A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor InteractionsBrock A. Luty, Zelda R. Wasserman, Pieter F.W. Stouten, C. Nicholas Hodge, Martin Zacharias and J. Andrew McCammonJournal of Computational Chemistry, Vol. 16, Issue 4, pp. 454-464 (1995)
We present a computational method for prediction of the conformation of
a ligand when bound to a macromolecular receptor. The method is intended
for use in systems in which the approximate location of the binding site
is known and no large-scale rearrangements of the receptor are expected
upon formation of the complex. The ligand is initially placed in the
vicinity of the binding site and the atomic motions of the ligand and
binding site are explicitly simulated, with solvent represented by an
implicit solvation model and using a grid representation for the bulk of
the receptor protein. These two approximations make the method
computationally efficient and yet maintain accuracy close to that of an
all-atom calculation. For the benzamidine/trypsin system, we ran 100
independent simulations, in many of which the ligand settled into the
low-energy conformation observed in the crystal structure of the
complex. The energy of these conformations was lower than and
well-separated from that of others sampled. Extensions of this method
are also discussed.
Conservative and Nonconservative Mutations in Proteins: Anomalous Mutations in a Transport Receptor Analyzed by Free Energy and Quantum Chemical CalculationsWilliam R. Cannon, James M. Briggs, Jian Shen, J. Andrew McCammon and Florante A. QuiochoProtein Science, Vol. 4, Issue 3, pp. 387-393 (1995) [PubMed 7795522]Experimental studies on a bacterial sulfate receptor have indicated
anomalous relative binding affinities for the mutations Ser(130) ->
Cys, Ser(130) -> Gly, and Ser(130) -> Ala. The loss of affinity
for sulfate in the former mutation was previously attributed to a
greater steric effect on the part of the Cys side chain relative to the
Ser side chain, whereas the relatively small loss of binding affinity
for the latter two mutations was attributed to the loss of a single
hydrogen bond. In this report we present quantum chemical and
statistical thermodynamic studies of these mutations. Qualitative
results from these studies indicate that for the Ser(130) -> Cys
mutation the large decrease in binding affinity is in part caused by
steric effects, but also significantly by the differential work required
to polarize the Cys thiol group relative to the Ser hydroxyl group. The
Gly mutant cobinds a water molecule in the same location as the Ser side
chain resulting in a relatively small decrease in binding affinity.
Results for the Ala mutant are in disagreement with experimental results
but are likely to be limited by insufficient sampling of configuration
space due to physical constraints applied during the simulation.
Binding of Cations and Protons in the Active Site of AcetylcholinesteraseStanislaw T. Wlodek, Jan Antosiewicz, J. Andrew McCammon and Michael K. GilsonIn "Modelling of Biomolecular Structures and Mechanisms," A. Pullman, J. Jortner, B. Pullman, Eds., Kluwer Academic Pub., Vol. 27, pp. 25-37 (1995)
The active site of acetylcholinesterase contains a number of ionizable
residues. The pKas of the catalytic histidine, His
440, is believed to be 6.3, based upon enzyme kinetic studies. However,
the pKas of the other residues have not been
measured. Here, we describe aclculations of the
pKa of the ionizable groups in this enzyme.
Interestingly, the initial calculations predict a
pKa of 9.3 for His 440. The deviation of 3
pKa units from the measured pKa
is traceable to the influence of Glu 199 and Glu 443 upon His 440. We
argue that the deviation does not represent a failure of the
computational method. Rather it points to the need for an adjustment in
the model of the protein. The adjustment we suggest involves a
monovalent cation bound in the active site, near Glu 199 and His 440.
Including such a cation in the calculations brings the computed
pKa of His 440 into agreement with the measured
value. Futhermore, the idea that a bound cation substantially reduces
the pKa of His 440 leads to satisfying explantions
of a number of otherwise puzzling experimental data.
Acetylcholinesterase: Diffusional Encounter Rate Constants for Dumbbell Models of LigandJan Antosiewicz, Michael K. Gilson, Irwin H. Lee and J. Andrew McCammonBiophysical Journal, Vol. 68, No. 1, pp. 62-68 (1995) [PubMed 7711269]For some enzymes, virtually every substrate molecule that encountersthe
entrance to the active site proceeds to reaction, at lowsubstrate
concentrations. Such diffusion-limited enzymes displayhigh apparent
bimolecular rate constants ((kcat/KM)), whichdepend strongly upon
solvent viscosity. Some experimental studiesprovide evidence that
acetylcholinesterase falls into this category.Interestingly, the
asymmetric charge distribution of acetylcholinesterase,apparent from the
crystallographic structure, suggests thatits electrostatic field
accelerates the encounter of its cationicsubstrate, acetylcholine, with
the entrance to the active site.Here we report simulations of the
diffusion of substrate inthe electrostatic field of
acetylcholinesterase. We find thatthe field indeed guides the substrate
to the mouth of the activesite. The computed encounter rate constants
depend upon theparticular relative geometries of substrate and enzyme
thatare considered to represent successful encounters. With
loosereaction criteria, the computed rates exceed those
measuredexperimentally, but the rate constants vary appropriately
withionic strength. Although more restrictive reaction criterialower the
computed rates, they also lead to unrealistic variationof the rate
constants with ionic strength. That these simulationsdo not agree well
with experiment suggests that the simple diffusionmodel is incomplete.
Structural fluctuations in the enzyme orevents after the encounter may
well contribute to rate limitation.
Parallelization of Poisson-Boltzmann and Brownian Dynamics CalculationsA. Ilin, B. Bagheri, L.R. Scott, J.M. Briggs and J.A. McCammonAmerican Chemical Society Symposium Series, No. 592, pp. 170-185 (1995)
Quantum-Classical Molecular Dynamics and Its Computer ImplementationP. Ba&Computers & Chemistry, Vol. 19, Issue 3, pp. 155-160 (1995)
Quantum-classical and quantum-stochastic molecular dynamics (QCMD/QSMD)
models are formulated and applied for quantum proton transfer processes.
The protein dynamics are described by the time-dependent Schroedinger
equation and the motion of classical atoms by the Newtonian or Langevin
equations of motion. Instantaneous positions of the classical atoms
determine the potential energy surface for the proton dynamics. In turn,
the proton wavefunction influences the classical atoms through
nonstationary Hellmann-Feynman forces (pubs90.html" target="_blank"
class="ref">Bala et al., 1994c). The QCMD/QSMD algorithm is
described and numerical results for a proton-bound ammonia-ammonia dimer
and an enzyme, phospholipase A2, are presented. In the case
of the enzyme molecule a valence-bond orbital method is used to compute
the potential energy function for the proton transfer. The methods are
found to be promising tools in studies of molecular and enzymatic
reactions in which quantum-dynamical effects cannot be neglected.
Secondary Structure Prediction of the H5-Pore of Potassium ChannelsK.V. Soman, J.A. McCammon and A.M. BrownProtein Engineering, Vol. 8, No. 4, pp. 397-401 (1995) [PubMed 7567925]The 'H5' segment located between the putative fifth and sixth
transmembrane helices is the most highly conserved region in
voltage-gated potassium channels and it is believed to constitute a
major part of the ion conduction path (pore). Here we present a two-step
procedure, comprising secondary structure prediction and hydrophobic
moment profiling, to predict the structure of this important region.
Combined results from the application of the procedure to the H5 region
of four voltage-gated and five other K
+ channel sequences
lead to the prediction of a β-strand-turn-(3-strand) structure for
H5. The reasons for the application of these soluble protein methods to
parts of membrane proteins are: (i) that pore-lining residues are
accessible to water and (ii) that a large enough database of
high-resolution membrane protein structures does not yet exist. The
results are compared with experimental results, in particular
spectroscopic studies of two peptides based on the H5 sequence of SHAKER
potassium channel. The procedure developed here maybe applicable to
water accessible regions of other membrane proteins.
Molecular Dynamics Simulation with a Continuum Electrostatic Model of the SolventMichael K. Gilson, J. Andrew McCammon and Jeffry D. MaduraJournal of Computational Chemistry, Vol. 16, Issue 9, pp. 1081-1095 (1995)
The accuracy and simplicity of the Poisson-Boltzmann electrostatics
model has led to the suggestion that it might offer an efficient solvent
model for use in molecular mechanics calculations on biomolecules. We
report a successful merger of the Poisson-Boltzmann and molecular
dynamics approaches, with illustrative calculations on the small solutes
dichloroethane and alanine dipeptide. The algorithm is implemented
within the program UHBD. Computational efficiency is achieved by the use
of rather coarse finite difference grids to solve the Poisson-Boltzmann
equation. Nonetheless, the conformational distributions generated by the
new method agree well with reference distributions obtained as Boltzmann
distributions from energies computed with fine finite difference grids.
The conformational distributions also agree well with the results of
experimental measurements and conformational analyses using more
detailed solvent models. We project that when multigrid methods are used
to solve the finite difference problem and the algorithm is implemented
on a vector supercomputer, the computation of solvent electrostatic
forces for a protein of modest size will add only about 0.1 s computer
time per simulation step relative to a vacuum calculation.
Simulation of Charge-Mutant AcetylcholinesterasesJan Antosiewicz, J. Andrew McCammon, Stanislaw T. Wlodek and Michael K. GilsonBiochemistry, Vol. 34, No. 13, pp. 4211-4219 (1995) [PubMed 7703233]A recent experimental study of human acetylcholinesterase has shown that
the mutation of surface acidic residues has little effect on the rate
constant for hydrolysis of acetylthiocholine. It was concluded, on this
basis, that the reaction is not diffusion controlled and that
electrostatic steering plays only a minor role in determining the rate.
Here we examine this issue through Brownian dynamics simulations on
Torpedo californica acetylcholinesterase in which the surface
acidic residues homologous with those mutated in the human enzyme are
artificially neutralized. The computed effects of the mutations on the
rate constants reproduce quite well the modest effects of the mutations
upon the measured encounter rates. Nonetheless, the electrostatic field
of the enzyme is found to increase the rate constants by about an order
of magnitude in both the wild type and the mutants. We therefore
conclude that the mutation experiments do not disprove that
electrostatic steering substantially affects the catalytic rate of
acetylcholinesterase.
Free Energy Simulations of the HyHEL-10/HEL Antibody-Antigen ComplexR. Pomés, R.C. Willson and J.A. McCammonProtein Engineering, Vol. 8, No. 7, pp. 663-675 (1995) [PubMed 8577695]Free energy simulations are reported for the N31
L-D
mutation, both in the HyHEL-10-HEL antibody-lysozyme complex and in the
unliganded antibody, using the thermo-dynamic-cycle perturbation method.
The present study suggests that the mutation would change the free
energy of binding of the complex by -5.6 kcal/mol (unrestrained free
energy simulations), by -0.5 kcal/mol (free energy simulations with a
restrained backbone) and by 1.8 kcal/mol (Poisson-Boltzmann
calculations, which also use a restrained geometry model). A detailed
structural analysis helps in estimating the contributions from various
residues and regions of the system. Enhanced recognition of HEL by the
mutant HyHEL-10 would arise from the combination of thermodynamically
more favorable conformational changes of the CDR loops upon association
and subsequent charge pairing with Lys96 in the antigen.
Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics ProgramJeffry D. Madura, James M. Briggs, Rebecca C. Wade, Malcolm E. Davis, Brock A. Luty, Andrew Ilin, Jan Antosiewicz, Michael K. Gilson, Babak Bagheri, L. Ridgway Scott and J. Andrew McCammonComputer Physics Communications, Vol. 91, Issues 1-3, pp. 57-95 (1995)
This paper is a follow-up to the initial communication (pubs00.html"
target="_blank" class="ref">Comput. Phys. Commun. 62 (1991) 187-197) on
the Brownian Dynamics/Electrostatics program UHBD developed at the
University of Houston. The program is now capable of computing
pKas of ionizable groups in proteins, performing
Brownian dynamics simulations with a flexible substrate and target, and
molecular mechanics/dynamics calculations using a continuum solvent.
These new capabilities and other features are discussed along with
selected applications which illustrate the capabilities of the current
version of UHBD.
Determination of the pKa Values of Titratable Groups of an Antigen-Antibody Complex: HyHEL5-HELShawn M. McDonald, Richard C. Willson and J. Andrew McCammonProtein Engineering, Vol. 8, No. 9, pp. 915-924 (1995) [PubMed 8746729]The titration behavior of the ionizable residues of the HyHEL-5-hen egg
lysozyme complex and its individual components has been studied using
continuum electrostatic calculations. Several residues of HyHEL-5 had
p
Ka values shifted away from model values for
isolated residues by more than three pH units. Shifts away from the
model values were smaller for the residues of hen egg lysozyme. A
moderate variation in the p
Ka values of the
titratable groups was observed upon increase of the ionic strength from
0 to 100 mM, amounting to 1-2 pH units in most cases. Under
physiological conditions, the net charge of HyHEL-5 was opposite that
for hen egg lysozyme. Several residues, including those involved in the
Arg-Glu salt bridges that have been proposed to be important in
antibody-antigen binding, had p
Ka values that were
changed significantly upon binding. The main titration event upon
antibody-antigen binding appears to be loss of a proton from residue
GluH50 of the Fv molecule. The limitations of our calculation methods
and the role they might play in the design of antibodies for use in
assays, sensors and separations are discussed
Electrostatic and Hydrodynamic Orientational Steering Effects in Enzyme-Substrate AssociationJ. Antosiewicz and J.A. McCammonBiophysical Journal, Vol. 69, No. 1, pp. 57-65 (1995) [PubMed 7669910]Diffusional encounters between a dumbbell model of a cleft enzyme and a
dumbbell model of an elongated ligand are simulated by Brownian
dynamics. The simulations take into account electrostatic and
hydrodynamic interactions between the molecules. It is shown that the
primary effect of inclusion of hydrodynamic interactions into the
simulation is an overall decrease in the rate constant. Hydrodynamic
orientational effects are of modest size for the systems considered
here. They are manifested when changes in the rate constants for
diffusional encounters favored by hydrodynamic interactions are compared
with those favored by electrostatic interactions as functions of the
overall strength of electrostatic interactions. The electrostatic
interactions modify the hydrodynamic torques by modifying the drift
velocity of the substrate toward the enzyme. We conclude that
simulations referring only to electrostatic interactions between an
enzyme and its ligand may yield rate constants that are somewhat (e.g.,
20%) too high, but provide realistic descriptions of the orientational
steering effects in the enzyme-ligand encounters.
I/O Limitations in Parallel Molecular DynamicsTerry W. Clark, L. Ridgway Scott, Stanislaw Wlodek and J. Andrew McCammonIn "Proceedings of the 1995 ACM/IEEE Supercomputing Conference," F. Baker and J. Wehmer, Eds., IEEE Computer Society Press, pp. 1-15 (1995, refereed)
We discuss data production rates and their impact on the performance of
scientific applications using parallel computers. On one hand, too high
rates of data production can be overwhelming, exceeding logistical
capacities for transfer, storage and analysis. On the other hand, the
rate limiting step in a computationally-based study should be the
human-guided analysis, not the calculation. We present performance data
for a biomolecular simulation of the enzyme, acetylcholinesterase, which
uses the parallel molecular dynamics program EulerGROMOS. The actual
production rates are compared against a typical time frame for results
analysis where we show that the rate limiting step is the simulation,
and that to overcome this will require improved output rates.
Sequence Dependent Hydration of DNA: Theoretical ResultsAdrian H. Elcock and J. Andrew McCammonJournal of the American Chemical Society, Vol. 117, No. 40, pp. 10161-10162 (1995)
Hydration effects are crucial to the static and dynamic behabior of DNA
and its interactions with other molecules. DNA hydration has been
studied by a variety of experimental methods: X-ray crystallography, NMR
spectroscopy, voumetric, and densitometric techniques have all been
employed. Despited such studies, however, there is little experimental
data regarding specifically the thermodynamics of hydration, largely
because of the difficulties in spearating out effects due soley to
hydration from those due to other causes. Drug-DNA binding equilibria,
for example, are governed by energetics of the drug-DNA interaction
itself, conformational changes in the drug and/or the DNA, and effects
due to changes in the ionic atmosphere, in addition to those resulting
soley from changes in hydration. In this paper we use a theoretical
method to focus entirely on this latter aspect and report on the
sequence dependence of solvation free energies calculated for DNA
oligonucleotides.