Mussel adhesive proteins (MAPs) have drawn interest for their ability to form strong adhesive bonds to a variety of substrates in wet environments. 1 There have been efforts to develop biomedical adhesives from these proteins, yet this has been hampered by the difficulty of isolation from biological sources. 2 Synthetic polymers are a potential source of functionally equivalent adhesives, yet little is known about how the MAPs function and therefore what must be incorporated into a synthetic analogue. The catechol functionality of L-3,4-dihydroxyphenylalanine, DOPA, residues is thought to be responsible for adhesion and cross-linking of the proteins; however, the mechanisms for these processes are unknown. The potential involvement of L-lysine and other polar residues in these reactions further complicates analytical efforts. 1 Speculation on the key components of these materials has been limited since no cross-link bond or specific bond to a substrate has been identified as yet. Through analysis of amino acid derivatives and simple copolypeptides under adhesive curing conditions, we have determined that DOPA is the only functional element required to reproduce the properties of MAPs. Furthermore, the primary roles of both catechol and o-quinone forms of DOPA can be assigned to adhesive bonding and cross-link formation, respectively.The most detailed studies on MAPs have focused on the blue mussel, Mytilus edulis. This organism anchors itself to surfaces by means of plaques on the ends of fibrous threads. A considerable variety of adhesive proteins have been isolated from uncured plaques. These proteins range in mass from ca. 5 to 120 kDa, and all contain high levels of DOPA (ca. 5-20 mol %). 3 Variants also contain elevated levels of other polar amino acids such as hydroxylated prolines, lysine, and 4-hydroxyarginine. The variability of these proteins, in terms of their chain lengths, sequences, and compositions, has made it difficult to identify the important components responsible for adhesion.It is known that catechol oxidase enzymes are present in MAP secretions that convert the catechol groups of DOPA into highly reactive o-quinone functionalities. 4 Numerous reactions have been proposed for cross-linking of the quinones (Scheme 1), yet none of these have been experimentally verified in MAPs. 1 The most often cited reaction is the Michael addition of side-chain amino groups of lysine residues to a DOPA-quinone residue. 5 Although all attempts to detect this product to date have been unsuccessful, the importance of the Michael addition in quinone chemistry has generated strong support for lysine cross-linking in MAPs. 6 Our goal was to experimentally identify the roles of amino acids that are active in the adhesive chemistry of MAPs. Problems

Water soluble copolypeptides containing l-dihydroxyphenylalanine (DOPA) and l-lysine were prepared by ring-opening polymerization of alpha-amino acid N-carboxyanhydride (NCA) monomers. We have prepared a range of different copolymers to probe the effects of functional group composition on adhesive and cross-linking behavior. Aqueous solutions of these copolymers, when mixed with a suitable oxidizing agent (e.g., O2, mushroom tyrosinase, Fe3+, H2O2, or IO4-), formed cross-linked networks that were found to form moisture-resistant adhesive bonds to a variety of substrates (e.g., aluminum, steel, glass, and plastics). It was found that successful adhesive formation was dependent on oxidation conditions, with chemical oxidants giving the best results. Optimized systems were found to form adhesive bonds that rival in strength those formed by natural marine adhesive proteins. Our synthetic systems are readily prepared in large quantities and require no enzymes or other biological components.

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GROMACS is a widely used package in molecular dynamics simulations of biological molecules such as proteins, and nucleic acids, etc. However, it requires many steps to run such simulations from the terminal window. This could be a challenge for those with minimum amount of computer skills. Although GROMACS provides some tools to perform the standard analysis such as density calculation, atomic fluctuation calculation, it does not have tools to give us information on the specific areas such as rigidity that could predict the property of the molecules. In this project, I have developed a user friendly program to carry out molecular dynamics simulations for proteins using GROMACS with an easy user input method. My program also allows one to analyze the rigidity of the proteins to get its property.