Electrostatic Potential (ESP) Measure polarization Electron Map density Electron distribution Dipole Moment Measure bond length/angle Measure bond strength Organic software for 3D model Click here download Rasmol Click here download PyMol Click 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 ✓
18
Embed
IB Chemistry on ICT, Protein Sequencing , Chimera, Jmol, Pymol for Internal Assessment on Hemoglobin, Myoglobin and Cytochrome
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Electrostatic Potential (ESP) Measure polarization Electron Map density Electron distribution
Dipole Moment Measure bond length/angle
Measure bond strength
Organic software for 3D model
Click here download Rasmol
Click here download PyMol Click 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)
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
Measuring using 3D modelling and Sequencing Technique
Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here NCBI Click here UCSC
Click here Ensembl
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
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
Fe
N
His F8
- Structural and sequence similarity for Hemo/Myo and cytochrome among
various species - Is His E7/F8 orientation similar for Hemoglobin, Myoglobin, Cytochrome - Is there any differences bet distance/position/orientation of porphyrin ring for
Hemoglobin, Myoglobin, Cytochrome - How is Fe2+ located, along or out of plane for Hemo/Myoglobin/Cytochrome - Is distance bet Fe and ligand N of porphyrin the same for
Hemoglobin/Myoglobin/Cytochrome - Investigate the conserved domain/regions in Hemo/Myo and Cytochrome that
are needed to ensure survival of species - Why His E7 and F8 are located in such a way across many different species? Is
their orientation highly conserved and why? - Sequence similarity among cytochromes found in diff species of organism
Structural and Sequence similarity for Hemo/Myoglobin and Cytochrome
Possible Research Question Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here NCBI Click here UCSC
Click here Ensembl
Myoglobin Hemoglobin Cytochrome
Chimera Swiss PDB
- Structural and sequence similarity for Hemo/Myo and cytochrome among
various species - Is His E7/F8 orientation similar for Hemoglobin, Myoglobin, Cytochrome - Is there any differences bet distance/position/orientation of porphyrin ring for
Hemoglobin, Myoglobin, Cytochrome - How is Fe2+ located, along or out of plane for Hemo/Myoglobin/Cytochrome - Is distance bet Fe and ligand N of porphyrin the same for
Hemoglobin/Myoglobin/Cytochrome - Investigate the conserved domain/regions in Hemo/Myo and Cytochrome that
are needed to ensure survival of species - Why His E7 and F8 are located in such a way across many different species? Is
their orientation highly conserved and why? - Sequence similarity among cytochromes found in diff species of organism
Structural and Sequence similarity for Hemo/Myoglobin and Cytochrome
Evaluation and Limitation using 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?
- 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
Porphyrin Heme = Fe + porphyrins ring
Heme
Heme A Heme B Heme C
Mitochondria - cytochrome c oxidase - electron transport
Mitochondria - cytochrome c oxidase - electron transport
Most abundant Hemoglobin and Myoglobin
Mitochondria - cytochrome c - electron transport
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 production via elec transport chain Many type cytochromes – Cyto a, b, c1, a3 Cytochrome c, 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 structure remain relatively unchanged
Fe in cytochrome Fe in cytochrome Cytochrome c – heme c
Hemoglobin A - 2 alpha and 2 beta chains Hemoglobin A2 - 2 alpha and 2 delta chains Hemoglobin F - 2 alpha and 2 gamma chains Heme (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
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
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 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.