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Riassumo le cose da fare nel mese di marzo (soprattutto con la metadinamica):

proj
Annexin I Binding S100/AnnI

Virtual screening N terminale

Yadamp2 Preparare script Yadamp/grimd per il folding di corti peptidi Lo script deve incorporare le idee del bias exchange metadynamics
APP Binding energy

Effetto della membrana

SMS1 Folding bias exchange
Valinomycin Best conformation

Calcolo binding energy VLM/met

Calcolo binding energy VM/memb

SMD Yasara

Metadynamics con la distanza VLM/Met come CV

Metadynamics con la distanza VLM/memb come CV

ALY/AzoALY Dinamiche in membrana/analisi

Binding energy membrana

Folding in membrana

metadyn
Assisted folding

 

Period Name Topic Location Key dates
Mar 4-6 CDDD Modeling Verona
Apr 2-4 CECAM How proteins can shape and sense membranes--a closer look at hybrid models FU Berlin
May 7-9 CECAM Dissipative Particle Dynamics: Foundations to Applications Lausanne
May 25-27 CBSB Computational biophysics Gdansk April 30
Jun 10-12 CECAM Binding free energy and kinetics: computation meets experiments IIT Genova
Jun 25-27 ETH Symposium
Sept 7-10 ECCB Computational biology Strasbourg March 28
Sept 22-25 POLYSOLVAT Polymers Salerno
Oct ?? BIONAM2014 Salerno
Nov 5-7 Antibiotic alternatives for the new millennium Antibiotics London Sept 20

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...
European journal of medicinal chemistry

 

List 1

Top 20 Articles, in the Domain of Article 22325123 and Keywords 'membrane molecular dynamics', Since its Publication (2012)

1. LAMBADA and InflateGRO2: efficient membrane alignment and insertion of membrane proteins for molecular dynamics simulations.

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Schmidt TH, Kandt C.
J Chem Inf Model; 2012 Oct 22;52(10):2657-69.

 

2. Structure and orientation of bovine lactoferrampin in the mimetic bacterial membrane as revealed by solid-state NMR and molecular dynamics simulation.
Tsutsumi A, Javkhlantugs N, Kira A, Umeyama M, Kawamura I, Nishimura K, Ueda K, Naito A.
Biophys J; 2012 Oct 17;103(8):1735-43.

 

3. Characterization of adenosine receptor in its native environment: insights from molecular dynamics simulations of palmitoylated/glycosylated, membrane-integrated human A(2B) adenosine receptor.
Mansourian M, Madadkar-Sobhani A, Mahnam K, Fassihi A, Saghaie L.
J Mol Model; 2012 Sep;18(9):4309-24.

 

4. Supramolecular structure of membrane-associated polypeptides by combining solid-state NMR and molecular dynamics simulations.
Weingarth M, Ader C, Melquiond AS, Nand D, Pongs O, Becker S, Bonvin AM, Baldus M.
Biophys J; 2012 Jul 3;103(1):29-37.

 

5. Insights into buforin II membrane translocation from molecular dynamics simulations.
Elmore DE.
Peptides; 2012 Dec;38(2):357-62.

Abstract | More from the author | Email delmore@ wellesley.edu | Citation export

 

6. Understanding the interaction between valsartan and detergents by NMR techniques and molecular dynamics simulation.
Cao C, Mao J, Li F, Yang M, He H, Jiang L, Liu M.
J Phys Chem B; 2012 Jun 28;116(25):7470-8.

 

7. Membrane active antimicrobial activity and molecular dynamics study of a novel cationic antimicrobial peptide polybia-MPI, from the venom of Polybia paulista.
Wang K, Yan J, Dang W, Liu X, Chen R, Zhang J, Zhang B, Zhang W, Kai M, Yan W, Yang Z, Xie J, Wang R.
Peptides; 2013 Jan;39:80-8.

 

8. Molecular dynamics simulation of cation-phospholipid clustering in phospholipid bilayers: possible role in stalk formation during membrane fusion.
Tsai HH, Lai WX, Lin HD, Lee JB, Juang WF, Tseng WH.
Biochim Biophys Acta; 2012 Nov;1818(11):2742-55.

 

9. Visualizing functional motions of membrane transporters with molecular dynamics simulations.
Shaikh SA, Li J, Enkavi G, Wen PC, Huang Z, Tajkhorshid E.
Biochemistry; 2013 Jan 29;52(4):569-87.

 

10. Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane-water partition coefficients.
Jakobtorweihen S, Ingram T, Smirnova I.
J Comput Chem; 2013 Jun 5;34(15):1332-40.

Abstract | More from the authors | Email jakobtorweihen@ tuhh.de | Citation export

 

11. The association of polar residues in the DAP12 homodimer: TOXCAT and molecular dynamics simulation studies.
Wei P, Zheng BK, Guo PR, Kawakami T, Luo SZ.
Biophys J; 2013 Apr 2;104(7):1435-44.

 

12. Molecular dynamics simulations of a new branched antimicrobial peptide: a comparison of force fields.
Li J, Lakshminarayanan R, Bai Y, Liu S, Zhou L, Pervushin K, Verma C, Beuerman RW.
J Chem Phys; 2012 Dec 7;137(21):215101.

Abstract | More from the authors | Email lijg@ bii.a-star.edu.sg | Citation export

 

13. Lipid interaction and membrane perturbation of human islet amyloid polypeptide monomer and dimer by molecular dynamics simulations.
Zhang Y, Luo Y, Deng Y, Mu Y, Wei G.
PLoS One; 2012;7(5):e38191.

 

14. Thermal decomposition of a honeycomb-network sheet: a molecular dynamics simulation study.
Paturej J, Popova H, Milchev A, Vilgis TA.
J Chem Phys; 2012 Aug 7;137(5):054901.

Abstract | More from the authors | Email jpaturej@ univ.szczecin.pl | Citation export

 

15. Membrane sculpting by F-BAR domains studied by molecular dynamics simulations.
Yu H, Schulten K.
PLoS Comput Biol; 2013 Jan;9(1):e1002892.

 

16. Structural analysis as an alternative to identify and determine mode of action of antimicrobial peptides: proposition of a kinetic model based on molecular dynamics studies.
Robles-Gomez EE, Flores-Villegas MC, Gonzalez-Manjarrez A, Soriano-Garcia M.
Protein Pept Lett; 2013 May;20(5):489-98.

 

17. Molecular Dynamics Simulations of Depth Distribution of Spin-Labeled Phospholipids within Lipid Bilayer.
Kyrychenko A, Ladokhin AS.
J Phys Chem B; 2013 May 16;117(19):5875-85.

 

18. Multiscale molecular dynamics simulations of membrane proteins.
Khalid S, Bond PJ.
Methods Mol Biol; 2013;924:635-57.

 

19. Free energy calculation of permeant-membrane interactions using molecular dynamics simulations.
Elvati P, Violi A.
Methods Mol Biol; 2012;926:189-202.

 

20. The activity of LE10 peptide on biological membranes using molecular dynamics, in vitro and in vivo studies.
Antunes E, Azoia NG, Matamá T, Gomes AC, Cavaco-Paulo A.
Colloids Surf B Biointerfaces; 2013 Jun 1;106:240-7.

 

 

List 2 Top 20 Articles, in the Domain of Article 22325123 and Keywords 'membrane molecular dynamics', in the Past 2 Months

1. Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane-water partition coefficients.
Jakobtorweihen S, Ingram T, Smirnova I.
J Comput Chem; 2013 Jun

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5;34(15):1332-40.

Abstract | More from the authors | Email jakobtorweihen@ tuhh.de | Citation export

 

2. The association of polar residues in the DAP12 homodimer: TOXCAT and molecular dynamics simulation studies.
Wei P, Zheng BK, Guo PR, Kawakami T, Luo SZ.
Biophys J; 2013 Apr 2;104(7):1435-44.

 

3. Structural analysis as an alternative to identify and determine mode of action of antimicrobial peptides: proposition of a kinetic model based on molecular dynamics studies.
Robles-Gomez EE, Flores-Villegas MC, Gonzalez-Manjarrez A, Soriano-Garcia M.
Protein Pept Lett; 2013 May;20(5):489-98.

 

4. Molecular Dynamics Simulations of Depth Distribution of Spin-Labeled Phospholipids within Lipid Bilayer.
Kyrychenko A, Ladokhin AS.
J Phys Chem B; 2013 May 16;117(19):5875-85.

 

5. Multiscale molecular dynamics simulations of membrane proteins.
Khalid S, Bond PJ.
Methods Mol Biol; 2013;924:635-57.

 

6. The activity of LE10 peptide on biological membranes using molecular dynamics, in vitro and in vivo studies.
Antunes E, Azoia NG, Matamá T, Gomes AC, Cavaco-Paulo A.
Colloids Surf B Biointerfaces; 2013 Jun 1;106:240-7.

 

7. Conformational changes of β-carotene and zeaxanthin immersed in a model membrane through atomistic molecular dynamics simulations.
Cerezo J, Zúñiga J, Bastida A, Requena A, Cerón-Carrasco JP.
Phys Chem Chem Phys; 2013 May 7;15(17):6527-38.

 

8. Molecular dynamics of water in the neighborhood of aquaporins.
Ozu M, Alvarez HA, McCarthy AN, Grigera JR, Chara O.
Eur Biophys J; 2013 Apr;42(4):223-39.

 

9. Simulation studies of the mechanism of membrane transporters.
Enkavi G, Li J, Mahinthichaichan P, Wen PC, Huang Z, Shaikh SA, Tajkhorshid E.
Methods Mol Biol; 2013;924:361-405.

 

10. Molecular dynamics simulations of the adenosine a2a receptor: structural stability, sampling, and convergence.
Ng HW, Laughton CA, Doughty SW.
J Chem Inf Model; 2013 May 24;53(5):1168-78.

 

11. Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel.
Ulmschneider MB, Bagnéris C, McCusker EC,

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Decaen PG, Delling M, Clapham DE, Ulmschneider JP, Wallace BA.
Proc Natl Acad Sci U S A; 2013 Apr 16;110(16):6364-9.

 

12. Behavior of fluorescent cholesterol analogues dehydroergosterol and cholestatrienol in lipid bilayers: a molecular dynamics study.
Robalo JR, do Canto AM, Carvalho AJ, Ramalho JP, Loura LM.
J Phys Chem B; 2013 May 16;117(19):5806-19.

 

13. SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein.
Dony N, Crowet JM, Joris B, Brasseur R, Lins L.
Int J Mol Sci; 2013;14(6):11510-26.

 

14. Molecular dynamics study of lipid bilayers modeling the plasma membranes of normal murine thymocytes and leukemic GRSL cells.
Andoh Y, Okazaki S, Ueoka R.
Biochim Biophys Acta; 2013 Apr;1828(4):1259-70.

 

15. The Glove-like Structure of the Conserved Membrane Protein TatC Provides Insight into Signal Sequence Recognition in Twin-Arginine Translocation.
Ramasamy S, Abrol R, Suloway CJ, Clemons WM Jr.
Structure; 2013 May 7;21(5):777-88.

 

16. Validation of Depth-Dependent Fluorescence Quenching in Membranes by Molecular Dynamics Simulation of Tryptophan Octyl Ester in POPC Bilayer.
Kyrychenko A, Tobias DJ, Ladokhin AS.
J Phys Chem B; 2013 May 2;117(17):4770-8.

 

17. Ab initio molecular dynamics.
Laasonen K.
Methods Mol Biol; 2013;924:29-42.

 

18. Molecular dynamics simulations of lipid bilayers: simple recipe of how to do it.
Martinez-Seara H, Róg T.
Methods Mol Biol; 2013;924:407-29.

 

19. The gating mechanism of the human aquaporin 5 revealed by molecular dynamics simulations.
Janosi L, Ceccarelli M.
PLoS One; 2013;8(4):e59897.

Abstract | More from the authors | Email Lorant.Janosi@ dsf.unica.it | Citation export

 

20. Protonation States in molecular dynamics simulations of Peptide folding and binding.
Ben-Shimon A, Shalev DE, Niv MY.
Curr Pharm Des; 2013;19(23):4173-81.

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Ci mancherai!

Per ottenere una analisi QSAR di tutti i peptidi antimicrobici e ottenere un modello matematico che trovasse una correlazione tra questi e la MIC ho utilizzato Material Studio. Dopo aver ordinato in un'unica tabella tutti i descrittori gia posseduti per ciascun AMP ho effettuato diverse suddivisioni.
Ho diviso gli AMP prima per quelli attivi su Gram+ e Gram-, poi li ho suddivisi ancora in base al loro organismo target. Una volta finito ho importato in material studio i file .mol degli AMP e li ho caricati nelle rispettive Study Table.

Per importare i file nel folder desiderato basta cliccare con il tasto destro su quest'ultimo (per es. Structures o Gram+) e selezionare "Import". Questo procedimento funziona anche con più file per volta l'importante è ricordarsi di salvare sempre dopo aver importato qualsiasi oggetto.

In seguito per calcolare altri descrittori ho creato una nuova Study Table -> ho selezionato la colonna in cui voglio inserirli e i file struttura di cui mi voglio calcolare i nuovi descrittori -> tasto destro e seleziono "Insert to" -> Poi clicco sul pulsante "Models" in alto a sinistra e seleziono i calcoli che voglio effettuare. Nel mio caso ho selezionato tutto tranne i "VAMP" e i "DMol3" in quanto questi sono descrittori quantistici il cui calcolo è estremamente lento.

Dopo aver ottenuto queste tabelle le ho ripulite manualmente da eventuali colonne di dati che non è stato possibile calcolare. Per esempio il Modello su E.Coli è stato generato in questo modo:

-> Ho creato una study table chiamata 'Modello_Coli' contenente 200 AMP attivi con 0 < MIC < 100 trovata sperimentalmente, 25 AMP con 101 < MIC > 499 e 13 AMP con una MIC arbitraria di 500 -> Ho selezionato la colonna della MIC (chiamata nel nostro caso 'Escherichia Coli') -> ho aperto il menu a tendina nella barra in alto 'Statistics', mouse su 'Model Building' e ho selezionato 'Genetic Function Approximation'.

-> All'interno della finestra che si è aperta ho: selezionato tutte le 'Periodic Variables'; in 'Equation Data' ho selezionato 'Use Quadratic Splines'; infine settato i 'Parameters' cosi come si può apprezzare dall'immagine in basso.

Al termine del calcolo ho ottenuto cinque e equazioni che una volta applicate, cliccando nel menu a tendina 'Modules' e su 'Apply Data' , forniscono una precisa previsione della MIC dei peptidi in studio, sia dei peptidi attivi che di quelli non attivi.

Intro.

Erano necessarie dei modelli molecolari di membrana in modo da poter effettuare test di binding di varie molecole e proteine;ho proceduto selezionando 14 tipi di membrane a diversa composizione:

  1. POPC
  2. POPE/POPC 50:50
  3. DMPC
  4. DOPC
  5. SM/CHOL 50:50
  6. SM/CHOL 60:40
  7. SM/CHOL 70:30
  8. SM/CHOL 80:20
  9. POhPC
  10. POhPE
  11. SMh/CHOL 50:50
  12. SMh/CHOL 60:40
  13. SMh/CHOL 70:30
  14. SMh/CHOL 80:20

Procedimento.Dopo aver scaricato i file .yob necessari e averli caricati sul programma sono andata a realizzare le varie membrane elencate, di dimensioni 100x100 Å, tramite il software CELLmicrocosmos MembraneEditor2 (http://89.46.69.105:9091/index.php/creazione-di-membrane-semplici-e-con-raft-lipidici-grazie-a-cell2microcosmos/) salvando i rispettivi file .pdb nella cartella C://MembraneEditor/Membrane_Files/Definitive.

In particolare per quanto riguarda le membrane costituite da POPE-POPC sono andata a realizzarne 3 differenti tipi in quanto ho usato sia lo .yob scaricato dal database sia uno modificato da me che ho chiamato POPE_Simona;sono state quindi sviluppate membrane con composizione:

  • POPE-POPC 50:50
  • POPE_Simona-POPC 50:50
  • POPE-POPE_Simona-POPC 25:25:50

Discorso analogo per le membrane contenenti POhPE.

In seguito ho caricato singolarmente i file su Yasara andando a definire un cella di simulazione di 0 Å intorno agli atomi;fatto ciò ho calcolato le dimensioni esatte della cella in Å (>Cell) ,il numero di residui dei singoli componenti (>CountRes) e,ove possibile,l'area occupata dai singoli lipidi.I risultati sono elencati nella tabella sottostante (Tab.1)

Tab.1

Membrane

Cell (100x100 Å)

Numero residui

Note (A=area)

POPC

97.75x63.00x97.27 Å

237

A= 51,40 Å2

POPE/POPC 50:50

97.08x62.75x97.54 Å

POC (111) POPE (110)

POPE_Simona-POPC 50:50

97.10x72.95x97.08 Å

POC (123) POPE_S (123)

POPE-POPE_Simona-POPC 25:25:50

95.97x72.96x97.45 Å

POC (113) POPE (113)

DMPC

97.90x63.07x97.85 Å

232

A=53,22 Å2

DOPC

97.30x68.46x96.69 Å

229

A=58,17 Å2

SM/CHOL 50:50

97.83x54.73x97.00 Å

BSM (135) CHL (137)

SM/CHOL 60:40

96.53x54.89x97.43 Å

BSM (146) CHL (99)

SM/CHOL 70:30

98.46x54.91x96.55 Å

BSM (164) CHL (72)

SM/CHOL 80:20

97.14x54.85x97.35 Å

BSM (175) CHL (44)

POhPC

97.50x62.86x97.22 Å

224

A=54,72 Å2

POhPE

97.85x51.70x97.09 Å

190

A=53,25 Å2

POhPE_Simona

97.37x72.96x97.59 Å

237

A=59,95 Å2

SMh/CHOL 50:50

97.68x62.58x97.60 Å

SMH (122) CHL (124)

SMh/CHOL 60:40

97.79x62.65x97.62 Å

SMH (136) CHL (91)

SMh/CHOL 70:30

97.95x62.68x97.89 Å

SMH (148) CHL (64)

SMh/CHOL 80:20

97.20x62.64x97.92 Å

SMH (159) CHL (41)

Le membrane dovranno essere ulteriormente compattate e modificate in modo da diventare modelli ideali per ulteriori esperimenti.