Computational design of peptide-Au cluster probe for sensitive detection of α(IIb)β3 integrin

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.

Biological Interaction and Imaging of Ultrasmall Gold Nanoparticles

The ultrasmall gold nanoparticles (AuNPs), serving as a bridge between small molecules and traditional inorganic nanoparticles, create significant opportunities to address many challenges in the health field. This review discusses the recent advances in the biological interactions and imaging of ultrasmall AuNPs. The challenges and the future development directions of the ultrasmall AuNPs are presented.

Visualization of integrin molecules by fluorescence imaging and techniques

Integrin molecules are transmembrane αβ heterodimers involved in cell adhesion, trafficking, and signaling. Upon activation, integrins undergo dynamic conformational changes that regulate their affinity to ligands. The physiological functions and activation mechanisms of integrins have been heavily discussed in previous studies and reviews, but the fluorescence imaging techniques -which are powerful tools for biological studies- have not. Here we review the fluorescence labeling methods, imaging techniques, as well as Förster resonance energy transfer assays used to study integrin expression, localization, activation, and functions.

Targeted peptide-Au cluster binds to epidermal growth factor receptor (EGFR) in both active and inactive states: a clue for cancer inhibition through dual pathways

The epidermal growth factor receptor (EGFR) has become an important target protein in anticancer drug development. Meanwhile, peptide-Au cluster has been proposed as potential targeted nano-drug assembled by targeting peptide. Here, we designed and synthesized a novel peptide-Au cluster as Au₁₀Peptide₅ to target to EGFR. We found Au₁₀Peptide₅ could target to the natural binding sites of all EGFRs at membrane in both active and inactive states by molecular simulations. Its targeted ability was further verified by the co-localization and blocking experiments. We also study the configuration modifications of both active and inactive EGFRs after binding by Au₁₀Peptide₅. For active EGFR, the absorbed Au₁₀Peptide₅ might replace the natural ligand in EGFR endocytosis process. Then, the peptide-Au cluster in endochylema could inhibit the cancer relating enzyme activity including thioredoxin reductase1 (TrxR1) and induce the oxidative stress mediated apoptosis in tumor cells. For inactive EGFR, it was retained in inactive state by Au₁₀Peptide₅ binding to inhibit dimerization of EGFR for anticancer. Both pathways might be applied in anticancer drug development based on the theoretical and experimental study here.

Homocysteine directly interacts and activates the angiotensin II type I receptor to aggravate vascular injury

Hyperhomocysteinemia (HHcy) is a risk factor for various cardiovascular diseases. However, the mechanism underlying HHcy-aggravated vascular injury remains unclear. Here we show that the aggravation of abdominal aortic aneurysm by HHcy is abolished in mice with genetic deletion of the angiotensin II type 1 (AT1) receptor and in mice treated with an AT1 blocker. We find that homocysteine directly activates AT1 receptor signalling. Homocysteine displaces angiotensin II and limits its binding to AT1 receptor. Bioluminescence resonance energy transfer analysis reveals distinct conformational changes of AT1 receptor upon binding to angiotensin II and homocysteine. Molecular dynamics and site-directed mutagenesis experiments suggest that homocysteine regulates the conformation of the AT1 receptor both orthosterically and allosterically by forming a salt bridge and a disulfide bond with its Arg¹⁶⁷ and Cys²⁸⁹ residues, respectively. Together, these findings suggest that strategies aimed at blocking the AT1 receptor may mitigate HHcy-associated aneurysmal vascular injuries.

High homocysteine plasma levels are associated with cardiovascular diseases. Here, Li and colleagues find that homocysteine aggravates vascular injury by direct binding to the angiotensin II type 1 receptor (AT1R), identifying AT1R inhibition as a potential strategy to counteract the deleterious vascular effects of hyperhomocysteinemia.

Peptide-templated noble metal catalysts: syntheses and applications

Noble metal catalysts have been widely used in many applications because of their high activity and selectivity. However, a controllable preparation of noble metal catalysts still remains as a significant challenge. To overcome this challenge, peptide templates can play a critical role in the controllable syntheses of catalysts owing to their flexible binding with specific metallic surfaces and self-assembly characteristics. By employing peptide templates, the size, shape, facet, structure, and composition of obtained catalysts can all be specifically controlled under the mild synthesis conditions. In addition, catalysts with spherical, nanofiber, and nanofilm structures can all be produced by associating with the self-assembly characteristics of peptide templates. Furthermore, the peptide-templated noble metal catalysts also reveal significantly enhanced catalytic behaviours compared with conventional catalysts because the electron conductivity, metal dispersion, and reactive site exposure can all be improved. In this review, we summarize the research progresses in the syntheses of peptide-templated noble metal catalysts. The applications of the peptide-templated catalysts in organic reactions, photocatalysis, and electrocatalysis are discussed, and the relationship between structure and activity of these catalysts are addressed. Future opportunities, including new catalytic materials designed by using biological principles, are indicated to achieve selective, eco-friendly, and energy neutral synthesis approaches.

Peptide-Au Clusters Induced Tumor Cells Apoptosis via Targeting Glutathione Peroxidase-1: The Molecular Dynamics Assisted Experimental Studies

The original motivation of the article is to give a systematic investigation on the protocol of combining computer simulation and accurate synthesis of serial peptide protected gold clusters for potent tumor targeting therapy. Glutathione peroxidase-1 (GPx-1) is a crucial antioxidant selenoenzyme that regulates cellular redox level, thus becomes a potential target in cancer treatment. We firstly utilize molecular dynamic (MD) simulation to rationally design and screen serial peptide-Au cluster compounds with special peptide sequences and precise gold atoms, which can recognize and bind specific domain of GPx-1 with high affinity. The theoretical simulations were further verified by the following peptide-Au clusters synthesis and GPx-1 activity suppression studies in buffer and cells, respectively. Further cytological experiments corroborated that peptide-Au clusters are promising nanoparticles inducing tumor cells apoptosis by suppressing GPx-1 activity and increasing higher cellular reactive oxygen species level to initiate tumor cell apoptosis through intrinsic mitochondrial pathway.

Design, fabrication, and biomedical applications of bioinspired peptide–inorganic nanomaterial hybrids

We presented the design, composition, and typical biomedical applications of bioinspired peptide–inorganic nanomaterial hybrids.