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Aggregation of Apo/Glycated Human Serum Albumins and Aptamer-Saturated Graphene Quantum Dot: A Simulation Study
... Additionally, our previous study has shown that aptamer saturation on the GQD surface is crucial for aptasensor performance. 38 Therefore, we employ an aptamersaturated GQD in this work. ...
... The topology of the GQD was obtained from a previous work. 38 GQD and aptamers were soaked in TIP3P water molecules and counterions and neutralized by 1 M NaCl. The system was equilibrated for 10 ns, followed by a 500 ns production run (the simulation setting can be seen in the Simulation Protocols section). ...
Microalbuminuria is a key indicator of chronic kidney disease (CKD), resulting from the leakage of albumin into urine. The accuracy of microalbuminuria measurement depends on urine freshness as improper storage and slow processing can lead to protease digestion of albumin. Recently, graphene-based aptasensors have been shown to detect albumin in aged urine samples, suggesting that albumin fragments can still be recognized by these sensors. To date, nine urinary albumin fragments (F1–F9) have been reported. Meanwhile, the graphene quantum dot (GQD) has emerged as a promising material due to its noncytotoxicity, high biocompatibility, and intrinsic fluorescence properties. Its comparable size to aptamers makes it particularly attractive for albumin detection. In this study, molecular dynamics (MD) simulations were performed to reveal the binding modes of urinary albumin fragments (F1–F9) to the aptamer-bound GQD (GQDA) complex. The study compares the binding behavior of nonaggregated (N_AG) and preaggregated (AG) albumin fragments with GQDA. The results demonstrate that the spontaneous clustering of GQDA and albumin fragments occurs in all cases. However, aggregated fragments exhibit reduced aptamer accessibility due to geometric confinement and structural rigidity. Lysine-rich regions were found to play a crucial role in fragment–aptamer interactions, with F1 and F8 displaying the highest number of aptamer contacts. Notably, F8, the most stable fragment, showed the strongest interactions with aptamers, highlighting its potential as a urinary biomarker for CKD detection. The findings from this study provide valuable molecular insights into the interactions between urinary albumin fragments and GQDA, paving the way for the development of highly selective and sensitive CKD diagnostic platforms.
In computational chemistry and molecular modeling, the interactions between biomolecules (BMs) and nanomaterials (NMs) play a crucial role in various physical and biological processes, and have significant implications in material discovery and development. While there is extensive literature on free energy calculations for drug-target interactions, reviews specifically addressing BM-NM interactions are relatively scarce. This manuscript aims to fill in this gap by presenting a comprehensive overview of the most widely used and well-established methods for free energy calculations. It provides a detailed analysis of the advantages and limitations of these methods and discusses their applicability to BM-NM systems. This work is intended to offer insights into free energy calculations and serve as a guide for future research in this field.
Diabetes mellitus is a chronic metabolic disease involving continued elevated blood glucose levels. It is a leading cause of mortality and reduced life expectancy. Glycated human serum albumin (GHSA) has been reported to be a potential diabetes biomarker. A nanomaterial-based aptasensor is one of the effective techniques to detect GHSA. Graphene quantum dots (GQDs) have been widely used in aptasensors as an aptamer fluorescence quencher due to their high biocompatibility and sensitivity. GHSA-selective fluorescent aptamers are first quenched upon binding to GQDs. The presence of albumin targets results in the release of aptamers to albumin and consequently fluorescence recovery. To date, the molecular details on how GQDs interact with GHSA-selective aptamers and albumin remain limited, especially the interactions of an aptamer-bound GQD (GQDA) with an albumin. Thus, in this work, molecular dynamics simulations were used to reveal the binding mechanism of human serum albumin (HSA) and GHSA to GQDA. The results show the rapid and spontaneous assembly of albumin and GQDA. Multiple sites of albumins can accommodate both aptamers and GQDs. This suggests that the saturation of aptamers on GQDs is required for accurate albumin detection. Guanine and thymine are keys for albumin-aptamer clustering. GHSA gets denatured more than HSA. The presence of bound GQDA on GHSA widens the entrance of drug site I, resulting in the release of open-chain glucose. The insight obtained here will serve as a base for accurate GQD-based aptasensor design and development.
Quantum dots (QDs) represent the promising new generation of luminophores owing to their size-, composition-, and surface-dependent tunable photoluminescence (PL) and photochemical stability. The development of various QD composites with high PL and good biocompatibility has facilitated the use of aptamer-functionalized QD biosensors for highly sensitive and specific detection of molecules in clinical and environmental settings. In addition to describing the recent advances in aptamer-based QD biosensor technology for the detection of diverse chemicals and biomolecules, this review provides recent examples of sensing strategies based on optical signal enhancement and quenching of QDs. It also discusses potential strategies for the development of biosensors to widen their practical applications across various scientific and technological fields.
Background:
Glycated albumin (GA), the non-enzymatic glycation product of albumin in plasma, became a glycemic marker in the beginning of the 21st century. The assay is not affected by hemoglobin levels and reflects the glycemic status over a shorter period as compared to HbA1c measurements. Thus, GA may contributes as an intermediate glucose index in the current diabetes mellitus (DM) diagnostic system.
Aim:
To search and summarize the available data on glycated albumin measurements required for the diagnosis of diabetes mellitus.
Methods:
Databases, including PubMed, Embase, Web of Science, and Cochrane Central Register of Controlled Trials (CENTRAL), among others, were systematically searched. The Quality Assessment of Diagnostic Accuracy Studies-2 tool was applied for the assessment of quality, and the bivariate model was used to pool the sensitivity and specificity. The hierarchical summary receiver operator characteristic curves (HSROC) model was utilized to estimate the summary receiver operating characteristics curve (SROC). Sensitivity analysis was performed to investigate the association of the study design and patient characteristics with the test accuracy and meta-regression to find the source of heterogeneity.
Results:
Three studies regarding gestational diabetes mellitus (GDM) and a meta-analysis of 16 non-GDM studies, comprising a total sample size of 12876, were included in the work. Results reveal that the average cut-off values of GA reported for the diagnosis of GDM diagnosis was much lower than those for non-GDM. For non-GDM cases, diagnosing DM with a circulating GA cut-off of 14.0% had a sensitivity of 0.766 (95%CI: 0.539, 0.901), specificity of 0.687 (95%CI: 0.364, 0.894), and area under the curve of 0.80 (95%CI: 0.76, 0.83) for the SROC. The estimated SROC at different GA cut-off values for non-GDM exhibited that the average location parameter lambda of 16 non-GDM studies was 2.354 (95%CI: 2.002, 2.707), and the scale parameter beta was -0.163 (95%CI: -0.614, 0.288). These non-GDM studies with various thresholds had substantial heterogeneity, which may be attributed to the type of DM, age, and body mass index as possible sources.
Conclusion:
Glycated albumin in non-DM exhibits a moderate diagnostic accuracy. Further research on the diagnostic accuracy of GA for GDM and combinational measurements of GA and other assays is suggested.
Glycated albumin (GA) has been previously introduced as a promising biomarker for glycemic monitoring in diabetes patients with thalassemia. In this study, a label-free graphene oxide (GO)-modified aptasensor was developed for the rapid detection of GA. The fabrication of the aptasensor was dependent on the covalent interaction of the amine-functionalized GA-specific aptamer with the carboxylic groups of GO. Square wave voltammetry (SWV) analysis was carried out for the measurement of GA-aptamer binding to their specific proteins. The peak current changes before and after incubation with GA protein were directly proportional to the concentration. The developed aptasensor exhibited a broad linearity (1–10,000 µg mL⁻¹), a low detection limit (LOD) of 0.031 µg mL⁻¹, and high selectivity for GA detection. In addition, the aptasensor was successfully applied to detect GA in both spiked and clinical serum samples. The comparison of the developed method with a commercial assay validated the reliability of the aptasensor for clinical application. Therefore, the newly developed aptasensor is a promising tool for GA measurements in diabetic patients with underlying thalassemia.
Background: Glycated hemoglobin (HbA1c) is commonly used in the diagnosis and evaluation of glycemic control in diabetes, and it may be influenced by several non-glycemic and glycemic factors, including albumin. This retrospective study investigated the influence of albumin on HbA1c and HbA1c-defined glycemic status.
Methods: The demographic, hematological, and biochemical data were collected for 11,922 patients undergoing routine physical examination. Univariate and multivariate linear regression analyses, stratified analyses and interaction analyses, and multiple logistic regression were conducted to identify the association between albumin and HbA1c in people with different glycemic status.
Results: HbA1c levels were inversely associated with serum albumin level ( P < 0.0001) in all participants. Risk factors leading to the association included age > 45 years, high fasting plasma glucose (≥7.0 mmol/L), and anemia. The negative association between HbA1c and albumin was curved ( P < 0.0001) and had a threshold effect in the HbA1c-defined diabetic population; the association was significantly stronger when the albumin level fell below 41.4 g/L (β: −0.31, 95% CI: −0.45 to −0.17, P < 0.0001). A 2 g/L increase in albumin reduced the odds of HbA1c-defined dysglycemia, diabetes, and poor glycemia control by 12% to 36%, after adjustment for all possible confounders.
Conclusions: HbA1c was inversely associated with albumin level in all participants, and the association was significantly stronger in people with diabetes (defined by HbA1c criteria). For diabetic patients with lower albumin level, there was an increased risk of an erroneous HbA1c-based identification and management of glycemic status.
The continuous decrease in the availability of fossil resources, along with an evident energy crisis, and the growing environmental impact due to their use, has pushed scientific research towards the development of innovative strategies and green routes for the use of renewable resources, not only in the field of energy production but also for the production of novel advanced materials and platform molecules for the modern chemical industry. A new class of promising carbon nanomaterials, especially graphene quantum dots (GQDs), due to their exceptional chemical-physical features, have been studied in many applications, such as biosensors, solar cells, electrochemical devices, optical sensors, and rechargeable batteries. Therefore, this review focuses on recent results in GQDs synthesis by green, easy, and low-cost synthetic processes from eco-friendly raw materials and biomass-waste. Significant advances in recent years on promising recent applications in the field of electrochemical sensors, have also been discussed. Finally, challenges and future perspectives with possible research directions in the topic are briefly summarized.
Abstract: Rapid and accurate diagnosis of various biomarkers associated with medical conditions
including early detection of viruses and bacteria with highly sensitive biosensors is currently a
research priority. Aptamer is a chemically derived recognition molecule capable of detecting and
binding small molecules with high specificity and its fast preparation time, cost effectiveness, ease of
modification, stability at high temperature and pH are some of the advantages it has over traditional
detection methods such as High Performance Liquid Chromatography (HPLC), Enzyme-linked
Immunosorbent Assay (ELISA), Polymerase Chain Reaction (PCR). Higher sensitivity and selectivity
can further be achieved via coupling of aptamers with nanomaterials and these conjugates called “aptasensors”
are receiving greater attention in early diagnosis and therapy. This review will highlight
the selection protocol of aptamers based on Traditional Systematic Evolution of Ligands by EXponential
enrichment (SELEX) and the various types of modified SELEX.We further identify both the
advantages and drawbacks associated with the modified version of SELEX. Furthermore, we describe
the current advances in aptasensor development and the quality of signal types, which are dependent
on surface area and other specific properties of the selected nanomaterials, are also reviewed.
Keywords: aptamer; gold nanoparticles; quantum dots; graphene; MoS2; carbon nanotubes; SELEX;
biomolecules; diagnosis; signal type; limit of detection
An immobilization-free electrochemical sensor coupled with a graphene oxide (GO)-based aptasensor was developed for glycated human serum albumin (GHSA) detection. The concentration of GHSA was monitored by measuring the electrochemical response of free GO and aptamer-bound GO in the presence of glycated albumin; their currents served as the analytical signals. The electrochemical aptasensor exhibited good performance with a base-10 logarithmic scale. The calibration curve was achieved in the range of 0.01–50 µg/mL. The limit of detection (LOD) was 8.70 ng/mL. The developed method was considered a one-drop measurement process because a fabrication step and the probe-immobilization process were not required. This simple sensor offers a cost-effective, rapid, and sensitive detection method, and could be an alternative approach for determination of GHSA levels.
A simple and sensitive graphene oxide-mediated fluorescence quenching aptasensor is developed to quantify albuminuria in urine samples. The developed aptasensor used the specific target binding property of aptamer and fluorescence quenching property of graphene oxide to determine the concentration of human serum albumin in urine. The limit of detection of the developed platform is 0.05 µg.mL⁻¹ and the detection range is 0.1–600 µg.mL⁻¹, which covers the albuminuria concentration range present in normal human urine and the urine of the patient with chronic kidney disease. This approach can be modified to measure albuminuria using a high-throughput quantification platform and portable point of care testing. In addition, the production cost for one reaction is cheaper than those for the standard automated method. Therefore, this aptasensor has significant potential for commercialization and public use.
•Our protocol is customized by using the fluorescence quenching property of graphene oxide and specific binding property of human serum albumin aptamer to detect human serum albumin in urine sample
•The limit of detection of our developed platform is 0.05 µg.mL⁻¹
•The detection range of our aptasensor is 0.1–600 µg.mL
A fast and sensitive carcinoembryonic antigen (CEA) aptasensor with multiple detection modes was developed. It is based on hollow gold nanoparticles (HGNPs) and horse radish peroxidase (HRP) as both labels and signal amplification elements. In fabrication, capture DNA (cpDNA) was modified on magnetic beads, and reporter DNA (rpDNA) and HRP were co-modified on HGNPs. A combination DNA, containing a DNA aptamer (GAC-P) segment, hybridized with cpDNA and rpDNA, forming a satellite-structured biosensor. In response to CEA, the aptamer switches its structure, releasing rpDNA/HGNPs/HRP under magnetic separation. The surface plasmon resonance of HGNPs and the HRP enzyme activity of the supernatant were observed/detected with naked eyes, UV–vis spectroscopy, and electrochemistry techniques. The assay time is as short as ~45 min. CEA levels can be differentiated with naked eyes. The absorbance at 677 nm is linearly proportional to CEA concentration from 10 to 250 ng mL⁻¹, with a limit of detection (LOD) of 8.6 ng mL⁻¹. In contrast, the differential pulse voltammetry (DPV) peak current at -0.057 V is linearly correlated with CEA concentration in the range of 2−250 ng mL⁻¹, with an LOD of 0.78 ng mL⁻¹. The LOD values are lower than cancer patient threshold levels. The aptasensor exhibits negligible responses to interfering proteins. In addition, it displays good reproducibility, stability, accuracy and easiness of usage. The recovery rate for CEA spiked human serum samples are 100±5%. The developed assay strategy should provide a general platform for detecting other interested biomarkers.
We developed a new nanozyme-based electrochemical immunoassay method for the monitoring of glycated albumin (GA) known to reflect short-term glycaemic levels. For this study, we synthesized urchin-like Pt nanozymes (uPtNZs) and applied them to colorimetric and electrochemical assays for sensitive determination of GA in total human serum albumin (tHSA) using 3,3′,5,5′-tetramethylbenzidine (TMB) and thionine as substrates, respectively. The uPtNZs showed peroxidase-mimic activity in the presence of hydrogen peroxide. Boronic acid (BA)-agarose bead was used to capture GA through specific cis-diol interactions. uPtNZs were modified with GA antibody (GA-Ab) to form sandwich complexes with GA/BA-agarose bead. The amount of Ab-uPtNZ/GA/BA-agarose bead complex increased with increasing percentage of GA in 50 mg/mL tHSA. The colorimetric assay exhibited linearity from 0.02 to 10% (10 µg/mL – 5 mg/mL) GA with an LOD of 0.02% (9.2 µg/mL). For electrochemical assay, GA was detected from 0.01 to 20% (5 µg/mL – 10 mg/mL) with an LOD of 0.008% (3.8 µg/mL). The recovery values of measured GA in human plasma samples were from 106 to 107%. These results indicate that electrochemical assay using uPtNZs is a promising method for determining GA.
In this paper, we propose a new field effect (FE) sensor for fast detection of glycated albumin (GA) based on thiol modified aptamer (TMA). A p-type Si/ (100 nm) SiO2 wafer was used, where the SiO2 layer acts as the gate insulator. This gate insulator is then decorated with a layer of randomly oriented ZnO nanorods, coated with 40 nm of Au to act as binding sites for the TMA. We have shown that the addition of GA significantly reduces the conductivity of the p-type Si channel, which can be used to determine the GA concentration in the test solution. The ZnO/Au/TMA/GA layer can induce negative charges in the Si channel underneath the gate insulator, which is followed by the depletion of the positively charged carriers of the Si, decreasing the conductivity. Accordingly, the charge carriers in the Si channel show a steady decline with increasing GA concentration. We have shown that this decrease in conductivity can be further tuned by varying the gate voltage. The sensor presented here can be used as a fast and reliable sensor for determination of GA.
Due to the proliferative cancer rates, cardiovascular diseases, neurodegenerative disorders, autoimmune diseases and a plethora of infections across the globe, it is essential to introduce strategies that can rapidly and specifically detect the ultralow concentrations of relevant biomarkers, pathogens, toxins and pharmaceuticals in biological matrices. Considering these pathophysiologies, various research works have become necessary to fabricate biosensors for their early diagnosis and treatment, using nanomaterials like quantum dots (QDs). These nanomaterials effectively ameliorate the sensor performance with respect to their reproducibility, selectivity as well as sensitivity. In particular, graphene quantum dots (GQDs), which are ideally graphene fragments of nanometer size, constitute discrete features such as acting as attractive fluorophores and excellent electro-catalysts owing to their photo-stability, water-solubility, biocompatibility, non-toxicity and lucrativeness that make them favorable candidates for a wide range of novel biomedical applications. Herein, we reviewed about 300 biomedical studies reported over the last five years which entail the state of art as well as some pioneering ideas with respect to the prominent role of GQDs, especially in the development of optical, electrochemical and photoelectrochemical biosensors. Additionally, we outline the ideal properties of GQDs, their eclectic methods of synthesis, and the general principle behind several biosensing techniques.
Graphene quantum dots (GQDs) are carbon‐based, nanoscale particles that exhibit excellent chemical, physical, and biological properties that allow them to excel in a wide range of applications in nanomedicine. The unique electronic structure of GQDs confers functional attributes onto these nanomaterials such as strong and tunable photoluminescence for use in fluorescence bioimaging and biosensing, a high loading capacity of aromatic compounds for small‐molecule drug delivery, and the ability to absorb incident radiation for use in the cancer‐killing techniques of photothermal and photodynamic therapy. Recent advances in the development of GQDs as novel, multifunctional biomaterials are presented with a focus on their physicochemical, electronic, magnetic, and biological properties, along with a discussion of technical progress in the synthesis of GQDs. Progress toward the application of GQDs in bioimaging, biosensing, and therapy is reviewed, along with a discussion of the current limitations and future directions of this exciting material. Recent advancements in the development of graphene quantum dots (GQDs) in the field of nanomedicine are reviewed. Following an overview of the properties of GQDs, progress in top‐down and bottom‐up synthesis methods are presented. Application of GQDs in various modes of bioimaging, biosensing, and therapy are also discussed, with a subsequent discussion of future directions.
Lung cancer is the most frequently occurring malignancy and the leading cause of cancer-related death for men in our country. The only recommended screening method is clinic based low-dose computed tomography (also called a low-dose CT scan, or LDCT). However, the effect of LDCT on overall mortality observed in lung cancer patients is not statistically significant. Over-diagnosis, excessive cost, risks associated with radiation exposure, false positive results and delay in the commencement of the treatment procedure questions the use of LDCT as a reliable technique for population-based screening. Therefore, identification of minimal-invasive biomarkers able to detect malignancies at an early stage might be useful to reduce the disease burden. Circulating nucleic acids are emerging as important source of information for several chronic pathologies including lung cancer. Of these, circulating cell free miRNAs are reported to be closely associated with the clinical outcome of lung cancer patients. Smaller size, sequence homology between species, low concentration and stability are some of the major challenges involved in characterization and specific detection of miRNAs. To circumvent these problems, synthesis of a quantum dot based nano-biosensor might assist in sensitive, specific and cost-effective detection of differentially regulated miRNAs. The wide excitation and narrow emission spectra of these nanoparticles result in excellent fluorescent quantum yields with a broader color spectrum which make them ideal bio-entities for fluorescence resonance energy transfer (FRET) based detection for sequential or simultaneous study of multiple targets. In addition, photo-resistance and higher stability of these nanoparticles allows extensive exposure and offer state-of-the art sensitivity for miRNA targeting. A major obstacle for integrating QDs into clinical application is the QD-associated toxicity. However, the use of non-toxic shells along with surface modification not only overcomes the toxicity issues, but also increases the ability of QDs to quickly detect circulating cell free miRNAs in a non-invasive mode. The present review illustrates the importance of circulating miRNAs in lung cancer diagnosis and highlights the translational prospects of developing QD-based nano-biosensor for rapid early disease detection.
Gestational diabetes mellitus (GDM) is a common complication of pregnancy; its rising incidence is a result of increased maternal obesity and older maternal age together with altered diagnostic criteria identifying a greater proportion of pregnant women with GDM. Its consequences are far-reaching, associated with poorer maternal and neonatal outcomes compared to non-GDM pregnancies, and GDM has implications for metabolic health in both mother and offspring. Objective markers to identify women at high risk for the development of GDM are useful to target therapy and potentially prevent its development. Established clinical risk factors for GDM include overweight/obesity, age, ethnicity, and family history of diabetes, though they lack specificity for its development. The addition of biomarkers to predictive models of GDM may improve the ability to identify women at risk of GDM prior to its development. These biomarkers reflect the pathophysiologic mechanisms of GDM involving insulin resistance, chronic inflammation, and altered placental function. In addition, the role of epigenetic changes in GDM pathogenesis highlights the complex interplay between genetic and environmental factors, potentially offering further refinement of the prediction of GDM risk. In this review, we will discuss the clinical challenges associated with the diagnosis of GDM and its current pathophysiologic basis, giving rise to potential biomarkers that may aid in its identification. While not yet validated for clinical use, we explore the possible clinical role of biomarkers in the future. We also explore novel diagnostic tools, including high throughput methodologies, that may have potential future application in the identification of women with GDM.
Glycated Albumin (GA) has been reported as an important biomarker for diabetes mellitus. This study investigates an optical sensor comprised of deoxyribonucleic acid (DNA) aptamer, semiconductor quantum dot and gold (Au) nanoparticle for the detection of GA. The system functions as a 'turn on' sensor because an increase in photoluminescence intensity is observed upon the addition of glycated albumin to the sensor. This is possibly because of the structure of the DNA aptamer, which folds to form a large hairpin loop before the addition of the analyte and is assumed to open up after the addition of target to the sensor in order to bind to GA. This pushes the quantum dot and the Au nanoparticle away causing an increase in photoluminescence. A linear increase in photoluminescence intensity and quenching efficiency of the sensor is observed as the GA concentration is varied between 0 nM to 14500 nM. Time based photoluminescence studies show the decrease in binding rate of the aptamer to the target within a specific time period. The sensor was found to have a higher selectivity towards GA than other control proteins. Further investigation of this simple sensor can open up avenues for an efficient diagnosis and monitoring of diabetes mellitus when used in conjunction with the traditional method of glucose level monitoring.
In the diagnosis of diabetes mellitus, hemoglobin A1c (HbA1c) is sometimes measured to determine the need of an oral glucose tolerance test (OGTT). However, HbA1c does not accurately reflect glycemic status in certain conditions. This study was performed to test the possibility that measurement of serum glycated albumin (GA) better assesses the need for OGTT. From 2006 to 2012, 1559 subjects not known to have diabetes or to use anti-diabetic medications were enrolled. Serum GA was measured, and a 75-g OGTT was then performed to diagnose diabetes. Serum GA correlated significantly to age (r = 0.27, p<0.001), serum albumin (r = -0.1179, age-adjusted p = 0.001), body mass index (r = -0.24, age-adjusted p<0.001), waist circumference (r = -0.16, age-adjusted p<0.001), and plasma GA (r = 0.999, p<0.001), but was unaffected by diet (p = 0.8). Using serum GA at 15% for diagnosis of diabetes, the sensitivity, specificity, and area under the receiver-operating characteristic curve were 74%, 85%, and 0.86, respectively. Applying a fasting plasma glucose (FPG) value of < 100 mg/dL to exclude diabetes and of ≥ 126 mg/dL to diagnose diabetes, 14.4% of the study population require an OGTT (OGTT%) with a sensitivity of 78.8% and a specificity of 100%. When serum GA value of 14% and 17% were used to exclude and diagnose diabetes, respectively, the sensitivity improved to 83.3%, with a slightly decrease in specificity (98.2%), but a significant increase in OGTT% (35%). Using combined FPG and serum GA cutoff values (FPG < 100 mg/dL plus serum GA < 15% to exclude diabetes and FPG ≥ 126 mg/dL or serum GA ≥ 17% to diagnose diabetes), the OGTT% was reduced to 22.5% and the sensitivity increased to 85.6% with no change in specificity (98.2%). In the diagnosis of diabetes, serum GA measurements can be used to determine the need of an OGTT.
Introduction:
The molecular mechanics energies combined with the Poisson-Boltzmann or generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods are popular approaches to estimate the free energy of the binding of small ligands to biological macromolecules. They are typically based on molecular dynamics simulations of the receptor-ligand complex and are therefore intermediate in both accuracy and computational effort between empirical scoring and strict alchemical perturbation methods. They have been applied to a large number of systems with varying success.
Areas covered:
The authors review the use of MM/PBSA and MM/GBSA methods to calculate ligand-binding affinities, with an emphasis on calibration, testing and validation, as well as attempts to improve the methods, rather than on specific applications.
Expert opinion:
MM/PBSA and MM/GBSA are attractive approaches owing to their modular nature and that they do not require calculations on a training set. They have been used successfully to reproduce and rationalize experimental findings and to improve the results of virtual screening and docking. However, they contain several crude and questionable approximations, for example, the lack of conformational entropy and information about the number and free energy of water molecules in the binding site. Moreover, there are many variants of the method and their performance varies strongly with the tested system. Likewise, most attempts to ameliorate the methods with more accurate approaches, for example, quantum-mechanical calculations, polarizable force fields or improved solvation have deteriorated the results.
Glucose reacts with proteins nonenzymatically under physiological conditions. Such glycation is exacerbated in diabetic patients
with high levels of blood sugar and induces various complications. Human albumin serum (HSA) is the most abundant protein
in plasma and is glycated by glucose. The glycation sites on HSA remain controversial among different studies. Here, we report
two protein crystal structures of HSA in complex with either glucose or fructose. These crystal structures reveal the presence
of linear forms of sugar for both monosaccharides. The linear form of glucose forms a covalent bond to Lys-195 of HSA, but
this is not the case for fructose. Based on these structures, we propose a mechanism for glucose ring opening involving both
residues Lys-195 and Lys-199. These results provide mechanistic insights to understand the glucose ring-opening reaction and
the glycation of proteins by monosaccharides.
Non-enzymatic glycosylation or glycation involves covalent attachment of reducing sugar residues to proteins without enzyme participation. Glycation of glucose to human serum albumin in vivo is related to diabetes and many other diseases. We present an approach using liquid chromatography coupled to an electrospray ionization source of a hybrid ion trap-time of flight (IT-TOF-MS/MS) tandem mass spectrometer to identify the glycation sites on serum albumin from both a healthy person and a diabetic patient. The MetID software, which is commonly used for screening metabolites, is adapted for peptide fingerprinting based on both m/z values and isotopic distribution profiles. A total of 21 glycation sites from the healthy person and 16 glycation sites from the diabetic patient were identified successfully. We also demonstrate the use of matrix assisted laser desorption ionization-time of flight mass spectrometry to estimate the incorporation ratio of glucose to albumin during glycation. Results from this study show that the glycation in healthy person is more complicated than previously thought. Further analysis of incorporation ratio distribution may be necessary to accurately reflect the change of serum albumin glycation in diabetic patients.
Human serum albumin (HSA) is a protein carrier in blood transporting metabolites and drugs. Glycated HSA (GHSA) acts as a potential biomarker for diabetes. Thus, many attempts have been made to detect GHSA. Glycation was reported to damage the structure and ligand binding capability, where no molecular detail is available. Recently, the crystal structure of GHSA has been solved, where two glucose isomers (pyranose/GLC and open-chain/GLO) are located at Sudlow's site I. GLO was found to covalently bind to K195, while GLC is trapped by noncontact interactions. GHSA exists in two forms (Schiff base (SCH) and Amadori (AMA) adducts), but how both disrupt albumin activity microscopically remains unknown. To this end, molecular dynamics simulations were performed here to explore the nature of SCH and AMA. Both forms are found to alter the main protein dynamics, resulting in (i) the widening of Sudlow's site I entrance, (ii) the size reduction of nine fatty acid-binding pockets, (iii) the enlargement of Sudlow's site I and the shrinking of Sudlow's site II, (iv) the enhancement of C34 reactivity, and (v) the change in the W214 microenvironment. These unique characteristics found here can be useful for understanding the effect of glycation on the albumin function in more detail and designing specific and selective GHSA detection strategies.
Human serum albumin (HSA) is a blood protein serving as a carrier for a wide range of drugs and nutrients. A level of glycated HSA (GHSA) is used as a diabetes biomarker. A graphene-based aptasensor is one of potential techniques to detect GHSA. Not only the interactions of albumin and aptamer, but the albumin-graphene (GRA) binding mechanism are also crucial for developing a diabetes aptasensor. In this work, Molecular Dynamics simulations (MD) were employed to explore the binding of GRA to both GHSA and HSA. The GRA binding from the back and front sides of an albumin are fast and spontaneous. The multiple GRA binding sites are identified. GRA causes more denaturation of helical characteristics in GHSA (∼12% reduction of helical structure). Both back and front GRA adhesions generate comparable degrees of helical unfolding. Importantly, the presence of bound GRA induces the release of glucose from drug sites implying the loss of ligand-binding affinity. This loss of drug site activity is independent on the GRA binding positions because all bound positions lead to the exit of sugars. The GRA binding deconstructs not only secondary structure, but also albumin function. Apparently, GRA is a non-biocompatible material for albumin. To construct a potential graphene-based aptasensor to detect GHSA, it is necessary to be certain that no free GRA surface is available because a bare GRA can bind and denature both HSA and GHSA which can cause misleading data.
Aims
Glycated albumin (GA) is a biomarker for short-term (2–3 weeks) glycemic control. However, the predictive utility of GA for diabetes and prediabetes is largely uncharacterized. We aimed to investigate the relationships of baseline serum GA levels with incident diabetes and prediabetes.
Methods
This was a longitudinal cohort study involving 516 subjects without diabetes or prediabetes at baseline. Blood glucose levels were observed during follow-up. Hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated using COX proportional hazard models. Receiver operating characteristic curves and areas under the curves (AUCs) were used to evaluate the discriminating abilities of glycemic biomarkers and prediction models.
Results
During a 9-year follow-up, 51 individuals (9.88%) developed diabetes and 92 (17.83%) prediabetes. Unadjusted HRs (95% CI) for both diabetes and prediabetes increased proportionally with increasing GA levels in a dose-response manner. Multivariable-adjusted HRs (95% CI) for diabetes were significantly elevated from 1.0 (reference) to 5.58 (1.86–16.74). However, the trend was no longer significant for prediabetes after multivariable adjustment. AUCs for GA, fasting blood glucose (FBG), and 2-h postprandial blood glucose (2h-PBG) for predicting diabetes were 0.698, 0.655, and 0.725, respectively. The AUCs for GA had no significant differences compared with those for FBG (P=0.376) and 2h-PBG (P=0.552). Replacing FBG or 2h-PBG or both with GA in diabetes prediction models made no significant changes to the AUCs of the models.
Conclusions
GA is of good prognostic utility in predicting diabetes. However, GA may not be a useful biomarker for predicting prediabetes.
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Monitoring of glycated human serum albumin (GHSA) as a glycemic marker for screening and monitoring of diabetes mellitus is widely practiced for patients with conditions that affect red blood cells. In this study, a complex comprising Pb ions adsorbed on graphene oxide (GO-Pb) was fabricated and utilized as a versatile probe in a fluorescence-electrochemical aptasensor for GHSA quantification. To simplify the aptasensor, the GO-Pb complex probe was prepared via an ion adsorption process. After modification with a fluorophore-labeled aptamer, the GO-Pb complex served as an excellent energy acceptor in fluorescence-based analysis, as well as generating a high current in the electrochemical transducer. Additionally, the proposed platform can detect GHSA via the dual technique from a single sample, allowing for precise and accurate results. Under optimal conditions, the fluorescence-electrochemical aptasensor exhibited a linear relationship with GHSA concentrations from 0.001 to 80 μg mL-1 and from 0.005 to 10 μg mL-1 for fluorescence and electrochemical detection, respectively. The corresponding detection limits were 8.80 ng mL-1 and 0.77 ng mL-1, respectively. The proposed aptasensor additionally displayed good selectivity and excellent stability. Moreover, its successful application in the analysis of clinical samples further demonstrated its utility. Therefore, the proposed platform has significant potential as a novel, facile, highly responsive, and low-cost monitoring method for the development of diabetes mellitus diagnostic devices intended for a clinical setting.
Increasing manufacturing and use of nanoparticles in industrial and biomedical applications creates the necessity to understand the impact of the interaction of nanoparticles with biomacromolecules. In the present study, graphene oxide nanosheets (GONS) were synthesized using modified Hummer’s method and further characterized employing X-ray diffraction (XRD), UV, FTIR, and Raman spectroscopy. After characterization, the interaction of GONS with human serum albumin (HSA) was investigated to delineate the binding mechanism employing different kinds of spectroscopic techniques. Intrinsic fluorescence spectroscopy revealed that complex formation is taking place between HSA and GONS. Fluorescence-based binding studies suggested that GONS binds to HSA with a significant binding affinity, and the interaction is governed by dynamic quenching. The evaluation of enthalpy change (ΔH) and entropy change (ΔS) suggested that the HSA-GONS complex formation is driven by hydrogen bonding and van der Waals interaction and hence complexation process is seemingly specific. Structural transition in the microenvironment of HSA was monitored using synchronous fluorescence spectroscopy and three-dimensional fluorescence spectroscopy, which showed that GONS binding to HSA influences the microenvironment around tyrosine and tryptophan residues. Secondary structural alterations in HSA upon binding to GONS were measured using circular dichroism (CD) spectroscopy. Additionally, molecular docking provided an insight into the critical residues involved in HSA-GONS interaction and further validated our in vitro observations affirming strong interaction between GONS and HSA. The significance of this study is attributable to the fact that HSA and GONS can be used as nanocarriers in drug delivery systems.
Serum albumin (SA) is the most abundant carrier protein in blood. SA carries a diverse range of nutrients, drugs, and metal ions. It has wide clinical and biochemical applications. Human serum albumin (HSA) can be used as a biomarker for kidney and liver diseases. Aptasensor is one of potential HSA detection methods. HSA‐specific aptamer was selected for HSA detection. In animals, bovine serum albumin (BSA) and canine serum albumins (CSA) share high sequence similarities to HSA. Thus, it is interesting to explore the possibility of using HSA‐selective aptamer for BSA and CSA aptasensor. In this study, molecular dynamics (MD) simulations were initially employed to investigate the binding of aptamer to BSA and CSA in comparison to HSA. Like HSA, both BSA and CSA can bind aptamer, but different binding affinities are observed. BSA shows the tighter binding to aptamer than CSA. Domain III is found to be the aptamer‐binding domain although no specific aptamer conformation is captured. However, in all cases, the aptamer utilizes the 3′‐end to attach on an albumin surface. Both nucleobases and phosphate backbones on a DNA aptamer are important for albumin‐aptamer complexation. Our results imply the possibility of using HSA‐specific aptamer for BSA detection due to tighter binding observed, but may be less effective in CSA. However, the test in actual complicated condition must be further studied.
Abstract
Diabetes mellitus is one of the most common chronic diseases worldwide. Generally, the levels of fasting or postprandial blood glucose and other biomarkers, such as glycated albumin, glycated hemoglobin, and 1,5-anhydroglucitol, are used to diagnose or monitor diabetes progression. In the present study, we developed a sensor to simultaneously detect the glucose levels and glycation ratios of human serum albumin using a lateral flow assay. Based on the specific enzymatic reactions and immunoassays, a spiked glucose solution, total human serum albumin, and glycated albumin were measured simultaneously. To test the performance of developed sensor, clinical serum samples from healthy subjects and patients with diabetes were analyzed. The glucose level and glycation ratios of the clinical samples were determined with reasonable correlation. The R-square values of glucose level and glycation ratio measurements were 0.932 and 0.930, respectively. The average detection recoveries of the sensor were 85.80% for glucose and 98.32% for the glycation ratio. The glucose level and glycation ratio in our results were crosschecked with reference diagnostic values of diabetes. Based on the outcomes of the present study, we propose that this novel platform can be utilized for the simultaneous detection of glucose and glycation ratios to diagnose and monitor diabetes mellitus.
Serum albumin (SA) is the most abundant protein in blood. SA carries a diverse range of nutrients and drugs. It has wide clinical and biochemical applications. Especially, administering human serum albumin (HSA) can increase albumin level and blood pressure in ill dogs and humans. Nonetheless, the use of HSA therapy is still controversial. Using albumin from other species is one of alternatives. Bovine serum albumin (BSA) is a homolog of HSA, but it shows different dynamics. Thus, understanding albumin properties from other species becomes crucial. Recently, the first crystal structure of canine serum albumin (CSA) has been solved. We thus employed Molecular Dynamics (MD) simulations to reveal structural and dynamic properties of CSA and BSA in comparison with HSA. The results indicate the motion of domains I and III is the key to define albumin characteristics. Among all, CSA is the most flexible. BSA and HSA are more alike in term of ligand-binding affinity. Many ligand-binding studies succeeded to employ BSA as a HSA substitute due to similar size and environment of binding pockets, however replacing HSA by BSA may fail in a dynamics-related process because of the more rigid BSA. For CSA, its properties deviate from BSA and HSA. CSA shows more flexibility and has larger and more water-exposed drug sites. Moreover, C34 on CSA is more reactive than that of BSA and HSA owing to more flexible side chain. An insight obtained can serve as a guideline for a future use of alternative albumins in clinical practice.
Albuminuria is a pathological condition wherein the human serum albumin (HSA) protein is present in abnormally excess amounts in the urine. A simple and sensitive graphene oxide-mediated fluorescence quenching aptasensor is developed to quantify albumin in urine samples and HSA in serum samples. The aptamer-bound HSA used in this aptasensor has hairpin structures, which are characteristic of the aptamer binding site. The limit of detection of the developed platform is 0.05 μg·mL-1 and the detection range is 0.1-14.0 μg·mL-1, which covers the albuminuria concentration range present in normal human urine and the urine of the patient with kidney diseases. This approach can be modified to measure HSA using a high-throughput quantification platform and portable point of care testing. In addition, the production cost for one reaction is cheaper than those for other standard automated methods. Therefore, this aptasensor has significant potential for commercialization and wide-scale public use.
Glycated albumin synthesized in a non-enzymatic reaction with high glucose levels in human plasma is a long-term biomarker for understanding average glucose levels over the past few weeks. Glycated albumin level determination requires an enzymatic assay involving an expensive, complicated, and laborious process, including the specific hydrolysis of albumin and the oxidation of glycated amino acids. In this study, we developed two advanced lateral flow immunoassays (LFIAs) for the simultaneous determination of total human serum albumin and glycated albumin concentrations using a colorimetric signal. Additionally, through a sequential reaction on our advanced LFIA, the selectivity of glycated albumin was improved. We quantified both HSA and GA with wide detection ranges of 1 ng/mL–1 mg/mL and 0.5 μg/mL–3.6 mg/mL, respectively. Various serum samples with different glycation ratios were analyzed using this sensor and demonstrated a reasonable recovery range. This indicated that our platform could directly determinate the glycation ratio of various samples, and therefore, be applicable in point-of-care glucose status monitoring.
Carbon-based nanomaterials have established a prime position as drug delivery carriers. It is very interesting to see that a carbon nanostructure could be used as a drug too, instead of its regular application as a drug delivery carrier. In this aspect, graphene quantum dots (GQDs) are now in the spotlight. GQDs are one of the recent entrants to the list of carbon-based nanomaterials. They are now reported useful in Parkinson's and Alzheimer's diseases. Furthermore, antibacterial and anti-diabetic potentials of GQDs are now known. In addition, they are now widely evaluated for drug delivery application. They have good potential for drug delivery across the blood-brain barrier. Tumor-targeted drug delivery is also possible with GQDs. Their biosensing and bioimaging applications are also under extensive study. In this review, the therapeutic, drug delivery, biosensing and bioimaging applications of GQDs are described. It would be very interesting to speculate the future of GQDs and how this carbon nanomaterial influences the future of nanobiomedicine. It is presumed that drug-GQD duo would be the next generation strategy for many unresolved therapeutic hurdles.
Glycated albumin (GHSA) is a medium‐term glycaemic control marker of diabetes, which can be used as an alternative to or together with glycated haemoglobin (HbA1c). Currently available methods for the measurement of GHSA are limited in clinical practice because they involve slow and cumbersome processes of sample preparation, proteolytic digestion, and thermal incubation, and they suffer from limited analytical performance, and/or a lack of normalization to total albumin (HSA) levels. In this paper, we developed a simple electrochemical biosensor to measure GHSA values based on two DNA aptamers that specifically bind to GHSA and HSA. We used square wave voltammetry (SWV) to measure binding of the target proteins to their specific biotinylated aptamers, which had been immobilised on separate streptavidin (STR)‐modified screen‐printed carbon electrodes (SPCEs), in the presence of the redox mediator ferricyanide (Fe(CN)63−). This electrochemical aptasensing system had a detection limit of 3 ng/ml for GHSA and 0.2 μg/ml for HSA. The results exhibited high selectivity for GHSA over other molecules present in the blood. The developed sensor was able to measure the amount of GHSA in plasma samples. A statistically significant difference was observed in the elevated plasma GHSA levels in diabetic versus non‐diabetic patients. Moreover, the trends in these GHSA levels were consistent with those obtained using the HbA1c test. The sensing system reported herein could be applied as a point‐of‐care‐testing (POCT) device for measurements of clinically relevant GHSA values.
The influence of solution chemistry on the adsorption of human serum albumin (HSA) proteins on graphene oxide (GO) was investigated through batch adsorption experiments and the use of a quartz crystal microbalance with dissipation (QCM-D). The conformation of HSA layers on GO was also examined with the QCM-D. Our results show that an increase in ionic strength under neutral pH conditions resulted in stronger binding between HSA and GO, as well as more compact HSA layers on GO, emphasizing the key role of electrostatic interactions in controlling HSA-GO interactions. Calcium ions also facilitated HSA adsorption likely through charge neutralization and bridging effect. At physiological ionic strength conditions (150 mM), maximum HSA adsorption was observed at the isoelectric point of HSA (4.7). Under acidic conditions, the adsorption of HSA on GO led to the formation of protein layers with a high degree of fluidity due to the extended conformation of HSA. Finally, the attachment of GO to a supported lipid bilayer that was composed of zwitterionic 1,2-dioleoyl-sn-glycero-3-phosphocholine, a model for cell membranes, was reduced in the presence of protein coronas. This reduction in GO attachment was influenced by the conformation of the protein coronas on GO.
A number of factors determine HbA1c other than the level of glucose exposure alone (1). In analysis of 941 diabetic persons with varying degrees of chronic kidney disease (CKD), and 724 not having CKD, from a subset of the Atherosclerosis Risk in Communities studywith mean age in the eighth decade, Jung and coworkers ask whether HbA1c is reliable as an indicator of glycemia in persons with kidney disease (CKD) to the same degree as in those not having kidney disease, andif not whether measures of glycated serum proteins might be more useful. The only available measure of glycemia for comparison was a single fasting glucose level, and the authors acknowledge that this gives an incomplete measure, particularly in persons with relatively mild diabetes, whose mean HbA1c was 6.4%, with the majority having levels of 7.5% or lower.
Human serum albumin (HSA) is the most abundant transport protein found in human blood. HSA is known to bind a wide range of drugs and monosaccharides, but where and how these molecules bind have been largely unknown. Recently, a crystal structure of glycated HSA has been obtained, and interestingly, found two glucose in pyranose (GLC) and open chain forms (GLO) bound in the same binding pocket (Sudlow site I). Molecular simulations also proposed two binding modes of GLC and GLO (either binding two ligands distantly or in close contact). Yet, how HSA binds sugars in general are poorly understood. To this end, here we study the mechanism for binding the glucose and its epimer galactose to HSA from alchemical free energy perturbation and molecular dynamics simulations to reveal why two sugar molecules appear in the bound state. We find that HSA does prefer glucose over galactose, in line with experiments, by binding glucose deeper in the pocket. Furthermore, out of the two possible binding modes suggested previously in molecular dynamics simulations, the binding of sugar to HSA becomes tighter when the two sugars are in contact; this is achieved by a hydrogen bond connecting the two sugars, and filling the large cavity of Sudlow site I as a dimer. We also find tight hydrogen bonds between the open chain glucose/galactose and HSA, which includes the possible glycation site K199, while the pyranose form does not strongly interact with any characteristic residue. Thus the current result highlights the importance of glucose/galactose to form a dimer in order to bind to HSA and possibly cause glycation/galactation.
Graphene quantum dots (GQDs) have gained significant interest in recent years due to their potential for biomedical applications, owing to their distinctive and tunable photoluminescence properties, remarkable physicochemical properties, high photostability, good biocompatibility, and small size. This article aims to explain the state-of-the-art outcomes in this rapidly evolving field and to deliver critical insights which will lead to further progress. In this article, the latest developments on synthesis, functionalization, key features, and cytotoxicity of GQDs have been presented followed by providing a focused overview on their current biological applications. Challenges and prospects in the developments of GQDs for biological applications are also discussed.
We selected and modified DNA aptamers specifically bound glycated human serum albumin (GHSA), which is an intermediate marker for diabetes mellitus. Our aptamer truncation study indicated that the hairpin-loop structure with 23 nucleotides length containing triple G-C hairpins and 15-nucleotide loop, plays an important role in GHSA binding. Fluorescent quenching graphene oxide (GO) and Cy5-labeled G8 aptamer were used in this study to develop simple and sensitive graphene based aptasensor for GHSA detection. The limit of detection (LOD) of our aptasensor was 50 μg/mL, which was lower than other existing methods. In addition, with the nuclease resistance system, our GHSA detection platform could also be used in clinical samples. Importantly, our approach could significantly reveal the higher levels of GHSA concentrations in diabetes than normal serums. These indicate that our aptasensor has a potential for diagnosis and monitoring of diabetes mellitus.
Molecular dynamics (MD) simulations are performed to investigate the adsorption mechanics and conformational dynamics of single and multiple bovine serum albumin (BSA) peptide segments on single-layer graphene through analysis of parameters such as the root-mean-square displacements, number of hydrogen bonds, helical content, interaction energies, and motions of mass center of the peptides. It is found that for the single segment system, destabilization of the helical structures in the form of the reduction in hydrogen bond numbers and α-helical content of the peptides occurred due to the strong interactions between BSA peptides and graphene. Similar destabilizations of the individual segments in the multi-segment system can occur as well, albeit with greater complexity and in a lesser degree due to the inter-segment interactions. Alleviation of decreases in the total helical content in the multi-segment system indicates protective capabilities of segment–segment interactions, which weaken their interactions with graphene. Diffusive motion upon adsorption of the segment(s) onto graphene is found to be highly confined, and the distance traversed by each segment in the multi-segment system was more significant than that in the single segment system, similarly attributable to reductions in their interactions with graphene due to inter-segment interactions.
Human serum albumin (HSA) is the most abundant protein found in blood serum. It carries essential metabolites and many drugs. The glycation of HSA causes abnormal biological effects. Importantly, glycated HSA (GHSA) is of interest as a biomarker for diabetes. Recently, the first HSA structure with bound pyranose (GLC) and open-chain (GLO) glucose at Sudlow site I has been crystallised. We therefore employed Molecular dynamics (MD) simulations and ONIOM calculations to study the dynamic nature of 2 bound glucose in a pre-glycated HSA (pGHSA) and observe how those sugars alter a protein structure comparing to wild type (Apo) and fatty acid-bound HSA (FA). Our analyses show that the overall structural stability of pGHSA is similar to Apo and FA, except Sudlow site II. Having glucose induces large protein flexibility at Sudlow site II. Besides, the presence of glucose causes W214 to reorient resulting in a change in W214 microenvironment. Considering sugars, both sugars are exposed to water, but GLO is more solvent-accessible. ONIOM results show that glucose binding is favoured for HSA (-115.04 kcal/mol) and GLO (-85.10 kcal/mol) is more preferable for Sudlow site I over GLC (-29.94 kcal/mol). GLO can strongly react with K195 and K199, whereas K195 and K199 provide slightly repulsive forces for GLC. This can confirm that an open-chain GLO is more favourable inside a pocket.
Diabetes is a major problem in the world. The proteins became modified during glycation after reacting with the reducing sugars (e.g. D-glucose) via non-enzymatic pathways. The glycated analogue of human serum albumin (HSA) has been characterized with the help of multi-spectroscopic methods. It has been observed that six glucose molecules can bind covalently to HSA under experimental condition. The binding affinity of the modified HSA towards the dietary polyphenols has been estimated using UV-vis and fluorescence spectroscopic techniques. The binding constant values of the ligands were found to decrease after the modification of HSA.
A novel biosensor platform was developed for detection of microRNAs (miRNAs) based on graphene quantum dots (GQDs) and pyrene-functionalized molecular beacon probes (py-MBs). Pyrene was introduced to trigger specifically fluorescence resonance energy transfer (FRET) between GQDs and fluorescent dyes labeled on py-MBs, and the unique fluorescent intensity change produced a novel signal for detection of the target. The platform realized detection of miRNAs in a wide range from 0.1 nM to 200 nM with great discrimination abilities, as well as multidetection of different kinds of miRNAs, which paved a brand new way for miRNA detection based on GQDs.
Human serum albumin (HSA) is chosen to investigate the interaction of graphene oxide-based nanosheets (GONS) with plasma proteins in terms of binding affinity, action mechanism, conformational change and function loss. We show that GONS inhibit HSA function via two routes: blocking protein active sites, or destroying protein structure.
Molecular Mechanics – Poisson Boltzmann Surface Area (MM-PBSA), a method to estimate interaction free energies, has been increasingly used in the study of bio-molecular interactions. Recently, this method has also been applied as a scoring function in computational drug design. Here a new tool g_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GROMACS and APBS packages is described. g_mmpbsa was developed as part of the Open Source Drug Discovery (OSDD) consortium. Its aim is to integrate high-throughput MD simulations with binding energy calculations. The tool provides options to select alternative atomic radii and different non-polar solvation models including models based on the solvent accessible surface area (SASA), solvent accessible volume (SAV) and a model which contains both repulsive (SASA-SAV) and attractive components (described using a Weeks-Chandler-Andersen like integral method). We showcase the effectiveness of the tool by comparing the calculated interaction energy of 37 structurally diverse HIV-1 protease inhibitor complexes with their experimental binding free energies. The effect of varying several combinations of input parameters such as atomic radii, dielectric constant, grid resolution, solute-solvent dielectric boundary definition and non-polar models was investigated. g_mmpbsa can also be used to estimate the energy contribution per residue to the binding energy. It has been used to identify those residues in HIV-1 protease that are most critical for binding a range of inhibitors.
We examined the association of serum albumin concentration with diabetes mellitus and other cardiovascular risk factors, prevalent cardiovascular disease, and ultrasonographically assessed carotid artery intima-media thickness using data from 45- to 64-year-old adults in the Atherosclerosis Risk in Communities (ARIC) Study. The mean albumin concentration was 0.04 to 0.12 g/L lower in participants with diabetes and 0.02 to 0.06 g/L lower in those with cardiovascular disease, compared to participants without these conditions. However, lower serum albumin level was also correlated with most traditional risk factors and hemostatic variables. On adjustment for these, there was essentially no association between serum albumin and prevalent cardiovascular disease. Likewise, there was no association between albumin and carotid intima-media thickness (a marker of atherosclerosis). While hypoalbuminemia may be a marker for chronic disease and perhaps renal loss of albumin, it seems unlikely that it is an important cause of atherosclerosis.
An N·log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems. The Journal of Chemical Physics is copyrighted by The American Institute of Physics.
In patients with diabetes, atherosclerosis is the main reason for impaired life expectancy, and diabetic nephropathy and retinopathy are the largest contributors to end-stage renal disease and blindness, respectively. An improved therapeutic approach to combat diabetic vascular complications might include blocking mechanisms of injury as well as promoting protective or regenerating factors, for example by enhancing the action of insulin-regulated genes in endothelial cells, promoting gene programs leading to induction of antioxidant or anti-inflammatory factors, or improving the sensitivity to vascular cell survival factors. Such strategies could help prevent complications despite suboptimal metabolic control.