Engineering Synthetic Antibody Inhibitors Specific for LD2 or LD4 Motifs of Paxillin

Targeting the hydrophobic pockets of FAK/PYK2 FAT domain: a highly effective inhibitory strategy suppressing tumor growth and eliminating metastasis

BACKGROUND

FAK is a non-receptor tyrosine kinase and an adaptor protein commonly overexpressed in cancer. It regulates multiple tumorigenic pathways through both kinase-dependent and kinase-independent scaffolding functions and thus represents a promising therapeutic target for various cancers. Several FAK kinase inhibitors shown to be effective in preclinical studies advanced to clinical trials, however none produced objective clinical responses. These results are in part attributed to drug resistance and the inability to simultaneously target kinase-dependent and kinase-independent functions of the protein, both of which have been shown to promote tumorigenesis. This has led to the development of scaffold inhibitors that could be used as adjuvants, none of which have so far reached the clinical stage. Importantly, FAK's closely related paralogue, PYK2, compensates for the loss of FAK thus it is also important to target both kinases. In the present study, we evaluate a novel strategy for the inhibition of kinase-dependent and kinase-independent functions of FAK and PYK2 through the expression of the FAT HP-site-specific LD2-LD4 peptide that leads to their displacement from focal adhesions.

METHODS

The impact of LD2-LD4 expression on FAK and PYK2 was assessed through co-immunoprecipitation experiments, Western Blot analysis and quantitative immunofluorescence. In vitro investigation of the effects of LD2-LD4 expression on tumor cell migration and proliferation was carried out using 2D migration, 3D invasion and proliferation assays. The preclinical experiments of this study were carried out using an orthotopic xenograft model, followed by immunohistochemical analysis.

RESULTS

We show that LD2-LD4 expression leads to the displacement of FAK and PYK2 from focal adhesions, blocking both enzymatic and non-enzymatic activities. It also dramatically inhibits 2D cell migration, as well as invasion in vitro. Importantly, LD2-LD4 exerts promising anti-tumor effects and nearly abolishes the appearance of metastatic foci. Finally, we show that an LD monomer can also displace both FAK and PYK2 from FAs suggesting that organic molecules with high affinity for the FAT HPs could mimic the LD2-LD4 activity.

CONCLUSIONS

Targeting the FAT domain hydrophobic patches of FAK/PYK2 is a highly effective inhibitory strategy that can overcome the limitations of existing ATP competitive inhibitors and lead to the development of novel inhibitors with strong antitumor and antimetastatic activity.

The Role of Paxillin Aberrant Expression in Cancer and Its Potential as a Target for Cancer Therapy

Paxillin is a multi-domain adaptor protein. As an important member of focal adhesion (FA) and a participant in regulating cell movement, paxillin plays an important role in physiological processes such as nervous system development, embryonic development, and vascular development. However, increasing evidence suggests that paxillin is aberrantly expressed in many cancers. Many scholars have also recognized that the abnormal expression of paxillin is related to the prognosis, metastases, invasion, survival, angiogenesis, and other aspects of malignant tumors, suggesting that paxillin may be a potential cancer therapeutic target. Therefore, the study of how aberrant paxillin expression affects the process of tumorigenesis and metastasis will help to develop more efficacious antitumor drugs. Herein, we review the structure of paxillin and its function and expression in tumors, paying special attention to the multifaceted effects of paxillin on tumors, the mechanism of tumorigenesis and progression, and its potential role in tumor therapy. We also hope to provide a reference for the clinical prognosis and development of new tumor therapeutic targets.

Synthetic Antibodies Detect Distinct Cellular States of Chromosome Passenger Complex Proteins

High performance affinity reagents are essential tools to enable biologists to profile the cellular location and composition of macromolecular complexes undergoing dynamic reorganization. To support further development of such tools, we have assembled a high-throughput phage display pipeline to generate Fab-based affinity reagents that target different dynamic forms of a large macromolecular complex, using the Chromosomal Passenger Complex (CPC), as an example. The CPC is critical for the maintenance of chromosomal and cytoskeleton processes during cell division. The complex contains 4 protein components: Aurora B kinase, survivin, borealin and INCENP. The CPC acts as a node to dynamically organize other partnering subcomplexes to build multiple functional structures during mitotic progression. Using phage display mutagenesis, a cohort of synthetic antibodies (sABs) were generated against different domains of survivin, borealin and INCENP. Immunofluorescence established that a set of these sABs can discriminate between the form of the CPC complex in the midbody versus the spindle. Others localize to targets, which appear to be less organized, in the nucleus or cytoplasm. This differentiation suggests that different CPC epitopes have dynamic accessibility depending upon the mitotic state of the cell. An Immunoprecipitation/Mass Spectrometry analysis was performed using sABs that bound specifically to the CPC in either the midbody or MT spindle macromolecular assemblies. Thus, sABs can be exploited as high performance reagents to profile the accessibility of different components of the CPC within macromolecular assemblies during different stages of mitosis suggesting this high throughput approach will be applicable to other complex macromolecular systems.

Quaternary structure independent folding of voltage-gated ion channel pore domain subunits

Every voltage-gated ion channel (VGIC) has a pore domain (PD) made from four subunits, each comprising an antiparallel transmembrane helix pair bridged by a loop. The extent to which PD subunit structure requires quaternary interactions is unclear. Here, we present crystal structures of a set of bacterial voltage-gated sodium channel (BacNa_V) 'pore only' proteins that reveal a surprising collection of non-canonical quaternary arrangements in which the PD tertiary structure is maintained. This context-independent structural robustness, supported by molecular dynamics simulations, indicates that VGIC-PD tertiary structure is independent of quaternary interactions. This fold occurs throughout the VGIC superfamily and in diverse transmembrane and soluble proteins. Strikingly, characterization of PD subunit-binding Fabs indicates that non-canonical quaternary PD conformations can occur in full-length VGICs. Together, our data demonstrate that the VGIC-PD is an autonomously folded unit. This property has implications for VGIC biogenesis, understanding functional states, de novo channel design, and VGIC structural origins.

Protein Engineering: Advances in Phage Display for Basic Science and Medical Research

Functional Protein Engineering became the hallmark in biomolecule manipulation in the new millennium, building on and surpassing the underlying structural DNA manipulation and recombination techniques developed and employed in the last decades of 20th century. Because of their prominence in almost all biological processes, proteins represent extremely important targets for engineering enhanced or altered properties that can lead to improvements exploitable in healthcare, medicine, research, biotechnology, and industry. Synthetic protein structures and functions can now be designed on a computer and/or evolved using molecular display or directed evolution methods in the laboratory. This review will focus on the recent trends in protein engineering and the impact of this technology on recent progress in science, cancer- and immunotherapies, with the emphasis on the current achievements in basic protein research using synthetic antibody (sABs) produced by phage display pipeline in the Kossiakoff laboratory at the University of Chicago (KossLab). Finally, engineering of the highly specific binding modules, such as variants of Streptococcal protein G with ultra-high orthogonal affinity for natural and engineered antibody scaffolds, and their possible applications as a plug-and-play platform for research and immunotherapy will be described.

Paxillin controls actin stress fiber formation and migration of vascular smooth muscle cells by directly binding to the active Fyn

Rho-kinase (ROK)-mediated migration of vascular smooth muscle cells plays a crucial role in cardiovascular diseases. Previously we demonstrated Fyn tyrosine kinase as an upstream molecule of ROK to mediate actin stress fiber formation that plays an important role in cell migration, but the molecular mechanism between the two kinases was unclear. To discover a novel signaling molecule that exists between Fyn and ROK, we identified paxillin acting downstream of the active Fyn by combined use of pulldown assay and mass spectrometry. Immunofluorescence staining confirmed co-localization of Fyn and paxillin at the ends of actin stress fibers in human coronary artery smooth muscle cells (CASMCs). Surface plasmon resonance assay demonstrated direct binding between constitutively active Fyn (CA-Fyn) and N-terminus of paxillin (N-pax). The sphingosylphosphorylcholine (SPC)-induced ROK activation, actin stress fiber formation and cell migration were inhibited by paxillin knockdown, which were rescued by full-length paxillin (FL-pax) but not N-pax. N-pax co-localized with CA-Fyn at the cytosol and overexpression of N-pax inhibited the SPC-induced actin stress fiber formation and cell migration, indicating that the direct binding of FL-pax and CA-Fyn at the ends of actin stress fibers is essential for the ROK-mediated actin stress fiber formation and cell migration. Paxillin, as a novel signalling molecule, mediates the SPC-induced actin stress fiber formation and migration in human CASMCs via the Fyn/paxillin/ROK signalling pathway by direct binding of active Fyn.

Paxillin family of focal adhesion adaptor proteins and regulation of cancer cell invasion

The paxillin family of proteins, including paxillin, Hic-5, and leupaxin, are focal adhesion adaptor/scaffolding proteins which localize to cell-matrix adhesions and are important in cell adhesion and migration of both normal and cancer cells. Historically, the role of these proteins in regulating the actin cytoskeleton through focal adhesion-mediated signaling has been well documented. However, studies in recent years have revealed additional functions in modulating the microtubule and intermediate filament cytoskeletons to affect diverse processes including cell polarization, vesicle trafficking and mechanosignaling. Expression of paxillin family proteins in stromal cells is also important in regulating tumor cell migration and invasion through non-cell autonomous effects on the extracellular matrix. Both paxillin and Hic-5 can also influence gene expression through a variety of mechanisms, while their own expression is frequently dysregulated in various cancers. Accordingly, these proteins may serve as valuable targets for novel diagnostic and treatment approaches in cancer.

Spatial arrangement of LD motif-interacting residues on focal adhesion targeting domain of Focal Adhesion Kinase determine domain-motif interaction affinity and specificity

BACKGROUND

Leucine rich Aspartate motifs (LD motifs) are molecular recognition motifs on Paxillin that recognize LD-motif binding domains (LDBD) of a number of focal adhesion proteins in order to carry out downstream signaling and actin cytoskeleton remodeling. In this study, we identified structural features within LDBDs that influence their binding affinity with Paxillin LD motifs.

METHODS

Various point mutants of focal adhesion targeting (FAT) domain of Focal Adhesion Kinase (FAK) were created by moving a key Lysine residue two and three helical turns in order to match the unique conformations as observed in LDBDs of two other focal adhesion proteins, Vinculin and CCM3.

RESULTS

This led to identify a mutant of FAT domain of FAK, named as FAT(NV) (Asn992 of FAT domain was replaced by Val), with remarkable high affinity for LD1 (K_d = 1.5 μM vs no-binding with wild type) and LD2 peptides (K_d = 7.2 μM vs 63 μM with wild type). Consistently, the focal adhesions of MCF7 cells expressing FAK(NV) were highly stable (turnover rate = 1.25 × 10^-5 μm²/s) as compared to wild type FAK transfected cells (turnover rate = 1.5 × 10^-3 μm²/s).

CONCLUSIONS

We observed that the relative disposition of key LD binding amino-acids at LDBD surface, hydrophobic burial of long Leucine side chains of LD-motifs and complementarity of charged surfaces are the key factors determining the binding affinities of LD motifs with LDBDs.

GENERAL SIGNIFICANCE

Our study will help in protein engineering of FAT domain of FAK by modulating FAK-LD motif interactions which have implications in cellular focal adhesions and cell migration.

The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability

Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.