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Akademický článek

Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces.

Autor: Maxime Louet, Christian Seifert, Ulf Hensen, Frauke Gräter

Publikováno v: PLoS Computational Biology, Vol 11, Iss 8, p e1004358 (2015)

The Catabolite Activator Protein (CAP) is a showcase example for entropic allostery. For full activation and DNA binding, the homodimeric protein requires the binding of two cyclic AMP (cAMP) molecules in an anti-cooperative manner, the source of whi

Externí odkaz: https://doaj.org/article/27e03949d2b249bc8a86cf8e5e0c71e0

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Akademický článek

Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.

Autor: Ulf Hensen, Tim Meyer, Jürgen Haas, René Rex, Gert Vriend, Helmut Grubmüller

Publikováno v: PLoS ONE, Vol 7, Iss 5, p e33931 (2012)

Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based o

Externí odkaz: https://doaj.org/article/2c79a227766d4d6bbab45a660db53b0c

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Akademický článek

Estimating absolute configurational entropies of macromolecules: the minimally coupled subspace approach.

Autor: Ulf Hensen, Oliver F Lange, Helmut Grubmüller

Publikováno v: PLoS ONE, Vol 5, Iss 2, p e9179 (2010)

We develop a general minimally coupled subspace approach (MCSA) to compute absolute entropies of macromolecules, such as proteins, from computer generated canonical ensembles. Our approach overcomes limitations of current estimates such as the quasi-

Externí odkaz: https://doaj.org/article/7955e90ef6104d01b66a16344a49cd1f

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How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered: β2-Adrenergic Receptor in the Spotlight

Autor: Ilpo Vattulainen, Waldemar Kulig, Matti Javanainen, Daniel J. Müller, Tomasz Róg, Ulf Hensen, Joona Tynkkynen, Moutusi Manna

Publikováno v: Manna, M, Kulig, W, Javanainen, M, Tynkkynen, J, Hensen, U, Muller, D J, Rog, T & Vattulainen, I 2015, ' How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered : β2-Adrenergic Receptor in the Spotlight ', Journal of Chemical Theory and Computation, vol. 11, no. 7, pp. 3432-3445 . https://doi.org/10.1021/acs.jctc.5b00070

Atomistic molecular dynamics (MD) simulations are used extensively to elucidate membrane protein properties. These simulations are based on three-dimensional protein structures that in turn are often based on crystallography. The protein structures r

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::df17a9eeccdb4f989a5f23adff72ebcf
https://doi.org/10.1021/acs.jctc.5b00070

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Quantitative Imaging of the Electrostatic Field and Potential Generated by a Transmembrane Protein Pore at Subnanometer Resolution

Autor: Daniel J. Müller, Ulf Hensen, Moritz Pfreundschuh

Publikováno v: Nano Letters

Elucidating the mechanisms by which proteins translocate small molecules and ions through transmembrane pores and channels is of great interest in biology, medicine, and nanotechnology. However, the characterization of pore forming proteins in their

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::614a97fba8754dd79a3c5645291119e3
https://doi.org/10.1021/nl403232z

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Protocol to Avoid Possible Artifacts in Atomistic Simulation of GPCR Proteins whose Crystal Structure is Heavily Engineered

Autor: Moutusi Manna, Tomasz Róg, Ulf Hensen, Waldemar Kulig, Matti Javanainen, Daniel J. Müller, Ilpo Vattulainen, Joona Tynkkynen

Publikováno v: Biophysical Journal. 110(3)

G protein-coupled receptors (GPCRs) are versatile signaling proteins that mediate diverse cellular responses. Atomistic molecular dynamics (MD) simulations are widely used to elucidate the properties of GPCRs. These simulations are based on three-dim

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e38f9c8a723fb74ee9d2ce121c4c3e6e

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