The Conformational Free Energy Landscape of β-<scp>d</scp>-Glucopyranose. Implications for Substrate Preactivation in β-Glucoside Hydrolases

Biarnés, Xevi; Ardèvol, Albert; Planas, Antoni; Rovira, Carme; Laio, Alessandro; Parrinello, Michele

doi:10.1021/ja068411o

Cited by 195 publications

(267 citation statements)

References 55 publications

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“…Here, protonated Glu95 forms a hydrogen bond of 1.98 Å with the O4 atom ( 25 This ring conformation pre-activates the substrate for catalysis by moving the glycosidic bond toward an axial position, increasing the charge of the C1′ atom 10 and removing steric conflict between the H1′ atom and the incoming nucleophilic water molecule.…”

Section: Reaction Free-energy Landscape and Minimalenergy Pathwaymentioning

confidence: 99%

“…5,6 The conformational interconversions that occur in the active sites of specific GHs have been the subject of many recent studies. [7][8][9][10][11][12][13][14] Nevertheless, direct evidence of conformational itineraries is still missing for many GH families. Furthermore, detailed structural features of the enzymatic transition state (TS) in GHs are still fairly unknown.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study

et al. 2009

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A detailed understanding of the catalytic strategy of cellulases is key to finding alternative ways to hydrolyze cellulose to mono-, di-, and oligosaccharides. Endoglucanases from glycoside hydrolase family 8 (GH8) catalyze the hydrolysis of β-1,4-glycosidic bonds in cellulose by an inverting mechanism believed to involve a oxacarbenium ion-like transition state (TS) with a boat-type conformation of the glucosyl unit in subsite −1. In this work, hydrolysis by Clostridium thermocellum endo-1,4-glucanase A was computationally simulated with quantum mechanics/molecular mechanics metadynamics based on density functional theory. Our calculations show that the glucosyl residue in subsite −1 in the Michaelis complex is in a distorted 2 S O / 2,5 B ring conformation, agreeing well with its crystal structure. In addition, our simulations capture the cationic oxacarbenium ion-like character of the TS with a partially formed double bond between the ring oxygen and C5′ carbon atoms. They also provide previously unknown structural information of important states along the reaction pathway. The simulations clearly show for the first time in GH8 members that the TS features a boattype conformation of the glucosyl unit in subsite −1. The overall catalytic mechanism follows a D N *A N -like mechanism and a β-2 S O → 2,5 B [TS] → α-5 S 1 conformational itinerary along the reaction coordinate, consistent with the anti-periplanar lone pair hypothesis. Because of the structural similarities and sequence homology among all GH8 members, our results can be extended to all GH8 cellulases, xylanases, and other endoglucanases. In addition, we provide evidence supporting the role of Asp278 as the catalytic proton acceptor (general base) for GH8a subfamily members. Disciplines Biochemical and Biomolecular Engineering | Biological Engineering | Chemical Engineering CommentsPosted with permission from The Journal of Physical Chemistry B, 113, no. 20 (2009) ReceiVed: December 29, 2008; ReVised Manuscript ReceiVed: March 18, 2009 A detailed understanding of the catalytic strategy of cellulases is key to finding alternative ways to hydrolyze cellulose to mono-, di-, and oligosaccharides. Endoglucanases from glycoside hydrolase family 8 (GH8) catalyze the hydrolysis of -1,4-glycosidic bonds in cellulose by an inverting mechanism believed to involve a oxacarbenium ion-like transition state (TS) with a boat-type conformation of the glucosyl unit in subsite -1. In this work, hydrolysis by Clostridium thermocellum endo-1,4-glucanase A was computationally simulated with quantum mechanics/molecular mechanics metadynamics based on density functional theory. Our calculations show that the glucosyl residue in subsite -1 in the Michaelis complex is in a distortedB ring conformation, agreeing well with its crystal structure. In addition, our simulations capture the cationic oxacarbenium ion-like character of the TS with a partially formed double bond between the ring oxygen and C5′ carbon atoms. They also provide previously unknown structural inf...

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Section: Reaction Free-energy Landscape and Minimalenergy Pathwaymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study

et al. 2009

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“…To our knowledge, Cremers-Pople coordinates have been employed as CVs to sample the puckering free energy landscape only in a recent work by Biarnés and coworkers [15], where the authors employed the Cartesian parametrization, though with an immaterial opposite sign for the phase φ.…”

Section: Puckering Coordinates As Collective Variablesmentioning

confidence: 99%

On the calculation of puckering free energy surfaces

Sega

Autieri

Pederiva

2009

The Journal of Chemical Physics

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Cremer-Pople puckering coordinates appear to be the natural candidate variables to explore the conformational space of cyclic compounds, and in literature different parametrizations have been used to this end. However, while every parametrization is equivalent in identifying conformations, it is not obvious that they can also act as proper collective variables for the exploration of the puckered conformations free energy surface. It is shown that only the polar parametrization is fit to produce an unbiased estimate of the free energy landscape. As an example, the case of a six-membered ring, glucuronic acid, is presented, showing the artefacts that are generated when a wrong parametrization is used.

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“…52 For this six-membered ring, the Cremer-Pople puckering coordinates 53 reduce to spherical coordinates (Q, θ, φ), and adequately describe its molecular flexibility with small fluctuations about the "radius" Q. See Appendix B for details.…”

Section: Six-membered Ringsmentioning

confidence: 99%

“…In Figure 11(d), we show that this correction, along θ and for any value of φ, is significant particularly at the pole and equator. In reality, although the variation along Q is small compared to θ and φ, 52 it is not negligible. Because the level sets of C 1 and C 2 are fundamentally different, the portion of configuration space that is integrated is also different, see Figure 11(e) and thus quantitatively comparing the free energies is meaningless (although observables computed from them are well-defined).…”

mentioning

confidence: 97%

Charting molecular free-energy landscapes with an atlas of collective variables

Hashemian

Millán

Arroyo

2016

The Journal of Chemical Physics

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Collective variables (CVs) are a fundamental tool to understand molecular flexibility, to compute free energy landscapes, and to enhance sampling in molecular dynamics simulations. However, identifying suitable CVs is challenging, and increasingly addressed with systematic data-driven manifold learning techniques. Here, we provide a flexible framework to model molecular systems in terms of a collection of locally valid and partially overlapping CVs: an atlas of CVs. The specific motivation for such a framework is to enhance the applicability and robustness of CVs based on manifold learning methods, which fail in the presence of periodicities in the underlying conformational manifold. More generally, using an atlas of CVs rather than a single chart may help us better describe different regions of conformational space. We develop the statistical mechanics foundation for our multi-chart description and propose an algorithmic implementation. The resulting atlas of data-based CVs are then used to enhance sampling and compute free energy surfaces in two model systems, alanine dipeptide and β-D-Glucopyranose, whose conformational manifolds have toroidal and spherical topology.

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The Conformational Free Energy Landscape of β-d-Glucopyranose. Implications for Substrate Preactivation in β-Glucoside Hydrolases

Cited by 195 publications

References 55 publications

Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study

Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study

On the calculation of puckering free energy surfaces

Charting molecular free-energy landscapes with an atlas of collective variables

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