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Morgan JE, Harden M, Phillips RS. Does routine surveillance imaging after completing treatment for childhood solid tumours cause more harm than good? A systematic review and meta-analysis protocol. Syst Rev 2019; 8:168. [PMID: 31300033 PMCID: PMC6624999 DOI: 10.1186/s13643-019-1096-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 07/02/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This systemic review aims to synthesise the current literature surrounding off-therapy surveillance imaging in children and young people with extra-cranial solid tumours, with a view to establishing if routine imaging studies after treatment for childhood cancer increase overall survival, increase the psychological distress caused to patients and families, result in other harms to patients and are cost-effective strategies. Within this manuscript, we also describe how patient and public involvement has impacted upon the protocol. METHODS The search will cover thirteen different databases, key conference proceedings and trial registers, as well as reference lists and forward citations of included papers. Prominent authors/clinicians in the field will be contacted. A full search strategy is provided. The study designs to be included in the review will be added in an iterative way (RCTs, quasi-randomised trials, prospective cohorts and retrospective cohorts). Qualitative studies will also be eligible for inclusion. We will include studies which examine a programme of surveillance imaging that aims to detect relapse in children or young people up to age 25 years who have completed treatment for a malignant extracranial solid tumour and have no evidence of active and ongoing disease at end of treatment. The primary outcome is overall survival, with secondary outcomes including psychological distress indicators, number of imaging tests performed, other harms of imaging and cost-effectiveness measures. Studies will be screened and data extracted by two researchers. Studies will be critically appraised using a stratified version of the ROBINS-I tool. Where appropriate, data will be synthesised using a random effects meta-analysis. A detailed analysis plan, including assessment of heterogeneity and publication bias, is provided. DISCUSSION The aim of routine surveillance imaging is to detect recurrence of disease before clinical symptoms and signs develop. Some studies have suggested that most relapses of childhood cancer are detected due to clinical symptoms or signs, particularly in those with extra-cranial solid tumours, and when these relapses are detected by imaging, there is no increase in survival. This review aims to establish whether routine surveillance imaging is beneficial, as well as evaluating the potential negative impacts of surveillance programmes. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD42018103764.
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Phillips RS, Crocker M, Lin R, Idowu OE, McCannon DK, Lima S. The roles of Ser-36, Asp-132 and Asp-201 in the reaction of Pseudomonas fluorescens Kynureninase. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2019; 1867:722-731. [PMID: 31100408 DOI: 10.1016/j.bbapap.2019.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/06/2019] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Abstract
Kynureninase from Pseudomonas fluorescens (Pfkynase) catalyzes the pyridoxal-5'-phosphate (PLP) dependent hydrolytic cleavage of L-kynurenine to give anthranilate and L-alanine. Asp-132 and Asp-201 are located in the structure near the pyridine NH of the PLP, with Asp-201 forming a hydrogen bond. Mutation of Asp-132 to alanine and glutamate and Asp-201 to glutamate results in reduced catalytic activity with L-kynurenine and β-benzoyl-L-alanine, but not O-benzoyl-l-serine. D132A, D132E D201E and S36A mutant Pfkynases all can form quinonoid and vinylogous amide intermediates with β-benzoyl-L-alanine, similar to wild-type enzyme. D132A, D132E, and D201E Pfkynase react more slowly with β-benzoyl-L-alanine and benzaldehyde to form an aldol product absorbing at 490 nm than wild-type, with D132E reacting the slowest. The 1H NMR spectra of wild-type and D201E Pfkynase are very similar in the low field region from 10 to 18 ppm, but that of D132A Pfkynase is missing a resonance at 13.1 ppm. These results show that these residues modulate the reactivity of the PLP at different stages during the reaction cycle. Ser-36 is located near the expected location of the carbonyl oxygen of the substrate. Mutation of Ser-36 to alanine results in a 230-fold reduction of kcat and 30-fold reduction in kcat/Km with L-kynurenine, but very little effect on the reaction of O-benzoyl-l-serine. Thus, the rate-determining step in the reaction of S36A Pfkynase is the Cβ-Cγ bond cleavage. These results support the hypothesis that Ser-36 together with Tyr-226 is part of an oxyanion hole that polarizes the carbonyl of the substrate in the catalytic mechanism of Pfkynase.
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Kudlac M, Sabol J, Kaiser K, Kane C, Phillips RS. Reliability and Validity of the Berg Balance Scale in the Stroke Population: A Systematic Review. PHYSICAL & OCCUPATIONAL THERAPY IN GERIATRICS 2019. [DOI: 10.1080/02703181.2019.1631423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Allaway Z, Phillips RS, Thursky KA, Haeusler GM. Nonneutropenic fever in children with cancer: A scoping review of management and outcome. Pediatr Blood Cancer 2019; 66:e27634. [PMID: 30724005 DOI: 10.1002/pbc.27634] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/17/2018] [Accepted: 01/10/2019] [Indexed: 12/17/2022]
Abstract
To date, very few studies have addressed nonneutropenic fever (NNF) in children with cancer, and there are no consensus guidelines. This scoping review aims to describe the rate of bacteremia, risk factors for infection and management, and outcomes of NNF in this population. Across 15 studies (n = 4106 episodes), the pooled-average bacteremia rate was 8.2%, and risk factors included tunneled external central venous catheter, clinical instability, and higher temperature. In two studies, antibiotics were successfully withheld in a subset of low-risk patients. Overall outcomes of NNF appear favorable; however, further research is required to determine its true clinical and economic impact.
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Mozzarelli A, Phillips RS. Editorial: Enzymes Regulating the Homeostasis of Agonists and Antagonists of the N-Methyl D-Aspartate Receptors. Front Mol Biosci 2019; 6:37. [PMID: 31192218 PMCID: PMC6546922 DOI: 10.3389/fmolb.2019.00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/07/2019] [Indexed: 11/13/2022] Open
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Han Q, Phillips RS, Li J. Editorial: Aromatic Amino Acid Metabolism. Front Mol Biosci 2019; 6:22. [PMID: 31024928 PMCID: PMC6468166 DOI: 10.3389/fmolb.2019.00022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 03/18/2019] [Indexed: 11/13/2022] Open
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Dwamena AK, Phillips RS, Kim CS. Impact of Expanded Small Alkyl-Binding Pocket by Triple Point Mutations on Substrate Specificity of Thermoanaerobacter ethanolicus Secondary Alcohol Dehydrogenase. J Microbiol Biotechnol 2019; 29:373-381. [DOI: 10.4014/jmb.1812.12016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Phillips RS, Iradukunda EC, Hughes T, Bowen JP. Modulation of Enzyme Activity in the Kynurenine Pathway by Kynurenine Monooxygenase Inhibition. Front Mol Biosci 2019; 6:3. [PMID: 30800661 PMCID: PMC6376250 DOI: 10.3389/fmolb.2019.00003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/21/2019] [Indexed: 11/13/2022] Open
Abstract
The kynurenine pathway is the major route for tryptophan metabolism in mammals. Several of the metabolites in the kynurenine pathway, however, are potentially toxic, particularly 3-hydroxykynurenine, 3-hydroxyanthranilic acid, and quinolinic acid. Quinolinic acid (QUIN) is an excitotoxic agonist at the NMDA receptor, and has been shown to be elevated in neurodegenerative diseases such as Alzheimer's Disease and Huntington's Disease. Thus, inhibitors of enzymes in the kynurenine pathway may be valuable to treat these diseases. Kynurenine monooxygenase (KMO) is the ideal target for an inhibitor, since inhibition of it would be expected to decrease the toxic metabolites and increase kynurenic acid (KynA), which is neuroprotective. The first generation of KMO inhibitors was based on structural analogs of the substrate, L-kynurenine. These compounds showed reduction of QUIN and increased KynA in vivo in rats. After the determination of the x-ray crystal structure of yeast KMO, inhibitor design has been facilitated. Benzisoxazoles with sub-nM binding to KMO have been developed recently. Some KMO ligands promote the reaction of NADPH with O2 without hydroxylation, resulting in uncoupled formation of H2O2. This potentially toxic side reaction should be avoided in the design of drugs targeting the kynurenine pathway for treatment of neurodegenerative disorders.
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Phillips RS, Poteh P, Krajcovic D, Miller KA, Hoover TR. Crystal Structure of d-Ornithine/d-Lysine Decarboxylase, a Stereoinverting Decarboxylase: Implications for Substrate Specificity and Stereospecificity of Fold III Decarboxylases. Biochemistry 2019; 58:1038-1042. [PMID: 30699288 DOI: 10.1021/acs.biochem.8b01319] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A newly discovered Fold III pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, d-ornithine/lysine decarboxylase (DOKDC), catalyzes decarboxylation of d-lysine and d-ornithine with inversion of stereochemistry. The X-ray crystal structure of DOKDC has been determined to 1.72 Å. DOKDC has a low level of sequence identity (<30%) with meso-diaminopimelate decarboxylase (DAPDC) and l-lysine/ornithine decarboxylase (LODC), but its three-dimensional structure is very similar. The distal binding site of DAPDC contains a conserved arginine that forms an ion pair with the l-carboxylate end of DAP. In both LODC and DOKDC, this distal site is modified by replacement of the arginine with aspartate, changing the substrate specificity. l-Ornithine decarboxylase (ODC) and LODC have a conserved phenylalanine on the re-face of the PLP complex that has been found to play a key role in the decarboxylation mechanism. We have found that both DAPDC and DOKDC have tyrosine instead of phenylalanine at this position, which precludes the binding of l-amino acids. Because the PLP-binding lysine in ODC, LODC, DAPDC, and DOKDC is located on the re-face of the PLP, we propose that this is the acid group responsible for protonation of the product, thus resulting in the observed retention of configuration for decarboxylation of l-amino acids and inversion for decarboxylation of d-amino acids. The reactions of DAPDC and DOKDC are likely accelerated by positive electrostatics on the re-face by the lysine ε-ammonium ion and on the si-face by closure of the lid over the active site, resulting in desolvation and destabilization of the d-amino acid carboxylate.
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Keul ND, Oruganty K, Schaper Bergman ET, Beattie NR, McDonald WE, Kadirvelraj R, Gross ML, Phillips RS, Harvey SC, Wood ZA. The entropic force generated by intrinsically disordered segments tunes protein function. Nature 2018; 563:584-588. [PMID: 30420606 PMCID: PMC6415545 DOI: 10.1038/s41586-018-0699-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 09/10/2018] [Indexed: 11/09/2022]
Abstract
Protein structures are dynamic and can explore a large conformational landscape1,2. Only some of these structural substates are important for protein function (such as ligand binding, catalysis and regulation)3-5. How evolution shapes the structural ensemble to optimize a specific function is poorly understood3,4. One of the constraints on the evolution of proteins is the stability of the folded 'native' state. Despite this, 44% of the human proteome contains intrinsically disordered peptide segments greater than 30 residues in length6, the majority of which have no known function7-9. Here we show that the entropic force produced by an intrinsically disordered carboxy terminus (ID-tail) shifts the conformational ensemble of human UDP-α-D-glucose-6-dehydrogenase (UGDH) towards a substate with a high affinity for an allosteric inhibitor. The function of the ID-tail does not depend on its sequence or chemical composition. Instead, the affinity enhancement can be accurately predicted based on the length of the intrinsically disordered segment, and is consistent with the entropic force generated by an unstructured peptide attached to the protein surface10-13. Our data show that the unfolded state of the ID-tail rectifies the dynamics and structure of UGDH to favour inhibitor binding. Because this entropic rectifier does not have any sequence or structural constraints, it is an easily acquired adaptation. This model implies that evolution selects for disordered segments to tune the energy landscape of proteins, which may explain the persistence of intrinsic disorder in the proteome.
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Phillips RS, Craig S. Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism. Biochemistry 2018; 57:6166-6179. [PMID: 30260636 DOI: 10.1021/acs.biochem.8b00724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyrosine phenol-lyase (TPL; EC 4.1.99.2) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the reversible hydrolytic cleavage of l-tyrosine to phenol and ammonium pyruvate. We have shown previously that F448A TPL has kcat and kcat/ Km values for l-tyrosine reduced by ∼104-fold [Phillips, R. S., Vita, A., Spivey, J. B., Rudloff, A. P., Driscoll, M. D., and Hay, S. (2016) ACS Catal. 6, 6770-6779]. We have now obtained crystal structures of F448A TPL and complexes with l-alanine, l-methionine, l-phenylalanine, and 3-F-l-tyrosine at 2.05-2.27 Å and the complex of wild-type TPL with l-phenylalanine at 1.8 Å. The small domain of F448A TPL, where Phe-448 is located, is more disordered in chain A than in wild-type TPL. The complexes of F448A TPL with l-alanine and l-phenylalanine are in an open conformation in both chains, while the complex with l-methionine is a 52:48 open:closed equilibrium mixture in chain A. Wild-type TPL with l-alanine is closed in chain A and open in chain B, and the complex with l-phenylalanine is a 56:44 open:closed mixture in chain A. Thus, the Phe-448 to alanine mutation affects the conformational equilibrium of open and closed active sites. The structure of the 3-F-l-tyrosine quinonoid complex of F448A TPL is unstrained and in an open conformation, with a hydrogen bond from the phenolic OH to Thr-124. These results support our previous conclusion that ground-state strain plays a critical role in the mechanism of TPL.
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Phillips RS, Buisman AA, Choi S, Hussaini A, Wood ZA. The crystal structure of Proteus vulgaris tryptophan indole-lyase complexed with oxindolyl-L-alanine: implications for the reaction mechanism. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:748-759. [DOI: 10.1107/s2059798318003352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 02/26/2018] [Indexed: 12/27/2022]
Abstract
Tryptophan indole-lyase (TIL) is a bacterial enzyme which catalyzes the reversible formation of indole and ammonium pyruvate from L-tryptophan. Oxindolyl-L-alanine (OIA) is an inhibitor of TIL, with a K
i value of about 5 µM. The crystal structure of the complex of Proteus vulgaris TIL with OIA has now been determined at 2.1 Å resolution. The ligand forms a closed quinonoid complex with the pyridoxal 5′-phosphate (PLP) cofactor. The small domain rotates about 10° to close the active site, bringing His458 into position to donate a hydrogen bond to Asp133, which also accepts a hydrogen bond from the heterocyclic NH of the inhibitor. This brings Phe37 and Phe459 into van der Waals contact with the aromatic ring of OIA. Mutation of the homologous Phe464 in Escherichia coli TIL to Ala results in a 500-fold decrease in k
cat/K
m for L-tryptophan, with less effect on the reaction of other nonphysiological β-elimination substrates. Stopped-flow kinetic experiments of F464A TIL show that the mutation has no effect on the formation of quinonoid intermediates. An aminoacrylate intermediate is observed in the reaction of F464A TIL with S-ethyl-L-cysteine and benzimidazole. A model of the L-tryptophan quinonoid complex with PLP in the active site of P. vulgaris TIL shows that there would be a severe clash of Phe459 (∼1.5 Å apart) and Phe37 (∼2 Å apart) with the benzene ring of the substrate. It is proposed that this creates distortion of the substrate aromatic ring out of plane and moves the substrate upwards on the reaction coordinate towards the transition state, thus reducing the activation energy and accelerating the enzymatic reaction.
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Hassan H, Rompola M, Glaser AW, Kinsey SE, Phillips RS. Systematic review and meta-analysis investigating the efficacy and safety of probiotics in people with cancer. Support Care Cancer 2018; 26:2503-2509. [PMID: 29704110 DOI: 10.1007/s00520-018-4216-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/13/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND/OBJECTIVES Probiotics are living microorganisms that confer a health benefit on the host when administered. This systematic review and meta-analysis investigates the efficacy and safety of probiotics in adult and paediatric patients diagnosed with cancer. METHODS A systematic review and meta-analysis was undertaken (PROSPERO registration: CRD42016050252). Randomised controlled trials (RCT), identified through screening multiple databases were included for analysis of efficacy. Non-randomised controlled trials and case reports were included for safety analysis. Outcomes included the reduction in the incidence and severity of diarrhoea, and adverse events. Where possible, data were combined for meta-analysis using a random-effects model. Planned subgroup analyses were not possible through marked heterogeneity of study characteristics. RESULTS Twenty one studies (N = 2982 participants) were included for assessment of efficacy. Probiotics may reduce the incidence of diarrhoea in patients with cancer [odds ratio (OR) = 0.52, 95% confidence interval (CI) 0.34-0.78, 95% prediction interval (PI) 0.3-0.92, I-sq 36.9%, 5 studies] and the duration of pyrexia [standardised mean difference 0.39 days, 95% CI 0.35-0.43, I-sq 0.01%, 5 studies]. Twenty five studies (N = 2242) were included in the safety analysis. Five case reports showed probiotic-related bacteraemia/fungaemia/positive blood cultures. Definitions and reporting of adverse events were variable and inconsistent. CONCLUSIONS There remain insufficient studies to assess the true effect of probiotics in people with cancer. Meta-analysis suggests probiotics may be beneficial but further studies are still required. Improved reporting of outcomes and adverse events in clinical trials are required to improve accuracy and confidence of conclusions drawn in future updates.
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Phillips RS, Ting SC, Tetsadjio AG, Anderson KL, Friez KM, Miller KA, Hoover TR. Properties and mechanism of d-glucosaminate-6-phosphate ammonia-lyase: An aminotransferase family enzyme with d-amino acid specificity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:799-805. [PMID: 29277660 DOI: 10.1016/j.bbapap.2017.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 11/28/2022]
Abstract
Salmonella enterica serovar Typhimurium utilizes a wide range of growth substrates, some of which are relatively novel. One of these unusual substrates is d-glucosaminate, which is metabolized by the enzymes encoded in the dga operon. d-Glucosaminate is transported and converted to d-glucosaminate-6-phosphate (G6P) by a phosphotransferase system, composed of DgaABCD. The protein product of dgaE, d-glucosaminate-6-phosphate ammonia lyase (DGL), converts G6P to 2-keto-3-deoxygluconate-6-phosphate, which undergoes a retroaldol reaction catalyzed by the DgaF protein to give d-glyceraldehyde-3-phosphate and pyruvate. We have now developed an improved synthesis of G6P which gives a higher yield. The DGL reaction is of mechanistic interest because it is one of only a few enzymes in the pyridoxal-5'-phosphate (PLP) dependent aminotransferase superfamily known to catalyze reaction of a d-amino acid substrate. The pH dependence of DGL shows an optimum at 7.5-8.5, suggesting a requirement for a catalytic base. α-Glycerophosphate and inorganic phosphate are weak competitive inhibitors, with Ki values near 30mM, and d-serine is neither a substrate nor an inhibitor. We have found in rapid-scanning stopped-flow experiments that DGL reacts rapidly with its substrate to form a quinonoid intermediate with λmax=480nm, within the dead time (ca. 2msec), which then rapidly decays (k=279s-1) to an intermediate with absorption between 330 and 350nm, probably an aminoacrylate complex. We suggest a mechanism for DGL and propose that the unusual stereochemistry of the DGL reaction requires a catalytic base poised on the opposite face of the PLP-substrate complex from the other members of the aminotransferase superfamily.
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Rossignoli G, Phillips RS, Astegno A, Menegazzi M, Voltattorni CB, Bertoldi M. Phosphorylation of pyridoxal 5'-phosphate enzymes: an intriguing and neglected topic. Amino Acids 2017; 50:205-215. [PMID: 29204749 DOI: 10.1007/s00726-017-2521-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 11/29/2017] [Indexed: 12/25/2022]
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes catalyze a wide range of reactions of amino acids and amines, with the exception of glycogen phosphorylase which exhibits peculiar both substrate preference and chemical mechanism. They represent about 4% of the gene products in eukaryotic cells. Although structure-function investigations regarding these enzymes are copious, their regulation by post-translational modifications is largely unknown. Protein phosphorylation is the most common post-translational modification fundamental in mediating diverse cellular functions. This review aims at summarizing the current knowledge on regulation of PLP enzymes by phosphorylation. Starting from the paradigmatic PLP-dependent glycogen phosphorylase, the first phosphoprotein discovered, we collect data in literature regarding functional phosphorylation events of eleven PLP enzymes belonging to different fold types and discuss the impact of the modification in affecting their activity and localization as well as the implications on the pathogenesis of diseases in which many of these enzymes are involved. The pivotal question is to correlate the structural consequences of phosphorylation among PLP enzymes of different folds with the functional modifications exerted in terms of activity or conformational changes or others. Although the literature shows that the phosphorylation of PLP enzymes plays important roles in mediating diverse cellular functions, our recapitulation of clue findings in the field makes clear that there is still much to be learnt. Besides mass spectrometry-based proteomic analyses, further biochemical and structural studies on purified native proteins are imperative to fully understand and predict how phosphorylation regulates PLP enzymes and to find the relationship between addition of a phosphate moiety and physiological response.
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Phillips RS, Poteh P, Miller KA, Hoover TR. STM2360 encodes a d-ornithine/d-lysine decarboxylase in Salmonella enterica serovar typhimurium. Arch Biochem Biophys 2017; 634:83-87. [PMID: 29024617 DOI: 10.1016/j.abb.2017.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/10/2017] [Accepted: 09/13/2017] [Indexed: 11/27/2022]
Abstract
STM2360 is a gene located in a small operon of undetermined function in Salmonella enterica serovar Typhimurium LT2. The amino acid sequence of STM2360 shows significant similarity (∼30% identity) to diaminopimelate decarboxylase (DapDC), a Fold III pyridoxal-5'-phosphate (PLP) dependent enzyme involved in l-lysine biosynthesis. We have found that the protein coded by STM2360 has a previously undocumented catalytic activity, d-ornithine/d-lysine decarboxylase (DOKDC). The reaction products, cadaverine and putrescine, respectively, were identified by NMR and mass spectrometry. The substrate specificity of DOKDC is d-Lysine > d-Ornithine. This is the first pyridoxal-5'-phosphate dependent decarboxylase identified to act on d-amino acids. STM2358, located in the same operon, has ornithine racemase activity. This suggests that the physiological substrate of the decarboxylase and the operon is ornithine. Homologs of STM2360 with high sequence identity (>80%) are found in other common enterobacteria, including species of Klebsiella, Citrobacter, Vibrio and Hafnia, as well as Clostridium in the Firmicutes, and Pseudomonas.
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Nealon CM, Kim CS, Dwamena AK, Phillips RS. Mutagenesis of Met-151 and Thr-153 to alanine in Thermoanaerobacter ethanolicus secondary alcohol dehydrogenase changes substrate specificity for acetophenones. Enzyme Microb Technol 2017; 105:59-63. [DOI: 10.1016/j.enzmictec.2017.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 06/12/2017] [Accepted: 06/16/2017] [Indexed: 10/19/2022]
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Abdelgadir IS, Phillips RS, Singh D, Moncreiff MP, Lumsden JL. Videolaryngoscopy versus direct laryngoscopy for tracheal intubation in children (excluding neonates). Cochrane Database Syst Rev 2017; 5:CD011413. [PMID: 28539007 PMCID: PMC6481531 DOI: 10.1002/14651858.cd011413.pub2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Direct laryngoscopy is the method currently used for tracheal intubation in children. It occasionally offers unexpectedly poor laryngeal views. Indirect laryngoscopy involves visualizing the vocal cords by means other than obtaining a direct sight, with the potential to improve outcomes. We reviewed the current available literature and performed a meta-analysis to compare direct versus indirect laryngoscopy, or videolaryngoscopy, with regards to efficacy and adverse effects. OBJECTIVES To assess the efficacy of indirect laryngoscopy, or videolaryngoscopy, versus direct laryngoscopy for intubation of children with regards to intubation time, number of attempts at intubation, and adverse haemodynamic responses to endotracheal intubation. We also assessed other adverse responses to intubation, such as trauma to oral, pharyngeal, and laryngeal structures, and we assessed vocal cord view scores. SEARCH METHODS We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), and trial registers (www.clinicaltrials.gov and www.controlledtrials) in November 2015. We reran the search in January 2017. We added new studies of potential interest to a list of 'Studies awaiting classification' and will incorporate them into formal review findings during the review update. We performed reference checking and citation searching and contacted the authors of unpublished data to ask for more information. We applied no language restrictions. SELECTION CRITERIA We included only randomized controlled trials. Participants were children aged 28 days to 18 years. Investigators performed intubations using any type of indirect laryngoscopes, or videolaryngoscopes, versus direct laryngoscopes. DATA COLLECTION AND ANALYSIS We used Cochrane standard methodological procedures. Two review authors independently reviewed titles, extracted data, and assessed risk of bias. MAIN RESULTS We included 12 studies (803 children) in this review and meta-analysis. We identified three studies that are awaiting classification and two ongoing studies.Trial results show that a longer intubation time was required when indirect laryngoscopy, or videolaryngoscopy, was used instead of direct laryngoscopy (12 trials; n = 798; mean difference (MD) 5.49 seconds, 95% confidence interval (CI) 1.37 to 9.60; I2 = 90%; very low-quality evidence). Researchers found no significant differences between direct and indirect laryngoscopy on assessment of success of the first attempt at intubation (11 trials; n = 749; risk ratio (RR) 0.96, 95% CI 0.91 to 1.02; I2 = 67%; low-quality evidence) and observed that unsuccessful intubation (five trials; n = 263) was significantly increased in the indirect laryngoscopy, or videolaryngoscopy, group (RR 4.93, 95% CI 1.33 to 18.31; I2 = 0%; low-quality evidence). Five studies reported the effect of intubation on oxygen saturation (n = 272; very low-quality evidence). Five children had desaturation during intubation: one from the direct laryngoscopy group and four from the indirect laryngoscopy, or videolaryngoscopy, group.Two studies (n = 100) reported other haemodynamic responses to intubation (very low-quality evidence). One study reported a significant increase in heart rate five minutes after intubation in the indirect laryngoscopy group (P = 0.007); the other study found that the heart rate change in the direct laryngoscopy group was significantly less than the heart rate change in the indirect laryngoscopy, or videolaryngoscopy, group (P < 0.001). A total of five studies (n = 244; very low-quality evidence) looked at evidence of trauma resulting from intubation. Investigators reported that only two children from the direct laryngoscopy group had trauma compared with no children in the indirect laryngoscopy, or videolaryngoscopy, group.Use of indirect laryngoscopy, or videolaryngoscopy, improved the percentage of glottic opening (five trials; n = 256). Studies noted no significant difference in Cormack and Lehane score (C&L) grade 1 (three trials; n = 190; RR 1.06, 95% CI 0.93 to 1.21; I2 = 59%). AUTHORS' CONCLUSIONS Evidence suggests that indirect laryngoscopy, or videolaryngoscopy, leads to prolonged intubation time with an increased rate of intubation failure when compared with direct laryngoscopy (very low-quality evidence due to imprecision, inconsistency, and study limitations). Review authors had difficulty reaching conclusions on adverse haemodynamic responses and other adverse effects of intubation, as only a few children were reported to have these outcomes. Use of indirect laryngoscopy, or videolaryngoscopy, might lead to improved vocal cord view, but marked heterogeneity between studies made it difficult for review authors to reach conclusions on this outcome.
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Reneker JC, Hassen A, Phillips RS, Moughiman MC, Donaldson M, Moughiman J. Feasibility of early physical therapy for dizziness after a sports-related concussion: A randomized clinical trial. Scand J Med Sci Sports 2017; 27:2009-2018. [PMID: 28211600 DOI: 10.1111/sms.12827] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2016] [Indexed: 12/30/2022]
Abstract
The purpose of this study was to (a) assess the feasibility of recruitment/retention of participants, protocol/resource management, and participant safety, and (b) estimate the size of the effect between the experimental and control groups. This was a feasibility study conducted as a prospective pilot double-blind randomized clinical trial. Subjects aged 10-23 years old with acute concussion and dizziness were enrolled from sports medicine centers. Forty-one participants were randomized into treatment and were seen for physical therapy beginning at 10 days post-concussion. Subjects in the experimental group received individually tailored, pragmatically delivered progressive interventions. Subjects in the control received prescriptive sham to minimally progressive interventions. The two primary outcomes were medical clearance for return-to-play and symptomatic recovery. The median number of days to medical clearance for the experimental group was 15.5 and for the control was 26. The median number of days to symptomatic recovery was 13.5 for the experimental group and was 17 for the control. According to Cox proportional hazards regression for time to medical release for return-to-play, the experimental group demonstrated a hazard ratio of 2.91 (95% CI: 1.01, 8.43) compared to the control. For time-to-symptomatic recovery, those in the experimental group demonstrated a hazard ratio of 1.99 (95% CI: 0.95, 4.15) compared to the control. The results indicate that it is feasible and safe to complete this type of intervention study. The results provide strong support for the allocation of resources to conduct well-powered randomized clinical trials of this intervention.
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Pini SA, Gibson F, Fern LA, Morgan SJ, Phillips RS, Stark DP. Multi-Professional Perspectives on Adolescent and Young Adult Oncology Across Europe: An e-Delphi Survey. J Adolesc Young Adult Oncol 2017; 6:178-185. [PMID: 28080182 DOI: 10.1089/jayao.2016.0051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The aims of this article are to describe the ongoing development of adolescent and young adult (AYA) cancer services within the European Union (EU), and to develop consensus on key areas within the field. This survey used an e-Delphi design. An initial survey was distributed via email to professionals working in Europe. A snowball sampling technique was used to promote distribution. Consensus was sought over three rounds from October 2012 to April 2015. Consensus was defined as >80% agreement ("agree" or "strongly agree"). Sixty professionals participated in round 1, 106 in round 2, and 61 in round 3. Twenty-six countries were represented across all rounds. Consensus was achieved for: the need for national policy guidance, the importance of patient choice, the validity of the International Charter of Rights for Young People, and some aspects of multi-disciplinary working. There was 75% agreement on a single definition of the patient age range within AYA cancer care. European professionals with expertise in AYA cancer care reached consensus on key elements of care for this group. The optimal AYA age range remained an elusive topic on which to agree. The broad engagement and interest in AYA cancer across the EU through the European Network for Cancer in Children and Adolescents (ENCCA) network was also demonstrated.
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Phillips RS, Vita A, Spivey JB, Rudloff AP, Driscoll MD, Hay S. Ground-State Destabilization by Phe-448 and Phe-449 Contributes to Tyrosine Phenol-Lyase Catalysis. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01495] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Miroddi M, Sterrantino C, Simmonds M, Caridi L, Calapai G, Phillips RS, Stewart LA. Systematic review and meta-analysis of the risk of severe and life-threatening thromboembolism in cancer patients receiving anti-EGFR monoclonal antibodies (cetuximab or panitumumab). Int J Cancer 2016; 139:2370-80. [PMID: 27450994 DOI: 10.1002/ijc.30280] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/26/2016] [Accepted: 07/12/2016] [Indexed: 01/20/2023]
Abstract
Cancer-associated thromboembolism is a substantial problem in clinical practice. An increase in the level of fibrinopeptide A (a substance associated with hypercoagulable states) has been observed in humans exposed to fluorouracil. Anti-EGFR monoclonal antibodies cetuximab and panitumumab, which are now widely used in patients with metastatic colorectal cancer, could prolong the uncovering of endothelial structures resulting from flouorouracil or other co-administered agents, thus favouring several factors leading to thromboembolism. We performed a systematic review and meta-analysis of randomised, controlled trials assessing whether cancer patients receiving anti-EGFR monoclonal antibodies cetuximab and panitumumab are at increased risk of thromboembolic events. We searched electronic databases (Medline, Embase, Web of Science, Central) and reference lists. Phase II/III randomised, controlled trials comparing standard anti-cancer regimens with or without anti-EGFR monoclonal antibodies and reporting serious venous thromboembolic events were included in the analysis. Seventeen studies (12,870 patients) were considered for quantitative analysis. The relative risk (RR) for venous thromboembolism (18 comparisons) was 1.46 (95% CI 1.26 to 1.69); the RR of pulmonary embolism, on the basis of eight studies providing nine comparisons, was 1.55 (1.20 to 2.00). Cancer patients receiving anti-EGFR monoclonal antibodies-containing regimens are approximately 1.5 times more likely to experience venous or pulmonary embolism, compared to those treated with the same regimens without anti-EGFR monoclonal antibodies. Clinicians should consider patient's baseline thromboembolic risk when selecting regimens that include cetuximab or panitumumab. Potential non-reporting of these important adverse events remains a concern. PROSPERO registration number is CRD42014009165.
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Do Q, Nguyen GT, Phillips RS. Inhibition of tyrosine phenol-lyase by tyrosine homologues. Amino Acids 2016; 48:2243-51. [DOI: 10.1007/s00726-016-2263-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 05/20/2016] [Indexed: 11/28/2022]
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Phillips RS, Sung L, Ammann RA, Riley RD, Castagnola E, Haeusler GM, Klaassen R, Tissing WJ, Lehrnbecher T, Chisholm J, Hakim H, Ranasinghe N, Paesmans M, Hann IM, Stewart LA. Predicting microbiologically defined infection in febrile neutropenic episodes in children: global individual participant data multivariable meta-analysis. Br J Cancer 2016; 114:e17. [PMID: 27228292 PMCID: PMC4984466 DOI: 10.1038/bjc.2016.137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Mohammadi-Abdar H, Ridgel AL, Discenzo FM, Phillips RS, Walter BL, Loparo KA. Test and Validation of a Smart Exercise Bike for Motor Rehabilitation in Individuals With Parkinson's Disease. IEEE Trans Neural Syst Rehabil Eng 2016; 24:1254-1264. [PMID: 27046905 DOI: 10.1109/tnsre.2016.2549030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To assess and validate the Smart Exercise Bike designed for Parkinson's Disease (PD) rehabilitation, 47 individuals with PD were randomly assigned to either the static or dynamic cycling group, and completed three sessions of exercise. Heart rate, cadence and power data were captured and recorded for each patient during exercise. Motor function for each subject was assessed with the UPDRS Motor III test before and after the three exercise sessions to evaluate the effect of exercise on functional abilities. Individuals who completed three sessions of dynamic cycling showed an average of 13.8% improvement in the UPDRS, while individuals in the static cycling group worsened by 1.6% in UPDRS. To distinguish the static and dynamic cycling groups by biomechanical and physiological features, the complexity of the recorded signals (cadence, power, and heart rate) was examined using approximate entropy (ApEn), sample entropy (SaEn) and spectral entropy (SpEn) as measures of variability. A multiple linear regression (MLR) model was used to relate these features to changes in motor function as measured by the UPDRS Motor III scale. Pattern variability in cadence was greater in the dynamic group when compared to the static group. In contrast, variability in power was greater for the static group. UPDRS Motor III scores predicted from the pattern variability data were correlated to measured scores in both groups. These results support our previous study which explained how variability analysis results for biomechanical and physiological parameters of exercise can be used to predict improvements in motor function.
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