Search

Understanding how the chemical environment modulatesthe predominantconformations and kinetics of flexible molecules is a core interestof biochemistry and a prerequisite for the rational design of syntheticcatalysts. This study combines molecular dynamics simulation and Markovstate models (MSMs) to a systematic computational strategy for investigatingthe effect of the chemical environment of a molecule on its conformationsand kinetics. MSMs allow quantities to be computed that are otherwisedifficult to access, such as the metastable sets, their free energies,and the relaxation time scales related to the rare transitions betweenmetastable states. Additionally, MSMs are useful to identify observablesthat may act as sensors for the conformational or binding state ofthe molecule, thus guiding the design of experiments. In the presentstudy, the conformation dynamics of UDP-GlcNAc are studied in vacuum,water, water + Mg2+, and in the protein UDP-GlcNAc 2-epimerase.It is found that addition of Mg2+significantly affectsthe conformational stability, thermodynamics, and kinetics of UDP-GlcNAc.In particular, the slowest structural process, puckering of the GlcNAcsugar, depends on the overall conformation of UDP-GlcNAc and may thusact as a sensor of whether Mg2+is bound or not. Interestingly,transferring the molecule from vacuum to water makes the protein-bindingconformations UDP-GlcNAc first accessible, while adding Mg2+further stabilizes them by specifically associating to binding-competentconformations. While Mg2+is not cocrystallized in theUDP-GlcNAc 2-epimerase complex, the selectively stabilized Mg2+/UDP-GlcNAc complex may be a template for the bound state,and Mg2+may accompany the binding-competent ligand conformationto the binding pocket. This serves as a possible explanation of theenhanced epimerization rate in the presence of Mg2+. Thisrole of Mg2+has previously not been described and opensthe question whether “binding co-factors” may be a conceptof general relevance for protein–ligand binding. [ABSTRACT FROM AUTHOR]

Base excision of mismatched or damaged nucleotides catalyzed by glycosylase enzymes is the first step of the base excision repair system, a machinery preserving the integrity of DNA. Thymine DNA glycosylase recognizes and removes mismatched thymine by cleaving the C1'-N1 bond between the base and the sugar ring. Our quantum mechanical/molecular mechanical calculations of this reaction in human thymine DNA glycosylase reveal a requirement for a positive charge in the active site to facilitate C1'-N1 bond scission: protonation of His151 significantly lowers the free energy barrier for C1'-N1 bond dissociation compared to the situation with neutral His151. Shuttling a proton from His151 to the thymine base further reduces the activation free energy for glycosidic bond cleavage. Classical molecular dynamics simulations of the H151A mutant suggest that the mutation to the smaller, neutral, residue increases the water accessibility of the thymine base, rendering direct proton transfer from the bulk feasible. Quantum mechanical/molecular mechanical calculations of the glycosidic bond cleavage reaction in the H151A mutant show that the activation free energy is slightly lower than in the wild-type enzyme, explaining the experimentally observed higher reaction rates in this mutant.

We study the exchange processes of the metabolite creatine, which is present in both tumorous and normal tissues and has NH2 and NH groups that can transfer protons to water. Creatine produces chemical exchange saturation transfer (CEST) contrast in magnetic resonance imaging (MRI). The proton transfer pathway from zwitterionic creatine to water is examined using a kinetic transition network constructed from the discrete path sampling approach and an approximate quantum-chemical energy function, employing the self-consistent-charge density-functional tight-binding (SCC-DFTB) method. The resulting potential energy surface is visualized by constructing disconnectivity graphs. The energy landscape consists of two distinct regions corresponding to the zwitterionic creatine structures and deprotonated creatine. The activation energy that characterizes the proton transfer from the creatine NH2 group to water was determined from an Arrhenius fit of rate constants as a function of temperature, obtained from harmonic transition state theory. The result is in reasonable agreement with values obtained in water exchange spectroscopy (WEX) experiments.