Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM

Abstract

The conformational dynamics of Candida antarctica lipase B (CALB) was investigated by molecular dynamics (MD) simulation, parallel cascade selection MD (PaCS-MD), and the Markov state model (MSM) and mainly focused on the lid-opening motion closely related to substrate binding. All-atom MD simulation of CALB was conducted in water and on the interface of water and tricaprylin. CALB initially situated in water and separated by layers of water from the interface is spontaneously adsorbed onto the tricaprylin surface during MD simulation. The opening and closing motions of the lid are simulated by PaCS-MD, and subsequent MSM analysis provided the free-energy landscape and time scale of the conformational transitions among the closed, semiopen, and open states. The closed state is the most stable in the water system, but the stable conformation in the interface system shifts to the semiopen state. These effects could explain the energetics and kinetics origin of the previously reported interfacial activation of CALB. These findings could help expand the application of CALB toward a wide variety of substrates.

PaCS-Toolkit: Optimized Software Utilities for Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Simulations and Subsequent Analyses

“…Parallel cascade selection molecular dynamics (PaCS-MD) is an enhanced conformational sampling method based on molecular dynamics (MD) simulation using only standard force fields, and consists of cycles of multiple MD simulations conducted in parallel using different conditions (replicas) and selections of the initial structures closest to a target for the next cycle. − This procedure can be considered as a “repetition of time leaps in parallel worlds” until reaching a target, which enables complete parallel execution of all the MD simulations for each cycle or computation with distributed computing. PaCS-MD has been shown to be very efficient in sampling large protein conformational change, ,,,− ,, peptide folding, the dissociation and association of protein/ligand, protein/peptide, and protein/DNA complexes ,,,,,, without applying any bias during each MD simulation.…”

“…MSM that assumes a Markov process is thus a suitable analysis method for PaCS-MD-generated trajectories. The PaCS-MD/MSM combination is widely used to calculate the free energy landscape of conformational changes, ,,,, standard binding free energy (Δ G °), ,,,,,, the association ( k on ) and dissociation rate constants ( k off ) of protein complexes, , and flux along conformational transition pathways. , If sampling is insufficient to construct an MSM, additional MD simulations can be added afterward. , In the MSM step, the sampled snapshots are grouped into discrete microstates based on certain features (termed MSM features hereafter), which are typically defined as collective coordinates that well characterize matters of interest. PaCS-MD accelerates dynamics along the selection feature but less so dynamics along other directions.…”

“… 1 − 14 This procedure can be considered as a “repetition of time leaps in parallel worlds” until reaching a target, which enables complete parallel execution of all the MD simulations for each cycle or computation with distributed computing. PaCS-MD has been shown to be very efficient in sampling large protein conformational change, 1 , 2 , 6 , 8 − 10 , 13 , 15 peptide folding, 1 the dissociation and association of protein/ligand, protein/peptide, and protein/DNA complexes 4 , 5 , 7 , 11 , 13 , 14 , 16 without applying any bias during each MD simulation.…”

“… 1 In contrast to t-PaCS-MD, rmsdPaCS-MD moves the system the farthest in RMSD from the initial structure. 13 The distance between two regions in a protein, such as an interdomain distance 6 or interlid distance, 15 are used as selection features to enhance the open-close motions of proteins. The intercenter-of-mass distance between two molecules ( d com ) 4 , 5 , 7 , 11 , 19 is also used as a selection feature to enhance intermolecular dynamics.…”

Lipase A from Bacillus subtilis: Substrate Binding, Conformational Dynamics, and Signatures of a Lid

“…Lipases are industrially important enzymes utilized in various chemical sectors such as pharmaceuticals, food, detergents, and bioenergy. − One characteristic feature of most lipases is the presence of a mobile subdomain over the catalytic site, known as the “lid”. − When the lid is open, the substrate can enter the active site and catalysis can proceed. However, in the closed state, lipases show a much reduced catalytic activity as the active site is not accessible to the substrate.…”