Hydrogen bond constraints

Pogozheva ID, Lomize AL, Mosberg HI. Opioid receptor three-dimensional structures from distance geometry calculations with hydrogen bonding constraints. Biophys J 1998 75 612-634. 

Clore et a/.81 calculated a structure of the B1 domain of the streptococcal protein G (56 residues) by RDCs (for 15N-Hn, l 5N l3C. and HN 13 C ) and 32 backbone hydrogen bond constraints (Section 8.3) without NOE-derived distances. They compared structural convergences for their calculations using 152 RDCs measured in tobacco mosaic virus, 150 RDCs measured in DMPC/DHPC (3 1) bicelles, and without RDCs. The rmsd values with RDCs were both improved significantly (four-fold). A further improvement was observed for calculations using the two sets of the constraints simultaneously by 20-30%. This indicated that the alignment mechanisms are different and complementary to the two medias. 

The molecular dynamics studies also show that, in the absence of hydrogen bond constraints, the antiparallel CGGA structure undergoes large... 

In the case of the retro Diels-Alder reaction, the nature of the activated complex plays a key role. In the activation process of this transformation, the reaction centre undergoes changes, mainly in the electron distributions, that cause a lowering of the chemical potential of the surrounding water molecules. Most likely, the latter is a consequence of an increased interaction between the reaction centre and the water molecules. Since the enforced hydrophobic effect is entropic in origin, this implies that the orientational constraints of the water molecules in the hydrophobic hydration shell are relieved in the activation process. Hence, it almost seems as if in the activated complex, the hydrocarbon part of the reaction centre is involved in hydrogen bonding interactions. Note that the... 

Plus 38 distance constraints derived from hydrogen bonds 131). 

---