Hippo

A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.

Hippo is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard openMP).

Download

Binaries will be publicly available from the Biowerkzeg.com download page for Linux, Windows, and Mac OS X (Intel platform only). For immediate access to beta-versions please email martin-AT-ulmschneider.com.

Features

Simulation methods

• Molecular dynamics (MD) in NVT, NPT, NVE ensembles
• Metropolis Monte Carlo (MC) in NVT and NPT ensembles JACS2004,JPhysChemB2006
• Replica exchange with MD and MC

Force fields

• OPLS-AA Jorgensen1996,Kaminski2001

Solvation models

• explicit solvent (water: TIP4P Jorgensen1985, SPC Berendsen1981)
• Generalized Born implicit solvent (GB/SA)
• Generalized Born implicit membrane (GB/IM) Proteins2007,BJ2007,Proteins2005

Enhanced productivity

A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes:

• seamless restarts
• intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology

Analysis

Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the translation+rotation energy scan analysis tool).

A growing number of analysis tools are built into Hippo, for instance

adiabatic translation+rotation energy scan

determines the Generalized Born energy of a peptide in a membrane MMB2008,BJ2006; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state

RMSD

calculates the root mean square deviation of trajectory frames to a reference structure

helicity

degree of helicity of segments along trajectory

Z - tilt - kink graph

Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. Cordes2002

cluster

Performs a cluster analysis using the pairwise method by Daura et al.Daura1999

fit to phase

recenters trajectory on the centre of mass of a phase (such as a lipid membrane)

fit solute to previous frames

Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame.

The Hippo output format is a binary xyz-movie (see the definition of the xyz format); thus many other analysis tools can also be used.

References

<biblio>

1. MMB2008 pmid=18428040
2. Proteins2007 pmid=17600830
3. BJ2007 pmid=17218457
4. BJ2006 pmid=16339877
5. JPhysChemB2006 pmid=16913813
6. Proteins2005 pmid=15723347
7. JACS2004 pmid=14871118
8. Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B, 105(28):6474–6487, 2001. 10.1021/jp003919d.
9. Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc., 118(45):11225–11236, 1996. 10.1021/ja9621760.
10. Jorgensen1985 W. L. Jorgensen and J. D. Madura. Temperature and size dependence for Monte-Carlo simulations of TIP4P water. Mol. Phys., 56(6):1381–1392, December 1985.
11. Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. Interaction models for water in relation to protein hydration. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981.
12. Cordes2002 pmid=12417206
13. Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. Peptide folding: When simulation meets experiment. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. 10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M.

</biblio>