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Yadavalli NS, Borodinov N, Choudhury CK, Quiñones-Ruiz T, Laradji AM, Tu S, Lednev IK, Kuksenok O, Luzinov I, Minko S. Thermal Stabilization of Enzymes with Molecular Brushes. ACS Catal 2017. [DOI: 10.1021/acscatal.7b03138] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nataraja S. Yadavalli
- Nanostructured
Materials Laboratory, The University of Georgia, Athens, Georgia 30602, United States
| | - Nikolay Borodinov
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Chandan K. Choudhury
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Tatiana Quiñones-Ruiz
- Department
of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Amine M. Laradji
- Nanostructured
Materials Laboratory, The University of Georgia, Athens, Georgia 30602, United States
| | - Sidong Tu
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Igor K. Lednev
- Department
of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Olga Kuksenok
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Igor Luzinov
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Sergiy Minko
- Nanostructured
Materials Laboratory, The University of Georgia, Athens, Georgia 30602, United States
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Zhang CY, Wu ZQ, Yin DC, Zhou BR, Guo YZ, Lu HM, Zhou RB, Shang P. A strategy for selecting the pH of protein solutions to enhance crystallization. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:821-6. [PMID: 23832217 PMCID: PMC3702334 DOI: 10.1107/s1744309113013651] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/17/2013] [Indexed: 11/10/2022]
Abstract
The pH of a solution is an important parameter in crystallization that needs to be controlled in order to ensure success. The actual pH of the crystallization droplet is determined by the combined contribution of the buffers in the screening and protein solutions, although the contribution of the latter to the pH is often ignored. In this study, the effects of the buffer and protein solution pH values on the results of screening are systematically investigated. It was found that these parameters significantly affected the results and thus the following strategy for the selection of appropriate pH values is proposed: (i) when screening with only one protein solution, the pH should be as low, as high or as divergent from the pI as possible for a basic, acidic or neutral protein, respectively, within its stable pH range; (ii) when screening with two protein solutions, the pH values should be well separated from one another; and (iii) when multiple pH values are utilized, an even distribution of pH values is the best approach to increase the success rate of crystallization.
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Affiliation(s)
- Chen-Yan Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, People’s Republic of China
| | - Zi-Qing Wu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, People’s Republic of China
| | - Da-Chuan Yin
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, People’s Republic of China
| | - Bo-Ru Zhou
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, People’s Republic of China
| | - Yun-Zhu Guo
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, People’s Republic of China
| | - Hui-Meng Lu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, People’s Republic of China
| | - Ren-Bin Zhou
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, People’s Republic of China
| | - Peng Shang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, People’s Republic of China
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Chu XQ, Gajapathy M, Weiss KL, Mamontov E, Ng JD, Coates L. Dynamic behavior of oligomeric inorganic pyrophosphatase explored by quasielastic neutron scattering. J Phys Chem B 2012; 116:9917-21. [PMID: 22804561 DOI: 10.1021/jp303127w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The purpose of this investigation is to determine whether a large oligomeric protein, inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens with quaternary structural complexity, would have distinguishable dynamic characteristics compared to those of the small simple monomeric model protein, lysozyme. In this study, the β-relaxational dynamics of the two proteins, IPPase and lysozyme, are compared in the 10 ps to 0.5 ns time interval using quasi-elastic neutron scattering (QENS). Both of the protein dynamics show a characteristic logarithmic-like decay in the intermediate scattering function (ISF) of the hydrogen atoms. Distinguishable dynamical behavior found between two proteins reveals local flexibility and conformational substates unique to oligomeric structures. Moreover, the temperature dependence of the mean square displacement (MSD) of the hydrogen atoms in protein molecules, which is a traditional way to determine the "softness" of the protein molecule, is measured and shows no difference for the two proteins.
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Affiliation(s)
- Xiang-qiang Chu
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Role of benzyl alcohol in the prevention of heat-induced aggregation and inactivation of hen egg white lysozyme. Eur J Pharm Biopharm 2009; 71:367-76. [DOI: 10.1016/j.ejpb.2008.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 08/19/2008] [Accepted: 09/13/2008] [Indexed: 11/21/2022]
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Ueda T, Yamada H, Hirata M, Imoto T. An intramolecular cross-linkage of lysozyme. Formation of cross-links between lysine-1 and histidine-15 with bis(bromoacetamide) derivatives by a two-stage reaction procedure and properties of the resulting derivatives. Biochemistry 1985; 24:6316-22. [PMID: 3936542 DOI: 10.1021/bi00343a042] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hen egg white lysozyme was treated at pH 5.5 with four bifunctional reagents, bis(bromoacetamide) derivatives [BrCH2CONH(CH2)nNHCOCH2Br, 1-n, n = 0, 2, 4, and 6], to alkylate His-15 monofunctionally. The excess bifunctional reagent was then removed, and the pH was raised to 9.0 to allow the other end of the reagent molecule to react. The shortest reagent (1-0) gave no intramolecularly cross-linked lysozyme derivative but only histidine-15-modified lysozyme monomer and intermolecularly cross-linked lysozyme dimer. However, the reagents with longer arms (1-2, 1-4, and 1-6) gave lysozyme derivatives cross-linked intramolecularly between the nitrogen at epsilon 2 of His-15 and the epsilon-amino group of Lys-1 without formation of any other intramolecularly cross-linked lysozyme derivative. These results are consistent with our previous proposal that lysozyme has a small hydrophobic pocket that binds small molecules in the direction from His-15 to Lys-1 [Yamada, H., Uozumi, F., Ishikawa, A., & Imoto, T. (1984) J. Biochem. (Tokyo) 95, 503-510]. The thermal stabilities of three cross-linked lysozymes thus obtained were investigated in 0.1 M acetate buffer containing 3 M guanidine hydrochloride at pH 5.5. All derivatives were stabilized but to different degrees. The derivative cross-linked with 1-4 was most stabilized (2.3 kcal/mol), but the derivatives cross-linked with the reagents both shorter (1-2) and longer (1-6) than 1-4 were less stabilized (both 1.6 kcal/mol).(ABSTRACT TRUNCATED AT 250 WORDS)
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Investigation of structure and conformational changes of proteins by inductive - resonance energy transfer method. ACTA ACUST UNITED AC 1979. [DOI: 10.1016/0378-4487(79)80045-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Delmotte FM, Privat JPD, Monsigny ML. Interactions glycanne-protéine. Synthése des 4-méthylombelliféryl-(2-acétamido-2-désoxy-β-D-glucopyranoside), -DI-N-acétyl-β-chitobioside et -tri-N-acétyl-β-chitotrioside. Interaction de ces osides avec le lysozyme. Carbohydr Res 1975. [DOI: 10.1016/s0008-6215(00)82616-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Tsai CS. Temperature dependent transition of lysozyme-beta-aryl di-N-acetylchitobioside complex. Biochem Biophys Res Commun 1973; 55:205-9. [PMID: 4783347 DOI: 10.1016/s0006-291x(73)80080-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Cysyk R, Prusoff WH. Alteration of Ultraviolet Sensitivity of Thymidine Kinase by Allosteric Regulators, Normal Substrates, and a Photo-Affinity Label, 5-Iodo-2′-deoxyuridine, a Metabolic Analog of Thymidine. J Biol Chem 1972. [DOI: 10.1016/s0021-9258(19)45458-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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