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Wang X, Shu J, Ni T, Xu C, Xu B, Liu X, Zhang K, Jiang W. Transesterification of RNA model induced by novel dinuclear copper (II) complexes with bis-tridentate imidazole derivatives. J Biol Inorg Chem 2023:10.1007/s00775-023-02000-6. [PMID: 37140680 DOI: 10.1007/s00775-023-02000-6] [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: 11/12/2022] [Accepted: 04/15/2023] [Indexed: 05/05/2023]
Abstract
Two novel bis-tridentate imidazole derivatives were conveniently synthesized using a 'one-pot' method. Their dinuclear (Cu2L1Cl4, Cu2L2Cl4) and mononuclear (CuL1Cl2, CuL2Cl2∙H2O) copper (II) complexes were synthesized to comparably evaluate their reactivities in the hydrolytic cleavage of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP) as a classic RNA model. Single crystals of Cu2L1Cl4 and Cu2L2Cl4 indicate that both of them are centrosymmetric, and each central copper ion is penta-coordinated. Regarding the transesterification of HPNP, both of dinuclear ones exhibited excess one order of magnitude rate enhancement in contrast with auto-hydrolysis reaction. Under comparable conditions, dinuclear complexes displayed no more than twofold increase in activity over their mononuclear analogues, which verifies the lack of binuclear cooperation effect due to long Cu-to-Cu space.
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Affiliation(s)
- Xiuyang Wang
- School of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, 643000, Sichuan, People's Republic of China
| | - Jun Shu
- School of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, 643000, Sichuan, People's Republic of China
| | - Tong Ni
- School of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, 643000, Sichuan, People's Republic of China
| | - Chengxu Xu
- School of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, 643000, Sichuan, People's Republic of China
| | - Bin Xu
- School of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, 643000, Sichuan, People's Republic of China
- Key Laboratory of Green Catalysis of Sichuan Institute of High Education, Sichuan University of Science and Engineering, Sichuan, 643000, Zigong, People's Republic of China
| | - Xiaoqiang Liu
- School of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, 643000, Sichuan, People's Republic of China
- Key Laboratory of Green Catalysis of Sichuan Institute of High Education, Sichuan University of Science and Engineering, Sichuan, 643000, Zigong, People's Republic of China
| | - Kaiming Zhang
- School of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, 643000, Sichuan, People's Republic of China
- Key Laboratory of Green Catalysis of Sichuan Institute of High Education, Sichuan University of Science and Engineering, Sichuan, 643000, Zigong, People's Republic of China
| | - Weidong Jiang
- School of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, 643000, Sichuan, People's Republic of China.
- Key Laboratory of Green Catalysis of Sichuan Institute of High Education, Sichuan University of Science and Engineering, Sichuan, 643000, Zigong, People's Republic of China.
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Zheng L, Liu Z, Zhang Q, Li S, Huang J, Zhang L, Zan B, Tyagi M, Cheng H, Zuo T, Sakai VG, Yamada T, Yang C, Tan P, Jiang F, Chen H, Zhuang W, Hong L. Universal dynamical onset in water at distinct material interfaces. Chem Sci 2022; 13:4341-4351. [PMID: 35509458 PMCID: PMC9006901 DOI: 10.1039/d1sc04650k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Interfacial water remains liquid and mobile much below 0 °C, imparting flexibility to the encapsulated materials to ensure their diverse functions at subzero temperatures. However, a united picture that can describe the dynamical differences of interfacial water on different materials and its role in imparting system-specific flexibility to distinct materials is lacking. By combining neutron spectroscopy and isotope labeling, we explored the dynamics of water and the underlying substrates independently below 0 °C across a broad range of materials. Surprisingly, while the function-related anharmonic dynamical onset in the materials exhibits diverse activation temperatures, the surface water presents a universal onset at a common temperature. Further analysis of the neutron experiment and simulation results revealed that the universal onset of water results from an intrinsic surface-independent relaxation: switching of hydrogen bonds between neighboring water molecules with a common energy barrier of ∼35 kJ mol−1. We demonstrated that the dynamical onset of interfacial water is an intrinsic property of water itself, resulting from a surface independent relaxation process in water with an approximately universal energy barrier of ∼35 kJ mol−1.![]()
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Affiliation(s)
- Lirong Zheng
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
| | - Zhuo Liu
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Zhang
- College of Chemistry and Materials Science, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia 028043, China
| | - Song Li
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Zhang
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Zan
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - He Cheng
- China Spallation Neutron Source (CSNS), Institute of High Energy Physics (IHEP), Chinese Academy of Science (CAS), Dongguan 523803, China
- Dongguan Institute of Neutron Science (DINS), Dongguan 523808, China
| | - Taisen Zuo
- China Spallation Neutron Source (CSNS), Institute of High Energy Physics (IHEP), Chinese Academy of Science (CAS), Dongguan 523803, China
- Dongguan Institute of Neutron Science (DINS), Dongguan 523808, China
| | - Victoria García Sakai
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Science & Technology Facilities Council, Didcot OX11 0QX, UK
| | - Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, 162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
| | - Chenxing Yang
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pan Tan
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan Jiang
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - Liang Hong
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
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3
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Thompson MC, Yeates TO, Rodriguez JA. Advances in methods for atomic resolution macromolecular structure determination. F1000Res 2020; 9:F1000 Faculty Rev-667. [PMID: 32676184 PMCID: PMC7333361 DOI: 10.12688/f1000research.25097.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. Here we highlight some of the latest advances and current challenges at the frontiers of atomic resolution methods for elucidating the structures and dynamical properties of macromolecules and their complexes.
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Affiliation(s)
- Michael C. Thompson
- Department of Chemistry and Chemical Biology, University of California, Merced, CA, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
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Zhou H, Li L, Zhan B, Wang S, Li J, Hu XJ. The Trp183 is essential in lactonohydrolase ZHD detoxifying zearalenone and zearalenols. Biochem Biophys Res Commun 2020; 522:986-989. [PMID: 31810602 DOI: 10.1016/j.bbrc.2019.11.178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 11/26/2019] [Indexed: 11/16/2022]
Abstract
Lactonohydrolase ZHD can detoxify oestrogenic mycotoxin zearalenone and zearalenols through hydrolysis and decarboxylation. The detail mechanism, especially the role of Trp183, which interacts with substrate through p-π interaction and one hydrogen bond, is still unknown. The Trp183 mutants abolished activity to ZEN, α-ZOL and β-ZOL, except that W183F mutant retained about 40% activity against α-ZOL. In two W183F-reactant complex structures the reactants still bind at the active position and it suggested that this p-π interaction takes responsible for the reactants recognization and allocation. Further, the ZHD-productant complex structures showed that the resorcinol ring of hydrolysed α-ZOL and hydrolysed β-ZOL move a distance of one ring as compare to the resorcinol ring of reactant α-ZOL and β-ZOL. The same movement also found in comparison of hydrolysed ZEN and ZEN. In the structure of W183F complex with hydrolysed α-ZOL the resorcinol ring of hydrolysed α-ZOL doesn't move as compare to the resorcinol ring of reactant α-ZOL. It suggested the Trp183 coordinated hydrogen bond takes responsible for the movement of the hydrolysed product. These functional and structural results suggested that Trp183 is essential for ZHD detoxifying zearalenone and zearalenols.
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Affiliation(s)
- Hujian Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Collaborateive Innovative Center of Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Long Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Collaborateive Innovative Center of Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Bowen Zhan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Collaborateive Innovative Center of Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Sen Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Collaborateive Innovative Center of Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Collaborateive Innovative Center of Genetics and Development, Fudan University, Shanghai, 200438, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China.
| | - Xiao-Jian Hu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Collaborateive Innovative Center of Genetics and Development, Fudan University, Shanghai, 200438, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China.
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5
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Xue G, Xie X, Zhou Y, Yuan C, Huang M, Jiang L. Insight to the residue in P2 position prevents the peptide inhibitor from being hydrolyzed by serine proteases. Biosci Biotechnol Biochem 2020; 84:1153-1159. [PMID: 32019421 DOI: 10.1080/09168451.2020.1723405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Peptidic inhibitors of proteases are attracting increasing interest not only as drug candidates but also for studying the function and regulation mechanisms of these enzymes. Previously, we screened out a cyclic peptide inhibitor of human uPA [Formula: see text] and found that Ala substitution of P2 residue turns upain-1 to a substrate. To further investigate the effect of P2 residue on the peptide behavior transformation, we constructed upain-1-W3F, which has Phe replacement in the P2 position. We determined KD and Ki of upain-1-W3F and found that upain-1-W3F might still exist as an inhibitor. Furthermore, the high-resolution crystal structure of upain-1-W3F·uPA reveals that upain-1-W3F indeed stays as an intact inhibitor bind to uPA. We thus propose that the P2 residue plays a nonnegligible role in the conversion of upain-1 to a substrate. These results also proposed a strategy to optimize the pharmacological properties of peptide-based drug candidates by hydrophobicity and steric hindrance.Abbreviations : uPA: urokinase-type plasminogen activator; SPD: serine protease domain; S1 pocket: specific substrate-binding pocket.
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Affiliation(s)
- Guangpu Xue
- College of Chemistry, Fuzhou University, Fuzhou, China.,National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou, China
| | - Xie Xie
- College of Chemistry, Fuzhou University, Fuzhou, China.,National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou, China
| | - Yang Zhou
- College of Chemistry, Fuzhou University, Fuzhou, China.,National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou, China
| | - Cai Yuan
- National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Mingdong Huang
- College of Chemistry, Fuzhou University, Fuzhou, China.,National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Longguang Jiang
- College of Chemistry, Fuzhou University, Fuzhou, China.,National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou, China
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6
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Qi Q, Yang WJ, Zhou HJ, Ming DM, Sun KL, Xu TY, Hu XJ, Lv H. The structure of a complex of the lactonohydrolase zearalenone hydrolase with the hydrolysis product of zearalenone at 1.60 Å resolution. Acta Crystallogr F Struct Biol Commun 2017; 73:376-381. [PMID: 28695844 PMCID: PMC5505240 DOI: 10.1107/s2053230x17007713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/24/2017] [Indexed: 11/24/2022] Open
Abstract
Zearalenone hydrolase (ZHD) is an α/β-hydrolase that detoxifies and degrades the lactone zearalenone (ZEN), a naturally occurring oestrogenic mycotoxin that contaminates crops. Several apoenzyme and enzyme-substrate complex structures have been reported in the resolution range 2.4-2.6 Å. However, the properties and mechanism of this enzyme are not yet fully understood. Here, a 1.60 Å resolution structure of a ZHD-product complex is reported which was determined from a C-terminally His6-tagged ZHD crystal soaked with 2 mM ZEN for 30 min. It shows that after the lactone-bond cleavage, the phenol-ring region moves closer to residues Leu132, Tyr187 and Pro188, while the lactone-ring region barely moves. Comparisons of the ZHD-substrate and ZHD-product structures show that the hydrophilic interactions change, especially Trp183 Nℇ1, which shifts from contacting O2 to O12', suggesting that Trp183 is responsible for the unidirectional translational movement of the phenol ring. This structure provides information on the final stage of the catalytic mechanism of zearalenone hydrolysis.
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Affiliation(s)
- Qi Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People’s Republic of China
| | - Wen-Jing Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People’s Republic of China
| | - Hu-Jian Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People’s Republic of China
| | - Deng-Ming Ming
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People’s Republic of China
| | - Kai-Lei Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People’s Republic of China
| | - Tian-Yu Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People’s Republic of China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, People’s Republic of China
| | - Xiao-Jian Hu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People’s Republic of China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, People’s Republic of China
| | - Hong Lv
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People’s Republic of China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, People’s Republic of China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai 200237, People’s Republic of China
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7
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Kim TH, Mehrabi P, Ren Z, Sljoka A, Ing C, Bezginov A, Ye L, Pomès R, Prosser RS, Pai EF. The role of dimer asymmetry and protomer dynamics in enzyme catalysis. Science 2017; 355:355/6322/eaag2355. [DOI: 10.1126/science.aag2355] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 12/05/2016] [Indexed: 01/19/2023]
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8
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Jiang L, Andersen LM, Andreasen PA, Chen L, Huang M. Insights into the serine protease mechanism based on structural observations of the conversion of a peptidyl serine protease inhibitor to a substrate. Biochim Biophys Acta Gen Subj 2015; 1860:599-606. [PMID: 26691138 DOI: 10.1016/j.bbagen.2015.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 12/02/2015] [Accepted: 12/11/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND Serine proteases are one of the most studied group of enzymes. Despite the extensive mechanistic studies, some crucial details remain controversial, for example, how the cleaved product is released in the catalysis reaction. A cyclic peptidyl inhibitor (CSWRGLENHRMC, upain-1) of a serine protease, urokinase-type plasminogen activator (uPA), was found to become a slow substrate and cleaved slowly upon the replacement of single residue (W3A). METHODS By taking advantage of the unique property of this peptide, we report the high-resolution structures of uPA in complex with upain-1-W3A peptide at four different pH values by X-ray crystallography. RESULTS In the structures obtained at low pH (pH4.6 and 5.5), the cyclic peptide upain-1-W3A was found to be intact and remained in the active site of uPA. At 7.4, the scissile bond of the peptide was found cleaved, showing that the peptide became a uPA substrate. At pH9.0, the C-terminal part of the substrate was no longer visible, and only the P1 residue occupying the S1 pocket was identified. CONCLUSIONS The analysis of these structures provides explanations why the upain-1-W3A is a slow substrate. In addition, we clearly identified the cleaved fragments of the peptide at both sides of the scissile bond in the active site of the enzyme, showing a slow release of the cleaved peptide. GENERAL SIGNIFICANCE This work indicates that the quick release of the cleaved P' fragment after the first step of hydrolysis may not always be needed for the second hydrolysis.
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Affiliation(s)
- Longguang Jiang
- State Key Lab of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yang Qiao West Road, Fuzhou, Fujian 350002, China; Danish-Chinese Centre for Proteases and Cancer, Denmark. http://www.proteasesandcancer.org
| | - Lisbeth Moreau Andersen
- Danish-Chinese Centre for Proteases and Cancer, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000-DK, Denmark. http://www.proteasesandcancer.org
| | - Peter A Andreasen
- Danish-Chinese Centre for Proteases and Cancer, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000-DK, Denmark. http://www.proteasesandcancer.org
| | - Liqing Chen
- University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Mingdong Huang
- State Key Lab of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yang Qiao West Road, Fuzhou, Fujian 350002, China; Danish-Chinese Centre for Proteases and Cancer, Denmark.
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Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G. Visualizing phosphodiester-bond hydrolysis by an endonuclease. Nat Struct Mol Biol 2014; 22:65-72. [PMID: 25486305 DOI: 10.1038/nsmb.2932] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/12/2014] [Indexed: 01/12/2023]
Abstract
The enzymatic hydrolysis of DNA phosphodiester bonds has been widely studied, but the chemical reaction has not yet been observed. Here we follow the generation of a DNA double-strand break (DSB) by the Desulfurococcus mobilis homing endonuclease I-DmoI, trapping sequential stages of a two-metal-ion cleavage mechanism. We captured intermediates of the different catalytic steps, and this allowed us to watch the reaction by 'freezing' multiple states. We observed the successive entry of two metals involved in the reaction and the arrival of a third cation in a central position of the active site. This third metal ion has a crucial role, triggering the consecutive hydrolysis of the targeted phosphodiester bonds in the DNA strands and leaving its position once the DSB is generated. The multiple structures show the orchestrated conformational changes in the protein residues, nucleotides and metals during catalysis.
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Affiliation(s)
- Rafael Molina
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Stefano Stella
- 1] Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. [2] Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pilar Redondo
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Hansel Gomez
- Joint Barcelona Computing Center (BSC)-Centre for Genomic Regulation (CRG)-Institute for Research in Biomedicine (IRB) Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
| | - María José Marcaida
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Modesto Orozco
- 1] Joint Barcelona Computing Center (BSC)-Centre for Genomic Regulation (CRG)-Institute for Research in Biomedicine (IRB) Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. [2] Departament de Bioquimica, Facultat de Biologia, University of Barcelona, Barcelona, Spain
| | - Jesús Prieto
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Guillermo Montoya
- 1] Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. [2] Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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10
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Conformational dynamics of threonine 195 and the S1 subsite in functional trypsin variants. J Mol Model 2012; 18:4941-54. [DOI: 10.1007/s00894-012-1541-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 07/16/2012] [Indexed: 12/25/2022]
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11
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Abstract
DNA synthesis has been extensively studied, but the chemical reaction itself has not been visualized. Here we follow the course of phosphodiester bond formation using time-resolved X-ray crystallography. Native human DNA polymerase η, DNA and dATP were co-crystallized at pH 6.0 without Mg(2+). The polymerization reaction was initiated by exposing crystals to 1 mM Mg(2+) at pH 7.0, and stopped by freezing at desired time points for structural analysis. The substrates and two Mg(2+) ions are aligned within 40 s, but the bond formation is not evident until 80 s. From 80 to 300 s structures show a mixture of decreasing substrate and increasing product of the nucleotidyl-transfer reaction. Transient electron densities indicate that deprotonation and an accompanying C2'-endo to C3'-endo conversion of the nucleophile 3'-OH are rate limiting. A third Mg(2+) ion, which arrives with the new bond and stabilizes the intermediate state, may be an unappreciated feature of the two-metal-ion mechanism.
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12
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Hansen G, Gielen-Haertwig H, Reinemer P, Schomburg D, Harrenga A, Niefind K. Unexpected active-site flexibility in the structure of human neutrophil elastase in complex with a new dihydropyrimidone inhibitor. J Mol Biol 2011; 409:681-91. [PMID: 21549129 DOI: 10.1016/j.jmb.2011.04.047] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 04/12/2011] [Accepted: 04/18/2011] [Indexed: 12/21/2022]
Abstract
Human neutrophil elastase (HNE), a trypsin-type serine protease, is of pivotal importance in the onset and progression of chronic obstructive pulmonary disease (COPD). COPD encompasses a group of slowly progressive respiratory disorders and is a major medical problem and the fifth leading cause of death worldwide. HNE is a major target for the development of compounds that inhibit the progression of long-term lung function decline in COPD patients. Here, we present the three-dimensional structure of a potent dihydropyrimidone inhibitor (DHPI) non-covalently bound to HNE at a resolution of 2.0 Å. The inhibitor binds to the active site in a unique orientation addressing S1 and S2 subsites of the protease. To facilitate further analysis of this binding mode, we determined the structure of the uncomplexed enzyme at a resolution of 1.86 Å. Detailed comparisons of the HNE:DHPI complex with the uncomplexed HNE structure and published structures of other elastase:inhibitor complexes revealed that binding of DHPI leads to large conformational changes in residues located in the S2 subsite. The rearrangement of residues Asp95-Leu99B creates a deep, well-defined cavity, which is filled by the P2 moiety of the inhibitor molecule to almost perfect shape complementarity. The shape of the S2 subsite in complex with DHPI clearly differs from all other observed HNE structures. The observed structural flexibility of the S2 subsite is a key feature for the understanding of the binding mode of DHPIs in general and the development of new HNE selective inhibitors.
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Affiliation(s)
- Guido Hansen
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Zülpicher Str. 47, D-50674 Cologne, Germany
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13
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Chung IYW, Paetzel M. Crystal structure of a viral protease intramolecular acyl-enzyme complex: insights into cis-cleavage at the VP4/VP3 junction of Tellina birnavirus. J Biol Chem 2011; 286:12475-82. [PMID: 21288899 PMCID: PMC3069450 DOI: 10.1074/jbc.m110.198812] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/10/2011] [Indexed: 11/06/2022] Open
Abstract
Viruses of the Birnaviridae family are characterized by their bisegmented double-stranded RNA genome that resides within a single-shelled non-enveloped icosahedral particle. They infect birds, aquatic organisms, and insects. Tellina virus 1 (TV-1) is an Aquabirnavirus isolated from the mollusk Tellina tenuis. It encodes a polyprotein (NH2-pVP2-X-VP4-VP3-COOH) that is cleaved by the self-encoded protease VP4 to yield capsid precursor protein pVP2, peptide X, and ribonucleoprotein VP3. Here we report the crystal structure of an intramolecular (cis) acyl-enzyme complex of TV-1 VP4 at 2.1-Å resolution. The structure reveals how the enzyme can recognize its own carboxyl terminus during the VP4/VP3 cleavage event. The methyl side chains of Ala830(P1) and Ala828(P3) at the VP4/VP3 junction point into complementary shallow and hydrophobic S1 and S3 binding pockets adjacent to the VP4 catalytic residues: nucleophile Ser738 and general base Lys777. The electron density clearly shows that the carbonyl carbon of Ala830 is covalently attached via an ester bond to the Oγ of Ser738. A highly ordered water molecule in the active site is coordinated in the proper position to act as the deacylating water. A comparative analysis of this intramolecular (cis) acyl-enzyme structure with the previously solved intermolecular (trans) acyl-enzyme structure of infectious pancreatic necrosis virus VP4 explains the narrower specificity observed in the cleavage sites of TV-1 VP4.
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Affiliation(s)
- Ivy Yeuk Wah Chung
- From the Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Mark Paetzel
- From the Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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14
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Glass DC, Krishnan M, Nutt DR, Smith JC. Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models. J Chem Theory Comput 2010. [DOI: 10.1021/ct9006508] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dennis C. Glass
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, and Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Marimuthu Krishnan
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, and Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - David R. Nutt
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, and Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Jeremy C. Smith
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, and Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
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15
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Structure of a serine protease poised to resynthesize a peptide bond. Proc Natl Acad Sci U S A 2009; 106:11034-9. [PMID: 19549826 DOI: 10.1073/pnas.0902463106] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The serine proteases are among the most thoroughly studied enzymes, and numerous crystal structures representing the enzyme-substrate complex and intermediates in the hydrolysis reactions have been reported. Some aspects of the catalytic mechanism remain controversial, however, especially the role of conformational changes in the reaction. We describe here a high-resolution (1.46 A) crystal structure of a complex formed between a cleaved form of bovine pancreatic trypsin inhibitor (BPTI) and a catalytically inactive trypsin variant with the BPTI cleavage site ideally positioned in the active site for resynthesis of the peptide bond. This structure defines the positions of the newly generated amino and carboxyl groups following the 2 steps in the hydrolytic reaction. Comparison of this structure with those representing other intermediates in the reaction demonstrates that the residues of the catalytic triad are positioned to promote each step of both the forward and reverse reaction with remarkably little motion and with conservation of hydrogen-bonding interactions. The results also provide insights into the mechanism by which inhibitors like BPTI normally resist hydrolysis when bound to their target proteases.
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16
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Iqbal A, Clifton IJ, Bagonis M, Kershaw NJ, Domene C, Claridge TDW, Wharton CW, Schofield CJ. Anatomy of a Simple Acyl Intermediate in Enzyme Catalysis: Combined Biophysical and Modeling Studies on Ornithine Acetyl Transferase. J Am Chem Soc 2008; 131:749-57. [DOI: 10.1021/ja807215u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aman Iqbal
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Ian J. Clifton
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Maria Bagonis
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Nadia J. Kershaw
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Carmen Domene
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Christopher W. Wharton
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Christopher J. Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K., Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K., School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
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17
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Brovchenko I, Oleinikova A. Which Properties of a Spanning Network of Hydration Water Enable Biological Functions? Chemphyschem 2008; 9:2695-702. [DOI: 10.1002/cphc.200800662] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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18
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Krishnan M, Kurkal-Siebert V, Smith JC. Methyl Group Dynamics and the Onset of Anharmonicity in Myoglobin. J Phys Chem B 2008; 112:5522-33. [DOI: 10.1021/jp076641z] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Krishnan
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany, and Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee
| | - V. Kurkal-Siebert
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany, and Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee
| | - Jeremy C. Smith
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany, and Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee
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19
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Oleinikova A, Smolin N, Brovchenko I. Origin of the dynamic transition upon pressurization of crystalline proteins. J Phys Chem B 2007; 110:19619-24. [PMID: 17004829 DOI: 10.1021/jp0629590] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We study the role of hydration water in the dynamic transition of low-hydrated proteins upon pressurization found recently (Meinhold, L.; Smith, J. C. Phys. Rev. E 2005, 72, 061908). Clustering and percolation of water in the hydration shells of protein molecules in crystalline Staphylococcal nuclease are analyzed at various pressures. The number of water molecules in the hydration shell increases and the hydrogen-bonded network of hydration water spans with increasing pressure. The dynamic transition of protein occurs when the spanning water network exists with the probability of about 50% and hydration water shows large density fluctuations. Formation of a spanning water network upon pressurization promotes protein dynamics as in the case of the dynamic transition with increasing hydration. Properties of hydration water in various thermodynamic states and their influence on biological function are discussed.
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Affiliation(s)
- Alla Oleinikova
- Department of Physical Chemistry, University of Dortmund, Otto-Hahn-Strasse 6, Dortmund D-44227, Germany.
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20
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Lee J, Feldman AR, Delmas B, Paetzel M. Crystal Structure of the VP4 Protease from Infectious Pancreatic Necrosis Virus Reveals the Acyl-Enzyme Complex for an Intermolecular Self-cleavage Reaction. J Biol Chem 2007; 282:24928-37. [PMID: 17553791 DOI: 10.1074/jbc.m701551200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Infectious pancreatic necrosis virus (IPNV), an aquatic birnavirus that infects salmonid fish, encodes a large polyprotein (NH(2)-pVP2-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease, VP4, to release the proteins pVP2 and VP3. pVP2 is further processed to give rise to the capsid protein VP2 and three peptides that are incorporated into the virion. Reported here are two crystal structures of the IPNV VP4 protease solved from two different crystal symmetries. The electron density at the active site in the triclinic crystal form, refined to 2.2-A resolution, reveals the acyl-enzyme complex formed with an internal VP4 cleavage site. The complex was generated using a truncated enzyme in which the general base lysine was substituted. Inside the complex, the nucleophilic Ser(633)Ogamma forms an ester bond with the main-chain carbonyl of the C-terminal residue, Ala(716), of a neighboring VP4. The structure of this substrate-VP4 complex allows us to identify the S1, S3, S5, and S6 substrate binding pockets as well as other substrate-VP4 interactions and therefore provides structural insights into the substrate specificity of this enzyme. The structure from the hexagonal crystal form, refined to 2.3-A resolution, reveals the free-binding site of the protease. Three-dimensional alignment with the VP4 of blotched snakehead virus, another birnavirus, shows that the overall structure of VP4 is conserved despite a low level of sequence identity ( approximately 19%). The structure determinations of IPNV VP4, the first of an acyl-enzyme complex for a Ser/Lys dyad protease, provide insights into the catalytic mechanism and substrate recognition of this type of protease.
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Affiliation(s)
- Jaeyong Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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21
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Ding X, Rasmussen BF, Petsko GA, Ringe D. Direct crystallographic observation of an acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of a peptidyl ester substrate: Exploiting the "glass transition" in protein dynamics. Bioorg Chem 2006; 34:410-23. [PMID: 17083959 PMCID: PMC1751290 DOI: 10.1016/j.bioorg.2006.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 10/10/2006] [Accepted: 10/10/2006] [Indexed: 11/28/2022]
Abstract
The crystal structure of the acyl complex of porcine pancreatic elastase with its peptidyl ester substrate N-acetyl-ala-ala-ala-methyl ester (Ac(Ala)3OMe) has been determined at 2.5 A resolution. The complex was stabilized by exploiting the "glass transition" in protein dynamics that occurs at around -53 degrees C (220 K). Substrate was flowed into the crystal in a cryoprotective solvent above this temperature, and then the crystal was rapidly cooled to a temperature below the transition to trap the species that formed. The use of a flow cell makes the experiment a kinetic one and means that the species prior to the rate determining transition state has a chance to accumulate. The resulting crystal structure shows an acyl-enzyme intermediate in which the leaving group is absent and the carbonyl carbon of the C-terminal alanine residue is covalently bound to the gamma oxygen of the active site serine. The ester carbonyl shows no significant distortion from planarity, with the carbonyl oxygen forming one hydrogen bond with the oxyanion hole. The tripeptide is bound in an extended antiparallel beta-sheet with main chain residues of the enzyme. The geometry and interactions of this acyl-enzyme suggest that it represents a productive intermediate. To test this hypothesis, the same crystal was then warmed above the glass transition temperature and a second data set was collected. The resulting electron density map shows no sign of the substrate, indicating hydrolysis of the intermediate followed by product release. This experiment provides direct evidence for the importance of dynamic properties in catalysis and also provides a blueprint for the stabilization of other short-lived species for direct crystallographic observation.
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Affiliation(s)
| | | | | | - Dagmar Ringe
- *To whom correspondence should be addressed. Telephone: (781) 736-4902; FAX: (781) 736-2405; E-MAIL:
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22
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Liu B, Schofield CJ, Wilmouth RC. Structural analyses on intermediates in serine protease catalysis. J Biol Chem 2006; 281:24024-35. [PMID: 16754679 DOI: 10.1074/jbc.m600495200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the subject of many studies, detailed structural information on aspects of the catalytic cycle of serine proteases is lacking. Crystallographic analyses were performed in which an acyl-enzyme complex, formed from elastase and a peptide, was reacted with a series of nucleophilic dipeptides. Multiple analyses led to electron density maps consistent with the formation of a tetrahedral species. In certain cases, apparent peptide bond formation at the active site was observed, and the electron density maps suggested production of a cis-amide rather than a trans-amide. Evidence for a cis-amide configuration was also observed in the noncovalent complex between elastase and an alpha1-antitrypsin-derived tetrapeptide. Although there are caveats on the relevance of the crystallographic data to solution catalysis, the results enable detailed proposals for the pathway of the acylation step to be made. At least in some cases, it is proposed that the alcohol of Ser-195 may preferentially attack the carbonyl of the cis-amide form of the substrate, in a stereoelectronically favored manner, to give a tetrahedral oxyanion intermediate, which undergoes N-inversion and/or C-N bond rotation to enable protonation of the leaving group nitrogen. The mechanistic proposals may have consequences for protease inhibition, in particular for the design of high energy intermediate analogues.
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Affiliation(s)
- Bin Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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23
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Abstract
The hydroxyl group of a serine residue at position 195 acts as a nucleophile in the catalytic mechanism of the serine proteases. However, the chemically similar residue, threonine, is rarely used in similar functional context. Our structural modeling suggests that the Ser 195 --> Thr trypsin variant is inactive due to negative steric interaction between the methyl group on the beta-carbon of Thr 195 and the disulfide bridge formed by cysteines 42 and 58. By simultaneously truncating residues 42 and 58 and substituting Ser 195 with threonine, we have successfully converted the classic serine protease trypsin to a functional threonine protease. Substitution of residue 42 with alanine and residue 58 with alanine or valine in the presence of threonine 195 results in trypsin variants that are 10(2) -10(4) -fold less active than wild type in kcat/KM but >10(6)-fold more active than the Ser 195 --> Thr single variant. The substitutions do not alter the substrate specificity of the enzyme in the P1'- P4' positions. Removal of the disulfide bridge decreases the overall thermostability of the enzyme, but it is partially rescued by the presence of threonine at position 195.
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Affiliation(s)
- Teaster T Baird
- University of California, San Francisco, Department of Pharmaceutical Chemistry, San Francisco, California 94143-2280, USA
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24
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Radisky ES, Lee JM, Lu CJK, Koshland DE. Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates. Proc Natl Acad Sci U S A 2006; 103:6835-40. [PMID: 16636277 PMCID: PMC1458980 DOI: 10.1073/pnas.0601910103] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Atomic resolution structures of trypsin acyl-enzymes and a tetrahedral intermediate analog, along with previously solved structures representing the Michaelis complex, are used to reconstruct events in the catalytic cycle of this classic serine protease. Structural comparisons provide insight into active site adjustments involved in catalysis. Subtle motions of the catalytic serine and histidine residues coordinated with translation of the substrate reaction center are seen to favor the forward progress of the acylation reaction. The structures also clarify the attack trajectory of the hydrolytic water in the deacylation reaction.
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Affiliation(s)
- Evette S. Radisky
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Justin M. Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Chia-Jung Karen Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Daniel E. Koshland
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
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25
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Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D, Petsko GA, Herschlag D. Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. PLoS Biol 2006; 4:e99. [PMID: 16602823 PMCID: PMC1413570 DOI: 10.1371/journal.pbio.0040099] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Accepted: 01/27/2006] [Indexed: 11/19/2022] Open
Abstract
A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole. The binding of substituted phenolates of constant molecular shape but increasing p
Ka models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0.50–0.76 ppm/p
Ka unit, suggesting a bond shortening of ˜0.02 Å/p
Ka unit. Nevertheless, there is little change in binding affinity across a series of substituted phenolates (ΔΔG = −0.2 kcal/mol/p
Ka unit). The small effect of increased charge localization on affinity occurs despite the shortening of the hydrogen bonds and a large favorable change in binding enthalpy (ΔΔH = −2.0 kcal/mol/p
Ka unit). This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of ˜300-fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution.
Enzymatic reactions require exquisitely detailed molecular interactions. Here the authors show that geometric complementarity is likely more important than electrostatic charge in contributing to the binding necessary for catalytic reactions.
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Affiliation(s)
- Daniel A Kraut
- 1Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Paul A Sigala
- 1Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Brandon Pybus
- 2Department of Biochemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Corey W Liu
- 3Stanford Magnetic Resonance Laboratory, Stanford University, Stanford, California, United States of America
| | - Dagmar Ringe
- 2Department of Biochemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Gregory A Petsko
- 2Department of Biochemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Daniel Herschlag
- 1Department of Biochemistry, Stanford University, Stanford, California, United States of America
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26
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Weik M, Vernede X, Royant A, Bourgeois D. Temperature derivative fluorescence spectroscopy as a tool to study dynamical changes in protein crystals. Biophys J 2004; 86:3176-85. [PMID: 15111430 PMCID: PMC1304182 DOI: 10.1016/s0006-3495(04)74365-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Motions through the energy landscape of proteins lead to biological function. At temperatures below a dynamical transition (150-250 K), some of these motions are arrested and the activity of some proteins ceases. Here, we introduce the technique of temperature-derivative fluorescence microspectrophotometry to investigate the dynamical behavior of single protein crystals. The observation of glass transitions in thin films of water/glycerol mixtures allowed us to demonstrate the potential of the technique. Then, protein crystals were investigated, after soaking the samples in a small amount of fluorescein. If the fluorophore resides within the crystal channels, temperature-dependent changes in solvent dynamics can be monitored. Alternatively, if the fluorophore binds to the protein, local dynamical transitions within the biomolecule can be probed directly. A clear dynamical transition was observed at 175 K in the active site of crystalline human butyrylcholinesterase. The results suggest that the dynamics of crystalline proteins is strongly dependent on solvent composition and confinement in the crystal channels. Beyond applications in the field of kinetic crystallography, the highly sensitive temperature-derivative fluorescence microspectrophotometry technique opens the way to many studies on the dynamics of biological nanosamples.
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Affiliation(s)
- Martin Weik
- Laboratoire de Biophysique Moléculaire and Laboratoire de Cristallographie et Cristallogenèse des Protéines, UMR 5075, Institut de Biologie Structurale, 38027 Grenoble, France
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27
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Becker T, Hayward JA, Finney JL, Daniel RM, Smith JC. Neutron frequency windows and the protein dynamical transition. Biophys J 2004; 87:1436-44. [PMID: 15345526 PMCID: PMC1304552 DOI: 10.1529/biophysj.104.042226] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Accepted: 05/14/2004] [Indexed: 11/18/2022] Open
Abstract
Proteins undergo an apparent dynamical transition on temperature variation that has been correlated with the onset of function. The transition in the mean-square displacement, , that is observed using a spectrometer or computer simulation, depends on the relationship between the timescales of the relaxation processes activated and the timescale accessible to the instrument or simulation. Models are described of two extreme situations---an "equilibrium" model, in which the long-time dynamics changes with temperature and all motions are resolved by the instrument used; and a "frequency window" model, in which there is no change in the long-time dynamics but as the temperature increases, the relaxation frequencies move into the instrumental range. Here we demonstrate that the latter, frequency-window model can describe the temperature and timescale dependences of both the intermediate neutron scattering function and derived from molecular dynamics simulations of a small protein in a cryosolution. The frequency-window model also describes the energy-resolution and temperature-dependences of obtained from experimental neutron scattering on glutamate dehydrogenase in the same solvent. Although equilibrium effects should also contribute to dynamical transitions in proteins, the present results suggests that frequency-window effects can play a role in the simulations and experiments examined. Finally, misquotations of previous findings are discussed in the context of solvent activation of protein dynamics and the possible relationship of this to activity.
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Affiliation(s)
- Torsten Becker
- Computational Molecular Biophysics, Interdisciplinary Center for Scientific Computing, Universität Heidelberg, D-69120 Heidelberg, Germany
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28
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McDonough MA, Schofield CJ. New structural insights into the inhibition of serine proteases by cyclic peptides from bacteria. ACTA ACUST UNITED AC 2004; 10:898-900. [PMID: 14583255 DOI: 10.1016/j.chembiol.2003.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Michael A McDonough
- The Dyson Perrins Laboratory and The Oxford Centre for Molecular Sciences, South Parks Road, Oxford OX1 3QY, United Kingdom
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29
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Ringe D, Petsko GA. The 'glass transition' in protein dynamics: what it is, why it occurs, and how to exploit it. Biophys Chem 2004; 105:667-80. [PMID: 14499926 DOI: 10.1016/s0301-4622(03)00096-6] [Citation(s) in RCA: 173] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
All proteins undergo a dramatic change in their dynamical properties at approximately 200 K. Above this temperature, their dynamic behavior is dominated by large-scale collective motions of bonded and nonbonded groups of atoms. At lower temperatures, simple harmonic vibrations predominate. The transition has been described as a 'glass transition' to emphasize certain similarities between the change in dynamic behavior of individual protein molecules and the changes in viscosity and other properties of liquids when they form a glass. The glass transition may reflect the intrinsic temperature dependence of the motions of atoms in the protein itself, in the bound solvent on the surface of the protein, or it may reflect contributions from both. Protein function is significantly altered below this transition temperature; a fact that can be exploited to trap normally unstable intermediates in enzyme-catalyzed reactions and stabilize them for periods long enough to permit their characterization by high-resolution protein crystallography.
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Affiliation(s)
- Dagmar Ringe
- Departments of Biochemistry and Chemistry, Brandeis University, MS 029, 415 South Street, Waltham, MA 02454-9110, USA
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30
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Hayward JA, Daniel RM, Finney JL, Smith JC. Use of computer simulation in the interpretation of elastic neutron scattering in complex molecular systems: a small protein in various environments. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00080-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Hayward JA, Finney JL, Daniel RM, Smith JC. Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution. Biophys J 2003; 85:679-85. [PMID: 12885619 PMCID: PMC1303193 DOI: 10.1016/s0006-3495(03)74511-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2002] [Accepted: 02/14/2003] [Indexed: 11/24/2022] Open
Abstract
Molecular dynamics simulations are performed of bovine pancreatic trypsin inhibitor in a cryosolution over a range of temperatures from 80 to 300 K and the origins identified of elastic dynamic neutron scattering from the solution. The elastic scattering and mean-square displacement calculated from the molecular dynamics trajectories are in reasonable agreement with experiments on a larger protein in the same solvent. The solvent and protein contributions to the scattering from the simulation model are determined. At lower temperatures (< approximately 200 K) or on shorter timescales ( approximately 10 ps) the scattering contributions are proportional to the isotopic nuclear scattering cross-sections of each component. However, for T > 200 K marked deviations from these cross-sections are seen due to differences in the dynamics of the components of the solution. Rapid activation of solvent diffusion leads to the variation with temperature of the total elastic intensity being determined largely by that of the solvent. At higher temperatures (>240 K) and longer times ( approximately 100 ps) the protein makes the only significant contribution to the scattering, the solvent scattering having moved out of the accessible time-space window. Decomposition of the protein mean-square displacement shows that the observed dynamical transition in the solution at 200-220 K involves activation of both internal motions and external whole-molecule rotational and translational diffusion. The proportion that the external dynamics contributes to the protein mean-square displacement increases to approximately 30 and 60% at 300 K on the 10- and 100-ps timescales, respectively.
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Affiliation(s)
- Jennifer A Hayward
- Interdisciplinary Centre for Computational Science (JWR), University of Heidelberg, Heidelberg, Germany
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Becker T, Smith JC. Energy resolution and dynamical heterogeneity effects on elastic incoherent neutron scattering from molecular systems. PHYSICAL REVIEW E 2003; 67:021904. [PMID: 12636712 DOI: 10.1103/physreve.67.021904] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2002] [Revised: 08/23/2002] [Indexed: 11/07/2022]
Abstract
Incoherent neutron scattering is widely used to probe picosecond-nanosecond time scale dynamics of molecular systems. In systems of spatially confined atoms the relatively high intensity of elastic incoherent neutron scattering is often used to obtain a first estimate of the dynamics present. For many complex systems, however, experimental elastic scattering is difficult to interpret unambiguously using analytical dynamical models that go beyond the determination of an average mean-square displacement. To circumvent this problem a description of the scattering is derived here that encompasses a variety of analytical models in a common framework. The framework describes the time-converged part of the dynamic structure factor [the elastic incoherent scattering function (EISF)] and lends itself to practical use by explicitly incorporating effects due to the finite energy resolution of the instrument used. The dependence of the elastic scattering on wave vector is examined, and it is shown how heterogeneity in the distribution of mean-square displacements can be related to deviations of the scattering from Gaussian behavior. In this case, a correction to fourth order in the scattering vector can be used to extract the variance of the distribution of mean-square displacements. The formalism is used in a discussion of measurements on dynamics accompanying the glass transition in molecular systems. By fitting to experimental data obtained on a protein solution the present methodology is used to show how the existence of a temperature-dependent relaxation frequency can lead to a transition in the measured mean-square displacement in the absence of an EISF change.
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Affiliation(s)
- Torsten Becker
- Computational Molecular Biophysics, Interdisciplinary Center for Computational Science (IWR), Universität Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany
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33
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Heyes DJ, Ruban AV, Wilks HM, Hunter CN. Enzymology below 200 K: the kinetics and thermodynamics of the photochemistry catalyzed by protochlorophyllide oxidoreductase. Proc Natl Acad Sci U S A 2002; 99:11145-50. [PMID: 12177453 PMCID: PMC123224 DOI: 10.1073/pnas.182274199] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2002] [Indexed: 11/18/2022] Open
Abstract
The chlorophyll biosynthesis enzyme protochlorophyllide reductase (POR) catalyzes the light-dependent reduction of protochlorophyllide (Pchlide) into chlorophyllide in the presence of NADPH. As POR is light-dependent, catalysis can be initiated by illumination of the enzyme-substrate complex at low temperatures, making it an attractive model for studying aspects of biological proton and hydride transfers. The early stages in the photoreduction, involving Pchlide binding and an initial photochemical reaction, have been studied in vitro by using low-temperature fluorescence and absorbance measurements. Formation of the ternary POR-NADPH-Pchlide complex produces red shifts in the fluorescence and absorbance maxima of Pchlide, allowing the dissociation constant for Pchlide binding to be measured. We demonstrate that the product of an initial photochemical reaction, which can occur below 200 K, is a nonfluorescent intermediate with a broad absorbance band at 696 nm (A696) that is suggested to represent an ion radical complex. The temperature dependence of the rate of A696 formation has allowed the activation energy for the photochemical step to be calculated and has shown that POR catalysis can proceed at much lower temperatures than previously thought. Calculations of differences in free energy between various reaction intermediates have been calculated; these, together with the quantum efficiency for Pchlide conversion, suggest a quantitative model for the thermodynamics of the light-driven step of Pchlide reduction.
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Affiliation(s)
- Derren J Heyes
- Robert Hill Institute for Photosynthesis and Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom.
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34
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Hayward JA, Smith JC. Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties. Biophys J 2002; 82:1216-25. [PMID: 11867439 PMCID: PMC1301925 DOI: 10.1016/s0006-3495(02)75478-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The temperature dependence of the internal dynamics of an isolated protein, bovine pancreatic trypsin inhibitor, is examined using normal mode analysis and molecular dynamics (MD) simulation. It is found that the protein exhibits marked anharmonic dynamics at temperatures of approximately 100-120 K, as evidenced by departure of the MD-derived average mean square displacement from that of the harmonic model. This activation of anharmonic dynamics is at lower temperatures than previously detected in proteins and is found in the absence of solvent molecules. The simulation data are also used to investigate neutron scattering properties. The effects are determined of instrumental energy resolution and of approximations commonly used to extract mean square displacement data from elastic scattering experiments. Both the presence of a distribution of mean square displacements in the protein and the use of the Gaussian approximation to the dynamic structure factor lead to quantified underestimation of the mean square displacement obtained.
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Affiliation(s)
- Jennifer A Hayward
- Lehrstuhl für Biocomputing, IWR, Universität Heidelberg, D-69120 Heidelberg, Germany
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35
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Tarek M, Tobias DJ. Effects of solvent damping on side chain and backbone contributions to the protein boson peak. J Chem Phys 2001. [DOI: 10.1063/1.1380708] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Ota N, Agard DA. Enzyme specificity under dynamic control II: Principal component analysis of alpha-lytic protease using global and local solvent boundary conditions. Protein Sci 2001; 10:1403-14. [PMID: 11420442 PMCID: PMC2374101 DOI: 10.1110/ps.800101] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2001] [Revised: 04/10/2001] [Accepted: 04/16/2001] [Indexed: 10/16/2022]
Abstract
The contributions of conformational dynamics to substrate specificity have been examined by the application of principal component analysis to molecular dynamics trajectories of alpha-lytic protease. The wild-type alpha-lytic protease is highly specific for substrates with small hydrophobic side chains at the specificity pocket, while the Met190-->Ala binding pocket mutant has a much broader specificity, actively hydrolyzing substrates ranging from Ala to Phe. Based on a combination of multiconformation analysis of cryo-X-ray crystallographic data, solution nuclear magnetic resonance (NMR), and normal mode calculations, we had hypothesized that the large alteration in specificity of the mutant enzyme is mainly attributable to changes in the dynamic movement of the two walls of the specificity pocket. To test this hypothesis, we performed a principal component analysis using 1-nanosecond molecular dynamics simulations using either a global or local solvent boundary condition. The results of this analysis strongly support our hypothesis and verify the results previously obtained by in vacuo normal mode analysis. We found that the walls of the wild-type substrate binding pocket move in tandem with one another, causing the pocket size to remain fixed so that only small substrates are recognized. In contrast, the M190A mutant shows uncoupled movement of the binding pocket walls, allowing the pocket to sample both smaller and larger sizes, which appears to be the cause of the observed broad specificity. The results suggest that the protein dynamics of alpha-lytic protease may play a significant role in defining the patterns of substrate specificity. As shown here, concerted local movements within proteins can be efficiently analyzed through a combination of principal component analysis and molecular dynamics trajectories using a local solvent boundary condition to reduce computational time and matrix size.
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Affiliation(s)
- N Ota
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, CA 94143-0448, USA
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37
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Metzler DE, Metzler CM, Sauke DJ. Transferring Groups by Displacement Reactions. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50015-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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38
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Réat V, Dunn R, Ferrand M, Finney JL, Daniel RM, Smith JC. Solvent dependence of dynamic transitions in protein solutions. Proc Natl Acad Sci U S A 2000; 97:9961-6. [PMID: 10963663 PMCID: PMC27638 DOI: 10.1073/pnas.97.18.9961] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2000] [Indexed: 11/18/2022] Open
Abstract
A transition as a function of increasing temperature from harmonic to anharmonic dynamics has been observed in globular proteins by using spectroscopic, scattering, and computer simulation techniques. We present here results of a dynamic neutron scattering analysis of the solvent dependence of the picosecond-time scale dynamic transition behavior of solutions of a simple single-subunit enzyme, xylanase. The protein is examined in powder form, in D(2)O, and in four two-component perdeuterated single-phase cryosolvents in which it is active and stable. The scattering profiles of the mixed solvent systems in the absence of protein are also determined. The general features of the dynamic transition behavior of the protein solutions follow those of the solvents. The dynamic transition in all of the mixed cryosolvent-protein systems is much more gradual than in pure D(2)O, consistent with a distribution of energy barriers. The differences between the dynamic behaviors of the various cryosolvent protein solutions themselves are remarkably small. The results are consistent with a picture in which the picosecond-time scale atomic dynamics respond strongly to melting of pure water solvent but are relatively invariant in cryosolvents of differing compositions and melting points.
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Affiliation(s)
- V Réat
- Department of Physics and Astronomy, University College London, Gower Street, London WCIE, 6BT, England
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39
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Nakanishi I, Kinoshita T, Sato A, Tada T. Structure of porcine pancreatic elastase complexed with FR901277, a novel macrocyclic inhibitor of elastases, at 1.6 A resolution. Biopolymers 2000; 53:434-45. [PMID: 10738204 DOI: 10.1002/(sici)1097-0282(20000415)53:5<434::aid-bip7>3.0.co;2-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Human leukocyte elastase (HLE) is a serine protease that contributes to tissue destruction in various disease states-for example, in emphysema. FR901277 is a natural product isolated from the culture filtrate of Streptomyces resistomicificus and is a potent inhibitor of both HLE and porcine pancreatic elastase (PPE). FR901277 consists of four normal amino acids and three unusual amino acids, and is a unique bicyclic peptide compound. The crystal structure of PPE complexed with FR901277 has been determined at 1.6 A resolution. The Ogamma atom of Ser-195 in PPE did not form a covalent bond with FR901277, but formed a hydrogen bond with the Nvarepsilon atom of His-57. On the other hand, the portion from L-Orn(1) through dehydroxyThr(3) in FR901277 formed an antiparallel beta-sheet structure with the backbone of the active site in PPE. The S4 through S2' binding subsites in PPE were all occupied by the hydrophobic side chains of the inhibitor molecule. Especially, the ethylidene moiety of FR901277 occupied the S1 specific pocket, indicating a CH/pi interaction. In addition, the isopropyl side chain of L-Val(7) was located at the enzyme surface between the S2 and S1' pockets with several van der Waals contacts. However, the amino acid (4) residue was not involved in a significant interaction with PPE. Comparison of inhibitor structures in different environments showed that FR901277 has a highly rigid bicyclic framework; however, it can slightly change its conformation according to the circumstances. The binding mode of FR901277 at the active site of PPE was directly applicable to that in HLE, after consideration of induced fit. The structure of the PPE-FR901277 complex provided much information regarding potential sites for modification of the physicochemical properties of FR901277.
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Affiliation(s)
- I Nakanishi
- Basic Research Laboratories, Fujisawa Pharmaceutical Co., Ltd., 2-1-6, Kashima, Yodogawa-ku, Osaka 532-8514, Japan
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40
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Petsko GA, Ringe D. Observation of unstable species in enzyme-catalyzed transformations using protein crystallography. Curr Opin Chem Biol 2000; 4:89-94. [PMID: 10679381 DOI: 10.1016/s1367-5931(99)00057-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent advances in rapid X-ray diffraction data collection methods, cryocrystallography, and other techniques have made it possible to visualize short-lived species in enzyme-catalyzed reactions directly at atomic resolution for a significant number of crystalline enzymes. The wide range of reaction types, intermediate lifetimes, and crystal characteristics means that different methods must be employed in each case, but there are enough examples now of successful structure determinations of normally unstable species to suggest guidelines for future investigations.
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Affiliation(s)
- G A Petsko
- Departments of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA.
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41
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42
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Kumaran S, Roy RP. Helix-enhancing propensity of fluoro and alkyl alcohols: influence of pH, temperature and cosolvent concentration on the helical conformation of peptides. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1999; 53:284-93. [PMID: 10231716 DOI: 10.1034/j.1399-3011.1999.00027.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have analyzed the effects of trifluoroethanol (TFE) and three other alcohols(1-propanol, 2-propanol and hexafluoro-2-propanol) on S-peptide (residues 1-20) of ribonuclease A, an analog of S-peptide (QHM-->AAA, Sa-peptide) and TC-peptide (residues 295-316) of thermolysin to assess the helix-enhancing propensity of fluoro and alkyl alcohols under different environmental conditions of cosolvent concentration, pH and temperature by circular dichroism (CD). The dependence of cosolvent concentration on helix-induction showed a plateauing effect in all cases. 1-Propanol and 2-propanol were as effective as TFE in all the three peptides. Hexafluoro-2-propanol (HFIP) was a better helix enhancer in all cases however, the relative effectiveness varied with the peptide sequence. The alcohol transitions were analyzed assuming a two-state transition. The free energy decreased linearly in the cosolvent concentration range of 0-5 m for all the three peptides. The m-value (constant of proportionality) varied between peptides but was similar for any given peptide for TFE, 1-propanol or 2-propanol. The m-values of HFIP for all three peptides was much higher compared to other cosolvents. The isothermal cosolvent helix-induction curves for the three peptides exhibited similar features of shape and character for 1-propanol, 2-propanol and TFE. The additivity of cosolvent-induced helix formation was observed for different blends of alkyl and/or fluoro cosolvents. The pH-dependence of helix formation was observed in both TFE and 1-propanol solutions for S-peptide and TC-peptide, respectively, while in Sa-peptide, which was designed to perturb the pH-effect, helix formation was unaffected. The overall results provide some insight into the mechanism of cosolvent-mediated helix-enhancement in protein segments and are likely to facilitate optimization of conditions for cosolvent usage in chemistry and biology.
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Affiliation(s)
- S Kumaran
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
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43
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Kaslik G, Westler WM, Gráf L, Markley JL. Properties of the His57-Asp102 dyad of rat trypsin D189S in the zymogen, activated enzyme, and alpha1-proteinase inhibitor complexed forms. Arch Biochem Biophys 1999; 362:254-64. [PMID: 9989934 DOI: 10.1006/abbi.1998.1035] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Structural and biochemical studies suggest that serpins induce structural rearrangements in their target serine-proteinases. Previous NMR studies of the complex between a serpin, alpha1-proteinase inhibitor, and a mutant of recombinant rat trypsin (the Asp189 to Ser mutant, D189S, which is much more stable than wild-type rat trypsin against autoproteolysis) provided information about the state of catalytic residues in this complex: the hydrogen bond between Asp102 and His57 remains intact in the complex, and spectral properties of His57 are more like those of the zymogen than of the activated enzyme (G. Kaslik, et al., 1997, Biochemistry 36, 5455-5464). Here we report the protonation and exchange behavior of His57 of recombinant rat trypsin D189S in three states: the zymogen, the active enzyme, and the complex with human alpha1-proteinase inhibitor and compare these with analogous behavior of His57 of bovine chymotrypsinogen and alpha-chymotrypsin. In these studies the pKa of His57 has been determined from the pH dependence of the 1H NMR signal from the Hdelta1 proton of histidine in the Asp102-His57 dyad, and a measure of the accessibility of this part of the active site has been obtained from the rate of appearance of this signal following its selective saturation. The activation of rat trypsinogen D189S (zymogen, pKa = 7.8 +/- 0.1; Hill coefficient = 0. 86 +/- 0.05) decreased the pKa of His57 by 1.1 unit and made the protonation process cooperative (active enzyme, pKa = 6.7 +/- 0.1; Hill coefficient = 1.37 +/- 0.08). The binding of alpha1-proteinase inhibitor to trypsin D189S led to an increase in the pKa value of His57 to a value higher than that of the zymogen and led to negative cooperativity in the protonation process (complex, pKa = 8.1 +/- 0. 1; Hill coefficient = 0.70 +/- 0.08), as was observed for the zymogen. In spite of these differences in the pKa of His57 in the zymogen, active enzyme, and alpha1-proteinase inhibitor complex, the solvent exchange lifetime of the His57 Hdelta1 proton was the same, within experimental error, in all three states (lifetime = 2 to 12.5 ms). The linewidth of the 1H NMR signal from the Hdelta1 proton of His57 was relatively sharp, at temperatures between 5 and 20 degrees C at both low pH (5.2) and high pH (10.0), in spectra of bovine alpha-chymotrypsin, recombinant rat trypsin D189S, and the complex between rat trypsin D189S and human alpha1-proteinase inhibitor; however, in spectra of the complex between alpha-chymotrypsin and human alpha1-proteinase inhibitor, the peak was broader and could be well-resolved only at the lower temperature (5 degrees C).
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Affiliation(s)
- G Kaslik
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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44
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Ordentlich A, Barak D, Kronman C, Ariel N, Segall Y, Velan B, Shafferman A. Functional characteristics of the oxyanion hole in human acetylcholinesterase. J Biol Chem 1998; 273:19509-17. [PMID: 9677373 DOI: 10.1074/jbc.273.31.19509] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The contribution of the oxyanion hole to the functional architecture and to the hydrolytic efficiency of human acetylcholinesterase (HuAChE) was investigated through single replacements of its elements, residues Gly-121, Gly-122 and the adjacent residue Gly-120, by alanine. All three substitutions resulted in about 100-fold decrease of the bimolecular rate constants for hydrolysis of acetylthiocholine; however, whereas replacements of Gly-120 and Gly-121 affected only the turnover number, mutation of residue Gly-122 had an effect also on the Michaelis constant. The differential behavior of the G121A and G122A enzymes was manifested also toward the transition state analog m-(N,N, N-trimethylammonio)trifluoroacetophenone (TMTFA), organophosphorous inhibitors, carbamates, and toward selected noncovalent active center ligands. Reactivity of both mutants toward TMTFA was 2000-11, 000-fold lower than that of the wild type HuAChE; however, the G121A enzyme exhibited a rapid inhibition pattern, as opposed to the slow binding kinetics shown by the G122A enzyme. For both phosphates (diethyl phosphorofluoridate, diisopropyl phosphorofluoridate, and paraoxon) and phosphonates (sarin and soman), the decrease in inhibitory activity toward the G121A enzyme was very substantial (2000-6700-fold), irrespective of size of the alkoxy substituents on the phosphorus atom. On the other hand, for the G122A HuAChE the relative decline in reactivity toward phosphonates (500-460-fold) differed from that toward the phosphates (12-95-fold). Although formation of Michaelis complexes with substrates does not seem to involve significant interaction with the oxyanion hole, interactions with this motif are a major stabilizing element in accommodation of covalent inhibitors like organophosphates or carbamates. These observations and molecular modeling suggest that replacements of residues Gly-120 or Gly-121 by alanine alter the structure of the oxyanion hole motif, abolishing the H-bonding capacity of residue at position 121. These mutations weaken the interaction between HuAChE and the various ligands by 2.7-5.0 kcal/mol. In contrast, variations in reactivity due to replacement of residue Gly-122 seem to result from steric hindrance at the active center acyl pocket.
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Affiliation(s)
- A Ordentlich
- Department of Biochemistry & Molecular Biology, Israel Institute for Biological Research, Ness-Ziona, 70450, Israel
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45
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Murphy JE, Stec B, Ma L, Kantrowitz ER. Trapping and visualization of a covalent enzyme-phosphate intermediate. NATURE STRUCTURAL BIOLOGY 1997; 4:618-22. [PMID: 9253408 DOI: 10.1038/nsb0897-618] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Using a mutant version of E. coli alkaline phosphatase, we succeeded in trapping and determining the structure of the phospho-enzyme intermediate. The X-ray structure also revealed the catalytic water molecule, bound to one of the active site zinc ions, positioned ideally for the apical attack necessary for the hydrolysis of the intermediate.
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46
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Mesecar AD, Stoddard BL, Koshland DE. Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences. Science 1997; 277:202-6. [PMID: 9211842 DOI: 10.1126/science.277.5323.202] [Citation(s) in RCA: 178] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Small structural perturbations in the enzyme isocitrate dehydrogenase (IDH) were made in order to evaluate the contribution of precise substrate alignment to the catalytic power of an enzyme. The reaction trajectory of IDH was modified (i) after the adenine moiety of nicotinamide adenine dinucleotide phosphate was changed to hypoxanthine (the 6-amino was changed to 6-hydroxyl), and (ii) by replacing Mg2+, which has six coordinating ligands, with Ca2+, which has eight coordinating ligands. Both changes make large (10(-3) to 10(-5)) changes in the reaction velocity but only small changes in the orientation of the substrates (both distance and angle) as revealed by cryocrystallographic trapping of active IDH complexes. The results provide evidence that orbital overlap produced by optimal orientation of reacting orbitals plays a major quantitative role in the catalytic power of enzymes.
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Affiliation(s)
- A D Mesecar
- Department of Molecular and Cell Biology, Stanley Hall, University of California, Berkeley, CA 94720, USA
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47
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Wilmouth RC, Clifton IJ, Robinson CV, Roach PL, Aplin RT, Westwood NJ, Hajdu J, Schofield CJ. Structure of a specific acyl-enzyme complex formed between beta-casomorphin-7 and porcine pancreatic elastase. NATURE STRUCTURAL BIOLOGY 1997; 4:456-62. [PMID: 9187653 DOI: 10.1038/nsb0697-456] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mass spectrometric screening reveals that an unmodified natural heptapeptide--human beta-casomorphin-7, an internal sequence of human beta-casein that possesses opioid-like activity--reacts with porcine pancreatic elastase to form an unusually stable acyl-enzyme complex at low pH. X-ray crystallographic analysis (to 1.9 A resolution) at pH 5 shows continuous electron density linking the C-terminal isoleucine of beta-casomorphin-7 to Ser 195 through an ester bond. The structure reveals a well defined water molecule (Wat 317), equidistant between the carbon of the ester carbonyl and N epsilon 2 of His 57. Deprotonation of Wat 317 will produce a hydroxide ion positioned to attack the ester carbonyl through the favoured Bürgi-Dunitz trajectory.
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48
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Affiliation(s)
- I Schlichting
- Abteilung Physikalische Biochemie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
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49
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50
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Stoddard BL, Dean A, Bash PA. Combining Laue diffraction and molecular dynamics to study enzyme intermediates. NATURE STRUCTURAL BIOLOGY 1996; 3:590-5. [PMID: 8673602 DOI: 10.1038/nsb0796-590] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Two separate techniques, Laue diffraction and computational molecular dynamics (MD) simulations, have been independently developed to allow the visualization and assessment of transient structural states. Recent studies on isocitrate dehydrogenase show that computational MD simulations of an enzymatic Michaelis complex are consistent with difference Fourier electron density maps of the same structure from a Laue experiment. The use of independent MD studies during crystallographic refinement has allowed us to assign with confidence a number of additional contacts and features important for hydride transfer. We find that unrestrained independent MD simulations provides a very useful method of cross-validation for highly mobile atoms in regions of experimental density that are poorly defined. Likewise, information from Laue difference maps provides information about substrate conformation and interactions that greatly facilitate MD simulations.
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Affiliation(s)
- B L Stoddard
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98104, USA
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