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The adaptability of the ion binding site by the Ag(I)/Cu(I) periplasmic chaperone SilF (2023)
Journal Article
Lithgo, R. M., Hanževački, M., Harris, G., Kamps, J. J. .. G., Holden, E., Gianga, T., …Scott, D. J. (2023). The adaptability of the ion binding site by the Ag(I)/Cu(I) periplasmic chaperone SilF. Journal of Biological Chemistry, 299(11), Article 105331. https://doi.org/10.1016/j.jbc.2023.105331

The periplasmic chaperone SilF has been identified as part of an Ag(I) detoxification system in Gram negative bacteria. Sil proteins also bind Cu(I), but with reported weaker affinity, therefore leading to the designation of a specific detoxification... Read More about The adaptability of the ion binding site by the Ag(I)/Cu(I) periplasmic chaperone SilF.

eIF4A1-dependent mRNAs employ purine-rich 5'UTR sequences to activate localised eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation (2023)
Journal Article
Schmidt, T., Dabrowska, A., Waldron, J. A., Hodge, K., Koulouras, G., Gabrielsen, M., …Bushell, M. (2023). eIF4A1-dependent mRNAs employ purine-rich 5'UTR sequences to activate localised eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation. Nucleic Acids Research, 51(4), 1859-1879. https://doi.org/10.1093/nar/gkad030

Altered eIF4A1 activity promotes translation of highly structured, eIF4A1-dependent oncogene mRNAs at root of oncogenic translational programmes. It remains unclear how these mRNAs recruit and activate eIF4A1 unwinding specifically to facilitate thei... Read More about eIF4A1-dependent mRNAs employ purine-rich 5'UTR sequences to activate localised eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation.

Flavour compounds affect protein structure: The effect of methyl anthranilate on bovine serum albumin conformation (2022)
Journal Article
Dinu, V., Borah, P. K., Muleya, M., Scott, D. J., Lithgo, R., Pattem, J., …Fisk, I. D. (2022). Flavour compounds affect protein structure: The effect of methyl anthranilate on bovine serum albumin conformation. Food Chemistry, 388, Article 133013. https://doi.org/10.1016/j.foodchem.2022.133013

This study aims to understand possible effects of flavour compounds on the structure and conformation of endogenous proteins. Using methyl anthranilate (a grape flavour compound added to drinks, confectionery, and vape-liquids) and bovine serum album... Read More about Flavour compounds affect protein structure: The effect of methyl anthranilate on bovine serum albumin conformation.

Thermodynamics of semi-specific ligand recognition: the binding of dipeptides to the E.coli dipeptide binding protein DppA (2021)
Journal Article
Zainol, M. K., Linforth, R. J., Winzor, D. J., & Scott, D. J. (2021). Thermodynamics of semi-specific ligand recognition: the binding of dipeptides to the E.coli dipeptide binding protein DppA. European Biophysics Journal, 50(8), 1103-1110. https://doi.org/10.1007/s00249-021-01572-y

This investigation of the temperature dependence of DppA interactions with a subset of three dipeptides (AA. AF and FA) by isothermal titration calorimetry has revealed the negative heat capacity (ΔCpo) that is a characteristic of hydrophobic interac... Read More about Thermodynamics of semi-specific ligand recognition: the binding of dipeptides to the E.coli dipeptide binding protein DppA.

Quantifying the concentration dependence of sedimentation coefficients for globular macromolecules: a continuing age-old problem (2021)
Journal Article
Winzor, D. J., Dinu, V., Scott, D. J., & Harding, S. E. (2021). Quantifying the concentration dependence of sedimentation coefficients for globular macromolecules: a continuing age-old problem. Biophysical Reviews, 13(2), 273-288. https://doi.org/10.1007/s12551-021-00793-x

This retrospective investigation has established that the early theoretical attempts to directly incorporate the consequences of radial dilution into expressions for variation of the sedimentation coefficient as a function of the loading concentratio... Read More about Quantifying the concentration dependence of sedimentation coefficients for globular macromolecules: a continuing age-old problem.

Engineering the Human Fc Region Enables Direct Cell Killing by Cancer Glycan-Targeting Antibodies without the Need for Immune Effector Cells or Complement (2020)
Journal Article
Vankemmelbeke, M., McIntosh, R. S., Chua, J. X., Kirk, T., Daniels, I., Patsalidou, M., …Durrant, L. G. (2020). Engineering the Human Fc Region Enables Direct Cell Killing by Cancer Glycan-Targeting Antibodies without the Need for Immune Effector Cells or Complement. Cancer Research, 80(16), 3399-3412. https://doi.org/10.1158/0008-5472.CAN-19-3599

©2020 American Association for Cancer Research. Murine IgG3 glycan-targeting mAb often induces direct cell killing in the absence of immune effector cells or complement via a proinflammatory mechanism resembling oncotic necrosis. This cancer cell kil... Read More about Engineering the Human Fc Region Enables Direct Cell Killing by Cancer Glycan-Targeting Antibodies without the Need for Immune Effector Cells or Complement.

Use of molecular crowding for the detection of protein self-association by size-exclusion chromatography (2019)
Journal Article
Mrozowich, T., Winzor, D. J., Scott, D. J., & Patel, T. R. (2019). Use of molecular crowding for the detection of protein self-association by size-exclusion chromatography. Analytical Biochemistry, 584, Article 113392. https://doi.org/10.1016/j.ab.2019.113392

The feasibility of employing molecular crowding cosolutes to facilitate the detection of protein self-association by zonal size exclusion chromatography is investigated. Theoretical considerations have established that although the cosolute-induced d... Read More about Use of molecular crowding for the detection of protein self-association by size-exclusion chromatography.

The carbonic anhydrase of Clostridium autoethanogenum represents a new subclass of β-carbonic anhydrases (2019)
Journal Article
Pander, B., Harris, G., Scott, D. J., Winzer, K., Köpke, M., Simpson, S. D., …Henstra, A. M. (2019). The carbonic anhydrase of Clostridium autoethanogenum represents a new subclass of β-carbonic anhydrases. Applied Microbiology and Biotechnology, 103(17), 7275-7286. https://doi.org/10.1007/s00253-019-10015-w

Carbonic anhydrase catalyses the interconversion of carbon dioxide and water to bicarbonate and protons. It was unknown if the industrial relevant acetogen Clostridium autoethanogenum possesses these enzymes. We identified two putative carbonic anhyd... Read More about The carbonic anhydrase of Clostridium autoethanogenum represents a new subclass of β-carbonic anhydrases.

Structural modeling of an outer membrane electron conduit from a metal-reducing bacterium suggests electron transfer via periplasmic redox partners (2018)
Journal Article
Edwards, M. J., White, G. F., Lockwood, C. W., Lawes, M. C., Martel, A., Harris, G., …Clarke, T. A. (2018). Structural modeling of an outer membrane electron conduit from a metal-reducing bacterium suggests electron transfer via periplasmic redox partners. Journal of Biological Chemistry, 293(21), https://doi.org/10.1074/jbc.RA118.001850

Many subsurface microorganisms couple their metabolism to the reduction or oxidation of extracellular substrates. For example, anaerobic mineral-respiring bacteria can use external metal oxides as terminal electron acceptors during respiration. Porin... Read More about Structural modeling of an outer membrane electron conduit from a metal-reducing bacterium suggests electron transfer via periplasmic redox partners.

Allowance for boundary sharpening in the determination of diffusion coefficients by sedimentation velocity: a historical perspective. (2018)
Journal Article
Winzor, D. J., & Scott, D. J. (2018). Allowance for boundary sharpening in the determination of diffusion coefficients by sedimentation velocity: a historical perspective. Biophysical Reviews, 10(1), 3-13. doi:10.1007/s12551-017-0384-1

This review summarizes endeavors undertaken in the middle of last century to employ the Lamm equation for quantitative analysis of boundary spreading in sedimentation velocity experiments on globular proteins, thereby illustrating the ingenuity requi... Read More about Allowance for boundary sharpening in the determination of diffusion coefficients by sedimentation velocity: a historical perspective..

Reconstructing promoter activity from Lux bioluminescent reporters (2017)
Journal Article
Iqbal, M., Doherty, N., Page, A. M., Qazi, S. N., Ajmera, I., Lund, P. A., …Stekel, D. J. (2017). Reconstructing promoter activity from Lux bioluminescent reporters. PLoS Computational Biology, 13(9), Article e1005731. https://doi.org/10.1371/journal.pcbi.1005731

The bacterial Lux system is used as a gene expression reporter. It is fast, sensitive and non-destructive, enabling high frequency measurements. Originally developed for bacterial cells, it has also been adapted for eukaryotic cells, and can be used... Read More about Reconstructing promoter activity from Lux bioluminescent reporters.

Intrinsic disorder in the partitioning protein KorB persists after co-operative complex formation with operator DNA and KorA (2017)
Journal Article
Hyde, E. I., Callow, P., Rajasekar, K. V., Timmins, P., Patel, T. P., Siligardi, G., …Scott, D. J. (2017). Intrinsic disorder in the partitioning protein KorB persists after co-operative complex formation with operator DNA and KorA. Biochemical Journal, 474(18), 3121-3135. https://doi.org/10.1042/BCJ20170281

© 2017 The Author(s). The ParB protein, KorB, from the RK2 plasmid is required for DNA partitioning and transcriptional repression. It acts co-operatively with other proteins, including the repressor KorA. Like many multifunctional proteins, KorB con... Read More about Intrinsic disorder in the partitioning protein KorB persists after co-operative complex formation with operator DNA and KorA.

Accounting for thermodynamic non-ideality in the Guinier region of small-angle scattering data of proteins (2016)
Journal Article
Scott, D. J. (2016). Accounting for thermodynamic non-ideality in the Guinier region of small-angle scattering data of proteins. Biophysical Reviews, 8(4), https://doi.org/10.1007/s12551-016-0235-5

Hydrodynamic studies of the solution properties of proteins and other biological macromolecules are often hard to interpret when the sample is present at a reasonably concentrated solution. The reason for this is that solutions exhibit deviations fro... Read More about Accounting for thermodynamic non-ideality in the Guinier region of small-angle scattering data of proteins.

STAT2 is a pervasive cytokine regulator due to its inhibition of STAT1 in multiple signaling pathways (2016)
Journal Article
Ho, J., Pelzel, C., Begitt, A., Mee, M., Elsheikha, H. M., Scott, D. J., & Vinkemeier, U. (2016). STAT2 is a pervasive cytokine regulator due to its inhibition of STAT1 in multiple signaling pathways. PLoS Biology, 14(10), 1-27. https://doi.org/10.1371/journal.pbio.2000117

STAT2 is the quintessential transcription factor for type 1 interferons (IFNs), where it functions as a heterodimer with STAT1. However, the human and murine STAT2-deficient phenotypes suggest important additional and currently unidentified type 1 IF... Read More about STAT2 is a pervasive cytokine regulator due to its inhibition of STAT1 in multiple signaling pathways.

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS) (2016)
Journal Article
Perkins, S. J., Wright, D. W., Zhang, H., Brookes, E. H., Chen, J., Irving, T. C., …Curtis, J. E. (2016). Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS). Journal of Applied Crystallography, 49(6), 1861-1875. https://doi.org/10.1107/S160057671601517X

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallog... Read More about Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS).

SilE is an intrinsically disordered periplasmic ‘molecular sponge' involved in bacterial silver resistance (2016)
Journal Article
Asiani, K. R., Williams, H. E. L., Bird, L., Jenner, M., Searle, M. S., Hobman, J. L., …Soultanas, P. (2016). SilE is an intrinsically disordered periplasmic ‘molecular sponge' involved in bacterial silver resistance. Molecular Microbiology, 101(5), 731-742. https://doi.org/10.1111/mmi.13399

Ag+ resistance was initially found on the Salmonella enetrica serovar Typhimurium multi-resistance plasmid pMG101 from burns patients in 1975. The putative model of Ag+ resistance, encoded by the sil operon from pMG101, involves export of Ag+ via an... Read More about SilE is an intrinsically disordered periplasmic ‘molecular sponge' involved in bacterial silver resistance.

Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator (2016)
Journal Article
Bingle, L. E., Rajasekar, K. V., Lovering, A. L., Dancea, F., Scott, D. J., Harris, S. A., …White, S. A. (2016). Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator. Nucleic Acids Research, 44(10), 4947-4956. https://doi.org/10.1093/nar/gkw191

The IncP (Incompatibility group P) plasmids are important carriers in the spread of antibiotic resistance across Gram-negative bacteria. Gene expression in the IncP-1 plasmids is stringently controlled by a network of four global repressors, KorA, Ko... Read More about Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator.

Defining the intrinsically disordered C-terminal domain of SSB reveals DNA-mediated compaction (2015)
Journal Article
Green, M., Hatter, L., Brookes, E., Soultanas, P., & Scott, D. (2016). Defining the intrinsically disordered C-terminal domain of SSB reveals DNA-mediated compaction. Journal of Molecular Biology, 428(2), 357-364. https://doi.org/10.1016/j.jmb.2015.12.007

The bacterial single-stranded DNA (ssDNA) binding protein SSB is a strictly conserved and essential protein involved in diverse functions of DNA metabolism, including replication and repair. SSB comprises a well-characterized tetrameric core of N-ter... Read More about Defining the intrinsically disordered C-terminal domain of SSB reveals DNA-mediated compaction.

Comparison of the Structure and Activity of Glycosylated and Aglycosylated Human Carboxylesterase 1 (2015)
Journal Article
Arena de Souza, V., Scott, D. J., Nettleship, J. E., Rahman, N., Charlton, M. H., Walsh, M. A., & Owens, R. J. (2015). Comparison of the Structure and Activity of Glycosylated and Aglycosylated Human Carboxylesterase 1. PLoS ONE, 10(12), e0143919. https://doi.org/10.1371/journal.pone.0143919

Human Carboxylesterase 1 (hCES1) is the key liver microsomal enzyme responsible for detoxification and metabolism of a variety of clinical drugs. To analyse the role of the single N-linked glycan on the structure and activity of the enzyme, authentic... Read More about Comparison of the Structure and Activity of Glycosylated and Aglycosylated Human Carboxylesterase 1.