Rustem I. Litvinov

Computational Design of Peptides That Target Transmembrane Helices

A variety of methods exist for the design or selection of antibodies and other proteins that recognize the water-soluble regions of proteins; however, companion methods for targeting transmembrane (TM) regions are not available. Here, we describe a method for the computational design of peptides that target TM helices in a sequence-specific manner. To illustrate the method, peptides were designed that specifically recognize the TM helices of two closely related integrins (αIIbβ3 and αvβ3) in micelles, bacterial membranes, and mammalian cells. These data show that sequence-specific recognition of helices in TM proteins can be achieved through optimization of the geometric complementarity of the target-host complex.

Multiscale Mechanics of Fibrin Polymer: Gel Stretching with Protein Unfolding and Loss of Water

<< Focusing on Fibrin Vascular injury initiates biochemical reactions that cause the blood protein, fibrin, to polymerize and help to stop bleeding and support wound healing. Fibrin can also be a scaffold for thrombi that lead to cardiovascular diseases. To maintain homeostasis, fibrin clots must be stiff, plastic, and, so that the network can be decompsed, permeable. Brown et al. (p. 741) investigated the behavior of fibrin clots at the macroscopic, single-fiber, and molecular scale. At relatively low strains, fibers aligned and formed bundles, and at higher strains, protein unfolding occurred. An integrated model provides a molecular basis for fibrin elasticity and extensibility. Protein unfolding in stretched fibrin blood clots creates porous gels that can withstand high strains. Blood clots and thrombi consist primarily of a mesh of branched fibers made of the protein fibrin. We propose a molecular basis for the marked extensibility and negative compressibility of fibrin gels based on the structural and mechanical properties of clots at the network, fiber, and molecular levels. The force required to stretch a clot initially rises linearly and is accompanied by a dramatic decrease in clot volume and a peak in compressibility. These macroscopic transitions are accompanied by fiber alignment and bundling after forced protein unfolding. Constitutive models are developed to integrate observations at spatial scales that span six orders of magnitude and indicate that gel extensibility and expulsion of water are both manifestations of protein unfolding, which is not apparent in other matrix proteins such as collagen.

Mechanisms of fibrin polymerization and clinical implications

Research on all stages of fibrin polymerization, using a variety of approaches including naturally occurring and recombinant variants of fibrinogen, x-ray crystallography, electron and light microscopy, and other biophysical approaches, has revealed aspects of the molecular mechanisms involved. The ordered sequence of fibrinopeptide release is essential for the knob-hole interactions that initiate oligomer formation and the subsequent formation of 2-stranded protofibrils. Calcium ions bound both strongly and weakly to fibrin(ogen) have been localized, and some aspects of their roles are beginning to be discovered. Much less is known about the mechanisms of the lateral aggregation of protofibrils and the subsequent branching to yield a 3-dimensional network, although the αC region and B:b knob-hole binding seem to enhance lateral aggregation. Much information now exists about variations in clot structure and properties because of genetic and acquired molecular variants, environmental factors, effects of various intravascular and extravascular cells, hydrodynamic flow, and some functional consequences. The mechanical and chemical stability of clots and thrombi are affected by both the structure of the fibrin network and cross-linking by plasma transglutaminase. There are important clinical consequences to all of these new findings that are relevant for the pathogenesis of diseases, prophylaxis, diagnosis, and treatment.

Binding strength and activation state of single fibrinogen-integrin pairs on living cells

Integrin activation states determine the ability of these receptors to mediate cell–matrix and cell–cell interactions. The prototypic example of this phenomenon is the platelet integrin, αIIbβ3. In unstimulated platelets, αIIbβ3 is inactive, whereas exposing platelets to an agonist such as ADP or thrombin enables αIIbβ3 to bind ligands such as fibrinogen and von Willebrand factor. To study the regulation of integrin activation states at the level of single molecules, we developed a model system based on laser tweezers, enabling us to determine the rupture forces required to separate single ligand-receptor pairs by using either purified proteins or intact living cells. Here, we show that rupture forces of individual fibrinogen molecules and either purified αIIbβ3 or αIIbβ3 on the surface of living platelets were 60 to 150 pN with a peak yield strength of 80–100 pN. Platelet stimulation using either ADP or the thrombin receptor-activating peptide enhanced the accessibility but not the adhesion strength of single αIIbβ3 molecules, indicating that there are only two states of αIIbβ3 activation. Thus, we found it possible to use laser tweezers to measure the regulation of forces between individual ligand-receptor pairs on living cells. This methodology can be applied to the study of other regulated cell membrane receptors using the ligand-receptor yield strength as a direct measure of receptor activation/inactivation state.

The Biochemical and Physical Process of Fibrinolysis and Effects of Clot Structure and Stability on the Lysis Rate

The effectiveness of fibrinolysis results from the combination of regulated enzymatic activity and the physical properties of the fibrin scaffold. Physiologically, clots or thrombi are dissolved from within via internal lysis. In contrast, with therapeutic thrombolysis, lytic agents are introduced at one surface and lysis proceeds across the thrombus. In the latter case, there are complex changes that take place at the lysis front in a narrow zone. However, at the microscopic level the mechanisms for either general type of fibrinolysis appear to be similar. Fibrinolysis proceeds by fibers being transected laterally, rather than digestion of fibers by surface erosion from the outside. A molecular model to account for these observations together with what is known from the biochemical characterization of fibrinolysis involves the movement of plasmin laterally across fibers, binding to sites created by its own proteolytic activity. Fibrin clots can have a great diversity of structural, biological, physical, and chemical properties depending on the conditions of formation, and the rate and nature of fibrinolysis is related to these properties. In general, the rate of lysis appears to be faster for clots made up of thicker fibers than for clots made up of thinner fibers, but the lysis rate is not simply a function of fiber diameter and also depends on other physical properties of the clot. Platelet aggregation and clot retraction have a dramatic effect on the structure of fibrin and hence on fibrinolysis.

Clot contraction: compression of erythrocytes into tightly packed polyhedra and redistribution of platelets and fibrin

Contraction of blood clots is necessary for hemostasis and wound healing and to restore flow past obstructive thrombi, but little is known about the structure of contracted clots or the role of erythrocytes in contraction. We found that contracted blood clots develop a remarkable structure, with a meshwork of fibrin and platelet aggregates on the exterior of the clot and a close-packed, tessellated array of compressed polyhedral erythrocytes within. The same results were obtained after initiation of clotting with various activators and also with clots from reconstituted human blood and mouse blood. Such close-packed arrays of polyhedral erythrocytes, or polyhedrocytes, were also observed in human arterial thrombi taken from patients. The mechanical nature of this shape change was confirmed by polyhedrocyte formation from the forces of centrifugation of blood without clotting. Platelets (with their cytoskeletal motility proteins) and fibrin(ogen) (as the substrate bridging platelets for contraction) are required to generate the forces necessary to segregate platelets/fibrin from erythrocytes and to compress erythrocytes into a tightly packed array. These results demonstrate how contracted clots form an impermeable barrier important for hemostasis and wound healing and help explain how fibrinolysis is greatly retarded as clots contract.

Protein-protein unbinding induced by force: single-molecule studies.

Experiments in which two specifically interacting protein molecules are dissociated by external force have yielded new insights into mechanisms involved in cell adhesion, leukocyte rolling, regulation of integrin activity, antigen-antibody interactions and other protein-mediated reactions contingent upon molecular recognition. Another important aspect of force-induced protein-protein unbinding studies is the new information being gleaned about the thermodynamics and kinetics of bond rupture.

Mechanism of Fibrin(ogen) Forced Unfolding

Fibrinogen, upon enzymatic conversion to monomeric fibrin, provides the building blocks for fibrin polymer, the scaffold of blood clots and thrombi. Little has been known about the force-induced unfolding of fibrin(ogen), even though it is the foundation for the mechanical and rheological properties of fibrin, which are essential for hemostasis. We determined mechanisms and mapped the free energy landscape of the elongation of fibrin(ogen) monomers and oligomers through combined experimental and theoretical studies of the nanomechanical properties of fibrin(ogen), using atomic force microscopy-based single-molecule unfolding and simulations in the experimentally relevant timescale. We have found that mechanical unraveling of fibrin(ogen) is determined by the combined molecular transitions that couple stepwise unfolding of the γ chain nodules and reversible extension-contraction of the α-helical coiled-coil connectors. These findings provide important characteristics of the fibrin(ogen) nanomechanics necessary to understand the molecular origins of fibrin viscoelasticity at the fiber and whole clot levels.

Loss of PIP5KIγ, unlike other PIP5KI isoforms, impairs the integrity of the membrane cytoskeleton in murine megakaryocytes

Phosphatidylinositol-4,5-bisphosphate (PIP(2)) is an abundant phospholipid that contributes to second messenger formation and has also been shown to contribute to the regulation of cytoskeletal dynamics in all eukaryotic cells. Although the alpha, beta, and gamma isoforms of phosphatidylinositol-4-phosphate-5-kinase I (PIP5KI) all synthesize PIP2, mammalian cells usually contain more than one PIP5KI isoform. This raises the question of whether different isoforms of PIP5KI fulfill different functions. Given the speculated role of PIP(2) in platelet and megakaryocyte actin dynamics, we analyzed murine megakaryocytes lacking individual PIP5KI isoforms. PIP5KIgamma(-/-) megakaryocytes exhibited plasma membrane blebbing accompanied by a decreased association of the membrane with the cytoskeleton. This membrane defect was rescued by adding back wild-type PIP5KIgamma, but not by adding a catalytically inactive mutant or a splice variant lacking the talin-binding motif. Notably, both PIP5KIbeta- and PIP5KIgamma(-/-) cells had impaired PIP(2) synthesis. However, PIP5KIbeta-null cells lacked the membrane-cytoskeleton defect. Furthermore, overexpressing PIP5KIbeta in PIP5KIgamma(-/-) cells failed to revert this defect. Megakaryocytes lacking the PIP5KIgamma-binding partner, talin1, mimicked the membrane-cytoskeleton defect phenotype seen in PIP5KIgamma(-/-) cells. These findings demonstrate a unique role for PIP5KIgamma in the anchoring of the cell membrane to the cytoskeleton in megakaryocytes, probably through a pathway involving talin. These observations further demonstrate that individual PIP5KI isoforms fulfill distinct functions within cells.

Computationally Designed Peptide Inhibitors of Protein-Protein Interactions in Membranes

We recently reported a computational method (CHAMP) for designing sequence-specific peptides that bind to the membrane-embedded portions of transmembrane proteins. We successfully applied this method to design membrane-spanning peptides targeting the transmembrane domains of the alpha IIb subunit of integrin alpha IIbbeta 3. Previously, we demonstrated that these CHAMP peptides bind specifically with reasonable affinity to isolated transmembrane helices of the targeted transmembrane region. These peptides also induced integrin alpha IIbbeta 3 activation due to disruption of the helix-helix interactions between the transmembrane domains of the alpha IIb and beta 3 subunits. In this paper, we show the direct interaction of the designed anti-alpha IIb CHAMP peptide with isolated full-length integrin alpha IIbbeta 3 in detergent micelles. Further, the behavior of the designed peptides in phospholipid bilayers is essentially identical to their behavior in detergent micelles. In particular, the peptides assume a membrane-spanning alpha-helical conformation that does not disrupt bilayer integrity. The activity and selectivity of the CHAMP peptides were further explored in platelets, comfirming that anti-alpha IIb activates wild-type alpha IIbbeta 3 in whole cells as a result of its disruption of the protein-protein interactions between the alpha and beta subunits in the transmembrane regions. These results demonstrate that CHAMP is a successful chemical biology approach that can provide specific tools for probing the transmembrane domains of proteins.