Adaptation of plasminogen activator sequences to known protease structures

Area of Science:

• Biochemistry
• Structural Biology
• Molecular Modeling

Background:

• Urokinase (UK) and tissue-type plasminogen activator (TPA) are serine proteases crucial for fibrinolysis.
• Understanding their structure-activity relationships is key to developing targeted therapies.
• Comparative analysis with other serine proteases like chymotrypsin, trypsin, and elastase provides a framework for structural insights.

Purpose of the Study:

• To elucidate the structural basis of plasminogen activation by UK and TPA.
• To compare the conserved and divergent structural features of UK and TPA with other related proteases.
• To identify key residues potentially involved in substrate recognition and specificity.

Main Methods:

• Sequence alignment of UK and TPA with chymotrypsin, trypsin, and elastase focusing on structurally conserved regions.
• Homology modeling of UK based on the chymotrypsin structure, incorporating disulfide bond patterns.
• Analysis of potential insertions and their surface accessibility in UK and TPA.

Main Results:

• UK was modeled using the chymotrypsin structure due to conserved disulfide patterns, despite trypsin-like specificity.
• An additional disulfide bond involving cysteines 50 and 111d was identified in UK.
• Specific residues (Asp 97, Lys 143, Arg 217/Leu in TPA) were highlighted as potentially critical for plasminogen activating specificity.
• Structural differences at the binding pocket edge may affect plasminogen-thrombin inhibitor (PTI) binding.

Conclusions:

• The structural framework of UK and TPA, particularly conserved disulfide bonds, influences their catalytic activity.
• Surface-accessible insertions in UK and TPA might play a role in plasminogen recognition.
• Specific amino acid variations at functional positions contribute to the distinct substrate specificities and inhibitor interactions of these enzymes.