Fibronectin is a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin. The major part of the sequence of fibronectin consists of the repetition of three types of domains, which are called type I, II, and III [1]. Type I domain (FN1) is approximately 40 residues in length. Four conserved cysteines are involved in disulfide bonds. Fibronectin contains 12 repeats of this domain.

The 3D structure of the FN1 domain has been determined (see <PDB:1FBR>) [2,3,4,5]. It consists of two antiparallel β-sheets, first a double-stranded one, that is linked by a disulfide bond to a triple-stranded β-sheet. The second conserved disulfide bridge links the C-terminal adjacent strands of the domain (see the schematic representation below).

                                          +--------+
              +---------------------------|-+      |
              |                           | |      |
            xxCxxxxxxxxaxxxxxax+xxxxxxxxxxCxCxxxxxxCxxx
              **************************************
              bbb    bbb    bbbbb      bbbbb      bbbbb

'C': conserved cysteine involved in a disulfide bond.
'a': often conserved aromatic amino acid.
'b': position of sheet-forming amino acids.
'+': positively charged amino acid.
'*': position of the pattern.

In human tissue plasminogen activator chain A, the FN1 domain together with the following epidermal growth factor (EGF)-like domain (see <PDOC00021>) are involved in fibrin-binding [6]. It has been suggested that these two modules form a single structural and functional unit [4]. The two domains keep their specific tertiary structure, but interact intimately to bury a hydrophobic core; the inter-module linker makes up the third strand of the EGF-module's major β-sheet.

The FN1 domain is also found as a single copy in the following mammalian proteins:

• Blood coagulation factor XII (Hageman factor), which is composed of a fibronectin type-II domain, two EGF-repeats, one fibronectin type-I domain, followed by a kringle.
• Hepatocyte growth factor (HGF) activator (EC 3.4.21.-), activates hepatocyte growth factor by converting it from a single chain to a heterodimeric form. It has the same modular architecture than the blood coagulation factor XII.
• Tissue-type plasminogen activator (t-PA), which contains a fibronectin type-I domain, one EGF-repeat, and two kringles.

We developed a pattern, that spans the domain between the first and the last conserved cysteine. We also developed a profile that covers the whole FN1 domain.