Insights on peptide topology in the computational design of protein ligands: the example of lysozyme binding peptides.

Herein, we compared the ability of linear and cyclic peptides generated in silico to target different protein sites: internal pockets and solvent-exposed sites. We selected human lysozyme (HuL) as a model target protein combined with the computational evolution of linear and cyclic peptides. The sequence evolution of these peptides was based on the PARCE algorithm. The generated peptides were screened based on their aqueous solubility and HuL binding affinity. The latter was evaluated by means of scoring functions and atomistic molecular dynamics (MD) trajectories in water, which allowed prediction of the structural features of the protein-peptide complexes. The computational results demonstrated that cyclic peptides constitute the optimal choice for solvent exposed sites, while both linear and cyclic peptides are capable of targeting the HuL pocket effectively. The most promising binders found in silico were investigated experimentally by surface plasmon resonance (SPR), nuclear magnetic resonance (NMR), and electrospray ionization mass spectrometry (ESI-MS) techniques. All tested peptides displayed dissociation constants in the micromolar range, as assessed by SPR; however, both NMR and ESI-MS suggested multiple binding modes, at least for the pocket binding peptides. A detailed NMR analysis confirmed that both linear and cyclic pocket peptides correctly target the binding site they were designed for.

The Independence of the Junior Scientist's Mind: At What Price?

When I was facing the daunting task of recounting my approximately 70 years of scientific career and some aspects of my personal life, I decided to write this autobiographical piece in a "different" way. After a section on the almost bare facts of my life (Section 1), I include several other parts, loosely connected in time, in each of which I make an almost self-contained point, decreasing in this way the need for consistency and coherence in the whole article. I discuss, for example, the importance of original ideas, the independence of junior colleagues, and my work with molecular beams and in nanomedicine. I end by acknowledging those I was lucky enough to learn from in my intellectual development as a research scientist and with a couple of recommendations that may be useful to my junior and not-so-junior colleagues.

Computational design of cyclic peptides for the customized oriented immobilization of globular proteins.

The oriented immobilization of proteins, key for the development of novel responsive biomaterials, relies on the availability of effective probes. These are generally provided by standard approaches based on in vivo maturation and in vitro selection of antibodies and/or aptamers. These techniques can suffer technical problems when a non-immunogenic epitope needs to be targeted. Here we propose a strategy to circumvent this issue by in silico design. In our method molecular binders, in the form of cyclic peptides, are computationally evolved by stochastically exploring their sequence and structure space to identify high-affinity peptides for a chosen epitope of a target globular protein: here a solvent-exposed site of ß2-microglobulin (ß2m). Designed sequences were screened by explicit solvent molecular dynamics simulations (MD) followed by experimental validation. Five candidates gave dose-response surface plasmon resonance signals with dissociation constants in the micromolar range. One of them was further analyzed by means of isothermal titration calorimetry, nuclear magnetic resonance, and 250 ns of MD. Atomic-force microscopy imaging showed that this peptide is able to immobilize ß2m on a gold surface. In short, we have shown by a variety of experimental techniques that it is possible to capture a protein through an epitope of choice by computational design.

In patients with metastatic breast cancer the identification of circulating tumor cells in epithelial-to-mesenchymal transition is associated with a poor prognosis.

BACKGROUND: Although recent models suggest that the detection of Circulating Tumor Cells (CTC) in epithelial-to-mesenchymal transition (EM CTC) might be related to disease progression in metastatic breast cancer (MBC) patients, current detection methods are not efficient in identifying this subpopulation of cells. Furthermore, the possible association of EM CTC with both clinicopathological features and prognosis of MBC patients has still to be demonstrated. Aims of this study were: first, to optimize a DEPArray-based protocol meant to identify, quantify and sort single, viable EM CTC and, subsequently, to test the association of EM CTC frequency with clinical data. METHODS: This prospective observational study enrolled 56 MBC patients regardless of the line of treatment. Blood samples, depleted of CD45(pos) leukocytes, were stained with an antibody cocktail recognizing both epithelial and mesenchymal markers. Four CD45(neg) cell subpopulations were identified: cells expressing only epithelial markers (E CTC), cells co-expressing epithelial and mesenchymal markers (EM CTC), cells expressing only mesenchymal markers (MES) and cells negative for every tested marker (NEG). CTC subpopulations were quantified as both absolute cell count and relative frequency. The association of CTC subpopulations with clinicopathological features, progression free survival (PFS), and overall survival (OS) was explored by Wilcoxon-Mann-Whitney test and Univariate Cox Regression Analysis, respectively. RESULTS: By employing the DEPArray-based strategy, we were able to assess the presence of cells pertaining to the above-described classes in every MBC patient. We observed a significant association between specific CD45(neg) subpopulations and tumor subtypes (e.g. NEG and triple negative), proliferation (NEG and Ki67 expression) and sites of metastatic spread (e.g. E CTC and bone; NEG and brain). Importantly, the fraction of CD45(neg) cells co-expressing epithelial and mesenchymal markers (EM CTC) was significantly associated with poorer PFS and OS, computed, this latter, both from the diagnosis of a stage IV disease and from the initial CTC assessment. CONCLUSION: This study suggests the importance of dissecting the heterogeneity of CTC in MBC. Precise characterization of CTC could help in estimating both metastatization pattern and outcome, driving clinical decision-making and surveillance strategies.

A Method for Detecting Circulating Tumor Cells Based on the Measurement of Single-Cell Metabolism in Droplet-Based Microfluidics.

The number of circulating tumor cells (CTCs) in blood is strongly correlated with the progress of metastatic cancer. Current methods to detect CTCs are based on immunostaining or discrimination of physical properties. Herein, a label-free method is presented exploiting the abnormal metabolic behavior of cancer cells. A single-cell analysis technique is used to measure the secretion of acid from individual living tumor cells compartmentalized in microfluidically prepared, monodisperse, picoliter (pL) droplets. As few as 10 tumor cells can be detected in a background of 200 000 white blood cells and proof-of-concept data is shown on the detection of CTCs in the blood of metastatic patients.

Ex vivo molecular rejuvenation improves the therapeutic activity of senescent human cardiac stem cells in a mouse model of myocardial infarction.

Cardiac stem cells (CSC) from explanted decompensated hearts (E-CSC) are, with respect to those obtained from healthy donors (D-CSC), senescent and functionally impaired. We aimed to identify alterations in signaling pathways that are associated with CSC senescence. Additionally, we investigated if pharmacological modulation of altered pathways can reduce CSC senescence in vitro and enhance their reparative ability in vivo. Measurement of secreted factors showed that E-CSC release larger amounts of proinflammatory cytokine IL1ß compared with D-CSC. Using blocking antibodies, we verified that IL1ß hampers the paracrine protective action of E-CSC on cardiomyocyte viability. IL1ß acts intracranially inducing IKKß signaling, a mechanism that via nuclear factor-κB upregulates the expression of IL1ß itself. Moreover, E-CSC show reduced levels of AMP protein kinase (AMPK) activating phosphorylation. This latter event, together with enhanced IKKß signaling, increases TORC1 activity, thereby impairing the autophagic flux and inhibiting the phosphorylation of Akt and cAMP response element-binding protein. The combined use of rapamycin and resveratrol enhanced AMPK, thereby restoring downstream signaling and reducing IL1ß secretion. These molecular corrections reduced E-CSC senescence, re-establishing their protective activity on cardiomyocytes. Moreover ex vivo treatment with rapamycin and resveratrol improved E-CSC capacity to induce cardiac repair upon injection in the mouse infarcted heart, leading to reduced cardiomyocyte senescence and apoptosis and increased abundance of endogenous c-Kit(+) CSC in the peri-infarct area. Molecular rejuvenation of patient-derived CSC by short pharmacologic conditioning boosts their in vivo reparative abilities. This approach might prove useful for refinement of CSC-based therapies.

Glioma-associated stem cells: a novel class of tumor-supporting cells able to predict prognosis of human low-grade gliomas.

BACKGROUND: Translational medicine aims at transferring advances in basic science research into new approaches for diagnosis and treatment of diseases. Low-grade gliomas (LGG) have a heterogeneous clinical behavior that can be only partially predicted employing current state-of-the-art markers, hindering the decision-making process. To deepen our comprehension on tumor heterogeneity, we dissected the mechanism of interaction between tumor cells and relevant components of the neoplastic environment, isolating, from LGG and high-grade gliomas (HGG), proliferating stem cell lines from both the glioma stroma and, where possible, the neoplasm. METHODS AND FINDINGS: We isolated glioma-associated stem cells (GASC) from LGG (n=40) and HGG (n=73). GASC showed stem cell features, anchorage-independent growth, and supported the malignant properties of both A172 cells and human glioma-stem cells, mainly through the release of exosomes. Finally, starting from GASC obtained from HGG (n=13) and LGG (n=12) we defined a score, based on the expression of 9 GASC surface markers, whose prognostic value was assayed on 40 subsequent LGG-patients. At the multivariate Cox analysis, the GASC-based score was the only independent predictor of overall survival and malignant progression free-survival. CONCLUSIONS: The microenvironment of both LGG and HGG hosts non-tumorigenic multipotent stem cells that can increase in vitro the biological aggressiveness of glioma-initiating cells through the release of exosomes. The clinical importance of this finding is supported by the strong prognostic value associated with the characteristics of GASC. This patient-based approach can provide a groundbreaking method to predict prognosis and to exploit novel strategies that target the tumor stroma.

A DNA-based nano-immunoassay for the label-free detection of glial fibrillary acidic protein in multicell lysates.

We have developed a quantitative approach to eventually enable precise and multiplexing protein analysis of very small systems, down to a single or a few cells. Through DNA-directed immobilization of DNA-protein conjugates we immobilized antibodies specific for a certain protein of interest, on a complementary DNA nanoarray fabricated by means of nanografting, a nanolithography technique based on atomic force microscopy (AFM). The proof of concept was realized for glial fibrillary acidic protein (GFAP), a biomarker crucial in cell's differentiation of astrocytes, and functional to grade classification of gliomas, the most common of primary malignant brain tumors. The efficiency of the nano-immuno sensing was tested by obtaining the immobilization of purified recombinant GFAP protein at different concentration in a standard solution then in a cellular lysate. A comparison of sensitivity between our technique and conventional ELISA assays is provided at the end of the paper. FROM THE CLINICAL EDITOR: This team developed a quantitative approach to enable precise and multiplexing protein analysis of very small systems, down to a single or a few cells, demonstrating the utility of this DNA-based nano-immunoassay in the detection of GFAP.

DNA as invisible ink for AFM nanolithography.

We have used nanografting, an atomic force microscopy (AFM)-based nanolithography technique, to fabricate thiolated DNA nanostructures on gold surfaces. The tip-guided assembly offers opportunities for locally controlling the packing order, density, and thus the thickness of the DNA patterns. By selecting proper nanografting parameters, we can embed single-stranded DNA (ssDNA) patches into a background composed of the same DNA molecule prepared by self-assembly, in which the patches remain topographically (and chemically) invisible but have much improved packing order. When the complementary DNA (cDNA) is added, the thickness of the nanografted layer increases much more dramatically than that of the self-assembled layer during the hybridization process, and as a result, the pattern emerges. Interestingly, the pattern can be reversibly hidden and shown with high fidelity simply by dehybridizing and appending the cDNA repeatedly.

Toward multiprotein nanoarrays using nanografting and DNA directed immobilization of proteins.

Atomic force microscopy nanografting was utilized to prepare DNA nanopatches of different sizes (200 x 200 to 1000 x 1000 nm(2)) onto which DNA-protein conjugates can be anchored through DNA-directed immobilization. Height measurements were used to assess the binding of the proteins as well as their subsequent interaction with other components, such as antibodies. The results indicate that nanografted patch arrays are well suited for application in biosensing and could enable the fabrication of multifeature protein nanoarrays.

Synthesis and characterization of a carbon nanotube-dendron series for efficient siRNA delivery.

A new series of dendron-functionalized multiwalled carbon nanotube (MWNT) derivatives, characterized by the presence of numerous positively charged tetraalkyl ammonium salts at the periphery of the dendron, has been synthesized. The positive charges on the MWNT surface, coupled with the unique ability of carbon nanotubes (CNTs) to penetrate cell membranes, make the new derivatives potentially ideal vectors for siRNA delivery. Using a fluorescently labeled, noncoding siRNA sequence, we demonstrate that cytoplasmic delivery of the nucleic acid is remarkably increased throughout the different dendron generations. The work reported here highlights the fact that dendron-functionalized CNTs can be rationally designed as efficient carriers of siRNA that can eventually lead to gene silencing.

Verification of biochemical activity for proteins nanografted on gold surfaces.

We demonstrate that the Atomic Force Microscope (AFM) can be used to immobilize a dicysteine-terminated protein (Maltose Binding Protein, MBP-cys-cys for short) at well-defined locations directly on gold substrates via nanografting and characterize the in situ bioactivity of these proteins within the fabricated nanopatterns. This method exploits the high spatial and orientational control of the protein monolayer assembly allowed by nanografting, combined with the high sensitivity of the AFM for detecting ligand-binding events. The maltose-mediated conformational changes within the MBP have been found to change the AFM-tip-protein interaction, therefore causing the frictional signal to change. Our measurements show that the protein ligand-binding function is maintained upon the immobilization process and is not affected by (a) the addition of the cysteine dipeptide, (b) the spatial confinement associated with nanografting, and (c) the interaction between the protein and the Au substrate. These surface-confined proteins can also be regenerated, and their frictional response is reproducible through several maltose exposure/washing cycles. By measuring the change in the frictional force above the protein nanopatterns as a function of maltose concentration, we determined the dissociation constant for the MBP-cys-cys/maltose system to be kd = (1 +/- 0.04) microM. Our results show that the MBP-cys-cys system provides a very sensitive surface-based, protein nanobiosensor for maltose detection at the attogram level (approximately 100 nM concentration). The implications of our study for the fabrication of molecular-scale biological sensors are discussed at the end of the paper.

Toward an accurate and efficient theory of physisorption. I. Development of an augmented density-functional theory model.

Currently available density functionals cannot describe the dispersion component of the interaction energy present in weakly bound complexes. Moreover, the exchange energy as obtained from the density-functional theory is often incorrect. Examples of problematic cases include clusters of van der Waals-bound rare-gas atoms and most hydrogen-bonded molecular systems. Thus, accurate ab initio methods to treat intermolecular forces should be used in such systems. These methods are, however, too slow to be applicable to the large systems needed to model adsorption. This is why DFT continues to be used, where, in addition, a quite common compensation of errors sometimes produces some sort of agreement with the corresponding experimental data. In this paper, we analyze in detail the inadequacy of standard DFT for describing the weak binding present in a few rare gas-rare gas, metal atom-rare gas, and metal atom-metal atom dimers.Inspired by the success of the Hartree-Fock plus (damped) dispersion (HFD) method, we test the use of an improved hybrid model in which to a density-functional interaction energy (with corrected exchange and avoidance of double-counting of dispersion), a (damped) dispersion expansion is added in the usual way.Comparisons with accurate theoretical or experimental benchmarks show that our DFdD method using the revPBEx or revPBEx+VWNc functionals and accurate dispersion coefficients is found to recover the interaction energy curves very well for many of the tested systems. The sec and paper in this series will describe the use of the DFdD method for physisorption for the previously well-studied (but not solved) case of Xe/Cu(111).

Emerging Technologies for Cancer Research: Towards Personalized Medicine with Microfluidic Platforms and 3D Tumor Models.

In the present review, we describe three hot topics in cancer research such as circulating tumor cells, exosomes, and 3D environment models. The first section is dedicated to microfluidic platforms for detecting circulating tumor cells, including both affinity-based methods that take advantage of antibodies and aptamers, and "label-free" approaches, exploiting cancer cells physical features and, more recently, abnormal cancer metabolism. In the second section, we briefly describe the biology of exosomes and their role in cancer, as well as conventional techniques for their isolation and innovative microfluidic platforms. In the third section, the importance of tumor microenvironment is highlighted, along with techniques for modeling it in vitro. Finally, we discuss limitations of two-dimensional monolayer methods and describe advantages and disadvantages of different three-dimensional tumor systems for cell-cell interaction analysis and their potential applications in cancer management.

Investigating the effect of cell substrate on cancer cell stiffness by optical tweezers.

The mechanical properties of cells are influenced by their microenvironment. Here we report cell stiffness alteration by changing the cell substrate stiffness for isolated cells and cells in contact with other cells. Polydimethylsiloxane (PDMS) is used to prepare soft substrates with three different stiffness values (173, 88 and 17kPa respectively). Breast cancer cells lines, namely HBL-100, MCF-7 and MDA-MB-231 with different level of aggressiveness are cultured on these substrates and their local elasticity is investigated by vertical indentation of the cell membrane. Our preliminary results show an unforeseen behavior of the MDA-MB-231 cells. When cultured on glass substrate as isolated cells, they are less stiff than the other two types of cells, in agreement with the general statement that more aggressive and metastatic cells are softer. However, when connected to other cells the stiffness of MDA-MB-231 cells becomes similar to the other two cell lines. Moreover, the stiffness of MDA-MB-231 cells cultured on soft PDMS substrates is significantly higher than the stiffness of the other cell types, demonstrating thus the strong influence of the environmental conditions on the mechanical properties of the cells.

Side-by-side characterization of electron tunneling through monolayers of isomeric molecules: a combined experimental and theoretical study.

We report a new experimental method for measuring relatively small differences in electron tunneling through two distinct monolayers. We place them side by side using scanning probe nanolithography and compare the tunneling currents by conductive probe atomic force microscopy under identical force, voltage, and tip contamination conditions. We demonstrate the validity of our approach by applying it to two isomeric molecules with similar length and functional groups, with only the position of two functional groups, one aromatic and the other aliphatic, being inverted with respect to each other. The relative values of the two tunneling currents, calculated using density functional theory and the Tersoff-Hamann approach, compare very well with the experimental data, providing us with an example of theory vs experiment agreement that is rather uncommon in this field.

Mismatch detection in DNA monolayers by atomic force microscopy and electrochemical impedance spectroscopy.

BACKGROUND: DNA hybridization is at the basis of most current technologies for genotyping and sequencing, due to the unique properties of DNA base-pairing that guarantee a high grade of selectivity. Nonetheless the presence of single base mismatches or not perfectly matched sequences can affect the response of the devices and the major challenge is, nowadays, to distinguish a mismatch of a single base and, at the same time, unequivocally differentiate devices read-out of fully and partially matching sequences. RESULTS: We present here two platforms based on different sensing strategies, to detect mismatched and/or perfectly matched complementary DNA strands hybridization into ssDNA oligonucleotide monolayers. The first platform exploits atomic force microscopy-based nanolithography to create ssDNA nano-arrays on gold surfaces. AFM topography measurements then monitor the variation of height of the nanostructures upon biorecognition and then follow annealing at different temperatures. This strategy allowed us to clearly detect the presence of mismatches. The second strategy exploits the change in capacitance at the interface between an ssDNA-functionalized gold electrode and the solution due to the hybridization process in a miniaturized electrochemical cell. Through electrochemical impedance spectroscopy measurements on extended ssDNA self-assembled monolayers we followed in real-time the variation of capacitance, being able to distinguish, through the difference in hybridization kinetics, not only the presence of single, double or triple mismatches in the complementary sequence, but also the position of the mismatched base pair with respect to the electrode surface. CONCLUSION: We demonstrate here two platforms based on different sensing strategies as sensitive and selective tools to discriminate mismatches. Our assays are ready for parallelization and can be used in the detection and quantification of single nucleotide mismatches in microRNAs or in genomic DNA.

Glucose is a key driver for GLUT1-mediated nanoparticles internalization in breast cancer cells.

The mesenchymal state in cancer is usually associated with poor prognosis due to the metastatic predisposition and the hyper-activated metabolism. Exploiting cell glucose metabolism we propose a new method to detect mesenchymal-like cancer cells. We demonstrate that the uptake of glucose-coated magnetic nanoparticles (MNPs) by mesenchymal-like cells remains constant when the glucose in the medium is increased from low (5.5 mM) to high (25 mM) concentration, while the MNPs uptake by epithelial-like cells is significantly reduced. These findings reveal that the glucose-shell of MNPs plays a major role in recognition of cells with high-metabolic activity. By selectively blocking the glucose transporter 1 channels we showed its involvement in the internalization process of glucose-coated MNPs. Our results suggest that glucose-coated MNPs can be used for metabolic-based assays aimed at detecting cancer cells and that can be used to selectively target cancer cells taking advantage, for instance, of the magnetic-thermotherapy.

Effect of neighboring cells on cell stiffness measured by optical tweezers indentation.

We report on the modification of mechanical properties of breast cancer cells when they get in contact with other neighboring cells of the same type. Optical tweezers vertical indentation was employed to investigate cell mechanics in isolated and contact conditions, by setting up stiffness as a marker. Two human breast cancer cell lines with different aggressiveness [MCF-7 (luminal breast cancer) and MDA-MB-231 (basal-like breast cancer)] and one normal immortalized breast cell line HBL-100 (normal and myoepithelial) were selected. We found that neighboring cells significantly alter cell stiffness: MDA-MB-231 becomes stiffer when in contact, while HBL-100 and MCF-7 exhibit softer character. Cell stiffness was probed at three cellular subregions: central (above nucleus), intermediate (cytoplasm), and near the leading edge. In an isolated condition, all cells showed a significant regional variation in stiffness: higher at the center and fading toward the leading edge. However, the regional variation becomes statistically insignificant when the cells were in contact with other neighboring cells. The proposed approach will contribute to understand the intriguing temporal sequential alterations in cancer cells during interaction with their surrounding microenvironment.

Correction: In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands.

[This corrects the article DOI: 10.1371/journal.pone.0133571.].