Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response DOI Creative Commons
Giacomo Salvadori, Patrizia Mazzeo, Davide Accomasso

и другие.

Journal of Molecular Biology, Год журнала: 2023, Номер 436(5), С. 168358 - 168358

Опубликована: Ноя. 7, 2023

In this review, we discuss the successes and challenges of atomistic modeling photoreceptors. Throughout our presentation, integrate explanations primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples their practical application specific systems. To enhance effectiveness analysis, focus has been directed towards examination applications across three distinct These include an example Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on pivotal role played matrix in fine-tuning initial photochemical event within embedded chromophore. Furthermore, investigate how localized perturbation initiates cascade events propagating binding pocket throughout entire structure, thanks intricate network interactions between chromophore protein.

Язык: Английский

Influence of pump laser fluence on ultrafast myoglobin structural dynamics DOI Creative Commons
Thomas R. M. Barends, A. Gorel, Swarnendu Bhattacharyya

и другие.

Nature, Год журнала: 2024, Номер 626(8000), С. 905 - 911

Опубликована: Фев. 14, 2024

Abstract High-intensity femtosecond pulses from an X-ray free-electron laser enable pump–probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging femtoseconds to milliseconds a variety biological systems, time-resolved serial crystallography (TR-SFX) has provided detailed structural data isomerization, breakage or formation chemical bonds electron transfer 1,2 . However, all ultrafast TR-SFX studies date have employed such high pump energies that nominally several photons were absorbed per chromophore 3–17 As multiphoton absorption may force protein response into non-physiological pathways, it is great concern 18,19 whether this experimental approach 20 allows valid conclusions be drawn vis-à-vis biologically relevant single-photon-induced reactions Here we describe SFX on photodissociation carboxymyoglobin, showing different fluences yield markedly results. In particular, dynamics observed indicators mechanistically important coherent oscillations Fe–CO bond distance (predicted by recent quantum wavepacket 21 ) are seen depend strongly energy, in line with analysis. Our results confirm both feasibility necessity performing linear photoexcitation regime. We consider starting point reassessing design interpretation insight emerges.

Язык: Английский

Процитировано

19
From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons DOI Creative Commons
Nicolas Caramello, Antoine Royant

Acta Crystallographica Section D Structural Biology, Год журнала: 2024, Номер 80(2), С. 60 - 79

Опубликована: Янв. 24, 2024

Over the last decade, development of time-resolved serial crystallography (TR-SX) at X-ray free-electron lasers (XFELs) and synchrotrons has allowed researchers to study phenomena occurring in proteins on femtosecond-to-minute timescale, taking advantage many technical methodological breakthroughs. Protein crystals various sizes are presented beam either a static or moving medium. Photoactive were naturally initial systems be studied TR-SX experiments using pump–probe schemes, where pump is pulse visible light. Other reaction initiations through small-molecule diffusion gaining momentum. Here, selected examples XFEL synchrotron studies will used highlight specificities instruments methods with respect time resolution, compared cryo-trapping studies.

Язык: Английский

Процитировано

11
A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics DOI Creative Commons
Yunbeom Lee, Key Young Oang, Doyeong Kim

и другие.

Structural Dynamics, Год журнала: 2024, Номер 11(3)

Опубликована: Май 1, 2024

The structure of molecules, particularly the dynamic changes in structure, plays an essential role understanding physical and chemical phenomena. Time-resolved (TR) scattering techniques serve as crucial experimental tools for studying structural dynamics, offering direct sensitivity to molecular structures through signals. Over past decade, advent x-ray free-electron lasers (XFELs) mega-electron-volt ultrafast electron diffraction (MeV-UED) facilities has ushered TR experiments into a new era, garnering significant attention. In this review, we delve basic principles experiments, especially focusing on those that employ x-rays electrons. We highlight variations conditions when employing vs electrons discuss their complementarity. Additionally, cutting-edge XFELs MeV-UED performed at are reviewed. As constructed existing ones undergo upgrades, landscape is poised further expansion. Through aim facilitate effective utilization these emerging opportunities, assisting researchers delving deeper intricate dynamics structures.

Язык: Английский

Процитировано

11
The time revolution in macromolecular crystallography DOI Creative Commons
Georgii Khusainov, J. Standfuss, Tobias Weinert

и другие.

Structural Dynamics, Год журнала: 2024, Номер 11(2)

Опубликована: Март 1, 2024

Macromolecular crystallography has historically provided the atomic structures of proteins fundamental to cellular functions. However, advent cryo-electron microscopy for structure determination large and increasingly smaller flexible signaled a paradigm shift in structural biology. The extensive sequence data from advanced sequencing techniques have been pivotal training computational models accurate prediction, unveiling general fold most proteins. Here, we present perspective on rise time-resolved as new frontier macromolecular determination. We trace evolution pioneering methods modern serial crystallography, highlighting synergy between rapid detection technologies state-of-the-art x-ray sources. These innovations are redefining our exploration protein dynamics, with high-resolution uniquely positioned elucidate dynamic processes at ambient temperatures, thus deepening understanding functionality. propose that integration machine learning advancements will unlock predictive capabilities kinetics, revolutionizing dynamics like revolutionized

Язык: Английский

Процитировано

9
Recent chemical mixing devices for time-resolved serial femtosecond crystallography DOI
Jaehyun Park, Ki Hyun Nam

TrAC Trends in Analytical Chemistry, Год журнала: 2024, Номер 172, С. 117554 - 117554

Опубликована: Янв. 26, 2024

Язык: Английский

Процитировано

8
A snapshot love story: what serial crystallography has done and will do for us DOI Creative Commons
Alessandra Henkel,

Dominik Oberthür

Acta Crystallographica Section D Structural Biology, Год журнала: 2024, Номер 80(8), С. 563 - 579

Опубликована: Июль 10, 2024

Serial crystallography, born from groundbreaking experiments at the Linac Coherent Light Source in 2009, has evolved into a pivotal technique structural biology. Initially pioneered X-ray free-electron laser facilities, it now expanded to synchrotron-radiation facilities globally, with dedicated experimental stations enhancing its accessibility. This review gives an overview of current developments serial emphasizing recent results time-resolved and discussing challenges shortcomings.

Язык: Английский

Процитировано

7
Reversibly switchable fluorescent proteins: “the fair switch project” DOI Creative Commons
Riccardo Nifosı̀, Barbara Storti, Ranieri Bizzarri

и другие.

Deleted Journal, Год журнала: 2024, Номер 47(2), С. 91 - 178

Опубликована: Фев. 1, 2024

Abstract Fluorescent proteins (FPs) have transformed cell biology through their use in fluorescence microscopy, enabling precise labeling of via genetic fusion. A key advancement is altering primary sequences to customize photophysical properties for specific imaging needs. particularly notable family engineered mutants constituted by Reversible Switching Proteins (RSFPs), i.e. variant whose optical can be toggled between a bright and dark state, thereby adding further dimension microscopy imaging. RSFPs strongly contributed the super-resolution (nanoscopy) revolution that has occurred last 20 years afforded new knowledge biochemistry at nanoscale. Beyond high-resolution applications, flexibility been exploited apply these other non-conventional schemes such as photochromic resonance energy transfer (FRET). In this work, we explore origins development behaviors FPs examine intricate relationships structure photoswitching ability. We also discuss simple mathematical model accounts observed kinetics. Although review most developed over past two decades, our main goal provide clear understanding switching phenotypes molecular bases. Indeed, comprehension crucial selecting right protein or engineer existing ones. To complete picture, highlight some detail exciting applications RSFPs, field microscopy.

Язык: Английский

Процитировано

5
Structural Characterization of Fluorescent Proteins Using Tunable Femtosecond Stimulated Raman Spectroscopy DOI Open Access
Cheng Chen,

J. Nathan Henderson,

Dmitry A. Ruchkin

и другие.

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(15), С. 11991 - 11991

Опубликована: Июль 26, 2023

The versatile functions of fluorescent proteins (FPs) as fluorescence biomarkers depend on their intrinsic chromophores interacting with the protein environment. Besides X-ray crystallography, vibrational spectroscopy represents a highly valuable tool for characterizing chromophore structure and revealing roles chromophore-environment interactions. In this work, we aim to benchmark ground-state signatures series FPs emission colors spanning from green, yellow, orange, red, well solvated model some these FPs, using wavelength-tunable femtosecond stimulated Raman (FSRS) in conjunction quantum calculations. We systematically analyzed discussed four factors underlying properties FP chromophores: sidechain structure, conjugation conformation, A prominent bond-stretching mode characteristic quinoidal resonance is found be conserved most investigated, which can used marker interpret interactions structural effects electronic chromophore. fundamental insights gained light-sensing units (e.g., active sites) substantiate unique powerful capability FSRS delineating high sensitivity resolution solution matrices. comprehensive characterization various across colorful palette could also serve solid foundation future spectroscopic studies rational engineering diverse improved functions.

Язык: Английский

Процитировано

11
Application of density matrix Wigner transforms for ultrafast macromolecular and chemical x-ray crystallography DOI Creative Commons
Samuel Perrett, Viktoria Chatrchyan, Tiago Buckup

и другие.

The Journal of Chemical Physics, Год журнала: 2024, Номер 160(10)

Опубликована: Март 8, 2024

Time-Resolved Serial Femtosecond Crystallography (TR-SFX) conducted at X-ray Free Electron Lasers (XFELs) has become a powerful tool for capturing macromolecular structural movies of light-initiated processes. As the capabilities XFELs advance, we anticipate that new range coherent control and Raman measurements will achievable. Shorter optical x-ray pulse durations increasingly more exotic regimes are becoming available free electron lasers. Moreover, with high repetition enabled by superconducting technology European XFEL (EuXFEL) Linac Coherent Light Source (LCLS-II) , it be possible to improve signal-to-noise ratio light-induced differences, allowing observation vibronic motion on sub-Angstrom level. To predict assign this motion, which is measurable technique, theoretical approaches must developed. In paper, present density matrix approach model various population dynamics system, considers molecular system parameters excitation conditions. We emphasize use Wigner transform time-dependent matrix, provides phase space representation can directly compared experimental positional displacements measured in TR-SFX experiment. Here, extend results from simple models include realistic schemes large relaxation terms. explore variety using multiple systems parameters. An open-source software package provided perform simulation transformations. The allows us define any arbitrary level as well electric field interaction Hamiltonian.

Язык: Английский

Процитировано

3
Advanced quantum and semiclassical methods for simulating photoinduced molecular dynamics and spectroscopy DOI Creative Commons
Shirin Faraji, David Picconi, Elisa Palacino‐González

и другие.

Wiley Interdisciplinary Reviews Computational Molecular Science, Год журнала: 2024, Номер 14(5)

Опубликована: Сен. 1, 2024

Abstract Molecular‐level understanding of photoinduced processes is critically important for breakthroughs in transformative technologies utilizing light, ranging from photomedicine to photoresponsive materials. Theory and simulation play a crucial role this task. Despite great advances hardware computational methods, the theoretical description phenomena presence complex environments external photoexcitation conditions still poses formidable challenges theoreticians there are numerous formal difficulties that must be overcome. The development predictive, accurate, at same time, computationally efficient approaches describe problems photochemistry photophysics an active field research contemporary chemistry. In advanced review, we discuss modern novel have been recently developed excited‐electronic structure multiscale modeling, with special emphasis on coupled electron‐nuclear dynamics spectroscopy, fully quantum semi‐classical methodologies—including dissipative effects, explicit light interaction, femtosecond time‐resolved software infrastructure. This article categorized under: Software > Quantum Chemistry Electronic Structure Combined QM/MM Methods Theoretical Physical Spectroscopy Molecular Modeling

Язык: Английский

Процитировано

3