peter siman v.5

Cross Talk Within Chemistry Disciplines

Dr. Peter Siman1

Peter Siman

2

Prof. Ashraf Brik

Nat. Chem. Biol. (2014)

Angew. Chem. Int. Ed. (2013)

Cell Reports (2013)

Chem. Sci. (2013)

Org. Lett (2012)

Org. Biomol. Chem. (2012)

ChemBioChem (2011).

ChemBioChem (2010)

Prof. Daniel Cohn

Biodegradable Polymerizable Adhesive

Compositions Comprising Cyanoacrylate

Monomers, WO-2010026590 (2009)

B.Sc. & M.Sc.

in Chemistry

Ph.D.

in Chemistry

3

Disease Related Aggregative Proteins

http://www.humpath.com/spip.php?article1586

4

New Tools for the Synthesis and Manipulation of

Aggregative Proteins

1) Difficulty in expression or synthesis

2) Lack of tools to control aggregation initiation

3) Complexity and variability in the aggregation processes

4) Difficulties in structural characterization

5) Difficulties in real time monitoring of aggregation

6) Unknown “hot spots” in the protein sequence

5

HIV-1 Rev

• A116 amino acid (13kDa) regulator

of expression of viral protein (Rev)

• Rev is a basic protein (pI 9.2) i.e.

positively charged binds RNA

• Rev specific RNA-binding protein

• Rev aggregates within 8 hours after

expression

M. A. DiMattia, et. al., Proc. Natl. Acad. Sci. 2010, 107,

5810-5814..

A. Dayton, Retrovirology 2011, 8, 62

V. W. Pollard, M. H. Malim, Annu. Rev. Microbiol.

1998, 52, 491-532

6

Total Synthesis of HIV-1 Rev from Three Fragments

P. Siman, O. Blatt, T. Moyal, T. Danieli, M. Lebendiker, H. A. Lashuel, A. Friedler, A. Brik, ChemBioChem 12, 1097-1104 (2011)

7

Racemization at Middle Fragment C-terminus (Serine)

P. Siman, O. Blatt, T. Moyal, T. Danieli, M. Lebendiker, H. A. Lashuel, A. Friedler, A. Brik, ChemBioChem 12, 1097-1104 (2011)

8

Racemization at Middle Fragment C-terminus (Serine)

P. Siman, O. Blatt, T. Moyal, T. Danieli, M. Lebendiker, H. A. Lashuel, A. Friedler, A. Brik, ChemBioChem 12, 1097-1104 (2011)

9

Racemization Free Synthesis of Middle Fragment

Challenges

P. Siman, O. Blatt, T. Moyal, T. Danieli, M. Lebendiker, H. A. Lashuel, A. Friedler, A. Brik, ChemBioChem 12, 1097-1104 (2011)

P. E. Dawson, et. al., Angew. Chem. Int.

Ed. 2008, 47, 6851-6855.

HPLC trace of Dbz activation

DCM

DMF

DCM, the conventional solvent causes aggregation of the peptide

DMF preserves the peptide, but causes the addition of 28 Da

10

NMR Study of the 28 Da Reveals Vilsmeier-Haack Reaction

P. Siman, O. Blatt, T. Moyal, T. Danieli, M. Lebendiker, H. A. Lashuel, A. Friedler, A. Brik, ChemBioChem 12, 1097-1104 (2011)

Proposed Mechanism of Dbz activation in DMF through Vilsmeier-Haack

11

Correctly Folded HIV-1 Rev Protein was Obtained Using Dbz

Approach

Circular Dichroism spectrum of recombinant Rev (A) and synthesized

Rev (B)

P. Siman, O. Blatt, T. Moyal, T. Danieli, M. Lebendiker, H. A. Lashuel, A. Friedler, A. Brik, ChemBioChem 12, 1097-1104 (2011)

T. Moyal,1 H. P. Hemantha,1 P. Siman, M. Refua and A. Brik, Chem. Sci., 4, 2496-2501, (2013)

12

Towards the Synthesis of Huntington Protein

N. V. Dokholyan, et. al., PLoS. Comput. Biol., 2010, 6, e1000772.

13

Native Chemical Ligation at γ-mercapto-Glutamine

P. Siman, S. V. Karthikeyan, A. Brik, Org. Lett. 2012, 14, 1520-1523

14

Chromatin & Histones

http://www.youtube.com/watch?v=eYrQ0EhVCYA

1. R. D. Kornberg, et. al., Science 1974, 184, 865-868.

2. R. Sperlinget. al., Biochemistry (Mosc). 1975, 14, 3322-3331.

3. Y. J. Jin, et. al., J. Biol. Chem. 1986, 261, 15805-15812.

4. A. D. Baxevanis, et. al., Biochemistry (Mosc). 1990, 29, 973-976.

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Lysine (34) Ubiquitinated H2B Protein

• Ubiquitination (Ub) of H2B at Lysine 34, was found to directly regulate

the methylation of Histone 3 (H3), which signals for DNA repair.

• Up to date, no report on neither the isolation nor production of K34-Ub-

H2B using other methods

L. Wu et al. , Mol. Cell, 43, 132-144 (2011)

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Total Synthesis of K34 Ubiquitinated H2B Protein

Siman P., Karthikeyan S. V., Nikolov M., Fischle W. and Brik A.* Angew. Chem. Int. Ed. 52, 8059-8063, (2013)

Shema-Yaacoby E.,# Nikolov M.,# Haj-Yahya M., Siman P., Allemand E., Yamaguchi Y., Muchardt C., Urlaub H., Brik A., Oren M.* and

Fischle W.* Cell Reports 4, 601-608, (2013)

MW= 24 kDa

256 chemical

reactions

Post-doc at the Yaghi Group

17

Siman P., Trickett C., Furukawa H., and Yaghi O. M., Chem. Commun., 2015, 51, 17463-17466.

Fracaroli A. M., Siman P., Nagib D. A., Suzuki M., Furukawa H., Toste F. D., and Yaghi O. M., J. Am. Chem. Soc.,

2016, 138 (27), pp 8352–8355.

Precise Control of Pore Environment Through Peptidic Linker

18

M+

Single Crystal (SC) Synthesis Using Methanol

Siman P., Trickett C., Furukawa H., and Yaghi O. M., Chem. Commun., 2015, 51, 17463-17466

Crystallographic Data of As-synthesized MOF-705

and MOF-706

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Sample MOF-705_as MOF-705_sc MOF-706_as MOF-706_sc

Chemical Formula C17 H18 N2 Na4 O12 C33.08 H33.70 N4 Na8 O25.71 C22.5 H18 N2 Na4 O12 C22.25 H19.25 N2 Na4 O11.5

Formula mass 534.29 1082.58 618.87 590.61

Crystal system monoclinic monoclinic monoclinic monoclinic

Space group P21 P21 P21 P21

[Å] 1.54178 0.77490 0.88560 1.03330

a [Å] 11.8894(4) 24.0448(19)a 12.0790(15) 11.9807(16)

b [Å] 5.2299(2) 5.2432(5) 5.2419(6) 5.2345(6)

c [Å] 17.4663(5) 16.9833(14) 21.254(3) 21.796(3)

β (degrees) 97.279(2) 103.366(6) 103.886(6) 99.274(10)

Z 2 2 2 2

V [Å3] 1077.3(1) 2083.1(3) 1306.4(3) 1349.1(3)

T [K] 100(2) 100(2) 100(2) 100(2)

density [g cm-3] 1.647 1.726 1.573 1.454

measured

reflections 23262 18857 7646 6359

unique reflections 4415 4815 1594 1980

parameters 334 623 327 345

restraints 34 19 106 130

Rint 0.0889 0.1078 0.1134 0.1002

range (degrees) 2.55 - 74.52 2.568 - 23.539 2.164 - 21.724 2.504 - 28.238

R1, wR2 0.0415, 0.0965 0.0684, 0.1878 0.0721, 0.2093 0.1176, 0.3174

S (GOF) 1.037 1.009 1.007 1.273

max / min res.

dens. [e Å-3] 0.366 / -0.241 0.692 / -0.346 0.535 / -0.457 0.732 / -0.673 a the unit cell is doubled due to superstructure in which water and methanol coordinate to Na(4)

Both MOFs Are Stable Upon Activation and Under Ambient

Conditions

21Siman P., Trickett C., Furukawa H., and Yaghi O. M., Chem. Commun., 2015, 51, 17463-17466

Higher Uptake of CO2 over N2 at 0 and 25 ºC

22Siman P., Trickett C., Furukawa H., and Yaghi O. M., Chem. Commun., 2015, 51, 17463-17466

CO2 and N2 isotherms for MOF-705. Filled and open

symbols represent adsorption and desorption branches

respectively

N2 isotherms are in orange (273 K) and green (298 K),

CO2 isotherms are in blue (273 K) and red (298 K).

Seven Post-synthetic Covalent Reactions in Tandem

Leading to Enzyme-like Complexity within Metal–Organic

Framework Crystals

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(a) Catalytic cleavage of pentapeptide 1 by Cat. C

[MTV-IRMOF-74-III-(CH3)0.6(CH2NH-Asp-

His-Cys-NH2)0.1] in the specific sequence

containing serine.

(b) Cartoon representation of the enzyme TEV

endoprotease, highlighting the three amino

acids that participate in the catalysis.

Fracaroli A. M., Siman P., Nagib D. A., Suzuki M., Furukawa H., Toste F. D., and Yaghi O. M., J. Am. Chem. Soc., 2016, 138 (27), pp 8352–8355.

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• GPC

• DSC/TGA

• NMR

• IR

• Mechanical characterization of polymers using Rheometer and related instruments

• HPLC

• MS-LCQ Fleet Ion Trap (Thermo Scientific)

• Peptide synthesizers of CSBio and CEM

• Powder X-ray diffraction (PXRD) - Bruker

• Single crystal X-ray diffraction (SC-XRD) - Bruker

Acquired Technical Knowledge