Determination of stereospecific assignments, torsion-angle constraints, and rotamer populations in proteins using the program AngleSearch.
A general program, AngleSearch, which calculates coupling constants and interproton distances for any molecular fragment and does a grid search to find torsion angles, rotamer populations, and stereospecific assignments which fit the measured data has been developed. The program takes full advantage of the fact that ratios of cross-peak intensities (measured in HNHB and HN(CO)HB experiments) can provide accurate ratios of coupling constants even for large molecules. AngleSearch is capable of: (a) analyzing any type of residue including protein, RNA, DNA, and ligand residues; (b) conformational grid searching in dihedral-angle space using 6 degree steps; (c) averaging coupling constants and (l/r6) distances for rotamers undergoing fast exchange; (d) grid or Monte Carlo searching for populations of staggered rotamers; (e) using all available distance-related data from ROESY and/or NOESY spectra; (f) using any available coupling constant data having known relationships to corresponding dihedral angles; and (g) directly using cross-peak intensities related to values of coupling constants. The program can also assist in the stereospecific assignment of the alpha-CH2 protons of glycine residues. The effects of the quality of the input data on the results of the AngleSearch calculations have been assessed.
Polshakov
V I
VI
Laboratory of Molecular Structure, National Institute for Medical Research, Mill Hill, London, United Kingdom.
Frenkiel
T A
TA
Birdsall
B
B
Soteriou
A
A
Feeney
J
J
D000409:Alanine / Q000737:chemistry; D000596:Amino Acids / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D002247:Carbon Isotopes; D004247:DNA / Q000737:chemistry; D005998:Glycine / Q000737:chemistry; D007780:Lacticaseibacillus casei / Q000737:chemistry; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D009587:Nitrogen Isotopes; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry; D012399:Rotation; D012984:Software
D000596:Amino Acids; D001426:Bacterial Proteins; D002247:Carbon Isotopes; D008024:Ligands; D009587:Nitrogen Isotopes; D012313:RNA; D004247:DNA; D000409:Alanine; D005998:Glycine