HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures

Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer prediction lack hydrogen coordinates. We present a new algorithm, HAAD, to predict the positions of hydrogen atoms based on the positions of heavy atoms. The algorithm is built on the basic rules of orbital hybridization followed by the optimization of steric repulsion and electrostatic interactions. We tested the algorithm using three independent data sets: ultra-high-resolution X-ray structures, structures determined by neutron diffraction, and NOE proton-proton distances. Compared with the widely used programs CHARMM and REDUCE, HAAD has a significantly higher accuracy, with the average RMSD of the predicted hydrogen atoms to the X-ray and neutron diffraction structures decreased by 26% and 11%, respectively. Furthermore, hydrogen atoms placed by HAAD have more matches with the NOE restraints and fewer clashes with heavy atoms. The average CPU cost by HAAD is 18 and 8 times lower than that of CHARMM and REDUCE, respectively. The significant advantage of HAAD in both the accuracy and the speed of the hydrogen additions should make HAAD a useful tool for the detailed study of protein structure and function. Both an executable and the source code of HAAD are freely available at http://zhang.bioinformatics.ku.edu/HAAD

Rotation analysis of the B-X 0-1 bands of GaO

The 0-1 band of the B-2 Sigma(+)-X(2) Sigma(+) system of (GaO)-Ga-69-O-16 and (GaO)-Ga-71-O-16 has been measured and rotationally assigned. Principal molecular constants (T-01, B-0, B-1 , B-e , D-0, D-1 , alpha(e) ) have been obtained

New rotational analysis of the B-2 Sigma(+)-X-2 Sigma(+) bands in (GaO)-Ga-69-O-16 and (GaO)-Ga-71-O-16

In the emission spectrum of the (GaO)-O-16 molecule, the 0-0 and 1-0 bands of the B-X system have been rephotographed by means of conventional high-resolution spectroscopy. Clear resolution on the rotational structure near the band origins made it possible to perform reanalysis of the bands and derive new molecular constants characterizing (GaO)-Ga-69-O-16 and (GaO)-Ga-71-O-16 in the B(2)Sigma(+) and X(2)Sigma(+) states, (C) 1999 Academic Press

Computational Prediction and Rationalization, and Experimental Validation of Handedness Induction in Helical Aromatic Oligoamide Foldamers

Metadynamics simulations were used to describe the conformational energy landscapes of several helically folded aromatic quinoline carboxamide oligomers bearing a single chiral group at either the C or Nterminus. The calculations allowed the prediction of whether a helix handedness bias occurs under the influence of the chiral group and gave insight into the interactions (sterics, electrostatics, hydrogen bonds) responsible for a particular helix sense preference. In the case of camphanyl-based and morpholine-based chiral groups, experimental data confirming the validity of the calculations were already available. New chiral groups with a proline residue were also investigated and were predicted to induce handedness. This prediction was verified experimentally through the synthesis of proline-containing monomers, their incorporation into an oligoamide sequence by solid phase synthesis and the investigation of handedness induction by NMR spectroscopy and circular dichroism