A survey of the 2006-2009 quartz crystal microbalance biosensor literature

Since the publication of the original review of piezoelectric acoustic sensors in this series there has been a consistent, gradual expansion in the number of published papers using 'quartz crystal microbalances' (QCM). Between 2001 and 2009, the number of QCM publications per annum has increased from 49 to 273, with a two-fold increase in papers per annum between 2004 and 2008. Within the field, comparing the time covered by the current to the previous review, there are trends towards increasing use of QCM in the study of protein adsorption to surfaces (93% increase), homeostasis (67% increase), protein-protein interactions (40% increase) and carbohydrates (43% increase). New commercial systems have been released that are driving the uptake of the technology for characterization of binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This paper highlights theoretical and practical aspects of the principles that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and membrane interfaces.     

A survey of the 2001 to 2005 quartz crystal microbalance biosensor literature: applications of acoustic physics to the analysis of biomolecular interactions

The widespread exploitation of biosensors in the analysis of molecular recognition has its origins in the mid-1990s following the release of commercial systems based on surface plasmon resonance (SPR). More recently, platforms based on piezoelectric acoustic sensors (principally 'bulk acoustic wave' (BAW), 'thickness shear mode' (TSM) sensors or 'quartz crystal microbalances' (QCM)), have been released that are driving the publication of a large number of papers analysing binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This article highlights salient theoretical and practical aspects of the technologies that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and lipidic and polymeric interfaces. Key differentiators between optical and acoustic sensing modalities are also reviewed.     

Validating and improving elastic network models with molecular dynamics simulations

Elastic network models (ENMs) are a class of simple models intended to represent the collective motions of proteins. In contrast to all‐atom molecular dynamics simulations, the low computational investment required to use an ENM makes them ideal for speculative hypothesis‐testing situations. Historically, ENMs have been validated via comparison to crystallographic B‐factors, but this comparison is relatively low‐resolution and only tests the predictions of relative flexibility. In this work, we systematically validate and optimize a number of ENM‐type models by quantitatively comparing their predictions to microsecond‐scale all‐atom simulations of three different G protein coupled receptors. We show that, despite their apparent simplicity, well‐optimized ENMs perform remarkably well, reproducing the protein fluctuations with an accuracy comparable to what one would expect from all‐atom simulations run for several hundred nanoseconds. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Sialylation enhancement of CTLA4‐Ig fusion protein in Chinese hamster ovary cells by dexamethasone

The importance of glycoprotein sialic acid levels is well known, as increased levels have been shown to increase in vivo serum half‐life profiles. Here we demonstrate for the first time that dexamethasone (DEX) was capable of improving the sialylation of a CTLA4‐Ig fusion protein produced by Chinese hamster ovary (CHO) cells. DEX was shown to enhance the intracellular addition of sialic acid by sialyltransferases as well as reduce extracellular removal of sialic acid by sialidase cleavage. We illustrated that DEX addition resulted in increased expression of the glycosyltransferases α2,3‐sialyltransferase (α2,3‐ST) and β1,4‐galactosyltransferase (β1,4‐GT) in CHO cells. Based upon our previous results showing DEX addition increased culture cell viability, we confirmed here that cultures treated with DEX also resulted in decreased sialidase activity. Addition of the glucocorticoid receptor (GR) antagonist mifepristone (RU‐486) was capable of blocking the increase in sialylation by DEX which further supports that DEX affected sialylation as well as provides evidence that the sialylation enhancement effects of DEX on recombinant CHO cells occurred through the GR. Finally, the effects of DEX on increasing sialylation were then confirmed in 5‐L controlled bioreactors. Addition of 1 µM DEX to the bioreactors on day 2 resulted in harvests with average increases of 16.2% for total sialic acid content and 15.8% in the protein fraction with N‐linked sialylation. DEX was found to be a simple and effective method for increasing sialylation of this CTLA4‐Ig fusion protein expressed in CHO cells. Biotechnol. Bioeng. 2010;107: 488–496. © 2010 Wiley Periodicals, Inc.     

Improving computational protein design by using structure‐derived sequence profile

Designing a protein sequence that will fold into a predefined structure is of both practical and fundamental interest. Many successful, computational designs in the last decade resulted from improved understanding of hydrophobic and polar interactions between side chains of amino acid residues in stabilizing protein tertiary structures. However, the coupling between main‐chain backbone structure and local sequence has yet to be fully addressed. Here, we attempt to account for such coupling by using a sequence profile derived from the sequences of five residue fragments in a fragment library that are structurally matched to the five‐residue segments contained in a target structure. We further introduced a term to reduce low complexity regions of designed sequences. These two terms together with optimized reference states for amino‐acid residues were implemented in the RosettaDesign program. The new method, called RosettaDesign‐SR, makes a 12% increase (from 34 to 46%) in fraction of proteins whose designed sequences are more than 35% identical to wild‐type sequences. Meanwhile, it reduces 8% (from 22% to 14%) to the number of designed sequences that are not homologous to any known protein sequences according to psi‐blast. More importantly, the sequences designed by RosettaDesign‐SR have 2–3% more polar residues at the surface and core regions of proteins and these surface and core polar residues have about 4% higher sequence identity to wild‐type sequences than by RosettaDesign. Thus, the proteins designed by RosettaDesign‐SR should be less likely to aggregate and more likely to have unique structures due to more specific polar interactions. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

The possible roles of B‐cell novel protein‐1 (BCNP1) in cellular signalling pathways and in cancer

B‐cell novel protein‐1 (BCNP1) or Family member of 129C (FAM129C) was identified as a B‐cell‐specific plasma‐membrane protein. Bioinformatics analysis predicted that BCNP1 might be heavily phosphorylated. The BCNP1 protein contains a pleckstrin homology (PH) domain, two proline‐rich (PR) regions and a Leucine Zipper (LZ) domain suggesting that it may be involved in protein‐protein interactions. Using The Cancer Genome Atlas (TCGA) data sets, we investigated the correlation of alteration of the BCNP1 copy‐number changes and mutations in several cancer types. We also investigated the function of BCNP1 in cellular signalling pathways. We found that BCNP1 is highly altered in some types of cancers and that BCNP1 copy‐number changes and mutations co‐occur with other molecular alteration events for TP53 (tumour protein P53), PIK3CA (Phosphatidylinositol‐4,5‐Bisphosphate 3‐Kinase, Catalytic Subunit Alpha), MAPK1 (mitogen‐activated protein kinase‐1; ERK: extracellular signal regulated kinase), KRAS (Kirsten rat sarcoma viral oncogene homolog) and AKT2 (V‐Akt Murine Thymoma Viral Oncogene Homolog 2). We also found that PI3K (Phoshoinositide 3‐kinase) inhibition and p38 MAPK (p38 mitogen‐activated protein kinase) activation leads to reduction in phosphorylation of BCNP1 at serine residues, suggesting that BCNP1 phosphorylation is PI3K and p38MAPK dependent and that it might be involved in cancer. Its degradation depends on a proteasome‐mediated pathway.     

ATM is involved in cell‐cycle control through the regulation of retinoblastoma protein phosphorylation

Ataxia telangiectasia mutated protein (ATM) is a member of the phosphatidylinositol‐3 kinase (PI3K) family, which has a role in the cellular response to DNA double‐strand breaks (DSBs). In the present study, we evaluated the role of ATM in cell‐cycle control in dopaminergic rat neuroblastoma B65 cells. For this purpose, ATM activity was either inhibited pharmacologically with the specific inhibitor KU‐55933, or the ATM gene was partially silenced by transfection with small interfering RNA (siRNA). Our data indicate that although ATM inhibition did not affect the cell cycle, both treatments specifically decreased the levels of cyclin A and retinoblastoma protein (pRb), phosphorylated at Ser780. Furthermore, ATM inhibition decreased the active form of p53, which is phosphorylated at Ser15, and also decreased Bax and p21 expression. Using H₂O₂ as a positive control of DSBs, caused a rapid pRb phosphorylation, this was prevented by KU‐55933 and siRNA treatment. Collectively, our data demonstrate how a new molecular network on ATM regulates the cell cycle through the control of pRb phosphorylation. These findings support a new target of ATM. J. Cell. Biochem. 110: 210–218, 2010. © 2010 Wiley‐Liss, Inc.     

Controlling Molecular Orientation of Naphthalenediimide‐Based Polymer Acceptors for High Performance All‐Polymer Solar Cells

Molecular orientation, with respect to donor/acceptor interface and electrodes, plays a critical role in determining the performance of all‐polymer solar cells (all‐PSCs), but is often difficult to rationally control. Here, an effective approach for tuning the molecular crystallinity and orientation of naphthalenediimide‐bithiophene‐based n‐type polymers (P(NDI2HD‐T2)) by controlling their number average molecular weights (M_n) is reported. A series of P(NDI2HD‐T2) polymers with different M_n of 13.6 ( P_L ), 22.9 ( P_M ), and 49.9 kg mol^?1 ( P_H ) are prepared by changing the amount of end‐capping agent (2‐bromothiophene) during polymerization. Increasing the M_n values of P(NDI2HD‐T2) polymers leads to a remarkable shift of dominant lamellar crystallite textures from edge‐on ( P_L ) to face‐on ( P_H ) as well as more than a twofold increase in the crystallinity. For example, the portion of face‐on oriented crystallites is dramatically increased from 21.5% and 46.1%, to 78.6% for P_L , P_M, and P_H polymers. These different packing structures in terms of the molecular orientation greatly affect the charge dissociation efficiency at the donor/acceptor interface and thus the short‐circuit current density of the all‐PSCs. All‐PSCs with PTB7‐Th as electron donor and P_H as electron acceptor show the highest efficiency of 6.14%, outperforming those with P_M (5.08%) and P_L (4.29%).     

SOFT‐MI: A novel microfabrication technique integrating soft‐lithography and molecular imprinting for tissue engineering applications

An innovative approach has been employed for the realization of bioactive scaffolds able to mimic the in vivo cellular microenvironment for tissue engineering applications. This method is based on the combination of molecular imprinting and soft‐lithography technology to enhance cellular adhesion and to guide cell growth and proliferation due to presence of highly specific recognition sites of selected biomolecules on a well‐defined polymeric microstructure. In this article polymethylmethacrylate (PMMA) scaffolds have been realized by using poly(dimethylsiloxane) (PDMS) microstructured molds imprinted with FITC‐albumin and TRITC‐lectin. In addition gelatin, an adhesion protein, was employed for the molecular imprinting of polymeric scaffolds for cellular tests. The most innovative aspect of this research was the molecular imprinting of whole cells for the development of substrates able to enhance the cell adhesion processes. Biotechnol. Bioeng. 2010;106: 804–817. © 2010 Wiley Periodicals, Inc.     

Indirubin-3'-monoxime, a derivative of a chinese antileukemia medicine, inhibits angiogenesis

Although the antiangiogenic activity of indirubin‐3‐monoxime (I3M), a derivative of a Chinese anti‐leukemia medicine, has been demonstrated using transgenic zebrafish, the detail molecular mechanism has not been elicited. To further establish its role in antiangiogenic activity, we tested its potential against human umbilical vein endothelial cells (HUVECs) and the in vivo Matrigel plug model was applied to evaluate new vessel formation. We also investigated the molecular mechanisms of I3M‐induced antiangiogenic effects in HUVECs. We found that I3M significantly inhibited HUVEC proliferation (2.5–20 µM), migration (2.5–20 µM), and tube formation (10–20 µM) in HUVECs. The number of microvessels growing from the aortic rings was suppressed by I3M treatment. Moreover, I3M suppressed neovascularization in Matrigel plugs in mice. The underlying antiangiogenic mechanism of I3M was correlated with down‐regulation of the vascular endothelial growth factor receptor‐2 activation, at least a part. These findings emphasize the potential use of I3M in pathological situations involving stimulated angiogenesis, such as tumor development. J. Cell. Biochem. 112: 1384–1391, 2011. © 2011 Wiley‐Liss, Inc.     

Cell culture media supplementation of infrequently used sugars for the targeted shifting of protein glycosylation profiles

Mammalian cells in culture rely on sources of carbohydrates to supply the energy requirements for proliferation. In addition, carbohydrates provide a large source of the carbon supply for supporting various other metabolic activities, including the intermediates involved in the protein glycosylation pathway. Glucose and galactose, in particular, are commonly used sugars in culture media for these purposes. However, there exists a very large repertoire of other sugars in nature, and many that have been chemically synthesized. These sugars are particularly interesting because they can be utilized by cells in culture in distinct ways. In the present work it has been found that many infrequently used sugars, and the corresponding cellular response towards them as substrates, led to differences in the protein N‐glycosylation profile of a recombinant glycoprotein. The selective media supplementation of raffinose, trehalose, turanose, palatinose, melezitose, psicose, lactose, lactulose, and mannose were found to be capable of redirecting N‐glycan oligosaccharide profiles. Despite this shifting of protein glycosylation, there were no other adverse changes in culture performance, including both cell growth and cellular productivity over a wide range of supplemented sugar concentrations. The approach presented highlights a potential means towards both the targeted shifting of protein glycosylation profiles and ensuring recombinant protein comparability, which up to this point in time has remained under‐appreciated for these under‐utilized compounds. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:511–522, 2017     

Refolding of denatured/reduced lysozyme at high concentrations by artificial molecular chaperone‐ion exchange chromatography

Development of high efficiency and low cost protein refolding methods is a highlighted research focus in biotechnology. Artificial molecular chaperone (AMC) and protein folding liquid chromatography (PFLC) are two attractive refolding methods developed in recent years. In the present work, AMC and one branch of PFLC, ion exchange chromatography (IEC), are integrated to form a new refolding method, artificial molecular chaperone‐ion exchange chromatography (AMC‐IEC). This new method is applied to the refolding of a widely used model protein, urea‐denatured/dithiothreitol‐reduced lysozyme. Many factors influencing the refolding of lysozyme, such as urea concentration, β‐cyclodextrin concentration, molar ratio of detergent to protein, mobile phase flow rate, and type of detergent, were investigated, respectively, to optimize the conditions for lysozyme refolding by AMC‐IEC. Compared with normal IEC refolding method, the activity recoveries of lysozyme obtained by AMC‐IEC were much higher in the investigated range of initial protein concentrations. Moreover, the activity recoveries obtained by using this newly developed refolding method were still quite high for denatured/reduced lysozyme at high initial concentrations. When the initial protein concentration was 200 mg mL^?1, the activity recovery was over 60%. In addition, the lifetime of the chromatographic column during AMC‐IEC was much longer than that during protein refolding by normal IEC. Therefore, AMC‐IEC is a high efficient and low cost protein refolding method. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

A molecularly imprinted nanofilm‐based quartz crystal microbalance sensor for the real‐time detection of pirimicarb

This study aimed to prepare a novel quartz crystal microbalance (QCM) sensor for the detection of pirimicarb. Pirimicarb‐imprinted poly (ethylene glycol dimethacrylate‐N‐metacryloyl‐(l )‐tryptophan methyl ester) [p (EGDMA‐MATrp)] nanofilm (MIP) on the gold surface of a QCM chip was synthesized using the molecular imprinting technique. A nonimprinted p (EGDMA‐MATrp) nanofilm (NIP) was also synthesized using the same experimental technique. The MIP and NIP nanofilms were characterized via Fourier transform infrared spectroscopy attenuated total reflectance spectroscopy, contact angle, atomic force microscopy, and an ellipsometer. A competitive adsorption experiment on the sensor was performed to display the selectivity of the nanofilm. An analysis of the QCM sensor showed that the MIP nanofilm exhibited high sensitivity and selectivity for pirimicarb determination. A liquid chromatography‐tandem mass spectrometry method was prepared and validated to determine the accuracy and precision of the QCM sensor. The accuracy and precision of both methods were determined by a comparison of six replicates at three different concentrations to tomato samples extracted by using a Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) method. The limit of detection of the QCM sensor was found to be 0.028 nM. In conclusion, the QCM sensor showed good accuracy, with recovery percentages between 91 and 94%. Also, the pirimicarb‐imprinted QCM sensor exhibited a fast response time, reusability, high selectivity and sensitivity, and a low limit of detection. Therefore, it offers a serious alternative to the traditional analytical methods for pesticide detection in both natural sources and aqueous solutions.     

Differentiation of human umbilical cord Wharton's jelly‐derived mesenchymal stem cells into germ‐like cells in vitro

Recent studies have demonstrated that mesenchymal stem cells could differentiate into germ cells under appropriate conditions. We sought to determine whether human umbilical cord Wharton's jelly‐derived mesenchymal stem cells (HUMSCs) could form germ cells in vitro. HUMSCs were induced to differentiate into germ cells in all‐trans retinoic acid, testosterone and testicular‐cell‐conditioned medium prepared from newborn male mouse testes. HUMSCs formed “tadpole‐like” cells after induction with different reagents and showed both mRNA and protein expression of germ‐cell‐specific markers Oct4 (POUF5), Ckit, CD49_f (α6), Stella (DDPA3), and Vasa (DDX4). Our results may provide a new route for reproductive therapy involving HUMSCs and a novel in vitro model to investigate the molecular mechanisms that regulate the development of the mammalian germ lineage. J. Cell. Biochem. 109: 747–754, 2010. © 2010 Wiley‐Liss, Inc.     

Gravimetric biosensors based on acoustic waves in thin polymer films

Most gravimetric biosensors use thin piezoelectric quartz crystals, either as resonating crystals (quartz crystal microbalance, QCM), or as bulk/surface acoustic wave (SAW) devices. In the majority of these the mass response is inversely proportional to the crystal thickness which, at a limit of about 150 microns, gives inadequate sensitivity. A new system is described in which acoustic waves are launched in very thin (10 microns) tensioned polymer films to produce an oscillatory device. A theoretical equation for this system is almost identical to the well-known Sauerbrey equation used in the QCM method. Because the polymer films are so thin, a 30-fold increase in sensitivity is predicted and verified by adding known surface masses. Temperature sensitivity is a problem so a separate control sensor and careful temperature regulation are necessary. Preliminary results showing the real time binding of protein (IgG), a step towards immunosensor development, and the use of mass enhancing particles are presented. Inexpensive materials are used so disposable gravimetric biosensors may become feasible.     

Macronutrients and obesity: Revisiting the calories in,calories out framework

Recent clinical research has studied weight responses to varying diet composition, but the contribution of changes in macronutrient intake and physical activity to rising population weight remains controversial. Research on the economics of obesity typically assumes a “calories in, calories out” framework, but a weight production model separating caloric intake into carbohydrates, fat, and protein, has not been explored in an economic framework. To estimate the contributions of changes in macronutrient intake and physical activity to changes in population weight, we conducted dynamic time series and structural VAR analyses of U.S. data between 1974 and 2006 and a panel analysis of 164 countries between 2001 and 2010. Findings from all analyses suggest that increases in carbohydrates are most strongly and positively associated with increases in obesity prevalence even when controlling for changes in total caloric intake and occupation-related physical activity. Our structural VAR results suggest that, on the margin, a 1% increase in carbohydrates intake yields a 1.01 point increase in obesity prevalence over 5 years while an equal percent increase in fat intake decreases obesity prevalence by 0.24 points.     

Tandem Cell‐Free Protein Synthesis as a Tool for Rapid Screening of Optimal Molecular Chaperones

A simple and flexible method is developed for rapid screening of molecular chaperones that enhance the functional expression of recombinant proteins. A panel of molecular chaperones are transiently expressed in a reaction mixture of cell‐free protein synthesis and then a target protein is subsequently expressed in the presence of these presynthesized molecular chaperones. The biological activity of the cell‐free synthesized target protein is compared to identify the effective molecular chaperones. This strategy successfully identifies individual and combinations of bacterial molecular chaperones that markedly improved the functional expression of horseradish peroxidase. The authors believe that the presented strategy provides a versatile platform for the optimal production of functional proteins, and can also be extended to studies of other interacting proteins.     

New protein–protein interactions of mitochondrial connexin 43 in mouse heart

Connexin 43 (Cx43), the gap junction protein involved in cell‐to‐cell coupling in the heart, is also present in the subsarcolemmal fraction of cardiomyocyte mitochondria. It has been described to regulate mitochondrial potassium influx and respiration and to be important for ischaemic preconditioning protection, although the molecular effectors involved are not fully characterized. In this study, we looked for potential partners of mitochondrial Cx43 in an attempt to identify new molecular pathways for cardioprotection. Mass spectrometry analysis of native immunoprecipitated mitochondrial extracts showed that Cx43 interacts with several proteins related with mitochondrial function and metabolism. Among them, we selected for further analysis only those present in the subsarcolemmal mitochondrial fraction and known to be related with the respiratory chain. Apoptosis‐inducing factor (AIF) and the beta‐subunit of the electron‐transfer protein (ETFB), two proteins unrelated to date with Cx43, fulfilled these conditions, and their interaction with Cx43 was proven by direct and reverse co‐immunoprecipitation. Furthermore, a previously unknown molecular interaction between AIF and ETFB was established, and protein content and sub‐cellular localization appeared to be independent from the presence of Cx43. Our results identify new protein–protein interactions between AIF‐Cx43, ETFB‐Cx43 and AIF‐ETFB as possible players in the regulation of the mitochondrial redox state.     

Crystal structures of MBP fusion proteins

Although chaperone‐assisted protein crystallization remains a comparatively rare undertaking, the number of crystal structures of polypeptides fused to maltose‐binding protein (MBP) that have been deposited in the Protein Data Bank (PDB) has grown dramatically during the past decade. Altogether, 102 fusion protein structures were detected by Basic Local Alignment Search Tool (BLAST) analysis. Collectively, these structures comprise a range of sizes, space groups, and resolutions that are typical of the PDB as a whole. While most of these MBP fusion proteins were equipped with short inter‐domain linkers to increase their rigidity, fusion proteins with long linkers have also been crystallized. In some cases, surface entropy reduction mutations in MBP appear to have facilitated the formation of crystals. A comparison of the structures of fused and unfused proteins, where both are available, reveals that MBP‐mediated structural distortions are very rare.