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MD Simulations of the Activation of the Adenovirus Proteinase
J.V. Stern, L. Slatest, J.W. Davenport, W.J. McGrath, and W.F. Mangel
The adenovirus proteinase (AVP) is a relatively inactive enzyme that can
be activated by an 11-amino-acid peptide cofactor, pVIc [1,2]. The binding
of pVIc increases the activity of AVP more than 3500-fold. The crystal
structure of the AVP-pVIc complex has been determined experimentally using
x-ray diffraction and the pVIc peptide was found to bind to AVP in an
extended conformation quite far from the active site, as shown in Figure 1
[3]. The peptide traverses the surface of the protein, ranging from 14 Å to
more than 30 Å away from the active site. This raises the question: how can
the peptide at such a large distance from the active site have such a
profound influence in the functioning of the enzyme?
Figure 1. Crystal structure of AVP-pVIc
(1NLN) (right). The active site His54 and Cys122 are in green. The 11
amino acidpeptide, pVIc is the yellow band at the bottom. The waters from
the crystal structure are shown in orange.
Recently, the crystal structure of AVP in the absence of the cofactor was
solved as well. Comparison of this structure to the structure of the
AVP-pVIc complex is revealing how pVIc activates the enzyme. We hypothesize
that in order for the binding of pVIc to activate the enzyme, a signal must
be transduced by a sequence of structural changes beginning at the pVIc
binding site on AVP and ending in the active site of AVP. Using molecular
dynamics simulations, it is hoped that the sequence of structural changes
that occur can be understood and exploited to provide targets for drugs. If
the binding of a drug to a target within the sequence of structural changes
can prevent the signal from being transduced, therefore preventing
activation, the drug could be an effective anti-viral agent..
Recently, the crystal structure of AVP in the absence of the
cofactor was solved as well. Comparison of this structure to the structure
of the AVP-pVIc complex is revealing how pVIc activates the enzyme. We
hypothesize that in order for the binding of pVIc to activate the enzyme, a
signal must be transduced by a sequence of structural changes beginning at
the pVIc binding site on AVP and ending in the active site of AVP. Using
molecular dynamics simulations, it is hoped that the sequence of structural
changes that occur can be understood and exploited to provide targets for
drugs. If the binding of a drug to a target within the sequence of
structural changes can prevent the signal from being transduced, therefore
preventing activation, the drug could be an effective anti-viral agent.
In the second set, an explicit water model was used [4]. Simulations were
started from the experimental AVP structure (without the pVIc) to which a
pVIc peptide had been docked. These simulations were run for ~ 3.7 nsec.
They illustrate further changes in the backbone structure including a most
interesting helix-coil transition. Using this approach, one possible step in
the activation mechanism has been observed. A third set of simulations was
run starting with the known AVP-pVIc complex but with the disulfide bond
that binds pVIc to AVP removed. The objective was to test a model describing
how pVIc binds to AVP by inducing a pocket in AVP, another possible step in
the activation mechanism. A simulation proceeding in the reverse direction,
unbinding, should therefore show some loss of the induced pocket. After ~100
picoseconds the last three amino acids of PVIc were indeed seen to leave the
induced pocket.
The explicit water model molecular dynamics (MD) simulations were performed
using NAMD [5], a parallel molecular dynamics code designed for
high-performance simulation of large biomolecular systems. AMBER force
fields [6] were used throughout. Our protein contains 204 amino acids plus
the 11 amino acid peptide cofactor. After protonation this constitutes about
3500 atoms. Adding water yields a total of 30,000 atoms. The implicit water
model MD simulations used a parameterization of the “OBC” model of
generalized Born [7], the AMBER force fields, and the AMBER parallel
molecular dynamics code [8]. Langevin dynamics with a collision frequency of
one inverse picosecond was employed to maintain a constant temperature of
310 K throughout the MD run. The fastest motion in the system, i.e. the bond
stretching freedom, was removed for bonds involving Hydrogen using the SHAKE
algorithm, thereby allowing a larger timestep (1 femtosecond) to be used.
We plan to continue these simulations to elucidate the transformations
involved in activating the enzyme and to discover sites along the pathway
that may serve as targets for drugs that will act as antiviral agents.
References
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[1] Mangel, W.F., McGrath, W.J. et al. Viral DNA and a viral peptide can act
as cofactors of adenovirus virion proteinase activity. Nature 361: 274-275
(1993).
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[2] Mangel, W.F., Baniecki, M.L., and McGrath, W. J. Specific interactions
of the adenovirus proteinase with the viral DNA, an 11-amino-acid viral
peptide, and the cellular protein actin, CMLS, Cell. Mol. Life Sci. 60:
2347-2355 (2003).
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[3] Ding, J., McGrath, W.J., et al. Crystal structure of the human
adenovirus proteinase with its 11 amino-acid cofactor. EMBO J. 15: 1778-1783
(1996).
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[4] Jorgensen, W.L., Chandrasekhar, J. et. al. Comparison of simple
potential functions for simulating liquid water. J. Chem. Phys. 79: 926-935
(1983).
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[5] Laxmikant, K.R., et al. NAMD2: Greater scalability for parallel
molecular dynamics. Journal of Computational Physics 151: 283-312 (1999).
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[6] Cornell, W.D., Cieplak, P. et al. A second generation force field for
the simulation of proteins, nucleic acids, and organic molecules. J. Am.
Chem. Soc. 117: 5179-5197 (1995).
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[7] Onufriev, A., Bashford, D., Case, D.A. Exploring protein native
states and large-scale conformational changes with a modified
generalized Born model. Proteins (2004).
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[8] Pearlman, D.A., Case, D.A. et. al. AMBER, a computer program for
applying molecular mechanics, normal mode analysis, molecular dynamics
and free energy calculations to elucidate the structures and energies of
molecules. Comp. Physics Commun. 91: 1-41 (1995).
Last Modified: January 31, 2008
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Claire Lamberti
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