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For over 20 years, peptide materials in their hydrogel or soluble fibril form have been used for biomedical applications such as drug delivery, cell culture, vaccines, and tissue regeneration. To facilitate the translation of these materials, key areas of research still need to be addressed. Their structural characterization lags compared to amyloid proteins. Many of the structural features designed to guide materials formation are primarily being characterized by their observation in atomic resolution structures of amyloid assemblies. Herein, these motifs are examined in relation to peptide designs identifying common interactions that drive assembly and provide structural specificity. Current efforts to design complex structures, as reviewed here, highlight the need to extend the structural revolution of amyloid proteins to peptide assemblies to validate design principles. With respect to clinical applications, the fundamental interactions and responses of proteins, cells, and the immune system to peptide materials are still not well understood. Only a few trends are just now emerging for peptide materials interactions with biological systems. Understanding how peptide material properties influence these interactions will enable the translation of materials towards current and emerging applications. [ABSTRACT FROM AUTHOR]

• Ni(OOH) catalysts decorated by iron oxide atomic layer deposition are demonstrated. • Surface iron on pm on Ni(OOH) catalystsis responsible for high OER OER activity. • Thick, high surface area Ni-Fe(OOH) catalysts require bulk iron for highest activity. • Ni-FeO x films deposited by ALD exhibit high OER activity and good corrosion resistance. Atomic layer deposition (ALD) has become a versatile tool in catalysis, allowing for precise synthesis of catalysts useful for gaining fundamental understanding of complex systems. In this work, ALD was used to perform surface-directed modification of Ni(OH) 2 /Ni(OOH) electrocatalysts for the oxygen evolution reaction (OER) to elucidate the different roles of iron as a surface dopant and of iron distributed throughout the NiOOH structure. Electrochemical and material characterization of FeO x ALD-modified Ni(OH) 2 indicates that iron is deposited on the surface of Ni(OH) 2 sheets without modifying its bulk properties. Sub-monolayer amounts of iron were deposited on the surface of Ni(OH) 2 using low cycle numbers of ALD. This surface iron results in high OER activity, characteristic of Ni-Fe(OOH) catalysts. Ni(OH) 2 /Ni(OOH) catalysts modified to incorporate iron throughout the structure were prepared by depositing large cycle numbers of FeO x ALD, which results in the deposition of a Fe 2 O 3 overlayer. Corrosion of this Fe 2 O 3 overlayer during electrochemical cycling in alkaline electrolyte leads to the incorporation of iron throughout the structure of Ni(OH) 2 /Ni(OOH) while leaving some iron at the surface. Incorporation of iron throughout the Ni(OH) 2 /Ni(OOH) structure was found to increase OER geometric activity for thick, high surface area Ni(OH) 2 /Ni(OOH) catalysts. Lastly, Ni-FeO x electrocatalysts synthesized fully by ALD were investigated for the OER; these catalysts demonstrated high OER activity and potential for photocatalysis applications. [ABSTRACT FROM AUTHOR]

Selectively targeting the membrane‐perturbing potential of peptides towards a distinct cellular phenotype allows one to target distinct populations of cells. We report the de novo design of a new class of peptide whose ability to perturb cellular membranes is coupled to an enzyme‐mediated shift in the folding potential of the peptide into its bioactive conformation. Cells rich in negatively charged surface components that also highly express alkaline phosphatase, for example many cancers, are susceptible to the action of the peptide. The unfolded, inactive peptide is dephosphorylated, shifting its conformational bias towards cell‐surface‐induced folding to form a facially amphiphilic membrane‐active conformer. The fate of the peptide can be further tuned by peptide concentration to affect either lytic or cell‐penetrating properties, which are useful for selective drug delivery. This is a new design strategy to afford peptides that are selective in their membrane‐perturbing activity. [ABSTRACT FROM AUTHOR]

Selectively targeting the membrane‐perturbing potential of peptides towards a distinct cellular phenotype allows one to target distinct populations of cells. We report the de novo design of a new class of peptide whose ability to perturb cellular membranes is coupled to an enzyme‐mediated shift in the folding potential of the peptide into its bioactive conformation. Cells rich in negatively charged surface components that also highly express alkaline phosphatase, for example many cancers, are susceptible to the action of the peptide. The unfolded, inactive peptide is dephosphorylated, shifting its conformational bias towards cell‐surface‐induced folding to form a facially amphiphilic membrane‐active conformer. The fate of the peptide can be further tuned by peptide concentration to affect either lytic or cell‐penetrating properties, which are useful for selective drug delivery. This is a new design strategy to afford peptides that are selective in their membrane‐perturbing activity. [ABSTRACT FROM AUTHOR]

Herein, peptide nucleic acids (PNAs) are employed in the design of a participatory duplex PNA‐peptide crosslinking agent. Biophysical and mechanical studies show that crosslinkers present during peptide assembly leading to hydrogelation participate in the formation of fibrils while simultaneously installing crosslinks into the higher‐order network that constitutes the peptide gel. The addition of 2 mol % crosslinker into the assembling system results in a ~100 % increase in mechanical stiffness without affecting the rate of peptide assembly or the local morphology of fibrils within the gel network. Stiffness enhancement is realized by only affecting change in the elastic component of the viscoelastic gel. A synthesis of the PNA‐peptide duplex crosslinkers is provided that allows facile variation in peptide composition and addresses the notorious hydrophobic content of PNAs. This crosslinking system represents a new tool for modulating the mechanical properties of peptide‐based hydrogels. [ABSTRACT FROM AUTHOR]

Herein, peptide nucleic acids (PNAs) are employed in the design of a participatory duplex PNA‐peptide crosslinking agent. Biophysical and mechanical studies show that crosslinkers present during peptide assembly leading to hydrogelation participate in the formation of fibrils while simultaneously installing crosslinks into the higher‐order network that constitutes the peptide gel. The addition of 2 mol % crosslinker into the assembling system results in a ~100 % increase in mechanical stiffness without affecting the rate of peptide assembly or the local morphology of fibrils within the gel network. Stiffness enhancement is realized by only affecting change in the elastic component of the viscoelastic gel. A synthesis of the PNA‐peptide duplex crosslinkers is provided that allows facile variation in peptide composition and addresses the notorious hydrophobic content of PNAs. This crosslinking system represents a new tool for modulating the mechanical properties of peptide‐based hydrogels. [ABSTRACT FROM AUTHOR]

Abstract: A synthetic route toward hybrid MoS2‐based materials that combines the 2D bonding of MoS2 with 3D networking of aliphatic carbon chains is devised, leading to a film with enhanced electrocatalytic activity. The hybrid inorganic–organic thin films are synthesized by combining atomic layer deposition (ALD) with molecular layer deposition (MLD) using the precursors molybdenum hexacarbonyl and 1,2‐ethanedithiol and characterized by in situ Fourier transform infrared spectroscopy, and the resultant material properties are probed by X‐ray photoelectron spectroscopy, Raman spectroscopy, and grazing incidence X‐ray diffraction. The process exhibits a growth rate of 1.3 Å per cycle, with an ALD/MLD temperature window of 155–175 °C. The hybrid films are moderately stable for about a week in ambient conditions, smooth (σRMS ≈ 5 Å for films 60 Å thick) and uniform, with densities ranging from 2.2–2.5 g cm−3. The material is both optically transparent and catalytically active for the hydrogen evolution reaction (HER), with an overpotential (294 mV at −10 mA cm−2) superior to that of planar MoS2. The enhancement in catalytic activity is attributed to the incorporation of organic chains into MoS2, which induces a morphological change during electrochemical testing that increases surface area and yields high activity HER catalysts without the need for deliberate nanostructuring. [ABSTRACT FROM AUTHOR]

Implantation of drug delivery depots into or proximal to targeted tissue is an effective method to deliver anticancer drugs in a sustained localized manner. Herein, syringe-injectable polydextran aldehyde (PDA)-based bioadhesive gels are prepared that can locally deliver cytotoxins upon their hydrolytic fragmentation. Adhesive gels are formed by mixing doxorubicin (DOX)-functionalized PDA (DOX-PDA) and bovine serum albumin (BSA) using a dual-barrel syringe. Upon mixing and delivery, the DOX-PDA reacts with the cross-linker BSA as well as the extracellular matrix via imine bond formation to define the cohesive and adhesive properties of the gel, respectively. Resulting gels are mechanically rigid (∼10 kPa) and adherent (adhesive stress ∼ 4 kPa). Once formed, the DOX-PDA-BSA gels undergo slow hydrolytic degradation (>2 months) locally releasing free DOX and DOX-PDA as expected. Surprisingly, we found that macromolecules composed of DOX, PDA, and BSA are also released from the bulk material. These DOX-PDA-BSA macromolecules, along with free DOX and DOX-PDA conjugate, are internalized by A549 lung carcinoma cells, resulting in potent cell death. [ABSTRACT FROM AUTHOR]

Many lead molecules identified in drug discovery campaigns are eliminated from consideration due to poor solubility and low cell permeability. These orphaned molecules could have clinical value if solubilized and delivered properly. SVS-1 is a de novo designed peptide that preferentially folds at the surface of tumor cells, adopting a β-hairpin conformation that rapidly translocates into the cytoplasm, and ultimately nucleus, of cells. SVS-1 is stable in serum and small molecules attached to the peptide are effectively delivered to cancer cells via mechanisms involving physical translocation and, to a lesser extent, clathrin-dependent endocytosis. For example, ligating the model hydrophobic drug Paclitaxel (PTX) to SVS-1 improved its aqueous solubility by ~ 1000-fold and successfully delivered and released PTX to cancer cells in vitro and tumors in vivo without toxic adjuvants. These results suggest that SVS-1 can serve as a simple, effective delivery platform for molecules with poor solubility and permeability. [ABSTRACT FROM AUTHOR]

According to the endosymbiotic hypothesis, the precursor of mitochondria invaded the precursor of eukaryotic cells, a process that began roughly 2 billion years ago. Since then, the majority of the genetic material translocated from the mitochondria to the nucleus, where now almost all mitochondrial proteins are expressed. Only a tiny amount of DNA remained in the mitochondria, known as mitochondrial DNA (mtDNA). In this study, we report that the transfer of mtDNA fragments to the nucleus of pluripotent stem cells is still ongoing. We show by in situ hybridization and agarose DNA two-dimensional gel technique that induced pluripotent stem (iPS) cells contain high levels of mtDNA in the nucleus. We found that a large proportion of the accumulated mtDNA sequences appear to be extrachromosomal. Accumulation of mtDNA in the nucleus is present not only in the iPS cells, but also in embryonic stem (ES) cells. However upon differentiation, the level of mtDNA in the nuclei of iPS and ES cells is substantially reduced. This reversible accumulation of mtDNA in the nucleus supports the notion that the nuclear copy number of mtDNA sequences may provide a novel mechanism by which chromosomal DNA is dynamically regulated in pluripotent stem cells. [ABSTRACT FROM AUTHOR]

DMD (Duchenne muscular dystrophy) is an incurable rapidly worsening neuromuscular degenerative disease caused by the absence of dystrophin. In skeletal muscle a lack of dystrophin disrupts the recruitment of neuronal NOS (nitric oxide synthase) to the sarcolemma thus affecting NO (nitric oxide) production. Utrophin is a dystrophin homologue, the expression of which is greatly up-regulated in the sarcolemma of dystrophin-negative fibres from mdx mice, a mouse model of DMD. Although cardiomyopathy is an important cause of death, little is known about the NO signalling pathway in the cardiac muscle of DMD patients. Thus we used cardiomyocytes and hearts from two month-old mdx and mdx:utrophin-/- (double knockout) mice (mdx:utr) to study key steps in NO signalling: L-arginine transporters, NOS and sGC (soluble guanylyl cyclase). nNOS did not co-localize with dystrophin or utrophin to the cardiomyocyte membrane. Despite this nNOS activity was markedly decreased in both mdx and mdx:utr mice, whereas nNOS expression was only decreased in mdx:utr mouse hearts, suggesting that utrophin up-regulation in cardiomyocytes maintains nNOS levels, but not function. sGC protein levels and activity remained at control levels. Unexpectedly, L-arginine transporter expression and function were significantly increased, suggesting a novel biochemical compensatory mechanism of the NO pathway and a potential entry site for therapeutics. [ABSTRACT FROM AUTHOR]

Limb-girdle muscular dystrophy-2F (LGMD-2F) is an incurable degenerative muscle disorder caused by a mutation in the sarcoglycan-δ (SGδ)-encoding gene (SGCD in humans). The lack of SGδ results in the complete disruption of the sarcoglycan complex (SGC) in the skeletal cardiac muscle within the larger dystrophin-glycoprotein complex (DGC). The long-term consequences of SG ablation on other members of the DGC are currently unknown. We produced mosaic mice through the injection of wild-type (WT) embryonic stem cells (ESCs) into SGδ-knockout (KO) blastocysts. ESC-derived SGδ was supplied to the sarcolemma of 18-month-old chimeric muscle which resulted in the restoration of the SGC. Despite SGC rescue contrary to previous observations obtained with WT/mdx chimeras (a mouse rescue paradigm for Duchenne muscular dystrophy) low levels of ESC incorporation were insufficient to produce histological corrections in SGd-KO skeletal muscle or heart. The inefficient process of ESC rescue was more evident in the SGδ-KO diaphragm which had reduced levels of dystrophin no compensatory utrophin needed almost full WT ESC reconstitution for histological improvement. The results suggest that the SGδ-KO mouse model of LGMD is not amenable to ESC treatment. [ABSTRACT FROM AUTHOR]

Embryonic stem cell (ESC) research is a promising area of investigation with enormous therapeutic potential. We have injected murine wild type (WT) ESCs into a variety of mutant murine blastocysts, which are predisposed to develop a human-like disease, such as muscular dystrophy or the embryonic lethal “thin myocardial syndrome”. In this review, we summarize data indicating that partial incorporation of ESCs is sufficient to prevent disease from occurring. We also present data indicating that blastocyst incorporation of ESCs may aid in the prevention of heart failure in stressed WT mice. In some cases, the rescue observed is predominantly non-cell autonomous and relies on the production of secreted factors from the ES-derived cells, but in others, cell replacement is required. Thus, congenital or acquired disease can be pre-emptively averted in mice by developmental injection of ESCs. [ABSTRACT FROM AUTHOR]

The article discusses the length of the space diagonal of a rectangular box with the given dimensions. A determination of its length requires two applications of the Pythagorean theorem or one application of the formula for the distance between two point in space in terms of their coordinates. One example of this problem includes a straw which is placed into a rectangular box that measures three inches by four inches by eight inches, if this straw fits exactly into the box diagonally, the length of the straw will then be measured to the nearest tenth of an inch. Accordingly, if a right circular cylinder with radius and the length fits in the box, then the right circular cylinder formed by reflecting through the midpoint also lies in the box.

Photolithography enables the precise construction of nanodevices in two-dimensional formats. However, self-assembly of designed molecules serves as an alternative for the construction of three-dimensional nanoscale systems and is particularly appealing in that material properties can potentially be engineered at the molecular level. Peptides and proteins hold promise as building blocks for self-assembled systems because of their exquisite three-dimensional structures and evolutionarily fine-tuned functions. [Copyright &y& Elsevier]

Three noncoding basic amino acids, mono-, di-, and trimethyldiaminopropionic acid (mmdap, dmdap, and tmdap), have been synthesized for use in protein design. Covalent modification of a diaminopropionic acid (dap) side chain with an increasing number of methyl moieties results in a family of residues displaying short basic side chains with varying degrees of enhanced hydrophobic character. These residues may be used to introduce charged/polar interactions into the confining hydrophobic interior or interfacial spaces of proteins. As a demonstration of their utility, the ability of these residues to promote interior salt bridge formation at the helix/helix interface of GCN4-p1, a dimeric two-stranded coiled coil, was assessed. Heterodimerization mediated by buried salt bridge formation between a GCN4-based peptide containing either mmdap, dmdap, or tmdap at position 16 and an analogous peptide containing aspartic acid at the same position was studied. Mmdap-derived heterodimers are 0.5 kcal/mol more stable than the corresponding dap-derived heterodimers. This result indicates that the addition of one methyl group to the dap side chain can stabilize the heterodimeric fold. The stabilization can most likely be attributed to a decrease in the desolvation penalty incurred upon folding as well as enhanced van der Waals contacts in the folded state. The addition of three methyl groups to the dap side chain results in heterodimers that are significantly less stable than the corresponding dap-derived heterodimers, suggesting that increased steric bulk is not well accommodated in the interior of this protein. Unexpectedly, the addition of two methyl groups leads to homotrimerization of the dmdap-peptide. The resulting trimer is relatively stable (ΔG[sub 37°C]º = 11.8 kcal/mol) and undergoes cooperative thermal unfolding. The GCN4-p1 system exemplifies how small incremental changes in size and hydrophobicity can alter the folding preferences of a protein.... [ABSTRACT FROM AUTHOR]

A general peptide design is presented that links the pH-dependent intramolecular folding of β-hairpin peptides to their propensity to self-assemble, affording hydrogels rich in β-sheet. Chemical responsiveness has been specifically engineered into the material by linking intramolecular folding to changes in solution pH, and mechanical responsiveness, by linking hydrogelation to self-assembly. Circular dichroic and infrared spectroscopies show that at low pH individual peptides are unstructured, affording a lowviscosity aqueous solution. Under basic conditions, intramolecular folding takes place, affording amphiphilic β-hairpins that intermolecularly self-assemble. Rheology shows that the resulting hydrogel is rigid but is shear-thinning. However, quick mechanical strength recovery after cessation of shear is observed due to the inherent self-assembled nature of the scaffold. Characterization of the gelation process, from the molecular level up through the macroscopic properties of the material, suggests that by linking the intramolecular folding of small designed peptides to their ability to self-assemble, responsive materials can be prepared. Cryo-transmission electron and laser scanning confocal microscopies reveal a water-filled porous scaffold on both the nano- and microscale. The environmental responsiveness, morphology, and peptidic nature make this hydrogel a possible material candidate for biomedical and engineering technology. [ABSTRACT FROM AUTHOR]

Dopamine is a small versatile molecule used for various biotechnological and biomedical applications. This neurotransmitter, in addition to its biological role, can undergo oxidative self-polymerization to yield polydopamine, a robust universal coating material. Herein, we harness dopamine self-polymerization to modulate the viscoelastic mechanical properties of peptide-based gels, expanding their ever-growing application potential. By combining rapid peptide assembly with slower dopamine auto-polymerization, a double network gel is formed, where the fibrillar peptide gel network serves as a scaffold for polydopamine deposition, allowing polydopamine to interpenetrate the gel network as well as establishing crosslinks within the matrix. We have shown that triggering the assembly of a lysine-rich peptide gelator in the presence of dopamine can increase the mechanical rigidity of the resultant gel by a factor of 90 in some cases, while retaining the gel's shear thin-recovery behavior. We further investigate how factors such as polymerization time, dopamine concentration and peptide concentration alter the mechanical properties of the resultant gel. The hybrid peptide–dopamine gel systems were characterized using rheological measurements, circular dichroism spectroscopy and transmission electron microscopy. Overall, triggering peptide gelation in the presence of dopamine represents a simple yet powerful approach to modulate the viscoelastic mechanical properties of peptide-based gels. [ABSTRACT FROM AUTHOR]

Presents information on a study which investigated the folding behavior of dimeric and covalently crosslinked versions of the 33-residue alpha-helical GCN4-p1 coiled coil derived from the leucine zipper region of the transcriptional activator GCN4. Materials and methods of the study; Results and discussion.

Provides information on a study focusing on the design of efficient ...-helical c-capping auxiliaries with various chain lengths based on alkyldiamines and monoguanylated diamines. Methodology used to conduct the study; Results of the study; Discussion on the results.

Describes the synthesis of four 6,6'-bis(acylamino)-2,2'-bipyridine-based amino acids. Ultraviolet visible studies; Circular dichroism studies; Matrix assisted laser desorption mass spectroscopy; Sedimentation equilibrium analytical ultracentrifugation.

Cell‐penetrating peptides (CPPs) are useful tools for the delivery of a wide variety of cargo into cells. Our lab has developed two classes of CPPs based on β‐hairpin sequences, one that folds at the surface of cell membranes and the other that is intrinsically disordered. Although these peptides can effectively deliver different types of cargo, their use in protein delivery has been hindered due to the presence of non‐natural D‐proline within the central turn region of both sequences, which prohibits functionalizing proteins with the CPPs via standard expression protocols. In this work, we describe new CPPs that replace the non‐natural turn region with natural turn motifs amenable to protein expression. We first investigate how these changes within the turn affect various CPP‐related properties in the absence of protein cargo, and then generate protein fusions for intracellular delivery. [ABSTRACT FROM AUTHOR]

Innentitelbild: De novo Design of Selective Membrane-Active Peptides by Enzymatic Control of Their Conformational Bias on the Cell Surface (Angew. Deren Fähigkeit zur Störung zellulärer Membranen an eine enzymvermittelte Verschiebung des Faltungspotentials des Peptids in eine membranaktive Konformation gekoppelt ist, wird von J. Shi und J. Schneider in ihrer Zuschrift auf S. 13844 vorgestellt. Einmal gefaltet, bestimmt die Konzentration des Peptids, ob es in Zellen eindringt oder sie durch Lyse abtötet. [Extracted from the article]

Structure‐based engineering starting from the antiparallel coiled coil domain of the Bcr‐Abl oncoprotein (BCR30‐65) afforded a new homodimeric antiparallel coiled coil whose folding is responsive to solution pH. The BCR30‐65 homodimer contains two glutamic acids (Glu52) buried in its hydrophobic core which one would expect to impart pH responsive folding behavior. Surprisingly, BCR30‐65 is resistant to thermal denaturation over a wide pH range. This behavior arises from stabilizing salt bridges formed between solvent‐exposed Arg55 and Glu52 that passivates the glutamates' negative charge within the protein's core. Replacing Arg55 with alanine imparts pH‐responsive folding behavior, but also results in the loss of directional specificity between the coiled coil's helices. We find that an Ile42Glu mutation preserves the salt bridges and imparts the desired pH responsive folding behavior. The Ile42Glu protein forms an antiparallel homodimeric coiled coil under acidic conditions but unfolds under basic conditions and is only marginally less thermally stable compared to BCR30‐65. [ABSTRACT FROM AUTHOR]

A synthetic route toward hybrid MoS2‐based materials that combines the 2D bonding of MoS2 with 3D networking of aliphatic carbon chains is devised, leading to a film with enhanced electrocatalytic activity. The hybrid inorganic–organic thin films are synthesized by combining atomic layer deposition (ALD) with molecular layer deposition (MLD) using the precursors molybdenum hexacarbonyl and 1,2‐ethanedithiol and characterized by in situ Fourier transform infrared spectroscopy, and the resultant material properties are probed by X‐ray photoelectron spectroscopy, Raman spectroscopy, and grazing incidence X‐ray diffraction. The process exhibits a growth rate of 1.3 Å per cycle, with an ALD/MLD temperature window of 155–175 °C. The hybrid films are moderately stable for about a week in ambient conditions, smooth (σRMS ≈ 5 Å for films 60 Å thick) and uniform, with densities ranging from 2.2–2.5 g cm−3. The material is both optically transparent and catalytically active for the hydrogen evolution reaction (HER), with an overpotential (294 mV at −10 mA cm−2) superior to that of planar MoS2. The enhancement in catalytic activity is attributed to the incorporation of organic chains into MoS2, which induces a morphological change during electrochemical testing that increases surface area and yields high activity HER catalysts without the need for deliberate nanostructuring. A new 3D MoS2‐like material is synthesized and applied to the hydrogen evolution reaction (HER), produced via atomic layer deposition/molecular layer deposition. The high HER activity of this [SCH2CH2S]2Mo material results from the film restructuring in situ during electrochemical testing, increasing surface area. [ABSTRACT FROM AUTHOR]

The nomenclatures used to describe HLA and killer‐cell immunoglobulin‐like receptor (KIR) alleles distinguish unique nucleotide and peptide sequences, and patterns of expression, but are insufficient for describing genotyping results, as description of ambiguities and relations across loci require terminology beyond allele names. The genotype list (GL) String grammar describes genotyping results for genetic systems with defined nomenclatures, like HLA and KIR, documenting what is known and unknown about a given genotyping result. However, the accuracy of a GL String is dependent on the reference database version under which it was generated. Here, we describe the GL string code (GLSC) system, which associates each GL String with meta‐data describing the specific reference context in which the GL String was created, and in which it should be interpreted. GLSC is a defined syntax for exchanging GL Strings in the context of a specific gene‐family namespace, allele‐name code‐system, and pertinent reference database version. GLSC allows HLA and KIR genotyping data to be transmitted, parsed and interpreted in the appropriate context, in an unambiguous manner, on modern data‐systems, including Health Level 7 Fast Healthcare Interoperability Resource systems. Technical specification for GLSC can be found at https://glstring.org. [ABSTRACT FROM AUTHOR]

The Genotype List (GL) String grammar for reporting HLA and Killer‐cell Immunoglobulin‐like Receptor (KIR) genotypes in a text string was described in 2013. Since this initial description, GL Strings have been used to describe HLA and KIR genotypes for more than 40 million subjects, allowing these data to be recorded, stored and transmitted in an easily parsed, text‐based format. After a decade of working with HLA and KIR data in GL String format, with advances in HLA and KIR genotyping technologies that have fostered the generation of full‐gene sequence data, the need for an extension of the GL String system has become clear. Here, we introduce the new GL String delimiter "?," which addresses the need to describe ambiguity in assigning a gene sequence to gene paralogs. GL Strings that do not include a "?" delimiter continue to be interpreted as originally described. This extension represents version 1.1 of the GL String grammar. [ABSTRACT FROM AUTHOR]

Abstract: Post‐translational modification is a common mechanism to affect conformational change in proteins, which in turn, regulates function. Herein, this principle is expanded to instruct the formation of supramolecular assemblies by controlling the conformational bias of self‐assembling peptides. Biophysical and mechanical studies show that an engineered phosphorylation/dephosphorylation couple can affectively modulate the folding of amphiphilic peptides into a conformation necessary for the formation of well‐defined fibrillar networks. Negative design principles based on the incompatibility of hosting residue side‐chain point charge within hydrophobic environments proved key to inhibiting the peptide's ability to adopt its low energy fold in the assembled state. Dephosphorylation relieves this restriction, lowers the energy barrier between unfolded and folded peptide, and allows the formation of self‐assembled fibrils that contain the folded conformer, thus ultimately enabling the formation of a cytocompatible hydrogel material. [ABSTRACT FROM AUTHOR]

Abstract: Post‐translational modification is a common mechanism to affect conformational change in proteins, which in turn, regulates function. Herein, this principle is expanded to instruct the formation of supramolecular assemblies by controlling the conformational bias of self‐assembling peptides. Biophysical and mechanical studies show that an engineered phosphorylation/dephosphorylation couple can affectively modulate the folding of amphiphilic peptides into a conformation necessary for the formation of well‐defined fibrillar networks. Negative design principles based on the incompatibility of hosting residue side‐chain point charge within hydrophobic environments proved key to inhibiting the peptide's ability to adopt its low energy fold in the assembled state. Dephosphorylation relieves this restriction, lowers the energy barrier between unfolded and folded peptide, and allows the formation of self‐assembled fibrils that contain the folded conformer, thus ultimately enabling the formation of a cytocompatible hydrogel material. [ABSTRACT FROM AUTHOR]

Tissue inhibitor of metalloproteinase 2 (TIMP-2) is an endogenous 22 kDa proteinase inhibitor, demonstrating antitumorigenic, antimetastatic and antiangiogenic activities in vitro and in vivo. Recombinant TIMP-2 is currently undergoing preclinical testing in multiple, murine tumor models. Here we report the development of an inert, injectable peptide hydrogel matrix enabling encapsulation and sustained release of TIMP-2. We studied the TIMP-2 release profile from four β-hairpin peptide gels of varying net electrostatic charge. A negatively charged peptide gel (designated AcVES3) enabling encapsulation of 4 mg/mL of TIMP-2, without effects on rheological properties, facilitated the slow sustained release (0.9%/d) of TIMP-2 over 28 d. Released TIMP-2 is structurally intact and maintains the ability to inhibit MMP activity, as well as suppress lung cancer cell proliferation in vitro. These findings suggest that the AcVES3 hydrogel will be useful as an injectable vehicle for systemic delivery of TIMP-2 in vivo for ongoing preclinical development. [ABSTRACT FROM AUTHOR]

Summary Although resistance toward small-molecule chemotherapeutics has been well studied, the potential of tumor cells to avoid destruction by membrane-lytic compounds remains unexplored. Anticancer peptides (ACPs) are a class of such agents that disrupt tumor cell membranes through rapid and non-stereospecific mechanisms, encouraging the perception that cellular resistance toward ACPs is unlikely to occur. We demonstrate that eukaryotic cells can, indeed, develop resistance to the model oncolytic peptide SVS-1, which preferentially disrupts the membranes of cancer cells. Utilizing fission yeast as a model organism, we show that ACP resistance is largely controlled through the loss of cell-surface anionic saccharides. A similar mechanism was discovered in mammalian cancer cells where removal of negatively charged sialic acid residues directly transformed SVS-1-sensitive cell lines into resistant phenotypes. These results demonstrate that changes in cell-surface glycosylation play a major role in tumor cell resistance toward oncolytic peptides. [ABSTRACT FROM AUTHOR]

Aim: A ‘Silver Standard’ for HLA data collection and reporting has been described at ImmPort (immport.niaid.nih.gov, “Proposal for HLA Data Validation”) to address ambiguity resolution in the recording and reporting of HLA typing results. While standards are critical for HLA data interoperability, they are not meaningful until useful tools are developed and made available for community use. We are developing distributable tools that implement this silver standard. Here we describe the development a web service to create, update, and retrieve HLA typing data in standardized formats without the need for NMDP allele codes and the corresponding inherent introduction of new ambiguities. Methods: ReST web services with HTTP negotiation are being developed employing a Java library that manages HLA typing data using standardized formats. These formats include the XML based Histoimmunogenetics Markup Language (HML) and a simple character-delimited string format (GL String) able to encode ambiguity within HLA typing. Resources are identified with a simple Uniform Resource Identifier (URI). Results: The services build on a foundation of an open access database schema for IMGT/HLA reference sequence data (updated quarterly), and objects such as alleles, lists of alleles, haplotypes, genotypes, lists of genotypes and multi-locus unphased genotypes. Public services include creating, updating, and retrieving these objects. Content negotiation allows data retrieval in a variety of formats including GL String, HML, HTML, JSON, and QR Code. Conclusions: The tools being developed here provide the HLA researcher, clinician and lab technician a common resource for managing HLA data in a standardized way. We envision these tools to augment workflows through creating new instances of HLA typing objects when needed, and retrieval of those objects and their associated metadata when called upon. [Copyright &y& Elsevier]

Unrelated stem cell registries have been collecting HLA typing of volunteer bone marrow donors for over 25 years. Donor selection for hematopoietic stem cell transplantation is based primarily on matching the alleles of donors and patients at five polymorphic HLA loci. As HLA typing technologies have continually advanced since the beginnings of stem cell transplantation, registries have accrued typings of varied HLA typing ambiguity. We present a new typing resolution score (TRS), based on the likelihood of self-match, that allows the systematic comparison of HLA typings across different methods, data sets and populations. We apply the TRS to chart improvement in HLA typing within the Be The Match Registry of the United States from the initiation of DNA-based HLA typing to the current state of high-resolution typing using next-generation sequencing technologies. In addition, we present a publicly available online tool for evaluation of any given HLA typing. This TRS objectively evaluates HLA typing methods and can help define standards for acceptable recruitment HLA typing. [ABSTRACT FROM AUTHOR]

The neuronal nitric-oxide synthase (nNOS) splice variant nNOSµ is essential for skeletal muscle function. Its localization is dependent on dystrophin, which stabilizes the dystrophin glycoprotein complex (DGC) at the sarcolemma of skeletal muscle fibers. In Duchenne muscular dystrophy (DMD) dystrophin is absent and sarcolemmal nNOS is lost. This leads to functional ischemia due to a decrease in contraction-induced vasodilation. In cardiomyocytes, nNOSµ is believed to be the predominant NOS isoform. However, the association of nNOS with the DGC in the heart is unclear. Here, we report nNOS localization at the intercalated discs (IDs) of cardiomyocytes, where utrophin is highly expressed. In mdx, mdx:utr, nNOSµ knock-out (KO), and mdx:nNOSµ KO mice, we observed a gradual reduction of nNOS at IDs and disrupted ID morphology, compared to wild-type. In mdx:nNOSµ KO mice, but not in mdx or nNOSµ KO mice, we also observed an early development of cardiac fibrosis. These findings suggest that nNOS localization in the heart may not depend exclusively on the presence of dystrophin. Additionally, the β1 subunit of soluble guanylyl cyclase (sGC), responsible for the production of cGMP through nitric oxide (NO) signaling, was also detected at the IDs. Together, our results suggest a new role of nNOS at the IDs for the cGMP-dependent NO pathway and the maintenance of ID morphology. [ABSTRACT FROM AUTHOR]

Most, if not all, peptide- and protein-based hydrogels formed by self-assembly can be characterized as kinetically trapped 3D networks of fibrils. The propensity of disease-associated amyloidforming peptides and proteins to assemble into polymorphic fibrils suggests that cross-β fibrils comprising hydrogels may also be polymorphic. We use solid-state NMR to determine the molecular and supramolecular structure of MAX1, a de novo designed gelforming peptide, in its fibrillar state. We find that MAX1 adopts a β-hairpin conformation and self-assembles with high fidelity into a double-layered cross-β structure. Hairpins assemble with an in-register Syn orientation within each β-sheet layer and with an Anti orientation between layers. Surprisingly, although the MAX1 fibril network is kinetically trapped, solid-state NMR data show that fibrils within this network are monomorphic and most likely represent the thermodynamic ground state. Intermolecular interactions not available in alternative structural arrangements apparently dictate this monomorphic behavior. [ABSTRACT FROM AUTHOR]

Hydrogels formed from self-assembling peptides are finding use in tissue engineering and drug delivery applications. Given the notorious difficulties associated with producing self-assembling peptides by recombinant expression, most are typically prepared by chemical synthesis. Herein, we report the design of a family of self-assembling β-hairpin peptides amenable to efficient production using an optimized bacterial expression system. Ex pressing peptides, EX1, EX2 and EX3 contain identical eight-residue amphiphilic β-strands connected by varying turn sequences that are responsible for ensuring chain reversal and the proper intramolecular folding and consequent self-assembly of the peptide into a hydrogel network under physiological conditions. EX1 was initially used to establish and optimize the bacterial expression system by which all the peptides could be eventually individually expressed. Expression clones were designed to allow exploration of possible fusion partners and investigate both enzymatic and chemical cleavage as means to liberate the target peptide. A systematic analysis of possible expression systems followed by fermentation optimization lead to a system in which all three peptides could be expressed as fusions with BAD-BH3, the BH3 domain of the proapoptotic BAD (Bcl-2 Associated Death) Protein. CNBr cleavage followed by purification afforded 50, 31, and 15 mg/L yields of pure EX1, EX2 and EX3, respectively. CD spectroscopy, TEM, and rheological analysis indicate that these peptides fold and assembled into well-defined fibrils that constitute hydrogels having shear-thin/recovery properties. [ABSTRACT FROM AUTHOR]

Abstract: Controlled biodegradation specific to matrix metalloproteinase-13 was incorporated into the design of self-assembling β-hairpin peptide hydrogels. Degrading Peptides (DP peptides) are a series of five peptides that have varying proteolytic susceptibilities toward MMP-13. These peptides undergo environmentally triggered folding and self-assembly under physiologically relevant conditions (150 mm NaCl, pH 7.6) to form self-supporting hydrogels. In the presence of enzyme, gels prepared from distinct peptides are degraded at rates that differ according to the primary sequence of the single peptide comprising the gel. Material degradation was monitored by oscillatory shear rheology over the course of 14 days, where overall degradation of the gels vary from 5% to 70%. Degradation products were analyzed by HPLC and identified by electrospray-ionization mass spectrometry. This data shows that proteolysis of the parent peptides constituting each gel occurs at the intended sequence location. DP hydrogels show specificity to MMP-13 and are only minimally cleaved by matrix metalloproteinase-3 (MMP-3), another common enzyme present during tissue injury. In vitro migration assays performed with SW1353 cells show that migration rates through each gel differs according to peptide sequence, which is consistent with the proteolysis studies using exogenous MMP-13. [Copyright &y& Elsevier]

As the prevalence of cancer and transmittable disease persists, the development of new and more advanced therapies remains a priority in medical research. An emerging platform for the treatment of these illnesses is the use of materials formed via peptide assembly where the bulk material itself acts as the therapeutic. Higher ordered peptide structures with defined chemistry are capable of cellular targeting, recognition, and internalization. Recent design efforts are being made to exploit the nanoscale definition of the materials formed by assembling peptides to target cancer and microbial cells and to function as vaccines. This review focuses on assembled peptide materials that actively participate in the biological processes important to cancer and transmittable diseases to exert an anticipated functional outcome. [Copyright &y& Elsevier]

Herein, we describe the design and surface-binding characterization of a de novo designed peptide, JAK1, which undergoes surface-induced folding at the hydroxyapatite (HA)-solution interface. JAK1 is designed to be unstructured in buffered saline solution, yet undergo HA-induced folding that is largely governed by the periodic positioning of γ-carboxyglutamic acid (Gla) residues within the primary sequence of the peptide. Circular dichroism (CD) spectroscopy and analytical ultracentrifugation indicate that the peptide remains unfolded and monomeric in solution under normal physiological conditions; however, CD spectroscopy indicates that in the presence of hydroxyapatite, the peptide avidly binds to the mineral surface adopting a helical structure. Adsorption isotherms indicate nearly quantitative surface coverage and Kd = 310 nM for the peptide-surface binding event. X-ray photoelectron spectroscopy (XPS) coupled with the adsorption isotherm data suggests that JAK1 binds to HA, forming a self-limiting monolayer. This study demonstrates the feasibility of using HA surfaces to trigger the intramolecular folding of designed peptides and represents the initial stages of defining the design rules that allow HA-induced peptide folding. [ABSTRACT FROM AUTHOR]

Abstract: A family of penta- and hexadentate metal ligating α-amino acids, suitably protected for Fmoc solid-phase chemistry, has been prepared. These residues incorporate the mono-amides of ethanolaminetriacetic acid, ethylenediaminetriacetic acid, and ethylenediaminetetraacetic acid as side chains. Side chains are tethered varying distances (n) from the Cα-carbon to allow metal binding events to occur at distinct distances from the peptide backbone. These residues are designed to allow the facile installation of metal chelates along a peptide backbone. [Copyright &y& Elsevier]

A synthetic peptide has been de novo designed that self-assembles into β-sheet fibrils exhibiting a nontwisted, stacked morphology. The stacked morphology is constituted by 2.5 nm wide filaments that laterally associate to form flat fibril laminates exceeding 50 nm in width and micrometers in length. The height of each fibril is limited to the length of exactly one peptide monomer in an extended β-strand conformation, approximately 7 nm. Once assembled, these highly ordered, 2-D structures are stable over a wide range of pH and temperature and exhibit characteristics similar to those of amyloid fibrils. Furthermore, the rate of assembly and degree of fibril lamination can be controlled with kinetic parameters of pH and temperature. Finally, the presence of a diproline peptide between two β-sheet-forming strands in the peptide sequence is demonstrated to be an important factor in promoting the nontwisting, laminated fibril morphology. [ABSTRACT FROM AUTHOR]

Structure-based iterative design was used to prepare a disulfide-containing nonapeptide as a fluorimetric probe for chemical and biochemical disulfide forming and breaking reactions. The peptide is composed entirely of natural amino acids and exhibits a marked (42%) change in fluorescence between its oxidized and its reduced states. The probe is easily synthesized and highly water soluble and exhibits well-behaved kinetics on reduction with the reductant tris–carboxyethylphosphine. The reduced peptide is an excellent substrate of the enzyme quiescin–sulfhydryl oxidase and may find utility in the characterization of other disulfide oxidoreductases. [Copyright &y& Elsevier]

As(Ill) displays a wide range of effects in cellular chemistry. Surprisingly, the structural consequences of arsenic binding to peptides and proteins are poorly understood. This study utilizes model α-helical peptides containing two cysteine (Cys) residues in various sequential arrangements and spatial locations to study the structural effects of arsenic binding. With i, and i + 1, i + 2, or i + 3 arrangements, CD spectroscopy shows that As(Ill) coordination causes helical destabitization when Cys residues are located at central or C-terminal regions of the helix. Interestingly, arsenic binding to i, i + 3 positions results in the elimination of helical structure and the formation of a relatively stable alternate fold. In contrast, helical stabilization is observed for peptides containing i, i + 4 Cys residues, with corresponding pseudo pairwise interaction energies (ΔG[sub pw]°) of -1.0 and -0.7 kcal/mol for C-terminal and central placements, respectively. Binding affinities and association rate constants show that As(Ill) binding is comparatively insensitive to the location of the Cys residues within these moderately stable helices. These data demonstrate that As(Ill) binding can be a significant modulator of helical secondary structure. [ABSTRACT FROM AUTHOR]

Allogeneic Hematopoietic Cell Transplantation (HCT) is a curative therapy for hematologic disorders and often requires human leukocyte antigen (HLA)-matched donors. Donor registries have recruited donors utilizing evolving technologies of HLA genotyping methods. This necessitates in-silico ambiguity resolution and statistical imputation based on haplotype frequencies estimated from donor data stratified by self-identified race and ethnicity (SIRE). However, SIRE has limited genetic validity and presents a challenge for individuals with unknown or mixed SIRE. We present MR-GRIMM "Multi-Race Graph IMputation and Matching" that simultaneously imputes the race/ethnic category and HLA genotype using a SIRE based prior. Additionally, we propose a novel method to impute HLA typing inconsistent with current haplotype frequencies. The performance of MR-GRIMM was validated using a dataset of 170,000 donor-recipient pairs. MR-GRIMM has an average 20 % lower matching error (1-AUC) than single-race imputation. The recall metric (sensitivity) of the race/ethnic category imputation from HLA was measured by comparing the imputed donor race with the donor-provided SIRE. Accuracies of 0.74 and 0.55 were obtained for the prediction of 5 broad and 21 detailed US population groups respectively. The operational implementation of this algorithm in a registry search could help improve match predictions and access to HLA-matched donors. [ABSTRACT FROM AUTHOR]