In this review, we aim to introduce the reader to the technique of electrical impedance spectroscopy (EIS) with a focus on its biological, biomaterials, and medical applications. We explain the theoretical and experimental aspects of the EIS with the details essential for biological studies, i.e., interaction of metal electrodes with biological matter and liquids, strategies of measurement rate increasing, noise reduction in bio-EIS experiments, etc. We also give various examples of successful bio-EIS practical implementations in science and technology, from whole-body health monitoring and sensors for vision prosthetic care to single living cell examination platforms, virus disease research, biomolecules detection, and implementation of novel biomaterials. The present review can be used as a bio-EIS tutorial for students as well as a handbook for scientists and engineers because of the extensive references covering the contemporary research papers in the field.

Rhodopsins are seven α-helical membrane proteins that are of great importance in chemistry, biology, and modern biotechnology. Any in silico study on rhodopsin properties and functioning requires a high-quality three-dimensional structure. Due to particular difficulties with obtaining membrane protein structures from the experiment, in silico prediction of the three-dimensional rhodopsin structure based only on its primary sequence is an especially important task. For the last few years, significant progress was made in the field of protein structure prediction, especially for methods based on comparative modeling. However, the majority of this progress was made for soluble proteins and further investigations are needed to achieve similar progress for membrane proteins. In this paper, we evaluate the performance of modern protein structure prediction methodologies (implemented in the Medeller, I-TASSER, and Rosetta packages) for their ability to predict rhodopsin structures. Three widely used methodologies were considered: two general methodologies that are commonly applied to soluble proteins and a methodology that uses constraints that are specific for membrane proteins. The test pool consisted of 36 target-template pairs with different sequence similarities that was constructed on the basis of 24 experimental rhodopsin structures taken from the RCSB database. As a result, we showed that all three considered methodologies allow obtaining rhodopsin structures with the quality that is close to the crystallographic one (root mean square deviation (RMSD) of the predicted structure from the corresponding X-ray structure up to 1.5 Å) if the target-template sequence identity is higher than 40%. Moreover, all considered methodologies provided structures of average quality (RMSD < 4.0 Å) if the target-template sequence identity is higher than 20%. Such structures can be subsequently used for further investigation of molecular mechanisms of protein functioning and for the development of modern protein-based biotechnologies.

Photopharmacology is a field of medicine and pharmacology that uses light to selectively activate or deactivate pharmaceutical agents. This approach significantly enhances and localizes the drug action and, therefore, reduces its side effects. Apart from the bioactive moiety, any photopharmacological compound should contain a photoactive group that must absorb light at the desired wavelength and reorganize the molecular structure after photoactivation. The design of an effective photopharmacological compound requires careful tuning of physical, chemical, and biological properties. The present review summarizes and analyzes the main approaches to the molecular design of photopharmacological drugs based on azobenzene or azoheteroarenes. The main ideas and methods used for tuning spectral and photochemical properties of compounds of this class are discussed. A comparative analysis of main computational methods for their in silico screening is carried out; the most common approaches to the synthesis of azobenzenes and azoheteroarenes derivatives are systematized. Special attention is given to the methods and approaches that are specific to the molecular design of photopharmacological compounds with required physicochemical and photochemical properties. The bibliography includes 212 references.

A typical feature of proteins from the rhodopsin family is the sensitivity of their absorption band maximum to protein amino acid composition. For this reason, studies of these proteins often require methodologies that determine spectral shift caused by amino acid substitutions. Generally, quantum mechanics/molecular mechanics models allow for the calculation of a substitution-induced spectral shift with high accuracy, but their application is not always easy and requires special knowledge. In the present study, we propose simple models that allow us to estimate the direct effect of a charged or polar residue substitution without extensive calculations using only rhodopsin three-dimensional structure and plots or tables that are provided in this article. The models are based on absorption maximum values calculated at the SORCI+Q level of theory for cis- and trans-forms of retinal protonated Schiff base in an external electrostatic field of charges and dipoles. Each value corresponds to a certain position of a charged or polar residue relative to the retinal chromophore. The proposed approach was evaluated against an example set consisting of twelve bovine rhodopsin and sodium pumping rhodopsin mutants. The limits of the applicability of the models are also discussed. The results of our study can be useful for the interpretation of experimental data and for the rational design of rhodopsins with required spectral properties.

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