Investigation of the NMR spin-spin coupling constants across the hydrogen bonds in ubiquitin: the nature of the hydrogen bond as reflected by the coupling mechanism.
نویسندگان
چکیده
The indirect scalar NMR spin-spin coupling constants across the H-bonds of the protein ubiquitin were calculated, including the Fermi contact, the diamagnetic spin-orbit, the paramagnetic spin-orbit, and the spin dipole term, employing coupled perturbed density functional theory in combination with the B3LYP functional and different basis sets: (9s,5p,1d/5s,1p)[6s,4p,1d/3s,1p] and (11s,7p,2d/5s,1p)[7s,6p,2d/4s,2p]. Four different models based on either the crystal or the aqueous solution structure of ubiquitin were used to describe H-bonding for selected residue pairs of ubiquitin. Calculated and measured 3hJ(NC') coupling constants differ depending on the model used, which is due to the fact that the geometry of ubiquitin is different in the solid state and in aqueous solution. Also, conformational averaging leads to a decrease of the magnitude of the measured 3hJ(NC') constants, which varies locally (larger for -sheets, smaller for -helix). Two different spin-spin coupling mechanisms were identified. While mechanism I transmits spin polarization via an electric field effect, mechanism II involves also electron delocalization from the lone pair of the carbonyl oxygen to the antibonding orbital of the N-H bond. Mechanism I is more important in the crystal structure of ubiquitin, while in aqueous solution, mechanism II plays a larger role. It is possible to set up simple relationships between the spin-spin coupling constants associated with the H bond in proteins and the geometrical features of these bonds. The importance of the 3hJ(NC') and 1J(N-H) constants as descriptors for the H-bond is emphasized.
منابع مشابه
Theoretical Study on Glycosyl Group Effect on Antioxidant Ability of Chrysin Bioflavonoid
Antioxidants are compounds which can prevent biological and chemical substances from oxidative damage by reactive oxygen species. Flavonoids are the most important class of polyphenolic compounds that because of their antioxidant characters possess biological activities and pharmacological effects. Chrysin-6-C-fucopyranoside and chrysin-3-malonyl-6-C-fucopyranoside are mono C-glycosyl derivativ...
متن کاملCoupling Constant Across an NHN Hydrogen Bond**
Since the discovery of NMR coupling constants across hydrogen bonds A H···B containing nuclei with spin =2, such as A, B= F, N, it has been established that these NMR parameters can not only be used to detect hydrogen bridges in biomolecules but also to determine the geometries of strong hydrogen bonds in solution. It has been shown experimentally and by ab initio calculations that scalar two-b...
متن کاملAnalysis of the NMR Spin-Spin Coupling Mechanism Across a H-Bond: Nature of the H-Bond in Proteins
The NMR spin-spin coupling constants (SSCCs) across the H-bond in proteins are sensitive to the electronic structure of the H-bonded system, i.e., the N-H‚‚‚OdC group in proteins. The spin-spin coupling mechanism across the H-bond involves a strong electric field effect, steric exchange interactions, and some weak covalent effects (transfer of electronic charge). The electric field effect is re...
متن کاملTheoretical study of - stacking interactions in substituted-coronene||cyclooctatetraene complexes: A system without direct electrostatic effects of substituents
Stability of the ;-; stacking interactions in the substituted-coronene||cyclooctatetraene complexes wasstudied using the computational quantum chemistry methods (where || denotes ;–; stackinginteraction, and substituted-coronene is coronene which substituted with four similar X groups; X =OH, SH, H, F, CN, and NO). There are meaningful correlations between changes of geometricalparameters and t...
متن کاملA theoretical study on quadrupole coupling parameters of HRPII Protein modeled as 310-helix & α-helix structures
A fragment of Histidine rich protein II (HRP II 215-236) was investigated by 14N and 17O electric field gradient, EFG, tensor calculations using DFT. This study is intended to explore the differences between 310-helix and α-helix of HRPII both in the gas phase and in solution. To achieve the aims, the 17O and 14N NQR parameters of a fragment of HRPII (215-236) for both structures are calculated...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Journal of the American Chemical Society
دوره 126 16 شماره
صفحات -
تاریخ انتشار 2004