Protein structural flexibility: molecular motionsRichard H. Henchman and J. Andrew McCammonIn "Encyclopedia of Life Sciences," John Wiley and Nature Publishing Group (2005)
Protein molecules are intrinsically flexible and typically undergo a
wide variety of motions at normal temperatures. The flexibility and
dynamics of proteins have been harnessed by evolution for a wide variety
of their activities, ranging from ligand binding to regulation of
function.
Computation of Non-covalent Binding AffinitiesJ. Andrew McCammonIn "Theory and Applications of Computational Chemistry," C. Dykstra, G. Frenking, K. Kim, and G. Scuseria, Eds., Elsevier, Amsterdam, Ch. 3, pp. 41-46 (2005)
The ability to accurately predict and analyze molecular recognition is
being achieved by advances in several areas of theoretical chemistry and
related fields such as applied mathematics and computational science.
This chapter provides an overview of the history, current state and
future prospects for computational studies of molecular recognition.
Rapid Estimation of Solvation Energy for Simulations of Protein-Protein AssociationDavid S. Cerutti, Lynn F. Ten Eyck and J. Andrew McCammonJournal of Chemical Theory and Computation, Vol. 1, No. 1, pp. 143-152 (2005)
We have formulated the Energy by Linear Superposition of Corrections
Approximation (ELSCA) for estimating the electrostatic and apolar
solvation energy of bringing two proteins into close proximity or into
contact as defined by the linearized Poisson-Boltzmann model and a
linear function of the solvent-accessible surface area. ELSCA utilizes
potentials of mean force between atom types found in the AMBER ff99
force field, a uniform distance-dependent dielectric, and a potential
that mimics the change in solvent accessible surface area for bringing
two solvated spheres into contact. ELSCA was trained by a linear
least-squares fit on more than 39 000 putative complexes, each formed
from pairs of nonhomologous proteins with a range of shapes, sizes, and
charges. The training set was also designed to capture various stages of
complex formation. ELSCA was tested against over 8000 non-native
complexes of 45 enzyme/inhibitor, antibody/antigen, and other systems
that are known to form complexes and gives an overall correlation of
0.962 with PBSA-derived energies for these complexes. The predictions
have a slope of 0.89 on the actual values with a bias of 11.1 kcal/mol.
When applied to native complexes of these 45 protein systems, ELSCA
reproduces PBSA results with a correlation of 0.787, a slope of 1.13,
and a bias of 13.0 kcal/mol. We report parameters for ELSCA in the
context of the AMBER ff99 parameter set. Our model is most useful in
macromolecular docking and protein association simulations, where large
portions of each molecule may be considered rigid.
Release of ADP from the catalytic subunit of protein kinase A: A molecular dynamics simulation studyBenzhuo Lu, Chung F. Wong and J. Andrew McCammonProtein Science, Vol. 14, Issue 1, pp. 159-168 (2005) [PubMed 15608120]Substrate phosphorylation by cAMP-dependent-protein kinase A (protein
kinase A, PKA) has been studied extensively. Phosphoryl transfer was
found to be fast, whereas ADP release was found to be the slow,
rate-limiting step. There is also evidence that ADP release may be
preceded by a partially rate-limiting conformational change. However,
the atomic details of the conformational change and the mode of ADP
release are difficult to obtain experimentally. In this work, we studied
ADP release from PKA by carrying out molecular dynamics simulations with
different pulling forces applied to the ligand. The detailed ADP release
pathway and the associated conformational changes were analyzed. The ADP
release process was found to involve a swinging motion with the
phosphate of ADP anchored to the Gly-rich loop, so that the more buried
adenine base and ribose ring came out before the phosphate. In contrast
to the common belief that a hinge-bending motion was responsible for the
opening of the ligand-binding cleft, our simulations showed that the
small lobe exhibited a large amplitude "rocking" motion when the ligand
came out. The largest conformational change of the protein was observed
at about the first quarter time point along the release pathway. Two
prominent intermediate states were observed in the release process.
Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: Accelerated molecular dynamics analysisDonald Hamelberg, Tongye Shen and J. Andrew McCammonJournal of the American Chemical Society, Vol. 127, No. 6, pp. 1969-1974 (2005) [PubMed 15701032]The presence of serine/threonine-proline motifs in proteins provides a
conformational switching mechanism of the backbone through the cis/trans
isomerization of the peptidyl-prolyl () bond. The reversible
phosphorylation of the serine/threonine modulates this switching in
regulatory proteins to alter signaling and transcription. However, the
mechanism is not well understood. This is partly because cis/trans
isomerization is a very slow process and, hence, difficult to study. We
have used our accelerated molecular dynamics method to study the
cis/trans proline isomerization, preferred backbone conformation of a
serine-proline motif, and the effects of phosphorylation of the serine
residue. We demonstrate that, unlike normal molecular dynamics, the
accelerated molecular dynamics allows for the system to escape very
easily from the trans isomer to cis isomer, and vice versa. Moreover,
for both the unphosphorylated and phosphorylated peptides, the
statistical thermodynamic properties are recaptured, and the results are
consistent with experimental values. Isomerization of the proline bond
is shown to be asymmetric and strongly dependent on the backbone angle
before and after phosphorylation. The rates of escape decrease after
phosphorylation. Also, the -helical backbone conformation is more
favored after phosphorylation. This accelerated molecular dynamics
approach provides a general approach for enhancing the conformational
transitions of molecular systems without having prior knowledge of the
location of the minima and barriers on the potential-energy landscape.
How does the cAMP-Dependent Protein Kinase Catalyze the Phosphorylation Reaction: an ab initio QM/MM StudyYuhui Cheng, Yingkai Zhang and J. Andrew McCammonJournal of the American Chemical Society, Vol. 127, No. 5, pp. 1553-1562 (2005) [PubMed 15686389]We have carried out density functional theory QM/MM calculations on the
catalytic subunit of cAMP-dependent protein kinase (PKA). The QM/MM
calculations indicate that the phosphorylation reaction catalyzed by PKA
is mainly dissociative, and Asp166 serves as the catalytic base to
accept the proton delivered by the substrate peptide. Among the key
interactions in the active site, the Mg2+ ions, glycine rich loop, and
Lys72 are found to stabilize the transition state through electrostatic
interactions. On the other hand, Lys168, Asn171, Asp184, and the
conserved waters bound to Mg2+ ions do not directly contribute to lower
the energy barrier of the phosphorylation reaction, and possible roles
for these residues are proposed. The QM/MM calculations with different
QM/MM partition schemes or different initial structures yield consistent
results. In addition, we have carried out 12 ns molecular dynamics
simulations on both wild type and K168A mutated PKA, respectively, to
demonstrate that the catalytic role of Lys168 is to keep ATP and
substrate peptide in the near-attack reactive conformation.
Ligand-Induced Conformational Change in the α7 Nicotinic Receptor Ligand Binding DomainRichard H. Henchman, Hai-Long Wang, Steven M. Sine, Palmer Taylor and J. Andrew McCammonBiophysical Journal, Vol. 88, No. 4, pp. 2564-2576 (2005) [PubMed 15665135]Implicit solvent models are a standard tool for assessing the
electrostatics of biomolecular systems. The accuracy of quantitative
predictions, such as pKa values, transfer free energies, binding
energies, and solvation forces, is strongly dependent on one's choice of
continuum parameters: the solute charges, dielectric coefficient, and
radii, which define the dielectric boundary. To ensure quantitative
accuracy, these parameters can be benchmarked against explicit solvent
simulations. Here we present two sets of optimized radii to define
either abrupt or cubic-spline smoothed dielectric boundaries in
Poisson-Boltzmann calculations of protein systems with AMBER (parm99)
charges. Spline smoothing stabilizes the electrostatic potential at the
molecular surface, allowing for continuum force calculations. Most
implementations, however, require significantly different radii than the
abrupt boundary surfaces. The optimal continuum radii are initially
approximated from the solvent radial charge distribution surrounding
each atom type. A genetic algorithm is then used to fine-tune the
starting values to reproduce charging free energies measured from
explicit solvent simulations. The optimized radii are tested on four
protein-like polypeptides. The results show increased accuracy of
molecular solvation energies and atomic forces relative to commonly used
continuum parameter sets. These radii are suitable for Poisson-Boltzmann
calculations with the AMBER force field and offer energetic congruence
to any model that combines molecular mechanics and Poisson-Boltzmann
solvation energies.
Agonist-mediated conformational changes in ACh-binding protein revealed by simulation and intrinsic tryptophan fluorescenceFan Gao, Nina Bren, Thomas P. Burghardt, Scott Hansen, Richard H. Henchman, Palmer Taylor, J. Andrew McCammon and Steven M. SineJournal of Biological Chemistry, Vol. 280, Issue 9, pp. 8443-8451 (2005) [PubMed 15591050]We delineated acetylcholine (ACh)-dependent conformational changes in a
prototype of the nicotinic receptor ligand binding domain by molecular
dynamics simulation and changes in intrinsic tryptophan (Trp)
fluorescence. Prolonged molecular dynamics simulation of ACh-binding
protein showed that binding of ACh establishes close register of Trps
from adjacent subunits, Trp143 and Trp53, and draws the peripheral
C-loop inward to occlude the entrance to the binding cavity. Close
register of Trp143 and Trp53 was demonstrated by ACh-mediated quenching
of intrinsic Trp fluorescence, elimination of quenching by mutation of
one or both Trps to Phe, and decreased lifetime of Trp fluorescence by
bound ACh. Occlusion of the binding cavity by the C-loop was
demonstrated by restricted access of an extrinsic quencher of binding
site Trp fluorescence by ACh. The collective findings showed that ACh
initially establishes close register of conserved Trps from adjacent
subunits and then draws the C-loop inward to occlude the entrance to the
binding cavity.
Tetrameric Mouse Acetylcholinesterase: Continuum Diffusion Rate Calculations by Solving the Steady-State Smoluchowski Equation Using Finite Element MethodsDeqiang Zhang, Jason Suen, Yongjie Zhang, Yuhua Song, Zoran Radi&Biophysical Journal, Vol. 88, No. 3, pp. 1659-1665 (2005) [PubMed 15626705]The tetramer is the most important form for acetylcholinesterase in
physiological conditions, i.e., in the neuromuscular junction and the
nervous system. It is important to study the diffusion of acetylcholine
to the active sites of the tetrameric enzyme to understand the overall
signal transduction process in these cellular components.
Crystallographic studies revealed two different forms of tetramers,
suggesting a flexible tetramer model for acetylcholinesterase. Using a
recently developed finite element solver for the steady-state
Smoluchowski equation, we have calculated the reaction rate for three
mouse acetylcholinesterase tetramers using these two crystal structures
and an intermediate structure as templates. Our results show that the
reaction rates differ for different individual active sites in the
compact tetramer crystal structure, and the rates are similar for
different individual active sites in the other crystal structure and the
intermediate structure. In the limit of zero salt, the reaction rates
per active site for the tetramers are the same as that for the monomer,
whereas at higher ionic strength, the rates per active site for the
tetramers are 67% - 75% of the rate for the monomer. By analyzing the
effect of electrostatic forces on ACh diffusion, we find that
electrostatic forces play an even more important role for the tetramers
than for the monomer. This study also shows that the finite element
solver is well suited for solving the diffusion problemwithin
complicated geometries.
Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systemsPeter A. Sims, Chung F. Wong, Danka Vuga, J. Andrew McCammon and Bartholomew M. SeftonJournal of Computational Chemistry, Vol. 26, Issue 7, pp. 668-681 (2005) [PubMed 15754303]In several previous studies, we performed sensitivity analysis to gauge
the relative importance of different atomic partial charges in
determining protein-ligand binding. In this work, we gain further
insights by decomposing these results into three contributions:
desolvation, intramolecular interactions, and intermolecular
interactions, again based on a Poisson continuum electrostatics model.
Three protein kinase-inhibitor systems have been analyzed:
CDK2-deschloroflavopiridol, PKA-PKI, and LCK-PP2. Although our results
point out the importance of specific intermolecular interactions to the
binding affinity, they also reveal the remarkable contributions from the
solvent-mediated intramolecular interactions in some cases. Thus, it is
necessary to look beyond analyzing protein-ligand interactions to
understand protein-ligand recognition or to gain insights into designing
ligands and proteins. In analyzing the contributions of the three
components to the overall binding free energy, the PKA-PKI system with a
much larger ligand was found to behave differently from the other two
systems with smaller ligands. In the former case, the intermolecular
interactions are very favorable, and together with the favorable
solvent-mediated intramolecular interactions, they overcome the large
desolvation penalties to give a favorable electrostatics contribution to
the overall binding affinity. On the other hand, the other two systems
with smaller ligands only present modest intermolecular interactions and
they are not or are only barely sufficient to overcome the desolvation
penalty even with the aid of the favorable intramolecular contributions.
As a result, the binding affinity of these two systems do not or only
barely benefit from electrostatics contributions.
Acetylcholinesterase: Pivotal Roles of its Long Omega Loop (Cys69-Cys96) in Regulating BindingJennifer M. Bui and J. Andrew McCammonChemico-Biological Interactions, Vol. 157-158, pp. 357-359 (2005) [PubMed 16429484]Modulation of synaptic activity is largely governed by the enzymatic
activity of acetylcholinesterase (AChE), which rapidly catalyzes the
hydrolysis of the neurotransmitter acetylcholine. One enigma that has
drawn much attention is the very fast (diffusion-controlled) kinetics of
the enzyme given that its catalytic triad is located at the bottom of a
20 Å deep and narrow gorge1,2. A large portion of the gorge is
formed by a number of residues from the long omega loop (Cys69-Cys96 in
mouse), and experimental studies3,4 have shown that conformational
variations of this loop accompany ligand binding. A 15ns molecular
dynamics simulation of mAChE in the presence of neurotoxin fasciculin-2
(FAS) is reported here and reveals a substantial increase in the
magnitude of fluctuations for mAChE. In particular, the long omega loop
is more flexible and its enhanced motions increase accessibility to the
active site. A formation of a hydrophobic patch (Leu76-Phe80) by
exposing its aromatic side chain to solvent surface, at the tip of this
long omega loop is detected. This new discovery might provide not only a
structural basis for interactions between a β-amyloid peptide and
AChE, but also insights into the associations of AChE in Alzheimer's
disease.
A gating mechanism proposed from a simulation of a human α7 nicotinic acetylcholine receptorRichard J. Law, Richard H. Henchman and J. Andrew McCammonProceedings of the National Academy of Sciences of the USA, Vol. 102, No. 19, pp. 6813-6818 (2005) [PubMed 15857954]The nicotinic acetylcholine receptor is a well characterized ligandgated
ion channel, yet a proper description of the mechanisms involved in
gating, opening, closing, ligand binding, and desensitization does not
exist. Until recently, atomic-resolution structural information on the
protein was limited, but with the production of the x-ray crystal
structure of the Lymnea stagnalis acetylcholine binding protein and the
EM image of the transmembrane domain of the torpedo electric ray
nicotinic channel, we were provided with a window to examine the
mechanism by which this channel operates. A 15-ns all-atom simulation of
a homology model of the homomeric human α7 form of the receptor
was conducted in a solvated
palmitoyl-2-oleoyl-sn-glycerol-phosphatidylcholine bilayer and examined
in detail. The receptor was unliganded. The structure undergoes a
twist-to-close motion that correlates movements of the C loop in the
ligand binding domain, via the β10-strand that connects the two,
with the 10° rotation and inward movement of two nonadjacent
subunits. The Cys loop appears to act as a stator around which the
α-helical transmembrane domain can pivot and rotate relative to
the rigid β-sheet binding domain. The M2-M3 loop may have a role in
controlling the extent or kinetics of these relative movements. All of
this motion, along with essential dynamics analysis, is suggestive of
the direction of larger motions involved in gating of the channel.
Substrate concentration dependence of the diffusion-controlled steady-state rate constantJ. Dzubiella and J.A. McCammonJournal of Chemical Physics, Vol. 122, Issue 18, article 184902, 7 pages (2005) [PubMed 15918760]The Smoluchowski approach to diffusion-controlled reactions is
generalized to interacting substrate particles by including the osmotic
pressure and hydrodynamic interactions of the nonideal particles in the
Smoluchoswki equation within a local-density approximation. By solving
the strictly linearized equation for the time-independent case with
absorbing boundary conditions, we present an analytic expression for the
diffusion-limited steady-state rate constant for small substrate
concentrations in terms of an effective second virial coefficient
B
2*. Comparisons to Brownian dynamics simulations
excluding hydrodynamic interactions show excellent agreement up to bulk
number densities of B
2* ρ
0 < 0.4
for hard sphere and repulsive Yukawa-like interactions between the
substrates. Our study provides an alternative way to determine the
second virial coefficient of interacting macromolecules experimentally
by measuring their steady-state rate constant in diffusion-controlled
reactions at low densities.
Pushing the limits: Editorial overviewJ. Andrew McCammon and Rebecca C. WadeCurrent Opinion in Structural Biology, Vol. 15, Issue 2, pp. 135-136 (2005)
Many of the contributions to the current section can be viewed as
communications from various fronts in our drive to increase the realism
of biomolecular simulations. Long-standing challenges have included
bridging the gaps between the spatial and temporal scales of typical
simulations (limited to tens of nanometers and tens of nanoseconds for
many popular simulation methods) and the scales of physiological
processes, which are often many orders of magnitudes larger. Other
challenges have included making the energy functions that are used in
typical simulations more accurate. This includes not only
“tweaking” the parameters in molecular mechanics or other
models, but also allowing for changes in the protonation state of
biopolymers that may be coupled with their conformational changes. As
will be seen, useful advances have been made recently in both
directions. Adequate sampling of molecular configurations is
particularly important in free energy simulations, and recent
theoretical progress has provided valuable new computational tools for
such simulations. Other contributions to the current section focus on
advances in applications of biomolecular simulations. Progress in this
area is leading to improved methods for understanding molecular
recognition and the activity of aquaporins.
Optimized radii for Poisson-Boltzmann calculations with the AMBER force fieldJessica M.J. Swanson, Stewart A. Adcock and J. Andrew McCammonJournal of Chemical Theory and Computation, Vol. 1, No. 3, pp. 484-493 (2005)
Implicit solvent models are a standard tool for assessing the
electrostatics of biomolecular systems. The accuracy of quantitative
predictions, such as pKa values, transfer free energies, binding
energies, and solvation forces, is strongly dependent on one's choice of
continuum parameters: the solute charges, dielectric coefficient, and
radii, which define the dielectric boundary. To ensure quantitative
accuracy, these parameters can be benchmarked against explicit solvent
simulations. Here we present two sets of optimized radii to define
either abrupt or cubic-spline smoothed dielectric boundaries in
Poisson-Boltzmann calculations of protein systems with AMBER (parm99)
charges. Spline smoothing stabilizes the electrostatic potential at the
molecular surface, allowing for continuum force calculations. Most
implementations, however, require significantly different radii than the
abrupt boundary surfaces. The optimal continuum radii are initially
approximated from the solvent radial charge distribution surrounding
each atom type. A genetic algorithm is then used to fine-tune the
starting values to reproduce charging free energies measured from
explicit solvent simulations. The optimized radii are tested on four
protein-like polypeptides. The results show increased accuracy of
molecular solvation energies and atomic forces relative to commonly used
continuum parameter sets. These radii are suitable for Poisson-Boltzmann
calculations with the AMBER force field and offer energetic congruence
to any model that combines molecular mechanics and Poisson-Boltzmann
solvation energies.
Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element methodBenzhuo Lu, Deqiang Zhang and J. Andrew McCammonJournal of Chemical Physics, Vol. 122, Issue 21, article 214102, 7 pages (2005) [PubMed 15974723]A rigorous approach is proposed to calculate the electrostatic forces
among an arbitrary number of solvated molecules in ionic solution
determined by the linearized Poisson-Boltzmann equation. The variational
principle is used and implemented in the frame of a boundary element
method. This approach does not require the calculation of the Maxwell
stress tensor on the molecular surface, therefore it totally avoids the
hypersingularity problem in the direct BEM whenever one needs to
calculate the gradient of the surface potential or the stress tensor.
This method provides an accurate and efficient way to calculate the full
inter-molecular electrostatic interaction energy and force, which could
potentially be used in Brownian dynamics simulation of biomolecular
association. The method has been tested on some simple cases to
demonstrate its reliability and efficiency, and parts of the results are
compared with analytical results and with those obtained by some known
methods such as adaptive Poisson-Boltzmann solver.
The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domainTongye Shen, Chenghang Zong, Donald Hamelberg, J. Andrew McCammon and Peter G. WolynesThe FASEB Journal, Vol. 19, Issue 11, pp. 1389-1395 (2005) [PubMed 16126906]An energy landscape approach predicts the conformational changes of the
configurations of the regulatory domain of the protein nuclear factor of
activated T cells (NFAT) caused by phosphorylation of specific multiple
sites. Structurally local effects and secondary structural changes are
modeled using all-atom Brownian dynamics to investigate the changes of
the backbone torsional distributions upon phosphorylation. For tertiary
and global changes, we employ a coarse-grained model to sample ensembles
of conformations both with and without phosphorylation. At the secondary
structure level, phosphorylation moderately increases the helical
propensity and gives a more rigid local backbone conformation. The
tertiary effects of phosphorylation caused by the extensive charge
modification are more pronounced and collectively change the
conformation of the regulatory domain of NFAT from a flexible globular
ensemble to a rather rigid helical bundle, blocking access to the
nuclear localization sequence. These studies give computational support
to one scenario conjectured from experiments.
Relating kinetic rates and local energetic roughness by accelerated molecular dynamics simulationsDonald Hamelberg, Tongye Shen and J. Andrew McCammonJournal of Chemical Physics, Vol. 122, Issue 24, article 241103, 4 pages (2005)
We show that our accelerated molecular dynamics (MD) approach can extend
the time scale in all-atom MD simulations of biopolymers. We also show
that this technique allows for kinetic rate information to be
recaptured. In deducing the kinetic rates, the relationship between the
local energetic roughness of the potential energy landscape and the
effective diffusion coefficient is established. These are demostrated on
a very slow but important biomolecular process: the dynamics of
cis-trans isomerization of Ser-Pro motifs. We do not only
recapture the slow kinetics rates, which is difficult in traditional MD;
but also obtain the underlying roughness of the energy landscape of
proteins at atomistic resolution.
Exploring Global Motions and Correlations in the RibosomeJoanna Trylska, Valentina Tozzini and J. Andrew McCammonBiophysical Journal, Vol. 89, No. 3, pp. 1455-1463 (2005) [PubMed 15951386]We studied slower global coupled motions of the ribosome with half a
microsecond of coarse-grained molecular dynamics. A low-resolution
anharmonic network model that allows for the evolution of tertiary
structure and long-scale sampling was developed and parameterized. Most
importantly, we find that functionally important movements of L7/L12 and
L1 lateral stalks are anticorrelated. Other principal directions of
motions include widening of the tRNA cleft and the rotation of the small
subunit which occurs as one block and is in phase with the movement of
L1 stalk. The effect of the dynamical correlation pattern on the
elongation process is discussed. Small fluctuations of the 3' tRNA
termini and anticodon nucleotides show tight alignment of substrates for
the reaction. Our model provides an efficient and reliable way to study
the dynamics of large biomolecular systems composed of both proteins and
nucleic acids.
A coarse grained model for the dynamics of the early stages of the binding mechanism of HIV-1 ProteaseValentina Tozzini and J. Andrew McCammonChemical Physics Letters, Vol. 413, Issue 1-3, pp. 123-128 (2005)
A coarse grained model for proteins is developed and applied to HIV-1
protease. Molecular dynamics simulations on the μsec timescale and
the use of a flexible force field allow study of the opening of the
"flaps" protecting the active site. The opening mechanism reveals
peculiar features that might be involved in the substrate capture. An
allosteric inhibition effect is demonstrated in specific regions of the
protein. This study indicates alternative conformations and target sites
to be used as basis for the design of novel inhibitor drugs.
Exploring Assembly Energetics of the 30S Ribosomal Subunit Using an Implicit Solvent ApproachJoanna Trylska, J. Andrew McCammon and Charles L. Brooks IIIJournal of the American Chemical Society, Vol. 127, No. 31, pp. 11125-11133 (2005) [PubMed 16076220]To explore the relationship between the assembly of the 30S ribosomal
subunit and interactions among the constituent components, 16S RNA and
proteins, relative binding free energies of the T. thermophilus 30S
proteins to the 16S RNA were studied based on an implicit solvent model
of electrostatic, nonpolar, and entropic contributions. The late binding
proteins in our assembly map were found not to bind to the naked 16S
RNA. The 5' domain early kinetic class proteins, on average, carry the
highest positive charge, get buried the most upon binding to 16S RNA,
and show the most favorable binding. Some proteins (S10/S14, S6/S18,
S13/S19) have more stabilizing interactions while binding as dimers. Our
computed assembly map resembles that of E. coli; however, the central
domain path is more similar to that of A. aeolicus, a hyperthermophilic
bacteria.
Molecular Docking of Balanol to Dynamics Snapshots of Protein Kinase AChung F. Wong, Jeremy Kua, Yingkai Zhang, T.P. Straatsma and J. Andrew McCammonProteins: Structure, Function, and Bioinformatics, Vol. 61, Issue 4, pp. 850-858 (2005) [PubMed 16245317]Even if the structure of a receptor has been determined experimentally,
it may not be a conformation to which a ligand would bind when induced
fit effects are significant. Molecular docking using such a receptor
structure may thus fail to recognize a ligand to which the receptor can
bind with reasonable affinity. Here, we examine one way to alleviate
this problem by using an ensemble of receptor conformations generated
from a molecular dynamics simulation for molecular docking. Two
molecular dynamics simulations were conducted to generate snapshots for
protein kinase A: one with the ligand bound, the other without. The
ligand, balanol, was then docked to conformations of the receptors
presented by these trajectories. The Lamarckian genetic algorithm in
Autodock
(http://dx.doi.org/10.1002/(SICI)1099-1352(199601)9:1%3C1::AID-JMR241%
3E3.0.CO;2-6" target="_blank" class="ref">Goodsell et al.,
J Mol
Recognit 1996; 9(1):1-5;
http://dx.doi.org/10.1002/(SICI)1096-987X(19981115)19:14%3C1639::AID-
JCC10%3E3.0.CO;2-B" target="_blank" class="ref">Morris et al.,
J
Comput Chem 1998;19(14):1639-1662) was used in the docking. Three
ligand models were used: rigid, flexible, and flexible with torsional
potentials. When the snapshots were taken from the molecular dynamics
simulation of the protein-ligand complex, the correct docking structure
could be recovered easily by the docking algorithm in all cases. This
was an easier case for challenging the docking algorithm because, by
using the structure of the protein in a protein-ligand complex, one
essentially assumed that the protein already had a pocket to which the
ligand can fit well. However, when the snapshots were taken from the
ligand-free protein simulation, which is more useful for a practical
application when the structure of the protein-ligand complex is not
known, several clusters of structures were found. Of the 10 docking runs
for each snapshot, at least one structure was close to the correctly
docked structure when the flexible-ligand models were used. We found
that a useful way to identify the correctly docked structure was to
locate the structure that appeared most frequently as the lowest energy
structure in the docking experiments to different snapshots.
The Entropic Cost of Protein-Protein Association: A Case Study on Acetylcholinesterase Binding to Fasciculin-2David D.L. Minh, Jennifer M. Bui, Chia-en Chang, Tushar Jain, Jessica M.J. Swanson and J. Andrew McCammonBiophysical Journal, Vol. 89, No. 4, pp. L25-L27 (2005) [PubMed 16100267]Protein-protein association is accompanied by a large reduction in
translational and rotational (external) entropy. Based on a 15 ns
molecular dynamics simulation of acetylcholinesterase (AChE) in complex
with fasciculin 2 (Fas2), we estimate the loss in external entropy using
quasiharmonic analysis and histogram-based approximations of the
probability distribution function. The external entropy loss of
AChE-Fas2 binding, ~30 cal/mol K, is found to be significantly larger
than most previously characterized protein-ligand systems. However, it
is less than the entropy loss estimated in an earlier study by A.V.
Finkelstein and J. Janin, which was based on atomic motions in crystals.
In Table 1 and 2, labels for translational and rotational degrees of
freedom are switched. Similarly, the sentence above figure 2, which
reads "the rotational entropy of the complex" should be "the
translational entropy of the complex." The end of the following
paragraph, which reads "artifactual motions in rotational phase space"
should be "artifactual motions in translational phase space."
Limitations of Atom-Centered Dielectric Functions in Implicit Solvent ModelsJessica M.J. Swanson, John Mongan and J. Andrew McCammonJournal of Physical Chemistry B, Vol. 109, No. 31, pp. 14769-14772 (2005) [PubMed 16852866]Many recent advances in Poisson-Boltzmann and generalized Born implicit
solvent models have used atom-centered polynomial or Gaussian functions
to define the boundary separating low and high dielectric regions. In
contrast to the Lee and Richards molecular surface, atom-centered
surfaces result in interatomic crevices and buried pockets of high
dielectric which are too small for a solvent molecule to occupy. We show
that these interstitial high dielectric regions are of significant
magnitude in globular proteins, that they artificially increase
solvation energies, and that they distort the free energy surface of
nonbonded interactions. These results suggest that implicit solvent
dielectric functions must exclude interstitial high dielectric regions
in order to yield physically meaningful results.
Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integralsBenzhuo Lu, Xiaolin Cheng, Tingjun Hou and J. Andrew McCammonJournal of Chemical Physics, Vol. 123, Issue 8, article 084904, 8 pages (2005) [PubMed 16164327]The electrostatic interaction among molecules solvated in ionic solution
is governed by the Poisson-Boltzmann equation (PBE). Here the
hypersingular integral technique is used in a boundary element method
(BEM) for the three-dimensional (3D) linear PBE to calculate the Maxwell
stress tensor on the solvated molecular surface, and then the PB forces
and torques can be obtained from the stress tensor. Compared with the
variational method (also in a BEM frame) that we proposed recently, this
method provides an even more efficient way to calculate the full
intermolecular electrostatic interaction force, especially for
macromolecular systems. Thus, it may be more suitable for the
application of Brownian dynamics methods to study the dynamics of
protein/protein docking as well as the assembly of large 3D
architectures involving many diffusing subunits. The method has been
tested on two simple cases to demonstrate its reliability and
efficiency, and also compared with our previous variational method used
in BEM.
Target Flexibility in Molecular RecognitionJ. Andrew McCammonBiochimica et Biophysica Acta, Vol. 1754, Issue 1-2, pp. 221-224 (2005, Special issue on Inhibitors of Protein Kinases) [PubMed 16181817]Induced-fit effects are well known in the binding of small molecules to
proteins and other macromolecular targets. Among other targets, protein
kinases are particularly flexible proteins, so that such effects should
be considered in attempts at structure-based inhibitor design for kinase
targets. This paper outlines some recent progress in methods for
including target flexibility in computational studies of molecular
recognition. A focus is the "relaxed complex method," in which ligands
are docked to an ensemble of conformations of the target, and the best
complexes are re-scored to provide predictions of optimal binding
geometries. Early applications of this method have suggested a new
approach to the development of inhibitors of HIV-1 Integrase.
Fast Peptidyl cis-trans Isomerization within the Flexible Gly-Rich Flaps of HIV-1 ProteaseDonald Hamelberg and J. Andrew McCammonJournal of the American Chemical Society, Vol. 127, No. 40, pp. 13778-13779 (2005) [PubMed 16201784]The catalytic aspartyl protease of the HIV-1 virus is a homodimer with
two flaps that control access to the active site and are known to be
flexible. However, knowledge of the atomistic mechanism of the
flexibility is lacking. We show that the Gly-Gly -bond in the
glycine-rich flap tips undergoes fast cis-trans isomerization on the
microsecond to millisecond time scale rather than in the usual seconds.
Further study reveals that the unexpectedly fast isomerization is a
direct consequence of the -hairpin loop structure of the flap tips,
which appears to be counterintuitive. After loop formation of a linear
peptide containing the Gly-Gly motif, the rate of isomerization is shown
to increase by many orders of magnitude.
Potent, Selective Pyrone-Based Inhibitors of Stromelysin-1David T. Puerta, John Mongan, Ba L. Tran, J. Andrew McCammon and Seth M. CohenJournal of the American Chemical Society, Vol. 127, No. 41, pp. 14148-14149 (2005) [PubMed 16218585]In an effort to develop alternatives to hydroxamate-based matrix
metalloproteinase inhibitors (MPIs), we have utilized the drug discovery
program LUDI enhanced with the structural coordinates of a bioinorganic
model complex. This method has yielded the first pyrone-based MPIs. The
inhibitors demonstrate nanomolar potency against MMP-3 and are selective
for MMP-3 over MMP-2 and MMP-1. We postulate that the potency and
unusual selectivity profile of these MPI is attributable to the pyrone
chelating group.
Induced Fit in Mouse Acetylcholinesterase upon Binding a Femtomolar Inhibitor: A Molecular Dynamics StudySanjib Senapati, Jennifer M. Bui and J. Andrew McCammonJournal of Medicinal Chemistry, Vol. 48, No. 26, pp. 8155-8162 (2005) [PubMed 16366597]A molecular dynamics simulation of mouse acetylcholinesterase (mAChE)
complexed with
syn-TZ2PA6, a femtomolar AChE inhibitor, is
compared to a simulation of unliganded mAChE. The simulation of the
complex was initiated by placing the inhibitor in its bound conformation
of the crystal complex into a structure of unliganded mAChE selected
from preliminary protein-ligand docking results. During a 2 ns period,
the enzyme subsequently displayed a substantial "induced fit" response
to yield a conformation very similar to that obtained by crystallography
(http://dx.doi.org/10.1073/pnas.0308206100" target="_blank"
class="ref">Bourne et al.
Proc. Natl. Acad. Sci. USA 2004,
101, 1449-1454). In this conformation of unique nature, the Trp
286 side chain of the enzyme flips out of the hydrophobic core and
becomes highly solvent exposed. The imidazole ring of His 287 is almost
orthogonal relative to its position in the unliganded enzyme, creating a
stable π stacking arrangement with the Trp 286 side chain. Other
major deviations among the active site residues include side chain
conformational changes of Trp 86, Tyr 133, Tyr 337, and Phe 338. These
residues in the complex deviate from their positions in unliganded mAChE
to better accommodate the inhibitor in the active site gorge.
The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode AnalysisDeqiang Zhang and J. Andrew McCammonPLoS Computational Biology, Vol. 1, Issue 6, pp. 484-491 (2005) [PubMed 16299589]Acetylcholinesterase (AChE) rapidly hydrolyzes acetylcholine in the
neuromuscular junctions and other cholinergic synapses to terminate the
neuronal signal. In physiological conditions, AChE exists as tetramers
associated with the proline-rich attachment domain (PRAD) of either
collagen-like Q subunit (ColQ) or proline-rich membrane-anchoring
protein. Crystallographic studies have revealed that different tetramer
forms may be present, and it is not clear whether one or both are
relevant under physiological conditions. Recently, the crystal structure
of the tryptophan amphiphilic tetramerization (WAT) domain of AChE
associated with PRAD (WAT4PRAD), which mimics the interface between ColQ
and AChE tetramer, became available. In this study we built a complete
tetrameric mouse AChET4-ColQ atomic structure model, based on the
crystal structure of the WAT4PRAD complex. The structure was optimized
using energy minimization. Block normal mode analysis was done to
investigate the low-frequency motions of the complex and to correlate
the structure model with the two known crystal structures of AChE
tetramer. Significant low-frequency motions among the catalytic domains
of the four AChE subunits were observed, while the WAT4PRAD part held
the complex together. Normal mode involvement analysis revealed that the
two lowest frequency modes were primarily involved in the conformational
changes leading to the two crystal structures. The first 30 normal modes
can account for more than 75% of the conformational changes in both
cases. The evidence further supports the idea of a flexible tetramer
model for AChE. This model can be used to study the implications of the
association of AChE with ColQ.