Artificial beta-sheets: chemical models of beta-sheets

Dissecting the Conformational Stability of a Glycan Hairpin

Systematic structural studies of model oligopeptides revealed important aspects of protein folding and offered design principles to access non-natural materials. In the same way, the rules that regulate glycan folding could be established by studying synthetic oligosaccharide models. However, their analysis is often limited due to the synthetic and analytical complexity. By utilizing a glycan capable of spontaneously folding into a hairpin conformation as a model system, we investigated the factors that contribute to its conformational stability in aqueous solution. The modular design of the hairpin model featured a trisaccharide turn unit and two β-1,4-oligoglucoside stacking strands that allowed for systematic chemical modifications of the glycan sequence, including the introduction of NMR labels and staples. Nuclear magnetic resonance assisted by molecular dynamics simulations revealed that stereoelectronic effects and multiple glycan-glycan interactions are the major determinants of folding stabilization. Chemical modifications in the glycan primary sequence (e.g., strand elongation) can be employed to fine-tune the rigidity of structural motifs distant from the modification sites. These results could inspire the design of other glycan architectures, with implications in glycobiology and material sciences.

Macrocyclic β-Sheets Stabilized by Hydrogen Bond Surrogates

Mimics of protein secondary and tertiary structure offer rationally-designed inhibitors of biomolecular interactions. β-Sheet mimics have a storied history in bioorganic chemistry and are typically designed with synthetic or natural turn segments. We hypothesized that replacement of terminal inter-β-strand hydrogen bonds with hydrogen bond surrogates (HBS) may lead to conformationally-defined macrocyclic β-sheets without the requirement for natural or synthetic β-turns, thereby providing a minimal mimic of a protein β-sheet. To access turn-less antiparallel β-sheet mimics, we developed a facile solid phase synthesis protocol. We surveyed a dataset of protein β-sheets for naturally observed interstrand side chain interactions. This bioinformatics survey highlighted an over-abundance of aromatic-aromatic, cation-π and ionic interactions in β-sheets. In correspondence with natural β-sheets, we find that minimal HBS mimics show robust β-sheet formation when specific amino acid residue pairings are incorporated. In isolated β-sheets, aromatic interactions endow superior conformational stability over ionic or cation-π interactions. Circular dichroism and NMR spectroscopies, along with high-resolution X-ray crystallography, support our design principles.

Synthesis of a glycan hairpin

The primary sequence of a biopolymer encodes the essential information for folding, permitting to carry out sophisticated functions. Inspired by natural biopolymers, peptide and nucleic acid sequences have been designed to adopt particular three-dimensional (3D) shapes and programmed to exert specific functions. In contrast, synthetic glycans capable of autonomously folding into defined 3D conformations have so far not been explored owing to their structural complexity and lack of design rules. Here we generate a glycan that adopts a stable secondary structure not present in nature, a glycan hairpin, by combining natural glycan motifs, stabilized by a non-conventional hydrogen bond and hydrophobic interactions. Automated glycan assembly enabled rapid access to synthetic analogues, including site-specific 13C-labelled ones, for nuclear magnetic resonance conformational analysis. Long-range inter-residue nuclear Overhauser effects unequivocally confirmed the folded conformation of the synthetic glycan hairpin. The capacity to control the 3D shape across the pool of available monosaccharides has the potential to afford more foldamer scaffolds with programmable properties and functions.

Molecular pathogenesis of a novel Met394Thr variant causing hemophilia B

BACKGROUND

Hemophilia B (HB), a rare bleeding disorder, shows X-linked recessive inheritance and is caused by heterogeneous variants in the FIX gene (F9) encoding coagulation factor IX (FIX). This study aimed to investigate the molecular pathogenesis of a novel Met394Thr variant causing HB.

METHODS

We used Sanger sequencing to analyze F9 sequence variants in members of a Chinese family with moderate HB. Subsequently, we performed in vitro experiments on the identified novel FIX-Met394Thr variant. In addition, we performed bioinformatics analysis of the novel variant.

RESULTS

We identified a novel missense variant (c.1181T>C, p.Met394Thr) in a Chinese family with moderate HB in the proband. The proband's mother and grandmother were carriers for the variant. The identified FIX-Met394Thr variant did not affect the transcription of F9 and the synthesis and secretion of FIX protein. The variant may, therefore, affect the physiological function of FIX protein by disrupting its spatial conformation. In addition, another variant (c.88+75A>G) in intron 1 of F9 was identified in the grandmother, which may also affect FIX protein function.

CONCLUSION

We identified FIX-Met394Thr as a novel causative variant of HB. Further understanding of the molecular pathogenesis underlying FIX deficiency may guide novel strategies for precision HB therapy.

Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions

Protein-protein interactions play crucial and subtle roles in many biological processes and modifications of their fine mechanisms generally result in severe diseases. Peptide derivatives are very promising therapeutic agents for modulating protein-protein associations with sizes and specificities between those of small compounds and antibodies. For the same reasons, rational design of peptide-based inhibitors naturally borrows and combines computational methods from both protein-ligand and protein-protein research fields. In this chapter, we aim to provide an overview of computational tools and approaches used for identifying and optimizing peptides that target protein-protein interfaces with high affinity and specificity. We hope that this review will help to implement appropriate in silico strategies for peptide-based drug design that builds on available information for the systems of interest.

An Improved Turn Structure for Inducing β-Hairpin Formation in Peptides

Although β-hairpins are widespread in proteins, there is no tool to coax any small peptide to adopt a β-hairpin conformation, regardless of sequence. Here, we report that δ-linked γ(R)-methyl-ornithine (^δ MeOrn) provides an improved β-turn template for inducing a β-hairpin conformation in peptides. We developed a synthesis of protected ^δ MeOrn as a building block suitable for use in Fmoc-based solid-phase peptide synthesis. The synthesis begins with l-leucine and affords gram quantities of the N^α -Boc-N^δ -Fmoc-γ(R)-methyl-ornithine building block. X-ray crystallography confirms that the ^δ MeOrn turn unit adopts a folded structure in a macrocyclic β-hairpin peptide. CD and NMR spectroscopy allow comparison of the ^δ MeOrn turn template to the δ-linked ornithine (^δ Orn) turn template that we previously introduced and to the popular d-Pro-Gly turn template. These studies show that the folding of the ^δ MeOrn turn template is substantially better than that of ^δ Orn and is comparable to d-Pro-Gly.

Identification of Secondary Binding Sites on Protein Surfaces for Rational Elaboration of Synthetic Protein Mimics

Minimal mimics of protein conformations provide rationally designed ligands to modulate protein function. The advantage of minimal mimics is that they can be chemically synthesized and coaxed to be proteolytically resistant; a key disadvantage is that minimization of the protein binding epitope may be associated with loss of affinity and specificity. Several approaches to overcome this challenge may be envisioned, including deployment of covalent warheads and use of nonnatural residues to improve contacts with the binding surface. Herein, we describe our computational and experimental efforts to enhance the minimal protein mimics with fragments that can contact undiscovered binding pockets on Mdm2 and MdmX-two well-studied protein partners of p53.

Hydrogen Bond Surrogate-Constrained Dynamic Antiparallel β-Sheets

Antiparallel β-sheets are important secondary structures within proteins that equilibrate with random-coil states; however, little is known about the exact dynamics of this process. Here, the first dynamic β-sheet models that mimic this equilibrium have been designed by using an H-bond surrogate that introduces constraint and torque into a tertiary amide bond. 2D NMR data sufficiently reveal the structure, kinetics, and thermodynamics of the folding process, thereby leading the way to similar analysis in isolated biologically relevant β-sheets.

Covalent Linkage and Macrocylization Preserve and Enhance Synergistic Interactions in Catalytic Amyloids

The self-assembly of short peptides into catalytic amyloid-like nanomaterials has proven to be a powerful tool in both understanding the evolution of early proteins and identifying new catalysts for practically useful chemical reactions. Here we demonstrate that both parallel and antiparallel arrangements of β-sheets can accommodate metal ions in catalytically productive coordination environments. Moreover, synergistic relationships, identified in catalytic amyloid mixtures, can be captured in macrocyclic and sheet-loop-sheet species, that offer faster rates of assembly and provide more complex asymmetric arrangements of functional groups, thus paving the way for future designs of amyloid-like catalytic proteins. Our findings show how initial catalytic activity in amyloid assemblies can be propagated and improved in more-complex molecules, providing another link in a complex evolutionary chain between short, potentially abiotically produced peptides and modern-day enzymes.

Fibril formation through self-assembly of a simple glycine derivative and X-ray diffraction study

N-(N-benzoyl glycinyl)-N,N′-dicyclohexylurea was synthesised by conjugating N-benzoyl glycine and dicyclohexylcarbodiimide (DCC) using triethylamine as base catalyst. A single crystal X-ray diffraction study reveals that the compound self-assembles into a supramolecular sheet structure by intermolecular N–H · · · O, C–H · · · O hydrogen bonding and non-bonding van der Waals interactions. A high resolution transmission electronic microscopic (HR-TEM) image of the compound exhibits formation of fibrils in the solid state.

Improved Stability and Tunable Functionalization of Parallel β-Sheets via Multicomponent N-Alkylation of the Turn Moiety

In contrast to the myriad of methods available to produce α-helices and antiparallel β-sheets in synthetic peptides, just a few are known for the construction of stable, non-cyclic parallel β-sheets. Herein, we report an efficient on-resin approach for the assembly of parallel β-sheet peptides in which the N-alkylated turn moiety enhances the stability and gives access to a variety of functionalizations without modifying the parallel strands. The key synthetic step of this strategy is the multicomponent construction of an N-alkylated turn using the Ugi reaction on varied isocyano-resins. This four-component process assembles the orthogonally protected turn fragment and incorporates handles serving for labeling/conjugation purposes or for reducing peptide aggregation. NMR and circular dichroism analyses confirm the better-structured and more stable parallel β-sheets in the N-alkylated peptides compared to the non-functionalized variants.

Variation in the Yaa position of collagen peptides containing azaGlycine

Herein, we report the systematic investigation of amino acid variation in the Yaa position of collagen peptides containing an adjacent azaGlycine residue. We demonstrate the reliability of azaGlycine as a glycine replacement and provide a sequence independent strategy for stabilizing the triple helical assembly of collagen peptides.

Uracil-amino acid as a scaffold for β-sheet peptidomimetics: Study of photophysics and interaction with BSA protein

We report herein the uracil-di-aza-amino acid (U^rAA) as a new family of molecular scaffold to induce β-hairpin structure with H-bonded β-sheet conformation in a short peptide. This has been demonstrated in two conceptual fluorescent pentapeptides wherein triazolylpyrenyl alanine and/or triazolylmethoxynapthyl alanine (^TPyAla_Do and/or ^TMNapAla_Do) are embedded into two arms of the uracil-amino acid via an intervening leucine. Conformational analysis by CD, IR, variable temperature and 2D NMR spectroscopy reveals the β-hairpin structures for both the peptides. Study of photophysical property reveals that the pentapeptide containing fluorescent triazolyl unnatural amino acids ^TMNapAla_Do and ^TPyAla_Do at the two termini exhibits dual path entry to exciplex emission-either via FRET from ^TMNapAla_Do to ^TPyAla_Do or via direct excitation of a FRET acceptor, ^TPyAla_Do. The other pentapeptide with ^TPyAla_Do/^TPyAla_Do pair shows excimer emission. Furthermore, both the peptides maintaining their fundamental photophysics are found to interact with BSA as only a test biomolecule.

Computational and Experimental Evaluation of Designed β-Cap Hairpins Using Molecular Simulations and Kinetic Network Models

Molecular simulation has been used to model the detailed folding properties of peptides, yet prospective computational peptide design by such approaches remains challenging and nontrivial. To test the accuracy of simulation-based hairpin design, we characterized the folding properties of a series of so-called β-cap hairpin peptides designed to mimic a conserved hairpin of LapD, a bacterial intracellular signaling protein, both experimentally by NMR spectroscopy and computationally by implicit-solvent replica-exchange molecular dynamics using three different AMBER force fields (ff96, ff99sb-ildn, and ff99sb-ildn-NMR). A unique challenge presented by these designs is the presence of both a terminal Trp-Trp capping motif and a conserved GWxQ motif in the hairpin turn required for binding to LapG. Consistent with previous studies, we found AMBER ff96 to be the most accurate when used with the OBC GBSA implicit solvent model, despite its known bias toward β-sheet conformations when used in explicit-solvent simulations. To gain microscopic insight into the folding landscape of the hairpin designs, we additionally performed parallel simulations on the Folding@home distributed computing platform using AMBER ff99sb-ildn-NMR with TIP3P explicit solvent. Markov state models (MSMs) built from trajectory data reveal a number of non-native interactions between Trp and other amino acid side chains, creating potential problems in achieving well-folded hairpin structures in solution.

Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions

We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala)_nn ≤ 5.

The conjugates of ferrocene-1,1'-diamine and amino acids. A novel synthetic approach and conformational analysis

A novel synthetic approach toward a poorly explored bioorganometallic consisting of ferrocene-1,1'-diamine bearing structurally and chirally diverse amino acid sequences is reported. Until now, ferrocene-1,1'-diamine was suitable for accommodating only identical amino acid sequences at its N-termini, leading to the symmetrically disubstituted homochiral products stabilized through a 14-membered intramolecular hydrogen-bonded ring as is seen in antiparallel β-sheet peptides. The key step of the novel synthetic pathway is the transformation of Ac-Ala-NH-Fn-COOH (5) (Fn = 1,1'-ferrocenylene) to orthogonally protected Ac-Ala-NH-Fn-NHBoc (7). The spectroscopic analysis (IR, NMR, CD) of the novel compounds, corroborated with DFT studies, suggests the interesting feature of the ferrocene-1,1'-diamine scaffold. The same hydrogen-bonding pattern, i.e. a 14-membered hydrogen-bonded ring, was determined both in solution and in the solid state, thus making them promising, yet simple scaffolds capable of mimicking β-sheet peptides. In vitro screening of potential anticancer activity in Hep G2 human liver carcinoma cells and Hs 578 T human breast cancer cells revealed a cytotoxic pattern for novel compounds (150-500 μM) with significantly decreased cell proliferation.

Peptide self-assembly triggered by metal ions

This review summarizes the recent development of structures, functions, as well as strategies of a peptide self-assembly induced by metal ions.

Phototriggerable peptidomimetics for the inhibition of Mycobacterium tuberculosis ribonucleotide reductase by targeting protein–protein binding

Peptidomimetic inhibitors with photomodulable affinity for the R1–R2 subunit association site were designed based on the R2-subunit C-terminal.

Design of monomeric water-soluble β-hairpin and β-sheet peptides

Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.

Small Molecule Probes That Perturb A Protein-protein Interface In Antithrombin

Small molecule probes for perturbing protein-protein interactions (PPIs) in vitro can be useful if they cause the target proteins to undergo biomedically relevant changes to their tertiary and quaternary structures. Application of the Exploring Key Orientations (EKO) strategy (J. Am. Chem. Soc., 2013, 135, 167 - 173) to a piperidinone-piperidine chemotype 1 indicated specific derivatives were candidates to perturb a protein-protein interface in the α-antithrombin dimer; those particular derivatives of 1 were prepared and tested. In the event, most of them significantly accelerated oligomerization of monomeric α-antithrombin, which is metastable in its oligomeric state. This assertion is supported by data from gel electrophoresis (non-denaturing PAGE; throughout) and probe-induced loss of α-antithrombin's inhibitor activity in a reaction catalyzed by thrombin. Kinetics of α-antithrombin oligomerization induced by the target compounds were examined. It was found that probes with O-benzyl-protected serine side-chains are the most active catalysts in the series, and reasons for this, based on modeling experiments, are proposed. Overall, this study reveals one of the first examples of small molecules designed to act at a protein-protein interface relevant to oligomerization of a serpin (ie α-antithrombin). The relevance of this to formation of oligomeric serpin fibrils, associated with the disease states known as "serpinopathies", is discussed.

The supramolecular chemistry of β-sheets

Interactions among β-sheets occur widely in protein quaternary structure, protein-protein interaction, and protein aggregation and are central in Alzheimer's and other amyloid-related diseases. This Perspective looks at the structural biology of these important yet under-appreciated interactions from a supramolecular chemist's point of view. Common themes in the supramolecular interactions of β-sheets are identified and richly illustrated though examples from proteins, amyloids, and chemical model systems. β-Sheets interact through edge-to-edge hydrogen bonding to form extended layers and through face-to-face hydrophobic or van der Waals interactions to form layered sandwich-like structures. Side chains from adjacent layers can fit together through simple hydrophobic contacts or can participate in complementary interdigitation or knob-hole interactions. The layers can be aligned, offset, or rotated. The right-handed twist of β-sheets provides additional opportunities for stabilization of edge-to-edge contacts and rotated layered structures.

Transient fibril structures facilitating nonenzymatic self-replication

An emerging new direction of research focuses on developing "self-synthesizing materials", those supramolecular structures that can promote their own formation by accelerating the synthesis of building blocks and/or an entire assembly. It was postulated recently that practical design of such systems can benefit from the ability to control the assembly of amphiphilic molecules into nanostructures. We describe here the self-assembly pathway of short amphiphilic peptides into various forms of soluble β-sheet structures--β-plates, fibrils, and hollow nanotubes--and their consequent activity as autocatalysts for the synthesis of monomeric peptides from simpler building blocks. A detailed kinetic analysis of both the self-assembly and self-replication processes allows us to suggest a full model and simulate the replication process, revealing that only specific structures, primarily fibrils that are stable within the solution for a time shorter than a few hours, can be active as catalysts. Interestingly, we have found that such a process also induces fibril reproduction, in a mechanism very similar to the propagation of prion proteins by transmission of misfolded states.

Computational design of a symmetric homodimer using β-strand assembly

Computational design of novel protein-protein interfaces is a test of our understanding of protein interactions and has the potential to allow modification of cellular physiology. Methods for designing high-affinity interactions that adopt a predetermined binding mode have proved elusive, suggesting the need for new strategies that simplify the design process. A solvent-exposed backbone on a β-strand is thought of as "sticky" and β-strand pairing stabilizes many naturally occurring protein complexes. Here, we computationally redesign a monomeric protein to form a symmetric homodimer by pairing exposed β-strands to form an intermolecular β-sheet. A crystal structure of the designed complex closely matches the computational model (rmsd = 1.0 Å). This work demonstrates that β-strand pairing can be used to computationally design new interactions with high accuracy.

Modular design in natural and biomimetic soft materials

Under eons of evolutionary and environmental pressure, biological systems have developed strong and lightweight peptide-based polymeric materials by using the 20 naturally occurring amino acids as principal monomeric units. These materials outperform their man-made counterparts in the following ways: 1) multifunctionality/tunability, 2) adaptability/stimuli-responsiveness, 3) synthesis and processing under ambient and aqueous conditions, and 4) recyclability and biodegradability. The universal design strategy that affords these advanced properties involves "bottom-up" synthesis and modular, hierarchical organization both within and across multiple length-scales. The field of "biomimicry"-elucidating and co-opting nature's basic material design principles and molecular building blocks-is rapidly evolving. This Review describes what has been discovered about the structure and molecular mechanisms of natural polymeric materials, as well as the progress towards synthetic "mimics" of these remarkable systems.

Four and a half LIM protein 1 gene mutations cause four distinct human myopathies: a comprehensive review of the clinical, histological and pathological features

Mutations in the four and a half LIM protein 1 (FHL1) gene were recently identified as the cause of four distinct skeletal muscle diseases. Since the initial report outlining the first fhl1 mutation in 2008, over 25 different mutations have been identified in patients with reducing body myopathy, X-linked myopathy characterized by postural muscle atrophy, scapuloperoneal myopathy and Emery-Dreifuss muscular dystrophy. Reducing body myopathy was first described four decades ago, its underlying genetic cause was unknown until the discovery of fhl1 mutations. X-linked myopathy characterized by postural muscle atrophy is a novel disease where fhl1 mutations are the only cause. This review will profile each of the FHL1, with a comprehensive analysis of mutations, a comparison of the clinical and histopathological features and will present several hypotheses for the possible disease mechanism(s).

Giant macrolactams based on β-sheet peptides

This paper reports the use of natural amino acids, the tripeptide β-strand mimic Hao, and the β-turn mimic δ-linked ornithine to generate water-soluble 54-, 78-, and 102-membered-ring macrolactams. These giant macrocycles were efficiently prepared by synthesis of the corresponding protected linear peptides, followed by solution-phase cyclization and deprotection. The protected linear peptide precursors were synthesized on 2-chlorotrityl chloride resin by conventional Fmoc-based solid-phase peptide synthesis. Macrocyclization was typically performed using HCTU and N,N-diisopropylethylamine in DMF at ca. 0.5 mM concentration. The macrocycles were isolated in 13-45% overall yield after HPLC purification and lyophilization. 1D, 2D TOCSY, and 2D ROESY (1)H NMR studies of the 54- and 78-membered-ring macrolactams establish that these compounds fold to form β-sheet structures in aqueous solutions.

Characteristics of amyloid-related oligomers revealed by crystal structures of macrocyclic β-sheet mimics

Protein amyloid oligomers have been strongly linked to amyloid diseases and can be intermediates to amyloid fibers. β-Sheets have been identified in amyloid oligomers. However, because of their transient and highly polymorphic properties, the details of their self-association remain elusive. Here we explore oligomer structure using a model system: macrocyclic peptides. Key amyloidogenic sequences from Aβ and tau were incorporated into macrocycles, thereby restraining them to β-strands, but limiting the growth of the oligomers so they may crystallize and cannot fibrillate. We determined the atomic structures for four such oligomers, and all four reveal tetrameric interfaces in which β-sheet dimers pair together by highly complementary, dry interfaces, analogous to steric zippers found in fibers, suggesting a common structure for amyloid oligomers and fibers. In amyloid fibers, the axes of the paired sheets are either parallel or antiparallel, whereas the oligomeric interfaces display a variety of sheet-to-sheet pairing angles, offering a structural explanation for the heterogeneity of amyloid oligomers.

Regioisomeric control induced by DABCO coordination to rotatable self-assembled bis- and tetraporphyrin α,γ-cyclic octapeptide dimers

The design and synthesis of two α,γ-cyclic octapeptides decorated with one and two Zn-porphyrin units in their periphery is described. In nonpolar organic solvents the α,γ-cyclic octapeptides quantitatively self-assemble into Zn-bis- or -tetraporphyrin architectures that could act as molecular tweezers. The self-assembly process, however, is not regioselective and affords a mixture of different regioisomers that are involved in chemical exchange processes. The regioisomers with the Zn-porphyrin units positioned in register with respect to each other are proposed to be the less abundant species in the solution mixture. It has been demonstrated that the coordination of 1,4-diazabicyclo[2.2.2]octane (DABCO) to the supramolecular bis- or tetraporphyrin tweezers is an effective way to achieve regioisomeric control of the self-assembled mixture of dimers. Thus, DABCO functions as an external molecular trigger and, when used under strict stoichiometric control with respect to the Zn-porphyrin units, provokes the exclusive formation of self-assembled dimers with a cofacial arrangement of Zn-porphyrin units through the formation of sandwich-type complexes. The use of excess DABCO fragments the sandwich complexes and affords open dimers of high stoichiometry with DABCO molecules axially monocoordinated to the Zn-porphyrin units, probably as a regioisomeric mixture. In the case of Zn-tetraporphyrin tweezers, the ditopic coordination of DABCO at the two binding sites shows a moderate positive cooperativity factor, αP=5. These assemblies have potential applications as light-induced energy and electron-transfer switches regulated by DABCO coordination; such applications would require the introduction of additional chromophores in the cyclic peptide scaffold.