In chemistry, an oligomer (\ə-ˈli-gə-mər\, ολιγος, or oligos, is Greek for "a few") is a molecular complex that consists of a few monomer units, in contrast to a polymer that, at least in principle, consists of a nearly unlimited number of monomers.[1] Dimers, trimers, and tetramers are, for
.
instance, oligomers respectively composed of two, three and four monomers
In the context of biochemistry, an oligomer is usually referred to a macromolecular complex formed by non-covalent bonding of few macromolecules like proteins or nucleic acids. In this sense, a homooligomer would be formed by few identical molecules and by contrast, a hetero-oligomer would be made of three different macromolecules. Collagen is an example of homo-oligomeric protein that is composed of three identical protein chains
Many oils are oligomeric, such as liquid paraffin. Plasticizers are oligomeric esters widely used to soften thermoplastics such as PVC. They may be made from monomers by linking them together, or by separation from the higher fractions of crude oil. Polybutene is an oligomeric oil used to make putty. Greek prefixes are often used to designate the number of monomer units in the oligomer, for
.
example a tetramer being composed of four units and a hexamer of six
In biochemistry, the term oligonucleotide - or, informally, "oligo" - is used for short, single-stranded nucleic acid fragments, such as DNA or RNA, or similar fragments of analogs of nucleic acids such as peptide nucleic acid or Morpholinos. Such oligos are used in hybridization experiments (bound to glass slides or nylon membranes), as probes for in situ hybridization or in antisense experiments such as gene knockdowns.[citation needed] It can also refer to a protein complex made of two or more subunits. In this case, a complex made of several different protein subunits is called a heterooligomer or heteromer. When only one type of protein subunit is used in the complex, it is called a
.
homo-oligomer or homomer
Oligomerization is a chemical process that converts monomers to macromolecular complexes through a finite degree of polymerization. The actual figure for degree of polymerization is a matter
] of debate, often a value between 10 and 100.[citation needed
When an oligomer forms as a result of chain transfer the oligomer is called a telomer and the process telomerization.[4] A telomere is a region of highly repetitive DNA at the end of a linear
.
chromosome
IUPAC definition

Oligomer molecule: A molecule of intermediate relative molecular mass, the structure of which essentially comprises a small plurality of units derived, actually
.
or conceptually, from molecules of lower relative molecular mass
Notes
A molecule is regarded as having an intermediate relative molecular mass if it .
1
.
has properties which do vary significantly with the removal of one or a few of the units
If a part or the whole of the molecule has an intermediate relative molecular mass .
2
, and essentially comprises a small plurality of units derived, actually or conceptually
, from molecules of lower relative molecular mass, it may be described as oligomeric
] or by oligomer used adjectivally.[2
Oligomerization: The process of converting a monomer or a mixture of monomers
.
into an oligomer
Note: An oligomerization by chain reaction carried out in the presence of a large amount
of chain-transfer agent, so that the end-groups are essentially fragments of the chain
] transfer agent, is termed telomerization. [3
Working With Oligomeric Proteins

In this section, you will learn to study models that contain more than one protein chain. For this
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section, obtain the file 3HHB.pdb from the PDB
.
Start DeepView and open 3HHB.pdb, a model of deoxyhemoglobin
Color: Chain
Many proteins are oligomeric -- composed of more than protein chain, or subunit. DeepView colors each subunit a different color. This command is a quick way to find out how many chains are in a
.
newly opened PDB file
Click on the Control Panel to activate it. Notice that letters A in the first column, the chain column.
Click on any A, then press return. Clicking in the chain column selects the entire A chain. Scroll down to the end of the list of A-chain residues and click on any B, then press return. Chain B appears and chain A disappears. The chain column provides for quick and easy selection and deselection of entire chains. If the protein has only one chain, this column is empty. Clicking in an empty chain column
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selects the whole model
Chains A and B in this model are the alpha and beta subunits of hemoglobin. You may be aware that hemoglobin consists of four subunits, two identical alpha and two identical beta. Some PDB files for oligomeric proteins contain only the unique subunits -- in this case, one each of alpha and beta.
Later, you will build the additional subunits. But first, you will examine the interface between the
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subunits
Color the chain A cyan (between blue and green on the color wheel) and the B chain magenta
.) (between red and blue
...
Select: Groups Close to another Chain
Use this dialog to select groups that are within 5 angstroms of another chain, and click OK. This amounts to selecting the residues within 5 angstroms of the subunit interface. Press return to
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eliminate other residues
Study the interactions in the subunit interface as follows. Color the selected sidechains (not backbones) by type, and then compute H-bonds. Zoom in for a close examination. The backbone

colors allow you to distinguish chains A and B, while sidechain colors suggest the types of interactions. Red side chains (negative) near blue (positive) suggests ionic interactions. Gray near gray implies hydrophobic interactions. Green dotted lines indicate H-bonds. Do you see any interchain H-bonds? Measure any potential ionic or hydrophobic interactions. Slabbing and showing
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surfaces of selected groups may help you to see more about how the subunits interact
When you are finished, redisplay the full model. Reset the Control Panel color menu to color
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backbone + sidechain, and color the model CPK. Turn off the display of H-bonds
If you want to examine A-A or B-B interactions, you need a model of the entire tetramer. If the proper information is provided in the PDB file, DeepView can help you build the full model. In the
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remainder of this section, your will build the full tetramer from two copies of the file 3HHB.pdb
) File: 3HHB.pdb (look for this file name near the bottom of the File menu
This command takes advantage of DeepView's list of recently used files. You have just used it to open a second copy of 3HHB. The two models are superimposed, so it appears that nothing new has
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been added
Wind: Layer Infos
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The Layer Information window allows you to control the display and properties of multiple layers
Color: Layer
> ctrl> - <tab>; <ctrl> - <tab>, <ctrl> - <tab <
.
You are cycling or blinking between the two models, which are now colored yellow and blue
These two models are called layers. On the Layer Infos window, both layers are listed as 3HHB. Blink to make the second 3HHB visible (check mark in vis column) and active (layer name red). Now you
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will rename the second 3HHB so you can more easily tell the two layers apart
...
Edit: Rename Current Layer
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Name the new layer 3HHBA'B' and click OK

Blink between the two layers. Stop with the new layer active -- red in the Layer Infos window. The
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name 3HHBA'B' should also be displayed at the top of the Control Panel
Make the Control Panel active and click on any A in the left-most column. You have selected all
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groups in chain A
...
Edit: Rename Current Layer
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Tab into the box labeled Rename Chain of Selected Groups, type C, and click OK
.
In the 3HHBA'B' layer, select chain B
...
Edit: Rename Current Layer
Tab into the box labeled Rename Chain of Selected Groups, type D, and click OK. You have renamed the A and B chains of the new 3HHBA'B' layer so that when you merge both files into one, the four chains will be named A and B (the first alpha/beta dimer), C and D (the second dimer). Now you will
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rotate the CD pair into the orientation of the second alpha/beta dimer
Select:All
With all groups in the new layer (3HHBA'B') selected, click the file icon on the graphics window
(beside the little earth icon) to display the PDB file. Scroll down to the beginning of the ATOM lines.
The last three lines, labeled MTRIX, before the first ATOM line give the information that DeepView needs to transform the coordinates of your CD dimer into the coordinates of the second, or A'B' pair.
All you need to do is click anywhere in these three lines, and click OK on the dialog box. Then close the file window, and you will find the current layer in its new orientation, with the original layer in
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the old orientation. Together, they make a full tetramer
Blink between the layers to see their relative orientation. In the Layer Infos window, put checkmarks in the vis column beside both layers to see them together. Next you will combine them into a single
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layer, and then save the tetramer in a new file
) shift> - Select: All (selects all in both layers -- recall that shift applies Select commands to all layers <
.
Check to be sure that all residues in both layers are selected

Edit: Create Merged Layer From Selection
This operation will take a few seconds. Notice that you now have a third layer, named "_merge_" .
.
Blink to make _merge_ the active the layer
Color: Chain
: You should see the four chains of the tetramer in different colors, like this
File: Save: Layer
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Save the _merge_ layer in a file named 3HHBTet.pdb
Close all files and then open your newly saved file. Rotate and study the way the four oligomers fit
.
together
Select: Groups Close to Another Chain
Use the dialog that appears to select groups that are within 5 angstroms of another chain, and click
.
OK
> return <
Now you can study all of the subunit interfaces of the tetramer, using the same tools you used
.
earlier to study the AB interface
Finally, look at the relative positions of the four hemes (and two phosphate ions) in the tetramer as
: follows
Select: Group Kind: HETATM
> return <

You should see only the four hemes and two phosphate ions. Use the measurement icon on the graphics window to measure all the distances between iron atoms in the various hemes. When you have measured them all, the six yellow lines will form an elongated tetrahedron, with its shortest
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sides connecting the two alpha/beta dimers you have combined to build this tetramer