1. Parastou Sadatmousavi§, & Ross C. Walker*
Calculating Activation Pathways of Adenovirus Protease Enzymes Using the Amber Molecular Dynamics Package on TeraGrid Resources
Parastou Sadatmousavi§, & Ross C. Walker*
San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA,
Method
Results
To predict the activation pathway of the Adenovirus Protease enzyme, the Nudged Elastic Band (NEB) method implemented within the Amber 11 package is being used. The calculations are being run on TeraGrid supercomputers.
NEB Background
In nudged elastic band (NEB), the minimum energy path for a conformational change is quantified with a series of images of the molecule describing the path. The images at the end points are fixed in space. Each image in-between is connected to the previous and next image by “springs” along the path that act to keep each image from sliding down the energy landscape onto adjacent images. The pathway represents the trajectory that a molecule follows through the conformational change and this pathway can be derived independently of the timescale of the conformational change (e.g. Figure 2). Along the direction of the path, the force on each image is governed by virtual springs that serve to fix the position of each image relative to the adjacent image so that the images follow the path. Perpendicular to the path, each image responds to the potential of the energy landscape as determined by the force field. The total force, F, is then:
where, N is the number of atoms per image, Fi is the force on image i, Pi is the 3N dimensional position vector of image i, ki is the spring constant between image i-1 and image i, V is the potential described by the force field, and ζ is the 3N dimensional tangent unit vector that describes the path.
Simulations run to date on the TeraGrid have provided an initial activation pathway prediction. This shows the formation of a possible intermediate involving the catalytic histidine (HIS54). Figure 3 shows 5 key structures in this pathway. 1 2 3
Inactive
His 54 Move 1
His 54 Move 2
Adenovirus Protease Inactive form
Figure 1
Adenovirus Protease Active form
Predicted Key Structures in the Pathway of AVP activation
Figure 3 4 5
Introduction
A detailed understanding of the reaction and activation pathways of enzymes is critical to the development of next generation pharmaceuticals. The ability to target specific locations on the activation pathway of an enzyme provides promising targets for novel drugs. The development of low energy pathway sampling methods, such as the nudged elastic band algorithm, has provided a mechanism by which constrained molecular dynamics simulations can be used to determine and then study enzyme activation pathways on an atomistic level. This work focuses on developing these methods, which require substantial computational resources and tightly coupled parallel HPC machines, and applying them to the determination of the activation pathway of the adenovirus protease enzyme.
The adenovirus protease (AVP) is essential for adeno virus replication and thus is a target for antiviral drugs aimed at treating infections such as avian and swine‐flu. The enzyme is activated upon the binding of a small peptide via a 53 amino acid signal transduction pathway. Recently obtained crystal structures of both the inactive and active forms of AVP provide the two end points of this pathway. This poster highlights continuing efforts to determine this pathway computationally and then the identification of potential drug binding locations along this pathway. The high computational complexity of these calculations has meant that the use of the TeraGrid has been vital.
Helix Unfold
Tyr 84 Move [Active]
Future Work
Understanding the activation process of the AVP will potentially allow new drugs to be designed that target the inactive form of the enzyme and prevent it from being activated. Keeping the enzyme inactive is a better approach than attempting to inactivate the already activated enzyme.
We are running additional simulations to further refine our understanding the activation pathway.
§P. Sadatmousavi is an BS/MS student in the bioengineering department at UCSD. This work is being conducted as part of a summer research experience for undergraduates program at the University of California.
Acknowledgements This work was supported in part by grant 09-LR WALR from the University of California Lab Fees program and through TeraGrid cost sharing funds to SDSC. Supercomputing time for this project is being provided under TeraGrid Award TG-MCB
Collaborators
We are extremely grateful to Prof. Walter Mangel and Dr. Bill McGrath of Brookhaven National Laboratory for providing us with the crystal structures used in this work and for acting as our experimental collaborators. Prof Mangel has worked for many years on adenovirus protease enzymes and we are very grateful to be collaborating with him on this work.
Classical MM Phi-Psi Map (AMBER FF03)
Figure 2
End Point
Start Point
* Correspondence to: (