The pseudomolecule method and the structure of globular proteins. II. The example of ribonuclease F1 and T1

• Published in: Biopolymers 2001-11, Vol.59 (6), p.402-410
• Main Authors: Peters, David, Peters, Jane
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Biopolymers - chemistry; Conserved Sequence; globular proteins; Hydrogen Bonding; Molecular Sequence Data; Point Mutation; Protein Conformation; pseudomolecule method; ribonuclease F1; ribonuclease T1; Ribonuclease T1 - chemistry; Ribonuclease T1 - genetics; Sequence Homology, Amino Acid; Water - chemistry
• ISSN: 0006-3525; 1097-0282
• DOI: 10.1002/1097-0282(200111)59:6<402::AID-BIP1045>3.0.CO;2-O

The pseudomolecule approach to the structure of globular proteins in which a small number of water molecules are incorporated into the “molecule” is tested again by comparing the ribbon of hydrogen bonds in two proteins, ribonuclease F1 and T1. These two molecules are 59% homologous and have the same backbone conformation both globally and locally. The two ribbons of hydrogen bonds that cover the whole of the backbone are conserved with an accuracy of some 95% providing that allowance is made for the intrusion into one of the pair of such extra factors as the presence of adducts or metal ions, the insertions and the absence of a few water molecules from one of the x‐ray data sets. Without these corrections, the conservation of the ribbon is some 85%. There are 35 conserved hydrogen‐bonding residues, nearly all of which show many unions to the backbone or interactions with the active site. There are 36 point mutations that involve one or two hydrogen‐bonding side chains and nearly all of these have either none or one hydrogen bond to the backbone. These are minor contributors to the ribbon of hydrogen bonds. Of the 71 residues involved in these two categories, all but six fit into the pseudomolecular picture of the structure of globular proteins. The remaining 30 residues almost all contain conserved hydrocarbon side chains that may have a second order effect on the structure through their space filling effects. © 2001 John Wiley & Sons, Inc. Biopolymers 59: 402–410, 2001