[InfiniteNow]

I've heard members in a number of threads use the term "left-handed" protiens, and that these are more common than "right-handed" protiens.

Before I ask the relevance of having more left-handed protiens than right-handed, can someone please describe what handedness has to do with protien structure? How this came to be and how it's used in practice?


Ambidextrous amino acids are my favorite.

[HydrogenBond]

If we take a protein, for example, and wind it into a left handed helix and then take a second protein and wind it into a right handed helix, the two helixes will not superimpose, even if you flip them. The atom count is the same but they exist differently in space.

What holds both protein helixes together is hydrogen bonding. One of the orientations contains more potential in the hydrogen bonding, while the other contains less potential. This is more obvious when we compare DNA with a lefthanded helix to DNA with a right handed helix. The left will show secondary hydrogen bonding features that will differ from the right handed helix.

[Southtown]

HydrogenBond said:

One of the orientations contains more potential in the hydrogen bonding, while the other contains less potential.

How is that exactly? Great info, by the way.

[Jay-qu]

Southtown said:

How is that exactly? Great info, by the way.

on the flip side different atoms will line up with the hydrogen, giving different potentials in the H-bonding.

A rough analogy would be the mirror image of the protein, though not entirely correct it can help you understand it better.

[Dov Henis]

I suggest the first link below for explanation of chirality and the second link for a most reasonable conjecture re the homochirality genesis of ALL Earth's organic matter produced via enzymatic involvement. To the homo-handedness explanation just add the comprehension that the initial handedness of the amino-acid(s) of the first replicating (life) chain(s) has determined-mandated that ALL consequent life must likewise be based on the same handedness.

Origin of life: the chirality problem

NAI: News Stories

Dov

[HydrogenBond]

Hydrogen bonding is a relatively strong secondary bond, but is weak enough to break and reform easily, allowing the fluid nature of life. If one looks at ameaboid motion, the cell sticks out a finger of material in the direction it wants to go (that way!). It then regrows itself into the new location. In this case, a ripple of potential softens the hydrogen bonds, allowing them to move and reform in the new location.

Hydrogen bonding is also a means for the cell to store potential within its structures. For example, enzymes are put into their active shapes by the hydrogen bonding. There are also secondary bonding features, such as charges, but these align due to the need to minimize overall hydrogen bonding potential. As proteins come off the ribosomes, the first little piece of protein forms its hydrogen bonds, with subsequent material building on this base. This building process helps to lower the overall hydrogen bonding potential.

The left handed helixes of proteins, DNA and RNA offer the best balance of fluidity and potential storage features. Right handed helixes tend to slant the features toward the potential storage side.

Below is a picture of left and right handed DNA

[Dov Henis]

Quoted from
Origin Of Life: Homochirality

" All protein molecules in all contemporary species, from bacteria to humans, are constructed from the same set of 20 amino acids. With the exception of glycine, which has a symmetric structure and is therefore achiral, all amino acid molecules are chiral; they can exist in two mirror image forms. However, in proteins they exist only in their levorotatory form. A similar point applies to other important biological macro-molecules including DNA; they are constructed from sub-units of uniform chirality. Such macro-molecules are described as homochiral.

The homochirality of biological macro-molecules such as DNA and proteins can be understood as a necessity for contemporary life-forms. Structure is crucial to the correct functioning of both DNA and proteins. Were a molecule of 'DNA' to be constructed from sub-units of different chirality, it would not correctly form the familiar double helix structure. A similar point can be made about proteins. These macro-molecules perform an enormous range of functions in living organisms, and in most (if not all) cases the physical shape of the protein plays a key role in determining its function. If a particular protein molecule is always constructed from amino acids of uniform chirality, then the polypeptide string formed by the amino acids will always fold in the same way so that the protein molecule formed will always have the same shape. If amino acids of randomly mixed chirality were used, then the resulting polypeptide string would hardly ever fold into the same shape, with the result that most of the 'protein' molecules formed would not be able to function effectively."

Forwarded by Dov

[InfiniteNow]

Well, that helps a bit to get me more into the knowledge fold. Thanks all.

[InfiniteNow]

From Dov's link in Post #6:

Quote

The molecular structure of all but one amino acid is an asymmetrical arrangement of atoms grouped around carbon. This arrangement means that there are two mirror-image forms of each amino acid; these forms are designated left-handed (L) and right-handed (D). All of the chemistry of living systems is distinguished by its selective use of these L and D, or chiral, molecules. Most scientists believe the first self-replicating organisms used L-amino acids, and today all living systems have proteins with only L-amino acids.

[Qfwfq]

HydrogenBond said:

One of the orientations contains more potential in the hydrogen bonding, while the other contains less potential.

Are you saying there isn't chiral invariance?

Surely it's governed essentially by EM interaction, which is fully chiral...

[somebody]

i don't know if you already got your answer but i am taking molecular biology and in the text they talk about L and D isomers of an amino acid so if amino acid has handedness then sure does the protien. MOst of our body protiens are L isomers becuase most of the time L amino acids are used.

[HydrogenBond]

The picture I posted that shows the left and right handed DNA double helix clearly demonstrates how the hydrogen bonding is different between the two version of DNA. It creates two very distinct hydrogen bonding structures. The left handed DNA better serves the type of hydrogen bonding needed for transcription on the DNA.

In other words, although consensus believes left handedness of proteins and DNA was just a flip of the coin, left handedness hydrogen boniding structures are much more condusive to the needs of life. This is the same path life would take again, if it had to form from scratch.

[Qfwfq]

That picture doesn't demonstrate anything very clearly and proves nothing. Are you claiming that electromagnetic interaction is not parity invariant, or that it isn't the only one relevant in biochemistry? I can't see any other possibilities, so please tell me which you mean.

[gribbon]

Right handed proteins are the “Stereoisomerism Isomer” of amino acids with chirality labelled "D" and not very many naturally occurring organic proteins are a such. Left handed, which are the specific “Stereoisomerism Isomer” of amino acids with labelled "L", and these make up most organic proteins. My understanding of this is that the Beta version of a helix is stabilised by inner hydrogen bonds, protein interactions and occasionally metal ions. The Alpha version has only a right handed coil, resembling a spring as far as my understanding goes. Wiki (see the link) supports this.

“every backbone N-H group donates a hydrogen bond to the backbone C = O group of the amino acid four residues earlier…”

Alpha helix - Wikipedia, the free encyclopedia

They are less stable, and the fact that they are quickly attacked by water is another important note to make. I don’t know whether it is the H-bonds on the N-H groups or the H-bonds on the C=O groups that do this, though…