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Chen D, Chen Q, Qin X, Tong P, Peng L, Zhang T, Xia C. Development and evolution of human glutaminyl cyclase inhibitors (QCIs): an alternative promising approach for disease-modifying treatment of Alzheimer's disease. Front Aging Neurosci 2023; 15:1209863. [PMID: 37600512 PMCID: PMC10435661 DOI: 10.3389/fnagi.2023.1209863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Human glutaminyl cyclase (hQC) is drawing considerable attention and emerging as a potential druggable target for Alzheimer's disease (AD) due to its close involvement in the pathology of AD via the post-translational pyroglutamate modification of amyloid-β. A recent phase 2a study has shown promising early evidence of efficacy for AD with a competitive benzimidazole-based QC inhibitor, PQ912, which also demonstrated favorable safety profiles. This finding has sparked new hope for the treatment of AD. In this review, we briefly summarize the discovery and evolution of hQC inhibitors, with a particular interest in classic Zinc binding group (ZBG)-containing chemicals reported in recent years. Additionally, we highlight several high-potency inhibitors and discuss new trends and challenges in the development of QC inhibitors as an alternative and promising disease-modifying therapy for AD.
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Affiliation(s)
- Daoyuan Chen
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Qingxiu Chen
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Xiaofei Qin
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Peipei Tong
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Liping Peng
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Tao Zhang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Institute of Basic Medicine, Fujian Medical University, Fuzhou, China
| | - Chunli Xia
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
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2
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Pyroglutamate Aβ cascade as drug target in Alzheimer's disease. Mol Psychiatry 2022; 27:1880-1885. [PMID: 34880449 PMCID: PMC9126800 DOI: 10.1038/s41380-021-01409-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 02/07/2023]
Abstract
One of the central aims in Alzheimer's disease (AD) research is the identification of clinically relevant drug targets. A plethora of potential molecular targets work very well in preclinical model systems both in vitro and in vivo in AD mouse models. However, the lack of translation into clinical settings in the AD field is a challenging endeavor. Although it is long known that N-terminally truncated and pyroglutamate-modified Abeta (AβpE3) peptides are abundantly present in the brain of AD patients, form stable and soluble low-molecular weight oligomers, and induce neurodegeneration in AD mouse models, their potential as drug target has not been generally accepted in the past. This situation has dramatically changed with the report that passive immunization with donanemab, an AβpE3-specific antibody, cleared aymloid plaques and stabilized cognitive deficits in a group of patients with mild AD in a phase II trial. This review summarizes the current knowledge on the molecular mechanisms of generation of AβpE, its biochemical properties, and the intervention points as a drug target in AD.
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3
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Hoi KK, Bada Juarez JF, Judge PJ, Yen HY, Wu D, Vinals J, Taylor GF, Watts A, Robinson CV. Detergent-free Lipodisq Nanoparticles Facilitate High-Resolution Mass Spectrometry of Folded Integral Membrane Proteins. NANO LETTERS 2021; 21:2824-2831. [PMID: 33787280 PMCID: PMC8050825 DOI: 10.1021/acs.nanolett.0c04911] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/04/2021] [Indexed: 05/04/2023]
Abstract
Integral membrane proteins pose considerable challenges to mass spectrometry (MS) owing to the complexity and diversity of the components in their native environment. Here, we use native MS to study the post-translational maturation of bacteriorhodopsin (bR) and archaerhodopsin-3 (AR3), using both octyl-glucoside detergent micelles and lipid-based nanoparticles. A lower collision energy was required to obtain well-resolved spectra for proteins in styrene-maleic acid copolymer (SMA) Lipodisqs than in membrane scaffold protein (MSP) Nanodiscs. By comparing spectra of membrane proteins prepared using the different membrane mimetics, we found that SMA may favor selective solubilization of correctly folded proteins and better preserve native lipid interactions than other membrane mimetics. Our spectra reveal the correlation between the post-translation modifications (PTMs), lipid-interactions, and protein-folding states of bR, providing insights into the process of maturation of the photoreceptor proteins.
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Affiliation(s)
- Kin Kuan Hoi
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Juan Francisco Bada Juarez
- Department
of Biochemistry, Biomembrane Structure Unit, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Peter J. Judge
- Department
of Biochemistry, Biomembrane Structure Unit, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Hsin-Yung Yen
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
- OMass
Therapeutics, The Schrödinger
Building, Oxford Science Park, Oxford OX4
4GE, United Kingdom
| | - Di Wu
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Javier Vinals
- Department
of Biochemistry, Biomembrane Structure Unit, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Garrick F. Taylor
- Department
of Biochemistry, Biomembrane Structure Unit, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anthony Watts
- Department
of Biochemistry, Biomembrane Structure Unit, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Carol V. Robinson
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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Lamers S, Feng Q, Cheng Y, Yu S, Sun B, Lukman M, Jiang J, Ruiz-Carrillo D. Structural and kinetic characterization of Porphyromonas gingivalis glutaminyl cyclase. Biol Chem 2021; 402:759-768. [PMID: 33823093 DOI: 10.1515/hsz-2020-0298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/16/2021] [Indexed: 11/15/2022]
Abstract
Porphyromonas gingivalis is a bacterial species known to be involved in the pathogenesis of chronic periodontitis, that more recently has been as well associated with Alzheimer's disease. P. gingivalis expresses a glutaminyl cyclase (PgQC) whose human ortholog is known to participate in the beta amyloid peptide metabolism. We have elucidated the crystal structure of PgQC at 1.95 Å resolution in unbound and in inhibitor-complexed forms. The structural characterization of PgQC confirmed that PgQC displays a mammalian fold rather than a bacterial fold. Our biochemical characterization indicates that PgQC uses a mammalian-like catalytic mechanism enabled by the residues Asp149, Glu182, Asp183, Asp218, Asp267 and His299. In addition, we could observe that a non-conserved Trp193 may drive differences in the binding affinity of ligands which might be useful for drug development. With a screening of a small molecule library, we have identified a benzimidazole derivative rendering PgQC inhibition in the low micromolar range that might be amenable for further medicinal chemistry development.
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Affiliation(s)
- Sebastiaan Lamers
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Qiaoli Feng
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Yili Cheng
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Sihong Yu
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Bo Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai201204, China
| | - Maxwell Lukman
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Jie Jiang
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - David Ruiz-Carrillo
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
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Taudte N, Linnert M, Rahfeld JU, Piechotta A, Ramsbeck D, Buchholz M, Kolenko P, Parthier C, Houston JA, Veillard F, Eick S, Potempa J, Schilling S, Demuth HU, Stubbs MT. Mammalian-like type II glutaminyl cyclases in Porphyromonas gingivalis and other oral pathogenic bacteria as targets for treatment of periodontitis. J Biol Chem 2021; 296:100263. [PMID: 33837744 PMCID: PMC7948796 DOI: 10.1016/j.jbc.2021.100263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 12/25/2022] Open
Abstract
The development of a targeted therapy would significantly improve the treatment of periodontitis and its associated diseases including Alzheimer’s disease, rheumatoid arthritis, and cardiovascular diseases. Glutaminyl cyclases (QCs) from the oral pathogens Porphyromonas gingivalis, Tannerella forsythia, and Prevotella intermedia represent attractive target enzymes for small-molecule inhibitor development, as their action is likely to stabilize essential periplasmic and outer membrane proteins by N-terminal pyroglutamination. In contrast to other microbial QCs that utilize the so-called type I enzymes, these oral pathogens possess sequences corresponding to type II QCs, observed hitherto only in animals. However, whether differences between these bacteroidal QCs and animal QCs are sufficient to enable development of selective inhibitors is not clear. To learn more, we recombinantly expressed all three QCs. They exhibit comparable catalytic efficiencies and are inhibited by metal chelators. Crystal structures of the enzymes from P. gingivalis (PgQC) and T. forsythia (TfQC) reveal a tertiary structure composed of an eight-stranded β-sheet surrounded by seven α-helices, typical of animal type II QCs. In each case, an active site Zn ion is tetrahedrally coordinated by conserved residues. Nevertheless, significant differences to mammalian enzymes are found around the active site of the bacteroidal enzymes. Application of a PgQC-selective inhibitor described here for the first time results in growth inhibition of two P. gingivalis clinical isolates in a dose-dependent manner. The insights gained by these studies will assist in the development of highly specific small-molecule bacteroidal QC inhibitors, paving the way for alternative therapies against periodontitis and associated diseases.
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Affiliation(s)
- Nadine Taudte
- Periotrap Pharmaceuticals GmbH, Halle (Saale), Germany
| | - Miriam Linnert
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Jens-Ulrich Rahfeld
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany.
| | - Anke Piechotta
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Daniel Ramsbeck
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Mirko Buchholz
- Periotrap Pharmaceuticals GmbH, Halle (Saale), Germany; Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Petr Kolenko
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Christoph Parthier
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - John A Houston
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, USA
| | - Florian Veillard
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sigrun Eick
- Department of Periodontology, School of Dental Medicine, University of Bern, Bern, Switzerland
| | - Jan Potempa
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, USA; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Stephan Schilling
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany; Angewandte Biowissenschaften und Prozesstechnik, Hochschule Anhalt, Köthen, Germany
| | - Hans-Ulrich Demuth
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Milton T Stubbs
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany; ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.
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6
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Niehaus TD, Elbadawi-Sidhu M, de Crécy-Lagard V, Fiehn O, Hanson AD. Discovery of a widespread prokaryotic 5-oxoprolinase that was hiding in plain sight. J Biol Chem 2017; 292:16360-16367. [PMID: 28830929 DOI: 10.1074/jbc.m117.805028] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/18/2017] [Indexed: 11/06/2022] Open
Abstract
5-Oxoproline (OP) is well-known as an enzymatic intermediate in the eukaryotic γ-glutamyl cycle, but it is also an unavoidable damage product formed spontaneously from glutamine and other sources. Eukaryotes metabolize OP via an ATP-dependent 5-oxoprolinase; most prokaryotes lack homologs of this enzyme (and the γ-glutamyl cycle) but are predicted to have some way to dispose of OP if its spontaneous formation in vivo is significant. Comparative analysis of prokaryotic genomes showed that the gene encoding pyroglutamyl peptidase, which removes N-terminal OP residues, clusters in diverse genomes with genes specifying homologs of a fungal lactamase (renamed prokaryotic 5-oxoprolinase A, pxpA) and homologs of allophanate hydrolase subunits (renamed pxpB and pxpC). Inactivation of Bacillus subtilis pxpA, pxpB, or pxpC genes slowed growth, caused OP accumulation in cells and medium, and prevented use of OP as a nitrogen source. Assays of cell lysates showed that ATP-dependent 5-oxoprolinase activity disappeared when pxpA, pxpB, or pxpC was inactivated. 5-Oxoprolinase activity could be reconstituted in vitro by mixing recombinant B. subtilis PxpA, PxpB, and PxpC proteins. In addition, overexpressing Escherichia coli pxpABC genes in E. coli increased 5-oxoprolinase activity in lysates ≥1700-fold. This work shows that OP is a major universal metabolite damage product and that OP disposal systems are common in all domains of life. Furthermore, it illustrates how easily metabolite damage and damage-control systems can be overlooked, even for central metabolites in model organisms.
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Affiliation(s)
- Thomas D Niehaus
- From the Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611,
| | - Mona Elbadawi-Sidhu
- the West Coast Metabolomics Center, University of California Davis, Davis, California 95616, and
| | - Valérie de Crécy-Lagard
- the Microbiology and Cell Science Department, University of Florida, Gainesville, Florida 32611
| | - Oliver Fiehn
- the West Coast Metabolomics Center, University of California Davis, Davis, California 95616, and
| | - Andrew D Hanson
- From the Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611,
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Identification of specific posttranslational O-mycoloylations mediating protein targeting to the mycomembrane. Proc Natl Acad Sci U S A 2017; 114:4231-4236. [PMID: 28373551 DOI: 10.1073/pnas.1617888114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The outer membranes (OMs) of members of the Corynebacteriales bacterial order, also called mycomembranes, harbor mycolic acids and unusual outer membrane proteins (OMPs), including those with α-helical structure. The signals that allow precursors of such proteins to be targeted to the mycomembrane remain uncharacterized. We report here the molecular features responsible for OMP targeting to the mycomembrane of Corynebacterium glutamicum, a nonpathogenic member of the Corynebacteriales order. To better understand the mechanisms by which OMP precursors were sorted in C. glutamicum, we first investigated the partitioning of endogenous and recombinant PorA, PorH, PorB, and PorC between bacterial compartments and showed that they were both imported into the mycomembrane and secreted into the extracellular medium. A detailed investigation of cell extracts and purified proteins by top-down MS, NMR spectroscopy, and site-directed mutagenesis revealed specific and well-conserved posttranslational modifications (PTMs), including O-mycoloylation, pyroglutamylation, and N-formylation, for mycomembrane-associated and -secreted OMPs. PTM site sequence analysis from C. glutamicum OMP and other O-acylated proteins in bacteria and eukaryotes revealed specific patterns. Furthermore, we found that such modifications were essential for targeting to the mycomembrane and sufficient for OMP assembly into mycolic acid-containing lipid bilayers. Collectively, it seems that these PTMs have evolved in the Corynebacteriales order and beyond to guide membrane proteins toward a specific cell compartment.
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8
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Structure of the host-recognition device of Staphylococcus aureus phage ϕ11. Sci Rep 2016; 6:27581. [PMID: 27282779 PMCID: PMC4901313 DOI: 10.1038/srep27581] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/17/2016] [Indexed: 12/16/2022] Open
Abstract
Phages play key roles in the pathogenicity and adaptation of the human pathogen Staphylococcus aureus. However, little is known about the molecular recognition events that mediate phage adsorption to the surface of S. aureus. The lysogenic siphophage ϕ11 infects S. aureus SA113. It was shown previously that ϕ11 requires α- or β-N-acetylglucosamine (GlcNAc) moieties on cell wall teichoic acid (WTA) for adsorption. Gp45 was identified as the receptor binding protein (RBP) involved in this process and GlcNAc residues on WTA were found to be the key component of the ϕ11 receptor. Here we report the crystal structure of the RBP of ϕ11, which assembles into a large, multidomain homotrimer. Each monomer contains a five-bladed propeller domain with a cavity that could accommodate a GlcNAc moiety. An electron microscopy reconstruction of the ϕ11 host adhesion component, the baseplate, reveals that six RBP trimers are assembled around the baseplate core. The Gp45 and baseplate structures provide insights into the overall organization and molecular recognition process of the phage ϕ11 tail. This assembly is conserved among most glycan-recognizing Siphoviridae, and the RBP orientation would allow host adhesion and infection without an activation step.
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Kolenko P, Koch B, Rahfeld JU, Schilling S, Demuth HU, Stubbs MT. Structure of glutaminyl cyclase from Drosophila melanogaster in space group I4. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:358-61. [PMID: 23545638 PMCID: PMC3614157 DOI: 10.1107/s1744309113005575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 02/26/2013] [Indexed: 05/06/2024]
Abstract
The structure of ligand-free glutaminyl cyclase (QC) from Drosophila melanogaster (DmQC) has been determined in a novel crystal form. The protein crystallized in space group I4, with unit-cell parameters a = b = 122.3, c = 72.7 Å. The crystal diffracted to a resolution of 2 Å at the home source. The structure was solved by molecular replacement and was refined to an R factor of 0.169. DmQC exhibits a typical α/β-hydrolase fold. The electron density of three monosaccharides could be localized. The accessibility of the active site will facilitate structural studies of novel inhibitor-binding modes.
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Affiliation(s)
- Petr Kolenko
- Department of Physical Biochemistry, Institute of Biochemistry and Biotechnology, MLU, Kurt-Mothes-Strasse 3, 06120 Halle, Germany.
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10
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Koch B, Kolenko P, Buchholz M, Carrillo DR, Parthier C, Wermann M, Rahfeld JU, Reuter G, Schilling S, Stubbs MT, Demuth HU. Crystal structures of glutaminyl cyclases (QCs) from Drosophila melanogaster reveal active site conservation between insect and mammalian QCs. Biochemistry 2012; 51:7383-92. [PMID: 22897232 DOI: 10.1021/bi300687g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glutaminyl cyclases (QCs), which catalyze the formation of pyroglutamic acid (pGlu) at the N-terminus of a variety of peptides and proteins, have attracted particular attention for their potential role in Alzheimer's disease. In a transgenic Drosophila melanogaster (Dm) fruit fly model, oral application of the potent competitive QC inhibitor PBD150 was shown to reduce the burden of pGlu-modified Aβ. In contrast to mammals such as humans and rodents, there are at least three DmQC species, one of which (isoDromeQC) is localized to mitochondria, whereas DromeQC and an isoDromeQC splice variant possess signal peptides for secretion. Here we present the recombinant expression, characterization, and crystal structure determination of mature DromeQC and isoDromeQC, revealing an overall fold similar to that of mammalian QCs. In the case of isoDromeQC, the putative extended substrate binding site might be affected by the proximity of the N-terminal residues. PBD150 inhibition of DromeQC is roughly 1 order of magnitude weaker than that of the human and murine QCs. The inhibitor binds to isoDromeQC in a fashion similar to that observed for human QCs, whereas it adopts alternative binding modes in a DromeQC variant lacking the conserved cysteines near the active center and shows a disordered dimethoxyphenyl moiety in wild-type DromeQC, providing an explanation for the lower affinity. Our biophysical and structural data suggest that isoDromeQC and human QC are similar with regard to functional aspects. The two Dm enzymes represent a suitable model for further in-depth analysis of the catalytic mechanism of animal QCs, and isoDromeQC might serve as a model system for the structure-based design of potential AD therapeutics.
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Affiliation(s)
- Birgit Koch
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
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11
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Bell JA, Ho KL, Farid R. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:935-52. [PMID: 22868759 PMCID: PMC3413210 DOI: 10.1107/s0907444912017453] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 04/19/2012] [Indexed: 11/12/2022]
Abstract
All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5-2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R(free) values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein-ligand interactions.
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Affiliation(s)
- Jeffrey A. Bell
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - Kenneth L. Ho
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - Ramy Farid
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
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12
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Ruiz-Carrillo D, Koch B, Parthier C, Wermann M, Dambe T, Buchholz M, Ludwig HH, Heiser U, Rahfeld JU, Stubbs MT, Schilling S, Demuth HU. Structures of Glycosylated Mammalian Glutaminyl Cyclases Reveal Conformational Variability near the Active Center. Biochemistry 2011; 50:6280-8. [DOI: 10.1021/bi200249h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David Ruiz-Carrillo
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Birgit Koch
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Christoph Parthier
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Michael Wermann
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Tresfore Dambe
- PSF AG, Robert-Roessle-Strasse 10, D-13092 Berlin, Germany
| | - Mirko Buchholz
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | | | - Ulrich Heiser
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | | | - Milton T. Stubbs
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
- Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
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