Adaptive Partitioning QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel.

Adaptive quantum-mechanics/molecular-mechanics (QM/MM) dynamics simulations feature on-the-fly reclassification of atoms as QM or MM continuously and smoothly as trajectories are propagated. This allows one to use small, mobile QM subsystems, the contents of which are dynamically updated as needed. In this work, we report the first adaptive QM/MM simulations of H+ transfer through a biological channel, in particular, the protein EcCLC, a chloride channel (CLC) Cl-/H+ antiporter derived from E. coli. To this end, the H+ indicator previously formulated for approximating the location of an excess H+ in bulk water was extended to include Cl- ions and carboxyl groups as H+ donors/acceptors. Furthermore, when setting up buffer groups, a new "sushi-roll" scheme was employed to group multiple water molecules, ions, and titratable residues along the one-dimensional channel for adaptive partitions. Our simulations reveal that the H+ relay path, which consists of water molecules in the pore, a bound Cl- ion at the central binding site (Cl-cen) of the protein, and the external gating residue E148, exhibits certain mobility within the channel. A two-stage journey of H+ migration was observed: the H+ moves toward Cl-cen and is then shared between Cl-cen and nearby water molecules in the first stage and departs from Cl-cen via nearly concerted transfer to protonate E148 in the second stage. Most of the simulated trajectories show the bound Cl- ion in the channel to be transiently protonated, a possibility that was previously suggested by experiments and computations. Comparisons with conventional QM/MM simulations revealed that both adaptive and conventional treatments yield similar qualitative pictures. This work demonstrates the feasibility of adaptive QM/MM in the simulations of H+ migration through biological channels.

Chloride Ion Transport by the E. coli CLC Cl-/H+ Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study.

We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl- ion migration through the transmembrane domain of a prototypical E. coli CLC Cl-/H+ antiporter by employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found to be critical for full access of the channel entrance by Cl-. Moving the anion into the external binding site (Sext) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl- traveled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl- exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl- along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing π bonds (e.g., the Tyr445 side chain), while the charges of the H atoms coordinating Cl- changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers (~10 kcal/mol) than the MM PMF (~2 kcal/mol). Binding energy calculations indicated that the interactions between Cl- and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing π bonds, missing the stabilizations of the Cl- ion due to electron delocalization. The results suggested that it is important to explore these quantum effects for accurate descriptions of the Cl- transport.

Investigation of In vitro Mineral forming bacterial isolates from supragingival calculus.

AIM: Although it is known that bacterial mechanisms are involved in dental calculus formation, which is a predisposing factor in periodontal diseases, there have been few studies of such associations, and therefore, information available is limited. The purpose of this study was to isolate and identify aerobic bacteria responsible for direct calcification from supragingival calculus samples. MATERIALS AND METHODS: The study was conducted using supragingival calculus samples from patients with periodontal disease, which was required as part of conventional treatment. Isolations were performed by sampling the supragingival calculus with buffer and inoculating the samples on media on which crystallization could be observed. The 16S recombinant DNA of the obtained pure cultures was then amplified and sequenced. RESULTS: A few bacterial species that have not previously been associated with mineralization or identified on bacterial plaque or calculus were detected. The bacteria that caused mineralization an aerobic environment are identified as Neisseria flava, Aggregatibacter segnis, Streptococcus tigurinus, and Morococcus cerebrosus. CONCLUSION: These findings proved that bacteria potentially play a role in the etiopathology of supragingival calculus. The association between the effects of the identified bacteria on periodontal diseases and calculus formation requires further studies.

Mesocorticolimbic dopamine functioning in primary psychopathy: A source of within-group heterogeneity.

Despite similar emotional deficiencies, primary psychopathic individuals can be situated on a continuum that spans from controlled to disinhibited. The constructs on which primary psychopaths are found to diverge, such as self-control, cognitive flexibility, and executive functioning, are crucially regulated by dopamine (DA). As such, the goal of this review is to examine which specific alterations in the meso-cortico-limbic DA system and corresponding genes (e.g., TH, DAT, COMT, DRD2, DRD4) might bias development towards a more controlled or disinhibited expression of primary psychopathy. Based on empirical data, it is argued that primary psychopathy is generally related to a higher tonic and population activity of striatal DA neurons and lower levels of D2-type DA receptors in meso-cortico-limbic projections, which may boost motivational drive towards incentive-laden goals, dampen punishment sensitivity, and increase future reward-expectancy. However, increasingly higher levels of DA activity in the striatum (moderate versus pathological elevations), lower levels of DA functionality in the prefrontal cortex, and higher D1-to-D2-type receptor ratios in meso-cortico-limbic projections may lead to increasingly disinhibited and impetuous phenotypes of primary psychopathy. Finally, in order to provide a more coherent view on etiological mechanisms, we discuss interactions between DA and serotonin that are relevant for primary psychopathy.

Prognostic significance of serum galectin-3 levels in patients with hepatocellular cancer and chronic viral hepatitis.

BACKGROUND/AIM: Galectins affect diverse physiological and pathophysiological processes such as development, inflammation, and tumor growth. We aimed to compare serum galectin-3 levels in three patient groups with chronic hepatitis B and C virus (HBV, HCV), cirrhosis secondary to HBV or HCV, and hepatocellular carcinoma (HCC) secondary to HBV or HCV and evaluate the role of galectin-3 during HCC progression. PATIENTS AND METHODS: Nineteen patients with hepatocellular cancer, 22 patients with cirrhosis, and 24 patients with chronic hepatitis B and C were included in this study. Serum galectin-3 levels in different liver diseases were assessed by enzyme-linked immunosorbent assay. RESULTS: The mean galectin-3 levels were 4.61 ng/mL (±2.32) in HCC patients, 5.68 ng/mL (±2,2) in cirrhotic patients, 1.98 ng/mL (±1.50) in chronic viral hepatitis group. There were no statistical differences between HCC and cirrhotic patients (P = 0.5), but lower in chronic hepatitis group statistically compared with cirrhosis and HCC (P < 0.001, P = 0.002, respectively). In case of cirrhotic patients, galectin-3 levels were significantly higher in patients with cirrhosis secondary to HCV compared with HBV (P = 0.03). When we evaluated galectin-3 levels in HCC patients, it was found to be 3.92 ng/mL in HCC secondary to hepatitis B and 5.37 ng/mL in HCC secondary to hepatitis C. CONCLUSION: Serum galectin-3 levels in patients with chronic HBV or HCV may guide us about progression to cirrhosis or HCC and prognosis of the disease. Especially, galectin-3 levels may be more pronounced in case of HCV.

Sodium tungstate alleviates biomechanical properties of diabetic rat femur via modulation of oxidative stress.

Diabetes mellitus leads to bone disorders such as osteopenia and osteoporosis that can increase fracture risk. On the other hand, sodium tungstate is an inorganic compound which exerts anti-diabetic activity in experimental studies due to its suggested insulin-mimetic or antioxidant activity. Therefore this study was designed to investigate the effect of tungstate on bone quality in diabetic rat femurs. The rats were divided into four groups: Control (C), tungstate-treated control (C+Tung), diabetes (STZ-D) and tungstate-treated diabetes (STZ-D+Tung). Diabetes mellitus was induced by single injection of streptozotocin (50 mg/kg). The treated rats received 150 mg/kg/day of sodium tungstate for 12 weeks. Sodium tungstate achieved a little (17%) but significant reduction on blood glucose levels, while it didn't recover the reduced body weights of diabetic rats. In addition, impaired bone mechanical quality was reversed, despite the unchanged mineral density. Sodium tungstate administration significantly lowered the 2-thiobarbituric acid reactive substances and restored the activity of tissue antioxidant enzymes such as glutathione peroxidase, catalase and superoxide dismutase in diabetic rats. On the other hand, glutathione levels didn't change in either case. These findings indicate that tungstate can improve the reduced mechanical quality of diabetic rat femurs due probably to reduction of reactive oxygen species and modulation of antioxidant enzymes as well as reduction in blood glucose levels.

Systematic review, structural analysis, and new theoretical perspectives on the role of serotonin and associated genes in the etiology of psychopathy and sociopathy.

Since its theoretical inception, psychopathy has been considered by philosophers, clinicians, theorists, and empirical researchers to be substantially and critically explained by genetic factors. In this systematic review and structural analysis, new hypotheses will be introduced regarding gene-gene and gene-environment interactions in the etiology of psychopathy and sociopathy. Theory and research from neurobiological and behavioral sciences will be integrated in order to place this work in a broader conceptual framework and promote synergy across fields. First, a between groups comparison between psychopathy and sociopathy is made based on their specific dysfunctions in emotional processing, behavioral profiles, etiological pathways, HPA-axis functioning, and serotonergic profiles. Next, it is examined how various polymorphisms in serotonergic genes (e.g., TPH, 5HTT, HTR1A, HTR2A, HTR2C, and HTR3) might contribute either individually or interactively to the development of these disorders and through which specific biological and behavioral endophenotypes this effect could be mediated. A short introduction is made into mediating variables such as GABAergic functioning and testosterone which could potentially alter the decisive effect of serotonergic genotypes on behavior and physiology. Finally, critical commentary is presented on how to interpret the hypotheses put forward in this review.

A review on the relationship between testosterone and life-course persistent antisocial behavior.

Life-course persistent antisocial behavior is 10 to 14 times more prevalent in males and it has been suggested that testosterone levels could account for this gender bias. Preliminary studies with measures of fetal testosterone find inconsistent associations with antisocial behavior, especially studies that use the 2D:4D ratio as a proxy for fetal testosterone. However, circulating testosterone consistently shows positive associations with antisocial behaviors throughout childhood, adolescence, and adulthood, particularly in males. It is suggested that high fetal/circulating testosterone interactively influence the maturation and functionality of mesolimbic dopaminergic circuitry, right orbitofrontal cortex, and cortico-subcortical connectivity, resulting in a strong reward motivation, low social sensitivity, and dampened regulation of strong motivational/emotional processes. The link between these testosterone induced endophenotypes and actual display of antisocial behavior is strongly modulated by different social (e.g., social rejection, low SES) and genetic (e.g., MAOA, 5HTT) risk factors that can disturb socio-, psycho-, and biological development and interact with testosterone in shaping behavior. When these additional risk factors are present, the testosterone induced endophenotypes may increase the risk for a chronic antisocial lifestyle. However, behavioral endophenotypes induced by testosterone can also predispose towards socially adaptive traits such as a strong achievement motivation, leadership, fair bargaining behaviors, and social assertiveness. These adaptive traits are more likely to emerge when the high testosterone individual has positive social experiences that promote prosocial behaviors such as strong and secure attachments with his caregivers, affiliation with prosocial peers, and sufficient socioeconomic resources. A theoretical model is presented, various hypotheses are examined, and future venues for research are discussed.

A review on the relationship between testosterone and the interpersonal/affective facet of psychopathy.

Testosterone (T) has received increasing interest in the recent years as a probable biological determinant in the etiology of male-biased clinical conditions such as psychopathy (i.e. psychopathy is more prevalent in men and leads to an earlier onset and more severe expression of antisocial and aggressive behavior in men compared to women). In this review, the authors evaluated the potential relationship between T and different constructs closely related to the core characteristics of psychopathy (affective empathy, fear-reactivity, and instrumental aggression). After a thorough examination of the literature, it is concluded that high T exposure in utero and high circulating T levels throughout important life phases (most notably adolescence) or in response to social challenges (e.g. social stress, competition) could be an important etiological risk factor in the emergence of psychopathic behavior. Nevertheless, studies consistently indicate that high T is not related to a significantly reduced fear-reactivity and is only indirectly associated with the increased levels of instrumental aggression observed in psychopathic individuals. Therefore, psychopathy is likely to arise from an interaction between high T levels and other biological and socio-psychological risk factors, such as a constitutionally based dampened fear-reactivity, insecure/disordered attachment processes in childhood, and social discrimination/rejection in adolescence and/or adulthood.

Effects of bovine milk lactoperoxidase system on some bacteria.

Bovine lactoperoxidase (LPO) was purified from skimmed milk using amberlite CG-50-H+ resin, CM sephadex C-50 ion-exchange chromatography, and sephadex G-100 gel filtration chromatography. Lactoperoxidase was purified 20.45-fold with a yield of 28.8%. Purity of enzyme checked by sodium dodecyl sulphate-polyacrylamide gel electrophoresis method and a single band was observed. Km was 0.25 mM at 20 degrees C, Vmax value was 7.95 micromol/ml min at 20 degrees C (pH 6.0). Antibacterial study was done by disk diffusion method of Kir-by-Bauer using Mueller-Hinton agar medium with slight modification. Bovine LPO showed high antibacterial activity in 100 mM thiocyanate-100 mM H2O2 medium for some bacteria (Brevibacillus centrosaurus, B. choshinensis, B. lyticum, Cedecea davisae, Chryseobacterium indoltheticum, Clavibacter michiganense pv. insidiosum, Kocuria erythromyxa, K. kristinae, K. rosea, K. varians, Paenibacillus validus, Pseudomonas syringae pv. populans, Ralstonia pickettii, Rhodococcus wratislaviensis, Serratia fonticola, Streptomyces violaceusniger, Vibrio cholerae-nonO1) respectively, and compared with well known antibacterial substances (levofloxacin, netilmicin). LPO system has inhibition effects on all type bacteria and concentration is really important such as LPO-100 mM thiocyanate-100 mM H2O2 system was proposed as an effective agent against many factors causing several diseases.

Impaired coronary microvascular function and increased intima-media thickness in rheumatoid arthritis.

BACKGROUND: Rheumatoid arthritis (RA) is associated with excessive cardiovascular mortality. Recently, some studies have shown endothelial dysfunction in RA patients with high inflammatory activity. In addition, it has been suggested that the chronic inflammatory state of RA contributes to accelerated atherosclerosis. Therefore, we aimed to evaluate whether coronary microvascular dysfunction and increased carotid artery intima-media thickness exist in patients with a long history and well controlled disease activity of RA lacking traditional cardiovascular risk factors. METHODS: Thirty RA patients (22 women; mean age 43.7+/-9.0) and 52 healthy volunteers (38 women; mean age 45.3+/-5.4) were included into the study. Using transthoracic echocardiography, each subject underwent echocardiographic examination including coronary flow reserve (CFR) and carotid intima-media thickness (IMT) measurement. RESULTS: CFR values were statistically reduced for RA patients as compared to controls (2.4+/-0.5 vs. 2.7+/-0.4, P=0.002) whereas IMT values were significantly increased (0.6+/-0.1 vs. 0.5+/-0.1, P=0.001). In RA patients, CFR positively correlated with lateral Em/Am ratio (r=0.399, P=0.029), and negatively correlated with lateral isovolumic relaxation time (IVRT) (r=-0.744, P=0.005), IMT (r=-0.542, P=0.002) and RA disease duration (r=-0.495, P=0.005). Reflecting LV diastolic function, mitral E-wave deceleration time and isovolumic relaxation time were borderline significant between the groups, however lateral Em/Am ratio and lateral IVRT were statistically different. CONCLUSIONS: Patients with RA had impaired CFR and increased carotid IMT, and these injurious effects correlated significantly with disease duration.

Important anatomical landmarks in the lateral nasal wall.

OBJECTIVE: The study aimed to investigate the anatomy of the lateral nasal wall to provide a set of measurements among some important anatomical landmarks and to reveal the relationship between them. METHODS: Fifty half heads were dissected to determine the distances between important landmarks in the lateral nasal wall for endoscopic sinus surgery. Landmarks were measured with an electronic caliper. This study was carried out between December 2002 and February 2003 at the Anatomy Research Laboratory, Faculty of Medicine, Akdeniz University, Antalya, Turkey. RESULTS: Results were provided as mean +/- standard deviation. In our study, some of the critical distances as in the lateral nasal wall were measured and results showed consistency to the data found in the literature. CONCLUSION: Our results are useful to achieve safe endoscopic sinus surgery.