1
|
Masuda T, Suzuki M, Inoue S, Song C, Nakane T, Nango E, Tanaka R, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Mikami B, Nureki O, Numata K, Iwata S, Sugahara M. Atomic resolution structure of serine protease proteinase K at ambient temperature. Sci Rep 2017; 7:45604. [PMID: 28361898 PMCID: PMC5374539 DOI: 10.1038/srep45604] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/01/2017] [Indexed: 01/24/2023] Open
Abstract
Atomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites.
Collapse
Affiliation(s)
- Tetsuya Masuda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.,RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mamoru Suzuki
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigeyuki Inoue
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Changyong Song
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Physics, POSTECH, Pohang 790-784, Korea
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takashi Kameshima
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takaki Hatsui
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Bunzo Mikami
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keiji Numata
- Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - So Iwata
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | | |
Collapse
|
2
|
Madala PK, Tyndall JDA, Nall T, Fairlie DP. Update 1 of: Proteases Universally Recognize Beta Strands In Their Active Sites. Chem Rev 2011; 110:PR1-31. [DOI: 10.1021/cr900368a] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Praveen K. Madala
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - Tessa Nall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - David P. Fairlie
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| |
Collapse
|
3
|
Liang L, Yang J, Li J, Mo Y, Li L, Zhao X, Zhang KQ. Cloning and homology modeling of a serine protease gene (PrC) from the nematophagous fungus Clonostachys rosea. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0166-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
4
|
Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10. World J Microbiol Biotechnol 2010; 26:1269-79. [DOI: 10.1007/s11274-009-0298-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Accepted: 12/22/2009] [Indexed: 10/20/2022]
|
5
|
De Franceschi G, Frare E, Bubacco L, Mammi S, Fontana A, de Laureto PP. Molecular insights into the interaction between alpha-synuclein and docosahexaenoic acid. J Mol Biol 2009; 394:94-107. [PMID: 19747490 DOI: 10.1016/j.jmb.2009.09.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 09/03/2009] [Accepted: 09/03/2009] [Indexed: 01/24/2023]
Abstract
alpha-Synuclein (alpha-syn) is a 140-residue protein of unknown function, involved in several neurodegenerative disorders, such as Parkinson's disease. Recently, the possible interaction between alpha-syn and polyunsaturated fatty acids has attracted a strong interest. Indeed, lipids are able to trigger the multimerization of the protein in vitro and in cultured cells. Docosahexaenoic acid (DHA) is one of the main fatty acids (FAs) in cerebral gray matter and is dynamically released following phospholipid hydrolysis. Moreover, it has been found in high levels in brain areas containing alpha-syn inclusions in patients affected by Parkinson's disease. Debated and unsolved questions regard the nature of the molecular interaction between alpha-syn and DHA and the effect exerted by the protein on the aggregated state of the FA. Here, we show that alpha-syn is able to strongly interact with DHA and that a mutual effect on the structure of the protein and on the physical state of the lipid derives from this interaction. alpha-Syn acquires an alpha-helical conformation in a simple two-state transition. The binding of the protein to the FA leads to a reduction of the size of the spontaneously formed aggregated species of DHA as well as of the critical aggregate concentration of the lipid. Specifically, biophysical methods and electron microscopy observations indicated that the FA forms oil droplets in the presence of alpha-syn. Limited proteolysis experiments showed that, when the protein is bound to the FA oil droplets, it is initially cleaved in the 89-102 region, suggesting that this chain segment is sufficiently flexible or unfolded to be protease-sensitive. Subsequent proteolytic events produce fragments corresponding to the first 70-80 residues that remain structured and show high affinity for the lipid. The fact that a region of the polypeptide chain remains accessible to proteases, when interacting with the lipid, suggests that this region could be involved in other interactions, justifying the ambivalent propensity of alpha-syn towards folding or aggregation in the presence of FAs.
Collapse
Affiliation(s)
- Giorgia De Franceschi
- CRIBI Biotechnology Centre, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
| | | | | | | | | | | |
Collapse
|
6
|
Larson SB, Day JS, Nguyen C, Cudney R, McPherson A. High-resolution structure of proteinase K cocrystallized with digalacturonic acid. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:192-8. [PMID: 19255463 DOI: 10.1107/s1744309109002218] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 01/19/2009] [Indexed: 11/10/2022]
Abstract
Proteinase K, a subtilisin-like fungal protease, was crystallized from a cocktail of small molecules containing digalacturonic acid (DGA). The crystal structure was determined to 1.32 A resolution and refined to an R factor of 0.158. The final model contained, beside the protein, two calcium ions, 379 water molecules, a molecule of DGA and a partially occupied HEPES molecule. The DGA molecule has one sugar moiety disposed exactly on a crystallographic twofold axis; the second ring was not observed. The DGA molecule is bound to two protein molecules across the twofold axis through hydrogen-bonding networks involving Ser150 and water molecules. One of the calcium-ion sites has not been reported previously. This study further illustrates the involvement of small molecules in the crystallization of macromolecules through their ability to form intermolecular lattice interactions.
Collapse
Affiliation(s)
- Steven B Larson
- Department of Molecular Biology and Biochemistry, The University of California, Irvine, 92697-3900, USA
| | | | | | | | | |
Collapse
|
7
|
Kagawa TF, O'Connell MR, Mouat P, Paoli M, O'Toole PW, Cooney JC. Model for Substrate Interactions in C5a Peptidase from Streptococcus pyogenes: A 1.9 Å Crystal Structure of the Active Form of ScpA. J Mol Biol 2009; 386:754-72. [DOI: 10.1016/j.jmb.2008.12.074] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 12/18/2008] [Accepted: 12/29/2008] [Indexed: 10/21/2022]
|
8
|
Tyndall JDA, Nall T, Fairlie DP. Proteases universally recognize beta strands in their active sites. Chem Rev 2005; 105:973-99. [PMID: 15755082 DOI: 10.1021/cr040669e] [Citation(s) in RCA: 301] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joel D A Tyndall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia.
| | | | | |
Collapse
|
9
|
Syed Ibrahim B, Pattabhi V. Trypsin inhibition by a peptide hormone: crystal structure of trypsin-vasopressin complex. J Mol Biol 2005; 348:1191-8. [PMID: 15854654 DOI: 10.1016/j.jmb.2005.03.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2005] [Revised: 03/07/2005] [Accepted: 03/15/2005] [Indexed: 10/25/2022]
Abstract
The large variety of serine protease inhibitors, available from various sources such as tissues, microorganisms, plants, etc., play an important role in regulating the proteolytic enzymes. The analysis of protease-inhibitor complexes helps in understanding the mechanism of action, as well as in designing inhibitors. Vasopressin, an anti-diuretic nonapeptide hormone, is found to be an effective inhibitor of trypsin, with a K(i) value of 5 nM. The crystal structure of the trypsin-vasopressin complex revealed that vasopressin fulfils all the important interactions for an inhibitor, without any break in the scissile peptide bond. The cyclic nature due to a disulfide bridge between Cys1 and Cys6 of vasopressin provides structural rigidity to the peptide hormone. The trypsin-binding site is located at the C terminus, while the neurophysin-binding site is at the N terminus of vasopressin. This study will assist in designing new peptide inhibitors. This study suggests that vasopressin inhibition of trypsin may have unexplored biological implications.
Collapse
Affiliation(s)
- B Syed Ibrahim
- Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | | |
Collapse
|
10
|
Ibrahim BS, Shamaladevi N, Pattabhi V. Trypsin activity reduced by an autocatalytically produced nonapeptide. J Biomol Struct Dyn 2005; 21:737-44. [PMID: 15106996 DOI: 10.1080/07391102.2004.10506964] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Trypsin, a serine protease enzyme plays a pivotal role in digestion and is autocatalytic. The crystal structure of a complex formed between porcine trypsin and an auto catalytically produced peptide is reported here. This complex shows a reduction in enzyme activity as compared to native beta-trypsin. The nonapeptide has a lysine, which is recognized by Asp 189 at the specificity pocket. The auto catalytically produced native nonapeptide is bound at the active site cleft like other trypsin inhibitors but the important interactions with the oxyanion hole are absent. The peptide covers only a part of the active site cleft and hence the enzyme activity is reduced rather than being inhibited.
Collapse
Affiliation(s)
- B S Ibrahim
- Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Guindy, Chennai-600025, India
| | | | | |
Collapse
|
11
|
Markert Y, Köditz J, Mansfeld J, Arnold U, Ulbrich-Hofmann R. Increased proteolytic resistance of ribonuclease A by protein engineering. PROTEIN ENGINEERING 2001; 14:791-6. [PMID: 11739898 DOI: 10.1093/protein/14.10.791] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Although highly stable toward unfolding, native ribonuclease A is known to be cleaved by unspecific proteases in the flexible loop region near Ala20. With the aim to create a protease-resistant ribonuclease A, Ala20 was substituted for Pro by site-directed mutagenesis. The resulting mutant enzyme was nearly identical to the wild-type enzyme in the near-UV and far-UV circular dichroism spectra, in its activity to 2',3'-cCMP and in its thermodynamic stability. However, the proteolytic resistance to proteinase K and subtilisin Carlsberg was extremely increased. Pseudo-first-order rate constants of proteolysis, determined by densitometric analysis of the bands of intact protein in SDS-PAGE, decreased by two orders of magnitude. In contrast, the rate constant of proteolysis with elastase was similar to that of the wild-type enzyme. These differences can be explained by the analysis of the fragments occurring in proteolysis with elastase. Ser21-Ser22 was identified as the main primary cleavage site in the degradation of the mutant enzyme by elastase. Obviously, this bond is not cleavable by proteinase K or subtilisin Carlsberg. The results demonstrate the high potential of a single mutation in protein stabilization to proteolytic degradation.
Collapse
Affiliation(s)
- Y Markert
- Department of Biochemistry/Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle, Germany
| | | | | | | | | |
Collapse
|
12
|
Singh RK, Gourinath S, Sharma S, Roy I, Gupta MN, Betzel C, Srinivasan A, Singh TP. Enhancement of enzyme activity through three-phase partitioning: crystal structure of a modified serine proteinase at 1.5 A resolution. PROTEIN ENGINEERING 2001; 14:307-13. [PMID: 11438752 DOI: 10.1093/protein/14.5.307] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Three-phase partitioning is fast developing as a novel bioseparation strategy with a wide range of applications including enzyme stability and enhancement of its catalytic activity. Despite all this, the enzyme behaviour in this process still remains unknown. A serine proteinase, proteinase K, was subjected to three-phase partitioning (TPP). A 3 ml volume of proteinase K solution (3 mg/ml in 0.05 M acetate buffer, pH 6.0) was brought to 30% (w/v) ammonium sulphate saturation by addition of saturated ammonium sulphate. tert-Butanol (6 ml) was added to this solution and the mixture was incubated at 25 degrees C for 1 h. The precipitated protein in the mid-layer was dissolved in 3 ml of 0.05 M acetate buffer, pH 6.0. The specific activity of the processed enzyme was estimated and was found to be 210% of the original enzyme activity. In order to understand the basis of this remarkable enhancement of the enzyme activity, the structure of the TPP-treated enzyme was determined by X-ray diffraction at 1.5 A resolution. The overall structure of the TPP-treated enzyme is similar to the original structure in an aqueous environment. The hydrogen bonding system of the catalytic triad is intact. However, the water structure in the substrate binding site has undergone a rearrangement as some of the water molecules are either displaced or completely absent. Two acetate ions were identified in the structure. One is located in the active site and seems to mimic the role of water in the enzyme activity and stability. The other is located at the surface of the molecule and is involved in stabilizing the local structure of the enzyme. The most striking observation in respect of the present structure pertains to a relatively higher overall temperature factor (B = 19.7 A(2)) than the value of 9.3 A(2) in the original enzyme. As a result of a higher B-factor, a number of residues, particularly their side chains, were found to adopt more than one conformation. It appears that the protein exists in an excited state which might be helping the enzyme to function more rapidly than the original enzyme in aqueous media. Summarily, the basis of increased enzymatic activity could be attributed to (i) the presence of an acetate ion at the active site and (ii) its excited state as reflected by an overall higher B-factor.
Collapse
Affiliation(s)
- R K Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Bagger S, Wagner K. Molecular recognition of cobalt(III)-ligated peptides by serine proteases: the role of electrostatic effects. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1998; 52:273-82. [PMID: 9832305 DOI: 10.1111/j.1399-3011.1998.tb01241.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of peptides with a positively charged cobalt(III)-complex group attached to the carboxylate terminal was synthesized. The behavior of these metallopeptides as acceptor nucleophiles in acyl transfer reactions catalyzed by the three serine proteases bovine pancreatic alpha-chymotrypsin, porcine pancreatic trypsin, and proteinase K from Tritirachium album was examined. The efficiency of the substrates was assessed by kinetic measurement of the partition between aminolysis and hydrolysis. The results are discussed with special reference to coulombic interactions between the metal-ligated substrates and charged residues on the enzyme surfaces. The idea of using the metallopeptides in practical enzymatic peptide synthesis is put forward.
Collapse
Affiliation(s)
- S Bagger
- Department of Chemistry, Technical University of Denmark, Lyngby.
| | | |
Collapse
|
14
|
Singh TP, Sharma S, Karthikeyan S, Betzel C, Bhatia KL. Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase K. Proteins 1998. [DOI: 10.1002/(sici)1097-0134(19981001)33:1<30::aid-prot3>3.0.co;2-p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
15
|
Rao GS, Arora S, Kataria S. A proteinase K inhibitor using alpha,beta-unsaturated (dehydro) residues: a presumptive model. J Biomol Struct Dyn 1998; 15:1053-8. [PMID: 9669551 DOI: 10.1080/07391102.1998.10509000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Enzymes of the subtilisin family, of which proteinase K is a member, have been studied extensively on account of their numerous biological applications. Specific inhibitors of the proteinases are of immense importance in regulating their activity so as to protect the cells against uncontrolled proteolysis. Using the specific design principles of peptides containing dehydro-Alanine (deltaAla), generated by our theoretical calculations, we present here the design of an inhibitor of proteinase K. Energy minimization and molecular modeling of the interaction of the designed tetrapeptide with the recognition site of proteinase K indicate that it is an effective inhibitor.
Collapse
Affiliation(s)
- G S Rao
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi.
| | | | | |
Collapse
|