84
BIOCHEMICAL E D U C A T I O N
would be happy to answer any questions readers might have concerning the tmplementatmn of this type of exercise m their laboratory program as well as indicating the types of cases we utdlze and some of the reference sources for the case h~stortes
REFERENCES i Saffran, M , J Med Educatmn 46, 1080 (1971) ZRubmstem, D , J Med Educatmn 47,198 (1972) 3Biochemical Education 3, 23 (1975) 4Macqueen, D , Chlgnell, D A , Dutton, G J , and Garland, P B , Medical Educatmn 10,418 (1976) SPearlmutter, A F , and Pearlmutter, F A , Biochemical Educatmn 5, 5 (1977) SBaggott, J , Lawrence, D M , Shaw, F , Galey, M , and Devhn, T M , J Med Education 52,157 (1977) 7Schwartz, P L , J Med Educatmn 50, 903 0975) BKarlson, P Biochemical Education 5, 1 (1977) 9Smith, A D , and Jepson, J B , Lancet, 2,585(1972) X°Berner, E S , Hamdton, L A and Best, W R , J Med Educatmn 49,666 (1974) lipalva, I P , Br J Med Educatmn 8, 52 (1974) ~2Blanchaer, M C , Biochemical EducaUon 3, 71 (1975) i3The Effective Climclan, Tumulty, P A , Saunders, Phfladelphm, PA, 1973 ~4fnterpretatmn of Dmgnostic Tests, second e&tion, Wallach, J , Little, Brown and Company, Boston, 1974 iSBiochemical Profiling m Dmgnostic Medicine, Preston, J A , and Troxel, D B , Technicon Instruments Corporation, Tarrytown, NY, 1971
P R O T E I N M O D E L S m A SIMPLE S T U D E N T EXERCISE
October 1978
Vol. 6
No. 4
t6ITatchle, R F , PaUent Care, May 15, 1974, 2 iTWard, P C J , Human Pathology 4, 47 (1973) ieReece, R L , and Hobble, R K , Amer J Clm Pathology 57, 664 (1972) igRamirez, G , Dram, R C , and Pnbor, H C , Comput Biol Med 2, 39 (1972) 2°Beeler, M F , Southern Med J 70, 1425 (1977) ZHnterpretation of Biochemical Multitest Profiles, Wolf P L , Masson Pub U S A , lnc , NY, 1977 22Practical Chnical Enzymology Techmques and Interpretation and Biochemical Profiling, Wolf, P L , Wilhams, D , Von der MuehU, E , John Wdey & Sons, NY, 1973 Z3The Metabohc Basts of Inherited Disease, fourth e&tion, Stanbury, J B , Wyngaarden, J B , and Fredrickson, D S , Editors, McGraw-Hall Book Company, NY, 1978 24Illustrated Dmgnosis of Localized Diseases, Collins, R D , J B Lippmcott Company, Phfladelphm, 1974 ZSlllustrated Diagnosis of Systemic Diseases, Collins, R D , J B Lappincott Company, Philadelphia, 1972 26Diagnotes, Lufkln Medical Laboratories, P O Box 629, Mmneapohs, MN, 55440, U S A 27Diagnostic Enzymology, Coodley, E L , editor, Lea & Febiger, Phdadelphia, 1970 ZeThe Bin-Science Handbook, llth e&hon, Bio-Science Laboratories, 7600 Tyrone Ave , Van Nuys, CA 91405, 1975 29Modern Urine Chemistry, Ames Company, Division Miles Laboratories, Inc , Elkhart, IN, 46514, U S A , 1976 3°Chmcal Chemistry m Diagnosis and Treatment, second e&tion, Zilva, J F and Pannall, P R , Year Book Medical Pubhshers, Inc Chicago, 1975
W U N G - W A I TSO Department of Biochemistry C h i n e s e U m v e r s l t y of H o n g K o n g
MAN-YIN W O N G Radioisotope Umt Umverstty of Hong Kong A three-dlmensmnal perspective of large complex molecules is essentml to an understanchng of bmchemlcal mechanisms In the past, many scientific workers (e g ref 1-3) have attempted to bring out a three dimensmnal perspective m two &mensional print using either Xograph or special stereoscopic wewers However, a complete detaded representation of molecular structure often demands a three dimensional model rather than a two dimensional picture Hence structural models, such as the space-fdhng type, the skeletal type, a combination of the space-fflhng and skeletal type as well as the pop-up type have been employed with success as aids m the visual presentatmn of the structural features and functional aspects of macromolecules4-7 For research purposes where a high degree of precision is reqmred, very often the space-filhng model is used The constructmn of this type of model has many disadvantages Not only are the matermls used for construction expensive, but also the constructmn procedures involved are very tedious Hence these types of models are hmited to the use of experienced scientific workers Moreover, a space-fdhng model suffers from the lack of transparency and unusually heavy weight6 Other types of models too have their drawbacks such as the need for auxiliary support and the inapplicability to complicated molecules 5 7 8 At present, we have developed in our laboratory a simple, colorful and attractive model which has none of the disadvantages mentioned above The bud&rig of this model requires only inexpensive and readily avadable materials This model we feel is most suitable for class demonstrations and student exercises at the undergraduate level The aim of this device is to encourage students to build their own models thus achieving the goal of learning the three-dimensional perspective from their own creations
Materials and Constructural Procedure 1 Colored Dymo tapes 9 m m width and each approximately 35 mm in length are employed to depict each of the 20 common Lamino acids Commercially 18 colors are avadable but addmonal codings can be obtained by marking the tapes w~th waterproof black ink as ln&cated in the table In practice, light colors are chosen for the hydrophdlc amino acids and dark colors for the hydrophobic ones For a protein of known primary structure, the number corresponding to the position in the sequence of each of the amino acids is embossed on the tape Usually, the colorations employed are adequate for all the amino acids listed m the table, but for beginners, addmonal one-letter amino acid symbols may also be included (see table) 2 White rubber coated electrical wire of great flexlblhty Is used as the backbone of the model Consequently the transparent Dymo tape which represents serine becomes white on this chosen backbone The length of the wire used is approximately 9 mm x the number of amino acid residues in the protein to be constructed Starting from the N-terminus, each Dymo tape representing the corresponding amino acid in the sequence is wrapped around the electrical wire backbone one after the other 3 The completed decorated colorful wire can then be looped according to published three-dimensional illustrations 2 If electrical wire of great flexlbdlty is used then a model such as this can reveal detads of secondary and tertmry structures In general, the thicker the rubber coating is, the less flexible is the wire for looping in model building 4 To prevent the Dymo tape from separating from the wire after looping, strips of thin polyethylene are used to wrap around the whole model In addition, corresponding cysteine residues were
BIOCHEMICAL EDUCATION
October 1978
"pa3xed u p " by the polyethylene strips so as to show the location of a disulfide bond 5 Since the model thus constructed depicts only the polypeptlde skeleton, the side chaans of the cratacal amino acids m the actwe sites can be further designated with the aid of "BluT a c k " clay This can be done by stackang a piece of the clay onto the corresponding amino acid to be emphasized
Features of the Model In this simple student exercise model, all the crucial amino acid residues and their positions can be easdy tdenlahed This is dehmtely an Improvement over the flag-hanging methods commonly used m three-thmensional model braiding 9 The model has an additional advantage m that the spahal location of the residue within an active site can be wsuahzed at a glance Furthermore, for compact molecules with many loops, the hght colored tapes which represent the hydrophdlc residues tend to exist predominantly on the surface as expected from the nature of protems l0 Figure 1 shows a lysozyme model built by a student using the method described above In this hgure we can see that m order to further dlustrate the action m e c h a m s m of the enzyme, a marker pen representing a lysozyme substrate was placed on the cleft of the lysozyme model Consequently, the two amino clds on the active site, glutamlc acid (at poslhon 35) and asparttc acid (at posRion 52) are m line with the glycoslthc bond (represented by the boundary of the two colors on the pen) on the substrate to be broken As a whole, the constructed model is colorful, mfurmalave, comprehensive and easdy c a m e d around for demonstration purpose As an exercise, students can be divided into groups, each assigned to work on a protein of known structural detads When the whole class has become enthuslashc about model building with wire and colorful tapes, the students are respired and ready to use their own models for learning more three-dimensional detads m biochemical reaction mechanisms
Vol. 6.
No. 4
85
Table 1 Color codes of the Amino acids
A m i n o acid
One-letter symbol
Color code
I A h p h a t w amino acids
Glycme Alanme Vahne Leucme Isoleucme
G A V L I
Day glow green Grey Ohve green Deep green Blue
S T
Transparent Yellow
Aspartic acid Asparagme* Glutamtc acid Glutamme"
D N E Q
Sliver Silver with strapes Gold Gold with stripes
IV Basw amino acids Lysme Argmme Hlstldme
K R H
Day glow red Orange Red
Y F W
Black Brown Purple
II Hydroxy amino acids Serane Threonme III Dwarboxyhc amino acids and derivatives
V A r o m a t w amino acids Tryptopban Phenylalanme Tyrosme
VI Sulfur-containing amino acids Cysteme C Methiomne M VII I m m o acid Prohne
P
Red with embossed stripes Blue with embossed strapes Wood
~Marked strapes are used for asparagme and glutamme, other colors are all commercially available
REFERENCES
Figure 1
Model of lysozyme with "substrate" budt by a student
Biochemical Nomenclature Documents, 1978
and
iHarte, R A , and Rupley, J A , J Blol C h e m , 243, 1663 (1968) z,,Cold Spring Harbor Symposia on Quantitative Biology", Cold Sprang Harbor Laboratory, Cold Sprang Harbor, New York, 1972, Vol XXXV1, Plate I - X X l X 3Dtckerson, R E , and Gels, I , "The Structure and Act,on of Proteins", Harper and Row, New York, 1969, p 70 4North, A C T , Blochem Educ , 1, 24 1973), Sebastian, J F , and Butkus, J C , J Chem E d u c , 52, 660 (1975), Clarke, F H , J Chem Edue , 54, 230 (1977), Huebner, J S , J Chem Educ , 54,171 (1977), Strong, C L , Scl Amer , 234, No 1,124(1976) SSmlth, I , Blochem Educ , 1, 9 (1972) SGurd, F R N , Blochem Educ , 2, 27(1974) ~Brown, B S , Blochem Educ , 2, 24 (1974) 7Walton, A , Progress in Stereochemlstry, 4,335 (1968) 9,,Cold Spring Harbor Symposia on Quantltahve Biology", Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1972, Vol XXXVI, p 132 I°Dlckerson, R E and Gets, I , "The Structure and Action of Proteins", Harper and Row, New York, 1969, p 73
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