These effects have been observed recently under two-dimensional (2D) van der Waals materials such as a graphene and boron nitride and for the case of supported 2D-porous oxides, including silicates, aluminosilicates and zeolite nanosheets. Interestingly, the Michael-type cross-linking generated less stable immobilized CAL-B, revealing the influence of a cross-linking mode on the resulting biocatalyst behavior. Spherical boundary conditions were used in the MD simulations, with a radius of 20 Å centered on the C4 atom of the cytidine. The EVB free-energy profiles are each averaged over 20 independent MD/EVB simulations of the enzyme (red curve) and water (blue curve) reactions at 300 K. To be able to compute thermodynamic activation parameters for the different steps of the cytidine deaminase reaction, we calibrated an EVB model of the entire catalytic reaction path (Fig. S5. Effects of Lid 1 Mutagenesis on Lid Displacement, Catalytic Performances and Thermostability of Cold-active Pseudomonas AMS8 Lipase in Toluene, Towards Rational Computational Engineering of Psychrophilic Enzymes, Importance of Entropic Contribution to Electrochemical Water Oxidation Catalysis, Opportunities in Catalysis over Metal-Zeotypes Enabled by Descriptions of Active Centers Beyond Their Binding Site, Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A 2A adenosine receptor binding site, Mechanistic Explanation of the Weak Carbonic Anhydrase's Esterase Activity, Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations, Influence of Dlutaraldehyde Cross-Linking Modes on the Recyclability of Immobilized Lipase B from Candida antarctica for Transesterification of Soy Bean Oil, Linear Eyring Plots Conceal a Change in Rate-Limiting Step in an Enzyme Reaction, Evolution of dynamical networks enhances catalysis in a designer enzyme, Modeling the adsorption of hydrogen, sodium, chloride and phthalate on goethite using a strict charge-neutral ion-exchange theory, Estimating configurational entropy and energy of molecular systems from computed spectral density, Molecular Dynamics Simulations on Aspergillus niger Monoamine Oxidase: Conformational Dynamics and Inter‐monomer Communication Essential for Its Efficient Catalysis, Protein Flexibility and Stiffness Enable Efficient Enzymatic Catalysis, Thermally‐Induced Reactions of Aromatic Crystalline Nitroso Compounds, Understanding the Entropic Effect in Chorismate Mutase Reaction Catalyzed by Isochorismate-Pyruvate Lyase from Pseudomonas Aeruginosa (PchB), Thermodynamic View of Proton Activated Electron Transfer in Reaction Center of Photosynthetic Bacteria, Chemistry in Confined Space through the eyes of surface science – Two-dimensional porous materials, GTP Hydrolysis without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases, Catalytic Adaptation of Psychrophilic Elastase, Uncovering the Relationship between the Change in Heat Capacity for Enzyme Catalysis and Vibrational Frequency through Isotope Effect Studies, Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering, Intertwined Chemistry of Hydroxyl Hydrogen-bond Donors, Epoxides and Isocyanates in the Organocatalytic Synthesis of Oxazolidinones versus Isocyanurates: Rational Catalytic Investigation and Mechanistic Understanding, Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome, Chemical reaction mechanisms in solution from brute force computational Arrhenius plots, Deducing the Kinetics of Protein Synthesis In Vivo from the Transition Rates Measured In Vitro, Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin, Quantitative exploration of the molecular origin of the activation of GTPase, Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and Chelate Effect. These three aspects that describe active centers at and beyond their binding sites must be accounted for in quantitative descriptions of the kinetic and thermodynamic factors that dictate catalysis over metal-containing zeotypes. Dispelling Circe's effect in enzyme catalysis, Binding energy, specificity, and enzymic catalysis: The Circe effect, Structural insights into peptide bond formation, Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect, Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate “anchor”, Chemical reaction mechanisms in solution from brute force computational Arrhenius plots, Cloning and nucleotide sequence of the Escherichia coli cytidine deaminase (ccd) gene, Cytidine deaminase. Their ability to proliferate in the cold is predicated on a capacity to synthesize cold-adapted enzymes. Movement in biological systems, such as muscle contraction and the active transport of ions, is generally brought about through a series of alternating chemical and vectorial steps that involve a series of changes in the specificity for catalysis of the chemical and vectorial reactions. Framework metal heteroatoms adopt various local configurations that are difficult to control synthetically and are susceptible to restructuring during reaction. It is therefore useful to verify that the EVB model can describe both the enzyme energetics and the enzyme’s catalytic effect with respect to the same mechanism in solution, even if the latter is not actually operational (17, 18). Such ground-state destabilization could, in principle, have different possible physical origins, such as reduction of translational, rotational, and conformational substrate entropies; steric and conformational strain; or electrostatic destabilization and desolvation effects (1).
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