Overview of the Molecule:


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1 Prtein Mdeling Event Guide t Scring the Invitatinal PreBuild Mdel Fr Science Olympiad 2016 Invitatinal Cmpetitin 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 Science Olympiad Invitatinal PreBuild MiniTber mdels f sepiapterin reductase, based n 1sep.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: Salmn alpha helices Yellw beta strands White  lps Blue tip Nterminus Red tip Cterminus αhelix #5 CTerminus 3 10 helix 2  ptinal αhelix #4 αhelix #3 βstrand #4 αhelix #2 β strand #3 β strand # helix 1  ptinal β strand #1 NTerminus αhelix #1a αhelix #1b 1
2 Nte abut Scring: As yu wrk thrugh this guide, it may be helpful t use bth the mdel and the images. Yu can quickly rient the mdel with the images by lining up the blue and red ends. 1. Order f Secndary Structures: (2.25 pts; 0.25 pts fr each bld bullet pint in the crrect rder) T receive these pints, the sequence f the secndary structures shuld be in the fllwing rder: N terminus β1 turn 1 (shrt 3 10 helix 1 turn 1a) α1a α1b [may appear as a single lng helix r tw helices with a tiny turn between] turn 2 β2 turn 3 (shrt 3 10 helix 2 turn 3a) α2 turn 4 β3 turn 5 α3 turn 6 α4 turn 7 α5 turn 8 β4 C terminus Deduct 0.25 pt fr each secndary structure (helix r βstrand) element that is nt in the crrect rder, r is missing. (If tw elements are reversed, deduct 0.5 pt. If a single element is missing, deduct 0.25 pt.) Secndary structures that are ut f rder shuld nt be cunted. Please refer t the figure n previus page, r t the physical mdel, t assist in scring the mdel. Nte that the 3 10 helices are nly 3 amin acids lng and may nt appear. D nt deduct pints fr the presence r absence f these helices. 2. Blue Cap n Nterminal Amin Acid (Leu93) (2 pts) The blue cap needs t be lcated at the Nterminus f the prtein, which is lcated at the beginning f beta strand #1. This end f the mlecule has a beta strand fllwed by a lng lp, then a lng alpha helix that runs parallel t this strand. Please see the figure t the right fr the crrect psitining f the blue end cap. Scring fr this feature is all r nne credit. NTerminus 2
3 3. Red Cap n Cterminal Amin Acid (Asp261) (2 pts) CTerminus T receive credit, the red cap needs t be lcated at the C terminus f the prtein, which is lcated at the end f beta strand #4. This end f the mlecule has a shrt beta strand preceded by a sharp turn, then tw alpha helices that lie at right angles t each ther. Please see the figure t the right fr the crrect psitining f the red end cap. Scring fr this feature is all r nne credit. 4. Mdel has 5 alpha helices accrding t Jml selectin criteria. (1 pt per helix fr a ttal f 5 pts) T receive these pints, there shuld be 5 helices within the mdel. Fr the purpses f scring, cnsider α1a and α1b as a single lng helix. Please see figure t the right fr the crrect lcatin f these helices. (Helices are clred salmn n the mdel and n the figure t the right.) Alpha helices 1a and 1b cunt as ne helix D nt cunt 3 10 helices Fr the purpses f this mdel, an alpha helix MUST have at least tw turns. Any lps in the mdel that are nt at least tw turns will nt be deemed an alpha helix. Deduct 1 pt fr each extra helix. Fr example, if a mdel has 6 helices, then the mdel wuld receive 4 pts rather than the full 5 pts. Alpha helices 5. Alpha helices are righthanded (1 pt each; ttal f 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 1 pt, fr a ttal f 5 pts if all five 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. Lefthanded vs righthanded helices 3
4 6. Mdel has 4 βstrands accrding t Jml selectin criteria (0.5 pt per βstrand fr a ttal f 2 pts) Beta strands T receive these pints, there shuld be 4 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 4 βstrands in the mdel, deduct 1 pt fr each extra strand. Fr example, if the mdel has 5 βstrands, the mdel shuld receive 3 pts, rather than the full 4 pts. 4
5 7. All βstrands are parallel. (1 pt; 0.25 pt per strand) βstrands need t have the same directinality frm N t C. If yu rient the mdel s the N terminus is at the bttm, as yu trace thrugh the mdel, each strand will be traced frm bttm t tp. Please see figure at right fr clarificatin. Fr each strand that is traced frm bttm t tp, award 0.25 pt. 8. Mdel has 1 βsheet. (1 pt) This mdel has 1 βsheet arranged frm the 4 βstrands. A βsheet is cmpsed f tw r mre strands lying parallel t each ther, thugh the plane f the βsheet may be twisted instead f flat. Nte that due t the twisting f the sheet, strands are essentially parallel t adjacent strands, but the end strands may nt be parallel t each ther. Please see the picture at the right and the mdel fr crrect alignment f the strands. T receive credit, the mdel must have a single βsheet. If ne f the strands des nt lie parallel t adjacent strands, deduct 0.25 pt. If there are tw sets f tw parallel strands, deduct 0.5 pt. Βsheet frms twisted plane; each strand is parallel t adjacent strands 5
6 Items #9  #14 refer t the 3dimensinal shape f the mdel. 9. Mdel has three distinct layers (1.5 pts fr each layer, fr a ttal f 4.5 pts) Layer 3 This prtein has three distinct layers. Layers 1 and 3 cnsist f alpha helices. Layer 2 cnsists f a single beta sheet. There is als a 3 10 helix in this layer; d nt deduct pints if the 3 10 helix is nt visible. Layer 2 If ne f the layers is nt clearly distinguishable frm the thers, please deduct 1.5 pts. If the beta sheet is nt sandwiched between the layers f alpha helices, deduct 1.5 pts. Layer 1 If the mdel has mre than three layers, then deduct 1.5 pts fr each additinal layer. Fr example, if the mdel has fur layers, the mdel shuld receive 3 pts, rather than the full 4.5 pts. 10. Layer 1 has tw lng helices. (1 pt each, fr a ttal f 2 pts) Layer 1 cnsists f helices 1a, 1b and 2. Helices 1a and 1b may be distinct r may appear as a single helix. Please see the mdel and image t right t identify these helices. Helix 2 The helices shuld lie in the same plane, but at abut a 15 angle relative t each ther. 15 If the images are in the same plane, but are nt at a 15 angle, deduct 0.5 pt. Helix 1a Helix 1b 6
7 11. Layer 2 cntains a furstranded βsheet. (2 pts) Strand 1 Strand 1 f the βsheet shuld be parallel and abve helix 1a. See mdel and figure at right t see this alignment. If strand 1 is nt parallel t helix 1a, deduct 0.5 pt. Helix 1a Strand 4 f the βsheet shuld be at a 45 angle relative t helix 5. See mdel and figure at right t see this alignment. 45 If strand 4 is nt at a 45 angle relative t helix 5, deduct 0.5 pt. 12. Layer 3 cntains 3 medium helices. (3 pts) Layer 3 cnsists f helices 3, 4 and 5; these helices are shrter than the helices in layer 1. Deduct 1 pt fr each helix that is nt clearly in this layer. Layer 3 Layer 3 is nt flat like layers 1 and 2, but instead frms a triangular peak. Please see mdel and image at right t identify this triangular peak. If layer 3 des nt have a triangular shape, deduct 0.5 pt. 7
8 Fr items #13  #14 please refer t the rientatin f the mdel in the image at the right. N terminus 13. N terminus is lcated in layer 2 (the middle layer) n the narrw side f the mlecule. (0.5 pt) When the mdel is rientated with the N terminus at the tp and facing yu, the structure shuld be brader at the base and narrwer at the tp, much like a pine tree. C terminus If the N terminus is nt lcated near the apex f the triangle, assign a scre f C terminus shuld be in the middle f the mdel and n the back side relative t the N terminus. (0.5 pt) When the mdel is riented as abve with the N terminus at 12 clck, the C terminus shuld be lcated at 3 clck. If the C terminus is nt lcated at 3 clck, deduct 0.25 pt. With the mdel riented as abve, with the N terminus in the frnt f the mdel, the C terminus shuld be in the back f the mdel. If the C terminus is nt n the ppsite f the mdel frm the N terminus, deduct 0.25 pt. 15. Students submitted a 3x5 card with explanatin f the mdel (1.25 pt) 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. If the card is larger than 3x5, r n 3x5 card is attached, award a scre f 0. If a card is attached but exceeds the 3x5 size, yu may use the infrmatin n the card t assess the creative additins t the mdel, but n credit will be assigned here. 8
9 16. Creative additins t the mdel. (Nte that there are many pssible creative additins t this mdel; each creative additin is wrth 1 pt; teams may have mre than 4 creative additins, but may earn n mre than 4 pts ttal in this sectin. If yu are using the electrnic scre sheet, it will autmatically calculate the sum f pints and recrd a maximum f 4 pts.) Beery Twin Mutatins and Implicatins (1 pt maximum) The Beery Twins are cmpund heterzygtes; each f them has tw different mutatins in their sepiapterin reductase alleles. One allele has the mutatin frm their Dad, and the ther allele has the mutatin frm their Mm. Teams may elect t display these mutatins and describe their effects n the prtein structure. The mdel built fr the cmpetitin is frm the muse, and there are slight variatins frm the human structure. Teams shuld be given full credit fr using EITHER the muse r the HUMAN numbering system as they describe these mutatins. Lys151 in βstrand 2 Asp145 in lp The first mutatin is at residue Arg150 (which crrespnds t Lys151 in the muse mdel here). The lcatin f this mutatin is in βstrand 2 in the mdel and the backbne is clred light green. This residue frms a salt bridge with Asp144 (Asp145 in the muse). This residue is lcated in the lp between helix 2 and β strand 2. In the image at the right, Asp145 has a purple backbne. This residue is NOT displayed n the mdel. Shuld be clse t interact Displaying Arg150 (Lys151) (0.25 pt) Displaying Asp144 (Asp145) (0.25 pt) If bth f these amin acids are displayed, they shuld be riented t display their interactin with each ther. See image at right fr clarificatin. (0.25 pt) The secnd mutatin results in changing Lys251 t a stp cdn. Lys251 (Phe251 in muse) is lcated in the lp between helix 5 and βstrand 4 near the C terminus. This mutatin results in early truncatin f the prtein. Sme f the residues in the C terminal regin are imprtant in substrate binding. Residue 251 is clred green in the mdel and in the image at the right. Truncatin at residue 251 Displaying Lys251 (Phe251) (0.25 pt) 9
10 Dimerizatin Dmain (1 pt maximum) Asn116 Sepiapterin reductase functins as a dimer. T receive credit fr this features, students nly have t display the prtins f the required mdel that interact with the secnd mnmer. Helices E and F f the prtein (labeled as 1a and 1b in the prebuild mdel) interact with the secnd mnmer. If teams mentin this interactin f helices n their 3x5 card, award 0.25 pt. (Nte teams d nt need t include the names f the helices t receive credit, but shuld mentin that the interactin with the ther mnmer is alng the helix.) Asn116 and Asn141 interact with the same Asn141 Dimerizatin regin amin acids n the secnd mnmer via charge interactins. These amin acids are displayed with a blue backbne in the image abve right, but NOT n the mdel. Teams shuld receive 0.25 pt fr each f these tw amin acids that is displayed in the prper lcatin n the prtein, fr a maximum f 0.5 pt. These amin acids shuld be arranged n the backbne s they face utward, away frm the mdel. They shuld be in an rientatin that wuld allw them t interact with a secnd prtein. Award 0.25 pt if bth are facing utward, r if nly ne f these amin acids is displayed and facing utward. If tw amin acids are displayed, and ne is facing utward and the ther is facing inward, award 0.1 pt. If bth amin acids are facing inward, n credit is awarded. Cfactr and Cfactr Binding Site (1 pt maximum) NADP is a required cfactr f sepiapterin reductase. It is displayed in range n the mdel and in the image at the right. Award 0.25 pt if NADP is displayed. Award 0.25 pt if NADP is the crrect lcatin and rientatin in the mdel. NADP is crdinated (held in place) by three residues, nly ne f which is in the truncated versin f the mdel. Leu127 is shwn in the image at the right (but nt n the mdel) with a purple backbne. Award 0.25 pt if Leu127 is displayed, and is riented twards NADP (r the pcket where NADP sits.) Arg43 and Leu71 als crdinate NADP, but they are nt part f the prtein that is mdeled fr the cmpetitin. If teams mentin that BOTH f these amin acids help t hld the NADP in place, award 0.25 pt. If they nly include ne f these amin acids, award 0.1 pt. 10
11 Catalytic Site (1 pt maximum) The catalytic site f sepiapterin reductase includes Tyr171, which is the amin acid needed fr prtein transfer, and Lys175 and Arg178, which may facilitate prtn transfer. All three f these residues are n helix 2 Helix 2 Award 0.25 pt fr each f the three residues that are displayed n helix 2 fr a maximum f 0.75 pt. Award 0.25 pt if the three residues are stacked ne n tp f the ther and facing twards the inside f the prtein. Please see image at right fr crrect psitining f these residues; these are NOT shwn n the mdel. Catalytic residues are displayed in cpk clring and the backbne is clred green. Binding Pcket (1 pt maximum) Stacked catalytic residues Substrate The substrate fits snugly int a binding pcket, which includes the catalytic residues, but several ther residues as well. These residues include: Leu105 Leu159 Cys160 Tyr165 Trp168 Met206 Leu219 Leu223 Leu226 Aps258 Tyr260 Each f these residues is depicted in the image t the right (but nt n the mdel). These amin acids have a purple backbne. Nte that all residues pint tward the bipterin substrate (shwn in image and n the judging mdel). All amin acids in active site shuld pint twards substrate T receive full credit, teams must display a minimum f three f these amin acids pinting tward the substrate (whether displayed r nt) and identify these amin acids n the 3x5 card. Award 0.25 pt fr each f the amin acids listed abve that are displayed, up t a maximum f three amin acids. (0.75 pt maximum) Award 0.25 pt if all amin acids in the active site are pinting twards the substrate (r the pcket where the substrate sits). Nte that the substrate des nt need t be displayed t receive credit. Deduct 0.25 pt if the amin acids are displayed, but are nt listed n the 3x5 card. 11
12 Substrate in Active Site (1 pt maximum) Bipterin is bund t sepiapterin reductase in the active site pcket. This is displayed in cpk clring in the mdel and in the image at the right. Assign 1 pt if bipterin is displayed in the mdel. Deduct 0.5 pt if bipterin is nt described n the 3x5 card but is displayed in the mdel. bipterin Additin f the Rest f the Prtein (1 pt maximum) The prebuild mdel cntains nly the Cterminal prtin f the prtein (amin acids ). Teams may include the rest f the prtein at the N terminus (amin acids 292). These additinal amin acids are depicted in the image at the right (but nt n the mdel). The lps f the added prtin are gray, the helices red, and the sheets bright yellw. T earn full credit the mdel must include: Layer 1: ne additinal, medium length helix adjacent t helix 1a and 1b. (0.25 pt) Layer 2: Three additinal beta strands, extending the single beta sheet. These strands shuld be added t the sheet n the side ppsite f the C terminus (red endcap). (0.25 pt) Layer 3: Tw additinal helices, running in the same directin as helix 5 and frming a twisted plane. (0.25 pt) The required mdel shuld be clearly distinguished frm the additinal sectin f the mdel. Teams may chse t use different clr backbnes, labels, r ther distinguishing features s it is clear what part f the mdel is the required mdel and what is an additinal feature. (0.25 pt) 12
13 Additin f a Secnd Mnmer t Frm a Dimer (1 pt maximum) Sepiapterin reductase functins as a dimer. Teams may pt t display a secnd mnmer t shw hw the dimer interacts. the image at right (secnd mnmer is in gray) t see the rientatin f the mnmers. T receive full credit fr this creative additin: See Layer 1 f the tw dimers must be face t face, with helices aligned. (0.25 pt). The secnd mnmer must have a triangular pine tree shape (see #13 fr an image f this triangular shape. (0.5 pt) The secnd mnmer must be upside dwn relative t the first. This can be easily sptted by lking fr the pine tree shape f the tw mnmers (ne will be upside dwn), and als bserving that the N termini f the tw mdels (blue endcap) will be diagnally ppsite in the dimer. (0.25 pt) Additinal Features Nt Described Abve (1 pt maximum) It is up t the event supervisr t determine whether the additin t the mdel is apprpriate and accurate. In rder t receive pints, the additins must be n the mdel and a cmplete descriptin and explanatin f significance must be included n the 3x5 nte card. 17. Additins t mdel are apprpriate t functin f the prtein (2 pt) 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 (r ther mdeling material) 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. 13
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