Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II

Mulholland, Sam; Turpin, Eleanor R.; Bonev, Boyan B.; Hirst, J.D.

doi:10.1038/srep21185

Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene (2020)
Journal Article
Jiang, L., Rogers, D. M., Hirst, J. D., & Do, H. (2020). Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene. Journal of Chemical Theory and Computation, 16(8), 5150-5162. https://doi.org/10.1021/acs.jctc.0c00399

Utilizing a force-matching procedure, we parametrize new force fields systematically for large conjugated systems. We model both conjugated polymers and molecular crystals that contain diketopyrrolopyrrole, thiophene, and thieno[3,2-b]thiophene units... Read More about Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene.

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.

Möbius and Hückel Cyclacenes with Dewar and Ladenburg Defects (2020)
Journal Article
Hanson-Heine, M. W., & Hirst, J. D. (2020). Möbius and Hückel Cyclacenes with Dewar and Ladenburg Defects. Journal of Physical Chemistry A, 124(26), 5408-5414. https://doi.org/10.1021/acs.jpca.0c04137

Copyright © 2020 American Chemical Society. Cyclacene nanobelts have not been synthesized in over 60 years and remain one of the last unsynthesized building blocks of carbon nanotubes. Recent work has predicted that Hückel-cyclacenes containing Dewar... Read More about Möbius and Hückel Cyclacenes with Dewar and Ladenburg Defects.

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.

Dewar Benzenoids Discovered in Carbon Nanobelts (2020)
Journal Article
Hanson-Heine, M. W., Rogers, D. M., Woodward, S., & Hirst, J. D. (2020). Dewar Benzenoids Discovered in Carbon Nanobelts. Journal of Physical Chemistry Letters, 11(10), 3769-3772. https://doi.org/10.1021/acs.jpclett.0c01027

© 2020 American Chemical Society. The synthesis of cyclacene nanobelts remains an elusive goal dating back over 60 years. These molecules represent the last unsynthesized building block of carbon nanotubes and may be useful both as seed molecules for... Read More about Dewar Benzenoids Discovered in Carbon Nanobelts.

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.

Active search for computer-aided drug design (2018)
Journal Article
Oglic, D., Oatley, S. A., Macdonald, S. J., McInally, T., Garnett, R., Hirst, J. D., & Gärtner, T. (in press). Active search for computer-aided drug design. Molecular Informatics, 37, https://doi.org/10.1002/minf.201700130

We consider lead discovery as active search in a space of labelled graphs. In particular, we extend our recent data-driven adaptive Markov chain approach, and evaluate it on a focused drug design problem, where we search for an antagonist of an av in... Read More about Active search for computer-aided drug design.

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.

Quantum chemical calculations of tryptophan→heme electron and excitation energy transfer rates in myoglobin (2017)
Journal Article
Suess, C. J., Hirst, J. D., & Besley, N. A. (2017). Quantum chemical calculations of tryptophan→heme electron and excitation energy transfer rates in myoglobin. Journal of Computational Chemistry, 38(17), 1495-1502. https://doi.org/10.1002/jcc.24793

The development of optical multidimensional spectroscopic techniques has opened up new possibilities for the study of biological processes. Recently, ultrafast two- dimensional ultraviolet spectroscopy experiments have determined the rates of tryptop... Read More about Quantum chemical calculations of tryptophan→heme electron and excitation energy transfer rates in myoglobin.

Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet (2017)
Journal Article
Li, Z., & Hirst, J. D. (in press). Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet. RSC Advances, https://doi.org/10.1039/C7SC00586E

Vibrational structure in the near-UV circular dichroism (CD) spectra of proteins is an important source of information on protein conformation and can be exploited to study structure and folding. A fully quantitative theory of the relationship betwee... Read More about Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet.

Computing infrared spectra of proteins using the exciton model (2016)
Journal Article
Husseini, F. S., Robinson, D., Hunt, N. T., Parker, A. W., & Hirst, J. (in press). Computing infrared spectra of proteins using the exciton model. Journal of Computational Chemistry, 38(16), https://doi.org/10.1002/jcc.24674

The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are... Read More about Computing infrared spectra of proteins using the exciton model.

Probing polyoxometalate-protein interactions using molecular dynamics simulations (2016)
Journal Article
Solé-Daura, A., Goovaerts, V., Stroobants, K., Absillis, G., Jiménez-Lozano, P., Poblet, J. M., …Carbó, J. J. (2016). Probing polyoxometalate-protein interactions using molecular dynamics simulations. Chemistry - A European Journal, 22(43), 15280-15289. https://doi.org/10.1002/chem.201602263

The molecular interactions between the Ce(IV)-substituted Keggin anion [PW11O39Ce(OH2)4]3- (CeK) and hen egg white lysozyme (HEWL), was investigated by molecular dynamics (MD) simulations. We compared the analysis of CeK with the Ce(IV)-substituted... Read More about Probing polyoxometalate-protein interactions using molecular dynamics simulations.

Simulation of Two-Dimensional Infrared Spectroscopy of Peptides Using Localized Normal Modes (2016)
Journal Article
Hanson-Heine, M. W. D., Husseini, F. S., Hirst, J. D., & Besley, N. A. (2016). Simulation of Two-Dimensional Infrared Spectroscopy of Peptides Using Localized Normal Modes. Journal of Chemical Theory and Computation, 12(4), 1905-1918. https://doi.org/10.1021/acs.jctc.5b01198

Non-linear two-dimensional infrared spectroscopy (2DIR) is most commonly simulated within the framework of the exciton method. The key parameters for these calculations include the frequency of the oscillators within their molecular environments and... Read More about Simulation of Two-Dimensional Infrared Spectroscopy of Peptides Using Localized Normal Modes.

Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II (2016)
Journal Article
Mulholland, S., Turpin, E. R., Bonev, B. B., & Hirst, J. (2016). Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II. Scientific Reports, 6(21185), https://doi.org/10.1038/srep21185

Lanthionine antibiotics are an important class of naturally-occurring antimicrobial peptides. The best-known, nisin, is a commercial food preservative. However, structural and mechanistic details on nisin/lipid II membrane complexes are currently lac... Read More about Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II.

All Outputs (71)