Parallel β-sheet secondary structure is stabilized and terminated by interstrand disulfide cross-linking

Structural conversion of the spidroin C-terminal domain during assembly of spider silk fibers

The major ampullate Spidroin 1 (MaSp1) is the main protein of the dragline spider silk. The C-terminal (CT) domain of MaSp1 is crucial for the self-assembly into fibers but the details of how it contributes to the fiber formation remain unsolved. Here we exploit the fact that the CT domain can form silk-like fibers by itself to gain knowledge about this transition. Structural investigations of fibers from recombinantly produced CT domain from E. australis MaSp1 reveal an α-helix to β-sheet transition upon fiber formation and highlight the helix No4 segment as most likely to initiate the structural conversion. This prediction is corroborated by the finding that a peptide corresponding to helix No4 has the ability of pH-induced conversion into β-sheets and self-assembly into nanofibrils. Our results provide structural information about the CT domain in fiber form and clues about its role in triggering the structural conversion of spidroins during fiber assembly.

Prolonged Linear Amplification of qPCR for the Correction of Amplification Variation and the Absolute Quantification without Standard Curves

The variable amplification efficiency of each thermal cycle of qPCR obeys the Poisson distribution, and the qPCR system dynamically changes, so there must be a detection error in its quantitative analysis. Here, more than 20 cycles of the linear amplification of qPCR can be produced as the BSA hydrogel is introduced to achieve the controlled release of Taq DNA polymerase. There is a significant negative correlation between the slope of linear amplification and Ct values (r = -0.9455), and it is well evident that the slope can reflect the amplification efficiency and a linear positive correlation exists between them. Through the change in the concentration of primers in the qPCR system, an exponential equation between Ct values and the slopes can be fitted (R2 = 0.9995). The slopes and Ct values of each qPCR system can be corrected by using this equation to guarantee that there will be significant consistency in their amplification efficiency because the degree of linear fitting (R2) between Ct values and the logarithm of their corresponding concentration of the DNA template increased significantly. By this time, the accurate amplification efficiency can be calculated in a known multiple of two initial concentrations of DNA templates. With the aid of the relationship between the known primer concentration and the fluorescence intensity at the end of PCR (End RFU), the initial concentrations of DNA templates can be reversely calculated in the absence of standard curves.

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.

Amyloid-like aggregation of recombinant β-lactoglobulin at pH 3.5 and 7.0: Is disulfide bond removal the key to fibrillation?

Functional nanofibrils from globular proteins are usually formed by heating for several hours at pH 2.0, which induces acidic hydrolysis and consecutive self-association. The functional properties of these micro-metre-long anisotropic structures are promising for biodegradable biomaterials and food applications, but their stability at pH > 2.0 is low. The results presented here show that modified β-lactoglobulin can also form nanofibrils by heating at neutral pH without prior acidic hydrolysis; the key is removing covalent disulfide bonds. The aggregation behaviour of various recombinant β-lactoglobulin variants was systemically studied at pH 3.5 and 7.0. The suppression of intra- and intermolecular disulfide bonds by eliminating one to three out of the five cysteines makes the non-covalent interactions more prevalent and allow for structural rearrangement. This stimulated the linear growth of worm-like aggregates. Full elimination of all five cysteines led to the transformation of worm-like aggregates into actual fibril structures (several hundreds of nanometres long) at pH 7.0. This understanding of the role of cysteine in protein-protein interactions will help to identify proteins and protein modifications to form functional aggregates at neutral pH.

Macrocyclization strategies for cyclic peptides and peptidomimetics

Peptides are a growing therapeutic class due to their unique spatial characteristics that can target traditionally "undruggable" protein-protein interactions and surfaces. Despite their advantages, peptides must overcome several key shortcomings to be considered as drug leads, including their high conformational flexibility and susceptibility to proteolytic cleavage. As a general approach for overcoming these challenges, macrocyclization of a linear peptide can usually improve these characteristics. Their synthetic accessibility makes peptide macrocycles very attractive, though traditional synthetic methods for macrocyclization can be challenging for peptides, especially for head-to-tail cyclization. This review provides an updated summary of the available macrocyclization chemistries, such as traditional lactam formation, azide-alkyne cycloadditions, ring-closing metathesis as well as unconventional cyclization reactions, and it is structured according to the obtained functional groups. Keeping peptide chemistry and screening in mind, the focus is given to reactions applicable in solution, on solid supports, and compatible with contemporary screening methods.

Cooperative Coupling of Oxidative Organic Synthesis and Hydrogen Production over Semiconductor-Based Photocatalysts

Merging hydrogen (H₂) evolution with oxidative organic synthesis in a semiconductor-mediated photoredox reaction is extremely attractive because the clean H₂ fuel and high-value chemicals can be coproduced under mild conditions using light as the sole energy input. Following this dual-functional photocatalytic strategy, a dreamlike reaction pathway for constructing C-C/C-X (X = C, N, O, S) bonds from abundant and readily available X-H bond-containing compounds with concomitant release of H₂ can be readily fulfilled without the need of external chemical reagents, thus offering a green and fascinating organic synthetic strategy. In this review, we begin by presenting a concise overview on the general background of traditional photocatalytic H₂ production and then focus on the fundamental principles of cooperative photoredox coupling of selective organic synthesis and H₂ production by simultaneous utilization of photoexcited electrons and holes over semiconductor-based catalysts to meet the economic and sustainability goal. Thereafter, we put dedicated emphasis on recent key progress of cooperative photoredox coupling of H₂ production and various selective organic transformations, including selective alcohol oxidation, selective methane conversion, amines oxidative coupling, oxidative cross-coupling, cyclic alkanes dehydrogenation, reforming of lignocellulosic biomass, and so on. Finally, the remaining challenges and future perspectives in this flourishing area have been critically discussed. It is anticipated that this review will provide enlightening guidance on the rational design of such dual-functional photoredox reaction system, thereby stimulating the development of economical and environmentally benign solar fuel generation and organic synthesis of value-added fine chemicals.

Bicyclic β-Sheet Mimetics that Target the Transcriptional Coactivator β-Catenin and Inhibit Wnt Signaling

Protein complexes are defined by the three-dimensional structure of participating binding partners. Knowledge about these structures can facilitate the design of peptidomimetics which have been applied for example, as inhibitors of protein-protein interactions (PPIs). Even though β-sheets participate widely in PPIs, they have only rarely served as the basis for peptidomimetic PPI inhibitors, in particular when addressing intracellular targets. Here, we present the structure-based design of β-sheet mimetics targeting the intracellular protein β-catenin, a central component of the Wnt signaling pathway. Based on a protein binding partner of β-catenin, a macrocyclic peptide was designed and its crystal structure in complex with β-catenin obtained. Using this structure, we designed a library of bicyclic β-sheet mimetics employing a late-stage diversification strategy. Several mimetics were identified that compete with transcription factor binding to β-catenin and inhibit Wnt signaling in cells. The presented design strategy can support the development of inhibitors for other β-sheet-mediated PPIs.

Revisiting bone morphogenetic protein-2 knuckle epitope and redesigning the epitope-derived peptides

The bone morphogenetic protein-2 (BMP2) plays a crucial role in bone formation, growth and regeneration, which adopts a conformational wrist epitope and a linear knuckle epitope to interact with its type-I (BRI) and type-II (BRII) receptors, respectively. In this study, we systematically examine the BRII-recognition site of BMP2 at structural, energetic and dynamic levels and accurately locate hotspots of the recognition at BMP2-BRII complex interface. It is revealed that the traditional knuckle epitope (BMP2 residue range 73-92) do fully match the identified hotspots; the BMP2-recognition site includes the C-terminal region of traditional knuckle epitope as well as its flanked β-strands. In addition, the protein context of full-length BMP2 is also responsible for the recognition by addressing conformational constraint on the native epitope segment. Therefore, we herein redefine the knuckle epitope to BMP2 residue range 84-102, which has a similar sequence length but is slid along the protein sequence by ~10 residues as compared to traditional knuckle epitope. The redefined one is also a linear epitope that is natively a double-stranded β-sheet with two asymmetric arms as compared to the natively single β-strand of the traditional version, although their sequences are partially overlapped to each other. It is revealed that the redefined epitope-derived peptide LN^84-102 exhibits an improved affinity by >3-fold relative to the traditional epitope-derived peptide KL^73-92 . Even so, the LN^84-102 peptide still cannot fully represent the BMP2 recognition event by BRII that has been reported to have a nanomolar affinity. We further introduce a disulfide bond across the two arms of double-stranded β-sheet to constrain the free LN^84-102 peptide conformation, which mimics the conformational constraint addressed by protein context. Consequently, several cyclic peptides are redesigned, in which the LN^84-102 (cyc89-101) is determined to exhibit a sub-micromolar affinity; this value is ~5-fold higher than its linear counterpart. Structural analysis also reveals that the cyclic peptide can interact with BRII in a similar binding mode with the redefined knuckle epitope region in full-length BMP2 protein.

Cyclic peptides bearing the d-Phe-2-Abz turn motif: Structural characterization and antimicrobial potential

The effect on secondary structure and antimicrobial activity of introducing different cyclic constraints in linear β-hairpin antimicrobial peptides has been investigated with the intention of generating cyclic β sheets as promising antimicrobials with improved therapeutic potential. The linear peptides were cyclized head to tail either directly or after the addition of either a second turn motif or a disulfide bridge. The propensity of these peptides to adopt a cyclic β-sheet structure has been correlated to their antibacterial activity. All cyclic peptides showed enhanced activity, compared with their linear counterparts against methicillin-resistant Staphylococcus aureus. Scanning electron microscopy and transmission electron microscopy studies showed that this family kills bacteria through membrane lysis. The peptide that showed the best efficacy against all strains (exhibiting nanomolar activity), while retaining low haemolysis, bears two symmetrical, homochiral d-phe-2-Abz-d-ala turns and adopted a flexible structure. Its twin peptide that bears heterochiral turns (one with d-ala and one with L-Ala) showed reduced antibacterial activity and higher percentage of haemolysis. Circular dichroism and nuclear magnetic resonance spectroscopy indicate that heterochirality in the two turns leads to oligomerization of the peptide at higher concentrations, stabilizing the β-sheet secondary structure. More rigid secondary structure is associated with lower activity against bacteria and loss of selectivity.

Structure-Property Relationship Study of N-(Hydroxy)Peptides for the Design of Self-Assembled Parallel β-Sheets

The design of novel and functional biomimetic foldamers remains a major challenge in creating mimics of native protein structures. Herein, we report the stabilization of a remarkably short β-sheet by incorporating N-(hydroxy)glycine (Hyg) residues into the backbone of peptides. These peptide-peptoid hybrids form unique parallel β-sheet structures by self-assembly upon hydrogenation. Our spectroscopic and crystallographic data suggest that the local conformational perturbations induced by N-(hydroxy)amides are outweighed by a network of strong interstrand hydrogen bonds.

Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank

Cysteine is a multifaceted amino acid that is central to the structure and function of many proteins. A disulfide bond formed between two cysteines restrains protein conformations through the strong covalent bond and torsions about the bond that prefer, energetically, ±90°. In this study, we transform over 30 000 Protein Databank files (PDBx/mmCIFs) into a single file, the SQLite database (Cys.sqlite). The database schema is designed to accommodate the structural information on both oxidized and reduced cysteines and to retain essential protein metadata to establish informational and biological provenance. Cys.sqlite contains over 95 000 peptide chains and 500 000 cysteines (700 000 structural conformers); there are over 265 000 cysteine disulfide bond conformations from structures solved with all available experimental methods. The structural information is analyzed with respect to sequence identity cutoff, the experimental method, and energetics of the disulfide. We find that as the experimental information becomes limiting and the influence of modeling becomes more pronounced, the observed average strain increases artificially. The database and analyses presented here can be used to improve the refinement of biological structures from experiments that are known to contain one or more disulfide bonds.

Rational Design of a Highly Potent and Selective Peptide Inhibitor of PACE4 by Salt Bridge Interaction with D160 at Position P3

PACE4, a member of the proprotein convertases (PCs) family of serine proteases, is a validated target for prostate cancer. Our group has developed a potent and selective PACE4 inhibitor: Ac-LLLLRVKR-NH₂ . In seeking for modifications to increase the selectivity of this ligand toward PACE4, we replaced one of its P3 Val methyl groups with a basic group capable of forming a salt bridge with D160 of PACE4. The resulting inhibitor is eight times more potent than the P3 Val parent inhibitor and two times more selective over furin, because the equivalent salt bridge with furin E257 is not optimal. Moreover, the β-branched nature of the new P3 residue favors the extended β-sheet conformation usually associated with substrates of proteases. This work provides new insight for better understanding of β-sheet backbone-backbone interactions between serine proteases and their peptidic ligands.

Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein

Heavy glycosylation of the envelope (Env) surface subunit, gp120, is a key adaptation of HIV-1; however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. Here we explore the patterns of HIV-1 Env gp120 glycosylation, and particularly the enrichment in glycosylation sites proximal to the disulfide linkages at the base of the surface-exposed variable domains. To dissect the influence of glycans on the conformation these regions, we focused on an antigenic peptide fragment from a disulfide bridge-bounded region spanning the V1 and V2 hyper-variable domains of HIV-1 gp120. We used replica exchange molecular dynamics (MD) simulations to investigate how glycosylation influences its conformation and stability. Simulations were performed with and without N-linked glycosylation at two sites that are highly conserved across HIV-1 isolates (N156 and N160); both are contacts for recognition by V1V2-targeted broadly neutralizing antibodies against HIV-1. Glycosylation stabilized the pre-existing conformations of this peptide construct, reduced its propensity to adopt other secondary structures, and provided resistance against thermal unfolding. Simulations performed in the context of the Env trimer also indicated that glycosylation reduces flexibility of the V1V2 region, and provided insight into glycan-glycan interactions in this region. These stabilizing effects were influenced by a combination of factors, including the presence of a disulfide bond between the Cysteines at 131 and 157, which increased the formation of beta-strands. Together, these results provide a mechanism for conservation of disulfide linkage proximal glycosylation adjacent to the variable domains of gp120 and begin to explain how this could be exploited to enhance the immunogenicity of those regions. These studies suggest that glycopeptide immunogens can be designed to stabilize the most relevant Env conformations to focus the immune response on key neutralizing epitopes.

Heavy glycosylation of the envelope surface subunit, gp120, is a key adaptation of HIV-1, however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. The network of glycans on gp120 is of particular interest with regards to vaccine design, because the glycans both serve as targets for many classes of broadly neutralizing antibodies, and contribute to patterns of immune evasion and escape during HIV-1 infection. In this manuscript, we report on how glycosylation influences an immunogenic but disordered region of gp120. Glycosylation stabilizes the pre-existing conformation, and reduces its propensity to form other secondary structures. It also stabilizes preformed conformation against thermal unfolding. These complementary effects originate from a combination of multiple factors, including the observation that having a glycosylation site adjacent to the disulfide bond further promotes the formation of beta-strand structure in this peptide.

Bridged Analogues for p53-Dependent Cancer Therapy Obtained by S-Alkylation

A small library of anticancer, cell-permeating, stapled peptides based on potent dual-specific antagonist of p53-MDM2/MDMX interactions, PMI-N8A, was synthesized, characterized and screened for anticancer activity against human colorectal cancer cell line, HCT-116. Employed synthetic modifications included: S-alkylation-based stapling, point mutations increasing hydrophobicity in key residues as well as improvement of cell-permeability by introduction of polycationic sequence(s) that were woven into the sequence of parental peptide. Selected analogue, ArB14Co, was also tested in vivo and exhibited potent anticancer bioactivity at the low dose (3.0 mg/kg). Collectively, our findings suggest that application of stapling in combination with rational design of polycationic short analogues may be a suitable approach in the development of physiologically active p53-MDM2/MDMX peptide inhibitors.

Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes

Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.

Vis/NIR light driven mild and clean synthesis of disulfides in the presence of Cu2(OH)PO4 under aerobic conditions

A highly efficient one-pot strategy has been developed for the synthesis of disulfide in the presence of air under the irradiation of Vis/NIR light.

Serendipitous discovery of an efficient method for the synthesis of dimeric-RGD analogues using DMAP-photoirradiation

We describe a novel disulfide reaction via UV/DMAP methodology for efficient construction of simple disulfides and structurally complex peptides.

Tightening up the structure, lighting up the pathway: Application of molecular constraints and light to manipulate protein folding, self-assembly and function

Chemical cross-linking provides an effective avenue to reduce the conformational entropy of polypeptide chains and hence has become a popular method to induce or force structural formation in peptides and proteins. Recently, other types of molecular constraints, especially photoresponsive linkers and functional groups, have also found increased use in a wide variety of applications. Herein, we provide a concise review of using various forms of molecular strategies to constrain proteins, thereby stabilizing their native states, gaining insight into their folding mechanisms, and/or providing a handle to trigger a conformational process of interest with light. The applications discussed here cover a wide range of topics, ranging from delineating the details of the protein folding energy landscape to controlling protein assembly and function.

Z-Selective olefin metathesis on peptides: investigation of side-chain influence, preorganization, and guidelines in substrate selection

Olefin metathesis has emerged as a promising strategy for modulating the stability and activity of biologically relevant compounds; however, the ability to control olefin geometry in the product remains a challenge. Recent advances in the design of cyclometalated ruthenium catalysts has led to new strategies for achieving such control with high fidelity and Z selectivity, but the scope and limitations of these catalysts on substrates bearing multiple functionalities, including peptides, remained unexplored. Herein, we report an assessment of various factors that contribute to both productive and nonproductive Z-selective metathesis on peptides. The influence of sterics, side-chain identity, and preorganization through peptide secondary structure are explored by homodimerization, cross metathesis, and ring-closing metathesis. Our results indicate that the amino acid side chain and identity of the olefin profoundly influence the activity of cyclometalated ruthenium catalysts in Z-selective metathesis. The criteria set forth for achieving high conversion and Z selectivity are highlighted by cross metathesis and ring-closing metathesis on diverse peptide substrates. The principles outlined in this report are important not only for expanding the scope of Z-selective olefin metathesis to peptides but also for applying stereoselective olefin metathesis in general synthetic endeavors.

Diphenylacetylene-linked peptide strands induce bidirectional β-sheet formation

In the search for synthetic mimics of protein secondary structures relevant to the mediation of protein-protein interactions, we have synthesized a series of tetrasubstituted diphenylacetylenes that display β-sheet structures in two directions. Extensive X-ray crystallographic and NMR solution phase studies are consistent with these proteomimetics adopting sheet structures, displaying both hydrophobic and hydrophilic amino acid side chains.

Convergent diversity-oriented side-chain macrocyclization scan for unprotected polypeptides

Here we describe a general synthetic platform for side-chain macrocyclization of an unprotected peptide library based on the SNAr reaction between cysteine thiolates and a new generation of highly reactive perfluoroaromatic small molecule linkers. This strategy enabled us to simultaneously "scan" two cysteine residues positioned from i, i + 1 to i, i + 14 sites in a polypeptide, producing 98 macrocyclic products from reactions of 14 peptides with 7 linkers. A complementary reverse strategy was developed; cysteine residues within the polypeptide were first modified with non-bridging perfluoroaryl moieties and then commercially available dithiol linkers were used for macrocyclization. The highly convergent, site-independent, and modular nature of these two strategies coupled with the unique chemoselectivity of a SNAr transformation allows for the rapid diversity-oriented synthesis of hybrid macrocyclic peptide libraries with varied chemical and structural complexities.

NMR investigation of disulfide containing peptides and proteins

Peptides and proteins with disulfide bonds are abundant in all kingdoms and play essential role in many biological events. Because small disulfide-rich peptides (proteins) are usually difficult to crystallize, nuclear magnetic resonance (NMR) is by far one of the most powerful techniques for the determination of their solution structure. Besides the “static” three-dimensional structure, NMR has unique opportunities to acquire additional information about molecular dynamics and folding at atomic resolution. Nowadays it is becoming increasingly evident, that “excited”, “disordered” or “fuzzy” protein states may exhibit biological function and disulfide proteins are also promising targets for such studies. In this short two-three years overview those disulfide peptides and proteins were cited from the literature that were studied by NMR. Though we may have missed some, their structural diversity and complexity as well as their wide repertoire of biological functions is impressive. We emphasised especially antimicrobial peptides and peptide based toxins in addition to some biologically important other structures. Besides the general NMR methods we reviewed some contemporary techniques suitable for disclosing the peculiar properties of disulfide bonds. Interesting dynamics and folding studies of disulfide proteins were also mentioned. It is important to disclose the essential structure, dynamics, function aspects of disulfide proteins since this aids the design of new compounds with improved activity and reduced toxicity. Undoubtedly, NMR has the potential to accelerate the development of new disulfide peptides/proteins with pharmacological activity.

Investigation of the ring-closing metathesis of peptides in water

A systematic study of the ring-closing metathesis (RCM) of unprotected oxytocin and crotalphine peptide analogues in water is reported. The replacement of cysteine with S-allyl cysteine enables RCM to proceed readily in water containing excess MgCl(2) with 30% t-BuOH as a co-solvent. The presence of the sulfur atom is vital for efficient aqueous RCM to occur, with non-sulfur containing analogues undergoing RCM in low yields.

Development of α-helical calpain probes by mimicking a natural protein-protein interaction

We have designed a highly specific inhibitor of calpain by mimicking a natural protein-protein interaction between calpain and its endogenous inhibitor calpastatin. To enable this goal we established a new method of stabilizing an α-helix in a small peptide by screening 24 commercially available cross-linkers for successful cysteine alkylation in a model peptide sequence. The effects of cross-linking on the α-helicity of selected peptides were examined by CD and NMR spectroscopy, and revealed structurally rigid cross-linkers to be the best at stabilizing α-helices. We applied this strategy to the design of inhibitors of calpain that are based on calpastatin, an intrinsically unstable polypeptide that becomes structured upon binding to the enzyme. A two-turn α-helix that binds proximal to the active site cleft was stabilized, resulting in a potent and selective inhibitor for calpain. We further expanded the utility of this inhibitor by developing irreversible calpain family activity-based probes (ABPs), which retained the specificity of the stabilized helical inhibitor. We believe the inhibitor and ABPs will be useful for future investigation of calpains, while the cross-linking technique will enable exploration of other protein-protein interactions.