Paul D. Barker

Find an error

Name:

Organization: University Chemical Laboratories and MRC Centre for Protein Engineering , England

Department: University Chemical Laboratories and MRC Centre for Protein Engineering

Title: Professor(PhD)

Chemicals
References

Selective Lability of Ruthenium(II) Arene Amino Acid Complexes

Co-reporter:Tom G. Scrase; Michael J. O’Neill; Andrew J. Peel; Paul W. Senior; Peter D. Matthews; Heyao Shi; Sally R. Boss

Inorganic Chemistry 2015 Volume 54(Issue 7) pp:3118-3124

Publication Date(Web):March 23, 2015

DOI:10.1021/ic502051y

A series of organometallic complexes of the form [(PhH)Ru(amino acid)]+ have been synthesized using amino acids able to act as tridentate ligands. The straightforward syntheses gave enantiomerically pure complexes with two stereogenic centers due to the enantiopurity of the chelating ligands. Complexes were characterized in the solid-state and/or solution-state where the stability of the complex allowed. The propensity toward labilization of the coordinatively saturated complexes was investigated. The links between complex stability and structural features are very subtle. Nonetheless, H/D exchange rates of coordinated amino groups reveal more significant differences in reactivity linked to metallocycle ring size resulting in decreasing stability of the metallocycle as the amino acid side-chain length increases. The behavior of these systems in acid is unusual, apparently labilizing the carboxylate residue of the amino acid. This acid-catalyzed hemilability in an organometallic is relevant to the use of Ru(II) arenes in medicinal contexts due to the relatively low pH of cancerous cells.

Folates are potential ligands for ruthenium compounds in vivo

Co-reporter:Tom G. Scrase, Simon M. Page, Paul D. Barker and Sally R. Boss

Dalton Transactions 2014 vol. 43(Issue 22) pp:8158-8161

Publication Date(Web):19 Mar 2014

DOI:10.1039/C4DT00081A

Under physiologically relevant conditions, cis-bis(2,2′-bipyridine)dichlororuthenium(II), [cis-Ru(2,2′-bipy)2Cl2] was observed to bind to folic acid via replacement of the two chloride ligands. This binding was shown to be pH dependent and afforded diastereomers, the structures of which were determined by 1- and 2D NMR spectroscopic techniques. We propose that when studying the cytotoxicity of labile ruthenium complexes in cells, folate coordination should be considered.

The Morphology of Decorated Amyloid Fibers is Controlled by the Conformation and Position of the Displayed Protein

Co-reporter:Christopher J. Forman, Adrian A. Nickson, Spencer J. Anthony-Cahill, Andrew J. Baldwin, Gillian Kaggwa, Urs Feber, Khizar Sheikh, Suzanne P. Jarvis, and Paul D. Barker

ACS Nano 2012 Volume 6(Issue 2) pp:1332

Publication Date(Web):January 25, 2012

DOI:10.1021/nn204140a

Self-assembled structures capable of mediating electron transfer are an attractive scientific and technological goal. Therefore, systematic variants of SH3-Cytochrome b562 fusion proteins were designed to make amyloid fibers displaying heme-b562 electron transfer complexes. TEM and AFM data show that fiber morphology responds systematically to placement of b562 within the fusion proteins. UV–vis spectroscopy shows that, for the fusion proteins under test, only half the fiber-borne b562 binds heme with high affinity. Cofactor binding also improves the AFM imaging properties and changes the fiber morphology through changes in cytochrome conformation. Systematic observations and measurements of fiber geometry suggest that longitudinal registry of subfilaments within the fiber, mediated by the interaction and conformation of the displayed proteins and their interaction with surfaces, gives rise to the observed morphologies, including defects and kinks. Of most interest is the role of small molecule modulation of fiber structure and mechanical stability. A minimum complexity model is proposed to capture and explain the fiber morphology in the light of these results. Understanding the complex interplay between these factors will enable a fiber design that supports longitudinal electron transfer.Keywords: AFM; amyloid; electron transfer; molecular electronics; self-assembly

Continued surprises in the cytochrome c biogenesis story

Co-reporter:Elizabeth B. Sawyer

Protein & Cell 2012 Volume 3( Issue 6) pp:405-409

Publication Date(Web):2012 June

DOI:10.1007/s13238-012-2912-x

Cytochromes c covalently bind their heme prosthetic groups through thioether bonds between the vinyl groups of the heme and the thiols of a CXXCH motif within the protein. In Gram-negative bacteria, this process is catalyzed by the Ccm (cytochrome c maturation) proteins, also called System I. The Ccm proteins are found in the bacterial inner membrane, but some (CcmE, CcmG, CcmH, and CcmI) also have soluble functional domains on the periplasmic face of the membrane. Elucidation of the mechanisms involved in the transport and relay of heme and the apocytochrome from the bacterial cytosol into the periplasm, and their subsequent reaction, has proved challenging due to the fact that most of the proteins involved are membrane-associated, but recent progress in understanding some key components has thrown up some surprises. In this Review, we discuss advances in our understanding of this process arising from a substrate’s point of view and from recent structural information about individual components.

Aberrant Attachment of Heme to Cytochrome by the Ccm System Results in a Cysteine Persulfide Linkage

Co-reporter:Elizabeth B. Sawyer ; Elaine Stephens ; Stuart J. Ferguson ; James W. A. Allen

Journal of the American Chemical Society 2010 Volume 132(Issue 14) pp:4974-4975

Publication Date(Web):March 23, 2010

DOI:10.1021/ja908241v

The system I cytochrome c maturation (Ccm) apparatus has been shown to handle a wide variety of apocytochrome substrates containing the CXnCH heme attachment sequence, where n = 2, 3, or 4 in natural sequences. When n = 5 or 6, the apparatus also appears to handle these substrates correctly, but close inspection reveals that the resulting mature cytochromes are mixtures of species containing extra mass. We have used accurate mass spectrometry to analyze peptide digests of matured Escherichia coli cytochrome cb562 with n = 1, 5, or 6 and shown that an extra sulfur is sometimes incorporated into the heme−protein linkage. These unprecedented, aberrant persulfide linkages may shed new light upon the mechanism of the attachment of heme to substrate apocytochrome within the Ccm complex of E. coli.

Controlling Self-Assembly by Linking Protein Folding, DNA Binding, and the Redox Chemistry of Heme

Co-reporter:D. Dafydd Jones

Angewandte Chemie 2005 Volume 117(Issue 39) pp:

Publication Date(Web):15 SEP 2005

DOI:10.1002/ange.200463035

Häm erkennt Gene: Ein Schritt hin zur elektronischen Steuerung des Lesens des DNA-Codes auf molekularer Ebene ist die Verknüpfung von Häm- und DNA-Erkennung durch das Falten eines Proteins (siehe Bild). Durch Überführen eines gezielt entworfenen, DNA bindenden Cytochroms in ein Heterodimer lässt sich die sequenzspezifische DNA-Erkennung über die Häm-Erkennung und die Oxidationsstufe des Eisenzentrums steuern.

Controlling Self-Assembly by Linking Protein Folding, DNA Binding, and the Redox Chemistry of Heme

Co-reporter:D. Dafydd Jones,Paul D. Barker

Angewandte Chemie International Edition 2005 44(39) pp:6337-6341

Publication Date(Web):

DOI:10.1002/anie.200463035

Design and Characterisation of an Artificial DNA-Binding Cytochrome

Co-reporter:D. Dafydd Jones Dr. Dr.

ChemBioChem 2004 Volume 5(Issue 7) pp:

Publication Date(Web):1 JUL 2004

DOI:10.1002/cbic.200300569

We aim to design novel proteins that link specific biochemical binding events, such as DNA recognition, with electron transfer functionality. We want these proteins to form the basis of new molecules that can be used for templated assembly of conducting cofactors or for thermodynamically linking DNA binding with cofactor chemistry for nanodevice applications. The first examples of our new proteins recruit the DNA-binding basic helix region of the leucine zipper protein GCN4. This basic helix region was attached to the N and C termini of cytochrome b₅₆₂(cyt b₅₆₂) to produce new, monomeric, multifunctional polypeptides. We have fully characterised the DNA and haem-binding properties of these proteins, which is a prerequisite for future application of the new molecules. Attachment of a single basic helix of GCN4 to either the N or C terminus of the cytochrome does not result in specific DNA binding but the presence of DNA-binding domains at both termini converts the cytochrome into a specific DNA-binding protein. Upon binding haem, this chimeric protein attains the spectral characteristics of wild-type cyt b₅₆₂. The three forms of the protein, apo, oxidised holo and reduced holo, all bind the designed (ATGAcgATGA) target DNA sequence with a dissociation constant, K_D, of approximately 90 nM. The protein has a lower affinity (K_Dca. 370 nM) for the wild-type GCN4 recognition sequence (ATGAcTCAT). The presence of only half the consensus DNA sequence (ATGAcgGGCC) shifts the K_Dvalue to more than 2500 nM and the chimera does not bind specifically to DNA sequences with no target recognition sites. Ultracentrifugation revealed that the holoprotein–DNA complex is formed with a 1:1 stoichiometry, which indicates that a higher-order protein aggregate is not responsible for DNA binding. Mutagenesis of a loop linking helices 2 and 3 of the cytochrome results in a chimera with a haem-dependent DNA binding affinity. This is the first demonstration that binding of a haem group to a designed monomeric protein can allosterically modulate the DNA binding affinity.