The name's bond......disulfide bond

A repeating theme in the structural biology of disulfide oxidants and isomerases is the extraordinary architectural similarity between functionally related proteins from prokaryotes and eukaryotes. The recently determined structure of full-length yeast protein disulfide isomerase (PDI) reveals a U-shaped molecule with two redox-active sites. It bears a remarkable resemblance to the V-shaped, but dimeric, bacterial disulfide isomerases DsbC and DsbG. Similarly, the much-anticipated structure of the bacterial membrane protein DsbB, the redox partner of DsbA, comprises a flexible redox loop embedded in an antiparallel four-helix bundle. This architecture is similar to that of soluble eukaryotic Ero1p and Erv2p proteins, the redox partners of PDI. Importantly, the DsbB crystal structure is a complex with DsbA, providing our first view of the molecular interactions between these two proteins.     

A study of dihydrogen bond interactions through three-centre bond and group indices

We report here an investigation into the correlation between dihydrogen bond energies, three-centre bond indices and group indices in some dihydrogen-bonded dimers. This kind of bond is generated by interaction between proton-donator and proton-acceptor groups, XH^σ+…H′^σ ? M, where X is a more electronegative atom and M a less electronegative atom than hydrogen. The different electronegativities of the X atoms, as well the M atoms, would affect the correlations between H^σ+…H′^σ ?  distances and bond energies of these systems. In this work it will be shown that three-centre bond indices and group indices exhibit a better correlation with bond energies when compared to H^σ+…H′^σ ?  distances for this kind of system.     

The neurobiology of pair bond formation,bond disruption,and social buffering

Enduring social bonds play an essential role in human society. These bonds positively affect psychological, physiological, and behavioral functions. Here, we review the recent literature on the neurobiology, particularly the role of oxytocin and dopamine, of pair bond formation, bond disruption, and social buffering effects on stress responses, from studies utilizing the socially monogamous prairie vole (Microtus ochrogaster).     

Non-empirical valence bond calculation of hydrogen bond energy in polypeptides

An approximate ab-initio valence bond calculation of hydrogen bond energy was carried out and the results are discussed. The total bond energy of a simplified N? H…O structure is calculated for various N? H and N…O distances and the potential energy profiles are obtained. The hydrogen bond energy, ie, the delocalization energy gained by the formation of one hydrogen bond is found to be 8.7–12.0 kcal/mole. The potential energy is characterized by a deep minimum at 1.6–1.8 a.u. from the nitrogen and the second trough is found to be considerably higher than the first.     

二硫键与蛋白质的结构

二硫键是肽链上2个半胱氨酸残基的巯基基团发生氧化反应形成的共价键．具有链内二硫键和链间二硫键2种形式。与氨基酸的氨基氮原子之间形成的稳定共价键不同．二硫键容易被还原而断裂,断裂后可再次氧化重新形成二硫键,因而是可以动态变化的化学键。二硫键是参与一级结构也是形成高级结构的重要化学键,对蛋白质折叠和高级结构的形成与维持十分重要。讨论了二硫键的形成和特征及其与蛋白质结构和功能之间的关系,并讨论了生物学教学中关于二硫键的一些疑问．     

Ribosomal tolerance and peptide bond formation

In the ribosome, the decoding and peptide bond formation sites are composed entirely of ribosomal RNA, thus confirming that the ribosome is a ribozyme. Precise alignment of the aminoacylated and peptidyl tRNA 3'-ends, which is the major enzymatic contribution of the ribosome, is dominated by remote interactions of the tRNA double helical acceptor stem with the distant rims of the peptidyl transferase center. An elaborate architecture and a sizable symmetry-related region within the otherwise asymmetric ribosome guide the A --> P passage of the tRNA 3'-end by a spiral rotatory motion, and ensures its outcome: stereochemistry suitable for peptide bond formation and geometry facilitating the entrance of newly formed proteins into their exit tunnel.     

Competition between tetrel bond and pnicogen bond in complexes of TX3-ZX2 and NH3

Journal of Molecular Modeling - The discovery or development of thermoalkalophilic lipases that show high levels of catalytic activity in organic solvents would have important industrial...     

Organocobaloximes: Cobalt-carbon bond stability and synthesis

Following the discovery that the naturally occurring vitamin B₁₂ coenzyme contained a stable CoC sigma bond and the further realization that porphyrin-like corrin was an important factor in the stabilization of the CoC bond, has led to the synthesis of a large number of organocobalt complexes. Inspite of the many known examples of such complexes in the literature, the synthesis of the CoC bond with new or modified structural features continues to be a fascinating field of study. Many synthetic routes have been reported and many new ones are frequently emerging. In this article, a complete analysis of the synthetic aspects of organocobalt compounds and organocobaloximes, in particular, is undertaken. The stability of the CoC bond, general methods of synthesis and experimental procedures are discussed.     

Enzyme-catalysed siloxane bond formation

Biosilicification occurs on a globally vast scale under mild conditions. Although research has progressed in the area of silica biosynthesis, the molecular mechanisms of these interactions are effectively unknown. The natural production of silica in the Tethya aurantia marine sponge, Cylindrotheca fusiformis diatom, and Equisetum telmateia plant appear to be similar. However, the studies were complicated mechanistic queries due to the use of silicic acid analogues. Given these complications, a carefully chosen model study was carried out to test the ability of enzymes to catalyse the formation of molecules with a single siloxane bond during the in vitro hydrolysis and condensation of alkoxysilanes. Our data suggest that homologous lipase and protease enzymes catalyse the formation of siloxane bonds under mild conditions. Non-specific interactions with trypsin promoted the in vitro hydrolysis of alkoxysilanes, while the active site was determined to selectively catalyse the condensation of silanols.     

A novel halogen bond and a better-known hydrogen bond cooperation of neonicotinoid and insect nicotinic acetylcholine receptor recognition

Neonicotinoid insecticides target the insect nicotinic acetylcholine receptor (nAChR) and are highly effective against the piercing-sucking pests. To explore the molecular interaction mechanism between the neonicotinoids and the insect nAChR, some key neonicotinoid compounds were docked into Aplysia californica acetylcholine binding protein (Ac-AChBP), which serves as a suitable structural surrogate of the insect nAChR. The binding mode study showed that the hydrogen bond force between the electronegative pharmacophore of the neonicotinoids and Cys190NH of the target binding pocket is crucial to the high efficiency of the neonicotinoids. Increasing the coplanarity between the guanidine or amidine and the electronegative pharmacophore of the neonicotinoids could increase the Π-Π stacking effect with Tyr188 of the Ac-AChBP and thus enhance the insecticidal potency. The introduction of an azide group to the chloropyridine ring of the neonicotinoids would reduce its binding ability due to the disappearance of a novel halogen bonding interaction. A series of novel neonicotinoid molecules were designed based on the halogen bonding interaction and two compounds with 6-bromopyridine-3-yl and 6-(trifluoromethyl)-3-pyridinyl were found to be with potential insecticidal activities.     

Isopeptide bond in collagen- and fibrinogen-binding MSCRAMMs

The internal isopeptide bonds are amide bonds formed autocatalytically between the side chains of Lys and Asn/Asp residues and have been discovered recently. These bonds are well conserved in Gram-positive bacterial pilin proteins and are also observed over a wide range of Gram-positive bacterial surface proteins. The presence of these bonds confers the pilus subunits with remarkable properties in terms of thermal stability and resistance to proteases. Like pili, microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) are also surface proteins found only in Gram-positive bacteria. They specifically interact with the extracellular matrix (ECM) molecules like collagen, fibrinogen, fibronectin, laminin, etc. Many biophysical and biochemical studies have been carried out to characterize the isopeptide bonds in pili proteins from Gram-positive bacteria, but no attempts have been made to study the isopeptide bonds in MSCRAMMs. This short review aims to study the significance of the isopeptide bonds in relation to their function, by analyzing the crystal structures of collagen- and fibrinogen-binding MSCRAMMs. In this analysis, interestingly, we observed that the putative isopeptide bonds are restricted to the collagen-binding MSCRAMMs. Based on analogy with bacterial pilus subunits, we hypothesize that the collagen-binding MSCRAMMs possessing putative isopeptide bonds exhibit similar structural properties, which could help the bacteria in colonizing the host and provide resistance against host–defense mechanisms.     

Quantitative comparison of the hydrogen bond network of A-state and native ubiquitin by hydrogen bond scalar couplings

The backbone hydrogen bond (H-bond) network of the partially folded A-state of ubiquitin (60% methanol, 40% water, pH 2) has been characterized quantitatively by (h3)J(NC)(') H-bond scalar couplings between the (15)N nuclei of amino acid H-bond donors and the (13)C carbonyl nuclei of the acceptors. Results on (h3)J(NC)(') couplings and the amide proton ((1)H(N)) chemical shifts for the A-state are compared quantitatively to the native state. The (h3)J(NC)(') correlations of the A-state show intact, nativelike H-bonds of the first beta-hairpin beta1/beta2 and the alpha-helix, albeit at lower strength, whereas the H-bonds in the C-terminal part change from a pure beta-structure to an all alpha-helical H(N)(i)-->O(i-4) connectivity pattern. A residue-specific analysis reveals that the conformations within the conserved secondary structure segments are much more homogeneous in the A-state than in the native state. Thus, the strong asymmetry of (h3)J(NC)(') couplings and (1)H(N) chemical shifts between the interior and exterior sides of the native state alpha-helix vanishes in the A-state. This indicates that the bend of this helix around the native state hydrophobic core is released in the homogeneous solvent environment of the A-state. Similarly, an irregularity in the behavior of H-bond I3-->L15 in hairpin beta1/beta2, which results from strong contacts to strand beta5 in the native state, is absent in the A-state. These findings rationalize the behavior of the (1)H(N) chemical shifts in both states and indicate that the A-state is in many aspects similar to the onset of thermal denaturation of the native state.     

Disulfide bond isomerization in prokaryotes

Proteins with multiple cysteine residues often require disulfide isomerization reactions before they attain their correct conformation. In prokaryotes this reaction is catalyzed mainly by DsbC, a protein that shares many similarities in structure and mechanism to the eukaryotic protein disulfide isomerase. This review discusses the current knowledge about disulfide isomerization in prokaryotes.