ib chemistry on ict, 3d software, chimera, jmol, swiss pdb, pymol for internal assessment on...
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Electrostatic Potential (ESP)Measure polarizationElectron Map densityElectron distribution
Dipole MomentMeasure bond length/angle
Measure bond strength
Organic software for 3D model
Click here download Rasmol
Click here download PyMolClick here download Jmol
Click here Chem EDDL
Click here chemical search. Click here CRC database
Modelling and 3D representation
Chemistry Database
Click here Spectra database(OhioState) Click here Spectra database (NIST)
Click here chem finder.
Spectroscopic Database
Click here down Swiss PDB
Modelling and 3D representation
Click here crystallography database.
✓ ✓
Click here NIST data
✓Click here download Arguslab
Click here chem axon
Click here download Avagrado
Click here chem EdDL
Click here download chimera✓
Measure polarizationElectron Map densityElectron distribution
Electrostatic Potential (ESP)Dipole Moment
Measure bond length/angleMeasure bond strength
Organic software for 3D model
Click here download Rasmol
Click here download PyMolClick here download Jmol
Click here Chem EDDL
Click here chemical search.
Modelling and 3D representation
Quick Chemistry Database Check
Click here down Swiss PDB
Modelling and 3D representation
✓ ✓
Click here NIST data
✓Click here download Arguslab
Click here chemaxon quick chem check
Click here download Avagrado
Click here chem EdDL
Click here for Visualization/3D sources
Click here download Marvin Sketch
Click here quick chemical checkClick here quick chemical check
Type PDB code – 4HHBRight click – select Hetero Select - HETATM – HEM
4 Heme is display from 4 chains
Measure bond length/angleMeasure number H2 bonds
Measure bond strengthProtein 1, 2 , 3O structure
Presence of disulfide bondPresence alpha and beta pleated sheet
Click here J mol protein video
Chemical viewer 3D structure (Jmol)
Uses molecular modelling
1
J mol executable file
Measure distance
Select measure – distance for porphyrin ringMeasure ring size/distance Fe from planeSelect protein – by residue – HistidineMeasure and locate His F8 Measure and locate His E7
final heme – click here
J mol executable file
1
Type 4HHB into protein data bank
Look for ligand Heme
Model kit to design molecule
Click here deoxyhemoglobin chimera
22
3
4
3
4
final productAll histidine shown
Get structure fromPDB and MOL
Measure bond length/angleMeasure number H2 bonds
Measure bond strengthProtein 1, 2 , 3O structure
Presence of disulfide bondPresence alpha and beta pleated sheet
Protein Data BankProtein database key in - PDB 4HHB
Click here Chimera tutorial
1
2
Uses molecular modelling
1
2
Chemical viewer 3D structure (Chimera)
Download PDB text file
File – fetch by ID- 4HHB
Select – residue – HEMSelect – chain A – Action – Ribbon – HideSelect – chain B,C,D - Action – ribbon HideDisplay only ligand Heme
Tool- structural analysis - DistanceSelect 2 atom -by press control/shift/left click select 2 pointsTool – structure analysis – create to get distance
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Check here 4HHB Chimera 1MBOSelect Histidine that are close to ringLocate His F8 and E7Make measurement
Click here download chimera
Tool – Sequence – choose sequence for 4 chainsIdentify amino acids of interest
4
Measure bond length/angleMeasure number H2 bonds
Measure bond strengthProtein 1, 2 , 3O structure
Presence of disulfide bondPresence alpha and beta pleated sheet
Organic software for 3D model (Pymol)
1 1
Click here - Protein Data BankProtein database key in - PDB 4 letter code
3
Click here download PyMol
Click here Pymol video tutorial
Click file – open your download pdb file from Protein Data bankGet to command term – Type fetch 4HHBH - Hide – S - Show cartoon – C – Type by ss
Select 4 Hem – Look for 4 HemesSelect 4HHB – H – hide everythingSelect Heme – Show stickLook His – select and name His F8 and His E7
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Press S – sequence at bottom screen.Right click – zoom inSelect HEM - hemoglobin
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Uses molecular modelling
2
Select heme – right click – action – around 5ALook for His F8 and E7 around hemeMake measure for distanceDouble click to display name of atom
Measure bond length/angleMeasure number H2 bonds
Measure bond strengthProtein 1, 2 , 3O structure
Presence of disulfide bondPresence alpha and beta pleated sheet
Protein Data BankProtein database key in - PDB 4HHB
Click here Swiss PDB tutorial
1
2
Uses molecular modelling
1
2
Chemical viewer 3D structure (Swiss PDB)
Download PDB text file
File – open 4HHB pdb downloaded from databank
Window – Control panelRemove – side chainSelect – Group kind – HETATMDisplay – stereo viewShow only selected 4 Heme
Click here down Swiss PDB
Select – Group kind – HistidineSelect – Residue – close to 2ALocate Histidine and make measurement
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Check for heme and Histidine only from control panel
Select Histidine that are close to ringLocate His F8 and E7 and make measurement
4
Heme
Hemoglobin - 4 chain - 4 heme (porphyrin) - 4 Fe 2+
Fe 2+
Heme (porphyrin)
Hemoglobin - 2 alpha chain - 144 amino acid - 2 beta chain - 146 amino acid
vs
Myoglobin - 1 chain – 1 heme (porphyrin) – 1 Fe2+
- 154 amino acids
HemoglobinMyoglobin
Fe 2+
Heme (porphyrin)
PDB code files
Oxyhemoglobin – 1GZX, 1JY7Deoxyhemoglobin – 1A3N, 4HHB, 2HHB, 1HBB, 1G9V, 101JMyoglobin – 4MBN, 3RGK, 5MBNFetal hemoglobin – 1FDMSickle cell Hemoglobin – 2HBS, 1NEJ
PDB file type for data analysis1
Analyze using Chimera/Pymol/Swiss PDB/Jmol1
Chimera Swiss PDB
JmolPymol
Possible Research Question
Measuring using 3D modelling
Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
-What is the distance bet Fe and His E7 and F8, and are they the same for diff heme found in hemoglobin/myoglobin-Is His E7/F8 orientation similar for Oxy, Deoxy and Myoglobin.-Is there any differences bet distance/position/orientation of porphyrin ring for Hemoglobin and Myoglobin-How is Fe2+ located, along or out of plane for Hemo/Myoglobin-Is the distance bet Fe and ligand N of porphyrin the same for Hemoglobin/Myoglobin-Is structure/size of porphyrin ring same for α and β chain-Is there any variation in terms of Fe and His E7/F8 for fetal hemoglobin and sickle cell hemoglobin-Why His E7 and F8 are located in such a way across many different species? Are their orientation highly conserved and why?
Click here NCBIClick here UCSC
Click here Ensembl
Structural similarity and differences bet Hemoglobin and Myoglobin
Myoglobin hemoglobin
Vs
Hemoglobin Chimera Pymol Jmol Swiss PDB Mean
Orientation His/Fe Similar Similar Similar Similar Similar
Bond length N - Fe 2.12A 1.90A 2.02A 2.02A 2.01A
Bond length Fe – E7 5.93A 5.80A 5.45A 5.42A 5.55A
Bond length Fe – F8 2.25A 2.05A 2.10A 2.21A 2.13A
Chimera Swiss PDB
Data source
Myoglobin Chimera Pymol Jmol Swiss PDB Mean
Orientation His/Fe Similar Similar Similar Similar Similar
Bond length N - Fe 2.02A 2.11A 2.15A 2.32 2.14A
Bond length Fe – E7 5.80A 5.71A 5.56A 5.25A 5.25A
Bond length Fe – F8 2.15A 2.25A 2.11A 2.21A 2.21A
His E7
His F8
Fe
N
Possible Research Question Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here NCBIClick here UCSC
Click here Ensembl
Structural similarity and differences bet Hemoglobin and Myoglobin
Myoglobin hemoglobin
vs
Chimera Swiss PDB
Evaluation and Limitation using 3D modelling
Must use a variety of sources/programme to verify/validate the validity and reliability of data collectedAverage is computed from diff software and checked with database to confirm.Check on methodological limitation using 3D model. (MUST perform 3D Optimization to most stable form structure.Critical and skeptical of result produced by computational chemistry. Major limitation of computation, they assume non-interacting molecule. (Ideal situation, ex molecule in vacuum or isolated state)Most appropriate molecule are those whose coordinates are not theoretical but derive from experimental structural determination(using X ray diffraction)Be careful of predicted arrangement from simulation /3D modelData sources are supported using diff method/3D model/databaseCertain database like NIST and CRC are more reliable source Check if there is a good agreement bet CRC, diff databases and 3D model prediction before making conclusionComputation programme is always based on approximation and we cannot conclusive prove anythingReflect of validity and reliability of dataIs model a true representation of reality?
-What is the distance bet Fe and His E7 and F8, and are they the same for diff heme found in hemoglobin/myoglobin-Is His E7/F8 orientation similar for Oxy, Deoxy and Myoglobin.-Is there any differences bet distance/position/orientation of porphyrin ring for Hemoglobin and Myoglobin-How is Fe2+ located, along or out of plane for Hemo/Myoglobin-Is the distance bet Fe and ligand N of porphyrin the same for Hemoglobin/Myoglobin-Is structure/size of porphyrin ring same for α and β chain-Is there any variation in terms of Fe and His E7/F8 for fetal hemoglobin and sickle cell hemoglobin-Why His E7 and F8 are located in such a way across many different species? Are their orientation highly conserved and why ?
- Porphyrin gp of heterocyclic made of 4 pyrrole subunit- Porphyrin macrocycle has 26 (delocalized) pi electron, obey Hückel rule - It is aromatic, 4n+2 π. (Highly conjugated system)
Heme
PorphyrinHeme = Fe + porphyrins ring
Heme
Heme A Heme B Heme C
Mitochondria- cytochrome c oxidase- electron transport
O2
Heme = Fe + porphyrin ring – carry O2
Fe2+ located
Most abundant Hemoglobin and Myoglobin
Mitochondria- cytochrome c - electron transport
Fetal Hemoglobin (2α22γ2)
Human Hemoglobin (2α2 2β2)
Sickle cell Hemoglobin (2α22βS
2)Myoglobin 1 α chain
Carbaminohemoglobin Carboxyhemoglobin Oxyhemoglobin
Hemoglobin A - 2 alpha and 2 beta chainsHemoglobin A2 - 2 alpha and 2 delta chainsHemoglobin F - 2 alpha and 2 gamma chainsHeme (porphyrin) bind to Fe2+ using 4 nitrogen atom (histidine gp) Porphyrin
- as electron-pair donor - polydentate ligandFe form 2 additional bonds, one on each side of the heme plane. These binding sites call fifth and sixth coordination sites. This hisitidine is referred as proximal Histidine F8The sixth coordination site bind oxygen with His E7 nearby
Deoxygenated hemoglobin formFe2+ - out planeCan’t fit the ring
Heme
Hemoglobin - 4 chain - 4 heme (porphyrin) - 4 Fe 2+
Fe 2+
Heme (porphyrin)
Oxygenated formFe2+ - located in planeFit the ring
Deoxyhemoglobin
Fe2+ out planeCan’t fit the ringOut by 0.06nm
Fe2+ in planeFit the ring
Human hemoglobin - 2 alpha chain - 144 amino acid - 2 beta chain - 146 amino acid
Fe bind to six ligand. 4 with N atom of porphyrinFifth ligand is donated by His 93 (F8) O2 add to Fe as sixth ligandO2 tilt relative to perpendicular of heme plane
His F8His F8 His F8
His E7His E7His E7
Oxyhemoglobin
Heme
Hemoglobin - 4 chain - 4 heme (porphyrin) - 4 Fe 2+
Fe 2+
Heme (porphyrin)
Hemoglobin - 2 alpha chain - 144 amino acid - 2 beta chain - 146 amino acid
Fe bind to six ligand. 4 with N atom of porphyrinFifth ligand is donated by His F8 O2 add to Fe as sixth ligandO2 tilt relative to perpendicular of heme plane
His E7 locate over Fe, force CO to bind to Fe at an angle. This steric hinderance reduce afinity of CO in hemoglobin. O2 bind to Fe at an angle, its binding not affected by presence of His E7.
His (E7)
His (F8)
vs
Myoglobin - 1 chain – 1 heme (porphyrin) - 1 Fe2+
- 154 amino acids
HemoglobinMyoglobin
Fe 2+
Heme (porphyrin)
His (F8)
His (E7)
C≡O