NAGA_Doha_M1ISDD_Internship_Presentation

By Doha Naga Scientific Responsable: Dr Jean Christophe Gelly

Co-supervised by Yassine Ghouzam

13/06/2016

Study of stability of « Protein units »

using Molecular Dynamics

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PROTEIN STRUCTURE

• Since Kendrew’s experiment

• Why studying protein structure? -Function

• How do Protein acquire architecture?

• how does a protein folds?

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Proteins Domains Secondary structures

30 aas50 aas 5 aas... ...

CLASSICAL VIEW

PROTEIN ARCHITECTURE

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Proteins Domains Secondary structures

30 aas50 aas 5 aas... ...

Protein Units

➡ Small motifs (Compact&Structured)

PROTEIN PEELING

Gelly J-C ; de Brevern, A. G. ; Hazout, S. (2006) BIOINFORMATICSGelly J-C ; de Brevern, A. G. ; Hazout, S. (2006) BIOINFORMATICS

NEW VISION

PROTEIN ARCHITECTURE

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PROTEIN UNITS CORE

• Recurrence

• PU Cores,PU non cores

• At least 1 PU core in almost all proteins

• Significance ?

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HYPOTHESIS

Protein units core are building blocks for proteins

Protein units core importance for folding

What are expected characteristics?

TENDENCY TO STABILITY

Assess by MD simulations6

PROTOCOL

• 27 PU’S (22 PU cores + 5 PU non cores)

• MD protocol (Charmm27 plus CMAP for proteins*,100 ns,300 K)

• Explicit solvent representation

• Temperature variation for some proteins(340K,398K)

• Analysis

*A.Mackerell(2004), JOURNAL OF COMPUTATIONAL CHEMISTRY, Vol. 25, No. 137

OVERVIEW OF PU TESTED

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OVERVIEW OF PU TESTEDPU CORE

PU NON CORE

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Stable UnstableNear-stable

PU CORE

PU NON CORE

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PU CORE

PU NON CORE

FOLDINGNUCLEI

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PU CORE

PU NON CORENEW MOTIF

FOLDINGNUCLEI

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PU CORE

PU NON CORENEW MOTIF

FOLDINGNUCLEI

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NON CORE PU

0 ns• 2H8PA protein unit (residue 33 to 71)

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NON CORE PU

0 ns 100 ns• 2H8PA protein unit (residue 33 to 71)

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NON CORE PUFr

eque

ncy

of n

ative

con

tact

s

Time (ps)20000 40000 60000 80000 100000

• 2H8PA protein unit (residue 33 to 71)

• Loss of native contact( around 80 %) 1 out of 3 replicas16

NON CORE PU

• 2H8PA protein unit (residue 33 to 71)

• Loss of native contact( around 80 %), 1 out of 3 replicas

• C-alpha RMSD variation around 7 Ångstroms

Freq

uenc

y of

nat

ive c

onta

cts

Time (ps)20000 40000 60000 80000 100000

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PROTEIN UNIT CORE: BAB

• Previous studies affirmed instability of BAB motif*

• Stable for 200 ns in our study

• Low of Variation of RMSD (1-2 Ångstroms) for each replica

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*Coincon M. et al.(2005), PROTEINS 60(4): 740-745

0 ns

BAB





• Native contact loss is less than 50 percent

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Freq

uenc

y of

nat

ive c

onta

cts

Time (ps)20000 40000 60000 80000 100000

BAB





• Native contact loss is less than 50 percent

• Reorientation of PhenylAlanine residue

200 ns

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0 ns

NEW MOTIF

The Jaw motif21

NEW MOTIF

The Jaw motif22

NEW MOTIF

23The Jaw motif

NEW MOTIF

24The Jaw motif

NEW MOTIF

C-alpha RMSD scores

1.15 Å

0.86 Å

1.50 Å

25The Jaw motif

FOLDING NUCLEI

. *Lo pez-Herna ndez, E. and Serrano, L. (1996) Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2. Fold. Des. 1, 43–55.

• Chy Folding nuclei (residue 8-57)*

• 0.51 phi value inside structural root motif and 0.07 phi value outside structural root motif

CheY protein

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FOLDING NUCLEI




• 3FZVA protein unit (residue 79-135)

CheY protein

Chy Folding nuclei superimposed with 3FZVA Protein unit

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FOLDING NUCLEI




• 3FZVA protein unit (residue 79-135)

Chy Folding nuclei superimposed with 3FZVA Protein unit

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CONCLUSION

Results are in agreement with our hypothesis

PU cores are more stable than PU non cores (statistically significant P-value: 0.001)

21 PU cores : 20 « stable » 1 unstable

5 PU non cores : 1 « stable » 5 unstable

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Draw backs

• Longer simulations

• Simulation of Mutants

• Different protocols

• More replicas

• Different methods (REMD for example)

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References• Coincon, M., A. Heitz, L. Chiche and P. Derreumaux (2005). "The betaalphabetaalphabeta

elementary supersecondary structure of the Rossmann fold from porcine lactate dehydrogenase exhibits characteristics of a molten globule." Proteins 60(4): 740-745.

• Efimov, A. V. (1996). "A structural tree for alpha-helical proteins containing alpha-alpha-corners and its application to protein classification." FEBS Lett 391(1-2): 167-170.

• Fersht, A. R. and S. Sato (2004). "Phi-value analysis and the nature of protein-folding transition states." Proc Natl Acad Sci U S A 101(21): 7976-7981.

• Garbuzynskiy, S. O. and M. S. Kondratova (2008). "Structural features of protein folding nuclei." FEBS Lett 582(5): 768-772.

• Kendrew, J. C., G. Bodo, H. M. Dintzis, R. G. Parrish, H. Wyckoff and D. C. Phillips (1958). "A three-dimensional model of the myoglobin molecule obtained by x-ray analysis." Nature 181(4610): 662-666.

• Lopez-Hernandez, E. and L. Serrano (1995). "Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2." Fold Des 1(1): 43-55.

• Sato, S., T. L. Religa, V. Daggett and A. R. Fersht (2004). "Testing protein-folding simulations by experiment: B domain of protein A." Proc Natl Acad Sci U S A 101(18): 6952-6956.

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Thank you for your attention

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NAGA_Doha_M1ISDD_Internship_Presentation

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