pKa Shift Effects on Backbone Amide Base-Catalyzed Hydrogen Exchange Rates in PeptidesF. Fogolari, G. Esposito, P. Viglino, J.M. Briggs and J.A. McCammonJournal of the American Chemical Society, Vol. 120, pp. 3735-3738 (1998)
Amide proton exchange (HX) rates are known to depend on protein primary
structure as well as local and global protein structure and dynamics.
Measurement of HX rates gives information on the local exposure of amide
protons to solvent and on local rates of structural openings. It has
long been recognized that the amide pKa directly influences the HX rate.
Using the finite- difference solution of the Poisson-Boltzmann equation,
we investigated the electrostatic effects on HX rates, via calculated
shifts in the amide pKa for model compounds (N-methylacetamide,
dipeptides entailing almost all amino acid sidechains, and a
tripeptide). Rather than shifts in the same compound with varying
environmental conditions, we address shifts in the HX rates of different
compounds relative to each other. The results for selected model
compounds which resemble Ala and Gly residues, with a standard choice of
parameters, agree to a high degree of accuracy with experimentally
determined rates. Application of the same methodology to naturally
occurring amino acids is promising but requires refinement to take into
account flexibility and inductive effects.
Correlation Between Rate of Enzyme-Substrate Diffusional Encounter and Average Boltzmann Factor Around Active SiteHuan-Xiang Zhou, James M. Briggs, Sylvia Tara and J. Andrew McCammonBiopolymers, Vol. 45, Issue 5, pp. 355-360 (1998) [PubMed 9530014]The utility of the average Boltzmann factor around the active site of an
enzyme as the predictor of the electrostatic enhancement of the
substrate binding rate is tested on a set of data on wild-type
acetylcholinesterase and 18 charge mutants recently obtained by Brownian
dynamics simulations. A good correlation between the average Boltzmann
factors and the substrate binding rate constants is found. The effects
of single charge mutations on both the Boltzmann factor and the
substrate binding rate constant are modest, i.e., <5 fold increase or
decrease. This is consistent with the experimental results of Shafferman
et al. but does not support their suggestion that the overall rate of
the catalytic reaction is not limited by the diffusional encounter of
acetylcholinesterase and its substrate.
Solvation Studies of DMP323 and A76928 Bound to HIV Protease: Analysis of Water Sites Using Grand Canonical Monte Carlo SimulationsTami J. Marrone, Haluk Resat, C. Nicholas Hodge, Chong-Hwan Chang and J. Andrew McCammonProtein Science, Vol. 7, Issue 3, pp. 573-579 (1998) [PubMed 9541388]We examine the water solvation of the complex of the inhibitors DMP323
and A76928 bound to HIV-I protease through grand canonical Monte Carlo
simulations, and demonstrate the ability of this method to reproduce
crystal waters and effectively predict water positions not seen in the
DMP323 or A76928 structures. The simulation method is useful for
identifying structurally important waters which may not be resolved in
the crystal structures. It can also be used to identify water positions
around a putative drug candidate docked into a binding pocket. Knowledge
of these water positions may be useful in designing drugs to utilize
them as bridging groups or displace them in the binding pocket. In
addition, the method should be useful in finding water sites in homology
models of enzymes for which crystal structures are unavailable.
Quantum Dynamics of Proton Transfer Processes in Enzymatic Reactions. Simulations of Phospholipase A2P. Ba&None
For the past few years we have been developing a theoretical model
capable of describing quantum dynamical processes which occur in
molecular systems and in enzymatic active sites. This, in particular,
includes proton transfer processes. Our most advanced studies have been
performed for phospholipase A2, an enzyme which hydrolyzes
phospholipids. The potential energy function for the active site is
computed using an Approximate Valence Bond (AVB) method. The dynamics of
the key proton in the enzyme's active site is described either by the
classical molecular dynamics (MD/AVB model) or by the time-dependent
Schroedinger equation. The dynamics of the remaining atoms of the enzyme
are described using classical MD. The coupling between the quantum
proton and the classical atoms is accomplished via Hellmann-Feynman
forces, as well as the time-dependence of the potential energy function
in the Schroedinger equation (QCMD/AVB model). The quantum proton
transfer from the water molecule to histidine is followed by a
nucleophilic attack of the created OH- group. The processes
are simulated using the parallelized QCMD code.
Theory of Biomolecular RecognitionJ.A. McCammonCurrent Opinion in Structural Biology, Vol. 8, pp. 245-249 (1998) [PubMed 9631300]Specific, noncovalent binding of biomolecules can only be understood by
consideration of structural, thermodynamic and kinetic issues. The
theoretical foundations for such analyses have been clarified in the
past year. Computational techniques for both particle-based models and
continuum models continue to improve, and yield useful insights to an
ever-wider range of biomolecular systems.
Correcting for Electrostatic Cutoffs in Free Energy Simulations: Toward Consistency Between Simulations with Different CutoffsH. Resat and J.A. McCammonJournal of Chemical Physics, Vol. 108, pp. 9617-9623 (1998)
The use of electrostatic cutoffs in calculations of free energy
differences by molecular simulations introduces errors. Even though both
solute-solvent and solvent-solvent cutoffs are known to create
discrepancies, past efforts have mostly been directed toward correcting
for the solute-solvent cutoffs. In this work, an approach based on the
generalized reaction field formalism is developed to correct for the
solvent-solvent cutoff errors as well. It is shown using a series of
simulation that when the cutoff lengths are significantly smaller than
the half unit cell size, and the solute-solvent cutoff is not much
larger than the solvent-solvent cutoff, the new algorithm is able to
yield better agreement among simulations employing different truncation
lengths.
Electrostatic Contributions to the Stability of Halophilic ProteinsA.H. Elcock and J.A. McCammonJournal of Molecular Biology, Vol. 280, pp. 731-748 (1998) [PubMed 9677300]Solution of the first crystal structures of proteins from a halophilic
organism suggest that an abundance of acidic residues distributed over
the protein surface is a key determinant of adaptation to high salt
conditions. Although one extant theory suggests that acidic residues are
favoured because of their superior water binding capacity, it is clear
that extensive repulsive electrostatic interactions will also be present
in such proteins at physiological pH. To investigate the magnitude and
importance of such electrostatic interactions, we conducted a
theoretical analysis of their contributions to the salt and pH
dependence of stability of two halophilic proteins. Our approach centers
around use of the Poisson-Boltzmann equation of classical
electrostatics, applied at an atomic level of detail to crystal
structures of the proteins. We first show that in using the method, it
is important to account for the fact that the dielectric constant of
water decreases at high salt concentrations, in order to reproduce
experimental changes in pKas of small acids and bases. We then conduct a
comparison of salt and pH effects on the stability of 2Fe-2S ferredoxins
from the halophile
Haloarcula marismortui and the non-halophile
anabaena. In both proteins, substantial upward shifts in pKas
accompany protein folding, though shifts are considerably larger on
average in the halophile. Upward shifts for basic residues occur because
of unfavourable electrostatic interactions with other acidic groups. Our
calculations suggest that at pH 7 the stability of the halophilic
protein is decreased by 18.2 kcal/mol on lowering the salt concentration
from 5M to 100mM, a result which is in line with the fact that
halophilic proteins generally unfold at low salt concentrations. For
comparison, the non-halophilic ferredoxin is calculated to be
destabilized by only 5.lkcal/mol over the same range. Analysis of the pH
stability curve suggests that lowering the pH should increase the
intrinsic stability of the halophilic protein at low salt
concentrations, although in practice this is not observed because of
aggregation effects. We also report the results of a similar analysis
carried out on the tetrameric malate dehydrogenase from
Haloarcula
marismortui. In this case we investigate the salt and pH dependence
of the various monomer-monomer interactions present in the tetramer. All
monomermonomer interactions are found to make substantial contributions
to the salt dependence of stability of the tetramer. Excellent agreement
is obtained between our calculated results for the stability of the
tetramer and experimental results. In particular, the finding that at 4M
NaCl, the tetramer is stable only between pH 4.8 and 10 is accurately
reproduced. Taken together, our results suggest that repulsive
electrostatic interactions between acidic residues are a major factor in
the destabilization of halophilic proteins in low salt conditions, and
that these interactions remain destabilizing even at high salt
concentrations. As a consequence, the role of acidic residues in
halophilic proteins appears to be more one of preventing aggregation
than making a positive contribution to intrinsic protein stability.
Analysis of Synaptic Transmission in the Neuromuscular Junction Using a Continuum Finite Element ModelJason L. Smart and J. Andrew McCammonBiophysical Journal, Vol. 75, No. 4, pp. 1679-1688 (1998) [PubMed 9746510]There is a steadily-growing body of experimental data describing the
diffusion of acetylcholine in the neuromuscular junction, and the
subsequent miniature end plate currents produced at the post-synaptic
membrane. In order to gain further insights into the structural features
governing synaptic transmission, we have performed calculations using a
simplified finite element model of the neuromuscular junction. The
diffusing acetylcholine molecules are modeled as a continuum, whose
spatial and temporal distribution is governed by the force-free
diffusion equation. The finite element method was adopted because of its
flexibility in modeling irregular geometries and complex boundary
conditions. The resulting simulations are shown to be in accord with
experiment, and with other simulations.
Conformation Gating as a Mechanism for Enzyme SpecificityHuan-Xiang Zhou, Stanislaw T. Wlodek and J. Andrew McCammonProceedings of the National Academy of Sciences of the USA, Vol. 95, No. 16, pp. 9280-9283 (1998) [PubMed 9689071]Acetylcholinesterasae (AChE), with an active site located at the bottom
of a narrow and deep gorge, provides a striking example of enzymes with
buried active sites. Recent molecular dynamics (MD) simulations showed
that reorientation of five aromatic rings leads to rapid opening and
closing of the gate to the active site. In the present study the MD
trajectory is used to quantitatively analyze the effect of the gate on
the substrate binding rate constant. For a 2.4 A probe modeling
acetylcholine, the gate is open only 2.4% of the time, but the
quantitative analysis reveals that the substrate binding rate is slowed
by merely a factor of 2. We rationalize this result by noting that the
substrate, by virtue of Brownian motion, will make repeated attempts to
enter the gate each time it is near the gate. If the gate is rapidly
switching between the open and closed states, one of these attempts will
coincide with an open state and then the substrate succeeds in entering
the gate. However, there is a limit on the extent to which rapid gating
dynamics can compensate for the small equilibrium probability of the
open state. Thus the gate is effective in reducing the binding rate for
a ligand 0.4 A bulkier by three orders of magnitude. This suggests a
mechanism for achieving enzyme specificity without sacrificing
efficiency.
Rapid Binding of a Cationic Active Site Inhibitor to Wild Type and Mutant Mouse Acetylcholinesterase: Brownian Dynamics Simulation Including Diffusion in the Active Site GorgeSylvia Tara, Adrian H. Elcock, Paul D. Kirchhoff, James M. Briggs, Zoran Radi&Biopolymers, Vol. 46, Issue 7, pp. 465-474 (1998) [PubMed http://www.ncbi.nlm.nih.gov/pubmed/9838872]PubMed: 9838872
It is known that anionic surface residues play a role in the long range electrostatic attraction between acetylcholinesterase and cationic ligands. In our current investigation, we show that anionic residues also play an important role in the behavior of the ligand within the active site gorge of acetylcholinesterase. Negatively charged residues near the gorge opening not only attract positively charged ligands from solution to the enzyme, but can also restrict the motion of the ligand once it is inside of the gorge. We use Brownian dynamics techniques to calculate the rate constant for wild type and mutant acetylcholinesterase with a positively charged ligand. These calculations are performed by allowing the ligand to diffuse within the active site gorge. This is an extension of previously reported work in which a ligand was allowed to diffuse only to the enzyme surface. By setting the reaction criteria for the ligand closer to the active site, better agreement with experimental data is obtained. Although a number of residues influence the movement of the ligand within the gorge, Asp74 is shown to play a particularly important role in this function. Asp74 traps the ligand within the gorge, and in this way helps to ensure a reaction.
Self-Organizing Neural Networks Bridge the Biomolecular Resolution GapW. Wriggers, R.A. Milligan, K. Schulten and J.A. McCammonJournal of Molecular Biology, Vol. 284, pp. 1247-1254 (1998) [PubMed 9878345]Topology representing neural networks are employed to generate
pseudo-atomic structures of large-scale protein assemblies by combining
high-resolution data with volumetric data at lower resolution. As an
application example, actin monomers and structural subdomains are
located in a 3D image reconstruction from electron micro-graphs. To test
the reliability of the method, the resolution of the atomic model of an
actin polymer is lowered to a level typically encountered in electron
microscopic reconstructions. The atomic model is restored with a
precision nine times the nominal resolution of the corresponding
low-resolution density. The presented self-organizing computing method
may be used as an information processing tool for the synthesis of
structural data from a variety of biophysical sources.
Exciting Green Fluorescent ProteinV. Helms, E.F.Y. Hom, T.P. Straatsma, J.A. McCammon and P. LanghoffIn "Combined Quantum Mechanical and Molecular Mechanical Methods," J. Gao, M.A. Thompson, Eds., ACS Symposium Series 712, American Chemical Society, Washington, DC, pp. 288-295 (1998)
Dynamical and luminescent properties of the Green Fluorescent Protein
(GFP) are being explored via molecular dynamics (MD) simulations and
quantum chemistry calculations with the aim of facilitating the rational
development of GFP as a probe for cellular functions. Results from an MD
simultion of wild type GFP demonstrate the rigidity of the structural
framework of GFP, and a very stable hydrogen bond network around the
chromophore. Furthermore, excited state calculations have been performed
on the chromophore in vacuum, and we report about our work in progress
here.
Brownian and Essential Dynamics Studies of the HIV-1 Integrase Catalytic DomainWolfgang Weber, Hagop Demirdjian, Roberto D. Lins, James M. Briggs, Ricardo Ferreira and J. Andrew McCammonJournal of Biomolecular Structure and Dynamics, Vol. 16, No. 3, pp. 733-745 (1998) [PubMed 10052629]The three-dimensional structure of the active site region of the enzyme
HIV-1 integrase is not unambiguously known. This region includes a
flexible peptide loop that cannot be well resolved in crystallographic
determinations. Here, we present two different computational approaches
with different levels of resolution and on different timescales to
understand this flexibility and to analyze the dynamics of this part of
the protein.
Computer Simulation Studies of Acetylcholinesterase Dynamics and ActivityJ.A. McCammon, S. Wlodek, T. Clark, P. Kirchhoff, L.R. Scott and S. TaraIn "Structure and Function of Cholinesterases and Related Proteins," B.P. Doctor, P. Taylor, D.M. Quinn, R.L. Rotundo, M.K. Gentry, Eds., Plenum Press, New York, pp. 327-329 (1998)
Computer simulations of the activity of acetylcholinesterase (AChE) are
shedding light on the origins of the selectivity, mechanism, and
efficiency of the enzyme. In the following, a brief discussion is
presented on two aspects of the the enzymatic activity: the role of the
electrostatic field of the enzyme in speeding its binding of cationic
substrates and inhibitors, and the role of fluctuations in the structure
of the enzyme in facilitating this binding.