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International audience; The activation of rhodopsin, the light-sensitive G-protein-coupled receptor responsible for dim-light vision in vertebrates, is driven by an ultrafast excited-state double-bond isomerization with a quantum efficiency of almost 70%. The origin of such light sensitivity is not understood and a key question is whether in-phase nuclear motion controls the quantum efficiency value. In this study we used hundreds of quantum-classical trajectories to show that, 15 fs after light absorption, a degeneracy between the reactive excited state and a neighbouring state causes the splitting of the rhodopsin population into subpopulations. These subpopulations propagate with different velocities and lead to distinct contributions to the quantum efficiency. We also show here that such splitting is modulated by protein electrostatics, thus linking amino acid sequence variations to quantum efficiency modulation. Finally, we discuss how such a linkage that in principle could be exploited to achieve higher quantum efficiencies would simultaneously increase the receptor thermal noise leading to a trade-off that may have played a role in rhodopsin evolution.

The use of light-responsive proteins to control both living or synthetic cells, is at the core of the expanding fields of optogenetics and synthetic biology. It is thus apparent that a richer reaction toolbox for the preparation of such systems is of fundamental importance. Here, we provide a proof-of-principle demonstration that Morita-Baylis-Hillman adducts can be employed to perform a facile site-specific, irreversible and diastereoselective click-functionalization of a lysine residue buried into a lipophilic binding pocket and yielding an unnatural chromophore with an extended π-system. In doing so we effectively open the path to the in vitro preparation of a library of synthetic proteins structurally reminiscent of xanthopsin eubacterial photoreceptors. We argue that such a library, made of variable unnatural chromophores inserted in an easy-to-mutate and crystallize retinoic acid transporter, significantly expand the scope of the recently introduced rhodopsin mimics as both optogenetic and "lab-on-a-molecule" tools.

Recently, progress in IR sources has led to the discovery that humans can detect infrared (IR) light. This is hypothesized to be due to the two-photon absorption (TPA) events promoting the retina dim-light rod photoreceptor rhodopsin to the same excited state populated via one-photon absorption (OPA). Here, we combine quantum mechanics/molecular mechanics and extended multiconfiguration quasi-degenerate perturbation theory calculations to simulate the TPA spectrum of bovine rhodopsin (Rh) as a model for the human photoreceptor. The results show that the TPA spectrum of Rh has an intense S0 → S1 band but shows also S0 → S2 and S0 → S3 transitions whose intensities, relative to the S0 → S1 band, are significantly increased when compared to the corresponding bands of the OPA spectrum. In conclusion, we show that IR light in the 950 nm region can be perceived by rod photoreceptors, thus supporting the two-photon origin of the IR perception. We also found that the same photoreceptor can perceive red (i.e., close to 680 nm) light provided that TPA induces population of S2.

Background The human ether a-go-go-related gene 1 (HERG1) is involved in tumor progression; however, its role in esophageal squamous cell carcinoma (ESCC) is not well studied. This study investigated HERG1 function in ESCC progression and elucidated the underlying mechanisms. Methods The prognostic value of HERG1 was determined by immunohistochemistry in ESCC biopsies. Cell growth and proliferation were analyzed by colony formation and methyl thiazolyl tetrazolium assays. Cell migration and invasion were analyzed by wound healing and Boyden transwell assays. Epithelial-mesenchymal transition (EMT) was evaluated by immunoblotting and quantitative polymerase chain reaction (qPCR). A xenograft mouse model was used to validate the tumorigenic and metastatic roles of HERG1 in vivo. Results HERG1 expression was overall higher in ESCC tissues compared to adjacent non-tumor tissues. A retrospective analysis of 349 patients with ESCC (stages I–IV) confirmed increased HERG1 expression was associated with disease progression and higher mortality rate. The overall survival of the patients was significantly worse when their tumors displayed higher HERG1 expression. HERG1 knockdown reduced tumor growth and metastasis in athymic mice. HERG1 affected the proliferation, migration, and invasion of two ESCC cell lines (TE-1 and KYSE-30). Changes in HERG1 expression affected the expression of cell cycle- and EMT-related proteins; these effects were reversed by altering the expression of thioredoxin domain-containing protein 5 (TXNDC5), which is also associated with the clinicopathological characteristics of patients with ESCC and is relevant to HERG1 in pathological biopsies. Additionally, HERG1 expression altered phosphoinositide 3-kinase (PI3K) and AKT phosphorylation, thereby affecting TXNDC5 expression. Conclusions HERG1 contributes to poor prognosis in patients with ESCC by promoting ESCC cell proliferation, migration, and invasion via TXNDC5 through the PI3K/AKT signaling pathway. Our findings provided novel insights into the pathology of ESCC and role of HERG1 in tumor progression, suggesting that targeting HERG1 has potential diagnostic and therapeutic value for ESCC treatment. Electronic supplementary material The online version of this article (10.1186/s13046-019-1284-y) contains supplementary material, which is available to authorized users.

This is the peer reviewed version of the following article: Mroginski, Adam, Amoyal, Barnoy, Bondar, ... Schapiro. (2020). Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochemistry and Photobiology, 97(2):243-269, which has been published in final form at https://doi.org/10.1111/php.13372. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited. This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.

The automatic building of quantum mechanical/molecular mechanical models (QM/MM) of rhodopsins has been recently proposed. This is a prototype of an approach that will be expanded to make possible the systematic computational investigation of biological photoreceptors. QM/MM models represent useful tools for biophysical studies and for protein engineering, but have the disadvantage of being time-consuming to construct, error prone and, also, of not being consistently constructed by researchers operating in different laboratories. These basic issues impair the possibility to comparatively study hundreds of photoreceptors of the same family, as typically required in biological or biotechnological studies. Thus, in order to carry out systematic studies of photoreceptors or, more generally, light-responsive proteins, some of the authors have recently developed the Automatic Rhodopsin Modeling (ARM) protocol for the fast generation of combined QM/MM models of photoreceptors formed by a single protein incorporating in its cavity a single chromophore. In this chapter, we review the results of such research effort by revising the building protocol and benchmark studies and by discussing selected applications.

This article introduces Web-ARM, a specialized tool, online available, designed to build quantum mechanical/molecular mechanical models of rhodopsins, a widely spread family of light-responsive proteins. Web-ARM allows the rapidly building of models of rhodopsins with a documented quality and the prediction of trends in UV-vis absorption maximum wavelengths, based on their excitation energies computed at the CASPT2//CASSCF/Amber level of theory. Web-ARM builds upon the recently reported, python-based a-ARM protocol [J. Chem. Theory Comput., 2019, 15, 3134-3152] and, as such, necessitates only a crystallographic structure or a comparative model in PDB format and a very basic knowledge of the studied rhodopsin system. The user-friendly web interface uses such input to generate congruous, gas-phase models of rhodopsins and, if requested, their mutants. We present two possible applications of Web-ARM, which showcase how the interface can be employed to assist both research and educational activities in fields at the interface between chemistry and biology. The first application shows how, through Web-ARM, research projects (e.g., rhodopsin and rhodopsin mutant screening) can be carried out in significantly less time with respect to using the required computational photochemistry tools via a command line. The second application documents the use of Web-ARM in a real-life educational/training activity, through a hands-on experience illustrating the concepts of rhodopsin color tuning.

Rhodopsins hosting synthetic retinal protonated Schiff base analogues are important for developing tools for optogenetics and high-resolution imaging. The ideal spectroscopic properties of such analogues include long-wavelength absorption/emission and fast/hindered photoisomerization. While the former may be achieved, for instance, by elongating the chromophore π-system, the latter requires a detailed understanding of the substituent effects (i.e. steric or electronic) on the chromophore light-induced dynamics. Below, we compare the results of QM/MM excited state trajectories of native and analogue-hosting microbial rhodopsins from the eubacterium Anabaena. The results uncover a relationship between nature of the substituent on the analogue (i.e. electron donating (a Me group) or withdrawing (a CF3 group)) and rhodopsin excited state lifetime. Most importantly, we show that electron donating or With drawing substituents cause a decrease or an increase in the electronic mixing of the first two excited states which, in turn, controls the photoisomerization speed.

Aerobic glycolysis plays an important role in cancer progression. New target genes regulating cancer aerobic glycolysis must be explored to improve patient prognosis. Mitochondrial topoisomerase I (TOP1MT) deficiency suppresses glucose oxidative metabolism but enhances glycolysis in normal cells. Here, we examined the role of TOP1MT in gastric cancer (GC) and attempted to determine the underlying mechanism. Using in vitro and in vivo experiments and analyzing the clinicopathological characteristics of patients with GC, we found that TOP1MT expression was lower in GC samples than in adjacent nonmalignant tissues. TOP1MT knockdown significantly promoted GC migration and invasion in vitro and in vivo. Importantly, TOP1MT silencing increased glucose consumption, lactate production, glucose transporter 1 expression and the epithelial-mesenchymal transition (EMT) in GC. Additionally, regulation of glucose metabolism induced by TOP1MT was significantly associated with lactate dehydrogenase A (LDHA) expression. A retrospective analysis of clinical data from 295 patients with GC demonstrated that low TOP1MT expression was associated with lymph node metastasis, recurrence and high mortality rates. TOP1MT deficiency enhanced glucose aerobic glycolysis by stimulating LDHA to promote GC progression.

In recent years, the potential energy surfaces of the penta-2,4-dieniminium cation have been investigated using several electronic structure methods. The resulting pool of geometrical, electronic, and energy data provides a suitable basis for the construction of a topographically correct analytical model of the molecule force field and, therefore, for a better understanding of this class of molecules, which includes the chromophore of visual pigments. In the present contribution, we report the construction of such a model for regions of the force field that drive the photochemical and thermal isomerization of the central double bound of the cation. While previous models included only two modes, it is here shown that the proposed three-mode model and corresponding set of parameters are able to reproduce the complex topographical and electronic structure features seen in electronically correlated data obtained at the XMCQDPT2//CASSCF/6-31G* level of theory.

Figure S1.â F-actin appearance of ESCC cells in different treatment groups was observed by immunofluorescence staining. Table S1. Primer sequences for HERG1 and TXNDC5 overexpression. Table S2. Short hairpin RNA (shRNA) sequences for HERG1 silencing. Table S3. Short interfering RNA (siRNA) sequences targeting TXNDC5. Table S4. Primers used for quantitative polymerase chain reaction (qPCR) analyses. Table S5. Clinicopathological characteristics of patients with ESCC exhibiting high, medium, and low intensity HERG1 immunohistochemical staining. Table S6. Clinicopathological characteristics of patients with ESCC exhibiting high, medium, and low intensity TXNDC5 immunohistochemical staining. (DOC 573 kb)

While the light-induced population dynamics of different photoresponsive proteins has been investigated spectroscopically, systematic computational studies have not yet been possible due to the phenomenally high cost of suitable high level quantum chemical methods and the need of propagating hundreds, if not thousands, of nonadiabatic trajectories. Here we explore the possibility of studying the photodynamics of rhodopsins by constructing and investigating quantum mechanics/molecular mechanics (QM/MM) models featuring reduced retinal chromophores. In order to do so we use the sensory rhodopsin found in the cyanobacterium Anabaena PCC7120 (ASR) as a benchmark system. We find that the basic mechanistic features associated with the excited state dynamics of ASR QM/MM models are reproduced using models incorporating a minimal (i.e., three double-bond) chromophore. Furthermore, we show that ensembles of nonadiabatic ASR trajectories computed using the same abridged models replicate, at both the CASPT2 and CASSCF levels of theory, the trends in spectroscopy and lifetimes estimated using unabridged models and observed experimentally at room temperature. We conclude that a further expansion of these studies may lead to low-cost QM/MM rhodopsin models that may be used as effective tools in high-throughput in silico mutant screening.

Vibronic coupling is key to efficient energy flow in molecular systems and a critical component of most mechanisms invoking quantum effects in biological processes. Despite increasing evidence for coherent coupling of electronic states being mediated by vibrational motion, it is not clear how and to what degree properties associated with vibrational coherence such as phase and coupling of atomic motion can impact the efficiency of light-induced processes under natural, incoherent illumination. Here, we show that deuteration of the H11–C11=C12–H12 double-bond of the 11-cis retinal chromophore in the visual pigment rhodopsin significantly and unexpectedly alters the photoisomerization yield while inducing smaller changes in the ultrafast isomerization dynamics assignable to known isotope effects. Combination of these results with non-adiabatic molecular dynamics simulations reveals a vibrational phase-dependent isotope effect that we suggest is an intrinsic attribute of vibronically coherent photochemical processes.

Spectral data show that the photoisomerization of retinal protonated Schiff base (rPSB) chromophores occurs on a 100 fs time scale or less in vertebrate rhodopsins, it is several times slower in microbial rhodopsins and it is between one and 2 orders of magnitude slower in solution. These time scale variations have been attributed to specific modifications of the topography of the first excited state potential energy surface of the chromophore. However, it is presently not clear which specific environment effects (e.g., electrostatic, electronic, or steric) are responsible for changing the surface topography. Here, we use QM/MM models and excited state trajectory computations to provide evidence for an increase in electronic mixing between the first and the second excited state of the chromophore when going from vertebrate rhodopsin to the solution environments. Ultimately, we argue that a correlation between the lifetime of the first excited state and electronic mixing between such state and its higher neighbor, may have been exploited to evolve rhodopsins toward faster isomerization and, possibly, light-sensitivity.

We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information on the protonation state of ionizable side chains and distributions of external counterions. Starting with such information, a model formed by a fixed environment system, a flexible cavity system, and a chromophore system is automatically generated. The results of the predicted vertical excitation energy for 27 different rhodopsins including vertebrate, invertebrate, and microbial pigments indicate that such basic models could be employed for predicting trends in spectral changes and/or correlate the spectral changes with structural variations in large sets of proteins.

We report here a clinical and molecular study on a case suffer from severe fever with thrombocytopenia syndrome (SFTS) due to a new type of bunyavirus, named SFTS bunyavirus (SFTSV), in Zhejiang Province China. The key clinical features of this patient include fever, lymphocytopenia and thrombocytopenia. We carried out a serological and molecular investigation in the indicated case and on relatives with close contact. The SFTSV infection was confirmed through amplification of viral genetic material using the polymerase chain reaction (PCR) from the patient's serum, but not relatives with close contact. Subsequently direct sequence of PCR product demonstrated a homology of 94-96% in the nucleotide sequence compared to a reference sequence previously reported, in which the majority of patients originated from an epidemic area of Central and Northeast China. Our results suggest that SFTSV can occur in a non-epidemic area due to a similar strain of SFTSV that apparently affect the blood system, implying the importance of dissecting the pathogenesis of SFTS as well as mode of infection.