Variation in one residue associated with the metal ion-dependent adhesion site regulates αIIbβ3 integrin ligand binding affinity

Calculating toxic pressure for mixtures of endocrine disruptors

Incidence of autoimmune disorders, birth defects, and neurological diseases rose over the past 50 years due to increasing variety and quantity of pollutants. To date, there appear few methods capable to evaluate and predict mixture effects by endocrine disruptors (EDs). For the first time, we have developed calculus to determine mixture effects by all kinds of EDs. Our method uses the golden ratio ϕ and draws from bifurcation and chaos theory. Using also the concept of molecular mimicry, we developed the equation: e f f e c t = 100 % 1 + e 5 · ∑ K i C i - n i ϕ 3 . We successfully tested the equation using a range of cohort studies and biomarkers, and for different pollutants like heavy metals, thyroid hormone mimickants, chromate/chlorate, etc. The equation is simple enough to use with only minor prior knowledge and understanding of basic algebra. The method is universal and calculation is data 'light', requiring only pollutant concentrations [C], potencies K and an integer n for endocrinal involvement. This study offers a comprehensive framework to assess the health effects of pollutant exposure across diverse populations, envisioning far-reaching impact, and presenting practical examples and insights.

Application of Funnel Metadynamics to the Platelet Integrin αIIbβ3 in Complex with an RGD Peptide

Integrin αIIbβ3 mediates platelet aggregation by binding the Arginyl-Glycyl-Aspartic acid (RGD) sequence of fibrinogen. RGD binding occurs at a site topographically proximal to the αIIb and β3 subunits, promoting the conformational activation of the receptor from bent to extended states. While several experimental approaches have characterized RGD binding to αIIbβ3 integrin, applying computational methods has been significantly more challenging due to limited sampling and the need for a priori information regarding the interactions between the RGD peptide and integrin. In this study, we employed all-atom simulations using funnel metadynamics (FM) to evaluate the interactions of an RGD peptide with the αIIb and β3 subunits of integrin. FM incorporates an external history-dependent potential on selected degrees of freedom while applying a funnel-shaped restraint potential to limit RGD exploration of the unbound state. Furthermore, it does not require a priori information about the interactions, enhancing the sampling at a low computational cost. Our FM simulations reveal significant molecular changes in the β3 subunit of integrin upon RGD binding and provide a free-energy landscape with a low-energy binding mode surrounded by higher-energy prebinding states. The strong agreement between previous experimental and computational data and our results highlights the reliability of FM as a method for studying dynamic interactions of complex systems such as integrin.

Effect of amino acids near the RGD sequence on binding activities between αIIbβ3 integrin and fibrinogen in the presence of RGD-containing synthetic peptides from elegantin and angustatin

Elegantin and angustatin, which were isolated from the snake venoms of Protobothrops elegans and Dendroaspis angusticeps, markedly inhibit binding between platelet integrins and fibrinogen via the Arg-Gly-Asp (RGD) sequence. Angustatin, which is a three-finger toxin containing the RGD sequence, inhibits platelet aggregation almost ten times more strongly than disintegrin isolated from the venoms of Viperidae and Crotalidae. The RGD sequences of both polypeptides are located at the top of hairpin loops, and the composition of the RGD loop is very important for binding to integrin. We investigated the effects of synthetic RGD loop peptides from angustatin and elegantin on ADP- or collagen-induced platelet aggregation and αIIbβ3-fibrinogen binding. Synthetic angustatin (PRGDMP)-type peptides inhibited platelet aggregation more strongly than elegantin (ARGDDX)-type peptides. In particular, the cyclic angustatin peptide (CPRGDMPC) inhibited ADP- and collagen-induced platelet aggregation at least 10-50 times more strongly than the other peptides. The cyclic angustatin peptide (CPRGDMPC) was also the strongest inhibitor of binding between αIIbβ3 and fibrinogen, the IC₅₀ of this peptide was approximately 2.58μM. Regarding the inhibition of binding between αIIbβ3 and fibrinogen, CPRGDMPC demonstrated a stronger inhibitory and more stable effect in the presence of Mg²⁺ than in the presence of Ca²⁺.

αIIbβ3: structure and function

During the past decade, advanced techniques in structural biology have provided atomic level information on the platelet integrin αIIbβ3 activation mechanism that results in it adopting a high-affinity ligand-binding conformation(s). This review focuses on advances in imaging intact αIIbβ3 in a lipid bilayer in the absence of detergent and new structural insights into the changes in the ligand-binding pocket with receptor activation and ligand binding. It concludes with descriptions of novel therapeutic αIIbβ3 antagonists being developed based on an advanced knowledge of the receptor's structure.