the computer bulletin b o a r d A Tutorial in Macromolecular Modeling Gale --...Rhades .... -. University of Southem Maine Portland, ME 04103
I have prepared a tutorial in mauomolecular graphics using widely available programs on Macintosh computers. Students who complete this tutorial- appropriate for use i n a n undergraduate biochemistry class or lab-are equipped to obtain and study all available crystallographic and NMR models of proteins, nucleic acids, and other biomolecules. Instructors mav acouire the tutorial and all necessary files and programs over the Internet, at no cost. Althoueh the tutorial is written for the Macintosh. a few of my stcdents obtained the Windows versions of 'the programs and carried out all their work on their own or campus PC-compatibles. They encountered a few minor differences but had no problems completing all the exercises.
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MAGE and PREKIN Some vears aeo. - . I introduced mauomolecular modeline.. as a regular part of my biochemistry lab course, using a RISC workstation. and research-level modeline software. Although I was happy that the students were ]&ing the tools of molecular graphics, I had the troubling suspicion that most of them never again would encounter either this program or this computer. In fact, some were intimidated by the complexity of the software and the unfriendliness of the UNM system. With the appearance of the programs MAGE and PREKIN, conceived a n d developed by J a n e and David Richardson of Duke University (1, 21,I found an attractive, user-friendly alternative that students can continue using beyond my course. MAGE displays are called kinetic images or kinemages. They include, in three separate display windows, iext, fi& captions, and figures in the form of interactive computer graphics. Kinemaaes are olain text files created usine PREKIN. which egtracts atomic coordinates from fil& available from the Protein Data Bank (3. 4 ) a t Brookhaven National Laboratory. Users can open P R E K I N - C I ~files ~~~~ with a word nrocessor and add text or c a ~ t i o n that s will appear in t h i appropriate windows in M ~ G E . MAGE, the display program, and PREKIN, its file-preparing companion, are available for both Macintosh and Windows o~eratinesvstems. in versions that are practically identical froma ker's point of view. Current versions are fast, robust, and tolerant of other programs in RAM. They are revised regularly to maintain compatibility with new releases of operating systems. Macintosh 68040 computers give fast, smooth-rotation and zooming, even with 100 or more atoms on the screen. What is more, the programs, instruction manuals, and sample kinemages-are available without charge over the 1nternet.l You may disIMAGE. PREKIN, and all related files for Macintosh are contained in the file MAGE-allsea available by anonymous FTP from orion.oac.uci.edu.
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Journal of Chemical Education
edited by
RUSSELH. BATT Kenyon College Gambier, OH 43022
tribute the programs freely or make them available over campus networks without a site license. In time for the Fall 1994 offering of my biochemistry lab course, I wrote a tutorial that guides the new user through a study of the structure of the enzyme lysozyme, using MAGE and PREKIN on Macintosh computers. The current version incorporates many helpful suggestions from my students. Designing a Tutorlal My stratem in desipning .. .. molecular modeling tutorials is to prepare step-by-step written procedure-that guides students through a study of an interesting small protein. I organize the study to give them experience with most of the tools in the modeling program. I hope that when students have comoleted the tutorial. thev have ( 11 learned a lot about a ty&cal protein, and'hence reinforced their classroom knowledee about omtein structure in eeneral. and (2, learned a 10; about th'e modeling program ;self, b i usine most of its ca~abilitiesand sceine the results of all the commands. ln'addition, I hope &at students find themselves equipped to start from scratch-that is, from a raw Protein Data Bank (PDB) file-and study any biomolecule that may interest them. For most students, a biomolecule is more interesting than a graphics program and can sustain interest and attention while providing repetitive practice. In my opinion, the best subiect for introducing modelii in a firshemester biochemi s t j course is a smali protein (140 residues) that includes a bound ligand (cofactnr or inhibitor), and most of the common elcments of secondary smcturc. I prefer a protein that is introduced, but not extensively covered, by the text I use in INture, so that students &discover sGctura1 features for themselves. Because much of my lab course is built around the e n m e Ivsome. " , I chose as the subiect of mv tutorial a complek of l$sozyme and the trisacch&de inhigitor tri-Naeetylchitotriose, or tri-NAG (3.
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Contents of the Tutorlal The tutorial consists of three sections: (1)An introduction to atomic coordinate files in Protein Data Bank format. Students use Internet tools tanonymous FTP) to obtain the PDB file PDBlHEW.ENT. which contains the coordinates of the lysozyme/tri-NAG complex, from the Brookhaven Protein Data Bank. Using a word processor, they read the "header" of introductory information to learn how the structure was determined and where it was published. They also learn to determine how many subunits or models are in the file, what non-protein ligands are present, and what residues are involved in disulfide bonds, alpha helixes, sheets, and turns. Finally, they examine the ATOM lines that contain atomic coordinates of each atom, and they see how all atoms are named and numbered. This prepares them to understand the labels that appear in modeling programs when the user selects snecific atoms and makes measurements of distance and geometry. (2) An introduction to the oroeram PREKIN. Usine the PDB file as input, students REKI RE KIN to prepare b e mage files for later viewing and modification with MAGE. Contents of the files include a ribbon diagram of the pro-
the computer bulletin board tein chain, the alpha-carbon backbone with disulfides and tri-NAG. all main-chain atoms and hvdroeen bonds. and all amino-acid side chains in separate sets-for instance, the set of all alanines. or the set of all ~lutamines-thatcan be turned on and off separately in M ~ ~ . (3) A tour of MAGE, in which students studv structure and bonding in the l y s & y m e / t r i - ~complex.-A6 ~~ the students work through the tutorial, they discover many structural details for themselves. For instance, they are required to find all hydrogen bonds between tri-NAG and &ozyrne main-chain or side-chain atoms. In doing so, they learn how to apply chemical, distance, and geometric criteria to recoenize noncovalent interactions in a comnuter model. The-tutorial directs students to employ the kajority of MAGE tools: display buttons, to turn specific parts of models on and off;rotating, centering, and zooming; z-slabbing, to control the display of background and foreground atoms; viewing in stereo and learning the important skill of using stereo without a viewer; labeling atoms and displaying their coordinates; measuring distances, bond angles. and dihedral aneles. to discover hvdroeen bonds and " other interactions; drawkg lines to represent bonds not shown a u t ~ m a t i c a l lsuch ~ as motein-lieand bonds: runing, to eliminate unwanted atoms fromyhe display; Ereating useful vicws and addine them to the displav . . menu: and sanng modified kinemage;. To complete the tutorial and reinforce newly acquired skills, I assign each student another small protein to study, using what they learned from the tutorial about how to explore a protein using PREKIN and MAGE. Then I ask them to write a report on the protein, illustrated with kinemages. They model their report after introductions to specific proteins in their biochemistry text. This follow-up assienment has the added advantaee of satisfvine our de" partment's requirement that all upper-division lab courses include at least one maior writine a s s i m e n t . in addition to routine lab reports.
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Several other introductions to MAGE are available. The Internet MAGE package (5) includes t h e file Demo3Xxa.kin, which introduces some of MAGE's display possibilities. In my tutorial, this file gives the students their first taste of MAGE functions. The Internet package also includes the file Cookbook.kin, a very brief introduction to PREKIN. A MAGE-based ancillary to Moran and Scrimgeour:Biochemistry (6, 7)contains the file Intmkin, which introduces the basics of viewing prepared files in MAGE. Finally, the kinemage supplement to Branden and Tooze: Introduction to Protein Structure (8,9) contains the file clBasic.kin, which introduces a few MAGE functions and ~rovidesan excellent interactive studv of ~ o l v o e ~ t i d e conf&mation. While all of these introduc&ons are useful and of hieh aualitv. none of them eive beeinnine students everything tiey need to become i;depenient explorers of macromolecular structure. includine an introduction to PDB files, hands-on experiknce a variety of disd a v files with PREKIN. and ex~lorationwith MAGE that eon%ncingly shows the'power of graphics for discovering details of molecular structure.
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How to Obtain the Tutorial
To obtain this tutorial with full instructions for teachers, set your W W W browser to gopher://gopher.usmacs.maine.edu:70/lle%3A/usm/chem and download the file MAGE.RTF. Tt)use Gopher instead, set a Gopher Journal of Chemical Education
Acknowledgment
Thanks to the students in the Fall 1994 section of my biochemistry laboratory for helping me to test and improve the tutorial. Macromolecular scientists and teachers everywhere should be grateful to Jane and David Richardson and to the management of The Protein Society, publishers of Protein Science, for free access to the excellent programs MAGE and PREKIN. Their efforts make it feasible to bring to every desk and classroom the vast resources of the Protein Data Bank. I can recall no greater single step forward for the teachine of macromolecular science. Editor's Note: versions of MAGE and PREKIN for PC comvuters running Windows V3.1 or ereater are contained in the self-expanding file MAGE.EX~obtainable as indicated in (5). Llterature Cited 1. Richardson,D. C.; Richardson,J. S. Rot. Sci. lm.1, a. 2. Richardson.D. C.: Richardson.J. S. &nda in Biahem S d 1984.19.13~138 3. Bemstein, b C.; E&tZle, T. F-wlliams, G. J. B.; Meyer, Jr,E. I?; Brice, J. R.;Rods. em.R.:Kennard. 0.:Shimsoouchi. T:T u s a m i M J . Mal. Bid. 1977.112.635542.
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6. Cheetham,J. C.;Artymiuk,PJ.;F'hiUipa.D.C. J. Mol. Bid 1998,224,613, 6. Moran, L. A ; Scz5mgrimsur.K G. Biahemisfry; Neil Psttermn: Englewod Cliffi, NJ, 1991. -~ I. Morao, L. A ; Scrimgwur, K G. Exploring M o k u l a r S m r c ~ r (lrinlrinage . supplement);Neil Patteram: Englewad Cliffa, NJ, 1994. 8. Blanden, C.; Iboze, J. Intmdudnn t o h t e i n Strudum; Garland: New York,1991. 9. Richardson, D. C.; Richardson, J. S. The Kimmzga Svpplemonf to Intmdution to Pmhin Struturn: Garland: New Y e 1991. ~
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The Sharp Electronic Organizer-A Warning
Other lntroductlonsto MAGE
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link to gopher.usmacs.maine.edu and open, in succession, the folders Campus Information by Department and CHEM. Then open the file MAGE.RTF and save it. Import the file with ClarisWorks (for best results) or other word processors. Send a message t o t h e a u t h o r a t rhodes~sm.maine.eduifyourunintotroub1e.
Thomas A. Eaton
Division of Science and Mathematics St. Thomas University 16400 N.W. 32nd Ave. Miami, FL 33054 The Sharp Electronic Organizer, Model YO-llO,34KB is a must for all scientists, engineers, and professionals. It has a calendar to remind you of birthdays, holidays, anniversaries, appointments, meetings, etc., and a schedule to help organize your day. There is a memo section to store jokes, quotations, equations, or whatever using the alphanumeric keypad. And with 34kB of memory, about half that of a Commodore, TRS 80 or Apple 11, it fits neatly into your pocket, the size of a pocket calculator. It has a port to interface with instruments, printers, or other microcomputers. No, this isnVta paid testimonial, although I'd be glad to write one in exchange for an electronic organizer and interfaces to my instruments and microcomputers. This is a warning to other chemistry professors to check your students' pocket calculators. I found this electronic marvel durine an exam in mv eenera1 chemistry class last week. ~ct&lly,I'd been &-the lookout for such devices for the vast w u ~ l eof vears. when students began to use the tbree-iich screen grapihia &leulators.They made me uncomfortable because one of mv tvDical organic chemistry exam questions is to draw a p~tentiaien-
