Abductin

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The inside of the shell where abductin is located. Valve-InternalView.png
The inside of the shell where abductin is located.

Abductin is a naturally occurring elastomeric protein found in the hinge ligament of bivalve mollusks. It is unique as it is the only natural elastomer with compressible elasticity, as compared to resilin, spider silk, and elastin. [1] Its name was proposed from the fact that it functions as the abductor of the valves of bivalve mollusks.

Contents

The properties of abductin vary across species of bivalves due to the specific use case of the species or the environment the species is found in. In spite of these differences, the same general function of acting opposite of the abductor muscles, where the resilin forces the shells into an open configuration.

Though patents for a specific protein sequences of abductin were approved by the United States Patent and Trademark Offices, there are no large scale commercial uses for abductin as of April 2022.

Structure

Amino acid composition of abductin compared to other elastomeric proteins. Amino Acid Residue of Abductin Compared To Other Elastomeric Proteins.png
Amino acid composition of abductin compared to other elastomeric proteins.

Amino acid composition

The amino acid composition of protein within the inner hinge ligament of bivalve mollusks was first discovered by Robert E. Kelly and Robert V. Rice in 1967, who subsequently proposed the protein’s name as abductin. [3] This was derived from its function as the abductor of the shells of bivalve mollusks. Kelly and Rice discovered that the protein lacked the presence of hydroxyproline and hydroxylysine, which are amino acids indicative of the common protein, collagen. Further analysis showed that abductin is made of three prominent amino acids: glycine, methionine, and phenylalanine, which are arranged in multiple repeating sequences throughout the molecule. [4] This was found in Placopecten magellanicus. Abductin is similar to elastin and resilin, but has a main difference having high concentrations of glycine and methionine. [3] The glycine and methionine, and other amino acid residues, vary in concentration with different species. In Argopecten irradians, for example, glycine and methionine make up 57.3% and 14.3% of the protein, respectively. [4] The high concentration of methionine found in abductin makes it unique because it is not a common occurrence in natural elastomeric proteins.

Protein structure

Amino acid sequence of abductin of Argopecten. Amino Acid Sequence of Abductin of Argopecten.jpg
Amino acid sequence of abductin of Argopecten.

Peptide sequences such as MGGG, FGGMG, FGGMGGG, GGFGGMGGG, and FGGMGGGNAG are repeated throughout the peptide chain. [3] It is to note that these peptide sequences all contain glycine. Additionally, in Argopecten irradians, the pentapeptide FGGMG is repeated throughout the molecule. [5] The main peptide sequence feature of abductin is the presence of many repeating sequences, all of which contain glycine residues. This is similar to that of the structure of elastin.

Abductin is lightly cross-linked, which gives it its high elasticity. The source of cross-linking has been researched, but no concrete explanation has been devised. The lack of tyrosine in the peptide chain suggests that cross-links are not formed through dityrosine links, like it is in resilin. [5] Hypotheses of the mechanism of cross-linking have been proposed by various researchers. One potential source of cross-linking is due to the presence of a methionine dimer, ½ cystine in some species, or other similar amino acids that contains a disulfide bridge, which creates the cross-link between peptide chains. [2] [3] Another study discovered that 3,3'-methylene-bistyrosine could be responsible for the cross-linkage in abductin, similar to how tyrosine and lysine residues are responsible for the cross-linking in resilin and elastin. [6]

Abductin is acellular and amorphous in structure, as discovered through microscopy and x-ray diffraction, respectively. [2] Since abductin is insoluble and its isolation from the hinge ligament is difficult, there is a lack of research concerning its structure at the protein level, such as secondary and hierarchical structures. [2] More recent research on synthetic peptides derived from abductin were found to have polyproline II helix structure in aqueous solutions and type II β-turn structure in hydrophobic solvents. [1] Combinations of both structures can also be observed for longer abductin-like peptide chains. [1]

Biological function

Bivalves swim by pushing jets of water out behind them Scallop swim.svg
Bivalves swim by pushing jets of water out behind them
Bivalve range of motion for the shell Purcell's swimming scallop with reciprocal motion.png
Bivalve range of motion for the shell

The use of abductin varies among the different species of mollusks in the world. Some, like scallops and file shells, are able to swim using a repetitive motion of opening and closing its shell, the motion of which rapidly intakes and expels water. [7] In other species of mollusks, the presence of abductin is usually located where the two shells come together to form a hinge. [8] Unlike the needs of scallops for efficient energy return for the purpose of movement, species like the Apylsia find it necessary to reduce energy return in favor of stability in opening and closing of the shells. [8] Abductin can be found within the resilium structure, which is used to store mechanical energy for this purpose. [7] The effectiveness of abductin is highly influenced by the morphological aspects of the mollusk's shell, such as its size and shape. [7] Other influences on the performance of abductin in mollusks is temperature, where there is a decrease in performance as the temperature of the surrounding environment decreases, and the presence of octopine - which acts as an analogous to lactic acid in mammals. [7] The implementation of the resilium structure of the clam can be modeled as an oscillatory system, where it works against the abductor muscle to open the shell of the organism; the resilium forces the shell open while the abductor muscle control the shell’s closure. [7]


Material properties

Little data exist on the structure and function of compressible elastomeric proteins such as abductin. An understanding of the underlying structural features of these proteins may lead to the development of a new class of highly tailored ‘‘compressible’ [9]

Solubility

By interpreting Hurst exponents as Flory, water results to be a poor solvent for the abductin peptides. [10] Predicting the functional solvent environment for insoluble proteins like abductin is particularly difficult because the protein’s hydrophobicity and the probable cross-linked nature suggest a less polar internal environment than the surrounding solvent. [9]

Conformation

The presence of both extended conformations (PPII) and folded conformations (β-turns) in equilibrium to describe abductin has been previously suggested. [9] Circular Dichroism (CD) spectra revealed that AMP1 (a 25 amino acid abductin sequence) adopts a dominant unordered conformation at 258 °C and a polyproline II (PPII) conformation at 0 °C and 458 °C with a possible minor amount of type II β-turn conformers. [9] This observation indicates that AMP1 undergoes an inverse temperature transition in that it goes from a dominant unordered conformation to a periodic, extended PPII conformation with increasing temperature. [9] The secondary structure of abductin was also investigated by Nuclear Magnetic Resonance (NMR) and CD studies of several synthetic peptides. Most synthetic abductin-based peptides adopted polyproline II (PPII) structures, which are left-handed helices, in aqueous solution, whereas they had type II β-turns in trifluoroethanol (TFE), which is a more hydrophobic (less polar) solvent. The coexistence of PPII and type II β-turns and temperature-induced multiconformational transitions were observed with longer synthetic abductin-like peptides such as (FGGMGGGNAG)4 in hexafluoroisopropanol (HFIP). [11] The secondary structure of AB12 was qualitatively analyzed by comparing the CD spectra to other peptides with known secondary structures. The CD spectra of aqueous solutions of AB12 shows a strong negative peak at 200 nm and a tendency toward positive values at ∼218 nm, which are characteristics of PPII helices. An isodichroic point at ∼208 nm suggests an equilibrium exists between the PPII structure and other conformations. In addition, because the peak at 218 nm never exceeds zero, the spectra suggest the coexistence of unordered structures and PPII helices. A small negative band can be observed at ∼225 nm, which likely results from the aromatic residue, phenylalanine, in the sequence. [11]

Temperature

The effect of temperature on the secondary structure was studied. With increasing temperature, the magnitude of both peaks in the CD spectra at 200 and 218 nm decreased, which is typical for PPII helix conformations. In addition, the change in structure because of temperature was fully reversible and did not display any hysteresis. The PPII conformation, which is widely present in elastomeric proteins such as elastin and titin, is believed to play an important role in determining the elasticity of these proteins. [11] The abductin-based protein possessed reversible Upper Critical Solution Temperature (UCST) behavior and formed a gel-like structure. At high temperatures, it displayed irreversible aggregation behavior. Thermal responsiveness is a useful property for engineering drug delivery systems because the encapsulation and release of drugs can easily be controlled via temperature change. [11]

Cytocompatibility

The abductin-based protein was cytocompatible, and cells spread slowly when first seeded on the abductin-based protein. [11] A LIVE/DEAD assay revealed that human umbilical vein endothelial cells had a viability of 98 ± 4% after being cultured for two days on the abductin-based protein. Initial cell spreading on the abductin-based protein was similar to that on bovine serum albumin. These studies thus demonstrate the potential of abductin-based proteins in tissue engineering and drug delivery applications due to the cytocompatibility and its response to temperature. [11]

Tensile and compressive moduli

Natural abductin has a tensile modulus of 1.25 MPa, which is higher than elastin (0.3−0.6 MPa) but on the same order of magnitude as resilin (0.6−2 MPa). [11] It has a compressive modulus of 4 MPa, which is higher than resilin (0.6−0.7 MPa). The superior mechanical properties of natural abductin offer the potential for designing protein-based biomaterials that can be utilized in a broader number of applications. [11]

Hydrodynamic volume and temperature relationship

A solution of AB12 (10 mg/mL in Milli-Q water) was visually observed to turn from transparent to opaque when cooled from room temperature to lower temperatures (incubated on ice). Dynamic Light Scattering (DLS) was used to further investigate the temperature responsiveness of AB12. An abrupt decrease in the hydrodynamic diameter (DH) of AB12 was observed when the protein solution was heated from 2 to 5 °C. This phenomenon is indicative of Upper Critical Solution Temperature (UCST) behavior. The change in DH at low temperatures was reversible and displayed some hysteresis. A moderate increase in DH was observed from 35 °C, and a sharper increase in DH occurred starting at 57 °C (aggregation temperature). Compared to the reversible UCST behavior, the transition that occurred at the aggregation temperature was irreversible. [11]

Extended-folded behavior

In the case of abductin, on compression, the equilibrium extended ⇄ folded should be shifted to the folded structures, decreasing the entropy. The uncompressed, multi-conformational state is recovered by a simple increase in entropy after the removal of the compression force. This is opposite to elastin’s behavior. [12]

Engineering applications

The first patent that is dedicated to the usage and implementation of abductin was accepted by the United States Patent and Trademark Office on October 3, 2000 (Patent No. 6,127,166). [13] The patent in question details the specific protein sequence of abductin to be manufactured through biological means and the possible applications of the polymer, suggesting possible uses as a copolymer for other naturally occurring polymers, a fabric material, or a material that binds with antibodies. [13] As of April 2022, there hasn’t been large-scale production, nor application, of polymers derived from the abductin or related polymeric sequences.

Related Research Articles

Amino acid Organic compounds containing amine and carboxylic groups

Amino acids are organic compounds that contain amino and carboxylate −CO−2 functional groups, along with a side chain specific to each amino acid. The elements present in every amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) (CHON); in addition sulfur (S) is present in the side chains of cysteine and methionine, and selenium (Se) in the less common amino acid selenocysteine. More than 500 naturally occurring amino acids are known to constitute monomer units of peptides, including proteins, as of 2020.

Alpha helix Type of secondary structure of proteins

The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues earlier along the protein sequence.

Collagen is the main structural protein in the extracellular matrix found in the body's various connective tissues. As the main component of connective tissue, it is the most abundant protein in mammals, making up from 25% to 35% of the whole-body protein content. Collagen consists of amino acids bound together to form a triple helix of elongated fibril known as a collagen helix. It is mostly found in connective tissue such as cartilage, bones, tendons, ligaments, and skin.

Collagen helix A structure in biochemistry

The collagen triple helix or type-2 helix is the primary secondary structure of various types of fibrous collagen, including type I collagen. It consists of a triple helix made of the repetitious amino acid sequence glycine-X-Y, where X and Y are frequently proline or hydroxyproline. Collagen folded into a triple helix is known as tropocollagen. Collagen triple helices are often bundled into fibrils which themselves form larger fibres, as in tendon.

Protein primary structure Linear sequence of amino acids in a peptide or protein

Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequences.

Protein secondary structure General three-dimensional form of local segments of proteins

Protein secondary structure is the three dimensional form of local segments of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure.

Proteinogenic amino acid Amino acid that is incorporated biosynthetically into proteins during translation

Proteinogenic amino acids are amino acids that are incorporated biosynthetically into proteins during translation. The word "proteinogenic" means "protein creating". Throughout known life, there are 22 genetically encoded (proteinogenic) amino acids, 20 in the standard genetic code and an additional 2 that can be incorporated by special translation mechanisms.

Elastin is a protein that in humans is encoded by the ELN gene. Elastin is a key component of the extracellular matrix in gnathostomes. It is highly elastic and present in connective tissue allowing many tissues in the body to resume their shape after stretching or contracting. Elastin helps skin to return to its original position when it is poked or pinched. Elastin is also an important load-bearing tissue in the bodies of vertebrates and used in places where mechanical energy is required to be stored. In humans, elastin is encoded by the ELN gene.

Protein structure Three-dimensional arrangement of atoms in an amino acid-chain molecule

Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers – specifically polypeptides – formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a residue indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of non-covalent interactions such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. This is the topic of the scientific field of structural biology, which employs techniques such as X-ray crystallography, NMR spectroscopy, cryo electron microscopy (cryo-EM) and dual polarisation interferometry to determine the structure of proteins.

Epitope mapping

Epitope mapping is the process of experimentally identifying the binding site, or "epitope", of an antibody on its target antigen. Identification and characterization of antibody binding sites aid in the discovery and development of new therapeutics, vaccines, and diagnostics. Epitope characterization can also help elucidate the mechanism of binding for an antibody and can strengthen intellectual property (patent) protection. Experimental epitope mapping data can be incorporated into robust algorithms to facilitate in silico prediction of B-cell epitopes based on sequence and/or structural data. Epitopes are generally divided into three classes: linear, conformational and discontinuous. Linear epitopes are formed by a continuous sequence of amino acids in a protein. In Conformational epitopes the binding residues are contained within certain key protein structural conformations, such as in helices, loops or beta sheets. The conformation of the epitope is important for bringing binding residues in the correct positions. Finally, discontinuous epitopes consist of parts of the antigen that are not close in the protein sequence but are brought together by three-dimensional protein folding. Discontinuous epitopes can harbour linear and conformational parts. B-cell epitope mapping studies suggest that most interactions between antigens and antibodies, particularly autoantibodies and protective antibodies, rely on binding to discontinuous epitopes.

Fibril

Fibrils are structural biological materials found in nearly all living organisms. Not to be confused with fibers or filaments, fibrils tend to have diameters ranging from 10-100 nanometers. Fibrils are not usually found alone but rather are parts of greater hierarchical structures commonly found in biological systems. Due to the prevalence of fibrils in biological systems, their study is of great importance in the fields of microbiology, biomechanics, and materials science.

Resilin

Resilin is an elastomeric protein found in many insects and other arthropods. It provides soft rubber-elasticity to mechanically active organs and tissue; for example, it enables insects of many species to jump or pivot their wings efficiently. Resilin was first discovered by Torkel Weis-Fogh in locust wing-hinges.

A polyproline helix is a type of protein secondary structure which occurs in proteins comprising repeating proline residues. A left-handed polyproline II helix is formed when sequential residues all adopt (φ,ψ) backbone dihedral angles of roughly and have trans isomers of their peptide bonds. This PPII conformation is also common in proteins and polypeptides with other amino acids apart from proline. Similarly, a more compact right-handed polyproline I helix is formed when sequential residues all adopt (φ,ψ) backbone dihedral angles of roughly and have cis isomers of their peptide bonds. Of the twenty common naturally occurring amino acids, only proline is likely to adopt the cis isomer of the peptide bond, specifically the X-Pro peptide bond; steric and electronic factors heavily favor the trans isomer in most other peptide bonds. However, peptide bonds that replace proline with another N-substituted amino acid are also likely to adopt the cis isomer.

Desmosine Chemical compound

Desmosine is an amino acid found uniquely in elastin, a protein found in connective tissue such as skin, lungs, and elastic arteries.

The Chou–Fasman method is an empirical technique for the prediction of tertiary structures in proteins, originally developed in the 1970s by Peter Y. Chou and Gerald D. Fasman. The method is based on analyses of the relative frequencies of each amino acid in alpha helices, beta sheets, and turns based on known protein structures solved with X-ray crystallography. From these frequencies a set of probability parameters were derived for the appearance of each amino acid in each secondary structure type, and these parameters are used to predict the probability that a given sequence of amino acids would form a helix, a beta strand, or a turn in a protein. The method is at most about 50–60% accurate in identifying correct secondary structures, which is significantly less accurate than the modern machine learning–based techniques.

Alpha sheet

Alpha sheet is an atypical secondary structure in proteins, first proposed by Linus Pauling and Robert Corey in 1951. The hydrogen bonding pattern in an alpha sheet is similar to that of a beta sheet, but the orientation of the carbonyl and amino groups in the peptide bond units is distinctive; in a single strand, all the carbonyl groups are oriented in the same direction on one side of the pleat, and all the amino groups are oriented in the same direction on the opposite side of the sheet. Thus the alpha sheet accumulates an inherent separation of electrostatic charge, with one edge of the sheet exposing negatively charged carbonyl groups and the opposite edge exposing positively charged amino groups. Unlike the alpha helix and beta sheet, the alpha sheet configuration does not require all component amino acid residues to lie within a single region of dihedral angles; instead, the alpha sheet contains residues of alternating dihedrals in the traditional right-handed (αR) and left-handed (αL) helical regions of Ramachandran space. Although the alpha sheet is only rarely observed in natural protein structures, it has been speculated to play a role in amyloid disease and it was found to be a stable form for amyloidogenic proteins in molecular dynamics simulations. Alpha sheets have also been observed in X-ray crystallography structures of designed peptides.

Photo-reactive amino acid analogs are artificial analogs of natural amino acids that can be used for crosslinking of protein complexes. Photo-reactive amino acid analogs may be incorporated into proteins and peptides in vivo or in vitro. Photo-reactive amino acid analogs in common use are photoreactive diazirine analogs to leucine and methionine, and para-benzoylphenylalanine. Upon exposure to ultraviolet light, they are activated and covalently bind to interacting proteins that are within a few angstroms of the photo-reactive amino acid analog.

Hydrophobicity scales are values that define the relative hydrophobicity or hydrophilicity of amino acid residues. The more positive the value, the more hydrophobic are the amino acids located in that region of the protein. These scales are commonly used to predict the transmembrane alpha-helices of membrane proteins. When consecutively measuring amino acids of a protein, changes in value indicate attraction of specific protein regions towards the hydrophobic region inside lipid bilayer.

Ligament (bivalve)

A hinge ligament is a crucial part of the anatomical structure of a bivalve shell, i.e. the shell of a bivalve mollusk. The shell of a bivalve has two valves and these are joined together by the ligament at the dorsal edge of the shell. The ligament is made of a strong, flexible and elastic, fibrous, proteinaceous material which is usually pale brown, dark brown or black in color.

Elastin-like polypeptides (ELPs) are synthetic biopolymers with potential applications in the fields of cancer therapy, tissue scaffolding, and protein purification. For cancer therapy, the addition of functional groups to ELPs can enable them to conjugate with cytotoxic drugs. Also, ELPs may be able to function as polymeric scaffolds, which promote tissue regeneration. This capacity of ELPs has been studied particularly in the context of bone growth. ELPs can also be engineered to recognize specific proteins in solution. The ability of ELPs to undergo morphological changes at certain temperatures enables specific proteins that are bound to the ELPs to be separated out from the rest of the solution via experimental techniques such as centrifugation.

References

  1. 1 2 3 R. S.-C. Su, J. N. Renner, and J. C. Liu, “Synthesis and characterization of recombinant abductin-based proteins,” Biomacromolecules, vol. 14, no. 12, pp. 4301–4308, 2013.
  2. 1 2 3 4 George A. Kahler, Frank M. Fisher, and Ronald L. Sass, “The chemical composition and mechanical properties of the hinge ligament in bivalve molluscs,” The Biological Bulletin, vol. 151, no. 1, pp. 161–181, 1976.
  3. 1 2 3 4 R. E. Kelly and R. V. Rice, “Abductin: A rubber-like protein from the internal triangular hinge ligament of pecten,” Science, vol. 155, no. 3759, pp. 208–210, 1967.
  4. 1 2 3 Q. Cao, Y. Wang, and H. Bayley, “Sequence of abductin, the molluscan ‘rubber’ protein,” Current Biology, vol. 7, no. 11, 1997.
  5. 1 2 H. Ehrlich, “Chapter 19: Abductin,” in Biological materials of marine origin: Vertebrates, Springer.
  6. S. O. ANDERSEN, “Isolation of a new type of cross link from the hinge ligament protein of molluscs,” Nature, vol. 216, no. 5119, pp. 1029–1030, 1967
  7. 1 2 3 4 5 Mark Denny, Luke Miller; Jet propulsion in the cold: mechanics of swimming in the Antarctic scallop Adamussium colbecki. J Exp Biol 15 November 2006; 209 (22): 4503–4514.
  8. 1 2 Sutton, G.P., Macknin, J.B., Gartman, S.S. et al. Passive hinge forces in the feeding apparatus of Aplysia aid retraction during biting but not during swallowing. J Comp Physiol A 190, 501–514 (2004).
  9. 1 2 3 4 5 Bochicchio, B., Jimenez-Oronoz, F., Pepe, A., Blanco, M., Sandberg, L. and Tamburro, A., 2005. Synthesis of and Structural Studies on Repeating Sequences of Abductin. Macromolecular Bioscience, [online] 5(6), pp.502-511
  10. Villani, V., 2003. Complexity of polypeptide dynamics: chaos, Brownian motion and elasticity in aqueous solution. Journal of Molecular Structure: THEOCHEM, [online] 621(1-2), pp.127-139.
  11. 1 2 3 4 5 6 7 8 9 Bochicchio, B., Pepe, A. and Tamburro, A., 2005. Circular dichroism studies on repeating polypeptide sequences of abductin. Chirality, [online] 17(7), pp.364-372.
  12. Su, R., Renner, J. and Liu, J., 2013. Synthesis and Characterization of Recombinant Abductin-Based Proteins. Biomacromolecules, [online] 14(12), pp.4301-4308.
  13. 1 2 U.S. Patent 6,127,166