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Mckerchar HJ, Lento C, Bennie RZ, Crowther JM, Dolamore F, Dyer JM, Clerens S, Mercadante D, Wilson DJ, Dobson RCJ. The protein dynamics of bovine and caprine β-lactoglobulin differ as a function of pH. Food Chem 2023; 408:135229. [PMID: 36563618 DOI: 10.1016/j.foodchem.2022.135229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/28/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
The properties of milk proteins differ between mammalian species. β-Lactoglobulin (βlg) proteins from caprine and bovine milk are sequentially and structurally highly similar, yet their physicochemical properties differ, particularly in response to pH. To resolve this conundrum, we compared the dynamics of both the monomeric and dimeric states for each homologue at pH 6.9 and 7.5 using hydrogen/deuterium exchange experiments. At pH 7.5, the rate of exchange is similar across both homologues, but at pH 6.9 the dimeric states of the bovine βlg B variant homologue have significantly more conformational flexibility compared with caprine βlg. Molecular dynamics simulations provide a mechanistic rationale for the experimental observations, revealing that variant-specific substitutions encode different conformational ensembles with different dynamic properties consistent with the hydrogen/deuterium exchange experiments. Understanding the dynamic differences across βlg homologues is essential to understand the different responses of these milks to processing, human digestion, and differences in immunogenicity.
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Affiliation(s)
- Hannah J Mckerchar
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Riddet Institute, based at Massey University, Palmerston North 4442, New Zealand; Protein and Metabolites Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Rachel Z Bennie
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jennifer M Crowther
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Fabian Dolamore
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jolon M Dyer
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; The New Zealand Institute for Plant and Food Research, Lincoln Research Centre, Lincoln 7608, New Zealand; Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln 7647, New Zealand
| | - Stefan Clerens
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Riddet Institute, based at Massey University, Palmerston North 4442, New Zealand; Protein and Metabolites Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada; Centre for Research in Mass Spectrometry, Toronto, Ontario M3J 1P3, Canada
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Riddet Institute, based at Massey University, Palmerston North 4442, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia.
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da Rocha L, Baptista AM, Campos SRR. Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the Dimerization of β-Lactoglobulin. J Chem Theory Comput 2022; 18:1982-2001. [PMID: 35171602 PMCID: PMC9775224 DOI: 10.1021/acs.jctc.1c01187] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein-protein association is often mediated by electrostatic interactions and modulated by pH. However, experimental and computational studies have often overlooked the effect of association on the protonation state of the protein. In this work, we present a methodological approach based on constant-pH molecular dynamics (MD), which aims to provide a detailed description of a pH-dependent protein-protein association, and apply it to the dimerization of β-lactoglobulin (BLG). A selection of analyses is performed using the data generated by constant-pH MD simulations of monomeric and dimeric forms of bovine BLG, in the pH range 3-8. First, we estimate free energies of dimerization using a computationally inexpensive approach based on the Wyman-Tanford linkage theory, calculated in a new way through the use of thermodynamically based splines. The individual free energy contribution of each titratable site is also calculated, allowing for identification of relevant residues. Second, the correlations between the proton occupancies of pairs of sites are calculated (using the Pearson coefficient), and extensive networks of correlated sites are observed at acidic pH values, sometimes involving distant pairs. In general, strongly correlated sites are also slow proton exchangers and contribute significantly to the pH-dependency of the dimerization free energy. Third, we use ionic density as a fingerprint of protein charge distribution and observe electrostatic complementarity between the monomer faces that form the dimer interface, more markedly at the isoionic point (where maximum dimerization occurs) than at other pH values, which might contribute to guide the association. Finally, the pH-dependent dimerization modes are inspected using PCA, among other analyses, and two states are identified: a relaxed state at pH 4-8 (with the typical alignment of the crystallographic structure) and a compact state at pH 3-4 (with a tighter association and rotated alignment). This work shows that an approach based on constant-pH MD simulations can produce rich detailed pictures of pH-dependent protein associations, as illustrated for BLG dimerization.
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Analytical ultracentrifugation: still the gold standard that offers multiple solutions. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 49:673-676. [PMID: 33211149 DOI: 10.1007/s00249-020-01483-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding the nature of macromolecules and their interactions in solution underpins many fields, including biology, chemistry and materials science. The 24th International Analytical Ultracentrifugation Workshop and Symposium (AUC2019, held in Christchurch, New Zealand, August 2019), brought together 77 international delegates to highlight recent developments in the field. There was a focus on analytical ultracentrifugation, although we recognise that this is but one of the key methods in the biophysicist's toolkit. Many of the presentations showcased the versatility of analytical ultracentrifugation and how such experiments are integrated with other solution techniques, such as small-angle X-ray scattering, cryo-electron microscopy, isothermal titration calorimetry and more. This special issue emphasises a wide range of themes covered in the meeting, including carbohydrate chemistry, protein chemistry, polymer science, and macromolecular interactions.
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Sawyer L. β-Lactoglobulin and Glycodelin: Two Sides of the Same Coin? Front Physiol 2021; 12:678080. [PMID: 34093238 PMCID: PMC8173191 DOI: 10.3389/fphys.2021.678080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/14/2021] [Indexed: 12/22/2022] Open
Abstract
The two lipocalins, β-lactoglobulin (βLg) and glycodelin (Gd), are possibly the most closely related members of the large and widely distributed lipocalin family, yet their functions appear to be substantially different. Indeed, the function of β-lactoglobulin, a major component of ruminant milk, is still unclear although neonatal nutrition is clearly important. On the other hand, glycodelin has several specific functions in reproduction conferred through distinct, tissue specific glycosylation of the polypeptide backbone. It is also associated with some cancer outcomes. The glycodelin gene, PAEP, reflecting one of its names, progestagen-associated endometrial protein, is expressed in many though not all primates, but the name has now also been adopted for the β-lactoglobulin gene (HGNC, www.genenames.org). After a general overview of the two proteins in the context of the lipocalin family, this review considers the properties of each in the light of their physiological functional significance, supplementing earlier reviews to include studies from the past decade. While the biological function of glycodelin is reasonably well defined, that of β-lactoglobulin remains elusive.
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Affiliation(s)
- Lindsay Sawyer
- School of Biological Sciences, IQB3, The University of Edinburgh, Edinburgh, United Kingdom
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