rotactors. Once you type in and correct the conrdinates, PICFILEMAKER suves them as a disk file, then srales the coordinates for the display program I'ICSYS-64, and saves the scaled set. PICSYS-64 loads scaled coordinate files and disnlavs . a high-resolution line drawing of the structure, either as a stereo pair (Fig. 1)or as a full-screen single view. The program displays the stereo pair for convergent viewing (3);that is. vou cross vour eves to s u ~ e r i m ~ o the s e views and see a three-dimensional idage. YO; can ;mily modify the display for divergent viewing, but then the views must be closer together, smaller, and thus at lower resolution. From the PICSYS-64 menu, you can rotate the model into any orientation. When you find an instructive view you want to save, PICSYS-64 creates a new scaled file in which this view is the default. In the mono viewing mode, you see one view of the stereo pair just as it will be printed. You can label the N and C termini and every tenth alpha carbon with depth-cued lahels, and you can add a figure legend. Then the SAVE PICTURE routine saves the full-screen memory map of each view of the stereo pair, properly positioned for side-hyside printing. he program STEREOPRINT loads these bitmaps and prints a stereo pair automatically (Fig. 21, using commands to the Grappler CD interface. You can also dump the maps to a ~ r i n t e by r standard screen-dump routines, but scaling. and positioning for stereo are not automatic. The PROTEIN SYSTEM 64 disk contains these three Droerams. documentation. at least 15 structure files. and the . .. 1'AI'F:RCI.IP 64 word processor file of a 20-page user's manual. There is mace on the disk fur Sunerhasic-64 and forsurh useful utilities ns Commodore's DOS wedge. I envision these uses of PROTEIN SYSTEM fi4 in undergraduate biochemistry classes and labs: 1) A simple means of studying protein conformations. Students can disdav or print sh%ures and learn t o recognize helical and sheet regions and larger structuralfeatures. 2) A source of illustrations for handouts and exams. On tests, I often ask students, to examine a stereo view of an unfamiliar protein and describe its structural features. With PROTEIN SYSTEM 64, I have a large source of such pictures and I am not limited to published views. 3) An aid in building models. Students in
PLASTDCYAWIH
my biochemistry laboratory select a protein for a conformational study and build a bent-wire model. Stereo views from PROTEIN SYSTEM 64 are excellent guides during the bending. 4) A simple introduction to molecular graphics. Computer graphics has almost completely replacedphysical models for fitting chemical models t o electron-density maps and for studvine conformations and interactions. " " nrotein . Because the programs in PROTEIN SYSTEM 64 are entirely in the BASIC language, you can see precisely how they use the coordinate set to produce a picture of the molecule, and how tbev mani~ulatethe coordinates to scale and rotate the structure. So these programs can be for you and your students what they have been for me: afirst step in understanding molecular graphics. All of these programs are heavily commented and easy to modify. The Commodore 64 is the cheapest commercially successful computer for which a protein graphics system is available. Among inexpensive computers, i t has the highest resolution for bitmapped graphics-320 by 200 picture elements. In addition, the Commodore 64 is quite fast, even in BASIC: PICSYS-64 rotates 100 atom coordinates in under five seconds. At current hardware prices, you can bring three dimensional screen displays and prints into your class or lab for less than $700. The PROTEIN SYSTEM 64 disk and manual are available from Project SERAPHIM on a SI4-in. disk. ~
Computer Simulated Metabolism: A StudentInteractive Program Lawrence J. Tirri and Peter W. Jurutka University of Nevada, Las Vegas Las Vegas. NV 89154 In biochemistry courses students are first introduced to metabolism through a study of the glycolytic and citric acid cycle pathways. This study usually includes discussions of the reactions and their mechanisms. Students mav studv these reactions diligently hut many experience some difficulty in understandina the factors affectine the flow of carbon through a seriesof reactions in apathwiy. In particu-
PLASTOCYAWIW
Figure 2. Stereo print of poplar plastocyanin(4)producedby STEREOPRINT with an midata 92 printer andGrappler CD parallel interface. The two views are arranged for divergent viewing with a stereo viewer.
Volume 63 Number 12 December 1966
1071
lar, how changes in metabolite concentrations andlor enzyme activities result in changes of other metaholite concentrations. The program desciihed here simulates &olvsis and oxidative phosphorylarion. It is written in FORTRAN VERSION 5 for usc.nn the CDC CYRER 172 mninfrnmennd run in the time-sharing mode. I t is menued and user friendIv. The . oroeram is interactive and allows the student user to " alter the parameters of certain zero-time metabolite concentrations and/or enzvme activities. Metabolite concentrations are computed as a function of time and are displayed next to control Darameter concentration values. The student user can see the effects of the parameter changes made during the computer experiment in a matter of minutes. This program is named GARFKEL in honor of David Garfinkel, University of Pennsylvania, a pioneer in computer metaholic simulation. GARFKEL is based upon the computer model reported by Garfinkel and Hess (5).I t is designed to compute the concentrations, in molesfliter, of each metaholite in the pathway a t microsecond time intervals using a Taylor expansion
In this equation C represents the concentration of a metaholite, t the time, d t the time increment of one microsecond, and k the rate constant. After cycling through a user-determined number of iterations i t will store the concentration values of each metaholite in storage arrays. The program then aoes throueh an additional 24 sets of iteration cvcles and fils the storage arrays with data representing concentrations of each metaholite a t 25 equally spaced time intervals. The time interval is determined by multiplying the number of iterations hv one microsecond. All concentrations are reset to the values for time zero. The student user is then presented with a menu of possible parameter changes in concentrations andlor enzyme activities (see Fig. 3). After entering the desired changes the program repeats the simulation, computes, and stores a new set of metaholite concentrations a t the same time points. Menus oromnt the student user to select the format to display thk computed data. Several options are possihle. A concentration data list for a single selected metabolite could he displayed andlor agraph produced. Data lists for both the original and altered set of parameters are disnlaved or minted.-The listing for each metabolite contains the zerd time concentration, the elapsed time for each of the 25 time points including their respective concentrations, and relative concentration values (RCV). The RCV is obtained by dividing each concentration by the zero time concentration value. This normalizes the data and provides convenient values for the graphing routines. Both sets of data are listed andlor graphed side by side for convenient comparison. Alternatively, data for all metabolites can he displayed as: 1) a data list followed by a question asking if a graph is desired; 2) a data list and graph; 3) all data graphed with no data listing. Options 2 and 3 are convenient when used with continuous-feed printers. The data plots are produced by a modification of a subroutine published by Dwight Tardy, University of Iowa (6),and used with his permission (7). 1his graphing rnutinc was selected because i; could produce a plot on n standard data terminal and would not require a special printerlplotter. Figure 4 is a representative example of data plotted by this program. Before a student is nermitted to interact with GARFKEL. the instructor shouldkxplain the fundamental design of the program and give the student a listine of the menu of rate : help the student get ionitant and concentration changes. T started the instructor should suggest a number of possible changes. The student is asked to consider these changes one at a time. Based upon his or her current understanding of metabolism the student then predicts the results of the parameter change or changes. For example, the student is ~
..
1072
Journal of Chemical Education
8 INC. P H Q S I H O I R U C T O X I W I S I L o w . s ~ u c r a o ~ r ~ a s kcrrvirr ~~~rr 9 oec. masmmtucmurs*se s INC. P R U C T O D I P H D S P H * T A S E LCTIYITY 10 I N C . P Y R U Y L T E X I N A S E ACTIVITY L 1 DEC. F Y X U V A T E Y T N A S E ACTIVITY 12 I N C . I O X Y G E N I 6 DEC. OX-PHOS ACTIVITY
s~
Figure 3. The program's menu. which lists the rate MnSlant and concentration changes.
2.360
+....+....+....+....+....+....+....+....+....+,...+
-.39
.79
(I * X 1 S ) X I O ' . TllE POINTS
~~~~~
L.96 L
-
TIHE P O I N T S 1 - 2 5 TIME P O I N T S 2 6 - 5 0 -
THERE A R E 100
3.!d
(Y *XIS)XIO"
6.31 -2
R E L A T I Y B CONCENTRATION
5.69
VALUES
O L D PARAMETERS WBW PARANETERS
~ICROSECONDS
BETYEEN rlne
porsrs
Figure 4. The program-producedplot of ConcenVationvalues for GLUCOSE-& PHOSPHATE versus time using old control parameters end altered new parameters. The time intewai between the time points is 100 microseconds. Total time required tocompile, execute and print Mis plot is 5 min. The altered new parameters are as follows: DEC. [ATP] 8 INC. [ADP]: [ ] ONLY DECREASED HEXOKINASE ACTIVITY INC. PHOSPHOFRUCTOKiNASE & DEC. FRUCTODIPHOSPHATASE ACTIVITY DEC. PYRUVATE KiNASE ACTIVITY
asked tonredict what effect. if anv. adecrease in ATP and an increasein ADP concentrationswould have on the rate of glucose-6-phosphate synthesis. He or she then runs GARFKEL and compares his or her predictions with the program's calculated results. At first, some students will need guidance. However, after students have been helped through a few computer experiments they should be canable of working on their own.. It should be emphasized that the goal of this uroeram is to use a working metabolic model as means t ~ - ~ r & i dstue dents an opportunity to test their understanding of the metabolic pathways. The data computed by this program, using altered parameters, was never intended to provide a simulated metaholic modelof anvin uiuo or in uitro resoirinesvstem . .. . and should not br considered as such. This program and the Garfinkel and Hess t . 5 ~model upon which it is hajed doesnot
a
include feedback or allosteric regulation. This is a desirable feature because it permits the student user the opportunity to alter those concentrations andlor enzyme activities in a way consistent with feedback or allosteric regulation. Although, GARFKEL is written in FORTRAN VERSION 5 for use on the CDC CYBER 172, i t should he compatible with any FORTRAN 5 or FORTRAN 4 complier. Minor modifiraticmx in statement and inpur-output formnttin$ may he required to run CAllFKEL on other systems. The nroaram uses douhlr urecision and reauires 75K hvtes 172. he (60 Gitsiyte) of memory u;hen run on the ~ Y B E R arravs are for data storaee " onlv and not used for data oroceasing. 'l'ht. initial metaholite concentrations and rate constantsare thosedesrribed by Carfinkel and Hesj 151. For the second set of computed data, where changes are made in concentrations and/or rate constants, values are usually changed by a factor of 100. However, the program can be modified and these values as well as the initial values can he changed by any factor desired. A source listing of GARFKEL is available from Lawrence J. Tirri, Department of Chemistry, University of Nevada, Las Vegas, Las Vegas, Nevada 89154. Write for additional information regarding the availability of this program on magnetic tape or floppy disks. Acknowledarnent -
The authors are grateful to the University of Nevada System Computin~Center and tu Sally A. Jarmow, user liaison, for their Galuable support and assistance in the development and operation of this program.
Interfacing an EM-360 NMR with an Apple lle Computer James C. Swailz and John T. Creed Thomas More College Crestview Hills, KY 41017 We have interfaced an Apple IIe microcomputer with our Varian EM-360 NMR spectrophotometer. This system, which was assembled as a senior research project, permits us to demonstrate data collection, signal averaging, data storage and retrieval, data analysis, and data manipulation. Similar interfaced systems have been reported 6 9 ) ;however, the one described here is significantly simpler with respect to the required hardware and software. The hardware consisted of an Apple IIe microcomputer with one disk drive, an ADALAB interface card1, a difference amplifier, an inverting amplifier, an X-Y plotter or Y-T Recorder, and a Varian EM-360 NMR spectrophotometer. The Varian EM-360 NMR is a relativelv simnle instrument to understand with respect to the mechanisms for scannine and recordine of spectra. The maenetic field sweep. by a potekometer that for the EM-360, is connected directlv to the X-axis of the NMR recorder, thus as the pen is moved across the X-axis by astepper motor, the magnetic field is automatically chanced. It require3 1000 p&es from the sweep time circuit t o t h e stepper motor to cover the entire range from 0 to 10 ppm. The magnetic field sweep, generated by the potentiometer, is a ramp that varies from about -3.10 V a t 10 ppm to 0 V a t 0 ppm. After each of the 4000 pulses, the Y-axis value (spectrum amplitude) is plotted on the recorder (10). An NMR spectrum can he recorded and stored by a computer, if after each of the recorder's 4000 X-axis positions the computer can measure and record the Y-axis value. On the EM-360 NMR, the Y-axis (spectrum amplitude) is ac-
' ADALAB is a trademark name of Interactive Microware Inc., P.O.
Box 139. State College, PA. 16804.
cessed through connector P 4 (the oscilloscope connector) located a t the rear of the instrument console. This was connected directly to the AID converter on the ADALAB interface card. Writing a program to collect the Y-axis value after each of the 4000 X-axis pulses is an extremely difficult task because the timing of the data collection by the program must perfectlv coincide with the seauence of the 4000 pulses for the x-axis. This problem can be solved if the computer either generates or controls the magnetic field sweep, and thus controls the X-axis values. Control of the X-axis was accomplished by minor modification of the EM-360 and the construction of the difference and inverting amplifiers, Figure 5. T o control the X-axis, it was necessary for the computerto generate a 4000-step ramp that ranged from -3.10 V to 0 V. The ADALAB interface card had a 12-hit (212or 4096 steps) D/A converter which was nearly ideal for producing the appropriate ramp. A major problem with the D/A converter was that its signal was symmetrical +2 to -2 V, as opposed to the needed values of -3 V to 0 V. The DIA converter was connected to a difference amplifier (which had a 2-V reference) and then to an inverting amplifier. By using avariable resistor in the circuit as the feedback resistor on the inverting amplifier, i t was possible t o vary the ramp from -3.10 to 0 V. The output from the inverting amplifier was then connected to the magnetic field sweep of the EM-360 via a single-throw-double-pole toggle switch. The field sweep potentiometer. which eenerates the maenetic field sweep. is located at the left rear of the recorder cf you are standing in front of the console) and can onlv he accessed hv removine the console cover. T o make the connection hetwien the inverting amplifier and the magnetic field sweep, you must unsolder thk wire connected tothe "wiper"of the fikld sweep potentiometer and then connect this wire to the middle post of the SPDT switch. A wire was then soldered to the "winer" of the field sweep potentiometer and connected to either of the remaining posts on the SPDT switch. Finally, the inverting amplifier is connected to the remaining post on the SPDT switch. With the SPDT toggle switch in position 1, the EM-360 will operate as usual. In position 2, all the controls on the EM-360 willoperate, hut the Y-axis (pen) will not respondas the pen carriage is moved left or right. The Y-axis is still connected, hut the X-axis has been disconnected and the magnetic field sweep is no longer controlled by the recorder of the EM-360. Instead i t is controlled by the computer. The actual program for signal averaging is extremely simple (less than 20 BASIC lines). The initial step is the dimensioning of arrays and configuring the ADALAB interface card. Using a loop, the X-axis is generated using the DIA converter and the Y-axis value is recorded using the A D converter. When all the data has been collected. it is "mani~
~~~
DIFFERENCE AMPLIFIER
~
~~~~~~~~~~~
~
.~
INVERTING AMPLIFIER
Figure
5. Schematic diagram for difference and inverting amplifiers. This Circuit is used to convert the +2-(-2)voltage of the D/A convertertoa (-3t0
wit ramp.
Volume 63
Number 12
December 1986
1073
