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Effect of Oriented Electric Fields on Biologically Relevant Iron–Sulfur Clusters: Tuning Redox Reactivity for Catalysis (2022)
Journal Article
Gaughan, S. J. H., Hirst, J. D., Croft, A. K., & Jäger, C. M. (2022). Effect of Oriented Electric Fields on Biologically Relevant Iron–Sulfur Clusters: Tuning Redox Reactivity for Catalysis. Journal of Chemical Information and Modeling, 62(3), 591-601. https://doi.org/10.1021/acs.jcim.1c00791

Enzyme-based iron-sulfur clusters, exemplified in families such as hydrogenases, nitrogenases, and radical S-Adenosylmethionine enzymes, feature in many essential biological processes. The functionality of biological iron-sulfur clusters extends beyo... Read More about Effect of Oriented Electric Fields on Biologically Relevant Iron–Sulfur Clusters: Tuning Redox Reactivity for Catalysis.

Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1 (2021)
Journal Article
Zhou, J., Wu, S., Lee, B. G., Chen, T., He, Z., Lei, Y., …Hirst, J. D. (2021). Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1. Molecules, 26(24), Article 7492. https://doi.org/10.3390/molecules26247492

A machine learning approach has been applied to virtual screening for lysine specific demethylase 1 (LSD1) inhibitors. LSD1 is an important anti-cancer target. Machine learning models to predict activity were constructed using Morgan molecular finger... Read More about Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1.

Kernel Methods for Predicting Yields of Chemical Reactions (2021)
Journal Article
Haywood, A. L., Redshaw, J., Hanson-Heine, M. W., Taylor, A., Brown, A., Mason, A. M., …Hirst, J. D. (2022). Kernel Methods for Predicting Yields of Chemical Reactions. Journal of Chemical Information and Modeling, 62(9), 2077-2092. https://doi.org/10.1021/acs.jcim.1c00699

The use of machine learning methods for the prediction of reaction yield is an emerging area. We demonstrate the applicability of support vector regression (SVR) for predicting reaction yields, using combinatorial data. Molecular descriptors used in... Read More about Kernel Methods for Predicting Yields of Chemical Reactions.

Benzene, Toluene, and Monosubstituted Derivatives: Diabatic Nature of the Oscillator Strengths of S1 ← S0 Transitions (2021)
Journal Article
Robinson, D., Alarfaji, S. S., & Hirst, J. D. (2021). Benzene, Toluene, and Monosubstituted Derivatives: Diabatic Nature of the Oscillator Strengths of S1 ← S0 Transitions. Journal of Physical Chemistry A, 125(24), 5237–5245. https://doi.org/10.1021/acs.jpca.1c01685

For benzene, toluene, aniline, fluorobenzene, and phenol, even sophisticated treatments of electron correlation, such as MRCI and XMS-CASPT2 calculations, show oscillator strengths typically lower than experiment. Inclusion of a simple pseudo-diabati... Read More about Benzene, Toluene, and Monosubstituted Derivatives: Diabatic Nature of the Oscillator Strengths of S1 ← S0 Transitions.

Structural variation of protein-ligand complexes of the first bromodomain of BRD4 (2021)
Journal Article
Guest, E. E., Pickett, S. D., & Hirst, J. D. (2021). Structural variation of protein-ligand complexes of the first bromodomain of BRD4. Organic and Biomolecular Chemistry, 19(25), 5632-5641. https://doi.org/10.1039/d1ob00658d

The bromodomain-containing protein 4 (BRD4), a member of the bromodomain and extra-terminal domain (BET) family, plays a key role in several diseases, especially cancers. With increased interest in BRD4 as a therapeutic target, many X-ray crystal str... Read More about Structural variation of protein-ligand complexes of the first bromodomain of BRD4.

Near-ultraviolet circular dichroism and two-dimensional spectroscopy of polypeptides (2021)
Journal Article
Segatta, F., Rogers, D. M., Dyer, N. T., Guest, E. E., Li, Z., Do, H., …Hirst, J. D. (2021). Near-ultraviolet circular dichroism and two-dimensional spectroscopy of polypeptides. Molecules, 26(2), Article 396. https://doi.org/10.3390/MOLECULES26020396

A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ul... Read More about Near-ultraviolet circular dichroism and two-dimensional spectroscopy of polypeptides.

A Machine Learning Protocol for Predicting Protein Infrared Spectra (2020)
Journal Article
Ye, S., Zhong, K., Zhang, J., Hu, W., Hirst, J. D., Zhang, G., …Jiang, J. (2020). A Machine Learning Protocol for Predicting Protein Infrared Spectra. Journal of the American Chemical Society, 142(45), 19071–19077. https://doi.org/10.1021/jacs.0c06530

© 2020 American Chemical Society. Infrared (IR) absorption provides important chemical fingerprints of biomolecules. Protein secondary structure determination from IR spectra is tedious since its theoretical interpretation requires repeated expensive... Read More about A Machine Learning Protocol for Predicting Protein Infrared Spectra.

Computed optical spectra of SARS-CoV-2 proteins (2020)
Journal Article
Li, Z., & Hirst, J. D. (2020). Computed optical spectra of SARS-CoV-2 proteins. Chemical Physics Letters, 758, Article 137935. https://doi.org/10.1016/j.cplett.2020.137935

© 2020 Elsevier B.V. Treatment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes Covid-19, may well be predicated on knowledge of the structures of protein of this virus. However, often these cannot be determined... Read More about Computed optical spectra of SARS-CoV-2 proteins.

Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid (2020)
Journal Article
Spankie, T. J., Haywood, A. L., Dottorini, T., Barrow, P. A., & Hirst, J. D. (2020). Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid. Journal of Molecular Graphics and Modelling, 101, Article 107723. https://doi.org/10.1016/j.jmgm.2020.107723

© 2020 Elsevier Inc. One promising strategy to combat antimicrobial resistance is to use bacteriophages that attach to the sex pili produced by transmissible antimicrobial resistance (AMR) plasmids, infect AMR bacteria and select for loss of the AMR... Read More about Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid.

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction (2020)
Journal Article
Baiz, C. R., Błasiak, B., Bredenbeck, J., Cho, M., Choi, J. H., Corcelli, S. A., …Zanni, M. T. (2020). Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chemical Reviews, 120(15), 7152–7218. https://doi.org/10.1021/acs.chemrev.9b00813

© 2020 American Chemical Society. Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have b... Read More about Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Unfolding Dynamics of a Photoswitchable Helical Peptide (2020)
Journal Article
Auvray, F., & Hirst, J. D. (2020). Unfolding Dynamics of a Photoswitchable Helical Peptide. Journal of Physical Chemistry B, 124(26), 5380-5392. https://doi.org/10.1021/acs.jpcb.0c04017

We present an atomistic force field for the azo-moiety of the photoswitchable FK-11-X peptide. We use the parameters to study the unfolding of the peptide through molecular dynamics simulations. The unfolded ensemble contains many different structure... Read More about Unfolding Dynamics of a Photoswitchable Helical Peptide.

Molecular Simulation of αvβ6 Integrin Inhibitors (2020)
Journal Article
Guest, E. E., Oatley, S. A., Macdonald, S. J. F., & Hirst, J. D. (2020). Molecular Simulation of αvβ6 Integrin Inhibitors. Journal of Chemical Information and Modeling, 60(11), 5487-5498. https://doi.org/10.1021/acs.jcim.0c00254

The urgent need for new treatments for the chronic lung disease idiopathic pulmonary fibrosis (IPF) motivates research into antagonists of the RGD binding integrin αvβ6, a protein linked to the initiation and progression of the disease. Molecular dyn... Read More about Molecular Simulation of αvβ6 Integrin Inhibitors.

Late-Stage Functionalization by Chan–Lam Amination: Rapid Access to Potent and Selective Integrin Inhibitors (2020)
Journal Article
Robinson, H., Oatley, S., Rowedder, J., Slade, P., Macdonald, S., Argent, S., …Moody, C. J. (2020). Late-Stage Functionalization by Chan–Lam Amination: Rapid Access to Potent and Selective Integrin Inhibitors. Chemistry - A European Journal, 26(34), 7678-7684. https://doi.org/10.1002/chem.202001059

© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim A late-stage functionalization of the aromatic ring in amino acid derivatives is described. The key step is a copper-catalysed diversification of a boronate ester by amination (Chan–Lam reaction) th... Read More about Late-Stage Functionalization by Chan–Lam Amination: Rapid Access to Potent and Selective Integrin Inhibitors.

Time resolved transient circular dichroism spectroscopy using synchrotron natural polarization (2019)
Journal Article
Auvray, F., Dennetiere, D., Giuliani, A., Jamme, F., Wien, F., Nay, B., …Réfrégiers, M. (2019). Time resolved transient circular dichroism spectroscopy using synchrotron natural polarization. Structural Dynamics, 6(5), Article 054307. https://doi.org/10.1063/1.5120346

Ultraviolet (UV) synchrotron radiation circular dichroism (SRCD) spectroscopy has made an important contribution to the determination and understanding of the structure of bio-molecules. In this paper, we report an innovative approach that we term ti... Read More about Time resolved transient circular dichroism spectroscopy using synchrotron natural polarization.

Electronic Circular Dichroism Spectroscopy of Proteins (2019)
Journal Article
Rogers, D. M., Jasim, S. B., Dyer, N. T., Auvray, F., Réfrégiers, M., & Hirst, J. D. (2019). Electronic Circular Dichroism Spectroscopy of Proteins. Chem, 5(11), 2751-2774. https://doi.org/10.1016/j.chempr.2019.07.008

Circular dichroism (CD) is an important spectroscopic technique that enables the characterization of protein secondary and tertiary structure. Proteins can undergo changes in their structure when they participate in processes, for example, ligand bin... Read More about Electronic Circular Dichroism Spectroscopy of Proteins.

Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra (2019)
Journal Article
Michaelis, M., Hildebrand, N., Meißner, R. H., Wurzler, N., Li, Z., Hirst, J. D., …Colombi Ciacchi, L. (2019). Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra. Journal of Physical Chemistry B, 123(31), 6694-6704. https://doi.org/10.1021/acs.jpcb.9b03932

Although successful in the structural determination of ordered biomolecules, the spectroscopic investigation of oligopeptides in solution is hindered by their complex and rapidly changing conformational ensemble. The measured circular dichroism (CD)... Read More about Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra.

Atomistic details of chymotrypsin conformational changes upon adsorption on silica (2018)
Journal Article
Hildebrand, N., Michaelis, M., Wurzler, N., Li, Z., Hirst, J. D., Micsonai, A., …Ciacchi, L. C. (2018). Atomistic details of chymotrypsin conformational changes upon adsorption on silica. ACS Biomaterials Science and Engineering, 4(12), 4036-4050. https://doi.org/10.1021/acsbiomaterials.8b00819

Adsorption of enzymes on solid surfaces may lead to conformational changes that reduce their catalytic conversion activity and are thus detrimental to the efficiency of biotechnology or biosensing applications. This work is a joint theoretical and expe... Read More about Atomistic details of chymotrypsin conformational changes upon adsorption on silica.

DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet (2017)
Journal Article
Jasim, S. B., Li, Z., Guest, E. E., & Hirst, J. D. (in press). DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet. Journal of Molecular Biology, https://doi.org/10.1016/j.jmb.2017.12.009

A fully quantitative theory connecting protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. The web-server DichroCalc (http://comp.chem.nottingham.ac.u... Read More about DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet.

Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis (2017)
Journal Article
Shaw, D., Hill, R., Simpson, N., Husseini, F., Robb, K., Greetham, G. M., …Hunt, N. (in press). Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis. Chemical Science, 8, https://doi.org/10.1039/C7SC03336B

Antimicrobial resistance represents a growing global health problem. The emergence of novel resistance mechanisms necessitates the development of alternative approaches to investigate the molecular fundamentals of resistance, leading ultimately to ne... Read More about Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis.