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1.
medRxiv ; 2024 Jan 09.
Article in English | MEDLINE | ID: mdl-38260255

ABSTRACT

SPOUT1/CENP-32 encodes a putative SPOUT RNA methyltransferase previously identified as a mitotic chromosome associated protein. SPOUT1/CENP-32 depletion leads to centrosome detachment from the spindle poles and chromosome misalignment. Aided by gene matching platforms, we identified 24 individuals with neurodevelopmental delays from 18 families with bi-allelic variants in SPOUT1/CENP-32 detected by exome/genome sequencing. Zebrafish spout1/cenp-32 mutants showed reduction in larval head size with concomitant apoptosis likely associated with altered cell cycle progression. In vivo complementation assays in zebrafish indicated that SPOUT1/CENP-32 missense variants identified in humans are pathogenic. Crystal structure analysis of SPOUT1/CENP-32 revealed that most disease-associated missense variants mapped to the catalytic domain. Additionally, SPOUT1/CENP-32 recurrent missense variants had reduced methyltransferase activity in vitro and compromised centrosome tethering to the spindle poles in human cells. Thus, SPOUT1/CENP-32 pathogenic variants cause an autosomal recessive neurodevelopmental disorder: SpADMiSS ( SPOUT1 Associated Development delay Microcephaly Seizures Short stature) underpinned by mitotic spindle organization defects and consequent chromosome segregation errors.

2.
Sci Rep ; 12(1): 19422, 2022 11 12.
Article in English | MEDLINE | ID: mdl-36371414

ABSTRACT

The interferon signalling system elicits a robust cytokine response against a wide range of environmental pathogenic and internal pathological signals, leading to induction of a subset of interferon-induced proteins. We applied DSS (disuccinimidyl suberate) mediated cross-linking mass spectrometry (CLMS) to capture novel protein-protein interactions within the realm of interferon induced proteins. In addition to the expected interferon-induced proteins, we identified novel inter- and intra-molecular cross-linked adducts for the canonical interferon induced proteins, such as MX1, USP18, OAS3, and STAT1. We focused on orthogonal validation of a cohort of novel interferon-induced protein networks formed by the HLA-A protein (H2BFS-HLA-A-HMGA1) using co-immunoprecipitation assay, and further investigated them by molecular dynamics simulation. Conformational dynamics of the simulated protein complexes revealed several interaction sites that mirrored the interactions identified in the CLMS findings. Together, we showcase a proof-of-principle CLMS study to identify novel interferon-induced signaling complexes and anticipate broader use of CLMS to identify novel protein interaction dynamics within the tumour microenvironment.


Subject(s)
Interferons , Proteins , Humans , Cross-Linking Reagents/chemistry , Proteins/chemistry , Mass Spectrometry/methods , HLA-A Antigens , HLA Antigens , Ubiquitin Thiolesterase
3.
Bioresour Technol ; 345: 126459, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34863843

ABSTRACT

Phycocyanin (PC) is a soluble blue pigment-protein primarily harvested from the cyanobacterium Arthrospira platensis. PC is in high demand from several industries, but its narrow stability range limits potential applications. Here, a pilot scale (120 L total) batch production, extraction and purification process for thermostable PC (Te-PC) from a Synechocystis sp. PCC 6803 'Olive' strain expressing the PC operon cpcBACD from Thermosynechococcus elongatus BP-1 on a self-replicating vector is presented. Batch cultivation without antibiotics had no impact on growth or Te-PC production and optimisation of growth conditions resulted in Te-PC contents of 75.3 ± 1.7 mg g DW-1. Wet biomass was harvested following chitosan-based flocculation with a 97 ± 2% efficiency, and Te-PC was extracted by high pressure homogenisation. Subsequent purification by heat-treatment and two-step ammonium sulfate precipitation removed chlorophyll and allophycocyanin contamination, resulting in Te-PC purities of 2.9 ± 0.7 and a mean Te-PC recovery of 84 ± 12%.


Subject(s)
Phycocyanin , Synechocystis , Biomass , Chlorophyll , Flocculation
4.
Nat Commun ; 12(1): 1052, 2021 02 16.
Article in English | MEDLINE | ID: mdl-33594070

ABSTRACT

The parasitic protist Trypanosoma brucei is the causative agent of Human African Trypanosomiasis, also known as sleeping sickness. The parasite enters the blood via the bite of the tsetse fly where it is wholly reliant on glycolysis for the production of ATP. Glycolytic enzymes have been regarded as challenging drug targets because of their highly conserved active sites and phosphorylated substrates. We describe the development of novel small molecule allosteric inhibitors of trypanosome phosphofructokinase (PFK) that block the glycolytic pathway resulting in very fast parasite kill times with no inhibition of human PFKs. The compounds cross the blood brain barrier and single day oral dosing cures parasitaemia in a stage 1 animal model of human African trypanosomiasis. This study demonstrates that it is possible to target glycolysis and additionally shows how differences in allosteric mechanisms may allow the development of species-specific inhibitors to tackle a range of proliferative or infectious diseases.


Subject(s)
Glycolysis/drug effects , Phosphofructokinases/antagonists & inhibitors , Protein Kinase Inhibitors/pharmacology , Trypanosoma/enzymology , Trypanosomiasis, African/metabolism , Trypanosomiasis, African/parasitology , Acute Disease , Allosteric Regulation/drug effects , Animals , Hep G2 Cells , Humans , Inhibitory Concentration 50 , Kaplan-Meier Estimate , Mice , Parasites/drug effects , Phosphofructokinases/chemistry , Phosphofructokinases/metabolism , Protein Binding/drug effects , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/pharmacokinetics , Protein Kinase Inhibitors/therapeutic use , Protein Multimerization , Structure-Activity Relationship , Trypanosoma/drug effects , Trypanosomiasis, African/drug therapy
5.
FEBS J ; 287(13): 2847-2861, 2020 07.
Article in English | MEDLINE | ID: mdl-31838765

ABSTRACT

Trypanosomatids possess glycosome organelles that contain much of the glycolytic machinery, including phosphofructokinase (PFK). We present kinetic and structural data for PFK from three human pathogenic trypanosomatids, illustrating intriguing differences that may reflect evolutionary adaptations to differing ecological niches. The activity of Leishmania PFK - to a much larger extent than Trypanosoma PFK - is reliant on AMP for activity regulation, with 1 mm AMP increasing the L. infantum PFK (LiPFK) kcat/K0.5F6P value by 10-fold, compared to only a 1.3- and 1.4-fold increase for T. cruzi and T. brucei PFK, respectively. We also show that Leishmania PFK melts at a significantly lower (> 15 °C) temperature than Trypanosoma PFKs and that addition of either AMP or ATP results in a marked stabilization of the protein. Sequence comparisons of Trypanosoma spp. and Leishmania spp. show that divergence of the two genera involved amino acid substitutions that occur in the enzyme's 'reaching arms' and 'embracing arms' that determine tetramer stability. The dramatic effects of AMP on Leishmania activity compared with the Trypanosoma PFKs may be explained by differences between the T-to-R equilibria for the two families, with the low-melting Leishmania PFK favouring the flexible inactive T-state in the absence of AMP. Sequence comparisons along with the enzymatic and structural data presented here also suggest there was a loss of AMP-dependent regulation in Trypanosoma species rather than gain of this characteristic in Leishmania species and that AMP acts as a key regulator in Leishmania governing the balance between glycolysis and gluconeogenesis.


Subject(s)
Adenosine Monophosphate/metabolism , Glycolysis , Guanosine Triphosphate/metabolism , Leishmania/enzymology , Phosphofructokinases/chemistry , Phosphofructokinases/metabolism , Trypanosoma brucei brucei/enzymology , Adenosine Monophosphate/chemistry , Amino Acid Sequence , Animals , Biological Evolution , Catalytic Domain , Crystallography, X-Ray , Gluconeogenesis , Guanosine Triphosphate/chemistry , Humans , Kinetics , Models, Molecular , Protein Conformation , Species Specificity , Substrate Specificity
6.
Chem Sci ; 10(2): 542-547, 2019 Jan 14.
Article in English | MEDLINE | ID: mdl-30746096

ABSTRACT

Cyclophilins (Cyps) are a major family of drug targets that are challenging to prosecute with small molecules because the shallow nature and high degree of conservation of the active site across human isoforms offers limited opportunities for potent and selective inhibition. Herein a computational approach based on molecular dynamics simulations and free energy calculations was combined with biophysical assays and X-ray crystallography to explore a flip in the binding mode of a reported urea-based Cyp inhibitor. This approach enabled access to a distal pocket that is poorly conserved among key Cyp isoforms, and led to the discovery of a new family of sub-micromolar cell-active inhibitors that offer unprecedented opportunities for the development of next-generation drug therapies based on Cyp inhibition. The computational approach is applicable to a broad range of organic functional groups and could prove widely enabling in molecular design.

7.
Biochem J ; 475(20): 3275-3291, 2018 10 31.
Article in English | MEDLINE | ID: mdl-30254098

ABSTRACT

We show here that the M2 isoform of human pyruvate kinase (M2PYK) is susceptible to nitrosation and oxidation, and that these modifications regulate enzyme activity by preventing the formation of the active tetrameric form. The biotin-switch assay carried out on M1 and M2 isoforms showed that M2PYK is sensitive to nitrosation and that Cys326 is highly susceptible to redox modification. Structural and enzymatic studies have been carried out on point mutants for three cysteine residues (Cys424, Cys358, and Cys326) to characterise their potential roles in redox regulation. Nine cysteines are conserved between M2PYK and M1PYK. Cys424 is the only cysteine unique to M2PYK. C424S, C424A, and C424L showed a moderate effect on enzyme activity with 80, 100, and 140% activity, respectively, compared with M2PYK. C358 had been previously identified from in vivo studies to be the favoured target for oxidation. Our characterised mutant showed that this mutation stabilises tetrameric M2PYK, suggesting that the in vivo resistance to oxidation for the Cys358Ser mutation is due to stabilisation of the tetrameric form of the enzyme. In contrast, the Cys326Ser mutant exists predominantly in monomeric form. A biotin-switch assay using this mutant also showed a significant reduction in biotinylation of M2PYK, confirming that this is a major target for nitrosation and probably oxidation. Our results show that the sensitivity of M2PYK to oxidation and nitrosation is regulated by its monomer-tetramer equilibrium. In the monomer state, residues (in particular C326) are exposed to oxidative modifications that prevent reformation of the active tetrameric form.


Subject(s)
Cysteine/metabolism , Pyruvate Kinase/metabolism , Crystallization , Humans , Isoenzymes/chemistry , Isoenzymes/metabolism , Nitrosation/physiology , Oxidation-Reduction , Protein Structure, Secondary , Pyruvate Kinase/chemistry
8.
Biochem J ; 475(10): 1821-1837, 2018 05 31.
Article in English | MEDLINE | ID: mdl-29748232

ABSTRACT

We have tested the effect of all 20 proteinogenic amino acids on the activity of the M2 isoenzyme of pyruvate kinase (M2PYK) and show that, within physiologically relevant concentrations, phenylalanine, alanine, tryptophan, methionine, valine, and proline act as inhibitors, while histidine and serine act as activators. Size exclusion chromatography has been used to show that all amino acids, whether activators or inhibitors, stabilise the tetrameric form of M2PYK. In the absence of amino-acid ligands an apparent tetramer-monomer dissociation Kd is estimated to be ∼0.9 µM with a slow dissociation rate (t1/2 ∼ 15 min). X-ray structures of M2PYK complexes with alanine, phenylalanine, and tryptophan show the M2PYK locked in an inactive T-state conformation, while activators lock the M2PYK tetramer in the active R-state conformation. Amino-acid binding in the allosteric pocket triggers rigid body rotations (11°) stabilising either T or R states. The opposing inhibitory and activating effects of the non-essential amino acids serine and alanine suggest that M2PYK could act as a rapid-response nutrient sensor to rebalance cellular metabolism. This competition at a single allosteric site between activators and inhibitors provides a novel regulatory mechanism by which M2PYK activity is finely tuned by the relative (but not absolute) concentrations of activator and inhibitor amino acids. Such 'allostatic' regulation may be important in metabolic reprogramming and influencing cell fate.


Subject(s)
Amino Acids/chemistry , Amino Acids/metabolism , Pyruvate Kinase/chemistry , Pyruvate Kinase/metabolism , Allosteric Regulation , Catalytic Domain , Cell Proliferation , Crystallography, X-Ray , Humans , Protein Conformation , Protein Multimerization
9.
EMBO Rep ; 18(6): 894-905, 2017 06.
Article in English | MEDLINE | ID: mdl-28377371

ABSTRACT

The centromere, a chromosomal locus that acts as a microtubule attachment site, is epigenetically specified by the enrichment of CENP-A nucleosomes. Centromere maintenance during the cell cycle requires HJURP-mediated CENP-A deposition, a process regulated by the Mis18 complex (Mis18α/Mis18ß/Mis18BP1). Spatial and temporal regulation of Mis18 complex assembly is crucial for its centromere association and function. Here, we provide the molecular basis for the assembly and regulation of the Mis18 complex. We show that the N-terminal region of Mis18BP1 spanning amino acid residues 20-130 directly interacts with Mis18α/ß to form the Mis18 complex. Within Mis18α/ß, the Mis18α MeDiY domain can directly interact with Mis18BP1. Mis18α/ß forms a hetero-hexamer with 4 Mis18α and 2 Mis18ß. However, only two copies of Mis18BP1 interact with Mis18α/ß to form a hetero-octameric assembly, highlighting the role of Mis18 oligomerization in limiting the number of Mis18BP1 within the Mis18 complex. Furthermore, we demonstrate the involvement of consensus Cdk1 phosphorylation sites on Mis18 complex assembly and thus provide a rationale for cell cycle-regulated timing of Mis18 assembly and CENP-A deposition.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , CDC2 Protein Kinase/metabolism , CDC2 Protein Kinase/pharmacokinetics , Centromere Protein A/metabolism , Gene Expression Regulation , Adaptor Proteins, Signal Transducing/genetics , CDC2 Protein Kinase/genetics , Cell Cycle/genetics , Centromere/genetics , Centromere/physiology , Chromosomal Proteins, Non-Histone/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Humans , Nucleosomes , Phosphorylation , Protein Binding
10.
FEBS Open Bio ; 7(4): 533-549, 2017 Apr.
Article in English | MEDLINE | ID: mdl-28396838

ABSTRACT

We have established a refined methodology for generating surface plasmon resonance sensor surfaces of recombinant his-tagged human cyclophilin-A. Our orientation-specific stabilisation approach captures his-tagged protein under 'physiological conditions' (150 mm NaCl, pH 7.5) and covalently stabilises it on Ni2+-nitrilotriacetic acid surfaces, very briefly activated for primary amine-coupling reactions, producing very stable and active surfaces (≥ 95% specific activity) of cyclophilin-A. Variation in protein concentration with the same contact time allows straightforward generation of variable density surfaces, with essentially no loss of activity, making the protocol easily adaptable for studying numerous interactions; from very small fragments, ~ 100 Da, to large protein ligands. This new method results in an increased stability and activity of the immobilised protein and allowed us to expand the thermo-kinetic analysis space, and to determine accurate and robust thermodynamic parameters for the cyclophilin-A-cyclosporin-A interaction. Furthermore, the increased sensitivity of the surface allowed identification of a new nonpeptide inhibitor of cyclophilin-A, from a screen of a fragment library. This fragment, 2,3-diaminopyridine, bound specifically with a mean affinity of 248 ± 60 µm. The X-ray structure of this 109-Da fragment bound in the active site of cyclophilin-A was solved to a resolution of 1.25 Å (PDB: 5LUD), providing new insight into the molecular details for a potential new series of nonpeptide cyclophilin-A inhibitors.

11.
PLoS One ; 10(12): e0146164, 2015.
Article in English | MEDLINE | ID: mdl-26717415

ABSTRACT

We developed an efficient, automated 2-step purification protocol for the production of milligram quantities of untagged recombinant rat lactate dehydrogenase A (rLDHA) from E. coli, using the ÄKTAxpress™ chromatography system. Cation exchange followed by size exclusion results in average final purity in excess of 93% and yields ~ 14 milligrams per 50 ml of original cell culture in EnPresso B media, in under 8 hrs, including all primary sample processing and column equilibration steps. The protein is highly active and coherent biophysically and a viable alternative to the more problematic human homolog for structural and ligand-binding studies; an apo structure of untagged rLDHA was solved to a resolution 2.29 Å (PDB ID 5ES3). Our automated methodology uses generic commercially available pre-packed columns and simple buffers, and represents a robust standard method for the production of milligram amounts of untagged rLDHA, facilitating a novel fragment screening approach for new inhibitors.


Subject(s)
L-Lactate Dehydrogenase/biosynthesis , Animals , Automation, Laboratory/methods , Chromatography, Affinity/methods , Chromatography, Liquid/methods , Crystallography, X-Ray/methods , Culture Media , Escherichia coli/metabolism , Isoenzymes/biosynthesis , Isoenzymes/isolation & purification , L-Lactate Dehydrogenase/isolation & purification , Lactate Dehydrogenase 5 , Rats , Recombinant Proteins/biosynthesis , Surface Plasmon Resonance/methods
12.
Biosci Rep ; 35(5)2015 Sep 01.
Article in English | MEDLINE | ID: mdl-26330616

ABSTRACT

Cyclophilin 40 (Cyp40) comprises an N-terminal cyclophilin domain with peptidyl-prolyl isomerase (PPIase) activity and a C-terminal tetratricopeptide repeat (TPR) domain that binds to the C-terminal-EEVD sequence common to both heat shock protein 70 (Hsp70) and Hsp90. We show in the present study that binding of peptides containing the MEEVD motif reduces the PPIase activity by ∼30%. CD and fluorescence assays show that the TPR domain is less stable than the cyclophilin domain and is stabilized by peptide binding. Isothermal titration calorimetry (ITC) shows that the affinity for the-MEEVD peptide is temperature sensitive in the physiological temperature range. Results from these biophysical studies fit with the MD simulations of the apo and holo (peptide-bound) structures which show a significant reduction in root mean square (RMS) fluctuation in both TPR and cyclophilin domains when-MEEVD is bound. The MD simulations of the apo-protein also highlight strong anti-correlated motions between residues around the PPIase-active site and a band of residues running across four of the seven helices in the TPR domain. Peptide binding leads to a distortion in the shape of the active site and a significant reduction in these strongly anti-correlated motions, providing an explanation for the allosteric effect of ligand binding and loss of PPIase activity. Together the experimental and MD results suggest that on heat shock, dissociation of Cyp40 from complexes mediated by the TPR domain leads to an increased pool of free Cyp40 capable of acting as an isomerase/chaperone in conditions of cellular stress.


Subject(s)
Cyclophilins/metabolism , HSP90 Heat-Shock Proteins/metabolism , Allosteric Regulation , Amino Acid Motifs , Catalytic Domain , Peptidyl-Prolyl Isomerase F , Cyclophilins/chemistry , HSP90 Heat-Shock Proteins/chemistry , Humans , Models, Molecular , Protein Denaturation , Protein Interaction Maps , Temperature
13.
DNA Repair (Amst) ; 31: 19-28, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25956741

ABSTRACT

ERCC1-XPF is a structure-specific endonuclease that is required for the repair of DNA lesions, generated by the widely used platinum-containing cancer chemotherapeutics such as cisplatin, through the Nucleotide Excision Repair and Interstrand Crosslink Repair pathways. Based on mouse xenograft experiments, where ERCC1-deficient melanomas were cured by cisplatin therapy, we proposed that inhibition of ERCC1-XPF could enhance the effectiveness of platinum-based chemotherapy. Here we report the identification and properties of inhibitors against two key targets on ERCC1-XPF. By targeting the ERCC1-XPF interaction domain we proposed that inhibition would disrupt the ERCC1-XPF heterodimer resulting in destabilisation of both proteins. Using in silico screening, we identified an inhibitor that bound to ERCC1-XPF in a biophysical assay, reduced the level of ERCC1-XPF complexes in ovarian cancer cells, inhibited Nucleotide Excision Repair and sensitised melanoma cells to cisplatin. We also utilised high throughput and in silico screening to identify the first reported inhibitors of the other key target, the XPF endonuclease domain. We demonstrate that two of these compounds display specificity in vitro for ERCC1-XPF over two other endonucleases, bind to ERCC1-XPF, inhibit Nucleotide Excision Repair in two independent assays and specifically sensitise Nucleotide Excision Repair-proficient, but not Nucleotide Excision Repair-deficient human and mouse cells to cisplatin.


Subject(s)
DNA Repair/drug effects , DNA-Binding Proteins/genetics , Drug Resistance, Neoplasm , Endonucleases/genetics , Catalytic Domain/drug effects , Cell Line, Tumor , Cisplatin/pharmacology , DNA-Binding Proteins/antagonists & inhibitors , DNA-Binding Proteins/metabolism , Endonucleases/antagonists & inhibitors , Endonucleases/metabolism , Female , Gene Expression Regulation, Neoplastic , High-Throughput Screening Assays , Humans , Ovarian Neoplasms/drug therapy , Ovarian Neoplasms/genetics , Reproducibility of Results , Sequence Analysis, DNA
14.
Biochem Biophys Res Commun ; 450(2): 936-41, 2014 Jul 25.
Article in English | MEDLINE | ID: mdl-24984149

ABSTRACT

Three structurally distinct forms of phosphoglycerate mutase from the trypanosomatid parasite Leishmania mexicana were isolated by standard procedures of bacterial expression and purification. Analytical size-exclusion chromatography coupled to a multi-angle scattering detector detected two monomeric forms of differing hydrodynamic radii, as well as a dimeric form. Structural comparisons of holoenzyme and apoenzyme trypanosomatid cofactor-independent phosphoglycerate mutase (iPGAM) X-ray crystal structures show a large conformational change between the open (apoenzyme) and closed (holoenzyme) forms accounting for the different monomer hydrodynamic radii. Until now iPGAM from trypanosomatids was considered to be only monomeric, but results presented here show the appearance of a dimeric form. Taken together, these observations are important for the choice of screening strategies to identify inhibitors of iPGAM for parasite chemotherapy and highlight the need to select the most biologically or functionally relevant form of the purified enzyme.


Subject(s)
Leishmania mexicana/enzymology , Phosphoglycerate Mutase/chemistry , Apoenzymes/chemistry , Chromatography, Gel , Chromatography, Ion Exchange , Crystallography, X-Ray , Holoenzymes/chemistry , Models, Molecular , Protein Conformation , Protein Multimerization , Substrate Specificity
15.
Org Biomol Chem ; 11(44): 7700-4, 2013 Nov 28.
Article in English | MEDLINE | ID: mdl-24108311

ABSTRACT

The natural amide bond found in all biotinylated proteins has been replaced with a triazole through CuAAC reaction of an alkynyl biotin derivative. The resultant triazole-linked adducts are shown to be highly resistant to the ubiquitous hydrolytic enzyme biotinidase and to bind avidin with dissociation constants in the low pM range. Application of this strategy to the production of a series of biotinidase-resistant biotin-Gd-DOTA contrast agents is demonstrated.


Subject(s)
Biotin/chemistry , Biotinidase/chemistry , Triazoles/chemistry , Cell Line, Tumor , Humans , Magnetic Resonance Spectroscopy , Spectrometry, Mass, Electrospray Ionization
16.
Structure ; 21(5): 844-53, 2013 May 07.
Article in English | MEDLINE | ID: mdl-23623732

ABSTRACT

Many pathogenic bacteria encase themselves in a polysaccharide capsule that provides a barrier to the physical and immunological challenges of the host. The mechanism by which the capsule assembles around the bacterial cell is unknown. Wzi, an integral outer-membrane protein from Escherichia coli, has been implicated in the formation of group 1 capsules. The 2.6 Å resolution structure of Wzi reveals an 18-stranded ß-barrel fold with a novel arrangement of long extracellular loops that blocks the extracellular entrance and a helical bundle that plugs the periplasmic end. Mutagenesis shows that specific extracellular loops are required for in vivo capsule assembly. The data show that Wzi binds the K30 carbohydrate polymer and, crucially, that mutants functionally deficient in vivo show no binding to K30 polymer in vitro. We conclude that Wzi is a novel outer-membrane lectin that assists in the formation of the bacterial capsule via direct interaction with capsular polysaccharides.


Subject(s)
Bacterial Capsules/chemistry , Bacterial Outer Membrane Proteins/chemistry , Escherichia coli Proteins/chemistry , Escherichia coli/metabolism , Antigens, Surface/chemistry , Antigens, Surface/metabolism , Bacterial Capsules/metabolism , Bacterial Outer Membrane Proteins/metabolism , Escherichia coli Proteins/metabolism , Lectins/chemistry , Lectins/metabolism , Phylogeny , Protein Conformation , Protein Folding
17.
Proc Natl Acad Sci U S A ; 110(15): 5881-6, 2013 Apr 09.
Article in English | MEDLINE | ID: mdl-23530218

ABSTRACT

We show that the M2 isoform of pyruvate kinase (M2PYK) exists in equilibrium between monomers and tetramers regulated by allosteric binding of naturally occurring small-molecule metabolites. Phenylalanine stabilizes an inactive T-state tetrameric conformer and inhibits M2PYK with an IC50 value of 0.24 mM, whereas thyroid hormone (triiodo-L-thyronine, T3) stabilizes an inactive monomeric form of M2PYK with an IC50 of 78 nM. The allosteric activator fructose-1,6-bisphosphate [F16BP, AC50 (concentration that gives 50% activation) of 7 µM] shifts the equilibrium to the tetrameric active R-state, which has a similar activity to that of the constitutively fully active isoform M1PYK. Proliferation assays using HCT-116 cells showed that addition of inhibitors phenylalanine and T3 both increased cell proliferation, whereas addition of the activator F16BP reduced proliferation. F16BP abrogates the inhibitory effect of both phenylalanine and T3, highlighting a dominant role of M2PYK allosteric activation in the regulation of cancer proliferation. X-ray structures show constitutively fully active M1PYK and F16BP-bound M2PYK in an R-state conformation with a lysine at the dimer-interface acting as a peg in a hole, locking the active tetramer conformation. Binding of phenylalanine in an allosteric pocket induces a 13° rotation of the protomers, destroying the peg-in-hole R-state interface. This distinct T-state tetramer is stabilized by flipped out Trp/Arg side chains that stack across the dimer interface. X-ray structures and biophysical binding data of M2PYK complexes explain how, at a molecular level, fluctuations in concentrations of amino acids, thyroid hormone, and glucose metabolites switch M2PYK on and off to provide the cell with a nutrient sensing and growth signaling mechanism.


Subject(s)
Cell Proliferation , Pyruvate Kinase/metabolism , Allosteric Site , Amino Acid Sequence , Catalytic Domain , Cell Line, Tumor , Crystallography, X-Ray , Dimerization , Humans , Inhibitory Concentration 50 , Molecular Sequence Data , Phenylalanine/chemistry , Protein Conformation , Protein Structure, Tertiary , Triiodothyronine/chemistry
18.
Biochem J ; 448(1): 67-72, 2012 Nov 15.
Article in English | MEDLINE | ID: mdl-22906073

ABSTRACT

PYK (pyruvate kinase) plays a central role in the metabolism of many organisms and cell types, but the elucidation of the details of its function in a systems biology context has been hampered by the lack of specific high-affinity small-molecule inhibitors. High-throughput screening has been used to identify a family of saccharin derivatives which inhibit LmPYK (Leishmania mexicana PYK) activity in a time- (and dose-) dependent manner, a characteristic of irreversible inhibition. The crystal structure of DBS {4-[(1,1-dioxo-1,2-benzothiazol-3-yl)sulfanyl]benzoic acid} complexed with LmPYK shows that the saccharin moiety reacts with an active-site lysine residue (Lys335), forming a covalent bond and sterically hindering the binding of ADP/ATP. Mutation of the lysine residue to an arginine residue eliminated the effect of the inhibitor molecule, providing confirmation of the proposed inhibitor mechanism. This lysine residue is conserved in the active sites of the four human PYK isoenzymes, which were also found to be irreversibly inhibited by DBS. X-ray structures of PYK isoforms show structural differences at the DBS-binding pocket, and this covalent inhibitor of PYK provides a chemical scaffold for the design of new families of potentially isoform-specific irreversible inhibitors.


Subject(s)
Adenosine Diphosphate/metabolism , Adenosine Triphosphate/metabolism , Pyruvate Kinase/antagonists & inhibitors , Animals , Arginine/metabolism , Benzoates/pharmacology , Catalytic Domain/drug effects , Conserved Sequence , Crystallography, X-Ray , Enzyme Inhibitors/pharmacology , High-Throughput Screening Assays , Humans , Isoenzymes/antagonists & inhibitors , Isoenzymes/chemistry , Isoenzymes/metabolism , Leishmania mexicana/enzymology , Lysine/chemistry , Lysine/metabolism , Models, Molecular , Protein Binding/drug effects , Protein Conformation , Pyruvate Kinase/chemistry , Pyruvate Kinase/metabolism , Recombinant Proteins/metabolism , Saccharin/analogs & derivatives , Saccharin/pharmacology , Species Specificity , Structure-Activity Relationship , Suramin/pharmacology
19.
J Biol Chem ; 287(39): 32381-93, 2012 Sep 21.
Article in English | MEDLINE | ID: mdl-22843697

ABSTRACT

Paralogs NDE1 (nuclear distribution element 1) and NDEL1 (NDE-like 1) are essential for mitosis and neurodevelopment. Both proteins are predicted to have similar structures, based upon high sequence similarity, and they co-complex in mammalian cells. X-ray diffraction studies and homology modeling suggest that their N-terminal regions (residues 8-167) adopt continuous, extended α-helical coiled-coil structures, but no experimentally derived information on the structure of their C-terminal regions or the architecture of the full-length proteins is available. In the case of NDE1, no biophysical data exists. Here we characterize the structural architecture of both full-length proteins utilizing negative stain electron microscopy along with our established paradigm of chemical cross-linking followed by tryptic digestion, mass spectrometry, and database searching, which we enhance using isotope labeling for mixed NDE1-NDEL1. We determined that full-length NDE1 forms needle-like dimers and tetramers in solution, similar to crystal structures of NDEL1, as well as chain-like end-to-end polymers. The C-terminal domain of each protein, required for interaction with key protein partners dynein and DISC1 (disrupted-in-schizophrenia 1), includes a predicted disordered region that allows a bent back structure. This facilitates interaction of the C-terminal region with the N-terminal coiled-coil domain and is in agreement with previous results showing N- and C-terminal regions of NDEL1 and NDE1 cooperating in dynein interaction. It sheds light on recently identified mutations in the NDE1 gene that cause truncation of the encoded protein. Additionally, analysis of mixed NDE1-NDEL1 complexes demonstrates that NDE1 and NDEL1 can interact directly.


Subject(s)
Carrier Proteins/chemistry , Microtubule-Associated Proteins/chemistry , Models, Molecular , Protein Folding , Protein Multimerization/physiology , Carrier Proteins/genetics , Carrier Proteins/metabolism , Humans , Microtubule-Associated Proteins/genetics , Microtubule-Associated Proteins/metabolism , Mutation , Protein Structure, Quaternary , Protein Structure, Tertiary
20.
Hum Mol Genet ; 21(15): 3374-86, 2012 Aug 01.
Article in English | MEDLINE | ID: mdl-22547224

ABSTRACT

Disrupted-In-Schizophrenia 1 (DISC1) was identified as a risk factor for psychiatric illness through its disruption by a balanced chromosomal translocation, t(1;11)(q42.1;q14.3), that co-segregates with schizophrenia, bipolar disorder and depression. We previously reported that the translocation reduces DISC1 expression, consistent with a haploinsufficiency disease model. Here we report that, in lymphoblastoid cell lines, the translocation additionally results in the production of abnormal transcripts due to the fusion of DISC1 with a disrupted gene on chromosome 11 (DISC1FP1/Boymaw). These chimeric transcripts encode abnormal proteins, designated CP1, CP60 and CP69, consisting of DISC1 amino acids 1-597 plus 1, 60 or 69 amino acids, respectively. The novel 69 amino acids in CP69 induce increased α-helical content and formation of large stable protein assemblies. The same is predicted for CP60. Both CP60 and CP69 exhibit profoundly altered functional properties within cell lines and neurons. Both are predominantly targeted to mitochondria, where they induce clustering and loss of membrane potential, indicative of severe mitochondrial dysfunction. There is currently no access to neural material from translocation carriers to confirm these findings, but there is no reason to suppose that these chimeric transcripts will not also be expressed in the brain. There is thus potential for the production of abnormal chimeric proteins in the brains of translocation carriers, although at substantially lower levels than for native DISC1. The mechanism by which inheritance of the translocation increases risk of psychiatric illness may therefore involve both DISC1 haploinsufficiency and mitochondrial deficiency due to the effects of abnormal chimeric protein expression. GenBank accession numbers: DISC1FP1 (EU302123), Boymaw (GU134617), der 11 chimeric transcript DISC1FP1 exon 2 to DISC1 exon 9 (JQ650115), der 1 chimeric transcript DISC1 exon 4 to DISC1FP1 exon 4 (JQ650116), der 1 chimeric transcript DISC1 exon 6 to DISC1FP1 exon 3a (JQ650117).


Subject(s)
Chromosomes, Human, Pair 11/genetics , Chromosomes, Human, Pair 1/genetics , Mood Disorders/genetics , Nerve Tissue Proteins/genetics , Schizophrenia/genetics , Translocation, Genetic , Animals , COS Cells , Chlorocebus aethiops , Haploinsufficiency , Humans , Mitochondrial Proteins/genetics , Nerve Tissue Proteins/chemistry , Transfection
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