scholarly journals Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps

IUCrJ ◽  
2021 ◽  
Vol 8 (4) ◽  
Author(s):  
Vinardas Kelpšas ◽  
Octav Caldararu ◽  
Matthew P. Blakeley ◽  
Nicolas Coquelle ◽  
Rikkert K. Wierenga ◽  
...  

Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. This simple reaction involves the shuttling of protons mediated by protolysable side chains. The catalytic power of TIM is thought to stem from its ability to facilitate the deprotonation of a carbon next to a carbonyl group to generate an enediolate intermediate. The enediolate intermediate is believed to be mimicked by the inhibitor 2-phosphoglycolate (PGA) and the subsequent enediol intermediate by phosphoglycolohydroxamate (PGH). Here, neutron structures of Leishmania mexicana TIM have been determined with both inhibitors, and joint neutron/X-ray refinement followed by quantum refinement has been performed. The structures show that in the PGA complex the postulated general base Glu167 is protonated, while in the PGH complex it remains deprotonated. The deuteron is clearly localized on Glu167 in the PGA–TIM structure, suggesting an asymmetric hydrogen bond instead of a low-barrier hydrogen bond. The full picture of the active-site protonation states allowed an investigation of the reaction mechanism using density-functional theory calculations.

2021 ◽  
Vol 03 (02) ◽  
pp. 090-096
Author(s):  
Yusuke Ishigaki ◽  
Kota Asai ◽  
Takuya Shimajiri ◽  
Tomoyuki Akutagawa ◽  
Takanori Fukushima ◽  
...  

The crystal structures of a series of tetracyanonaphthoquinodimethanes fused with a selenadiazole or thiadiazole ring revealed that their molecular packing is determined mainly by two intermolecular interactions: chalcogen bond (ChB) and weak hydrogen bond (WHB). ChB between Se and a cyano group dictates the packing of selenadiazole derivatives, whereas the S-based ChB is much weaker and competes with WHB in thiadiazole analogues. This difference can be explained by different electrostatic potentials as revealed by density functional theory calculations. A proper molecular design that weakens WHB can change the contribution of ChB in determining the crystal packing of thiadiazole derivatives.


2019 ◽  
Author(s):  
Hassan Harb ◽  
Lee Thompson ◽  
Hrant Hratchian

Lanthanide hydroxides are key species in a variety of catalytic processes and in the preparation of corresponding oxides. This work explores the fundamental structure and bonding of the simplest lanthanide hydroxide, LnOH (Ln=La-Lu), using density functional theory calculations. Interestingly, the calculations predict that all structures of this series will be linear. Furthermore, these results indicate a valence electron configuration featuring an occupied sigma orbital and two occupied pi orbitals for all LnOH compounds, suggesting that the lanthanide-hydroxide bond is best characterized as a covalent triple bond.


2019 ◽  
Author(s):  
Hassan Harb ◽  
Lee Thompson ◽  
Hrant Hratchian

Lanthanide hydroxides are key species in a variety of catalytic processes and in the preparation of corresponding oxides. This work explores the fundamental structure and bonding of the simplest lanthanide hydroxide, LnOH (Ln=La-Lu), using density functional theory calculations. Interestingly, the calculations predict that all structures of this series will be linear. Furthermore, these results indicate a valence electron configuration featuring an occupied sigma orbital and two occupied pi orbitals for all LnOH compounds, suggesting that the lanthanide-hydroxide bond is best characterized as a covalent triple bond.


2019 ◽  
Author(s):  
Anshuman Kumar ◽  
Reinhard Schweitzer-Stenner ◽  
Bryan Wong

In this work, we carry out new time-dependent density functional theory calculations on the cationic tripeptide GAG in implicit and explicit water to determine the transitions that give rise to the observed CD signals of polyproline II and β-strand conformations. Our results reveal a plethora of electronic transitions that are governed by configurational interactions between multiple molecular orbital transitions of comparable energy. We also show that reproducing the CD spectra of polyproline II and β-strand conformations requires the explicit consideration of water molecules. The structure dependence of delocalized occupied orbitals contributes to the experimentally-observed invalidation of Flory’s isolated pair hypothesis.


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