Protein effects in non-heme iron enzyme catalysis: insights from multiscale models

Abstract

PostprintThis is the accepted version of a paper published in Journal of Biological Inorganic Chemistry. This paper has been peer-reviewed but does not include the final publisher proof-corrections or journal pagination. Citation for the original published paper (version of record):Vedin, N P., Lundberg, M. (2016) Protein effects in non-heme iron enzyme catalysis: insights from multiscale models. from second-sphere residues. The long-range electrostatic effects on reaction barriers are small for many systems. In the systems where large electrostatic effects have been reported, these lead to higher barriers. There is thus no evidence of any significant long-range electrostatic effects contributing to the catalytic efficiency of non-heme iron enzymes. However, the correct evaluation of electrostatic contributions is challenging, and the correlation between calculated residue contributions and the effects of mutation experiments is not very strong. The largest benefits of QM/MM models are thus the improved active-site geometries, rather than the calculation of accurate energies. Reported differences in mechanistic predictions between QM and QM/MM models can be explained by differences in hydrogen bonding patterns in and around the active site. Correctly constructed cluster models can give results with similar accuracy as those from multiscale models, but the latter reduces the risk of drawing the wrong mechanistic conclusions based on incorrect geometries and are preferable for all types of modeling, even when using very large QM parts. Journal of Biological Inorganic

The Protein’s Role in Substrate Positioning and Reactivity for Biosynthetic Enzyme Complexes: The Case of SyrB2/SyrB1

“…Computational modeling can provide complementary insight into transient interactions and in cases where structural characterization is incomplete. However, most modeling has been carried out on cluster models of SyrB2 with few exceptions, , despite the wider use of whole-protein multiscale modeling for other non-heme iron enzymes. − To date, no SyrB2/SyrB1 complexes have been simulated, with the largest models using truncated ,− PPant- S -Thr models placed in SyrB2 by rotating or mutating F196.…”

Hydrothermal Synthesis of Nitrogen-Doped and Excitation-Dependent Carbon Quantum Dots for Selective Detection of Fe3+ in Blood Plasma

“…Ferric ion (Fe 3+ ) is an essential element for human beings and has important roles in many physiological activities such as the action of enzymes, hemoglobin synthesis, electron transfer, and oxygen transportation [2,[45][46][47]. Iron deficiency is the most common dietary deficiency worldwide and may create symptoms such as tiredness, lack of energy, shortness of breath, pale skin, and limitations in motor and mental growth as well as various disorders and physiological damage in humans [48,49].…”