IB Chemistry on ICT, 3D software, Chimera, Jmol, Swiss PDB, Pymol for Internal Assessment on Hemoglobin, Myoglobin and Cytochrome

1. Electrostatic Potential (ESP)
Measure polarization
Electron Map density
Electron distribution
Dipole Moment
Measure bond length/angle
Measure bond strength
Organic softwarefor 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
✓

2. Measure polarization
Electron Map density
Electron distribution
Electrostatic Potential (ESP)
Dipole Moment
Measure bond length/angle
Measure bond strength
Organic softwarefor 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 DatabaseCheck
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 check
Click here quick chemical check

3. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Protein Data Bank
Protein database key in - PDB 4HHB
Click here Chimera tutorial
1
2
Uses molecular modelling
1
2
Chemicalviewer 3D structure(Chimera)
Download PDB text file
File – fetch by ID- 4HHB
Select – residue – HEM
Select – chain A – Action – Ribbon – Hide
Select – chain B,C,D - Action – ribbon Hide
Display only ligand Heme
Tool- structural analysis - Distance
Select 2 atom
-by press control/shift/left click select 2 points
Tool – structure analysis – create to get distance
3
Check here 4HHB Chimera 1MBO
Select Histidine that are close to ring
Locate His F8 and E7
Make measurement
Click here download chimera
Tool – Sequence – choose sequence for 4 chains
Identify amino acids of interest
4

4. Type PDB code – 4HHB
Right click – select Hetero
Select - HETATM – HEM
4 Heme is display from 4 chains
Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence 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 ring
Measure ring size/distance Fe from plane
Select protein – by residue – Histidine
Measure 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
2
2
3
4
3
4
final product
All histidine shown
Get structure from
PDB and MOL

5. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Organic softwarefor 3D model (Pymol)
1 1
Click here - Protein Data Bank
Protein 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 bank
Get to command term – Type fetch 4HHB
H - Hide – S - Show cartoon – C – Type by ss
Select 4 Hem – Look for 4 Hemes
Select 4HHB – H – hide everything
Select Heme – Show stick
Look His – select and name His F8 and His E7
2
Press S – sequence at bottom screen.
Right click – zoom in
Select HEM - hemoglobin
4
Uses molecular modelling
2
Select heme – right click – action – around 5A
Look for His F8 and E7 around heme
Make measure for distance
Double click to display name of atom

6. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Protein Data Bank
Protein database key in - PDB 4HHB
Click here Swiss PDB tutorial
1
2
Uses molecular modelling
1
2
Chemicalviewer 3D structure(Swiss PDB)
Download PDB text file
File – open 4HHB pdb downloaded from databank
Window – Control panel
Remove – side chain
Select – Group kind – HETATM
Display – stereo view
Show only selected 4 Heme
Click here down Swiss PDB
Select – Group kind – Histidine
Select – Residue – close to 2A
Locate Histidine and make measurement
3
Check for heme and Histidine
only from control panel
Select Histidine that are close to ring
Locate His F8 and E7 and make measurement
4

7. Heme
Hemoglobin - 4 chain - 4 heme - 4 Fe 2+
Fe2+
Heme
(porphyrin)
Hemoglobin - 2 alpha chain - 144 amino acid
- 2 beta chain - 146 amino acid
Myoglobin - 1 chain – 1 heme – 1 Fe2+
- 154 amino acids
HemoglobinMyoglobin
Fe2+
Heme
(porphyrin)
PDB code files
Oxyhemoglobin – 1GZX, 1JY7
Deoxyhemoglobin – 1A3N, 4HHB, 2HHB, 1HBB, 1G9V, 101J
Myoglobin – 4MBN, 3RGK, 5MBN
Fetal hemoglobin – 1FDM
Sickle cell Hemoglobin - 2HBS, 1NEJ
Cytochrome(bovine) - 2B4Z
Cytochrome(horse) - 1HRC
Cytochrome(yeast) - 1YCC
Cytochrome(human) - 3NWV
PDB file type for data analysis
1
Analyze using Chimera/Pymol/Swiss PDB/Jmol
1
Chimera Swiss PDB
JmolPymol
Fe in cytochrome
1 polypeptide chain
Fe2+
Cytochrome c

8. Possible ResearchQuestion
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/Cytochrome
- Is His E7/F8 orientation similar for Hemoglobin, Myoglobin, Cytochrome
- Is there any differencesbet distance/position/orientationof porphyrin ring for
Hemoglobin, Myoglobin, Cytochrome
- How is Fe2+located, along or out of plane for Hemo/Myoglobin/Cytochrome
- Is distancebet Fe and ligand N of porphyrin the same for
Hemoglobin/Myoglobin/Cytochrome
- Is there any variation in terms of Fe and His E7/F8 for
Hemoglobin/Myoglobin/Cytochrome
- Why His E7 and F8 are locatedin such a way across many different species? Is
their orientation highly conserved and why?
- Similarity among cytochromes found in diff species of organism
Click here NCBI
Click here UCSC
Click here Ensembl
Structuralsimilarity and diff bet Hemoglobin/Myoglobin and Cytochrome
Myoglobin Hemoglobin Cytochrome
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

9. Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here NCBI
Click here UCSC
Click here Ensembl
Structuralsimilarity and differences bet Hemoglobin and Myoglobin
Myoglobin hemoglobin
vs
Chimera Swiss PDB
Evaluationand Limitationusing 3D modelling
Must use a variety of sources/programme to verify/validate the validity and reliability of data collected
Average 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 model
Data sources are supported using diff method/3D model/database
Certain 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 conclusion
Computation programme is always based on approximation and we cannot conclusive prove anything
Reflect of validity and reliability of data
Is 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 differencesbet distance/position/orientationof porphyrin
ring for Hemoglobinand 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/sizeof 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 locatedin such a way across many different
species? Are their orientation highly conserved and why ?

10. - Porphyrin gp of heterocyclic made of 4 pyrrole subunit
- Porphyrin macrocyclehas 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
- cytochromec oxidase
- electrontransport
O2
Heme = Fe + porphyrin ring – carry O2
Fe2+ located
Most abundant
Hemoglobin and Myoglobin
Mitochondria
- cytochromec
- electrontransport
Fetal Hemoglobin
(2α22γ2)
Human Hemoglobin
(2α2 2β2)
Sickle cell Hemoglobin
(2α22βS
2)
Myoglobin
1 α chain
Carbaminohemoglobin Carboxyhemoglobin Oxyhemoglobin

11. Heme
Heme A Heme B Heme C
Mitochondria
- cytochromec oxidase
- electrontransport
Most abundant
Hemoglobin and Myoglobin
Mitochondria
- cytochromec
- electrontransport
Fetal Hemoglobin
(2α22γ2)
Human Hemoglobin
(2α2 2β2)
Sickle cell Hemo
(2α22βS
2)
Myoglobin
1 α chain
Cytochrome
Heme in cytochrome,highly conjugated ring sys surrounding Fe
Cytochrome- REDOX rxn – mitochondria – ATP/energy productionvia elec transport chain
Many type cytochromes – Cyto a, b, c1, a3
Cytochromec, an ancient protein, developed early in the evolution of life. Essential protein for energy/ATP
HIGHLY CONSERVED has changed little in millions of years.
Many variation – but structureremain relatively unchanged
Fe in cytochrome Fe in cytochrome Cytochrome c – heme c

12. Hemoglobin A - 2 alpha and 2 beta chains
Hemoglobin A2 - 2 alpha and 2 delta chains
Hemoglobin F - 2 alpha and 2 gamma chainsHeme (porphyrin) bind to Fe2+using 4 nitrogen atom (histidine gp) Porphyrin
- as electron-pair donor - polydentate ligand
Fe 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 F8
The sixth coordination site bind oxygen with His E7 nearby
Deoxyhemoglobin
Fe2+- out plane
Can’t fit the ring
Heme
Hemoglobin - 4 chain - 4 heme (porphyrin) - 4 Fe 2+
Fe2+
Heme
(porphyrin)
Oxyhemoglobin
Fe2+- located in plane
Fit the ring
Deoxyhemoglobin
Fe2+ out plane
Can’t fit the ring
Out by 0.06nm
Fe2+ in plane
Fit 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 porphyrin
Fifth ligand is donated by His F8
O2 add to Fe as sixth ligand
O2 tilt relative to perpendicular of heme plane
His F8His F8 His F8
His E7
His E7
His E7
Oxyhemoglobin

13. Heme
Hemoglobin - 4 chain - 4 heme (porphyrin) - 4 Fe 2+
Fe2+
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 porphyrin
Fifth ligand is donated by His F8
O2 add to Fe as sixth ligand
O2 tilt relative to perpendicularof heme plane
His E7 locateover 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
Fe2+
Heme
(porphyrin)
His (F8)
His (E7)