subsequently converts
to the final complex as observed in crystal structures. Formation of the
intermediate complex has also been independently captured in a separate
20-ns molecular dynamics simulation of the encounter complex.
Conformational transitions between the apo and liganded states of
fasciculin-2 in the presence and absence of acetylcholinesterase are
described in terms of their relative free energy profiles that link
these two states. The transitions of fascisculin-2 after binding to
acetylcholinesterase are significantly faster than in the absence of
acetylcholinesterase; the energy barrier between the two conformational
states is reduced by half. Conformational rearrangements of fasciculin-2
to the final liganded form not only bring the
fasciculin-2/acetylcholinesterase complex to lower energy states, but by
controlling transient motions that lead to opening or closing one of the
alternative passages to the active site of the enzyme, also maximize the
ligand's inhibition of the enzyme.
On the Application of Accelerated Molecular Dynamics to Liquid Water SimulationsCésar Augusto F. de Oliveira, Donald Hamelberg and J. Andrew McCammonJournal of Physical Chemistry B, Vol. 110, No. 45, pp. 22695-22701 (2006) [PubMed 17092018]Our group recently proposed a robust bias potential function that can be
used in an efficient all-atom accelerated molecular dynamics (MD)
approach to simulate the transition of high energy barriers without any
advance knowledge of the potential-energy landscape. The main idea is to
modify the potential-energy surface by adding a bias, or boost,
potential in regions close to the local minima, such that all
transitions rates are increased. By applying the accelerated MD
simulation method to liquid water, we observed that this new simulation
technique accelerates the molecular motion without losing its
microscopic structure and equilibrium properties. Our results showed
that the application of a small boost energy on the potential-energy
surface significantly reduces the statistical inefficiency of the
simulation while keeping all the other calculated properties unchanged.
On the other hand, although aggressive acceleration of the dynamics
simulation increases the self-diffusion coefficient of water molecules
greatly and dramatically reduces the correlation time of the simulation,
configurations representative of the true structure of liquid water are
poorly sampled. Our results also showed the strength and robustness of
this simulation technique, which confirm this approach as a very useful
and promising tool to extend the time scale of the all-atom simulations
of biological system with explicit solvent models. However, we should
keep in mind that there is a compromise between the strength of the
boost applied in the simulation and the reproduction of the ensemble
average properties.
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implicationsIvaylo Ivanov, Brian R. Chapados, J. Andrew McCammon and John A. TainerNucleic Acids Research, Vol. 34, No. 20, pp. 6023-6033 (2006) [PubMed 17071716]Proliferating cell nuclear antigen (PCNA) acts as a biologically
essential processivity factor that encircles DNA and provides binding
sites for polymerase, flap endonuclease-1 (FEN-1) and ligase during DNA
replication and repair. We have computationally characterized the
interactions of human and Archaeoglobus fulgidus PCNA trimer with
double-stranded DNA (ds DNA) using multi-nanosecond classical molecular
dynamics simulations. The results reveal the interactions of DNA passing
through the PCNA trimeric ring including the contacts formed, overall
orientation and motion with respect to the sliding clamp. Notably, we
observe pronounced tilting of the axis of dsDNA with respect to the PCNA
ring plane reflecting interactions between the DNA phosphodiester
backbone and positively charged arginine and lysine residues lining the
PCNA inner surface. Covariance matrix analysis revealed a pattern of
correlated motions within and between the three equivalent subunits
involving the PCNA C-terminal region and linker strand associated with
partner protein binding sites. Additionally, principal component
analysis identified low frequency global PCNA subunit motions suitable
for translocation along duplex DNA. The PCNA motions and interactions
with the DNA minor groove, identified here computationally, provide an
unexpected basis for PCNA to act in the coordinated handoff of
intermediates from polymerase to FEN-1 to ligase during DNA replication
and repair.
Order N algorithm for computation of electrostatic interactions in biomolecular systemsBenzhuo Lu, Xiaolin Cheng, Jingfang Huang and J. Andrew McCammonProceedings of the National Academy of Sciences of the USA, Vol. 103, No. 51, pp. 19314-19319 (2006) [PubMed 17148613]Poisson-Boltzmann (PB) electrostatics is a well established model in
biophysics, however its application to large scale biomolecular
processes such as protein-protein encounter is still limited by the
efficiency and memory constraints of existing numerical techniques. In
this paper, we present an efficient and accurate scheme which
incorporates recently developed numerical techniques to enhance our
computational ability. In particular, a boundary integral equation (BIE)
approach is applied to discretize the linearized PB equation; the
resulting integral formulas are well conditioned and are extended to
systems with arbitrary numbers of biomolecules. The solution process is
accelerated by Krylov subspace methods and a new version of the fast
multipole method (FMM). In addition to the electrostatic energy, fast
calculations of the forces and torques are made possible by using an
interpolation procedure. Numerical experiments show that the implemented
algorithm is asymptotically optimal $O(N)$ in both CPU time and required
memory, and application to the acetylcholinesterase-fasciculin complex
is illustrated.