Looking at Molecules—An Essay on Art and Science

  • Published on
    06-Jun-2016

  • View
    213

  • Download
    0

Embed Size (px)

Transcript

  • ESSAY

    ChemBioChem 2003, 4, 1293 1298 DOI: 10.1002/cbic.200300747 2003 Wiley-VCH Verlag GmbH&Co. KGaA, Weinheim 1293

    Introduction

    As you leaf through the pages of thisjournal, you will be presented with allmanner of illustrations. The fields that wework inchemistry, biochemistry, molec-ular biologyare particularly amenableto illustration. After all, most of our workboils down to understanding the arrange-ment of atoms in space. So, we usesketches, illustrations, and advanced com-puter graphics to examine our particulararrangement of atoms, and to present ouratoms to other researchers and to thepublic.

    Take a moment to think about howamazing this is. We are able to synthesizepictures of the arrangement of atoms inmatter, both animate and inanimate. Weare revealing an invisible world, where theconcept of vision has no meaning, in away that is interpretable by our senses.

    Tools of the Trade

    Today, manipulation and illustration ofatomic structure is fast, easy, and remark-ably fun. The computer forms a facileinterface to atomic data (of which there isenough for a lifetime of exploration),allowing us to delve into structures,compare them to others, and ultimatelycreate pictures of what we have discov-ered.

    If you are a chemist, you will be dealingwith hoards of chemical diagrams. Fortu-nately, there is a long tradition of how torepresent these diagrams. Even more

    fortunately, these diagrams are codifiedto a sufficient extent to allow computersto understand the rules. By sticking to thistradition, every chemist will understandyour atoms and their covalent connec-tions. We even can use some shorthand tosimplify these already parsimonious dia-grams: the familiar hexagon with a circleinside represents a more complex under-lying aromaticity, we don't have to put aC at every carbon position in a hydro-carbon, and often, we don't even have toshow the hydrogens at all. Turn-key soft-ware running on personal computersallows us to churn out clear, preciseversions of these diagrams.

    If you are a biochemist, you will prob-ably be dealing with larger fish, so you'llneed to use a bigger hook. Protein andnucleic acid structures have hundreds orthousands of atomseach essentialsowe need advanced tools to look at them.Over the years, researchers and illustratorshave tried many ways of simplifying thesestructures. The goal is to simplify therepresentation to make the picture moreinterpretable, throwing out informationthat is not needed. We have to be careful,though, not to throw out too much, or thepicture will be useless. This is the artistryand pedagogy of molecular illustration.

    Three basic representations, shown inFigure 1, have withstood the test of time.Covalent diagrams, such as wireframes orball-and-stick diagrams, are direct exten-sions from the chemical tradition, show-ing the underlying chemistry of themolecule. Everything is there for theexploring, but often it can be too much,and the image becomes a sprawl ofoverlapping lines. Spacefilling represen-tations (and other surfacing or solventaccessible variants) combat this sprawlby obscuring all interior detail. Thesediagrams look at the size and shape ofmolecules, and are great for thinkingabout interactions between different

    molecules. Their strength, however, is alsotheir major limitation: they are the bestway to show the shape of the moleculebut all of the interesting connectionsinside are hidden. Ribbon diagrams roundout our representational bag-of-tricks.They strip away all of the distractingatomic information and present the to-pology of a protein or nucleic acid chain.Ribbon diagrams are arguably the mostbeautiful of the representations, and thusfind their way into most popular accountsof biomolecular structure. When you thinkof the structure of DNA, the familiarladder diagram, first shown in that famousNature paper,[1] is the picture that comesto mind. Today, you can find the curlyprotein ribbons and arrows on the coverof nearly any journal.

    Researchers are Doing It forThemselves

    Molecular graphics software is availableoff the shelf, so today many images ofmolecules are created in the laboratorywhere they are being studied (Figure 2).These programs range from basic molec-ular viewing to advanced rendering. Myfavorite place to start is the programRasMol (links to all of the softwaredescribed in this section may be foundat the Protein Data Bank: http://www.pdb.org). With two clicks of themouse, you have a molecule on thescreen and you can start exploring. Otherpopular programs, such as Molscript andRaster3D, allow the creation of high-quality images for publication. They re-quire a bit more practice, but the resultsare well worth the effort.

    Because interactivity is so important inbiomolecular graphics, clever researchershave also developed a number of power-ful methods to incorporate interactivefigures into publications and presenta-

    Looking at MoleculesAn Essayon Art and ScienceDavid S. Goodsell*[a]

    [a] Prof. D. S. GoodsellDepartment of Molecular BiologyThe Scripps Research Institute10550 N. Torrey Pines Road, La JollaCA 92102 (USA)Fax: (1) 858-784-2860E-mail : goodsell@scripps.edu

  • D. S. Goodsell

    1294 2003 Wiley-VCH Verlag GmbH&Co. KGaA, Weinheim www.chembiochem.org ChemBioChem 2003, 4, 1293 1298

    tions. David and Jane Richardson pio-neered the approach with the programMage. It allows authors to create akinemage, an animated, interactive fig-ure. The reader is given some basic free-dom to interact with the figure, but notand this is importanttotal freedom. Theauthor designs the kinemage to pave theway for the reader, picking the bestrepresentations to display the particulartopic at hand, and removing options thatmight cause the reader to get lost.

    More recently, the Chime plug-in forNetscape has moved interactive molec-ular graphics into the world wide web.With Chime, authors can place interactivewindows into web pages, allowing per-fect integration between interactive ex-ploration of the structure and any explan-atory text or links to other sites.

    State-of-the-Art

    Molecular graphics is an active field,undergoing significant changes. A majorthrust in current development is to im-prove the modularity and reusability ofgraphics methods. The idea is to create acollection of modular tools that can beconnected together to perform customfunctions. We no longer create ponder-ous, monolithic programs that do every-thing, instead, we take an atomic co-ordinate manager and have it feed data toa molecular dynamics tool, and hook it upto a molecular viewer so we can watchwhat is happening.

    For example, Michel Sanner is using thePython programming language as theglue to connect these diverse modules.[2]

    He has created a visual programming

    Figure 2. Amazingly powerful molecular graphics programs are available on personal computers. A snapshotof RasMol (http://www.bernstein-plus-sons.com/software/rasmol) in action is shown here. It allows interactivemanipulation of this enormous ribosome structure, which includes nearly a hundred thousand atoms, and avariety of options for coloring and representation. With RasMol and other similar programs, molecularstructures are at anybody's fingertips. Coordinates were taken from entry 1jj2 at the Protein Data Bank.

    Figure 1. Ever since the first protein structure wassolved, researchers have looked for ways to displayand explore these complex molecules. Today, threebasic representations are commonly used. The first,shown at the top, is a modification of traditionalchemical diagrams that uses lines or cylinders toshow the covalent structure of the molecule. This isthe workhorse of biomolecular research, and isparticularly useful when viewed on an interactivecomputer graphics system, allowing manipulationof the three-dimensional image. The spacefillingrepresentation, shown in the middle, was designedby Linus Pauling[5] to reveal the bulk of themolecule. If we were able, somehow, to see amolecule, we might expect it to look something likethis (without, perhaps, the shiny highlights!).Ribbon diagrams, codified for proteins by JaneRichardson,[6] radically simplify the structure,showing the topology of the chain and revealingregions of specific secondary structure. These areideal for thinking about protein folding andevolutionary relationships. These imageswere created with the Python Molecule Viewer(http://www.scripps.edu/~sanner/python/pmv), byusing coordinates from entry 1mbn at the ProteinData Bank (http://www.pdb.org).

  • Looking at Molecules ESSAY

    ChemBioChem 2003, 4, 1293 1298 www.chembiochem.org 2003 Wiley-VCH Verlag GmbH&Co. KGaA, Weinheim 1295

    environment that allows the networkingof different modules to form customapplications. The use of Python is thekey advantage over previous data net-work methods (such as AVS), because itallows, with modest coding effort, thewrapping of other applications to allowthem to communicate their results to thenetwork. The center of this network isPMV, the Python Molecule Viewer, whichtakes care of all of the graphics tasks.Figure 3 shows an example of using aWWW-based service to direct the render-ing of molecules. In other applications,symmetry information, molecular dynam-ics, electrostatics, quantum mechanics,and many other sources of data havebeen linked into the networks.

    Molecular Models

    Wooden or plastic ball-and-stick modelsplay an indispensable role when teachingabout covalent bonding and stereochem-istry. These modelsan adult form ofTinkertoysprovide hours of fun andinsight. But until recently, physical modelswere limited to the world of chemistry.

    Snap-together models get too unwieldywhen you try to build trypsin or aribosome.

    Researchers are now borrowing tech-nologies from engineering to create phys-ical models of proteins and large molec-ular assemblies. These technologies weredesigned for rapid prototyping, to buildand test car parts and the like. They buildup a model one layer at a time bysquirting on tiny dots of molten plastic,by cutting and gluing together layer afterlayer of paper, or by gluing down thinlayers of gypsum powder with an ink-jetprinter. After a little programming, three-dimensional printers are now being usedby biologists to provide a tangible alter-native to computer graphics. The result isa perfect three-dimensional model of anydesired molecule (Figure 4). These modelsare irresistible: researchers and studentsalike are finding that it is impossible notto handle and explore them.

    Collaboration with an Artist

    Now that these exciting tools are availableon our desktop, why would a scientist

    need to go to an artist? Desktop molec-ular graphics are superb for the represen-tations that they are designed to create,but only for those. Artists are essential incases where the subject is just too com-plex for routine graphics. Artists figuredprominently in the first few decades ofprotein structure, when scientists andreaders struggled to understand for thefirst time the complex three-dimensionalarrangement of atoms of myoglobin andlysozyme. The collaboration of Irving Geisand Richard Dickerson is a milestone:working as one, they created illustrationsthat brought this new world to life.[3]

    In other cases, the artist/scientist col-laboration can benefit both the imagebeing created and the science beingpresented. A perfect example is theillustration by Graham Johnson, shownin Figure 5. He was approached by RonVale to create a picture showing thecurrent state of knowledge of motorproteins. Graham was able to synthesizestructural information frommany sources:from atomic structures, ultrastructuralinformation from microscopy, and, forsome pieces, simple molecular weights.These are combined into a coherent,interpretable picture, with very little fab-rication. The animations by Drew Berry(Figure 6), or my own paintings of mole-

    Figure 3. A visual programming environment is used to link services on the WWW with a molecular viewer.Here, a WWW-based resource, ConSurf, provides values for evolutionary conservation of amino acids in aprotein. They are then used to modulate the color of the chain representation in the Molecular Viewer. TheNetwork Builder allows many different options to be explored: pulling in data from a variety of resources andusing it to modulate any of the parameters of rendering. Figure provided by Michel Sanner, the ScrippsResearch Institute.

    Figure 4. Rapid prototyping methods are beingused to create physical models of large molecules.This model of chymotrypsin (notice the deep, darkspecificity pocket) was created by using machineryfrom Z-Corporation. The machinery lays down thinlayers of gypsum powder and sprays on coloredglue with an ink-jet printer, building the model uplayer-by-layer from bottom to top. The hand-sizedmodel allows direct, tactile exploration of theprotein structure.

  • D. S. Goodsell

    1296 2003 Wiley-VCH Verlag GmbH&Co. KGaA, Weinheim www.chembiochem.org ChemBioChem 2003, 4, 1293 1298

    cules in cells (Figure 7) are other examplesof the utility of this approach.

    Note that this process is a two-waystreet. The collaboration is an opportunityfor the scientist to compile an exhaustiveset of information: after all, Grahamneeded to know what information wasavailable for every part in each structure,and Drew needed to know where andhow fast the parts of the polymerase wereacting. The artist/scientist collaborationforces us to reveal both the parts that arewell understood, and the parts thatrequire further scientific scrutiny.

    One Size Does Not Fit All

    Today, we can easily turn out colorful,accurate illustrations to support our re-search projects. These are perfect toaccompany our journal articles, but wemay run into trouble when we move toother audiences. We often make themistake of using the same imagery whenfaced with less technical audiences, andlose their interest in the process. The

    Figure 6. Drew Berry tackled the challenge ofanimating a DNA replication fork in action. Based onthe many atomic structures of the players, heassembled this model of the DNA replisome. As withall complex models, parts are based firmly in data,and parts, such as the geometry of the polymerases,primases, and clamps in the overall complex, are stillthe subject of speculation and study. Since the overallprocess -most notably, the discontinuous primingand replication of the lagging strandis modeledaccurately, the animation is an excellent teachingtool. It is also a boon to science, forcing researchersto look at all of the steps in this process, and developtests to decide if Drew's particular model is com-pletely correct.

    Figure 5. Ron Vale went to Graham Johnson tocreate this atlas of motor proteins for an article inCell.[7] This is a challenging task, since parts of theseproteins are known in great detail, and parts are lesswell defined. After digging up all currently-availablestructural data, Graham developed a style thatshows high detail where warranted and smootherrepresentations for domains and coiled-coils whereonly amino acid sequences and molecular weightsare known.

  • Looking at Mol...

Recommended

View more >