Probing structure and reaction dynamics of proteins using time-resolved resonance Raman spectroscopy

D Buhrke, P Hildebrandt - Chemical reviews, 2019 - ACS Publications
The mechanistic understanding of protein functions requires insight into the structural and
reaction dynamics. To elucidate these processes, a variety of experimental approaches are …

Reactive molecular dynamics: From small molecules to proteins

M Meuwly - Wiley Interdisciplinary Reviews: Computational …, 2019 - Wiley Online Library
The current status of reactive molecular dynamics (MD) simulations is summarized. Both,
methodological aspects and applications to problems ranging from gas phase reaction …

High-dimensional potential energy surfaces for molecular simulations: from empiricism to machine learning

OT Unke, D Koner, S Patra, S Käser… - … Learning: Science and …, 2020 - iopscience.iop.org
An overview of computational methods to describe high-dimensional potential energy
surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy …

Femtosecond X-ray emission study of the spin cross-over dynamics in haem proteins

D Kinschel, C Bacellar, O Cannelli, B Sorokin… - Nature …, 2020 - nature.com
In haemoglobin the change from the low-spin (LS) hexacoordinated haem to the high spin
(HS, S= 2) pentacoordinated domed deoxy-myoglobin (deoxyMb) form upon ligand …

The H-NOX protein structure adapts to different mechanisms in sensors interacting with nitric oxide

BK Yoo, SG Kruglik, JC Lambry, I Lamarre… - Chemical …, 2023 - pubs.rsc.org
Some classes of bacteria within phyla possess protein sensors identified as homologous to
the heme domain of soluble guanylate cyclase, the mammalian NO-receptor. Named H-NOX …

Direct observation of subpicosecond vibrational dynamics in photoexcited myoglobin

C Ferrante, E Pontecorvo, G Cerullo, MH Vos… - Nature Chemistry, 2016 - nature.com
Determining the initial pathway for ultrafast energy redistribution within biomolecules is a
challenge, and haem proteins, for which energy can be deposited locally in the haem moiety …

[HTML][HTML] Observing heme doming in myoglobin with femtosecond X-ray absorption spectroscopy

M Levantino, HT Lemke, G Schirò, M Glownia… - Structural …, 2015 - pubs.aip.org
We report time-resolved X-ray absorption measurements after photolysis of carbonmonoxy
myoglobin performed at the LCLS X-ray free electron laser with nearly 100 fs (FWHM) time …

[HTML][HTML] Non-conventional force fields for applications in spectroscopy and chemical reaction dynamics

D Koner, SM Salehi, P Mondal… - The Journal of chemical …, 2020 - pubs.aip.org
Extensions and improvements of empirical force fields are discussed in view of applications
to computational vibrational spectroscopy and reactive molecular dynamics simulations …

Time-resolved resonance Raman spectroscopy: exploring reactive intermediates

SK Sahoo, S Umapathy, AW Parker - Applied Spectroscopy, 2011 - opg.optica.org
The study of reaction mechanisms involves systematic investigations of the correlation
between structure, reactivity, and time. The challenge is to be able to observe the chemical …

The transcriptional repressor REV-ERB as a novel target for disease

A Uriz-Huarte, A Date, H Ang, S Ali, HJM Brady… - Bioorganic & Medicinal …, 2020 - Elsevier
REV-ERB is a member of the nuclear receptor superfamily of transcription factors involved in
the regulation of many physiological processes, from circadian rhythm, to immune function …