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 Nterminus Red tip Cterminus 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: Nterminus βstrand #1 turn βstrand #2 Turn αhelix #1 turn βstand #3 turn βstrand #4 turn αhelix #2 turn βstrand #5 turn βstrand #6 turn αhelix #3 Cterminus
2 1. Blue Cap n Nterminal Amin Acid (Thr399) (0.5 pt) T receive credit, the blue cap needs t be lcated at the Nterminus 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 Cterminal Amin Acid (Phe483) (0.5 pt) T receive credit, the red cap needs t be lcated at the Cterminus 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 βstrand, 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 righthanded (0.5 pt each; ttal f 1.5 pts) Alpha helices are righthanded. Check each alpha helix in the mdel t cnfirm that the helix is righthanded. Fr each righthanded 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 righthanded, 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 handrail, 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 righthanded helix. If yu wuld put yur left hand n the tber, yu have a lefthanded 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 34 turns. Each helix that is the crrect length shuld receive 0.5 pints, fr a ttal f 1.5 pints. 6. Mdel has 6 βstrands accrding t Jml selectin criteria (0.5 pt per βstrand fr a ttal f 3 pints) T receive these pints, there shuld be 6 βstrands within the mdel. Please see figure t the right fr the crrect lcatin f these beta strands. (βstrands are clred yellw n the mdel and n the figure t the right.) βstrands need t be clearly distinguishable frm lps; there may be sme slight zigzag flding f the tber t indicate the upanddwn psitining f the amin acids. Alternately, teams might clrcde their beta strands t distinguish them frm lps r write n the tber indicating the lcatin f the βstrands. Please see phts belw depicting βstrands mdeled using tbers. If there are mre than 6 βstrands in the mdel, 0.5 pt shuld be deducted fr each extra strand. Fr example, if the mdel has 7 βstrands, 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: Nterminus βstrand #1 Turn βstrand #2 Turn αhelix #1 Turn βstrand #3 Turn βstrand #4 Turn αhelix #2 Turn βstrand #5 Turn βstrand #6 Turn αhelix #3 Cterminus Each secndary structure (helix r βstrand), 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 3dimensinal shape f the mdel. 8. Mdel has 3 βsheets (0.5 pt fr each sheet fr a ttal f 1.5 pts) This prtein has tw βsheets arranged frm the 6 βstrands. A βsheet is cmpsed f tw r mre βstrands lying parallel t each ther, thugh the plane f the βsheet may be twisted instead f flat. β sheet #2 β sheet #3 βsheet #1 is cmpsed f βstrands #1 and #2. β sheet #1
5 βsheet #2 is cmpsed f βstrands #3 and #4. βsheet #3 is cmpsed f βstrands #5 and #6. T receive credit, the mdel shuld have three distinct βsheets. If the mdel has mre than three βsheets, then deduct 0.5 pt fr each additinal sheet. Fr example, if the mdel has fur βsheets, 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 Ctermini 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 Nterminus and the Cterminus 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 Nterminus psitined facing tward yu and the Cterminus is behind the Nterminus (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.
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