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The main cysteine protease (M pro ) of coronavirus SARS-CoV-2 has become a promising target for computational development in anti-COVID-19 treatments. Here, we benchmarked the performance of six biomolecular molecular dynamics (MD) force fields (OPLS-AA, CHARMM27, CHARMM36, AMBER03, AMBER14SB and GROMOS G54A7) and three water models (TIP3P, TIP4P and SPC) for reproducing the native fold and the enzymatic activity of M pro as monomeric and dimeric units. The MD sampling up to 1 μs suggested that the proper choice of the force fields and water models plays an essential role in reproducing the tertiary structure and the inter-residue distance between the catalytic dyad His41-Cys145. We found that while most benchmarked all-atom force fields reproduce well the native fold of M pro , the CHARMM27/TIP3P and OPLS-AA/TIP4P setups revealed a good performance in reproducing the structure of the catalytic domain. In addition, these FF setups were also well-adopted for MD sampling of M pro at the physiologic conditions by mimicking the presence of 100 mM NaCl and the elevated temperature of 310 K. Finally, both FFs were also performed well in reproducing the native fold of M pro in a dimeric form. Therefore, comparing the preservation of the native fold of M pro and the stability of its catalytic site architecture, our MD benchmarking suggests that the OPLS-AA/TIP4P and CHARMM27/TIP3P MD setups at the physiologic conditions may be well-suited for rapid in silico screening and developing broad-spectrum anti-coronaviral therapeutic agents., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

Acute myocarditis remains a diagnostic issue with a wide spectrum of clinical manifestations that could mimic ST-elevation myocardial infarction (STEMI). We present a case of a 26-year-old male with left-sided intense squeezing chest pain associated with elevated troponin, ST-segment elevations, and reduced ejection fraction. The patient was initially suspected of having a STEMI with non-obstructed coronary arteries (MINOCA). However, due to positive pair troponin tests, increased inflammatory markers there was suspected myocarditis and cardiac MRI confirmed this diagnosis. This case highlights the clinical significance of assessment of laboratory markers and cardiac MRI in diagnostics of myocarditis.

Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods., (© 2023 The Chemical Society of Japan & Wiley-VCH GmbH.)

The pandemic caused by the coronavirus SARS-CoV-2 led to a global crisis in the world healthcare system. Despite some progress in the creation of antiviral vaccines and mass vaccination of the population, the number of patients continues to grow because of the spread of new SARS-CoV-2 mutations. There is an urgent need for direct-acting drugs capable of suppressing or stopping the main mechanisms of reproduction of the coronavirus SARS-CoV-2. Several studies have shown that the successful replication of the virus in the cell requires proteolytic cleavage of the protein structures of the virus. Two proteases are crucial in replicating SARS-CoV-2 and other coronaviruses: the main protease (Mpro) and the papain-like protease (PLpro). In this review, we summarize the essential viral proteins of SARS-CoV-2 required for its viral life cycle as targets for chemotherapy of coronavirus infection and provide a critical summary of the development of drugs against COVID-19 from the drug repurposing strategy up to the molecular design of novel covalent and non-covalent agents capable of inhibiting virus replication. We overview the main antiviral strategy and the choice of SARS-CoV-2 Mpro and PLpro proteases as promising targets for pharmacological impact on the coronavirus life cycle., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Natural flavonoids are capable of inhibiting glucosidase activity, so they can be used for treating diabetes mellitus and hypertension. However, molecular-level details of their interactions with glucosidase enzymes remain poorly understood. This paper describes the synthesis and spectral characterization of a series of fluorescent flavonols and their interaction with the β-glucosidase enzyme. To tune flavonol-enzyme interaction modes and affinity, we introduced different polar halogen-containing groups or bulky aromatic/alkyl substituents in the peripheral 2-aryl ring of a flavonol moiety. Using fluorescence spectroscopy methods in combination with molecular docking and molecular dynamics simulations, we examined the binding affinity and identified probe binding patterns, which are critical for steric blockage of the key catalytic residues of the enzyme. Using a fluorescent assay, we demonstrated that the binding of flavonol 2e to β-glucosidase decreased its enzymatic activity up to 3.5 times. In addition, our molecular docking and all-atom molecular dynamics simulations suggest that the probe binding is driven by hydrophobic interactions with aromatic Trp and Tyr residues within the catalytic glycone binding pockets of β-glucosidase. Our study provides a new insight into structure-property relations for flavonol-protein interactions, which govern their enzyme binding, and outlines a framework for a rational design of new flavonol-based potent inhibitors for β-glucosidases., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Protonation of key histidine residues has been long implicated in the acid-mediated cellular action of the diphtheria toxin translocation (T-) domain, responsible for the delivery of the catalytic domain into the cell. Here, we use a combination of computational (constant-pH Molecular Dynamics simulations) and experimental (NMR, circular dichroism, and fluorescence spectroscopy along with the X-ray crystallography) approaches to characterize the initial stages of conformational change happening in solution in the wild-type T-domain and in the H223Q/H257Q double mutant. This replacement suppresses the acid-induced transition, resulting in the retention of a more stable protein structure in solutions at pH 5.5 and, consequently, in reduced membrane-disrupting activity. Here, for the first time, we report the pK a values of the histidine residues of the T-domain, measured by NMR-monitored pH titrations. Most peaks in the histidine side chain spectral region are titrated with pK a s ranging from 6.2 to 6.8. However, the two most up-field peaks display little change down to pH 6, which is a limiting pH for this protein in solution at concentrations required for NMR. These peaks are absent in the double mutant, suggesting they belong to H223 and H257. The constant-pH simulations indicate that for the T-domain in solution, the pK a values for histidine residues range from 3.0 to 6.5, with those most difficult to protonate being H251 and H257. Taken together, our experimental and computational data demonstrate that previously suggested cooperative protonation of all six histidines in the T-domain does not occur.

Permeabilization of the mitochondrial outer membrane-a point of no return in apoptotic regulation-is tightly controlled by proteins of the Bcl-2 family. Apoptotic inhibitor Bcl-xL is an important member of this family, responsible for blocking the permeabilization, and is also a promising target for anti-cancer drugs. Bcl-xL exists in the following conformations, each believed to play a role in the inhibition of apoptosis: (i) a soluble folded conformation, (ii) a membrane-anchored (by its C-terminal α8 helix) form, which retains the same fold as in solution and (iii) refolded membrane-inserted conformations, for which no structural data are available. In this review, we present the summary of the application of various methods of fluorescence spectroscopy for studying membrane interaction of Bcl-xL, and specifically the formation of the refolded inserted conformation. We discuss the application of environment-sensitive probes, Förster resonance energy transfer, fluorescence correlation spectroscopy, and fluorescent quenching for structural, thermodynamic, and functional characterization of protein-lipid interactions, which can benefit studies of other members of Bcl-2 (e.g., Bax, BAK, Bid). The conformational switching between various conformations of Bcl-xL depends on the presence of divalent cations, pH and lipid composition. This insertion-refolding transition also results in the release of the BH4 regulatory domain from the folded structure of Bcl-xL, which is relevant to the lipid-regulated conversion between canonical and non-canonical modes of apoptotic inhibition., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors.)

The purpose of the study - to conduct an analysis of the disability of ATO/JFO participants in 2014-2021 with a detailed comparative analysis of data of 2021 and determination of the needs of the mentioned contingent in rehabilitation devices. Operational information was collected according to the statistic form of ATO/OOS participants examined at the medical and social expert commissions: developed by the authors statistical form "Report on the causes of disability, indications for medical, professional and social rehabilitation in ATO participants for _____ year", which was summarized and processed. Materials were collected from 2014 to 2021. More than a half of those recognized for the first time as disabled, 2,997 people in 2021 (86.0%), 2,624 people in 2020 (81.2%), 3,297 people in 2019 (79.3%), 2,848 people (75.5%) in 2018 and 1,859 people (65.0%) in 2017 - received the disability group not as a result of traumatic injuries, but for other unspecified reasons that did not have a traumatization factor. The main causes of disability were diseases of the circulatory system (47.9%), musculoskeletal system (13.4%), mental and behavioral disorders (7.2%), neoplasms (3.8%), diseases of the nervous system (3.3%), endocrine diseases, nutritional disorders, and metabolic disorders (3.2%), diseases of the digestive organs (2.0%), some infectious and parasitic diseases (1.6%), respiratory diseases (1.3%) and other reasons (0.7%). In 2021, less than ¼ (14.0%) of ATO/JFO participants were initially recognized as disabled due to various traumatic injuries, which is 25.5% less than in 2020. Among the patients with injuries of the musculoskeletal system, prevailed the victims with injuries of the lower extremities - 92 people, with injuries of the upper extremities - 44 people, polytraumas 38 people, combined injuries - 22 people. Traumatic lesions of the spinal cord led to the onset of disability in 7 persons, traumatic eye lesions in 12 persons. Medical rehabilitation services, including restorative treatment, reconstructive surgery, and orthotics, were the most needed among the examined ATO/JFO participants. More than half of the participants of ATO/JFO received the disability group due to other reasons that did not have a trauma factor, not traumatic injuries. Traumatic brain lesions accounted for 6.9% of the total number of ATO/JFO participants recognized as disabled, musculoskeletal injuries - 3.9%. 1.1% were recognized as disabled due to polytraumas, 0.2% due to combined injuries. Traumatic lesions of the spinal cord led to the onset of disability in 0.2%. With a traumatic eye injury, 0.3% were recognized as disabled. Complicated limb injuries with damage to peripheral nerves accounted for 0.1% and blood vessels - 0.1%. Medical rehabilitation services, including restorative treatment, reconstructive surgery, and orthotics, were the most needed among ATO/JFO participants examined. The increase in the number of ATO/JFO participants initially recognized as disabled due to reasons not related to traumatic lesions requires further careful analysis, determination of the reasons for such a situation and the development of effective measures for the prevention of disability and the return of lost functionality in the specified contingent, which will become the topic of further research.

Dynamic disorder of the lipid bilayer presents a challenge for establishing structure-function relationships in membrane proteins, especially to those that insert by refolding from soluble states, e.g., bacterial toxins and Bcl-2 apoptotic regulators. Because many high-resolution structural techniques cannot be easily applied to such systems, methods like depth-dependent fluorescence quenching gained prominence. Over three decades ago, Prof. Erwin London and his co-workers revolutionized the studies of membrane protein insertion by introducing a quantitative approach to the analysis of membrane quenching data and inspired many researchers to continue this work. Here, we illustrate how the application of the quantitative analysis yields new insights into previously published results. We have used the method of distribution analysis (DA) to calculate the precise immersion depth of NBD fluorophores selectively attached to various single-cysteine mutants of the apoptotic factor BAX from quenching data obtained with a series of spin-labeled lipids. The original qualitative analysis interpreted the higher quenching determined for shallower probes in positions flanking the helix 9 of BAX as evidence of a transmembrane helix 9 topology. The quantitative DA, however, revealed that a transmembrane topology of helix 9 of BAX is unlikely, as it would require labeling sites that are only 15 residues apart in a helical conformation to be separated by a transverse distance of over 45 Å., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The problem of interaction between aseptic necrosis of the femoral head (ANFH) and mental disorders is of interest according to modern research. It is known that with ANFH, altered brain activity is detected in areas related to pain, emotions, and cognition, which proves the influence of joint disease on the formation of non-psychotic mental disorders (NPD). The current NPR along with somatic symptoms, affect the quality of life of patients. Quality of life is related to health and can be used to assess the quality of health, diagnose the nature, severity and prognosis of the disease, and evaluate the results of treatment.; Purpose - studying the quality of life of patients with ANFH and non-psychotic mental disorders in the course of treatment; 137 patients (92 men (67.2%), of whom 96 completed the study) were included in the study. A clinical-psychopathological study was conducted to determine the leading syndrome of non-psychotic mental disorders, and socio-anamnestic data were collected. Quality of life was assessed using a questionnaire quality of life SF-12 Patients of the first clinical group included participants with a duration of ANFH up to 5 years, and the second main clinical group included patients with a duration of ANFH of more than 5 years.; The average index of the mental component of the quality of life for the duration of ANFH up to 5 years was 43.46±9.00 points, and for the duration of more than 5 years - 36.55±10.35 points. The obtained results of the quality-of-life indicator of the patients in the study indicate a lower quality of life compared to the average population indicator (50±10 points). As the duration of ANFH increases, the quality of life deteriorates, and the mental component to a greater extent than the physical. Considering the selected leading syndromes, correction of NPR psychological and psychopharmacological interventions (antidepressants and/or anxiolytics depending on the clinical form of NPR) was carried out. Under the influence of the NPR correction, the following features were revealed: in the first main group, the physical component of the quality of life improved by 3.25 points (p<0.05), the mental component of the quality of life increased by 6.4 points (p<0.05). In the second main group, the physical component of the quality of life increased by 4.55 points (p<0.05), and the mental component of the quality of life changed positively by 10.55 points (p<0.05).; When the duration of the disease is up to 5 years, the leading syndrome of NPR affects the quality of life in various ways. In the presence of anxiety-depressive or depressive-hypochondriac syndromes, it is possible to restore the mental component of QoL to a normal level. The leading astheno-apathetic syndrome does not affect the quality of life of patients. When the duration of ANFH is more than 5 years, the mental component of QOL is most reduced in leading anxiety-depressive and depressive-hypochondriac disorders.

Cancerous tissues undergo extensive changes to their cellular environments that differentiate them from healthy tissues. These changes include changes in extracellular pH and Ca 2+ concentrations, and the exposure of phosphatidylserine (PS) to the extracellular environment, which can modulate the interaction of peptides and proteins with the plasma membrane. Deciphering the molecular mechanisms of such interactions is critical for advancing the knowledge-based design of cancer-targeting molecular tools, such as pH-low insertion peptide (pHLIP). Here, we explore the effects of PS, Ca 2+ , and peptide protonation state on the interactions of pHLIP with lipid membranes. Cellular studies demonstrate that exposed PS on the plasma membrane promotes pHLIP targeting. The magnitude of this effect is dependent on extracellular Ca 2+ concentration, indicating that divalent cations play an important role in pHLIP targeting in vivo. The targeting mechanism is further explored with a combination of fluorescence and circular dichroism experiments in model membranes and microsecond-timescale all-atom molecular dynamics simulations. Our results demonstrate that Ca 2+ is engaged in coupling peptide-lipid interactions in the unprotonated transmembrane conformation of pHLIP. The simulations reveal that while the pH-induced insertion leads to a strong depletion of PS around pHLIP, the Ca 2+ -induced insertion has the opposite effect. Thus, extracellular levels of Ca 2+ are crucial to linking cellular changes in membrane lipid composition with the selective targeting and insertion of pHLIP. The characterized Ca 2+ -dependent coupling between pHLIP sidechains and PS provides atomistic insights into the general mechanism for lipid-coupled regulation of protein-membrane insertion by divalent cations., (© 2022 The Protein Society.)

The purpose of this article is to study individual aspects of the impact of the COVID-19 pandemic on the mental state of PLHIV. The study covered 146 patients with HIV-related diseases who attended the outpatient department of the communal enterprise "Dnepropetrovsk Regional Center for Socially Significant Diseases of the Dnepropetrovsk Regional Council" during September-October 2020. HIV-infected were interviewed using a self-developed questionnaire. We used integrative test of anxiety by A.P. Bizyuk to investigate anxiety. The frequency of increased anxiety over the past half year among respondents is 15.75%; frequency of insomnia, weight loss, eating disorders - 12.32%; In 10.42% (n=15) cases, PLHIV had episodes of acute feelings of fear, palpitations, shortness of breath, chest tightness, panic while watching news about COVID-19. A high level of average value of situational anxiety among PLHIV was revealed - 7.8 (1.3) stanins - M (SD), in the structure of which "social defense reactions", a phobic component and anxious assessment of prospects prevail. 74.6% of HIV-infected strictly adhered to additional protection against COVID-19; 63.01% - considered crowded places a threat to their health; 52.74% were afraid to get sick with COVID-19; 49.31% - had an increased interest of PLHIV in COVID-19 in Ukraine and the world. The respondents used the following additional methods of protection: self-isolation (60%), strict adherence to distance (75%), disinfection of their belongings and household items (10%). The mental state of PLHIV during the coronavirus pandemic indicates the presence of symptoms of distress: the manifestations of anxiety-depressive disorders, insomnia have increased, a fixation has appeared on their physical condition, social isolation and distancing have increased. Further research into the characteristics of the psychoemotional state of PLHIV will help improve the organization of medical and social assistance in the current situation of the COVID-19 pandemic.

Regulation of apoptosis is tightly linked with the targeting of numerous Bcl-2 proteins to the mitochondrial outer membrane (MOM), where their activation or inhibition dictates cell death or survival. According to the traditional view of apoptotic regulation, BH3-effector proteins are indispensable for the cytosol-to-MOM targeting and activation of proapoptotic and antiapoptotic members of the Bcl-2 protein family. This view is challenged by recent studies showing that these processes can occur in cells lacking BH3 effectors by as yet to be determined mechanism(s). Here, we exploit a model membrane system that recapitulates key features of MOM to demonstrate that the proapoptotic Bcl-2 protein BAX and antiapoptotic Bcl-xL have an inherent ability to interact with membranes in the absence of BH3 effectors, but only in the presence of cellular concentrations of Mg 2+ /Ca 2+ Under these conditions, BAX and Bcl-xL are selectively targeted to membranes, refolded, and activated in the presence of anionic lipids especially the mitochondrial-specific lipid cardiolipin. These results provide a mechanistic explanation for the mitochondrial targeting and activation of Bcl-2 proteins in cells lacking BH3 effectors. At cytosolic Mg 2+ levels, the BH3-independent activation of BAX could provide localized amplification of apoptotic signaling at regions enriched in cardiolipin (e.g., contact sites between MOM and mitochondrial inner membrane). Increases in MOM cardiolipin, as well as cytosolic [Ca 2+ ] during apoptosis could further contribute to its MOM targeting and activity. Meanwhile, the BH3-independent targeting and activation of Bcl-xL to the MOM is expected to counter the action of proapoptotic BAX, thereby preventing premature commitment to apoptosis., Competing Interests: The authors declare no competing interest.

The anti-apoptotic protein Bcl-xL regulates apoptosis by preventing the permeation of the mitochondrial outer membrane by pro-apoptotic pore-forming proteins, which release apoptotic factors into the cytosol that ultimately lead to cell death. Two different membrane-integrated Bcl-xL constructs have been identified: a membrane-anchored and a membrane-inserted conformation. Here, we use molecular dynamics simulations to study the effect of the mitochondrial specific lipid cardiolipin and the protein protonation state on the conformational dynamics of membrane-anchored Bcl-xL. The analysis reveals that the protonation state of the protein and cardiolipin content of the membrane modulate the orientation of the soluble head region (helices α1 through α7) and hence the exposure of its BH3-binding groove, which is required for its interaction with pro-apoptotic proteins.

Objective: Generalized tonic-clonic (GTC) seizures are the most common type of generalized seizure and more common in children than adults. This phase 3 study evaluated the efficacy and safety of pregabalin for GTC seizures in adults and children with epilepsy., Methods: This randomized, double-blind, multicenter study evaluated pregabalin (5 mg/kg/day or 10 mg/kg/day) vs placebo as adjunctive therapy for 10 weeks (following a 2-week dose escalation), in pediatric and adult patients (aged 5-65 years) with GTC seizures. Primary endpoint was change in log-transformed 28-day seizure rate during active treatment. Secondary endpoints included responder rates, defined as proportion of patients with ≥50% reduction in 28-day GTC seizure rate from baseline. Safety was monitored throughout., Results: Of 219 patients, 75, 72, and 72 were randomized to adjunctive pregabalin 5 mg/kg/day, 10 mg/kg/day, and placebo, respectively. Fifteen, 11, and 6 patients discontinued from the 5 mg/kg/day, 10 mg/kg/day, and placebo arms, respectively, most commonly due to adverse events (AEs; 10.7%, 6.9%, and 5.6%, respectively). A nonsignificant change in log-transformed mean 28-day seizure rate was seen with pregabalin 10 mg/kg/day vs placebo (least-squares [LS] mean difference -0.01 [95% confidence interval (CI) -0.19 to 0.16]; P = .8889) and with pregabalin 5 mg/kg/day vs placebo (LS mean difference 0.02 [CI -0.15 to 0.19]; P = .8121). Similar observations were noted for adults and children. No significant differences were seen for secondary endpoints with pregabalin vs placebo, including responder rate. The most common AEs (≥10%) were dizziness, headache, and somnolence. Most were of mild/moderate intensity. Seven patients had serious AEs, with one death in the placebo arm (sudden unexpected death in epilepsy)., Significance: Adjunctive pregabalin treatment did not change GTC seizure rate in adults or children. The safety profile of pregabalin was similar to that known; treatment was well tolerated with few discontinuations due to AEs., (© 2021 The Authors. Epilepsia Open published by Wiley Periodicals LLC on behalf of International League Against Epilepsy.)

In recent years, the chemistry of flavonoid glycosylation has undergone significant developments. This mini-review is devoted to summarizing existing strategies and methods for glycosylation of natural and synthetic flavonoids. Herein we overviewed the reaction conditions of flavonoid glycosylation depending on the position of hydroxyl groups in a parent molecule, the degree of it conjugation with the π-system, the presence of steric factors, the formation of intramolecular hydrogen bonds, etc. Especial attention was given to the choice of the glycosyl donor moiety, which has a significant effect on the yield of the final glycosidated products. Finally, a general strategy for regioselective glycosylation of flavonoids containing several hydroxyl groups is outlined., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Khodzhaieva, Gladkov, Kyrychenko and Roshal.)

Diphtheria toxin is among many bacterial toxins that utilize the endosomal pathway of cellular entry, which is ensured by the bridging of the endosomal membrane by the toxin's translocation (T) domain. Endosomal acidification triggers a series of conformational changes of the T-domain, that take place first in aqueous and subsequently in membranous milieu. These rearrangements ultimately result in establishing membrane-inserted conformation(s) and translocation of the catalytic moiety of the toxin into the cytoplasm. We discuss here the strategy for combining site-selective labeling with various spectroscopic methods to characterize structural and thermodynamic aspects of protonation-dependent conformational switching and membrane insertion of the diphtheria toxin T-domain. Among the discussed methods are FRET, FCS and depth-dependent fluorescence quenching with lipid-attached bromine atoms and spin probes. The membrane-insertion pathway of the T-domain contains multiple intermediates and is governed by staggered pH-dependent transitions involving protonation of histidines and acidic residues. Presented data demonstrate that the lipid bilayer plays an active part in T-domain functioning and that the so-called Open-Channel State does not constitute the translocation pathway, but is likely to be a byproduct of the translocation. The spectroscopic approaches presented here are broadly applicable to many other systems of physiological and biomedical interest for which conformational changes can lead to membrane insertion (e.g., other bacterial toxins, host defense peptides, tumor-targeting pHLIP peptides and members of Bcl-2 family of apoptotic regulators)., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Diphtheria toxin, an exotoxin secreted by Corynebacterium that causes disease in humans by inhibiting protein synthesis, enters the cell via receptor-mediated endocytosis. The subsequent endosomal acidification triggers a series of conformational changes, resulting in the refolding and membrane insertion of the translocation (T-)domain and ultimately leading to the translocation of the catalytic domain into the cytoplasm. Here, we use X-ray crystallography along with circular dichroism and fluorescence spectroscopy to gain insight into the mechanism of the early stages of pH-dependent conformational transition. For the first time, we present the high-resolution structure of the diphtheria toxin at a mildly acidic pH (5-6) and compare it to the structure at neutral pH (7). We demonstrate that neither catalytic nor receptor-binding domains change their structure upon this acidification, while the T-domain undergoes a conformational change that results in the unfolding of the TH2-3 helices. Surprisingly, the TH1 helix maintains its conformation in the crystal of the full-length toxin even at pH 5. This contrasts with the evidence from the new and previously published data, obtained by spectroscopic measurements and molecular dynamics computer simulations, which indicate the refolding of TH1 upon the acidification of the isolated T-domain. The overall results imply that the membrane interactions of the T-domain are critical in ensuring the proper conformational changes required for the preparation of the diphtheria toxin for the cellular entry.

The problem of studying, diagnosing and correcting stress-associated disorders resulting from exposure to psychogenic factors, the sources of which are various traumatic events, is one of the most relevant.; The purpose of the work is to create a psychological portrait of a combat participant for the subsequent development of preventive measures for stress-associated disorders. To study the psychological characteristics and psycho-emotional state, a comprehensive clinical and psychological examination of 147 military personnel was carried out after mostly mine-blast injuries received while performing official duties in the ATO zone.; The state of mental functions, and the emotional-volitional sphere and personality traits were evaluated. The points and characteristics of the test methods were analyzed, the total number of points was calculated separately on each scale.; A generalization of the results of the study allowed us to determine the main aspects of the psychological portrait of a military man. The essence of the portrait consists in harmonious restructuring from conscious to unconscious psychological attitudes and vice versa, in changing the subjective hierarchy of values and also to note that the character of the traumatic situation is not important in the portrait of the ATO participant, but the personal attitude of the participant and his environment.

Objective: To evaluate the efficacy and safety of pregabalin as adjunctive treatment for children (aged 1 month-<4 years) with focal onset seizures (FOS) using video-electroencephalography (V-EEG)., Methods: This randomized, placebo-controlled, international study included V-EEG seizure monitoring (48-72 hours) at baseline and over the last 3 days of 14-day (5-day dose escalation; 9-day fixed dose) double-blind pregabalin treatment (7 or 14 mg/kg/d in three divided doses). This was followed by a double-blind 1-week taper. The primary efficacy endpoint was log-transformed seizure rate (log e [24-hour seizure rate + 1]) for all FOS recorded during the double-blind V-EEG monitoring, evaluated in subjects who took ≥1 dose of study medication, experienced ≥1 baseline seizure(s), and had a treatment phase V-EEG. Safety and tolerability were assessed by adverse events (AEs), clinical laboratory data, physical/neurological examinations, vital signs, and electrocardiograms., Results: Overall, 175 patients were randomized (mean age = 28.2 months; 59% male, 69% white, 30% Asian) in a 2:1:2 ratio to pregabalin 7 or 14 mg/kg/d (n = 71 or n = 34, respectively), or placebo (n = 70). Pregabalin 14 mg/kg/d (n = 28) resulted in a statistically significant 35% reduction of log e (24-hour seizure rate + 1) versus placebo (n = 53; P = .022), an effect that was not observed with pregabalin 7 mg/kg/d (n = 59; P = .461). The most frequently reported treatment-emergent AEs for pregabalin 7 mg/kg/d, 14 mg/kg/d, and placebo, respectively, were somnolence (11.3%, 17.6%, and 5.7%) and upper respiratory tract infection (7.0%, 11.8%, and 11.4%). All AEs were mild to moderate in severity., Significance: Pregabalin 14 mg/kg/d (but not 7 mg/kg/d) significantly reduced seizure rate in children with FOS, when assessed using V-EEG, compared with placebo. Both pregabalin dosages were generally safe and well tolerated in children 1 month to <4 years of age with FOS. Safety and tolerability were consistent with the known profile of pregabalin in older children with epilepsy., (Wiley Periodicals, Inc. © 2020 International League Against Epilepsy.)

The inhibition of mitochondrial permeabilization by the anti-apoptotic protein Bcl-xL is crucial for cell survival and homeostasis. Its inhibitory role requires the partitioning of Bcl-xL to the mitochondrial outer membrane from an inactive state in the cytosol, leading to its extensive refolding. The molecular mechanisms behind these events and the resulting conformations in the bilayer are unclear, and different models have been proposed to explain them. In the most recently proposed non-canonical model, the active form of Bcl-xL employs its N-terminal BH4 helix to bind and block its pro-apoptotic target. Here, we used a combination of various spectroscopic techniques to study the release of the BH4 helix (α1) during the membrane insertion of Bcl-xL. This refolding was characterized by a gradual increase in helicity due to the lipid-dependent partitioning-coupled folding and formation of new helix αX (presumably in the originally disordered loop between helices α1 and α2). Notably, a comparison of various fluorescence and circular dichroism measurements suggested the presence of multiple Bcl-xL conformations in the bilayer. This conclusion was explicitly confirmed by single-molecule measurements of Fӧrster Resonance Energy Transfer from Alexa-Fluor-488-labeled Bcl-xL D189C to a mCherry fluorescent protein attached at the N-terminus. These measurements clearly indicated that the refolding of Bcl-xL in the bilayer is not a two-state transition and involves multiple membranous intermediates of variable compactness., Competing Interests: The authors declare no conflict of interest.

The characterization of the behavior of lipid-attached spin probes in a bilayer is of fundamental importance for correct interpretation of the results of both EPR and fluorescence studies of protein-membrane interactions. The knowledge of the immersion depth of TEMPO spin probe attached to lipid headgroup in TEMPO-PC is critical for the determination of the transverse location of fluorescence probes attached to proteins and peptides. The question of bilayer penetration of TEMPO moiety in TEMPO-PC has recently came into prominence in two studies of interfacial solvation (Cheng et al. in Biophys J 109:330-339, 2015; Lee et al. in Biophys J 111:2481-2491, 2016). Here, we re-examine the arguments on TEMPO penetration using the cross-validation of MD simulations and depth-dependent fluorescence-quenching experiments, which confirms that TEMPO in TEMPO-PC penetrates below the level of phosphate groups. The proper analysis of fluorescence quenching requires the use of Tempo position below the level of phosphate groups; and failure to do so will result in substantial systematic errors in determining the penetration of the labeled site on a membrane protein.

Native and modified cyclodextrins (CDs) are routinely used as a capping agent upon the preparation of gold nanoparticles (AuNP); however, their role in the synthesis remains unresolved. Here, the adsorption behavior of β-cyclodextrin (β-CD) onto AuNP was studied by all-atom molecular dynamics (MD) simulations. We found that β-CD binding onto the AuNP surface occurs through multiple non-covalent interactions, among which non-covalent binding of the aliphatic carbon moieties and the hydroxyl oxygen atoms plays a vital role. Surprisingly, the MD analysis revealed that the most preferred binding mode of the β-CD molecules onto the gold surface corresponds to the toroid side geometry. Only minor populations of β-CD molecules were observed, in which the adsorbate molecules are bound onto AuNP by either its primary or secondary rims, respectively. The adsorbed β-CDs formed the multiple-layer coating on AuNP, composed up to three adsorbate layers. We found that for AuNP of the size of 2.9 nm, the maximum water-protecting efficiency of the adsorbate coating occurs upon reaching a value of 40 β-CD molecules, the further increase in the adsorbate content resulted in some self-aggregation of β-CD molecules onto the gold surface. Our findings provide the molecular-level understanding of the adsorption behavior of β-CD onto gold, which is relevant for various applications of CD-capped gold nanostructures., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Thermoresponsive poly(N-vinylcaprolactam) (PVCL) has received growing interest due to a temperature-induced phase transition, which switches its solubility in aqueous solutions. However, the lower critical solution temperature (LCST) of PVCL is greatly influenced by the molecular weight, morphology and the environment. Therefore, despite of numerous experimental studies of the thermal response of PVCL, a driving force and a molecular origin of conformation transitions in solution remain far less studied. To get a better understanding of the coil-to-globule conformation transition of PVCL in aqueous solution, we examined the structure and conformation dynamics of a single-chain PVCL 30 in a temperature range of 280-360 K by using atomistic molecular dynamics (MD) simulations. The united-atom GROMOS G53a6 force field was re-parameterized and fine-tuned by DFT calculations to reproduce the experimental LCST transition of PVCL. Our MD model reproduces the LCST transition of PVCL 30 to occur within a temperature range of 34.6-38.5°. MD simulation results suggest a significant difference between the hydration state of the carbonyl group of PVCL below and above the LCST threshold. The analysis of the number of hydrogen bonds of PVCL with water molecules demonstrates that dehydration of the polymer plays an important role and drives the temperature-induced polymer collapse. Finally, the developed MD model and FF parameters were successfully tested for large-scale systems, such as mixture PVCL 30 oligomer and single-chain PVCL 816 polymer, respectively., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Polymeric nanoparticles are increasingly used as biocompatible carriers for drugs and imaging agents. Understanding their self-assembly dynamics and morphology is of ultimate importance to develop nanoformulations with optimal characteristics. To achieve better performance, it is vital to account for cargo-carrier interactions at the molecular level. The self-assembly dynamics were studied and the internal structure of nanoparticles derived from a series of hydrophobically modified hyaluronic acid was revealed. Environment-sensitive ratiometric fluorescent probes provide valuable information about the nanoparticle's interior morphology, and molecular dynamics simulations complement the overall picture with insights into intramolecular and intermolecular interactions of the polymer, as well as its interactions with the small-molecule load. van der Waals and π-π interactions of the hydrophobic side fragments play a leading role in self-assembly and loading of hydrophobic small molecules. Aliphatic substituents form more extensive hydrophobic domains, while aromatic moieties allow more interaction of the loaded small molecules with the surrounding solvent.

Dynamic disorder of the lipid bilayer presents a challenge for establishing structure-function relationships in membranous systems. The resulting structural heterogeneity is especially evident for peripheral and spontaneously inserting membrane proteins, which are not constrained by the well-defined transmembrane topology and exert their action in the context of intimate interaction with lipids. Here, we propose a concerted approach combining depth-dependent fluorescence quenching with Molecular Dynamics simulation to decipher dynamic interactions of membrane proteins with the lipid bilayers. We apply this approach to characterize membrane-mediated action of the diphtheria toxin translocation domain. First, we use a combination of the steady-state and time-resolved fluorescence spectroscopy to characterize bilayer penetration of the NBD probe selectively attached to different sites of the protein into membranes containing lipid-attached nitroxyl quenching groups. The constructed quenching profiles are analyzed with the Distribution Analysis methodology allowing for accurate determination of transverse distribution of the probe. The results obtained for 12 NBD-labeled single-Cys mutants are consistent with the so-called Open-Channel topology model. The experimentally determined quenching profiles for labeling sites corresponding to L350, N373, and P378 were used as initial constraints for positioning TH8-9 hairpin into the lipid bilayer for Molecular Dynamics simulation. Finally, we used alchemical free energy calculations to characterize protonation of E362 in soluble translocation domain and membrane-inserted conformation of its TH8-9 fragment. Our results indicate that membrane partitioning of the neutral E362 is more favorable energetically (by ~ 6 kcal/mol), but causes stronger perturbation of the bilayer, than the charged E362.

2'-Hydroxy derivatives of 2,5-diaryl-1,3-oxazole are known as environment-sensitive ratiometric excited-state intramolecular proton transfer (ESIPT) fluorescent probes, which are used to monitor physicochemical properties of lipid membranes. However, because of their heterogeneous membrane distribution, accurate experimental determination of the probe position is difficult. To estimate the location of the ESIPT probes in lipid membranes we have performed fluorescence measurements and molecular dynamics (MD) simulations. In the series composed of 2-(2'-hydroxy-phenyl)-5-phenyl-1,3-oxazole (1), 2-(2'-hydroxy-phenyl)-5-(4'-biphenyl)-1,3-oxazole (2), and 2-(2'-hydroxy-phenyl)-phenanthro[9,10-d]-1,3-oxazole (3), the structure of the ESIPT-moiety of 2-(2'-hydroxy-phenyl)-oxazole was varied by either aromatic ring substitution or annealing, leading to the systematical increase in the hydrophobic character of the probes. The comparison of the fluorescence behavior of probes 1-3 in a wide variety of solvents with those in phospholipid vesicles revealed that all three probes prefer to reside inside a membrane. Our MD results demonstrate that the probes locate from the glycerol residues and the polar carbonyl groups of phospholipids up to hydrophobic acyl chain units. It has been found that the probe location correlates well with the size of the aromatic moiety, being gradually shifted from 11.1 Å to 7.6 Å from the bilayer center for probes 1 to 3, respectively. Our results may be useful for the design of novel fluorescent probes for fluorescence sensing of specific regions within a lipid membrane., (Copyright © 2018 Elsevier B.V. All rights reserved.)

The advent of nanomedicine has rejuvenated the need for increased understanding of the fundamental physicochemical properties of polymeric amphiphiles. Hyaluronic acid (HA) is a hydrophilic polysaccharide that is frequently conjugated to hydrophobic moieties and then used to entrap dyes and therapeutics. Here, we develop computational models to examine the effects of the hydrophobic modification on supramolecular behavior among three systematically designed HA derivatives substituted with alkyl chains of increasing length. Our simulations coalesce with experimentally obtained results to demonstrate the dependence of supramolecular behavior on intramolecular forces. We show that the formation of clearly defined hydrophobic domains in samples of octadecylamine-modified HA compared to HA conjugates with shorter alkyl chains is a result of more favorable hydrophobic interactions. Trends in hydrodynamic radius and polydispersity are observed in experimental results that coalesce with theoretical calculations, suggesting that supramolecular properties are dependent on the physicochemical characteristics of individual polymer strands., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Fluorescent nanomaterials require high colloidal stability for effective use in imaging and sensing applications. We herein report the synthesis of carbazole-based organic fluorescent nanoaggregates, and demonstrate the superior colloidal stability of alkyl-substituted dye aggregates over their non-alkylated analogs. The role of alkyl chains in self-assembly and stability of such nanoaggregates is discussed based on both experimental and molecular dynamics simulation data, and spectral characteristics of the precursor dyes and their aggregates are described. The obtained results provide new insights on development of colloidally stable organic fluorescent nanomaterials with low polydispersity., Competing Interests: Conflict of Interests The authors declare no conflicting financial interests.

This article supplies raw data related to a research article entitled "Joint refinement of FRET measurements using spectroscopic and computational tools" (Kyrychenko et al., 2017) [1], in which we demonstrate the use of molecular dynamics simulations to estimate FRET orientational factors in a benchmark donor-linker-acceptor system of enhanced cyan (ECFP) and enhanced yellow (EYFP) fluorescent proteins. This can improve the recalculation of donor-acceptor distance information from single-molecule FRET measurements.

The variability of the orientation factor is a long-standing challenge in converting FRET efficiency measurements into donor-acceptor distances. We propose the use of molecular dynamics (MD) simulations to characterize orientation distributions and thus improve the accuracy of distance measurements. Here, we test this approach by comparing experimental and simulated FRET efficiencies for a model donor-acceptor pair of enhanced cyan and enhanced yellow FPs connected by a flexible linker. Several spectroscopic techniques were used to characterize FRET in solution. In addition, a series of atomistic MD simulations of a total length of 1.5 μs were carried out to calculate the distances and the orientation factor in the FRET-pair. The resulting MD-based and experimentally measured FRET efficiency histograms coincided with each other, allowing for direct comparison of distance distributions. Despite the fact that the calculated average orientation factor was close to 2/3, the application of the average κ 2 to the entire histogram of FRET efficiencies resulted in a substantial artificial broadening of the calculated distribution of apparent donor-acceptor distances. By combining single pair-FRET measurements with computational tools, we demonstrate that accounting for the donor and acceptor orientation heterogeneity is critical for accurate representation of the donor-acceptor distance distribution from FRET measurements., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Chemical modification of silver nanoparticles (AgNPs) with a stabilizing agent, such as poly(vinyl alcohol) (PVA), plays an important role in shape-controlled seeded-growth and colloidal stability. However, theoretical aspects of the stabilizing mechanism of PVA are still poorly understood. To gain a better understanding of the role of PVA in water protecting effects for silver nanoparticles, we developed an atomistic model of a AgNP grafted with single-chain PVA of various lengths. Our model, designed for classical molecular dynamics (MD) simulations, approximates the AgNP as a quasi-spherical silver nanocrystal with 3.9 nm diameter and uses a united-atom representation for PVA with its polymer chain length varying from 220 up to 1540 repeating units. We found that PVA adsorbs onto the AgNP surface through multiple non-covalent interactions, among which non-covalent bonding of the hydroxyl groups plays a key role. The analysis of adsorption isotherms by using the Hill, Scatchard, and McGhee & von Hippel models exhibits evidence for positive binding cooperativity with the cooperativity parameter varying from 1.55 to 2.12. Our results indicate that the size of the PVA polymer rather than its structure plays a crucial role in providing water protecting effects for the AgNP core, varying from 40% up to 91%. The water-protecting efficiency was well approximated by the Langmuir-Freundlich equation, allowing us to predict that the saturated coverage of the nanoparticle of a given diameter of 3.9 nm should occur when the PVA molecular weight approaches 115 kDa, which corresponds to the number of vinyl alcohol monomers being equal to 3100 units.

The analysis of Ukrainian isolate of beet necrotic yellow vein virus has been performed. The partial nucleotide sequence of cDNA corresponding to RNA-2 of BNYVV isolates were analyzed and Ukrainian isolate AG9 of BNYVV was assigned to type A strains based on DNA sequences. The nucleotide sequence of gene encoding a coat protein of Ukrainian isolate of BNYVV was compared with appropriate nucleotide sequences existing in the GeneBank and the phylogenetic analysis of investigated virus was done. It was shown that Ukrainian isolate AG9 of BNYVV has 100 % homology to isolate originating from Sweden.

Fluorescence techniques have become powerful and widely used tools for studies of biochemical and biophysical processes occurring in biological membranes. Various fluorescence methods have played and continue to play key roles in modern membrane science, so that there have been several focused reviews on this topic. Here, I present the progress and recent achievements in various fluorescence approaches commonly utilized in studies of biological membranes. Applications of numerous fluorescence methods have been reviewed, including single molecule detection, confocal scanning fluorescence microscopy and fluorescence lifetime imaging. I focus on the benefits and limitations of various fluorescence techniques and their combinations, as well as the available methods of in vivo studying. A separate section is dedicated to discussing and comparing different classes of fluorescent membrane probes and their applications to the study of biological membranes. The review should provide researchers from chemistry, biochemistry, and biophysics with the necessary background to identify a range of suitable fluorescence methods in order to successfully design and conduct experimental studies on model lipid bilayers and biological membranes.

Determination of the depth of membrane penetration provides important information for studies of membrane protein folding and protein-lipid interactions. Here, we use a combination of molecular dynamics (MD) simulations and depth-dependent fluorescence quenching to calibrate the methodology for extracting quantitative information on membrane penetration. In order to investigate the immersion depth of the fluorescent label in lipid bilayer, we studied 7-nitrobenz-2-oxa-1,3-diazole (NBD) attached to the lipid headgroup in NBD-PE incorporated into POPC bilayer. The immersion depth of NBD was estimated by measuring steady-state and time-resolved fluorescence quenching with spin-labeled lipids co-incorporated into lipid vesicles. Six different spin-labeled lipids were utilized: one with headgroup-attached Tempo probe (Tempo-PC) and five with acyl chain-labeled n-Doxyl moieties (n-Doxyl-PC where n is a chain labeling position equal to 5, 7, 10, 12, and 14, respectively). The Stern-Volmer analysis revealed that NBD quenching in membranes occurs by both static and dynamic collisional quenching processes. Using the methodology of Distribution Analysis, the immersion depth and the apparent half-width of the transversal distributions of the NBD moiety were estimated to be 14.7 and 6.7 Å, respectively, from the bilayer center. This position is independently validated by atomistic MD simulations of NBD-PE lipids in a POPC bilayer (14.4 Å). In addition, we demonstrate that MD simulations of the transverse overlap integrals between dye and quencher distributions can be used for proper analysis of the depth-dependent quenching profile. Finally, we illustrate the application of this methodology by determining membrane penetration of site selectively labeled mutants of diphtheria toxin T-domain.

The diphtheria toxin translocation (T) domain inserts into the endosomal membrane in response to the endosomal acidification and enables the delivery of the catalytic domain into the cell. The insertion pathway consists of a series of conformational changes that occur in solution and in the membrane and leads to the conversion of a water-soluble state into a transmembrane state. In this work, we utilize various biophysical techniques to characterize the insertion pathway from the thermodynamic perspective. Thermal and chemical unfolding measured by differential scanning calorimetry, circular dichroism, and tryptophan fluorescence reveal that the free energy of unfolding of the T-domain at neutral and mildly acidic pH differ by 3-5 kcal/mol, depending on the experimental conditions. Fluorescence correlation spectroscopy measurements show that the free energy change from the membrane-competent state to the interfacial state is approximately -8 kcal/mol and is pH-independent, while that from the membrane-competent state to the transmembrane state ranges between -9.5 and -12 kcal/mol, depending on the membrane lipid composition and pH. Finally, the thermodynamics of transmembrane insertion of individual helices was tested using an in vitro assay that measures the translocon-assisted integration of test sequences into the microsomal membrane. These experiments suggest that even the most hydrophobic helix TH8 has only a small favorable free energy of insertion. The free energy for the insertion of the consensus insertion unit TH8-TH9 is slightly more favorable, yet less favorable than that measured for the entire protein, suggesting a cooperative effect for the membrane insertion of the helices of the T-domain.

The potential of gold nanoparticles (AuNPs) in therapeutic and diagnostic cancer applications is becoming increasingly recognized, which focuses on their efficient and specific delivery from passive accumulation in tumour tissue to directly targeting tumor-specific biomarkers. AuNPs functionalized by pH low insertion peptide (pHLIP) have recently revealed the capability of targeting acidic tissues and inserting into cell membranes. However, the structure of AuNP-pHLIP conjugates and fundamental gold-peptide interactions still remain unknown. In this study, we have developed a series of molecular dynamics (MD) models reproducing a small gold nanoparticle coupled to pHLIP. We focus on Au135 nanoparticles that comprise a nearly spherical Au core (diameter ∼ 1.4 nm) functionalized with a monomaleimide moiety, mimicking a commercially available monomaleimido NANOGOLD® labelling agent. To probe the structure and folding of pHLIP, which is attached covalently to the maleimide NANOGOLD particle, we have benchmarked the performances of a series of popular, all-atom force fields (FF), including those of OPLS-AA, AMBER03, three variations of CHARMM FFs, as well as united-atom GROMOS G53A6 FF. We found that CHARMMs and OPLSAA FFs predict that in an aqueous salt solution at a neutral pH, pHLIP is partially bound onto the gold surface through some short hydrophobic peptide stretches, while at the same time, a large portion of peptide remains in solution. In contrast, AMBER03 and G53A6 FFs revealed the formation of compact, tightly bound peptide configurations adsorbed onto the nanoparticle core. To reproduce the experimental physical picture of the peptide adsorption onto gold in unfolded and unstructured conformations, our study suggests CHARMM36 and OPLS-AA FFs as a tool of choice for the computational studies of NANOGOLD decorated by pHLIP.

The pH low insertion peptide (pHLIP) is an important tool for drug delivery and visualization of acidic tissues produced by various maladies, including cancer, inflammation, and ischemia. Numerous studies indicate that pHLIP exists in three states: unfolded and soluble in water at neutral pH (State I), unfolded and bound to the surface of a phosphatidylcholine membrane at neutral pH (State II), and inserted across the membrane as an α-helix at low pH (State III). Here we report how changes in lipid composition modulate this insertion scheme. First, the presence of either anionic lipids, cholesterol, or phosphoethanolamine eliminates membrane binding at neutral pH (State II). Second, the apparent pKa for the insertion transition (State I → State III) is increased with increasing content of anionic lipids, suggesting that electrostatic interactions in the interfacial region modulate protonation of acidic residues of pHLIP responsible for transbilayer insertion. These findings indicate a possibility for triggering protonation-coupled conformational switching in proteins at membrane interfaces through changes in lipid composition., (Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

The excited-state dynamics of a diketopyrrolopyrrole (DPP) derivative with push-pull substituents has been investigated in a variety of solvents and at the dodecane/water and dodecane/heavy-water interfaces using a combination of ultrafast spectroscopic techniques, including transient electronic absorption and time-resolved surface second-harmonic generation. Whereas the photophysics of a nonpolar DPP analogue is mostly independent of the solvent, the fluorescence decay of the push-pull DPP accelerates strongly by going from aprotic to protic solvents. As this effect increases with the polarity and the hydrogen-bond-donating ability of the solvent, it is attributed to the occurrence of H-bond-assisted nonradiative deactivation induced by the charge-transfer character of the excited state that favors the coupling of the molecule to the H-bond network of the solvent. At the dodecane/water interface, the excited-state lifetime is longer by a factor of ca. 20 than that estimated in pure water and increases further by a factor of about 3 when going to the dodecane/heavy-water interface. This isotope effect, that is more than twice as strong as that measured in bulk solutions, and molecular dynamic simulations indicate that the slowing down of the dynamics at the interface cannot be solely ascribed to a reduced accessibility of the DPP molecule to the aqueous phase. The slower excited-state decay is rather assigned to the conjunction of several effects, such as the strengthening of the H-bond network formed by the interfacial water molecules and the lower local polarity of the interfacial region.

We use a number of computational and experimental approaches to investigate the membrane topology of the membrane-interacting C-terminal domain of the HIV-1 gp41 fusion protein. Several putative transmembrane regions are identified using hydrophobicity analysis based on the Wimley-White scales, including the membrane-proximal external region (MPER). The MPER region is an important target for neutralizing anti-HIV monoclonal antibodies and is believed to have an interfacial topology in the membrane. To assess the possibility of a transmembrane topology of MPER, we examined the membrane interactions of a peptide corresponding to a 22-residue stretch of the MPER sequence (residues 662-683) using fluorescence spectroscopy and oriented circular dichroism. In addition to the previously reported interfacial location, we identify a stable transmembrane conformation of the peptide in synthetic lipid bilayers. All-atom molecular dynamics simulations of the MPER-derived peptide in a lipid bilayer demonstrate a stable helical structure with an average tilt of 24 degrees, with the five tryptophan residues sampling different environments inside the hydrocarbon core of the lipid bilayer, consistent with the observed spectral properties of intrinsic fluorescence. The degree of lipid bilayer penetration obtained by computer simulation was verified using depth-dependent fluorescence quenching of a selectively attached fluorescence probe. Overall, our data indicate that the MPER sequence can have at least two stable conformations in the lipid bilayer, interfacial and transmembrane, and suggest a possibility that external perturbations can switch the topology during physiological functioning., (Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Accurate determination of the depth of membrane penetration of a fluorescent probe, attached to a lipid, protein, or other macromolecule of interest, using depth-dependent quenching methodology is complicated by thermal motion in the lipid bilayer. Here, we suggest that a combination of steady-state and time-resolved measurements can be used to generate a static quenching profile that reduces the contribution from transverse diffusion occurring during the excited-state lifetime. This procedure results in narrower quenching profiles, compared with those obtained by traditional measurements, and thus improves precision in determination of the underlying depth distribution of the probe., (Copyright © 2013 Elsevier Inc. All rights reserved.)

This paper presents data on BYMV effects on some physiological processes of Glycine soja L. cultivated in the right-bank forest-steppe regions. Pigment content (chlorophyll a, b and carotenoids), soluble proteins and water soluble carbohydrates were estimated and, as has been shown, are subjected to significant changes as compared with control plants, namely: a decrease in the content of chlorophyll a, b and carotenoids was 64%, 53% and 36% compared with the control plants. The significant increase in carbohydrates (56% compared to the control) was observed at the end of the test period.

The modulation of the properties and function of cell membranes by small volatile substances is important for many biomedical applications. Despite available experimental results, molecular mechanisms of action of inhalants and organic solvents, such as acetone, on lipid membranes remain not well understood. To gain a better understanding of how acetone interacts with membranes, we have performed a series of molecular dynamics (MD) simulations of a POPC bilayer in aqueous solution in the presence of acetone, whose concentration was varied from 2.8 to 11.2 mol%. The MD simulations of passive distribution of acetone between a bulk water phase and a lipid bilayer show that acetone favors partitioning into the water-free region of the bilayer, located near the carbonyl groups of the phospholipids and at the beginning of the hydrocarbon core of the lipid membrane. Using MD umbrella sampling, we found that the permeability barrier of ~0.5 kcal/mol exists for acetone partitioning into the membrane. In addition, a Gibbs free energy profile of the acetone penetration across a bilayer demonstrates a favorable potential energy well of -3.6 kcal/mol, located at 15-16Å from the bilayer center. The analysis of the structural and dynamics properties of the model membrane revealed that the POPC bilayer can tolerate the presence of acetone in the concentration range of 2.8-5.6 mol%. The accumulation of the higher acetone concentration of 11.2 mol% results, however, in drastic disordering of phospholipid packing and the increase in the membrane fluidity. The acetone molecules push the lipid heads apart and, hence, act as spacers in the headgroup region. This effect leads to the increase in the average headgroup area per molecule. In addition, the acyl tail region of the membrane also becomes less dense. We suggest, therefore, that the molecular mechanism of acetone action on the phospholipid bilayer has many common features with the effects of short chain alcohols, DMSO, and chloroform., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

pH-induced conformational switching is essential for functioning of diphtheria toxin, which undergoes a membrane insertion/translocation transition triggered by endosomal acidification as a key step of cellular entry. In order to establish the sequence of molecular rearrangements and side-chain protonation accompanying the formation of the membrane-competent state of the toxin's translocation (T) domain, we have developed and applied an integrated approach that combines multiple techniques of computational chemistry [e.g., long-microsecond-range, all-atom molecular dynamics (MD) simulations; continuum electrostatics calculations; and thermodynamic integration (TI)] with several experimental techniques of fluorescence spectroscopy. TI calculations indicate that protonation of H257 causes the greatest destabilization of the native structure (6.9 kcal/mol), which is consistent with our early mutagenesis results. Extensive equilibrium MD simulations with a combined length of over 8 μs demonstrate that histidine protonation, while not accompanied by the loss of structural compactness of the T-domain, nevertheless results in substantial molecular rearrangements characterized by the partial loss of secondary structure due to unfolding of helices TH1 and TH2 and the loss of close contact between the C- and N-terminal segments. The structural changes accompanying the formation of the membrane-competent state ensure an easier exposure of the internal hydrophobic hairpin formed by helices TH8 and TH9, in preparation for its subsequent transmembrane insertion., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Spin-labeled lipids are commonly used as fluorescence quenchers in studies of membrane penetration of dye-labeled proteins and peptides using depth-dependent quenching. Accurate calculations of depth of the fluorophore rely on the use of several spin labels placed in the membrane at various positions. The depth of the quenchers (spin probes) has to be determined independently; however, experimental determination of transverse distributions of spin probe depths is difficult. In this Article, we use molecular dynamics (MD) simulations to study the membrane behavior and depth distributions of spin-labeled phospholipids in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. To probe different depths within the bilayer, a series containing five Doxyl-labeled lipids (n-Doxyl PC) has been studied, in which a spin moiety was covalently attached to nth carbon atoms (where n = 5, 7, 10, 12, and 14) of the sn-2 stearoyl chain of the host phospholipid. Our results demonstrate that the chain-attached spin labels are broadly distributed across the model membrane and their environment is characterized by a high degree of mobility and structural heterogeneity. Despite the high thermal disorder, the depth distributions of the Doxyl labels were found to correlate well with their attachment positions, indicating that the distribution of the spin label within the model membrane is dictated by the depth of the nth lipid carbon atom and not by intrinsic properties of the label. In contrast, a much broader and heterogeneous distribution was observed for a headgroup-attached Tempo spin label of Tempo-PC lipids. MD simulations reveal that, due to the hydrophobic nature, a Tempo moiety favors partitioning from the headgroup region deeper into the membrane. Depending on the concentration of Tempo-PC lipids, the probable depth of the Tempo moiety could span a range from 14.4 to 18.2 Å from the membrane center. Comparison of the MD-estimated immersion depths of Tempo and n-Doxyl labels with their suggested experimental depth positions allows us to review critically the possible sources of error in depth-dependent fluorescence quenching studies.

Depth-dependent fluorescence quenching is an important tool for studying the penetration of proteins and peptides into lipid bilayers. Extracting quantitative information from quenching data is, however, complicated by (1) a limited number of experimentally available quenchers and (2) thermal disorder resulting in broad distributions of the transverse positions of both quenchers and fluorophores. Here we validate and refine a general approach to determining the location of a fluorescent probe along the bilayer normal from quenching data, based on a molecular dynamics (MD) simulation of a model compound, tryptophan octyl ester (TOE), in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. The TOE ring was found to lie deeply within the bilayer (most probable position of 13.3 Å and center-of-weight of the distribution of 14.8 Å from the bilayer center), and it was very broadly distributed (with 9 Å depth distribution width), which is consistent with previous experimental observations. The depth-dependent quenching profiles were simulated by treating carbon atoms of the lipid acyl chain of POPC as "pseudo-quenchers" and calculating appropriate transverse overlaps and collision rates with indole atoms of TOE. These simulated quenching profiles were well fitted by a Gaussian function of depth, as is routinely done with experimental data subjected to the distribution analysis procedure [Methods Enzymol. 1997, 278, 462-473]. Comparison of the collisional pseudoquenching profiles with the actual profiles of the indole moiety of TOE allows for testing of the validity of the data analysis and identification of the possible sources of error in calculating depths of membrane penetration from quenching data.

Elucidation of the factors underlying nucleotide substitution types and rates in genomes is of significance for improving the prevalent models for molecular evolution, and is essential in studying the evolution process, distinguishing the coding and noncoding RNAs, identifying biologically significant motifs such as replication signals, control regions and so on. However, many questions concerning the factors that affect the nucleotide substitutions in plant virus genomes still remain unclear. In this paper a comparative computer analysis of nucleotide substitution in genomic sequences of 10 pairs of closely related potato virus X (PVX) strains having equal genome and gene length has been carried out. A significant frequency variation of nucleotide substitutions, depending on nucleotide and strain pairs, length and localization of genome and gene regions as well as substitution types and their codon positions, was found. The highest relations of substitution frequency are found in different nucleotide pairs (u-->c/c-->g, 1240), codon positions (third/second, 17.3) and substitution types (transitions/transversions, 5.8), the least ones - in forward and back substitutions in the same nucleotide pairs (1.03-1.6). The transversion frequencies are generally significantly lower but more variable than the transition one, and there is no direct relationship between gene (region) length and transversion frequency.

Computational analysis of codon usage bias and spontaneous nucleotide substitutions in six strains of soybean dwarf virus was performed. It was shown that synonymous codon usage in the virus genes varies widely depending on the gene, gene overlapping, codon, codon's two first nucleotides, mononucleotide context located upstream and downstream of the codon, GC-content in virus-encoded genes and in the third codon position. Overlapping of genes causes a 2.5-fold decrease of the total number of nucleotide substitutions, 2.8-4.3-fold decrease of the number of synonymous substitutions in the third codon position, 1.4-1.6-fold decrease of the dicodon content in genes. At the same time there is a significant increase of nonsynonymous substitutions in the second codon position as well as a high codon bias (Fop = 0.94-1.0) and correlation between the nucleotide content in genes and in the third codon positions (r = 0.73-0.74). The results obtained evidence for selection of dicodons in the viral genes.

Solubilizing membrane proteins for functional, structural and thermodynamic studies is usually achieved with the help of detergents, which, however, tend to destabilize them. Several classes of non-detergent surfactants have been designed as milder substitutes for detergents, most prominently amphipathic polymers called 'amphipols' and fluorinated surfactants. Here we test the potential usefulness of these compounds for thermodynamic studies by examining their effect on conformational transitions of the diphtheria toxin T-domain. The advantage of the T-domain as a model system is that it exists as a soluble globular protein at neutral pH yet is converted into a membrane-competent form by acidification and inserts into the lipid bilayer as part of its physiological action. We have examined the effects of various surfactants on two conformational transitions of the T-domain, thermal unfolding and pH-induced transition to a membrane-competent form. All tested detergent and non-detergent surfactants lowered the cooperativity of the thermal unfolding of the T-domain. The dependence of enthalpy of unfolding on surfactant concentration was found to be least for fluorinated surfactants, thus making them useful candidates for thermodynamic studies. Circular dichroism measurements demonstrate that non-ionic homopolymeric amphipols (NAhPols), unlike any other surfactants, can actively cause a conformational change of the T-domain. NAhPol-induced structural rearrangements are different from those observed during thermal denaturation and are suggested to be related to the formation of the membrane-competent form of the T-domain. Measurements of leakage of vesicle content indicate that interaction with NAhPols not only does not prevent the T-domain from inserting into the bilayer, but it can make bilayer permeabilization even more efficient, whereas the pH-dependence of membrane permeabilization becomes more cooperative. This article is part of a Special Issue entitled: Protein Folding in Membranes., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Accurate determination of the free energy of transfer of a helical segment from an aqueous into a transmembrane (TM) conformation is essential for understanding and predicting the folding and stability of membrane proteins. Until recently, direct thermodynamically sound measurements of free energy of insertion of hydrophobic TM peptides were impossible due to peptide aggregation outside the lipid bilayer. Here, we overcome this problem by using fluorinated surfactants that are capable of preventing aggregation but, unlike detergents, do not themselves interact with the bilayer. We have applied the fluorescence correlation spectroscopy methodology to study surfactant-chaperoned insertion into preformed POPC (palmitoyloleoylphosphatidylcholine) vesicles of the two well-studied dye-labeled TM peptides of different lengths: WALP23 and WALP27. Extrapolation of the apparent free-energy values measured in the presence of surfactants to a zero surfactant concentration yielded free-energy values of -9.0±0.1 and -10.0±0.1 kcal/mol for insertion of WALP23 and WALP27, respectively. Circular dichroism measurements confirmed helical structure of peptides in lipid bilayer, in the presence of surfactants, and in aqueous mixtures of organic solvents. From a combination of thermodynamic and conformational measurements, we conclude that the partitioning of a four-residue L-A-L-A segment in the context of a continuous helical conformation from an aqueous environment into the hydrocarbon core of the membrane has a favorable free energy of 1 kcal/mol. Our measurements, combined with the predictions of two independent experimental hydrophobicity scales, indicate that the per-residue cost of transfer of the helical backbone from water to the hydrocarbon core of the lipid bilayer is unfavorable and is equal to +2.13±0.17 kcal/mol., (Copyright © 2012 Elsevier Ltd. All rights reserved.)