The Nogly Lab uses time-resolved serial crystallography to watch proteins move — capturing the structural rearrangements that underlie light sensing, ion transport, and signal transduction at atomic resolution, across timescales from femtoseconds to milliseconds. We combine X-ray crystallography with spectroscopy and computation to address mechanistic questions that static structures simply cannot answer.
If you are an ambitious postdoc or PhD candidate looking to push the boundaries of dynamic structural biology experimentally, we want to hear from you.
Studying small and fast
The challenge
Studying molecular mechanisms behind protein function is demanding because a detailed understanding of complex protein dynamics requires very high spatial and temporal resolution. The recent development of X-ray free-electron laser (XFEL) facilities has opened new opportunities for dynamic structural biology.
Our toolkit
Their intense and ultrashort 10–70 fs X-ray pulses enable pump–probe experiments with unprecedented temporal resolution. Time-resolved serial femtosecond crystallography (TR-SFX) can provide atomic-level details of proteins in action while probing events from femtoseconds to milliseconds after activation. We carry out TR-SFX experiments at leading XFEL facilities including European XFEL and SwissFEL.
Capturing proteins in motion
Bacteriorhodopsin as a model system
Our group builds in particular on recent experiments focused on the dynamics of bacteriorhodopsin. This work demonstrated sample-efficient TR-SFX at XFELs using high-viscosity injectors while providing unique insights into activation and photocycle dynamics .
From XFEL to synchrotron
Bacteriorhodopsin was also used to perform serial crystallography experiments at the synchrotron. Combined with a pump laser, this provides an excellent tool to probe slower protein dynamics at more widely available X-ray sources through time-resolved serial synchrotron crystallography (TR-SSX), including at MAX IV .
Unravelling halorhodopsin transport
The combination of TR-SFX and TR-SSX enabled us to unravel the complex structural dynamics that drive chloride transport in halorhodopsin from Nonlabens marinus, NmHR . This comprehensive study was complemented by spectroscopy and QM/MM calculations to describe the mode of light energy utilization in transport initiation, the mechanism controlling transport unidirectionality, and the transport pathway itself.
Overview of major events during chloride transport by NmHR captured by time-resolved serial X-ray crystallography. For details, check our publication Mous et al. Science 2022.
The first molecular events in vision
In collaboration with the Gebhard Schertler and Valerie Panneels teams from the Paul Scherrer Institute, we used the TR-SFX approach to gain insight into the first molecular events in vision .
Changes of chromophore binding in bovine rhodopsin probed by TR-SFX. Interactions between the retinal and the binding-pocket residues are substantially reduced by 1 ps after photoactivation in this G-protein coupled receptor. For details, check our publication Gruhl et al. Nature 2023.
Understanding signal conversion in receptors at the atomic level
A central mechanistic question
The central question driving the Nogly Lab — a Dioscuri Centre of Scientific Excellence — is how different input signals, including light, pH change, and ligand binding, are converted at the molecular level into distinct output signals. Recently, we started to study Light-Oxygen-Voltage (LOV) proteins.
LOV proteins as optogenetic tools
These proteins act as blue-light antennae and activate various effector proteins such as kinases, phosphatases, phosphodiesterases, and many others. Due to their universal utility, LOV proteins have also found important application as optogenetic tools for controlling cellular physiology with light .
Photoactivation of the LOV domain leads to the formation of a covalent bond between the Cys residue and the chromophore, followed by the activation of effector proteins with various functions. See our review Flores-Ibarra et al. JMB 2024.
Slow LOV dynamics by TR-SSX
Our first insights from TR-SSX show the slow dynamics of the LOV domain and structural changes associated with the initial stages of signal transduction .
TR-SSX experiment on the LOV domain shows the structural dynamics associated with signal transduction in milliseconds after photoactivation. See our paper Gotthard et al. IUCrJ 2024 (a).
Fixed-target TR-SFX at XFELs
We also used this protein system to demonstrate the first successful TR-SFX experiments at XFELs using fixed-target sample delivery as a way to drastically reduce sample requirements for this type of experiment .
Different experimental setups were tested before we successfully demonstrated the TR-SFX experiment with LOV crystals delivered on a fixed target to drastically reduce sample consumption. See our paper Gotthard et al. IUCrJ 2024 (b).
Open questions
Other exciting questions include the ultrafast protein activation mechanism involving formation of a covalent thioether link to the chromophore, signal transduction to diverse effector domains, and the molecular mechanisms that define distinct functional outputs.
Studying dynamics of non-photoactive proteins
Beyond light-activated systems
We extend TR-SFX experiments to non-photoactive proteins such as ionotropic receptors, using fast mixing techniques or photoswitchable ligands to study structural dynamics at atomic resolution, including in medically relevant receptor systems.
Join Us
We are actively looking for exceptional postdoctoral researchers to contribute to our ongoing projects in time-resolved crystallography, photoreceptor biology, and membrane transporter mechanisms. If you are driven by fundamental mechanistic questions and want to work at the forefront of dynamic structural biology, please get in touch.