CHIRALITY IN BIOMOLECULES

SYMMETRY AND ASYMMETRY IN NATURE

CIRCULAR DICHROISM AND O.R.D

Biofisica ws 2006, Roma, pl luisi

 

M. Escher

Aminoacids and sugars are chiral

HN

O

R

OHH

H

Peptides, proteins, nucleotides, nucleic acids, sugars, polysaccarides and glycerophospholipid (from glycerol, which is pro-chiral) are intrinsecally chiral due to their primary structure.

PHOSPHOLIPID MOLECULE is the primary structural element in all cell membranes. Four main kinds of phospholipid are found in animal-cell-membranes. The one shown at the left in the diagram is phosphatidylcholine, but the other tree differ from it and from one another only in the chemical structure of their head groups, which are diagrammed here as colored spheres. The electric charge in each head group makes the group hydrophilic. The head group is connected to a glycerol group, and two hydrocarbon chains are attached in turn o glycerol. The hydrocarbon chains are oily and therefore hydrophobic.

Chirality criteria

OPERATIONAL CRITERIUM:

Chiral objects are not superimposeable to their mirror images.

Operationally:

1. Build (or imagine) the mirror image of the object.

2. If the object and its mirror image are superimposeable, then the object is not chiral. Theoretically (Group Theory

applied to chemical compounds):

1. Chirality derives from the lack of symmetry elements.

2. Axis of rotation are possible in chiral objects. Other symmetry elements (such as plane of symmetry, inversion center and axis of roto-reflection are not possible)

Chirality

H3NO

O

RH

O R

XO

OP

O

O

O

OHHOO

OH

aminoacid

nucleic acid

sugar

R-

R----R S----S

R----S S----R

R---R---R S S S

R---S---S R---R---S

ENANTIOMERSR---R R----S

R---R---R R—S---R

S---S---R S---R---S

DIASTEREOMERS

STEREO- ISOMERS, OPTICAL ISOMERS,

aminio acid peptide bond+H3N

COO-

helix

sheet

hydrogen bond

a. Primary structure

b. Secondary structure

c.Tertiary structure d. Quaternary structure

disulfide bond

Levels of Protein Stucture

OH

O–PO–CH2

O

O

OH

O–PO–CH2

O

O

OH

O–PO–CH2

O

O

OH

O–PO–CH2

O

O

U

C

G

C

5'

RNA

1

2

Secondary structure chirality

protein -helix (right-handed)

double stranded DNA helix, B-form (right-handed)

Helices and chirality

Note that the handness is retained when the helices are turned upside down.

Enantiomers and Diasteroisomers

right-handed -

helix

left-handed -helix

m

enantiomers

LL

L

L

L

L

L

L

m

RL

L

L

L

R

R

R

enantiomers diastereoisomers

TAKE A PEPTIDE WITH 10 AMINO-ACIDS

ASSUME THAT BOTH D AND L FORMS ARE ALLOWED

HOW MANY STEREOISOMERS ARE POSSIBLE?

AND FOR A CHAIN WITH 50 AMINO-ACIDS?

FOR A CHAIN WITH 50 racemic AMINO ACIDS, THE POSSIBLE NUMBER IS

2 To the power of 50Many many billions......

What is the number when only one form is allowed?

Thins number is : ONE!!

NH3+ COO-

RH NH3+ COO-

H R

L D

Asymmetry as a powerful ordering factor

Hormone with 10 residues

N = 2 x 2 x 2 x 2 ................................. 210 = 103

if L and D isomers had the same probability.But since only L-isomers are allowed, N = 1

For a chain with 50 residues ( Insulin ... )

N = 250 1015 1 !

only L-residues

L - Asp - L - PheOMe Aspartame (sweet)L DD LD D } bitter

Macroscopic systems are highly symmetric

WHAT IS THE ORIGIN OF HOMOCHIRALITY IN NATURE?

DE LEGE ( determinism)And random –stochastic- mechanisms

The chirality of the molecules of life Most probably another example of contingency

Developments from the Rutherford-Soddy (1904) theory of the spontaneous transmutation of the radioactive elements led to the discovery of two new natural forces, the strong and the weak nuclear interaction. An accumulation of anomalies in elementary particle physics led Lee and Yang (1956) to conclude that mirror-image symmetry, is not a property of the weak nuclear interaction. A consequence of the proposed parity violation, the asymmetric -decay of radionucleides, was soon observed in the decay of 60Co to 60Ni . …The asymmetry found showed the electron to possess an intrinsic left-handedness and the positron an inherent righthandedness

The unified electroweak interaction violates parity through the electromagnetic interaction, which primarily governs the binding of electrons to the nucleus in an atom and the bonding of the atoms in a molecule.The main atomic and molecular expectations from the electroweak interaction are, firstly, universal optical activity and, secondly, a difference between the electronic binding energy of two enantiomeric molecules in either a stationary or a transition state. The universal optical activity arising from the electroweak interaction is the more important for the heavier atoms, and high sensitivity polarization-rotation studies of thallium, lead and bismuth atoms in the gas phase give an optical rotation with the correct sign and order of magnitude5. 

The electroweak interaction in chiral molecules gives rise to a parity-violating shift of the electronic binding energy, Epv , which is positive for one isomer and negative for its enantiomer. The energy shift, Epv , like the optical activity, is dependent, not only upon the overall stereochemical configuration, but also upon the detailed molecular conformation. Ab initio calculations for the two main regular conformations of the proteins… indicate that the polypeptides based upon the naturally occurring L-amino acids are stabilised relative to the corresponding D-enantiomers by some 10-14 J mol-1 per peptide unit. For the conformation preferred in aqueous solution, the L-isomer is similarly the more stable of the two alanine enantiomers…The parity violating energy difference between the enantiomers, Epv, is very small relative to the thermal energy, kT. The advantage factor, given by the ratio, (Epv / kT), has the approximate value of 10–17, which is equivalent to an enantiomeric excess of some 106 molecules of the L-polypeptide, or the L-amino acid, per mole of the corresponding racemate in thermodynamic equilibrium at ambient temperatures6. 

The origin of the homochirality of biological molecules (the use in living organisms of only left-handed or L-amino acids and right-handed or D-sugars) has puzzled scientists since the chirality of molecules was discovered by Louis Pasteur more than 150 years ago. Recently it has been discovered that an excess of L-amino acids is present in the Murchison and Murray meteorites indicating that a preference for L-amino acids existed in solar system material before there was life on Earth. This supports an idea, first proposed by Rubenstein et al. (1983, Nature 306, 118), for an extraterrestrial origin for homochirality.  

In this model the action of circular polarized light on interstellar chiral molecules introduced a left handed excess into molecules in the material from which the solar system formed. Some of this organic material then finds its way onto Earth via impacts of comets, meteorites and dust particles during the heavy bombardment phase in the first few hundred million years of the solar system. These molecules were then part of the prebiotic material available for the origin of life, and tipped the scales for life to develop with L-amino acids and D-sugars.

Total chiral symmetry breaking by bifurcation from racemic

systems: when “left” and “right” cannot coexist

Dilip Kondepudi

Description of Research A general theory of spontaneous chiral symmetry breaking in chemical systems has been formulated. The fundamental equations of this theory depend only on the two-fold mirror-image symmetry and not on the details of the chemical kinetics. Close to equilibrium, the system will be in a symmetric state in which the amounts of the two enantiomers of all chiral molecules are equal. When the system is driven away from equilibrium by a flow of chemicals, a point is reached at which the system becomes unstable to small fluctuation in the difference in the amount of the two enantiomers. As a consequence, a small random fluctuation in the difference in the amount of the two enantiomers spontaneously grows and the system makes a transition to an asymmetric state. The general theory describes this phenomenon in the vicinity of the transition point. --

Up to now it was believed that total chiral symmetry breaking during crystallization of sodium chlorate occurs via the production of secondary crystals of the same handedness from an initial single chiral crystal or “mother crystal” that seeds the solution. Here we report that a solution of sodium chlorate with a large and “symmetric” population of D- and Lcrystals moves into complete chiral purity disappearing one of the enantiomers.This result shows: (i) a new symmetry breaking process, incompatible with the hypothesis of an initial single chiral crystal; (ii) that complete symmetry breaking and total chiral purity can be achieved from an initial system with both enantiomers. These findings demand a new explanation to the process of total symmetry breaking in crystallization without the intervention of an initial single chiral phase and open the debate on this fascinating phenomenon. …

Plane-polarized light

Polarization of light

100

180

MM

cd

nn RL

specific rotationd in dm; c in g/mL

molar rotation

Left- and right-handed polarized light

Linearly polarized light can be seen as composed by right- and left-handed circularly polarized light.

A chiral compound interacts with these two kinds of light in a different manner.

As consequence, the emerging light carries the information (ellipticity) about the chirality of the system.

Optical Rotatory Dispersion & Circular Dichroism

Interaction between E and molecules (electrons) has two effects on E

reducing the velocityof propagation

decreasing the amplitudeof E

cd

M

DL

DL

10][

3300

circular dichroism(elliptically polarized light

results)

molar ellipticity deg cm2 dmol-1

DL

DL

DL

nnd

nn

nn

180

Positive Cotton Effect

Negative Cotton Effect

Absorption spectrum

CD bands can be positive or negative

Absorption

()

Differential Absorption

(L- R)

CD band can have a positive or negative sign because is related to the difference:

RL

and molar ellipticities are related by the relation:

3298][

-Helix

Myoglobin

-Sheet

CD of proteins

CD spectra of secondary structure models. Reference CD

spectra

The CD spectrum in the region of the amide bond absorption is a sensitive probe to study the secondary structure of a protein.

Evaluation of the secondary structure

ccppp ][][][][

1 cppp

0.683

0.047

0.270

Generally the fit is done with four or five basis spectra: -helix, -sheet, -turns, random coil, and eventually including aromatic contribution

pH-induced denaturation of myoglobin

pH

[]

2.6 3.8 6.25.0

CD in the near-UV region (aromatic residues)

10 000

0

-10 000

100

0

100

200 220 240 280 320nm nm

[] []Native

Denaturated

CD of nucleic acids

250 300 350 400

-20

0

20

40

60

[] 1

0-3, d

egre

es c

m2 d

mol

-1

Wavelength, nm

Compacted DNA (psi form) in lecithin reverse micelles

w0 = 5w0 = 7

w0 = 10w0 = 13

water phase

Ontological Levels and Symmetry BreakingGyorgy DarvasThe Institute for Advanced Symmetry Studies, Budapest, Hungaryh492dar@ella.hu, symmetry@mailhost.net                                                                                   ABSTRACT: I discuss the role of symmetry breaking in a philosophical context, and formulate laws of symmetry breaking. I deal with their conceptual and ontological background, limits of validity, their relation to the theories of evolution and reductionism and to level theories. Level theories are used to make a sequential arrangement of the forms of appearance of moving matter. Aspects of symmetry or symmetry breaking have never been involved in the treatment of these theories. Here, I first attempt to bring knowledges of different origins together. There are two types of level theories: a general one (in philosophy) and particular ones (in the inanimate, the organic nature and in the human society). Particular level theories differ from each other in the three fundamental ontological spheres, and in their description and contents . At the same time they may have common features, e.g., all are particular theories concerning their width of validity, and all are based on an arrangement by a common concept, namely the forms of interaction. The clarification of these conceptual problems was necessary to understand the laws of symmetry breaking. The law of correspondence between the ontological levels and their potential symmetry properties is formulated in four constituent statements and two concluding laws are also presented. The new features of this treatment will link level theories with (dis)symmetry principles, and formulate the laws of symmetry breaking.