Design for Solubility May Reveal Induction of Amide Hydrogen/Deuterium Exchange by Protein Self-Association. 2022

Kyle Trainor, and Colleen M Doyle, and Avril Metcalfe-Roach, and Julia Steckner, and Daša Lipovšek, and Heather Malakian, and David Langley, and Stanley R Krystek, and Elizabeth M Meiering
Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada.

Structural heterogeneity often constrains the characterization of aggregating proteins to indirect or low-resolution methods, obscuring mechanistic details of association. Here, we report progress in understanding the aggregation of Adnectins, engineered binding proteins with an immunoglobulin-like fold. We rationally design Adnectin solubility and measure amide hydrogen/deuterium exchange (HDX) under conditions that permit transient protein self-association. Protein-protein binding commonly slows rates of HDX; in contrast, we find that Adnectin association may induce faster HDX for certain amides, particularly in the C-terminal β-strand. In aggregation-prone proteins, we identify a pattern of very different rates of amide HDX for residues linked by reciprocal hydrogen bonds in the native structure. These results may be explained by local loss of native structure and formation of an inter-protein interface. Amide HDX induced by self-association, detected here by deliberate modulation of propensity for such interactions, may be a general phenomenon with the potential to expose mechanisms of aggregation by diverse proteins.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D011485 Protein Binding The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments. Plasma Protein Binding Capacity,Binding, Protein
D011506 Proteins Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. Gene Products, Protein,Gene Proteins,Protein,Protein Gene Products,Proteins, Gene
D003903 Deuterium The stable isotope of hydrogen. It has one neutron and one proton in the nucleus. Deuterons,Hydrogen-2,Hydrogen 2
D006859 Hydrogen The first chemical element in the periodic table with atomic symbol H, and atomic number 1. Protium (atomic weight 1) is by far the most common hydrogen isotope. Hydrogen also exists as the stable isotope DEUTERIUM (atomic weight 2) and the radioactive isotope TRITIUM (atomic weight 3). Hydrogen forms into a diatomic molecule at room temperature and appears as a highly flammable colorless and odorless gas. Protium,Hydrogen-1
D006860 Hydrogen Bonding A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds. Hydrogen Bonds,Bond, Hydrogen,Hydrogen Bond
D000577 Amides Organic compounds containing the -CO-NH2 radical. Amides are derived from acids by replacement of -OH by -NH2 or from ammonia by the replacement of H by an acyl group. (From Grant & Hackh's Chemical Dictionary, 5th ed) Amide
D000595 Amino Acid Sequence The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION. Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D012995 Solubility The ability of a substance to be dissolved, i.e. to form a solution with another substance. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Solubilities

Related Publications

Kyle Trainor, and Colleen M Doyle, and Avril Metcalfe-Roach, and Julia Steckner, and Daša Lipovšek, and Heather Malakian, and David Langley, and Stanley R Krystek, and Elizabeth M Meiering
January 2002, Rapid communications in mass spectrometry : RCM,
Kyle Trainor, and Colleen M Doyle, and Avril Metcalfe-Roach, and Julia Steckner, and Daša Lipovšek, and Heather Malakian, and David Langley, and Stanley R Krystek, and Elizabeth M Meiering
August 2019, Rapid communications in mass spectrometry : RCM,
Kyle Trainor, and Colleen M Doyle, and Avril Metcalfe-Roach, and Julia Steckner, and Daša Lipovšek, and Heather Malakian, and David Langley, and Stanley R Krystek, and Elizabeth M Meiering
June 1965, Journal of the American Chemical Society,
Kyle Trainor, and Colleen M Doyle, and Avril Metcalfe-Roach, and Julia Steckner, and Daša Lipovšek, and Heather Malakian, and David Langley, and Stanley R Krystek, and Elizabeth M Meiering
December 2008, The Journal of biological chemistry,
Kyle Trainor, and Colleen M Doyle, and Avril Metcalfe-Roach, and Julia Steckner, and Daša Lipovšek, and Heather Malakian, and David Langley, and Stanley R Krystek, and Elizabeth M Meiering
September 2009, Proteins,
Kyle Trainor, and Colleen M Doyle, and Avril Metcalfe-Roach, and Julia Steckner, and Daša Lipovšek, and Heather Malakian, and David Langley, and Stanley R Krystek, and Elizabeth M Meiering
September 2022, Analytical biochemistry,
Kyle Trainor, and Colleen M Doyle, and Avril Metcalfe-Roach, and Julia Steckner, and Daša Lipovšek, and Heather Malakian, and David Langley, and Stanley R Krystek, and Elizabeth M Meiering
November 1962, Science (New York, N.Y.),
Kyle Trainor, and Colleen M Doyle, and Avril Metcalfe-Roach, and Julia Steckner, and Daša Lipovšek, and Heather Malakian, and David Langley, and Stanley R Krystek, and Elizabeth M Meiering
October 2025, Chemphyschem : a European journal of chemical physics and physical chemistry,
Kyle Trainor, and Colleen M Doyle, and Avril Metcalfe-Roach, and Julia Steckner, and Daša Lipovšek, and Heather Malakian, and David Langley, and Stanley R Krystek, and Elizabeth M Meiering
September 2009, Biochemistry,
Kyle Trainor, and Colleen M Doyle, and Avril Metcalfe-Roach, and Julia Steckner, and Daša Lipovšek, and Heather Malakian, and David Langley, and Stanley R Krystek, and Elizabeth M Meiering
January 2007, Rapid communications in mass spectrometry : RCM,
Copied contents to your clipboard!