Mol Biosyst [JOURNAL]
Sun
200 papers
Structure-based design of novel combinatorially generated NBTIs as potential DNA gyrase inhibitors against various Staphylococcus aureus mutant strains.
Kolaric A, Minovski N
Mol Biosyst · 2017 Jun · PMID 28590495 · Publisher ↗
Although intercalating agents such as quinolones have had proven therapeutic success as antibacterial agents for more than 40 years, new forms of quinolone-based resistance in bacteria are continually emerging. To allevi...
Although intercalating agents such as quinolones have had proven therapeutic success as antibacterial agents for more than 40 years, new forms of quinolone-based resistance in bacteria are continually emerging. To alleviate this problem, a new class of antibacterials is urgently needed; recently, novel bacterial topoisomerase inhibitors (NBTIs) have been found to be particularly important. Based on 67 experimentally evaluated NBTIs against wild-type (WT) DNA gyrase originating from Staphylococcus aureus, a predictive QSAR model was initially constructed and validated and was later used for in silico prediction of biological activities for an in house designed compound library of 548 novel drug-like NBTI combinatorial analogs. To evaluate the influence of gyrA alterations on NBTI resistance, various mutant homology models were constructed; meanwhile, their resistance profiles were assessed and validated relative to that of WT enzyme by structure-based virtual screening (VS) of known NBTIs. Surprisingly, the M121K mutant model was recognized as the most selective due to an additional established cation-π interaction between K121-NH (not found in the WT) and the aromatic moiety of the NBTI right-hand site (RHS) fragment; this finding was additionally supported by VS of our combinatorially generated NBTIs. Moreover, we identified several attractive, synthetically feasible RHS building blocks that may enable the development of new NBTIs.
Literature-based prediction of novel drug indications considering relationships between entities.
Jang G, Lee T, Lee BM … +1 more , Yoon Y
Mol Biosyst · 2017 Jun · PMID 28581007 · Publisher ↗
There have been many attempts to identify and develop new uses for existing drugs, which is known as drug repositioning. Among these efforts, text mining is an effective means of discovering novel knowledge from a large...
There have been many attempts to identify and develop new uses for existing drugs, which is known as drug repositioning. Among these efforts, text mining is an effective means of discovering novel knowledge from a large amount of literature data. We identify a gene regulation by a drug and a phenotype based on the biomedical literature. Drugs or phenotypes can activate or inhibit gene regulation. We calculate the therapeutic possibility that a drug acts on a phenotype by means of these two types of regulation. We assume that a drug treats a phenotype if the genes regulated by the phenotype are inversely correlated with the genes regulated by the drug. Based on this hypothesis, we identify drug-phenotype associations with therapeutic possibility. To validate the drug-phenotype associations predicted by our method, we make an enrichment comparison with known drug-phenotype associations. We also identify candidate drugs for drug repositioning from novel associations and thus reveal that our method is a novel approach to drug repositioning.
Mathematical modeling reveals differential regulation of MAPK activity by phosphatase proteins in the yeast pheromone response pathway.
Dyjack N, Azeredo-Tseng C, Yildirim N
Mol Biosyst · 2017 Jun · PMID 28581003 · Publisher ↗
To prevent indefinite cellular responses to external signals, cells utilize various adaptation mechanisms. The yeast mating-response pathway is a model cellular system that exhibits adaptation to persistent external sign...
To prevent indefinite cellular responses to external signals, cells utilize various adaptation mechanisms. The yeast mating-response pathway is a model cellular system that exhibits adaptation to persistent external signals. This pathway employs a mitogen-activated protein kinase (MAPK) cascade which is composed of two well-known negative feedback inhibitions that involve the yeast phosphatase proteins Ptp3 and Msg5. The phosphorylated form of the yeast MAPK protein Fus3 (pFus3) triggers the phosphorylation of both phosphatases, but transcriptionally upregulates only Msg5. To study the biological rationale for the existence of two distinct negative feedback inhibitions acting on pFus3, we used published experimental data to develop a mathematical model which quantifies the inhibitory roles of these phosphatase proteins on pFus3. Our analyses show that the inhibition of pFus3 due to Ptp3 is largely independent of the signal profile, and is most impactful at early time points after pheromone induction. Conversely, the feedback inhibition due to Msg5 is highly dependent on the signal profile, and is most influential after pFus3 attains its maximum cellular abundance. Similarly, Ptp3 reduces the variation in the pFus3 dynamics at early time points while the noise-reduction effects of Msg5 become stronger as time passes.
What shapes eukaryotic transcriptional bursting?
Nicolas D, Phillips NE, Naef F
Mol Biosyst · 2017 Jun · PMID 28573295 · Publisher ↗
Isogenic cells in a common environment present a large degree of heterogeneity in gene expression. Part of this variability is attributed to transcriptional bursting: the stochastic activation and inactivation of promote...
Isogenic cells in a common environment present a large degree of heterogeneity in gene expression. Part of this variability is attributed to transcriptional bursting: the stochastic activation and inactivation of promoters that leads to the discontinuous production of mRNA. The diversity in bursting patterns displayed by different genes suggests the existence of a connection between bursting and gene regulation. Experimental strategies such as single-molecule RNA FISH, MS2-GFP or short-lived protein reporters allow the quantification of transcriptional bursting and the comparison of bursting kinetics between conditions, allowing therefore the identification of molecular mechanisms modulating transcriptional bursting. In this review we recapitulate the impact on transcriptional bursting of different molecular aspects of transcription such as the chromatin environment, nucleosome occupancy, histone modifications, the number and affinity of regulatory elements, DNA looping and transcription factor availability. More specifically, we examine their role in tuning the burst size or the burst frequency. While some molecular mechanisms involved in transcription such as histone marks can affect every aspect of bursting, others predominantly influence the burst size (e.g. the number and affinity of cis-regulatory elements) or frequency (e.g. transcription factor availability).
The effect of global transcriptional regulators on the anaerobic fermentative metabolism of Escherichia coli.
Kargeti M, Venkatesh KV
Mol Biosyst · 2017 Jun · PMID 28573283 · Publisher ↗
Global transcription factors are known to regulate the anaerobic growth of Escherichia coli on glucose. These transcription factors help the organism to sense oxygen and accordingly regulate the synthesis of mixed acid p...
Global transcription factors are known to regulate the anaerobic growth of Escherichia coli on glucose. These transcription factors help the organism to sense oxygen and accordingly regulate the synthesis of mixed acid producing enzymes. Five global transcription factors, namely ArcA, Fnr, IhfA-B, Crp and Fis, are known to play an important role in the growth phenotype of the organism in the transition from anaerobic to aerobic conditions. The effect of deletion of most of these global transcription factors on the growth phenotype has not been characterized under strict anaerobic fermentation conditions. In order to enumerate the role of global transcription factors in central carbon metabolism, experiments were performed using single deletion mutants of the above mentioned global transcription regulators. The mutants demonstrated lower growth rates, ranging from 3-75% lower growth as compared to the wild-type strain along with varying glucose uptake rates. Global transcription regulators help in lowering formate and acetate synthesis, thereby effectively channeling the carbon towards redox balance (through ethanol formation) and biomass synthesis. Flux analysis of mutant strains indicated that deletion of a single transcription factor alone does not play a significant role in the normalized flux distribution of the central carbon metabolism.
Dynamic properties of the growth hormone releasing hormone receptor (GHRHR) and molecular determinants of GHRH binding.
Matsoukas MT, Spyroulias GA
Mol Biosyst · 2017 Jun · PMID 28561845 · Publisher ↗
The growth hormone-releasing hormone receptor (GHRHR) is a member of the class B GPCR subfamily. GHRH, a 44-residue neuropeptide produced in the hypothalamus, regulates the secretion of growth hormone through its binding...
The growth hormone-releasing hormone receptor (GHRHR) is a member of the class B GPCR subfamily. GHRH, a 44-residue neuropeptide produced in the hypothalamus, regulates the secretion of growth hormone through its binding to GHRHR. It has recently been associated with several types of cancer such as prostate, breast, pancreatic and ovarian cancer. Family B GPCR peptides bind in a two-step model, where first the C-terminal region of the peptide interacts with the extracellular domain (ECD) of the receptor and subsequently, the N-terminal interacts with the seven transmembrane domain (TMD), resulting in activation. Structural information on family B GPCRs is limited; therefore, the use of computational methods may assist their efficient targeting towards new therapeutics. Here, we have utilized several computational tools, such as homology modelling, docking, large-scale molecular dynamics and principal component analysis (PCA), in order to: (a) gain information on the dynamic properties of the receptor domains and (b) propose a structural model for the interactions between GHRH and the ECD and TMD regions of GHRHR respectively. We conclude that PCA analysis can be used for studying such relative movements in family B GPCRs and provide a structural model, which may assist in the design of highly anticipated non-peptide antagonists against GHRHR.
vhfRNAi: a web-platform for analysis of host genes involved in viral infections discovered by genome wide RNAi screens.
Thakur A, Qureshi A, Kumar M
Mol Biosyst · 2017 Jun · PMID 28561835 · Publisher ↗
Knockdown of host genes using high-throughput genome-wide RNA interference screens has identified numerous host factors that affect viral infections, which would be helpful in understanding host-virus interactions. We ha...
Knockdown of host genes using high-throughput genome-wide RNA interference screens has identified numerous host factors that affect viral infections, which would be helpful in understanding host-virus interactions. We have developed a vhfRNAi web resource based on genome-wide RNAi experiments for viruses. It contains experimental details of 12 249 entries (host factors + restriction factors) for 18 viruses. Simultaneously, this resource encompasses analysis of overlapping genes, genome wide association studies, gene ontology (GO), pathogen interacting proteins, interaction networks and pathway enrichment. Using overlap analysis, it was found that Influenza A virus shared overlapping host genes with the majority of viruses including Hepatitis C virus and Dengue virus 2. In the genome wide association studies analysis, 429 diseases/traits were mapped, of which obesity-related traits were the most common. GO analysis revealed that the major categories belonged to metabolic processes, molecule transport, signal transduction, proteolysis, etc. In the pathogen interacting protein analysis, protein interaction data from different resources can be explored for further understanding of host-virus biology. By pathway enrichment analysis, a total of 8955 genes were mapped on 303 pathways with most of the hits coming from metabolic pathways. We have found 491 genes that are not essential for the host but essential for the virus and can be targeted to inhibit the virus. These may be explored as potential candidates for drug targets. The resource is freely accessible at and will be useful in understanding host-virus biology as well as identification of targets for the development of antiviral therapeutics.
Crystal structure of Aquifex aeolicus gene product Aq1627: a putative phosphoglucosamine mutase reveals a unique C-terminal end-to-end disulfide linkage.
Sridharan U, Kuramitsu S, Yokoyama S … +2 more , Kumarevel T, Ponnuraj K
Mol Biosyst · 2017 Jun · PMID 28548163 · Publisher ↗
The Aq1627 gene from Aquifex aeolicus, a hyperthermophilic bacterium has been cloned and overexpressed in Escherichia coli. The protein was purified to homogeneity and its X-ray crystal structure was determined to 1.3 Å...
The Aq1627 gene from Aquifex aeolicus, a hyperthermophilic bacterium has been cloned and overexpressed in Escherichia coli. The protein was purified to homogeneity and its X-ray crystal structure was determined to 1.3 Å resolution using multiple wavelength anomalous dispersion phasing. The structural and sequence analysis of Aq1627 is suggestive of a putative phosphoglucosamine mutase. The structural features of Aq1627 further indicate that it could belong to a new subclass of the phosphoglucosamine mutase family. Aq1627 structure contains a unique C-terminal end-to-end disulfide bond, which links two monomers and this structural information can be used in protein engineering to make proteins more stable in different applications.
Structure based in silico identification of potentially non-steroidal brassinosteroids mimics.
Lei B, Heng N, Dang X … +3 more , Liu J, Yao X, Zhang C
Mol Biosyst · 2017 Jun · PMID 28540949 · Publisher ↗
Brassinosteroids (BRs) are a class of plant steroid hormones that play indispensable roles in cell elongation, division and plant development. To date, the numerous synthesis of BRs analogs and structure-activity relatio...
Brassinosteroids (BRs) are a class of plant steroid hormones that play indispensable roles in cell elongation, division and plant development. To date, the numerous synthesis of BRs analogs and structure-activity relationship investigations have clearly revealed the key substituent groups relevant to the steroidal activity of BRs. However, due to the limited chemical space studied, the efforts for alternative non-steroidal compounds have produced no remarkable results. To identify potentially non-steroidal BR mimics in this study, vital interacting pharmacophore features were extracted starting from several complex structures of BRs that bound with the receptor Brassinosteroid-Insentive 1 (BRI1) and co-receptor BRI1-associated kinase 1 (BAK1), which were characterized and merged into one comprehensive pharmacophore model. In silico screening of a commercial compound database was carried out by combing pharmacophore modeling, molecular docking and visual analysis. Finally, six non-steroidal molecules were identified and subjected to the in vivo radish hypocotyl elongation assay. As a positive control, the hypocotyls elongation for the naturally most active BR brassinolide (BL) is 152 ± 3% at 100 nM. Moreover, two candidates (4 and 6) show good BRs-like activity with the hypocotyls elongation of 143 ± 1% and 128 ± 3% at the same dose, respectively. Most remarkably, compounds 4 and 6, which have different structures, are predicted to share similar binding modes and proven to exhibit potential BRs-like activity. The two compounds obtained could be valuable leads for the development of BRs-like plant growth regulators.
Covalent inhibition of protein tyrosine phosphatases.
Ruddraraju KV, Zhang ZY
Mol Biosyst · 2017 Jun · PMID 28534914 · Full text
Protein tyrosine phosphatases (PTPs) are a large family of 107 signaling enzymes that catalyze the hydrolytic removal of phosphate groups from tyrosine residues in a target protein. The phosphorylation status of tyrosine...
Protein tyrosine phosphatases (PTPs) are a large family of 107 signaling enzymes that catalyze the hydrolytic removal of phosphate groups from tyrosine residues in a target protein. The phosphorylation status of tyrosine residues on proteins serve as a ubiquitous mechanism for cellular signal transduction. Aberrant function of PTPs can lead to many human diseases, such as diabetes, obesity, cancer, and autoimmune diseases. As the number of disease relevant PTPs increases, there is urgency in developing highly potent inhibitors that are selective towards specific PTPs. Most current efforts have been devoted to the development of active site-directed and reversible inhibitors for PTPs. This review summarizes recent progress made in the field of covalent inhibitors to target PTPs. Here, we discuss the in vivo and in vitro inactivation of various PTPs by small molecule-containing electrophiles, such as Michael acceptors, α-halo ketones, epoxides, and isothiocyanates, etc. as well as oxidizing agents. We also suggest potential strategies to transform these electrophiles into isozyme selective covalent PTP inhibitors.
Proteomic analysis of prognostic plasma biomarkers in peripheral arterial occlusive disease.
Yang CS, Wei YS, Tsai HL … +5 more , Cheong IS, Chang SJ, Chou HC, Lee YR, Chan HL
Mol Biosyst · 2017 Jun · PMID 28530744 · Publisher ↗
Peripheral arterial occlusive disease (PAOD), one of the major manifestations of systemic atherosclerosis, causes intermittent claudication and rest pain. Patients with PAOD not only have reduced quality of life, but als...
Peripheral arterial occlusive disease (PAOD), one of the major manifestations of systemic atherosclerosis, causes intermittent claudication and rest pain. Patients with PAOD not only have reduced quality of life, but also have a substantial risk of cardiovascular morbidity and death. In this study, we adopted a proteomics-based approach using 2D-DIGE and MALDI-TOF MS to compare the differential plasma proteome between good and poor prognosis of PAOD. We identified 196 plasma proteins, which represent 42 unique gene products. These proteins mainly have roles in the inflammatory response and coagulation. This approach identified several potential prognostic plasma markers in PAOD, including transthyretin and complement factor B, which may be associated with the evaluation of good/poor prognosis of PAOD. In conclusion, we report a comprehensive patient-based plasma proteomic approach for the identification of potential plasma biomarkers for the screening and detection of good/poor prognosis of PAOD. Among these, transthyretin and complement factor B are potential markers for monitoring the PAOD disease in the plasma.
FOCuS: a metaheuristic algorithm for computing knockouts from genome-scale models for strain optimization.
Mutturi S
Mol Biosyst · 2017 Jun · PMID 28530276 · Publisher ↗
Although handful tools are available for constraint-based flux analysis to generate knockout strains, most of these are either based on bilevel-MIP or its modifications. However, metaheuristic approaches that are known f...
Although handful tools are available for constraint-based flux analysis to generate knockout strains, most of these are either based on bilevel-MIP or its modifications. However, metaheuristic approaches that are known for their flexibility and scalability have been less studied. Moreover, in the existing tools, sectioning of search space to find optimal knocks has not been considered. Herein, a novel computational procedure, termed as FOCuS (Flower-pOllination coupled Clonal Selection algorithm), was developed to find the optimal reaction knockouts from a metabolic network to maximize the production of specific metabolites. FOCuS derives its benefits from nature-inspired flower pollination algorithm and artificial immune system-inspired clonal selection algorithm to converge to an optimal solution. To evaluate the performance of FOCuS, reported results obtained from both MIP and other metaheuristic-based tools were compared in selected case studies. The results demonstrated the robustness of FOCuS irrespective of the size of metabolic network and number of knockouts. Moreover, sectioning of search space coupled with pooling of priority reactions based on their contribution to objective function for generating smaller search space significantly reduced the computational time.
Correction: Metabolomic profiling and biochemical evaluation of the follicular fluid of endometriosis patients.
Santonastaso M, Pucciarelli A, Costantini S … +7 more , Caprio F, Sorice A, Capone F, Natella A, Iardino P, Colacurci N, Chiosi E
Mol Biosyst · 2017 May · PMID 28524204 · Publisher ↗
Correction for 'Metabolomic profiling and biochemical evaluation of the follicular fluid of endometriosis patients' by Marianna Santonastaso et al., Mol. BioSyst., 2017, DOI: 10.1039/c7mb00181a.
Correction for 'Metabolomic profiling and biochemical evaluation of the follicular fluid of endometriosis patients' by Marianna Santonastaso et al., Mol. BioSyst., 2017, DOI: 10.1039/c7mb00181a.
Tumor suppressors microRNA-302d and microRNA-16 inhibit human glioblastoma multiforme by targeting NF-κB and FGF2.
Wang F, Yang L, Sun J … +4 more , Zheng J, Shi L, Zhang G, Cui N
Mol Biosyst · 2017 Jun · PMID 28497156 · Publisher ↗
Glioblastoma multiforme (GBM) is a highly malignant cancer in the brain with a median survival time of approximately one year. However, the mechanisms underlying GBM development and occurrence are poorly understood. Rece...
Glioblastoma multiforme (GBM) is a highly malignant cancer in the brain with a median survival time of approximately one year. However, the mechanisms underlying GBM development and occurrence are poorly understood. Recently, miRNAs were reported to play important roles in GBM. We performed microRNA profiling by comparing the human GBM cell line T98G and control cell line HCN1A. MicroRNA assays, PCR and Western blot analysis were performed to detect the expressions of microRNAs, mRNAs and proteins of target genes, respectively. Cell migration and invasion assays were conducted. A murine in situ xenograft tumor model was used to evaluate tumor growth in vivo. Glioblastoma tissues were examined to investigate the clinical relevance of our findings. MiR-302d and miR-16 levels were found to be decreased in T98G cells. MiR-302d and miR-16 inhibited the expressions of p65 and FGF2, respectively, by binding to the 3'-UTR of their mRNAs. Over-expression of miR-302d and miR-16 inhibited T98G cell migration and invasion in vitro, and tumorigenesis in the xenograft tumor mouse model in vivo, by suppressing p65 and FGF2. Negative correlations between miR-302d and p65 and between miR-16 and FGF2 were observed in patient glioblastoma tissues. MiR-302d and miR-16 inhibit tumorigenesis by down-regulating p65 and FGF2, which potentially contributes to the treatment of glioblastoma with clinical relevance.
Emergent properties of extracellular vesicles: a holistic approach to decode the complexity of intercellular communication networks.
Gho YS, Lee C
Mol Biosyst · 2017 Jun · PMID 28488707 · Publisher ↗
Shedding of nano-sized bilayered extracellular vesicles and extracellular vesicle-mediated intercellular communication are evolutionarily conserved biological processes. Communication between cells and the environment is...
Shedding of nano-sized bilayered extracellular vesicles and extracellular vesicle-mediated intercellular communication are evolutionarily conserved biological processes. Communication between cells and the environment is an essential process in living organisms and dysregulation of intercellular communication leads to various diseases. Thus, systematic studies on extracellular vesicles, also known as exosomes, microvesicles, and outer membrane vesicles, are critical for a deeper understanding of intercellular communication networks that are crucial for decoding the exact causes of various difficult-to-cure diseases. Recent progress in this emerging field reveals that extracellular vesicles are endogenous carriers of specific subsets of proteins, mRNAs, miRNAs, and other bioactive materials, as well as play diverse pathophysiological roles. However, certain issues regarding diverse subtypes and the complex pathophysiological roles of extracellular vesicles are not yet clearly elucidated. In this review, we first briefly introduce the complexity of extracellular vesicles in terms of their vesicular cargos and protein-protein interaction networks, their diverse subtypes, and multifaceted pathophysiological functions. Then, we introduce the limitation of reductionist approaches in understanding the complexity of extracellular vesicles. We finally suggest that molecular systems biology approaches based on the concept of emergent properties are essential for a comprehensive understanding of the complex pathophysiological functions of heterogeneous extracellular vesicles, either at the single vesicle level or at a systems level as a whole.
GeneSPIDER - gene regulatory network inference benchmarking with controlled network and data properties.
Tjärnberg A, Morgan DC, Studham M … +2 more , Nordling TEM, Sonnhammer ELL
Mol Biosyst · 2017 Jun · PMID 28485748 · Publisher ↗
A key question in network inference, that has not been properly answered, is what accuracy can be expected for a given biological dataset and inference method. We present GeneSPIDER - a Matlab package for tuning, running...
A key question in network inference, that has not been properly answered, is what accuracy can be expected for a given biological dataset and inference method. We present GeneSPIDER - a Matlab package for tuning, running, and evaluating inference algorithms that allows independent control of network and data properties to enable data-driven benchmarking. GeneSPIDER is uniquely suited to address this question by first extracting salient properties from the experimental data and then generating simulated networks and data that closely match these properties. It enables data-driven algorithm selection, estimation of inference accuracy from biological data, and a more multifaceted benchmarking. Included are generic pipelines for the design of perturbation experiments, bootstrapping, analysis of linear dependence, sample selection, scaling of SNR, and performance evaluation. With GeneSPIDER we aim to move the goal of network inference benchmarks from simple performance measurement to a deeper understanding of how the accuracy of an algorithm is determined by different combinations of network and data properties.
Systematic comparison of the response properties of protein and RNA mediated gene regulatory motifs.
Iyengar BR, Pillai B, Venkatesh KV … +1 more , Gadgil CJ
Mol Biosyst · 2017 May · PMID 28485414 · Publisher ↗
We present a framework enabling the dissection of the effects of motif structure (feedback or feedforward), the nature of the controller (RNA or protein), and the regulation mode (transcriptional, post-transcriptional or...
We present a framework enabling the dissection of the effects of motif structure (feedback or feedforward), the nature of the controller (RNA or protein), and the regulation mode (transcriptional, post-transcriptional or translational) on the response to a step change in the input. We have used a common model framework for gene expression where both motif structures have an activating input and repressing regulator, with the same set of parameters, to enable a comparison of the responses. We studied the global sensitivity of the system properties, such as steady-state gain, overshoot, peak time, and peak duration, to parameters. We find that, in all motifs, overshoot correlated negatively whereas peak duration varied concavely with peak time. Differences in the other system properties were found to be mainly dependent on the nature of the controller rather than the motif structure. Protein mediated motifs showed a higher degree of adaptation i.e. a tendency to return to baseline levels; in particular, feedforward motifs exhibited perfect adaptation. RNA mediated motifs had a mild regulatory effect; they also exhibited a lower peaking tendency and mean overshoot. Protein mediated feedforward motifs showed higher overshoot and lower peak time compared to the corresponding feedback motifs.
Differential flap dynamics in l,d-transpeptidase2 from mycobacterium tuberculosis revealed by molecular dynamics.
Fakhar Z, Govender T, Maguire GEM … +4 more , Lamichhane G, Walker RC, Kruger HG, Honarparvar B
Mol Biosyst · 2017 Jun · PMID 28480928 · Publisher ↗
Despite the advances in tuberculosis treatment, TB is still one the most deadly infectious diseases and remains a major global health quandary. Mycobacterium tuberculosis (Mtb) is the only known mycobacterium with a high...
Despite the advances in tuberculosis treatment, TB is still one the most deadly infectious diseases and remains a major global health quandary. Mycobacterium tuberculosis (Mtb) is the only known mycobacterium with a high content of 3→3 crosslinks in the biosynthesis of peptidoglycan, which is negligible in most bacterial species. An Mtb lacking Ldt leads to alteration of the colony morphology and loss of virulence which makes this enzyme an attractive target. Regardless of the vital role of Ldt for cell wall survival, the impact of ligand binding on the dynamics of the β-hairpin flap is still unknown. Understanding the structural and dynamical behaviour of the flap regions provides clear insight into the design of the effective inhibitors against Ldt. Carbapenems, an specific class of β-lactam family, have been shown to inactivate this enzyme. Herein a comprehensive investigation of the flap dynamics of Ldt complex with substrate and three carbapenems namely, ertapenem, imipenem and meropenem is discussed and analyzed for the first account using 140 ns molecular dynamics simulations. The structural features (RMSD, RMSF and R) derived by MD trajectories were analyzed. Distance analysis, particularly tip-tip SER135-ASN167 index, identified conformational changes in terms of flap opening and closure within binding process. Principal component analysis (PCA) was employed to qualitatively understand the divergent effects of different inhibitors on the dominant motion of each residue. To probe different internal dynamics induced by ligand binding, dynamic cross-correlation marix (DCCM) analysis was used. The binding free energies of the selected complexes were assessed using MM-GBSA method and per residue free energy decomposition analysis were performed to characterize the contribution of the key residues to the total binding free energies.
Metabolomic profiling and biochemical evaluation of the follicular fluid of endometriosis patients.
Marianna S, Alessia P, Susan C … +7 more , Francesca C, Angela S, Francesca C, Antonella N, Patrizia I, Nicola C, Emilio C
Mol Biosyst · 2017 Jun · PMID 28475193 · Publisher ↗
Diseases are complex systems that can be studied through the integration of data derived from different disciplines to obtain a global and reliable picture of the biological phenomenon under investigation. Based on the r...
Diseases are complex systems that can be studied through the integration of data derived from different disciplines to obtain a global and reliable picture of the biological phenomenon under investigation. Based on the recent observations that the metabolomics profiling of follicular fluids reflects the ovarian microenvironment of women and that endometriosis represents an example of complex diseases, clearly diagnosed by laparoscopy, we thought that the follicular fluids of endometriosis patients can represent a study model to evaluate the possibility of integrating data obtained by different approaches. Hence, the aim of this work was to analyze and integrate different clinical chemistry parameters with specific reference to the metabolic profile, inflammatory state and cell damage by a H-NMR approach and biochemical analysis in the follicular fluids of women with different stages of endometriosis (I-II and III-IV) subjected to the In Vitro Fertilization (IVF) cycle. Our analysis evidenced that in the follicular fluids of endometriosis patients the levels of phospholipids, lactate, insulin, PTX3, CXCL8, CXCL10, CCL11 and VEGF were higher whereas those of some fatty acids, lysine, choline, glucose, aspartate, alanine, leucine, valine, proline, phosphocholine, total LDH as well its LDH-3 isoform were lower in comparison to the control group. The levels of LDHB, PTX3 and insulin receptor were also confirmed by RT-PCR applied on cumulus cells surrounding oocytes retrieved from the patients. The reduced oocyte quality observed in patients with endometriosis can be certainly correlated to the different levels of these molecules. These data represent how the integration of different experimental approaches may be useful for understanding the underlying mechanisms of a complex disease and can lead to a better clinical management of endometriosis.
Characterization of the structure, dynamics and allosteric pathways of human NPP1 in its free form and substrate-bound complex from molecular modeling.
Barbeau X, Mathieu P, Paquin JF … +1 more , Lagüe P
Mol Biosyst · 2017 May · PMID 28474020 · Publisher ↗
The ectonucleotide phosphodiesterase/pyrophosphatase-1 (NPP1) is a type II transmembrane glycoprotein that regulates extracellular inorganic purine nucleotide and inorganic diphosphate levels through the hydrolysis of AT...
The ectonucleotide phosphodiesterase/pyrophosphatase-1 (NPP1) is a type II transmembrane glycoprotein that regulates extracellular inorganic purine nucleotide and inorganic diphosphate levels through the hydrolysis of ATP into AMP and diphosphate. NPP1 is a promising drug target as it plays a role in several disorders. In the present work, we report the 3D structure modeling and extensive molecular dynamics simulations of NPP1-h, both in its free and ATP-bound forms. We identified the key residues involved in the binding of the ATP and the binding modes. The simulations suggest that NPP1-h is a rigid enzyme except for specific residues or segments, with the most mobile residues located in the unstructure "lasso loop" (LSO) domain. The binding of ATP significantly affected the dynamics of NPP1-h, with a rigidification of the phosphodiesterase (PDE) catalytic domain and an increase in mobility for the residues of the Nuclease-like (NUC) and the LSO domains. A dynamical network analysis identified that the most prevalent edges of the networks were located between the PDE and the NUC domains. In presence of ATP the networks became scattered through the PDE domain while the networks converged into a specific path that stretched from the PDE-NUC interdomain up to the middle of the LSO loop throughout the NUC domain. We suggest that these sections of the dynamical network may host potential allosteric inhibition sites. These results provide an improved understanding of the structure and dynamics of NPP1-h and will contribute to the rational design of NPP1-h inhibitors.
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