1
|
Liang Z, Yu Y, Zou B, Fu M, Hu T, Yin X, Wang J, Xu Y, Cheng L. The effect of structural changes on the activity of peroxidase with different initial state under high-pressure freezing. Food Chem 2024; 459:140314. [PMID: 39024881 DOI: 10.1016/j.foodchem.2024.140314] [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: 02/03/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024]
Abstract
The combined impact of initial state, pressure, and freezing on peroxidase denaturation during high-pressure freezing (HPF) processing of enzyme-containing foods remains unclear. This study investigated solid-liquid (initial low/high concentration) biphasic peroxidase using spectroscopic and computer simulation techniques to analyze structural changes affecting peroxidase (POD) activity under HPF. The results indicate that the primary factors determining POD activity during HPF treatment can be ranked as follows: concentration > physical state > pressure > freezing. Higher initial concentrations strengthen protein interactions, leading to a 1% increase in the molecular diameter and a 34% increase in molecular height of HL-POD, thereby increasing aggregation likelihood during crystallization and facilitating structural changes that activate enzymes by 6-17%. The amide I peak proves to be a reliable indicator for monitoring both POD activity and structural alterations. This study offers valuable insights for optimizing HPF technology in food processing.
Collapse
Affiliation(s)
- Zhanhong Liang
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China; School of Food Science, Guangdong Pharmaceutical University, Zhongshan 528400, China
| | - Yuanshan Yu
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China
| | - Bo Zou
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China
| | - Manqin Fu
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China
| | - Tenggen Hu
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China
| | - Xiaomeng Yin
- Guangzhou Conghua District Agriculture and rural Bureau, Guangzhou 510610, China
| | - Jin Wang
- Guangzhou Conghua District Agriculture and rural Bureau, Guangzhou 510610, China
| | - Yujuan Xu
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China.
| | - Lina Cheng
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China.
| |
Collapse
|
2
|
Kurakin S, Ivankov O, Dushanov E, Murugova T, Ermakova E, Efimov S, Mukhametzyanov T, Smerdova S, Klochkov V, Kuklin A, Kučerka N. Calcium ions do not influence the Aβ(25-35) triggered morphological changes of lipid membranes. Biophys Chem 2024; 313:107292. [PMID: 39018778 DOI: 10.1016/j.bpc.2024.107292] [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: 03/06/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024]
Abstract
We have studied the effect of calcium ions (Ca2+) at various concentrations on the structure of lipid vesicles in the presence of amyloid-beta peptide Aβ(25-35). In particular, we have investigated the influence of calcium ions on the formation of recently documented bicelle-like structures (BLSs) emerged as a result of Aβ(25-35) triggered membrane disintegration. First, we have shown by using small-angle X-ray and neutron scattering that peptide molecules rigidify the lipid bilayer of gel phase DPPC unilamellar vesicles (ULVs), while addition of the calcium ions to the system hinders this effect of Aβ(25-35). Secondly, the Aβ(25-35) demonstrates a critical peptide concentration at which the BLSs reorganize from ULVs due to heating and cooling the samples through the lipid main phase transition temperature (Tm). However, addition of calcium ions does not affect noticeably the Aβ-induced formation of BLSs and their structural parameters, though the changes in peptide's secondary structure, e.g. the increased α-helix fraction, has been registered by circular dichroism spectroscopy. Finally, according to 31P nuclear magnetic resonance (NMR) measurements, calcium ions do not affect the lipid-peptide arrangement in BLSs and their ability to align in the magnetic field of NMR spectrometer. The influences of various concentrations of calcium ions on the lipid-peptide interactions may prove biologically important because their local concentrations vary widely in in-vivo conditions. In the present work, calcium ions were investigated as a possible tool aimed at regulating the lipid-peptide interactions that demonstrated the disruptive effect of Aβ(25-35) on lipid membranes.
Collapse
Affiliation(s)
- Sergei Kurakin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia.
| | - Oleksandr Ivankov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Ermuhammad Dushanov
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Department of Biophysics, Dubna State University, Universitetskaya 19, Dubna, Moscow Region 141982, Russia
| | - Tatiana Murugova
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Elena Ermakova
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Sergey Efimov
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Timur Mukhametzyanov
- Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Svetlana Smerdova
- Kazan National Research Technological University, Karl Marx 68, Kazan 420015, Russia
| | - Vladimir Klochkov
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Alexander Kuklin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Moscow Institute of Physics and Technology, Instytutskiy Pereulok 9, Dolgoprudny, Moscow Region 141701, Russia
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Odbojárov 10, Bratislava 832 32, Slovakia.
| |
Collapse
|
3
|
Zhang Z, Zhao Y, Han Y, Teng H, Xu Q. Crucial effect of ovomucin on alkali-induced egg white gel formation: Properties, structure and facilitation mechanism. Int J Biol Macromol 2024; 277:134507. [PMID: 39111502 DOI: 10.1016/j.ijbiomac.2024.134507] [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: 06/04/2024] [Revised: 07/29/2024] [Accepted: 08/03/2024] [Indexed: 08/10/2024]
Abstract
Alkali-induced preserved egg gel formation is a dynamic process that involves complex protein changes. Ovomucin (OVM) is closely associated with the gel properties of egg white. In this study, the effect of OVM in alkali-induced egg white gel (AEWG) formation was investigated. The results suggested that OVM reduced the gel formation time by 15 %. The mechanical properties of the fully formed gel were also improved by OVM. Specifically, OVM increased the storage modulus (G') of the gel by 1.5-fold, while the hardness significantly increased from 78.90 ± 4.24 g to 99.80 ± 9.23 g. Low-field nuclear magnetic resonance (LF-NMR) demonstrated that OVM significantly shortened T23 relaxation time and reduced the water mobility, thus increasing the water holding capacity (WHC). Meanwhile, the presence of OVM resulted in a more homogeneous and denser microscopic morphology of the gel. Selective solubility experiments revealed that disulfide bonds are the primary force in gel formation. OVM promoted the formation of more disulfide bonds, which increased the strength and stability of the gel network. Overall, this research proved OVM plays a critical role in the performance improvement of AEWG, which provides a new insight into the quality control of preserved egg and protein gel foods.
Collapse
Affiliation(s)
- Zhenqing Zhang
- Institute of advanced cross-field science, College of Life Science, Qingdao University, Qingdao, Shandong province 266800, People's Republic of China
| | - Yuhan Zhao
- Institute of advanced cross-field science, College of Life Science, Qingdao University, Qingdao, Shandong province 266800, People's Republic of China
| | - Yumeng Han
- Institute of advanced cross-field science, College of Life Science, Qingdao University, Qingdao, Shandong province 266800, People's Republic of China
| | - Haoye Teng
- Institute of advanced cross-field science, College of Life Science, Qingdao University, Qingdao, Shandong province 266800, People's Republic of China
| | - Qi Xu
- Institute of advanced cross-field science, College of Life Science, Qingdao University, Qingdao, Shandong province 266800, People's Republic of China.
| |
Collapse
|
4
|
Pan F, Li X, Chen H, Liu M, Fang X, Peng W, Tian W. Exploring the effect of high-pressure processing conditions on the deaggregation of natural major royal jelly proteins (MRJPs) fibrillar aggregates. Food Chem 2024; 452:139611. [PMID: 38749141 DOI: 10.1016/j.foodchem.2024.139611] [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: 02/29/2024] [Revised: 04/18/2024] [Accepted: 05/07/2024] [Indexed: 06/01/2024]
Abstract
High pressure processing is a safe and green novel non-thermal processing technique for modulating food protein aggregation behavior. However, the systematic relationship between high pressure processing conditions and protein deaggregation has not been sufficiently investigated. Major royal jelly proteins, which are naturally highly fibrillar aggregates, and it was found that the pressure level and exposure time could significantly promote protein deaggregation. The 100-200 MPa treatment favoured the deaggregation of proteins with a significant decrease in the sulfhydryl group content. Contrarily, at higher pressure levels (>400 MPa), the exposure time promoted the formation of disordered agglomerates. Notably, the inter-conversion of α-helix and β-strands in major royal jelly proteins after high pressure processing eliminates the solvent-free cavities inside the aggregates, which exerts a 'collapsing' effect on the fibrillar aggregates. Furthermore, the first machine learning model of the high pressure processing conditions and the protein deaggregation behaviour was developed, which provided digital guidance for protein aggregation regulation.
Collapse
Affiliation(s)
- Fei Pan
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Xiangxin Li
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Hualei Chen
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Mengyao Liu
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Xiaoming Fang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Wenjun Peng
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China.
| | - Wenli Tian
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China.
| |
Collapse
|
5
|
Bhatt M, Masi HA, Patel A, Singh NK, Joshi C. Heterologous expression, purification and single step efficient refolding of recombinant tissue plasminogen activator (Reteplase) from E. coli. Protein Expr Purif 2024; 221:106504. [PMID: 38782082 DOI: 10.1016/j.pep.2024.106504] [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: 01/19/2024] [Revised: 04/19/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Reteplase (recombinant plasminogen activator, rPA) is a mutant non-glycosylated tissue-type plasminogen activator (tPA) containing 355 amino acids with longer half-life and promising thrombolytic activity than its original counterpart, full length tPA. In this study, we aimed to produce and optimize the purification process of recombinant tissue-type plasminogen activator (tPA) known as Reteplase (rPA). Reteplase cDNA synthesized from total mRNA isolated from human placenta was PCR amplified, cloned into a pET-28a(+) E. coli expression vector and expressed in Rosetta-gami 2 E. coli (NovagenⓇ) host. rPA was expressed as an inclusion body in E. coli and its biological activity was achieved after single step solubilization, purification and refolding. We exploited the strategy of Slow Refolding using Gradual Dialysis (SRGD) in which a refolding buffer containing glutathione oxidized (1 mM GSSG) and glutathione reduced (3 mM GSH) and pH 9.0 was used. Using the SRGD method, we were able to successfully obtain the protein in its active form. We obtained 4.26 mg of active refolded protein from a 50 mL culture that was scaled up in a bioreactor. The purity and homogeneity of rPA was evaluated by SDS-PAGE, Western blotting and mass spectrometry. Circular dichroism spectroscopy was conducted to evaluate the refolding and stability of the refolded rPA in comparison to reference standard rPA. The thrombolytic potential of rPA was assessed by fibrin plate assay and In Vitro clot lysis assay. The presented protocol offers a viable approach for enhancing both the yield and refolding efficiency of reteplase, potentially resulting in an increase in yield.
Collapse
Affiliation(s)
- Meha Bhatt
- Gujarat Biotechnology Research Centre, Department of Science & Technology, MS Building, 6th Floor, GH Road, Sector - 11, Gandhinagar, Gujarat, 382011, India
| | - Haidar Abbas Masi
- Gujarat Biotechnology Research Centre, Department of Science & Technology, MS Building, 6th Floor, GH Road, Sector - 11, Gandhinagar, Gujarat, 382011, India
| | - Amrutlal Patel
- Gujarat Biotechnology Research Centre, Department of Science & Technology, MS Building, 6th Floor, GH Road, Sector - 11, Gandhinagar, Gujarat, 382011, India.
| | - Niraj Kumar Singh
- Gujarat Biotechnology Research Centre, Department of Science & Technology, MS Building, 6th Floor, GH Road, Sector - 11, Gandhinagar, Gujarat, 382011, India.
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Department of Science & Technology, MS Building, 6th Floor, GH Road, Sector - 11, Gandhinagar, Gujarat, 382011, India.
| |
Collapse
|
6
|
Tian Q, Hao L, Song X, Liu Y, Fan C, Zhao Q, Zhang H, Hou H. Isolation and differential structure characteristics of calcium-binding peptides derived from Pacific cod bones by hydroxyapatite affinity. Food Chem 2024; 451:139268. [PMID: 38663247 DOI: 10.1016/j.foodchem.2024.139268] [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: 12/25/2023] [Revised: 03/17/2024] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
Calcium-chelating peptides were found in Pacific cod bone, but their binding structure and properties have not been elucidated. Novel calcium-binding peptides were isolated by hydroxyapatite affinity chromatography (HAC), and their binding structure and properties were investigated by isothermal titration calorimetry (ITC), multispectral techniques, and mass spectrometry. Based on multiple purifications, the calcium binding capacity (CBC) of Pacific cod bone peptides (PBPs) was increased from 1.71 ± 0.15 μg/mg to 7.94 ± 1.56 μg/mg. Peptides with a molecular weight of 1-2 kDa are closely correlated with CBC. After binding to calcium, the secondary structure of peptides transitioned from random coil to β-sheet, resulting in a loose and porous microstructure. Hydrogen bonds, electrostatic interaction, and hydrophobic interaction contribute to the formation of peptide‑calcium complexes. The F21 contained 42 peptides, with repeated "GE" motif. Differential structure analysis provides a theoretical basis for the targeted preparation of high CBC peptides.
Collapse
Affiliation(s)
- Qiaoji Tian
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No.1299, San Sha Road, Qingdao, Shandong Province, 266404, PR China
| | - Li Hao
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No.1299, San Sha Road, Qingdao, Shandong Province, 266404, PR China
| | - Xue Song
- Technology Center of Qingdao Customs District, No. 83, Xinyue Road, Qingdao, Shandong Province 266109, PR China
| | - Yang Liu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No.1299, San Sha Road, Qingdao, Shandong Province, 266404, PR China
| | - Chaozhong Fan
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No.1299, San Sha Road, Qingdao, Shandong Province, 266404, PR China
| | - Qianqian Zhao
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No.1299, San Sha Road, Qingdao, Shandong Province, 266404, PR China
| | - Hongwei Zhang
- Technology Center of Qingdao Customs District, No. 83, Xinyue Road, Qingdao, Shandong Province 266109, PR China
| | - Hu Hou
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No.1299, San Sha Road, Qingdao, Shandong Province, 266404, PR China; Laboratory for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, Shandong Province 266237, PR China; Sanya Oceanographic Institution, Ocean University of China, Sanya, Hainan Province 572024, PR China.
| |
Collapse
|
7
|
Folimonova V, Chen X, Negi H, Schwieters CD, Li J, Byrd RA, Taylor N, Youkharibache P, Walters KJ. CD28 hinge used in chimeric antigen receptor (CAR) T-cells exhibits local structure and conformational exchange amidst global disorder. Commun Biol 2024; 7:1072. [PMID: 39217198 PMCID: PMC11365992 DOI: 10.1038/s42003-024-06770-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
T-cell therapies based on chimeric antigen receptor (CAR) targeting of a tumor-specific antigen offer hope for patients with relapsed or refractory cancers. CAR hinge and transmembrane regions link antigen recognition domains to intracellular signal transduction domains. Here, we apply biophysical methods to characterize the structure and dynamic properties of the CD28 CAR hinge (CD28H) used in an FDA-approved CD19 CAR for the treatment of B-lineage leukemia/lymphoma. By using nuclear Overhauser effect spectroscopy (NOESY), which detects even transiently occupied structural motifs, we observed otherwise elusive local structural elements amidst overall disorder in CD28H, including a conformational switch from a native β-strand to a 310-helix and polyproline II helix-like structure. These local structural motifs contribute to an overall loosely formed extended geometry that could be captured by NOESY data. All FDA-approved CARs use prolines in the hinge region, which we find in CD28, and previously in CD8α, isomerize to promote structural plasticity and dynamics. These local structural elements may function in recognition and signaling events and constrain the spacing between the transmembrane and antigen recognition domains. Our study thus demonstrates a method for detecting local and transient structure within intrinsically disordered systems and moreover, our CD28H findings may inform future CAR design.
Collapse
Affiliation(s)
- Varvara Folimonova
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Xiang Chen
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Hitendra Negi
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Charles D Schwieters
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jess Li
- Macromolecular NMR Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - R Andrew Byrd
- Macromolecular NMR Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Naomi Taylor
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Philippe Youkharibache
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
| |
Collapse
|
8
|
Li J, Eagles DA, Tucker IJ, Pereira Schmidt AC, Deplazes E. Secondary structure propensities of the Ebola delta peptide E40 in solution and model membrane environments. Biophys Chem 2024; 314:107318. [PMID: 39226875 DOI: 10.1016/j.bpc.2024.107318] [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: 02/17/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/05/2024]
Abstract
The Ebola delta peptide is an amphipathic, 40-residue peptide encoded by the Ebola virus, referred to as E40. The membrane-permeabilising activity of the E40 delta peptide has been demonstrated in cells and lipid vesicles suggesting the E40 delta peptide likely acts as a viroporin. The lytic activity of the peptide increases in the presence of anionic lipids and a disulphide bond in the C-terminal part of the peptide. Previous in silico work predicts the peptide to show a partially helical structure, but there is no experimental information on the structure of E40. Here, we use circular dichroism spectroscopy to report the secondary structure propensities of the reduced and oxidised forms of the E40 peptide in water, detergent micelles, and lipid vesicles composed of neutral and anionic lipids (POPC and POPG, respectively). Results indicate that the peptide is predominately a random coil in solution, and the disulphide bond has a small but measurable effect on peptide conformation. Secondary structure analysis shows large uncertainties and dependence on the reference data set and, in our system, cannot be used to accurately determine the secondary structure motifs of the peptide in membrane environments. Nevertheless, the spectra can be used to assess the relative changes in secondary structure propensities of the peptide depending on the solvent environment and disulphide bond. In POPC-POPG vesicles, the peptide transitions from a random coil towards a more structured conformation, which is even more pronounced in negatively charged SDS micelles. In vesicles, the effect depends on the peptide-lipid ratio, likely resulting from vesicle surface saturation. Further experiments with zwitterionic POPC vesicles and DPC micelles show that both curvature and negatively charged lipids can induce a change in conformation, with the two effects being cumulative. Electrostatic screening from Na+ ions reduced this effect. The oxidised form of the peptide shows a slightly lower propensity for secondary structure and retains a more random coil conformation even in the presence of PG-PC vesicles.
Collapse
Affiliation(s)
- Jiayu Li
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Australia
| | - David A Eagles
- Institute of Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Isaac J Tucker
- Institute of Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | | | - Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Australia.
| |
Collapse
|
9
|
Sarangi AN, Gupta AN. Impedance Spectroscopy Unveiled the Surfactant-Induced Unfolding and Subsequent Refolding of Human Serum Albumin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 39189867 DOI: 10.1021/acs.langmuir.4c01886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Protein-surfactant interaction is a dynamic interplay of electrostatic and hydrophobic forces that ensues from the folding of a protein. We employ impedance spectroscopy (IS), a label-free method, to investigate the unfolding and refolding of human serum albumin (HSA), a globular plasma protein, in the presence of two surfactants: polysorbate-20 (Tween-20), a nonionic surfactant, and sodium dodecyl sulfate (SDS), an anionic surfactant. The equivalent electrical analog circuit was predicted from impedance spectra of HSA in an aqueous solution at physiological pH and room temperature, focusing on varying the concentration of codissolved surfactants. A change in the dielectric constant (ε') and ionic conductivity (κ) is observed by comparing the surfactant-treated protein samples to the bare surfactant solutions to assess the conformational changes induced by surfactants in HSA. Far-UV circular dichroism analysis revealed a decrease in α-helices and an increase in β-sheets and random coils upon SDS addition, which were reversed by Tween-20. Dynamic light scattering supported the findings by measuring changes in the hydrodynamic diameter (dh) of HSA. Unfolding and refolding of HSA with surfactants were also observed through photoluminescence spectroscopy by examining the microenvironment surrounding the single tryptophan (W) within the protein, and the thermodynamic parameters were obtained using the modified Stern-Volmer equation. Our research explores the intriguing domain of protein-surfactant interactions, offering insights with promising applications across diverse biological processes and IS as a suitable alternative technique for investigating protein conformational changes by studying the electrical response of the samples.
Collapse
Affiliation(s)
- Akshay Narayan Sarangi
- Biophysics and Soft Matter Laboratory, Department of Physics, IIT Kharagpur, Kharagpur 721302, India
| | - Amar Nath Gupta
- Biophysics and Soft Matter Laboratory, Department of Physics, IIT Kharagpur, Kharagpur 721302, India
| |
Collapse
|
10
|
Ocampo CMM, Villaraza AJL. A Gd(III)-labelled self-assembling peptide as a potential pH-responsive MRI contrast agent. Dalton Trans 2024. [PMID: 39189442 DOI: 10.1039/d4dt01773k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
A marine-derived peptide labelled with a Gd(III)-chelate was found to self-assemble depending on the solution pH, accompanied by changes in T1-relaxivity (r1) values when in the dispersed or self-assembled form. Such pH-responsive behavior can be advantageous in the development of macromolecular magnetic resonance imaging (MRI) contrast agents which monitor the tissue physiology.
Collapse
|
11
|
Li J, Zeng C, Guan J, Suryanarayanan R. Effect of surfactants on lactate dehydrogenase aqueous solutions: A comparative study of poloxamer 188, polysorbate 20 and 80. Int J Pharm 2024; 661:124374. [PMID: 38909927 DOI: 10.1016/j.ijpharm.2024.124374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
The effect of three commonly used surfactants, poloxamer 188 (P188), polysorbate 20 and 80 (PS20 and PS80), on the stability of a model protein, lactate dehydrogenase (LDH), was compared in aqueous solutions. In the absence of a surfactant, protein solution revealed a gradual decrease in surface tension as a function of time. The addition of surfactant resulted in a rapid decrease in the surface tension. This suggested that the surface behavior was dictated by the surfactant. PS20 and PS80 were more effective than P188 in preventing LDH adsorption on the solution surface. The advantage of polysorbates over P188 was also evident from the higher LDH tetramer recovery after shaking (room temperature, 30 h), especially when the surfactants were used at concentrations ≤ 0.01% w/v. However, PS20 and PS80 accelerated protein unfolding during quiescent storage at 40 °C. Based on circular dichroism results, polysorbates perturbed the tertiary structure of LDH but not the secondary structure, while P188 did not impact the protein structure and stability. Polysorbates were more effective in stabilizing LDH against mechanical stress (shaking), but their adverse effects on protein conformational stability need to be carefully evaluated.
Collapse
Affiliation(s)
- Jinghan Li
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, United States
| | - Chaowang Zeng
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, United States
| | - Jibin Guan
- Masonic Cancer Center, University of Minnesota, Minneapolis, 55455, United States
| | - Raj Suryanarayanan
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, United States.
| |
Collapse
|
12
|
Tsuchiya K, Fujita S, Numata K. Ampholytic Peptides Consisting of an Alternating Lysine/Glutamic Acid Sequence for the Simultaneous Formation of Polyion Complex Vesicles. ACS POLYMERS AU 2024; 4:320-330. [PMID: 39156560 PMCID: PMC11328329 DOI: 10.1021/acspolymersau.4c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 08/20/2024]
Abstract
Nanoarchitectures such as micelles and vesicles that self-assemble via electrostatic interactions between their charged polymeric components have been widely used as material delivery platforms. In this work, ampholytic peptides with a sequence of alternating lysine and glutamic acid residues were designed and synthesized via chemoenzymatic polymerization. This alternating sequence was achieved by trypsin-catalyzed polymerization of a dipeptide monomer. Due to the electrostatic interaction between the anionic and cationic residues, the prepared ampholytic peptides spontaneously formed nanosized assemblies with a size of 100-200 nm in water. Modification with tetra(ethylene glycol) (TEG) at the N-terminus of these ampholytic alternating peptides resulted in the formation of stable nanosized assemblies, while peptides consisting of random sequences of lysine and glutamic acid formed large aggregates with deteriorated stability even with TEG modification. Morphological observations using a field-emission scanning electron microscope and an atomic force microscope revealed that the obtained assemblies were spherical and hollow, indicating the spontaneous formation of vesicles from the TEG-modified ampholytic alternating peptides. These vesicles were able to encapsulate a model fluorescent protein within their hollow structures without structural collapse causing loss of fluorescence, demonstrating the potential of these nanocarriers for use in material delivery systems.
Collapse
Affiliation(s)
- Kousuke Tsuchiya
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1
Hirosawa, Wako, Saitama 351-0198, Japan
| | - Seiya Fujita
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Keiji Numata
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1
Hirosawa, Wako, Saitama 351-0198, Japan
| |
Collapse
|
13
|
Cheong HH, Zuo W, Chen J, Un CW, Si YW, Wong KH, Kwok HF, Siu SWI. Identification of Anticancer Peptides from the Genome of Candida albicans: in Silico Screening, in Vitro and in Vivo Validations. J Chem Inf Model 2024; 64:6174-6189. [PMID: 39008832 DOI: 10.1021/acs.jcim.4c00501] [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: 07/17/2024]
Abstract
Anticancer peptides (ACPs) are promising future therapeutics, but their experimental discovery remains time-consuming and costly. To accelerate the discovery process, we propose a computational screening workflow to identify, filter, and prioritize peptide sequences based on predicted class probability, antitumor activity, and toxicity. The workflow was applied to identify novel ACPs with potent activity against colorectal cancer from the genome sequences of Candida albicans. As a result, four candidates were identified and validated in the HCT116 colon cancer cell line. Among them, PCa1 and PCa2 emerged as the most potent, displaying IC50 values of 3.75 and 56.06 μM, respectively, and demonstrating a 4-fold selectivity for cancer cells over normal cells. In the colon xenograft nude mice model, the administration of both peptides resulted in substantial inhibition of tumor growth without causing significant adverse effects. In conclusion, this work not only contributes a proven computational workflow for ACP discovery but also introduces two peptides, PCa1 and PCa2, as promising candidates poised for further development as targeted therapies for colon cancer. The method as a web service is available at https://app.cbbio.online/acpep/home and the source code at https://github.com/cartercheong/AcPEP_classification.git.
Collapse
Affiliation(s)
- Hong-Hin Cheong
- Department of Computer and Information Science, Faculty of Science and Technology, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
| | - Weimin Zuo
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
| | - Jiarui Chen
- Department of Computer and Information Science, Faculty of Science and Technology, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
| | - Chon-Wai Un
- Department of Computer and Information Science, Faculty of Science and Technology, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
| | - Yain-Whar Si
- Department of Computer and Information Science, Faculty of Science and Technology, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
| | - Koon Ho Wong
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
| | - Hang Fai Kwok
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
| | - Shirley W I Siu
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, R. de Luís Gonzaga Gomes, Macau SAR 999078, China
- Institute of Science and Environment, University of Saint Joseph, Estrada Marginal da Ilha Verde 14-17, Macau SAR 999078, China
| |
Collapse
|
14
|
Li Y, Li C, Pan F, Wang K, Weng S, Zhao M, Li Q, Wang D, Zhao L, Liu X, Hu Z. High hydrostatic pressure reduces inflammation induced by litchi thaumatin-like protein via altering active domain. Food Chem 2024; 461:140858. [PMID: 39173258 DOI: 10.1016/j.foodchem.2024.140858] [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: 04/18/2024] [Revised: 07/27/2024] [Accepted: 08/11/2024] [Indexed: 08/24/2024]
Abstract
Thaumatin-like proteins (TLP), existing in various fruits, have allergenic and pro-inflammatory activities. The current research attempts to reduce the pro-inflammatory activity of litchi TLP (LcTLP) through high hydrostatic pressure (HHP). This study demonstrated that HHP (250-500 MPa, 5-10 min) was a potential technique to reduce the pro-inflammatory activity of LcTLP, which was attributed to the irreversible destruction of the active domain, ie., V-cleft. SDS-PAGE showed no change in the protein profile. Continuous HHP treatment promoted LcTLP unfolding and then reassembling (400 MPa was the transition pressure), and the content of β-sheets decreased from 35.4% to 31.1%. HHP treatment could mitigate inflammatory responses of LcTLP, as confirmed by ELISA and western blot. Molecular dynamics simulations showed significant changes in the residue network under HHP, thereby affecting the V-cleft. These findings provide a theoretical explanation and structural insights into the HHP-induced reduction of pro-inflammatory activity of LcTLP.
Collapse
Affiliation(s)
- Yun Li
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Chuyuan Li
- Guangzhou Pharmaceutical Holding Limited, Guangzhou 510130, China
| | - Fei Pan
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China
| | - Kai Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Shaoquan Weng
- Guangzhou Wanglaoji Great Health Industry Co., Ltd., Guangzhou 510623, China
| | - Min Zhao
- Guangzhou Wanglaoji Great Health Industry Co., Ltd., Guangzhou 510623, China
| | - Qian Li
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan, Hubei, 430068, China
| | - Dongwei Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Lei Zhao
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Xuwei Liu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China.
| | - Zhuoyan Hu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
15
|
Balboni B, Marotta R, Rinaldi F, Milordini G, Varignani G, Girotto S, Cavalli A. An integrative structural study of the human full-length RAD52 at 2.2 Å resolution. Commun Biol 2024; 7:956. [PMID: 39112549 PMCID: PMC11306251 DOI: 10.1038/s42003-024-06644-1] [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: 02/11/2024] [Accepted: 07/27/2024] [Indexed: 08/10/2024] Open
Abstract
Human RAD52 (RAD52) is a DNA-binding protein involved in many DNA repair mechanisms and genomic stability maintenance. In the last few years, this protein was discovered to be a promising novel pharmacological target for anticancer strategies. Although the interest in RAD52 has exponentially grown in the previous decade, most information about its structure and mechanism still needs to be elucidated. Here, we report the 2.2 Å resolution cryo-EM reconstruction of the full-length RAD52 (FL-RAD52) protein. This allows us to describe the hydration shell of the N-terminal region of FL-RAD52, which is structured in an undecamer ring. Water molecules coordinate with protein residues to promote stabilization inside and among the protomers and within the inner DNA binding cleft to drive protein-DNA recognition. Additionally, through a multidisciplinary approach involving SEC-SAXS and computational methods, we comprehensively describe the highly flexible and dynamic organization of the C-terminal portion of FL-RAD52. This work discloses unprecedented structural details on the FL-RAD52, which will be critical for characterizing its mechanism of action and inhibitor development, particularly in the context of novel approaches to synthetic lethality and anticancer drug discovery.
Collapse
Affiliation(s)
- Beatrice Balboni
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Roberto Marotta
- Electron Microscopy Facility (EMF), Istituto Italiano di Tecnologia, Genoa, Italy
| | - Francesco Rinaldi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giulia Milordini
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Giulia Varignani
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Stefania Girotto
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy.
- Structural Biophysics Facility, Istituto Italiano di Tecnologia, Genoa, Italy.
| | - Andrea Cavalli
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy.
- CECAM, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
| |
Collapse
|
16
|
Sundaram R, Gandhi S, Jonak C, Vasudevan D. Characterization of the Arabidopsis thaliana chromatin remodeler DEK3 for its interaction with histones and DNA. Biochimie 2024:S0300-9084(24)00177-9. [PMID: 39097158 DOI: 10.1016/j.biochi.2024.07.018] [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: 06/03/2024] [Revised: 07/04/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Chromatin structure and dynamics regulate all DNA-templated processes, such as transcription, replication, and repair. Chromatin binding factors, chromatin architectural proteins, and nucleosome remodelers modulate chromatin structure and dynamics and, thereby, the various DNA-dependent processes. Arabidopsis thaliana DEK3, a member of the evolutionarily conserved DEK domain-containing chromatin architectural proteins, is an important factor for chromatin structure and function, involved in transcriptional programming to regulate flowering time and abiotic stress tolerance. AtDEK3 contains an uncharacterized N-terminal domain, a middle SAF domain (winged helix-like domain), and a C-terminal DEK domain, but their role in the interaction of AtDEK3 with histones and DNA remained poorly understood. Using biochemical and biophysical analyses, we provide a comprehensive in vitro characterization of the different AtDEK3 domains for their interaction with histone H3/H4 and DNA. AtDEK3 directly interacts with histone H3/H4 tetramers through its N-terminal domain and the C-terminal DEK domain in a 1:1 stoichiometry. Upon interaction with H3/H4, the unstructured N-terminal domain of AtDEK3 undergoes a conformational change and adopts an alpha-helical conformation. In addition, the in-solution envelope structures of the AtDEK3 domains and their complex with H3/H4 have been characterized. The SAF and DEK domains associate with double-stranded and four-way junction DNA. As DEK3 possesses a histone-interacting domain at the N- and the C-terminus and a DNA-binding domain in the middle and at the C-terminus, the protein might play a complex role as a chromatin remodeler.
Collapse
Affiliation(s)
- Rajivgandhi Sundaram
- Institute of Life Sciences, Bhubaneswar, 751023, India; Manipal Academy of Higher Education, Manipal, 576104, India
| | - Surajit Gandhi
- Institute of Life Sciences, Bhubaneswar, 751023, India; Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Claudia Jonak
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Bioresources Unit, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Dileep Vasudevan
- Institute of Life Sciences, Bhubaneswar, 751023, India; Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, India.
| |
Collapse
|
17
|
Ciesiołkiewicz A, Lizandra Perez J, Skalniak L, Noceń P, Berlicki Ł. Miniprotein engineering for inhibition of PD-1/PD-L1 interaction. Protein Sci 2024; 33:e5106. [PMID: 39012010 PMCID: PMC11250529 DOI: 10.1002/pro.5106] [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: 01/15/2024] [Revised: 06/07/2024] [Accepted: 06/23/2024] [Indexed: 07/17/2024]
Abstract
Miniproteins constitute an excellent basis for the development of structurally demanding functional molecules. The engrailed homeodomain, a three-helix-containing miniprotein, was applied as a scaffold for constructing programmed cell death protein 1/programmed death-ligand 1 (PD-1/PD-L1) interaction inhibitors. PD-L1 binders were initially designed using the computer-aided approach and subsequently optimized iteratively. The conformational stability was assessed for each obtained miniprotein using circular dichroism spectroscopy, indicating that numerous mutations could be introduced. The formation of a sizable hydrophobic surface at the inhibitor that fits the molecular target imposed the necessity for the incorporation of additional charged amino acid residues to retain its appropriate solubility. Finally, the miniprotein effectively binding to PD-L1 (KD = 51.4 nM) that inhibits PD-1/PD-L1 interaction in cell-based studies with EC50 = 3.9 μM, was discovered.
Collapse
Affiliation(s)
| | - Juan Lizandra Perez
- Department of Bioorganic ChemistryWrocław University of Science and TechnologyWrocławPoland
| | | | - Paweł Noceń
- Department of Bioorganic ChemistryWrocław University of Science and TechnologyWrocławPoland
| | - Łukasz Berlicki
- Department of Bioorganic ChemistryWrocław University of Science and TechnologyWrocławPoland
| |
Collapse
|
18
|
Riva D, Orlando M, Rabattoni V, Pollegioni L. On the quaternary structure of human D-3-phosphoglycerate dehydrogenase. Protein Sci 2024; 33:e5089. [PMID: 39012001 PMCID: PMC11250409 DOI: 10.1002/pro.5089] [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: 04/10/2024] [Revised: 05/27/2024] [Accepted: 06/10/2024] [Indexed: 07/17/2024]
Abstract
D-3-phosphoglycerate dehydrogenase (PHGDH) catalyzes the NAD+-dependent conversion of D-3-phospho-glycerate to 3-phosphohydroxypyruvate, the first step in the phosphorylated pathway for L-serine (L-Ser) biosynthesis. L-Ser plays different relevant metabolic roles in eukaryotic cells: alterations in L-Ser metabolism have been linked to serious neurological disorders. The human PHGDH (hPHGDH), showing a homotetrameric state in solution, is made of four domains, among which there are two regulatory domains at the C-terminus: the aspartate kinase-chorismate mutase-tyrA prephenate dehydrogenase (ACT) and allosteric substrate-binding (ASB) domains. The structure of hPHGDH was solved only for a truncated, dimeric form harboring the N-terminal end containing the substrate and the cofactor binding domains. A model ensemble of the tetrameric hPHGDH was generated using AlphaFold coupled with molecular dynamics refinement. By analyzing the inter-subunit interactions at the tetrameric interface, the residues F418, L478, P479, R454, and Y495 were selected and their role was studied by the alanine-scanning mutagenesis approach. The F418A variant modifies the putative ASB, slightly alters the activity, the fraction of protein in the tetrameric state, and the protein stability; it seems relevant in dimers' recognition to yield the tetrameric oligomer. On the contrary, the R454A, L478A, P479A, and Y495A variants (ACT domain) determine a loss of the tetrameric assembly, resulting in low stability and misfolding, triggering the aggregation and hampering the activity. The predicted tetrameric interface seems mediated by residues at the ACT domain, and the tetramer formation seems crucial for proper folding of hPHGDH, which, in turn, is essential for both stability and functionality.
Collapse
Affiliation(s)
- Daniele Riva
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
| | - Marco Orlando
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
- Present address:
Department of Biotechnology and BiosciencesUniversity of Milano‐BicoccaMilanItaly
| | - Valentina Rabattoni
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
| | - Loredano Pollegioni
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
| |
Collapse
|
19
|
Shen Y, Fang L, Liu C, Wang J, Wu D, Zeng Q, Leng Y, Min W. Effect of bi-enzyme hydrolysis on the properties and composition of hydrolysates of Manchurian walnut dreg protein. Food Chem 2024; 447:138947. [PMID: 38492294 DOI: 10.1016/j.foodchem.2024.138947] [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: 05/15/2023] [Revised: 02/08/2024] [Accepted: 02/24/2024] [Indexed: 03/18/2024]
Abstract
Walnut dreg (WD) active peptides are an important source of dietary antioxidants; however, the products of conventional hydrolysis have limited industrial output owing to poor flavour and low bioactivity. To this end, in this study, we aimed to employ bvLAP, an aminopeptidase previously identified in our research, as well as commercially available Alcalase for bi-enzyme digestion. The flavour, antioxidant activity, and structures of products resulting from various digestion methods were compared. The results showed that the bi-enzyme digestion products had enhanced antioxidant activity, increased β-sheet content, and reduced bitterness intensity from 9.65 to 6.93. Moreover, bi-enzyme hydrolysates showed a more diverse amino acid composition containing 1640 peptides with distinct sequences. These results demonstrate that bi-enzyme hydrolysis could be a potential process for converting WD into functional food ingredients. Additionally, our results provide new concepts that can be applied in waste processing and high-value utilisation of WD.
Collapse
Affiliation(s)
- Yue Shen
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China; National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, PR China
| | - Li Fang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China; National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, PR China
| | - Chunlei Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China; National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, PR China
| | - Ji Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China; National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, PR China
| | - Dan Wu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China; National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, PR China
| | - Qi Zeng
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China; National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, PR China
| | - Yue Leng
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China; National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, PR China.
| | - Weihong Min
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China; National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, PR China.
| |
Collapse
|
20
|
de Andrades D, Alnoch RC, Alves GS, Salgado JCS, Almeida PZ, Berto GL, Segato F, Ward RJ, Buckeridge MS, Polizeli MDLTM. Recombinant GH3 β-glucosidase stimulated by xylose and tolerant to furfural and 5-hydroxymethylfurfural obtained from Aspergillus nidulans. BIORESOUR BIOPROCESS 2024; 11:77. [PMID: 39073555 PMCID: PMC11286919 DOI: 10.1186/s40643-024-00784-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/03/2024] [Indexed: 07/30/2024] Open
Abstract
The β-glucosidase gene from Aspergillus nidulans FGSC A4 was cloned and overexpressed in the A. nidulans A773. The resulting purified β-glucosidase, named AnGH3, is a monomeric enzyme with a molecular weight of approximately 80 kDa, as confirmed by SDS-PAGE. Circular dichroism further validated its unique canonical barrel fold (β/α), a feature also observed in the 3D homology model of AnGH3. The most striking aspect of this recombinant enzyme is its robustness, as it retained 100% activity after 24 h of incubation at 45 and 50 ºC and pH 6.0. Even at 55 °C, it maintained 72% of its enzymatic activity after 6 h of incubation at the same pH. The kinetic parameters Vmax, KM, and Kcat/KM for ρ-nitrophenyl-β-D-glucopyranoside (ρNPG) and cellobiose were also determined. Using ρNPG, the enzyme demonstrated a Vmax of 212 U mg - 1, KM of 0.0607 mmol L - 1, and Kcat/KM of 4521 mmol L - 1 s - 1 when incubated at pH 6.0 and 65 °C. The KM, Vmax, and Kcat/KM using cellobiose were 2.7 mmol L - 1, 57 U mg - 1, and 27 mmol -1 s - 1, respectively. AnGH3 activity was significantly enhanced by xylose and ethanol at concentrations up to 1.5 mol L - 1 and 25%, respectively. Even in challenging conditions, at 65 °C and pH 6.0, the enzyme maintained its activity, retaining 100% and 70% of its initial activity in the presence of 200 mmol L - 1 furfural and 5-hydroxymethylfurfural (HMF), respectively. The potential of this enzyme was further demonstrated by its application in the saccharification of the forage grass Panicum maximum, where it led to a 48% increase in glucose release after 24 h. These unique characteristics, including high catalytic performance, good thermal stability in hydrolysis temperature, and tolerance to elevated concentrations of ethanol, D-xylose, furfural, and HMF, position this recombinant enzyme as a promising tool in the hydrolysis of lignocellulosic biomass as part of an efficient multi-enzyme cocktail, thereby opening new avenues in the field of biotechnology and enzymology.
Collapse
Affiliation(s)
- Diandra de Andrades
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | - Robson C Alnoch
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
- Department of Biochemistry and Immunology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Gabriela S Alves
- Department of Biochemistry and Immunology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
- Laboratory of Enzymology and Molecular Biology of Microorganisms, Institute of Biology, Campinas State University (UNICAMP), Campinas, 13083-970, SP, Brazil
| | - Jose C S Salgado
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | - Paula Z Almeida
- Department of Biochemistry and Immunology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Gabriela Leila Berto
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, 12602-810, Brazil
| | - Fernando Segato
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, 12602-810, Brazil
| | - Richard J Ward
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | | | - Maria de Lourdes T M Polizeli
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14040-901, Brazil.
- Department of Biochemistry and Immunology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil.
| |
Collapse
|
21
|
Baumgartner L, Ipsaro JJ, Hohmann U, Handler D, Schleiffer A, Duchek P, Brennecke J. Evolutionary adaptation of an HP1-protein chromodomain integrates chromatin and DNA sequence signals. eLife 2024; 13:RP93194. [PMID: 38995818 PMCID: PMC11245307 DOI: 10.7554/elife.93194] [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] [Indexed: 07/14/2024] Open
Abstract
Members of the diverse heterochromatin protein 1 (HP1) family play crucial roles in heterochromatin formation and maintenance. Despite the similar affinities of their chromodomains for di- and tri-methylated histone H3 lysine 9 (H3K9me2/3), different HP1 proteins exhibit distinct chromatin-binding patterns, likely due to interactions with various specificity factors. Previously, we showed that the chromatin-binding pattern of the HP1 protein Rhino, a crucial factor of the Drosophila PIWI-interacting RNA (piRNA) pathway, is largely defined by a DNA sequence-specific C2H2 zinc finger protein named Kipferl (Baumgartner et al., 2022). Here, we elucidate the molecular basis of the interaction between Rhino and its guidance factor Kipferl. Through phylogenetic analyses, structure prediction, and in vivo genetics, we identify a single amino acid change within Rhino's chromodomain, G31D, that does not affect H3K9me2/3 binding but disrupts the interaction between Rhino and Kipferl. Flies carrying the rhinoG31D mutation phenocopy kipferl mutant flies, with Rhino redistributing from piRNA clusters to satellite repeats, causing pronounced changes in the ovarian piRNA profile of rhinoG31D flies. Thus, Rhino's chromodomain functions as a dual-specificity module, facilitating interactions with both a histone mark and a DNA-binding protein.
Collapse
Affiliation(s)
- Lisa Baumgartner
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Jonathan J Ipsaro
- Howard Hughes Medical Institute, W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Ulrich Hohmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Schleiffer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| |
Collapse
|
22
|
Carter BM, Day GJ, Zhang WH, Sessions RB, Jackson CJ, Perriman AW. Partitioning of an Enzyme-Polymer Surfactant Nanocomplex into Lipid-Rich Cellular Compartments Drives In Situ Hydrolysis of Organophosphates. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401982. [PMID: 38992997 DOI: 10.1002/smll.202401982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/30/2024] [Indexed: 07/13/2024]
Abstract
Most organophosphates (OPs) are hydrophobic, and after exposure, can sequester into lipophilic regions within the body, such as adipose tissue, resulting in long term chronic effects. Consequently, there is an urgent need for therapeutic agents that can decontaminate OPs in these hydrophobic regions. Accordingly, an enzyme-polymer surfactant nanocomplex is designed and tested comprising chemically supercharged phosphotriesterase (Agrobacterium radiobacter; arPTE) electrostatically conjugated to amphiphilic polymer surfactant chains ([cat.arPTE][S-]). Experimentally-derived structural data are combined with molecular dynamics (MD) simulations to provide atomic level detail on conformational ensembles of the nanocomplex using dielectric constants relevant to aqueous and lipidic microenvironments. These show the formation of a compact admicelle pseudophase surfactant corona under aqueous conditions, which reconfigures to yield an extended conformation at a low dielectric constant, providing insight into the mechanism underpinning cell membrane binding. Significantly, it demonstrated that [cat.arPTE][S-] spontaneously binds to human mesenchymal stem cell membranes (hMSCs), resulting in on-cell OP hydrolysis. Moreover, the nanoconstruct can endocytose and partition into the intracellular fatty vacuoles of adipocytes and hydrolyze sequestered OP.
Collapse
Affiliation(s)
- Benjamin M Carter
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Graham J Day
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - William H Zhang
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | | | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT, 2601, Australia
| | - Adam W Perriman
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| |
Collapse
|
23
|
Wang C, Lu Y, Xia B, Li X, Huang X, Dong C. Complexation of bovine lactoferrin with selected phenolic acids via noncovalent interactions: Binding mechanism and altered functionality. J Dairy Sci 2024; 107:4189-4204. [PMID: 38369115 DOI: 10.3168/jds.2023-24088] [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: 08/15/2023] [Accepted: 01/16/2024] [Indexed: 02/20/2024]
Abstract
Noncovalent interactions of 4 selected phenolic acids, including gallic acid (GA), caffeic acid (CA), chlorogenic acid (CGA), and rosmarinic acid (RA) with lactoferrin (LF) were investigated. Compound combined with LF in the binding constant of CA > GA > RA > CGA, driven by van der Waals and hydrogen bonding for GA, and hydrophobic forces for others. Conformation of LF was affected at secondary and ternary structure levels. Molecular docking indicated that GA and CA located in the same site near the iron of the C-lobe, whereas RA and CGA bound to the C2 and N-lobe, respectively. Significantly enhanced antioxidant activity of complexes was found compared with pure LF, as demonstrated by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azinobis(2-ethylbenzothiazoline-6-sulfonate) (ABTS), and ferric reducing antioxidant power (FRAP) models. Caffeic acid, CGA, and RA significantly decreased the emulsifying stability index and improved foam ability of LF, and the effect of CA and RA was the most remarkable, respectively.
Collapse
Affiliation(s)
- Cuina Wang
- Department of Food Science, College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, China.
| | - Yingcong Lu
- Department of Food Science, College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, China
| | - Boxue Xia
- Department of Food Science, College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, China
| | - Xiang Li
- Department of Food Science, College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, China
| | - Xin Huang
- Department of Food Science, College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, China
| | - Chao Dong
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, Jilin, 130021, China.
| |
Collapse
|
24
|
Miller C, Huntoon D, Kaley N, Ogutu I, Fiedler AT, Bennett B, Liu D, Holz R. Role of second-sphere arginine residues in metal binding and metallocentre assembly in nitrile hydratases. J Inorg Biochem 2024; 256:112565. [PMID: 38677005 DOI: 10.1016/j.jinorgbio.2024.112565] [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: 02/09/2024] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024]
Abstract
Two conserved second-sphere βArg (R) residues in nitrile hydratases (NHase), that form hydrogen bonds with the catalytically essential sulfenic and sulfinic acid ligands, were mutated to Lys and Ala residues in the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) and the Fe-type NHase from Rhodococcus equi TG328-2 (ReNHase). Only five of the eight mutants (PtNHase βR52A, βR52K, βR157A, βR157K and ReNHase βR61A) were successfully expressed and purified. Apart from the PtNHase βR52A mutant that exhibited no detectable activity, the kcat values obtained for the PtNHase and ReNHase βR mutant enzymes were between 1.8 and 12.4 s-1 amounting to <1% of the kcat values observed for WT enzymes. The metal content of each mutant was also significantly decreased with occupancies ranging from ∼10 to ∼40%. UV-Vis spectra coupled with EPR data obtained on the ReNHase mutant enzyme, suggest a decrease in the Lewis acidity of the active site metal ion. X-ray crystal structures of the four PtNHase βR mutant enzymes confirmed the mutation and the low active site metal content, while also providing insight into the active site hydrogen bonding network. Finally, DFT calculations suggest that the equatorial sulfenic acid ligand, which has been shown to be the catalytic nucleophile, is protonated in the mutant enzyme. Taken together, these data confirm the necessity of the conserved second-sphere βR residues in the proposed subunit swapping process and post-translational modification of the α-subunit in the α activator complex, along with stabilizing the catalytic sulfenic acid in its anionic form.
Collapse
Affiliation(s)
- Callie Miller
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Delanie Huntoon
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Nicholas Kaley
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Irene Ogutu
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Adam T Fiedler
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, WI 53233, USA
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Richard Holz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| |
Collapse
|
25
|
Huang Y, Lin T, Dadmohammadi Y, He Y, Khongkomolsakul W, Noack CE, Abbaspourrad A. Lactoferrin thermal stabilization and iron(II) fortification through ternary complex fabrication with succinylated sodium caseinate. Food Chem X 2024; 22:101498. [PMID: 38911915 PMCID: PMC11190486 DOI: 10.1016/j.fochx.2024.101498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024] Open
Abstract
A thermally stable co-delivery system for lactoferrin (LF) and iron(II) was developed to address iron deficiency anemia. Complexes were formed between LF, succinylated sodium caseinate (S.NaCas) and FeSO4 with high yield (∼85%). LF-S.NaCas-Fe complexes achieved loading capacities for iron(II) between 2.5 and 12 mg g-1and LF loading capacities between 250 and 690 mg g-1, depending upon initial Fe2+ concentrations and LF ratios. The LF-S.NaCas complex mixtures appeared as smooth cubic particles in SEM, and gradually aggregated to amorphous particles as th iron(II) concentration increased due to iron-facilitated cross-linking. The complexation significantly improved LF thermal stability and addressed the poor solubility of iron(II) under neutral pH. After thermal treatment (95 °C, 5 min), the rehydrated complexes retained 68%-90% LF, with <10% iron(II) release. Circular dichroism spectra showed the secondary structure of the complexed LF was well retained during thermal treatment. This thermally stable system showed great potential in LF thermal protection and iron(II) fortification.
Collapse
Affiliation(s)
- Yunan Huang
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Tiantian Lin
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Younas Dadmohammadi
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Yanhong He
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Waritsara Khongkomolsakul
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Claire Elizabeth Noack
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Alireza Abbaspourrad
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| |
Collapse
|
26
|
Mitra A, Naik L, Dhiman R, Sarkar N. Protonation-State Dependent Modulation of Hen Egg-White Lysozyme Fibrillation under the Influence of a Short Synthetic Peptide. J Phys Chem B 2024; 128:5995-6013. [PMID: 38875472 DOI: 10.1021/acs.jpcb.4c01578] [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: 06/16/2024]
Abstract
Under the influence of various conditions, misfolding of soluble proteins occurs, leading to the formation of toxic insoluble amyloids. The formation and deposition of such amyloids within the body are associated with detrimental biological consequences such as the onset of several amyloid-related diseases. Previously, we established a strategy for the rational design of peptide inhibitors against amyloid formation based on the amyloidogenic-prone region of the protein. In the current study, we have designed and identified an Asp-containing rationally designed hexapeptide (SqP4) as an excellent inhibitor of hen egg-white lysozyme (HEWL) amyloid progression in vitro. First, SqP4 showed strong affinity toward the native monomeric HEWL leading to the stabilization of the native form and restriction in the unfolding process of monomeric HEWL. Second, SqP4 was found to arrest the amyloidogenic misfolded structure of HEWL in a nonfibrillar monomer-like stage. We also observed the differential effect of the protonation state of the charged amino acid (Asp) within the peptide inhibitor on the amyloid formation of HEWL and explored the reason behind the observations. The findings of this study can be implemented in future strategies for the development of potent therapeutics against other amyloid-related diseases.
Collapse
Affiliation(s)
- Amit Mitra
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Lincoln Naik
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Nandini Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| |
Collapse
|
27
|
Shaik L, Chakraborty S. Sequential Pulsed Light and Ultrasound Treatments for the Inactivation of Saccharomyces cerevisiae and PPO and the Retention of Bioactive Compounds in Sweet Lime Juice. Foods 2024; 13:1996. [PMID: 38998503 PMCID: PMC11241773 DOI: 10.3390/foods13131996] [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: 04/30/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 07/14/2024] Open
Abstract
Designing a pasteurization con dition for sweet lime juice while ensuring microbial safety, enzymatic stability, and high nutritional quality is crucial for satisfying stakeholder demands. The present research investigates the effects of matrix pH, ultrasound treatments, and sequential pulsed light on the microbial population, enzyme activity, and bioactive chemicals in sweet lime juice. The sequential pulsed light (PL: 0.6-0.84 J/cm2) and ultrasound (US: 0.2-0.4 W/cm3) treatments for sweet lime juice were optimized using response surface methodology (RSM). A three-factor full factorial design was used for this purpose. The independent variables encompassed pH (X1), PL effective fluence (X2, J/cm2), and US intensity (X3, W/cm3). The responses assessed included the inactivation of Saccharomyces cerevisiae (Y1, log cfu/mL) and polyphenol oxidase (PPO: Y2 in %) and the retention of vitamin C (Y3, %). The polynomial models were optimized using numerical optimization to attain the maximum desirability value (0.89). The optimized PL + US sample (0.8 J/cm2 + 0.4 W/cm3, respectively) at pH 3.5 resulted in a 5-log cycle reduction in S. cerevisiae count and a 90% inactivation in PPO activity and retained 95% of its vitamin C content. This optimized sample underwent further analysis, including phenolic profiling, assessment of microbial cell morphology, and examination of enzyme conformational changes. After sequential pulsed-light (0.8 J/cm2) and ultrasound (0.4 W/cm3) treatments, yeast cells showed unusual structural changes, indicating additional targets besides membranes. Following PL + US treatment, the PPO composition changed to 2.7 ± 0.1% α-helix, 33.9 ± 0.3% β-sheet, 1.4 ± 0.2% β-turn, and 62 ± 0.7% random coil. Impressively, the optimized PL + US sample maintained a sensory acceptance level similar to that of the untreated sample.
Collapse
Affiliation(s)
- Lubna Shaik
- Department of Food Engineering and Technology, Institute of Chemical Technology, Matunga, Mumbai 400019, India
- School of Biosciences and Bioengineering, D Y Patil International University, Akurdi, Pune 411044, India
| | - Snehasis Chakraborty
- Department of Food Engineering and Technology, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| |
Collapse
|
28
|
Nazeer N, Kooner N, Ghimire A, Rainey JK, Lubell WD, Meneksedag-Erol D, Ahmed M. Secondary Structure Stabilization of Macrocyclic Antimicrobial Peptides via Cross-Link Swapping. J Med Chem 2024; 67:8693-8707. [PMID: 38771638 DOI: 10.1021/acs.jmedchem.4c00005] [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: 05/23/2024]
Abstract
Lactam cross-links have been employed to stabilize the helical secondary structure and enhance the activity and physiological stability of antimicrobial peptides; however, stabilization of β-sheets via lactamization has not been observed. In the present study, lactams between the side chains of C- and N-terminal residues have been used to stabilize the β-sheet conformation in a short ten-residue analogue of chicken angiogenin-4. Designed using a combination of molecular dynamics simulations and Markov state models, the lactam cross-linked peptides are shown to adopt stabilized β-sheet conformations consistent with simulated structures. Replacement of the peptide side-chain Cys-Cys disulfide by a lactam cross-link enhanced the broad-spectrum antibacterial activity compared to the parent peptide and exhibited greater propensity to induce proinflammatory activity in macrophages. The combination of molecular simulations and conformational and biological analyses of the synthetic peptides provides a useful paradigm for the rational design of therapeutically active peptides with constrained β-sheet structures.
Collapse
Affiliation(s)
- Nauman Nazeer
- Department of Chemistry, University of Prince Edward Island, Charlottetown C1A 4P3, Prince Edward Island, Canada
| | - Navjote Kooner
- Department of Chemistry and Biochemistry, Concordia University, Montreal H4B 1R6, Quebec, Canada
| | - Anupama Ghimire
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
| | - Jan K Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
- Department of Chemistry, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
- School of Biomedical Engineering, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
| | - William D Lubell
- Département de Chimie, Université de Montréal, 1375 Ave. Thérèse-Lavoie-Roux, Montréal H2 V 0B3, Québec, Canada
| | - Deniz Meneksedag-Erol
- Department of Chemistry and Biochemistry, Concordia University, Montreal H4B 1R6, Quebec, Canada
- Department of Chemical and Materials Engineering, Concordia University, Montreal H4B 1R6, Quebec, Canada
| | - Marya Ahmed
- Department of Chemistry, University of Prince Edward Island, Charlottetown C1A 4P3, Prince Edward Island, Canada
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Charlottetown C1A 4P3, Prince Edward Island, Canada
| |
Collapse
|
29
|
Han Z, Migheli Q, Kong Q. Fusion Expression of Peptides with AflR Binuclear Zinc Finger Motif and Their Enhanced Inhibition of Aspergillus flavus: A Study of Engineered Antimicrobial Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:13360-13370. [PMID: 38830379 DOI: 10.1021/acs.jafc.4c01259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
This study reports a peptide design model for engineering fusion-expressed antimicrobial peptides (AMPs) with the AflR dinuclear zinc finger motif to improve the defense against aflatoxins and Aspergillus flavus. The study identified AflR, a Zn2Cys6-type sequence-specific DNA-binding protein, as a key player in the regulation of aflatoxin biosynthesis. By integrating the AflR motif into AMPs, we demonstrate that these novel fusion peptides significantly lower the minimum inhibitory concentrations (MICs) and reduce aflatoxin B1 and B2 levels, outperforming traditional AMPs. Comprehensive analysis, including bioinformatics and structural determination, elucidates the enhanced structure-function relationship underlying their efficacy. Furthermore, the study reveals the possibility that the fusion peptides have the potential to bind to the DNA binding sites of transcriptional regulators, binding DNA sites of key transcriptional regulators, thereby inhibiting genes critical for aflatoxin production. This research not only deepens our understanding of aflatoxin inhibition mechanisms but also presents a promising avenue for developing advanced antifungal agents, which are essential for global food safety and crop protection.
Collapse
Affiliation(s)
- Zhuoyu Han
- College of Food Science and Engineering, Ocean University of China, Qingdao 266000, China
| | - Quirico Migheli
- Dipartimento di Agraria and Nucleo di Ricerca sulla Desertificazione, Università degli Studi di Sassari, Sassari 07100, Italy
| | - Qing Kong
- College of Food Science and Engineering, Ocean University of China, Qingdao 266000, China
| |
Collapse
|
30
|
Andretto V, Rosso A, Zilio S, Sidi-Boumedine J, Boschetti G, Sankar S, Buffier M, Miele AE, Denis M, Choffour PA, Briançon S, Nancey S, Kryza D, Lollo G. Peptide-Based Hydrogel for Nanosystems Encapsulation: the Next Generation of Localized Delivery Systems for the Treatment of Intestinal Inflammations. Adv Healthc Mater 2024; 13:e2303280. [PMID: 38445812 DOI: 10.1002/adhm.202303280] [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: 09/27/2023] [Revised: 02/10/2024] [Indexed: 03/07/2024]
Abstract
Conventional therapies for inflammatory bowel diseases are mainly based on systemic treatments which cause side effects and toxicity over long-term administration. Nanoparticles appear as a valid alternative to allow a preferential accumulation in inflamed tissues following oral administration while reducing systemic drug exposure. To increase their residence time in the inflamed intestine, the nanoparticles are here associated with a hydrogel matrix. A bioadhesive peptide-based hydrogel is mixed with nanoemulsions, creating a hybrid lipid-polymer nanocomposite. Mucopenetrating nanoemulsions of 100 nm are embedded in a scaffold constituted of the self-assembling peptide hydrogel product PuraStat. The nanocomposite is fully characterized to study the impact of lipid particles in the hydrogel structure. Rheological measurements and circular dichroism analyses are performed to investigate the system's microstructure and physical properties. Biodistribution studies demonstrate that the nanocomposite acts as a depot in the stomach and facilitates the slow release of the nanoemulsions in the intestine. Efficacy studies upon oral administration of the drug-loaded system show the improvement of the disease score in a mouse model of intestinal inflammation.
Collapse
Affiliation(s)
- Valentina Andretto
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
| | - Annalisa Rosso
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
| | - Serena Zilio
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
- SATT, Ouest Valorisation, 14C Rue du Patis Tatelin, Renne, 35708, France
| | - Jacqueline Sidi-Boumedine
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
| | - Gilles Boschetti
- Department of Gastroenterology, Lyon Sud Hospital, Hospices Civil de Lyon and CIRI, Lyon, 69495, France
| | - Sharanya Sankar
- 3-D Matrix Europe SAS, Medical Technology, Caluire-et-Cuire, 69300, France
| | - Marie Buffier
- 3-D Matrix Europe SAS, Medical Technology, Caluire-et-Cuire, 69300, France
| | - Adriana Erica Miele
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ISA UMR 5280, 5 rue de la Doua, Villeurbanne, F-69100, France
- Dept Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, Rome, I-00185, Italy
| | - Morgane Denis
- Univ Lyon, Université Claude Bernard Lyon, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69008, France
- Antineo, R&D Department, Lyon, 69008, France
| | | | - Stéphanie Briançon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
| | - Stéphane Nancey
- Department of Gastroenterology, Lyon Sud Hospital, Hospices Civil de Lyon and CIRI, Lyon, 69495, France
| | - David Kryza
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
- Hospices Civils de Lyon, Lyon, 69437, France
| | - Giovanna Lollo
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 Boulevard du 11 Novembre 1918, Villeurbanne, F-69622, France
| |
Collapse
|
31
|
Janarthanam C, Clabaugh G, Wang Z, Melvin BR, Scheibe I, Jin H, Anantharam V, Urbauer RJB, Urbauer JL, Ma J, Kanthasamy A, Huang X, Donadio V, Zou W, Kanthasamy AG. High-Yield α-Synuclein Purification and Ionic Strength Modification Pivotal to Seed Amplification Assay Performance and Reproducibility. Int J Mol Sci 2024; 25:5988. [PMID: 38892177 PMCID: PMC11172462 DOI: 10.3390/ijms25115988] [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: 04/16/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Alpha-synuclein seed amplification assays (αSyn-SAAs) have emerged as promising diagnostic tools for Parkinson's disease (PD) by detecting misfolded αSyn and amplifying the signal through cyclic shaking and resting in vitro. Recently, our group and others have shown that multiple biospecimens, including CSF, skin, and submandibular glands (SMGs), can be used to seed the aggregation reaction and robustly distinguish between patients with PD and non-disease controls. The ultrasensitivity of the assay affords the ability to detect minute quantities of αSyn in peripheral tissues, but it also produces various technical challenges of variability. To address the problem of variability, we present a high-yield αSyn protein purification protocol for the efficient production of monomers with a low propensity for self-aggregation. We expressed wild-type αSyn in BL21 Escherichia coli, lysed the cells using osmotic shock, and isolated αSyn using acid precipitation and fast protein liquid chromatography (FPLC). Following purification, we optimized the ionic strength of the reaction buffer to distinguish the fluorescence maximum (Fmax) separation between disease and healthy control tissues for enhanced assay performance. Our protein purification protocol yielded high quantities of αSyn (average: 68.7 mg/mL per 1 L of culture) and showed highly precise and robust αSyn-SAA results using brain, skin, and SMGs with inter-lab validation.
Collapse
Affiliation(s)
- Chelva Janarthanam
- Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of Georgia, Athens, GA 30602, USA; (C.J.); (G.C.); (I.S.); (H.J.); (V.A.); (A.K.)
| | - Griffin Clabaugh
- Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of Georgia, Athens, GA 30602, USA; (C.J.); (G.C.); (I.S.); (H.J.); (V.A.); (A.K.)
| | - Zerui Wang
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
| | - Bradley R. Melvin
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA;
| | - Ileia Scheibe
- Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of Georgia, Athens, GA 30602, USA; (C.J.); (G.C.); (I.S.); (H.J.); (V.A.); (A.K.)
| | - Huajun Jin
- Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of Georgia, Athens, GA 30602, USA; (C.J.); (G.C.); (I.S.); (H.J.); (V.A.); (A.K.)
| | - Vellareddy Anantharam
- Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of Georgia, Athens, GA 30602, USA; (C.J.); (G.C.); (I.S.); (H.J.); (V.A.); (A.K.)
| | - Ramona J. B. Urbauer
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA; (R.J.B.U.); (J.L.U.)
| | - Jeffrey L. Urbauer
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA; (R.J.B.U.); (J.L.U.)
| | - Jiyan Ma
- Chinese Institute for Brain Research, Beijing 102206, China;
| | - Arthi Kanthasamy
- Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of Georgia, Athens, GA 30602, USA; (C.J.); (G.C.); (I.S.); (H.J.); (V.A.); (A.K.)
| | - Xuemei Huang
- Department of Neurology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA;
| | - Vincenzo Donadio
- IRCCS Institute of Neurological Sciences of Bologna, Complex Operational Unit Clinica Neurologica, 40138 Bologna, Italy;
| | - Wenquan Zou
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
| | - Anumantha G. Kanthasamy
- Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of Georgia, Athens, GA 30602, USA; (C.J.); (G.C.); (I.S.); (H.J.); (V.A.); (A.K.)
| |
Collapse
|
32
|
Pepanian A, Sommerfeld P, Binbay FA, Fischer D, Pietsch M, Imhof D. In-depth analysis of Gαs protein activity by probing different fluorescently labeled guanine nucleotides. Biol Chem 2024; 405:297-309. [PMID: 38353111 DOI: 10.1515/hsz-2023-0321] [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: 10/10/2023] [Accepted: 01/10/2024] [Indexed: 05/04/2024]
Abstract
G proteins are interacting partners of G protein-coupled receptors (GPCRs) in eukaryotic cells. Upon G protein activation, the ability of the Gα subunit to exchange GDP for GTP determines the intracellular signal transduction. Although various studies have successfully shown that both Gαs and Gαi have an opposite effect on the intracellular cAMP production, with the latter being commonly described as "more active", the functional analysis of Gαs is a comparably more complicated matter. Additionally, the thorough investigation of the ubiquitously expressed variants of Gαs, Gαs(short) and Gαs(long), is still pending. Since the previous experimental evaluation of the activity and function of the Gαs isoforms is not consistent, the focus was laid on structural investigations to understand the GTPase activity. Herein, we examined recombinant human Gαs by applying an established methodological setup developed for Gαi characterization. The ability for GTP binding was evaluated with fluorescence and fluorescence anisotropy assays, whereas the intrinsic hydrolytic activity of the isoforms was determined by a GTPase assay. Among different nucleotide probes, BODIPY FL GTPγS exhibited the highest binding affinity towards the Gαs subunit. This work provides a deeper understanding of the Gαs subunit and provides novel information concerning the differences between the two protein variants.
Collapse
Affiliation(s)
- Anna Pepanian
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Paul Sommerfeld
- Institutes I & II of Pharmacology, Center of Pharmacology, Faculty of Medicine and University Hospital Cologne, University of Cologne, D-50931 Cologne, Germany
| | - Furkan Ayberk Binbay
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Dietmar Fischer
- Institutes I & II of Pharmacology, Center of Pharmacology, Faculty of Medicine and University Hospital Cologne, University of Cologne, D-50931 Cologne, Germany
| | - Markus Pietsch
- Institutes I & II of Pharmacology, Center of Pharmacology, Faculty of Medicine and University Hospital Cologne, University of Cologne, D-50931 Cologne, Germany
- Faculty of Applied Natural Sciences, TH Köln-University of Applied Sciences, Campus Leverkusen, D-51379 Leverkusen, Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| |
Collapse
|
33
|
Liu Y, Xu J, Ma M, You T, Ye S, Liu S. Computational design towards a boiling-resistant single-chain sweet protein monellin. Food Chem 2024; 440:138279. [PMID: 38159314 DOI: 10.1016/j.foodchem.2023.138279] [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: 07/19/2023] [Revised: 12/18/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Sweet proteins offer a promising solution as sugar substitutes by providing a sugar-like sweetness without the negative health impacts linked to sugar or artificial sweeteners. However, the low thermal stability of sweet proteins has hindered their applications. In this study, we took a computational approach utilizing ΔΔG calculations in PyRosetta to enhance the thermostability of single-chain monellin (MNEI). By generating and characterizing 21 variants with single mutation, we identified 11 variants with higher melting temperature (Tm) than that of MNEI. To further enhance the thermal stability, we conducted structural analysis and designed an additional set of 14 variants with multiple mutations. Among these variants, four exhibited a significant improvement in thermal stability, with an increase of at least 20 °C (Tm > 96 °C) compared to MNEI, while maintaining their sweetness. Remarkably, these variants remained soluble even after being heated in boiling water for one hour. Moreover, they displayed exceptional stability across alkaline, acidic and neutral environments. These findings highlight the tremendous potential of these variants for applications in the food and beverage industry. Additionally, this study provides valuable strategies for protein engineering to enhance the thermal stability of sweet proteins.
Collapse
Affiliation(s)
- Yanmei Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Jiayu Xu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Mingxue Ma
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Tianjie You
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China.
| | - Si Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China.
| |
Collapse
|
34
|
Ding J, Qi L, Zhong L, Shang S, Zhu C, Lin S. Conformation-Activity Mechanism of Alcalase Hydrolysis for Reducing In Vitro Allergenicity of Instant Soy Milk Powder. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10627-10639. [PMID: 38664940 DOI: 10.1021/acs.jafc.4c00767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
Effective reduction of the allergenicity of instant soy milk powder (ISMP) is practically valuable for expanding its applications. This study optimized the enzymolysis technology of ISMP using single-factor experiments and response surface methodology, combined serological analysis, cellular immunological models, bioinformatics tools, and multiple spectroscopy techniques to investigate the effects of alcalase hydrolysis on allergenicity, spatial conformation, and linear epitopes of ISMP. Under the optimal process, special IgE and IgG1 binding abilities and allergenic activity to induce cell degranulation of alcalase-hydrolyzed ISMP were reduced by (64.72 ± 1.76)%, (56.79 ± 3.72)%, and (73.3 ± 1.19)%, respectively (P < 0.05). Moreover, the spatial conformation of instant soy milk powder hydrolysates (ISMPH) changed, including decreased surface hydrophobicity, a weaker peak of amide II band, lower contents of α-helix and β-sheet, and an enhanced content of random coil. Furthermore, the linear epitopes of major soy allergens, 9 from glycinin and 13 from β-conglycinin, could be directionally disrupted by alcalase hydrolysis. Overall, the structure-activity mechanism of alcalase hydrolysis to reduce ISMP allergenicity in vitro was preliminarily clarified. It provided a new research direction for the breakthrough in the desensitization of ISMP and a theoretical basis for revealing the potential mechanism of alcalase enzymolysis to reduce the allergenicity of ISMP.
Collapse
Affiliation(s)
- Jie Ding
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- Engineering Research Center of Food of Liaoning Province, Engineering Research Center of Special Dietary Food of Liaoning Province, Dalian 116034, P. R. China
| | - Libo Qi
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Limin Zhong
- Ganzhou Quanbiao Biological Technology Co. Ltd., Ganzhou 341100, P. R. China
| | - Shan Shang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Chunyan Zhu
- Ganzhou Quanbiao Biological Technology Co. Ltd., Ganzhou 341100, P. R. China
| | - Songyi Lin
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- Engineering Research Center of Food of Liaoning Province, Engineering Research Center of Special Dietary Food of Liaoning Province, Dalian 116034, P. R. China
- Ganzhou Quanbiao Biological Technology Co. Ltd., Ganzhou 341100, P. R. China
| |
Collapse
|
35
|
Brytan W, Shortall K, Duarte F, Soulimane T, Padrela L. Contribution of a C-Terminal Extension to the Substrate Affinity and Oligomeric Stability of Aldehyde Dehydrogenase from Thermus thermophilus HB27. Biochemistry 2024; 63:1075-1088. [PMID: 38602394 PMCID: PMC11080044 DOI: 10.1021/acs.biochem.3c00698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024]
Abstract
Aldehyde dehydrogenase enzymes (ALDHs) are widely studied for their roles in disease propagation and cell metabolism. Their use in biocatalysis applications, for the conversion of aldehydes to carboxylic acids, has also been recognized. Understanding the structural features and functions of both prokaryotic and eukaryotic ALDHs is key to uncovering novel applications of the enzyme and probing its role in disease propagation. The thermostable enzyme ALDHTt originating fromThermus thermophilus, strain HB27, possesses a unique extension of its C-terminus, which has been evolutionarily excluded from mesophilic counterparts and other thermophilic enzymes in the same genus. In this work, the thermophilic adaptation is studied by the expression and optimized purification of mutant ALDHTt-508, with a 22-amino acid truncation of the C-terminus. The mutant shows increased activity throughout production compared to native ALDHTt, indicating an opening of the active site upon C-terminus truncation and giving rationale into the evolutionary exclusion of the C-terminal extension from similar thermophilic and mesophilic ALDH proteins. Additionally, the C-terminus is shown to play a role in controlling substrate specificity of native ALDH, particularly in excluding catalysis of certain large and certain aromatic ortho-substituted aldehydes, as well as modulating the protein's pH tolerance by increasing surface charge. Dynamic light scattering and size-exclusion HPLC methods are used to show the role of the C-terminus in ALDHTt oligomeric stability at the cost of catalytic efficiency. Studying the aggregation rate of ALDHTt with and without a C-terminal extension leads to the conclusion that ALDHTt follows a monomolecular reaction aggregation mechanism.
Collapse
Affiliation(s)
- Wiktoria Brytan
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
| | - Kim Shortall
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
| | - Francisco Duarte
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
| | - Tewfik Soulimane
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
- SSPC
− The Science Foundation Ireland Research Centre for Pharmaceuticals, Limerick V94 T9PX,Ireland
| | - Luis Padrela
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
- SSPC
− The Science Foundation Ireland Research Centre for Pharmaceuticals, Limerick V94 T9PX,Ireland
| |
Collapse
|
36
|
Zhu R, Stone T, Wang Y. The role of shear rates on amyloid formation from biofilm peptide phenol-soluble modulins. Biophys J 2024; 123:1106-1115. [PMID: 38549371 PMCID: PMC11079943 DOI: 10.1016/j.bpj.2024.03.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/28/2024] [Accepted: 03/26/2024] [Indexed: 04/15/2024] Open
Abstract
Biofilms, microbial communities enclosed in the self-produced extracellular matrix, have a significant impact on human health, environment, and industry. The pathogen Staphylococcus aureus (S. aureus) is recognized as one of the most frequent causes of biofilm-related infections. Phenol-soluble modulins (PSMs) serve as a crucial component, fortifying S. aureus biofilm matrix through self-assembly into amyloid fibrils, which enhances S. aureus colonization and resistance to antibiotics. However, the role of shear rate, one of the critical physiological factors within blood vessels, on the formation of PSM amyloids remains poorly understood. In this work, using a combination of thioflavin T fluorescence kinetic studies, circular dichroism spectrometry, and electron microscopy, we demonstrated that shear rates ranging from 150 to 300 s-1 accelerate fibrillation of PSMα1, α3, and α4 into amyloids, resulting in elongated amyloid structures. Furthermore, PSMα1, α3, and α4 predominantly self-assembled into amyloid fibers with a cross-α structure under shear conditions, deviating from the typical β-sheet configuration of PSM amyloids. These findings imply the role of shear rates within the bloodstream on enhancing PSM self-assembly that is associated with S. aureus biofilm formation.
Collapse
Affiliation(s)
- Runyao Zhu
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana
| | - Trevor Stone
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana; Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia
| | - Yichun Wang
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana.
| |
Collapse
|
37
|
Jones C. Impact of imperfect data on protein secondary structure estimates from Far-UV circular dichroism spectra. Anal Biochem 2024; 688:115483. [PMID: 38360171 DOI: 10.1016/j.ab.2024.115483] [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: 10/27/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
Circular dichroism [CD] is widely used to rapidly assess protein structure. Deconvolution of the far-UV CD spectrum is widely used to quantify the secondary structural elements [SSEs]. Multiple algorithms are available for this. Imperfections in the experimental CD spectra arising from spectral noise, instrument miscalibration, spectral offsets and non-linearity will impact on the accuracy and precision of derived secondary structure estimates. Analytical validation for use in regulated environments, such as biopharmaceuticals, requires that the impact of imperfect data on these estimates be understood. Limited information on the impact of poor data were available. A series of noise-free simulated spectral datasets with modified intensity, wavelength, noise and intensity linearity and offsets were created from entries in the Protein Circular Dichroism Data Bank. These datasets were analysed using the BeStSel, on-line resource to estimate secondary structure. Data imperfections caused significant change in SSEs, but the spectral range is also important. This study emphasises the importance of analytical method validation and justifiable estimates of uncertainty when reporting results. The datasets created are made available as a resource to validate other secondary structure estimation programs.
Collapse
|
38
|
Meloni M, Rossi J, Fanti S, Carloni G, Tedesco D, Treffon P, Piccinini L, Falini G, Trost P, Vierling E, Licausi F, Giuntoli B, Musiani F, Fermani S, Zaffagnini M. Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1054-1070. [PMID: 38308388 DOI: 10.1111/tpj.16651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/07/2024] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Abstract
Alcohol dehydrogenases (ADHs) are a group of zinc-binding enzymes belonging to the medium-length dehydrogenase/reductase (MDR) protein superfamily. In plants, these enzymes fulfill important functions involving the reduction of toxic aldehydes to the corresponding alcohols (as well as catalyzing the reverse reaction, i.e., alcohol oxidation; ADH1) and the reduction of nitrosoglutathione (GSNO; ADH2/GSNOR). We investigated and compared the structural and biochemical properties of ADH1 and GSNOR from Arabidopsis thaliana. We expressed and purified ADH1 and GSNOR and determined two new structures, NADH-ADH1 and apo-GSNOR, thus completing the structural landscape of Arabidopsis ADHs in both apo- and holo-forms. A structural comparison of these Arabidopsis ADHs revealed a high sequence conservation (59% identity) and a similar fold. In contrast, a striking dissimilarity was observed in the catalytic cavity supporting substrate specificity and accommodation. Consistently, ADH1 and GSNOR showed strict specificity for their substrates (ethanol and GSNO, respectively), although both enzymes had the ability to oxidize long-chain alcohols, with ADH1 performing better than GSNOR. Both enzymes contain a high number of cysteines (12 and 15 out of 379 residues for ADH1 and GSNOR, respectively) and showed a significant and similar responsivity to thiol-oxidizing agents, indicating that redox modifications may constitute a mechanism for controlling enzyme activity under both optimal growth and stress conditions.
Collapse
Affiliation(s)
- Maria Meloni
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Jacopo Rossi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Silvia Fanti
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
| | - Giacomo Carloni
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
| | - Daniele Tedesco
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), 40129, Bologna, Italy
| | - Patrick Treffon
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Luca Piccinini
- Department of Biology, University of Pisa, Pisa, 56127, Italy
- Center for Plant Sciences, Scuola Superiore Sant'Anna, Pisa, 56124, Italy
| | - Giuseppe Falini
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Elizabeth Vierling
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | | | - Beatrice Giuntoli
- Department of Biology, University of Pisa, Pisa, 56127, Italy
- Center for Plant Sciences, Scuola Superiore Sant'Anna, Pisa, 56124, Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Simona Fermani
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
- Interdepartmental Centre for Industrial Research Health Sciences & Technologies, University of Bologna, 40064, Bologna, Italy
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| |
Collapse
|
39
|
Huang F, Dai Q, Zheng K, Ma Q, Liu Y, Jiang S, Jiang W, Yan X. Exploring the inhibitory potential of KPHs-AL-derived GLLF peptide on pancreatic lipase and cholesterol esterase activities. Food Chem 2024; 439:138108. [PMID: 38061297 DOI: 10.1016/j.foodchem.2023.138108] [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: 09/15/2023] [Revised: 11/25/2023] [Accepted: 11/26/2023] [Indexed: 01/10/2024]
Abstract
The effective modulation of pancreatic lipase and cholesterol esterase activities proves critical in maintaining circulatory triglycerides and cholesterol levels within physiological boundaries. In this study, peptides derived from KPHs-AL, produced through the enzymatic hydrolysis of skipjack tuna dark muscle using alkaline protease, have a specific inhibitory effect on pancreatic lipase and cholesterol esterase. It is hypothesized that these peptides target and modulate the activities of enzymes by inducing conformational changes within their binding pockets, potentially impacting the catalytic functions of both pancreatic lipase and cholesterol esterase. Results revealed these peptides including AINDPFIDL, FLGM, GLLF and WGPL, were found to nestle into the binding site groove of pancreatic lipase and cholesterol esterase. Among these, GLLF stood out, demonstrating potent inhibition with IC50 values of 0.1891 mg/mL and 0.2534 mg/mL for pancreatic lipase and cholesterol esterase, respectively. The kinetics studies suggested that GLLF competed effectively with substrates for the enzyme active sites. Spectroscopic analyses, including ultraviolet-visible, fluorescence quenching, and circular dichroism, indicated that GLLF binding induced conformational changes within the enzymes, likely through hydrogen bond formation and hydrophobic interactions, thereby increasing structural flexibility. Molecular docking and molecular dynamics simulations supported these findings, showing GLLF's stable interaction with vital active site residues. These findings position GLLF as a potent inhibitor of key digestive enzymes, offering insights into its role in regulating lipid metabolism and highlighting its potential as functional ingredient.
Collapse
Affiliation(s)
- Fangfang Huang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China; Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China; Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Qingfei Dai
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Kewei Zheng
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Qingbao Ma
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Yu Liu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Shuoqi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Li-Hu Road, Bin-Hu District, Wuxi, Jiangsu, China
| | - Wei Jiang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China; Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China.
| | - Xiaojun Yan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China; Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| |
Collapse
|
40
|
Kuang X, Deng Z, Feng B, He R, Chen L, Liang G. The mechanism of epigallocatechin-3-gallate inhibiting the antigenicity of β-lactoglobulin under pH 6.2, 7.4 and 8.2: Multi-spectroscopy and molecular simulation methods. Int J Biol Macromol 2024; 268:131773. [PMID: 38657930 DOI: 10.1016/j.ijbiomac.2024.131773] [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: 12/18/2023] [Revised: 03/01/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
The antigenicity of β-lactoglobulin (β-LG) can be influenced by pH values and reduced by epigallocatechin-3-gallate (EGCG). However, a detailed mechanism concerning EGCG decreasing the antigenicity of β-LG at different pH levels lacks clarity. Here, we explore the inhibition mechanism of EGCG on the antigenicity of β-LG at pH 6.2, 7.4 and 8.2 using enzyme-linked immunosorbent assay, multi-spectroscopy, mass spectrometry and molecular simulations. The results of Fourier transform infrared spectroscopy (FTIR) and circular dichroism (CD) elucidate that the noncovalent binding of EGCG with β-LG induces variations in the secondary structure and conformations of β-LG. Moreover, EGCG inhibits the antigenicity of β-LG the most at pH 7.4 (98.30 %), followed by pH 6.2 (73.18 %) and pH 8.2 (36.24 %). The inhibitory difference is attributed to the disparity in the number of epitopes involved in the interacting regions of EGCG and β-LG. Our findings suggest that manipulating pH conditions may enhance the effectiveness of antigenic inhibitors, with the potential for further application in the food industry.
Collapse
Affiliation(s)
- Xiaoyu Kuang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400045, China
| | - Zhifen Deng
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400045, China
| | - Bowen Feng
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400045, China
| | - Ran He
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400045, China
| | - Lang Chen
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400045, China
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400045, China.
| |
Collapse
|
41
|
Armanious GP, Lemieux MJ, Espinoza-Fonseca LM, Young HS. Missense variants in phospholamban and cardiac myosin binding protein identified in patients with a family history and clinical diagnosis of dilated cardiomyopathy. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119699. [PMID: 38387507 DOI: 10.1016/j.bbamcr.2024.119699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/07/2023] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
As the genetic landscape of cardiomyopathies continues to expand, the identification of missense variants in disease-associated genes frequently leads to a classification of variant of uncertain significance (VUS). For the proper reclassification of such variants, functional characterization is an important contributor to the proper assessment of pathogenic potential. Several missense variants in the calcium transport regulatory protein phospholamban have been associated with dilated cardiomyopathy. However, >40 missense variants in this transmembrane peptide are currently known and most remain classified as VUS with little clinical information. Similarly, missense variants in cardiac myosin binding protein have been associated with hypertrophic cardiomyopathy. However, hundreds of variants are known and many have low penetrance and are often found in control populations. Herein, we focused on novel missense variants in phospholamban, an Ala15-Thr variant found in a 4-year-old female and a Pro21-Thr variant found in a 60-year-old female, both with a family history and clinical diagnosis of dilated cardiomyopathy. The patients also harbored a Val896-Met variant in cardiac myosin binding protein. The phospholamban variants caused defects in the function, phosphorylation, and dephosphorylation of this calcium transport regulatory peptide, and we classified these variants as potentially pathogenic. The variant in cardiac myosin binding protein alters the structure of the protein. While this variant has been classified as benign, it has the potential to be a low-risk susceptibility variant because of the structural change in cardiac myosin binding protein. Our studies provide new biochemical evidence for missense variants previously classified as benign or VUS.
Collapse
Affiliation(s)
- Gareth P Armanious
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - L Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Howard S Young
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
| |
Collapse
|
42
|
Sania A, Muhammad MA, Sajed M, Azim N, Ahmad N, Aslam M, Tang XF, Rashid N. Structural and functional analyses of an L-asparaginase from Geobacillus thermopakistaniensis. Int J Biol Macromol 2024; 263:130438. [PMID: 38408579 DOI: 10.1016/j.ijbiomac.2024.130438] [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: 11/14/2023] [Revised: 01/29/2024] [Accepted: 02/23/2024] [Indexed: 02/28/2024]
Abstract
Genome sequence of Geobacillus thermopakistaniensis contains an open reading frame annotated as a type II L-asparaginase (ASNaseGt). Critical structural analysis disclosed that ASNaseGt might be a type I L-asparaginase. In order to determine whether it is a type I or type II L-asparaginase, we have performed the structural-functional characterization of the recombinant protein as well as analyzed the localization of ASNaseGt in G. thermopakistaniensis. ASNaseGt exhibited optimal activity at 52 °C and pH 9.5. There was a > 3-fold increase in activity in the presence of β-mercaptoethanol. Apparent Vmax and Km values were 2735 U/mg and 0.35 mM, respectively. ASNaseGt displayed high thermostability with >80 % residual activity even after 6 h of incubation at 55 °C. Recombinant ASNaseGt existed in oligomeric form. Addition of β-mercaptoethanol lowered the degree of oligomerization and displayed that tetrameric form was the most active, with a specific activity of 4300 U/mg. Under physiological conditions, ASNaseGt displayed >50 % of the optimal activity. Localization studies in G. thermopakistaniensis revealed that ASNaseGt is a cytosolic protein. Structural and functional characterization, and localization in G. thermopakistaniensis displayed that ASNaseGt is not a type II but a type I L-asparaginase.
Collapse
Affiliation(s)
- Ayesha Sania
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Majida Atta Muhammad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Muhammad Sajed
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naseema Azim
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Nasir Ahmad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Mehwish Aslam
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Xiao-Feng Tang
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei Province, China
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan.
| |
Collapse
|
43
|
Stefan A, Mucchi A, Hochkoeppler A. The catalytic action of human d-lactate dehydrogenase is severely inhibited by oxalate and is impaired by mutations triggering d-lactate acidosis. Arch Biochem Biophys 2024; 754:109932. [PMID: 38373542 DOI: 10.1016/j.abb.2024.109932] [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: 11/03/2023] [Revised: 01/29/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
d-lactate dehydrogenases are known to be expressed by prokaryotes and by eukaryotic invertebrates, and over the years the functional and structural features of some bacterial representatives of this enzyme ensemble have been investigated quite in detail. Remarkably, a human gene coding for a putative d-lactate dehydrogenase (DLDH) was identified and characterized, disclosing the occurrence of alternative splicing of its primary transcript. This translates into the expression of two human DLDH (hDLDH) isoforms, the molecular mass of which is expected to differ by 2.7 kDa. However, no information on these two hDLDH isoforms is available at the protein level. Here we report on the catalytic action of these enzymes, along with a first analysis of their structural features. In particular, we show that hDLDH is strictly stereospecific, with the larger isoform (hDLDH-1) featuring higher activity at the expense of d-lactate when compared to its smaller counterpart (hDLDH-2). Furthermore, we found that hDLDH is strongly inhibited by oxalate, as indicated by a Ki equal to 1.2 μM for this dicarboxylic acid. Structurally speaking, hDLDH-1 and hDLDH-2 were determined, by means of gel filtration and dynamic light scattering experiments, to be a hexamer and a tetramer, respectively. Moreover, in agreement with previous studies performed with human mitochondria, we identified FAD as the cofactor of hDLDH, and we report here a model of FAD binding by the human d-lactate dehydrogenase. Interestingly, the mutations W323C and T412 M negatively affect the activity of hDLDH, most likely by impairing the enzyme electron-acceptor site.
Collapse
Affiliation(s)
- Alessandra Stefan
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy
| | - Alberto Mucchi
- Department of Industrial Chemistry "Toso Montanari", Viale Risorgimento 4, 40136, Bologna, Italy
| | - Alejandro Hochkoeppler
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy.
| |
Collapse
|
44
|
Dávalos AL, Rivera Echeverri JD, Favaro DC, Junio de Oliveira R, Penteado Battesini Carretero G, Lacerda C, Midea Cuccovia I, Cangussu Cardoso MV, Farah CS, Kopke Salinas R. Uncovering the Association Mechanism between Two Intrinsically Flexible Proteins. ACS Chem Biol 2024; 19:669-686. [PMID: 38486495 DOI: 10.1021/acschembio.3c00649] [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: 03/19/2024]
Abstract
The understanding of protein-protein interaction mechanisms is key to the atomistic description of cell signaling pathways and for the development of new drugs. In this context, the mechanism of intrinsically disordered proteins folding upon binding has attracted attention. The VirB9 C-terminal domain (VirB9Ct) and the VirB7 N-terminal motif (VirB7Nt) associate with VirB10 to form the outer membrane core complex of the Type IV Secretion System injectisome. Despite forming a stable and rigid complex, VirB7Nt behaves as a random coil, while VirB9Ct is intrinsically dynamic in the free state. Here we combined NMR, stopped-flow fluorescence, and computer simulations using structure-based models to characterize the VirB9Ct-VirB7Nt coupled folding and binding mechanism. Qualitative data analysis suggested that VirB9Ct preferentially binds to VirB7Nt by way of a conformational selection mechanism at lower temperatures. However, at higher temperatures, energy barriers between different VirB9Ct conformations are more easily surpassed. Under these conditions the formation of non-native initial encounter complexes may provide alternative pathways toward the native complex conformation. These observations highlight the intimate relationship between folding and binding, calling attention to the fact that the two molecular partners must search for the most favored intramolecular and intermolecular interactions on a rugged and funnelled conformational energy landscape, along which multiple intermediates may lead to the final native state.
Collapse
Affiliation(s)
- Angy Liseth Dávalos
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | | | - Denize C Favaro
- Department of Organic Chemistry, State University of Campinas, Campinas, 13083-862, Brazil
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York 10031, United States
| | - Ronaldo Junio de Oliveira
- Department of Physics, Institute of Exact, Natural and Educational Sciences, Federal University of Triângulo Mineiro, Uberaba, 38064-200, Brazil
| | | | - Caroline Lacerda
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Iolanda Midea Cuccovia
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | | | - Chuck S Farah
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Roberto Kopke Salinas
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| |
Collapse
|
45
|
Heber S, McClintock MA, Simon B, Mehtab E, Lapouge K, Hennig J, Bullock SL, Ephrussi A. Tropomyosin 1-I/C coordinates kinesin-1 and dynein motors during oskar mRNA transport. Nat Struct Mol Biol 2024; 31:476-488. [PMID: 38297086 PMCID: PMC10948360 DOI: 10.1038/s41594-024-01212-x] [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: 03/16/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Dynein and kinesin motors mediate long-range intracellular transport, translocating towards microtubule minus and plus ends, respectively. Cargoes often undergo bidirectional transport by binding to both motors simultaneously. However, it is not known how motor activities are coordinated in such circumstances. In the Drosophila female germline, sequential activities of the dynein-dynactin-BicD-Egalitarian (DDBE) complex and of kinesin-1 deliver oskar messenger RNA from nurse cells to the oocyte, and within the oocyte to the posterior pole. We show through in vitro reconstitution that Tm1-I/C, a tropomyosin-1 isoform, links kinesin-1 in a strongly inhibited state to DDBE-associated oskar mRNA. Nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and structural modeling indicate that Tm1-I/C suppresses kinesin-1 activity by stabilizing its autoinhibited conformation, thus preventing competition with dynein until kinesin-1 is activated in the oocyte. Our work reveals a new strategy for ensuring sequential activity of microtubule motors.
Collapse
Affiliation(s)
- Simone Heber
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mark A McClintock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Eve Mehtab
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany
| | - Simon L Bullock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| |
Collapse
|
46
|
Vásquez-Suárez A, Muñoz-Flores C, Ortega L, Roa F, Castillo C, Romero A, Parra N, Sandoval F, Macaya L, González-Chavarría I, Astuya A, Starck MF, Villegas MF, Agurto N, Montesino R, Sánchez O, Valenzuela A, Toledo JR, Acosta J. Design and functional characterization of Salmo salar TLR5 agonist peptides derived from high mobility group B1 acidic tail. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109373. [PMID: 38272332 DOI: 10.1016/j.fsi.2024.109373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/21/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024]
Abstract
Toll-like receptor 5 (TLR5) responds to the monomeric form of flagellin and induces the MyD88-depending signaling pathway, activating proinflammatory transcription factors such as NF-κB and the consequent induction of cytokines. On the other hand, HMGB1 is a highly conserved non-histone chromosomal protein shown to interact with and activate TLR5. The present work aimed to design and characterize TLR5 agonist peptides derived from the acidic tail of Salmo salar HMGB1 based on the structural knowledge of the TLR5 surface using global molecular docking platforms. Peptide binding poses complexed on TLR5 ectodomain model from each algorithm were filtrated based on docking scoring functions and predicted theoretical binding affinity of the complex. Circular dichroism spectra were recorded for each peptide selected for synthesis. Only intrinsically disordered peptides (6W, 11W, and SsOri) were selected for experimental functional assay. The functional characterization of the peptides was performed by NF-κB activation assays, RT-qPCR gene expression assays, and Piscirickettsia salmonis challenge in SHK-1 cells. The 6W and 11W peptides increased the nuclear translation of p65 and phosphorylation. In addition, the peptides induced the expression of genes related to the TLR5 pathway activation, pro- and anti-inflammatory response, and differentiation and activation of T lymphocytes towards phenotypes such as TH1, TH17, and TH2. Finally, it was shown that the 11W peptide protects immune cells against infection with P. salmonis bacteria. Overall, the results indicate the usefulness of novel peptides as potential immunostimulants in salmonids.
Collapse
Affiliation(s)
- Aleikar Vásquez-Suárez
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Carolina Muñoz-Flores
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Leonardo Ortega
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Francisco Roa
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Carolina Castillo
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Alex Romero
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
| | - Natalie Parra
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Felipe Sandoval
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Luis Macaya
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Iván González-Chavarría
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Allisson Astuya
- Laboratorio de Genómica Marina y Cultivo Celular, Departamento de Oceanografía y COPAS Sur-Austral, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - María Francisca Starck
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Milton F Villegas
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Niza Agurto
- Laboratorio de Piscicultura y Patología Acuática, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Raquel Montesino
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Oliberto Sánchez
- Laboratorio de Biofármacos Recombinantes, Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Ariel Valenzuela
- Laboratorio de Piscicultura y Patología Acuática, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Jorge R Toledo
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
| | - Jannel Acosta
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
| |
Collapse
|
47
|
Zhang J, Li Y, Gao H, Zhang H, Zhang X, Rao Z, Xu M. N-terminal truncation (N-) and directional proton transfer in an old yellow enzyme enables tunable efficient producing (R)- or (S)-citronellal. Int J Biol Macromol 2024; 262:130129. [PMID: 38354939 DOI: 10.1016/j.ijbiomac.2024.130129] [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: 11/05/2023] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
(R)-Citronellal is a valuable molecule as the precursor for the industrial synthesis of (-)-menthol, one of the worldwide best-selling compounds in the flavors and fragrances field. However, its biocatalytic production, even from the optically pure substrate (E)-citral, is inherently limited by the activity of Old Yellow Enzyme (OYE). Herein, we rationally designed a different approach to increase the activity of OYE in biocatalytic production. The activity of OYE from Corynebacterium glutamicum (CgOYE) is increased, as well as superior thermal stability and pH tolerance via truncating the different lengths of regions at N-terminal of CgOYE. Next, we converted the truncation mutant N31-CgOYE, a protein involved in proton transfer for the asymmetric hydrogenation of CC bonds, into highly (R)- and (S)-stereoselective enzymes using only three mutations. The mixture of racemic (E/Z)-citral is reduced into the (R)-citronellal with ee and conversion up to 99 % by the mutant of CgOYE, overcoming the problem of the reduction for the mixtures of (E/Z)-citral in biocatalytic reaction. The present work provides a general and effective strategy for improving the activity of OYE, in which the partially conserved histidine residues provide "tunable gating" for the enantioselectivity for both the (R)- and (S)-isomerases.
Collapse
Affiliation(s)
- Jie Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yueshu Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Hui Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Hengwei Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China..
| |
Collapse
|
48
|
Shu E, Wang S, Kong X, Sun X, Yang Q, Chen Q, Niu B. Effects of Flavourzyme and Alkaline Protease Treatment on Structure and Allergenicity of Peanut Allergen Ara h 1. Food Technol Biotechnol 2024; 62:4-14. [PMID: 38601963 PMCID: PMC11002447 DOI: 10.17113/ftb.62.01.24.8064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 12/18/2023] [Indexed: 04/12/2024] Open
Abstract
Research background Peanut allergy poses a significant threat to human health due to the increased risk of long-term morbidity at low doses. Modifying protein structure to affect sensitization is a popular topic. Experimental approach In this study, the purified peanut allergen Ara h 1 was enzymatically hydrolysed using Flavourzyme, alkaline protease or a combination of both. The binding ability of Ara h 1 to antibodies, gene expression and secretion levels of the proinflammatory factors interleukin-5 and interleukin-6 in Caco-2 cells was measured. Changes in the secondary and tertiary structures before and after treatment with Ara h 1 were analysed by circular dichroism and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Results and conclusions The results indicated a decrease of the allergenicity and proinflammatory ability of Ara h 1. The evaluation showed that the Flavourzyme and alkaline protease treatments caused particle shortening and aggregation. The fluorescence emission peak increased by 3.4-fold after the combined treatment with both proteases. Additionally, the secondary structure underwent changes and the hydrophobicity also increased 8.95-fold after the combined treatment. Novelty and scientific contribution These findings partially uncover the mechanism of peanut sensitization and provide an effective theoretical basis for the development of a new method of peanut desensitization.
Collapse
Affiliation(s)
- Erlian Shu
- School of Life Sciences, Shanghai University, No. 99, Shangda Road, Baoshan District, 200444 Shanghai, PRChina
| | - Shuo Wang
- School of Life Sciences, Shanghai University, No. 99, Shangda Road, Baoshan District, 200444 Shanghai, PRChina
| | - Xiangxiang Kong
- School of Life Sciences, Shanghai University, No. 99, Shangda Road, Baoshan District, 200444 Shanghai, PRChina
| | - Xiaodong Sun
- School of Medicine, Shanghai University, No. 99, Shangda Road, Baoshan District, 200444 Shanghai, PRChina
| | - Qiaoling Yang
- School of Environmental and Chemical Engineering, Shanghai University, No. 99, Shangda Road, Baoshan District, 200444 Shanghai, PRChina
| | - Qin Chen
- School of Life Sciences, Shanghai University, No. 99, Shangda Road, Baoshan District, 200444 Shanghai, PRChina
| | - Bing Niu
- School of Life Sciences, Shanghai University, No. 99, Shangda Road, Baoshan District, 200444 Shanghai, PRChina
| |
Collapse
|
49
|
Tsukada K, Jones SE, Bannister J, Durin MA, Vendrell I, Fawkes M, Fischer R, Kessler BM, Chapman JR, Blackford AN. BLM and BRCA1-BARD1 coordinate complementary mechanisms of joint DNA molecule resolution. Mol Cell 2024; 84:640-658.e10. [PMID: 38266639 DOI: 10.1016/j.molcel.2023.12.040] [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: 03/18/2023] [Revised: 10/10/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The Bloom syndrome helicase BLM interacts with topoisomerase IIIα (TOP3A), RMI1, and RMI2 to form the BTR complex, which dissolves double Holliday junctions and DNA replication intermediates to promote sister chromatid disjunction before cell division. In its absence, structure-specific nucleases like the SMX complex (comprising SLX1-SLX4, MUS81-EME1, and XPF-ERCC1) can cleave joint DNA molecules instead, but cells deficient in both BTR and SMX are not viable. Here, we identify a negative genetic interaction between BLM loss and deficiency in the BRCA1-BARD1 tumor suppressor complex. We show that this is due to a previously overlooked role for BARD1 in recruiting SLX4 to resolve DNA intermediates left unprocessed by BLM in the preceding interphase. Consequently, cells with defective BLM and BRCA1-BARD1 accumulate catastrophic levels of chromosome breakage and micronucleation, leading to cell death. Thus, we reveal mechanistic insights into SLX4 recruitment to DNA lesions, with potential clinical implications for treating BRCA1-deficient tumors.
Collapse
Affiliation(s)
- Kaima Tsukada
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Samuel E Jones
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Julius Bannister
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Mary-Anne Durin
- MRC Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Matthew Fawkes
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - J Ross Chapman
- MRC Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
| |
Collapse
|
50
|
Kava E, Garbelotti CV, Lopes JLS, Costa-Filho AJ. Myristoylated GRASP55 dimerizes in the presence of model membranes. J Biomol Struct Dyn 2024:1-12. [PMID: 38361284 DOI: 10.1080/07391102.2024.2317973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
The Golgi Reassembly and Stacking Proteins (GRASPs) are engaged in various functions within the cell, both in unconventional secretion mechanisms and structuring and organizing the Golgi apparatus. Understanding their specific role in each situation still requires more structural and functional data at the molecular level. GRASP55 is one of the GRASP members in mammals, anchored to the membrane via the myristoylation of a Gly residue at its N-terminus. Therefore, co-translational modifications, such as myristoylation, are fundamental when considering a strategy to obtain detailed information on the interactions between GRASP55 and membranes. Despite its functional relevance, the N-terminal myristoylation has been underappreciated in the studies reported to date, compromising the previously proposed models for GRASP-membrane interactions. Here, we investigated the synergy between the presence of the membrane and the formation of oligomeric structures of myristoylated GRASP55, using a series of biophysical techniques to perform the structural characterization of the lipidated GRASP55 and its interaction with biological lipid model membranes. Our data fulfill an unexplored gap: the adequate evaluation of the presence of lipidations and lipid membranes on the structure-function dyad of GRASPs.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Emanuel Kava
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Carolina V Garbelotti
- Laboratório de Fisiologia Ecológica de Plantas, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - José Luiz S Lopes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| |
Collapse
|