Predicting the magnitude of the reflex response to insertions in ubiquitin.
The ability to predict the structural response of a protein to an insertion would be a significant advance for the fields of homology modeling and protein design. However, the effects of insertions on protein conformation are not well understood. Previous work has demonstrated that for two loops in ubiquitin, the primary determinant of the structural adaptation to insertions is the insertion site rather than the sequence of the insertion; this phenomenon was termed the reflex response of loops to insertions. We report herein the analysis of ubiquitin mutants with insertions in two other loops. This study demonstrates that the insertion site is the primary determinant of the response to insertions for these two new loops as well, which further supports the reflex response hypothesis. We also attempted to predict the relative magnitudes of the responses at each site but were unsuccessful. Using the additional data collected in this work, we have refined our predictive hypothesis.
Ferraro
Debra M
DM
Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
Robertson
Andrew D
AD
D000595:Amino Acid Sequence; D006859:Hydrogen / Q000378:metabolism; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D016254:Mutagenesis, Insertional; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular; D016133:Polymerase Chain Reaction; D011237:Predictive Value of Tests; D011487:Protein Conformation; D015202:Protein Engineering; D017433:Protein Structure, Secondary; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013696:Temperature; D013698:Templates, Genetic; D025801:Ubiquitin / Q000737:chemistry / Q000235:genetics*
D025801:Ubiquitin; D006859:Hydrogen