Astbury Centre for Structural Molecular Biology

EM and schematic of dynein motion

Annual Report 2002
© University of Leeds 2003

Astbury logo


Front cover illustration:
The power stroke of the dynein molecular motor.
The left panel shows a superposition of two conformational states of dynein seen for the first time before and after its power stroke. These conformations were produced by the presence and absence respectively of ADP.vanadate. The molecule consists of an elongated stem and stalk connected to a ring-like head. The arrow indicates that a 15 nm displacement of the tip of the stalk is apparent when the other parts are superposed. The images were generated by negative stain electron microscopy, followed by single-particle image processing. This isoform of dynein was purified from flagella of the alga Chlamydomonas reinhardtii in the laboratory of Dr K. Oiwa, KARC, Kobe, Japan.

The right panel shows a new model of the dynein structure and how it interacts with its microtubule track (microtubule not drawn to scale). The model combines the new image data with the domain structure deduced from dynein sequences. Four highly-conserved AAA domains are indicated, the first of which is the site of ATP hydrolysis. The ATP-sensitive microtubule-binding domain is at the tip of the anti-parallel coiled coil stalk, 28 nm away.

Burgess, S.A., Walker, M.L., Sakakibara, H., Knight, P.J. and Oiwa, K. (2003) “Dynein structure and power stroke” Nature, 421, 715-718.

Acknowledgement

The Astbury Centre for Structural Molecular Biology thanks its many sponsors for support of the work, its members for writing these reports and Jenny Gilmartin for her hard work in collating and type-setting this report. The report is edited by Alan Berry.

This report is also available electronically via http://www.astbury.leeds.ac.uk


Mission Statement

The Astbury Centre for Structural Molecular Biology will promote interdisciplinary research of the highest standard on the structure and function of biological molecules, biomolecular assemblies and complexes using physico-chemical, molecular biological and computational approaches.

Introduction

It is once again a great privilege as the Director of the Astbury Centre for Structural Molecular Biology (ACSMB) to write the introduction to our Annual Report (2002). The ACSMB is an interdisciplinary research centre of the University of Leeds founded in 1999 to carry out research in all aspects of structural molecular biology. ACSMB brings together over fifty academic staff from the faculties of Biological Sciences, Chemistry, Physics and Medicine to examine the molecular mechanisms of life. It is named after W.T. (Bill) Astbury, a biophysicist who laid many of the foundations of the field during a long research career at the University of Leeds (1928-1961). Astbury originally identified the two major recurring patterns of protein structure (alpha and beta), took the first X-ray fibre diffraction pictures of DNA (in 1938) and is widely credited with the definition of the field of molecular biology. As I write in 2003, we are celebrating the 50th anniversary of the publication of the double helical structure of DNA by the Cambridge and King’s College, London groups, a result that put molecular descriptions at the heart of all Biology. The explosive progress that has occurred following this structural insight fully illustrates Astbury’s vision of the new field. As an outsider to the dramatic developments that occurred in our field in 1953, it has always struck me as significant that progress was the result of interdisciplinary interactions. Careful and painstaking experimental work by Franklin, Wilkins and their colleagues, coupled to the relatively new theory behind helical diffraction (Crick & Stokes), together with the deep understanding that the structure must say something profound about genetics (Watson) came together, sometimes controversially, to yield the “big picture”. I believe that ACSMB continues to provide an excellent interdisciplinary environment for continued progress to be made. I’m sure that the pages that follow show ample proof that this is the case.

This report describes some of the highlights of our work over the last year. These reports have largely been written by our younger researchers. Their tremendous enthusiasm for this kind of interdisciplinary work augurs well for our future. I was particularly struck by the breadth of activity in the Centre ranging from the sophisticated applications of synthetic organic chemistry to the developments in single molecule biophysics. In between these extremes you will find groundbreaking activity in many traditional areas for structural biology. ACSMB has always been outward looking and this tradition continues with the many external collaborations acknowledged in these pages, both from within the UK and beyond. We would welcome discussions with anyone wishing to collaborate or simply to make use of our facilities, the details of which can be found on our web page (http://www.astbury.leeds.ac.uk/).

These brief summaries, however, only scratch the surface of the work of the Centre. I hope you enjoy reading them, and if you wish to learn more please visit our website or contact the Director.

This annual report is also available as a 7.25MB PDF document that can be downloaded.

Peter G. Stockley
Director, Astbury Centre for Structural Molecular Biology
Leeds, May 2003

INDEX TO THE 2002 REPORT

Ashcroft - Mass spectrometry facility

Ashcroft - Protein structure and aggregation studied by mass spectrometry

Baldwin - Bacterial nucleoside transporters as models for mammalian transporters of chemotherapeutic nucleoside drugs

Baldwin - Structure and cell biology of a membrane trafficking complex - the exocyst

Baron - Analytical centrifuge facility

Berry - Directed evolution of aldolase

Berry - Partial sequential resonance assignment of the 78kDa Class II fructose-1,6-bisphosphate aldolase and investigation of its dynamics

Donnelly - Structure/function studies of glucagon-like peptide-1 and exendin 4

Harris - Structural and functional studies on the Hepatitis C virus non-structural NS5A protein

Harris - Structural and functional studies on the HIV-1 Nef protein

Hewitt - The transporter associated with antigen processing (TAP)

Homans - Derivation of per-residue thermodynamic parameters for ligand-protein interactions

Homans - Dissecting the cholera toxin-ganglioside GM1 interaction by isothermal titration calorimetry

Homans - Molecular dynamics in mouse urinary protein by NMR methods

Homans, Henderson and Herbert - Solution state NMR studies on a large alpha-helical membrane protein

Homans - The NMR solution structure of the VMA-7 subunit of the vacuolar H+-ATPase from Saccharomyces cerevisiae

Jackson - A new method for comparing lignad binding sites in biomolecules

Jackson - Analysis of SH2 domain phosphopeptide interactions

Jackson - Q-fit: A method for docking molecular fragments by sampling low energy conformational space

Jaeger - Crystallographic studies of (+) strand RNA-directed RNA polymerases

Jaeger - Functional analysis of nucleotide import in Hepatitis C virus RNA polymerase

Jaeger - Structural determinants of polymerase fidelity and nucleotide discrimination in mammalian DNA pol beta

Keen - Proteomics and allied technologies

Knight - Dynein structure and power stroke

McDowall - An essential activity at the centre of a macromolecular machine

McPherson - Cofactor processing in galactose oxidase

Nelson - Macrocyclic bisindoylmaleimides: synthesis, conformation and potential as tools for studying protein kinases

Phillips - Crystal structure of a catalytically impaired mutant of T7 endonuclease I (K67A) that retains the ability to bind metal ions

Phillips - Crystal structures of MS2 and Qbeta RNA stemloop operators complexed with a bacteriophage MS2 coat protein mutant

Ponnambalam - Regulation of membrane protein function in human blood vessel formation

Radford - Biophysical studies of beta2-microglobulin amyloid formation

Radford - Characterisation of amyloid fibrils by atomic force microscopy

Radford - Characterising the factors that describe the mechanical resistance of proteins

Radford - Transition states and intermediates in the folding of the four-helix bundle proteins Im7 and Im9

Rowlans - Targeting the Hepatitis C virus ion channel p7 for anti-viral therapy

Smith - Single molecule spectroscopy to probe folding of individual proteins

Stockley - In vitro studies of MetJ structure-function relationships

Stockley - Microarray studies of gene expression in the methionine biosynthetic pathway of Escherichia coli

Stockley - Protein-RNA interactions and virus assembly studied by mass spectrometry

Stockley - Small molecular weight mimics of MetJ

Stonehouse - Molecular interactions in the bacteriophage phi29 DNA packaging motor

Thomas - New crystals of replication initiator proteins

Thomas - Molecular mechanism of Staphylococcal plasmid transfer

Thomas - Dimerisation determinants of replication initiator proteins

Thomson - Atomic force microscopy of DNA-protein interactions

Trinick - The force producing mechanism of myosin

Trinick - Self-association properties of the elastic region of the giant protein titin

Westhead - Application of machine learning methods to aggregation, protein structure and SNP data

Westhead - Automated metabolic reconstruction from genomic DNA

Westhead - Derivation and refinement of global sequence motifs for the integral membrane proteins

Westhead - Protein surface descriptions and function

Astbury Seminars 2002

Last year's report (2001) is still available as a large pdf file - download here.