Tripeptides adopt stable structures in water. A combined polarized visible Raman,FTIR, and VCD spectroscopy study

We have measured the band profile of amide I in the infrared, isotropic, and anisotropic Raman spectra of L-alanyl-D-alanyl-L-alanine, acetyl-L-alanyl-L-alanine, L-vanyl-L-vanyl-L-valine, L-seryl-L-seryl-L-serine, and L-lysyl-L-lysyl-L-lysine at acid, neutral, and alkaline pD. The respective intensity ratios of the two amide I bands depend on the excitonic coupling between the amide I modes of the peptide group. These intensity ratios were obtained from a self-consistent spectral decomposition and then were used to determine the dihedral angles between the two peptide groups by means of a recently developed algorithm (Schweitzer-Stenner, R. Biophys. J. 2002, 83, 523-532). The validity of the obtained structures were checked by measuring and analyzing the vibrational circular dichroism of the two amide I bands. Thus, we found two solutions for all protonation states of trialanine. Assuming a single conformer, one obtains a very extended beta-helix-like structure. Alternatively, the data can be explained by the coexistence of a 3(1)(PII) and a beta-sheet-like structure. Acetyl-L-alanyl-L-alanine exhibits a structure which is very similar to that obtained for trialanine. The tripeptide with the central D-alanine adopts an extended structure with a negative psi and a positive phi angle. Trivaline and triserine adopt single beta(2)-like structures such as that identified in the energy landscape of the alanine dipeptide. Trilysine appears different from the other investigated homopeptides in that it adopts a left-handed helix which at acid pD is in part stabilized by hydrogen bonding between the protonated carboxylate (donor) and the N-terminal peptide carbonyl. Our result provides compelling evidence for the capability of short peptides to adopt stable structures in an aqueous solution, which at least to some extent reflect the intrinsic structural propensity of the respective amino acids in proteins. Furthermore, this paper convincingly demonstrates that the combination of different vibrational spectroscopies provides a powerful tool for the determination of the secondary structure of peptides in solution.     

Sequence, structure, and function of peptide self-assembled monolayers

Cysteine is commonly used to attach peptides onto gold surfaces. Here we show that the inclusion of an additional linker with a length of four residues (-PPPPC) and a rigid, hydrophobic nature is a better choice for forming peptide self-assembled monolayers (SAMs) with a well-ordered structure and high surface density. We compared the structure and function of the nonfouling peptide EKEKEKE-PPPPC-Am with EKEKEKE-C-Am. Circular dichroism, attenuated total internal reflection Fourier transform IR spectroscopy, and molecular dynamics results showed that EKEKEKE-PPPPC-Am forms a secondary structure while EKEKEKE-C-Am has a random structure. Surface plasmon resonance sensor results showed that protein adsorption on EKEKEKE-PPPPC-Am/gold is very low with small variation while protein adsorption on EKEKEKE-C-Am/gold is high with large variation. X-ray photoelectron spectroscopy results showed that both peptides have strong gold-thiol binding with the gold surface, indicating that their difference in protein adsorption is due to their assembled structures. Further experimental and simulation studies were performed to show that -PPPPC is a better linker than -PC, -PPC, and -PPPC. Finally, we extended EKEKEKE-PPPPC-Am with the cell-binding sequence RGD and demonstrated control over specific versus nonspecific cell adhesion without using poly(ethylene glycol). Adding a functional peptide to the nonfouling EK sequence avoids complex chemistries that are used for its connection to synthetic materials.     

Building a metal binding domain,one half at a time

The recently determined structure of a zinc binding peptide reveals that a particular sequence can adopt one stable fold as an isolated peptide but adopt an alternative structure as part of a larger protein domain.     

Characterization and Applications of Red Mud,an Aluminum Industry Waste Material,in the Construction and Building Industries,as well as Catalysis

The disposal of red mud (RM), a waste material generated by the aluminum industry, remains a global environmental concern because of its high alkalinity and smaller particle size, which have the potential to pollute air, soil, and water. Recently, efforts have been made to develop a strategy for reusing industrial byproducts, such as RM, and turning waste into value-added products. The use of RM as (i) a supplementary cementitious material for construction and building materials, such as cement, concrete, bricks, ceramics, and geopolymers, and (ii) a catalyst is discussed in this review. Furthermore, the physical, chemical, mineralogical, structural, and thermal properties of RM, as well as its environmental impact, are also discussed in this review. It is possible to conclude that using RM in catalysis, cement, and construction industries is the most efficient way to recycle this byproduct on a large scale. However, the low cementitious properties of RM can be attributed to a reduction in the fresh and mechanical properties of composites incorporating RM. On the other hand, RM can be used as an efficient active catalyst to synthesize organic molecules and reduce air pollution, which not only makes use of solid waste but also lowers the price of the catalyst. The review provides basic information on the characterization of RM and its suitability in various applications, paving the way for more advanced research on the sustainable disposal of RM waste. Future research perspectives on the utilization of RM are also addressed.     

Bond length contraction in gold nanoparticles

The structure of nanoparticles typically differs from its bulk counterpart. Predominantly, the structures of gold nanoparticles have been under exceedingly intense discussion since the discovery of their high catalytic activity. We found an increasing bond length contraction with decreasing particle size for citrate-stabilized gold nanoparticles in aqueous solution as determined by in situ extended X-ray absorption fine structure (EXAFS) spectroscopy. Particle sizes and size distributions were determined by small-angle X-ray scattering. The analysis of the obtained EXAFS spectra employing ab initio calculations reveals that the Au–Au bond length undergoes a contraction of 2 pm for nanoparticles with a radius of 2.9 nm. NIST reference material RM 8011 gold nanoparticles with a radius of 4.4 nm exhibit a smaller contraction of approximately 1 pm. Finally, gold atoms in RM 8013 particles with a radius of 25.7 nm show distances of 288 pm—identical to the distance in gold foil—and exhibits bulk-like properties. The observed bond length contraction of gold nanoparticles in solution is significantly smaller than previously reported for gold nanoparticle deposited on surfaces, which is up to 15 pm. This indicates that the bond length contraction effect of “free” and “surface-immobilized” nanoparticles differ fundamentally. Such difference could be essential for the understanding of nanoparticle-supported catalysis.     

Modified reverse microemulsion synthesis for iron oxide/silica core–shell colloidal particles

Iron oxide/silica core–shell colloidal particles were prepared by basic reverse microemulsion (RM) method and two modified RM methods. By basic RM method, maximum particle size obtained was mere 40 nm. For building photonic crystals working in the visible range, the colloidal particles must be larger than 100 nm. Thus two modified RM methods were used. By alcohol modified RM method, short chain alcohols were used as co-surfactant. The particle size rose to near 100 nm, but the core–shell structure was comparatively poor. By emulsifier pair modified RM method, the particle size leapt to over 200 nm and a narrow growth window was found favorable to enhance the stability and rigidity of the surfactants layers. The core–shell mechanism was also discussed and a new four-step mechanism was proposed.     

A novel artificial loop scaffold for the noncovalent constraint of peptides

BACKGROUND: Few examples exist of peptides of < 35 residues that form a stable tertiary structure without disulfide bonds. A method for stabilization and noncovalent constraint of relatively short peptides may allow the construction and use of intracellular peptide libraries containing protein minidomains. RESULTS: We have examined a novel method for the noncovalent constraint of peptides by attaching the peptide EFLIVKS (single-letter amino acid code), which forms dimers, to the amino and carboxyl termini of different peptide inserts. An 18 residue random coil taken from the inhibitor loop of barley chymotrypsin inhibitor 2 was inserted between the peptides to produce a 32-mer minidomain that is attacked only slowly by elastase, has numerous slowly exchanging protons, contains a high beta-structure content and has a T(m) above 37 degrees C. A point mutation disrupting the hydrophobic interior in both dimerizing peptides causes a loss of all slowly exchanging protons and of secondary structure. Adding specific charged residues to each terminus substantially increased the T(m), as did point mutants designed to add interdimerizer ion pairs. Three flexible epitope tag inserts and a nonamer insert do not appear to be folded in a stable structure by EFLIVKS. The properties of two peptides selected for expression in HeLa cells suggest they do form a stable tertiary structure. CONCLUSIONS: Attaching short dimerizing peptides to both the amino and carboxyl termini of several 18-mer peptides appears to create stable monomeric tertiary structures. Mutations in the dimerizers can either destabilize or significantly stabilize a standard 18-mer insert. Dimerizing peptides flanking random insert sequences could be used as a strategy to generate heterogeneous peptide libraries with both extended and folded members.     

Extended sugar-assisted glycopeptide ligations: development, scope, and applications

Recently, we reported the development of sugar-assisted ligation (SAL), a novel peptide ligation method for the synthesis of glycopeptides. After screening a large number of glycoprotein sequences in a glycoprotein database, it became evident that a large proportion (approximately 53%) of O-glycosylation sites contain amino acid residues that will not undergo SAL reactions. To overcome these inherent limitations and broaden the scope of the method we report here the development of an extended SAL method. Glycopeptides containing up to six amino acid extensions N-terminal to the glycosylated residue were shown to facilitate ligation reactions with peptide thioesters, and these products were isolated in good yields. Kinetic analysis was used to show that as glycopeptides were extended by further amino acid residues, ligation reactions became slower. This finding was rationalized by molecular dynamics simulations using AMBER9. These studies suggested a general trend whereby the proximal distance between the reactive sites of the thioester intermediate (the N-terminal amine and the carbonyl carbon of the thioester) increased as glycopeptides were extended, thus slowing down the ligation rate. Each of the extended SAL methods showed broad tolerance to a number of different amino acid combinations at the ligation junction. Re-evaluation of the glycoprotein database suggested that 95% of the O-linked glycosylation sites can now be utilized to facilitate SAL or extended SAL reactions. As such, this method represents an extremely valuable tool for the synthesis of naturally occurring glycopeptides and glycoproteins. To demonstrate the applicability of the method, extended SAL was successfully implemented in the synthesis of the starting unit of the cancer-associated MUC1 glycoprotein.     

Beta-hairpin folding by a model amyloid peptide in solution and at an interface

The development of specific agents against amyloidoses requires an understanding of the conformational distribution of fibrillogenic peptides at a microscopic level. Here, I present molecular dynamics simulations of the model amyloid peptide LSFD with sequence LSFDNSGAITIG-NH2 in explicit water and at a water/vapor interface for a total time scale of approximately 1.8 micros. An extended structure was used as initial peptide configuration. At approximately 290 K, solvated LSFD was kinetically trapped in diverse misfolded beta-sheet/coil conformations. At 350 K, in contrast, the same type II' beta-hairpin in equilibrium with less ordered but also U-shaped conformations was observed for the core residues DNSGAITI in solution and at the interface in multiple independent simulations. The most stable structural unit of the beta-hairpin was the two residue turn (GA). The core residues exhibited a well-defined folded state in which the beta-hairpin was stabilized by a hydrogen bond between the side chain of Asn-385 and the main chain carbonyl group of Gly-387. My results suggest that beta-sheet conformations indicated from previous Fourier-transform infrared spectroscopy measurements immediately after preparation of the peptide solution may not arise from protofilaments as speculated by others but are a property of LSFD monomers. In addition, combined with previous results from X-ray scattering, my findings suggest that interfacial aggregation of LSFD implies a transition from U-shaped to extended peptide conformations. This work including the first simulations of reversible beta-hairpin folding at an interface is an essential step toward a microscopic understanding of interfacial peptide folding and self-assembly. Knowledge of the main conformation of the peptide core may facilitate the design of possible inhibitors of LSFD aggregation as a test ground for future computational therapeutic strategies against amyloid diseases.     

Micelle‐Triggered β‐Hairpin to α‐Helix Transition in a 14‐Residue Peptide from a Choline‐Binding Repeat of the Pneumococcal Autolysin LytA

Choline‐binding modules (CBMs) have a ββ‐solenoid structure composed of choline‐binding repeats (CBR), which consist of a β‐hairpin followed by a short linker. To find minimal peptides that are able to maintain the CBR native structure and to evaluate their remaining choline‐binding ability, we have analysed the third β‐hairpin of the CBM from the pneumococcal LytA autolysin. Circular dichroism and NMR data reveal that this peptide forms a highly stable native‐like β‐hairpin both in aqueous solution and in the presence of trifluoroethanol, but, strikingly, the peptide structure is a stable amphipathic α‐helix in both zwitterionic (dodecylphosphocholine) and anionic (sodium dodecylsulfate) detergent micelles, as well as in small unilamellar vesicles. This β‐hairpin to α‐helix conversion is reversible. Given that the β‐hairpin and α‐helix differ greatly in the distribution of hydrophobic and hydrophilic side chains, we propose that the amphipathicity is a requirement for a peptide structure to interact and to be stable in micelles or lipid vesicles. To our knowledge, this “chameleonic” behaviour is the only described case of a micelle‐induced structural transition between two ordered peptide structures.     

Anchored Mediator Enabling Shuttle‐Free Redox Mediation in Lithium‐Oxygen Batteries

Redox mediators (RMs) are considered an effective countermeasure to reduce the large polarization in lithium‐oxygen batteries. Nevertheless, achieving sufficient enhancement of the cyclability is limited by the trade‐offs of freely mobile RMs, which are beneficial for charge transport but also trigger the shuttling phenomenon. Here, we successfully decoupled the charge‐carrying redox property of RMs and shuttling phenomenon by anchoring the RMs in polymer form, where physical RM migration was replaced by charge transfer along polymer chains. Using PTMA (poly(2,2,6,6‐tetramethyl‐1‐piperidinyloxy‐4‐yl methacrylate)) as a polymer model system based on the well‐known RM tetramethylpiperidinyloxyl (TEMPO), it is demonstrated that PTMA can function as stationary RM, preserving the redox activity of TEMPO. The efficiency of RM‐mediated Li₂O₂ decomposition remains remarkably stable without the consumption of oxidized RMs or degradation of the lithium anode, resulting in an improved performance of the lithium‐oxygen cell.     

De novo design of a redox-active minimal rubredoxin mimic

Metal-binding sites in metalloproteins frequently occur at the interfaces of elements of secondary structure, which has enabled the retrostructural analysis of natural proteins and the de novo design of helical bundles that bind metal ion cofactors. However, the design of metalloproteins containing beta-structure is less well developed, despite the frequent occurrence of beta-conformations in natural metalloproteins. Here, we describe the design and construction of a beta-protein, RM1, that forms a stable, redox-active 4-Cys thiolate Fe(II/III) site analogous to the active site of rubredoxin. The protein folds into a beta-structure in the presence and absence of metal ions and binds Fe(II/III) to form a redox-active site that is stable to repeated cycles of oxidation and reduction, even in an aerobic environment.     

RM1: a reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I

Twenty years ago, the landmark AM1 was introduced, and has since had an increasingly wide following among chemists due to its consistently good results and time-tested reliability--being presently available in countless computational quantum chemistry programs. However, semiempirical molecular orbital models still are of limited accuracy and need to be improved if the full potential of new linear scaling techniques, such as MOZYME and LocalSCF, is to be realized. Accordingly, in this article we present RM1 (Recife Model 1): a reparameterization of AM1. As before, the properties used in the parameterization procedure were: heats of formation, dipole moments, ionization potentials and geometric variables (bond lengths and angles). Considering that the vast majority of molecules of importance to life can be assembled by using only six elements: C, H, N, O, P, and S, and that by adding the halogens we can now build most molecules of importance to pharmaceutical research, our training set consisted of 1736 molecules, representative of organic and biochemistry, containing C, H, N, O, P, S, F, Cl, Br, and I atoms. Unlike AM1, and similar to PM3, all RM1 parameters have been optimized. For enthalpies of formation, dipole moments, ionization potentials, and interatomic distances, the average errors in RM1, for the 1736 molecules, are less than those for AM1, PM3, and PM5. Indeed, the average errors in kcal x mol(-1) of the enthalpies of formation for AM1, PM3, and PM5 are 11.15, 7.98, and 6.03, whereas for RM1 this value is 5.77. The errors, in Debye, of the dipole moments for AM1, PM3, PM5, and RM1 are, respectively, 0.37, 0.38, 0.50, and 0.34. Likewise, the respective errors for the ionization potentials, in eV, are 0.60, 0.55, 0.48, and 0.45, and the respective errors, in angstroms, for the interatomic distances are 0.036, 0.029, 0.037, and 0.027. The RM1 average error in bond angles of 6.82 degrees is only slightly higher than the AM1 figure of 5.88 degrees, and both are much smaller than the PM3 and PM5 figures of 6.98 degrees and 9.83 degrees, respectively. Moreover, a known error in PM3 nitrogen charges is corrected in RM1. Therefore, RM1 represents an improvement over AM1 and its similar successor PM3, and is probably very competitive with PM5, which is a somewhat different model, and not fully disclosed. RM1 possesses the same analytical construct and the same number of parameters for each atom as AM1, and, therefore, can be easily implemented in any software that already has AM1, not requiring any change in any line of code, with the sole exception of the values of the parameters themselves.     

Effects of the water content on the growth rate of AgCl nanoparticles in a reversed micelle system

The effects of water content on the growth rate and the final particle size of AgCl nanoparticles in a reversed micelle (RM) system of polyoxyethylene (6) nonylphenyl ether (NP-6)/water/cyclohexane were investigated using a double-jet technique, in which RM solutions of AgNO(3) and KCl were added concurrently to a RM solution containing the excess concentration of chloride ion. As a result, the particle growth rate and the final particle size at a constant Rw ( identical with[water]/[surfactant]) below 5 were found to be in excellent agreement with our theoretical prediction based on a dynamic Ostwald ripening mechanism governed by the overall solubility of the solid and the diffusivity of the reversed micelles, whereas the final particle size was far beyond the size of the water pool of a reversed micelle. Thus, the dramatic reduction of the particle size in the RM system can be explained by the drastic reduction of the overall solubility of the solid and the small diffusivity of the bulky reversed micelles as a carrier of silver ion, and not by the size of the water pool of a reversed micelle as conventionally explained. Some additional contribution of a coagulation process was also suggested in a high Rw range above 5. Significant coagulation of AgCl particles was observed in a RM system with AOT in place of NP-6 even under the standard conditions for the NP-6 system.     

Development of bovine muscle, liver and urine reference materials for zeranol – preparation, homogeneity and stability

 Samples of bovine muscle, liver and urine, zeranol-free (RM 508, RM 509 and RM 510, respectively) and zeranol-containing (RM 511, RM 512 and RM 513, respectively) were prepared and tested as candidate reference materials. Preliminary studies on achievement of target zeranol content, intercomparison of analytical methods (HPLC-RIA and GC-MS) and effects of lyophilisation and irradiation on zeranol content are described. The preparation of the materials and testing for homogeneity and stability of zeranol in the materials are discussed. The coefficients of variation for zeranol determinations for between-vial homogeneity (4.0%, 4.4% and 4.6% for muscle, liver and urine, respectively) are similar to those for the analytical method (4.0%, 7.3% and 6.8% for muscle, liver and urine, respectively) indicating that the materials are homogeneous. Stability data over a 12-month storage period at temperatures ranging from −18 °C to +37 °C indicate that the materials are sufficiently stable for use as reference materials. This paper is dedicated to the memory of Dr Hilary Stevenson (The Queen’s University of Belfast/DANI) who, together with Mr. W. Graham, facilitated the irradiation of the lyophilised materials.--> Received: 18 June 1996/Revised: 19 August 1996/Accepted: 23 August 1996     

Development of bovine muscle, liver and urine reference materials for zeranol – preparation, homogeneity and stability

 Samples of bovine muscle, liver and urine, zeranol-free (RM 508, RM 509 and RM 510, respectively) and zeranol-containing (RM 511, RM 512 and RM 513, respectively) were prepared and tested as candidate reference materials. Preliminary studies on achievement of target zeranol content, intercomparison of analytical methods (HPLC-RIA and GC-MS) and effects of lyophilisation and irradiation on zeranol content are described. The preparation of the materials and testing for homogeneity and stability of zeranol in the materials are discussed. The coefficients of variation for zeranol determinations for between-vial homogeneity (4.0%, 4.4% and 4.6% for muscle, liver and urine, respectively) are similar to those for the analytical method (4.0%, 7.3% and 6.8% for muscle, liver and urine, respectively) indicating that the materials are homogeneous. Stability data over a 12-month storage period at temperatures ranging from −18 °C to +37 °C indicate that the materials are sufficiently stable for use as reference materials. This paper is dedicated to the memory of Dr Hilary Stevenson (The Queen’s University of Belfast/DANI) who, together with Mr. W. Graham, facilitated the irradiation of the lyophilised materials.--> Received: 18 June 1996/Revised: 19 August 1996/Accepted: 23 August 1996     

Reversible thermal transition of polydiacetylene based on KTTKS collagen sequence

Here we explore the physico-chemical properties of a peptide amphiphile obtained by chemical conjugation of the collagen-stimulating peptide KTTKS with 10,12-pentacosadiynoic acid which photopolymerizes as a stable and extended polydiacetylene. We investigate the self-assembly of this new polymer and rationalize its peculiar behavior in terms of a thermal conformational transition. Surprisingly, this polymer shows a thermal transition associated with a non-cooperative increase in β-sheet content at high temperature.     

Anchored Mediator Enabling Shuttle-Free Redox Mediation in Lithium-Oxygen Batteries

Redox mediators (RMs) are considered an effective countermeasure to reduce the large polarization in lithium-oxygen batteries. Nevertheless, achieving sufficient enhancement of the cyclability is limited by the trade-offs of freely mobile RMs, which are beneficial for charge transport but also trigger the shuttling phenomenon. Here, we successfully decoupled the charge-carrying redox property of RMs and shuttling phenomenon by anchoring the RMs in polymer form, where physical RM migration was replaced by charge transfer along polymer chains. Using PTMA (poly(2,2,6,6-tetramethyl-1-piperidinyloxy-4-yl methacrylate)) as a polymer model system based on the well-known RM tetramethylpiperidinyloxyl (TEMPO), it is demonstrated that PTMA can function as stationary RM, preserving the redox activity of TEMPO. The efficiency of RM-mediated Li₂O₂ decomposition remains remarkably stable without the consumption of oxidized RMs or degradation of the lithium anode, resulting in an improved performance of the lithium-oxygen cell.     

Peptoid oligomers with alpha-chiral, aromatic side chains: sequence requirements for the formation of stable peptoid helices.

The achiral backbone of oligo-N-substituted glycines or "peptoids" lacks hydrogen-bond donors, effectively preventing formation of the regular, intrachain hydrogen bonds that stabilize peptide alpha-helical structures. Yet, when peptoids are N-substituted with alpha-chiral, aromatic side chains, oligomers with as few as five residues form stable, chiral, polyproline-like helices in either organic or aqueous solution. The adoption of chiral secondary structure in peptoid oligomers is primarily driven by the steric influence of these bulky, chiral side chains. Interestingly, peptoid helices of this class exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have taken advantage of this distinctive spectroscopic signature to investigate sequence-related factors that favor and disfavor stable formation of peptoid helices of this class, through a comparison of more than 30 different heterooligomers with mixed chiral and achiral side chains. For this family of peptoids, we observe that a composition of at least 50% alpha-chiral, aromatic residues is necessary for the formation of stable helical structure in hexameric sequences. Moreover, both CD and 1H-13C HSQC NMR studies reveal that these short peptoid helices are stabilized by the placement of an alpha-chiral, aromatic residue on the carboxy terminus. Additional stabilization can be provided by the presence of an "aromatic face" on the helix, which can be patterned by positioning aromatic residues with three-fold periodicity in the sequence. Extending heterooligomer chain length beyond 12-15 residues minimizes the impact of the placement, but not the percentage, of alpha-chiral aromatic side chains on overall helical stability. In light of these new data, we discuss implications for the design of helical, biomimetic peptoids based on this structural motif.