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Thalhammer A, Bröker NK. Biophysical Approaches for the Characterization of Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:199-229. [PMID: 36178628 DOI: 10.1007/978-1-0716-2624-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.
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Affiliation(s)
- Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Potsdam, Germany.
| | - Nina K Bröker
- Physical Biochemistry, University of Potsdam, Potsdam, Germany
- Health and Medical University Potsdam, Potsdam, Germany
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Bondarenko P, Nichols AC, Xiao G, Shi RL, Chan PK, Dillon TM, Garces F, Semin DJ, Ricci MS. Identification of critical chemical modifications and paratope mapping by size exclusion chromatography of stressed antibody-target complexes. MAbs 2021; 13:1887629. [PMID: 33615991 PMCID: PMC7899697 DOI: 10.1080/19420862.2021.1887629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Therapeutic proteins including antibodies and Fc-fusion proteins undergo a large number of chemical modifications during cell culture, purification, storage and in human circulation. They are also exposed to harsh conditions during stress studies, including elevated temperature, extremes of pH, forced oxidation, physiological pH, UV light to assess the possible degradation pathways and suitability of methods for detecting them. Some of these modifications are located on residues in binding regions, leading to loss of binding and potency and classified as critical quality attributes. Currently, criticality of modifications is assessed by a laborious process of collecting antibody fractions from the soft chromatography techniques ion exchange and hydrophobic interaction chromatography and characterizing the fractions one-by-one for potency and chemical modifications. Here, we describe a method for large-scale, parallel identification of all critical chemical modifications in one experiment. In the first step, the antibody is stressed by one or several stress methods. It is then mixed with target protein and separated by size-exclusion chromatography (SEC) on bound antibody-target complex and unbound antibody. Peptide mapping of fractions and statistical analysis are performed to identify modifications on amino acid residues that affect binding. To identify the modifications leading to slight decreases in binding, competitive SEC of antibody and antigen mixtures was developed and described in a companion study by Shi et al, where target protein is provided at lower level, below the stoichiometry. The newly described method was successfully correlated to crystallography for assessing criticality of chemical modifications and paratope mapping. It is more sensitive to low-level modifications, better streamlined and platform ready.
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Affiliation(s)
- Pavel Bondarenko
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Andrew C Nichols
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Gang Xiao
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Rachel Liuqing Shi
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Pik Kay Chan
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Thomas M Dillon
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Fernando Garces
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc , Thousand Oaks, CA, USA
| | - David J Semin
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Margaret S Ricci
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
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