Dr Jane Allison staff profile picture

Contact details +64 (09) 414 0800  ext. 43617

Dr Jane Allison

Senior Lecturer

Institute of Natural and Mathematical Sciences

I obtained a BSc (Hons) in Biochemistry from the University of Canterbury in 2003, conducting my Honours research and spending the subsequent year as a research assistant in the protein biochemistry laboratory of Prof. Juliet Gerrard. After being awarded one of the inaugural Woolf Fisher scholarships, I moved to the UK in 2004 to study towards a PhD with Prof. Chris Dobson in the Department of Chemistry at Cambridge University. Upon completing my PhD in late 2007 I moved to Zürich, Switzerland to work as a postdoctoral research assistant in the computer-aided chemistry group of Prof. Wilfred van Gunsteren at the ETH. In January 2012, I took up a Lectureship at Massey University, where I am also a member of the Centre for Theoretical Chemistry and Physics. I am also an Associate Investigator with the Biomolecular Interaction Centre at the University of Canterbury, and with the Maurice Wilkins Centre for Molecular Biodiscovery. In 2015, I was awarded a Rutherford Discovery Fellowship from the Royal Society of New Zealand.

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Professional

Contact details

  • Ph: +64 9 414 0800 extn. 41451
    Location: 11, Building 14
    Campus: Oteha Rohe

Qualifications

  • Doctor of Philosophy - Cambridge University (2008)
  • Bachelor of Science with 1st Class Honours - University of Canterbury (2003)

Research Expertise

Research Interests

My research involves the development and application of computational methods for exploring the conformational dynamics of proteins. Investigating the relationship between the physico-chemical nature of biological molecules and their behaviour, in terms of structure, dynamics and thermodynamics, is crucial for understanding the function and malfunction of biological systems. Computer simulations are extremely valuable for probing these aspects at both the detailed molecular and ensemble level, as well as uniquely allowing direct and simultaneous visualisation of structure and dynamics.

Area of Expertise

Field of research codes
Biochemistry and Cell Biology (060100): Biological Sciences (060000):
Biomolecular Modelling and Design (030402): Characterisation of Biological Macromolecules (030403): Chemical Science (030000): Medicinal and Biomolecular Chemistry (030400): Physical Chemistry (incl. Structural (030600): Proteins and Peptides (030406):
Structural Biology (incl. Macromolecular Modelling) (060112):
Theoretical and Computational Chemistry (030700)

Keywords

Biomolecular Modelling

Molecular Dynamics Simulations

Protein Biochemistry

Structural Biology

Computational Chemistry

Research Projects

Summary of Research Projects

Position Current Completed
Project Leader 2 5

Current Projects

Project Title: Rutherford Discovery Fellowship - Deciphering molecular choreography

Date Range: 2016 - 2021

Funding Body: Royal Society of New Zealand

Project Team:

Project Title: Probing the protein membrane interface of an oncogenic cell signalling system

Date Range: 2016 - 2019

Funding Body: University of Auckland

Project Team:

Completed Projects

Project Title: Summer Student Scholarship 2013 - 2014: Making movies of membranes

Biomolecules, the molecules from which organisms are built, are inherently dynamic, undergoing structural changes at a range of scales that are critical to their function. Characterising how biomolecules move is therefore essential to understanding how biological entities work. Additionally, many diseases are caused by these molecules forming incorrect structures and failing to carry out their function, hence by understanding both normal and abnormal biomolecular dynamics, effective strategies for combating disease can be developed. Computer simulations are a very useful tool for investigating how biomolecules move: essentially, they allow "movies" to be made that show how the atoms in these molecules move around. Existing computer models are rather detailed and therefore computationally expensive, so only small-scale motion of single molecules can be investigated. One way of overcoming these limitations is to use detailed models for the molecules that are of most interest, and less detailed ("coarse-grained") and computationally cheaper models for their surroundings. The aim of this summer student project is to take a by creating such coarse-grained models for the molecules that make up cell membranes.
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Date Range: 2013 - 2014

Funding Body: Massey University

Project Team:

Research Outputs

Journal

Wirz, LN., & Allison, JR. (2017). Block-restraining of residual dipolar couplings to allow fluctuating relative alignments of molecular subdomains. Progress in Biophysics and Molecular Biology. 128, 133-141
[Journal article]Authored by: Allison, J.
Allison, JR. (2017). Using simulation to interpret experimental data in terms of protein conformational ensembles. Current Opinion in Structural Biology. 43, 79-87
[Journal article]Authored by: Allison, J.
Lee, J., Joshi, N., Pasini, R., Dobson, RCJ., Allison, J., & Leustek, T. (2016). Inhibition of Arabidopsis growth by the allelopathic compound azetidine-2-carboxylate is due to the low amino acid specificity of cytosolic prolyl-tRNA synthetase. Plant Journal. 88(2), 236-246
[Journal article]Authored by: Allison, J.
van Gunsteren, WF., Allison, JR., Daura, X., Dolenc, J., Hansen, N., Mark, AE., . . . Smith, LJ. (2016). Deriving Structural Information from Experimentally Measured Data on Biomolecules. Angewandte Chemie - International Edition. 55(52), 15990-16010
[Journal article]Authored by: Allison, J.
Zare, D., Allison, JR., & McGrath, KM. (2016). Molecular Dynamics Simulation of β-Lactoglobulin at Different Oil/Water Interfaces. Biomacromolecules. 17(5), 1572-1581
[Journal article]Authored by: Allison, J.
Allison, JR. (2016). Let the Powers Combine. Structure. 24(1), 5-6
[Journal article]Authored by: Allison, J.
Allison, JR., Lechner, M., Hoeppner, MP., & Poole, AM. (2016). Positive selection or free to vary? Assessing the functional significance of sequence change using molecular dynamics. PLoS ONE. 11(2)
[Journal article]Authored by: Allison, J.
Pichugina, T., Sugawara, T., Kaykov, A., Schierding, W., Masuda, K., Uewaki, J., . . . O'Sullivan, JM. (2016). A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe. Scientific Reports. 6
[Journal article]Authored by: Allison, J.
Wirz, LN., & Allison, JR. (2015). Comment on "a Tensor-Free Method for the Structural and Dynamic Refinement of Proteins using Residual Dipolar Couplings". Journal of Physical Chemistry B. 119(25), 8223-8224
[Journal article]Authored by: Allison, J.
Zare, D., McGrath, KM., & Allison, JR. (2015). Deciphering β-lactoglobulin interactions at an oil-water interface: A molecular dynamics study. Biomacromolecules. 16(6), 1855-1861
[Journal article]Authored by: Allison, J.
Wirz, LN., & Allison, JR. (2015). Fitting alignment tensor components to experimental RDCs, CSAs and RQCs. Journal of Biomolecular NMR. 62(1), 25-29
[Journal article]Authored by: Allison, J.
Allison, JR., Rivers, RC., Christodoulou, JC., Vendruscolo, M., & Dobson, CM. (2014). A relationship between the transient structure in the monomeric state and the aggregation propensities of α-synuclein and β-synuclein. Biochemistry. 53(46), 7170-7183
[Journal article]Authored by: Allison, J.
Grand, RS., Pichugina, T., Gehlen, LR., Jones, MB., Tsai, P., Allison, JR., . . . O'Sullivan, JM. (2014). Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure. Nucleic acids research. 42(20), 12585-12599
[Journal article]Authored by: Allison, J., Jones, M.
Smith, LJ., Roby, Y., Allison, JR., & Van Gunsteren, WF. (2013). Molecular dynamics simulations of barley and maize lipid transfer proteins show different ligand binding preferences in agreement with experimental data. Biochemistry. 52(30), 5029-5038
[Journal article]Authored by: Allison, J.
Hansen, N., Allison, JR., Hodel, FH., & Van Gunsteren, WF. (2013). Relative free enthalpies for point mutations in two proteins with highly similar sequences but different folds. Biochemistry. 52(29), 4962-4970
[Journal article]Authored by: Allison, J.
Smith, LJ., Van Gunsteren, WF., & Allison, JR. (2013). Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12. Protein Science. 22(1), 56-64
[Journal article]Authored by: Allison, J.
Müller, MM., Allison, JR., Hongdilokkul, N., Gaillon, L., Kast, P., van Gunsteren, WF., . . . Hilvert, D. (2013). Directed Evolution of a Model Primordial Enzyme Provides Insights into the Development of the Genetic Code. PLoS Genetics. 9(1)
[Journal article]Authored by: Allison, J.
Allison, JR. (2012). Assessing and refining molecular dynamics simulations of proteins with nuclear magnetic resonance data. Biophysical Reviews. 4(3), 189-203
[Journal article]Authored by: Allison, J.
Allison, JR., Hertig, S., Missimer, JH., Smith, LJ., Steinmetz, MO., & Dolenc, J. (2012). Probing the structure and dynamics of proteins by combining molecular dynamics simulations and experimental NMR data. Journal of Chemical Theory and Computation. 8(10), 3430-3444
[Journal article]Authored by: Allison, J.
Kleinjung, J., Scott, WRP., Allison, JR., Van Gunsteren, WF., & Fraternali, F. (2012). Implicit solvation parameters derived from explicit water forces in large-scale molecular dynamics simulations. Journal of Chemical Theory and Computation. 8(7), 2391-2403
[Journal article]Authored by: Allison, J.
Steiner, D., Allison, JR., Eichenberger, AP., & Van Gunsteren, WF. (2012). On the calculation of <sup>3</sup>Jαβ-coupling constants for side chains in proteins. Journal of Biomolecular NMR. 53(3), 223-246
[Journal article]Authored by: Allison, J.
Riniker, S., Allison, JR., & Van Gunsteren, WF. (2012). On developing coarse-grained models for biomolecular simulation: A review. Physical Chemistry Chemical Physics. 14(36), 12423-12430
[Journal article]Authored by: Allison, J.
Kunz, APE., Allison, JR., Geerke, DP., Horta, BAC., Hünenberger, PH., Riniker, S., . . . Van Gunsteren, WF. (2012). New functionalities in the GROMOS biomolecular simulation software. Journal of Computational Chemistry. 33(3), 340-353
[Journal article]Authored by: Allison, J.
Allison, JR., Riniker, S., & Van Gunsteren, WF. (2012). Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol. Journal of Chemical Physics. 136(5)
[Journal article]Authored by: Allison, J.
Schmid, N., Allison, JR., Dolenc, J., Eichenberger, AP., Kunz, APE., & Van Gunsteren, WF. (2011). Biomolecular structure refinement using the GROMOS simulation software. Journal of Biomolecular NMR. 51(3), 265-281
[Journal article]Authored by: Allison, J.
Eichenberger, AP., Allison, JR., Dolenc, J., Geerke, DP., Horta, BAC., Meier, K., . . . Van Gunsteren, WF. (2011). GROMOS++ software for the analysis of biomolecular simulation trajectories. Journal of Chemical Theory and Computation. 7(10), 3379-3390
[Journal article]Authored by: Allison, J.
Allison, JR., Boguslawski, K., Fraternali, F., & Van Gunsteren, WF. (2011). A refined, efficient mean solvation force model that includes the interior volume contribution. Journal of Physical Chemistry B. 115(15), 4547-4557
[Journal article]Authored by: Allison, J.
Allison, JR., Bergeler, M., Hansen, N., & Van Gunsteren, WF. (2011). Current computer modeling cannot explain why two highly similar sequences fold into different structures. Biochemistry. 50(50), 10965-10973
[Journal article]Authored by: Allison, J.
Allison, JR., Müller, M., & Van Gunsteren, WF. (2010). A comparison of the different helices adopted by α- and β-peptides suggests different reasons for their stability. Protein Science. 19(11), 2186-2195
[Journal article]Authored by: Allison, J.
Allison, JR., Moll, GP., & Van Gunsteren, WF. (2010). Investigation of stability and disulfide bond shuffling of lipid transfer proteins by molecular dynamics simulation. Biochemistry. 49(32), 6916-6927
[Journal article]Authored by: Allison, J.
Allison, JR., Varnai, P., Dobson, CM., & Vendruscolo, M. (2009). Determination of the free energy landscape of α-synuclein using spin label nuclear magnetic resonance measurements. Journal of the American Chemical Society. 131(51), 18314-18326
[Journal article]Authored by: Allison, J.
Allison, JR., & Van Gunsteren, WF. (2009). A method to explore protein side chain conformational variability using experimental data. ChemPhysChem. 10(18), 3213-3228
[Journal article]Authored by: Allison, J.

Thesis

Allison, JR. (2008). Computational Methods for Characterising Disordered States of Proteins. (Doctoral Thesis, Cambridge University)
[Doctoral Thesis]Authored by: Allison, J.

Conference

Allison, JR. (2015, November). Supercalifragilisticexpialidocious: a magical approach to automated parameter optimisation. Presented at Molecular Graphics and Modelling Society Conference 2015. Singapore.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR. (2015, February). Statistically sound structural phylogenetics. Presented at Portobello '15 Phylogenomics. Portobello.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR. (2015, November). Simulate all the things! But how...?. Presented at Cluster Fest 2014. Great Barrier Island.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR. (2014, October). Variety is the spice of life: parameterise all the things!. Presented at BIC Computing Symposium. University of Canterbury, Christchurch.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR. (2014, April). Let the powers combine: Hybrid methods in structural biology. Presented at Crystal29. Lamington National Park.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR., & Wirz, L. (2014). Disorder and (dis)orientation. Poster session presented at the meeting of Molecular Modelling 2014. Lamington National Park
[Conference Poster]Authored by: Allison, J.
Allison, JR., & Wirz, L. (2014). Disorder and (dis)orientation. Poster session presented at the meeting of International Biophysics Congress. Brisbane
[Conference Poster]Authored by: Allison, J.
Allison, JR. (2013, September). Can Ensemble-Restrained Simulations Rationalise the Different Aggregation Propensities of Two Related Intrinsicaly Disordered Proteins?. Presented at CECAM workshop on "Intrinsically Disordered Proteins: Connecting Computation, Physics and Biology". ETH Zürich.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR. (2013, August). Alice in molecular-land: an evolutionary arms race in sequence and structure space. Presented at E3: Enzyme Engineering and Evolution. Queenstown.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR. (2013, May). Back to the future: lysozyme revisited. Presented at Retirement Symposium of Prof. Wilfred van Gunsteren. ETH Zürich.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR. (2012, August). Enhancing biomolecular simulations with experimental data (and vice versa). Presented at Molecular Modelling 2012. Queenstown.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR. (2012, April). What biomolecular modelling can (and cannot) do for you. Presented at BIC Symposium. University of Canterbury.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR. (2011, September). The art of coarse-graining. Presented at 21st International BIOMOS Symposium. Ausserberg.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR., & van Gunsteren, WF. (2011). Local elevation biasing of NMR 3J-couplings. Poster session presented at the meeting of 9th International NCCR Symposium on New Trends in Structural Biology. Zuerich, Switzerland
[Conference Poster]Authored by: Allison, J.
Allison, JR., & van Gunsteren, WF. (2011). Local elevation biasing of NMR 3J-couplings. Poster session presented at the meeting of 9th Triennial Congress of the World Association of Theoretical and Computational Chemists. Santiago de Compostela, Spain
[Conference Poster]Authored by: Allison, J.
Allison, JR. (2010, April). Overcoming frustration with local elevation: a method for enhancing biomolecular simulations biased with experimental data. Presented at Hünfeld Workshop on Computer Simulation and Theory of Macromolecules. Hünfeld, Germany.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR. (2010, September). The intriguing sensitivity of RDCs. Presented at 20th International BIOMOS Symposium. Burg Arras, Germany.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR., & van Gunsteren, WF. (2010). Exploring the information content of NMR 3J-couplings. Poster session presented at the meeting of 8th International NCCR Symposium on New Trends in Structural Biology. Zuerich, Switzerland
[Conference Poster]Authored by: Allison, J.
Allison, JR. (2009, September). What’s with RDCs? (What are they and what can we do with them?). Presented at 19th International BIOMOS Symposium. Burg Arras, Germany.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR., & van Gunsteren, WF. (2009). Clarifying the relationship between experimental data and structural properties of molecules. Poster session presented at the meeting of C4 Workshop, Novartis Institute for Biomedical Research. Basel, Switzerland
[Conference Poster]Authored by: Allison, J.
Allison, JR., & van Gunsteren, WF. (2009). Clarifying the relationship between experimental data and structural properties of molecules. Poster session presented at the meeting of Hünfeld Workshop on Computer Simulation and Theory of Macromolecules. Huenfeld, Germany
[Conference Poster]Authored by: Allison, J.
Allison, JR., & van Gunsteren, WF. (2009). Clarifying the relationship between experimental data and structural properties of molecules. . Zuerich, Switzerland
[Conference Poster]Authored by: Allison, J.
Allison, JR., & van Gunsteren, WF. (2009). Clarifying the relationship between experimental data and structural properties of molecules. Poster session presented at the meeting of 7th International NCCR Symposium on New Trends in Structural Biology. Zuerich, Switzerland
[Conference Poster]Authored by: Allison, J.
Allison, JR. (2008, August). Raising RDCs to new heights using local elevation. Presented at 18th International BIOMOS Symposium. Burg Arras, Germany.
[Conference Oral Presentation]Authored by: Allison, J.
Allison, JR., & van Gunsteren, WF. (2008). Interpretation of NMR experiments using MD simulations. Poster session presented at the meeting of 6th International NCCR Symposium on New Trends in Structural Biology. Zuerich, Switzerland
[Conference Poster]Authored by: Allison, J.
Allison, JR., Vendruscolo, M., & Lindorff-Larsen, K. (2005). Determination of the conformational preferences of α-synuclein in solution. Poster session presented at the meeting of 19th Annual Symposium of the Protein Society. Boston, MA, USA
[Conference Poster]Authored by: Allison, J.

Supervision and Teaching

Summary of Doctoral Supervision

Position Current Completed
Supervisor 5 1
CoSupervisor 0 1

Teaching

Undergraduate

246.201 Systems and Models in the Natural Sciences

246.101 Science and Sustainability

122.102 Biochemistry of Cells

123.172 Chemistry for Biological Systems

122.231 Genes and Gene Expression

Postgraduate

122.704 Molecular Cell Biology

162.760 Research Methods in Molecular Biosciences

Current Doctoral Supervision

Supervisor of:

  • Shamim Shadfar - PhD
    Molecular dynamics simulation of inter-molecular interactions
  • Ashar Jamil Malik - PhD
    Exploring Deep Phylogenies Using Protein Structures
  • William Irvine - PhD
    Molecular Dynamics Simulations of Protein-Membrane Interactions Focusing on PI3Ká and Its Oncogenic Mutants
  • Ivan Welsh - PhD
    On Using Automated Algorithms to Parameterise Molecules for Molecular Dynamics Simulations and Investigating Suitable Ensembles for the Simulation of Naphthalimide Monolayers

Completed Doctoral Supervision

Supervisor of:

  • 2014 - Mayank Saraswat - PhD
    In search of novel folds:Protein evolution via non-homologous recombination

CoSupervisor of:

  • 2015 - Lukas Nico Wirz - PhD
    Graph Theoretic and Electronic Properties of Fullerenes and Biasing Molecular Modelling Simulations with Experimental Residual Dipolar Couplings

Media and Links

Media

  • 30 Oct 2013 - Online
    Featured on Royal Society of NZ website.
    Featured on the Royal Society of NZ website as a highlight of the 2013 Marsden funding round.
  • 27 Sep 2014 - Community Service
    Metagenomics 2014
    Assisted in running the Metagenomics workshop run for high school biology students at Massey University Auckland.
  • 27 Sep 2014 - Community Service
    The wiggling and jiggling of molecules
    Gave a talk to students attending the Metagenomics workshop for high school biology students at Massey University Auckland.
  • 23 Apr 2013 - Community Service
    Watching proteins wobble
    Gave a talk to students attending a Biology Olympiad training camp at Massey University.
  • 21 Sep 2013 - Community Service
    Metagenomics 2013
    Assisted in running the Metagenomics workshop run for high school biology students at Massey University Auckland.
  • 20 Mar 2014 - Community Service
    Molecular CGI: making movies of molecules
    Spoke to careers advisers from Auckland schools about the kind of research being done at Massey University Auckland.
  • 18 Feb 2014 - Newspaper
    NZ Herald article
    Featured in an article in the NZ Herald about the Marsden fund.
  • 16 Jun 2014 - Community Service
    Molecular CGI: making movies of molecules
    Gave a talk at Orewa College as part of the Massey Science Research Roadshow.
  • 16 Jan 2014 - Community Service
    How to watch proteins wobble: molecular CGI
    Spoke to students attending the Rotary Science programme at Massey University Auckland.
  • 13 Apr 2015 - Community Service
    Watching proteins wobble
    Gave a talk to students attending a Biology Olympiad training camp at Massey University.
  • 12 Apr 2014 - Community Service
    Watching proteins wobble
    Gave a talk to students attending a Biology Olympiad training camp at Massey University.
  • 10 Mar 2014 - Online
    Featured in eResearch2020
    Interviewed for opinion piece on the future of e-research in NZ.

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