Molegro Molecular Viewer (MMV) Program de vizualizare off-line a proteinelor si a interactiunii ligand - proteina
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1 Molegro Molecular Viewer (MMV) Program de vizualizare off-line a proteinelor si a interactiunii ligand - proteina
2 Molegro Molecular Viewer - aplicatie pentru studiul si analiza interactiunii dintre liganzi si proteine (macromolecule). Programul permite deschiderea fisierelor cu extensia pdb, salvate din baza de date RCSB Protein Data Bank (rcsb.org/pdb).
3 Fisierele proteinei de interes se descarca de pe site-ul (rcsb.org), din pe pagina dedicate proteinei respective. Pentru deschiderea fisierului unei proteine se foloseste comanda import
4 MMV se bazeaza pe notiunea de "workspaces". Un "spatiu de lucru" poate fi salvat, curatat, inlocuit sau lipit la alte "spatii de lucru".
5 Molegro Molecular Viewer toolbar: - usureaza accesul la actiunile uzuale de vizualizare a unor molecule. Import molecule Fit to screen Screen capture Search Label dialog Visualization settings Hydrogens On/Off
6 Fereastra Workspace Explorer: contine informatii despre: - molecule (proteine, liganzi, moleculele de apa) - etichete (labels), - suprafete, - scheletul proteinei (backbones), - cavitati Butonul dreapta al mouse-ului (context menu) permite: Exportul moleculei (format PDB, Mol2, SDF) Editare in fereastra Workspace Properties Redenumirea moleculei Eliminarea unor elemente din fereastra activa Clonarea ligandului sau a proteinei (copy) Convertirea proteinei la ligand Prepararea de molecule Crearea de etichete, suprafete si schelete (backbones) Fitarea moleculei in Visualization Window
7 Fereastra Workspace Explorer poate fi folosita pentru a inspecta molecula in Visualization Window (click pe molecula de interes)
8 Properties Window contine informatii despre obiectele selectate in Visualization Window
9 Visualization Window: pentru vizualizarea de proteine, liganzi, suprafete, cavitati, molecule de apa (doar oxigen), etichete, notatii, scheletul proteinei, legaturi de hidrogen,... Modificarea modului de afisare se face activand Visualization settings : - stilul si culoarea moleculelor, - rendering options, - legaturile de hydrogen, - interactiunile electrostatice
10 Style and color : moleculele pot fi reprezentate ca - ball-and-sticks, - sticks, - space-fill (CPK), - wireframe Ball and Stick : atomii sunt sfere iar legaturile sunt reprezentate ca cilindrii. Atom Scale seteaza fractia razei Van der Waals care este folosita ca raza a sferelor. Bond Scale este diametrul legaturii in Angstrom Reprezentarea Ball-and-stick este folosita pentru prepararea liganzilor: legatura vizualizata indica ordinul legaturii, culoarea ne spune daca legatura este rigida (brown or red) sau flexibila (green). Stick : legaturile sunt figurate ca cilindrii. Bond Scale este diametrul legaturii in Angstrom Spacefill (CPK). Atomii sunt figurati ca sfere. Legaturile nu sunt vizualizate Atom Scale seteaza fractia razei Van der Waals care este folosita ca raza a sferelor. Wireframe cel mai rapid mod de desenare a moleculelor: legaturile sunt fogurate ca linii intre atomi. Atomii nu sunt figurati (dar este posibil sa fie selectati). Toate legaturile sunt desenate cu o singura linie indifferent daca sunt duble, simple sau delocalizate.
11 Setari coloring styles ce pot fi aplicate tuturor moleculelor Fixed Color Color By Element (CPK) Color By Id (or Chain) Color By Id (carbons only) Color By Hydrogen Bond Type (rosu = donori, verde = acceptori, galben = atomi capabili si sa doneze si sa accepte atomi de hidrogen). Color By Partial Charge (albastru = pozitiv, rosu = negativ) Setari coloring styles ce pot fi aplicate numai proteinelor Color By Temperature (B-Factor) (albastru = Tmin, rosu = Tmax) factorul B (Temperatura) indica masura in care atomul vibreaza in jurul pozitiei de echilibru Color By Amino Acid Type Color By Shapely Residue Color By Residue ID (rainbow effect). Color By Secondary Structure (rosu = -helices, albastru = -strands, galben = -turns. Color By Hydrophobicity (rosu = aminoacid hydrophilic, albastru = amoinoacid hydrophobic.
12 Rendering: modificarea setarilor de afisaj: fog, 3D projection, background, label Interactions: hydrogen bonds; electrostatic interactions Views: moduri presetate de reprezentare
13 Toate rotatiile se fac in jurul unui centru de rotatie care poate fi ales: Set as Rotational Center Toate obiectele din Visualization Window (spatiul 3D) pot fi actionate prin "context menu" (click dreapta)
14 Console Window (in josul ecranului) afiseaza informatiii, avertizari si erori
15 Se pot crea vizualizari ale suprafetei moleculei: Tools ; Surfaces. Se selecteaza molecula dorita (proteina, ligand, etc) Se selecteaza tipul de suprafata (electrostatic, hidrofobicitate, )
16 Clipping Planes: modificarea planului de vizualizare (ex. pentru vizualizarea interiorului unei proteine) Se activeaza din meniul Window : Se ajusteaza planul apropiat si cel indepartat pana cand este vizualizata regiunea dorita.
17 Search Space: poate fi folosit pentru a crea o suprafata moleculara partiala: - se ascund moleculele in exteriorul spatiului creat; Se seteaza centrul suprafetei: - centrul proteinei - centrul ligandului (daca exista) Se seteaza raza sferei
18 Hide Residues permite ascunderea reziduurilor (aminoacizilor) din exteriorul unei sfere predefinite (centru, raza) Crop molecules: stergerea unor parti din molecula (eliminarea regiunilor nerelevante). Workspace Finder: cautarea rapida a reziduurilor/atomilor sau a moleculelor.
19 Sequence Viewer: (se activeaza din "Tools" sau "Window"): permite inspectarea rezidurilor proteinei. Pentru evidentiere se selecteaza aminoacidul Pentru informatii se plaseaza cursorul pe aminoacidul respectiv
20 Masuratori si notatii: Daca se selecteaza 2 atomi: - in Properties Window este afisata distanta dintre ei. Daca se selecteaza 3 atomi conectati: - in Properties Window este afisat unghiul dintre ei. Daca se selecteaza o legatura: - in Properties Window este afisat unghiul de torsiune definit prin aceasta legatura. Pentru a face diferite notatii: - se selecteaza 1 atom "click dreapta Create Point Annotation - se selecteaza 2 atomi "click dreapta Create Distance Annotation - se selecteaza 3 atomi "click dreapta Create Angle Annotation - se selecteaza 4 atomi "click dreapta Create Dihedral Angle Annotation
21 - Create Backbone: din "context menu" (click dreapta) pe categoria "Protein" in Workspace Explorer - cartoon style (vizualizarea structurii secundare) - tube style (scheletul proteinei este reprezentat ca o curba polinomiala ce trece prin carbonii α ai fiecarui aminoacid)
22 - Create surface (electrostatic, hidrofobicitate,...) - din "Context menu" - Create labels (la proteina sau la ligand) - din "Context menu"
23 Structural Protein Alignment: se face prin identificarea rezidurilor identice din doua proteine si calcularea translatiilor si rotatiilor ce minimizeaza RMSD (root mean standard deviation) dintre carbonii alfa ai reziduurilor identice. - se selecteaza Tools, apoi Structural Protein Alignment. Proteina "target" este proteina ce va fi translatata si reorientata (in Visualization window).
24 Energy Map Visualization: se vizualizeaza campul de forte Steric favorable: regiunile favorabile plasarii unui atom nepolar. Potential electrostatic: rosu (sarcina electrostatica negativa), albastru (sarcina electrostatica pozitiva)
25 Model activitate practica: Vizualizarea unei proteinei (si a liganzilor) folosind "Molegro Molecular Viewer" 1) proteina :
26 2) Liganzii proteinei distanta dintre atomii C(8) si O(13) din: 1,20 A: unghiul dintre 2 legaturi adiacente: (C5-Se6-C7=102,14)
27 3) vizualizarea aminoacizilor aflati la 7 Å de centrul proteinei;
28 3) aminoacizii aflati la 10 Å de centrul ligandului;
29 4) aminoacidul din pozitia 10: Glycina, Structura secundara: Coil
30 4) aminoacidul din pozitia 166: Lysina, Structura secundara: Beta sheet
31 5) structura secundara a proteinei: fara ligand; "color by residue" cu ligand; "color by structure"
32 6) Etichetarea aminoaciziilor
33 7) Crearea suprafetei proteinei din punct de vedere electrostatic din punct de vedere al hidrofobicitatii
34 8) vizualizarea (concomitenta) suprafetei proteinei (solid), a unei portiuni a lantului de aminoacizi si a ligandului:
35 9) harti energetice (1EMA) sarcina electrostatica zone favorabile steric
36 zone favorabile acceptarii atomilor de hidrogen zone favorabile donarii atomilor de hidrogen
37 Suprapunerea celor 4 reprezentari energetice Molecula in reprezentare Backbone (cartoon, color by residue)
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