Heparin is a complex carbohydrate that occurs naturally and is used medically to prevent the formation of blood clots. It belongs to a class of linear polysaccharides known as glycosaminoglycans. Found in the mast cells of various animal tissues, the heparin used for medical purposes is sourced from porcine intestines or bovine lungs. The molecule’s intricate structure is directly responsible for its biological activity.
The Polysaccharide Chain
Heparin is a polymer, a long chain of repeating disaccharide units composed of two linked sugar molecules. The chain is built from alternating units of a D-glucosamine and a uronic acid, which can be either L-iduronic acid or D-glucuronic acid. The linkage between these sugars occurs at specific carbon atoms, creating a linear, unbranched polysaccharide chain similar to heparan sulfate.
Extensive chemical modifications that occur after the initial chain is formed define heparin’s structure. A primary modification is sulfation, the addition of sulfate groups to various positions on the sugar rings. These modifications include N-sulfation on the glucosamine unit and O-sulfation on both the glucosamine and uronic acid residues. A common repeating unit is a trisulfated disaccharide.
The numerous sulfate and carboxyl groups along the chain give heparin the highest negative charge density of any known biological molecule. This dense negative charge is not an incidental feature; it is fundamental to how heparin interacts with other molecules in the body. These interactions are the basis for its anticoagulant effects.
The Antithrombin-Binding Sequence
The primary anticoagulant function of heparin is mediated through its interaction with a protein called antithrombin. While the heparin polysaccharide can be long, its ability to activate antithrombin relies on a specific, shorter structural element within the chain. This feature is a unique pentasaccharide sequence, a specific arrangement of five sugar units that creates a high-affinity binding site for antithrombin. Only about one-third of heparin chains contain this sequence.
This specific five-sugar sequence acts as a molecular key. The central component of this sequence is a rare, 3-O-sulfated glucosamine residue. The presence and specific arrangement of this and other sulfate groups within the pentasaccharide allow it to fit precisely into a binding pocket on the antithrombin protein. Amino acids such as arginine and lysine on the antithrombin surface form hydrogen bonds with the sulfate and carboxyl groups of the pentasaccharide, securing the connection.
When this binding occurs, it induces a conformational change in the antithrombin protein. This change alters the shape of antithrombin’s reactive center loop, making it a much more efficient inhibitor of blood clotting enzymes, particularly Factor Xa. The binding of the pentasaccharide sequence accelerates the rate at which antithrombin can inactivate these clotting factors by several orders of magnitude.
Structural Heterogeneity and Conformation
A sample of heparin is not a single, uniform molecule but a diverse population of polysaccharide chains. This structural heterogeneity arises from two main sources: variations in chain length and differences in the sulfation pattern. The biosynthesis process is not perfectly uniform, resulting in chains with molecular weights that can range from 5,000 to over 40,000 Daltons. The exact placement and number of sulfate groups can also differ from one chain to another, meaning a pharmaceutical preparation of heparin contains a vast collection of distinct molecular structures.
In solution, the heparin chain adopts a flexible, helical structure. This conformation is not rigid, as fluctuations in the iduronic acid rings allow for considerable internal motion. This flexibility is important because it enables the pentasaccharide binding sequence to orient itself correctly in three-dimensional space. The ability of the chain to present this binding site effectively is necessary for its interaction with antithrombin.
Fractionated vs Unfractionated Heparin
The natural, heterogeneous mixture of heparin chains isolated from animal tissue is known as unfractionated heparin (UFH). UFH contains the full spectrum of chain lengths, from short to very long, with molecular weights averaging around 15,000 Daltons. This mixture of different-sized molecules contributes to its broad biological effect.
Low-molecular-weight heparin (LMWH) is a derivative created by breaking down UFH into smaller pieces through chemical or enzymatic depolymerization. This process results in shorter polysaccharide chains with a more uniform and predictable size, averaging between 4,500 and 5,000 Daltons. While these shorter chains still contain the antithrombin-binding pentasaccharide, their reduced length alters their mechanism of action.
The difference in function lies in how chain length affects interactions with clotting factors. To inactivate the clotting enzyme thrombin, the heparin chain must be long enough—at least 18 saccharide units—to bind to both antithrombin and thrombin simultaneously, forming a bridge. Many chains in LMWH are too short to do this effectively.
However, these shorter chains are still fully capable of binding to antithrombin to accelerate the inactivation of another clotting factor, Factor Xa. This interaction does not require the bridging mechanism. This structural difference gives LMWH a more targeted activity and more predictable pharmacokinetic properties compared to UFH.