Reactant Product Energy Landscape

EcoRV

Phosphodiester hydrolysis H2OH2O

“Reactant State” Crystal Structure Cleavage Site Water Oxygen 3.7Å Ala 92 (Mutated from Lys)

Molecular Dynamics of Wild Type Lys 92 Water Molecule PETRA IMHOF

MD I Molecular Dynamics of Wild Type PETRA IMHOF

MD II

Principal Components I Principal Component

Molecular Dynamics of Wild-Type Deprotonated Lys 92 Water Molecule

Muscle Contraction Thick filamentThin filament

ATP Hydrolysis by Myosin SONJA SCHWARZL

Serine Protease Melanie Böttcher

Index Definition Digestive enzymes Blood clotting Complement system

Serine Protease Cutting of certain peptide bonds in other proteins Activity depends on a set of amino acid residues in the active site of the enzyme Based on nucleophilic attack of the targeted peptidic bond by a serine

Serine Amino acid alcohol as residue

Digestive enzymes Chymotrypsin, Trypsin, Elastase closely-similar structures different substrate specificities Pancreatic proteases  proenzymes trypsinogen and chymotrypsinogen  synthesized in the pancreas and secreted into the lumen of the small intestine

Mechanism

Active site

Trypsinogen-Trypsin loss of six amino acids from one end overall structures remain similar Ca++ for thermal stability activated enzyme does have more of its structure organized into sheets

Trypsin Trypsin cleaves peptide bonds on the C-terminal side of arginines and lysines  Alcaline amino acids Activation by enteropeptidase or through protoelyse Optimum pH 7 to 8

Chymotrypsinogen-Chymotrypsin Chain is clipped in four places  release of 2 dipeptides  creation of two breaks in the backbone 1-13 segment retained as part of the active enzyme, linked on by a disulfide bond Activation by trypsin

Chymotrypsin Active site: His57-Ser195-Asp102 Chymotrypsin cuts on the C- terminal side of tyrosine, phenylalanine, and tryptophan residues hydrolysis of bonds of leucyl, methionyl, asparaginyl and glutamyl residues.

Elastase cuts peptide bonds next to small, uncharged side chains such as those of alanine, serine, valine and threonin cuts collagen

Blood Clotting System Cascade of several mechanism  Involved Serine Proteases  Thrombin  Plasmin  Factor 10 a  Factor 11 b

Human Thrombin with the Amino acids of Hirudin Thrombin Inactivated Prothrombin cleaves into activated Thrombin Thrombins cuts Paraglobuline (= fibrinoplastic substance) and forms the soluble state of it Precipitation by plasmasalt in unsoluble state

Serpins Serine Protease Inhibitors inhibit the action of their respective serine protease  serine protease binds the serpin instead of its normal substrate  protease makes a cut in the serpin leading to –the formation of a covalent bond linking the two molecules –a massive allosteric change in the tertiary structure of the serpin which moves the attached protease to a site where it can be destroyed

Serine ProteaseSerpin Chymotrypsinalpha-1-antichymotrypsin Complement factor C1s C1 Inhibitor (C1INH) Elastase (secreted by neutrophils)alpha-1-antitrypsin Clotting factor 10 (X)antithrombin III Thrombinantithrombin III Plasminalpha-2-antiplasmin Trypsinpancreatic trypsin inhibitor

Occurrence/ Function stop proteolytic activity blood plasma clotting complement systems where a tiny initial activating event leads to a rapidly amplifying cascade of activity

Serpin Deficiencies inherited diseases mutation in the encoding gene for serpin examples

Alpha-1-Antitrypsin Serpin for Elastase secreted by neutrophils (lung infection)  emphysema  liver damage tests are running

The Others Other Serine Proteases –Subtilisin –Acetylcholinesterase Serpinlike Molecules –Angiotensinogen –Chicken Ovalbumin