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.

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 β3/α12, β4/α13, β5/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.

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.