Sculpting proteins with a virtual chisel

COMPUTER CORNER

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OCTOBER 1996

allow Sculpt TMto be very fast and therefore, to be used interactively- the number of calculations is proportional to the number of atoms (not to the cube of the number of atoms, as would be the case with a more rigorous algorithm). You can see what the molecule is 'doing' as you change the structure, including a graphical and numerical estiUse a Macintosh to do molecular mod- others) of any size, but at above about mate of the energy of the whole system. eling? Even a year ago I would have 80 amino acids, its performance drops Sculpt TM also displays local energy by scoffed, but times have changed. to about one update per second on a lighting up hemispheres of VDW radii Moore's Law (which states that CPU PowerMac 8500 (120MHz, 604 PPC when the atoms involved begin to interpower doubles and prices halve every processor; about equal to the 200 MHz, act strongly (repulsion shown by red, 18 months) and some recent software R4400 MIPS processor in many SGIs). attraction, by blue; see Fig. 1). have given me pause. The processing When modeling very large molecules, Homology modeling, As the number of power previously available in high-end interactive speeds can be maintained entries of the Brookhaven Protein Data workstations (and even aging super- by 'freezing' the molecule and 'thawing' Bank (PDB) increases, homology modelcomputers) is now packed into Macs (doing the calculations for) only those ing2 (see also, http://expasy.hcuge.ch/cgiand PCs, and authors are starting to parts that you are currently modifying; bin/seqanalr-search.de?HOMOLOGY) write programs that can tap this power you can also thaw by proximity; for ex- is becoming more popular as a way to for useful work. ample, 'thaw within 20 of 236' will thaw estimate the structures of proteins reOne such program is Sculpt TM from all atoms within 20]~ of residue 236. In lated by sequence to solved structures. Interactive Simulations (contact infor- handling typical ligands and small pep- This involves threading the new semation can be found at either: tides, real time, interactive speeds quence onto the coordinates of the http://www.intsim.com or sculpt@intsim. could be supported by any PowerMac. close relative whose structure has been coin). Sculpt TMis an interactive molecuForce fields, In order to understand solved and then rationalizing the differlar modeling program for PowerMac (re- how SculpU Mworks, you have to know ences in sidechains, insertions and viewed), Windows (95, NT) and Silicon a bit about force fields, how they are deletions, in much the same way that Graphics, which is both exceptionally represented in Sculpt TMand what liber- an ill-fitting suit is snugged and looseasy to use and surprisingly powerful ties Sculpt TM takes with them. As this ened on a mannequin of the correct The first time I saw SculptTMin action a article is for the bench scientist rather proportions (except that in this case, few years ago was thoroughly amazing: than the computational chemist, I'll the mannequin is modified to fit the tickling my retina was a 20-residue describe it briefly and refer you to the suit). Sculpt T" is particularly invaluable peptide being tugged into a different original (quite readable) paper for a in this process, because of the ease and configuration, energy-minimized in real complete description 1. speed with which it is possible to set time. Impossible?! The author, Mark The force field that models molecular and test alternative structures. Surles, convinced me it was indeed interactions is composed of a series of possible, but it did require a powerful terms for each atom describing the Other features, present or missing platform on which to run it - a Silicon various forces that act on it. Sculpt TM SculpffM allows you to do standard Graphics (SGI)workstation; this power (like many such programs) views these graphical operations on the model such is now hidden in the PowerMac on your forces as a series of springs and angles as zoom, pan in X and Y, do orthogonal desk, at a quarter of the price of the SGI. that connects and influences the sur- or perspective views, change the viewrounding atoms. In Sculpt TM, when you ing slab width, move the model through What Sculpt TM does tug on an atom using the mouse, you ef- the slab, and view in split-screen stereo. While Sculpt TM allows you to freely fectively attach a 'virtual spring' to the It also allows some standard Mac operturn the computer-generated model of a atom, which has the magnitude and di- ations such as copy and paste (mainmolecule in three dimensions, in much rection you supply with the mouse. The taining three-dimensional information the same way performed by other visu- resultant integration of all the forces re- for a number of programs), and the alization tools [RASMOL, MAGE, Foldit, sults in the movement of the tugged recording of QuicktimeTMmovies at one SwissPdbviewer and others*, Sculpt TM atom and the atoms influenced by it. frame per screen update, a useful teachalone does one very significant thing: it Simplification. Sculpt TM simplifies the ing tool much like a Kinemage [a graphiallows you to pull the structure of the force field considerably. It considers cal data format used by Protein Science model into different shapes directly by covalent bonds as rigid, so they are (http://www.prosci.uci.edu)]. 'tugging' at the atoms themselves. therefore not considered in the force You can explicitly group residues (by Sculpt TMalso does local minimization of calculation. It ignores VDW forces con- secondary structure, for example) and both van der Waals (VDW) and electro- tributed by atoms more than 6A away manipulate them as units, very useful static forces in near real time. It can, in from the atom under consideration. It when you are trying to rough out a theory (and with enough RAM), handle also uses a linear cut-off for the effects structure, but maintain certain conmolecules (nucleic acids, proteins and of close atoms, instead of calculating straints. You can superimpose one the complete Lennard-Jones equation. structure over another by linking homFinally, it ignores the contribution of ologous atoms; SculpU M will bring the *These and related programs are described and two structures into alignment based on further referenced at: http://hornet.bio.uci.edu/ electrostatic forces from atoms more ~bjm/projects/tibs_scutpt.html) than 10]k away. These simplifications the tie points. However, it will not give

Sculpting proteins with a virtual chisel

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you a numerical estimate of the similarity, such as an RMS difference. One feature I would like to see, is the ability to color residues by specification (by polarity, by hydropathy, etc.) as is possible with RASMOL, Setor, and Insightll*. As SculptTM considers only local interactions (<10 ]k), it cannot be used as a tool to verify large scale structural assignments. Such reverse-folding analysis has to be done outside of Sculpt TM with a tool such as the Profiles3D method 3 (which does not yet exist in a Mac form). Also, Sculpt TM buys speed at the expense of accuracy and obtaining a careful minimization is not as easy as clicking a 'Now do it carefully' button. You must export the structure to another program and minimize it there. Sculpt TM is primarily a tool for model-building, not verification, and there are very few programs that give you both in one package on any platform for less than several thousand dollars. The interface of Sculpt TM on the SGI platform is spare (or elegant, depending on your preference) - menu items are few, complex commands must be typed and the keyboard and mouse are needed in combination to control tugging, zooming and panning. The Macintosh version has been made considerably more intuitive: you click on buttons to select the mode (retained until another is selected), much like you would in a drawing program. Mac Sculpt TM also retains some of the SGI's command line interface to specify residues to group, freeze or thaw, selectable using a menu.

SculptTM Chem3DTM. Sculpt TM

used with ChemDrawTM and The current version of does not allow you to modify

molecules; unfortunate in such an otherwise remarkable program. However, to address this, Interactive Simulations has bundled the Cambridge Software Suite (ChemDraw TM and Chem3D TM) with Sculpt TM, SO that you can build and modify molecules to submit to Sculpt TM. Although suspicious of such interprogram gymnastics, 1 found it was remarkably easy to use them in concert. ChemDraw TM uses a vector drawing approach to sketching molecules as you would on paper. Copy and paste them into Chem3D TM and they are given three-dimensional attributes (although you might have to correct stereochemistry). Copy and paste that model into Sculpt TM and you are ready to minimize. It is surprisingly fast. In a fortuitous coincidence, a colleague wanted my help in making figures for some glutamate agonists and

Figure 1 Screen shot of SculptTM 2.0. Part of the backbone of a 202-residue protein is shown; only non-carbon, heavy atoms of the sidechains are shown. The green lines are force vectors being applied to the oxygen at their vertex. The red dot and line hemispheres (of van der Waals radii) indicate repulsive forces between atoms, blue indicates attractive forces. Purple lines indicate hydrogen bonds. The icons at upper left set the manipulation modes; the green bar at bottom indicates local energy. The set of icons at the bottom simplify complex commands and call up online help.

antagonists. From tearing off the shrinkwrap to presenting him with twodimensional and (SculptTM-minimized) three-dimensional images of seven molecules took about three hours. I estimate it would now take me about five minutes per molecule.

SwissPdbViewer. In

this

context,

a

notable (and free) program is SwissPdbViewer*. It is the only Mac program I have seen that allows you to mutate amino acids on screen. You can select a residue in three dimensions with the mouse and immediately change it to another residue, although the new sidechain is not placed in favorable configuration (a situation calling for a program just like SculptTM). Data can be exchanged with Sculpt TM through a PDB file, although not by the more convenient 'cut and paste'. Teaching, As a teaching tool, Sculpt TM is one of the best ways I have seen to teach students about how molecules interact. There are several tutorial data sets included with Sculpt TM, all of which are arresting and intuitive (included in the free, working demo). One of these tutorials is nothing more than several water molecules tightly packed as the file is opened. Click on an oxygen, apply a tug and the whole field

explodes to reasonable separation distances. Drag an ion through the field of water and watch how the water molecules rearrange and realign in response. To summarize, with 'minimization off', Sculpt TM iS a very fast, model building tool, allowing you to twist a protein chain into place intuitively and with tremendous ease, applying multiple threedimensional forces on the molecule at once. With 'minimization on', it allows you to do considerable error checking and experimentation before you dedicate a long minimizer run for more accurate analysis, or even worse, dedicate graduate students to follow up an idea requiring several thousands dollars of reagents and hundreds of their hours.

References 1 Surles,M. C., Richardson,D. C., Richardson,J. S. and Brooks, F. P., Jr (1994) Protein Sci. 3, 198-210 2 Blundell,T. L. et al. (1988) Eur. J. Biochem. 172, 513-520 3 Luethy, R., Bowie,J. U. and Eisenberg, D. (1992) Nature 356, 83-85

HARRY MANGALAM Developmental and Cellular Biology, School of Biological Sciences, UC Irvine, Irvine, CA 92697, USA.

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