Dr Steven Hayward
| Job Title | Contact | Location |
|---|---|---|
| Senior Lecturer |
Steven dot Hayward at uea dot ac dot uk
Tel: +44 (0)1603 59 3542 |
Biology 2.14 |
Key Research Interests
The general area of my research concerns conformational change in proteins and protein structure. In particular I am interested in the relationship between the two. We use various computational methods including, biogeometry, molecular dynamics simulation, and bioinformatics based approaches.
A main focus concerns domain motions in enzymes. Using molecular dynamics simulation we have shown that for some enzymes a domain-locking mechanism operates which keeps domains open in the absence of a functional ligand. The exact nature and purpose of the locking mechanism in alcohol dehydrogenase was elucidated recently.
Another thread of my research on domain proteins concerns the creation of a database of protein domain movements based on my DynDom software (see http://www.cmp.uea.ac.uk/dyndom). This is the foremost database for protein domain motions and forms the foundation to a bioinformatics based approaches to understanding protein conformational change.
We have recently become interested in the little known secondary structure α-sheet which was a structure predicted by Pauling and Corey in 1951 but hardly found in proteins at all. However, recently interest in this “poor cousin” has been rekindled by the finding that it may be involved in amyloid diseases such as Alzheimer’s disease, Parkinson’s Huntington’s, Type II diabetes and the prion diseases such as BSE (mad cow). We were the first to calculate the geometrical properties of a strand of α-sheet.
Steven Hayward is part of the Computational Biology Group
PhD Projects
The following opportunity exists to pursue a PhD with Dr. Hayward on the project:
Mechanisms of Domain Closure in Enzymes
Selected Publications
Hayward, S. and Milner-White, E.J., The geometry of alpha-sheet: Implications for its possible function as amyloid precursor in proteins. Proteins-Structure, Function and Bioinformatics, Volume 71, Number 1, Page(s) 415 - 425, 2008.
Hayward, S. and Kitao, A., Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase. Biophysical Journal, Volume 91, Issue 5, Page(s) 1823-1831, 2006.
Qi, G., Lee, R., and Hayward, S., A comprehensive and non-redundant database of protein domain movements. Bioinformatics, Volume 21, Number 12, Page(s) 2832-2838, 2005.
Hayward, S., Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements. Journal of Molecular Biology, Volume 339, Issue 4, Page(s) 1001-1021, 2004.
List all publications by Dr Steven Hayward (Eprints)Collaborators
Dr A. Kitao, University of Tokyo
Dr H. Ishida, Japan Atomic Energy Agency
Professor K. Yura, Ochanomizu University
Professor J. Milner-White, Glasgow
Dr Danilo Roccatano, Jakobs University, Germany
Dr Bert de Groot, Max Planck Institute for Biophysical Chemistry
Professor A. Day, UEA
Dr S. Laycock, UEA
Dr. A. Matumoto, Japan Atomic Energy Agency
Research Group Members
Current members
Mr Daniel Taylor
Past members
Dr Guoying Qi
Dr Guru Poornam
Dr Catherine Snow
Past Research Projects and Grants
| Project Title | Start Date | End Date | Funding Body | Project Members |
|---|---|---|---|---|
| Advancing Machine Learning Methodology for New Classes of Prediction Problems | 25/2/2008 | 24/2/2011 | EPSRC | Steven Hayward, Gavin Cawley, Geoff Moore |
| Changes in protein hydration structure during ligand-driven domain closure | 1/4/2007 | 30/9/2007 | Royal Society | N/A |
| Understanding ligand-induced domain closure in proteins | 27/6/2005 | 26/6/2008 | BBSRC | N/A |
| Predicting protein disorder with advanced machine learning tools | 1/9/2004 | 31/8/2005 | MRC (Medical Research Council) | Steven Hayward, Gavin Cawley, Geoff Moore |
| Understanding and predicting protein domain motions using a new database | 1/9/2001 | 31/8/2003 | EPSRC | Steven Hayward, Moe Razaz, Richard Lee |
| JIF: Biophysical Chemistry at UEA | 1/6/2001 | 31/12/2006 | Wellcome Trust | Steven Hayward, Andrew Hemmings, David Richardson, Nick Watmough, Andrew Thomson, Julea Butt, Myles Cheesman, Geoff Moore, Nick Le Brun |
Article
Hayward, S and James Milner-White, E (2011) Simulation of the β- to α-sheet transition results in a twisted sheet for antiparallel and an α-nanotube for parallel strands: Implications for amyloid formation. Proteins: Structure, Function, and Bioinformatics. n/a-n/a. ISSN 08873585 (In Press)
Stocks, Matthew, Laycock, Stephen and Hayward, Steven (2011) Applying forces to elastic network models of large biomolecules using a haptic feedback device. Journal of Computer-Aided Molecular Design, 25 (3). pp. 203-211.
Hayward, S. and Kitao, A. (2010) Effect of end constraints on protein loop kinematics. Biophysical Journal, 98 (9). pp. 1976-1985.
Stocks, Matthew B., Hayward, Steven and Laycock, Stephen D. (2009) Interacting with the biomolecular solvent accessible surface via a haptic feedback device. BMC Structural Biology, 9. p. 69. ISSN 1472-6807
Poornam, Guru Prasad, Matsumoto, Atsushi, Ishida, Hisashi and Hayward, Steven (2009) A method for the analysis of domain movements in large biomolecular complexes. Proteins: Structure, Function, and Bioinformatics, 76 (1). pp. 201-212. ISSN 0887-3585
Nishima, W., Qi, G., Hayward, S. and Kitao, A. (2009) DTA: Dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins. Bioinformatics, 25 (5). pp. 628-635.
Qi, Guoying and Hayward, Steven (2009) Database of ligand-induced domain movements in enzymes. BMC Structural Biology, 9. p. 13. ISSN 1472-6807
Yura, K. and Hayward, S. (2009) The interwinding nature of protein-protein interfaces and its implication for protein complex formation. Bioinformatics, 25 (23). pp. 3108-3113. ISSN 1367-4803
Hayward, S and Milner-White, EJ (2008) The geometry of alpha-sheet: Implications for its possible function as amyloid precursor in proteins. Proteins: Structure, Function, and Bioinformatics, 71 (1). 415 - 425. ISSN 0887-3585
Ishida, H. and Hayward, S. (2008) Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome. Biophysical Journal, 95 (12). pp. 5962-5973.
Snow, Catherine, Qi, Guoying and Hayward, Steven (2007) Essential dynamics sampling study of adenylate kinase: Comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions. Proteins-Structure Function and Bioinformatics, 67 (2). pp. 325-337. ISSN 1097-0134
Hayward, Steven and Kitao, Akio (2006) Molecular dynamics simulations of NAD(+)-induced domain closure in horse liver alcohol dehydrogenase. Biophysical Journal, 91 (5). pp. 1823-1831.
Milner-White, J. E., Watson, J. D., Qi, G. and Hayward, S. (2006) Amyloid Formation May Involve α- to β Sheet Interconversion via Peptide Plane Flipping. Structure, 14 (9). pp. 1369-1376. ISSN 0969-2126
Qi, Guoying, Lee, Richard and Hayward, Steven (2005) A comprehensive and non-redundant database of protein domain movements. Bioinformatics, 21 (12). pp. 2832-2838.
Daidone, Isabella, Roccatano, Danilo and Hayward, Steven (2004) Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling. Journal of Molecular Biology, 339 (3). pp. 515-525. ISSN 0022-2836
Hayward, Steven (2004) Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements. Journal of Molecular Biology, 339 (4). pp. 1001-1021. ISSN 0022-2836
Lee, Richard, Razaz, Moe and Hayward, Steven (2003) The DynDom database of protein domain motions. Bioinformatics, 19 (10). pp. 1290-1291. ISSN 1367-4803
Hayward, Steven and Lee, Richard A. (2002) Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. Journal of Molecular Graphics and Modelling, 21 (3). pp. 181-183. ISSN 1093-3263
Hayward, Steven (2001) Peptide-Plane Flipping in Proteins. Protein Science, 10 (11). pp. 2219-2227. ISSN 1469-896X
Roccatano, Danilo, Mark, Alan E. and Hayward, Steven J. (2001) Investigation of the Mechanism of Domain Closure in Citrate Synthase by Molecular Dynamics Simulation. Journal of Molecular Biology, 301 (5). pp. 1039-1053. ISSN 0022-2836
Berendsen, H. J. C. and Hayward, S. (2000) Collective protein dynamics in relation to function. Current Opinions in Structural Biology, 10 (2). pp. 165-169. ISSN 0959-440X
Hayward, S. (1999) Structural Principles Governing Domain Motions in Proteins. Proteins, Structure, Function and Genetics, 36 (4). pp. 425-435.
Hayward, S. and Berendsen, H. J. C. (1998) Systematic Analysis of Domain Motions in Proteins from Conformational Change: New Results on Citrate Synthase and T4 Lysozyme. Proteins, Structure, Function and Genetics, 30 (2). pp. 144-154.
Kitao, A., Hayward, S. and Go, N. (1998) Energy Landscape of a Native Protein : Jumping-Among-Minima Model. Proteins, Structure, Function and Genetics, 33 (4). pp. 496-517.
de Groot, B.L., Hayward, S., van Aalten, V., Amadei, A. and Berendsen, H.J.C. (1998) Domain Motions in Bacteriophage T4 Lysozyme; a Comparison between Molecular Dynamics and Crystallographic Data. Proteins, Structure, Function and Genetics, 31 (2). pp. 116-127.
Hayward, S., Kitao, A. and Berendsen, H. J. C. (1997) Model-Free Methods of Analyzing Domain Motions in Proteins from Simulation: A Comparison of Normal Mode Analysis and Molecular Dynamics Simulation of Lysozyme. Proteins: Structure, Function, and Bioinformatics, 27 (3). pp. 425-437. ISSN 0887-3585
van der Spoel, D., de Groot, B.L., Hayward, S., Berendsen, H.J.C. and Vogel, H.J. (1996) Bending of the Calmodulin Central Helix: A Theoretical Study. Protein Science, 5 (10). pp. 2044-2053.
Hayward, Steven and Gō, Nobuhiro (1995) Collective Variable Description of Native Protein Dynamics. Annual Review in Physical Chemistry, 46. pp. 223-250.
Hayward, S., Kitao, A. and Go, N. (1995) Harmonicity and Anharmonicity in Protein Dynamics: A Normal Mode Analysis and Principal Component Analysis. Proteins, Structure, Function and Genetics, 23 (2). pp. 177-186.
Kitao, Akio, Hayward, Steven and Go, Nobuhiro (1994) Comparison of Normal Mode Analysis on a Small Globular Protein in Dihedral Angle Space and Cartesian Coordinate Space. Biophysical Chemistry, 52 (2). pp. 107-114. ISSN 0301-4622
Hayward, Steven, Kitao, Akio and Gō, Nobuhiro (1994) Harmonic and Anharmonic Aspects in the Dynamics of BPTI: A Normal Mode Analysis and Principal Component Analysis. Protein Science, 3 (6). pp. 936-943. ISSN 1469-896X
Hayward, S., Kitao, A., Hirata, F. and Go, N. (1993) Effect of Solvent on the Collective Motions in Globular Protein. Journal of Molecular Biology, 234. pp. 1207-1217.
Hayward, S. and Collins, J. F. (1992) Limits on Alpha-Helix Prediction with Neural Network Models. Proteins: Structure, Function, and Bioinformatics, 14 (3). pp. 372-381. ISSN 0887-3585
Hayward, S., Heermann, D. W. and Binder, K. (1987) Dynamic Percolation Transition Induced by Phase Separation: A Monte Carlo Analysis. Journal of Statistical Physics, 49 (5-6). pp. 1053-1081. ISSN 0022-4715
Book Section
Hayward, S and de Groot, B (2008) Normal Modes and Essential Dynamics. In: Molecular Modeling of Proteins. Methods in Molecular Biology, 443 . The Humana Press Inc, USA, pp. 89-106. ISBN 978-1-59745-177-2
Hayward, Steven (2001) Normal Mode Analysis of Biological Molecules. In: Computational Biochemistry and Biophysics. Marcel Dekker, New York, pp. 153-168. ISBN 978-0824704551
Hayward, S., Kitao, A., Hirata, F. and Go, N. (1993) The Effect of Water on the Low Frequency Motions in BPTI. In: Computer Aided Innovation of New Materials II. Elsevier Science Publications B.V..
Conference or Workshop Item
Laycock, S.D., Stocks, M.B. and Hayward, S. (2010) Navigation and exploration of large data-sets using a haptic feedback device. In: ACM Siggraph: Posters.
External Activities and Indicators of Esteem
- Regular invited speaker: Workshop on Molecular Theories and Simulations, Gaeta, Italy, May 2002-6
- Invited speaker: Theory and simulation of biomolecular nano-machines International Conference, Kobe, Japan 2006
- Visiting scientist: Information Technology Based Laboratory (ITBL), Japanese Atomic Energy Agency (JAEA), Kizu, Japan, 2003 and 2007
