Astbury Centre for Structural Molecular Biology

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Annual Report 2000
© University of Leeds 2001

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Front cover illustration:
RNA aptamer complexed to MS2 bacteriophage coat protein The image shows an RNA aptamer molecule (gold), corresponding to a stem-loop structure, complexed to two coat protein subunits (blue and green) of the icosahedral bacteriophage MS2. The structure was determined by X-ray crystallography using synchrotron radiation collected at the Daresbury Laboratory (UK) and the ESRF (Grenoble, France). The two subunits shown correspond to a small part of the spherical virus shell that consists of a total of 180 subunits. The view is from the inside of the virus and the RNA is clinging to the inside surface of the shell. The structure is one of a series determined to elucidate rules for protein-RNA recognition in the system.
Convery, M.A., Rowsell, S., Stonehouse, N.J., Ellington, A.D., Hirao, I., Murray, J.B., Peabody, D.S., Phillips, S.E.V. and Stockley, P.G. (1998) "The crystal structure of an RNA aptamer-protein complex at 2.8 resolution" Nature Struct. Biol., 5, 133-139.
Rowsell, S., Stonehouse, N.J., Convery, M.A., Adams, C.J., Ellington, A.D., Hirao, I., Peabody, D.S., Stockley, P.G. and Phillips, S.E.V. (1998) "Crystal structures of a series of RNA aptamers complexed to the same protein target" Nature Struct. Biol., 5, 970-975.

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 Walker for her hard work in collating and type-setting this report.

 

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

The Astbury Centre for Structural Molecular Biology (ACSMB) is an interdisciplinary research centre of the University of Leeds. It was 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 itself. 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 (a and b), 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.

The ACSMB today continues this tradition and focuses on the determination of the atomic structures of biological macromolecules using all of the current major techniques (X-ray diffraction, nuclear magnetic resonance spectroscopy and electron microscopy). ACSMB also specialises in new biophysical techniques such as measuring the mechanical folding properties of individual protein molecules using atomic force microscopy. These studies are combined with analyses of biological function with the ultimate aim of understanding the molecular basis of life itself. During the year, ACSMB was designated a Marie Curie Research Training Centre by the European Union, allowing young scientists from all over Europe to visit us and receive training in our structural techniques.

Structural molecular biology plays a pivotal role in modern biology, both in the fundamental understanding of living things and in the design of new treatments for disease. It is currently undergoing a revolution in both scale and scope. The publication of the human genome sequence holds out the prospect of using structural molecular biology techniques to determine the exact molecular structure of every protein in our bodies. New drugs are frequently designed by analysing the molecular structures of the proteins they target, so this promises to generate dramatic advances in healthcare. It is notable that the original observation by Astbury of transitions in fibrous proteins between a and b forms remains relevant today since devastating amyloid diseases such as Alzheimer's, BSE and CJD are linked to such transitions in brain proteins.

In the pages that follow, you will find highlights of our work over the last year. The reports have largely been written by our younger researchers, whose enthusiasm for their work augurs well for our future. Noteworthy examples include the first observation of the beginning of the power stroke in myosin, the motor protein that drives muscle, the structure determination of RNA polymerase from Hepatitis C as a target for antiviral drug design, elucidation of the interaction of the E. coli O157 verotoxin B with its receptor and new insights into amyloid formation. These brief reports, 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 9MB PDF document which can download.

Simon E.V. Phillips
Director, Astbury Centre for Structural Molecular Biology
Leeds, February 2001

 

INDEX

Ashcroft - Mass spectrometry facility

Baldwin - Molecular studies on active nucleoside transport proteins

Baldwin - Purine transporters in human and protozoan parasites

Berry - Biophysical studies of the dynamics and mechanisms of Class II fructose 1,6- bisphosphate aldolase

Berry - Protein engineering of aldolase and the sialic acid synthesising enzymes

Findlay - Structure-function analysis of G protein- coupled receptors

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

Harris - Structural and functional studies on Hepatitis C virus non-structural proteins

Henderson - Investigation of the ligand binding site in the glucuronide-H+ symporter, GusB, in Escherichia coli using chemical and solid state NMR spectroscopy approaches

Homans - The NMR Facility

Homans - NMR studies of the structure of the Verotoxin B subunit from E. coli 0157 with its REceptor Gb3 26

Homans - The structure of Mycobacterium tuberculosis lipoarabinomannan (LAM)

Homans - Efficient resonance assignment and global fold determination of backbone labelled proteins

Jager - Subtle changes in the fingers domain of DNA polymerase: influences nucleotide discrimination and fidelity

Jager - The crystal structure of Hepatitis C virus RNA polymerase complexed with nucleotides and metal ions

Johnson - Further development and applications of computer programs for de novo ligand design.

Keen - Proteomics and allied technologies

Nelson - A general, two-directional synthesis of C-alpha(1® 6)-linked disaccharides

Phillips - Biology of bacterial peptidoglycan synthesis

Phillips - Crystallographic studies of copper amine oxidase

Phillips - Crystal Structure of the Holliday junction-resolving enzyme T7 endonuclease 1 at 2.1Å resolution

Phillips - Structural determination of a chemically modified RNA translation operator complexed with bacteriophage MS2 coat protein

Phillips - Structural studies of AhrC, the arginine activator/repressor from Bacillus subtilis

Phillips - Structural studies of processing in galactose oxidase

Ponnambalam - Control of peripheral and integral membrane protein localisation in eukaryotes

Radford - Biophysical studies of the beta2-microglobulin amyloid formation

Radford - Searching for the native structure

Radford - Single molecule techniques in protein folding

Smith - Fast folding kinetics of apomyoglobin initiated by a nanosecond temperature jump

Smith - Single molecule spectroscopy to probe folding of individual proteins

Stockley - Reflection-selection of RNA aptamers

Stockley - RNA-protein recognition/virus assembly

Stockley - Transcriptional control

Stonehouse - Molecular interactions in the assembly of bacteriophage O 29

Thomas - Replication and maintenance of Staphylococcal plasmids

Thomson - Atomic force microscopy of protein-protein and DNA-protein interactions

Trinick - Titin project

Trinick - Myosin V project

Westhead - Bioinformatics of macromolecular sequence and structure

Astbury Seminars 2000