Guide t Using the Rubric t Scre the Myc/Max ON-SITE Build Mdel fr Science Olympiad 2011 NATIONAL Turnament These instructins are t help the event supervisr and scring judges t use the rubric develped by the MSOE enter fr BiMlecular Mdeling when scring the 2010 2011 Science Olympiad Natinal On Site Build Mini Tber mdels f Myc and Max, based n 1nkp.pdb. Each categry n the rubric is addressed within these instructins and is accmpanied by a shrt descriptin and picture, if apprpriate. Overview f the Mlecule: lr de: Magenta alpha helices Gray lps Blue tip N terminus Red tip terminus terminus; terminus; α helix #2; α helix #2; 1nkp.pdb has tw chains in it is Myc and is Max. Order f Secndary Structures Fr bth A and B chains: N terminus α helix #1 Turn α helix #2 terminus α helix #1; α helix #1; N Terminus; N Terminus; 1
1. Blue cap n N terminal Amin Acids (Glu897 () and Asp202 ()) (1 pt per end cap, fr a ttal f 2 pts) T receive credit, this mdel shuld have tw blue caps psitined t identify the N terminus f each f the tw chains in the prtein. Fr bth chains, the blue cap needs t be lcated at the N terminus f the prtein, which is lcated at the end f the shrter f the tw helices in this prtein. Please see the figure t the right fr the crrect psitining f the blue end caps. The mdel shuld receive 1 pt fr each crrectly placed blue end cap. If a blue end cap is near the lnger f the tw alpha helices, then the mdel des nt receive credit fr this feature. N Terminus 2. Red cap n terminal Amin Acids (ys984 () and ys284 ()) (1 pt per end cap, fr a ttal f 2 pts) Terminus T receive credit, this mdel shuld have tw red caps psitined t identify the terminus f each f the tw chains in the prtein. Fr bth chains, the red cap needs t be lcated at the terminus f the prtein, which is lcated at the end f the lnger f the tw helices in this prtein. Please see the figure t the right fr the crrect psitining f the red end caps. The mdel shuld receive 1 pt fr each crrectly placed red end cap. If a red end cap is near the shrter f the tw alpha helices, then the mdel des nt receive credit fr this feature. 2
3. Mdel has 4 alpha helices accrding t Jml selectin criteria; 2 helices n each chain (1 pt per helix fr a ttal f 4 pints) T receive these pints, there shuld be 4 helices within the mdel. Please see figure t the right fr the crrect lcatin f these helices. (Helices are clred magenta n the mdel and n the figure t the right.) Deduct 1 pint fr each extra helix. Fr example, if a mdel has 5 helices, then the mdel wuld receive 3 pts rather than the full 4 pints. 4. Alpha helices are right handed (1 pt each; ttal f 4 pts) Alpha helices are right handed. heck each alpha helix in the mdel t cnfirm that the helix is right handed. Fr each right handed helix, the mdel shuld receive 1 pint, fr a ttal f 4 pints if all fur helices are crrect. T determine if the helix is right handed, find ne f the ends f the helix and imagine that the helix is a spiral staircase. Pretend that yu are climbing that staircase and yu need t have a handrail and the helix is the hand rail, which is always n the utside edge f the staircase. If yu wuld put yur right hand n the tber as yu g up the staircase, yu have a right handed helix. If yu wuld put yur left hand n the tber, yu have a lefthanded helix and the mdeled helix wuld nt receive the pints. Left handed vs righthanded helices 5. Alpha helices are f the crrect length. (1 pt each; ttal f 4 pts) Helix #1 n bth chains shuld have apprximately 9 10 turns. Helix #2 n bth chains shuld have apprximately 11 12 turns. Each helix that is the crrect length shuld receive 1 pt. 3
Items #6 #13 refer t the 3 dimensinal shape f the mdel. The psitining f the secndary structures is very imprtant t the verall 3 dimensinal fld f the prtein. Prteins are nt flat; therefre the mdel shuld have a 3 dimensinal lk t it. 6. rrect psitining f Helix #1 and Helix #2 n relative t ne anther (2 pts) Hld the mdel s that N termini are pinting dwn and the termini are pinting upward. Please see figure t the right fr prper rientatin. cnsists f tw helices separated by a small turn. T receive credit fr this feature, shuld be arranged s that the terminus f Helix #1 is psitined higher than the N terminus f Helix #2. In the figure t the right, has been clred gray and nly the helices n chain A are clred magenta. N 7. rrect psitining f Helix #1 and Helix #2 n chain B relative t ne anther (2 pts) Hld the mdel s that N termini are pinting dwn and the termini are pinting upward. Please see figure t the right fr prper rientatin. cnsists f tw helices separated by a small turn. T receive credit fr this feature, shuld be arranged s that the terminus f Helix #1 is psitined higher than the N terminus f Helix #2. In the figure t the right, has been clred gray and nly the helices n are clred magenta. N 4
8. Helix #2 n wraps slightly arund Helix #2 n t frm leucine zipper (2 pts) Hld the mdel s that N termini are pinting dwn and the termini are pinting upward. Please see figure t the right fr prper rientatin. Helix #2 n each chain shuld wrap arund each ther t frm a leucine zipper. Helix #2 n chain B (clred white n the image t right) is wrapping arund Helix #2 n chain A (clred green in figure). The N terminus f Helix #2 n chain B (clred white in image t right) starts n the right side f the mdel and the terminus f the helix is n the left side f the mdel and slightly behind Helix #2 n chain A (clred green in image t right). N If the mdel has the tw helices wrapped arund each ther several times, then the mdel shuld nt receive credit fr this feature. 9. Leucine zipper has a left handed twist (1 pt) Hld the mdel s that N termini are pinting dwn and the termini are pinting upward. Please see figure t the right fr prper rientatin. terminus The tw helices frm a left handed twist. Each helix shuld be right handed (see Rubric Pint 4 fr an explanatin f right vs left handed helices), but when the tw helices intertwine with each ther, they frm a left handed twist. 10. N termini are psitined far away frm ne anther (1 pt) Hld the mdel s that N termini are pinting dwn and the termini are pinting upward. Please see figure t the right fr prper rientatin. The tw N termini (indicated by blue caps) shuld be psitined apart frm ne anther. Helix #1 n each chain interacts with DNA, therefre these helices (and thus the N termini) shuld be far enugh apart that a mlecule f DNA culd fit between these helices. The N termini shuld be psitined arund 6 inches away frm each ther. If the N termini are psitined very clse t ne anther (less than 2 inches apart frm ne anther), the mdel shuld nt receive credit fr this feature. N terminus 5
11. termini are lcated near ne anther as part f the leucine zipper (1 pt) Hld the mdel s that N termini are pinting dwn and the termini are pinting upward. Please see figure t the right fr prper rientatin. The tw termini (indicated by red caps) shuld be psitined very near t ne anther. The termini shuld be apprximately an inch apart frm ne anther. If the termini are psitined very far way frm anther (mre than 3 inches apart frm ne anther), the mdel shuld nt receive credit fr this feature. 12. The lp/turn between helix #1 and Helix #2 n bth chains are ppsite f ne anther t frm handles n the quarternary structure (1 pt) Hld the mdel s that N termini are pinting dwn and the termini are pinting upward. Please see figure t the right fr prper rientatin. The lp regin cnnecting Helix #1 and Helix #2 n each f the chains shuld extend ut away frm the helices. In the image t the right, the handles are clred green (chain A) and yellw (chain B). The N terminus (beginning f the handle) shuld be psitined higher (clser t Helices #2 n each chain) than the terminus (end f the handle). The end f the handles shuld be psitined clser t Helices #1 f each chain. Handle ; terminus Handle ; N terminus 6
13. rrect psitining f 4 sidechains (Arg914 and Arg215; Leu967 and Leu267) (4 pts) The prvided amin acids shuld be psitined crrectly within the sequence f the prtein (Arg914 at psitin 914 n chain A, Arg215 at psitin 215 n chain B, Leu967 at psitin 967 n chain A and Leu267 at psitin 267 n chain B). (0.5 pt fr each sidechain crrectly psitined at the right lcatin in the prtein; ttal f 2 pts) Arg914 and Arg215 are psitined in the middle f Helix #1 n their respective chains. Leu967 and Leu267 are psitined apprximately 2/ 3 up the helix, near the termini n their respective chains. The amin acids shuld als be riented crrectly within 3 dimensinal space. (0.5 pt fr each sidechain crrectly riented; ttal f 2 pts) Arg914 and Arg215 shuld be facing the center f the V created by helices #1 n hains A and B. This prtein is a transcriptin factr that interacts with DNA and these Arg residues plays a rle in that DNA/prtein interface. Therefre, the sidechains fr Arg914 and Arg215 shuld be pinting utward, away frm the prtein, as if it might bind with smething else. Leu967 and Leu267 interact with ne anther in the leucine zipper. These sidechains shuld be facing each ther and be psitined ppsite f ne anther n the tw chains, as if frming the zipper teeth. Please see figure t the right and the physical mdel fr prper lcatin and psitining. Leu267 and Leu967 Arg215 and Arg915 7