Comparative studies of structure and dynamics of caprine, leporine, ovine, and equine serum albumins.

Serum albumin (SA) is the most prevalent protein found in blood. Human albumin was used as an albumin substitute in hypoalbuminemia pets due to high sequence similarity. SAs from furry animals were also reported to be the major indoor allergens. Sensitizing to one of SAs coupled with high sequence identity can lead to cross-reactive antibodies in allergic individuals. Thus, understanding the structural and dynamic characters of SAs is crucial for not only albumin substitution but also allergen therapy. Herein, Molecular dynamics (MD) simulations were performed to elucidate the structural and dynamic dissimilarity and similarity of economic animals [equine (ESA), caprine (CASA), ovine (OSA), and leporine (LSA)] to albumins from human (HSA), bovine (BSA), porcine (PSA), and pets [cat (FSA) and dog (CSA)]. The aim is to explore the feasibility of HSA substitution and understand how albumins cause the cross-reactivity. Generally, all albumins studied here show the scissoring motion like other mammalian albumins. The uniqueness of each albumin is defined by different sequence identity of domain I. Also, the drug binding affinity of studied albumins differs from HSA, CSA, FSA, BSA, and PSA. Especially, LSA displays the most deviated behavior from the group. So, such albumin may not be suitable for albumin therapy for pets and humans. CASA, OSA, and ESA share similar characteristics, therefore it is possible to use them to monitor the osmotic pressure among their species, but the allergenic response must be seriously considered. An insight obtained here can be useful to develop albumin therapy and understand clinical allergy.Communicated by Ramaswamy H. Sarma.

Molecular dynamics simulations of human α-defensin 5 (HD5) crossing gram-negative bacterial membrane.

Human α-defensin 5 (HD5) is a cationic antimicrobial peptide exhibiting a wide range of antimicrobial activities. It plays an important role in mucosal immunity of the small intestine. HD5 exerts its bactericidal activities through multiple mechanisms, one of which involves HD5 inducing the formation of pores in the bacterial membrane, subsequently allowing the peptide to enter the bacterial cytoplasm. Nevertheless, the precise molecular intricacies underlying its bactericidal mechanisms remain inadequately understood. In this work, the Potential of Mean Force (PMF) was computed to delve into the energetic properties governing the movement of HD5 across the lipopolysaccharide (LPS) membrane, which is a representative model of the gram-negative bacterial membrane. Our findings indicate that the most favorable free energy is attained when HD5 binds to the surface of the LPS membrane. This favorable interaction is primarily driven by the strong interactions between arginine residues in HD5 and the charged head groups of LPS, serving as the predominant forces facilitating the adhesion of HD5 to the membrane. Our analysis reveals that a dimeric form of HD5 alone is sufficient to create a water-filled channel in the membrane; however, achieving the complete lysis of the gram-negative bacterial membrane requires higher-order oligomerization of HD5. Our results suggest that HD5 employs the toroidal pore formation mechanism to disrupt the integrity of the LPS membrane. Furthermore, we identified that the primary energy barrier obstructing HD5 from traversing the membrane is localized within the hydrophobic core of the membrane, which is also observed for other defensins. Additionally, our study demonstrates that a mixture of HD5-LPS leads to a thinning of the membrane. Taken together, this work provides a deeper insight into the molecular intricacies governing the behavior of HD5 as it translocates through the gram-negative bacterial membrane.

Binding Modes of Carnostatine, Homocarnosine, and Ophidine to Human Carnosinase 1.

Carnosine (CAR), anserine (ANS), homocarnosine (H-CAR), and ophidine (OPH) are histidine-containing dipeptides that show a wide range of therapeutic properties. With their potential physiological effects, these bioactive dipeptides are considered as bioactive food components. However, such dipeptides display low stability due to their rapid degradation by human serum carnosinase 1 (CN1). A dimeric CN1 hydrolyzes such histidine-containing compounds with different degrees of reactivities. A selective CN inhibitor, carnostatine (CARN), was reported to effectively inhibit CN's activity. To date, the binding mechanisms of CAR and ANS have been recently reported, while no clear information about H-CAR, OPH, and CARN binding is available. Thus, in this work, molecular dynamics simulations were employed to elucidate the binding mechanism of H-CAR, OPH, and CARN. Among all, the amine end and imidazole ring are the main players for trapping all of the ligands in a pocket. OPH shows the poorest binding affinity, while CARN displays the tightest binding. Such firm binding is due to the longer amine chain and the additional hydroxyl (-OH) group of CARN. H-CAR and CARN are analogous, but the absence of the -OH moiety in H-CAR significantly enhances its mobility, resulting in the reduction in binding affinity. For OPH which is an ANS analogue, the methylated imidazole ring destroys the OPH-CN1 interaction network at this region, consequentially leading to the poor binding ability. An insight into how CN recognizes and binds its substrates obtained here will be useful for designing an effective strategy to prolong the lifetime of CAR and its analogues after ingestion.

Structural and dynamic properties of urinary human serum albumin fragments: a molecular dynamics study.

A microalbuminuria level acts as a good index to screen and monitor diabetes and renal failure. However, the urinary albumin loss after sample preservation and storage is the major bottleneck to obtain the accurate microalbuminuria test. Such loss is due to the rapid albumin fragmentation by urinary proteases. Some fragments were suggested to be bioactive biomarkers of diabetes and renal disease, but no structural and dynamical properties of albumin fragments are available. Thus, in this work, the structural and dynamical properties of reported albumin fragments are revealed using molecular dynamics simulations. The properties of nine fragments (F1-F9) discovered recently were studied at the real pH conditions of urine samples (pH 4.5, 7 and 8). The complete loss of secondary structure is found in short fragments (F1-F6), while large-sized polypeptides (F7-F9) can somehow maintain their folds. Especially, F8 (subdomain IIIB) is the most stable fragment. The difference in histidine protonation states has no impact on the structural stability of albumin fragments. The ability of F8 (subdomain IIIB) to maintain its stability and folds suggests it as an alternative albumin biomarker in urine. An insight obtained here will become the fundamental importance for understanding clinical assays for albumin detection, sample stability and peptidomics analysis of urine.Communicated by Ramaswamy H. Sarma.

Binding of Apo and Glycated Human Serum Albumins to an Albumin-Selective Aptamer-Bound Graphene Quantum Dot Complex.

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.

Structural and Dynamic Alteration of Glycated Human Serum Albumin in Schiff Base and Amadori Adducts: A Molecular Simulation Study.

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.

Exploring the structural and dynamic differences between human carnosinase I (CN1) and II (CN2).

Human carnosinases (CNs) are dimeric dipeptidases in the metallopeptidase M20 family. Two isoforms of carnosinases (Zn2+ -containing carnosinase 1 (CN1) found in serum and Mn2+ -carnosinase 2 (CN2) in tissue) were identified. Both CNs cleave histidine-containing (Xaa-His) dipeptides such as carnosine where CN2 was found to accept a broader spectrum of substrates. A loss of CN function, resulting in a high carnosine concentration, reduces risk for diabetes and neurological disorders. Although several studies on CN activities and its Michaelis complex were conducted, all shed the light on CN1 activity where the CN2 data is limited. Also, the molecular details on CN1 and CN2 similarity and dissimilarity in structure and function remain unclear. Thus, in this work, molecular dynamics (MD) simulations were employed to study structure and dynamics of human CN1 and CN2 in comparison. The results show that the different catalytic ability of both CNs is due to their pocket size and environment. CN2 can accept a wider range of substrate due to the wider mouth of a binding pocket. The L1 loop seems to play a role in gating activity. Comparing to CN2, CN1 provides more electronegative entrance, more wettability, and higher stability of catalytic metal ion-pair in the active site which allow more efficient water-mediated catalysis. The microscopic understanding obtained here can serve as a basis for CN inhibition strategies resulting in higher carnosine levels and consequently mitigating complications associated with diseases such as diabetes and neurological disorder.

What make malarial adenosine deaminase from PLASMODIUM VIVAX recognise adenosine and 5'-methylthioadenosine: simulation studies.

Malaria is a life-threatening disease in humans caused by Plasmodium parasites. Plasmodium vivax (P. vivax) is one of the prevalent species found worldwide. An increase in an anti-malarial drug resistance suggests the urgent need for new drugs. Zn2+-containing adenosine deaminase (ADA) is a promising drug target because the ADA inhibition is fatal to the parasite. Malarial ADA accepts both adenosine (ADN) and 5'-methylthioadenosine (MTA) as substrates. The understanding of the substrate binding becomes crucial for an anti-malarial drug development. In this work, ADA from P. vivax (pvADA) is of interest due to its prevalence worldwide. The binding of ADN and MTA are studied here using Molecular Dynamics (MD) simulations. Upon binding, the open and closed states of pvADA are captured. The displacement of α7, linking loops of ß3/α12, ß4/α13, ß5/α15, and α10/α11 is involved in the cavity closure and opening. Also, the inappropriate substrate orientation induces a failure in a complete cavity closure. Interactions with D46, D172, S280, D310, and D311 are important for ADN binding, whereas only hydrogen bonds with D172 and D311 are sufficient to anchor MTA inside the pocket. No Zn2+-coordinated histidine residues is acquired for substrate binding. D172 is found to play a role in ribose moiety recognition, while D311 is crucial for trapping the amine group of an adenine ring towards the Zn2+ site. Comparing between ADN and MTA, the additional interaction between D310 and an amine nitrogen on ADN supports a tighter fit that may facilitate the deamination.Communicated by Ramaswamy H. Sarma.

Elucidating structure and dynamics of glutathione S-transferase from Rhipicephalus (Boophilus) microplus.

Rhipicephalus (Boophilus) microplus is tick parasite that affects the cattle industry worldwide. In R. (B.) microplus, acaricide resistance develops rapidly against many commercial acaricides. One of main resistance strategies is to enhance the metabolic detoxification mediated by R. (B.) microplus glutathione-S-transferase (RmGST). RmGST detoxifies acaricides by catalyzing the conjugation of glutathione to acaricides. Although structural and dynamic details of RmGST are expected to elucidate the biologic activity of this molecule, these data have not been available to date. Thus, Molecular Dynamics simulations were employed to study ligand-free RmGST at an atomic level. Like other m-class GSTs, the flexible m loop (m1) of RmGST was observed. M1 seems to shield the active sites from the bulk. A RmGST dimer is stabilized by the lock-and-key motif (F57 as "key") and hydrogen bonds of R82-E91 and R82-D98 at the dimer interface. Without substrates, conserved catalytic Y116 and N209 can interact with V112, G210 (for Y116) and F215 (for N209). Overall, most residues involving in RmGST function and stability are similar to other m-class GSTs. This implies similar structural stability and catalytic activity of RmGST to other GSTs. An insight obtained here will be useful for management of acaricide resistance and tick control.Communicated by Ramaswamy H. Sarma.

Observing How Glutathione and S-Hexyl Glutathione Bind to Glutathione S-Transferase from Rhipicephalus (Boophilus) microplus.

Rhipicephalus (Boophilus) microplus is one of the most widespread ticks causing a massive loss to livestock production. The long-term use of acaracides rapidly develops acaracide resistance. In R. microplus, enhancing the metabolic activity of glutathione S-transferase (RmGST) is one of the mechanisms underlying acaracide resistance. RmGST catalyzes the conjugation of glutathione (GSH) to insecticides causing an easy-to-excrete conjugate. The active RmGST dimer contains two active sites (hydrophobic co-substrate binding site (H-site) and GSH binding site (G-site)) in each monomer. To preserve the insecticide efficacy, s-hexyl glutathione (GTX), a GST inhibitor, has been used as a synergist. To date, no molecular information on the RmGST-GSH/GTX complex is available. The insight is important for developing a novel RmGST inhibitor. Therefore, in this work, molecular dynamics simulations (MD) were performed to explore the binding of GTX and GSH to RmGST. GSH binds tighter and sits rigidly inside the G-site, while flexible GTX occupies both active sites. In GSH, the backbone mainly interacts with W8, R43, W46, K50, N59, L60, Q72, and S73, while its thiol group directs to Y7. In contrast, the aliphatic hexyl of GTX protrudes into the H-site and allows a flexible peptide core to form various interactions. Such high GTX flexibility and the protrusion of its hexyl moiety to the H-site suggest the dual role of GTX in preventing the conjugation reaction and the binding of acaracide. This insight can provide a better understanding of an important insecticide-resistance mechanism, which may in turn facilitate the development of novel approaches to tick control.

Effects of Boric Acid and Storage Temperature on the Analysis of Microalbumin Using Aptasensor-Based Fluorescent Detection.

The instability of human serum albumin (HSA) in urine samples makes fresh urine a requirement for microalbumin analyses using immunoturbidimetry. Here, we determined the ability of an aptasensor-based fluorescent platform to detect microalbumin in old, boric acid-preserved urine samples. Our results show that the cleavage site of protease enzymes on urine albumin protein differed from the binding position of the aptamer on HSA protein, suggesting the aptasensor may be effective for albumin detection in non-fresh urine. Furthermore, the addition of boric acid in urine samples over a short term (at ambient temperature (Ta) and 4 °C), long term (-20 and -80 °C), and following freeze-thawing (1-3 cycles) did not significantly affect albumin stability, as analyzed using the aptasensor. Therefore, boric acid stabilized has in urine stored over a short- and long-term. Thus, the aptasensor developed by us is applicable for HSA detection in boric acid-preserved urine that has been stored for 7-d at Ta and 4 °C, and in the long-term at -80 °C.

The aggregation of multiple miR-29a cancer biomarkers induced by graphene quantum dots: Molecular dynamics simulations.

MicroRNAs (miRNAs) are small non-coding RNAs that play a role in regulating gene expression. MiRNAs are focused on as potential cancer biomarkers due to their involvement in the cancer development. New effective techniques for extracting miRNA from a biological matrix is important. Recently, graphene quantum dots (GQDs) have been used to detect DNA/RNA in many sensor platforms, but the application in miRNA extraction remains limited. To extract miRNAs, the miRNA adsorption and desorption on GQD are the key. Thus, in this work, the adsorption mechanism of excess miRNA on GQD in solution is revealed using Molecular dynamics simulations. The miRNA assemblies on one and two GQDs were studied to explore the possibility of using GQD for miRNA extraction. The folded miR-29a molecule, one of key cancer biomarkers, is used as an miRNA model. Three systems with one (6miR) and two GQDs (with parallel (6miR_2GP) and sandwich (6miR_2GS) organisations) in six-miR-29a solution were set. The data show excess miR-29a can reduce the miR-29a-GQD binding efficiency. The opening of intrabase pairing of GQD-absorbed miR-29a facilitates the interbase coupling resulting in the self-aggregation of miR-29a. The GQD organisation also affects the miR-29a adsorption ability. The additional GQDs result in the tighter miR-29a adsorption which can retard the miR-29a desorption. The proper GQD concentration is thus important to successfully collect all miR-29a and accommodate the easy miR-29a dissociation. Our results can be useful for a design of DNA probe and choosing decent nanosized GRA concentration for experimental setups.

The binding of apo and glucose-bound human serum albumins to a free graphene sheet in aqueous environment: Simulation studies.

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.

Evaluation of the Binding Mechanism of Human Defensin 5 in a Bacterial Membrane: A Simulation Study.

Human α-defensin 5 (HD5) is a host-defense peptide exhibiting broad-spectrum antimicrobial activity. The lipopolysaccharide (LPS) layer on the Gram-negative bacterial membrane acts as a barrier to HD5 insertion. Therefore, the pore formation and binding mechanism remain unclear. Here, the binding mechanisms at five positions along the bacterial membrane axis were investigated using Molecular Dynamics. (MD) simulations. We found that HD5 initially placed at positions 1 to 3 moved up to the surface, while HD5 positioned at 4 and 5 remained within the membrane interacting with the middle and inner leaflet of the membrane, respectively. The arginines were key components for tighter binding with 3-deoxy-d-manno-octulosonic acid (KDO), phosphates of the outer and inner leaflets. KDO appeared to retard the HD5 penetration.

The penetration of human defensin 5 (HD5) through bacterial outer membrane: simulation studies.

Human α-defensin 5 (HD5) is one of cationic antimicrobial peptides which plays a crucial role in an innate immune system in human body. HD5 shows the killing activity against a broad spectrum of pathogenic bacteria by making a pore in a bacterial membrane and penetrating into a cytosol. Nonetheless, its pore-forming mechanisms remain unclear. Thus, in this work, the constant-velocity steered molecular dynamics (SMD) simulation was used to simulate the permeation of a dimeric HD5 into a gram-negative lipopolysaccharide (LPS) membrane model. Arginine-rich HD5 is found to strongly interact with a LPS surface. Upon arrival, arginines on HD5 interact with lipid A head groups (a top part of LPS) and then drag these charged moieties down into a hydrophobic core resulting in the formation of water-filled pore. Although all arginines are found to interact with a membrane, Arg13 and Arg32 appear to play a dominant role in the HD5 adsorption on a gram-negative membrane. Furthermore, one chain of a dimeric HD5 is required for HD5 adhesion. The interactions of arginine-lipid A head groups play a major role in adhering a cationic HD5 on a membrane surface and retarding a HD5 passage in the meantime.

Modeling the Adsorption of the miR-29a Cancer Biomarker on a Graphene Quantum Dot.

MicroRNAs (miRNAs) are small noncoding RNA molecules associated with the regulation of gene expression in organisms. MiRNAs are focused on as potential cancer biomarkers due to their involvement in cancer development. New potential techniques for miRNA detection are rapidly developed, while there is a lack of effective extraction approaches, especially for miRNAs. Recently, graphene quantum dots (GQDs) have been involved in many disease biosensor platforms including miRNA detection, but no application in miRNA extraction is studied. To extract miRNAs, miRNA adsorption and desorption on GQDs are the key. Thus, in this work, the adsorption mechanism of miRNA on GQDs in solution is revealed using molecular dynamics simulations. The aim is to explore the possibility of using GQDs for miRNA extraction. The folded miR-29a molecule, one of the key cancer biomarkers, is used as a miRNA model. Two systems with one (1miR) and four (4miR) chains of miR-29a were set. MiR-29a molecules in all systems are simultaneously adsorbed on the GQD surface. Our finding highlights the ability of the GQD in collecting miRNAs in solution. In 1miR, the whole miR-29a chain sits on the GQD face, whereas all miR-29a molecules in 4miR show the "clamping" conformation. No "lying flat" orientation of miR-29a is observed due to the existence of the preserved hairpin region. Interestingly, the 5' end shows tighter binding than the 3' terminus. A design of complementary DNA with the recognition segment involving the sequences close to the 3' end can promote effective miR-29a desorption.

How human serum albumin-selective DNA aptamer binds to bovine and canine serum albumins.

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.

What Happens When a Complementary DNA Meets miR-29a Cancer Biomarker in Complex with a Graphene Quantum Dot.

MicroRNAs (miRNAs), short single-stranded noncoding RNA molecules, serve as potential cancer biomarkers due to their involvement in cancer development. One of the strategies to extract miRNAs is to perform the miRNA adsorption on nanomaterials and dissociation by a complementary DNA strand (DNA probe). Recently, graphene quantum dots (GQDs) were found to show a good ability to absorb miRNAs. Thus, in this work, the mechanism of the GQD-adhered miRNA capture by its complementary DNA is revealed using molecular dynamics simulations. miR-29a, a potential cancer biomarker, is used as a miRNA model. Three systems containing one and four chains of miR-29a in addition to one and four complementary DNA probes (1R1D, 1R4D, and 4R4D) were studied. GQDs are the prime targets of a DNA attack. The full coverage of GQDs is required to protect the adsorption of DNA probes on the GQD face. The nucleobase-backbone interactions are the main contributors to miR-DNA interactions in this work. The interbase paring becomes small because most nucleobases of miR-29a and their probe are stacked to maintain their secondary structures, and some are absorbed on the GQD surface. Apparently, weakening of the nucleobase-GQD π-π stacking and the intrabase-pairing strength is needed for extracting miR-29a by a probe. Although no GQD-absorbed miR-29a desorption is found here, the basic principles obtained can be useful for further utilization of GQDs and their derivatives for miRNA extraction and detection.

Albuminuria detection using graphene oxide-mediated fluorescence quenching aptasensor.

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-1.

Exploring how structural and dynamic properties of bovine and canine serum albumins differ from human serum albumin.

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.