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Gilbert J, Ermilova I, Nagao M, Swenson J, Nylander T. Effect of encapsulated protein on the dynamics of lipid sponge phase: a neutron spin echo and molecular dynamics simulation study. NANOSCALE 2022; 14:6990-7002. [PMID: 35470842 DOI: 10.1039/d2nr00882c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lipid membranes are highly mobile systems with hierarchical, time and length scale dependent, collective motions including thickness fluctuations, undulations, and topological membrane changes, which play an important role in membrane interactions. In this work we have characterised the effect of encapsulating two industrially important enzymes, β-galactosidase and aspartic protease, in lipid sponge phase nanoparticles on the dynamics of the lipid membrane using neutron spin echo (NSE) spectroscopy and molecular dynamics (MD) simulations. From NSE, reduced membrane dynamics were observed upon enzyme encapsulation, which were dependent on the enzyme concentration and type. By fitting the intermediate scattering functions (ISFs) with a modified Zilman and Granek model including nanoparticle diffusion, an increase in membrane bending rigidity was observed, with a larger effect for β-galactosidase than aspartic protease at the same concentration. MD simulations for the system with and without aspartic protease showed that the lipids relax more slowly in the system with protein due to the replacement of the lipid carbonyl-water hydrogen bonds with lipid-protein hydrogen bonds. This indicates that the most likely cause of the increase in membrane rigidity observed in the NSE measurements was dehydration of the lipid head groups. The dynamics of the protein itself were also studied, which showed a stable secondary structure of protein over the simulation, indicating no unfolding events occurred.
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Affiliation(s)
- Jennifer Gilbert
- Division of Physical Chemistry, Department of Chemistry, Naturvetarvägen 14, Lund University, 22362 Lund, Sweden.
- NanoLund, Lund University, Professorsgatan 1, 223 63 Lund, Sweden
| | - Inna Ermilova
- Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Michihiro Nagao
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA
| | - Jan Swenson
- Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Tommy Nylander
- Division of Physical Chemistry, Department of Chemistry, Naturvetarvägen 14, Lund University, 22362 Lund, Sweden.
- NanoLund, Lund University, Professorsgatan 1, 223 63 Lund, Sweden
- Lund Institute of Advanced Neutron and X-Ray Science, Scheelevägen 19, 223 70 Lund, Sweden
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2
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Kneller DW, Phillips G, Kovalevsky A, Coates L. Room-temperature neutron and X-ray data collection of 3CL M pro from SARS-CoV-2. Acta Crystallogr F Struct Biol Commun 2020; 76:483-487. [PMID: 33006576 PMCID: PMC7531248 DOI: 10.1107/s2053230x20011814] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/27/2020] [Indexed: 01/16/2023] Open
Abstract
The replication of SARS-CoV-2 produces two large polyproteins, pp1a and pp1ab, that are inactive until cleavage by the viral chymotrypsin-like cysteine protease enzyme (3CL Mpro) into a series of smaller functional proteins. At the heart of 3CL Mpro is an unusual catalytic dyad formed by the side chains of His41 and Cys145 and a coordinated water molecule. The catalytic mechanism by which the enzyme operates is still unknown, as crucial information on the protonation states within the active site is unclear. To experimentally determine the protonation states of the catalytic site and of the other residues in the substrate-binding cavity, and to visualize the hydrogen-bonding networks throughout the enzyme, room-temperature neutron and X-ray data were collected from a large H/D-exchanged crystal of ligand-free (apo) 3CL Mpro.
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Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA
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Valldeperas M, Talaikis M, Dhayal SK, Velička M, Barauskas J, Niaura G, Nylander T. Encapsulation of Aspartic Protease in Nonlamellar Lipid Liquid Crystalline Phases. Biophys J 2019; 117:829-843. [PMID: 31422820 DOI: 10.1016/j.bpj.2019.07.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 02/04/2023] Open
Abstract
Encapsulation of proteins within lipid inverse bicontinuous cubic phases (Q2) has been widely studied for many applications, such as protein crystallization or drug delivery of proteins for food and pharmaceutical purposes. However, the use of the lipid sponge (L3) phase for encapsulation of proteins has not yet been well explored. Here, we have employed a lipid system that forms highly swollen sponge phases to entrap aspartic protease (34 kDa), an enzyme used for food processing, e.g., to control the cheese-ripening process. Small-angle x-ray scattering showed that although the L3 phase was maintained at low enzyme concentrations (≤15 mg/mL), higher concentration induces a transition to more curved structures, i.e., transition from L3 to inverse bicontinuous cubic (Q2) phase. The Raman spectroscopy data showed minor conformational changes assigned to the lipid molecules that confirm the lipid-protein interactions. However, the peaks assigned to the protein showed that the structure was not significantly affected. This was consistent with the higher activity presented by the encapsulated aspartic protease compared to the free enzyme stored at the same temperature. Finally, the encapsulation efficiency of aspartic protease in lipid sponge-like nanoparticles was 81% as examined by size-exclusion chromatography. Based on these results, we discuss the large potential of lipid sponge phases as carriers for proteins.
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Affiliation(s)
- Maria Valldeperas
- Physical Chemistry, Department of Chemistry, Lund University, Lund, Sweden; NanoLund, Lund University, Lund, Sweden
| | - Martynas Talaikis
- Department of Bioelectrochemistry and Biospectroscopy, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Martynas Velička
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Vilnius, Lithuania
| | | | - Gediminas Niaura
- Department of Bioelectrochemistry and Biospectroscopy, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Tommy Nylander
- Physical Chemistry, Department of Chemistry, Lund University, Lund, Sweden; NanoLund, Lund University, Lund, Sweden.
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El Arnaout T, Soulimane T. Targeting Lipoprotein Biogenesis: Considerations towards Antimicrobials. Trends Biochem Sci 2019; 44:701-715. [PMID: 31036406 DOI: 10.1016/j.tibs.2019.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/14/2019] [Accepted: 03/25/2019] [Indexed: 12/25/2022]
Abstract
Decades have passed without approval of a new antibiotic class. Several companies have recently halted related discovery efforts because of multiple obstacles. One promising route under research is to target the lipoprotein maturation pathway in light of major recent findings and the virulence roles of lipoproteins. To support the future design of selective drugs, considerations and priority-setting are established for the main lipoprotein processing enzymes (Lgt, LspA, and Lnt) based on microbiology, biochemistry, structural biology, chemical design, and pharmacology. Although not all bacterial species will be similarly impacted by drug candidates, several advantages make LspA a top target to pursue in the development of novel antibiotics effective against bacteria that are resistant to existing drugs.
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Affiliation(s)
- Toufic El Arnaout
- Kappa Crystals Ltd, Dublin, Ireland; School of Food Science and Environmental Health, Technological University (TU) Dublin City Campus, TU, Dublin, Dublin, Ireland.
| | - Tewfik Soulimane
- Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland; Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland
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Lin J, Pozharski E, Wilson MA. Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons. Biochemistry 2017; 56:391-402. [PMID: 27989121 PMCID: PMC5805389 DOI: 10.1021/acs.biochem.6b00906] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor-acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [⟨dO-O⟩ = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.
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Affiliation(s)
- Jiusheng Lin
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE, 68588
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD, 21201,Institute for Bioscience and Biotechnology Research, Rockville, MD 20850,To whom correspondence can be addressed: Edwin Pozharski: or Mark A. Wilson:
| | - Mark A. Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE, 68588,To whom correspondence can be addressed: Edwin Pozharski: or Mark A. Wilson:
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Fadel F, Zhao Y, Cachau R, Cousido-Siah A, Ruiz FX, Harlos K, Howard E, Mitschler A, Podjarny A. New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM. ACTA ACUST UNITED AC 2015; 71:1455-70. [PMID: 26143917 DOI: 10.1107/s139900471500783x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/21/2015] [Indexed: 11/10/2022]
Abstract
Chitotriosidase (CHIT1) is a human chitinase belonging to the highly conserved glycosyl hydrolase family 18 (GH18). GH18 enzymes hydrolyze chitin, an N-acetylglucosamine polymer synthesized by lower organisms for structural purposes. Recently, CHIT1 has attracted attention owing to its upregulation in immune-system disorders and as a marker of Gaucher disease. The 39 kDa catalytic domain shows a conserved cluster of three acidic residues, Glu140, Asp138 and Asp136, involved in the hydrolysis reaction. Under an excess concentration of substrate, CHIT1 and other homologues perform an additional activity, transglycosylation. To understand the catalytic mechanism of GH18 chitinases and the dual enzymatic activity, the structure and mechanism of CHIT1 were analyzed in detail. The resolution of the crystals of the catalytic domain was improved from 1.65 Å (PDB entry 1waw) to 0.95-1.10 Å for the apo and pseudo-apo forms and the complex with chitobiose, allowing the determination of the protonation states within the active site. This information was extended by hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. The results suggest a new mechanism involving changes in the conformation and protonation state of the catalytic triad, as well as a new role for Tyr27, providing new insights into the hydrolysis and transglycosylation activities.
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Affiliation(s)
- Firas Fadel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Raul Cachau
- Leidos Biomedical Research Inc. Advanced Biomedical Computer Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alexandra Cousido-Siah
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Francesc X Ruiz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Eduardo Howard
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Andre Mitschler
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Alberto Podjarny
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
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Bhaumik P, Gustchina A, Wlodawer A. Structural studies of vacuolar plasmepsins. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1824:207-23. [PMID: 21540129 PMCID: PMC3154504 DOI: 10.1016/j.bbapap.2011.04.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Revised: 04/11/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
Abstract
Plasmepsins (PMs) are pepsin-like aspartic proteases present in different species of parasite Plasmodium. Four Plasmodium spp. (P. vivax, P. ovale, P. malariae, and the most lethal P. falciparum) are mainly responsible for causing human malaria that affects millions worldwide. Due to the complexity and rate of parasite mutation coupled with regional variations, and the emergence of P. falciparum strains which are resistant to antimalarial agents such as chloroquine and sulfadoxine/pyrimethamine, there is constant pressure to find new and lasting chemotherapeutic drug therapies. Since many proteases represent therapeutic targets and PMs have been shown to play an important role in the survival of parasite, these enzymes have recently been identified as promising targets for the development of novel antimalarial drugs. The genome of P. falciparum encodes 10 PMs (PMI, PMII, PMIV-X and histo-aspartic protease (HAP)), 4 of which (PMI, PMII, PMIV and HAP) reside within the food vacuole, are directly involved in degradation of human hemoglobin, and share 50-79% amino acid sequence identity. This review focuses on structural studies of only these four enzymes, including their orthologs in other Plasmodium spp.. Almost all original crystallographic studies were performed with PMII, but more recent work on PMIV, PMI, and HAP resulted in a more complete picture of the structure-function relationship of vacuolar PMs. Many structures of inhibitor complexes of vacuolar plasmepsins, as well as their zymogens, have been reported in the last 15 years. Information gained by such studies will be helpful for the development of better inhibitors that could become a new class of potent antimalarial drugs. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.
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Affiliation(s)
- Prasenjit Bhaumik
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alla Gustchina
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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8
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Behnen J, Köster H, Neudert G, Craan T, Heine A, Klebe G. Experimental and computational active site mapping as a starting point to fragment-based lead discovery. ChemMedChem 2011; 7:248-61. [PMID: 22213702 DOI: 10.1002/cmdc.201100490] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 11/23/2011] [Indexed: 11/06/2022]
Abstract
Small highly soluble probe molecules such as aniline, urea, N-methylurea, 2-bromoacetate, 1,2-propanediol, nitrous oxide, benzamidine, and phenol were soaked into crystals of various proteins to map their binding pockets and to detect hot spots of binding with respect to hydrophobic and hydrophilic properties. The selected probe molecules were first tested at the zinc protease thermolysin. They were then applied to a wider range of proteins such as protein kinase A, D-xylose isomerase, 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, endothiapepsin, and secreted aspartic protease 2. The crystal structures obtained clearly show that the probe molecules populate the protein binding pockets in an ordered fashion. The thus characterized, experimentally observed hot spots of binding were subjected to computational active site mapping using HotspotsX. This approach uses knowledge-based pair potentials to detect favorable binding positions for various atom types. Good agreement between the in silico hot spot predictions and the experimentally observed positions of the polar hydrogen bond forming functional groups and hydrophobic portions was obtained. Finally, we compared the observed poses of the small-molecule probes with those of much larger structurally related ligands. They coincide remarkably well with the larger ligands, considering their spatial orientation and the experienced interaction patterns. This observation confirms the fundamental hypothesis of fragment-based lead discovery: that binding poses, even of very small molecular probes, do not significantly deviate or move once a ligand is grown further into the binding site. This underscores the fact that these probes populate given hot spots and can be regarded as relevant seeds for further design.
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Affiliation(s)
- Jürgen Behnen
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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9
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Bhaumik P, Xiao H, Hidaka K, Gustchina A, Kiso Y, Yada RY, Wlodawer A. Structural insights into the activation and inhibition of histo-aspartic protease from Plasmodium falciparum. Biochemistry 2011; 50:8862-79. [PMID: 21928835 PMCID: PMC3501826 DOI: 10.1021/bi201118z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Histo-aspartic protease (HAP) from Plasmodium falciparum is a promising target for the development of novel antimalarial drugs. The sequence of HAP is highly similar to those of pepsin-like aspartic proteases, but one of the two catalytic aspartates, Asp32, is replaced with histidine. Crystal structures of the truncated zymogen of HAP and of the complex of the mature enzyme with inhibitor KNI-10395 have been determined at 2.1 and 2.5 Å resolution, respectively. As in other proplasmepsins, the propeptide of the zymogen interacts with the C-terminal domain of the enzyme, forcing the N- and C-terminal domains apart, thereby separating His32 and Asp215 and preventing formation of the mature active site. In the inhibitor complex, the enzyme forms a tight domain-swapped dimer, not previously seen in any aspartic proteases. The inhibitor is found in an unprecedented conformation resembling the letter U, stabilized by two intramolecular hydrogen bonds. Surprisingly, the location and conformation of the inhibitor are similar to those of the fragment of helix 2 comprising residues 34p-38p in the prosegments of the zymogens of gastric aspartic proteases; a corresponding helix assumes a vastly different orientation in proplasmepsins. Each inhibitor molecule is in contact with two molecules of HAP, interacting with the carboxylate group of the catalytic Asp215 of one HAP protomer through a water molecule, while also making a direct hydrogen bond to Glu278A' of the other protomer. A comparison of the shifts in the positions of the catalytic residues in the inhibitor complex presented here with those published previously gives further hints regarding the enzymatic mechanism of HAP.
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Affiliation(s)
- Prasenjit Bhaumik
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Huogen Xiao
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Koushi Hidaka
- Department of Medicinal Chemistry and Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607–8412, Japan
- Laboratory of Medicinal Chemistry, Kobe Gakuin University, 1-1–3 Minatojima, Chuo-ku, Kobe 650–8586, Japan
| | - Alla Gustchina
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Yoshiaki Kiso
- Department of Medicinal Chemistry and Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607–8412, Japan
- Laboratory of Medicinal Chemistry, Kobe Gakuin University, 1-1–3 Minatojima, Chuo-ku, Kobe 650–8586, Japan
- Laboratory of Peptide Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526–0829, Japan
| | - Rickey Y. Yada
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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Deniau G, Seebach D. Preparation ofN-Fmoc-Protected (S)-5-Amino-4,4-difluoro-7-methyloctanoic Acid, a Possible Dipeptide Isostere. Helv Chim Acta 2009. [DOI: 10.1002/hlca.200900215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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11
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Bhaumik P, Xiao H, Parr CL, Kiso Y, Gustchina A, Yada RY, Wlodawer A. Crystal structures of the histo-aspartic protease (HAP) from Plasmodium falciparum. J Mol Biol 2009; 388:520-40. [PMID: 19285084 DOI: 10.1016/j.jmb.2009.03.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 02/25/2009] [Accepted: 03/05/2009] [Indexed: 02/07/2023]
Abstract
The structures of recombinant histo-aspartic protease (HAP) from malaria-causing parasite Plasmodium falciparum as apoenzyme and in complex with two inhibitors, pepstatin A and KNI-10006, were solved at 2.5-, 3.3-, and 3.05-A resolutions, respectively. In the apoenzyme crystals, HAP forms a tight dimer not seen previously in any aspartic protease. The interactions between the monomers affect the conformation of two flexible loops, the functionally important "flap" (residues 70-83) and its structural equivalent in the C-terminal domain (residues 238-245), as well as the orientation of helix 225-235. The flap is found in an open conformation in the apoenzyme. Unexpectedly, the active site of the apoenzyme contains a zinc ion tightly bound to His32 and Asp215 from one monomer and to Glu278A from the other monomer, with the coordination of Zn resembling that seen in metalloproteases. The flap is closed in the structure of the pepstatin A complex, whereas it is open in the complex with KNI-10006. Although the binding mode of pepstatin A is significantly different from that in other pepsin-like aspartic proteases, its location in the active site makes unlikely the previously proposed hypothesis that HAP is a serine protease. The binding mode of KNI-10006 is unusual compared with the binding of other inhibitors from the KNI series to aspartic proteases. The novel features of the HAP active site could facilitate design of specific inhibitors used in the development of antimalarial drugs.
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Affiliation(s)
- Prasenjit Bhaumik
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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Singh R, Barman A, Prabhakar R. Computational Insights into Aspartyl Protease Activity of Presenilin 1 (PS1) Generating Alzheimer Amyloid β-Peptides (Aβ40 and Aβ42). J Phys Chem B 2009; 113:2990-9. [DOI: 10.1021/jp811154w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Rajiv Singh
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
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13
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Witt AC, Lakshminarasimhan M, Remington BC, Hasim S, Pozharski E, Wilson MA. Cysteine pKa depression by a protonated glutamic acid in human DJ-1. Biochemistry 2008; 47:7430-40. [PMID: 18570440 DOI: 10.1021/bi800282d] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human DJ-1, a disease-associated protein that protects cells from oxidative stress, contains an oxidation-sensitive cysteine (C106) that is essential for its cytoprotective activity. The origin of C106 reactivity is obscure, due in part to the absence of an experimentally determined p K a value for this residue. We have used atomic-resolution X-ray crystallography and UV spectroscopy to show that C106 has a depressed p K a of 5.4 +/- 0.1 and that the C106 thiolate accepts a hydrogen bond from a protonated glutamic acid side chain (E18). X-ray crystal structures and cysteine p K a analysis of several site-directed substitutions at residue 18 demonstrate that the protonated carboxylic acid side chain of E18 is required for the maximal stabilization of the C106 thiolate. A nearby arginine residue (R48) participates in a guanidinium stacking interaction with R28 from the other monomer in the DJ-1 dimer and elevates the p K a of C106 by binding an anion that electrostatically suppresses thiol ionization. Our results show that the ionizable residues (E18, R48, and R28) surrounding C106 affect its p K a in a way that is contrary to expectations based on the typical ionization behavior of glutamic acid and arginine. Lastly, a search of the Protein Data Bank (PDB) produces several candidate hydrogen-bonded aspartic/glutamic acid-cysteine interactions, which we propose are particularly common in the DJ-1 superfamily.
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Affiliation(s)
- Anna C Witt
- Department of Biochemistry and Redox Biology Center, The University of Nebraska, Lincoln, Nebraska 68588-0664, USA
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14
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Understanding the structure–function role of specific catalytic residues in a model food related enzyme: Pepsin. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.08.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Coates L, Erskine PT, Mall S, Gill R, Wood SP, Myles DAA, Cooper JB. X-ray, neutron and NMR studies of the catalytic mechanism of aspartic proteinases. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2006; 35:559-66. [PMID: 16673078 DOI: 10.1007/s00249-006-0065-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2006] [Revised: 03/24/2006] [Accepted: 04/04/2006] [Indexed: 11/24/2022]
Abstract
Current proposals for the catalytic mechanism of aspartic proteinases are largely based on X-ray structures of bound oligopeptide inhibitors possessing non-hydrolysable analogues of the scissile peptide bond. Until recent years, the positions of protons on the catalytic aspartates and the ligand in these complexes had not been determined with certainty due to the inadequate resolution of these analyses. There has been much interest in locating the catalytic protons at the active site of aspartic proteinases since this has major implications for detailed understanding of the mechanism of action and the design of improved transition state mimics for therapeutic applications. In this review we discuss the results of studies which have shed light on the locations of protons at the catalytic centre. The first direct determination of the proton positions stemmed from neutron diffraction data collected from crystals of the fungal aspartic proteinase endothiapepsin bound to a transition state analogue (H261). The neutron structure of the complex at a resolution of 2.1 A provided evidence that Asp 215 is protonated and that Asp 32 is the negatively charged residue in the transition state complex. Atomic resolution X-ray studies of inhibitor complexes have corroborated this finding. A similar study of the native enzyme established that it, unexpectedly, has a dipeptide bound at the catalytic site which is consistent with classical reports of inhibition by short peptides and the ability of pepsins to catalyse transpeptidation reactions. Studies by NMR have confirmed the findings of low-barrier and single-well hydrogen bonds in the complexes with transition state analogues.
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Affiliation(s)
- Leighton Coates
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton, SO16 7PX, England
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16
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Davis IW, Arendall WB, Richardson DC, Richardson JS. The backrub motion: how protein backbone shrugs when a sidechain dances. Structure 2006; 14:265-74. [PMID: 16472746 DOI: 10.1016/j.str.2005.10.007] [Citation(s) in RCA: 200] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2005] [Revised: 10/10/2005] [Accepted: 10/12/2005] [Indexed: 11/16/2022]
Abstract
Surprisingly, the frozen structures from ultra-high-resolution protein crystallography reveal a prevalent, but subtle, mode of local backbone motion coupled to much larger, two-state changes of sidechain conformation. This "backrub" motion provides an influential and common type of local plasticity in protein backbone. Concerted reorientation of two adjacent peptides swings the central sidechain perpendicular to the chain direction, changing accessible sidechain conformations while leaving flanking structure undisturbed. Alternate conformations in sub-1 angstroms crystal structures show backrub motions for two-thirds of the significant Cbeta shifts and 3% of the total residues in these proteins (126/3882), accompanied by two-state changes in sidechain rotamer. The Backrub modeling tool is effective in crystallographic rebuilding. For homology modeling or protein redesign, backrubs can provide realistic, small perturbations to rigid backbones. For large sidechain changes in protein dynamics or for single mutations, backrubs allow backbone accommodation while maintaining H bonds and ideal geometry.
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Affiliation(s)
- Ian W Davis
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
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17
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Prade L, Jones AF, Boss C, Richard-Bildstein S, Meyer S, Binkert C, Bur D. X-ray Structure of Plasmepsin II Complexed with a Potent Achiral Inhibitor. J Biol Chem 2005; 280:23837-43. [PMID: 15840589 DOI: 10.1074/jbc.m501519200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The malaria parasite Plasmodium falciparum degrades host cell hemoglobin inside an acidic food vacuole during the blood stage of the infectious cycle. A number of aspartic proteinases called plasmepsins (PMs) have been identified to play important roles in this degradation process and therefore generated significant interest as new antimalarial targets. Several x-ray structures of PMII have been described previously, but thus far, structure-guided drug design has been hampered by the fact that only inhibitors comprising a statine moiety or derivatives thereof have been published. Our drug discovery efforts to find innovative, cheap, and easily synthesized inhibitors against aspartic proteinases yielded some highly potent non-peptidic achiral inhibitors. A highly resolved (1.6 A) x-ray structure of PMII is presented, featuring a potent achiral inhibitor in an unprecedented orientation, contacting the catalytic aspartates indirectly via the "catalytic" water. Major side chain rearrangements in the active site occur, which open up a new pocket and allow a new binding mode of the inhibitor. Moreover, a second inhibitor molecule could be located unambiguously in the active site of PMII. These newly obtained structural insights will further guide our attempts to improve compound properties eventually leading to the identification of molecules suitable as antimalarial drugs.
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Affiliation(s)
- Lars Prade
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
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18
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Rajamani R, Reynolds CH. Modeling the protonation states of the catalytic aspartates in beta-secretase. J Med Chem 2004; 47:5159-66. [PMID: 15456259 DOI: 10.1021/jm049817j] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Beta-secretase (BACE) is a critical enzyme in the production of beta-amyloid, a protein that has been implicated as a potential cause of Alzheimer's disease (AD). There are two aspartic acid residues (Asp 32 and Asp 228) present in the catalytic region of BACE that can adopt multiple protonation states. The protonation state and precise location of the protons for these two residues, particularly in the presence of an inhibitor, are subjects of great interest since they have a direct bearing on the mechanism of aspartyl proteases and efforts to model beta-secretase. We have carried out full liner-scaling quantum mechanical (QM) calculations that include Poisson-Boltzmann solvation in order to identify the preferred protonation state and proton location in the presence and absence of an inhibitor. These calculations favor the monoprotonated state in the presence of ligand, and di-deprotonated state in the absence of ligand. Further the proton in the monoprotonated state is located on the inner oxygen of Asp 228. These results have implications for the catalytic mechanism of BACE and related aspartyl proteases. They also provide a reference state for the protein in structure-based modeling studies of this therapeutically important target.
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Affiliation(s)
- Ramkumar Rajamani
- Johnson & Johnson Pharmaceutical R&D, Welsh and McKean Roads, PO Box 776, Spring House, PA 19477, USA
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19
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Coburn CA, Stachel SJ, Li YM, Rush DM, Steele TG, Chen-Dodson E, Holloway MK, Xu M, Huang Q, Lai MT, DiMuzio J, Crouthamel MC, Shi XP, Sardana V, Chen Z, Munshi S, Kuo L, Makara GM, Annis DA, Tadikonda PK, Nash HM, Vacca JP, Wang T. Identification of a Small Molecule Nonpeptide Active Site β-Secretase Inhibitor That Displays a Nontraditional Binding Mode for Aspartyl Proteases. J Med Chem 2004; 47:6117-9. [PMID: 15566281 DOI: 10.1021/jm049388p] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A small molecule nonpeptide inhibitor of beta-secretase has been developed, and its binding has been defined through crystallographic determination of the enzyme-inhibitor complex. The molecule is shown to bind to the catalytic aspartate residues in an unprecedented manner in the field of aspartyl protease inhibition. Additionally, the complex reveals a heretofore unknown S(3) subpocket that is created by the inhibitor. This structure has served an important role in the design of newer beta-secretase inhibitors.
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Affiliation(s)
- Craig A Coburn
- Department of Medicinal Chemistry, Merck Research Laoratories, West Point, PA 19486-0004, USA.
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