Introduction to Salt Bridge

Using the crystal structure, molecular dynamics simulations, and mutagenesis, we identify a conserved interdomain salt bridge that prevents premature intramolecular cleavage at higher pH values and may thus present a control switch for the observed pH sensitivity of proenzyme cleavage in (trypanosomal) CathL-like proteases.

Molecular docking and molecular dynamics simulation demonstrate that CLR01 is attached with Lysine222 nitrogen by π-cation interaction of its nine aromatic rings and formation of salt bridge/hydrogen bond of one of the two rotatable peripheral anionic phosphate groups.

The antibody recognizes the MenX fragment by binding all six repeating units of the oligosaccharide via hydrogen bonding, salt bridges, and hydrophobic interactions.

In per-residue energy decomposition analysis, four residues, K362, R376, Y436, and K439 in hcGAS were found to contribute significantly to the binding with inhibitors via hydrogen bonding, salt bridges, and various π interactions, such as π· · ·π stacking, cation· · ·π, hydroxyl· · ·π, and alkyl· · ·π interactions.

2 nm; 4) hydrogen bonds, salt bridges, interactions among aromatic side-chains, burial and tight packing of hydrophobic side-chains, and aqueous solvent exposure of hydrophilic side-chains are relatively optimal; and 5) residues that are identical among distantly related homologous proteins cluster in the interior of most oligomers whereas residues that are hypervariable are exposed on protein surfaces.

2 nm; 4) hydrogen bonds, salt bridges, interactions among aromatic side-chains, burial and tight packing of hydrophobic side-chains, and aqueous solvent exposure of hydrophilic side-chains are relatively optimal; and 5) residues that are identical among distantly related homologous proteins cluster in the interior of most oligomers whereas residues that are hypervariable are exposed on protein surfaces.

From the analysis of a set of  bonding descriptors firmly rooted in the formalism of quantum mechanics, including Natural Bond Orbitals (NBO), Quantum Theory of Atoms In Molecules (QTAIM) and highly correlated energies within the Domain Based Local Pair Natural Orbital Coupled Cluster Method (DLPNO-CCSD(T)), and from a set of computed electronic spectral patterns with environmental effects, we show that the new variants improve their ability to recognize available sites to either hydrogen bond or to form salt bridges with residues in the ACE2 receptor of the host cells.

Structural analysis revealed a molecular basis for the higher stability of the CBH‐I structure in which A65R and G415R substitutions form salt bridges (D64 … R65, E411 … R415) and S181F forms π–π interaction (Y155 … F181), leading to stabilize surface‐exposed flexible α‐helixes and loop in the multidomain β‐jelly roll fold structure, respectively.

91kcal/mol by forming Salt Bridge at LYS143, Hydrogen bond at ALA8, VAL45, HIS47, SER142, ASN277, ASN359, and TRP363.

Moreover, the GV971 components mainly interact directly with the charged residues D1, R5, K16, and K28 by forming salt bridges and hydrogen bonds, which specifically bind to the N-terminal region of Aβ42.

Cytoplasmic access of water to the ion-binding site is accompanied by a remarkable loss of secondary structure of the KdpB N-terminus and disruption of a key salt bridge between Glu87 in the A domain and Arg212 in the P domain.

We found that this conformational transition is brought about by the loss of a key salt bridge between Lys353 and Asp358 due to the phosphorylation at Ser356 that results in the reorganization of the dimeric interface.

the introduction of a tyrosine corner in a helix-loop-helix segment and the formation of a novel surface salt bridge network possibly explaining the enhanced thermal stability.

The stabilizing effect can be attributed to the formation of additional surface salt bridges between Arg‐residues and pS111 not present in the native structure.

2% agar salt bridge connected the chambers.

In this work single chamber microbial fuel cell (SCMFC) incorporating agar salt bridge pipe were used to investigate the interaction mechanisms between bacterial growth, Congo red decolorization, and bioelectricity generation.

In all cases, our MD simulations produced protein clusters that were stabilized by intermolecular salt bridges.

An interfilament interface exists between residues K60‒F94 and Q62‒I88 with an intermolecular salt bridge between K80 and E83.

A novel salt bridge is also discovered, which can mediate contact between the spike tip and fulcrum even in closed conformations, revealing a mechanism of direct communication across these domains.

Our study also identified a novel salt bridge in CRTC1 with an important function in binding 14-3-3, expanding the understanding of the interaction between 14-3-3 and its ligands.

Our results indicate that the E484Q mutation disrupts the conserved salt bridge formed between Lys31 of hACE2 and Glu484 of S protein.

A structurally conserved glutamate in the ECL2 anchors the peptides by a conserved salt bridge to the arginine of the RFamide motif.

Our findings indicate that histone H4 tails engage in a fuzzy interaction with nucleosomal DNA, underpinned by a variable pattern of short-lived salt bridges and hydrogen bonds, which persists at low ionic strength (0-100 mM NaCl).

Microsecond molecular dynamics simulations of KRAS4b on PS and PIP2 containing membranes show that the dynamics of the G-domain at the bilayer sur-face are significantly altered in the presence of PIP2, due to the formation of long lived salt bridges with basic residues on the G-domain.

Further investigation indicates that betaine and taurine can enhance the quinary interaction between the protein and cellular environment and manifestly weaken the electrostatic attraction in protein salt bridges.

In addition to traditional stacking interactions between aromatic rings, stacking interactions involving heterocyclic drug fragments and protein salt bridges have also been observed.

Only in one CB[7]@Aβ1-42 complex was observed stable Asp23-Lys28 salt bridge with an average distance of 0.

Our results demonstrate that although the overall secondary structure population is similar with Aβ42 and Aβ42(G37V), Aβ42(G37V) shows an increase in the β-turn and β-hairpin at residues 36-37 and the flexibility of the Asp23-Lys28 salt bridge.

Though it is not clear how the linkers affecting the activity, structure analysis indicated that the stability improvement is dependent on the additional salt bridge, H-bond, and the subunit interface area increasing due to the linker insertion, among which the additional salt bridge and interface area were more important factors.

Additional salt bridges, hydrogen bonds, and a high number of non-bonded contacts (i.

JA is converted to JA-Ile which shows strong binding with COI1 and COI1-JA-Ile complex docked with JAZ which showed strong interaction with five hydrogens and one salt bridge bond.

The selected docked complex showed five hydrogen bonds and one salt bridge.

Analysis of side chain-side chain salt bridges suggests that the overestimation of the helical content may be, in part, due to such interactions.

Hb Hope is characterized by a comparable charge altering mutation (β136 Gly→Asp) and the intra chain salt bridge so formed between the carboxyl group of β136 Asp and the charged α-amino group of β1 valine.

Our results suggest that deamidation creates a new intramolecular salt bridge in NEDD8 to destabilize the NEDD8/WHB complex and reduce CRL activity.

The structure of the closed state of the core complex SctR5S4T1 revealed that several of these residues form inter- and intramolecular salt bridges, some of which have to be broken for pore opening.

We studied the stability of two salt bridges between hen egg-white lysozyme (HEL) and its antibody, HyHEL-10, by using molecular dynamics simulations.

Within the active site of FGFR4, the ligand 5b interacted with four H-bonds with Asp630 (carbonyl function), Glu520 (with amide NH and ArNH), and Ile609 (phenol function), while an imine “N” showed two salt bridges with Asp630 and Glu520.

Our results demonstrate several molecular structural and dynamics changes at around the transition pH values, including the isomerization of proline-threonine backbone configuration, breaking of arginine-aspartic acid salt bridge and the formation of arginine-lipid interactions, and an universal decreasing of dynamics in lipid headgroups and alkyl chains.

The Spike protein bound with human receptor, an amino acid salt bridge and a potential furin cleavage site were found in the SARS-CoV-2 using molecular modeling.

These changes include (i) the H3A1 binding region, (ii) strand β1 that forms an intermolecular β-sheet with the H3 peptide, and (iii) an aspartate-containing motif involved in salt bridge interaction with H3K4, which together appear to abrogate recognition of H3K4 by the VIM1 PHD finger.

Molecular docking using the C-I-TASSER-predicted TMPRSS2 catalytic domain model suggested that the guanidinobenzoyl or aminidinobenzoyl group in all the drugs could form putative salt bridge interactions with the side-chain carboxyl group of Asp435 located in the S1 pocket of TMPRSS2.

Using computational simulations we discovered that the substitutions at 155th and 171st positions changed the amino acids involved in salt bridge formation, hydrogen-bond occupancy, interactome clusters, and the stability of the protein.

In addition, molecular docking analysis revealed that this peptide interacted with DNA gyrase and dihydrofolate reductase by salt bridge formation, hydrogen bond interactions, and metal contact.

Our results indicate that the E484Q mutation disrupts the conserved salt bridge formed between Lys31 of hACE2 and Glu484 of S protein.

Molecular dynamics simulations performed indicated that the mutant protein AI loop structure was stabilized by salt bridge formed between D615 and R602.

Furthermore, we found increased flexibility in direct spatial proximity of the fusion peptide due to salt bridge rearrangements induced by the D614G mutation in B.

This increase in flexibility is due to salt bridge rearrangements induced by the D614G mutation in B.