CapZ-lipid membrane interactions: a computer analysis

The phosphoinositide code is read by a plethora of protein domains

INTRODUCTION

The proteins that decipher nucleic acid- and protein-based information are well known, however, those that read membrane-encoded information remain understudied. Here we report 70 different human, microbial and viral protein folds that recognize phosphoinositides (PIs), comprising the readers of a vast membrane code.

AREAS COVERED

Membrane recognition is best understood for FYVE, PH and PX domains, which exemplify hundreds of PI code readers. Comparable lipid interaction mechanisms may be mediated by kinases, adjacent C1 and C2 domains, trafficking arrestin, GAT and VHS modules, membrane-perturbing annexin, BAR, CHMP, ENTH, HEAT, syntaxin and Tubby helical bundles, multipurpose FERM, EH, MATH, PHD, PDZ, PROPPIN, PTB and SH2 domains, as well as systems that regulate receptors, GTPases and actin filaments, transfer lipids and assembled bacterial and viral particles.

EXPERT OPINION

The elucidation of how membranes are recognized has extended the genetic code to the PI code. Novel discoveries include PIP-stop and MET-stop residues to which phosphates and metabolites are attached to block phosphatidylinositol phosphate (PIP) recognition, memteins as functional membrane protein apparatuses, and lipidons as lipid "codons" recognized by membrane readers. At least 5% of the human proteome senses such membrane signals and allows eukaryotic organelles and pathogens to operate and replicate.

Mechanosignaling pathways alter muscle structure and function by post-translational modification of existing sarcomeric proteins to optimize energy usage

A transduced mechanical signal arriving at its destination in muscle alters sarcomeric structure and function. A major question addressed is how muscle mass and tension generation are optimized to match actual performance demands so that little energy is wasted. Three cases for improved energy efficiency are examined: the troponin complex for tuning force production, control of the myosin heads in a resting state, and the Z-disc proteins for sarcomere assembly. On arrival, the regulation of protein complexes is often controlled by post-translational modification (PTM), of which the most common are phosphorylation by kinases, deacetylation by histone deacetylases and ubiquitination by E3 ligases. Another branch of signals acts not through peptide covalent bonding but via ligand interactions (e.g. Ca²⁺ and phosphoinositide binding). The myosin head and the regulation of its binding to actin by the troponin complex is the best and earliest example of signal destinations that modify myofibrillar contractility. PTMs in the troponin complex regulate both the efficiency of the contractile function to match physiologic demand for work, and muscle mass via protein degradation. The regulation of sarcomere assembly by integration of incoming signaling pathways causing the same PTMs or ligand binding are discussed in response to mechanical loading and unloading by the Z-disc proteins CapZ, α-actinin, telethonin, titin N-termini, and others. Many human mutations that lead to cardiomyopathy and heart disease occur in the proteins discussed above, which often occur at their PTM or ligand binding sites.

CapZ integrates several signaling pathways in response to mechanical stiffness

Changes in mechanical load, hormones, or metabolic stress provoke remodeling of the actin-based thin filaments within muscle fibers. Solís and Russell show that several signaling pathways converge at the actin-capping protein CapZ to regulate muscle fiber growth in response to mechanical stiffness and neurohumoral signaling.

Muscle adaptation is a response to physiological demand elicited by changes in mechanical load, hormones, or metabolic stress. Cytoskeletal remodeling processes in many cell types are thought to be primarily regulated by thin filament formation due to actin-binding accessory proteins, such as the actin-capping protein. Here, we hypothesize that in muscle, the actin-capping protein (named CapZ) integrates signaling by a variety of pathways, including phosphorylation and phosphatidylinositol 4,5-bisphosphate (PIP2) binding, to regulate muscle fiber growth in response to mechanical load. To test this hypothesis, we assess mechanotransduction signaling that regulates muscle growth using neonatal rat ventricular myocytes cultured on substrates with the stiffness of the healthy myocardium (10 kPa), fibrotic myocardium (100 kPa), or glass. We investigate how PIP2 signaling affects CapZ using the PIP2 sequestering agent neomycin and the effect of PKC-mediated CapZ phosphorylation using the PKC-activating drug phorbol 12-myristate 13-acetate (PMA). Molecular simulations suggest that close interactions between PIP2 and the β-tentacle of CapZ are modified by phosphorylation at T267. Fluorescence recovery after photobleaching (FRAP) demonstrates that the kinetic binding constant of CapZ to sarcomeric thin filaments in living muscle cells increases with stiffness or PMA treatment but is diminished by PIP2 reduction. Furthermore, CapZ with a deletion of the β-tentacle that lacks the phosphorylation site T267 shows increased FRAP kinetics with lack of sensitivity to PMA treatment or PIP2 reduction. Förster resonance energy transfer (FRET) probes the molecular interactions between PIP2 and CapZ, which are decreased by PIP2 availability or by the β-tentacle truncation. These data suggest that CapZ is bound to actin tightly in the idle, locked state, with little phosphorylation or PIP2 binding. However, this tight binding is loosened in growth states triggered by mechanical stimuli such as substrate stiffness, which may have relevance to fibrotic heart disease.

Targeting Focal Adhesion Kinase Using Inhibitors of Protein-Protein Interactions

Focal adhesion kinase (FAK) is a cytoplasmic non-receptor protein tyrosine kinase that is overexpressed and activated in many human cancers. FAK transmits signals to a wide range of targets through both kinase-dependant and independent mechanism thereby playing essential roles in cell survival, proliferation, migration and invasion. In the past years, small molecules that inhibit FAK kinase function have been developed and show reduced cancer progression and metastasis in several preclinical models. Clinical trials have been conducted and these molecules display limited adverse effect in patients. FAK contain multiple functional domains and thus exhibit both important scaffolding functions. In this review, we describe the major FAK interactions relevant in cancer signalling and discuss how such knowledge provide rational for the development of Protein-Protein Interactions (PPI) inhibitors.

Phosphatidylinositol 4,5-bisphosphate regulates CapZβ1 and actin dynamics in response to mechanical strain

Mechanical stress causes filament remodeling leading to myocyte hypertrophy and heart failure. The actin capping protein Z (CapZ) tightly binds to the barbed end of actin filaments, thus regulating actin assembly. The hypothesis is that the binding between CapZ and the actin filament is modulated through phosphatidylinositol 4,5-bisphosphate (PIP2) and how the COOH-terminus of CapZβ1 regulates this binding. Primary neonatal rat ventricular myocytes (NRVMs) were strained at 10% amplitude and 1-Hz frequency. Dot blotting measured the PIP2 amount, and affinity precipitation assay assessed the direct interaction between PIP2 and CapZβ1. Fluorescence recovery after photobleaching of green fluorescent protein-CapZβ1 and actin-green fluorescent protein after 1 h of strain shows the dynamics significantly increased above the unstrained group. The increases in CapZ and actin dynamics were blunted by neomycin, suggesting PIP2 signaling is involved. The amount of PIP2 dramatically increased in NRVMs strained for 1 h. With a ROCK or RhoA inhibitor, changes were markedly reduced. Subcellular fractionation and antibody localization showed PIP2 distributed to the sarcomeres. More PIP2-bound CapZβ1 was found in strained NRVMs. Less PIP2 bound to the CapZβ1 with its COOH-terminus intact than in the COOH-terminal mutant of CapZβ1, suggesting some inhibitory role for the COOH-terminus. Myocyte hypertrophy normally induced by 48 h of cyclic strain was blunted by dominant negative RhoA or neomycin. This suggests that after many hours of cyclic strain, a possible mechanism for cell hypertrophy is the accumulation of thin filament assembly triggered partially by the increased PIP2 level and its binding to CapZ.

Modeling morphodynamic phenotypes and dynamic regimes of cell motion

Many cellular processes and signaling pathways converge onto cell morphology and cell motion, which share important components. The mechanisms used for propulsion could also be responsible for shape changes, if they are capable of generating the rich observed variety of dynamic regimes. Additionally, the analysis of cell shape changes in space and time promises insight into the state of the cytoskeleton and signaling pathways controlling it. While this has been obvious for some time by now, little effort has been made to systematically and quantitatively explore this source of information. First pioneering experimental work revealed morphodynamic phenotypes which can be associated with dynamic regimes like oscillations and excitability. Here, we review the current state of modeling of morphodynamic phenotypes, the experimental results and discuss the ideas on the mechanisms driving shape changes which are suggested by modeling.

Mechanical stress-induced sarcomere assembly for cardiac muscle growth in length and width

A ventricular myocyte experiences changes in length and load during every beat of the heart and has the ability to remodel cell shape to maintain cardiac performance. Specifically, myocytes elongate in response to increased diastolic strain by adding sarcomeres in series, and they thicken in response to continued systolic stress by adding filaments in parallel. Myocytes do this while still keeping the resting sarcomere length close to its optimal value at the peak of the length-tension curve. This review focuses on the little understood mechanisms by which direction of growth is matched in a physiologically appropriate direction. We propose that the direction of strain is detected by differential phosphorylation of proteins in the costamere, which then transmit signaling to the Z-disc for parallel or series addition of thin filaments regulated via the actin capping processes. In this review, we link mechanotransduction to the molecular mechanisms for regulation of myocyte length and width.

Single Molecule Kinetic Analysis of Actin Filament Capping

We investigated how heterodimeric capping proteins bind to and dissociate from the barbed ends of actin filaments by observing single muscle actin filaments by total internal reflection fluorescence microscopy. The barbed end rate constants for mouse capping protein (CP) association of 2.6 x 10(6) M(-1) s(-1) and dissociation of 0.0003 s(-1) agree with published values measured in bulk assays. The polyphosphoinositides (PPIs), phosphatidylinositol 3,4-bisphosphate (PI(3,4)P(2)), PI(4,5)P(2), and PI(3,4,5)P(3), prevent CP from binding to barbed ends, but three different assays showed that none of these lipids dissociate CP from filaments at concentrations that block CP binding to barbed ends. The affinity of fission yeast CP for barbed ends is a thousandfold less than mouse CP, because of a slower association rate constant (1.1 x 10(5) M(-1) s(-1)) and a faster dissociation rate constant (0.004 s(-1)). PPIs do not inhibit binding of fission yeast CP to filament ends. Comparison of homology models revealed that fission yeast CP lacks a large patch of basic residues along the actin-binding surface on mouse CP. PPIs binding to this site might interfere sterically with capping, but this site would be inaccessible when CP is bound to the end of a filament.

Structure/function analysis of the interaction of phosphatidylinositol 4,5-bisphosphate with actin-capping protein: implications for how capping protein binds the actin filament

The heterodimeric actin-capping protein (CP) can be inhibited by polyphosphoinositides, which may be important for actin polymerization at membranes in cells. Here, we have identified a conserved set of basic residues on the surface of CP that are important for the interaction with phosphatidylinositol 4,5-bisphosphate (PIP(2)). Computational docking studies predicted the identity of residues involved in this interaction, and functional and physical assays with site-directed mutants of CP confirmed the prediction. The PIP(2) binding site overlaps with the more important of the two known actin-binding sites of CP. Correspondingly, we observed that loss of PIP(2) binding correlated with loss of actin binding among the mutants. Using TIRF (total internal reflection fluorescence) microscopy, we observed that PIP(2) rapidly converted capped actin filaments to a growing state, consistent with uncapping. Together, these results extend our understanding of how CP binds to the barbed end of the actin filament, and they support the idea that CP can "wobble" when bound to the barbed end solely by the C-terminal "tentacle" of its beta-subunit.