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Articles 1 - 14 of 14
Full-Text Articles in Social and Behavioral Sciences
High-Yield Cell-Free Protein Synthesis For Site-Specific Incorporation Of Unnatural Amino Acids At Two Sites, Kiyoshi Ozawa, Karin V. Loscha, Kekini V. Kuppan, Choy Theng Loh, Nicholas E. Dixon, Gottfried Otting
High-Yield Cell-Free Protein Synthesis For Site-Specific Incorporation Of Unnatural Amino Acids At Two Sites, Kiyoshi Ozawa, Karin V. Loscha, Kekini V. Kuppan, Choy Theng Loh, Nicholas E. Dixon, Gottfried Otting
Faculty of Science - Papers (Archive)
Using aminoacyl-tRNA synthetase/suppressor tRNA pairs derived from Methanocaldococcus jannaschii, an Escherichia coli cell-free protein production system affords proteins with site-specifically incorporated unnatural amino acids (UAAs) in high yields through the use of optimized amber suppressor tRNACUA opt and optimization of reagent concentrations. The efficiency of the cell-free system allows the incorporation of trifluoromethyl-phenylalanine using a polyspecific synthetase evolved previously for p-cyanophenylalanine, and the incorporation of UAAs at two different sites of the same protein without any re-engineering of the E. coli cells used to make the cell-free extract.
Fragment-Based Screening By Protein Crystallography: Successes And Pitfalls, Zorik Chilingaryan, Zhou Yin, Aaron J. Oakley
Fragment-Based Screening By Protein Crystallography: Successes And Pitfalls, Zorik Chilingaryan, Zhou Yin, Aaron J. Oakley
Faculty of Science - Papers (Archive)
Fragment-based drug discovery (FBDD) concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper, the rationale and technology behind the use of X-ray crystallography in fragment based screening (FBS) will be described, including fragment library design and use of synchrotron radiation and robotics for high-throughput X-ray data collection. Some recent uses of crystallography in FBS will be described in detail, including interrogation of the drug targets β-secretase, phenylethanolamine N-methyltransferase, phosphodiesterase …
Protein Chemistry Of Amyloid Fibrils And Chaperones: Implications For Amyloid Formation And Disease, Justin J. Yerbury, Janet R. Kumita
Protein Chemistry Of Amyloid Fibrils And Chaperones: Implications For Amyloid Formation And Disease, Justin J. Yerbury, Janet R. Kumita
Faculty of Science - Papers (Archive)
Understanding the mechanisms by which amyloid fibrils are formed, both in vivo and in vitro, is vital for developing methods to treat and prevent debilitating deposition diseases such as Alzheimer's disease, Parkinson's disease, type II diabetes and systemic amyloidoses. In recent years, computer modelling and biophysical studies have broadened our understanding of the biochemical mechanisms underpinning protein aggregation. As a result, it is now believed that the ability to form fibrils is an intrinsic property of polypeptide chains and not isolated to disease-related proteins or peptides. Molecular chaperones are a diverse group of functionally related proteins well known for their …
Modulation Of Amyloid Precursor Protein Processing By Synthetic Ceramide Analogues, Hongyun Li, Woojin Scott Kim, Gilles Guillemin, Andrew F. Hill, Genevieve Evin, Brett Garner
Modulation Of Amyloid Precursor Protein Processing By Synthetic Ceramide Analogues, Hongyun Li, Woojin Scott Kim, Gilles Guillemin, Andrew F. Hill, Genevieve Evin, Brett Garner
Faculty of Science - Papers (Archive)
Previous studies suggest that membrane lipids may regulate proteolytic processing of the amyloid precursor protein (APP) to generate amyloid-beta peptide (Abeta). In the present study, we have assessed the capacity for a series of structurally related synthetic ceramide analogues to modulate APP processing in vitro. The compounds tested are established glucosylceramide synthase (GS) inhibitors based on the D-1-phenyl-2-decanoylamino-3-morpholino-1-propanol (PDMP) structure. PDMP and related compounds PPMP and EtDO-P4 inhibited Abeta secretion from Chinese hamster ovary cells expressing human APP (CHO-APP) with approximate IC50 values of 15, 5, and 1 mu M, respectively. A trend for reduced secretion of the APP alpha-secretase …
Synthesis And Applications Of Covalent Protein-Dna Conjugates, Patrick M. Schaeffer, Nicholas E. Dixon
Synthesis And Applications Of Covalent Protein-Dna Conjugates, Patrick M. Schaeffer, Nicholas E. Dixon
Faculty of Science - Papers (Archive)
Synthetic protein-DNA conjugates are valuable tools with applications in fields including nanobiotechnology, bioanalytical chemistry, and molecular diagnostics, and various synthetic methods for their production have been developed during the past three decades. The present article reviews current methodologies for the synthesis of covalent protein-DNA conjugates with particular focus on the regiospecificity and stoichiometry of these reactions.
Structural Characterization Of Clusterin-Chaperone Client Protein Complexes, Amy R. Wyatt, Justin J. Yerbury, Mark R. Wilson
Structural Characterization Of Clusterin-Chaperone Client Protein Complexes, Amy R. Wyatt, Justin J. Yerbury, Mark R. Wilson
Faculty of Science - Papers (Archive)
Clusterin (CLU) is a potent extracellular chaperone that inhibits protein aggregation and precipitation otherwise caused by physical or chemical stresses (e.g. heat, reduction). This action involves CLU forming soluble high molecular weight (HMW) complexes with the client protein. Other than their unquantified large size, the physical characteristics of these complexes were previously unknown. In this study, HMW CLU-citrate synthase (CS), HMW CLU-fibrinogen (FGN), and HMW CLU-glutathione S-transferase (GST) complexes were generated in vitro, and their structures studied using size exclusion chromatography (SEC), ELISA, SDS-PAGE, dynamic light scattering (DLS), bisANS fluorescence, and circular dichroism spectrophotometry (CD). Densitometry of …
Macroglobulin And Haptoglobin Suppress Amyloid Formation By Interacting With Prefibrillar Protein Species, Justin J. Yerbury, Janet R. Kumita, Sarah Meehan, Christopher M. Dobson, Mark R. Wilson
Macroglobulin And Haptoglobin Suppress Amyloid Formation By Interacting With Prefibrillar Protein Species, Justin J. Yerbury, Janet R. Kumita, Sarah Meehan, Christopher M. Dobson, Mark R. Wilson
Faculty of Science - Papers (Archive)
α2-Macroglobulin (α2M) and haptoglobin (Hp) are both abundant secreted glycoproteins that are best known for their protease trapping and hemoglobin binding activities, respectively. Like the small heat shock proteins, both these glycoproteins have in common the ability to protect a range of proteins from stress-induced amorphous aggregation and have been described as extracellular chaperones. Using an array of biophysical techniques, this study establishes that in vitro at substoichiometric levels and under physiological conditions α2M and Hp both inhibit the formation of amyloid fibrils from a range of proteins. We also provide evidence that both …
Therapeutic Targets In Extracellular Protein Deposition Diseases, Amy R. Wyatt, Justin J. Yerbury, Stephen Poon, Mark R. Wilson
Therapeutic Targets In Extracellular Protein Deposition Diseases, Amy R. Wyatt, Justin J. Yerbury, Stephen Poon, Mark R. Wilson
Faculty of Science - Papers (Archive)
Many litres of fluids are found outside cells in the human body. These fluids are rich in dissolved proteins that each have a characteristic three dimensional shape, necessary for normal function, which has been attained by the correct folding of their polypeptide chain(s). The structure of these extracellular proteins can be damaged by a variety of environmental stresses (e. g. heat and oxidation) leading to their partial unfolding and aggregation. This in turn can produce toxic soluble aggregates and/or large insoluble protein deposits, either of which can disrupt normal body function (e. g. in Alzheimer's disease and the systemic amyloidoses). …
Unraveling The Mysteries Of Protein Folding And Misfolding, Heath Ecroyd, John A. Carver
Unraveling The Mysteries Of Protein Folding And Misfolding, Heath Ecroyd, John A. Carver
Faculty of Science - Papers (Archive)
This mini-review focuses on the processes and consequences of protein folding and misfolding. The latter process often leads to protein aggregation and precipitation with the aggregates adopting either highly ordered (amyloid fibril) or disordered (amorphous) forms. In particular, the amyloid fibril is discussed because this form has gained considerable notoriety due to its close links to a variety of debilitating diseases including Alzheimer's, Parkinson's, Huntington's, and Creutzfeldt-Jakob diseases, and type-II diabetes. In each of these diseases a different protein forms fibrils, yet the fibrils formed have a very similar structure. The mechanism by which fibrils form, fibril structure, and the …
Effect Of Protein Stabilization On Charge State Distribution In Positive- And Negative Ion Electrospray Ionization Mass Spectra, Stephen J. Watt, Margaret Sheil, Jennifer L. Beck, Pavel Prosselkov, Gottfried Otting, Nicholas E. Dixon
Effect Of Protein Stabilization On Charge State Distribution In Positive- And Negative Ion Electrospray Ionization Mass Spectra, Stephen J. Watt, Margaret Sheil, Jennifer L. Beck, Pavel Prosselkov, Gottfried Otting, Nicholas E. Dixon
Faculty of Science - Papers (Archive)
Changes in protein conformation are thought to alter charge state distributions observed in electrospray ionization mass spectra (ESI-MS) of proteins. In most cases, this has been demonstrated by unfolding proteins through acidification of the solution. This methodology changes the properties of the solvent so that changes in the ESI-MS charge envelopes from conformational changes are difficult to separate from the effects of changing solvent on the ionization process. A novel strategy is presented enabling comparison of ESI mass spectra of a folded and partially unfolded protein of the same amino acid sequence subjected to the same experimental protocols and conditions. …
Anisotropic Atomic Motions In High-Resolution Protein Crystallography Molecular Dynamics Simulations, Conrad J. Burden, Aaron J. Oakley
Anisotropic Atomic Motions In High-Resolution Protein Crystallography Molecular Dynamics Simulations, Conrad J. Burden, Aaron J. Oakley
Faculty of Science - Papers (Archive)
Molecular dynamics (MD) simulations using empirical force fields are popular for the study of proteins. In this work, we compare anisotropic atomic fluctuations in nanosecond-timescale MD simulations with those observed in an ultra-high-resolution crystal structure of crambin. In order to make our comparisons, we have developed a compact graphical technique for assessing agreement between spatial atomic distributions determined by MD simulations and observed anisotropic temperature factors.
Targeting C-Reactive Protein For The Treatment Of Cardiovascular Disease, Mark B. Pepys, Gideon M. Hirschfield, Glenys A. Tennent, J Ruth Gallimore, Melvyn C. Kahan, Vittorio Bellotti, Philip N. Hawkins, Rebecca M. Myers, Martin D. Smith, Alessandra Polara, Alexander J. A Cobb, Steven V. Ley, J. Andrew Aquilina, Carol V. Robinson, Isam Sharif, Gillian A. Gray, Caroline A. Sabin, Michelle C. Jenvey, Simon E. Kolstoe, Darren Thompson, Stephen P. Wood
Targeting C-Reactive Protein For The Treatment Of Cardiovascular Disease, Mark B. Pepys, Gideon M. Hirschfield, Glenys A. Tennent, J Ruth Gallimore, Melvyn C. Kahan, Vittorio Bellotti, Philip N. Hawkins, Rebecca M. Myers, Martin D. Smith, Alessandra Polara, Alexander J. A Cobb, Steven V. Ley, J. Andrew Aquilina, Carol V. Robinson, Isam Sharif, Gillian A. Gray, Caroline A. Sabin, Michelle C. Jenvey, Simon E. Kolstoe, Darren Thompson, Stephen P. Wood
Faculty of Science - Papers (Archive)
Complement-mediated inflammation exacerbates the tissue injury of ischaemic necrosis in heart attacks and strokes, the most common causes of death in developed countries. Large infarct size increases immediate morbidity and mortality and, in survivors of the acute event, larger non-functional scars adversely affect long-term prognosis. There is thus an important unmet medical need for new cardioprotective and neuroprotective treatments. We have previously shown that human C-reactive protein (CRP), the classical acute-phase protein that binds to ligands exposed in damaged tissue and then activates complement1, increases myocardial and cerebral infarct size in rats subjected to coronary or cerebral artery ligation, respectively2,3. …
The Epididymal Soluble Prion Protein Forms A High-Molecular-Mass Complex In Association With Hydrophobic Proteins, Heath W. Ecroyd, Maya Belghazi, Jean-Louis Dacheux, Jean-Luc Gatti
The Epididymal Soluble Prion Protein Forms A High-Molecular-Mass Complex In Association With Hydrophobic Proteins, Heath W. Ecroyd, Maya Belghazi, Jean-Louis Dacheux, Jean-Luc Gatti
Faculty of Science - Papers (Archive)
We have shown previously that a 'soluble' form of PrP (prion protein), not associated with membranous vesicles, exists in the male reproductive fluid [Ecroyd, Sarradin, Dacheux and Gatti (2004) Biol. Reprod. 71, 993-1001]. Attempts to purify this 'soluble' PrP indicated that it behaves like a high-molecular-mass complex of more than 350 kDa and always co-purified with the same set of proteins. The main associated proteins were sequenced by MS and were found to match to clusterin (apolipoprotein J), BPI (bacterial permeability-increasing protein), carboxylesterase-like urinary excreted protein (cauxin), beta-mannosidase and beta-galactosidase. Immunoblotting and enzymatic assay confirmed the presence of clusterin and …
Molecular Dynamics Simulations Of Peptides Containing An Unnatural Amino Acid: Dimerization, Folding, And Protein Binding, Haibo Yu, Xavier Daura, Wilfred Van Gunsteren
Molecular Dynamics Simulations Of Peptides Containing An Unnatural Amino Acid: Dimerization, Folding, And Protein Binding, Haibo Yu, Xavier Daura, Wilfred Van Gunsteren
Faculty of Science - Papers (Archive)
We have performed molecular dynamics (MD) simulations to study the dimerization, folding, and binding to a protein of peptides containing an unnatural amino acid. NMR studies have shown that the substitution of one residue in a tripeptide β-strand by the unnatural amino acid Hao (5-HO2CCONH-2-MeO-C6H3-CO-NHNH2) modifies the conformational flexibility of the β-strand and the hydrogen-bonding properties of its two edges: The number of hydrogen-bond donors and acceptors increases at one edge, whereas at the other, they are sterically hindered. In simulations in chloroform, the Hao-containing peptide 9 (i-PrCO-Phe-Hao-Val-NHBu) forms a β-sheet–like hydrogen-bonded dimer, in good agreement with the available experimental …