Difference between revisions of "Jmol-Application/C4/3D-Models-of-Enzymes/Khasi"

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(Created page with "{| border=1 || '''Time''' || '''Narration''' |- ||00:01 ||Khublei ïaphi baroh. Pdiang sngewbha sha kane ka tutorial halor '''3D Models of Enzymes in Jmol '''. |- ||00:08...")
 
 
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||Ka '''Input''' dialogue-box ka paw haka screen. Type ïaki saw tylli ki dak '''PDB code''' na bynta ka '''hexokinase''',  kata, '''3IDH'''  haka text-box.  
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||Ka '''Input''' dialog-box ka paw haka screen. Type ïaki saw tylli ki dak '''PDB code''' na bynta ka '''hexokinase''',  kata, '''3IDH'''  haka text-box.  
  
 
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Latest revision as of 15:51, 28 October 2020

Time Narration
00:01 Khublei ïaphi baroh. Pdiang sngewbha sha kane ka tutorial halor 3D Models of Enzymes in Jmol .
00:08 Ha kane ka tutorial, ngin pule ban: * Load structure jong Human Pancreatic Hexokinase haka Jmol panel
00:16 Pynpher ia ka display jong ka secondary structure
00:20 Highlight ki amino acid residue haka active site.
00:25 Highlight substrate bad ki cofactor jong ki enzyme.
00:30 Bad, peit ka Ramachandran plot na bynta u protein.
00:35 Ban bud ïa kane ka tutorial, phi dei ban don ka jing tip ïaka basic biochemistry
00:41 bad tip bha shaphang ka rukom treikam naka Jmol Application window.
00:46 Sngewbha peit ïaka tutorial Proteins and Macromolecules haka Jmol Application series.
00:53 lah ban ioh ïaka na ka link harum.
00:57 Ban record ïa kane ka tutorial, nga pyndonkam ka:* Ubuntu Operating System version 12.04
01:05 Jmol version 12.2.2.
01:08 Java version 7 bad * Mozilla Firefox browser 22.0.
01:16 Plie ïaka Jmol window bad load ka structure jong u hexokinase enzyme.
01:22 Nga long connect sha ka internet. Te, ngan load beit ïaka structure beit beit naka PDB website.
01:28 Ban leh kumta, plie ïaka File menu, hiar shapoh bad click ha u jingjied Get PDB.
01:37 Ka Input dialog-box ka paw haka screen. Type ïaki saw tylli ki dak PDB code na bynta ka hexokinase, kata, 3IDH haka text-box.
01:50 ïa une u code la ioh na ka website jong ka Protein Data Bank.
01:55 Lada phim don ka internet connection ba long: plie ïaka file pdb pyndonkam da u icon Open a file ha u tool bar.
02:06 Click ha u jingshon OK.
02:09 ïa ki 3D structure jong u hexokinase bala tip ruh kum ka glucokinase la plie haka screen.
02:16 Plie ïaka Console window pyndonkam daka File menu.
02:21 Kumba la pyni ha ka Console, ka structure haka panel ka dei naka bynta ka Human Pancreatic Glucokinase ryngkat ka substrate Glucose.
02:31 Khang noh ka Console.
02:34 Haka panel, ngi don ïaka model ball and stick jong ka hexokinase.
02:40 Weng ïaki water molecules na ka protein model haka panel.
02:44 ïa Kane ka rukom la batai bniah bha haka Jmol tutorial Proteins and macromolecules.
02:53 Shaphang u hexokinase Enzyme-
02:56 Hexokinase u dei u monomeric protein jong ki 465 amino acids.
03:02 u don artylli ki domains, Ka domain baheh bad ka domain barit.
03:07 Ka active-site na bynta kane ka enzyme la pynshong haka cleft hapdeng ki artylli ki domain.
03:14 Ka Active-site na bynta ka hexokinase ka don 3 tylli ki amino acid residue: Aspergine ha 204, Aspergine haka kyrdan ba 231 bad Glutamic acid ha 256.
03:30 U Alpha-D-Glucose u dei u substrate naka bynta une u enzyme.
03:34 Mynta to ngin leit phai pat sha ka Jmol panel.
03:38 Ngi lah ban jied bad highlight ïa ki jingpynlong jong u enzymes kum Substrate, Cofactors lane Amino acid residues haka active site.
03:49 Ban jied ïa uno uno u component- plie ïaka pop-up menu dakaba pyndonkam u right-click.
03:55 Hiar sha u jingjied Select.
03:57 Naka sub-menu, Proteins, jied By Residue name.
04:04 Ngi don ki amino acid residue ba marwei bala list hangne.
04:10 Click haka kyrteng jong u amino acid ban jied ïa u.
04:14 ïa ki amino acids ruh la group hapoh ki heading kum: Polar, Non-polar, Basic, Acidic, Uncharged ter ter.
04:26 Kiba la List haka Hetero menu, ki long ki metal ion potassium bad substrate glucose.
04:34 Ngi lah ban pynpher ïaka display jong u enzyme ban lap suk ïa ka substrate binding site.`
04:41 To ngin pynkylla ïaka display bad ka rong jong ki atoms jong ki protein.
04:46 Plie ïaka pop-up menu, leit sha Select bad hiar sha u jingjied Protein. Click ha All.
04:55 Plie biang ïaka pop-up menu, Hiar sha u Style, nangta sha u Scheme. bAd click ha u jingjied Sticks.
05:05 Mynta ngi don haka panel, ïa ka protein haka sticks display.
05:11 Mynta ban pynkylla ïa ka rong, - plie biang ïaka pop-up menu, leit sha Color >> Atoms bad click ha u jingjied Blue.
05:23 Ngi don haka screen ïaka model jong ka hexokinase haka rong blue bad haka sticks display.
05:30 Khmih thuh ïa u substrate Alfa-D-Glucose haka ball and stick display haka cleft.
05:38 Ban highlight ïa ka substrate- plie ïaka pop-up menu, leit sha Select, nangta Hetero bad click ha GLC-ALFA-D-GLUCOSE.
05:52 Plie biang ïaka pop-up menu, Hiar sha Style >> Scheme bad click ha u jingjied Sticks.
06:00 Ban pynkylla ïaka rong – Plie biang ïaka pop-up menu, Hiar sha Color >> Atoms bad click ha u jingjied White.
06:12 Haka panel, ïa u model jong ka hexokinase ryngkat ka jaka shong jong u substrate la highlight shai bha.
06:20 Ngi lah ban pynkylla ïa ka rong jong ki amino acids haka active site ban highlight ïaki.
06:26 ban leh kumta, ngi donkam ban type ki command ha ka Console window.
06:32 Kumba la la batai mynne, ki amino acids kiba don haka active-site ki long u Aspergine ha ka kyrdan ba 204, Aspergine haka kyrdan ba 231 bad Glutamic acid ha 256.
06:50 Plie ïaka console window pyndonkam ka File menu. Click ha Console.
06:57 Nga pyndonkam ka Kmag Screen magnifier ban pyni heh ïaka console window.
07:03 Ha u $ (dollar) prompt, type: "select" hapoh ki square brackets "Asn" na bynta u aspergine bad khang noh u bracket, "204" kata, ka kyrdan semicolon "color atoms orange".
07:25 ñion Enter.
07:27 Khmih thuh ba ki atom jong u aspargine residue mynta ki long rong orange.
07:33 ñion ïa u up-arrow button haka key board bad edit ïaka command.
07:39 Edit ïaka jaka shong u amino acid sha 231 bad ka rong jong ki atom sha rong saw.
07:48 ñion Enter.
07:51 ñion biang ïa u up-arrow key bad edit ïaka kyrteng jong u amino acid sha GLU, kata u, glutamic acid bad ka kyrdan sha 256.
08:06 bad, ka rong jong ki atom sha rong green bad ñion Enter.
08:13 Ngi don haka panel ïa ka 3D model jong ka hexokinase ryngkat ka substrate bad ka active site bala highlight.
08:23 Bala highlight ruh haka model u dei u potassium atom bala pyni hangne,haka rong purple.
08:30 Ngi lah ruh ban pyni ïa ki ramachandran plots na bynta u protein bala thmu haka jmol.
08:36 Ha ka console, ha u dollar($) prompt, type: plot ramachandran
08:45 ñion Enter.
08:47 Ha ka screen, ngi don ka ramachandran plot na ka bynta ka hexokinase.
08:54 Pyrshang ban load ïa ki enzymes bapher bapher pyndonkam da ki pdb files naka database.
09:00 Pynkylla ïaka display jong ka secondary structure.
09:04 To ngin Batai lyngkot. Ha kane ka tutorial, ngi la pule ban:: * Load ki structure jong ka Human Pancreatic Hexokinase pyndonkam u PDB code.
09:14 Pynpher ïaka display jong ka secondary structure.
09:17 Highlight ki amino acid residue haka active site.
09:21 Highlight ki substrate bad ki cofactor jong ki enzyme.
09:25 Bad,Peit ïa ka ramachandran plot naka bynta ki proteins.
09:30 Kum ka assignment: Load ïa ka dot pdb file jong u enzyme Lysozyme haka Jmol panel.
09:38 Highlight ïa u substrate bala khum sha u enzyme.
09:42 Highlight ki amino acids haka active site.
09:46 Hint: Shim ïa ka pdb file jong Lysozyme naka PDB database.
09:52 Peit ïaka video badon ha kane ka URL:
09:56 Ka batai lyngkot ïaka Spoken Tutorial project.
10:00 Lada phim don ka bandwidth ba biang, phi lah ban download bad peit ïaka.
10:04 Ka Spoken Tutorial project team:
10:07 Ka pynlong workshop bad Ka sam certificates.
10:10 Ban tip kham bniah, sngewbha thoh sha ngi
10:14 Spoken Tutorial project kadei shi bynta jong ka ‘‘‘Talk to a Teacher project.
10:19 La kyrshan ïaka daka National Mission on Education Lyngba ka ICT, MHRD, Sorkar India.
10:25 Khambun ka jingtip halor kane ka mission kadon ha kane ka link:
10:30 ïa kane ka script la pynkylla sha ka ktien Khasi da I Hezekiah Lyngdoh na Shillong. Khublei ba phi la ïasnohlang.

Contributors and Content Editors

Hezekiah2016, PoojaMoolya

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