2. CONTENTS
● Objective
● Protein threading
● Ab initio method
● I-TASSER
● MUSTER
● DALI server
● Robetta
● Validation
● Result and discussion
● Conclusion
● References
3. ●We have to geerate a model of given sequence Ecdl
[Emeicella rugulosa] have 604 residue.
●This protein have not shown significant alignment with
any solved structure .
●On other hand, it can be modeled with either Fold
recognition method or Ab intio method.
OBJECTIVE
5. Protein Threading
●Also known as Fold recognition method.
●It is a Template Based Model.
●It is a method of protein modeling which is used to model those
proteins which have the same fold as protein of known structures,
but don't have homologous proteins with known structure.
●There are many popular software for Fold Recognotion-
- I-TASSER
- MUSTER
- PHYRE2
- RaptorX server
6. Ab intio method
●It is a Template Free Model.
● It done when we have not any information about
structure of our protein of intrest.
●The most popular software for ab initio are -
- Robetta
7. I-TASSER
●Iterative - Threading ASSEmbly Refinement
●It is web appliocation for protein structure & function
prediction.
●Model are built based on Multiple threading alignment by
LOMETS (Local Meta Threading Server) and iterative TASSER
simulation.
●It was ranked as the No 1 server in recent CASP7
(Critical Assessment of technique for protein Structure Prediction)
and CASP8 experiment.
8. Steps of I-TASSER
1. Threading
2. Structral assembly
3. Model Selection and Refinment
4. Structral based Functional Annotation
10. MUSTER
●Muti-Source ThreER
●It is also one of best software for new protein to
identify the templates structure from the PDB library.
●It generate sequence template alignment by
comninig sequence profile-profile alignment (PPA)
with multiple structural information.
●It was successful for TBM in CASP experiment.
11. Steps of MUSTER
1. Scoring Function
2. Sequence Profile
3. Secondary Stucture Match
4. Stucture Profile
5. Solvent Accesiability
6. Backbon of Dihyral Angle
7. Hydrophobic Scoring Matrix
8. Dynamic Programming
9. Template taking scheme
13. Result of I-TASSER and MUSTER
●The result of I-TASSER and MUSTER both give the
model of our protein based on template – 4PL0A.
●“I consider 4PL0A this model for our protein of intrest”.
16. ● Structure of an antibacterial peptide ATP-binding
cassette transporter.
●Molecular Description :-
Classification: Transport Protein
Molecule: Microcin-J25 export ATP-
binding/permease protein
McjD
Type: protein
Length: 580
Chains: A, B
Organism: Escherichia coli
4Pl0A
17. DALI Server
●Distance mAtrix aLIgnment
●The Dali server is a network service for comparing
protein structures in 3D.
●Be used to imply evolutionary relationship between
protein that share very little common sequence.
●The output of sructural Alignment are : -
1.Z score- Structural similarity is measured by Doli z-score.
18. DALI Server result
2. Super positionof atomic co ordinate set - Its use to
compare multiple conformation of same protein and to
evaluate the quality of alignment produced using only two or
more known sequences .
3. Minimal RMSD between structure - RMSD of two align
stucture shows the divergance from one to another.
4. Nresu - its show the number of align residue.
5. Lali - its the number of align position.
19. DALI result
“Low rmsd and high nres shows the better alignment.”
●If both rmsd and nres is high or low, not possible to establish
an order between the alignment.
●Rmsd- It is the measure of the average deviation in distance
between aligned alpha carbons (i.e, calculate the diversance
from one to another b/w two sequences)
●Note:- DALI package is based on Fartran programming and
perl script.
“The best alignment shows with low rmsd 0.6 and high
lali score 403.”
22. Ab initio by Robetta
● I am going to used Robetta server for Ab initio structure
prediction.
● At first, we go on robetta server.
● Register on Robetta home server.
● Open id with username or email.
● Paste protein sequence.
● Filling the all field which is neccessaey .
● Submit.
● After submiting, we received a job id 54467 on date 24 march
2015.
● Check result by clicking Queue on Robetta page.
23. Robetta
Steps of Robetta -
1. After giving target sequence it will start doing Profile -
profile alignment based on fragments library.
2. phase 1 : Monte Carlo fragment assembly
Low resolution model ( predict of strc with about near
accuracy )
3. Phase 2 : physics base atomic refinement
High resolution model (absolute accuracy)
4. Final atomic model
26. Robetta result
● Robetta generate 3 model -
Sl. no. Protein ID Discription
1 4p79 ● Crystal str of cloudin provides insight into the architecture
of tight junction
● Ion channel regulator, alpha helical
● Membrane protein
2 1ni0 ● Hydrolase
● Restriction endonuclease PuvII from proteus vulgaris,
class alpha/beta protein
● EC 3.1.21.4
3 4m1m ● Multidrug resistant protein
● ATP binding cassate transpoter
● Pgp
28. ANOLEA
● Atomic Non-Local Environment Assessment
● It check the non local environment of protein itself with
their different amino acid on the basis of energy with
Euclidean distance (7°A) with 11 residue Amino acid.
33. PROSA
● Protein Structure Analysis
● It check the quality of c alpha carbon.
● Output of prosa shows-
1. Z score- it shows the overall quality of model value display of
all experimentally determined protein chain in PDB.
"more negative z score- best structure.
more positive z score not well structure."
2. Plot of residue score- shows local quality of model by plotting
energy as sum of AA sequence position i (take window size 40)
34. PROSA
– Positive value correspond problematic part
of structure.
3. Prosa web visualizer picture 3D model (J mol c-alpha
trace)- the 3D structure of protein of interest is visualised
by the use molecular viewer Jmol.
– Residue are colored from blue to red in order of
increasing residue energy.
● The Z score of this model is -6.41
38. Result and Discussion
●As the given instructions the given sequence Ecdl having 604 aa long
can't modeling by homology modeling.
●Thus, we have to move towards on the other method of prediction either
Fold recognition methid or Ab initio method.
●Threading method was done by MUSTER and I-TASSER server which
gives common reslutt .
●And the Ab initio method was done by Robetta server,as the result we get
information about domain and generate structure on the basis of founded
domain.
●With the help of prosa/ Procheck , analysed the ramachandran plot of the
model.and validate our model by the using of other tools ti check quality of
model.
●We found the many protein of ABC transporter and p glyco protein as
result.
39. Conclusion
Result of I-TASSER and MUSTER which for
fold recognition and Robetta for ab initio
structure prediction shows the given protein
is higher similar to those protein which are -
●ABC transporter super family protein (ATP binding
Cassette )
●Transmembrane protein
