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Jang YJ, Qin QQ, Huang SY, Peter ATJ, Ding XM, Kornmann B. Accurate prediction of protein function using statistics-informed graph networks. Nat Commun 2024; 15:6601. [PMID: 39097570 PMCID: PMC11297950 DOI: 10.1038/s41467-024-50955-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/15/2024] [Indexed: 08/05/2024] Open
Abstract
Understanding protein function is pivotal in comprehending the intricate mechanisms that underlie many crucial biological activities, with far-reaching implications in the fields of medicine, biotechnology, and drug development. However, more than 200 million proteins remain uncharacterized, and computational efforts heavily rely on protein structural information to predict annotations of varying quality. Here, we present a method that utilizes statistics-informed graph networks to predict protein functions solely from its sequence. Our method inherently characterizes evolutionary signatures, allowing for a quantitative assessment of the significance of residues that carry out specific functions. PhiGnet not only demonstrates superior performance compared to alternative approaches but also narrows the sequence-function gap, even in the absence of structural information. Our findings indicate that applying deep learning to evolutionary data can highlight functional sites at the residue level, providing valuable support for interpreting both existing properties and new functionalities of proteins in research and biomedicine.
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Affiliation(s)
- Yaan J Jang
- Department of Biochemistry, University of Oxford, Oxford, UK.
- AmoAi Technologies, Oxford, UK.
| | - Qi-Qi Qin
- AmoAi Technologies, Oxford, UK
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Si-Yu Huang
- AmoAi Technologies, Oxford, UK
- Oxford Martin School, University of Oxford, Oxford, UK
- School of Systems Science, Beijing Normal University, Beijing, China
| | | | - Xue-Ming Ding
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Benoît Kornmann
- Department of Biochemistry, University of Oxford, Oxford, UK.
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2
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Ghanta KP, Bandyopadhyay S. Counteraction Effects of Ammonium-Based Ionic Liquids on Urea-Induced Denaturation of α-Lactalbumin: A Comprehensive Molecular Simulation Study. J Phys Chem B 2023; 127:7251-7265. [PMID: 37574910 DOI: 10.1021/acs.jpcb.3c03223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Ionic liquids (ILs) are known to stabilize protein conformations in aqueous medium. Importantly, ILs can also act as refolding additives in urea-driven denaturation of proteins. However, despite the importance of the problem, detailed microscopic understanding of the counteraction effects of ILs on urea-induced protein denaturation remains elusive. In this work, atomistic molecular dynamics (MD) simulations of the protein α-lactalbumin have been carried out in pure aqueous medium, in 8 M binary urea-water solution and in ternary urea-IL-water solutions containing ammonium-based ethyl ammonium acetate (EAA) as the IL at different concentrations (1-4 M). Attempts have been made to quantify detailed molecular-level understanding of the origin behind the counteraction effects of the IL on urea-induced partial unfolding of the protein. The calculations revealed significant conformational changes of the protein with multiple free energy minima due to its partial unfolding in binary urea-water solution. The counteraction effect of the IL was evident from the enhanced structural rigidity of the protein with propensity to transform into a single native free energy minimum state in ternary urea-IL-water solutions. Such an effect has been found to be associated with preferential direct binding of the IL components with the protein and simultaneous expulsion of urea from the interface, thereby providing additional stabilization of the protein in ternary solutions. Most importantly, modified rearrangement of the hydrogen bond network at the interface due to the formation of stronger protein-cation (PC) and protein-anion (PA) hydrogen bonds by breaking relatively weaker protein-urea (PU) and protein-water (PW) hydrogen bonds has been recognized as the microscopic origin behind the counteraction effects of EAA on urea-induced partial unfolding of the protein.
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Affiliation(s)
- Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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3
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Evaluation of a Raman Chemometric Method for Detecting Protein Structural Conformational Changes in Solution. J Pharm Sci 2023; 112:573-586. [PMID: 36152698 DOI: 10.1016/j.xphs.2022.09.006] [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: 02/22/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 01/18/2023]
Abstract
Raman scattering shows promise as a powerful routine tool, to determine both secondary and the smaller tertiary structural changes that precede aggregation in both solutions and solids. A method was developed utilizing principal component analysis (PCA) of Raman spectra for detection of small, but meaningful, pH induced changes in tertiary protein structure linked to aggregate formation using α-lactalbumin solutions as a model. The sample preparation and spectral parameters, were optimized for a bulk Raman probe. Analysis of large regions (600-1850 cm-1) yielded principal component (PC) scores useful for semi-quantitative comparison of protein conformation between formulations. PC loadings corresponded to specific structural peaks known to change with solution pH. PCA of circular dichroism (CD) spectra of dilute solutions yielded similar results. Sucrose is a common formulation excipient with a Raman spectrum that overlaps many protein peaks. With sucrose in the protein solution, the ability of PCA to discern protein structural changes from the Raman spectra was somewhat reduced. Analysis of a more limited spectral region (1530-1780 cm-1) with negligible sucrose spectral contribution improved the discrimination of protein conformational states. The new Raman method accurately distinguished differences in protein structure in concentrated solutions. The long-term goal is to explore Raman characterization as a routine monitoring tool of protein stability in both solution and solid states.
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4
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Zhao Z, Liang X, Li Q. Oleic acid-induced structural changes of buffalo apo-α-lactalbumin. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2022.114323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Ghanta KP, Mondal S, Bandyopadhyay S. Exploring the Dynamic Heterogeneity at the Interface of a Protein in Aqueous Ionic Liquid Solutions. J Phys Chem B 2022; 126:7271-7285. [DOI: 10.1021/acs.jpcb.2c03940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sandip Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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6
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Meng Y, Lou L, Shao Z, Chen J, Li Y, Zhang T. Antibacterial Activity and Mechanism of Action of Whey Protein-ε-Polylysine Complexes against Staphylococcus aureus and Bacillus subtilis. Foods 2022; 11:foods11152311. [PMID: 35954078 PMCID: PMC9367709 DOI: 10.3390/foods11152311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/23/2022] [Accepted: 07/27/2022] [Indexed: 12/01/2022] Open
Abstract
ε-Polylysine (ε-PL) is a cationic antimicrobial peptide, which easily forms complexes with food polyanions to weaken its antibacterial activity. A whey protein-ε-PL complex delivery system was found to be able to solve this problem. This study investigated the antimicrobial activity of the complexes and their mechanism against Gram-positive bacteria. The minimal inhibitory concentration of the complexes with different ε-PL contents against Staphylococcus aureus and Bacillus subtilis were 19.53–31.26 and 3.90–7.81 μg/mL, respectively, which were similar to free ε-PL. Furthermore, the whey protein-ε-PL complexes had a strong bactericidal effect on Bacillus subtilis. The inhibition zone diameters of the complexes against Staphylococcus aureus and Bacillus subtilis containing 5000 μg/mL of ε-PL were 14.14 and 16.69 mm, respectively. The results of scanning electron microscopy showed that the complexes could destroy the cell membrane structure in Bacillussubtilis, resulting in holes on the surface, but not in Staphylococcus aureus. The results of molecular dynamics simulation showed that under electrostatic interaction, the complexes captured the phospholipid molecules of the bacterial membrane through the hydrogen bonds. Parts of the ε-PL molecules of the complexes were embedded in the bilayer membrane, and parts of the ε-PL molecules could penetrate the bilayer membrane and enter the bacterial internal environment, forming holes on the surface of the bacteria. The antibacterial results in fresh meat showed that the whey protein-ε-PL complexes could reduce the total mesophilic and Staphylococcus aureus counts. This study on the antibacterial activity mechanism of whey protein-ε-PL complexes could provide a reference for the application of ε-PL in protein food matrices.
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Affiliation(s)
- Yuecheng Meng
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China; (Y.M.); (L.L.); (J.C.); (T.Z.)
| | - Li Lou
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China; (Y.M.); (L.L.); (J.C.); (T.Z.)
| | - Zhipeng Shao
- Research and Development Center, Wuxi Biortus Biosciences Co., Ltd., Jiangyin 214437, China;
| | - Jie Chen
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China; (Y.M.); (L.L.); (J.C.); (T.Z.)
| | - Yanhua Li
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China; (Y.M.); (L.L.); (J.C.); (T.Z.)
- Correspondence: ; Tel.: +86-158-6912-2579
| | - Tianqi Zhang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China; (Y.M.); (L.L.); (J.C.); (T.Z.)
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Insight into binding behavior, structure, and foam properties of α-lactalbumin/glycyrrhizic acid complex in an acidic environment. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107411] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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8
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Diao M, Liang Y, Zhao J, Zhang J, Zhang T. Complexation of ellagic acid with α-lactalbumin and its antioxidant property. Food Chem 2022; 372:131307. [PMID: 34634588 DOI: 10.1016/j.foodchem.2021.131307] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 11/04/2022]
Abstract
Ellagic acid possesses numerous bioactivities such as antioxidant activity and anti-inflammatory effect. In this work, the binding interaction between ellagic acid and α-lactalbumin was investigated by multi-spectroscopy and the results suggested that ellagic acid could change the conformation of α-lactalbumin. Chromatographic analysis proved the interaction of α-lactalbumin with ellagic acid taken place in less than 30 min and this interaction was stable. Computer simulations showed that both aromatic clusters Ⅰ and Ⅱ of α-lactalbumin were active sites for ellagic acid. Interestingly, both the results of molecular docking and molecular dynamics simulations suggested that ellagic acid tended to bind to aromatic cluster Ⅱ rather than aromatic cluster Ⅰ. Moreover, α-lactalbumin could enhance the antioxidant property of ellagic acid, indicating that the solubility of ellagic acid might be improved by combining α-lactalbumin. Overall, this work suggested that α-lactalbumin exhibited binding affinity for ellagic acid and enhanced its antioxidant property.
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Affiliation(s)
- Mengxue Diao
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Yuan Liang
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Jingqi Zhao
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun 130062, China.
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Characterization of the binding behavior, structure and foaming properties of bovine α-lactalbumin combined with saponin by the multi-spectroscopic and silico approaches. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107259] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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10
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Tejaswi Naidu K, Prakash Prabhu N. An able-cryoprotectant and a moderate denaturant: distinctive character of ethylene glycol on protein stability. J Biomol Struct Dyn 2022; 40:820-832. [DOI: 10.1080/07391102.2020.1819422] [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]
Affiliation(s)
- K. Tejaswi Naidu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - N. Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
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11
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Characterization of Conjugates between α-Lactalbumin and Benzyl Isothiocyanate-Effects on Molecular Structure and Proteolytic Stability. Molecules 2021; 26:molecules26206247. [PMID: 34684828 PMCID: PMC8539348 DOI: 10.3390/molecules26206247] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/27/2022] Open
Abstract
In complex foods, bioactive secondary plant metabolites (SPM) can bind to food proteins. Especially when being covalently bound, such modifications can alter the structure and, thus, the functional and biological properties of the proteins. Additionally, the bioactivity of the SPM can be affected as well. Consequently, knowledge of the influence of chemical modifications on these properties is particularly important for food processing, food safety, and nutritional physiology. As a model, the molecular structure of conjugates between the bioactive metabolite benzyl isothiocyanate (BITC, a hydrolysis product of the glucosinolate glucotropaeolin) and the whey protein α-lactalbumin (α-LA) was investigated using circular dichroism spectroscopy, anilino-1-naphthalenesulfonic acid fluorescence, and dynamic light scattering. Free amino groups were determined before and after the BITC conjugation. Finally, mass spectrometric analysis of the BITC-α-LA protein hydrolysates was performed. As a result of the chemical modifications, a change in the secondary structure of α-LA and an increase in surface hydrophobicity and hydrodynamic radii were documented. BITC modification at the ε-amino group of certain lysine side chains inhibited tryptic hydrolysis. Furthermore, two BITC-modified amino acids were identified, located at two lysine side chains (K32 and K113) in the amino acid sequence of α-LA.
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12
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Ghanta KP, Mondal S, Mondal S, Bandyopadhyay S. Contrasting Effects of Ionic Liquids of Varying Degree of Hydrophilicity on the Conformational and Interfacial Properties of a Globular Protein. J Phys Chem B 2021; 125:9441-9453. [PMID: 34433280 DOI: 10.1021/acs.jpcb.1c04167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ionic liquids (ILs), depending on their cation-anion combinations, are known to influence the conformational properties and activities of proteins in a nonuniform manner. To obtain microscopic understanding of such influence, it is important to characterize protein-IL interactions and explore the modified solvation environment around the protein. In this work, molecular dynamics (MD) simulations of the globular protein α-lactalbumin have been carried out in aqueous IL solutions containing 1-butyl-3-methylimidazolium cations (BMIM+) in combination with a series of anions with varying degree of hydrophilicity, namely, hexafluorophosphate (PF6-), ethyl sulfate (ETS-), acetate (OAc-), chloride (Cl-), dicyanamide (DCA-), and nitrate (NO3-) . The calculations revealed that ILs with hydrophobic and hydrophilic anions have contrasting influence on conformational flexibility of the protein. It is further observed that the BMIM+ cations exhibit site-specific orientations at the interface depending on the hydrophilicity of the anion component. Most importantly, the results demonstrated enhanced propensity of hydrophilic ILs to replace relatively weaker protein-water hydrogen bonds by stronger protein-IL hydrogen bonds at the protein surface as compared to the hydrophobic ILs. Such breaking of protein-water hydrogen bonds at a greater extent leads to greater loss of water hydrating the protein in the presence of hydrophilic ILs, thereby reducing the protein's stability.
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Affiliation(s)
- Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Souvik Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sandip Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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13
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Darmawan KK, Karagiannis TC, Hughes JG, Small DM, Hung A. In silico modelling of apo-lactoferrin under simulated gastric conditions: Structural dynamics, binding with β-lactoglobulin and α-lactalbumin, and functional implications. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111726] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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14
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De Oliveira TV, Polêto MD, Barbosa SV, Coimbra JSDR, De Oliveira EB. Impacts of Ca 2+ cation and temperature on bovine α-lactalbumin secondary structures and foamability - Insights from computational molecular dynamics. Food Chem 2021; 367:130733. [PMID: 34375890 DOI: 10.1016/j.foodchem.2021.130733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/19/2022]
Abstract
We used computational molecular dynamics (MD) to assess molecular conformations of apo- and holo-forms (respectively without and with Ca2+) of bovine α-lactalbumin (α-La) at different temperatures, and to correlate them with the protein's foaming properties. At 4 °C and 25 °C no major protein conformation changes occurred. At 75 °C, lots of changes were evidenced: the Ca2+ depletion triggered the complete loss of h2b, h3c helices and S1, S2 and S3 β-sheets, and partial losses of H1, H2 and H3 α-helices. The absence of Ca2+ in apo-α-La and its leaving from holo-α-La triggered electrostatic repulsion among Asp82, Asp84 and Asp87, leading to the formation of a hydrophobic cluster involving Phe9, Phe31, Ile1, Va42, Ile55, Phe80 and Leu81. These conformational changes were related to an interfacial tension decrease and to a foaming capacity increase, for both apo-α-La and holo-α-La. This study exemplifies how powerful MD is as a tool to provide a better understanding of the molecular origins of food proteins' techno-functionalities.
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Affiliation(s)
- Thomás Valente De Oliveira
- Departamento de Tecnologia de Alimentos (DTA), Universidade Federal de Viçosa (UFV), Campus Universitário, CEP 36570-900 Viçosa, MG, Brazil.
| | - Marcelo Depólo Polêto
- Departamento de Biologia Geral (DBG), Universidade Federal de Viçosa (UFV), Campus Universitário, CEP 36570-900 Viçosa, MG, Brazil
| | - Samuel Vieira Barbosa
- Departamento de Química (DEQ), Universidade Federal de Viçosa (UFV), Campus Universitário, CEP 36570-900 Viçosa, MG, Brazil
| | - Jane Sélia Dos Reis Coimbra
- Departamento de Tecnologia de Alimentos (DTA), Universidade Federal de Viçosa (UFV), Campus Universitário, CEP 36570-900 Viçosa, MG, Brazil.
| | - Eduardo Basílio De Oliveira
- Departamento de Tecnologia de Alimentos (DTA), Universidade Federal de Viçosa (UFV), Campus Universitário, CEP 36570-900 Viçosa, MG, Brazil.
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15
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Sadovnikova A, Garcia SC, Hovey RC. A Comparative Review of the Cell Biology, Biochemistry, and Genetics of Lactose Synthesis. J Mammary Gland Biol Neoplasia 2021; 26:181-196. [PMID: 34125364 PMCID: PMC8236053 DOI: 10.1007/s10911-021-09490-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 05/20/2021] [Indexed: 12/18/2022] Open
Abstract
Lactose is the primary carbohydrate in the milk of most mammals and is unique in that it is only synthesized by epithelial cells in the mammary glands. Lactose is also essential for the development and nutrition of infants. Across species, the concentration of lactose in milk holds a strong positive correlation with overall milk volume. Additionally, there is a range of examples where the onset of lactose synthesis as well as the content of lactose in milk varies between species and throughout a lactation. Despite this diversity, the precursors, genes, proteins and ions that regulate lactose synthesis have not received the depth of study they likely deserve relative to the significance of this simple and abundant molecule. Through this review, our objective is to highlight the requirements for lactose synthesis at the biochemical, cellular and temporal levels through a comparative approach. This overview also serves as the prelude to a companion review describing the dietary, hormonal, molecular, and genetic factors that regulate lactose synthesis.
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Affiliation(s)
- Anna Sadovnikova
- Graduate Group in Nutritional Biology, Physician Scientist Training Program, University of California, Davis, CA, USA.
- Department of Animal Science, University of California, Davis, CA, USA.
| | - Sergio C Garcia
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Russell C Hovey
- Department of Animal Science, University of California, Davis, CA, USA
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16
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Diao M, Liang Y, Zhao J, Zhao C, Zhang J, Zhang T. Enhanced cytotoxicity and antioxidant capacity of kaempferol complexed with α-lactalbumin. Food Chem Toxicol 2021; 153:112265. [PMID: 34004225 DOI: 10.1016/j.fct.2021.112265] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 01/25/2023]
Abstract
As a dietary polyphenol, kaempferol exhibits numerous biological activities such as antioxidant and anticancer properties. However, its application is limited because of its poor solubility and low permeability. This work aims to investigate the interaction of kaempferol with α-lactalbumin. Multiple-spectroscopic techniques were used to prove the interaction between kaempferol and α-lactalbumin. UV-vis absorption spectra suggested that the conformation of α-lactalbumin could be changed via binding with kaempferol. The fluorescence quenching test showed that kaempferol significantly quenched the intrinsic fluorescence of α-lactalbumin. Circular dichroism spectroscopy showed that the percent helicity of α-lactalbumin secondary structure increased when combined with kaempferol. In addition, the α-lactalbumin-kaempferol complex showed stronger inhibition ability on the growth of HeLa cells compared with kaempferol alone. The complex also showed higher antioxidant capacity than kaempferol alone. Molecular docking provided three predicted binding sites of α-lactalbumin for kaempferol, as well as five predicted binding poses of kaempferol. The weak intermolecular interactions were the main forces to stabilize the α-lactalbumin-kaempferol complex. Besides, the binding stability between α-lactalbumin and kaempferol was explored by molecular dynamics simulation. In conclusion, this work provides a basis for the potential application of α-lactalbumin as a delivery carrier for kaempferol owing to its nontoxic and biocompatible properties.
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Affiliation(s)
- Mengxue Diao
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Yuan Liang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Jingqi Zhao
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Changhui Zhao
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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17
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Pintér G, Hohmann K, Grün J, Wirmer-Bartoschek J, Glaubitz C, Fürtig B, Schwalbe H. Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:291-320. [PMID: 37904763 PMCID: PMC10539803 DOI: 10.5194/mr-2-291-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/07/2021] [Indexed: 11/01/2023]
Abstract
The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.
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Affiliation(s)
- György Pintér
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
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18
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α-Lactalbumin, Amazing Calcium-Binding Protein. Biomolecules 2020; 10:biom10091210. [PMID: 32825311 PMCID: PMC7565966 DOI: 10.3390/biom10091210] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023] Open
Abstract
α-Lactalbumin (α-LA) is a small (Mr 14,200), acidic (pI 4–5), Ca2+-binding protein. α-LA is a regulatory component of lactose synthase enzyme system functioning in the lactating mammary gland. The protein possesses a single strong Ca2+-binding site, which can also bind Mg2+, Mn2+, Na+, K+, and some other metal cations. It contains several distinct Zn2+-binding sites. Physical properties of α-LA strongly depend on the occupation of its metal binding sites by metal ions. In the absence of bound metal ions, α-LA is in the molten globule-like state. The binding of metal ions, and especially of Ca2+, increases stability of α-LA against the action of heat, various denaturing agents and proteases, while the binding of Zn2+ to the Ca2+-loaded protein decreases its stability and causes its aggregation. At pH 2, the protein is in the classical molten globule state. α-LA can associate with membranes at neutral or slightly acidic pH at physiological temperatures. Depending on external conditions, α-LA can form amyloid fibrils, amorphous aggregates, nanoparticles, and nanotubes. Some of these aggregated states of α-LA can be used in practical applications such as drug delivery to tissues and organs. α-LA and some of its fragments possess bactericidal and antiviral activities. Complexes of partially unfolded α-LA with oleic acid are cytotoxic to various tumor and bacterial cells. α-LA in the cytotoxic complexes plays a role of a delivery carrier of cytotoxic fatty acid molecules into tumor and bacterial cells across the cell membrane. Perhaps in the future the complexes of α-LA with oleic acid will be used for development of new anti-cancer drugs.
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19
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Darmawan KK, Karagiannis TC, Hughes JG, Small DM, Hung A. High temperature induced structural changes of apo-lactoferrin and interactions with β-lactoglobulin and α-lactalbumin for potential encapsulation strategies. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2020.105817] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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Shao Z, Yang Y, Fang S, Li Y, Chen J, Meng Y. Mechanism of the antimicrobial activity of whey protein-ε-polylysine complexes against Escherichia coli and its application in sauced duck products. Int J Food Microbiol 2020; 328:108663. [PMID: 32454366 DOI: 10.1016/j.ijfoodmicro.2020.108663] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 05/12/2020] [Accepted: 05/16/2020] [Indexed: 10/24/2022]
Abstract
ε-Polylysine (ε-PL) is a natural and highly effective cationic antimicrobial, of which antibacterial activity is limited in food matrix because of ε-PL's charged amino groups that form complexes with food polyanions. Whey protein-ε-PL complexes delivery system was found to be able to solve the problem and keep the antibacterial activity. This study investigated the antibacterial activity of the complexes and its mechanism against Escherichia coli. The minimal inhibitory concentration of ε-PL was in the range 11.72-25.00 g/mL for the complexes containing different amount of ε-PL and was similar to that of free ε-PL. The results of scanning electron microscopy showed that the complexes could destroy the structure of E. coli cell membrane surface, leaving holes on the surface of the bacteria, leading to the death of the bacteria. The molecular dynamics simulation results showed that the mechanism of the antibacterial activity of the complexes was as follows: under electrostatic interaction, the complexes captured the phospholipid molecules of the bacterial membrane through the hydrogen bonds between the positively charged amino groups of ε-PL and the oxygen atom of the phosphate head groups of the membrane, which could create holes on the surface of the bacteria and lead to the death of the bacteria. The results of activity on real food systems showed that the complexes kept the number of E. coli within 5.8 log10 CFU/g after 7 d storage in sauced duck products, while the positive control (ε-PL) was 6.5 log10 CFU/g and negative control (sterile water) was 7.8 log10 CFU/g. Overall, this study confirmed the antibacterial activity of the complexes and provided fundamental knowledge of its antibacterial activity mechanism.
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Affiliation(s)
- Zhipeng Shao
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035, People's Republic of China
| | - Yi Yang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035, People's Republic of China
| | - Sheng Fang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035, People's Republic of China
| | - Yanhua Li
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035, People's Republic of China
| | - Jie Chen
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035, People's Republic of China.
| | - Yuecheng Meng
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035, People's Republic of China.
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21
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Ghanta KP, Pal T, Mondal S, Bandyopadhyay S. Microscopic Understanding of the Effect of Ionic Liquid on Protein from Molecular Simulation Studies. J Phys Chem B 2020; 124:3909-3921. [PMID: 32302476 DOI: 10.1021/acs.jpcb.0c02001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have performed molecular dynamics (MD) simulations of the protein α-lactalbumin in aqueous solution containing the ionic liquid (IL) 1-butyl-3-methyl imidazolium tetrafluoroborate ([BMIM][BF4]) as the cosolvent at different concentrations. Attempts have been made to obtain quantitative understanding of the effects of the IL on the conformational features of the protein as well as the distributions of the IL and water around it. The calculations revealed enhanced rigidity of the protein with reduced conformational fluctuations and increasingly correlated local motions in the presence of the IL. Nonuniform relative population of the BMIM+ and BF4- ions at the protein surface with respect to that in the bulk solution has been observed. It is demonstrated that exchange of water by the IL around the protein results in rearrangement of the hydrogen bond network at the interface with breaking of protein-water hydrogen bonds and formation of protein-IL hydrogen bonds. Importantly, it is found that the protein forms increased number of stronger salt bridges in the presence of IL. This shows that the formation of a greater number of such stronger salt bridges is the origin behind the enhanced rigidity of the protein in the presence of the IL.
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Affiliation(s)
- Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Tamisra Pal
- Centre for Computational and Data Sciences, Indian Institute of Technology, Kharagpur 721302, India
| | - Sandip Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India.,Centre for Computational and Data Sciences, Indian Institute of Technology, Kharagpur 721302, India
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22
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Disentangling the role of solvent polarity and protein solvation in folding and self-assembly of α-lactalbumin. J Colloid Interface Sci 2020; 561:749-761. [DOI: 10.1016/j.jcis.2019.11.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/29/2019] [Accepted: 11/14/2019] [Indexed: 12/31/2022]
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23
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Depicting the Non-Covalent Interaction of Whey Proteins with Galangin or Genistein Using the Multi-Spectroscopic Techniques and Molecular Docking. Foods 2019; 8:foods8090360. [PMID: 31450792 PMCID: PMC6770871 DOI: 10.3390/foods8090360] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/17/2019] [Accepted: 08/21/2019] [Indexed: 12/16/2022] Open
Abstract
The non-covalent interactions between a commercial whey protein isolate (WPI) and two bioactive polyphenols galangin and genistein were studied at pH 6.8 via the multi-spectroscopic assays and molecular docking. When forming these WPI-polyphenol complexes, whey proteins had changed secondary structures while hydrophobic interaction was the major driving force. Detergent sodium dodecyl sulfate destroyed the hydrophobic interaction and thus decreased apparent binding constants of the WPI-polyphenol interactions. Urea led to hydrogen-bonds breakage and protein unfolding, and therefore increased apparent binding constants. Based on the measured apparent thermodynamic parameters like ΔH, ΔS, ΔG, and donor-acceptor distance, galangin with more planar stereochemical structure and random B-ring rotation showed higher affinity for WPI than genistein with location isomerism and twisted stereochemical structure. The molecular docking results disclosed that β-lactoglobulin of higher average hydrophobicity had better affinity for the two polyphenols than α-lactalbumin of lower average hydrophobicity while β-lactoglobulin possessed very similar binding sites to the two polyphenols. It is concluded that polyphenols might have different non-covalent interactions with food proteins, depending on the crucial polyphenol structures and protein hydrophobicity.
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24
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Cytotoxicity of apo bovine α-lactalbumin complexed with La 3+ on cancer cells supported by its high resolution crystal structure. Sci Rep 2019; 9:1780. [PMID: 30741951 PMCID: PMC6370903 DOI: 10.1038/s41598-018-38024-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/11/2018] [Indexed: 11/08/2022] Open
Abstract
Cancer remains one of the biggest threats to human society. There are massive demands for compounds to selectively kill cancerous cells. Earlier studies have shown that bovine α -lactalbumin made lethal to tumor cells (BAMLET) becomes cytotoxic against cancer cells in complex with oleic acid {Hoque, M. et. al., PLoSOne8, e68390 (2013)}. In our study, we obtained bovine α-lactalbumin complexed with lanthanum ion (La3+-B-α-LA) and determined its high resolution crystal structure. The natural calcium binding site of bovine α-lactalbumin is replaced by lanthanum. The La3+ complex formation by B-α-apo-LA was also supported by various biophysical methods. Interestingly, our complex, La3+-B-α-LA exhibits much greater anticancer activity against breast cancer cells as compared to the reported BAMLET-oleic acid complex. This study shows that La3+-B-α-LA complex is preferentially more toxic to MCF-7 cells as compared to KB (oral cancer) and HeLa (cervical) cells, while almost non-toxic to the healthy cells that we studied. Our data indicates that the cytotoxicity of La3+-B-α-LA against cancer cells is through apoptotic path way. The higher anticancer activity of La3+-B-α-LA is attributable to the requisite structural changes induced in the protein by La3+ binding as supported by the crystal structure of the complex.
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25
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Shao Z, Fang S, Li Y, Chen J, Meng Y. Physicochemical properties and formation mechanism of electrostatic complexes based on ε-polylysine and whey protein: Experimental and molecular dynamics simulations study. Int J Biol Macromol 2018; 118:2208-2215. [DOI: 10.1016/j.ijbiomac.2018.07.086] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 01/30/2023]
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26
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Cheung DL. Adsorption and conformations of lysozyme and α-lactalbumin at a water-octane interface. J Chem Phys 2018; 147:195101. [PMID: 29166117 DOI: 10.1063/1.4994561] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
As proteins contain both hydrophobic and hydrophilic amino acids, they will readily adsorb onto interfaces between water and hydrophobic fluids such as oil. This adsorption normally causes changes in the protein structure, which can result in loss of protein function and irreversible adsorption, leading to the formation of protein interfacial films. While this can be advantageous in some applications (e.g., food technology), in most cases it limits our ability to exploit protein functionality at interfaces. To understand and control protein interfacial adsorption and function, it is necessary to understand the microscopic conformation of proteins at liquid interfaces. In this paper, molecular dynamics simulations are used to investigate the adsorption and conformation of two similar proteins, lysozyme and α-lactalbumin, at a water-octane interface. While they both adsorb onto the interface, α-lactalbumin does so in a specific orientation, mediated by two amphipathic helices, while lysozyme adsorbs in a non-specific manner. Using replica exchange simulations, both proteins are found to possess a number of distinct interfacial conformations, with compact states similar to the solution conformation being most common for both proteins. Decomposing the different contributions to the protein energy at oil-water interfaces suggests that conformational change for α-lactalbumin, unlike lysozyme, is driven by favourable protein-oil interactions. Revealing these differences between the factors that govern the conformational change at interfaces in otherwise similar proteins can give insight into the control of protein interfacial adsorption, aggregation, and function.
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Affiliation(s)
- David L Cheung
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
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27
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Stender EGP, Koutina G, Almdal K, Hassenkam T, Mackie A, Ipsen R, Svensson B. Isoenergic modification of whey protein structure by denaturation and crosslinking using transglutaminase. Food Funct 2018; 9:797-805. [DOI: 10.1039/c7fo01451a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural effect of denaturation of whey protein by heat or pH and subsequent crosslinking by transglutaminase.
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Affiliation(s)
- Emil G. P. Stender
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- Denmark
| | - Glykeria Koutina
- Department of Food Science
- University of Copenhagen
- Copenhagen
- Denmark
| | - Kristoffer Almdal
- Department of Micro- and Nanotechnology
- Technical University of Denmark
- Denmark
| | - Tue Hassenkam
- Department of Chemistry
- University of Copenhagen
- Copenhagen
- Denmark
| | - Alan Mackie
- Institute of Food Research
- Norwich Research Park
- Colney
- UK
- School of Food Science and Nutrition
| | - Richard Ipsen
- Department of Food Science
- University of Copenhagen
- Copenhagen
- Denmark
| | - Birte Svensson
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- Denmark
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28
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Tian P, Best RB. How Many Protein Sequences Fold to a Given Structure? A Coevolutionary Analysis. Biophys J 2017; 113:1719-1730. [PMID: 29045866 PMCID: PMC5647607 DOI: 10.1016/j.bpj.2017.08.039] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 12/23/2022] Open
Abstract
Quantifying the relationship between protein sequence and structure is key to understanding the protein universe. A fundamental measure of this relationship is the total number of amino acid sequences that can fold to a target protein structure, known as the "sequence capacity," which has been suggested as a proxy for how designable a given protein fold is. Although sequence capacity has been extensively studied using lattice models and theory, numerical estimates for real protein structures are currently lacking. In this work, we have quantitatively estimated the sequence capacity of 10 proteins with a variety of different structures using a statistical model based on residue-residue co-evolution to capture the variation of sequences from the same protein family. Remarkably, we find that even for the smallest protein folds, such as the WW domain, the number of foldable sequences is extremely large, exceeding the Avogadro constant. In agreement with earlier theoretical work, the calculated sequence capacity is positively correlated with the size of the protein, or better, the density of contacts. This allows the absolute sequence capacity of a given protein to be approximately predicted from its structure. On the other hand, the relative sequence capacity, i.e., normalized by the total number of possible sequences, is an extremely tiny number and is strongly anti-correlated with the protein length. Thus, although there may be more foldable sequences for larger proteins, it will be much harder to find them. Lastly, we have correlated the evolutionary age of proteins in the CATH database with their sequence capacity as predicted by our model. The results suggest a trade-off between the opposing requirements of high designability and the likelihood of a novel fold emerging by chance.
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Affiliation(s)
- Pengfei Tian
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.
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29
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L. S, Vasu P. In silico designing of therapeutic protein enriched with branched-chain amino acids for the dietary treatment of chronic liver disease. J Mol Graph Model 2017; 76:192-204. [DOI: 10.1016/j.jmgm.2017.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 02/07/2023]
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30
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Cheison SC, Kulozik U. Impact of the environmental conditions and substrate pre-treatment on whey protein hydrolysis: A review. Crit Rev Food Sci Nutr 2017; 57:418-453. [PMID: 25976220 DOI: 10.1080/10408398.2014.959115] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Proteins in solution are subject to myriad forces stemming from interactions with each other as well as with the solvent media. The role of the environmental conditions, namely pH, temperature, ionic strength remains under-estimated yet it impacts protein conformations and consequently its interaction with, and susceptibility to, the enzyme. Enzymes, being proteins are also amenable to the environmental conditions because they are either activated or denatured depending on the choice of the conditions. Furthermore, enzyme specificity is restricted to a narrow regime of optimal conditions while opportunities outside the optimum conditions remain untapped. In addition, the composition of protein substrate (whether mixed or single purified) have been underestimated in previous studies. In addition, protein pre-treatment methods like heat denaturation prior to hydrolysis is a complex phenomenon whose progression is influenced by the environmental conditions including the presence or absence of sugars like lactose, ionic strength, purity of the protein, and the molecular structure of the mixed proteins particularly presence of free thiol groups. In this review, we revisit protein hydrolysis with a focus on the impact of the hydrolysis environment and show that preference of peptide bonds and/or one protein over another during hydrolysis is driven by the environmental conditions. Likewise, heat-denaturing is a process which is dependent on not only the environment but the presence or absence of other proteins.
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Affiliation(s)
| | - Ulrich Kulozik
- b Chair for Food Process Engineering and Dairy Technology Department , ZIEL Technology Section, Technische Universität München , Weihenstephaner Berg 1, Freising , Germany
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31
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α-Lactalbumin and sodium dodecyl sulfate aggregates: Denaturation, complex formation and time stability. Food Hydrocoll 2017. [DOI: 10.1016/j.foodhyd.2016.07.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Al-Hanish A, Stanic-Vucinic D, Mihailovic J, Prodic I, Minic S, Stojadinovic M, Radibratovic M, Milcic M, Cirkovic Velickovic T. Noncovalent interactions of bovine α-lactalbumin with green tea polyphenol, epigalocatechin-3-gallate. Food Hydrocoll 2016. [DOI: 10.1016/j.foodhyd.2016.05.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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33
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Nguyen TTP, Bhandari B, Cichero J, Prakash S. In vitro digestion of infant formulations with hydrolysed and non-hydrolysed proteins from dairy and soybean. Food Funct 2016; 7:4908-4919. [DOI: 10.1039/c6fo01240j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Digestion of hydrolysed and non-hydrolysed dairy (casein and whey proteins) and soy proteins commonly used in infant formulations was studied underin vitrogastrointestinal (without lipases) conditions for 60 and 120 minutes in the stomach and small intestine, respectively.
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Affiliation(s)
- Thao T. P. Nguyen
- School of Agriculture and Food Sciences
- The University of Queensland
- Brisbane
- Australia
| | - Bhesh Bhandari
- School of Agriculture and Food Sciences
- The University of Queensland
- Brisbane
- Australia
| | - Julie Cichero
- School of Pharmacy
- Pharmacy Australia Centre of Excellence
- The University of Queensland
- Brisbane
- Australia
| | - Sangeeta Prakash
- School of Agriculture and Food Sciences
- The University of Queensland
- Brisbane
- Australia
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34
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Larda ST, Pichugin D, Prosser RS. Site-Specific Labeling of Protein Lysine Residues and N-Terminal Amino Groups with Indoles and Indole-Derivatives. Bioconjug Chem 2015; 26:2376-83. [DOI: 10.1021/acs.bioconjchem.5b00457] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sacha Thierry Larda
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
| | - Dmitry Pichugin
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
| | - Robert Scott Prosser
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
- Department
of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
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35
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Madende M, Osthoff G, Patterton HG, Patterton HE, Martin P, Opperman DJ. Characterization of casein and alpha lactalbumin of African elephant (Loxodonta africana) milk. J Dairy Sci 2015; 98:8308-18. [PMID: 26454297 DOI: 10.3168/jds.2014-9195] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 08/14/2015] [Indexed: 11/19/2022]
Abstract
The current research reports partial characterization of the caseins and α-lactalbumin (α-LA) of the African elephant with proposed unique structure-function properties. Extensive research has been carried out to understand the structure of the casein micelles. Crystallographic structure elucidation of caseins and casein micelles is not possible. Consequently, several models have been developed in an effort to describe the casein micelle, specifically of cow milk. Here we report the characterization of African elephant milk caseins. The κ-caseins and β-caseins were investigated, and their relative ratio was found to be approximately 1:8.5, whereas α-caseins were not detected. The gene sequence of β-casein in the NCBI database was revisited, and a different sequence in the N-terminal region is proposed. Amino acid sequence alignment and hydropathy plots showed that the κ-casein of African elephant milk is similar to that of other mammals, whereas the β-casein is similar to the human protein, and displayed a section of unique AA composition and additional hydrophilic regions compared with bovine caseins. Elephant milk is destabilized by 62% alcohol, and it is speculated that the β-casein characteristics may allow maintenance of the colloidal nature of the casein micelle, a role that was previously only associated with κ-casein. The oligosaccharide content of milk was reported to be low in dairy animals but high in some other species such as humans and elephants. In the milk of the African elephant, lactose and oligosaccharides both occur at high levels. These levels are typically related to the content of α-LA in the mammary gland and thus point to a specialized carbohydrate synthesis, where the whey protein α-LA plays a role. We report the characterization of African elephant α-LA. Homology modeling of the α-LA showed that it is structurally similar to crystal structures of other mammalian species, which in turn may be an indication that its functional properties, such as lactose synthesis, should not be impaired.
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Affiliation(s)
- M Madende
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
| | - G Osthoff
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa.
| | - H-G Patterton
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
| | - H E Patterton
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
| | - P Martin
- UMR1313 Génétique Animale et Biologie Integrative, Institut National de la Recherche Agronomique, Domaine de Vilvert - Bâtiment 221, 78350 Jouy-en-Josas, France
| | - D J Opperman
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
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36
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Zheng H, Mandal A, Shumilin IA, Chordia MD, Panneerdoss S, Herr JC, Minor W. Sperm Lysozyme-Like Protein 1 (SLLP1), an intra-acrosomal oolemmal-binding sperm protein, reveals filamentous organization in protein crystal form. Andrology 2015; 3:756-71. [PMID: 26198801 PMCID: PMC5040164 DOI: 10.1111/andr.12057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 01/07/2023]
Abstract
Sperm lysozyme-like protein 1 (SLLP1) is one of the lysozyme-like proteins predominantly expressed in mammalian testes that lacks bacteriolytic activity, localizes in the sperm acrosome, and exhibits high affinity for an oolemmal receptor, SAS1B. The crystal structure of mouse SLLP1 (mSLLP1) was determined at 2.15 Å resolution. mSLLP1 monomer adopts a structural fold similar to that of chicken/mouse lysozymes retaining all four canonical disulfide bonds. mSLLP1 is distinct from c-lysozyme by substituting two essential catalytic residues (E35T/D52N), exhibiting different surface charge distribution, and by forming helical filaments approximately 75 Å in diameter with a 25 Å central pore comprised of six monomers per helix turn repeating every 33 Å. Cross-species alignment of all reported SLLP1 sequences revealed a set of invariant surface regions comprising a characteristic fingerprint uniquely identifying SLLP1 from other c-lysozyme family members. The fingerprint surface regions reside around the lips of the putative glycan-binding groove including three polar residues (Y33/E46/H113). A flexible salt bridge (E46-R61) was observed covering the glycan-binding groove. The conservation of these regions may be linked to their involvement in oolemmal protein binding. Interaction between SLLP1 monomer and its oolemmal receptor SAS1B was modeled using protein-protein docking algorithms, utilizing the SLLP1 fingerprint regions along with the SAS1B conserved surface regions. This computational model revealed complementarity between the conserved SLLP1/SAS1B interacting surfaces supporting the experimentally observed SLLP1/SAS1B interaction involved in fertilization.
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Affiliation(s)
- Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Arabinda Mandal
- Department of Cell Biology, Center for Research in Contraceptive and Reproductive Health, University of Virginia, Charlottesville, VA 22908, USA
| | - Igor A. Shumilin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Mahendra D. Chordia
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Subbarayalu Panneerdoss
- Department of Cell Biology, Center for Research in Contraceptive and Reproductive Health, University of Virginia, Charlottesville, VA 22908, USA
| | - John C. Herr
- Department of Cell Biology, Center for Research in Contraceptive and Reproductive Health, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence: Wladek Minor, Ph.D., Department of Molecular Physiology and Biological Physics, University of Virginia, P.O. Box 800736, Charlottesville, Virginia 22908-0736, USA. Ph: +1 434 243-6865; Fax: +1 434 982-1616; , John C. Herr, Ph.D., Department of Cell Biology, University of Virginia, P.O. Box 800732, Charlottesville, Virginia 22908, USA. Ph: +1 434 924-2007; Fax: +1 434 982-3912;
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence: Wladek Minor, Ph.D., Department of Molecular Physiology and Biological Physics, University of Virginia, P.O. Box 800736, Charlottesville, Virginia 22908-0736, USA. Ph: +1 434 243-6865; Fax: +1 434 982-1616; , John C. Herr, Ph.D., Department of Cell Biology, University of Virginia, P.O. Box 800732, Charlottesville, Virginia 22908, USA. Ph: +1 434 924-2007; Fax: +1 434 982-3912;
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Sapir L, Harries D. Macromolecular Stabilization by Excluded Cosolutes: Mean Field Theory of Crowded Solutions. J Chem Theory Comput 2015; 11:3478-90. [DOI: 10.1021/acs.jctc.5b00258] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Liel Sapir
- Institute of Chemistry and
The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and
The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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Sapir L, Harries D. Is the depletion force entropic? Molecular crowding beyond steric interactions. Curr Opin Colloid Interface Sci 2015. [DOI: 10.1016/j.cocis.2014.12.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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39
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Thawari AG, Hinge VK, Temgire M, Rao CP. Mercuration of apo-α-lactalbumin: binding of Hg2+followed by protein-mediated nanoparticle formation. RSC Adv 2014. [DOI: 10.1039/c4ra07156e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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40
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Tetens JL, Qanbari S, Drögemüller C, Pimentel ECG, Bennewitz J, Thaller G, Tetens J. Bos indicus introgression into (peri-)alpine cattle breeds - evidence from the analysis of bovine whey protein variants. Anim Genet 2014; 45:585-8. [PMID: 24931299 DOI: 10.1111/age.12185] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2014] [Indexed: 11/28/2022]
Abstract
The major bovine whey proteins, α-lactalbumin (α-LA) and β-lactoglobulin (β-LG), exhibit breed-specific genetic variation. The aim of this study was to identify possible new protein variants and determine the distribution of variants across a variety of 18 taurine and indicine cattle breeds applying a DNA-based sequencing approach. To this end, the open reading frames of the respective genes (LALBA and LGB) were sequenced in 476 animals. Within the LALBA gene, a previously unknown synonymous and a previously undesignated non-synonymous nucleotide exchange were identified. Furthermore, two known α-LA variants (A and B) and four known β-LG variants (A, B, C and W) were determined. The occurrence of typical indicine variants in some taurine cattle breeds, such as Suisse Eringer, German Hinterwälder and Hungarian Grey Steppe, further supports the hypothesis of ancient Bos indicus introgression into (peri-)alpine cattle breeds.
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Affiliation(s)
- J L Tetens
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, D-24118, Kiel, Germany
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41
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Zhai JL, Day L, Aguilar MI, Wooster TJ. Protein folding at emulsion oil/water interfaces. Curr Opin Colloid Interface Sci 2013. [DOI: 10.1016/j.cocis.2013.03.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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The biological activities of protein/oleic acid complexes reside in the fatty acid. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1125-43. [DOI: 10.1016/j.bbapap.2013.02.041] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/18/2013] [Accepted: 02/20/2013] [Indexed: 12/12/2022]
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43
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Aprodu I, Stănciuc N, Banu I, Bahrim G. Probing thermal behaviour of microbial transglutaminase with fluorescence and in silico methods. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2013; 93:794-802. [PMID: 22836726 DOI: 10.1002/jsfa.5799] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/17/2012] [Accepted: 06/12/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND Knowledge of transglutaminase behaviour at thermal treatment allows efficient applications in food processing. The heat-induced conformational changes of microbial transglutaminase were studied by fluorescence spectroscopy and a molecular modelling approach. RESULTS The experimental results indicate the unfolding of transglutaminase in a single-phase reaction, at temperatures over 60 °C. The incidence of conformational changes is also supported by the increase of both intrinsic and 1-anilino-8-naphthalene sulfonate fluorescence intensity with temperature. Changes in the secondary and tertiary structure of transglutaminase were outlined after running molecular dynamics simulations at temperatures ranging from 25 °C to 80 °C. CONCLUSION The motif's particularities varied with the temperature, suggesting structural rearrangements of the protein, mainly in helices. The largest deviation from the structure equilibrated at 25 °C was observed at 80 °C.
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Affiliation(s)
- Iuliana Aprodu
- Dunarea de Jos University of Galati, Faculty of Food Science and Engineering, Galati, Romania
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44
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Stroobants K, Moelants E, Ly HGT, Proost P, Bartik K, Parac-Vogt TN. Polyoxometalates as a Novel Class of Artificial Proteases: Selective Hydrolysis of Lysozyme under Physiological pH and Temperature Promoted by a Cerium(IV) Keggin-Type Polyoxometalate. Chemistry 2013; 19:2848-58. [DOI: 10.1002/chem.201203020] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 11/15/2012] [Indexed: 11/10/2022]
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45
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Batista ANL, Batista Jr JM, Bolzani VS, Furlan M, Blanch EW. Selective DMSO-induced conformational changes in proteins from Raman optical activity. Phys Chem Chem Phys 2013; 15:20147-52. [DOI: 10.1039/c3cp53525h] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Makabe K, Nakamura T, Kuwajima K. Structural insights into the stability perturbations induced by N-terminal variation in human and goat -lactalbumin. Protein Eng Des Sel 2012; 26:165-70. [DOI: 10.1093/protein/gzs093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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47
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Spolaore B, Raboni S, Ramos Molina A, Satwekar A, Damiano N, Fontana A. Local unfolding is required for the site-specific protein modification by transglutaminase. Biochemistry 2012; 51:8679-89. [PMID: 23083324 DOI: 10.1021/bi301005z] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The transglutaminase (TGase) from Streptomyces mobaraensis catalyzes transamidation reactions in a protein substrate leading to the modification of the side chains of Gln and Lys residues according to the A-CONH(2) + H(2)N-B → A-CONH-B + NH(3) reaction, where both A and B can be a protein or a ligand. A noteworthy property of TGase is its susbstrate specificity, so that often only a few specific Gln or Lys residues can be modified in a globular protein. The molecular features of a globular protein dictating the site-specific reactions mediated by TGase are yet poorly understood. Here, we have analyzed the reactivity toward TGase of apomyoglobin (apoMb), α-lactalbumin (α-LA), and fragment 205-316 of thermolysin. These proteins are models of protein structure and folding that have been studied previously using the limited proteolysis technique to unravel regions of local unfolding in their amino acid sequences. The three proteins were modified by TGase at the level of Gln or Lys residues with dansylcadaverine or carbobenzoxy-l-glutaminylglycine, respectively. Despite these model proteins containing several Gln and Lys residues, the sites of TGase derivatization occur over restricted chain regions of the protein substrates. In particular, the TGase-mediated modifications occur in the "helix F" region in apoMb, in the β-domain in apo-α-LA in its molten globule state, and in the N-terminal region in fragment 205-316 of thermolysin. Interestingly, the sites of limited proteolysis are located in the same chain regions of these proteins, thus providing a clear-cut demonstration that chain flexibility or local unfolding overwhelmingly dictates the site-specific modification by both TGase and a protease.
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Affiliation(s)
- Barbara Spolaore
- CRIBI Biotechnology Centre, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy.
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48
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Visker MHPW, Heck JML, van Valenberg HJF, van Arendonk JAM, Bovenhuis H. Short communication: A new bovine milk-protein variant: α-lactalbumin variant D. J Dairy Sci 2012; 95:2165-9. [PMID: 22459861 DOI: 10.3168/jds.2011-4794] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 12/01/2011] [Indexed: 01/24/2023]
Abstract
Capillary zone electrophoresis of 1,948 Holstein-Friesian cows suggested the presence of an unknown protein variant of α-lactalbumin (α-LA) in the milk of 1 cow. Sequencing genomic DNA of this cow showed a polymorphism in the α-LA gene (LAA) that appears to be responsible for this protein variant. This single nucleotide polymorphism g.600G > T was located in exon 2 of LAA and causes the amino acid change 65Gln > His in the α-LA protein. This α-LA protein variant is a new protein variant and should be called α-LA protein variant D. This amino acid change is not expected to affect protein function. Genomic DNA of 156 bulls of various dairy cattle breeds was screened to examine the presence of the new α-LA protein variant D. Single nucleotide polymorphism g.600G > T, responsible for α-LA protein variant D, was not found in any of the 156 bulls. However, 10 other polymorphisms in the coding and promoter regions of LAA were detected that were used to construct haplotypes.
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Affiliation(s)
- M H P W Visker
- Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, 6700 AH Wageningen, The Netherlands.
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49
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Fang B, Zhang M, Jiang L, Jing H, Ren FZ. Influence of pH on the Structure and Oleic Acid Binding Ability of Bovine α-Lactalbumin. Protein J 2012; 31:564-72. [DOI: 10.1007/s10930-012-9434-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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50
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Tomoyori K, Nakamura T, Makabe K, Maki K, Saeki K, Kuwajima K. Sequential four-state folding/unfolding of goat α-lactalbumin and its N-terminal variants. Proteins 2012; 80:2191-206. [PMID: 22577070 DOI: 10.1002/prot.24109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/11/2012] [Accepted: 04/25/2012] [Indexed: 11/09/2022]
Abstract
Equilibria and kinetics of folding/unfolding of α-lactalbumin and its two N-terminal variants were studied by circular dichroism spectroscopy. The two variants were wild-type recombinant and Glu1-deletion (E1M) variants expressed in Escherichia coli. The presence of an extra methionine at the N terminus in recombinant α-lactalbumin destabilized the protein by 2 kcal/mol, while the stability was recovered in the E1M variant in which Glu1 was replaced by Met1. Kinetic folding/unfolding reactions of the proteins, induced by stopped-flow concentration jumps of guanidine hydrochloride, indicated the presence of a burst-phase in refolding, and gave chevron plots with significant curvatures in both the folding and unfolding limbs. The folding-limb curvature was interpreted in terms of accumulation of the burst-phase intermediate. However, there was no burst phase observed in the unfolding kinetics to interpret the unfolding-limb curvature. We thus assumed a sequential four-state mechanism, in which the folding from the burst-phase intermediate takes place via two transition states separated by a high-energy intermediate. We estimated changes in the free energies of the burst-phase intermediate and two transition states, caused by the N-terminal variations and also by the presence of stabilizing calcium ions. The Φ values at the N terminus and at the Ca(2+)-binding site thus obtained increased successively during folding, demonstrating the validity of the sequential mechanism. The stability and the folding behavior of the E1M variant were essentially identical to those of the authentic protein, allowing us to use this variant as a pseudo-wild-type α-lactalbumin in future studies.
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Affiliation(s)
- Katsuaki Tomoyori
- Department of Physics, School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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