scholarly journals Transition Path Sampling Study of the Feruloyl Esterase Mechanism

2021 ◽  
Vol 125 (8) ◽  
pp. 2018-2030
Author(s):  
Rodrigo L. Silveira ◽  
Brandon C. Knott ◽  
Caroline S. Pereira ◽  
Michael F. Crowley ◽  
Munir S. Skaf ◽  
...  
Author(s):  
Michael P. Allen ◽  
Dominic J. Tildesley

The development of techniques to simulate infrequent events has been an area of rapid progress in recent years. In this chapter, we shall discuss some of the simulation techniques developed to study the dynamics of rare events. A basic summary of the statistical mechanics of barrier crossing is followed by a discussion of approaches based on the identification of reaction coordinates, and those which seek to avoid prior assumptions about the transition path. The demanding technique of transition path sampling is introduced and forward flux sampling and transition interface sampling are considered as rigorous but computationally efficient approaches.


ACS Omega ◽  
2020 ◽  
Vol 5 (34) ◽  
pp. 21374-21384
Author(s):  
Pavel Janoš ◽  
Igor Tvaroška ◽  
Christoph Dellago ◽  
Jaroslav Koča

2018 ◽  
Vol 108 ◽  
pp. 74-88 ◽  
Author(s):  
Ian H. Moskowitz ◽  
Warren D. Seider ◽  
Amish J. Patel ◽  
Jeffrey E. Arbogast ◽  
Ulku G. Oktem

2018 ◽  
Vol 115 (27) ◽  
pp. E6209-E6216 ◽  
Author(s):  
Rajesh K. Harijan ◽  
Ioanna Zoi ◽  
Dimitri Antoniou ◽  
Steven D. Schwartz ◽  
Vern L. Schramm

Transition path-sampling calculations with several enzymes have indicated that local catalytic site femtosecond motions are linked to transition state barrier crossing. Experimentally, femtosecond motions can be perturbed by labeling the protein with amino acids containing 13C, 15N, and nonexchangeable 2H. A slowed chemical step at the catalytic site with variable effects on steady-state kinetics is usually observed for heavy enzymes. Heavy human purine nucleoside phosphorylase (PNP) is slowed significantly (kchemlight/kchemheavy = 1.36). An asparagine (Asn243) at the catalytic site is involved in purine leaving-group activation in the PNP catalytic mechanism. In a PNP produced with isotopically heavy asparagines, the chemical step is faster (kchemlight/kchemheavy = 0.78). When all amino acids in PNP are heavy except for the asparagines, the chemical step is also faster (kchemlight/kchemheavy = 0.71). Substrate-trapping experiments provided independent confirmation of improved catalysis in these constructs. Transition path-sampling analysis of these partially labeled PNPs indicate altered femtosecond catalytic site motions with improved Asn243 interactions to the purine leaving group. Altered transition state barrier recrossing has been proposed as an explanation for heavy-PNP isotope effects but is incompatible with these isotope effects. Rate-limiting product release governs steady-state kinetics in this enzyme, and kinetic constants were unaffected in the labeled PNPs. The study suggests that mass-constrained femtosecond motions at the catalytic site of PNP can improve transition state barrier crossing by more frequent sampling of essential catalytic site contacts.


2019 ◽  
Vol 47 (21) ◽  
pp. 11069-11076 ◽  
Author(s):  
Jocelyne Vreede ◽  
Alberto Pérez de Alba Ortíz ◽  
Peter G Bolhuis ◽  
David W H Swenson

Abstract DNA predominantly contains Watson–Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In HG, the purine is rotated ∼180° relative to the WC motif. The transitions between WC and HG may play a role in recognition and replication, but are difficult to investigate experimentally because they occur quickly, but only rarely. To gain insight into the mechanisms for this process, we performed transition path sampling simulations on a model nucleotide sequence in which an AT pair changes from WC to HG. This transition can occur in two ways, both starting with loss of hydrogen bonds in the base pair, followed by rotation around the glycosidic bond. In one route the adenine base converts from WC to HG geometry while remaining entirely within the double helix. The other route involves the adenine leaving the confines of the double helix and interacting with water. Our results indicate that this outside route is more probable. We used transition interface sampling to compute rate constants and relative free energies for the transitions between WC and HG. Our results agree with experiments, and provide highly detailed insights into the mechanisms of this important process.


2012 ◽  
Vol 1383 ◽  
Author(s):  
Massimiliano Picciani ◽  
Manuel Athènes ◽  
Mihai-Cosmin Marinica

ABSTRACTPredicting the microstructural evolution of radiation damage in materials requires handling the physics of infrequent-events, in which several time scales are involved. The reactions rates characterizing these events are the main ingredient for simulating the kinetics of materials under irradiation over large time scales and high irradiation doses. We propose here an efficient, finite temperature method to compute reaction rate constants of thermally activated processes. The method consists of two steps. Firstly, rare reactive trajectories in phase-space are sampled using a transition path sampling (TPS) algorithm supplemented with a local Lyapunov bias favoring diverging trajectories. This enables the system to visit transition regions separating stable configurations more often, and thus enhances the probability of observing transitions between stable states during relatively short simulations. Secondly, reaction constants are estimated from the unbiased fraction of reactive trajectories, yielded by an appropriate statistical data analysis tool, the multistate Bennett acceptance ratio (MBAR) package. We apply our method to the calculation of reaction rates for vacancy and di-vacancy migration in α-Iron crystal, using an Embedded Atom Model potential, for temperatures ranging from 300 K to 800 K.


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