The creation of native-like macromolecules in copying nature's way represents a fascinating challenge in protein chemistry today. In the absence of a detailed knowledge of the complex folding pathway the ultimate goal in protein de novo design, the construction of artificial proteins with predetermined three-dimensional structure and tailor-made functions based on a defined, generally valid set of rules, appears to be still out of reach. With progress in synthesis strategies and biostructural characterization methods, topological templates have become a versatile tool for inducing and stabilizing secondary and tertiary structures, such as protein loops, beta-turns, alpha-helices, beta-sheets and a variety of folding motifs. In this article, we extend the concept of template-assembled synthetic proteins for the construction of protein-like topologies with multiply bridged, oligocyclic chain architectures termed locked-in tertiary folds that exhibit unique physicochemical and folding properties because of the highly confined conformational space. Furthermore, we show that some fundamental questions in protein assembly can be approached applying the template concept. Using covalent template trapping of self-associated peptide assemblies in aqueous solution the structural and physical forces guiding protein folding, supramolecular assembly and molecular recognition processes can be studied on a molecular level.

Platelet adhesion, the initial step of platelet activation, is mediated by the interaction of von Willebrand factor (VWF) with its platelet receptor, the GPIb–IX complex. The binding of VWF to GPIb–IX is induced either by increased shear stress or by exogenous modulators, such as botrocetin. At a molecular level, this interaction takes place between the A1 domain of VWF and the GPIbα chain of the GPIb–IX complex. We report here the design and functional characteristics of a VWF template‐assembled synthetic protein (TASP), a chimeric four‐helix‐bundle TASP scaffold mimicking the surface of the A1 domain. Twelve residues located on helices α3 and α4 in the native A1 domain were grafted onto a surface formed by two neighboring helices of the TASP. VWF TASP was found to inhibit specifically botrocetin‐induced platelet aggregation and to bind both botrocetin and GPIbα. However, in contrast to the native A1 domain, VWF TASP did not bind simultaneously to both ligands. Modeling studies revealed that the relative orientation of the α helices in VWF TASP led to a clash of bound botrocetin and GPIbα. These results demonstrate that a chimeric four‐helix‐bundle TASP as a scaffold offers a suitable surface for presenting crucial residues of the VWF A1 domain; the potential of the TASP approach for de novo protein design and mimicry is thereby illustrated.

The construction of protein-like folding motifs as structurally stable scaffolds for the introduction of function represents a major goal in protein design. The use of topol. templates allows the bypass of the well-known folding problem of linear polypeptides and offers a way to mimic native packing topologies by the template directed self-assembly of helical and/or b-sheeted peptide blocks. In conceptually sepg. structure from function, a chimeric 4-helix bundle TASP (Template Assembled Synthetic Protein) derived from the ROP protein and the cell adhesion glycoprotein E-selectin has been designed and synthesized, aimed at inhibiting an early stage in cell adhesion processes, in particular leukocyte adhesion. [on SciFinder (R)]

Pseudo-proline building blocks exert a dual functionality in enhancing and stabilizing the relevant polyproline II (PPII) conformation and increasing and optimizing van der Waals contacts and hydrogen bonding to the receptor mols. thus modifying affinity and specificity. They are highly useful in studying ligand recognition mediated by Src homol. 3 domains essential in cellular regulation and protein-protein interactions. The 2-C substituents promote the induction of the required PPII helix and allow for optimal complementation of the SH3 topog. [on SciFinder (R)]

Pseudoprolines (ΨPro) have been developed as tools for inducing bioactive conformations that allow for optimal spatial complementation in protein-protein interactions. This dual function of ΨPro was explored for tuning proline-rich peptides as potent ligands for SH3 domains.

Specific protein-protein interactions are essential facets in cellular communication and the formation and specific assembly of multicomponent protein complexes often is regulated by binding to proline (Pro)-rich peptide sequences. Pro-rich ligands adopt a left-handed polyproline II helical conformation (PPII, all trans amide bonds) and bind to a highly conserved patch of aromatic amino acids of e.g. Src homology (SH3) domains [1]. The essential feature of SH3 binding ligands is the consensus sequence Pro-Xaa-Xaa-Pro (Xaa representing variable amino acids). In the search for novel inhibitors, recently introduced pseudoprolines (ΨPro), i.e. Ser, Thr, Cys derived proline-ring structures with enhanced inherent properties of L-Pro, were used to study ligand receptor interactions of Pro-rich peptides [2]. Binding affinities in the order typically found for SH3-mediated interactions and most notably, enhanced binding specificity as well as inhibition of Grb2 SH3 (N)-SoS complex formation (Figure 1) illustrate that ΨPro building blocks exert a dual functionality, i.e. i) increase and optimization of van der Waals contacts and hydrogen bonding to the receptor molecule, and ii) enhancement of the relevant PPII conformation [3]. To further optimize ligand-receptor interactions in the search of potent SH3 ligands, 2C-substituted ΨPro libraries applying post-insertion strategies have been generated allowing for rapid screening of ligands that optimally complement the SH3 topography.

An experimental system is described, permitting a detailed and systematic analysis of the factors governing self-assembly of amphipathic helices, e.g. to a four-helical bundle, a subject of major relevance for tertiary structure formation, protein folding and design. Following the Template Assembled Synthetic Proteins (TASP) approach, helices of different packing potential are competitively assembled in solution with a preformed two-helix TASP molecule, and after equilibration are covalently attached ('template trapping') via chemoselective thioether formation. The quantitative analysis of the individual TASP molecules by high performance liquid chromatography (HPLC) and electrospray mass spectrometry (ES-MS) allows the delineation of the role of complementary packing in helix bundle formation. The procedure established represents a general tool for the experimental verification of modern concepts in molecular recognition.

Pseudoproline (ΨPro) dienen als vielseitige Bausteine, die in der Lage sind, die bioaktive Konformation eines Peptidliganden sowie die für eine Protein-Protein-Wechselwirkung komplementäre Oberflächenstruktur zu induzieren. Diese duale Funktion von ΨPro wurde an prolinreichen Peptiden als effizienten Liganden für SH3-Domänen aufgezeigt (siehe Bild).

Creating functional biological molecules de novo requires a detailed understanding of the intimate relationship between primary sequence, folding mechanism, and packing topology, and remains up to now a most challenging goal in protein design and mimicry. As a consequence, the use of well-defined robust macromolecules as scaffolds for the introduction of function by grafting surface residues has become a major objective in protein engineering and de novo design. In this article, the concept of scaffolds is demonstrated on some selected examples, illustrating that novel types of functional molecules can be generated. Reengineered proteins and, most notably, de novo designed peptide scaffolds exhibiting molecular function, are ideal tools for structure-function studies and as leads in drug design.

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Experience has shown that protein redesigns (using the backbone from a known protein structure) are far more likely to produce well-ordered, native-like structures than are true de novo designs. Therefore, to design a four-helix bundle made of identical short helices, we here proceed by an extensive redesign of the ROP protein. A fully symmetrical SymROP sequence derived from ROP was chosen by modeling ideal-geometry side chains, including hydrogens, while maintaining the "goodness-of-fit" of side-chain packing by calculating all-atom contact surfaces with the Reduce and Probe programs. To estimate the probable extent of backbone movement and side-chain mobility, restrained molecular dynamics simulations were compared for candidate sequences and controls, including substitution of Abu for all or half the core Ala residues. The resulting 17-residue designed sequence is 41% identical to the relevant regions in ROP. SymROP is intended for construction by the Template Assembled Synthetic Proteins approach, to control the bundle topology, to use short helices, and to allow blocked termini and unnatural amino acids. ROP protein has been a valuable system for studying helical protein structure because of its simplicity and regularity within a structure large enough to have a real hydrophobic core. The SymROP design carries that simplicity and regularity even further.

The design and synthesis of cyclic mimetics of VCAM-1 protein that reproduce the integrin-binding domain are presented. The unprotected peptide precursor 37–43, Thr-Gln-Ile-Asp-Ser-Pro-Leu, was grafted onto functional templates of type naphthalene, biphenyl and benzyl through the chemoselective formation of C- and N-terminal oximes resulting in a mixture of four isomeric forms due to syn–anti isomerism of the oxime bonds. Some isomers could be monitored by HPLC and identified by NMR. The molecule containing a naphthalene-derived template was found to inhibit the VCAM-1/VLA-4 interaction more efficiently than previously reported for sulfur-bridged cyclic peptides containing similar sequences. The finding confirms the importance of incorporating conformational constraints between the terminal ends of the peptide loop 37–43 in the design of synthetic inhibitors of the VCAM-1/integrin interaction. Copyright © 1999 European Peptide Society and John Wiley & Sons, Ltd.