Lid closure dynamics of porcine pancreatic lipase in aqueous solution

• Published in: Biochimica et biophysica acta Vol. 1860; no. 10; pp. 2313 - 2325
• Main Authors: Haque, Neshatul, Prabhu, N. Prakash
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.10.2016
• Subjects: Amino Acid Sequence - genetics; amino acids; Animals; aqueous solutions; bile salts; Binding Sites; Colipase; Colipases - chemistry; Colipases - genetics; Colipases - metabolism; detergents; dietary fat; energy; Hydrolysis; Lid closure; Lipase - chemistry; Lipase - genetics; Lipase - metabolism; Molecular Dynamics Simulation; Molecular simulation; Mutagenesis, Site-Directed; Pancreas - enzymology; Pancreatic lipase; Protein Conformation; Substrate Specificity; swine; Swine - genetics; triacylglycerol lipase; Water; Water - chemistry; Molecular simulation; Water; PPL-O; Pancreatic lipase; PPL-Cl; Colipase; RMSF; PPL+colip; Lid closure; RMSD; PPL-colip; PCA; Rg; SASA
• ISSN: 0304-4165; 0006-3002; 1872-8006
• DOI: 10.1016/j.bbagen.2016.05.004

Pancreatic lipases hydrolyze fatty acids in dietary pathway. The activity of porcine pancreatic lipase (PPL) is controlled by lid domain along with a coenzyme, colipase. The active open-state conformation of the protein could be induced by detergents or bile salts which would be further stabilized by binding of colipase. In the absence of these interactions, the lid preferably attains a closed conformation in water. Molecular dynamic simulation was used to monitor the lid movement of PPL in open and closed conformations in water. Free energy surface was constructed from the simulation. Energy barriers and major structural changes during lid opening were evaluated. The lid closure of PPL in water from its open conformation might be initiated by columbic interactions which initially move the lid away from domain 1. This is followed by major dihedral changes on the lid residues which alter the trajectory of motion. The lid then swirls back towards domain 1 to attain closed conformation. This is accompanied with conformational changes around β5- and β9-loops as well. However, PPL in closed conformation shows only the domain movements and the lid remains in its closed conformation. PPL in closed conformation is stable in water and the open conformation is driven towards closed state. The lid follows a swirling trajectory during the closure. Conformational state of the lid regulates the activity and substrate specificity of PPL. Hence, it is essential to understand the lid dynamics and the role of specific amino acid residues involved. •MD simulation studies on lid-closure dynamics of porcine pancreatic lipase in water•Free energy surface was constructed and energy barriers were identified.•Trajectory of lid closing movement and the role of specific residues were analyzed.•Lipase in closed conformation shows only domain–domain movement.