Index of papers in April 2015 that mention
  • hydrogen bond
Tomáš Trnka, Stanislav Kozmon, Igor Tvaroška, Jaroslav Koča
Important interactions stabilizing the transition state
Among the structural interactions there are several hydrogen bonds coordinating the Gal-NAc moiety: a bond between the amidic backbone hydrogen of Gly309 and the N-acetyl carbonyl oxygen, two hydrogen bonds between Glu334 and the O4 and O6 hydrogens of GalNAc and a hydrogen bond between Arg208 and the O4 GalNAc oxygen.
Important interactions stabilizing the transition state
Apart from the electrostatic effects of the metal cation and hydrogen bonding with the water molecules coordinated to this ion, the leaving group is additionally forming a strong hydrogen bond with Tyr367, a hydrogen bond with Arg362 and another, relatively weak hydrogen bond with the amidic hydrogen of the acceptor threonine.
Important interactions stabilizing the transition state
There is also an important intramolecular hydrogen bond between a phosphate oxygen and the amidic hydrogen of Gal-NAc that further contributes to keeping the saccharide moiety suitably rotated.
Introduction
[4, 14] Recent experimental evidence for the retaining glycosyltransferase, trehalose-6-phosphate synthase (OtsA) [12, 15] is consistent with the SNi mechanism and also supports the theory that the hydrogen bond between the phosphate group and the acceptor hydroxyl plays a role in stabilizing the transition state suggested by calculations.
Methods
Furthermore, water molecules present in the active site were manually rotated to create a network of hydrogen bonds where possible.
Methods
Three of these water molecules are located close to the metal ion with one of them directly serving as a ligand and the other two forming a hydrogen bond network between the first water molecule and neighboring active site residues.
Path optimisation
On the other hand, the hydrogen bond between threonine hydrogen and phosphate oxygen shortens visibly by about 0.2 A, as this bond is made stronger by the increased negative charge on the oxygen atom after the heterolytic cleavage of the C1-01 bond.
Path optimisation
o The proton is transferred to the phosphate, While maintaining an exceptionally strong hydrogen bond to threonine With a bond length of only 1.34 A.
Transition state optimisation
The proton is still attached to the acceptor oxygen, but at the same time it participates in a very strong hydrogen bond with the leaving group.
hydrogen bond is mentioned in 12 sentences in this paper.
Topics mentioned in this paper:
Noorain Khan, Narendar Kolimi, Thenmalarchelvi Rathinavelan
Base pair nonisomorphism is the key factor for inducing Z-DNA conformation by A. . .A mismatch
.A mismatch is single hydrogen bonded , it exhibits enormous flexibility for base extrusion and flipping, facilitating the formation of Z-DNA through Zipper mechanism.
Mechanism of formation of 8-2 junction
An intriguing observation is that a single hydrogen bonded noncanonical A. .
Periodic B-Z junction in (CAG)6. (CAG)6 duplex
.G hydrogen bonding pattern (818 Fig).
Results
As the Z-DNA formation happens due to the sugar-phosphate flipping, hydrogen bond between A8&A23 undergoes minor changes (82 Fig).
Results
.N6(A23) hydrogen bond persists, whereas, between 16.5-100ns, N1(A23).
Results
.N6(A8) hydrogen bond is predominantly favored due to the slight movement of A23 towards the minor groove.
hydrogen bond is mentioned in 17 sentences in this paper.
Topics mentioned in this paper:
Nils A. Berglund, Thomas J. Piggot, Damien Jefferies, Richard B. Sessions, Peter J. Bond, Syma Khalid
Discussion
Unlike the LPS system, PMB1 appeared to have no effect upon intra-lipid A hydrogen bonding , but instead the DAB residues interacted with phosphate groups, pushing them apart, leading to local membrane deformation and creating a region of reduced membrane-surface charge density that may no longer inhibit fatty acid tail insertion.
Inner Membrane Model
Hydrogen bonding interactions were formed between the DAB residues of the peptide and the phospholipid headgroups within a few nanoseconds.
Inner Membrane Model
The side chains accounted for 46% (81 Table) of the total hydrogen bonds formed between the whole PMB1 molecules and the lipid head-groups.
Inner Membrane Model
After PMB1 insertion into the membrane core however, this value dropped dramatically and DAB accounted for only 17% of hydrogen bonds formed between the entire PMB1 molecule and the lipid headgroups.
Re LPS Outer Membrane Model
The DAB side chain alone accounts for 43% of the total number of hydrogen bonds formed (SI Table) between any part of the peptide and the LPS sugars during the initial 300 ns of simulation, despite only making up 25% of the total number of atoms in PMB1.
Re LPS Outer Membrane Model
Moreover, during the last 500 ns of these simulations, the DAB residues were responsible for over 50% of the hydrogen bonds formed between the whole PMB1 and the LPS sugars.
Re LPS Outer Membrane Model
This was stabilized by PMB1-sugar hydrogen bonding interactions, with an average of ~8 hydrogen bonds per PMB1 molecule present at any one time during the final 500 ns (S2 Table).
hydrogen bond is mentioned in 9 sentences in this paper.
Topics mentioned in this paper: