Publications

December 2017 - January 2018

Fibroblast growth factor 9 subfamily and the heart

Shen Wang, Yong Li, Chao Jiang, Haishan Tian

ABSTRACT - The fibroblast growth factor (FGF) 9 subfamily is a member of the FGF family, including FGF9, 16, and 20, potentially sharing similar biochemical functions due to their high degree of sequence homology. Unlike other secreted proteins which have a cleavable N-terminal secreted signal peptide, FGF9/16/20 have non-cleaved N-terminal signal peptides.

 

Approaches to ab initio molecular replacement of alpha-helical transmembrane proteins

Thomas, JMH; Simkovic, F; Keegan, R; Mayans, O; Zhang, CX; Zhang, Y; Rigden, DJ

ABSTRACT - alpha-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving alpha-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information

 

New Perspectives, Opportunities, and Challenges in Exploring the Human Protein Kinome

Leah J. Wilson, Adam Linley, Dean E. Hammond, Fiona E. Hood, Judy M. Coulson, David J. MacEwan, Sarah J. Ross, Joseph R. Slupsky, Paul D. Smith, Patrick A. Eyers and Ian A. Prior

ABSTRACT - The human protein kinome comprises 535 proteins that, with the exception of approximately 50 pseudokinases, control intracellular signaling networks by catalyzing the phosphorylation of multiple protein substrates

 

In vitro investigations on the effects of semi-synthetic, sulphated carbohydrates on the immune status of cultured common carp (Cyprinus carpio) leucocytes

N. Kareema, E. Yates, M. Skidmore, D. Hoole

ABSTRACT - The rapid emergence of drug resistance, unfavourable immunosuppression and mounting evidence to suggest the deleterious accumulation of drug breakdown residues within animal tissues has driven a strong desire to move away from these current methods of disease control.

 

Optimising the chick chorioallantoic membrane xenograft model of neuroblastoma for drug delivery

Rasha Swadi, Grace Mather, Barry L. Pizer, Paul D. Losty, Violaine See and Diana Moss

ABSTRACT - Neuroblastoma is a paediatric cancer that despite multimodal therapy still has a poor outcome for many patients with high risk tumours

 

Back to the future: new target-validated Rab antibodies for evaluating LRRK2 signalling in cell biology and Parkinson's disease

Patrick A. Eyers

ABSTRACT - The addition of phosphate groups to substrates allows protein kinases to regulate a myriad of biological processes, and contextual analysis of protein-bound phosphate is important for understanding how kinases contribute to physiology and disease

 

Understanding protein–drug interactions using ion mobility–mass spectrometry

Claire E Eyers, Matthias Vonderach, Samantha Ferries, Kiani Jeacock, Patrick A Eyers

ABSTRACT - Ion mobility–mass spectrometry (IM–MS) is an important addition to the analytical toolbox for the structural evaluation of proteins, and is enhancing many areas of biophysical analysis.

 

November 2017 - December 2017

Structure and function of Per-ARNT-Sim domains and their possible role in the life-cycle biology of Trypanosoma cruzi

Maura Rojas-Pirelaa, Daniel J. Rigden, Paul A. Michels, Ana J. Cáceres, Wilfredo Quiñones

ABTRACT - Per-ARNT-Sim (PAS) domains of proteins play important roles as modules for signalling and cellular regulation processes in widely diverse organisms such as Archaea, Bacteria, protists, plants, yeasts, insects and vertebrates. These domains are present in many proteins where they are used as sensors of stimuli and modules for protein interactions.

 

Using an NMR metabolomics approach to investigate the pathogenicity of amyloid-beta and alpha-synuclein

Phelan, M. M.; Caamano-Gutierrez, E.; Gant, M. S.; Grosman, R. X.; Madine, J.

ABSTRACT - The pathogenicity at differing points along the aggregation pathway of many fibril-forming proteins associated with neurodegenerative diseases is unclear. Understanding the effect of different aggregation states of these proteins on cellular processes is essential to enhance understanding of diseases and provide future options for diagnosis and therapeutic intervention.

 

Medin Amyloid, but Not β-amyloid, Induces Pro-Inflammatory Signaling in Endothelial Cells That is Synergistic With Palmitic Acid

Nina Karamanova, Seth Truran, Jillian Madine, Hannah Davies, Jenna Anderson, Daniel A Franco, Geidy Serrano, Thomas Beach, Raymond Q Migrino

ABSTRACT - Medin is the most common human amyloid protein and accumulates in vessels with aging yet little is known about the pathophysiology of medin and its role in vascular aging. We previously showed that medin, β-amyloid (Aβ42) and saturated fatty acid palmitic acid (PA) induce profound endothelial dysfunction in ex-vivo human adipose and leptomeningeal arterioles, suggesting potential interactions that could provide the missing link between cardiovascular risk factors (CVRFs) and amyloid proteins in inducing vascular dysfunction leading to atherosclerosis and cognitive dysfunction.

 

Medin Amyloid Protein-Induced Human Leptomeningeal Arteriole Endothelial Dysfunction and Pro-Inflammatory Signaling are Reversed by Monosialoganglioside Nanoliposomes

Seth Truran, Nina Karamanova, Jillian Madine, Hannah Davies, Diana Guzman-Villanueva, Geidy Serrano, Daniel A Franco, Thomas Beach, Volkmar Weissig, Raymond Q Migrino

ABSTRACT - Medin is a 50 amino acid peptide that forms amyloid deposits in the vasculature. It is the most common human amyloid protein and was reported to be present in almost all tested patients above 55 years old. It has been implicated as a potential novel etiologic risk factor for vascular aging yet we know little about its pathophysiology or treatment.

 

Targeting SxIP-EB1 interaction: An integrated approach to the discovery of small molecule modulators of dynamic binding sites

T. B. Almeida, A. J. Carnell, I. L. Barsukov, N.G. Berry

ABSTRACT - End binding protein 1 (EB1) is a key element in the complex network of protein-protein interactions at microtubule (MT) growing ends, which has a fundamental role in MT polymerisation. EB1 is an important protein target as it is involved in regulating MT dynamic behaviour, and has been associated with several disease states, such as cancer and neuronal diseases.

 

An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase

Thomas P. Halsted, Keitaro Yamashita, Kunio Hirata, Hideo Ago, Go Ueno, Takehiko Tosha Robert R. Eady Svetlana V. Antonyuk Masaki Yamamoto and S. Samar Hasnain

ABSTRACT - Synchrotron-based X-ray structural studies of ligand-bound enzymes are powerful tools to further our understanding of reaction mechanisms. For redox enzymes, it is necessary to study both the oxidized and reduced active sites to fully elucidate the reaction, an objective that is complicated by potential X-ray photoreduction. In the presence of the substrate, this can be exploited to construct a structural movie of the events associated with catalysis.

 

Approaches to ab initio molecular replacement of α-helical transmembrane proteins

J. M. H. Thomas, F. Simkovic, R. Keegan, O. Mayans, C. Zhang, Y. Zhang and D. J. Rigden

ABSTRACT - Transmembrane proteins are an important class of proteins that are estimated to comprise about 30% of the proteome (Tusnády et al., 2004)  They reside t least partly and often predominantly, within the hydrophobic cell membrane, sandwiched between the aqueous cell interior and exterior

 

The Muscle Stem Cell Niche in Health and Disease

Omid Mashinchian, Addolorata Pisconti, Emmeran Le Moal§, C. Florian Bentzinger

ABSTRACT - The regulation of stem cells that maintain and regenerate postnatal tissues depends on extrinsic signals originating from their microenvironment, commonly referred to as the stem cell niche.

 

October 2017 - November 2017

Homo-PROTACs: bivalent small-molecule dimerizers of the VHL E3 ubiquitin ligase to induce self-degradation

Maniaci C1,2, Hughes SJ1, Testa A1, Chen W1, Lamont DJ1, Rocha S3, Alessi DR2, Romeo R4, Ciulli A5

ABTRACT - E3 ubiquitin ligases are key enzymes within the ubiquitin proteasome system which catalyze the ubiquitination of proteins, targeting them for proteasomal degradation. E3 ligases are gaining importance as targets to small molecules, both for direct inhibition and to be hijacked to induce the degradation of non-native neo-substrates using bivalent compounds known as PROTACs (for 'proteolysis-targeting chimeras'). We describe Homo-PROTACs as an approach to dimerize an E3 ligase to trigger its suicide-type chemical knockdown inside cells

 

MEERCAT: Multiplexed Efficient Cell Free Expression of Recombinant QconCATs For Large Scale Absolute Proteome Quantification.

Nobuaki Takemori1, Ayako Takemori1, Yuki Tanaka2, Yaeta Endo1, Jane L. Hurst3, Guadalupe Gómez- Baena4, Victoria M Harman4 and Robert J Beynon4

ABSTRACT - A major challenge in proteomics is the absolute accurate quantification of large numbers of proteins. QconCATs, artificial proteins that are concatenations of multiple standard peptides, are well established as an efficient means to generate standards for proteome quantification

 

Using an NMR metabolomics approach to investigate the pathogenicity of amyloid-beta and alpha-synuclein

M. M. Phelan, E. Caamaño-Gutiérrez, M. S. Gant, R. X. Grosman, J. Madine

ABSTRACT - The pathogenicity at differing points along the aggregation pathway of many fibril-forming proteins associated with neurodegenerative diseases is unclear. Understanding the effect of different aggregation states of these proteins on cellular processes is essential to enhance understanding of diseases and provide future options for diagnosis and therapeutic intervention

 

Identification of Heparin Modifications and Polysaccharide Inhibitors of Plasmodium falciparum Merozoite Invasion That Have Potential for Novel Drug Development 

Boyle, MJ; Skidmore, M; Dickerman, B; Cooper, L; Devlin, A ; Yates, E; Horrocks, P; Freeman, C; Chai, WG; Beeson, JG.

ABSTRACT - Despite recent successful control efforts, malaria remains a leading global health burden. Alarmingly, resistance to current antimalarials is increasing and the development of new drug families is needed to maintain malaria control. Current antimalarials target the intraerythrocytic developmental stage of the Plasmodium falciparum life cycle. However, the invasive extracellular parasite form, the merozoite, is also an attractive target for drug development

 

September 2017 - October 2017

Kinome-wide transcriptional profiling of uveal melanoma reveals new vulnerabilities to targeted therapeutics

Fiona P Bailey, Kim Clarke, Helen Kalirai, Jenna Kenyani, Haleh Shahidipour, Francesco Falciani, Judy M Coulson, Joseph J Sacco, Sarah E Coupland, Patrick A Eyers 

ABSTRACT - Metastatic uveal melanoma (UM) is invariably fatal, usually within a year of diagnosis. There are currently no effective therapies, and clinical studies employing kinase inhibitors have so far demonstrated limited success.

 

The Wnt5a Receptor, Receptor Tyrosine Kinase-Like Orphan Receptor 2, Is a Predictive Cell Surface Marker of Human Mesenchymal Stem Cells with an Enhanced Capacity for Chondrogenic Differentiation

Sally C. Dickenson, Catherine A. Sutton, Kyla Brady, Anna Salerno, Theoni Ktopodi, Rhys L. Williams, Christopher C. West, Denis Evseenko, Ling Wu, Suzanna Pang, Roberto Ferro de Godoy, Allen E. Goodship, Bruno PE Ault, Ashley W Blom, Wael Kafienah, Anthony P. Hollander

ABSTRACTMultipotent mesenchymal stem cells (MSCs) have enormous potential in tissue engineering and regenerative medicine.  However, until now their development for clinical use has been severely limited as they are a mixed population of cells with varying capacities for lineage differentiation and tissue formation  

 

Extensive non-canonical phosphorylation in human cells revealed using strong-anion exchange-mediated phosphoproteomics

Gemma Hardman, Simon Perkins, Zheng Ruan, Natarajan Kannan, Philip Brownridge, Dominic P Byrne, Patrick A Eyers, Andrew R Jones, Claire E Eyers

ABSTRACT - Protein phosphorylation is a ubiquitous post-translational modification (PTM) that regulates all aspects of life. To date, investigation of human cell signalling has focussed on canonical phosphorylation of serine (Ser), threonine (Thr) and tyrosine (Tyr) residues. However, mounting evidence suggests that phosphorylation of histidine also plays a central role in regulating cell biology

 

Expression and purification of an FGF9 fusion protein in E. coli, and the effects of the FGF9 subfamily on human hepatocellular carcinoma cell proliferation and migration

Shen Wang, Haipeng Lin, Tiantian Zhao, Sisi Huang, David G. Fernig, Nuo Xu, Fenfang Wu, Mi Zhou, Chao Jiang, Haishan Tian

ABSTRACT - Fibroblast growth factor (FGF) 9 has oncogenic activity and plays an important role in the development of ovarian, lung, prostate, and gastric cancers

 

Identification of heparin modifications and polysaccharide inhibitors of Plasmodium falciparum merozoite invasion that have potential for novel drug development

Michelle J. Boyle, Mark Skidmore, Benjamin Dickerman, Lynsay Cooper, Antony Devlin, Edwin Yates, Paul Horrocks, Craig Freeman, Wengang Chai and James G. Beeson

ABSTRACT - Despite recent successful control efforts, malaria remains a leading global health burden. Alarmingly, resistance to current antimalarials is increasing, and the development of new drug families is needed to maintain malaria control.

 

August 2017

Local protein kinase A action proceeds through intact holoenzymes
Smith, F.D., Esseltine, J.L., Nygren, P.J., Veesler, D., Byrne, D.P., Vonderach, M., Strashnov, I., Eyers, C.E., Eyers, P.A., Langeberg, L.K., Scott, J.D. (2017) Local protein kinase A action proceeds through intact holoenzymes. Science. doi: 10.1126/science.aaj1669

Dynamic changes in heparan sulfate during muscle differentiation and ageing regulate myoblast cell fate and FGF2 signalling
Ghadiali, R.S., Guimond, S.E., Turnbull, J.E., Pisconti, A. (2017). Dynamic changes in heparan sulfate during muscle differentiation and ageing regulate myoblast cell fate and FGF2 signalling. Matrix Biology. doi: 10.1016/j.matbio.2016.07.007

MRL proteins cooperate with activated Ras in glia to drive distinct oncogenic outcomes
Taylor, E., Alqadri, N., Dodgson, L., Mason, D., Lyulcheva, E., Messina, G., Bennett, D. (2017). MRL proteins cooperate with activated Ras in glia to drive distinct oncogenic outcomes. Oncogene. doi: 10.1038/onc.2017.68

SHANK proteins limit integrin activation by directly interacting with Rap1 and R-Ras
Lilja, J., Zacharchenko, T., Georgiadou, M., Jacquemet, G., Franceschi, N.D., Peuhu, E., Hamidi, H., Pouwels, J., Martens, V., Nia, F.H., Beifuss, M., Boeckers, T., Kreienkamp, H.-J., Barsukov, I.L., Ivaska, J. (2017). SHANK proteins limit integrin activation by directly interacting with Rap1 and R-Ras. Nature Cell Biology. doi: 10.1038/ncb3487