A Network of Coiled-Coil Associations Derived from Synthetic GCN4 Leucine-Zipper Arrays

Systematic Mutagenesis of Oncocin Reveals Enhanced Activity and Insights into the Mechanisms of Antimicrobial Activity

Oncocin is a proline-rich antimicrobial peptide that inhibits protein synthesis by binding to the bacterial ribosome. In this work, the antimicrobial activity of oncocin was improved by systematic peptide mutagenesis and activity evaluation. We found that a pair of cationic substitutions (P4K and L7K/R) improves the activity by 2-4 fold (p<0.05) against multiple Gram-negative bacteria. An in vitro transcription / translation assay indicated that the increased activity was not because of stronger ribosome binding. Rather a cellular internalization assay revealed a higher internalization rate for the optimized analogs thereby suggesting a mechanism to increase potency. In addition, we found that the optimized peptides' benefit is dependent upon nutrient-depleted media conditions. The molecular design and characterization strategies have broad potential for development of antimicrobial peptides.

Determination of the Substrate Specificity of Protein Kinases with Peptide Micro- and Macroarrays

Elucidation of the key determinants for the phosphorylation site specificities of protein kinases facilitates identification of their physiological substrates, and serves to better define their critical roles in the signaling networks that underlie a multitude of cellular activities. Albeit with some apparent limitations, such as the lack of contextual information for secondary substrate-binding sites, the synthetic peptide-based approach has been adopted widely for the kinase specificity profiling studies, especially when they are used in an array format, which permits the screening of large numbers of potential peptide substrates in parallel. In this chapter, we present detailed protocols for determining protein kinase substrate specificity using an approach that involves both peptide microarrays and macroarrays. In particular, SPOT synthesis on macroarrays can be used to follow up on in silico predictions of protein kinase substrate specificity with predictive algorithms.

Analysis of selected and designed chimeric D- and L-α-helix assemblies

D-peptides have been attributed pharmacological advantages over regular L-peptides, yet design rules are largely unknown. Based on a designed coiled coil-like D/L heterotetramer, named L-Base/D-Acid, we generated a library offering alternative residues for interaction with the D-peptide. Phage display selection yielded one predominant peptide, named HelixA, that differed at 13 positions from the scaffold helix. In addition to the observed D-/L-heterotetramers, ratio-dependent intermediate states were detected by isothermal titration calorimetry. Importantly, the formation of the selected HelixA/D-Acid bundle passes through fewer intermediate states than L-Base/D-Acid. Back mutation of HelixA core residues to L-Base (HelixLL) revealed that the residues at e/g-positions are responsible for the different intermediates. Furthermore, a Val-core variant (PeptideVV) was completely devoid of binding D-Acid, whereas an Ile-core helix (HelixII) interacted with D-Acid in a significantly more specific complex than L-Base.

Synthetic peptide arrays for investigating protein interaction domains

Synthetic peptide array technology was first developed in the early 1990s by Ronald Frank. Since then the technique has become a powerful tool for high throughput approaches in biology and biochemistry. Here, we focus on peptide arrays applied to investigate the binding specificity of protein interaction domains such as WW, SH3, and PDZ domains. We describe array-based methods used to reveal domain networks in yeast, and briefly review rules as well as ideas about the synthesis and application of peptide arrays. We also provide initial results of a study designed to investigate the nature and evolution of SH3 domain interaction networks in eukaryotes.

Complex networks govern coiled-coil oligomerization--predicting and profiling by means of a machine learning approach

Understanding the relationship between protein sequence and structure is one of the great challenges in biology. In the case of the ubiquitous coiled-coil motif, structure and occurrence have been described in extensive detail, but there is a lack of insight into the rules that govern oligomerization, i.e. how many α-helices form a given coiled coil. To shed new light on the formation of two- and three-stranded coiled coils, we developed a machine learning approach to identify rules in the form of weighted amino acid patterns. These rules form the basis of our classification tool, PrOCoil, which also visualizes the contribution of each individual amino acid to the overall oligomeric tendency of a given coiled-coil sequence. We discovered that sequence positions previously thought irrelevant to direct coiled-coil interaction have an undeniable impact on stoichiometry. Our rules also demystify the oligomerization behavior of the yeast transcription factor GCN4, which can now be described as a hybrid--part dimer and part trimer--with both theoretical and experimental justification.

A study to assess the cross-reactivity of cellulose membrane-bound peptides with detection systems: an analysis at the amino acid level

The growing demand for binding assays to study protein-protein interaction can be addressed by peptide array-based methods. The SPOT technique is a widespread peptide-array technology, which is able to distinguish semi-quantitatively the binding affinities of peptides to defined protein targets within one array. The quality of an assay system used for probing peptide arrays depends on the well-balanced combination of screening and read-out methods. The former address the steady-state of analyte capture, whereas the latter provide the means to detect captured analyte. In all cases, however, false-positive results can occur when challenging a peptide array with analyte or detecting captured analyte with label conjugates. Little is known about the cross-reactivity of peptides with the detection agents. Here, we describe at the amino acid level the potential of (i) 5-(and 6)-carboxytetramethylrhodamine (5(6)-TAMRA), (ii) fluoresceinisothiocyanate in form of the peptide-bound fluorescein-substituted thiourea derivative (FITC), and (iii) biotin/streptavidin-POD to cross-react with individual amino acids in a peptide sequence.

Heterotrimeric coiled coils with core residue urea side chains

We report several coiled coil heterotrimers with varying core residue buried polar groups, all with T(m) values >43 degrees C. Introduction of new synthetic side chain structures, including some terminating in monosubstituted ureas, diversifies the pool of viable core residue candidates. A study of core charge pairings demonstrates that, unlike dimeric systems, trimeric coiled coils do not tolerate guanidine-guanidine contacts, even in the presence of a compensating carboxylate. Overall, the roster of feasible coiled coil designs is significantly expanded.

Structural specificity in coiled-coil interactions

Coiled coils have a rich history in the field of protein design and engineering. Novel structures, such as the first seven-helix coiled coil, continue to provide surprises and insights. Large-scale datasets quantifying the influence of systematic mutations on coiled-coil stability are a valuable new asset to the area. Scoring methods based on sequence and/or structure can predict interaction preferences in coiled-coil-mediated bZIP transcription factor dimerization. Experimental and computational methods for dealing with the near-degeneracy of many coiled-coil structures appear promising for future design applications.

Orthogonal recognition in dimeric coiled coils via buried polar-group modulation

We describe the design and exploration of new buried polar groups to control coiled-coil dimerization. Employing our recently described method for on-resin guanidinylation, we have prepared coiled-coil peptides with a single core guanidine, spaced from the backbone by 1-3 methylene groups. Heterodimeric mixtures of these sequences with guanidine, amide, and carboxylic acid binding partners form a large number of reasonably stable coiled coils (T(m) > or = 60 degrees C). A detailed stability trend examination reveals that asparagine/acid pairs are sharply sensitive to acid residue chain length (Asn/Asp much worse than Asn/Glu), while guanidine/acid pairs are largely insensitive. This has been exploited to create orthogonal recognition pairs which establish the capacity to form two distinct heterodimeric coiled coils by simple mixing of four different peptides. One dimer has buried core asparagines, while the other pairs aspartic acid with any of three guanidinylated side chains. Specificity of this behavior is underscored by failure of glutamic acid substituted sequences to perform accordingly. The successful alternate pairs are further characterized by various biophysical methods (circular dichroism, ultracentrifugation, thermal and chemical denaturation, affinity tags).

Pharmacological interference with protein-protein interactions mediated by coiled-coil motifs

Coiled coils are bundles of intertwined alpha-helices that provide protein-protein interaction sites for the dynamic assembly and disassembly of protein complexes. The coiled-coil motif combines structural versatility and adaptability with mechanical strength and specificity. Multimeric proteins that rely on coiled-coil interactions are structurally and functionally very diverse, ranging from simple homodimeric transcription factors to elaborate heteromultimeric scaffolding clusters. Several coiled-coil-bearing proteins are of outstanding pharmacological importance, most notably SNARE proteins involved in vesicular trafficking of neurotransmitters and viral fusion proteins. Together with their crucial roles in many physiological and pathological processes, the structural simplicity and reversible nature of coiled-coil associations render them a promising target for pharmacological interference, as successfully exemplified by botulinum toxins and viral fusion inhibitors. The alpha-helical coiled coil is a ubiquitous protein domain that mediates highly specific homo- and heteromeric protein-protein interactions among a wide range of proteins. The coiled-coil motif was first proposed by Crick on the basis of X-ray diffraction data on alpha-keratin more than 50 years ago (Crick 1952, 1953) and nowadays belongs to the best-characterized protein interaction modules. By definition, a coiled coil is an oligomeric protein assembly consisting of several right-handed amphipathic alpha-helices that wind around each other into a superhelix (or a supercoil) in which the hydrophobic surfaces of the constituent helices are in continuous contact, forming a hydrophobic core. Both homomeric and heteromeric coiled coils with different stoichiometries are possible, and the helices can be aligned in either a parallel or an antiparallel topology (Harbury et al. 1993, 1994). Stoichiometry and topology are governed by the primary structure, that is, the sequence of the polypeptide chains, and a given protein can participate in multiple assembly-disassembly equilibria among several coiled coils differing in stoichiometry and topology (Portwich et al. 2007). Protein complexes whose oligomeric quaternary structures - and, hence, biological activities - depend on coiled-coil interactions include transcription factors, tRNA synthetases (Biou et al. 1994; Cusack et al. 1990), cytoskeletal and signal-transduction proteins, enzyme complexes, proteins involved in vesicular trafficking, viral coat proteins, and membrane proteins (Langosch and Heringa 1998). It is thus not surprising that coiled-coil motifs have gained great attention as potential targets for modulating protein-protein interactions implicated in a large number of diseases. In this review, we will first discuss some fundamental functional and structural aspects of a simple and well-characterized representative of coiled-coil transcription factors (Sect. 1) before considering two more complex coiled coils found in scaffolding proteins involved in mitosis and meiosis and vesicular trafficking Sect. 2). This will set the stage for addressing the role of coiled coils in viral infection (Sect. 3) as well as strategies of interfering with such protein-protein interactions therapeutically (Sect. 4 and 5).

Mapping Putative Contact Sites Between Subunits in a Bacterial ATP-binding Cassette (ABC) Transporter by Synthetic Peptide Libraries

The maltose ATP-binding cassette transporter of Salmonella typhimurium is composed of the soluble periplasmic receptor, MalE, and a membrane-associated complex comprising one copy each of the pore-forming hydrophobic subunits, MalF and MalG, and of a homodimer of the ATP-hydrolyzing subunit, MalK. During the transport process the subunits are thought to undergo conformational changes that might transiently alter molecular contacts between MalFG and MalK(2). In order to map sites of subunit-subunit interactions we have used a comprehensive peptide mapping approach comprising large-scale microsynthesis of labelled probes and array techniques. In particular, we screened the binding of (i) MalFG-derived soluble biotinylated peptides to immobilized MalK, and (ii) radiolabelled MalK to MalFG-derived cellulose membrane-bound peptides. The first approach identified seven peptides (10mers) each of MalF and MalG that specifically bound to MalK. The peptides were localized to TMDs 3 and 6, periplasmic loop P4 and cytoplasmic loops C2 and C3 of MalF, while MalG-derived peptides localized to the N terminus, TMDs 4-6, periplasmic loop P1 and cytoplasmic loop C2. Peptides from C3 and C2, respectively, of MalF and MalG partially encompass the conserved EAA-motif, known to be crucial for interaction with MalK. These results were basically confirmed by screening MalFG-derived peptide arrays consisting of 16mers or 31mers with radiolabelled MalK. This approach also allowed us to perform complete substitutional analyses of peptides in question. The results led to the construction of MalFG variants that were subsequently analyzed for functional consequences in vivo. Growth experiments revealed that most of the mutations had no phenotype, suggesting that the mutated residues themselves are not critical but part of a discontinuous binding site. However, two novel mutations affecting residues from the EAA motifs of MalF (Ile417Glu) and MalG (Phe203Gln/Asn), respectively, displayed severe growth defects, indicating their functional importance. Together, these experimental outcomes identify specific molecular contacts made between MalK and MalFG that extend beyond the well-characterized EAA motif.