St. George’s mushroom, Calocybe gambosa (Fr.) Donk: A promising source of nutrients and biologically active compounds

The composition of biologically active compounds of Calocybe gambosa (Lyophyllaceae) was analysed, and the antioxidant and cytotoxic activities were tested in vitro. C. gambosa was low in energy, fat, and carbohydrates, but rich in proteins and fibres. The total polyphenol content in the extracts was low (23.08 ± 0.67 in aqueous and 24.99 ± 4.25 μg GA mg−1 of extract in methanolic extract). The methanolic extract showed anti-DPPH radical activity with an IC50 of 626.10 ± 25.20 μg mL−1. The sample of C. gambosa is rich in nucleotides and amino acids responsible for its pleasant taste. The nucleoside and 5′-monophosphates contents were 0.97 mg g−1 and 2.32 mg g−1 of dry mushroom, respectively. The contents of essential and non-essential amino acids were 18.41 ± 0.06 and 41.75 ± 0.30 mg g−1 d.w., respectively. The percentages of saturated and unsaturated fatty acids were 42.6% and 57.4%, respectively. The most abundant water-soluble and fat-soluble vitamins were B1 and E, respectively. Cytotoxic effect of the extracts was examined against different cancer cell lines, and the best cytotoxicity was showed by the peptide extract against colon cancer cell line LS174.

White blood cell subsets in HER2-positive breast cancer patients treated with trastuzumab in relation to clinical outcome

To examine whether HER2+ breast cancer patients who have decreased immune effector cells could respond well to trastuzumab, we evaluated the alterations in circulating immune system cell subsets: CD16+ and/or CD56+ lymphocytes, lymphocytes and granulocytes in these patients before and after treatment with trastuzumab-based regimens in relation to clinical response to therapy. The study involved 55 patients with HER2+ breast cancer before and 2 months after the initiation of the therapy. Progressive disease was confirmed in nine out of 55 patients (non-responders), while other patients achieved complete or partial response, or stable disease (responders). Control group consisted of up to 52 healthy individuals. Significantly lower percentages of total lymphocytes, CD16+, CD56+, and CD16+CD56+ lymphocytes as well as higher percentage of granulocytes and a higher ratio of granulocyte to lymphocyte percentages were found in patients before therapy and 2 months after the initiation of the therapy, compared with those in healthy individuals. Responder subgroup showed significantly lower percentages of CD16+, CD56+, and CD16+CD56+ lymphocytes before therapy, compared with those in healthy controls. Two months after the initiation of the therapy, the percentages of immune cell subsets remained significantly lower in responders in comparison with those in the healthy donors, while a significantly decreased percentages of CD56+ and CD16+CD56+ lymphocytes were observed in non-responders, in comparison with those in healthy controls. Our study demonstrated that HER2+ breast cancer patients who have decreased percentages of CD16+, CD56+, and CD16+CD56+ lymphocytes may achieve response to trastuzumab-containing treatment.

3D HeLa spheroids as a model for investigating the anticancer activity of Biginelli-hybrids

In previous study, we examined the anticancer effects of novel Biginelli-hybrids against HeLa cell line on 2D monolayer culture. The five most effective compounds were chosen for further analysis of their anticancer activity against HeLa spheroids. Using the 3D models implies the possible differences in anticancer effects and mechanisms of activity of tested compounds. The compounds 4c and 4d exerted the strongest activity against 3D HeLa spheroids and induced to some extent loosened cell-cell contacts in spheroids, leading to the largest reduction in the diameter of the spheroids. Additionally, the highest accumulation of the cells in the subG1 phase of the cell cycle was observed after the treatment with compounds 4d and 4c, while the compound 4f led to the G2/M arrest. The invasion potential of treated HeLa cells in spheroids was monitored by imaging of spheroids embedded in a matrix made of matrigel and collagen and by determination of MMP2, MMP9, and VEGF gene expression levels. The compound 4l did not show invasion-suppressive activity, while the compounds 4c and 4d exerted the strongest anti-invasive activity.

Influence of selective acid-etching on functionality of halloysite-chitosan nanocontainers for sustained drug release

The functionality of halloysite (Hal) nanotubes as drug carriers can be improved by lumen enlargement and polymer modification. This study investigates the influence of selective acid etching on Hal functionalization with cationic biopolymer chitosan. Hal was subjected to lumen etching under mild conditions, loaded under vacuum with nonsteroidal antiinflammatory drug aceclofenac, and incubated in an acidic solution of chitosan. The functionality of pristine and etched Hal before and upon polymer functionalization was assessed by ζ-potential measurements, structural characterization (FT-IR, DSC and XRPD analysis), cell viability assay, drug loading and drug release studies. Acid etching increased specific surface area, pore volume and pore size of Hal, decreased ζ-potential and facilitated binding of the cationic polymer. XRPD and DSC analysis revealed crystalline structure of etched Hal. Successful chitosan binding and drug entrapment were further confirmed by FT-IR and DSC studies. XRPD showed surface polymer binding. DSC and FT-IR analyses confirmed the presence of the entrapped drug in its crystalline form. Drug loading was increased for ≈81% by selective lumen etching. Slight decrease of drug content occurred during chitosan functionalization due to aceclofenac diffusion in the polymer solution. The drug release was more sustained from etched Hal nanocomposites (up to ≈87% for 12 h) than from pristine Hal (up to ≈97% for 12 h) due to more intensive chitosan binding. High human fibroblast survival rates upon exposure to pristine and etched Hal before and after chitosan functionalization (>90% in the concentration of 1000 μg/mL) confirmed that both lumen etching under mild conditions and polymer functionalization had no significant effect on cytocompatibility. Based on these findings, selective lumen etching in combination with polycation modification appears to be a promising approach for improvement of Hal nanotubes functionality by increasing payload, polymer binding capacity, and sustained release properties with no significant effect on their cytocompatibility.

Mahonia aquifolium Extracts Promote Doxorubicin Effects against Lung Adenocarcinoma Cells In Vitro

Mahonia aquifolium and its secondary metabolites have been shown to have anticancer potential. We performed MTT, scratch, and colony formation assays; analyzed cell cycle phase distribution and doxorubicin uptake and retention with flow cytometry; and detected alterations in the expression of genes involved in the formation of cell-cell interactions and migration using quantitative real-time PCR following treatment of lung adenocarcinoma cells with doxorubicin, M. aquifolium extracts, or their combination. MTT assay results suggested strong synergistic effects of the combined treatments, and their application led to an increase in cell numbers in the subG1 phase of the cell cycle. Both extracts were shown to prolong doxorubicin retention time in cancer cells, while the application of doxorubicin/extract combination led to a decrease in MMP9 expression. Furthermore, cells treated with doxorubicin/extract combinations were shown to have lower migratory and colony formation potentials than untreated cells or cells treated with doxorubicin alone. The obtained results suggest that nontoxic M. aquifolium extracts can enhance the activity of doxorubicin, thus potentially allowing the application of lower doxorubicin doses in vivo, which may decrease its toxic effects in normal tissues.

Mechanisms of Chemotherapy Resistance in Triple-Negative Breast Cancer-How We Can Rise to the Challenge

Triple-negative (TNBC) is the most lethal subtype of breast cancer owing to high heterogeneity, aggressive nature, and lack of treatment options. Chemotherapy remains the standard of care for TNBC treatment, but unfortunately, patients frequently develop resistance. Accordingly, in recent years, tremendous effort has been made into elucidating the mechanisms of TNBC chemoresistance with the goal of identifying new molecular targets. It has become evident that the development of TNBC chemoresistance is multifaceted and based on the elaborate interplay of the tumor microenvironment, drug efflux, cancer stem cells, and bulk tumor cells. Alterations of multiple signaling pathways govern these interactions. Moreover, TNBC's high heterogeneity, highlighted in the existence of several molecular signatures, presents a significant obstacle to successful treatment. In the present, in-depth review, we explore the contribution of key mechanisms to TNBC chemoresistance as well as emerging strategies to overcome them. We discuss novel anti-tumor agents that target the components of these mechanisms and pay special attention to their current clinical development while emphasizing the challenges still ahead of successful TNBC management. The evidence presented in this review outlines the role of crucial pathways in TNBC survival following chemotherapy treatment and highlights the importance of using combinatorial drug strategies and incorporating biomarkers in clinical studies.

Biological Potential of Novel Methoxy and Hydroxy Substituted Heteroaromatic Amides Designed as Promising Antioxidative Agents: Synthesis, 3D-QSAR Analysis, and Biological Activity

This paper discusses antioxidative and biological activities of 25 novel amidino substituted benzamides with a variety of heteroaromatic nuclei attached to the benzamide moiety and with a variable number of methoxy or hydroxy substituents. Targeted compounds, bearing either amidino or 2-imidazolinyl substituent, were obtained in the Pinner reaction from cyano precursors. 3D-QSAR models were generated to predict antioxidative activity of the 25 novel aromatic and heteroaromatic benzamide derivatives. The compounds were tested for antioxidative activity using in vitro spectrophotometric assays. Direct validation of 3D-QSAR approach for predicting activities of novel benzamide derivatives was carried out by comparing experimental and computationally predicted antioxidative activity. Experimentally determined activities for all novel compounds were found to be within a standard deviation of error of the models. Following this, structure-activity relationships among the synthesized compounds are discussed. Furthermore, antiproliferative activity in vitro against HeLa cells as well as antibacterial and antifungal activity was tested to confirm the other biological activities of the prepared compounds.

Integration of dry-column flash chromatography with NMR and FTIR metabolomics to reveal cytotoxic metabolites from Amphoricarpos autariatus

Metabolomics generate a profile of small molecules from plant extracts, which could be directly responsible for bioactivity effects. Using dry-column flash chromatography enabled a rapid and inexpensive method for the very efficient separation of plant extract with a high resolution. This separation method coupled to NMR and FTIR-based metabolomics is applied to identify bioactive natural products. OPLS multivariate analysis method, was used for correlation the chemical composition of the plant extracts, Amphoricarpos autariatus, with the results of cytotoxic activity against Human cervical adenocarcinoma cell line (HeLa) and epithelial lung cancer cell line (A549). In this way, the highest contribution to the cytotoxic activity was recorded for the guaianolide sesquiterpene lactones named amphoricarpolides. The compounds indicated as bioactive after metabolomics analysis were tested, and their cytotoxic activity were confirmed.

Association of uPA and PAI-1 tumor levels and 4G/5G variants of PAI-1 gene with disease outcome in luminal HER2-negative node-negative breast cancer patients treated with adjuvant endocrine therapy

BACKGROUND

The aim of this study was to evaluate the prognostic potential of urokinase-type plasminogen activator (uPA) and plasminogen activator inhibitor type 1 (PAI-1) tumor tissue levels and examine the association between these biomarkers and classical prognostic factors in early node-negative luminal breast cancer patients. The clinical value of 4G/5G variants of PAI-1 gene was evaluated.

PATIENTS AND METHODS

This study involved 81 node-negative, estrogen receptor-positive and/or progesterone receptor-positive and human epidermal growth factor receptor 2-negative operable breast cancer patients who underwent radical surgical resection and received adjuvant endocrine therapy. Determination of uPA and PAI-1 concentrations in the breast cancer tissue extracts was performed using FEMTELLE® uPA/PAI-1 ELISA. An insertion (5G)/deletion (4G) polymorphism at position - 675 of the PAI-1 gene was detected by PCR-RFLP analysis.

RESULTS

Our research showed that patients with uPA tumor tissue levels higher than 3 ng/mg of protein had significantly reduced disease-free survival (DFS) and overall survival (OS) when compared to patients with uPA tumor tissue levels lower or equal to 3 ng/mg of protein. Patients with PAI-1 tumor tissue levels higher than 14 ng/mg of protein had significantly decreased OS in comparison with patients with PAI-1 tumor tissue levels lower or equal to 14 ng/mg of protein. ROC analysis confirmed the uPA and PAI-1 discriminative potential for the presence/absence of relevant events in these patients and resulted in higher cut-off values (5.65 ng/mg of protein for uPA and 27.10 ng/mg of protein for PAI-1) than standard reference cut-off values for both biomarkers. The prognostic importance of uPA and PAI-1 ROC cut-off values was confirmed by the impact of uPA higher than 5.65 ng/mg of protein and PAI-1 higher than 27.10 ng/mg of protein on poorer DFS, OS and event-free survival (EFS). We observed that patients with dominant allele in PAI-1 genotype (heterozygote and dominant homozygote, - 675 4G/5G and - 675 5G/5G) had significantly increased DFS, OS and EFS when compared with patients with recessive homozygote genotype (- 675 4G/4G).

CONCLUSION

Our study indicates that uPA and PAI-1 tumor tissue levels and 4G/5G variants of PAI-1 gene might be of prognostic significance in early node-negative luminal HER2-negative breast cancer patients treated with adjuvant endocrine therapy.

Comparative in vitro studies of the biological potential and chemical composition of stems, leaves and berries Aronia melanocarpa's extracts obtained by subcritical water extraction

Preparation of functional products as well as natural-based products requires non-toxic but effective extraction techniques. In this study, subcritical water extraction was used for the extraction of different aronia parts in order to explore their potential. Stems, leaves and berries of Aronia melanocarpa were extracted under the following conditions: temperature 130 °C; pressure 35 bar; time 20 min. The total phenols and flavonoid contents of the produced extracts were evaluated by conventional spectrophotometric methods. Additionally, the main phenolic compounds were also identified and quantified by high performance liquid chromatography with diode array detection (HPLC-DAD). The biological potential of the extracts was evaluated by determining their antioxidant (DPPH, ABTS and lipid peroxidation assays), antimicrobial, enzyme inhibitory (cholinesterase and elastase) and cytotoxic effects (HeLa, A-549, LS-174T, MRC-5 cell lines). The results indicate that leaves and berries extracts exhibited stronger antioxidant action when compared with stems. The strongest cholinesterase and elastase inhibitory activity was also found in berries extract. Similarly, the extracts obtained from leaves and berries showed considerable cytotoxic effects against tested cell lines. A moderate antimicrobial effects was observed too. Demonstrated biological potential of all three aronia parts can trace a new road map for developing newly designed functional products.

Synthesis, characterization and biological evaluation of Pd(ii), Cu(ii), Re(i) and 99mTc(i) thiazole-based complexes

A new thiazole-containing multidentate ligand 2-((2-phenylthiazol-4-yl)methylthio)ethanamine, L, was synthesized and used to prepare new complexes of the formula Pd^IILCl₂ (Pd-L), Cu^IIL₂Cl₂ (Cu-L) and fac-[Re/^99mTc^I(CO)₃(L)]⁺ (Re/^99mTc-L). The ligand L and the metal complexes were characterized spectroscopically. Furthermore, the structures of Re-L and Cu-L were elucidated by X-ray crystallography. Ligand L acts as a bidentate (N_th, S) chelator in Pd-L, as a bidentate (N, S) chelator in Cu-L and as a tridentate (N_th, S, N) chelator in Re-L. The radiotracer ^99mTc-L was synthesized in high yield and characterised by HPLC comparison with the Re-L analog. The synthesized compounds were evaluated for their anti-inflammatory and cytotoxic properties. The compounds exhibited low anti-inflammatory activity with Pd-L showing the highest activity among them. The cytotoxic activity of the ligand and the complexes against several human cancer cell lines (cervical adenocarcinoma HeLa, colorectal adenocarcinoma LS-174T, lung adenocarcinoma A549, breast adenocarcinoma MDA-MB-231 and normal human lung fibroblast cell line MRC-5) was examined using the MTT assay. The complex Cu-L exhibited the highest cytotoxicity and the complex Pd-L showed the best tumor selectivity. The changes in the cell cycle phase distribution were determined by flow cytometry and it was found that ligand L shows the highest apoptotic activity. The biodistribution studies of ^99mTc-L in mice showed fast tissue clearance. Of all the thiazole-containing compounds, the palladium complex appears to be more promising for future efforts.

Peripheral White Blood Cell Subsets in Metastatic Colorectal Cancer Patients Treated with Cetuximab: The Potential Clinical Relevance

It was demonstrated that cetuximab-induced tumor regression is based on the effects exerted by immune cells included mainly in the innate immune response. Therefore, the focus of this study was to explore the alterations in the percentages of CD16+, and/or CD56+ lymphocytes, which are comprised of NK cells, and minority of CD56+CD3+ cells, in patients with metastatic colorectal cancer before or 2 months after the treatment with cetuximab-based regimens associated with the response to therapy. The changes in the percentages of lymphocytes and granulocytes in these patients were evaluated as well. We enrolled 50 patients with wild-type KRAS metastatic colorectal cancer. Disease progression was observed in 11/50 patients (non-responders), while other patients achieved partial response or stable disease (responders). Control groups included up to 72 healthy individuals. A significant decrease in the percentages of CD56+ and CD16+CD56+ lymphocytes together with a significant decrease in the percentage of lymphocytes and an increase in the ratio of granulocyte to lymphocyte percentages were observed in patients with metastatic colorectal cancer before therapy, compared with those in the healthy individuals. In contrast to those in the responders, the percentage of CD16+ lymphocytes in the overall white blood cell pool was shown to be significantly decreased in the non-responders, together with a significantly decreased percentage of lymphocytes, a significantly increased percentage of granulocytes, and an increased ratio of granulocyte to lymphocyte percentages before treatment compared with those in the healthy controls. Two months after the initiation of the treatment, significantly decreased percentages of CD16+, CD56+, and CD16+CD56+ lymphocytes were observed in patients, compared with those determined in the healthy controls. The same changes in the amounts of circulating immune cells were also observed in the responder subgroup, but the percentages of CD16+, CD56+, and CD16+CD56+ lymphocytes 2 months after treatment in the non-responder group did not differ significantly in comparison with healthy individuals. Considerable alterations of immune cell percentages observed in patients with metastatic colorectal cancer with disease progression indicate that the assessment of peripheral white blood cell architecture before treatment initiation may be clinically relevant.

Enhancing constant-pH simulation in explicit solvent with a two-dimensional replica exchange method

We present a new method for enhanced sampling for constant-pH simulations in explicit water based on a two-dimensional (2D) replica exchange scheme. The new method is a significant extension of our previously developed constant-pH simulation method, which is based on enveloping distribution sampling (EDS) coupled with a one-dimensional (1D) Hamiltonian exchange method (HREM). EDS constructs a hybrid Hamiltonian from multiple discrete end state Hamiltonians that, in this case, represent different protonation states of the system. The ruggedness and heights of the hybrid Hamiltonian's energy barriers can be tuned by the smoothness parameter. Within the context of the 1D EDS-HREM method, exchanges are performed between replicas with different smoothness parameters, allowing frequent protonation-state transitions and sampling of conformations that are favored by the end-state Hamiltonians. In this work, the 1D method is extended to 2D with an additional dimension, external pH. Within the context of the 2D method (2D EDS-HREM), exchanges are performed on a lattice of Hamiltonians with different pH conditions and smoothness parameters. We demonstrate that both the 1D and 2D methods exactly reproduce the thermodynamic properties of the semigrand canonical (SGC) ensemble of a system at a given pH. We have tested our new 2D method on aspartic acid, glutamic acid, lysine, a four residue peptide (sequence KAAE), and snake cardiotoxin. In all cases, the 2D method converges faster and without loss of precision; the only limitation is a loss of flexibility in how CPU time is employed. The results for snake cardiotoxin demonstrate that the 2D method enhances protonation-state transitions, samples a wider conformational space with the same amount of computational resources, and converges significantly faster overall than the original 1D method.

Metformin effects on malignant cells and healthy PBMC; the influence of metformin on the phenotype of breast cancer cells

The aim of research was to determine the effects of maximally therapeutically achievable concentrations of metformin on malignant cells and healthy peripheral blood mononuclear cells (PBMC). Eight patients with T2D or hyperglycemia and nine healthy volunteers were included in the study. For determination of the influence of metformin on the phenotype of breast carcinoma, 1,410 patients with surgically removed tumors were included. From this group 37 breast cancer patients had DM type 2 or hyperglycemia and were pretreated with metformin alone or sometimes in combination with other antidiabetic drugs. Our results proved that metformin at low concentrations induced mild decrease in survival of malignant cells and PBMC stimulated for proliferation, but it didn't affect survival of resting PBMC. The effects of plasma of hyperglycemic patients who were under metformin therapy on autologous PBMC-induced decrease in survival of MDA-MB-361 cells, was noticeable in some patients. Metformin pretreatment for 24 h of HER2+ MDA-MB-361 cells, which were subsequently treated for 48 h with Herceptin, induced additional decline in cell survival. The analysis of influence of metformin on phenotype of breast cancer cells revealed significantly lower number of diabetic cancer patients treated with metformin with overexpressed HER2+ tumors (p < 0.013), while the number of patients with ER+PR+ tumors was not significantly changed (p < 0.832). In conclusion, therapeutically used concentrations of metformin exhibit mild cytotoxic action on malignant and dividing normal cells pointing to its preferred role in malignant and autoimmune diseases. The use of metformin was associated with pronounced decrease in HER2 overexpressing tumors.

Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation states. A smoothness parameter s is used to control the heights of energy barriers of the hybrid-state energy landscape. A small s value facilitates state transitions by lowering energy barriers. Replica exchange between EDS potentials with different s values allows us to readily obtain a thermodynamically accurate ensemble of multiple protonation states with frequent state transitions. The analysis is performed with an ensemble obtained from an EDS Hamiltonian without smoothing, s = ∞, which strictly follows the minimum energy surface of the end states. The accuracy and efficiency of this method is tested on aspartic acid, lysine, and glutamic acid, which have two protonation states, a histidine with three states, a four-residue peptide with four states, and snake cardiotoxin with eight states. The pKa values estimated with the EDS-HREX method agree well with the experimental pKa values. The mean absolute errors of small benchmark systems range from 0.03 to 0.17 pKa units, and those of three titratable groups of snake cardiotoxin range from 0.2 to 1.6 pKa units. This study demonstrates that EDS-HREX is a potent theoretical framework, which gives the correct description of multiple protonation states and good calculated pKa values.

Serum activity of DPPIV and its expression on lymphocytes in patients with melanoma and in people with vitiligo

Background

Dipeptidyl peptidase IV, a multifunctional serine protease, is implicated in regulation of malignant transformation, promotion and further progression of cancer, exerting tumor-suppressing or even completely opposite - tumor-promoting activities.

The aim of present research was to determine the serum DPPIV activity, as well as the percentages of CD26+ lymphocytes, CD26+ overall white blood cells and the mean fluorescence intensity of CD26 expression on lymphocytes in patients with melanoma, people with vitiligo and in healthy controls.

Methods

The activity of DPPIV in serum was determined by colorimetric test. Expression of DPPIV (as CD26) on immunocompetent peripheral white blood cells was done using flow cytometry analysis.

Results

Data from our study show for the first time statistically significant decrease: in the serum DPPIV activity, in the percentage of CD26+ overall white blood cells and in the percentage of lymphocytes in patients with melanoma in comparison to healthy control people. In addition, significantly lower serum DPPIV activity was found in the group of patients with melanoma in relation to people with vitiligo too.

Conclusion

This study indicates the need for exploring the cause and the importance of the disturbances in the serum DPPIV activity and in the CD26 expression on immunocompetent cells in complex molecular mechanisms underlying the development and progression of melanoma.

Immunity to melanin and to tyrosinase in melanoma patients, and in people with vitiligo

Background

The aim of this study was to determine the presence and the intensity of humoral immunity to melanoma-associated antigens: tyrosinase and melanin, in patients with melanoma, in persons with vitiligo and in control healthy people.

Methods

The study involved 63 patients with melanoma and 19 persons with vitiligo. Control group consisted up to 41 healthy volunteers. Mushroom tyrosinase and synthetic melanin were used as the antigens.

Results

ELISA test showed significantly (p < 0.0000004 and p < 0.04) lower levels of IgM anti-tyrosinase autoantibodies, in melanoma and vitiligo patients respectively, compared to controls.

Although there was no significant difference between the levels of IgA anti-melanin autoantibodies in melanoma or vitiligo patients in comparison with controls, the enhanced concentrations of anti-melanin IgA autoantibodies were preferentially found in melanoma patients with metastatic disease. Significantly high percentage in the Fc alphaRI (CD89) positive cells was determined in melanoma patients (p < 0.002 and p < 0.008) in comparison to that found in healthy people or in patients with vitiligo, in the already mentioned order, pointing that IgA dependent cellular cytotoxicity is not important for the immune action against melanoma, even more that it is included in some immune suppression.

Levels of IgG autoantibodies to mentioned antigens in melanoma patients although low were not significantly lower from controls. These findings analyzed together with the statistically significant low percentage of FcgammaRIII, (CD16) positive immunocompetent cells (p < 0.0007 and p < 0.003), which was found in patients with melanoma compared with healthy or vitiligo people respectively, and statistically significant low percentage of (CD16 + CD56+) natural killer (NK) cells (p < 0.005) found in melanoma patients in comparison to healthy controls pointed to the low probability for anti-melanoma IgG mediated, antibody mediated cellular cytotoxicity, (ADCC) and NK cytotoxicity. Moreover the ratio of the percentages of granulocytes and percentage of lymphocytes was statistically higher in patients with melanoma in relation to healthy people as well as to people with vitiligo (p < 0.0007 and p < 0.05 respectively).

Conclusion

Autoantibodies to tyrosinase and to melanin which are found even in healthy people, point that consummation of edible mushrooms that carry the antigen tyrosinase and melanin, could influence the humoral anti-melanoma immune response.

Levels of different immunoglobulin classes of anti-melanin and anti-tyrosinase antibodies varied depending on the presence and the stage of studied diseases. Besides, the statistically enhanced ratio of the percentages of granulocytes and percentage of lymphocytes, together with statistically decreased percentage of NK cells is found in analyzed melanoma patients.

pH replica-exchange method based on discrete protonation states

We propose a new algorithm for obtaining proton titration curves of ionizable residues. The algorithm is a pH replica-exchange method (PHREM), which is based on the constant pH algorithm of Mongan et al. (J Comput Chem 2004;25:2038-2048). In the original replica-exchange method, simulations of different replicas are performed at different temperatures, and the temperatures are exchanged between the replicas. In our PHREM, simulations of different replicas are performed at different pH values, and the pHs are exchanged between the replicas. The PHREM was applied to a blocked amino acid and to two protein systems (snake cardiotoxin and turkey ovomucoid third domain), in conjunction with a generalized Born implicit solvent. The performance and accuracy of this algorithm and the original constant pH method (PHMD) were compared. For a single set of simulations at different pHs, the use of PHREM yields more accurate Hill coefficients of titratable residues. By performing multiple sets of constant pH simulations started with different initial states, the accuracy of predicted pK(a) values and Hill coefficients obtained with PHREM and PHMD methods becomes comparable. However, the PHREM algorithm exhibits better samplings of the protonation states of titratable residues and less scatter of the titration points and thus better precision of measured pK(a) values and Hill coefficients. In addition, PHREM exhibits faster convergence of individual simulations than the original constant pH algorithm.

Conformational relaxation and water penetration coupled to ionization of internal groups in proteins

Molecular dynamics simulations were used to examine the effects of ionization of internal groups on the structures of eighteen variants of staphylococcal nuclease (SNase) with internal Lys, Asp, or Glu. In most cases the RMSD values of internal ionizable side chains were larger when the ionizable moieties were charged than when they were neutral. Calculations of solvent-accessible surface area showed that the internal ionizable side chains were buried in the protein interior when they were neutral and moved toward crevices and toward the protein-water interface when they were charged. The only exceptions are Lys-36, Lys-62, and Lys-103, which remained buried even after charging. With the exception of Lys-38, the number of internal water molecules surrounding the ionizable group increased upon charging: the average number of water oxygen atoms within the first hydration shell increased by 1.7 for Lys residues, by 5.2 for Asp residues, and by 3.2 for Glu residues. The polarity of the microenvironment of the ionizable group also increased when the groups were charged: the average number of polar atoms of any kind within the first hydration shell increased by 2.7 for Lys residues, by 4.8 for Asp residues, and by 4.0 for Glu residues. An unexpected correlation was observed between the absolute value of the shifts in pK(a) values measured experimentally, and several parameters of structural relaxation: the net difference in the polarity of the microenvironment of the charged and neutral forms of the ionizable groups, the net difference in hydration of the charged and neutral forms of the ionizable groups, and the difference in RMSD values of the charged and neutral forms of the ionizable groups. The effects of ionization of internal groups on the conformation of the backbone were noticeable but mostly small and localized to the area immediately next to the internal ionizable moiety. Some variants did exhibit local unfolding.

Self-guided Langevin dynamics study of regulatory interactions in NtrC

Multiple self-guided Langevin dynamics (SGLD) simulations were performed to examine structural and dynamical properties of the receiver domain of nitrogen regulatory protein C (NtrC(r)). SGLD and MD simulations of the phosphorylated active form structure suggest a mostly stable but broad structural ensemble of this protein. The finite difference Poisson-Boltzmann calculations of the pK(a) values of the active site residues suggest an increase in the pK(a) of His-84 on phosphorylation of Asp-54. In SGLD simulations of the phosphorylated active form with charged His-84, the average position of the regulatory helix alpha4 is found closer to the starting structure than in simulations with the neutral His-84. To model the transition pathway, the phosphate group was removed from the simulations. After 7 ns of simulations, the regulatory helix alpha4 was found approximately halfway between positions in the NMR structures of the active and inactive forms. Removal of the phosphate group stimulated loss of helix alpha4, suggesting that the pathway of conformational transition may involve partial unfolding mechanism. The study illustrates the potential utility of the SGLD method in studies of the coupling between ligand binding and conformational transitions.

SCHIZOPHRENIA AND POLYMORPHIC CAG REPEATS ARRAY OF CALCIUM-ACTIVATED POTASSIUM CHANNEL (KCNN3) GENE IN SERBIAN POPULATION

KCNN3 might be a candidate gene for schizophrenia. The KCNN3 cDNA sequence contains two stretches of CAG trinucleotide repeats encoding two separate polyglutamine segments near the N-terminus of this channel protein. The second CAG repeat is highly polymorphic in the Caucasian population from both Europe and United States. The authors carried out a study to compare the allelic frequency distribution of the CAG repeat in KCNN3 gene in 55 Serbian schizophrenic patients and 46 controls. The data indicate a significant association between longer CAG repeats in second polymorphic KCNN3 region and schizophrenia in the Serbian population.

Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study

Pathways of structural relaxation triggered by ionization of internal groups in staphylococcal nuclease (SNase) were studied through multiple self-guided Langevin dynamics (SGLD) simulations. Circular dichroism, steady-state Trp fluorescence, and nuclear magnetic resonance spectroscopy have shown previously that variants of SNase with internal Glu, Asp, and Lys at positions 66 or 92, and Arg at position 66, exhibit local reorganization or global unfolding when the internal ionizable group is charged. Except for Arg-66, these internal ionizable groups have unusual pKa values and are neutral at physiological pH. The structural trends observed in the simulations are in general agreement with experimental observations. The I92D variant, which unfolds globally upon ionization of Asp-92, in simulations often exhibits extensive hydration of the protein core, and sometimes also significant perturbations of the beta-barrel. In the crystal structure of the V66R variant, the beta1 strand from the beta-barrel is domain-swapped; in the simulations, the beta1 strand is sometimes partially released. The V66K variant, which in solutions shows reorganization of six residues at the C-terminus of helix alpha1 and perturbations in the beta-barrel structure, exhibits fraying of three residues of helix alpha1 in one simulation, and perturbations and partial unfolding of three beta-strands in a few other simulations. In sharp contrast, very small structural changes were observed in simulations of the wild-type protein. The simulations indicate that charging of internal groups frequently triggers penetration of water into the protein interior. The pKa values of Asp-92 and Arg-66 calculated with continuum methods on SGLD-relaxed structures reached the normal values in most simulations. Detailed analysis of accuracy and performance of SGLD demonstrates that SGLD outperforms LD in sampling of alternative protein conformations without loss of the accuracy and level of detail characteristic of regular LD.

Open science grid study of the coupling between conformation and water content in the interior of a protein

Computational grids are a promising resource for modeling complex biochemical processes such as protein folding, penetration of gases or water into proteins, or protein structural rearrangements coupled to ligand binding. We have enabled the molecular dynamics program CHARMM to run on the Open Science Grid. The implementation is general, flexible, easily modifiable for use with other molecular dynamics programs and other grids and automated in terms of job submission, monitoring, and resubmission. The usefulness of grid computing was demonstrated through the study of hydration of the Glu-66 side chain in the interior of protein staphylococcal nuclease. Multiple simulations started with and without two internal water molecules shown crystallographically to be associated with the side chain of Glu-66 yielded two distinct populations of rotameric states of Glu-66 that differed by as much as 20%. This illustrates how internal water molecules can bias protein conformations. Furthermore, there appeared to be a temporal correlation between dehydration of the side chain and conformational transitions of Glu-66. This example demonstrated how difficult it is to get convergence even in the relatively simple case of a side chain oscillating between two conformations. With grid computing, we also benchmarked the self-guided Langevin dynamics method against the Langevin dynamics method traditionally used for temperature control in molecular dynamics simulations and showed that the two methods yield comparable results.

A buried lysine that titrates with a normal pKa: role of conformational flexibility at the protein-water interface as a determinant of pKa values

Previously we reported that Lys, Asp, and Glu residues at positions 66 and 92 in staphylococcal nuclease (SNase) titrate with pK(a) values shifted by up to 5 pK(a) units in the direction that promotes the neutral state. In contrast, the internal Lys-38 in SNase titrates with a normal pK(a). The crystal structure of the L38K variant shows that the side chain of Lys-38 is buried. The ionizable moiety is approximately 7 A from solvent and ion paired with Glu-122. This suggests that the pK(a) value of Lys-38 is normal because the energetic penalty for dehydration is offset by a favorable Coulomb interaction. However, the pK(a) of Lys-38 was also normal when Glu-122 was replaced with Gln or with Ala. Continuum electrostatics calculations were unable to reproduce the pK(a) of Lys-38 unless the protein was treated with an artificially high dielectric constant, consistent with structural reorganization being responsible for the normal pK(a) value of Lys-38. This reorganization must be local because circular dichroism and NMR spectroscopy indicate that the L38K protein is native-like under all conditions studied. In molecular dynamics simulations, the ion pair between Lys-38 and Glu-122 is unstable. The simulations show that a minor rearrangement of a loop is sufficient to allow penetration of water to the amino moiety of Lys-38. This illustrates both the important roles of local flexibility and water penetration as determinants of pK(a) values of ionizable groups buried near the protein-water interface, and the challenges faced by structure-based pK(a) calculations in reproducing these effects.

Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins

Molecular dynamics simulations of Staphylococcal nuclease and of 10 variants with internal polar or ionizable groups were performed to investigate systematically the molecular determinants of hydration of internal cavities and pockets in proteins. In contrast to apolar cavities in rigid carbon structures, such as nanotubes or buckeyballs, internal cavities in proteins that are large enough to house a few water molecules will most likely be dehydrated unless they contain a source of polarity. The water content in the protein interior can be modulated by the flexibility of protein elements that interact with water, which can impart positional disorder to water molecules, or bias the pattern of internal hydration that is stabilized. This might explain differences in the patterns of hydration observed in crystal structures obtained at cryogenic and room temperature conditions. The ability of molecular dynamics simulations to determine the most likely sites of water binding in internal pockets and cavities depends on its efficiency in sampling the hydration of internal sites and alternative protein and water conformations. This can be enhanced significantly by performing multiple molecular dynamics simulations as well as simulations started from different initial hydration states.

Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes

A general approach for calculating spectral and optical properties of pigment-protein complexes of known atomic structure is presented. The method, that combines molecular dynamics simulations, quantum chemistry calculations, and statistical mechanical modeling, is demonstrated by calculating the absorption and circular dichroism spectra of the B800-B850 bacteriochlorophylls of the LH2 antenna complex from Rs. molischianum at room temperature. The calculated spectra are found to be in good agreement with the available experimental results. The calculations reveal that the broadening of the B800 band is mainly caused by the interactions with the polar protein environment, while the broadening of the B850 band is due to the excitonic interactions. Since it contains no fitting parameters, in principle, the proposed method can be used to predict optical spectra of arbitrary pigment-protein complexes of known structure.

Molecular dynamics study of water penetration in staphylococcal nuclease

The ionization properties of Lys and Glu residues buried in the hydrophobic core of staphylococcal nuclease (SN) suggest that the interior of this protein behaves as a highly polarizable medium with an apparent dielectric constant near 10. This has been rationalized previously in terms of localized conformational relaxation concomitant with the ionization of the internal residue, and with contributions by internal water molecules. Paradoxically, the crystal structure of the SN V66E variant shows internal water molecules and the structure of the V66K variant does not. To assess the structural and dynamical character of interior water molecules in SN, a series of 10-ns-long molecular dynamics (MD) simulations was performed with wild-type SN, and with the V66E and V66K variants with Glu66 and Lys66 in the neutral form. Internal water molecules were identified based on their coordination state and characterized in terms of their residence times, average location, dipole moment fluctuations, hydrogen bonding interactions, and interaction energies. The locations of the water molecules that have residence times of several nanoseconds and display small mean-square displacements agree well with the locations of crystallographically observed water molecules. Additional, relatively disordered water molecules that are not observed crystallographically were found in internal hydrophobic locations. All of the interior water molecules that were analyzed in detail displayed a distribution of interaction energies with higher mean value and narrower width than a bulk water molecule. This underscores the importance of protein dynamics for hydration of the protein interior. Further analysis of the MD trajectories revealed that the fluctuations in the protein structure (especially the loop elements) can strongly influence protein hydration by changing the patterns or strengths of hydrogen bonding interactions between water molecules and the protein. To investigate the dynamical response of the protein to burial of charged groups in the protein interior, MD simulations were performed with Glu66 and Lys66 in the charged state. Overall, the MD simulations suggest that a conformational change rather than internal water molecules is the dominant determinant of the high apparent polarizability of the protein interior.

Energy transfer in photosystem I of cyanobacteria Synechococcus elongatus: model study with structure-based semi-empirical Hamiltonian and experimental spectral density

We model the energy transfer and trapping kinetics in PSI. Rather than simply applying Förster theory, we develop a new approach to self-consistently describe energy transfer in a complex with heterogeneous couplings. Experimentally determined spectral densities are employed to calculate the energy transfer rates. The absorption spectrum and fluorescence decay time components of the complex at room temperature were reasonably reproduced. The roles of the special chlorophylls (red, linker, and reaction center, respectively) molecules are discussed. A formally exact expression for the trapping time is derived in terms of the intrinsic trapping time, mean first passage time to trap, and detrapping time. The energy transfer mechanism is discussed and the slowest steps of the arrival at the primary electron donor are found to contain two dominant steps: transfer-to-reaction-center, and transfer-to-trap-from-reaction-center. The intrinsic charge transfer time is estimated to be 0.8 approximately 1.7 ps. The optimality with respect to the trapping time of the calculated transition energies and the orientation of Chls is discussed.

The quantum physics of photosynthesis

Biological cells contain nanoscale machineries that exhibit a unique combination of high efficiency, high adaptability to changing environmental conditions, and high reliability. Recent progress in obtaining atomically resolved structures provide an opportunity for an atomic-level explanation of the biological function of cellular machineries and the underlying physical mechanisms. A prime example in this regard is the apparatus with which purple bacteria harvest the light of the sun. Its highly symmetrical architecture and close interplay of biological functionality with quantum physical processes allow an illuminating demonstration of the fact that properties of living beings ultimately rely on and are determined by the laws of physics.

Excitons in a photosynthetic light-harvesting system: a combined molecular dynamics, quantum chemistry, and polaron model study

The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with an approach that combines molecular dynamics simulations with quantum chemistry calculations and a polaron model analysis. The molecular dynamics simulation of light-harvesting (LH) complexes was performed on an 87 055 atom system comprised of a LH-II complex of Rhodospirillum molischianum embedded in a lipid bilayer and surrounded with appropriate water layers. For each of the 16 B850 bacteriochlorophylls (BChls), we performed 400 ab initio quantum chemistry calculations on geometries that emerged from the molecular dynamical simulations, determining the fluctuations of pigment excitation energies as a function of time. From the results of these calculations we construct a time-dependent Hamiltonian of the B850 exciton system from which we determine within linear response theory the absorption spectrum. Finally, a polaron model is introduced to describe both the excitonic and coupled phonon degrees of freedom by quantum mechanics. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function, are derived from the molecular dynamics and quantum chemistry simulations. The model predicts that excitons in the B850 BChl ring are delocalized over five pigments at room temperature. Also, the polaron model permits the calculation of the absorption and circular dichroism spectra of the B850 excitons from the sole knowledge of the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined molecular dynamics and quantum chemistry simulations. The obtained results are found to be in good agreement with the experimentally measured absorption and circular dichroism spectra.

Photosynthetic apparatus of purple bacteria

1. Introduction 2

2. Structure of the bacterial PSU 5

2.1 Organization of the bacterial PSU 5

2.2 The crystal structure of the RC 9

2.3 The crystal structures of LH-II 11

2.4 Bacteriochlorophyll pairs in LH-II and the RC 13

2.5 Models of LH-I and the LH-I-RC complex 15

2.6 Model for the PSU 17

3. Excitation transfer in the PSU 18

3.1 Electronic excitations of BChls 22

3.1.1 Individual BChls 22

3.1.2 Rings of BChls 22

3.1.2.1 Exciton states 22

3.1.3 Effective Hamiltonian 24

3.1.4 Optical properties 25

3.1.5 The effect of disorder 26

3.2 Theory of excitation transfer 29

3.2.1 General theory 29

3.2.2 Mechanisms of excitation transfer 32

3.2.3 Approximation for long-range transfer 34

3.2.4 Transfer to exciton states 35

3.3 Rates for transfer processes in the PSU 37

3.3.1 Car→BChl transfer 37

3.3.1.1 Mechanism of Car→BChl transfer 39

3.3.1.2 Pathways of Car→BChl transfer 40

3.3.2 Efficiency of Car→BChl transfer 40

3.3.3 B800-B850 transfer 44

3.3.4 LH-II→LH-II transfer 44

3.3.5 LH-II→LH-I transfer 45

3.3.6 LH-I→RC transfer 45

3.3.7 Excitation migration in the PSU 46

3.3.8 Genetic basis of PSU assembly 49

4. Concluding remarks 53

5. Acknowledgments 55

6. References 55

Life as we know it today exists largely because of photosynthesis, the process through which light energy is converted into chemical energy by plants, algae, and photosynthetic bacteria (Priestley, 1772; Barnes, 1893; Wurmser, 1925; Van Niel, 1941; Clayton & Sistrom, 1978; Blankenship et al. 1995; Ort & Yocum, 1996). Historically, photosynthetic organisms are grouped into two classes. When photosynthesis is carried out in the presence of air it is called oxygenic photosynthesis (Ort & Yocum, 1996). Otherwise, it is anoxygenic (Blankenship et al. 1995). Higher plants, algae and cyanobacteria perform oxygenic photosynthesis, which involves reduction of carbon dioxide to carbohydrate and oxidation of water to produce molecular oxygen. Some photosynthetic bacteria, such as purple bacteria, carry out anoxygenic photosynthesis that involves oxidation of molecules other than water. In spite of these differences, the general principles of energy transduction are the same in anoxygenic and oxygenic photosynthesis (Van Niel, 1931, 1941; Stanier, 1961; Wraight, 1982; Gest, 1993). The primary processes of photosynthesis involve absorption of photons by light-harvesting complexes (LHs), transfer of excitation energy from LHs to the photosynthetic reaction centers (RCs), and the primary charge separation across the photosynthetic membrane (Sauer, 1975; Knox, 1977; Fleming & van Grondelle, 1994; van Grondelle et al. 1994). In this article, we will focus on the anoxygenic photosynthetic process in purple bacteria, since its photosynthetic system is the most studied and best characterized during the past 50 years.

Excitation transfer in the peridinin-chlorophyll-protein of Amphidinium carterae

Peridinin-chlorophyll-protein (PCP) is a unique light-harvesting protein that uses carotenoids as its primary light-absorbers. This paper theoretically investigates excitation transfer between carotenoids and chlorophylls in PCP of the dinoflagellate Amphidinium carterae. Calculations based on a description of the electronic states of the participating chromophores and on the atomic level structure of PCP seek to identify the mechanism and pathways of singlet excitation flow. After light absorption the optically allowed states of peridinins share their electronic excitation in excitonic fashion, but are not coupled strongly to chlorophyll residues in PCP. Instead, a gateway to chlorophyll Q(y) excitations is furnished through a low-lying optically forbidden excited state, populated through internal conversion. Carbonyl group and non-hydrogen side groups of peridinin are instrumental in achieving the respective coupling to chlorophyll. Triplet excitation transfer to peridinins, mediated by electron exchange, is found to efficiently protect chlorophylls against photo-oxidation.

Efficient light harvesting through carotenoids

We review the factors that control the efficiency of carotenoid-chlorophyll excitation transfer in photosynthetic light harvesting. For this we summarize first the recently developed theory that describes electronic couplings between carotenoids and chlorophylls and we outline in particular the influence of length of conjugated system and of symmetry breaking on the couplings. We focus hereby on the structurally solved lycopene-BChl system of LH 2 from Rhodospirillum molischianum and the peridinin-Chl a system of PCP from Amphidinium carterae. In addition, we review recent spectroscopic data for neurosporene, spheroidene and lycopene, three carotenoids with different lengths of conjugated systems. On the basis of the measured energies, emission lineshapes, solution and protein environment lifetimes for their 2A ( g ) (-) and 1B ( u ) (+) states as well as of the theoretically determined couplings, we conclude that the transfer efficiencies from the 2A ( g ) (-) state are controlled by the Car(2A ( g ) (-) )-BChl(Q(g)) electronic couplings and the 2A ( g ) (-) --> 1A ( g ) (-) internal conversion rates. We suggest that symmetry breaking and geometry rather than length of conjugated system dominate couplings involving the 2A ( g ) (-) state. Differences in transfer efficiencies from the 1B ( u ) (+) state in LH 2 and PCP are found to be dominated by the differences in spectral overlap. The role of the 1B ( u ) (+) state is likely to be influenced by a lower-lying (in longer polyenes), optically forbidden 1B ( u ) (-) state.

Architecture and mechanism of the light-harvesting apparatus of purple bacteria

Photosynthetic organisms fuel their metabolism with light energy and have developed for this purpose an efficient apparatus for harvesting sunlight. The atomic structure of the apparatus, as it evolved in purple bacteria, has been constructed through a combination of x-ray crystallography, electron microscopy, and modeling. The detailed structure and overall architecture reveals a hierarchical aggregate of pigments that utilizes, as shown through femtosecond spectroscopy and quantum physics, elegant and efficient mechanisms for primary light absorption and transfer of electronic excitation toward the photosynthetic reaction center.

[Gilles de la Tourette's syndrome]

Gilles de la Tourette's syndrome (GTS) is characterized with motor and vocal tics, initiating before 21 years of age, lasting for over a year and are associated with diverse behavioral disorders. The study analyzes features of 12 our GTS patients with mean age at the onset of the disease of 12.0 years, while the exact diagnosis was established only after 9.5 years (2-33 years). In 11 out of 12 patients the disease started with motor or vocal tics, while in completely developed clinical picture of GTS the permanently present tics were associated with coprolalia (6 patients), echolalia, copropraxia (in 2 patients, respectively), attention deficits (9 patients), obsessive-compulsive disorders (8 patients) etv. The role of neuroleptic therapy was discussed according to our experience and other reported studies. In our study, haloperidol had good therapeutical effect in 64% of the treated patients.