arXiv subjects

Peter Hamm

Publications and source records attributed to Peter Hamm.

At least 19 recordsLinked to original sources

arXiv2026

Local molecular motions encode time-resolved infrared spectra of proteins

Time-resolved infrared spectroscopy probes protein dynamics over timescales spanning more than ten orders of magnitude, yet the molecular motions underlying the observed kinetic signatures have remained elusive. Here we combine transient infrared spectroscopy with nonequilibrium molecular dynamics simulations to establish a direct connection between experimental relaxation times and local structural motions. Studying single-domain allosteric proteins, we find that inter-residue contact distances provide the structural representation that most faithfully reproduces the experimental dynamics. Correlation analysis identifies localized networks of coordinated contacts that mediate communication between secondary-structure elements. The characteristic timescales of these contact networks quantitatively match the experimentally observed relaxation processes, enabling each kinetic step to be assigned to a specific molecular motion. Applied to allosteric signal propagation in PDZ3 and photoinduced ligand unbinding in PDZ2, this framework provides an atomistic picture of hierarchical protein relaxation and establishes a general framework for connecting transient infrared spectroscopy with the molecular mechanisms of protein dynamics.

cond-mat.soft↗

arXiv2026

Anharmonic phonon coupling enabled by local inversion symmetry breaking at domain walls in ferroelastics

In ferroelastic materials, spontaneous symmetry breaking leads to the formation of twin domains. Although the bulk crystal typically remains centrosymmetric, inversion symmetry can be locally broken at the domain walls, potentially changing phonon selection rules and enabling local anharmonic phonon coupling. Here we report direct evidence of such anharmonic coupling in ferroelastic LaAlO$_3$ using two-dimensional Raman-terahertz spectroscopy. We attribute the cross-peaks observed in the two-dimensional spectra to both mechanical and electrical anharmonicity between the $A_{1g}$ Raman-active phonon and the $E_g$ phonon, which acquires finite infrared activity through local inversion symmetry breaking at ferroelastic domain walls. These findings provide new insight into the complex lattice dynamics of ferroelastic materials and highlight the potential of two-dimensional Raman-terahertz spectroscopy to uncover subtle symmetry breaking through the detection of intrinsically weak anharmonic signals.

cond-mat.mtrl-sci↗

arXiv2024

Force Fields for Deep Eutectic Mixtures: Application to Structure and 2D-Infrared Spectroscopy

Parametrizing energy functions for ionic systems can be challenging. Here, the total energy function for an eutectic system consisting of water, SCN$^-$, K$^+$ and acetamide is improved vis-a-vis experimentally measured properties. Given the importance of electrostatic interactions, two different types of models are considered: the first (model M0) uses atom-centered multipole whereas the other two (models M1 and M2) are based on fluctuating minimal distributed charges (fMDCM) that respond to geometrical changes of SCN$^-$. The Lennard-Jones parameters of the anion are adjusted to best reproduce experimentally known hydration free energies and densities which are matched to within a few percent for the final models irrespective of the electrostatic model. Molecular dynamics simulations of the eutectic mixtures with varying water content (between 0% and 100%) yield radial distribution functions and frequency correlation functions for the CN-stretch vibration. Comparison with experiments indicate that models based on fMDCM are considerably more consistent that those using multipoles. Computed viscosities from models M1 and M2 are within 30% of measured values and their change with increasing water content is consistent with experiments. This is not the case for model M0.

physics.chem-ph↗

arXiv2024

$χ^{(2)}$-Induced Artifact Overwhelming the Third-Order Signal in 2D Raman-THz Spectroscopy of Non-Centrosymmetric Materials

Through comprehensive data analysis, we demonstrate that a $χ^{(2)}$-induced artifact, arising from imperfect balancing in the conventional electro-optic sampling (EOS) detection scheme, contributes significantly to the measured signal in 2D Raman-THz spectroscopy of non-centrosymmetric materials. The artifact is a product of two 1D responses, overwhelming the desired 2D response. We confirm that by analyzing the 2D Raman-THz response of a x-cut beta barium borate (BBO) crystal. We furthermore show that this artifact can be effectively suppressed by implementing a special detection scheme. We successfully isolate the desired third-order 2D Raman-THz response, revealing a distinct cross-peak feature, whose frequency position suggests the coupling between two crystal phonons.

physics.optics↗

arXiv2023

A billion years of evolution manifest in nanosecond protein dynamics

Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a structurally and functionally conserved protein across species separated by almost a billion years, investigating ten homologs in complex with their ligand. By inducing a photo-triggered destabilization of the ligand inside the binding pocket, we resolved distinct kinetic footprints for each homolog via transient infrared spectroscopy . Strikingly, we found a cascade of rearrangements within the protein complex which manifest in three discrete time points of dynamic activity, conserved over hundreds of millions of years within a narrow window. Among these processes, one displays a subtle temporal shift correlating with evolutionary divergence, suggesting reduced selective pressure in the past. Our study not only uncovers the impact of evolution on molecular processes in a specific case, but has also the potential to initiate a novel field of scientific inquiry within molecular paleontology, where species are compared and classified based on the rapid pace of protein dynamic processes; a field which connects the shortest conceivable time scale in living matter (10^-9 s) with the largest ones (10^16 s).

physics.bio-ph↗

arXiv2023

Transient 2D IR spectroscopy and multiscale simulations reveal vibrational couplings in the Cyanobacteriochrome Slr1393-g3

Cyanobacteriochromes are bi-stable photoreceptor proteins with desirable photochemical properties for biotechnological applications such as optogenetics or fluorescence microscopy. Here, we investigated Slr1393-g3, a cyanobacteriochrome that reversibly photo-switches between a red-absorbing (Pr) and green-absorbing (Pg) form. We applied advanced IR spectroscopic methods to track the sequence of intermediates during the photocycle over many orders in magnitude in time. In the conversion from Pg to Pr, we have revealed a new intermediate which precedes the Pr formation by using transient IR spectroscopy. In addition, stationary and transient 2D~IR experiments measured the vibrational couplings between different groups of the chromophore and the protein during these intermediate states. Anharmonic QM/MM calculations predict spectra in close-to-quantitative agreement with experimental 2D~IR spectra of the initial and the final state of the photocycle. They facilitate the assignment of the IR spectra and provide an atomistic insight into the coupling mechanism. This serves as a basis for the interpretation of the spectroscopic results and suggests structural changes of the intermediates along the photocycle.

physics.bio-ph↗

arXiv2023

Versatile Femtosecond Laser Synchronization for Multiple-Timescale Transient IR Spectroscopy

Several ways to electronically synchronize different types of amplified femtosecond laser systems are presented, based on a single freely programmable electronics hardware: Arbitrary-detuning asynchronous optical sampling, as well as actively locking two femtosecond laser oscillators, albeit not necessarily to the same round-trip frequency. They allow us to rapidly probe a very wide range of timescales, from picoseconds to potentially seconds, in a single transient absorption experiment without the need to move any delay stage. Experiments become possible that address a largely unexplored aspect of many photochemical reactions, in particular in the context of photo-catalysis as well as photoactive proteins, where an initial femtosecond trigger very often initiates a long-lasting cascade of follow-up processes. The approach is very versatile, and allows us to synchronize very different lasers, such as a Ti:Sa amplifier and a 100~kHz Yb-laser system. The jitter of the synchronisation, and therewith the time-resolution in the transient experiment, lies in the range from 1~ps to 3~ps, depending on the method. For illustration, transient IR measurements of the excited state solvation and decay of a metal carbonyl complex as well as the full reaction cycle of bacteriorhodopsin are shown. The pros and cons of the various methods are discussed, with regard to the scientific question one might want to address, and also with regard to the laser systems that might be already existent in a laser lab.

physics.optics↗

arXiv2023

Breaking Barriers in Ultrafast Spectroscopy and Imaging Using 100 kHz Amplified Yb-Laser Systems

Ultrafast spectroscopy and imaging have become tools utilized by a broad range of scientists involved in materials, energy, biological, and chemical sciences. Commercialization of ultrafast spectrometers including transient absorption spectrometers, vibrational sum frequency generation spectrometers, and even multidimensional spectrometers have put these advanced spectroscopy measurements into the hands of practitioners originally outside the field of ultrafast spectroscopy. There is a technology shift occurring in ultrafast spectroscopy, made possible by new Yb-based lasers, that is opening exciting new experiments in the chemical and physical sciences. Amplified Yb-based lasers operate at many times the repetition rate of the previous generation of Ti:Sapphire amplifier technology, enabling improvements to long-standing techniques, new experiments, and the transformation of spectroscopies to microscopies. The impact of this technology will be felt across a great swath of the scientific communities. This review focuses on amplified Yb-based laser systems used in conjunction with 100 kHz spectrometers operating with shot-to-shot pulse shaping and detection. The shift to 100 kHz lasers is a transformative step in nonlinear spectroscopy and imaging, much like the dramatic expansion that occurred with the commercialization of Ti:Sapphire laser systems in the 1990s.

physics.chem-ph↗

arXiv2022

MCL-1 promiscuity and the structural resilience of its binding partners

MCL-1 and its natural inhibitors, the BH3-only proteins PUMA, BIM, and NOXA regulate apoptosis by interacting promiscuously within an entangled binding network. Little is known about the transient processes and dynamic conformational fluctuations that are the basis for the formation and stability of the MCL-1/BH3-only complex. In this study, we designed photoswitchable versions of MCL-1/PUMA and MCL-1/NOXA, and investigated the protein response after an ultrafast photo-perturbation with transient infrared spectroscopy. We observed partial $α$-helical unfolding in all cases, albeit on strongly varying timescales (1.6~ns for PUMA, 9.7~ns for the previously studied BIM, and 85~ns for NOXA). These differences are interpreted as a BH3-only-specific "structural resilience" to defy the perturbation while remaining in MCL-1's binding pocket. Thus, the presented insights could help to better understand the differences between PUMA, BIM, and NOXA, the promiscuity of MCL-1 in general, and the role of the proteins in the apoptotic network.

physics.bio-ph↗

arXiv2022

Structure, Organization and Heterogeneity of Water-Containing Deep Eutectic Solvents

The spectroscopy and structural dynamics of a deep eutectic mixture (KSCN/acetamide) with varying water content is investigated from 2D IR (with the C-N stretch vibration of the SCN$^-$ anions as the reporter) and THz spectroscopy. Molecular dynamics simulations correctly describe the non-trivial dependence of both spectroscopic signatures depending on water content. For the 2D IR spectra, the MD simulations relate the steep increase in the cross relaxation rate at high water content to parallel alignment of packed SCN$^-$ anions. Conversely, the non-linear increase of the THz absorption with increasing water content is mainly attributed to the formation of larger water clusters. The results demonstrate that a combination of structure sensitive spectroscopies and molecular dynamics simulations provides molecular-level insights into emergence of heterogeneity of such mixtures by modulating their composition.

physics.chem-ph↗

arXiv2022

Hydration Dynamics and IR Spectroscopy of 4-Fluorophenol

Halogenated groups are relevant in pharmaceutical applications and potentially useful spectroscopic probes for infrared spectroscopy. In this work, the structural dynamics and infrared spectroscopy of $para$-fluorophenol (F-PhOH) and phenol (PhOH) is investigated in the gas phase and in water using a combination of experiment and molecular dynamics (MD) simulations. The gas phase and solvent dynamics around F-PhOH and PhOH is characterized from atomistic simulations using empirical energy functions with point charges or multipoles for the electrostatics, Machine-Learning (ML) based parametrization and with full $\textit{ab initio}$ (QM) and mixed Quantum Mechanical/Molecular Mechanics (QM/MM) simulations with a particular focus on the CF- and OH-stretch region. The CF-stretch band is heavily mixed with other modes whereas the OH-stretch in solution displays a characteristic high-frequency peak around 3600 cm$^{-1}$ most likely associated with the -OH group of PhOH and F-PhOH together with a characteristic progression below 3000 cm$^{-1}$ due to coupling with water modes which is also reproduced by several of the simulations. Solvent and radial distribution functions indicate that the CF-site is largely hydrophobic except for simulations using point charges which renders them unsuited for correctly describing hydration and dynamics around fluorinated sites.

physics.chem-ph↗

arXiv2021

Using Azobenzene Photocontrol to Set Proteins in Motion

Controlling the activity of proteins with azobenzene photoswitches is a potent tool for manipulating their biological function. With the help of light, one can change e.g. binding affinities, control allostery or temper with complex biological processes. Additionally, due to their intrinsically fast photoisomerisation, azobenzene photoswitches can serve as triggers to initiate out-of-equilibrium processes. Such switching of the activity, therefore, initiates a cascade of conformational events, which can only be accessed with time-resolved methods. In this Review, we will show how combining the potency of azobenzene photoswitching with transient spectroscopic techniques helps to disclose the order of events and provide an experimental observation of biomolecular interactions in real-time. This will ultimately help us to understand how proteins accommodate, adapt and readjust their structure to answer an incoming signal and it will complete our knowledge of the dynamical character of proteins.

physics.chem-ph↗

arXiv2021

Sequence of Events During Peptide Unbinding from RNase S: A Complete Experimental Description

The photo-triggered unbinding of the intrinsically disordered S-peptide from the RNase S complex is studied with the help of transient IR spectroscopy, covering a wide range of time scales from 100 ps to 10 ms. To that end, an azobenzene moiety has been linked to the S-peptide in a way that its helicity is disrupted by light, thereby initiating its complete unbinding. The full sequence of events is observed, starting from unfolding of the helical structure of the S-peptide on a 20 ns timescale while still being in the binding pocket of the S-protein, S-peptide unbinding after 300 microseconds, and the structural response of the S-protein after 3 ms. With regard to the S-peptide dynamics, the binding mechanism can be classified as an induced fit, while the structural response of the S-protein is better described as conformational selection.

physics.bio-ph↗

arXiv2021

Intrinsic Dynamics of Protein-Peptide Unbinding

The dynamics of peptide-protein binding and unbinding of a variant of the RNase S system has been investigated. To initiate the process, a photoswitchable azobenzene moiety has been covalently linked to the S-peptide, thereby switching its binding affinity to the S-protein. Transient fluorescence quenching was measured with the help of a time-resolved fluorometer, which has been specifically designed for these experiments and is based on inexpensive LED's and laser diodes only. One mutant shows on-off behaviour with no specific binding detectable in one of the states of the photoswitch. Unbinding is faster by at least two orders of magnitudes, as compared to other variants of the RNase S system. It is concluded that unbinding is essentially barrier-less in that case, revealing the intrinsic dynamics of the unbinding event, which occurs on a few 100 microseconds timescale in a strongly stretched-exponential manner.

physics.bio-ph↗

arXiv2021

The Speed of Allosteric Signaling Within a Single-Domain Protein

While much is known about different allosteric regulation mechanisms, the nature of the "allosteric signal", and the timescale on which it propagates, remains elusive. The PDZ3 domain from postsynaptic density-95 protein is a small protein domain with a terminal third alpha helix -- the $α$3-helix, which is known to be allosterically active. By cross-linking the allosteric helix with an azobenzene moiety, we obtained a photocontrollable PDZ3 variant. Photoswitching triggers its allosteric transition, resulting in a change in binding affnity of a peptide to the remote binding pocket. Using time-resolved infrared and UV/Vis spectroscopy, we follow the allosteric signal transduction and reconstruct the timeline in which the allosteric signal propagates through the protein within 200 ns.

physics.bio-ph↗

arXiv2021

Nanosecond protein dynamics in a red/green Cyanobacteriochrome revealed by transient IR spectroscopy

Over the last decades, photoreceptive proteins were extensively studied with biophysical methods to gain a fundamental understanding of their working mechanisms and further guide the development of optogenetic tools from them. Time-resolved infrared (IR) spectroscopy is one of the key methods to access their functional non-equilibrium processes with high temporal resolution, but has the major drawback that experimental data is usually highly complex. Linking the spectral response to specific molecular events is a major obstacle. Here, we investigate a cyanobacteriochrome (CBCR) photoreceptor with a combined approach of transient absorption spectroscopy in the Visible and IR spectral regions. We obtain kinetic information in both spectral regions by analysis with two different fitting methods, global multiexponential fitting and lifetime analysis. We investigate the ground state dynamics that follow photoexcitation in both directions of the bi-stable photocycle (Pr* and Pg*) in the nanosecond and microsecond time regime. We find two ground state intermediates associated with the decay of Pr* and four with Pg* and report the macroscopic time constants of their interconversions. One of these processes is assigned to a structural change in the protein backbone. At later delay times, the spectroscopic responses are stretched out in time, an effect that can be better described by the lifetime analysis than the global fit. We ascribe it to the intrinsic ruggedness of the free energy landscape of proteins.

physics.bio-ph↗

arXiv2020

Real-time observation of ligand-induced allosteric transitions in a PDZ domain

While allostery is of paramount importance for protein regulation, the underlying dynamical process of ligand (un)binding at one site, resulting time evolution of the protein structure, and change of the binding affinity at a remote site is not well understood. Here the ligand-induced conformational transition in a widely studied model system of allostery, the PDZ2 domain, is investigated by transient infrared spectroscopy accompanied by molecular dynamics simulations. To this end, an azobenzene derived photoswitch is linked to a peptide ligand in a way that its binding affinity to the PDZ2 domain changes upon switching, thus initiating an allosteric transition in the PDZ2 domain protein. The subsequent response of the protein, covering four decades of time ranging from $\sim$1~ns to $\sim$10~$μ$s, can be rationalize by a remodelling of its rugged free energy landscape, with ver subtle shifts in the populations of a small number of structurally well defined states. It is proposed that structurally and dynamically driven allostery, often discussed as limiting scenarios of allosteric communication, actually go hand-in-hand, allowing the protein to adapt its free energy landscape to incoming signals.

physics.bio-ph↗

arXiv2018

Feynman Diagram Description of 2D-Raman-THz Spectroscopy Applied to Water

2D-Raman-THz spectroscopy of liquid water, which has been presented recently (Proc. Natl. Acad. Sci. USA 110, 20402 (2013)), directly probes the intermolecular degrees of freedom of the hydrogen-bond network. However, being a relatively new technique, its information content is not fully explored as to date. While the spectroscopic signal can be simulated based on molecular dynamics simulation in connection with a water force field, it is difficult to relate spectroscopic signatures to the underlying microscopic features of the force field. Here, a completely different approach is taken that starts from an as simple as possible model, i.e., a single vibrational mode with electrical and mechanical anharmonicity augmented with homogeneous and inhomogeneous broadening. An intuitive Feynman diagram picture is developed for all possible pulse sequences of hybrid 2D-Raman-THz spectroscopy. It is shown that the model can explain the experimental data essentially quantitatively with a very small set of parameters, and it is tentatively concluded that the experimental signal originates from the hydrogen-bond stretching vibration around 170 cm$^{-1}$. Furthermore, the echo observed in the experimental data can be quantified by fitting the model. A dominant fraction of its linewidth is attributed to quasi-inhomogeneous broadening in the slow-modulation limit with a correlation time of 370 fs, reflecting the lifetime of the hydrogen-bond networks giving rise the absorption band.

physics.chem-ph↗