RESUMEN
Carbon bonds (C-bonds) are the highly directional noncovalent interactions between carbonyl-oxygen acceptors and sp3 -hybridized-carbon σ-hole donors through nâσ* electron delocalization. We have shown the ubiquitous existence of C-bonds in proteins with the help of careful protein structure analysis and quantum calculations, and have precisely determined C-bond energies. The importance of conventional noncovalent interactions such as hydrogen bond (H-bonds) and halogen bond (X-bonds) in the structure and function of biological molecules are well established, while carbon bonds C-bonds have still to be recognized. We have shown that C-bonds are present in proteins, contribute enthalpically to the overall hydrophobic interaction and play a significant role in the photodissociation mechanism of myoglobin and the binding of nucleobases to proteins.
Asunto(s)
Carbono/química , Proteínas/química , Animales , Caballos , Enlace de Hidrógeno , Interacciones Hidrofóbicas e Hidrofílicas , Modelos Moleculares , Mioglobina/química , Teoría Cuántica , TermodinámicaRESUMEN
Thioamides are used as potential surrogates of amides to study the structure and dynamics of proteins and nucleic acids. However, incorporation of thioamides in biomolecules leads to changes in their structures and conformations mostly attributed to the strength of the amide-N-H···SâC hydrogen bond. In most cases, it is considered weak owing to the small electronegativity of sulfur, and in some cases, it is as strong as conventional H-bonds. Herein, adopting PDB structure analysis, NMR spectroscopy, and quantum chemistry calculations, we have shown that thioamides in a geometrical and structural constraint-free environment are capable of forming strong H-bonds like their amide counterparts. These studies also enabled us to determine the amide-N-H···SâC H-bond enthalpy (ΔH) very precisely. The estimated ΔH for the amide-N-H···SâC H-bond is â¼-30 kJ/mol, which suggests that the amide-N-H···SâC H-bond is a strong H-bond and merits its inclusion in computational force fields for biomolecular structure simulations to explore the role of amide-N-H···SâC H-bonds in nucleobase pairing and protein folding.
Asunto(s)
Ácidos Nucleicos/química , Proteínas/química , Amidas/química , Hidrógeno/química , Enlace de Hidrógeno , Espectroscopía de Resonancia Magnética , Conformación Molecular , Pliegue de Proteína , Azufre , TermodinámicaRESUMEN
Careful protein structure analysis unravels many unknown and unappreciated noncovalent interactions that control protein structure; one such unrecognized interaction in protein is selenium centered hydrogen bonds (SeCHBs). We report, for the first time, SeCHBs involving the amide proton and selenium of selenomethionine (Mse), i.e., amide-N-H···Se H-bonds discerned in proteins. Using mass selective and conformer specific high resolution vibrational spectroscopy, gold standard quantum chemical calculations at CCSD(T), and in-depth protein structure analysis, we establish that amide-N-H···Se and amide-N-H···Te H-bonds are as strong as conventional amide-NH···O and amide-NH···OâC H-bonds despite smaller electronegativity of selenium and tellurium than oxygen. It is in fact, electronegativity, atomic charge, and polarizability of the H-bond acceptor atoms are at play in deciding the strength of H-bonds. The amide-N-H···Se and amide-N-H···Te H-bonds presented here are not only new additions to the ever expanding world of noncovalent interactions, but also are of central importance to design new force-fields for better biomolecular structure simulations.
Asunto(s)
Enlace de Hidrógeno , Modelos Moleculares , Resonancia Magnética Nuclear Biomolecular/métodos , Proteínas/química , Selenio/química , Selenometionina/química , Amidas/química , Cristalografía por Rayos X , Hidrógeno/química , Nitrógeno/química , Oxígeno/química , ProtonesRESUMEN
Gas-phase vibrational spectroscopy, coupled cluster (CCSD(T)), and dispersion corrected density functional (B97-D3) methods are employed to characterize surprisingly strong sulfur center H-bonded (SCHB) complexes between cis and trans amide NH and S atom of methionine and cysteine side chain. The amide N-H···S H-bonds are compared with the representative classical σ- and π-type H-bonded complexes such as N-H···O, N-H···OâC and N-H···π H-bonds. With the spectroscopic, theoretical, and structural evidence, amide N-H···S H-bonds are found to be as strong as the classical σ-type H-bonds, despite the smaller electronegativity of sulfur in comparison to oxygen. The strength of backbone-amide N-H···S H-bonds in cysteine and methionine containing peptides and proteins are also investigated and found to be of similar magnitudes as those observed in the intermolecular model complexes studied in this work. All such SCHBs also confirm that the electronegativities of the acceptors are not the sole criteria to predict the H-bond strength.