POLYMER DYNAMERS, CONSTITUTIONAL DYNAMIC AND

ADAPTATIVE CHEMISTRY

G. S. Georgiev

University of Sofia, Faculty of Chemistry

Laboratory of Water-Soluble Polymers,

Polyelectrolytes and Biopolymers

1, James Bourchier Avenue1164-Sofia, Bulgaria

LAYOUT OF THE REPORT1. Definitions of dynamer (D) and cosntitutional dynamic chemistry (CDC).

2. Dynamer`s characteristics: D as multi-equilibrium, multi-constitutient system; D -selectivity, adaptation ability (AA), multivalent ability, critical state, constituen’s (C) -adaptation potentials and efficiency.

3. Polymer D (PD): definition, conformation and equilibrium states of PD constituents, PD selectivity, adaptation ability, multivalent ability and critical states.

4. Critical states of PD constituent (Cp) and PD.

5. Relationship between CDC, Polymer and adaptation chemistry.

6. PD examples: i. Ribosome as mixed biopolymer D; ii. Proteasome as protein D;

iii. Photozymes as synthetic copolymer D; IV. Chromosome as protein-DNA D.

7. Conclusions.

THE AIM OF THIS REPORT IS TO REVEAL THE RELATIONSHIP BETWEEN THE POLYMER AND ADAPTATIVE CHEMISTRY.

1.D and CDC definitions1.1. D is dynamic associates whose components (constituents, C) are molecules, linked

through weak, reversible connections and have therefore a capacity to modify their constitution, by exchange and modification of its components (constituents).

Figure 1. Dynamer with 3 constituents (C) and 4 weak reversible bonds.

1.2. Constitutional Dynamic Chemistry (CDC) studies the D’s characteristics and their dynamic behaviour as a result of the chemical reactions, molecular orientations, conformation transitionsand constitutional dynamics, related to constitution changes through dissociation and reconstitutioninto same or different entities.

[J. -M. Lehn, Prog. Polym. Sci., 30, 814 (2005); Chem. Soc. Rev., 36 151 (2007)]

Figure 2. Two different equilibrium states of D with 3 constituents; the first one (left) with 4 weak bonds, while the second (right) with 2 weak bonds.

2. D-characteristics2.1. D is a dynamic object having a set of equilibrium states

Figure 3. Three different equilibrium states of D with 3 constituents and their free Gibbs energies.

G

G1G2G3

+

G(D1+Ss)

G(Ds1)-(ΔG)= GDs1+ G(D+Ss)

- ΔG°RTK1=e

G

D1+Ss Ds1

K1

K1

Ds1

Ss

D1

2.2. D-selectivity

+K2

Ss

D2 Ds2

D2+Ss Ds2

K2

G(D2+Ss)

G(Ds2)-(ΔG)= GDs2- G(D2+Ss)

RTK2=eG

- ΔG°

Max l GDS-G(Di+Ss)lFigure 4. D-selectivity as a result of that each Ss can select the equilibrium state with

2.3. D-adaptation ability

D Ds

The fraction of the new-forming bonds between D and substrate (Ss) is a possible measure for the adaptation (self-turning) ability (AA) of D towards Ss.

Figure 5. D adaptation ability towards Ss could be measured by the number fraction of the new-

forming weak bonds between D and Ss or by the ratio between them and the breaking weak bonds in D during Ss adoption.

AA has a dominating contribution in a D-selectivity.

Ss

2.4. D-multivalent adaptation ability

Different AA of D towards different Ss provides different D-selectivity towards them and multivalent selectivities of D.

Figure 6. D has different AA towards different Ss. A. The ratio between new-forming

and breaking bonds is 2.5; B. The ratio, above mentioned, in this case is 1.5.

D Ds1

K1

A

Ss1

D Ds2

K2

B

Ss2

Dcr

2.5. D critical stateDefinition: D in a critical state (Dcr) is a network with C as junction points, connected by weak bonds, and having a nonlinear, great, cooperative, and coherent response on the external perturbation.

Figure 7. Heterogeneous D with 2 6-bonding sites and 2 3-bonding sites constituents. Transition between noncritical (D1) and critical (Dcr) states of D. In Dcr there is not D-fragments connecting with one weak bond only.

D1

2 local responses Cooperative, nonlinear and coherent response of D as an intact body

Dncr

Dscr

Dcr

2.6. Subdivision of D equilibrium sates into two subsets

Figure 8. Subdivision of D equilibrium states into two subsets : noncritical subset of states ({Dncr}) and subcritical subset of states ({Dscr}) with Hncr > Hcr; Sncr > Scr and Hscr < Hcr; Sscr < Scr, respectively.

Hncr > Hcr; Sncr > Scr; and Gncr > Gcr when TISncr – ScrI < IHncr – HcrI

Gcr (Hcr, Scr)

Hscr < Hcr; Sscr < Scr; and Gscr < Gcr

when TISscr –ScrI < IHscr - HcrI

2.7. Difference between transition probabilities from {Dncr} and {Dscr}

If Di belongs to {Dscr}, the external Ss effect (Ss addition to Di) is an increase of the crosslinking degree of the formed already D network. As a result of this Pscr,scr > Pncr,scr.

Figure 9. The general tendency Pi,scr > Pi, ncr is enhanced considerably when Di

belongs to {Dscr} subdivision set.

{{

{Dncr} {Dncr} {Dscr}Pncr,ncr Pncr,scr

{Dncr} {Dscr} {Dscr}Pscr,ncr Pscr,scr

2.8. Adaptation potential of D-constituents

Definition: The ratio between the numbers of the inter- [(Nc,inter)cr]- and intra-[(Nc,intra)cr] constituent weak bonds for a given Ci in a critical state defines its adaptation potential (APc) – its ability to form weak bonds with an external Ss.

APc = (Nc,inter)cr

(Nc,tot)cr

=1

1+ (Nc,intra)cr/(Nc,inter)cr

Figure 10. Dynamer with 3 constituents, 3 interconstituent and 3 intraconstituent bonds.

In all of the examples discussed above the weak bonds were bonds between different C of D. However, such weak bonds could be formed between the active sites of a given C also (intraconstituent bonds).

Intraconstituent bond

Interconstituent bond

2.9. Partial adaptation potential of C to given Ss

APcs = (Ncs, inter)cr

(Nc,tot)cr

• (Ncs, inter)cr is the number of the intercontacts between C an Ss if C is in a critical state.• (Nc,tot)cr is the total number of C contacts.

Figure 11. The APcs values are 0.66 for both border and 0.33 for the central constituents of D presented.

The relationship between APcs and AA of D towards Ss is under a development now.

Ss

2.10. Adaptation efficiency of D constituents

Definition: Adaptation efficiency of D constituents (AEc) is a number fraction of the C inter-bonds among the total number of such bonds of all of the D constituents.

AEc = (Nc,inter)cr

∑(Nci, inter)cri

• (Nci,inter)cr is the number of the inter-contacts of the i-th D constituent in the critical state of D.

X

X

XX

X

3. Polymer dymamer (PD)3.1. Definition

PD is D with macromolecular coustituents.

Figure 12. PD with two macromolecular constituents and subsets of intra- and inter-constituent weak bonds.

Polymer chains

Interconstituent weak bonds

Intraconstituent weak bonds

3.2. Infinite conformation and equilibrium states of PD

The number of conformation and equilibrium states of each macromolecular constituents and PD as a whole is practically infinite, which means that:

• PD selectivity,

• PD adaptation ability (AA),

• PD multivalent adaptation ability and selectivity and

• adaptation potentials of PD macromolecular constituents (APc) are very large.

3.3. Critical state of the single PD constituent (Cp)

Definition: In contrast to low molecular weight C, Cp has a critical state which is its conformation state forming a response on the external perturbation as an intact body.

Figure 13. Transition between noncritical (left) and critical (right) Cp states as a result of the macromolecular contraction around the external substrate.

Local responses of CP segments

Collective, nonlinear and coherent response of CP

A crucial characteristic for the transition intoa CP critical state is the mole fraction of theIntra-constitutional weak bonds:

Xintra =NCP,intra

NCP,total

If Xintra > Xcr CP is in a critical or subcritical state.If Xintra < Xcr is in a noncritical sate.

4. Critical states of PD

The set of PD critical states includes the critical states of the individual (macromolecular constituents) critical states and one common critical state characterizing the PD response as an intact compact body on the external perturbations. Therefore, it could be subdivided into the following subclasses:• Subclass I – the PD states with only one CP in a critical state,• Subclass II – the PD states with two CP in a critical state, ……………………….....................• Subclass n – the PD state when all CP are in critical states, coinciding with PD critical one.

This large variety of PD critical states is a very important reason for the large values of PD AA, selectivity and multivalent adaptation ability. 4.1. CP is C with controllable conformation transitions and Xintra

Another CP peculiarity against to low molecular weight C is the possibility for the easy control the set of the conformation (equilibrium) CP states by: i. Macromolecular chemical composition; ii. Macromolecular tacticity; iii. Molecular weight characteristics; IV. Degree of brunching and cross-linking; V. Functionality of the chain ends and side groups; VI. Mass and composition characteristics of the inter-branch and inter-node segments. These possibilities are the fundamental advantages of CP against C for the target regulation of PD AA, selectivity and multivalent adaptation selectivity (ability).

4.2. Adaptation potentials of the PD constituents (CP) The huge set of the different classes PD critical states requires the definition if only two different types of constituent’s adaptation potentials (ACP,S): 4.2.1. AP of C related to critical states of different CP

(APCP,S)CP,cr=(NCP,S,inter)CP,cr

(NCP, tot)CP,cr

• (NCP,S,inter)CP,cr is the number of the inter-contacts

between CP and Ss in a critical state of this CP.

4.2.2. AP of C related to a critical state of PD as a whole

(APCP,S)PD,cr = (NCP,S, inter)PD,cr

(NCP, tot)PD,cr

••• (NCP,S,inter)PD,cr is the number of the inter-contacts between CP and Ss in a critical of PD as a whole.

• (N CP, tot )PD,cr is the total number of the inter- and inter-contacts of CP in the same PD critical state.

Adaptive chemistry

Polymer chemistry

Constitutional Dynamic chemistry

5. Relationship between Constitutional Dynamic, Polymer and Adaptation Chemistry

Figure 14. Schematic representation of the Adaptive chemistry (AC) as a intersection between Polymer (PC) and Constitutional Dynamic chemistry (CDC).

AC = CDC ∩ PC

This relationship was proved in nature already, and the next examples aim to demonstrate this statement.

6.1 Ribosome as a mixed biopolymer dynamer

• Ribosomes as complexes of RNA and proteins are mixed biopolymer dynamers.• They are 20 nm in diameter and composed of 65% ribosomal RNA (rRNA) and 35% ribosomal proteins.• Ribosomes consist of two subunits; small (40S) and large (60S) in eukaryotes.

• Large subunit is composed of a 5S RNA (102 nucleotides), 28S RNA (4700 nucleotides) and 5.8S (160

nucleotides) RNA and 49 ribosomal proteins (52 C), bounded together as a result of weak hydrophobic, electrostatic and stacking interactions.

• Small subunit has 18S RNA (1800 nucleotides) and 33

proteins (34 constituents), bounded together by the same weak non-covalent bonds

Figure 15. Large (red, 1) and small (blue, 2) ribosomal subunits, working as one during the protein synthesis as a result of weak interaction between them.

6. PD examples

6.1.1. Ribosomes are the workhorses of the protein synthesis

Protein biosynthesis is a translation of the messenger RNA (mRNA) into a protein macromolecule. Translation has four phases: activation, initiation, elongation and termination. Each of them is performed by four different equilibrium states of the ribosome dynamer.

Figure16. Translation of mRNA (1) by a ribosome (2) into a polypeptide chain (3).

The mRNA begins with a codon (AUG) and ends with a stop codon (UAG).

• The small ribosomal subunit, bound to a tRNA containing methionine, binds to AUG codon on the mRNA and recruits the large ribosomal subunit• The large ribosomal subunit contains three tRNA sites A,P and E sites.

Figure 17. The peptidyl-transferase center is localized in the 50S subunit and creates suitable conditions for the α-amino group of aminoacyl-tRNA attack to the carbonyl carbon of the peptidyl-tRNA in the P site.

A site binds an aminoacyl-tRNA, bound to an amino acidP site Binds a peptidyl-tRNA, bound to the peptide being synthrsised.E site binds a free tRNA

before it exits the ribosome

6.1.2. Peptidyl-transferase center (PTC) as an entropy trap

GUCGGG

Figure 18. Coordinative-insertion mechanism of the protein chain elongation and transition from Pto A site. Different intermediates are different equilibrium states of ribosome D. The acceleration of this reaction is 107 times against the same out of ribosome D. So, the latter was called RIBOZYME.

δ+δ-

Aminoacyl-tRNA attack of the carbonyl carbon atom in PTC

6.2. Proteasome as a protein dynamer

Proteasome (Pz) is a large multi-subunit PROTEIN complex localized in the cell

nucleus and cytosol that selectively degrades unneeded and damaged intracellular proteins by proteolysis, a reaction breaking peptide bonds. Therefore, PZ is an example of protein D.

6.2.1. Pz structure. Pz is a barrel like 26S (around 15 nm) D, conforming 20S core of 4 heptametric stocked rings (blue) around a central pore (Ø=5.3nm) and 19S regulation caps (red).

Figure 18. Proteasome representation; active sites are sheltered inside the tube (blue)

and regular cups are red.

Figure 19. A schematic diagram of the Pz 20S core.

Proteins are tagged for degradation by a small protein called UBIQUITIN (8.5 kDa). The reaction of the latter with this target protein is an ubiquitination reaction.

Figure 19. The ubiquitination pathway.

Due to a Pz AA the demonstrated system (called ubiquitine-proteasome system) provides protein ubiquitination, next its recognition and proteasomal degradation.

6.2.2. Ubiquitination

6.3. Photozyme D

6.3.1. Definition: Photozymes are new type copolymer photo-catalysts, capable to reproduce the elements of the photosynthetic reaction. They are amphiphilic copolymers with chromophoric hydrophobic monomer units, capable of light absorption and transmitting the excitation energy by means of the antenna effect to selected traps within the micelle core. Hydrophobic interaction provides this capability

of self-organization and so, photozymes are copolymer D.

Figure 20. Comparison between the caring natural photosynthesis in a thylakoid membrane

(A) and the high–harvesting photocatalysts in the photozyme micelles, produced

from the amphiphile copolymers (B).

A B

K = CT

core

CTsolution

Figure 21. Photozyme core engineering including 1,8-naphtalimide monomer units in it.

6.3.2. Photozyme applications• Poly(sodium styrenesulfonate-co-N-vinylcarbazole) photozyme (0.1 wt.%) was used for an effective photo-degradation of hexachlorbenzene in a waste water.• Poly(sodium styrenesulfonate-co-vinylnaphthalene) was applied for the purification of water contaminated by cyanide ions.• Naphtalimide-contained photozumes was synthesized in our laboratory and tested for the water purification also [λFl = 442nm; ΦFl = 0.58].

6.3.3. Photozyme core engineering

mnlToluene

80ºC,DBPO

Figure 22. Photozyme’s core engineering including porphyrine- and phtalocyanine-

light-harvesting monomer units in it.

Figure 23. Poly(styrene sulfonate-co-N-vinylcarbazole-co-dimethylaminoethyl-

methacryloylpropanesulfonate) – the first photozyme with zwitterion

units in the hydrophilic shell.

6.3.4. Photozyme shell engineering

Figure 24. Xanthene-containing photozymes covalently, bounded to the Merrifield support surface, through two steps surface modifications, included a

graft copolymerization also.

6.3.5. Heterogeneous photozymes

6.4. Chromosome D

Each chromosome contains extremely long DNA molecule that is packaged by 5 kinds of histones, protein rich in positive charged lysine and arginine residues. For this reason they bind tightly to the negatively-charged phosphates in DNA by electrostatical noncovalent bonds. By this way, the chromosomes COULD BE REGARDED AS MIXED BIOPOLYMER PD AGAIN.

Chromosome changes its conformation, size and degree of compaction throughout the cell cycle. Due this compaction 2m long DNA macromolecules in cell nucleus are packaged in a chromosome with diameter of 5µm only.

This drastic decrease of DNA size indicates a

• Nonlinear

• Co-operative and

• Coherent response

of the chromosome D on the external perturbation during the cell cycle.

Figure 25. Compactation step of chromosomal DNA as a result of their interaction with histones.

7. Conclusions1. Original quality theory of the constitutional dynamic chemistry is

proposed which explains the dynamer selectivity, multivalent adaptation ability and large adaptation ability on the basis of dynamer great set of equilibrium states, easy transitions between them and transition to a critical equilibrium state of each dynamer.

2. The peculiarities of the polymer dynamers are underlined and used for the explanation of their huge adaptation ability and selectivity.

3. The relationship between constitutional dynamer chemistry, polymer and adaptation chemistry is proposed.

4. The examples of biopolymer and synthetic copolymer dynamers are discussed to confirm the close relationship between polymer and adaptation chemistry.

ACKNOWLEDGEMENTS: Thanks my colleagues from Laboratory of Water-Soluble Polymers, Polyelectrolytes and Biopolymers

for the collaboration, and EC (PhotoNanoTech project NMP4-ct-2007-033168)

for the financial support.

THANK YOU FOR YOUR ATTENTION

AND ENDURANCE!

Figure 17. The peptidyl-transferase center is localized in the 50S subunit and creates suitable conditions for the α-amino group of aminoacyl-tRNA to attac the

carbonyl carbon of the peptidyl-tRNA in the P site.

• A site binds an aminoacyl-tRNA, bound to an amino acid.• P site binds a peptidyl-tRNA, bound to the peptide being synthrsised.• E site binds a free tRNA

before it exits the ribosome.

Peptidyl-transferase center• The small ribosomal subunit, bound to a tRNA containing methionine, binds to AUG codon on the mRNA and recruits the large ribosomal subunit.• The large ribosomal subunit contains three tRNA sites A,P and E sites.

Structure: Pz is a barrel like 26S (around 15 nm) D, conforming 20S core of 4 heptametric stocked rings around a central pore (Ø=5.3nm) and 19S regulation caps.

Figure 17. Representation of proteasome. Active sites are sheltered inside the tube (blue) and regular cups are red.