1
|
Puławski W, Koliński A, Koliński M. Integrative modeling of diverse protein-peptide systems using CABS-dock. PLoS Comput Biol 2023; 19:e1011275. [PMID: 37405984 DOI: 10.1371/journal.pcbi.1011275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023] Open
Abstract
The CABS model can be applied to a wide range of protein-protein and protein-peptide molecular modeling tasks, such as simulating folding pathways, predicting structures, docking, and analyzing the structural dynamics of molecular complexes. In this work, we use the CABS-dock tool in two diverse modeling tasks: 1) predicting the structures of amyloid protofilaments and 2) identifying cleavage sites in the peptide substrates of proteolytic enzymes. In the first case, simulations of the simultaneous docking of amyloidogenic peptides indicated that the CABS model can accurately predict the structures of amyloid protofilaments which have an in-register parallel architecture. Scoring based on a combination of symmetry criteria and estimated interaction energy values for bound monomers enables the identification of protofilament models that closely match their experimental structures for 5 out of 6 analyzed systems. For the second task, it has been shown that CABS-dock coarse-grained docking simulations can be used to identify the positions of cleavage sites in the peptide substrates of proteolytic enzymes. The cleavage site position was correctly identified for 12 out of 15 analyzed peptides. When combined with sequence-based methods, these docking simulations may lead to an efficient way of predicting cleavage sites in degraded proteins. The method also provides the atomic structures of enzyme-substrate complexes, which can give insights into enzyme-substrate interactions that are crucial for the design of new potent inhibitors.
Collapse
Affiliation(s)
- Wojciech Puławski
- Bioinformatics Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | | | - Michał Koliński
- Bioinformatics Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
2
|
Comparison of the interactions of fanetizole with pepsin and trypsin: Spectroscopic and molecular docking approach. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
3
|
Ree BJ, Satoh Y, Jin KS, Isono T, Satoh T. Unimodal and Well-Defined Nanomicelles Assembled by Topology-Controlled Bicyclic Block Copolymers. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c01916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brian J. Ree
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Yusuke Satoh
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Kyeong Sik Jin
- PLS-II Beamline Division, Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Takuya Isono
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Toshifumi Satoh
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| |
Collapse
|
4
|
Investigation on the interaction behavior between safranal and pepsin by spectral and MD simulation studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
5
|
Evaluation of interaction between citrus flavonoid, naringenin, and pepsin using spectroscopic analysis and docking simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116763] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
6
|
Niu C, Wan X. Engineering a Trypsin-Resistant Thermophilic α-Galactosidase to Enhance Pepsin Resistance, Acidic Tolerance, Catalytic Performance, and Potential in the Food and Feed Industry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10560-10573. [PMID: 32829638 DOI: 10.1021/acs.jafc.0c02175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
α-Galactosidase has potential applications, and attempts to improve proteolytic resistance of enzymes have important values. We use a novel strategy for genetic manipulation of a pepsin-sensitive region specific for a pepsin-sensitive but trypsin-resistant high-temperature-active Gal27B from Neosartorya fischeri to screen mutants with enhanced pepsin resistance. All enzymes were produced in Pichia pastoris to identify the roles of loop 4 (Gal27B-A23) and its key residue at position 156 (Gly156Arg/Pro/His) in pepsin resistance. Gal27B-A23 and Gly156Arg/Pro/His elevated pepsin resistance, thermostability, stability at low pH, activity toward raffinose (5.3-6.9-fold) and stachyose (about 1.3-fold), and catalytic efficiencies (up to 4.9-fold). Replacing the pepsin cleavage site Glu155 with Gly improved pepsin resistance but had no effect on pepsin resistance when Arg/Pro/His was at position 156. Thus, pepsin resistance could appear to occur through steric hindrance between the residue at the altered site and neighboring pepsin active site. In the presence of pepsin or trypsin, all mutations increased the ability of Gal27B to hydrolyze galactosaccharides in soybean flour (up to 9.6- and 4.3-fold, respectively) and promoted apparent metabolizable energy and nutrient digestibility in soybean meal for broilers (1.3-1.8-fold). The high activity and tolerance to heat, low pH, and protease benefit food and feed industry in a cost-effective way.
Collapse
Affiliation(s)
- Canfang Niu
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
| |
Collapse
|
7
|
El-Sayed N, Schneider M. Advances in biomedical and pharmaceutical applications of protein-stabilized gold nanoclusters. J Mater Chem B 2020; 8:8952-8971. [PMID: 32901648 DOI: 10.1039/d0tb01610a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
The interest in using gold nanoclusters (AuNCs) as imaging probes is growing, covering wide ranges of applications. The stabilization of AuNCs with protein ligands enhances their biomedical and pharmaceutical applications. This is due to the biocompatibility, water solubility and bioactivity of proteins. Different factors can control the optical properties of AuNCs such as protein size, amino acids content and conformational structure. Controlling the synthesis conditions can result in tuning the AuNCs excitation, emission, fluorescence intensity and physicochemical properties to fulfill different applications. NIR-emitting protein-stabilized AuNCs are promising as imaging agents for targeting and visualization of cancer in vitro and in vivo. They are promising to be included as an important part of multifunctional theranostic nanosystems, due to their potential dual functions as imaging and photosensitizing agent for photodynamic therapy. Additionally, the protein around AuNCs represents a rich environment of active functional groups that are susceptible for conjugation with various biomolecules. Protein-AuNCs can act as fluorescent probes for rapid and selective analysis of different analytes in solution, cells or biological fluids. In conclusion, the variability of protein-AuNC applications can advance research in different biomedical and pharmaceutical fields.
Collapse
Affiliation(s)
- Nesma El-Sayed
- Department of Pharmacy, Biopharmaceutics and Pharmaceutical Technology, Saarland University, Campus C4 1, D-66123 Saarbrücken, Germany. and Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt.
| | - Marc Schneider
- Department of Pharmacy, Biopharmaceutics and Pharmaceutical Technology, Saarland University, Campus C4 1, D-66123 Saarbrücken, Germany.
| |
Collapse
|
8
|
Guo Y, Amunyela HTNN, Cheng Y, Xie Y, Yu H, Yao W, Li HW, Qian H. Natural protein-templated fluorescent gold nanoclusters: Syntheses and applications. Food Chem 2020; 335:127657. [PMID: 32738539 DOI: 10.1016/j.foodchem.2020.127657] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 07/01/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022]
Abstract
For the past decades, the synthesis of metal nanoclusters has been a great interest for research, for their unique physicochemical properties and great contributions to the catalytic, electrical and biomedical applications. Protein-templated gold nanoclusters (AuNCs) is a kind of fluorescent nanomaterials with good solubility, excellent stability, biocompatibility, decent quantum yields and active groups (-COOH, -NH2) for facilitating modifications. Natural proteins are easily available, commercially affordable, diverse and multitudinous in animals, plants and foods, which provide a template pool for the exploration of AuNCs. This is one of the few reviews of specifically focusing on the natural protein-templated fluorescent AuNCs. The syntheses, properties and applications of different AuNCs were enumerated. Prospects were given on utilizing structure-modified proteins, bioactive enzymes, antibodies which should endow the AuNCs more favourable fluorescence performances and functional characteristics. The applications of AuNCs in analytical, biomedical and food sciences would be further heightened.
Collapse
Affiliation(s)
- Yahui Guo
- State Key Laboratory of Food Science and Technology, National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Helena T N N Amunyela
- State Key Laboratory of Food Science and Technology, National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yuliang Cheng
- State Key Laboratory of Food Science and Technology, National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yunfei Xie
- State Key Laboratory of Food Science and Technology, National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hang Yu
- State Key Laboratory of Food Science and Technology, National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology, National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hung-Wing Li
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
| | - He Qian
- State Key Laboratory of Food Science and Technology, National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
9
|
Zhang S, Zhang X, Su Z. Biomolecule conjugated metal nanoclusters: bio-inspiration strategies, targeted therapeutics, and diagnostics. J Mater Chem B 2020; 8:4176-4194. [DOI: 10.1039/c9tb02936b] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To help those suffering from viral infections and cancers, scientists are exploring enhanced therapeutic methods via metal nanoclusters (MNCs).
Collapse
Affiliation(s)
- Shan Zhang
- State Key Laboratory of Chemical Resource Engineering
- Beijing Key Laboratory of Advanced Functional Polymer Composites
- Beijing University of Chemical Technology
- 100029 Beijing
- China
| | - Xiaoyuan Zhang
- Faculty of Physics and Astronomy
- Friedrich-Schiller University Jena
- 07743 Jena
- Germany
| | - Zhiqiang Su
- State Key Laboratory of Chemical Resource Engineering
- Beijing Key Laboratory of Advanced Functional Polymer Composites
- Beijing University of Chemical Technology
- 100029 Beijing
- China
| |
Collapse
|
10
|
Rho Y, Kim JH, Min B, Jin KS. Chemically Denatured Structures of Porcine Pepsin using Small-Angle X-ray Scattering. Polymers (Basel) 2019; 11:polym11122104. [PMID: 31847418 PMCID: PMC6961028 DOI: 10.3390/polym11122104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 11/16/2022] Open
Abstract
Porcine pepsin is a gastric aspartic proteinase that reportedly plays a pivotal role in the digestive process of many vertebrates. We have investigated the three-dimensional (3D) structure and conformational transition of porcine pepsin in solution over a wide range of denaturant urea concentrations (0–10 M) using Raman spectroscopy and small-angle X-ray scattering. Furthermore, 3D GASBOR ab initio structural models, which provide an adequate conformational description of pepsin under varying denatured conditions, were successfully constructed. It was shown that pepsin molecules retain native conformation at 0–5 M urea, undergo partial denaturation at 6 M urea, and display a strongly unfolded conformation at 7–10 M urea. According to the resulting GASBOR solution models, we identified an intermediate pepsin conformation that was dominant during the early stage of denaturation. We believe that the structural evidence presented here provides useful insights into the relationship between enzymatic activity and conformation of porcine pepsin at different states of denaturation.
Collapse
Affiliation(s)
- Yecheol Rho
- Chemical Analysis Center, Korea Research Institute of Chemical Technology, 141, Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea;
| | - Jun Ha Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-beongil, Nam-Gu, Pohang, Kyungbuk 37673, Korea; (J.H.K.); (B.M.)
| | - Byoungseok Min
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-beongil, Nam-Gu, Pohang, Kyungbuk 37673, Korea; (J.H.K.); (B.M.)
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-beongil, Nam-Gu, Pohang, Kyungbuk 37673, Korea; (J.H.K.); (B.M.)
- Correspondence: ; Tel.: +82-54-279-1573; Fax: +82-54-279-1599
| |
Collapse
|
11
|
Wang X, Yue Y, Zhang Y, Wang Z, Liu J, Tang Q. Probing the interaction of pepsin with imidacloprid via DFT calculation, spectroscopic approaches and molecular docking. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.07.061] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
12
|
Vergauwe RMA, Thomas A, Nagarajan K, Shalabney A, George J, Chervy T, Seidel M, Devaux E, Torbeev V, Ebbesen TW. Modification of Enzyme Activity by Vibrational Strong Coupling of Water. Angew Chem Int Ed Engl 2019; 58:15324-15328. [PMID: 31449707 PMCID: PMC6856831 DOI: 10.1002/anie.201908876] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/23/2019] [Indexed: 01/06/2023]
Abstract
Vibrational strong coupling (VSC) has recently emerged as a completely new tool for influencing chemical reactivity. It harnesses electromagnetic vacuum fluctuations through the creation of hybrid states of light and matter, called polaritonic states, in an optical cavity resonant to a molecular absorption band. Here, we investigate the effect of vibrational strong coupling of water on the enzymatic activity of pepsin, where a water molecule is directly involved in the enzyme's chemical mechanism. We observe an approximately 4.5-fold decrease of the apparent second-order rate constant kcat /Km when coupling the water stretching vibration, whereas no effect was detected for the strong coupling of the bending vibration. The possibility of modifying enzymatic activity by coupling water demonstrates the potential of VSC as a new tool to study biochemical reactivity.
Collapse
Affiliation(s)
| | - Anoop Thomas
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
| | - Kalaivanan Nagarajan
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
| | | | - Jino George
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
- Present address: Department of Chemical SciencesIndian Institute of Science Education and Research MohaliKnowledge city, Sector 81, SAS Nagar, ManauliPO 140306MohaliIndia
| | - Thibault Chervy
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
- Present address: Institute for Quantum ElectronicsETH ZurichOtto-Stern-Weg 18093ZurichSwitzerland
| | - Marcus Seidel
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
| | - Eloïse Devaux
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
| | - Vladimir Torbeev
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
| | - Thomas W. Ebbesen
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
| |
Collapse
|
13
|
Vergauwe RMA, Thomas A, Nagarajan K, Shalabney A, George J, Chervy T, Seidel M, Devaux E, Torbeev V, Ebbesen TW. Modification of Enzyme Activity by Vibrational Strong Coupling of Water. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908876] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Anoop Thomas
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
| | - Kalaivanan Nagarajan
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
| | | | - Jino George
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
- Present address: Department of Chemical Sciences Indian Institute of Science Education and Research Mohali Knowledge city, Sector 81, SAS Nagar, Manauli PO 140306 Mohali India
| | - Thibault Chervy
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
- Present address: Institute for Quantum Electronics ETH Zurich Otto-Stern-Weg 1 8093 Zurich Switzerland
| | - Marcus Seidel
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
| | - Eloïse Devaux
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
| | - Vladimir Torbeev
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
| | - Thomas W. Ebbesen
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
| |
Collapse
|
14
|
Liu Z, Wang L, Shi L, Chen X, Chang Y, Cao Y, Zhao L. Investigation on the Interaction Behavior Between Oenothein B and Pepsin by Isothermal Titration Calorimetry and Spectral Studies. J Food Sci 2019; 84:2412-2420. [PMID: 31429484 DOI: 10.1111/1750-3841.14678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/11/2019] [Accepted: 05/11/2019] [Indexed: 01/17/2023]
Abstract
Oenothein B (OeB) is a dimeric macrocyclic ellagitannin isolated from Herbs and fruits that have a variety of biological activities. In order to better understand the effect of OeB on the activity of the digestive enzyme pepsin, interactions between OeB and pepsin were investigated in vitro under simulated physiological conditions based on enzyme inhibition studies, fluorescence, isothermal titration calorimetry, CD, and molecular docking. It was found OeB is an effective inhibitor of pepsin, likely acting in a reversible manner through both competitive and noncompetitive inhibition. Fluorescence quenching of pepsin by OeB was a static quenching. CD spectra showed the addition of OeB causes the main chain of pepsin to loosen and expand and the partial β-sheet structure to be converted to a disordered structure. Isothermal titration calorimetry and docking studies revealed the main binding mechanism of OeB and pepsin was through noncovalent interactions, hydrophobic interactions with OeB and the internal hydrophobic group of pepsin, and then hydrogen bonding between OeB and the Val243 and Asp77 residues of pepsin. Noncovalent bonds between OeB and pepsin change the polarity and structure of enzymes, decreasing enzymatic activity. Compared with small molecular polyphenols, OeB has a weaker hydrophobic interaction with pepsin and less effect on the secondary structure of pepsin. These findings are the first direct elucidation of the interactions between the oligomer ellagitannin OeB and pepsin, further contributing to understanding binding between oligomer ellagitannins and digestive enzymes. PRACTICAL APPLICATION: The results of this study indicate that the interaction between OeB and pepsin has a certain inhibitory effect on pepsin. In order to reduce the impact of OeB on human digestion and its own activities, nano-encapsulation technology can be used in the future to protect oligomeric ellagitannin such as OeB.
Collapse
Affiliation(s)
- Zitao Liu
- College of Food Science, South China Agricultural Univ., Guangzhou, Guangdong, 510642, PR China
| | - Li Wang
- College of Food Science, South China Agricultural Univ., Guangzhou, Guangdong, 510642, PR China.,Inst. of Food Safety and Nutrition, Jinan Univ., Guangzhou, Guangdong, 510632, PR China
| | - Lei Shi
- Inst. of Food Safety and Nutrition, Jinan Univ., Guangzhou, Guangdong, 510632, PR China
| | - Xun Chen
- Inst. of Food Safety and Nutrition, Jinan Univ., Guangzhou, Guangdong, 510632, PR China
| | - Yanlei Chang
- Inst. of Food Safety and Nutrition, Jinan Univ., Guangzhou, Guangdong, 510632, PR China
| | - Yong Cao
- College of Food Science, South China Agricultural Univ., Guangzhou, Guangdong, 510642, PR China
| | - Lichao Zhao
- College of Food Science, South China Agricultural Univ., Guangzhou, Guangdong, 510642, PR China.,Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China Univ. of Technology, Guangzhou, Guangdong, 510640, PR China
| |
Collapse
|
15
|
Yue Y, Wang Z, Zhang Y, Wang Z, Lv Q, Liu J. Binding of triclosan and triclocarban to pepsin: DFT, spectroscopic and dynamic simulation studies. CHEMOSPHERE 2019; 214:278-287. [PMID: 30265935 DOI: 10.1016/j.chemosphere.2018.09.108] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/29/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
The use of antibacterial agents, triclosan (TCS) and triclocarban (TCC), in personal care products can result in direct human exposure. Density Functional Theory (DFT) was utilized to evaluate the electronic properties of TCS and TCC, and the determined energetically accessible transitions across the HOMO-LUMO gap. Choosing pepsin as a model protein, we explored the binding effects of TCS or TCC on pepsin by molecular docking and dynamic simulations. Titration of pepsin with TCS or TCC at pH 2.2 led to quenching of the pepsin intrinsic fluorescence via formation of a ground-state complex. The binding constants of the TCS/TCC-pepsin complexes, determined at 296 K, were (7.053 ± 0.030) × 104 M-1 and (6.233 ± 0.060) × 104 M-1, respectively. Analysis of the thermodynamic properties of each system at various temperatures demonstrated that the binding reaction is a spontaneous process driven by hydrophobic interactions. The spectroscopic results revealed that changes in the secondary structure of pepsin are induced by TCS or TCC. The thermal stability of pepsin was evaluated, and no change in thermal stability was observed upon substrate binding. However, the binding of either TCS or TCC to pepsin effectively reduced the activity.
Collapse
Affiliation(s)
- Yuanyuan Yue
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, PR China.
| | - Zhiyue Wang
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Yanyan Zhang
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Zhixian Wang
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Qingzhang Lv
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Jianming Liu
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, PR China.
| |
Collapse
|
16
|
Meti MD, Xu Y, Xie J, Chen Y, Wu Z, Liu J, Han Q, He Z, Hu Z, Xu H. Multi-spectroscopic studies on the interaction between traditional Chinese herb, helicid with pepsin. Mol Biol Rep 2018; 45:1637-1646. [DOI: 10.1007/s11033-018-4306-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/10/2018] [Indexed: 11/30/2022]
|
17
|
Yue Y, Zhao S, Liu J, Yan X, Sun Y. Probing the binding properties of dicyandiamide with pepsin by spectroscopy and docking methods. CHEMOSPHERE 2017; 185:1056-1062. [PMID: 28764101 DOI: 10.1016/j.chemosphere.2017.07.115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 06/07/2023]
Abstract
Dicyandiamide (DCD), considered to be a nitrification inhibitor, poses threat to human's health with exposure from milk, infant formula and other food products. In this work, DCD was investigated for its binding reaction with pepsin using spectroscopy and docking methods. Fluorescence experiments indicated DCD quenched the fluorescence of pepsin through a static process. Thermodynamic analysis of the binding data (ΔH0 = -21.72 kJ mol-1 and ΔS0 = 17.61 J mol-1 K-1) suggested the involvement of hydrophobic and hydrogen bonding in the complex formation. The pepsin interacted with DCD at a hydrophobic cavity, leading to a conformational changes in the pepsin, as revealed from UV-vis absorption, Fourier transform infrared, the time-resolved fluorescence, three-dimensional fluorescence and circular dichroism spectral results.
Collapse
Affiliation(s)
- Yuanyuan Yue
- Henan Key Laboratory of Green Chemicals Media and Reactions, Ministry of Education, Key Laboratory of Green Chemical Media and Reactions, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering Institution, Henan Normal University, 453007, Xinxiang, China.
| | - Shufang Zhao
- Henan Key Laboratory of Green Chemicals Media and Reactions, Ministry of Education, Key Laboratory of Green Chemical Media and Reactions, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering Institution, Henan Normal University, 453007, Xinxiang, China
| | - Jianming Liu
- Henan Key Laboratory of Green Chemicals Media and Reactions, Ministry of Education, Key Laboratory of Green Chemical Media and Reactions, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering Institution, Henan Normal University, 453007, Xinxiang, China.
| | - Xuyang Yan
- Henan Key Laboratory of Green Chemicals Media and Reactions, Ministry of Education, Key Laboratory of Green Chemical Media and Reactions, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering Institution, Henan Normal University, 453007, Xinxiang, China
| | - Yangyang Sun
- Henan Key Laboratory of Green Chemicals Media and Reactions, Ministry of Education, Key Laboratory of Green Chemical Media and Reactions, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering Institution, Henan Normal University, 453007, Xinxiang, China
| |
Collapse
|
18
|
Lau HH, Murney R, Yakovlev NL, Novoselova MV, Lim SH, Roy N, Singh H, Sukhorukov GB, Haigh B, Kiryukhin MV. Protein-tannic acid multilayer films: A multifunctional material for microencapsulation of food-derived bioactives. J Colloid Interface Sci 2017; 505:332-340. [PMID: 28601742 DOI: 10.1016/j.jcis.2017.06.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 10/19/2022]
Abstract
The benefits of various functional foods are often negated by stomach digestion and poor targeting to the lower gastrointestinal tract. Layer-by-Layer assembled protein-tannic acid (TA) films are suggested as a prospective material for microencapsulation of food-derived bioactive compounds. Bovine serum albumin (BSA)-TA and pepsin-TA films demonstrate linear growth of 2.8±0.1 and 4.2±0.1nm per bi-layer, correspondingly, as shown by ellipsometry. Both multilayer films are stable in simulated gastric fluid but degrade in simulated intestinal fluid. Their corresponding degradation constants are 0.026±0.006 and 0.347±0.005nm-1min-1. Milk proteins possessing enhanced adhesion to human intestinal surface, Immunoglobulin G (IgG) and β-Lactoglobulin (BLG), are explored to tailor targeting function to BSA-TA multilayer film. BLG does not adsorb onto the multilayer while IgG is successfully incorporated. Microcapsules prepared from the multilayer demonstrate 2.7 and 6.3 times higher adhesion to Caco-2 cells when IgG is introduced as an intermediate and the terminal layer, correspondingly. This developed material has a great potential for oral delivery of numerous active food-derived ingredients.
Collapse
Affiliation(s)
- Hooi Hong Lau
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, #08-03, 138634, Singapore
| | - Regan Murney
- AgResearch Limited, Ruakura Research Centre, Bisley Road, Private Bag 3123, Hamilton 3240, New Zealand
| | - Nikolai L Yakovlev
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, #08-03, 138634, Singapore
| | - Marina V Novoselova
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, #08-03, 138634, Singapore; N.G. Chernyshevsky Saratov State University, 83 Astrakhanskaya Street, Saratov 410012, Russia
| | - Su Hui Lim
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, #08-03, 138634, Singapore
| | - Nicole Roy
- AgResearch Limited, Ruakura Research Centre, Bisley Road, Private Bag 3123, Hamilton 3240, New Zealand; Riddet Institute, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Harjinder Singh
- Riddet Institute, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Gleb B Sukhorukov
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Brendan Haigh
- AgResearch Limited, Ruakura Research Centre, Bisley Road, Private Bag 3123, Hamilton 3240, New Zealand
| | - Maxim V Kiryukhin
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, #08-03, 138634, Singapore.
| |
Collapse
|
19
|
Engineering the residual side chains of HAP phytases to improve their pepsin resistance and catalytic efficiency. Sci Rep 2017; 7:42133. [PMID: 28186144 PMCID: PMC5301473 DOI: 10.1038/srep42133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/06/2017] [Indexed: 11/08/2022] Open
Abstract
Strong resistance to proteolytic attack is important for feed enzymes. Here, we selected three predicted pepsin cleavage sites, L99, L162, and E230 (numbering from the initiator M of premature proteins), in pepsin-sensitive HAP phytases YkAPPA from Yersinia kristensenii and YeAPPA from Y. enterocolitica, which corresponded to L99, V162, and D230 in pepsin-resistant YrAPPA from Y. rohdei. We constructed mutants with different side chain structures at these sites using site-directed mutagenesis and produced all enzymes in Escherichia coli for catalytic and biochemical characterization. The substitutions E230G/A/P/R/S/T/D, L162G/A/V, L99A, L99A/L162G, and L99A/L162G/E230G improved the pepsin resistance. Moreover, E230G/A and L162G/V conferred enhanced pepsin resistance on YkAPPA and YeAPPA, increased their catalytic efficiency 1.3–2.4-fold, improved their stability at 60 °C and pH 1.0–2.0 and alleviated inhibition by metal ions. In addition, E230G increased the ability of YkAPPA and YeAPPA to hydrolyze phytate from corn meal at a high pepsin concentration and low pH, which indicated that optimization of the pepsin cleavage site side chains may enhance the pepsin resistance, improve the stability at acidic pH, and increase the catalytic activity. This study proposes an efficient approach to improve enzyme performance in monogastric animals fed feed with a high phytate content.
Collapse
|
20
|
Zeng HJ, Yang D, Hu GZ, Yang R, Qu LB. Studies on the binding of pepsin with three pyrethroid insecticides by multi-spectroscopic approaches and molecular docking. J Mol Recognit 2016; 29:476-84. [PMID: 27135781 DOI: 10.1002/jmr.2547] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/17/2016] [Accepted: 04/06/2016] [Indexed: 11/08/2022]
Abstract
In this study, the molecular interactions between pepsin and three pyrethroid insecticides, including fenvalerate, cyhalothrin and deltamethrin, were investigated by multi-spectroscopic and molecular docking methods under mimic physiological pH conditions. The results indicated that all of these insecticides could interact with pepsin to form insecticide-pepsin complexes. The binding constants, number of binding sites and thermodynamic parameters measured at different temperatures indicated that these three pyrethroid insecticides could spontaneously bind with pepsin mainly through electrostatic forces and hydrophobic interactions with one binding site. According to the theory of Föster's non-radioactive energy transfer, the distance (r) between pepsin and three pyrethroid insecticides were all found to be less than 7 nm, which implied that the energy transfer occurred between pepsin and these insecticides, leading to the quenching of pepsin fluorescence. Synchronous and three-dimensional fluorescence, CD spectra and molecular docking results indicated that all tested pyrethroid insecticides bound directly into the enzyme cavity site and the binding of insecticides into the cavity influenced the microenvironment of the pepsin activity site which resulted in the extension of peptide strands of pepsin with loss of α-helix structures.Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Hua-Jin Zeng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Dan Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Gui-Zhou Hu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Ran Yang
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Ling-Bo Qu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, 450001, PR China
| |
Collapse
|
21
|
Probing the binding mechanisms of α-tocopherol to trypsin and pepsin using isothermal titration calorimetry, spectroscopic, and molecular modeling methods. J Biol Phys 2016; 42:415-34. [PMID: 27094449 DOI: 10.1007/s10867-016-9415-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 03/09/2016] [Indexed: 10/21/2022] Open
Abstract
α-Tocopherol is a required nutrient for a variety of biological functions. In this study, the binding of α-tocopherol to trypsin and pepsin was investigated using isothermal titration calorimetry (ITC), steady-state and time-resolved fluorescence measurements, circular dichroism (CD) spectroscopy, and molecular modeling methods. Thermodynamic investigations reveal that α-tocopherol binds to trypsin/pepsin is synergistically driven by enthalpy and entropy. The fluorescence experimental results indicate that α-tocopherol can quench the fluorescence of trypsin/pepsin through a static quenching mechanism. The binding ability of α-tocopherol with trypsin/pepsin is in the intermediate range, and one molecule of α-tocopherol combines with one molecule of trypsin/pepsin. As shown by circular dichroism (CD) spectroscopy, α-tocopherol may induce conformational changes of trypsin/pepsin. Molecular modeling displays the specific binding site and gives information about binding forces and α-tocopherol-tryptophan (Trp)/tyrosine (Tyr) distances. In addition, the inhibition rate of α-tocopherol on trypsin and pepsin was studied. The study provides a basic data set for clarifying the binding mechanisms of α-tocopherol with trypsin and pepsin and is helpful for understanding its biological activity in vivo.
Collapse
|
22
|
Li X, Geng M. Probing the binding of procyanidin B3 to trypsin and pepsin: A multi-technique approach. Int J Biol Macromol 2016; 85:168-78. [DOI: 10.1016/j.ijbiomac.2015.12.075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 12/23/2022]
|
23
|
Marchenko NY, Sikorskaya E, Marchenkov V, Kashparov I, Semisotnov G. Affinity chromatography of chaperones based on denatured proteins: Analysis of cell lysates of different origin. Protein Expr Purif 2016; 119:117-23. [DOI: 10.1016/j.pep.2015.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/19/2015] [Accepted: 11/24/2015] [Indexed: 11/29/2022]
|
24
|
Marchenkov V, Marchenko N, Kaysheva A, Kotova N, Kashparov I, Semisotnov G. Dataset concerning GroEL chaperonin interaction with proteins. Data Brief 2016; 6:619-24. [PMID: 26909376 PMCID: PMC4735476 DOI: 10.1016/j.dib.2016.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 12/28/2015] [Accepted: 01/06/2016] [Indexed: 11/21/2022] Open
Abstract
GroEL chaperonin is well-known to interact with a wide variety of polypeptide chains. Here we show the data related to our previous work (http://dx.doi.org/10.1016/j.pep.2015.11.020[1]), and concerning the interaction of GroEL with native (lysozyme, α-lactalbumin) and denatured (lysozyme, α-lactalbumin and pepsin) proteins in solution. The use of affinity chromatography on the base of denatured pepsin for GroEL purification from fluorescent impurities is represented as well.
Collapse
|
25
|
Li X, Ni T. Binding of glutathione and melatonin to pepsin occurs via different binding mechanisms. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 45:165-74. [PMID: 26507952 DOI: 10.1007/s00249-015-1085-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/15/2015] [Accepted: 10/01/2015] [Indexed: 01/06/2023]
Abstract
Glutathione is a hydrophilic antioxidant and melatonin is a hydrophobic antioxidant, thus, the binding mechanism of the two antioxidants interacting with protease may be different. In this study, binding of glutathione and melatonin to pepsin has been studied using isothermal titration calorimetry (ITC), equilibrium microdialysis, UV-Vis absorption spectroscopy, circular dichroism (CD) spectroscopy, and molecular modeling. Thermodynamic investigations reveal that the binding of glutathione/melatonin to pepsin is driven by favorable enthalpy and unfavorable entropy, and the major driving forces are hydrogen bond and van der Waals force. ITC, equilibrium microdialysis, and molecular modeling reveal that the binding of glutathione to pepsin is characterized by a high number of binding sites. For melatonin, one molecule of melatonin combines with one molecule of pepsin. These results confirm that glutathione/melatonin interact with pepsin through two different binding mechanisms. In addition, the UV-Vis absorption and CD experiments indicate that glutathione and melatonin may induce conformational and microenvironmental changes of pepsin. The conformational changes of pepsin may affect its biological function as protease.
Collapse
Affiliation(s)
- Xiangrong Li
- Department of Chemistry, School of Basic Medicine, Xinxiang Medical University, 601 Jin-sui Road, Hong Qi District, Xinxiang, 453003, Henan, People's Republic of China.
| | - Tianjun Ni
- Department of Chemistry, School of Basic Medicine, Xinxiang Medical University, 601 Jin-sui Road, Hong Qi District, Xinxiang, 453003, Henan, People's Republic of China
| |
Collapse
|
26
|
Li X, Li P. Study on the interaction of β-carotene and astaxanthin with trypsin and pepsin by spectroscopic techniques. LUMINESCENCE 2015; 31:782-92. [DOI: 10.1002/bio.3024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/13/2015] [Accepted: 08/05/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Xiangrong Li
- Department of Chemistry, School of Basic Medicine; Xinxiang Medical University; Xinxiang Henan 453003 People's Republic of China
| | - Peihong Li
- The Clinical Skills Training Center; Xinxiang Medical University; Xinxiang Henan 453003 People's Republic of China
| |
Collapse
|
27
|
Liu S, Wang H, Cheng Z, Liu H. Facile synthesis of near infrared fluorescent trypsin-stabilized Ag nanoclusters with tunable emission for 1,4-dihydronicotinamide adenine dinucleotide and ethanol sensing. Anal Chim Acta 2015; 886:151-6. [PMID: 26320647 DOI: 10.1016/j.aca.2015.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 07/01/2015] [Accepted: 07/03/2015] [Indexed: 10/23/2022]
Abstract
A facile chemical synthetic route was developed to prepare near-infrared fluorescent trypsin-stabilized Ag nanoclusters (Try-Ag NCs). The fluorescence emission wavelength of the produced Try-Ag NCs is tunable by simple adjusting pH value of the synthesis system, and the Try-Ag NCs offer a symmetric fluorescent excitation and emission peak. The fluorescence of Try-Ag NCs remains constant in the presence of various ions and molecules, and it can be effectively quenched by 1,4-dihydronicotinamide adenine dinucleotide (NADH) instead of its oxidized forms nicotinamide adenine dinucleotide (NAD(+)). This property enables the Try-Ag NCs to be a novel analytical platform to monitor biological reaction involved with NADH. In this work, the Try-Ag NCs was also applied to analyze ethanol based on the generation of NADH which was the product of NAD(+) and ethanol in the catalysis of alcohol dehydrogenase. And the proposed platform allowed ethanol to be determined in the range from 10 to 300 μmol/L with 5 μmol/L detection limit.
Collapse
Affiliation(s)
- Siyu Liu
- Institute of Molecular Medicine, College of Life and Health Sciences, Northeastern University, Shenyang 110000, China
| | - Hui Wang
- Institute of Molecular Medicine, College of Life and Health Sciences, Northeastern University, Shenyang 110000, China
| | - Zhen Cheng
- Molecular Imaging Program at Stanford, Stanford University, Palo Alto, CA 94305, USA
| | - Hongguang Liu
- Institute of Molecular Medicine, College of Life and Health Sciences, Northeastern University, Shenyang 110000, China.
| |
Collapse
|
28
|
Fang Y, Xu H, Shen L, Huang F, Yibulayin S, Huang S, Tian S, Hu Z, He Z, Li F, Li Y, Zhou K. Study on the mechanism of the interaction between acteoside and pepsin using spectroscopic techniques. LUMINESCENCE 2015; 30:859-66. [DOI: 10.1002/bio.2833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 10/28/2014] [Accepted: 11/19/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Yifeng Fang
- College of Life Sciences; Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University; Shenzhen 518060 China
| | - Hong Xu
- College of Life Sciences; Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University; Shenzhen 518060 China
| | - Liangliang Shen
- College of Life Sciences; Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University; Shenzhen 518060 China
| | - Fengwen Huang
- College of Life Sciences; Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University; Shenzhen 518060 China
| | - Shadaiti Yibulayin
- College of Life Sciences; Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University; Shenzhen 518060 China
| | - Songyang Huang
- College of Life Sciences; Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University; Shenzhen 518060 China
| | - Shengli Tian
- College of Life Sciences; Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University; Shenzhen 518060 China
| | - Zhangli Hu
- College of Life Sciences; Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University; Shenzhen 518060 China
| | - Zhendan He
- School of Medicine; Shenzhen University; Shenzhen 518060 China
| | - Fangrong Li
- Shenzhen Entry-Exit inspection and Quarantine Bureau; Shenzhen 518001 China
| | - Yinong Li
- Shenzhen Entry-Exit inspection and Quarantine Bureau; Shenzhen 518001 China
| | - Kai Zhou
- Shenzhen Marine Environment and Resource Monitoring Center; Shenzhen 518060 China
| |
Collapse
|
29
|
Shen L, Xu H, Huang F, Li Y, Xiao H, Yang Z, Hu Z, He Z, Zeng Z, Li Y. Investigation on interaction between Ligupurpuroside A and pepsin by spectroscopic and docking methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 135:256-263. [PMID: 25078459 DOI: 10.1016/j.saa.2014.06.087] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/02/2014] [Accepted: 06/06/2014] [Indexed: 06/03/2023]
Abstract
Ligupurpuroside A is one of the major glycoside in Ku-Din-Cha, a type of Chinese functional tea. In order to better understand its digestion and metabolism in humans, the interaction between Ligupurpuroside A and pepsin has been investigated by fluorescence spectra, UV-vis absorption spectra and synchronous fluorescence spectra along with molecular docking method. The fluorescence experiments indicate that Ligupurpuroside A can effectively quench the intrinsic fluorescence of pepsin through a combined quenching way at the low concentration of Ligupurpuroside A, and a static quenching procedure at the high concentration. The binding constant, binding sites of Ligupurpuroside A with pepsin have been calculated. The thermodynamic analysis suggests that non-covalent reactions, including electrostatic force, hydrophobic interaction and hydrogen bond are the main forces stabilizing the complex. According to the Förster's non-radiation energy transfer theory, the binding distance between pepsin and Ligupurpuroside A was calculated to be 3.15 nm, which implies that energy transfer occurs between pepsin and Ligupurpuroside A. Conformation change of pepsin was observed from UV-vis absorption spectra and synchronous fluorescence spectra under experimental conditions. In addition, all these experimental results have been validated by the protein-ligand docking studies which show that Ligupurpuroside A is located in the cleft between the domains of pepsin.
Collapse
Affiliation(s)
- Liangliang Shen
- College of Life Sciences, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen 518060, China
| | - Hong Xu
- College of Life Sciences, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen 518060, China.
| | - Fengwen Huang
- College of Life Sciences, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen 518060, China
| | - Yi Li
- College of Life Sciences, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen 518060, China
| | - Huafeng Xiao
- College of Life Sciences, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen 518060, China
| | - Zhen Yang
- College of Life Sciences, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen 518060, China
| | - Zhangli Hu
- College of Life Sciences, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen 518060, China
| | - Zhendan He
- School of Medicine, Shenzhen University, Shenzhen 518060, China.
| | - Zheling Zeng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Yinong Li
- Center of Inspection and Quarantine of Shenzhen Entry & Exit Animal, Plant & Food, Shenzhen 518000, China
| |
Collapse
|
30
|
Chen LY, Wang CW, Yuan Z, Chang HT. Fluorescent Gold Nanoclusters: Recent Advances in Sensing and Imaging. Anal Chem 2014; 87:216-29. [DOI: 10.1021/ac503636j] [Citation(s) in RCA: 544] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Li-Yi Chen
- Department
of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Chia-Wei Wang
- Department
of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Zhiqin Yuan
- Department
of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Huan-Tsung Chang
- Department
of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| |
Collapse
|
31
|
Ree M. Probing the self-assembled nanostructures of functional polymers with synchrotron grazing incidence X-ray scattering. Macromol Rapid Commun 2014; 35:930-59. [PMID: 24706560 DOI: 10.1002/marc.201400025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Indexed: 11/09/2022]
Abstract
For advanced functional polymers such as biopolymers, biomimic polymers, brush polymers, star polymers, dendritic polymers, and block copolymers, information about their surface structures, morphologies, and atomic structures is essential for understanding their properties and investigating their potential applications. Grazing incidence X-ray scattering (GIXS) is established for the last 15 years as the most powerful, versatile, and nondestructive tool for determining these structural details when performed with the aid of an advanced third-generation synchrotron radiation source with high flux, high energy resolution, energy tunability, and small beam size. One particular merit of this technique is that GIXS data can be obtained facilely for material specimens of any size, type, or shape. However, GIXS data analysis requires an understanding of GIXS theory and of refraction and reflection effects, and for any given material specimen, the best methods for extracting the form factor and the structure factor from the data need to be established. GIXS theory is reviewed here from the perspective of practical GIXS measurements and quantitative data analysis. In addition, schemes are discussed for the detailed analysis of GIXS data for the various self-assembled nanostructures of functional homopolymers, brush, star, and dendritic polymers, and block copolymers. Moreover, enhancements to the GIXS technique are discussed that can significantly improve its structure analysis by using the new synchrotron radiation sources such as third-generation X-ray sources with picosecond pulses and partial coherence and fourth-generation X-ray laser sources with femtosecond pulses and full coherence.
Collapse
Affiliation(s)
- Moonhor Ree
- Department of Chemistry, Division of Advanced Materials Science, Pohang Accelerator Laboratory, Center for Electro-Photo Behaviors in Advanced Molecular Systems, Polymer Research Institute, and BK School of Molecular Science, Pohang University of Science & Technology, Pohang, 790-784, Republic of Korea
| |
Collapse
|
32
|
Zeng HJ, Liang HL, You J, Qu LB. Study on the binding of chlorogenic acid to pepsin by spectral and molecular docking. LUMINESCENCE 2013; 29:715-21. [DOI: 10.1002/bio.2610] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 10/02/2013] [Accepted: 10/11/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Hua-jin Zeng
- School of Pharmaceutical Sciences; Zhengzhou University; Zhengzhou 450001 People's Republic of China
| | - Hui-li Liang
- School of Pharmaceutical Sciences; Zhengzhou University; Zhengzhou 450001 People's Republic of China
| | - Jing You
- School of Pharmaceutical Sciences; Zhengzhou University; Zhengzhou 450001 People's Republic of China
| | - Ling-bo Qu
- School of Chemistry and Chemical Engineering; Henan University of Technology; Zhengzhou 450001 People's Republic of China
| |
Collapse
|
33
|
A study of the feasibility of single molecule scattering analysis with X-ray free electron lasers. Macromol Res 2013. [DOI: 10.1007/s13233-014-2015-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
34
|
Ciolkowski M, Rozanek M, Bryszewska M, Klajnert B. The influence of PAMAM dendrimers surface groups on their interaction with porcine pepsin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1982-7. [PMID: 23851144 DOI: 10.1016/j.bbapap.2013.06.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/10/2013] [Accepted: 06/25/2013] [Indexed: 01/08/2023]
Abstract
In this study the ability of three polyamidoamine (PAMAM) dendrimers with different surface charge (positive, neutral and negative) to interact with a negatively charged protein (porcine pepsin) was examined. It was shown that the dendrimer with a positively charged surface (G4 PAMAM-NH2), as well as the dendrimer with a neutral surface (G4 PAMAM-OH), were able to inhibit enzymatic activity of pepsin. It was also found that these dendrimers act as mixed partially non-competitive pepsin inhibitors. The negatively charged dendrimer (G3.5 PAMAM-COOH) was not able to inhibit the enzymatic activity of pepsin, probably due to the electrostatic repulsion between this dendrimer and the protein. No correlation between changes in enzymatic activity of pepsin and alterations in CD spectrum of the protein was observed. It indicates that the interactions between dendrimers and porcine pepsin are complex, multidirectional and not dependent only on disturbances of the secondary structure.
Collapse
Affiliation(s)
- Michal Ciolkowski
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland
| | | | | | | |
Collapse
|
35
|
Ahn J, Cao MJ, Yu YQ, Engen JR. Accessing the reproducibility and specificity of pepsin and other aspartic proteases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:1222-9. [PMID: 23063535 DOI: 10.1016/j.bbapap.2012.10.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 09/28/2012] [Accepted: 10/02/2012] [Indexed: 10/27/2022]
Abstract
The aspartic protease pepsin is less specific than other endoproteinases. Because aspartic proteases like pepsin are active at low pH, they are utilized in hydrogen deuterium exchange mass spectrometry (HDX MS) experiments for digestion under hydrogen exchange quench conditions. We investigated the reproducibility, both qualitatively and quantitatively, of online and offline pepsin digestion to understand the compliment of reproducible pepsin fragments that can be expected during a typical pepsin digestion. The collection of reproducible peptides was identified from >30 replicate digestions of the same protein and it was found that the number of reproducible peptides produced during pepsin digestion becomes constant above 5-6 replicate digestions. We also investigated a new aspartic protease from the stomach of the rice field eel (Monopterus albus Zuiew) and compared digestion efficiency and specificity to porcine pepsin and aspergillopepsin. Unique cleavage specificity was found for rice field eel pepsin at arginine, asparagine, and glycine. Different peptides produced by the various proteases can enhance protein sequence coverage and improve the spatial resolution of HDX MS data. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.
Collapse
Affiliation(s)
- Joomi Ahn
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | | | | | | |
Collapse
|
36
|
Chaudhari K, Xavier PL, Pradeep T. Understanding the evolution of luminescent gold quantum clusters in protein templates. ACS NANO 2011; 5:8816-27. [PMID: 22010989 DOI: 10.1021/nn202901a] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We show that the time-dependent biomineralization of Au(3+) by native lactoferrin (NLf) and bovine serum albumin (BSA) resulting in near-infrared (NIR) luminescent gold quantum clusters (QCs) occurs through a protein-bound Au(1+) intermediate and subsequent emergence of free protein. The evolution was probed by diverse tools, principally, using matrix-assisted laser desorption ionization mass spectrometry (MALDI MS), X-ray photoelectron spectroscopy (XPS), and photoluminescence spectroscopy (PL). The importance of alkaline pH in the formation of clusters was probed. At neutral pH, a Au(1+)-protein complex was formed (starting from Au(3+)) with the binding of 13-14 gold atoms per protein. When the pH was increased above 12, these bound gold ions were further reduced to Au(0) and nucleation and growth of cluster commenced, which was corroborated by the beginning of emission; at this point, the number of gold atoms per protein was ~25, suggesting the formation of Au(25). During the cluster evolution, at certain time intervals, for specific molar ratios of gold and protein, occurrence of free protein was noticed in the mass spectra, suggesting a mixture of products and gold ion redistribution. By providing gold ions at specific time of the reaction, monodispersed clusters with enhanced luminescence could be obtained, and the available quantity of free protein could be utilized efficiently. Monodispersed clusters would be useful in obtaining single crystals of protein-protected noble metal quantum clusters where homogeneity of the system is of primary concern.
Collapse
Affiliation(s)
- Kamalesh Chaudhari
- Department of Biotechnology, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India
| | | | | |
Collapse
|
37
|
Campana PT, Barbosa LRS, Itri R. Conformational stability of peanut agglutinin using small angle X-ray scattering. Int J Biol Macromol 2011; 48:398-402. [DOI: 10.1016/j.ijbiomac.2010.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 12/07/2010] [Accepted: 12/09/2010] [Indexed: 11/29/2022]
|
38
|
Composition-dependent phase segregation and cocrystallization behaviors of blends of metallocene-catalyzed octene-LLDPE(D) and LDPE(H). POLYMER 2010. [DOI: 10.1016/j.polymer.2010.09.075] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
39
|
Jin KS, Shin SR, Ahn B, Jin S, Rho Y, Kim H, Kim SJ, Ree M. Effect of C(60) fullerene on the duplex formation of i-motif DNA with complementary DNA in solution. J Phys Chem B 2010; 114:4783-8. [PMID: 20218585 DOI: 10.1021/jp9122453] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural effects of fullerene on i-motif DNA were investigated by characterizing the structures of fullerene-free and fullerene-bound i-motif DNA, in the presence of cDNA and in solutions of varying pH, using circular dichroism and synchrotron small-angle X-ray scattering. To facilitate a direct structural comparison between the i-motif and duplex structures in response to pH stimulus, we developed atomic scale structural models for the duplex and i-motif DNA structures, and for the C(60)/i-motif DNA hybrid associated with the cDNA strand, assuming that the DNA strands are present in an ideal right-handed helical conformation. We found that fullerene shifted the pH-induced conformational transition between the i-motif and the duplex structure, possibly due to the hydrophobic interactions between the terminal fullerenes and between the terminal fullerenes and an internal TAA loop in the DNA strand. The hybrid structure showed a dramatic reduction in cyclic hysteresis.
Collapse
Affiliation(s)
- Kyeong Sik Jin
- Pohang Accelerator Laboratory, Department of Chemistry, National Research Lab for Polymer Synthesis and Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, Division of Advanced Materials Science, Polymer Research Institute, and BK School of Molecular Science, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Republic of Korea
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Jin S, Higashihara T, Jin KS, Yoon J, Rho Y, Ahn B, Kim J, Hirao A, Ree M. Synchrotron X-ray Scattering Characterization of the Molecular Structures of Star Polystyrenes with Varying Numbers of Arms. J Phys Chem B 2010; 114:6247-57. [DOI: 10.1021/jp911928b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sangwoo Jin
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Tomoya Higashihara
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Kyeong Sik Jin
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Jinhwan Yoon
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Yecheol Rho
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Byungcheol Ahn
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Jehan Kim
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Akira Hirao
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Moonhor Ree
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| |
Collapse
|
41
|
Dee DR, Yada RY. The prosegment catalyzes pepsin folding to a kinetically trapped native state. Biochemistry 2010; 49:365-71. [PMID: 20000477 DOI: 10.1021/bi9014055] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Investigations of irreversible protein unfolding often assume that alterations to the unfolded state, rather than the nature of the native state itself, are the cause of the irreversibility. However, the present study describes a less common explanation for the irreversible denaturation of pepsin, a zymogen-derived aspartic peptidase. The presence of a large folding barrier combined with the thermodynamically metastable nature of the native state, the formation of which depends on a separate prosegment (PS) domain, is the source of the irreversibility. Pepsin is unable to refold to the native state upon return from denaturing conditions due to a large folding barrier (24.6 kcal/mol) and instead forms a thermodynamically stable, yet inactive, refolded state. The native state is kinetically stabilized by an unfolding activation energy of 24.5 kcal/mol, comparable to the folding barrier, indicating that native pepsin exists as a thermodynamically metastable state. However, in the presence of the PS, the native state becomes thermodynamically stable, and the PS catalyzes pepsin folding by stabilizing the folding transition state by 14.7 kcal/mol. Once folded, the PS is removed, and the native conformation exists as a kinetically trapped state. Thus, while PS-guided folding is thermodynamically driven, without the PS the pepsin energy landscape is dominated by kinetic barriers rather than by free energy differences between native and denatured states. As pepsin is the archetype of a broad class of aspartic peptidases of similar structure and function, and many require their PS for correct folding, these results suggest that the occurrence of native states optimized for kinetic rather than thermodynamic stability may be a common feature of protein design.
Collapse
Affiliation(s)
- Derek R Dee
- Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | | |
Collapse
|