Exploring the pH-Dependent Structure–Dynamics–Function Relationship of Human Renin

Abstract

Renin is a pepsin-like aspartyl protease and an important drug target for the treatment of hypertension; despite three decades' research, its pH-dependent structure-function relationship remains poorly understood. Here we employed the continuous constant pH molecular dynamics (CpHMD) simulations to decipher the acid/base roles of renin's catalytic dyad and the conformational dynamics of the flap, which is a common structural feature among aspartyl proteases. The calculated pK a 's suggest that the catalytic Asp38 and Asp226 serve as the general base and acid, respectively, in agreement with experiment and supporting the hypothesis that renin's neutral optimum pH is due to the substrate-induced pK a shifts of the aspartic dyad. The CpHMD data confirmed our previous hypothesis that hydrogen bond formation is the major determinant of the dyad pK a order. Additionally, our simulations showed that renin's flap remains open regardless of pH, although a Tyr-inhibited state is occasionally formed above pH 5. These findings are discussed in comparison to the related aspartyl proteases, including β-secretases 1 and 2, capthepsin D, and plasmepsin II. Our work represents a first step towards a systematic understanding of the pH-dependent structure-dynamics-function relationships of pepsin-like aspartyl proteases that play important roles in biology and human disease states.Renin-angiotensin-aldosterone system (RAAS) is a critical regulator for blood pressure and systemic vascular resistance. 1,2 As a part of the RAAS system, the aspartic protease renin cleaves a protein called angiotensinogen to generate an inactive decapeptide, angiotensin I, which is further cleaved by the angiotensin converting enzyme (ACE) to produce shorter peptides, including the octapeptide angiotensin II which binds and activates the angiotensin II type 1 (AT 1 ) and type 2 (AT 2 ) receptors. The primary effects of AT 1 receptor activation include vasoconstriction and stimulation of aldosterone synthesis and release with subsequent sodium and fluid retention, which tend to elevate blood pressure. 1 Because of its essential role in the function of RAAS and the high specificity for its only known substrate angiotensinogen, renin is an attractive drug target for the treatment of hypertension. Despite

Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems

“…Recent CpHMD simulations showed that the population of hydrogen bonds in pepsin-like aspartic proteases depends on the pH through the varying protonation of the aspartic dyad. 43 …”

“…We speculate that the population of normal and flipped states depends on the protonation states of catalytic aspartates. Recent CpHMD simulations showed that the population of hydrogen bonds in pepsin-like aspartic proteases depends on the pH through the varying protonation of the aspartic dyad …”

Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments

“…Due to their similarity, either DIST2 or z can be applicable in PAPs to capture the extent of flap opening. Recently Shen and co-workers 23 proposed the following distance parameters to measure the extent of flap opening in human renin: (1) distance between Tyr-83-OH and Asp-38-CG and (2) distance between Ser-84-CB and Asp-226-CG ( Fig. 27 in ESI † ).…”

Exploring the pH- and Ligand-Dependent Flap Dynamics of Malarial Plasmepsin II

“…Pepstatin A binds plasmepsin II by forming hydrogen bonds with the catalytic dyad and acts as a transition-state analogue. ,, Interestingly, the X-ray structure of plasmepsin II in complex with pepstatin A shows that the flap, which is a long β-hairpin loop (residues 72–85) that lays over the active site, is in a closed conformation (Figure A). The flap is a common structural feature for aspartyl proteases such as human β-secretase 1 (BACE1), CatD, and renin; the flap dynamics is an important aspect in the design of potent and selective inhibitors. , The X-ray crystal structures of plasmepsin II in complex with various inhibitors showed that the flap can adopt both open and closed states; , inhibitors have been discovered to target the specific flap conformations . Recently, a conventional MD study suggested that the flaps of apo plasmepsins I–V, IX, and X are all flexible; , however, the details of how a ligand and, potentially, pH modulate the flap conformation have not been examined.…”