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Although a large number of databases are available for regulatory elements, a bottleneck has been created by the lack of bioinformatics tools to predict the interaction modes of regulatory elements. To reduce this gap, we developed the Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool–liquid/liquid phase separation (LLPS), oligomerization, GO analysis (ART FOUNDATION-LOG), a useful toolkit for protein–nucleic acid interaction (PNI) and protein–protein interaction (PPI) analysis based on domain–domain interactions (DDIs). LLPS, protein oligomerization, the structural properties of protein domains, and protein modifications are major components in the orchestration of the spatiotemporal dynamics of PPIs and PNIs. Our goal is to integrate PPI/PNI information into the development of a prediction model for identifying important genetic variants in peaches. Our program unified interdatabase relational keys based on protein domains to facilitate inference from the model species. A key advantage of this program lies in the integrated information of related features, such as protein oligomerization, LOG analysis, structural characterizations of domains (e.g., domain linkers, intrinsically disordered regions, DDIs, domain–motif (peptide) interactions, beta sheets, and transmembrane helices), and post-translational modification. We provided simple tests to demonstrate how to use this program, which can be applied to other eukaryotic organisms. [ABSTRACT FROM AUTHOR]

Peptides and nucleic acids can self‐assemble to give supramolecular structures that find application in different fields, ranging from the delivery of drugs to the obtainment of materials endowed with optical properties. Forces that stabilize the "suprastructures" typically are hydrogen bonds or aromatic interactions; in case of nucleic acids, Watson‐Crick pairing drives self‐assembly while, in case of peptides, backbone hydrogen bonds and interactions between aromatic side chains trigger the formation of structures, such as nanotubes or ribbons. Molecules containing both aromatic peptides and nucleic acids could in principle exploit different forces to self‐assemble. In this work we meant to investigate the self‐assembly of mixed systems, with the aim to understand which forces play a major role and determine formation/structure of aggregates. We therefore synthesized conjugates of the peptide FF to the peptide nucleic acid dimer "gc" and characterized their aggregates by different spectroscopic techniques, including NMR, CD and fluorescence. [ABSTRACT FROM AUTHOR]

Ultrasound can be used in the biomaterial field due to its high efficiency, easy operation, no chemical treatment, repeatability and high level of control. In this work, we demonstrated that ultrasound is able to quickly regulate protein structure at the solution assembly stage to obtain the designed properties of protein-based materials. Silk fibroin proteins dissolved in a formic acid-CaCl2 solution system were treated in an ultrasound with varying times and powers. By altering these variables, the silks physical properties and structures can be fine-tuned and the results were investigated with Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscopy (SEM), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), dynamic mechanical analysis (DMA), gas permeability and water contact angle measurements. Ultrasonic treatment aids the interactions between the calcium ions and silk molecular chains which leads to increased amounts of intermolecular β-sheets and α-helix. This unique structural change caused the silk film to be highly insoluble in water while also inducing a hydrophilic swelling property. The ultrasound-regulated silk materials also showed higher thermal stability, better biocompatibility and breathability, and favorable mechanical strength and flexibility. It was also possible to tune the enzymatic degradation rate and biological response (cell growth and proliferation) of protein materials by changing ultrasound parameters. This study provides a unique physical and non-contact material processing method for the wide applications of protein-based biomaterials.

A safe and effective delivery system is considered a key to the success of nucleic acid therapeutics. It has been reported that pulmonary surfactants or their components could facilitate the uptake of small interfering RNA (siRNA) into the lung epithelial cells. Previously, our group investigated the use of KL4 peptide, a synthetic cationic peptide that simulates the structural properties of surfactant protein B (SP-B), as siRNA delivery vector. Although KL4 peptide exhibits good in vitro siRNA transfection efficiency on lung epithelial cells, its therapeutic potential is limited by its poor aqueous solubility due to the presence of a high proportion of hydrophobic leucine residues. In this study, we aim to address the solubility issue, designing five different modified peptides by replacing the hydrophobic leucine with alanine or valine, and assess their potential as siRNA delivery vectors. While the modified peptides retain the overall cationic property, their siRNA binding is also affected and their transfection efficiency is inferior to the parent KL4 peptide. A closer examination of the conformation of these peptides by circular dichroism shows that substitution of leucine residues leads to the change of the secondary structure from α-helical content to either β-sheet or more disordered, β-turn conformations. Relatively conservative amino acid substitutions, in terms of hydrophobicity bulk, lead to substantial conformational alteration, heavily impacting siRNA binding and release, cellular uptake, and transfection efficiency. Although the peptide modification strategy employed in this study was unsuccessful in developing an improved version of KL4 peptide for siRNA delivery, it highlights the importance of the α-helical conformation for efficient siRNA transfection, providing useful insights for future development of peptide-based RNA delivery system. [ABSTRACT FROM AUTHOR]

Protein-based adhesives could have several advantages over petroleum-derived alternatives, including substantially lower toxicity, smaller environmental footprint, and renewable sourcing. Here, we report that non-covalently crosslinked bovine serum albumin and recombinant spider silk proteins have high adhesive strength on glass (8.53 and 6.28 MPa, respectively) and other transparent substrates. Moreover, the adhesives have high visible transparency and showed no apparent degradation over a period of several months. The mechanism of adhesion was investigated and primarily attributed to dehydration-induced reorganization of protein secondary structure, resulting in the supramolecular association of β-sheets into a densely hydrogen-bonded network.

The modulation of structural fibrous protein and polysaccharide biopolymers for the design of biomaterials is still relatively challenging due to the non-trivial nature of the transformation from a biopolymer's native state to a more usable form. To gain insight into the nature of the molecular interaction between silk and cellulose chains, we characterized the structural, thermal and morphological properties of silk-cellulose biocomposites regenerated from the ionic liquid, 1-ethyl-3-methylimidazolium acetate (EMIMAc), as a function of increasing coagulation agent concentrations. We found that the cellulose crystallinity and crystal size are dependent on the coagulation agent, hydrogen peroxide solution. The interpretation of our results suggests that the selection of a proper coagulator is a critical step for controlling the physicochemical properties of protein-polysaccharide biocomposite materials. [ABSTRACT FROM AUTHOR]

Summary Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology. [ABSTRACT FROM AUTHOR]

Redescribimos taxonómicamente el gusano Macroperipatus geagy Bouvier 1899, a partir de 15 especímenes recolectados en los cafetales de hacienda El Roble, Santander, Colombia. De acuerdo con la reconstrucción en tres dimensiones de la superficie dorsal del cuerpo, las papilas primarias y accesorias de M. geagy se distribuyen sin formar un patrón determinado. Características diagnósticas: un diente accesorio y un diente principal en la mandíbula externa; y un diente principal, un diente accesorio y siete dentículos en la sierra de la mandíbula interna. Cuerpo: longitud (X=45.66; S=26.10 mm), peso (X= 0.95; S= 2.21) y pares de lobopodos (X= 28.13; S= 1.30). Se elaboró una clave para seis especies de Macroperipatus. La secreción adhesiva en estado líquido perdió 60% del peso inicial al alcanzar los 70 ºC, la muestra sólida perdió el 13% del peso cerca de los 90 ºC, la fase de estabilidad térmica de la secreción estuvo entre los 90 y 280 ºC en la secreción líquida y entre los 100 y 205 ºC en la sólida. La temperatura de inicio de la degradación de las muestras se registró a los 355 ºC. En comparación con la araña Nephila sp., el onicóforo perdió mayor porcentaje de peso y alcanzó la fase de degradación a temperaturas más bajas. Los cambios en el flujo de calor en la secreción adhesiva sólida y líquida de M. geagy fueron confirmados con el comportamiento de las muestras en el análisis de termogravimetría. La proporción de láminas beta calculado en el espectro infrarrojo de la secreción adhesiva fue del 59%. La presencia de este tipo de conformación de la estructura secundaria de las proteínas en la secreción adhesiva de M. geagy conferiría extensibilidad y resistencia a la tracción, en similitud con las fibras de seda tejidas por las arañas para depredación.Velvet worm taxonomy from Santander, Colombia and thermogravimetry, differential scanning calorimetry and infrared spectroscopy of the adhesive secretion (Onychophora: Peripatidae). Onychophoran worms are terrestrial organisms that have changed relatively little since the mid-Cambrian. We collected Macroperipatus geagy in coffee plantations at "Hacienda El Roble", Santander, Colombia, and here redescribe the species based on 15 individuals. A digital three-dimensional reconstruction of the ventral side of the body indicates that the primary and accessory papillae lack a defined distribution pattern. Diagnostic characters: one main tooth and one accessory tooth in the outer jaw, and one main tooth, one accessory tooth and seven denticles in the internal jaw. Measurements: length (X=45.66 mm; SD=26.10), weight (X= 0.95 g; SD= 2.21) and number of lobopods (X= 28.13 pairs; SD= 1.30). We present a taxonomic key for six species of Macroperipatus. The liquid adhesive secretion lost 60% of the initial weight at 70 oC (solid: 13% close to 90 oC). The stability phase of the liquid secretion was within 90-280 oC (100 oC -205 oC in the solid secretion). The starting degradation temperature of the sample was 355 oC. Heat flow changes in the solid and liquid secretions were confirmed by the sample behavior during thermogravimetric analysis. The percentage of β sheets calculated by infrared spectrum was 59%. In comparison with Nephila spiders, the onychophoran secretion lost more weight and entered the phase of degradation at lower temperatures. This secondary structure of proteins gives the onychophoran adhesive secretion a tensile strength and extensibility similar to those of the silk produced by spiders for prey-capture. Rev. Biol. Trop. 57 (3): 567-588. Epub 2009 September 30.

The dissipative and self-healing properties of mussel byssal threads are critical for their function as anchoring fibers in wave-battered habitats and central to their emergence as an exciting model system for bio-inspired polymers. Much is now understood about the structure-function relationships defining this remarkable proteinaceous bio-fiber; however, the molecular mechanisms underlying the distinctive tough, viscoelastic and self-healing behavior are still unclear. Here, we investigate elastic and dissipative contributions from the primary load-bearing proteins in the distal region of byssal threads (the preCols) using X-ray diffraction (XRD) combined with in situ tensile testing. Specifically, we identified cross β-sheet structure in the preCol flanking domains that functions as an elastic framework, providing hidden length. Dissipative behavior was associated with a strain-rate dependent phase transition of a sacrificial network stabilized by strong, reversible cross-links. Based on these findings, we posit a new model for byssal thread deformation and self-healing. [ABSTRACT FROM AUTHOR]

Three different tetraphenylalanine (FFFF) based peptides that differ at the N- and C-termini have been synthesized by using standard procedures to study their ability to form different nanoassemblies under a variety of conditions. The FFFF peptide assembles into nanotubes that show more structural imperfections at the surface than those formed by the diphenylalanine (FF) peptide under the same conditions. Periodic DFT calculations (M06L functional) were used to propose a model that consists of three FFFF molecules defining a ring through head-to-tail NH3+⋅⋅⋅−OOC interactions, which in turn stack to produce deformed channels with internal diameters between 12 and 16 Å. Depending on the experimental conditions used for the peptide incubation, N-fluorenylmethoxycarbonyl (Fmoc) protected FFFF self-assembles into a variety of polymorphs: ultra-thin nanoplates, fibrils, and star-like submicrometric aggregates. DFT calculations indicate that Fmoc-FFFF prefers a parallel rather than an antiparallel β-sheet assembly. Finally, coexisting multiple assemblies (up to three) were observed for Fmoc-FFFF-OBzl (OBzl = benzyl ester), which incorporates aromatic protecting groups at the two peptide terminals. This unusual and noticeable feature is attributed to the fact that the assemblies obtained by combining the Fmoc and OBzl groups contained in the peptide are isoenergetic. [ABSTRACT FROM AUTHOR]

Understanding protein beta structures has been hindered by the challenge of designing small, well‐folded β‐sheet systems. A β‐capping motif was previously designed to help solve this problem, but not without limitations, as the termini of this β‐cap were not fully available for chain extension. Combining Coulombic side chain attractions with a Trp/Trp edge‐to‐face interaction we produced a new capping motif that provided greater β‐sheet stability. This stability was maintained even in systems lacking a turn locus with a high propensity for chain direction reversal. The Coulombic cap was shown to improve β‐sheet stability in a number of difficult systems, hence providing an additional tool for protein structure and folding studies.An improved capping motif is introduced for stabilizing β sheets. This β‐cap contains attractive Coulombic forces and an indole/indole interaction. The β‐cap stabilizes hairpins and antiparallel strands connected by long loops. [ABSTRACT FROM AUTHOR]

This work advances bottom-up design of bioinspired materials built from peptide-amphiphiles, which are a class of bioconjugates in which a biofunctional peptide is covalently attached to a hydrophobic moiety that drives self-assembly in aqueous solution. Specifically, this work highlights the importance of peptide contour length in determining the equilibrium secondary structure of the peptide as well as the self-assembled (i.e., micelle) geometry. Peptides used here repeat a seven-amino acid sequence between one and four times to vary peptide contour length while maintaining similar peptide-peptide interactions. Without a hydrophobic tail, these peptides all exhibit a combination of random coil and α-helical structure. Upon self-assembly in the crowded environment of a micellar corona, however, short peptides are prone to β-sheet structure and cylindrical micelle geometry while longer peptides remain helical in spheroidal micelles. The transition to β-sheets in short peptides is rapid, whereby amphiphiles first self-assemble with α-helical peptide structure, then transition to their equilibrium β-sheet structure at a rate that depends on both temperature and ionic strength. These results identify peptide contour length as an important control over equilibrium peptide secondary structure and micelle geometry. Furthermore, the time-dependent nature of the helix-to-sheet transition opens the door for shape-changing bioinspired materials with tunable conversion rates. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 573-581, 2013. [ABSTRACT FROM AUTHOR]

Steric zipper refers to a structural motif where the residues of two neighboring beta-sheet layers are tightly interdigitated. Recently, steric zippers have been proposed as the fundamental structural units of amyloid fibrils. The steric zipper formed by polypeptides containing the palindromic sequence AGAAAAGA may have considerable biological relevance because the fragment AGAAAAGA is highly conserved in prion proteins of different species. The fibril core formed by AGAAAAGA has a distinctive structural feature that the distance between two interdigitated beta-sheet layers is comparable to the inter-strand distance of the individual beta sheet. In this work, the amyloid fibrils formed by the polypeptides of PrP(113-127), viz. Ac-AGAAAAGAVVGGLGG-NH2, are taken as the model compound for the solid-state NMR study of the formation of steric zipper. Near the end stage of the zipper formation, the NMR data show that there is a layer of water molecules trapped in between the two closely stacking β-sheet layers. The zipper formation is completed upon the depletion of the water molecules between the interdigitated β-sheet layers. On the basis of the NMR measurements and molecular dynamics simulations, we suggest that the residues A118 of the two neighboring beta sheets would first come into contact upon the zipper formation. [ABSTRACT FROM AUTHOR]

Abstract: We investigated the site-specific local structure of an amyloid peptide, NH2–GSNKGAIIGLM–COOH [Aβ(25–35)], one of the active fragments of amyloid β peptide that is known to be responsible for Alzheimer''s disease, in the fibrillar aggregated state. Isotope-assisted infrared vibrational circular dichroism (VCD) and absorption (VA) spectroscopy were used for the parent Aβ(25–35) peptide, along with doubly 13C labeled peptides at the carbonyl groups of residues 29 (Gly) and 30 (Ala) [Aβ(25–35:13C-29/30)] and at the carbonyl groups of residues 33 (Gly) and 34 (Leu) [Aβ(25–35:13C-33/34)]. The present results confirm that Aβ(25–35) peptide fibrils adopt a β-sheet structure and isotopic dilution experiments suggest a parallel β-sheet structure. The isotopic shifts suggest that the microenvironment of residues 29 (Gly) and 30 (Ala) could be different from that of residues 33 (Gly) and 34 (Leu). An unusual enhancement for the amide II′ VCD intensities of Aβ(25–35:13C-29/30) and Aβ(25–35:13C-33/34) peptide fibrils, considered to originate from inter-strand coupling, was found for the first time. The structural information reported in this manuscript has important implications in understanding the role of this peptide in the development of Alzheimer''s disease. [Copyright &y& Elsevier]

The accuracy of the secondary structure element (SSE) identification from volumetric protein density maps is critical for de-novo backbone structure derivation in electron cryo-microscopy (cryoEM). It is still challenging to detect the SSE automatically and accurately from the density maps at medium resolutions (∼5-10 Å). We present a machine learning approach, SSELearner, to automatically identify helices and β-sheets by using the knowledge from existing volumetric maps in the Electron Microscopy Data Bank. We tested our approach using 10 simulated density maps. The averaged specificity and sensitivity for the helix detection are 94.9% and 95.8%, respectively, and those for the β-sheet detection are 86.7% and 96.4%, respectively. We have developed a secondary structure annotator, SSID, to predict the helices and β-strands from the backbone Cα trace. With the help of SSID, we tested our SSELearner using 13 experimentally derived cryo-EM density maps. The machine learning approach shows the specificity and sensitivity of 91.8% and 74.5%, respectively, for the helix detection and 85.2% and 86.5% respectively for the β-sheet detection in cryoEM maps of Electron Microscopy Data Bank. The reduced detection accuracy reveals the challenges in SSE detection when the cryoEM maps are used instead of the simulated maps. Our results suggest that it is effective to use one cryoEM map for learning to detect the SSE in another cryoEM map of similar quality. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 698-708, 2012. [ABSTRACT FROM AUTHOR]

Abstract: The study of the folding of single domains, in the context of their multidomain environment, is important because more than 70% of eukaryotic proteins are composed of multiple domains. The structures of the tandem immunoglobulin (Ig) domain pairs A164–A165 and A168–A169, from the A-band of the giant muscle protein titin, reveal that they form tightly associated domain arrangements, connected by a continuous β-strand. We investigate the thermodynamic and kinetic properties of these tandem domain pairs. While A164–A165 apparently behaves as a single cooperative unit at equilibrium, unfolding without the accumulation of a large population of intermediates, domains in A168–A169 behave independently. Although A169 appears to be stabilized in the tandem protein, we show that this is due to nonspecific stabilization by extension. We elucidate the folding and unfolding pathways of both tandem pairs and show that cooperativity in A164–A165 is a manifestation of the relative refolding and unfolding rate constants of each individual domain. We infer that the differences between the two tandem pairs result from a different pattern of interactions at the domain/domain interface. [Copyright &y& Elsevier]

Abstract: Here we describe bispidine as a scaffold for inducing open turn-like and beta sheet conformations on the attached peptides depending on the mode of attachment of peptides to the scaffold. Various bispidine–peptide conjugates were designed and synthesized to demonstrate the versatility of the scaffold. [Copyright &y& Elsevier]

Abstract: Isotope-assisted vibrational circular dichroism (VCD) investigations have been used to probe the site specific local structure of an amyloid peptide for the first time. A seven residue peptide, NH2-KLVFFAE-COOH, which represents the Aβ(16–22) fragment of the Alzheimer’s amyloid β peptide, was used for these investigations. 13C labels were introduced separately at the carbonyl group of leucine (residue 17), alanine (residue 21) and also at both sites together. Since VCD spectra provide structure dependent signs, band shapes and frequencies, the isotope-assisted VCD spectroscopy revealed information on site specific secondary structure of the polypeptide. Isotope dilution VCD experiments provided a means to distinguish between parallel and anti-parallel nature of the β-sheet structure formed by the Aβ(16–22) fragment. The current results establish the usefulness of isotope-assisted VCD analysis in determining the site specific secondary structure of amyloid peptides. [Copyright &y& Elsevier]

An exercise using simple paper strips to illustrate protein helical and sheet secondary structures is presented. Drawing on the rich historical context of the use of physical models in protein biochemistry by early practitioners, in particular Linus Pauling, the purpose of this activity is to cultivate in students a hands-on, intuitive sense of protein secondary structure and to complement the common computer-based structural portrayals often used in teaching biochemistry. As students fold these paper strips into model secondary structures, they will better grasp how intramolecular hydrogen bonds form in the folding of a polypeptide into secondary structure, and how these hydrogen bonds direct the overall shape of helical and sheet structures, including the handedness of the α-helix and the difference between right- and the left-handed twist. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION Vol. 39, No. 3, pp. 221-225, 2011. [ABSTRACT FROM AUTHOR]

Abstract: The ability of a single polypeptide sequence to grow into multiple stable amyloid fibrils sets these aggregates apart from most native globular proteins. The existence of multiple amyloid forms is the basis for strain effects in yeast prion biology, and might contribute to variations in Alzheimer''s disease pathology. However, the structural basis for amyloid polymorphism is poorly understood. We report here five structurally distinct fibrillar aggregates of the Alzheimer''s plaque peptide Aβ(1–40), as well as a non-fibrillar aggregate induced by Zn2+. Each of these conformational forms exhibits a unique profile of physical properties, and all the fibrillar forms breed true in elongation reactions under a common set of growth conditions. Consistent with their defining cross-β structure, we find that in this series the amyloid fibrils containing more extensive β-sheet exhibit greater stability. At the same time, side chain packing outside of the β-sheet regions contributes to stability, and to differences of stability between polymorphic forms. Stability comparison is facilitated by the unique feature that the free energy of the monomer (equivalent to the unfolded state in a protein folding reaction) does not vary, and hence can be ignored, in the comparison of ΔG° of elongation values for each polymorphic fibril obtained under a single set of conditions. [Copyright &y& Elsevier]

Abstract: Silk proteins are a promising material for drug delivery due to their aqueous processability, biocompatibility, and biodegradability. A simple aqueous preparation method for silk fibroin particles with controllable size, secondary structure and zeta potential is reported. The particles were produced by salting out a silk fibroin solution with potassium phosphate. The effect of ionic strength and pH of potassium phosphate solution on the yield and morphology of the particles was determined. Secondary structure and zeta potential of the silk particles could be controlled by pH. Particles produced by salting out with 1.25 m potassium phosphate pH 6 showed a dominating silk II (crystalline) structure whereas particles produced at pH 9 were mainly composed of silk I (less crystalline). The results show that silk I-rich particles possess chemical and physical stability and secondary structure which remained unchanged during post treatments even upon exposure to 100% ethanol or methanol. A model is presented to explain the process of particle formation based on intra- and intermolecular interactions of the silk domains, influenced by pH and kosmotropic salts. The reported silk fibroin particles can be loaded with small molecule model drugs, such as alcian blue, rhodamine B, and crystal violet, by simple absorption based on electrostatic interactions. In vitro release of these compounds from the silk particles depends on charge–charge interactions between the compounds and the silk. With crystal violet we demonstrated that the release kinetics are dependent on the secondary structure of the particles. [Copyright &y& Elsevier]

Mounting evidence points to soluble peptide oligomers as the primary agents in various amyloid and prion diseases. Multiple mechanisms appear to contribute to the cytotoxic effects of these oligomers. Here, an additional, general mechanism is proposed - that soluble amyloid peptide oligomers serve as “all-purpose”β strands that can interact with transiently unfolded or nascent proteins where interior β-sheet edges are exposed. The proteins, trapped in misfolded states through this interaction, become substrates for ubiquitination, targeting them for proteasomal degradation. The increased load of ubiquitinated proteins could contribute to the impairment of the ubiquitin/proteasome system (UPS) seen in many amyloid-related diseases. This “misfolding trap” mechanism could be especially stressful in the endoplasmic reticulum, where the amyloid oligomers would compete with chaperones for nascent β-sheet proteins. If the bound amyloid oligomer dissociates at some point after the misfolded protein is committed to the UPS pathway, the oligomer could then repeat the process, adding a catalytic aspect to the misfolding mechanism. Direct proof of this proposed mechanism requires detection of amyloid oligomer-β-sheet protein complexes, and a co-immunoprecipitation experiment is proposed. This hypothesis supports therapies that increase amyloid oligomer degradation or sequestration, as well as therapies that upregulate chaperone activity, for combating amyloid-related diseases. [ABSTRACT FROM AUTHOR]

Abstract: Can two unrelated proteins with deliberately compromised folding abilities, marked propensities to aggregate upon increase of protein concentration, and proclivities towards beta sheet formation, be caused to hetero-aggregate? We address this question here using the ‘designer’ backbone-reversed forms of two model all-beta sheet proteins, E. coli CspA and C. elegans HSP12.6, both earlier created and characterized by our group. These were covalently labeled with fluorescent dyes of well-resolved spectral characteristics [retro-CspA with FITC, and retro-HSP12.6 with TRITC] and then allowed to aggregate within the same reaction vessel. The resultant aggregates are shown by spectrofluorimetry-coupled confocal laser scanning microscopy to constitute uniform mixtures of both proteins, existing within every cylindrical volume element of ≈200nm diameter, and comparable height, in all sections of the co-aggregated material suggesting that the two proteins do not selectively associate with copies of themselves during aggregation. Thus, it would appear that aggregation can occur without reference to protein molecular identity. [Copyright &y& Elsevier]

Molecular dynamics (MD) simulations of the interactions of a beta-strand antimicrobial peptide, protegrin-1, with model lipid bilayers of different hydrophobic widths show that protegrin-1 possesses at least two distinct binding modes in the trans-membrane orientation. In one of the modes, three of the cationic arginine residues bind to one bilayer leaflet and the other three arginine residues bind to the opposite leaflet, while in the second binding mode, four arginines bind to one leaflet and two to the other. The existence of multiple binding modes is facilitated by the high conformational flexibility of the first four residues of the N-terminal region, with a sequence of RGGR. One of the binding modes causes a larger bilayer disruption than the other, and in either mode, the bilayer disruption is smaller for lipid membranes with smaller bilayer widths. Simulations of the self-assembly of initially random lipid/water mixtures in the presence of PG-1 peptides show that the system evolves into a bilayer, with a stable water pore spanning the two lipid leaflets. Lipid head groups and the PG-1 peptide stabilize the water pore. [ABSTRACT FROM AUTHOR]

The cis Gly–Gly peptidic bond observed in dihydrofolate reductase, which takes place between a beta sheet and an alpha helix is chosen as an example to study the various factors which influence this conformation. The peptidic chain of 16 amino acids is studied by a QM/MM scheme (6-31+G* B3LYP—Amber 99). Both electronic and classical contributions to the total energy take part to the stabilization of the cis conformation. A special role is played by the alpha helix when it is bonded to the carbonyl group of the bond of interest. [ABSTRACT FROM AUTHOR]

Abstract: Glycation, a local covalent interaction, leads to alterations in secondary and tertiary structures of hemoglobin, the changes produced by fructose being more pronounced than those caused by glucose. The Stokes diameter of hemoglobin increases upon glycation from 7 to 14 nm and a concurrent inter-chain cross-linking and heme loss are also observed, particularly in the later stage of glycation. An initial increase of tryptophan (trp) fluorescence was observed in both glucation and fructation. In case of frucation however there was a decrease in tryptophan fluorescence that was accompanied by an increase in fluorescence of the advanced glycosylation end products (AGEs). This fluorescence behavior is indicative of energy transfer between tryptophan and the AGEs formed during the late stage of glycation. Emergence of an isosbestic point in the fluorescence spectra (taken at different time intervals) implies existence of two distinct glycation stages. The late glycation stage is also marked by an increase of  beta structure and random coil at the expense of alpha helix. It is further observed that this compensatory loss of alpha helix (reported for the first time) and increase in beta sheet and random coil elements depend on the number of solvent-accessible glycation sites (rather than total number of such sites) and the subunit assembly of the protein. [Copyright &y& Elsevier]

To address questions of protein stability, researchers have increasingly turned to combinatorial approaches that permit the rapid analysis of libraries of protein variants. Phage- display has proved to be a powerful tool for analyzing protein stability due to the large library size and the robustness of the phage particle to a variety of denaturing conditions. With the B! domain of protein G (GB!) and a carnelid heavy chain antibody as model systems, we are using phage-display lib- raries to experimentally address questions that have generally been addressed in silico, either through computational studies or statistical analysis of known protein structures. One effort has focused on identifying novel solutions to repacking the hydrophobic core of GB1, while maintaining stability comparable to the wild type protein. In a second study, a small set of substitutions in complimentarity-determining region 3 was found to stabilize the framework of the camelid antibody. Another major focus has been to obtain quantitative data on 13-sheet stability determinants. We have successfully adapted a phage-display method for quantitating affinities of protein variants (shotgun alanine scanning) to analysis of GB1 stability. Using this method, we have analyzed the energetic contributions of cross-strand side chain- side chain interactions. Finally, we discuss parameters to consider in using phage-display to discriminate subtle stability differences among fully folded variants. Overall, this method provides a fast approach for quantitatively addressing biophysical questions. [ABSTRACT FROM AUTHOR]

Self-assembling polypeptide molecules have been designed to explore aspects of hierarchical or multiscale long-range order, and the interactions that occur at various length scales that drive order and patterning in complex materials. Three peptides were synthesized with repetitive motifs loosely based on insect silks. Thin films were obtained from each peptide using a solvent templating technique. Smectic layers were observed in the thin films and in bulk materials prepared for comparison. A variety of additional effects, including chirality and interfacial anchoring at the helix, compete in the thin films, resulting in complex but regular patterns within the materials over a hierarchy of length scales spanning several orders of magnitude. The relative magnitude of these effects can be tuned through sequence design, as can the smectic layer thickness. Thus, many parameters describing the patterns in the materials can be controlled at the molecular design level, allowing complex patterns of nanoscale to microscale topography and chemistry to be created through self-assembly. In addition to the potential for designer materials, there may be some biological relevance to the observed phenomena. The silk-like molecules used fold into “hairpins,” providing a rigid unit that can drive liquid crystalline phase behavior. A similar process could be at work in silks and other structurally similar proteins that form textured materials. Chiral smectic order and multiscale patterns that can often result are clearly rich areas, worthy of further exploration. [ABSTRACT FROM AUTHOR]

We present a unified potential-energy model that successfully reproduces the hydrogen bonding effect in proteins and can be used to represent well-defined secondary structures, both α-helices and β-sheets. The native structures of the model contain both α-helices and β-sheets and are entirely dependent on the sequence of the modelled protein. The model provides structural insight into the physical mechanism of such problems as structural conversion due to mutation and double native conformations with different α-helix and β-sheet contents. [Copyright &y& Elsevier]

Because poly-l-lysine (PLL) can exist in the α-helix or β-sheet conformation depending on solution preparation and solution conditions, PLL is a suitable candidate to probe the dependence of protein interactions on secondary structure. The osmotic second virial coefficient and weight-average molecular weight are reported from low-angle laser-light scattering measurements for PLL as a function of NaCl concentration, pH, and α-helix or β-sheet content. Interactions between PLL molecules become more attractive as salt concentration increases due to screening of PLL charge by salt ions and at low salt concentration become more attractive as pH increases due to decreased net charge on PLL. The experimental results show that interactions are stronger for the β-sheet conformation than for the α-helix conformation. A spherically-symmetric model for the potential of mean force is used to account for specific interactions not described by DLVO theory and to show how differences in secondary structure affect PLL interactions. [Copyright &y& Elsevier]

• β−sheets and their unfolding are monitored by infrared spectroscopy. • We present a tripeptide capable of reversing β−sheet formation in other peptides. • Our inhibitor can completely eliminate β−sheets from α−Synuclein-derived peptides. • Our inhibitor can dramatically reduce β−sheet formation in Aβ(16−22). A wide array of protein misfolding diseases all follow a similar pathogenic mechanism that includes, as an early step, the formation of β−sheet-rich monomers and oligomers. Thus, interruption of β−sheets is a promising strategy for preventing and reversing these diseases. We have identified a tri-peptide that is capable of interacting with peptides that can form β−sheets in isolation, and causing their unfolding. Using infrared spectroscopy, we studied the effect of Ac-GGA-NH 2 , a disordered peptide, on four β−sheet peptides derived from stretches of amyloidogenic proteins. In each case, less β−sheet is observed in the experimental mixture of these peptides and Ac-GGA-NH 2 than is predicted mathematically from averaging the individual spectra of the two peptides. In the case of the two peptides we used that are derived from α−Synuclein, complete unfolding of the β−sheets is induced by the presence of equimolar concentrations of Ac-GGA-NH 2. [ABSTRACT FROM AUTHOR]

Silk is an especially appealing biomaterial due to its adaptable mechanical properties, allowing it to be used in a wide range of tissue engineering applications. However, processing conditions play a critical role in determining silk's mechanical properties, biodegradability, and biocompatibility. While bulk properties of silk have been widely explored, focusing on microscopic features is becoming increasingly important, as modifications at this scale largely affect the resulting regenerative properties of the biomaterial. Structural changes caused by the silk source, extraction, and processing should be carefully considered, as they will affect the biocompatibility and degradability of silk fibroin. Processing techniques and physical properties of silk that make it an ideal material for many biomedical applications will be explored. This article is categorized under: Implantable Materials and Surgical Technologies > Nanotechnology in Tissue Repair and ReplacementImplantable Materials and Surgical Technologies > Nanomaterials and Implants Silk's highly tunable range of mechanical properties, degradation rates, and material formats arise from subtle changes at the microscopic level. [ABSTRACT FROM AUTHOR]