1
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Carlos JP, Carlos GC, Sergio AS, Lorena GR, Gabriela RS, Mariano GG, Alma CG. Evaluation of the pH effect on complex formation between bovine β-lactoglobulin and aflatoxin M1: a molecular dynamic simulation and molecular docking study. J Biomol Struct Dyn 2023:1-11. [PMID: 37817538 DOI: 10.1080/07391102.2023.2268178] [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: 07/05/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023]
Abstract
The aim of this work was to evaluate interaction between aflatoxin M1 (AFM1) and structural models of β-lactoglobulin (β-LG) at pH 4.0 and 6.5. This information would provide an explanation of the variability in AFM1 during cheese production. Once β-LG models were optimized using molecular dynamic (MD) simulation, it was found that a region of the Calyx cavity underwent conformational changes, at the E-F loop, from the closed conformation at pH 6.5 to the open at pH 4.0. No differences in Site C conformation were observed at both pH. The binding free energy (ΔGb) of the β-LG-AFM1 complexes at the different pHs were determined by molecular docking. The ΔGb values obtained for the Calyx cavity showed that at pH 4.0 there is a more stable complex formation compared to pH 6.5 with values of -42.6 and -32.0 kJ mol-1, respectively. On the contrary, in the complexes formed in Site C at both pH´s there were no differences. Likewise, the ΔGb in the dimer interface was evaluated, obtaining a value of -29.3 kJ mol-1, like those obtained at Site C. In addition, by the MD simulations of the β-LG-AFM1 complexes, it was observed that at acidic pH the binding of AFM1 with β-LG is more stable. In conclusion, the computational tools showed that the most stable complex was formed at the Calyx cavity at pH 4.0. This suggests that during cheese production using acidic coagulation, the whey proteins show higher affinity toward AFM1 which may explain the observed variability of mycotoxin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiménez-Pérez Carlos
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, México, México
| | - Gómez-Castro Carlos
- Área Académica de Química, Universidad Autónoma del Estado de Hidalgo, Unidad Universitaria, Pachuca-Hidalgo, México
| | | | - Gómez-Ruiz Lorena
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, México, México
| | | | - García-Garibay Mariano
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, México, México
- Departamento de Ciencias de la Alimentación, Universidad Autónoma Metropolitana-Lerma. Av, México, México
| | - Cruz-Guerrero Alma
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, México, México
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2
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Bonarek P, Mularczyk D, Loch JI, Kurpiewska K, Dziedzicka-Wasylewska M. β-Lactoglobulin variants as potential carriers of pramoxine: Comprehensive structural and biophysical studies. J Mol Recognit 2023; 36:e3052. [PMID: 37610054 DOI: 10.1002/jmr.3052] [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] [Received: 04/12/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
β-Lactoglobulin (BLG) is a member of the lipocalin family. As other proteins from this group, BLG can be modified to bind specifically compounds of medical interests. The aim of this study was to evaluate the role of two mutations, L39Y and L58F, in the binding of topical anesthetic pramoxine (PRM) to β-lactoglobulin. Circular dichroism spectroscopy, isothermal titration calorimetry (ITC), and X-ray crystallography were used to understand the mechanisms of BLG-PRM interactions. Studies were performed for three new BLG mutants: L39Y, L58F, and L39Y/L58F. ITC measurements indicated a significant increase in the affinity to the PRM of variants L58F and L39Y. Measurements taken for the double mutant L39Y/L58F showed the additivity of two mutations leading to about 80-fold increase in the affinity to PRM in comparison to natural protein BLG from bovine milk. The determined crystal structures revealed that pramoxine is accommodated in the β-barrel interior of BLG mutants and stabilized by hydrophobic interactions. The observed additive effect of two mutations on drug binding opens the possibility for further designing of new BLG variants with high affinity to selected drugs.
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Affiliation(s)
- Piotr Bonarek
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
| | - Dorota Mularczyk
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
| | - Joanna I Loch
- Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Jagiellonian University, Kraków, Poland
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Jagiellonian University, Kraków, Poland
| | - Marta Dziedzicka-Wasylewska
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
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3
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Madsen M, Prestel A, Madland E, Westh P, Tøndervik A, Sletta H, Peters GHJ, Aachmann FL, Kragelund BB, Svensson B. Molecular insights into alginate β-lactoglobulin A multivalencies-The foundation for their amorphous aggregates and coacervation. Protein Sci 2023; 32:e4556. [PMID: 36571497 PMCID: PMC9847093 DOI: 10.1002/pro.4556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/06/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
For improved control of biomaterial property design, a better understanding of complex coacervation involving anionic polysaccharides and proteins is needed. Here, we address the initial steps in condensate formation of β-lactoglobulin A (β-LgA) with nine defined alginate oligosaccharides (AOSs) and describe their multivalent interactions in structural detail. Binding of AOSs containing four, five, or six uronic acid residues (UARs), either all mannuronate (M), all guluronate (G), or alternating M and G embodying the block structural components of alginates, was characterized by isothermal titration calorimetry, nuclear magnetic resonance spectroscopy (NMR), and molecular docking. β-LgA was highly multivalent exhibiting binding stoichiometries decreasing from five to two AOSs with increasing degree of polymerization (DP) and similar affinities in the mid micromolar range. The different AOS binding sites on β-LgA were identified by NMR chemical shift perturbation analyses and showed diverse compositions of charged, polar and hydrophobic residues. Distinct sites for the shorter AOSs merged to accommodate longer AOSs. The AOSs bound dynamically to β-LgA, as concluded from saturation transfer difference and 1 H-ligand-targeted NMR analyses. Molecular docking using Glide within the Schrödinger suite 2016-1 revealed the orientation of AOSs to only vary slightly at the preferred β-LgA binding site resulting in similar XP glide scores. The multivalency coupled with highly dynamic AOS binding with lack of confined conformations in the β-LgA complexes may help explain the first steps toward disordered β-LgA alginate coacervate structures.
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Affiliation(s)
- Mikkel Madsen
- Enzyme and Protein Chemistry, Department of Biotechnology and BiomedicineTechnical University of DenmarkKgs. LyngbyDenmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Eva Madland
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food ScienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Peter Westh
- Interfacial Enzymology, Department of Biotechnology and BiomedicineTechnical University of DenmarkKgs. LyngbyDenmark
| | - Anne Tøndervik
- Department of Biotechnology and Nanomedicine, SINTEF IndustryTrondheimNorway
| | - Håvard Sletta
- Department of Biotechnology and Nanomedicine, SINTEF IndustryTrondheimNorway
| | - Günther H. J. Peters
- Biophysical and Biomedicinal Chemistry, Department of ChemistryTechnical University of DenmarkKgs. LyngbyDenmark
| | - Finn L. Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food ScienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and BiomedicineTechnical University of DenmarkKgs. LyngbyDenmark
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4
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Zhang W, Guan H, Huang D, Zou H, Li D. Effects of preheating temperatures on
β
‐lactoglobulin structure and binding interaction with dihydromyricetin. EFOOD 2022. [DOI: 10.1002/efd2.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Wenyuan Zhang
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian China
| | - Hui Guan
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian China
| | - Dongjie Huang
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian China
| | - Hui Zou
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian China
| | - Dapeng Li
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian China
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5
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Solution behavior of native and denatured beta lactoglobulin in presence of pyridinium based ionic liquids: A biophysical perspective of folding and refolding pattern of the protein. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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6
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Loch JI, Barciszewski J, Śliwiak J, Bonarek P, Wróbel P, Pokrywka K, Shabalin IG, Minor W, Jaskolski M, Lewiński K. New ligand-binding sites identified in the crystal structures of β-lactoglobulin complexes with desipramine. IUCRJ 2022; 9:386-398. [PMID: 35546795 PMCID: PMC9067113 DOI: 10.1107/s2052252522004183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
The homodimeric β-lactoglobulin belongs to the lipocalin family of proteins that transport a wide range of hydrophobic molecules and can be modified by mutagenesis to develop specificity for novel groups of ligands. In this work, new lactoglobulin variants, FAF (I56F/L39A/M107F) and FAW (I56F/L39A/M107W), were produced and their interactions with the tricyclic drug desipramine (DSM) were studied using X-ray crystallography, calorimetry (ITC) and circular dichroism (CD). The ITC and CD data showed micromolar affinity of the mutants for DSM and interactions according to the classical one-site binding model. However, the crystal structures unambiguously showed that the FAF and FAW dimers are capable of binding DSM not only inside the β-barrel as expected, but also at the dimer interface and at the entrance to the binding pocket. The presented high-resolution crystal structures therefore provide important evidence of the existence of alternative ligand-binding sites in the β-lactoglobulin molecule. Analysis of the crystal structures highlighted the importance of shape complementarity for ligand recognition and selectivity. The binding sites identified in the crystal structures of the FAF-DSM and FAW-DSM complexes together with data from the existing literature are used to establish a systematic classification of the ligand-binding sites in the β-lactoglobulin molecule.
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Affiliation(s)
- Joanna I. Loch
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Jakub Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Joanna Śliwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Piotr Bonarek
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Paulina Wróbel
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Kinga Pokrywka
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Mariusz Jaskolski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Krzysztof Lewiński
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
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7
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Probing the ligand-binding pocket of recombinant β-lactoglobulin: Calorimetric and spectroscopic studies. Biophys Chem 2022; 283:106770. [DOI: 10.1016/j.bpc.2022.106770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/23/2022]
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8
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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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9
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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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10
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Birch J, Khan S, Madsen M, Kjeldsen C, Møller MS, Stender EGP, Peters GJ, Duus JØ, Kragelund BB, Svensson B. Binding Sites for Oligosaccharide Repeats from Lactic Acid Bacteria Exopolysaccharides on Bovine β-Lactoglobulin Identified by NMR Spectroscopy. ACS OMEGA 2021; 6:9039-9052. [PMID: 33842774 PMCID: PMC8028130 DOI: 10.1021/acsomega.1c00060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/11/2021] [Indexed: 05/26/2023]
Abstract
Lactic acid bacterial exopolysaccharides (EPS) are used in the food industry to improve the stability and rheological properties of fermented dairy products. β-Lactoglobulin (BLG), the dominant whey protein in bovine milk, is well known to bind small molecules such as fatty acids, vitamins, and flavors, and to interact with neutral and anionic polysaccharides used in food and pharmaceuticals. While sparse data are available on the affinity of EPS-milk protein interactions, structural information on BLG-EPS complexes, including the EPS binding sites, is completely lacking. Here, binding sites on BLG variant A (BLGA), for oligosaccharides prepared by mild acid hydrolysis of two EPS produced by Streptococcus thermophilus LY03 and Lactobacillus delbrueckii ssp. bulgaricus CNRZ 1187, respectively, are identified by NMR spectroscopy and supplemented by isothermal titration calorimetry (ITC) and molecular docking of complexes. Evidence of two binding sites (site 1 and site 2) on the surface of BLGA is achieved for both oligosaccharides (LY03-OS and 1187-OS) through NMR chemical shift perturbations, revealing multivalency of BLGA for EPS. The affinities of LY03-OS and 1187-OS for BLGA gave K D values in the mM range obtained by both NMR (pH 2.65) and ITC (pH 4.0). Molecular docking suggested that the BLGA and EPS complexes depend on hydrogen bonds and hydrophobic interactions. The findings provide insights into how BLGA engages structurally different EPS-derived oligosaccharides, which may facilitate the design of BLG-EPS complexation, of relevance for formulation of dairy products and improve understanding of BLGA coacervation.
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Affiliation(s)
- Johnny Birch
- Enzyme
and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Sanaullah Khan
- Enzyme
and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Mikkel Madsen
- Enzyme
and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Christian Kjeldsen
- NMR
Spectroscopy, Department of Chemistry, Technical
University of Denmark, Kemitorvet 207, DK-2800 Kgs. Lyngby, Denmark
| | - Marie Sofie Møller
- Enzyme
and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Emil G. P. Stender
- Enzyme
and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Günther
H. J. Peters
- Biophysical
and Biomedicinal Chemistry, Department of Chemistry, Technical University of Denmark, Kemitorvet 206, DK-2800
Kgs. Lyngby, Denmark
| | - Jens Ø. Duus
- NMR
Spectroscopy, Department of Chemistry, Technical
University of Denmark, Kemitorvet 207, DK-2800 Kgs. Lyngby, Denmark
| | - Birthe B. Kragelund
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Birte Svensson
- Enzyme
and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
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11
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Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Arch Biochem Biophys 2021; 699:108750. [PMID: 33421379 DOI: 10.1016/j.abb.2020.108750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 01/14/2023]
Abstract
Bovine β-lactoglobulin, an abundant protein in whey, is a promising nanocarrier for peroral administration of drug-like hydrophobic molecules, a process that involves transit through the different acidic conditions of the human digestive tract. Among the several pH-induced conformational rearrangements that this lipocalin undergoes, the Tanford transition is particularly relevant. This transition, which occurs with a midpoint around neutral pH, involves a conformational change of the E-F loop that regulates accessibility to the primary binding site. The effect of this transition on the ligand binding properties of this protein has scarcely been explored. In this study, we carried out an energetic and structural characterization of β-lactoglobulin molecular recognition at pH values above and below the zone in which the Tanford transition occurs. The combined analysis of crystallographic, calorimetric, and molecular dynamics data sheds new light on the interplay between self-association, ligand binding, and the Tanford pre- and post-transition conformational states, revealing novel aspects underlying the molecular recognition mechanism of this enigmatic lipocalin.
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12
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Small angle X-ray scattering analysis of ligand-bound forms of tetrameric apolipoprotein-D. Biosci Rep 2021; 41:227100. [PMID: 33399852 PMCID: PMC7786332 DOI: 10.1042/bsr20201423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 11/17/2022] Open
Abstract
Human apolipoprotein-D (apoD) is a glycosylated lipocalin that plays a protective role in Alzheimer's disease due to its antioxidant function. Native apoD from human body fluids forms oligomers, predominantly a stable tetramer. As a lipocalin, apoD binds and transports small hydrophobic molecules such as progesterone, palmitic acid and sphingomyelin. Oligomerisation is a common trait in the lipocalin family and is affected by ligand binding in other lipocalins. The crystal structure of monomeric apoD shows no major changes upon progesterone binding. Here, we used small-angle X-ray scattering (SAXS) to investigate the influence of ligand binding and oxidation on apoD oligomerisation and conformation. As a solution-based technique, SAXS is well suited to detect changes in oligomeric state and conformation in response to ligand binding. Our results show no change in oligomeric state of apoD and no major conformational changes or subunit rearrangements in response to binding of ligands or protein oxidation. This highlights the highly stable structure of the native apoD tetramer under various physiologically relevant experimental conditions.
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13
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Broersen K. Milk Processing Affects Structure, Bioavailability and Immunogenicity of β-lactoglobulin. Foods 2020; 9:foods9070874. [PMID: 32635246 PMCID: PMC7404694 DOI: 10.3390/foods9070874] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022] Open
Abstract
Bovine milk is subjected to various processing steps to warrant constant quality and consumer safety. One of these steps is pasteurization, which involves the exposure of liquid milk to a high temperature for a limited amount of time. While such heating effectively ameliorates consumer safety concerns mediated by pathogenic bacteria, these conditions also have an impact on one of the main nutritional whey constituents of milk, the protein β-lactoglobulin. As a function of heating, β-lactoglobulin was shown to become increasingly prone to denaturation, aggregation, and lactose conjugation. This review discusses the implications of such heat-induced modifications on digestion and adsorption in the gastro-intestinal tract, and the responses these conformations elicit from the gastro-intestinal immune system.
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Affiliation(s)
- Kerensa Broersen
- Department of Applied Stem Cell Technologies, TechMed Centre, University of Twente, Postbus 217, 7500 AE Enschede, The Netherlands
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14
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Bonarek P, Loch JI, Tworzydło M, Cooper DR, Milto K, Wróbel P, Kurpiewska K, Lewiński K. Structure-based design approach to rational site-directed mutagenesis of β-lactoglobulin. J Struct Biol 2020; 210:107493. [PMID: 32169624 DOI: 10.1016/j.jsb.2020.107493] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/30/2022]
Abstract
Recombinant proteins play an important role in medicine and have diverse applications in industrial biotechnology. Lactoglobulin has shown great potential for use in targeted drug delivery and body fluid detoxification because of its ability to bind a variety of molecules. In order to modify the biophysical properties of β-lactoglobulin, a series of single-site mutations were designed using a structure-based approach. A 3-dimensional structure alignment of homologous molecules led to the design of nine β-lactoglobulin variants with mutations introduced in the binding pocket region. Seven stable and correctly folded variants (L39Y, I56F, L58F, V92F, V92Y, F105L, M107L) were thoroughly characterized by fluorescence, circular dichroism, isothermal titration calorimetry, size-exclusion chromatography, and X-ray structural investigations. The effects of the amino acid substitutions were observed as slight rearrangements of the binding pocket geometry, but they also significantly influenced the global properties of the protein. Most of the mutations increased the thermal/chemical stability without altering the dimerization constant or pH-dependent conformational behavior. The crystal structures reveal that the I56F and F105L mutations reduced the depth of the binding pocket, which is advantageous since it can reduce the affinity to endogenous fatty acids. The F105L mutant created a unique binding mode for a fatty acid, supporting the idea that lactoglobulin can be altered to bind unique molecules. Selected variants possessing a unique combination of their individual properties can be used for further, more advanced mutagenesis, and the presented results support further research using β-lactoglobulin as a therapeutic delivery agent or a blood detoxifying molecule.
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Affiliation(s)
- Piotr Bonarek
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa 7, 30-387 Kraków, Poland
| | - Joanna I Loch
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Magdalena Tworzydło
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa 7, 30-387 Kraków, Poland
| | - David R Cooper
- University of Virginia, Department of Molecular Physiology and Biological Physics, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Katažyna Milto
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa 7, 30-387 Kraków, Poland
| | - Paulina Wróbel
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Katarzyna Kurpiewska
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Krzysztof Lewiński
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland.
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15
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Rizzuti B, Bartucci R, Guzzi R. Effects of Polar Head Nature and Tail Length of Single-Chain Lipids on the Conformational Stability of β-Lactoglobulin. J Phys Chem B 2020; 124:944-952. [PMID: 31968169 DOI: 10.1021/acs.jpcb.9b09925] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interaction between β-lactoglobulin and single-chain lipids, differing for either the length of the aliphatic chain or the molecular properties of the headgroup, was investigated at neutral and acidic pH to determine the impact on the thermal stability of the protein. Differential scanning calorimetry results with different fatty acids (from C10:0 to C18:0) show a correlation of both melting temperature and unfolding enthalpy of the protein with the ligand binding affinity, and the maximum effect was found for palmitic acid (PLM). The influence of the lipid polar head was investigated by comparing PLM with lyso-palmitoylphosphatidylcholine (LPC), which possesses the same aliphatic chain. At neutral pH, the stabilizing effect of LPC is less favorable compared to PLM. However, fluorescence results revealed that LPC can bind into the protein calyx even at acidic pH, at variance with fatty acids. Molecular dynamics simulations indicated that this difference is due to the ability of the polar head of LPC to interact with the protein loop that regulates the shift (Tanford transition) between open and closed state of the binding site of β-lactoglobulin. The results provide a rationale for how a ligand has the ability to access the protein active site at acidic conditions by overcoming the Tanford transition, and they demonstrate that β-lactoglobulin can deliver ligands with tailored properties of the polar head in a wide pH range.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics , University of Calabria , 87036 Rende , Italy
| | - Rosa Bartucci
- Department of Chemistry and Chemical Technologies and Molecular Biophysics Laboratory , University of Calabria , 87036 Rende , Italy
| | - Rita Guzzi
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics , University of Calabria , 87036 Rende , Italy.,Department of Physics, Molecular Biophysics Laboratory , University of Calabria , 87036 Rende , Italy
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16
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Gómez-Velasco H, Rojo-Domínguez A, García-Hernández E. Enthalpically-driven ligand recognition and cavity solvation of bovine odorant binding protein. Biophys Chem 2020; 257:106315. [DOI: 10.1016/j.bpc.2019.106315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/05/2019] [Accepted: 12/08/2019] [Indexed: 11/29/2022]
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17
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Rodrigues RM, Claro B, Bastos M, Pereira RN, Vicente AA, Petersen SB. Multi-step thermally induced transitions of β-lactoglobulin – An in situ spectroscopy approach. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2019.104562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Singh R, Meena NK, Das T, Sharma RD, Prakash A, Lynn AM. Delineating the conformational dynamics of intermediate structures on the unfolding pathway of β-lactoglobulin in aqueous urea and dimethyl sulfoxide. J Biomol Struct Dyn 2019; 38:5027-5036. [PMID: 31744390 DOI: 10.1080/07391102.2019.1695669] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The funnel shaped energy landscape model of the protein folding suggests that progression of folding proceeds through multiple pathways, having the multiple intermediates which leads to multidimensional free-energy surface. Herein, we applied all-atom MD simulation to conduct a comparative study on the structure of β-lactoglobulin (β-LgA) in aqueous mixture of 8 M urea and 8 M dimethyl sulfoxide (DMSO), at different temperatures. The cumulative results of multiple simulations suggest a common unfolding pathway of β-LgA, occurred through the stable and meta-stable intermediates (I), in both urea and DMSO. However, the free-energy landscape (FEL) analyses show that the structural transitions of I-states are energetically different. In urea, FEL shows distinct ensemble of intermediates, I1 and I2, separated by the energy barrier of ∼3.0 kcal mol-1. Similarly, we find the population of two distinct I1 and I2 states in DMSO, however, the I1 appeared transiently around ∼30-35 ns and is short-lived. But, the I2 ensemble is observed structurally compact and long-lived (∼50-150 ns) as compared to unfolding in urea. Furthermore, the I1 and I2 are separated through a high energy barrier of ∼6.0 kcal mol-1. Thus, our results provide the structural insights of intermediates which essentially bear the signature of a different unfolding pathway of β-LgA in urea and DMSO.Abbreviationsβ-LgAβ-lactoglobulinDMSOdimethyl sulfoxideFELfree-energy landscapeGdmClguanidinium chlorideIintermediate stateMGmolten globule statePMEparticle mesh EwaldQfraction of native contactsRMSDroot mean square deviationRMSFroot mean square fluctuationRgradius of gyrationSASAsolvent Accessible Surface AreascSASAthe side chain SASATrptryptophanCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ruhar Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naveen Kumar Meena
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Trishala Das
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Datta Sharma
- Amity Institute of Integrative Sciences and Health, Amity University, Haryana, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University, Haryana, India
| | - Andrew M Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Nnyigide OS, Lee SG, Hyun K. In Silico Characterization of the Binding Modes of Surfactants with Bovine Serum Albumin. Sci Rep 2019; 9:10643. [PMID: 31337814 PMCID: PMC6650617 DOI: 10.1038/s41598-019-47135-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 07/09/2019] [Indexed: 01/10/2023] Open
Abstract
The binding interactions of the surfactants: anionic sodium dodecyl sulphate (SDS), cationic cetyltrimethylammonium bromide (CTAB), non-ionic octyl glucoside (OG), and zwitterionic 3-[Hexadecyl(dimethyl)ammonio]-1-propanesulfonate (HPS), with bovine serum albumin (BSA) were investigated by computer simulation. The results disclosed that the surfactants bound stably between hydrophobic subdomain IIA and IIIA where tryptophan-213 residue, an important intrinsic fluorophore in BSA is housed. The interactions of the surfactants with the BSA were electrostatic and hydrophobic interactions. The head-groups of SDS, HPS and OG formed hydrogen bonds with the BSA, while that of CTAB was shielded from intermolecular hydrogen-bonding due to intervening methyl groups. Subsequently, molecular dynamics (MD) simulation of the protein-surfactant complexes revealed that hydrogen bonds formed by OG were stronger than those of SDS and HPS. However, the decomposed force-field energies showed that OG had the least interaction energy with the BSA. In addition to MD simulation, it was found by density functional theory (DFT) that the differences in the coulomb interaction energies can be attributed to charge distribution in the surfactants. Overall, free energies calculated by linear interaction energy (LIE) proved that the binding of each surfactant was dominated by differences between van der Waals interactions in bound and free states.
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Affiliation(s)
- Osita Sunday Nnyigide
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Korea
| | - Sun-Gu Lee
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Korea.
| | - Kyu Hyun
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Korea.
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20
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Pandey P, Meena NK, Prakash A, Kumar V, Lynn AM, Ahmad F. Characterization of heterogeneous intermediate ensembles on the guanidinium chloride-induced unfolding pathway of β-lactoglobulin. J Biomol Struct Dyn 2019; 38:1042-1053. [PMID: 30880641 DOI: 10.1080/07391102.2019.1593245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Folding pathway of β-LgA (β-lactoglobulin) evolves through the conformational α→β transition. The α→β transition is a molecular hallmark of various neurodegenerative diseases. Thus, β-LgA may serve as a good model for understanding molecular mechanism of protein aggregation involved in neurodegenerative diseases. Here, we studied the conformational dynamics of β-LgA in 6 M GdmCl at different temperatures using MD simulations. Structural order parameters such as RMSD, Rg, SASA, native contacts (Q), hydrophobic distal-matrix and free-energy landscape (FEL) were used to investigate the conformational transitions. Our results show that GdmCl destabilizes secondary and tertiary structure of β-LgA by weakening the hydrophobic interactions and hydrogen bond network. Multidimensional FEL shows the presence of different unfolding intermediates at 400 K. I1 is long-lived intermediate which has mostly intact native secondary structure, but loose tertiary structure. I2 is structurally compact intermediate formed after the partial loss of secondary structure. The transiently and infrequently buried evolution of W19 shows that intermediate conformational ensembles are structurally heterogeneous. We observed that the intermediate conformations are largely stabilized by non-native H-bonds. The outcome of this work provides the molecular details of intermediates trapped due to non-native interactions that may be regarded as pathogenic conformations involved in neurodegenerative diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Preeti Pandey
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naveen Kumar Meena
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Amresh Prakash
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, India
| | - Andrew M Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Faizan Ahmad
- Jamia Millia Islamia, Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
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21
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Rennie ML, Crowley PB. A Thermodynamic Model of Auto‐regulated Protein Assembly by a Supramolecular Scaffold. Chemphyschem 2019; 20:1011-1017. [DOI: 10.1002/cphc.201900153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Martin L. Rennie
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
- Present address: Institute of Molecular Cell and System BiologyUniversity of Glasgow University Avenue Glasgow UK
| | - Peter B. Crowley
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
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22
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Brotzakis ZF, Bolhuis PG. Unbiased Atomistic Insight into the Mechanisms and Solvent Role for Globular Protein Dimer Dissociation. J Phys Chem B 2019; 123:1883-1895. [PMID: 30714378 PMCID: PMC6581425 DOI: 10.1021/acs.jpcb.8b10005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 01/30/2019] [Indexed: 12/18/2022]
Abstract
Association and dissociation of proteins are fundamental processes in nature. Although simple to understand conceptually, the details of the underlying mechanisms and role of the solvent are poorly understood. Here, we investigate the dissociation of the hydrophilic β-lactoglobulin dimer by employing transition path sampling. Analysis of the sampled path ensembles reveals a variety of mechanisms: (1) a direct aligned dissociation (2) a hopping and rebinding transition followed by unbinding, and (3) a sliding transition before unbinding. Reaction coordinate and transition-state analysis predicts that, besides native contact and neighboring salt-bridge interactions, solvent degrees of freedom play an important role in the dissociation process. Bridging waters, hydrogen-bonded to both proteins, support contacts in the native state and nearby lying transition-state regions, whereas they exhibit faster dynamics in further lying transition-state regions, rendering the proteins more mobile and assisting in rebinding. Analysis of the structure and dynamics of the solvent molecules reveals that the dry native interface induces enhanced populations of both disordered hydration water near hydrophilic residues and tetrahedrally ordered hydration water nearby hydrophobic residues. Although not exhaustive, our sampling of rare unbiased reactive molecular dynamics trajectories enhances the understanding of protein dissociation via complex pathways including (multiple) rebinding events.
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Affiliation(s)
| | - P. G. Bolhuis
- Van’t Hoff Institute
for Molecular Sciences, Universiteit van
Amsterdam, Science Park 904, 1090 GD Amsterdam, The Netherlands
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23
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24
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Bonarek P, Polit A. Systematic calorimetric studies of proton exchange associated with binding of beta-lactoglobulin with ligand. Int J Biol Macromol 2018; 120:128-134. [DOI: 10.1016/j.ijbiomac.2018.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 01/05/2023]
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25
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Glasgow BJ, Abduragimov AR. Ligand binding complexes in lipocalins: Underestimation of the stoichiometry parameter (n). BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:1001-1007. [PMID: 30037780 PMCID: PMC6481938 DOI: 10.1016/j.bbapap.2018.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/15/2018] [Accepted: 07/03/2018] [Indexed: 11/18/2022]
Abstract
The stoichiometry of a ligand binding reaction to a protein is given by a parameter (n). The value of this parameter may indicate the presence of protein monomer or dimers in the binding complex. Members of the lipocalin superfamily show variation in the stoichiometry of binding to ligands. In some cases the stoichiometry parameter (n) has been variously reported for the same protein as mono- and multimerization of the complex. Prime examples include retinol binding protein, β lactoglobulin and tear lipocalin, also called lipocalin-1(LCN1). Recent work demonstrated the stoichiometric ratio for ceramide:tear lipocalin varied (range n = 0.3-0.75) by several different methods. The structure of ceramide raises the intriguing possibility of a lipocalin dimer complex with each lipocalin molecule attached to one of the two alkyl chains of ceramide. The stoichiometry of the ceramide-tear lipocalin binding complex was explored in detail using size exclusion chromatography and time resolved fluorescence anisotropy. Both methods showed consistent results that tear lipocalin remains monomeric when bound to ceramide. Delipidation experiments suggest the most likely explanation is that the low 'n' values result from prior occupancy of the binding sites by native ligands. Lipocalins such as tear lipocalin that have numerous binding partners are particularly prone to an underestimated apparent stoichiometry parameter.
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Affiliation(s)
- Ben J Glasgow
- Departments of Ophthalmology, Pathology and Laboratory Medicine, Jules Stein Eye Institute, University of California, Los Angeles, 100 Stein Plaza Rm. BH 623, Los Angeles, CA 90095, United States.
| | - Adil R Abduragimov
- Departments of Ophthalmology, Pathology and Laboratory Medicine, Jules Stein Eye Institute, University of California, Los Angeles, 100 Stein Plaza Rm. BH 623, Los Angeles, CA 90095, United States
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26
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Kielkopf CS, Low JKK, Mok YF, Bhatia S, Palasovski T, Oakley AJ, Whitten AE, Garner B, Brown SHJ. Identification of a novel tetrameric structure for human apolipoprotein-D. J Struct Biol 2018; 203:205-218. [PMID: 29885491 DOI: 10.1016/j.jsb.2018.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/18/2018] [Accepted: 05/30/2018] [Indexed: 10/14/2022]
Abstract
Apolipoprotein-D is a 25 kDa glycosylated member of the lipocalin family that folds into an eight-stranded β-barrel with a single adjacent α-helix. Apolipoprotein-D specifically binds a range of small hydrophobic ligands such as progesterone and arachidonic acid and has an antioxidant function that is in part due to the reduction of peroxidised lipids by methionine-93. Therefore, apolipoprotein-D plays multiple roles throughout the body and is protective in Alzheimer's disease, where apolipoprotein-D overexpression reduces the amyloid-β burden in Alzheimer's disease mouse models. Oligomerisation is a common feature of lipocalins that can influence ligand binding. The native structure of apolipoprotein-D, however, has not been conclusively defined. Apolipoprotein-D is generally described as a monomeric protein, although it dimerises when reducing peroxidised lipids. Here, we investigated the native structure of apolipoprotein-D derived from plasma, breast cyst fluid (BCF) and cerebrospinal fluid. In plasma and cerebrospinal fluid, apolipoprotein-D was present in high-molecular weight complexes, potentially in association with lipoproteins. In contrast, apolipoprotein-D in BCF formed distinct oligomeric species. We assessed apolipoprotein-D oligomerisation using native apolipoprotein-D purified from BCF and a suite of complementary methods, including multi-angle laser light scattering, analytical ultracentrifugation and small-angle X-ray scattering. Our analyses showed that apolipoprotein-D predominantly forms a ∼95 to ∼100 kDa tetramer. Small-angle X-ray scattering analysis confirmed these findings and provided a structural model for apolipoprotein-D tetramer. These data indicate apolipoprotein-D rarely exists as a free monomer under physiological conditions and provide insights into novel native structures of apolipoprotein-D and into oligomerisation behaviour in the lipocalin family.
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Affiliation(s)
- Claudia S Kielkopf
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.
| | - Surabhi Bhatia
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia.
| | - Tony Palasovski
- Illawarra and Shoalhaven Local Health District (ISLHD), Wollongong, NSW, Australia; Specialist Breast Clinic Sutherland Shire and Wollongong, NSW, Australia; Integrated Specialist Health Care Sutherland Shire, NSW, Australia
| | - Aaron J Oakley
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia; School of Chemistry, University of Wollongong, Wollongong, NSW, Australia.
| | - Andrew E Whitten
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia.
| | - Brett Garner
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
| | - Simon H J Brown
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
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27
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Mehraban MH, Odooli S, Yousefi R, Roghanian R, Motovali-Bashi M, Moosavi-Movahedi AA, Ghasemi Y. The interaction of beta-lactoglobulin with ciprofloxacin and kanamycin; a spectroscopic and molecular modeling approach. J Biomol Struct Dyn 2016; 35:1968-1978. [PMID: 27562530 DOI: 10.1080/07391102.2016.1203819] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A vast research has been conducted to find suitable and safe carriers for vital and pH-sensitive drugs including antibiotics. This article reports the use of easily accessible and abundant purified beta-lactoglobulin (β-LG) protein as the potential carrier of widely used Kanamycin (Kana) and Ciprofloxacin (Cip) antibiotics. Spectroscopic techniques (Fluorescence, UV-vis, Circular Dichroism) combined with molecular docking were used to determine the binding mechanism of these drugs. Fluorescence studies showed moderate binding affinity with the calculated binding constants KCip = 60.1 (±0.2) × 103 M-1 and Kkana = 2.5 (±0.6) × 103 M-1 with the order of Cip > Kana. Results of UV-vis were consistent with fluorescence measurements and demonstrated a stronger complexation for Cip rather than Kana. The secondary structure of β-LG was preserved upon interaction with Kana; however, a reduction in β-sheet content from 39.1 to 31.9% was convoyed with an increase in α-helix from 12.8 to 20.5% due to complexation of Cip. Molecular docking studies demonstrated that preferred binding sites of these drugs are not the same and several amino acids are involved in stabilizing the interaction. Based on the achieved results, Kana and Cip can spontaneously bind to β-LG and this protein may serve as their transport vehicle.
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Affiliation(s)
- Mohammad Hossein Mehraban
- a Pharmaceutical Sciences Research Center, School of Pharmacy , Shiraz University of Medical Sciences , Shiraz , Iran.,b Genetics Division, Biology Department , Faculty of Sciences , University of Isfahan , Isfahan , Iran
| | - Salman Odooli
- a Pharmaceutical Sciences Research Center, School of Pharmacy , Shiraz University of Medical Sciences , Shiraz , Iran.,c Department of Biology, Faculty of Sciences , University of Isfahan , Isfahan , Iran
| | - Reza Yousefi
- d Protein Chemistry Laboratory (PCL), Department of Biology , College of Sciences, Shiraz University , Shiraz , Iran
| | - Rasoul Roghanian
- c Department of Biology, Faculty of Sciences , University of Isfahan , Isfahan , Iran
| | - Majid Motovali-Bashi
- b Genetics Division, Biology Department , Faculty of Sciences , University of Isfahan , Isfahan , Iran
| | | | - Younes Ghasemi
- a Pharmaceutical Sciences Research Center, School of Pharmacy , Shiraz University of Medical Sciences , Shiraz , Iran.,f Department of Pharmaceutical Biotechnology , School of Pharmacy, Shiraz University of Medical Sciences , Shiraz , Iran
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28
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Benigni P, Marin R, Molano-Arevalo JC, Garabedian A, Wolff JJ, Ridgeway ME, Park MA, Fernandez-Lima F. Towards the Analysis of High Molecular Weight Proteins and Protein complexes using TIMS-MS. INTERNATIONAL JOURNAL FOR ION MOBILITY SPECTROMETRY : OFFICIAL PUBLICATION OF THE INTERNATIONAL SOCIETY FOR ION MOBILITY SPECTROMETRY 2016; 19:95-104. [PMID: 27818614 PMCID: PMC5091298 DOI: 10.1007/s12127-016-0201-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 05/26/2016] [Accepted: 05/29/2016] [Indexed: 01/02/2023]
Abstract
In the present work, we demonstrate the potential and versatility of TIMS for the analysis of proteins, DNA-protein complexes and protein-protein complexes in their native and denatured states. In addition, we show that accurate CCS measurement are possible and in good agreement with previously reported CCS values using other IMS analyzers (<5% difference). The main challenges for the analysis of high mass proteins and protein complexes in the mobility and m/z domain are described. That is, the analysis of high molecular weight systems in their native state may require the use of higher electric fields or a compromise in the TIMS mobility resolution by reducing the bath gas velocity in order to effectively trap at lower electric fields. This is the first report of CCS measurements of high molecular weight biomolecules and biomolecular complexes (~ 150 kDa) using TIMS-MS.
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Rebecca Marin
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | - Alyssa Garabedian
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
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29
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Li H, Wei J, Dong Y, Yu Z. Interaction between 2-( p-toluidino)-6-naphthalenesulfonic acid sodium salt (TNS) and β-lactoglobulin. CAN J CHEM 2016. [DOI: 10.1139/cjc-2015-0450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The major bovine milk protein β-lactoglobulin (β-LG), a member of the lipocalin superfamily, can bind a wide range of ligands and act as a transporter. In the present study, the combination of the hydrophobic molecule 2-(p-toluidino)-6-naphthalenesulfonic acid sodium salt (TNS) with β-LG was analyzed using fluorescence spectroscopy and AutoDock modeling to discern the major binding sites of the protein and to determine the capacity of other small ligands to bind with β-LG by utilizing TNS as a reference. The experimental data indicate that in a neutral pH environment, TNS is located in the hydrophobic domain of the protein, 2.5 nm away from the Trp19 residues of β-LG. The binding constant of the small molecule to β-LG is (3.30 ± 0.32) × 106 (mol L–1)−1. An interaction model between the ligand and β-LG was developed, and AutoDock modeling also demonstrates that the ligand is located in the central hydrophobic calyx of β-LG within the regions covered by the Förster radius of the Trp19–ligand pair. Although the interaction between the ligand and β-LG is affected by increasing ion strength, pH change, and heat treatment, the complex is maintained until the secondary structure of β-LG is destroyed. Additionally, the ligand binding stabilizes the folding of β-LG. The binding constants of sodium dodecyl sulfate (SDS) and sodium dodecylbenzene sulfonate (SDBS) to β-LG were obtained using competitive ligand binding measurements. With a sensitive fluorescence signal and stable complex, the ligand could be utilized as a reference to detect the binding of other small ligands to β-LG.
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Affiliation(s)
- Huiqing Li
- Chemistry Department, Xinzhou Teachers’ University, Xinzhou, Heping Street, Xinzhou City, PR, China
- Chemistry Department, Xinzhou Teachers’ University, Xinzhou, Heping Street, Xinzhou City, PR, China
| | - Jing Wei
- Chemistry Department, Xinzhou Teachers’ University, Xinzhou, Heping Street, Xinzhou City, PR, China
- Chemistry Department, Xinzhou Teachers’ University, Xinzhou, Heping Street, Xinzhou City, PR, China
| | - Youming Dong
- Chemistry Department, Xinzhou Teachers’ University, Xinzhou, Heping Street, Xinzhou City, PR, China
- Chemistry Department, Xinzhou Teachers’ University, Xinzhou, Heping Street, Xinzhou City, PR, China
| | - Zhiyue Yu
- Chemistry Department, Xinzhou Teachers’ University, Xinzhou, Heping Street, Xinzhou City, PR, China
- Chemistry Department, Xinzhou Teachers’ University, Xinzhou, Heping Street, Xinzhou City, PR, China
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Bello M, Fragoso-Vázquez MJ, Correa Basurto J. Energetic and conformational features linked to the monomeric and dimeric states of bovine BLG. Int J Biol Macromol 2016; 92:625-636. [PMID: 27456117 DOI: 10.1016/j.ijbiomac.2016.07.071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 07/15/2016] [Accepted: 07/21/2016] [Indexed: 11/16/2022]
Abstract
Bovine β-lactoglobulin (BLG) belong to the lipocalin family. This is a group of proteins involved in the binding and transporting of hydrophobic molecules. Experimental and theoretical reports have stated its complex structural behavior in solution, with coupled effects between homodimerization and ligand recognition. Nonetheless, structural evidence at the atomic level about the cause of this coupled effect has not been reported to date. To address this issue microsecond molecular dynamics (MD) simulations were combined with the molecular mechanics generalized Born surface area (MM/GBSA) approach, clustering analysis and principal component analysis (PCA), to explore the conformational complexity of BLG protein-protein self-association and palmitic acid (PLM) or dodecyl sulfate (SDS) ligand recognition in the monomeric and dimeric state. MD simulations, coupled to the MM/GBSA method, revealed that dimerization exerts contrasting effects on the ligand-binding capacity of BLG. Protein dimerization decreases PLM affinity, promoting dimer association. For SDS the dimeric state increases affinity, enhancing dimer dissociation. MD simulations based on PCA revealed that while few differences in the conformational subspace are observed between the free and bound monomer and dimer coupling for PLM, substantial changes are observed between the free and bound monomer and dimer coupling for SDS.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico City CP: 11340, Mexico.
| | - M Jonathan Fragoso-Vázquez
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico City CP: 11340, Mexico
| | - José Correa Basurto
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico City CP: 11340, Mexico
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Bello M. Structural and energetic requirements for a second binding site at the dimeric β-lactoglobulin interface. J Biomol Struct Dyn 2016; 34:1884-902. [DOI: 10.1080/07391102.2015.1094413] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, CP 11340 México, D. F., Mexico
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Engineered β-Lactoglobulin Produced in E. coli: Purification, Biophysical and Structural Characterisation. Mol Biotechnol 2016; 58:605-618. [PMID: 27380951 PMCID: PMC5035327 DOI: 10.1007/s12033-016-9960-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Functional recombinant bovine β-lactoglobulin has been produced by expression in E. coli using an engineered protein gene and purified to homogeneity by applying a new protocol. Mutations L1A/I2S introduced into the protein sequence greatly facilitate in vivo cleavage of the N-terminal methionine, allowing correctly folded and soluble protein suitable for biochemical, biophysical and structural studies to be obtained. The use of gel filtration on Sephadex G75 at the last purification step enables protein without endogenous ligand to be obtained. The physicochemical properties of recombinant β-lactoglobulin such as CD spectra, ligand binding (n, K a, ΔH, TΔS, ΔG), chemical and thermal stability (ΔG D, C mid) and crystal structure confirmed that the protein obtained is almost identical to the natural one. The substitutions of N-terminal residues did not influence the binding properties of the recombinant protein so that the lactoglobulin produced and purified according to our protocol is a good candidate for further engineering and potential use in pharmacology and medicine.
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Sahihi M. In-Silico Study on the Interaction of Saffron Ligands and Beta-Lactoglobulin by Molecular Dynamics and Molecular Docking Approach. J MACROMOL SCI B 2015. [DOI: 10.1080/00222348.2015.1125066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Khosravi I, Heidari-Koholi Z. In Silico Study on the Interaction of Thiazolidinediones and β-Lactoglobulin by Molecular Dynamics and Docking Approach. J MACROMOL SCI B 2015. [DOI: 10.1080/00222348.2015.1061883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Keppler JK, Martin D, Garamus VM, Schwarz K. Differences in binding behavior of (−)-epigallocatechin gallate to β-lactoglobulin heterodimers (AB) compared to homodimers (A) and (B). J Mol Recognit 2015; 28:656-66. [DOI: 10.1002/jmr.2480] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Julia K. Keppler
- Christian-Albrechts-University of Kiel; Institute of Human Nutrition and Food Science, Division of Food Technology; Kiel Germany
| | - Dierk Martin
- Max Rubner-Institut (MRI); Department of Safety and Quality of Milk and Fish Products; Kiel Germany
| | - Vasil M. Garamus
- Helmholtz-Zentrum Geesthacht; Zentrum für Material- und Küstenforschung GmbH; Geesthacht Germany
| | - Karin Schwarz
- Christian-Albrechts-University of Kiel; Institute of Human Nutrition and Food Science, Division of Food Technology; Kiel Germany
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Loch JI, Bonarek P, Polit A, Świątek S, Czub M, Ludwikowska M, Lewiński K. Conformational variability of goat β-lactoglobulin: Crystallographic and thermodynamic studies. Int J Biol Macromol 2015; 72:1283-91. [DOI: 10.1016/j.ijbiomac.2014.10.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
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37
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Lech FJ, Steltenpool P, Meinders MB, Sforza S, Gruppen H, Wierenga PA. Identifying changes in chemical, interfacial and foam properties of β-lactoglobulin–sodium dodecyl sulphate mixtures. Colloids Surf A Physicochem Eng Asp 2014. [DOI: 10.1016/j.colsurfa.2014.08.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Kontopidis G, Nordle Gilliver A, Sawyer L. Ovine β-lactoglobulin at atomic resolution. Acta Crystallogr F Struct Biol Commun 2014; 70:1498-503. [PMID: 25372816 PMCID: PMC4231851 DOI: 10.1107/s2053230x14020950] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 09/19/2014] [Indexed: 11/10/2022] Open
Abstract
The crystal structure of the triclinic form of the milk protein β-lactoglobulin from sheep (Ovis aries) at 1.1 Å resolution is described together with a comparison of the triclinic structures of the low-pH bovine and high-pH ovine proteins. All three structures are remarkably similar, despite the well known pH-dependent conformational transition described for the bovine and porcine proteins that occurs in solution. The high resolution of the present structure determination has allowed a more accurate description of the protein than has hitherto been possible, but it is still not clear whether flexibility changes in the external loops can compensate for the presence of a significant void in the unliganded interior of the structure.
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Affiliation(s)
- George Kontopidis
- Structural Biochemistry Group, Institute of Cell and Molecular Biology, The University of Edinburgh, Swann Building, King’s Buildings, Mayfield Road, Edinburgh EH10 3BF, Scotland
| | - Anna Nordle Gilliver
- Structural Biochemistry Group, Institute of Cell and Molecular Biology, The University of Edinburgh, Swann Building, King’s Buildings, Mayfield Road, Edinburgh EH10 3BF, Scotland
| | - Lindsay Sawyer
- Structural Biochemistry Group, Institute of Cell and Molecular Biology, The University of Edinburgh, Swann Building, King’s Buildings, Mayfield Road, Edinburgh EH10 3BF, Scotland
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Vega S, Abian O, Velazquez-Campoy A. A unified framework based on the binding polynomial for characterizing biological systems by isothermal titration calorimetry. Methods 2014; 76:99-115. [PMID: 25305413 DOI: 10.1016/j.ymeth.2014.09.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 01/10/2023] Open
Abstract
Isothermal titration calorimetry (ITC) has become the gold-standard technique for studying binding processes due to its high precision and sensitivity, as well as its capability for the simultaneous determination of the association equilibrium constant, the binding enthalpy and the binding stoichiometry. The current widespread use of ITC for biological systems has been facilitated by technical advances and the availability of commercial calorimeters. However, the complexity of data analysis for non-standard models is one of the most significant drawbacks in ITC. Many models for studying macromolecular interactions can be found in the literature, but it looks like each biological system requires specific modeling and data analysis approaches. The aim of this article is to solve this lack of unity and provide a unified methodological framework for studying binding interactions by ITC that can be applied to any experimental system. The apparent complexity of this methodology, based on the binding polynomial, is overcome by its easy generalization to complex systems.
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Affiliation(s)
- Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain; IIS Aragón, Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain.
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain; Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain; Fundacion ARAID, Government of Aragon, Spain.
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Keppler JK, Sönnichsen FD, Lorenzen PC, Schwarz K. Differences in heat stability and ligand binding among β-lactoglobulin genetic variants A, B and C using 1H NMR and fluorescence quenching. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1083-93. [DOI: 10.1016/j.bbapap.2014.02.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 01/25/2014] [Accepted: 02/10/2014] [Indexed: 11/25/2022]
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41
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Loch JI, Molenda M, Kopeć M, Świątek S, Lewiński K. Structure of two crystal forms of sheep β‐lactoglobulin with EF‐loop in closed conformation. Biopolymers 2014; 101:886-94. [DOI: 10.1002/bip.22471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/31/2014] [Accepted: 02/07/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Joanna I. Loch
- Department of Crystal Chemistry and Crystal PhysicsFaculty of Chemistry Jagiellonian University in KrakówIngardena 3Kraków30–060 Poland
| | - Marta Molenda
- Department of Crystal Chemistry and Crystal PhysicsFaculty of Chemistry Jagiellonian University in KrakówIngardena 3Kraków30–060 Poland
| | - Magdalena Kopeć
- Department of Crystal Chemistry and Crystal PhysicsFaculty of Chemistry Jagiellonian University in KrakówIngardena 3Kraków30–060 Poland
| | - Sylwia Świątek
- Department of Crystal Chemistry and Crystal PhysicsFaculty of Chemistry Jagiellonian University in KrakówIngardena 3Kraków30–060 Poland
| | - Krzysztof Lewiński
- Department of Crystal Chemistry and Crystal PhysicsFaculty of Chemistry Jagiellonian University in KrakówIngardena 3Kraków30–060 Poland
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42
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Loch JI, Bonarek P, Polit A, Swiątek Ś, Dziedzicka-Wasylewska M, Lewiński K. The differences in binding 12-carbon aliphatic ligands by bovine β-lactoglobulin isoform A and B studied by isothermal titration calorimetry and X-ray crystallography. J Mol Recognit 2014; 26:357-67. [PMID: 23784992 DOI: 10.1002/jmr.2280] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 04/19/2013] [Accepted: 04/21/2013] [Indexed: 01/23/2023]
Abstract
Isoforms A (LGB-A) and B (LGB-B) of bovine lactoglobulin, the milk protein, differ in positions 64 (D↔G) and 118 (V↔A). Interactions of LGB-A and LGB-B with sodium dodecyl sulfate (SDS), dodecyltrimethylammonium chloride (DTAC) and lauric acid (LA), 12-carbon ligands possessing differently charged polar groups, were investigated using isothermal titration calorimetry and X-ray crystallography, to study the proton linkage phenomenon and to distinguish between effects related to different isoforms and different ligand properties. The determined values of ΔS and ΔH revealed that for all ligands, binding is entropically driven. The contribution from enthalpy change is lower and shows strong dependence on type of buffer that indicates proton release from the protein varying with protein isoform and ligand type and involvement of LA and Asp64 (in isoform A) in this process. The ligand affinities for both isoforms were arranged in the same order, DTAC < LA < SDS, and were systematically lower for variant B. The entropy change of the complexation process was always higher for isoform A, but these values were compensated by changes in enthalpy, resulting in almost identical ΔG for complexes of both isoforms. The determined crystal structures showed that substitution in positions 64 and 118 did not influence the overall structure of LGB complexes. The chemical character of the ligand polar group did not affect the position of its aliphatic chain in protein β-barrel, indicating a major role of hydrophobic interactions in ligand binding that prevailed even with the repulsion between positively charged DTAC and lysine residues located at binding site entrance.
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Affiliation(s)
- Joanna I Loch
- Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Ingardena 3, 30-060 Kraków, Poland
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43
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Bello M, García-Hernández E. Ligand entry into the calyx of β-lactoglobulin. Biopolymers 2014; 101:744-57. [DOI: 10.1002/bip.22454] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/06/2013] [Accepted: 12/17/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular y Bioinformática de la Escuela Superior de Medicina; Instituto Politécnico Nacional, México. Plan de San Luis Y Diaz Mirón S/N; Col. Casco de Santo Tomas, 11340 México, D. F. México
| | - Enrique García-Hernández
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; 04360 México, D. F. México
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Engelhardt K, Weichsel U, Kraft E, Segets D, Peukert W, Braunschweig B. Mixed Layers of β-Lactoglobulin and SDS at Air–Water Interfaces with Tunable Intermolecular Interactions. J Phys Chem B 2014; 118:4098-105. [DOI: 10.1021/jp501541q] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Kathrin Engelhardt
- Institute of Particle Technology
(LFG), University of Erlangen-Nuremberg, Cauerstrasse 4, 91058 Erlangen, Germany
| | - Ulrike Weichsel
- Institute of Particle Technology
(LFG), University of Erlangen-Nuremberg, Cauerstrasse 4, 91058 Erlangen, Germany
| | - Elena Kraft
- Institute of Particle Technology
(LFG), University of Erlangen-Nuremberg, Cauerstrasse 4, 91058 Erlangen, Germany
| | - Doris Segets
- Institute of Particle Technology
(LFG), University of Erlangen-Nuremberg, Cauerstrasse 4, 91058 Erlangen, Germany
| | - Wolfgang Peukert
- Institute of Particle Technology
(LFG), University of Erlangen-Nuremberg, Cauerstrasse 4, 91058 Erlangen, Germany
| | - Björn Braunschweig
- Institute of Particle Technology
(LFG), University of Erlangen-Nuremberg, Cauerstrasse 4, 91058 Erlangen, Germany
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Binding study of novel anti-diabetic pyrimidine fused heterocycles to β-lactoglobulin as a carrier protein. Colloids Surf B Biointerfaces 2013; 112:374-9. [DOI: 10.1016/j.colsurfb.2013.08.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 08/02/2013] [Accepted: 08/09/2013] [Indexed: 12/29/2022]
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46
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Banach M, Roterman I, Prudhomme N, Chomilier J. Hydrophobic core in domains of immunoglobulin-like fold. J Biomol Struct Dyn 2013; 32:1583-600. [PMID: 23998258 DOI: 10.1080/07391102.2013.829756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This work analyzes proteins which contain an immunoglobulin fold, focusing on their hydrophobic core structure. The "fuzzy oil drop" model was used to measure the regularity of hydrophobicity distribution in globular domains belonging to proteins which exhibit the above-mentioned fold. Light-chain IgG domains are found to frequently contain regular hydrophobic cores, unlike the corresponding heavy-chain domains. Enzymes and DNA binding proteins present in the data-set are found to exhibit poor accordance with the hydrophobic core model.
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Affiliation(s)
- M Banach
- a Department of Bioinformatics and Telemedicine , Collegium Medicum, Jagiellonian University , Krakow , Poland
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47
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Bello M, Correa-Basurto J, Rudiño-Piñera E. Simulation of the cavity-binding site of three bacterial multicopper oxidases upon complex stabilization: interactional profile and electron transference pathways. J Biomol Struct Dyn 2013; 32:1303-17. [DOI: 10.1080/07391102.2013.817954] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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