A direct dynamics study of the deprotonated guanine·cytosine base pair: intra-base pair proton transfer, thermal dissociation vs. collision-induced dissociation, and comparison with experiment

2017 ◽  
Vol 19 (45) ◽  
pp. 30616-30626 ◽  
Author(s):  
Jianbo Liu
Keyword(s):  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Base Pair ◽  
Collisional Activation ◽  
Thermal Dissociation ◽  
Collision Induced Dissociation ◽  
Thermal Excitation ◽  
Direct Dynamics ◽  
Comparison With Experiment

Dynamics of intra-base pair hydrogen bonds upon random thermal excitation vs. non-random collisional activation.

Transient proton transfer of base pair hydrogen bonds induced by intense terahertz radiation

2020 ◽  
Vol 22 (17) ◽  
pp. 9316-9321
Author(s):  
Kaicheng Wang ◽  
Lixia Yang ◽  
Shaomeng Wang ◽  
Lianghao Guo ◽  
Jialu Ma ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Terahertz Radiation ◽  
Base Pair ◽  
Quantum Simulation ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs

Intense terahertz radiation was applied to trigger transient proton transfer in DNA base pairs through quantum simulation.

Mass spectrometry and computational study of collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation: intra-base-pair proton transfer and hydrogen transfer, non-statistical dissociation, and reaction with a water ligand

2020 ◽  
Vol 22 (26) ◽  
pp. 14875-14888 ◽  
Author(s):  
Yan Sun ◽  
May Myat Moe ◽  
Jianbo Liu
Keyword(s):  
Mass Spectrometry ◽  
Proton Transfer ◽  
Radical Cation ◽  
Base Pair ◽  
Hydrogen Transfer ◽  
Theoretical Study ◽  
Computational Study ◽  
Collision Induced Dissociation ◽  
Water Ligand

A combined experimental and theoretical study is presented on the collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation ([9MG·1MC]˙+) and its monohydrate ([9MG·1MC]˙+·H2O) with Xe and Ar gases.

WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

2013 ◽  
Vol 12 (08) ◽  
pp. 1341002 ◽  
Author(s):  
XIN ZHANG ◽  
MING LEI
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Glutamic Acid ◽  
Active Site ◽  
Nucleophilic Attack ◽  
Zinc Ions ◽  
Initial Model ◽  
Dynamics Simulations

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

scholarly journals 5-Nitrosalicylic Acid and its Proton-Transfer Compounds with Aliphatic Lewis Bases

2005 ◽  
Vol 58 (1) ◽  
pp. 47 ◽  
Author(s):  
Graham Smith ◽  
Andy W. Hartono ◽  
Urs D. Wermuth ◽  
Peter C. Healy ◽  
Jonathan M. White ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Lewis Base ◽  
Unusual Structure ◽  
Lewis Bases ◽  
Carboxylate Oxygen ◽  
Hydrogen Bonding Interactions ◽  
Polymer Compound ◽  
Proton Transfer Compounds ◽  
Centrosymmetric Dimers

The crystal structures of the proton-transfer compounds of 5-nitrosalicylic acid (5-nsa) with morpholine (morph), hexamethylenetetramine (hmt), and ethylenediamine (en) have been determined and their solid-state packing structures described. The compounds are [(morph)+(5-nsa)–] 1, [(hmt)+(5-nsa)–·H2O] 2, and [(en)2+2(5-nsa)–·H2O] 3. In all compounds, protonation of the hetero-nitrogen of the Lewis base occurs. With 1, the 5-nsa anions and the morpholine cations lie, respectively, in or across crystallographic mirror planes and are linked within the planes by hydrogen-bonding interactions through the aminium group and the carboxylic and phenolic oxygens of the anionic 5-nsa species giving a two-dimensional sheet polymer. Compound 2 is an unusual structure with the planar 5-nsa anions lying within pseudo mirror planes and cyclically linked by duplex water bridges through a single carboxylate oxygen into centrosymmetric dimers. The hmt cation molecules are disordered across the pseudo mirror and are strongly linked by N+–H···O hydrogen bonds only to the water molecules with peripheral weak hmt C–H···O hydrogen bonds extending the dimer within and between the dimer planes. Compound 3 is a network polymer comprised of the 5-nsa anions, the en dianions, and the water molecule in an extensive hydrogen-bonded structure.

Three-centre C—H...O hydrogen bonds in the DNA minor groove: analysis of oligonucleotide crystal structures

1999 ◽  
Vol 55 (12) ◽  
pp. 2005-2012 ◽  
Author(s):  
Anirban Ghosh ◽  
Manju Bansal
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Base Pair ◽  
Minor Groove ◽  
Local Geometry ◽  
Data Sets ◽  
Base Pairs ◽  
Dna Minor Groove ◽  
Close Proximity ◽  
Using Data

AA·TT and GA·TC dinucleotide steps in B-DNA-type oligomeric crystal structures and in protein-bound DNA fragments (solved using data with resolution <2.6 Å) show very small variations in their local dinucleotide geometries. A detailed analysis of these crystal structures reveals that in AA·TT and GA·TC steps the electropositive C2—H2 group of adenine is in very close proximity to the keto O atoms of both the pyrimidine bases in the antiparallel strand of the duplex structure, suggesting the possibility of intra-base pair as well as cross-strand inter-base pair C—H...O hydrogen bonds in the DNA minor groove. The C2—H2...O2 hydrogen bonds in the A·T base pairs could be a natural consequence of Watson–Crick pairing. However, the cross-strand interactions between the bases at the 3′-end of the AA·TT and GA·TC steps obviously arise owing to specific local geometry of these steps, since a majority of the H2...O2 distances in both data sets are considerably shorter than their values in the uniform fibre model (3.3 Å) and many are even smaller than the sum of the van der Waals radii. The analysis suggests that in addition to already documented features such as the large propeller twist of A·T base pairs and the hydration of the minor groove, these C2—H2...O2 cross-strand interactions may also play a role in the narrowing of the minor groove in A-tract regions of DNA and help explain the high structural rigidity and stability observed for poly(dA)·poly(dT).

scholarly journals Crystal structure and hydrogen bonding in the water-stabilized proton-transfer salt brucinium 4-aminophenylarsonate tetrahydrate

2016 ◽  
Vol 72 (5) ◽  
pp. 751-755 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Network Structure ◽  
Three Dimensional ◽  
Water Molecules ◽  
Arsanilic Acid ◽  
Dimensional Network

In the structure of the brucinium salt of 4-aminophenylarsonic acid (p-arsanilic acid), systematically 2,3-dimethoxy-10-oxostrychnidinium 4-aminophenylarsonate tetrahydrate, (C23H27N2O4)[As(C6H7N)O2(OH)]·4H2O, the brucinium cations form the characteristic undulating and overlapping head-to-tail layered brucine substructures packed along [010]. The arsanilate anions and the water molecules of solvation are accommodated between the layers and are linked to them through a primary cation N—H...O(anion) hydrogen bond, as well as through water O—H...O hydrogen bonds to brucinium and arsanilate ions as well as bridging water O-atom acceptors, giving an overall three-dimensional network structure.

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