A new paradigm for electrostatic catalysis of radical reactions in vitamin B
            <sub>12</sub>
            enzymes

Sharma, Pramod Kumar; Chu, Zhen T.; Olsson, Mats H. M.; Warshel, Arieh

doi:10.1073/pnas.0702238104

Cited by 96 publications

(136 citation statements)

References 33 publications

(44 reference statements)

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“…However, enzymes that have evolved during a long time found ways to exploit electrostatic effects, even when the charge changes are not localized; the best example is vitamin B12 enzymes, where the enzyme found a remarkable way to exploit electrostatic TS stabilization with no change in the charge distribution of the bond that is being broken (see ref. 28). Overall, it is not clear if directed evolution explores all options and it is clear the group contribution approach cannot be very effective with the TS charge distribution of our system (see, however, below).…”

Section: Discussionmentioning

confidence: 99%

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

Frushicheva

Cao

Chu

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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One of the fundamental challenges in biotechnology and in biochemistry is the ability to design effective enzymes. Doing so would be a convincing manifestation of a full understanding of the origin of enzyme catalysis. Despite an impressive progress, most of the advances on this front have been made by placing the reacting fragments in the proper places, rather than by optimizing the environment preorganization, which is the key factor in enzyme catalysis. Rational improvement of the preorganization would require approaches capable of evaluating reliably the actual catalytic effect. This work takes apreviously designed kemp eliminases as a benchmark for a computer aided enzyme design, using the empirical valence bond as the main screening tool. The observed absolute catalytic effect and the effect of directed evolution are reproduced and analyzed (assuming that the substrate is in the designed site). It is found that, in the case of kemp eliminases, the transition state charge distribution makes it hard to exploit the active site polarity, even with the ability to quantify the effect of different mutations. Unexpectedly, it is found that the directed evolution mutants lead to the reduction of solvation of the reactant state by water molecules rather that to the more common mode of transition state stabilization used by naturally evolved enzymes. Finally it is pointed out that our difficulties in improving Kemp eliminase are not due to overlooking exotic effect, but to the challenge in designing a preorganized environment that would exploit the small change it charge distribution during the formation of the transition state.computer aided enzyme design | empirical valence bond | directed evolution R ational enzyme design is expected to have a great potential in industrial application and eventually in medicine (1). Furthermore, the ability to design efficient enzymes might be considered as the best manifestation of a true understanding of enzyme catalysis. However, at present there has been a limited success in most attempts of rational enzyme design, and the resulting constructs have been much less effective than the corresponding natural enzymes (1). Furthermore, despite the progress in directed evolution (e.g., ref.2), we do not have unique rationales for the resulting rate enhancements.Most attempts to identify the problems with the current rational design approaches (for review, see ref. 1) have not been based on actual simulations of the given effect. In fact, it has been argued (3,4), that the problems are due to the incomplete modeling of the transition state (TS) and to the limited awareness to the key role of the reorganization energy. Even a recent attempt to use a molecular orbital-combined quantum mechanical /molecular mechanics (MO-QM/MM) approach (5) has not provided a reasonable estimate of the observed catalytic effect or the trend of the mutational effects in an artificially design enzyme. Thus, reproducing the effect of directed evolution and eventually obtaining better performance in enzyme de...

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Section: Discussionmentioning

confidence: 99%

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

Frushicheva

Cao

Chu

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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113

181

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“…To be able to draw a quantitative picture of these results requires application of free-energy methods. These methods attempt an extensive sampling of the energetics of system (36), but this type of approach is beyond the scope of the current study.…”

Section: Resultsmentioning

confidence: 99%

A quantum-chemical picture of hemoglobin affinity

Alcantara

Spiro

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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Understanding the molecular mechanism of hemoglobin cooperativity remains an enduring challenge. Protein forces that control ligand affinity are not directly accessible by experiment. We demonstrate that computational quantum mechanics/molecular mechanics methods can provide reasonable values of ligand binding energies in Hb, and of their dependence on allostery. About 40% of the binding energy differences between the relaxed state and tense state quaternary structures result from strain induced in the heme and its ligands, especially in one of the pyrrole rings. The proximal histidine also contributes significantly, in particular, in the ␣-chains. The remaining energy difference resides in protein contacts, involving residues responsible for locking the quaternary changes. In the ␣-chains, the most important contacts involve the FG corner, at the ''hinge'' region of the ␣1␤2 quaternary interface. The energy differences are spread more evenly among the ␤-chain residues, suggesting greater flexibility for the ␤-than for the ␣-chains along the quaternary transition. Despite this chain differentiation, the chains contribute equally to the relaxed substitute state energy difference. Thus, nature has evolved a symmetric response to the quaternary structure change, which is a requirement for maximum cooperativity, via different mechanisms for the two kinds of chains.allostery ͉ cooperativity ͉ heme ͉ quantum mechanics/molecular mechanics H emoglobin has been a paradigm for our understanding of multisubunit proteins, beginning with the pioneering work of Adair (1) and then with the elucidation of the oxygenated and deoxygenated crystal structures of Hb by Perutz (2), some four decades ago. Interest in Hb continues to the present, with new experimental and theoretical methods aimed at characterizing intermediate ligation states of the molecule (3-5) and at gaining a deeper understanding of its allosteric transition (6-11).The Hb molecule is composed of four chains that contain a heme group capable of reversibly binding CO or O 2 . The molecule is arranged as a dimer of dimers, where each dimer is made up of an ␣-and a ␤-chain (denoted as ␣ 1 ␤ 1 or ␣ 2 ␤ 2 ) with a hydrophobic intradimer interface. Adair observed that Hb binds oxygen in a cooperative manner, successive ligation events occurring with higher affinity. For some time it was believed that such cooperativity could be explained by direct interaction of the closely packed heme groups. However the 1960s saw the appearance of the first allosteric models for Hb cooperativity. In particular, the Monod-Wyman-Changeux (12) model postulated the existence of two states of the molecule: the relaxed (R) state with high ligand affinity and the tense (T) state with low affinity. Ligand binding preferentially stabilized the R form and led to cooperativity. Early Hb crystallization attempts revealed that deoxy crystals would shatter when exposed to oxygen, which suggested that a quaternary rearrangement was associated with the T-R transition of the molecule.Crystal structure...

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“…To accelerate Co-C bond homolysis, substrate binding likely modulates the interactions between the protein and the 5Ј-dAdo, for example by inducing large scale conformational changes such as the TIM barrel motions or by altering active site electrostatics or dynamics to destabilize the C2Ј-endo form or to stabilize the C3Ј-endo form (55,68,69). It is unclear how many molecular mechanisms AdoCbl enzymes use to afford the substantial 10 12 enhancement in Co-C bond homolysis that accompanies substrate binding (1,3,70).…”

Section: Discussionmentioning

confidence: 99%

Structural Basis for Substrate Specificity in Adenosylcobalamin-dependent Isobutyryl-CoA Mutase and Related Acyl-CoA Mutases

Jost

Born

Cracan

et al. 2015

Journal of Biological Chemistry

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Background: Acyl-CoA mutases catalyze radical-based carbon skeleton rearrangements. Results: Crystal structures of isobutyryl-CoA mutase in complex with four different substrates reveal active site architecture and determinants of substrate specificity. Conclusion: Identification of specificity-determining residues allows for prediction of new acyl-CoA mutase activities. Significance: Improved understanding of acyl-CoA mutase substrate specificity is critical for biotechnological and engineering applications.

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A new paradigm for electrostatic catalysis of radical reactions in vitamin B ₁₂ enzymes

Cited by 96 publications

References 33 publications

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

A quantum-chemical picture of hemoglobin affinity

Structural Basis for Substrate Specificity in Adenosylcobalamin-dependent Isobutyryl-CoA Mutase and Related Acyl-CoA Mutases

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A new paradigm for electrostatic catalysis of radical reactions in vitamin B 12 enzymes

Cited by 96 publications

References 33 publications

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

A quantum-chemical picture of hemoglobin affinity

Structural Basis for Substrate Specificity in Adenosylcobalamin-dependent Isobutyryl-CoA Mutase and Related Acyl-CoA Mutases

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A new paradigm for electrostatic catalysis of radical reactions in vitamin B ₁₂ enzymes