Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase

Kamp, Marc W. van der; Perruccio, Francesca; Mulholland, Adrian J.

doi:10.1016/j.jmgm.2007.04.002

Cited by 24 publications

(35 citation statements)

References 91 publications

(180 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An additional requirement is that the p K a s of the donor and acceptor are very similar 27. Short hydrogen‐bond distances have been observed in some atomic resolution crystal structures,47, 60 but the importance of such strong hydrogen bonds for transition‐state stabilization remains a topic of discussion 61–64. In the TIM–PGH active site, LBHB‐like interactions are observed between the N1O1 moiety of PGH and the carboxylate oxygen atoms of Glu167 (see Fig.…”

Section: Discussionmentioning

confidence: 99%

Atomic resolution crystallography of a complex of triosephosphate isomerase with a reaction‐intermediate analog: New insight in the proton transfer reaction mechanism

Alahuhta

Wierenga

2010

Proteins

View full text Add to dashboard Cite

Enzymes achieve their catalytic proficiency by precisely positioning the substrate and catalytic residues with respect to each other. Atomic resolution crystallography is an excellent tool to study the important details of these geometric active-site features. Here, we have investigated the reaction mechanism of triosephosphate isomerase (TIM) using atomic resolution crystallographic studies at 0.82-A resolution of leishmanial TIM complexed with the well-studied reaction-intermediate analog phosphoglycolohydroxamate (PGH). Remaining unresolved aspects of the reaction mechanism of TIM such as the protonation state of the first reaction intermediate and the properties of the hydrogen-bonding interactions in the active site are being addressed. The hydroxamate moiety of PGH interacts via unusually short hydrogen bonds of its N1-O1 moiety with the carboxylate group of the catalytic glutamate (Glu167), for example, the distance of N1(PGH)-OE2(Glu167) is 2.69 +/- 0.01 A and the distance of O1(PGH)-OE1(Glu167) is 2.60 +/- 0.01 A. Structural comparisons show that the side chain of the catalytic base (Glu167) can move during the reaction cycle in a small cavity, located above the hydroxamate plane. The structure analysis suggests that the hydroxamate moiety of PGH is negatively charged. Therefore, the bound PGH mimics the negatively charged enediolate intermediate, which is formed immediately after the initial proton abstraction from DHAP by the catalytic glutamate. The new findings are discussed in the context of the current knowledge of the TIM reaction mechanism.

show abstract

Section: Discussionmentioning

confidence: 99%

Atomic resolution crystallography of a complex of triosephosphate isomerase with a reaction‐intermediate analog: New insight in the proton transfer reaction mechanism

Alahuhta

Wierenga

2010

Proteins

View full text Add to dashboard Cite

show abstract

“…1). This type of reaction coordinate is known to describe similar proton transfers reasonably accurately [11,26,27,45].…”

Section: Am1/charmm27 Potential Energy Profilesmentioning

confidence: 99%

“…A LBHB is therefore not necessary to explain the high reaction rate in KSI. LBHBs were suggested as important for catalysis in enzymes that catalyse similar reactions, but QM/MM modelling has indicated that they are not involved in catalysis in citrate synthase [26,27] or triosephosphate isomerase [28,29].…”

Section: Introductionmentioning

confidence: 99%

QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis

2013

Self Cite

View full text Add to dashboard Cite

-3-keto steroid isomerase or steroid D-isomerase) is a highly efficient enzyme at the centre of current debates on enzyme catalysis. We have modelled the reaction mechanism of the isomerization of 3-oxo-D 5 -steroids into their D 4-conjugated isomers using high-level combined quantum mechanics/molecular mechanics (QM/MM) methods, and semi-empirical QM/MM molecular dynamics simulations. Energy profiles were obtained at various levels of QM theory (AM1, B3LYP and SCS-MP2). The high-level QM/MM profile is consistent with experimental data. QM/MM dynamics simulations indicate that active site closure and desolvation of the catalytic Asp38 occur before or during formation of dienolate intermediates. These changes have a significant effect on the reaction barrier. A low barrier to reaction is found only when the active site is closed, poising it for catalysis. This conformational change is thus integral to the whole process. The effects on the barrier are apparently largely due to changes in solvation. The combination of high-level QM/MM energy profiles and QM/MM dynamics simulation shows that the reaction involves active site closure, desolvation of the catalytic base, efficient isomerization and re-opening of the active site. These changes highlight the transition between the ligand binding/releasing form and the catalytic form of the enzyme. The results demonstrate that electrostatic interactions (as a consequence of pre-organization of the active site) are crucial for stabilization during the chemical reaction step, but closure of the active site is essential for efficient catalysis to occur.

show abstract

“…These arguments are very difficult to settle, because the complexity and large size of enzymes make experimental analysis very difficult. Recent controversies include the possible role of protein dynamics in catalysis [2,3], 'lowbarrier' hydrogen bonds [5][6][7][8][9], 'near-attack conformations' [4,[10][11][12], quantum tunnelling [13], substrate polarization [14] and on the contribution of entropy [3]. These arguments have included questioning the applicability of transition state theory (a basic tool from chemical physics for understanding molecular reaction rates) for enzyme reactions.…”

Section: Introductionmentioning

confidence: 99%

Computational enzymology: modelling the mechanisms of biological catalysts

Mulholland

2008

Biochemical Society Transactions

View full text Add to dashboard Cite

Simulations and modelling [e.g. with combined QM/MM (quantum mechanics/molecular mechanics) methods] are increasingly important in investigations of enzyme-catalysed reaction mechanisms. Calculations offer the potential of uniquely detailed, atomic-level insight into the fundamental processes of biological catalysis. Highly accurate methods promise quantitative comparison with experiments, and reliable predictions of mechanisms, revolutionizing enzymology.

show abstract

Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase

Cited by 24 publications

References 91 publications

Atomic resolution crystallography of a complex of triosephosphate isomerase with a reaction‐intermediate analog: New insight in the proton transfer reaction mechanism

Atomic resolution crystallography of a complex of triosephosphate isomerase with a reaction‐intermediate analog: New insight in the proton transfer reaction mechanism

QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis

Computational enzymology: modelling the mechanisms of biological catalysts

Contact Info

Product

Resources

About