Guide to Using the Rubric to Score the Klf4 PREBUILD Model for Science Olympiad National Competitions

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1 Guide t Using the Rubric t Scre the Klf4 PREBUILD Mdel fr Science Olympiad Natinal Cmpetitins These instructins are t help the event supervisr and scring judges use the rubric develped by the MSOE Center fr BiMlecular Mdeling when scring the 2011 Science Olympiad Natinal Pre Build Mini Tber mdels f Klf4, based n 2wbu.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: Clr Cde: Magenta alpha helices Yellw beta strands Gray - lps Blue tip N-terminus Red tip C-terminus β strand #4 β strand #3 α helix #2 β strand #2 β strand #6 α helix #1 β strand #5 β strand #1 α helix #3 C Terminus N Terminus Order f Secndary Structures: N-terminus β-strand #1 turn β-strand #2 Turn α-helix #1 turn β-stand #3 turn β-strand #4 turn α-helix #2 turn β-strand #5 turn β-strand #6 turn α-helix #3 C-terminus

2 1. Blue Cap n N-terminal Amin Acid (Thr399) (0.5 pt) T receive credit, the blue cap needs t be lcated at the N-terminus f the prtein, which is lcated at the beginning f beta strand #1. Please see the figure t the right fr the crrect psitining f the blue end cap. If the blue end cap is by a helix, then the mdel des nt receive credit fr this feature. N Terminus 2. Red Cap n C-terminal Amin Acid (Phe483) (0.5 pt) T receive credit, the red cap needs t be lcated at the C-terminus f the prtein, which is lcated at the end f helix #3. Please see the figure t the right fr the crrect psitining f the red end cap. If the red end cap is psitined n a β-strand, then the mdel des nt receive credit fr this feature. C Terminus 3. Mdel has 3 alpha helices accrding t Jml selectin criteria (0.5 pt per helix fr a ttal f 1.5 pints) T receive these pints, there shuld be 3 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 0.5 pints fr each extra helix. Fr example, if a mdel has 4 helices, then the mdel wuld receive 1 pint rather than the full 1.5 pints. Three alpha helices

3 4. Alpha helices are right-handed (0.5 pt each; ttal f 1.5 pts) Alpha helices are right-handed. Check each alpha helix in the mdel t cnfirm that the helix is right-handed. Fr each right-handed helix, the mdel shuld receive 0.5 pints, fr a ttal f 1.5 pints if all three 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 hand-rail 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 left-handed helix and the mdeled helix wuld nt receive credit. Left handed vs righthanded helices 5. Alpha helices are f the crrect length. (0.5 pt each; ttal f 1.5 pts) Helix #1, Helix #2 and Helix #3 are apprximately the same length. Each helix shuld have apprximately 3-4 turns. Each helix that is the crrect length shuld receive 0.5 pints, fr a ttal f 1.5 pints. 6. Mdel has 6 β-strands accrding t Jml selectin criteria (0.5 pt per β-strand fr a ttal f 3 pints) T receive these pints, there shuld be 6 β-strands within the mdel. Please see figure t the right fr the crrect lcatin f these beta strands. (β-strands are clred yellw n the mdel and n the figure t the right.) β-strands need t be clearly distinguishable frm lps; there may be sme slight zig-zag flding f the tber t indicate the up-and-dwn psitining f the amin acids. Alternately, teams might clr-cde their beta strands t distinguish them frm lps r write n the tber indicating the lcatin f the β-strands. Please see phts belw depicting β-strands mdeled using tbers. If there are mre than 6 β-strands in the mdel, 0.5 pt shuld be deducted fr each extra strand. Fr example, if the mdel has 7 β-strands, the mdel shuld receive 2.5 pints, rather than the full 3 pints.

4 7. Psitining f secndary structures in prper rder (0.5 pt each; fr a ttal f 4.5 pts) T receive these pints, the sequence f the secndary structures shuld be in the fllwing rder: N-terminus β-strand #1 Turn β-strand #2 Turn α-helix #1 Turn β-strand #3 Turn β-strand #4 Turn α-helix #2 Turn β-strand #5 Turn β-strand #6 Turn α-helix #3 C-terminus Each secndary structure (helix r β-strand), if in the crrect rder, shuld receive 0.5 pt, fr a ttal f 4.5 pts. Secndary structures that are ut f rder shuld nt be cunted. Please refer t the figure at right, r t the physical mdel, t assist in scring the mdel. Items #8 - #12 refer t the 3-dimensinal shape f the mdel. 8. Mdel has 3 β-sheets (0.5 pt fr each sheet fr a ttal f 1.5 pts) This prtein has tw β-sheets arranged frm the 6 β-strands. A β-sheet is cmpsed f tw r mre β-strands lying parallel t each ther, thugh the plane f the β-sheet may be twisted instead f flat. β sheet #2 β sheet #3 β-sheet #1 is cmpsed f β-strands #1 and #2. β sheet #1

5 β-sheet #2 is cmpsed f β-strands #3 and #4. β-sheet #3 is cmpsed f β-strands #5 and #6. T receive credit, the mdel shuld have three distinct β-sheets. If the mdel has mre than three β-sheets, then deduct 0.5 pt fr each additinal sheet. Fr example, if the mdel has fur β-sheets, the mdel shuld receive 1 pt, rather than the full 1.5 pts. 9. Mdel has three distinguishable zinc fingers (0.5 pt each; fr a ttal f 1.5 pts) 2 A zinc finger is a cmmn structural mtif stabilized by the presence f a zinc in. In Klf4, this mtif is characterized by 1 helix and 1 sheet. Please see figure t the right illustrating a single zinc finger mtif fund in the Klf4 prtein. T receive these pints, the mdel shuld have 3 distinguishable zinc finger mtifs. Each zinc finger present in the mdel shuld receive 0.5 pt, up t 1.5 pts. Please see physical mdel and figure t the right t identify the three zinc fingers. 1 3 If a mdel has mre than 3 zinc fingers, deduct 0.5 fr each additinal zinc finger mtif. Fr example, if a mdel has 4 zinc fingers, the mdel shuld nly receive 1 pt, rather than the full 1.5 pts. 10. Zinc fingers are arranged t frm a V shape (1 pt) Hld the mdel s that the N and C-termini are pinting upward. Pleas see figure t the right fr prper rientatin. The three zinc finger mtifs shuld be arranged s that the mdel has a V shape. Please see physical mdel r image n the right. The N-terminus and the C-terminus shuld frm the tips f the V, with the 2 nd zinc finger frming the apex f the angle. If a mdel has all three zinc fingers in a straight line, the mdel will nt receive the pints. If the N and C termini are directly adjacent t ne anther (frming a hairpin lp, rather than a V), the mdel will nt receive credit fr this feature

6 11. The prtein is cmpact and flat (1pt) The Klf4 prtein is arranged such that the three zinc fingers lay in the same basic plane (see physical mdel r figure t the right). If yu place the mdel n a flat surface with the N-terminus psitined facing tward yu and the C-terminus is behind the N-terminus (see figure abve), then the mdel shuld nt have any prtins f the prtein extending far abve the table r cause the mdel nt t lie flat n the table. If a mdel has regins that prject abve r belw the table when lying n the surface, the mdel shuld nt receive credit fr this feature. 12. The zinc fingers are psitined crrectly next t ne anther (2 pts) Helix #2 The zinc fingers are psitined s that the turn between the sheet and helix f each zinc finger are pinting twards the helices f the previus mtif. Turn #5 shuld be pinting twards helix #1 Turn #8 Turn #5 Turn #8 shuld be pinting twards helix #2 Award 1 pt fr each crrectly psitined zinc finger. Helix #1 13. Students submitted a 3x5 card with explanatin f the mdel (2 pts) The 3x5 card submitted with the mdel shuld describe the mdel in terms f what additinal features have been added t the mdel s that the judge is nt left guessing what the mdel represents.

7 4. Creative additins t the mdel. (Nte that there are many pssible creative additins t this mdel; each creative additin is wrth 4 pints; teams may have mre than 4 creative additins, but may earn n mre than 16 pints in this sectin. If yu are using the electrnic scre sheet, it will autmatically calculate the sum f pints and recrd a maximum f 16 pints.) DNA (4 pts) DNA Klf4 is a transcriptin factr, which means that it has the ability t bind t DNA. Teams may elect t add DNA t their mdel f Klf4 t reflect this functin. The PDB file (2wbu.pdb) that was used t develp the mdels includes data n hw Klf4 interacts with DNA. Please see the figure t the right, which is based n the PDB file 2wbu, t see hw the prtein interacts with the DNA. Klf4 binds in the majr grve f the DNA. Zinc Atms (4 pts) The zinc finger mtif is stabilized by the presence f a zinc in. Teams may elect t include zinc atms in their mdel t illustrate the stabilizing prperty f this in. On the figure t the right, and n the physical mdel, the zinc ins are shwn in spacefill and are clred green. Each finger shuld have a zinc in assciated with it. T receive full credit, the mdel must display all three zinc ins. If nly ne r tw atms are displayed, deduct 2 pt. Zinc ins

8 Zinc Atm Crdinatin (4 pts) The zinc ins are held in place thrugh crdinatin with sidechains f the prtein. In Klf4, the zinc ins interact with tw histidine and tw cysteine sidechains in each zinc finger mtif. T receive credit, each finger shuld have 2 histidine and 2 cysteines sidechains displayed and interacting with the zinc in. Please see the figure t the right, and the physical mdel, t see where these sidechains are psitined relative t the zinc ins. Sidechains that interact with DNA (4 pts) In rder t functin as a transcriptin factr, Klf4 has t interact with the DNA; this is accmplished thrugh sidechain interactin with the nucleic acid. Award 1pt t the mdel if the mdel has at least 2 arginine residues psitined n the Klf4 prtein that wuld enable the sidechains t interact directly with the DNA. Arginine is shwn in green in the figure t the right. DNA Mst frequently, this arginine is psitined at the tp f the helix. Klf4 has 3 arginine residues n the 2 nd zinc finger n the helix that interact with the DNA. The mdel may have as many as 5 arginines indicated, but the mdel shuld have at least 2 t receive this pint.

9 Sidechains that stabilize the structure f the prtein (4pts) Hydrphbic amin acids stabilize the fld f this prtein. Award 1 pt if the mdel has a hydrphbic cre shwn n the 3 zinc fingers this cre is typically cmpsed f at least ne phenylalanine and ne leucine residue. These amin acids shuld be psitined t stabilize the alpha helix near the beta sheet. Please see figure t the right (hydrphbic amin acids shwn in cyan). Additinal features that are nt listed abve may be added t the prtein. It is up t the event supervisr t determine whether the additin t the mdel is apprpriate and accurate. A mdel cannt receive mre than 16 pts ttal fr this sectin. 15. Additins t mdel are apprpriate t functin f the prtein (2 pts) T receive credit fr this feature, the creative additins need t be relevant t telling the functinal stry f the prtein. Credit shuld be awarded t thse prteins that meet the fllwing criteria: Mdel has creative additins Mdels that are just the tber will nt receive credit Additins are apprpriate t the functin f the prtein Mdels that have ALL sidechains displayed shuld nt receive credit. If all sidechains are displayed, the team did nt recgnize the significance f a select few amin acids t the enzyme functin. The fcus f adding the amin acids shuld be n the nes that play a rle in the functin f the prtein. Additinally, credit shuld nt be awarded if amin acids utside f thse that play a specific functinal rle in the prtein are displayed.