Hydrogen bonding catalysis by water in epoxide ring opening reaction

Ahsan, Mohd; Pindi, Chinmai; Senapati, Sanjib

doi:10.1016/j.jmgm.2021.107894

Cited by 7 publications

(11 citation statements)

References 39 publications

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“…As suggested by the authors, the RDG isosurface (isovalue = 0.5) is mapped by the function: sign (λ 2 )ρ. ρ represents the electron density and is multiplied with the sign of λ 2 (second Hessian eigenvalue of the Laplacian of electron density (Δ 2 ρ)). The negative sign of λ 2 indicates H-bonding (blue-color surface), the positive sign of λ 2 shows steric crowding (red-color surface), while close to zero λ 2 would indicate the dispersion interaction (green-color surface); , these calculations were performed using the Multiwfn program Figure B clearly shows a dark-blue surface between O6 and Mg 2+ , which denotes a very strong interaction, while this is replaced by a green-color surface between O6 and K + , representing a weaker interaction.…”

Section: Resultsmentioning

confidence: 99%

Structural Insights into the Antiparallel G-Quadruplex in the Presence of K⁺ and Mg²⁺ Ions

2023

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G-Quadruplex (GQ) is a secondary structural unit of DNA, formed at the telomere region of the chromosome with a high guanine content. It is reported that the GQs can hinder many biological processes. Thus, research thrives to explore the structural stability of GQs. Studies based on circular dichroism (CD) and nuclear magnetic resonance (NMR) experiments established the vital role of cations such as K+ and Mg2+ in the stability of antiparallel G-quadruplexes (AGQs). However, there is a need to understand how stability in AGQ is attained in the presence of cations. Here, we employed molecular dynamics (MD) simulations, steered MD (SMD) simulations, and QM/MM calculations to understand the biophysical and electronic bases of the stability imparted to AGQs via cation binding. Our results showed that Mg2+ prefers to bind in the plane with the guanine tetrad, whereas K+ binds in between the AGQ tetrads. Thus, three Mg2+ cations or two K+ ions are needed to stabilize an AGQ molecule, where each and every tetrad binds to Mg2+ more robustly with a higher binding affinity. SMD revealed that the traversal of K+ through the AGQ central channel required less force than that of Mg2+, illustrating the presence of more strong interactions between Mg2+ and AGQ tetrads compared to K+. The stabilization in the AGQ tetrads due to cation binding is reassessed by employing ab initio simulations. Mixed QM/MM calculations confirmed that Mg2+ binds strongly to AGQ compared to K+, and it induces higher interactions between the guanine tetrads. However, K+ binding to AGQ induces a higher stabilization energy than Mg2+ binding to AGQ tetrads. Despite the higher binding energy, Mg2+ binding imparts lower stabilization to AGQ due to its unfavorable fermionic quantum energy.

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Section: Resultsmentioning

confidence: 99%

Structural Insights into the Antiparallel G-Quadruplex in the Presence of K⁺ and Mg²⁺ Ions

2023

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“…It has been reported that low potential hydrogen bonding (<2.6 Å) occurs in the double proton transfer mechanism. 19 , 20 , 21 , 22 , 23 , 24 Although the acidic amino acid Glu261 is adjacent to Arg262, charge repulsion between Glu261 and the phosphate group prevents this residue from participating in proton transfer with His273. A similar phenomenon is observed in the cytomegalovirus protease 25 , 26 of the S21 family, which can use histidine as both an acid and a base in the triplet to form a serine‐histidine‐histidine (S‐H‐H) triplet.…”

Section: Discussionmentioning

confidence: 99%

“…Although nucleophilic residues used for covalent catalysis are generally acid‐base‐nucleophilic triplets, the shorter hydrogen bond (2.3 Å) between arginine and histidine removes the barrier to proton transfer, allowing protons to be shared in a broad single‐potential well (Figure S13A). It has been reported that low potential hydrogen bonding (<2.6 Å) occurs in the double proton transfer mechanism 19–24 . Although the acidic amino acid Glu261 is adjacent to Arg262, charge repulsion between Glu261 and the phosphate group prevents this residue from participating in proton transfer with His273.…”

Section: Discussionmentioning

confidence: 99%

Structural insights into the catalytic and inhibitory mechanisms of the flavin transferase FmnB in Listeria monocytogenes

Zheng

Dou

et al. 2022

MedComm

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Listeria monocytogenes , a food‐borne Gram‐positive pathogen, often causes diseases such as gastroenteritis, bacterial sepsis, and meningitis. Newly discovered extracellular electron transfer (EET) from L. monocytogenes plays critical roles in the generation of redox molecules as electron carriers in bacteria. A Mg 2+ ‐dependent protein flavin mononucleotide (FMN) transferase (FmnB; UniProt: LMRG_02181) in EET is responsible for the transfer of electrons from intracellular to extracellular by hydrolyzing cofactor flavin adenine dinucleotide (FAD) and transferring FMN. FmnB homologs have been investigated in Gram‐negative bacteria but have been less well studied in Gram‐positive bacteria. In particular, the catalytic and inhibitory mechanisms of FmnB homologs remain elusive. Here, we report a series of crystal structures of apo‐FmnB and FmnB complexed with substrate FAD, three inhibitors AMP, ADP, and ATP, revealing the unusual catalytic triad center (Asp301‐Ser257‐His273) of FmnB. The three inhibitors indeed inhibited the activity of FmnB in varying degrees by occupying the binding site of the FAD substrate. The key residue Arg262 of FmnB was profoundly affected by ADP but not AMP or ATP. Overall, our studies not only provide insights into the promiscuous ligand recognition behavior of FmnB but also shed light on its catalytic and inhibitory mechanisms.

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“…Journal of Advanced Scientific Research, 2022; 13 (1): Feb.-2022 water molecules with the epoxide ring, reduce the intrinsic reaction barrier while structurally remains unperturbed. Later on Ahsan et al [27] attempt to unravel the electronic basis of the co-catalytic role of water in the epoxide ring opening reaction.…”

Section: Discussionmentioning

confidence: 99%

“On-Water” Ring Opening Reactions: A Review

Verma¹

2022

JASR

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The replacement of current organic chemical processes with more environmentally benign alternatives is an important goal from an ecological point of view. The study is aimed with the goal of promoting water as a solvent in organic synthesis. In recent years, extensive industrial and scholarly research has been promoted for the development of organic reactions in aqueous media. Using water as a solvent often promotes considerable rate enhancements and operational simplicity. Environmental benefits of using water are additionally highlighted in relation to the Twelve Principles of Green Chemistry.

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Hydrogen bonding catalysis by water in epoxide ring opening reaction

Cited by 7 publications

References 39 publications

Structural Insights into the Antiparallel G-Quadruplex in the Presence of K⁺ and Mg²⁺ Ions

Structural Insights into the Antiparallel G-Quadruplex in the Presence of K⁺ and Mg²⁺ Ions

Structural insights into the catalytic and inhibitory mechanisms of the flavin transferase FmnB in Listeria monocytogenes

“On-Water” Ring Opening Reactions: A Review

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Hydrogen bonding catalysis by water in epoxide ring opening reaction

Cited by 7 publications

References 39 publications

Structural Insights into the Antiparallel G-Quadruplex in the Presence of K+ and Mg2+ Ions

Structural Insights into the Antiparallel G-Quadruplex in the Presence of K+ and Mg2+ Ions

Structural insights into the catalytic and inhibitory mechanisms of the flavin transferase FmnB in Listeria monocytogenes

“On-Water” Ring Opening Reactions: A Review

Contact Info

Product

Resources

About

Structural Insights into the Antiparallel G-Quadruplex in the Presence of K⁺ and Mg²⁺ Ions

Structural Insights into the Antiparallel G-Quadruplex in the Presence of K⁺ and Mg²⁺ Ions