Conformational ensemble of human α-synuclein physiological form predicted by molecular simulations.

We perform here enhanced sampling simulations of N-terminally acetylated human α-synuclein, an intrinsically disordered protein involved in Parkinson's disease. The calculations, consistent with experiments, suggest that the post-translational modification leads to the formation of a transient amphipathic α-helix. The latter, absent in the non-physiological form, alters protein dynamics at the N-terminal and intramolecular interactions.

Hydration of chloride anions in the NanC Porin from Escherichia coli: a comparative study by QM/MM and MD simulations.

Chloride anions permeate the bacterial NanC porin in physiological processes. Here we present a DFT-based QM/MM study of this porin in the presence of these anions. Comparison is made with classical MD simulations on the same system. In both QM/MM and classical approaches, the anions are almost entirely solvated by water molecules. However, the average water-Cl(-) distance is significantly larger in the first approach. Polarization effects of protein groups close to Cl(-) anion are sizeable. These effects might modulate the anion-protein electrostatic interactions, which in turn play a central role for selectivity mechanisms of the channel.

Survey of Oral Hygiene Habits and Knowledge among School Children: a cross-sectional study from Italy.

AIM: This study is aimed to investigate the oral hygiene practice, knowledge and attitude of young adults, assessing their awareness about the impact of a certain "risk" behaviour on their oral and dental health. MATERIALS: This is a cross-sectional survey study conducted on 829 students (350 males and 479 females, mean age 13-20 years) attending high school in Milan and surrounding areas. They were asked to complete anonymous questionnaire during the first semester of the 2019-2020 school year, under the supervision of a teacher and/or an assigned interviewer. The questionnaire was created by "Laboratorio Adolescenza", in collaboration with the International Alliance of Responsible Drinking (IARD) Research Institute and the University of Milan. All of the data was compiled into table or graph form and analysed. CONCLUSION: There is a general awareness among Italian school children about the risks of bad oral habits, however, there is a need to improve the oral health knowledge, attitude and practices in the target population with emphasis on improvement of oral hygiene practices.

What is the use of nutraceuticals in dentistry? A scoping review.

OBJECTIVE: Recently, nutraceuticals have been widely explored in many medical fields and their use is also increasing in oral and dental problems. Since the nutraceutical evidence landscape in the literature has not been fully elucidated yet, this review aims to examine the effects of commercially available nutraceuticals and their potential evidence and applications in dentistry. MATERIALS AND METHODS: A scoping review was conducted following the "Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR)" checklist. The electronic search was performed using PubMed/MEDLINE, EMBASE, the Cochrane Library, and Web of Science on March 2022. The inclusion criteria include humans, clinical trials, randomized controlled trials (RCT), reviews, and systematic reviews published over the last ten years. RESULTS: 18 studies met the eligibility criteria. There were 2 RCTs, 11 systematic reviews, and four narrative reviews. In most studies, the clinical indications were oral leucoplakia, periodontitis, osseointegration of implants, oral mucositis, oral clefts, and oral health. Probiotics, prebiotics, polyunsaturated fatty acids, and vitamins A, B, C, D, and E were the most common nutraceuticals used in dentistry. CONCLUSIONS: Nutraceuticals are foods that, according to the literature, may be useful for preventing and treating dental diseases.

Modeling the allosteric modulation on a G-Protein Coupled Receptor: the case of M2 muscarinic Acetylcholine Receptor in complex with LY211960.

Allosteric modulation is involved in a plethora of diverse protein functions, which are fundamental for cells' life. This phenomenon can be thought as communication between two topographically distinct site of a protein structure. How this communication occurs is still matter of debate. Many different descriptions have been presented so far. Here we consider a specific case where any significant conformational change is involved upon allosteric modulator binding and the phenomenon is depicted as a vibrational energy diffusion process between distant protein regions. We applied this model, by employing computational tools, to the human muscarinic receptor M2, a transmembrane protein G-protein coupled receptor known to undergo allosteric modulation whose recently X-ray structure has been recently resolved both with and without the presence of a particular allosteric modulator. Our calculations, performed on these two receptor structures, suggest that for this case the allosteric modulator modifies the energy current between functionally relevant regions of the protein; this allows to identify the main residues responsible for this modulation. These results contribute to shed light on the molecular basis of allosteric modulation and may help design new allosteric ligands.

Vibrational Energy in Proteins Correlates with Topology.

The exchange of vibrational energy in proteins is crucial for their function. Here, we establish a connection between quantities related to it with geometry-based properties such as the proteins' residues coordination number. This relation is proven by molecular simulation in a neuro-pharmacologically relevant transmembrane receptor. The connection demonstrated here paves the way to studies of protein allostery and conformational changes based solely on protein structure.

Protonation state and substrate binding to B2 metallo-beta-lactamase CphA from Aeromonas hydrofila.

The zinc enzymes metallo beta-lactamases counteract the beneficial action of beta-lactam antibiotics against bacterial infections, by hydrolyzing their beta-lactam rings. To understand structure/function relationships on a representative member of this class, the B2 M beta L CphA, we have investigated the H-bond pattern at the Zn enzymatic active site and substrate binding mode by molecular simulation methods. Extensive QM calculations at the DFT-BLYP level on eleven models of the protein active site, along with MD simulations of the protein in aqueous solution, allow us to propose two plausible protonation states for the unbound enzyme, which are probably in equilibrium. Docking procedures along with MD simulations and QM calculations suggest that in the complex between the enzyme and its substrate (biapenem), the latter is stable in only one of the two protonation states, in addition it exhibits two different binding modes, of which only one agrees with previous proposals. In both cases, the substrate is polarized as in aqueous solution. We conclude that addressing mechanistic issues on this class of enzymes requires a careful procedure to assign protonation states and substrate docking modes.

Unwinding the helical linker of calcium-loaded calmodulin: a molecular dynamics study.

The fold of calmodulin (CaM) consists of two globular domains connected by a helical segment (the linker), whose conformational properties play a crucial role for the protein's molecular recognition processes. Here we investigate the structural properties of the linker by performing a 11.5 ns molecular dynamics (MD) simulation of calcium-loaded human CaM in aqueous solution. The calculations are based on the AMBER force field. The calculated S2 order parameters are in good accord with NMR data: The structure of the linker in our simulations is much more flexible than that emerging from the Homo sapiens X-ray structure, consistently with the helix unwinding observed experimentally in solution. This process occurs spontaneously in a nanosecond timescale, as observed also in a very recent simulation based on the GROMOS force field. A detailed description of the mechanism that determines the linker unwinding is provided, in which electrostatic contacts between the two globular domains play a critical role. The orientation of the domains emerging from our MD calculations is consistent both with former X-ray scattering data and a recent NMR work. Based on our findings, a rationale for the experimentally measured entropy cost associated to binding to the protein's cellular partners is also given.

Crystal structure of the complex between carboxypeptidase A and the biproduct analog inhibitor L-benzylsuccinate at 2.0 A resolution.

The X-ray crystal structure of the carboxypeptidase A-L-benzylsuccinate complex has been refined at 2.0 A resolution to a final R-factor of 0.166. One molecule of the inhibitor binds to the enzyme active site. The terminal carboxylate forms a salt link with the guanidinium group of Arg145 and hydrogen bonds with Tyr248 and Asn144. The second carboxylate group binds to the zinc ion in an asymmetric bidentate fashion replacing the water molecule of the native structure. The zinc ion moves 0.5 A from its position in the native structure to accommodate the inhibitor binding. The overall stereochemistry around the zinc can be considered a distorted tetrahedron, although six atoms of the co-ordinated groups lie within 3.0 A from the zinc ion. The key for the strong inhibitory properties of L-benzylsuccinate can be found in its ability both to co-ordinate the zinc and to form a short carboxyl-carboxylate-type hydrogen bond (2.5 A) with Glu270.

Ab initio molecular dynamics studies on HIV-1 reverse transcriptase triphosphate binding site: implications for nucleoside-analog drug resistance.

Quantum-chemical methods are used to shed light on the functional role of residues involved in the resistance of HIV-1 reverse transcriptase against nucleoside-analog drugs. Ab initio molecular dynamics simulations are carried out for models representing the adduct between the triphosphate substrate and the nucleoside binding site. The triphosphate is considered either deprotonated or protonated at the gamma-position. Although the protonated form already experiences large rearrangements in the ps time scale, the fully deprotonated state exhibits a previously unrecognized low-barrier hydrogen bond between Lys65 and gamma-phosphate. Absence of this interaction in Lys65-->Arg HIV-1 RT might play a prominent role in the resistance of this mutant for nucleoside analogs (Gu Z et al., 1994b, Antimicrob Agents Chemother 38:275-281; Zhang D et al., 1994, Antimicrob Agents Chemother 38:282-287). Water molecules present in the active site, not detected in the X-ray structure, form a complex H-bond network. Among these waters, one may be crucial for substrate recognition as it bridges Gln151 and Arg72 with the beta-phosphate. Absence of this stabilizing interaction in Gln151-->Met HIV-1 RT mutant may be a key factor for the known drug resistance of this mutant toward dideoxy-type drugs and AZT (Shirasaka T et al., 1995, Proc Natl Acad Sci USA 92:2398-2402: Iversen AK et al., 1996, J Virol 70:1086-1090).

Reaction mechanism of caspases: insights from QM/MM Car-Parrinello simulations.

Caspases are fundamental targets for pharmaceutical interventions in a variety of diseases involving disregulated apoptosis. Here, we present a quantum mechanics/molecular mechanics Car-Parrinello study of key steps of the enzymatic reaction for a representative member of this family, caspase-3. The hydrolysis of the acyl-enzyme complex is described at the density functional (BLYP) level of theory while the protein frame and solvent are treated using the GROMOS96 force field. These calculations show that the attack of the hydrolytic water molecule implies an activation free energy of ca. DeltaF(A) approximately equal 19 +/- 4 kcal/mol in good agreement with experimental data and leads to a previously unrecognized gem-diol intermediate that can readily (DeltaF(A) approximately equal 5 +/- 3 kcal/mol) evolve to the enzyme products. Our findings assist in elucidating the striking difference in catalytic activity between caspases and other structurally well-characterized cysteine proteases (papains and cathepsins) and may help design novel transition-state analog inhibitors.

Water and potassium dynamics inside the KcsA K(+) channel.

Molecular dynamics simulations and electrostatic modeling are used to investigate structural and dynamical properties of the potassium ions and of water molecules inside the KcsA channel immersed in a membrane-mimetic environment. Two potassium ions, initially located in the selectivity filter binding sites, maintain their position during 2 ns of dynamics. A third potassium ion is very mobile in the water-filled cavity. The protein appears engineered so as to polarize water molecules inside the channel cavity. The resulting water induced dipole and the positively charged potassium ion within the cavity are the key ingredients for stabilizing the two K(+) ions in the binding sites. These two ions experience single file movements upon removal of the potassium in the cavity, confirming the role of the latter in ion transport through the channel.

Increased oxidative modification of albumin when illuminated in vitro in the presence of a common sunscreen ingredient: protection by nitroxide radicals.

We previously reported on the ability of dibenzoylmethane (DBM) and a relative, Parsol 1789, used as a ultraviolet A (UVA)-absorbing sunscreen, to generate free radicals upon illumination, and as a consequence, to inflict strand breaks in plasmid DNA in vitro. This study has now been extended to determine the effects of Parsol 1789 and DBM on proteins, under UVA illumination, with the sole purpose of gaining more knowledge on the photobiological effects of sunscreen chemicals. Parsol 1789 (100 microM) caused a 2-fold increase in protein carbonyl formation (an index of oxidative damage) in bovine serum albumin (BSA) when exposed to illumination, and this damage was both concentration- and time-dependent. The degree of protein damage was markedly reduced by the presence of free radical scavengers, namely piperidinic and indolinonic nitroxide radicals, in accordance with our previous study. Vitamin E had no effect under the conditions used. The results obtained corroborate the fact that Parsol 1789 generates free radicals upon illumination and that these are, most probably, responsible for the protein damage observed under the conditions used in our system. However, at present, we cannot extrapolate from these results the relevance to human use of sunscreens; therefore, further studies should be necessary to determine the efficacy at the molecular and cellular level of this UVA-absorber in order to ascertain protection against photocarcinogenic risk.

Effects of indolinic and quinolinic aminoxyls on protein and lipid peroxidation of rat liver microsomes.

A study on peroxyl radical induced oxidation of rat liver microsomal membranes in the presence of different indolinic and quinolinic aminoxyls (Scheme 1) was carried out in order to test their efficiency as antioxidants in lipid and protein peroxidation. The extent of lipid peroxidation was quantified by the amount of malondialdehyde (MDA) produced, and the measurement of carbonyl residues was used as an index of microsomal protein oxidation. The results obtained suggest that lipid soluble indolinic and quinolinic aminoxyls are efficient in protecting lipids and proteins of biological membranes against oxidation. The efficacy of these aminoxyls as protectors of lipids and proteins was much higher than the water soluble TEMPOL. Moreover, the hydrophobic aminoxyls were more effective in preventing protein than lipid oxidation at low concentrations (1-20 microM). However, at high concentration (100 microM), lipid as opposed to protein oxidation was almost completely inhibited. The data supports the hypothesis that proteins probably have a different oxidation pattern from lipids.

Vitamin E consumption induced by oxidative stress in red blood cells is enhanced by melatonin and reduced by N-acetylserotonin.

The effect of melatonin and its precursor N-acetylserotonin was studied in a model of lipid peroxidation induced in human red blood cells by incubation with cumene hydroperoxide (CHP) and H2O2. The oxidative stress was expressed as vitamin E consumption in the presence of melatonin or N-acetylserotonin (concentration ranging from 0.3 to 400 microM): incubation with melatonin not only lacked any protective effect but it induced a dose-dependent extra vitamin E consumption with both CHP and H2O2. On the contrary, N-acetylserotonin showed a strong antioxidant effect at concentrations between 100 and 400 microM. The hydrogen-donating capacity of melatonin and N-acetylserotonin was also evaluated from the decay of the ESR signal of galvinoxyl radical used as hydrogen abstractor. Lack of hydrogen-donating capacity was observed with melatonin, whereas N-acetylserotonin showed a significant hydrogendonating capacity although inferior to vitamin E, thus suggesting that N-acetylserotonin acts by the classical antioxidant mechanism of hydrogen donation. The measurement of the oxidation potential and the specific molecular structure suggest that the vitamin E consumption effect observed with melatonin could be due to the interactions of its radical cation or derivatives on vitamin E.

Reactivity of an indolinonic aminoxyl with superoxide anion and hydroxyl radicals.

The increasing knowledge on the participation of free radicals in many diverse clinical and pathological conditions, has consequently expanded the search for new and versatile antioxidants aimed at combating oxidative stress. Our interest in this field concerns aromatic indolinonic aminoxyls (nitroxides) which efficiently react with alkoxyl, peroxyl, aminyl, arylthiyl and alkyl radicals to give non-paramagnetic species. This prompted us to test their antioxidant activity on different biological systems exposed to free radical-induced oxidative stress and the results obtained so far have been very promising. However little is known about their behaviour towards superoxide and hydroxyl radicals. Here, we report on the reactivity of an indolinonic aminoxyl, with the two above mentioned radicals using hypoxanthine/xanthine oxidase and potassium superoxide for generating the former and the Fenton reagent for the latter. Besides performing the deoxyribose assay for studying the reaction of the aminoxyl with hydroxyl radical and monitoring spectral changes of the aminoxyl in the presence of superoxide radical, macroscale reactions were performed in both cases and the products of the reactions isolated and identified. The EPR technique was used in this study to help elucidate the data obtained. The results show that this compound efficiently reacts with both hydroxyl and superoxide radicals and furthermore, it is capable of maintaining iron ions in its oxidized form. The results thus contribute to increasing the knowledge on the reactivity of indolinonic aminoxyls towards free radical species and as a consequence, these compounds and/or other aminoxyl derivatives, may be considered as complementary, and sometimes alternative sources for combating oxidative damage.

Quinolinic aminoxyl protects albumin against peroxyl radical mediated damage.

A study of peroxyl radical-mediated bovine serum albumin oxidation in the presence of the quinolinic aminoxyl 1,2-dihydro-2,2-diphenyl-4-ethoxy-quinoline-1-oxyl (QAO) was carried out in order to test its efficiency as a protein antioxidant. Albumin oxidation was induced by the tert-butylhydroperoxide/PbO2 system. The extent of protein oxidation, measured by monitoring the formation of carbonyl groups, was considerably reduced in the presence of QAO. ESR measurements were carried out to confirm the consumption of the nitroxide during oxidation and its incorporation in the protein. The data obtained indicate that the quinolinic aminoxyl function can be used as an effective antioxidant in biological systems.

Evaluation of intramolecular equilibria in complexes formed between substituted imidazole ligands and nickel (II), copper (II) or zinc (II).

The metal ion-binding properties of imidazole-4-acetate (ImA-), 4(5)-aminoimidazole-5(4)-carboxamide (AImC), 2,2'biimidazole(BiIm) (I. Török et al., J. Inorg. Biochem. 71 (1998) 7-14), and bis (imidazol-2-yl)methane(BiImM) (K. Várnagy et al., J. Chem. Soc., Dalton Trans. (1994) 2939-2945) have been evaluated by using the recently published stability constants and by applying the recently established log K(ML)M versus pK(HL)H straight-line plots (L. E. Kapinos et al., Inorg. Chim. Acta 280 (1998) 50-56) which hold for simple imidazole-type ligands. The indicated analysis regarding the intramolecular equilibrium between a monodentatally imidazole-nitrogen-coordinated (open) species and a chelated isomer provides helpful insights, e.g., the formation degree of chelates is more favored if six-membered rings can be formed, as in the case with M(BiImM)2+ compared to M(BiIm)2+, though in both instances the formation degree of the chelates is large. The formation degree of chelates in the M(ImA)+ complexes increases in the series Zn(ImA)+ (87%)

Large-scale motions and electrostatic properties of furin and HIV-1 protease.

We present a comparative study between two members of serine and aspartic proteases complexed with a peptide substrate. The same computational setup is used to characterize the structural, electrostatic, and electronic properties for the Michaelis complex of furin, a serine protease, and of the aspartic protease from HIV-1. In both cases plane-wave density functional theory (PW-DFT) and empirical force-field-based molecular dynamics calculations are used. For furin, calculations are extended to the complex with the intermediate of the first step of the reaction. Comparisons are also made with results from recent PW-DFT investigations on both families of enzymes and with the same chemical groups in an aqueous environment. It is found that the substrate carbonyl group is more polarized in the furin complex than in the HIV-1 protease one. A further difference regards the large-scale motions of the complexes as a whole and local conformational fluctuations at the active site. The global and local fluctuations are well coupled for HIV-1 protease but not for furin. Thus, despite some chemical analogies in the first step of the reaction mechanism, furin and HIV-1 protease complexes appear to be characterized by a different interplay of electrostatics and conformational fluctuations.