Integrin αIIbβ3

Data-driven prediction of αIIbβ3 integrin activation paths using manifold learning and deep generative modeling

The integrin heterodimer is a transmembrane protein critical for driving cellular process and is a therapeutic target in the treatment of multiple diseases linked to its malfunction. Activation of integrin involves conformational transitions between bent and extended states. Some of the conformations that are intermediate between bent and extended states of the heterodimer have been experimentally characterized, but the full activation pathways remain unresolved both experimentally due to their transient nature and computationally due to the challenges in simulating rare barrier crossing events in these large molecular systems. An understanding of the activation pathways can provide new fundamental understanding of the biophysical processes associated with the dynamic interconversions between bent and extended states and can unveil new putative therapeutic targets. In this work, we apply nonlinear manifold learning to coarse-grained molecular dynamics simulations of bent, extended, and two intermediate states of αIIbβ3 integrin to learn a low-dimensional embedding of the configurational phase space. We then train deep generative models to learn an inverse mapping between the low-dimensional embedding and high-dimensional molecular space and use these models to interpolate the molecular configurations constituting the activation pathways between the experimentally characterized states. This work furnishes plausible predictions of integrin activation pathways and reports a generic and transferable multiscale technique to predict transition pathways for biomolecular systems.

The investigation into the effect of the length of RGD peptides and temperature on the interaction with the αIIbβ3 integrin: a molecular dynamic study

The tripeptide Arg-Gly-Asp acid (RGD) is a protein sequence in the binding of proteins to cell surfaces, and is involved in various biological processes such as cell adhesion to the extracellular matrix, platelet activation, hemostasis, etc. The C2 domain of the Von Willebrand Factor (VWF), containing the RGD motif, plays an important role in the initial homeostasis process. It binds to the αIIbβ3 integrin and stimulates platelet aggregation. We have investigated, using the molecular Dynamic (MD) simulation method, the effect of the RGD-peptide length, and temperature variation, on the binding to the αIIbβ3 integrin receptor. We examined 10 different structural modes of the αIIbβ3 at three different temperatures; 237 K, 310 K and 318 K. Our findings show that the amino acids that form a binding pocket include Asp₂₂₄, Tyr₂₃₄, Ser₂₂₆, Tyr₁₉₀, Tyr₁₈₉, Trp₂₆₀, Trp₂₆₂, Asp_259, Lys₂₅₃, Arg₂₁₄, Asp₂₁₇, Ser₁₆₁ and Ala₂₁₈ and that the ligand-receptor interaction was increased at higher temperatures. It was also found that the increase in the number of ligands' amino acids and their types (% glycine) plays an important role in the stability, conformation, and ligand-receptor interaction.Communicated by Ramaswamy H. Sarma.

Platelets and Their Role in Hemostasis and Thrombosis-From Physiology to Pathophysiology and Therapeutic Implications

Hemostasis is a physiological process critical for survival. Meanwhile, thrombosis is amongst the leading causes of death worldwide, making antithrombotic therapy one of the most crucial aspects of modern medicine. Although antithrombotic therapy has progressed tremendously over the years, it remains far from ideal, and this is mainly due to the incomplete understanding of the exceptionally complex structural and functional properties of platelets. However, advances in biochemistry, molecular biology, and the advent of 'omics' continue to provide crucial information for our understanding of the complex structure and function of platelets, their interactions with the coagulation system, and their role in hemostasis and thrombosis. In this review, we provide a comprehensive view of the complex role that platelets play in hemostasis and thrombosis, and we discuss the major clinical implications of these fundamental blood components, with a focus on hemostatic platelet-related disorders and existing and emerging antithrombotic therapies. We also emphasize a number of questions that remain to be answered, and we identify hotspots for future research.

Comprehensive phenotyping of human platelets by single-cell cytometry

Platelets are small anucleate blood cells that contribute to hemostasis, immunity, and inflammation. Circulating platelets are heterogeneous in size, age, receptor expression, and reactivity. They inherit many features from megakaryocytes and are further modified on exposure to bioactive substances in the bloodstream. Among these substances, prothrombotic agonists, vasodilators, and bloodborne pathogens modulate platelet phenotypes via distinct signaling cascades. The ability of platelets to respond to (patho)physiologic signals is incompletely understood but likely depends on their repertoire of surface receptors, which may partition them into discrete subsets with specialized functions and divergent abilities. The single-cell resolution of flow and mass cytometry is ideal for immunophenotyping and allows the identification of platelet subsets in remarkable detail. In this report, we describe the surface markers and gating strategies needed for the comprehensive characterization of platelets.

Platelet Immunophenotyping by High-Dimensional Mass Cytometry

Platelets are small blood cells that contribute to hemostasis, immunity, and inflammation. Characterization of platelet surface markers allows for differentiation of activated platelets from resting platelets, diagnosis of platelet disorders, and investigation of platelet biology and pathology. In this article, we describe the use of mass cytometry or "CyTOF" (mass spectroscopy detection of metal-tagged antibodies on individual cells) to measure a large number of markers on each platelet and to identify platelet subsets based on the shared expression of multiple markers. This powerful new approach provides a vastly more detailed picture of platelet immunophenotypes than conventional flow cytometry and enables investigation of the roles of platelet subsets in health and disease. © 2021 Wiley Periodicals LLC. Basic Protocol: Platelet immunophenotyping by high-dimensional mass cytometry Support Protocol: Data preprocessing.

Cancer-associated-platelet-inspired nanomedicines for cancer therapy

Platelets, with hemostasis and thrombosis activities, are one of the key components in the blood circulation. As a guard, they rapidly respond to any abnormal blood vessel injury signal and release their granules' contents, which induce their adhesion and aggregation on wound site for hemostasis. Recently, increasing evidence has indicated that platelets are critically involved in the growth and metastasis of cancer cells by releasing a variety of cytokines and chemokines to stimulate cancer cell proliferation and various angiogenic regulators to accelerate tumor angiogenesis. Platelets also secrete active transforming growth factor beta (TGF-β) to promote the epithelial-mesenchymal transition of cancer cells and their extravasation from primary site, and form microthrombus on the surface of cancer cells to protect them from immune attack and high-speed shear force in the circulation. Therefore, blocking platelet-cancer cell interaction may be an attractive strategy to treat primary tumor and/or prevent cancer metastasis. However, systemic inhibition or depletion of platelets brings risk of severe bleeding complication. Cancer-associated-platelets-targeted nanomedicines and biomimetic nanomedicines coated with platelet membrane can be used for targeted anticancer drug delivery, due to their natural targeting ability to tumor cells and platelets. In the current review, we first summarized the platelet mechanisms of action in physiological condition and their multiple roles in cancer progression and conventional antiplatelet therapeutics. We then highlighted the recent progress on the design and fabrication of cancer-associated-platelet-targeted nanomedicines and platelet membrane coating nanomedicines for cancer therapy. Finally, we discussed opportunities and challenges and offered our thoughts for the future development. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Biology-Inspired Nanomaterials > Lipid-Based Structures.

Kindlin Assists Talin to Promote Integrin Activation

Integrin αIIbβ3 is a predominant type of integrin abundantly expressed on the surface of platelets and its activation regulates the process of thrombosis. Talin and kindlin are cytoplasmic proteins that bind to integrin and modulate its affinity for extracellular ligands. Although the molecular details of talin-mediated integrin activation are known, the mechanism of kindlin involvement in this process remains elusive. Here, we demonstrate that the interplay between talin and kindlin promotes integrin activation. Our all-atomic molecular dynamics simulations on complete transmembrane and cytoplasmic domains of integrin αIIbβ3, talin1 F2/F3 subdomains, and the kindlin2 FERM domain in an explicit lipid-water environment over a microsecond timescale unraveled the role of kindlin as an enhancer of the talin interaction with the membrane proximal region of β-integrin. The cooperation of kindlin with talin results in a complete disruption of salt bridges between R995 on αIIb and D723/E726 on β3. Furthermore, kindlin modifies the molecular mechanisms of inside-out activation by decreasing the crossing angle between transmembrane helices of integrin αIIbβ3, which eventually results in parallelization of integrin dimer. In addition, our control simulation featuring integrin in complex with kindlin reveals that kindlin binding is not sufficient for unclasping the inner-membrane and outer-membrane interactions of integrin dimer, thus ruling out the possibility of solitary action of kindlin in integrin activation.