Tad A. Holak

Lifeact: a versatile marker to visualize F-actin.

Live imaging of the actin cytoskeleton is crucial for the study of many fundamental biological processes, but current approaches to visualize actin have several limitations. Here we describe Lifeact, a 17-amino-acid peptide, which stained filamentous actin (F-actin) structures in eukaryotic cells and tissues. Lifeact did not interfere with actin dynamics in vitro and in vivo and in its chemically modified peptide form allowed visualization of actin dynamics in nontransfectable cells.

Structure of the IGF-binding domain of the insulin-like growth factor-binding protein-5 (IGFBP-5): implications for IGF and IGF-I receptor interactions.

Binding proteins for insulin‐like growth factors (IGFs) IGF‐I and IGF‐II, known as IGFBPs, control the distribution, function and activity of IGFs in various cell tissues and body fluids. Insulin‐like growth factor‐binding protein‐5 (IGFBP‐5) is known to modulate the stimulatory effects of IGFs and is the major IGF‐binding protein in bone tissue. We have expressed two N‐terminal fragments of IGFBP‐5 in Escherichia coli; the first encodes the N‐terminal domain of the protein (residues 1–104) and the second, mini‐IGFBP‐5, comprises residues Ala40 to Ile92. We show that the entire IGFBP‐5 protein contains only one high‐affinity binding site for IGFs, located in mini‐IGFBP‐5. The solution structure of mini‐IGFBP‐5, determined by nuclear magnetic resonance spectroscopy, discloses a rigid, globular structure that consists of a centrally located three‐stranded anti‐parallel β‐sheet. Its scaffold is stabilized further by two inside packed disulfide bridges. The binding to IGFs, which is in the nanomolar range, involves conserved Leu and Val residues localized in a hydrophobic patch on the surface of the IGFBP‐5 protein. Remarkably, the IGF‐I receptor binding assays of IGFBP‐5 showed that IGFBP‐5 inhibits the binding of IGFs to the IGF‐I receptor, resulting in reduction of receptor stimulation and autophosphorylation. Compared with the full‐length IGFBP‐5, the smaller N‐terminal fragments were less efficient inhibitors of the IGF‐I receptor binding of IGFs.

Structures of low molecular weight inhibitors bound to MDMX and MDM2 reveal new approaches for p53-MDMX/MDM2 antagonist drug discovery

Intensive anticancer drug discovery efforts have been made to develop small molecule inhibitors of the p53-MDM2 and p53-MDMX interactions. We present here the structures of the most potent inhibitors bound to MDM2 and MDMX that are based on the new imidazo-indole scaffold. In addition, the structure of the recently reported spiro-oxindole inhibitor bound to MDM2 is described. The structures indicate how the substituents of a small molecule that bind to the three subpockets of the MDM2/X-p53 interaction should be optimized for effective binding to MDM2 and/or MDMX. While the spiro-oxindole inhibitor triggers significant ligand-induced changes in MDM2, the imidazo-indoles share similar binding modes for MDMX and MDM2, but cause only minimal induced-fit changes in the structures of both proteins. Our study includes the first structure of the complex between MDMX and a small molecule and should aid in developing efficient scaffolds for binding to MDMX and/or MDM2.

Structure of the Stapled p53 Peptide Bound to Mdm2

Mdm2 is a major negative regulator of the tumor suppressor p53 protein, a protein that plays a crucial role in maintaining genome integrity. Inactivation of p53 is the most prevalent defect in human cancers. Inhibitors of the Mdm2-p53 interaction that restore the functional p53 constitute potential nongenotoxic anticancer agents with a novel mode of action. We present here a 2.0 Å resolution structure of the Mdm2 protein with a bound stapled p53 peptide. Such peptides, which are conformationally and proteolytically stabilized with all-hydrocarbon staples, are an emerging class of biologics that are capable of disrupting protein-protein interactions and thus have broad therapeutic potential. The structure represents the first crystal structure of an i, i + 7 stapled peptide bound to its target and reveals that rather than acting solely as a passive conformational brace, a staple can intimately interact with the surface of a protein and augment the binding interface.

Relaxation matrix refinement of the solution structure of squash trypsin inhibitor

The structure of the small squash trypsin inhibitor CMTI-I is refined by directly minimizing the difference between the observed two-dimensional nuclear Overhauser enhancement (NOE) intensities and those calculated by the full relaxation matrix approach. To achieve this, a term proportional to this difference was added to the potential energy function of the molecular dynamics program X-PLOR. Derivatives with respect to atomic co-ordinates are calculated analytically. Spin diffusion effects are thus accounted for fully during the refinement. Initial structures for the refinement were those determined recently by solution nuclear magnetic resonance using the isolated two-spin approximation to derive distance range estimates. The fits to the nuclear magnetic resonance data improve significantly with only small shifts in the refined structures during a few cycles of conjugate gradient minimization. However, larger changes (approximately 1 A) in the conformation occur during simulated annealing, which is accompanied by a further reduction of the difference between experimental and calculated two-dimensional NOE intensities. The refined structures are closer to the X-ray structure of the inhibitor complexed with trypsin than the initial structures. The root-mean-square difference for backbone atoms between the initial structures and the X-ray structure is 0.96 A, and that between the refined structures and the X-ray structure 0.61 A.

Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain

The Mdmx oncoprotein has only recently emerged as a critical - independent to Mdm2 - regulator of p53 activation. We have determined the crystal structure of the N-terminal domain of human Mdmx bound to a 15-residue transactivation domain peptide of human p53. The structure shows why antagonists of the Mdm2 binding to p53 are ineffective in the Mdmx-p53 interaction.

Mutational analysis of the putative nucleic acid‐binding surface of the cold‐shock domain, CspB, revealed an essential role of aromatic and basic residues in binding of single‐stranded DNA containing the Y‐box motif

The major cold‐shock protein of Bacillus subtilis, CspB, is a member of a protein family widespread among prokaryotes and eukaryotes that share the highly conserved cold‐shock domain (CSD). The CSD domain is involved in transcriptional and translational regulation and was shown to bind the Y‐box motif, a cis‐element that contains the core sequence ATTGG, with high affinity. The three‐dimensional structure of CspB, a prototype of this protein family, revealed that this hydrophilic CSD domain creates a surface rich in aromatic and basic amino acids that may act as the nucleic acid‐binding site. We have analysed the potential role of conserved aromatic and basic residues in nucleic acid binding by site‐directed mutagenesis. In gel retardation and ultraviolet cross‐linking experiments, the ability of CspB mutants to bind single‐stranded oligonucleotides (ssDNA) that contain the Y‐box motif was investigated. Single substitutions of three highly conserved phenylalanine residues (Phe‐15, Phe‐17, Phe‐27) by alanine and substitution of one histidine (His‐29) by glutamine, all located within the putative RNA‐binding sites RNP‐1 and RNP‐2, abolished the nucleic acid‐binding activity of CspB. Conservative substitutions of Phe‐15 to tyrosine (F15Y) showed a small increase in binding affinity, whereas separate replacement of Phe‐17 and Phe‐27 by tyrosine caused a reduction in binding activity. These and other substitutions including the conserved basic residues Lys‐7, Lys‐13 and Arg‐56 as well as the aromatic residues Trp‐8 and Phe‐30 strongly suggest that CspB uses the sidechains of these amino acids for specific interaction with nucleic acids. Ultraviolet cross‐linking experiments for CspB mutants with ssDNA supported the idea of specific CspB/nucleic acid interaction and indicated an essential role for the aromatic and basic residues in this binding. In addition, two‐dimensional nuclear magnetic resonance studies with F17A, K13Q, F15Y and F27Y revealed that the mutants have the same overall structure as the wild‐type CspB protein.

Protein solubility

MOTIVATION Obtaining soluble proteins in sufficient concentrations is a recurring limiting factor in various experimental studies. Solubility is an individual trait of proteins which, under a given set of experimental conditions, is determined by their amino acid sequence. Accurate theoretical prediction of solubility from sequence is instrumental for setting priorities on targets in large-scale proteomics projects. RESULTS We present a machine-learning approach called PROSO to assess the chance of a protein to be soluble upon heterologous expression in Escherichia coli based on its amino acid composition. The classification algorithm is organized as a two-layered structure in which the output of primary support vector machine (SVM) classifiers serves as input for a secondary Naive Bayes classifier. Experimental progress information from the TargetDB database as well as previously published datasets were used as the source of training data. In comparison with previously published methods our classification algorithm possesses improved discriminatory capacity characterized by the Matthews Correlation Coefficient (MCC) of 0.434 between predicted and known solubility states and the overall prediction accuracy of 72% (75 and 68% for positive and negative class, respectively). We also provide experimental verification of our predictions using solubility measurements for 31 mutational variants of two different proteins.

Molecular basis for the inhibition of p53 by Mdmx.

The oncoprotein Mdm2, and the recently intensely studied, homologues protein Mdmx, are principal negative regulators of the p53 tumor uppressor. The mechanisms by which they regulate the stability and activity of p53 are not fully established. We have determined the crystal structure of the N-terminal domain of Mdmx bound to a 15-residue p53 peptide. The structure reveals that although the principle features of the Mdm2-p53 interaction are preserved in the Mdmx-p53 complex, the Mdmx hydrophobic cleft on which the p53 peptide binds is significantly altered: a part of the cleft is blocked by sidechains of Met and Tyr of the p53-binding pocket of Mdmx. Thus specific inhibitors of Mdm2-p53 would not be optimal for binding to Mdmx. Our binding assays show indeed that nutlins, the newly discovered, potent antagonists of the Mdm2-p53 interaction, are notcapable to efficiently disrupt the Mdmx-p53 interaction. To achieve full activation of p53 in tumor cells, compounds that are specific for Mdmx are necessary to complement the Mdm2 specific binders.

Structural basis for the inhibition of insulin-like growth factors by insulin-like growth factor-binding proteins.

Insulin-like growth factor-binding proteins (IGFBPs) control bioavailability, activity, and distribution of insulin-like growth factor (IGF)1 and -2 through high-affinity IGFBP/IGF complexes. IGF-binding sites are found on N- and C-terminal fragments of IGFBPs, the two conserved domains of IGFBPs. The relative contributions of these domains to IGFBP/IGF complexation has been difficult to analyze, in part, because of the lack of appropriate three-dimensional structures. To analyze the effects of N- and C-terminal domain interactions, we determined several x-ray structures: first, of a ternary complex of N- and C-terminal domain fragments of IGFBP4 and IGF1 and second, of a “hybrid” ternary complex using the C-terminal domain fragment of IGFBP1 instead of IGFBP4. We also solved the binary complex of the N-terminal domains of IGFBP4 and IGF1, again to analyze C- and N-terminal domain interactions by comparison with the ternary complexes. The structures reveal the mechanisms of IGF signaling regulation via IGFBP binding. This finding supports research into the design of IGFBP variants as therapeutic IGF inhibitors for diseases of IGF disregulation. In IGFBP4, residues 1–38 form a rigid disulphide bond ladder-like structure, and the first five N-terminal residues bind to IGF and partially mask IGF residues responsible for the type 1 IGF receptor binding. A high-affinity IGF1-binding site is located in a globular structure between residues 39 and 82. Although the C-terminal domains do not form stable binary complexes with either IGF1 or the N-terminal domain of IGFBP4, in the ternary complex, the C-terminal domain contacts both and contributes to blocking of the IGF1 receptor-binding region of IGF1.