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[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object]
[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],Sequenze MIC E.coli Alog P Energia torsionale Energia elettrostatica Flessibilità molecolare FLPLILRKIVTA 69 1,564 0,682 193,406 42,293 INLKAIAALAKKLL 57 -2,820 1,331 341,265 46,604 LKLKSIVSWAKKVL -3,764 0,778 494,964 47,185 RLCRIVVIRVCR -4,427 47,166 FFPVIGRILNGIL 83 1,483 38,758 FCTMIPIPRCY 11 -1,243 2,462 25,048 34,074 RVCFAIPLPICH -0,419 0,857 169,099 33,404 RVCYAIPLPIC 43 -0,621 1,877 69,482 32,164 RVCYAIPLPICY -0,193 NFLGTLINLAKKIM 33,5 -3,139 FLPILINLIHKGLL 42,7 2,702 1,304 108,156 FFPIGVFCKIFKTC 0,535 1,236 171,877 PKRKSATKGDEPA -8,499 1,790 262,402 40,050 AKRHHGYKRKFH 23,8 -8,966 41,609 KWKLFKKIPKFLHSAKKF -4,4947 3,828 1,017e+003 61,386
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Database Paese Sito Web (http://) Anno Numero di sequenze AMSDb ITALIA www.bbcm.units.it/~tossi/pag1.htm 2002 804 APPDb IRLANDA ercbinfo1.ucd.ie/APPDb/ 2002 SAPD FINLANDIA oma.terkko.helsinki.fi:8080/~SAPD 2002 ~200 ANTIMIC SINGAPORE research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/ 2004 1700 APD USA aps.unmc.edu/AP/main.html 2004 526 Peptaibols UK www.cryst.bbk.ac.uk/peptaibol 2004 307 Defensins SINGAPORE defensins.bii.a-star.edu.sg/ 2006 350 PenBase FRANCIA penbase.immunaqua.com/ 2006 200
(http://193.205.186.243/progetto)
 
 
 
 
Sappiamo che gli AMP interagiscono con particolari domini di membrana ma non è possibile determinare sperimentalmente il meccanismo In ogni organismo sono presenti sequenze peptidiche transmembrana
[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],Il server Phobius è in grado di prevedere la topologia delle sequenze amminoacidiche  costituenti una proteina e di  definire le porzioni transmembrana.  L’architettura del software Phobius è basata  sull’ HMM (Hidden Markov Models)
GYMGGILFSDIITNSLYA FLLYSCFLSVLISIALSRIA  YLDFLVGAISSLVVIGLAFIL  FLPNPFNLILSIYLLKSSFAIR VIAPLFYYLIFGLPGVVYRAV LNFVPARITVLLFLSLG IAAMSAVLGVWLEKPNY YWIIVVEFLLIVAIILYGG WMLPLLTPLTAFIPSLILYLNI SILSLYWVIGLLHLDGLA VNTGIAGTFAVVMILLIQVYSL YSIYLAELNSKMAMLLALATK VFLGGVLYALLLIPILLY IGLWVTGLLMAFLTGLLVGIGYLI IIAFTIALFMNFFSYWFS LIQTIAAVLAGAIMVLVNFARWSLW VALILAIILAPIAATLIQLAI LILTGGLVGQLFTLAKGFDLG LTVLFIAIMLLSVVPVHFVS LLALIVAFAVLTAGCLGS PILLITILLGFAMAWAIGA QAVIIAGVLEFMGAYFFG … A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V 1  0  1  1  0  0  0  3  0  3  2  0  1  0  1  2  1  0  2  0 2  1  0  0  1  0  0  0  0  3  5  0  0  0  2  4  0  0  1  1 2  0  0  1  0  0  0  2  0  3  5  0  0  0  2  2  0  0  1  3 1  1  2  0  0  0  0  0  0  3  5  1  0  2  3  3  0  0  1  0 2  1  0  0  0  0  0  2  0  2  3  0  0  2  2  0  0  0  3  4 1  1  1  0  0  0  0  1  0  1  5  0  0  1  2  1  1  0  0  2 3  0  1  0  0  0  1  1  0  1  2  1  1  1  0  1  0  1  1  2 1  0  0  0  0  0  1  2  0  5  3  0  0  0  1  0  0  1  2  3 1  0  1  0  0  0  0  0  0  3  7  0  1  3  1  1  2  1  1  0 1  0  0  1  0  0  0  2  1  2  6  0  0  0  0  2  0  1  1  1 2  0  1  0  0  1  0  2  0  3  3  0  1  0  1  1  2  0  1  4 A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V 15  4  6  3  1  0  2  13  1  26  43  2  3  9  14  16  4  4  13  16 23  1  4  1  0  4  1  15  1  24  42  3  7  3  13  8  11  4  7  18 22  0  1  0  1  1  1  25  0  29  23  2  5  4  12  7  7  7  8  17 20  2  2  4  1  3  0  24  4  26  29  4  3  6  12  7  14  6  5  20 11  1  3  0  2  1  1  18  2  40  40  3  1  5  19  9  15  3  16  14 26  1  6  3  0  0  1  21  0  42  28  1  3  8  11  13  13  5  13  17 13  2  3  0  0  1  0  17  0  29  42  1  8  5  20  16  6  2  6  29 20  0  5  2  2  4  1  12  1  30  41  3  7  4  15  18  10  1  8  14 15  1  3  1  1  1  2  13  1  32  32  3  5  10  10  15  11  3  12  19 15  3  7  1  0  2  0  23  0  28  31  1  6  6  28  15  6  5  6  16 23  0  4  3  0  0  1  14  2  35  38  0  2  7  14  11  11  2  8  23 18  3  4  3  0  1  3  17  0  16  35  1  9  6  22  6  11  3  7  15 9  7  8  9  1  5  12  14  3  16  20  11  4  10  10  8  8  1  5  13
mean(A)  median(A)  trimmean  iqr(A)  mad(A)  range(A)  std(A) A  9.946969  9.895833  9.850927  3.109966  1.895804  15.386686  2.459542 R  0.994661  0.990099  0.772769  0.956998  0.594214  4.838710  0.794100 N  1.426511  1.136364  1.334014  1.526390  0.784821  4.787234  0.981287 D  0.684437  0.529101  0.515462  1.063830  0.525710  5.172414  0.679448 C  0.232200  0.000000  0.127124  0.520159  0.307689  1.895735  0.369977 Q  0.732651  0.531915  0.544379  0.571629  0.511893  3.141361  0.662653 E  0.943068  0.938967  0.703481  0.652138  0.611739  6.896552  0.881986 G  8.324893  8.241758  8.243749  3.367347  1.938552  12.629773  2.418436 H  0.548854  0.518135  0.380092  0.979197  0.438348  3.428571  0.604753 I  13.926745  14.070352  13.913042  3.832976  2.225817  14.260175  2.768701 L  19.148035  19.021739  19.118976  4.230597  2.447674  15.633075  3.041508
conteggio aminoacidi A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V 187 15  42  17  8  17  9  183 10  315 364 23  47  64  163 128 99  41  98  187 conteggio dimeri  LI  56 LL  55 IL  50 LA  43 IG  40 GL  39 II  38 AI  35 IA  34 FL  32 VL  31 conteggio trimeri  IGL 13 LIL 12 LLL 10 LLA 9 VIG 9 FLL 8 GLA 8 IAG 8
L’analisi attualmente condotta su Pyrococcus furiosus e su eritrociti umani sarà completata sugli organismi suindicati L’analisi su tutti gli ennameri presenti in tutti i peptidi antimicrobici presenti nel database metterà le premesse per una estesa analisi computazionale degli AMP L’analisi statistica della composizione aa dei proteomi transmembrana ha mostrato differenze statisticamente significative. Sarà ricercata la correlazione tra la  tossicità esibita da alcuni peptidi e la differenza tra TPM di batteri e quelli di eritrocita  Dei nuovi descrittori molecolari, basati sulla distanza di Mahalanobis tra i diversi TPM, saranno impiegati nella nuova generazioni di modelli QSAR di attività antimicrobica.
Studio sulla composizione amminoacidica delle proteine di membrana ,[object Object],[object Object]

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Bianchino I Anno

  • 1.
  • 2.
  • 3.
  • 4.
  • 5.
  • 6.
  • 7. Database Paese Sito Web (http://) Anno Numero di sequenze AMSDb ITALIA www.bbcm.units.it/~tossi/pag1.htm 2002 804 APPDb IRLANDA ercbinfo1.ucd.ie/APPDb/ 2002 SAPD FINLANDIA oma.terkko.helsinki.fi:8080/~SAPD 2002 ~200 ANTIMIC SINGAPORE research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/ 2004 1700 APD USA aps.unmc.edu/AP/main.html 2004 526 Peptaibols UK www.cryst.bbk.ac.uk/peptaibol 2004 307 Defensins SINGAPORE defensins.bii.a-star.edu.sg/ 2006 350 PenBase FRANCIA penbase.immunaqua.com/ 2006 200
  • 9.  
  • 10.  
  • 11.  
  • 12.  
  • 13. Sappiamo che gli AMP interagiscono con particolari domini di membrana ma non è possibile determinare sperimentalmente il meccanismo In ogni organismo sono presenti sequenze peptidiche transmembrana
  • 14.
  • 15.
  • 16.
  • 17.
  • 18. GYMGGILFSDIITNSLYA FLLYSCFLSVLISIALSRIA YLDFLVGAISSLVVIGLAFIL FLPNPFNLILSIYLLKSSFAIR VIAPLFYYLIFGLPGVVYRAV LNFVPARITVLLFLSLG IAAMSAVLGVWLEKPNY YWIIVVEFLLIVAIILYGG WMLPLLTPLTAFIPSLILYLNI SILSLYWVIGLLHLDGLA VNTGIAGTFAVVMILLIQVYSL YSIYLAELNSKMAMLLALATK VFLGGVLYALLLIPILLY IGLWVTGLLMAFLTGLLVGIGYLI IIAFTIALFMNFFSYWFS LIQTIAAVLAGAIMVLVNFARWSLW VALILAIILAPIAATLIQLAI LILTGGLVGQLFTLAKGFDLG LTVLFIAIMLLSVVPVHFVS LLALIVAFAVLTAGCLGS PILLITILLGFAMAWAIGA QAVIIAGVLEFMGAYFFG … A R N D C Q E G H I L K M F P S T W Y V 1 0 1 1 0 0 0 3 0 3 2 0 1 0 1 2 1 0 2 0 2 1 0 0 1 0 0 0 0 3 5 0 0 0 2 4 0 0 1 1 2 0 0 1 0 0 0 2 0 3 5 0 0 0 2 2 0 0 1 3 1 1 2 0 0 0 0 0 0 3 5 1 0 2 3 3 0 0 1 0 2 1 0 0 0 0 0 2 0 2 3 0 0 2 2 0 0 0 3 4 1 1 1 0 0 0 0 1 0 1 5 0 0 1 2 1 1 0 0 2 3 0 1 0 0 0 1 1 0 1 2 1 1 1 0 1 0 1 1 2 1 0 0 0 0 0 1 2 0 5 3 0 0 0 1 0 0 1 2 3 1 0 1 0 0 0 0 0 0 3 7 0 1 3 1 1 2 1 1 0 1 0 0 1 0 0 0 2 1 2 6 0 0 0 0 2 0 1 1 1 2 0 1 0 0 1 0 2 0 3 3 0 1 0 1 1 2 0 1 4 A R N D C Q E G H I L K M F P S T W Y V 15 4 6 3 1 0 2 13 1 26 43 2 3 9 14 16 4 4 13 16 23 1 4 1 0 4 1 15 1 24 42 3 7 3 13 8 11 4 7 18 22 0 1 0 1 1 1 25 0 29 23 2 5 4 12 7 7 7 8 17 20 2 2 4 1 3 0 24 4 26 29 4 3 6 12 7 14 6 5 20 11 1 3 0 2 1 1 18 2 40 40 3 1 5 19 9 15 3 16 14 26 1 6 3 0 0 1 21 0 42 28 1 3 8 11 13 13 5 13 17 13 2 3 0 0 1 0 17 0 29 42 1 8 5 20 16 6 2 6 29 20 0 5 2 2 4 1 12 1 30 41 3 7 4 15 18 10 1 8 14 15 1 3 1 1 1 2 13 1 32 32 3 5 10 10 15 11 3 12 19 15 3 7 1 0 2 0 23 0 28 31 1 6 6 28 15 6 5 6 16 23 0 4 3 0 0 1 14 2 35 38 0 2 7 14 11 11 2 8 23 18 3 4 3 0 1 3 17 0 16 35 1 9 6 22 6 11 3 7 15 9 7 8 9 1 5 12 14 3 16 20 11 4 10 10 8 8 1 5 13
  • 19. mean(A) median(A) trimmean iqr(A) mad(A) range(A) std(A) A 9.946969 9.895833 9.850927 3.109966 1.895804 15.386686 2.459542 R 0.994661 0.990099 0.772769 0.956998 0.594214 4.838710 0.794100 N 1.426511 1.136364 1.334014 1.526390 0.784821 4.787234 0.981287 D 0.684437 0.529101 0.515462 1.063830 0.525710 5.172414 0.679448 C 0.232200 0.000000 0.127124 0.520159 0.307689 1.895735 0.369977 Q 0.732651 0.531915 0.544379 0.571629 0.511893 3.141361 0.662653 E 0.943068 0.938967 0.703481 0.652138 0.611739 6.896552 0.881986 G 8.324893 8.241758 8.243749 3.367347 1.938552 12.629773 2.418436 H 0.548854 0.518135 0.380092 0.979197 0.438348 3.428571 0.604753 I 13.926745 14.070352 13.913042 3.832976 2.225817 14.260175 2.768701 L 19.148035 19.021739 19.118976 4.230597 2.447674 15.633075 3.041508
  • 20. conteggio aminoacidi A R N D C Q E G H I L K M F P S T W Y V 187 15 42 17 8 17 9 183 10 315 364 23 47 64 163 128 99 41 98 187 conteggio dimeri LI 56 LL 55 IL 50 LA 43 IG 40 GL 39 II 38 AI 35 IA 34 FL 32 VL 31 conteggio trimeri IGL 13 LIL 12 LLL 10 LLA 9 VIG 9 FLL 8 GLA 8 IAG 8
  • 21. L’analisi attualmente condotta su Pyrococcus furiosus e su eritrociti umani sarà completata sugli organismi suindicati L’analisi su tutti gli ennameri presenti in tutti i peptidi antimicrobici presenti nel database metterà le premesse per una estesa analisi computazionale degli AMP L’analisi statistica della composizione aa dei proteomi transmembrana ha mostrato differenze statisticamente significative. Sarà ricercata la correlazione tra la tossicità esibita da alcuni peptidi e la differenza tra TPM di batteri e quelli di eritrocita Dei nuovi descrittori molecolari, basati sulla distanza di Mahalanobis tra i diversi TPM, saranno impiegati nella nuova generazioni di modelli QSAR di attività antimicrobica.
  • 22.

Editor's Notes

  1. L’obiettivo principale di questo lavoro di dottorato è la progettazione di nuovi farmaci (peptidi o peptidomimetici) con attività antimicrobica e/o antifungina.
  2. L’obiettivo principale di questo lavoro di dottorato è la progettazione di nuovi farmaci (peptidi o peptidomimetici) con attività antimicrobica e/o antifungina.
  3. Studiando i peptidi ad azione antimicrobica ci si è imbattuti nell’evidenza che molte delle banche date che raccolgono sequenze attive non forniscono sufficienti informazioni sui metodi sperimentali che hanno portato ad isolare e a caratterizzare le sequenze stesse. I database oggi disponibili non consentono di effettuare ricerche molto dettagliate, ad esempio, sulla base della MIC propria di ogni sequenza, o relative all’azione su uno specifico agente patogeno. Nella seguente tabella sono riportate le maggiori banche dati di peptidi antimicrobici oggi disponibili nel Web, alcune di queste sono consultabili gratuitamente.
  4. Da un punto di vista computazionale risulterebbe estremamente complesso simulare modelli di membrane a causa dell’eterogeneità dei lipidi che le costituiscono. Si è pensato per questo di intraprendere lo studio delle proteine di membrana….
  5. VANTAGGI Da un punto di vista computazionale risulterebbe estremamente complesso simulare modelli di membrane a causa dell’eterogeneità dei lipidi che le costituiscono. Si è pensato per questo di intraprendere lo studio delle proteine di membrana….
  6. Per poter isolare le sequenze proteiche transmembrana relative ai seguenti organismi batterici e archeobatterici abbiamo dovuto disporre dell’intero proteoma degli stessi. Per proteoma si intende la totalità delle proteine espresse e modificate dopo l’espressione da un genoma durante l’arco dell’intera vita di una cellula o di un tessuto. Nella serie d’eventi regolatori che da un gene portano ad una proteina attiva, il proteoma rappresenta il prodotto finale del genoma. I dati ottenuti dall'analisi del proteoma, in particolare i dati di spettrometria di massa, sono inseriti in banche dati che in alcuni casi , come quello dell’ HAMAP , sono pubbliche.