Cu(I) luminescence from the tetranuclear Cu4S4 cofactor of a synthetic 4-helix bundle

The addition of Cu(I) to the random-coil peptide, C16C19-GGY, produces a self-organized, metal-bridged 4-helix bundle which displays an intense room-temperature luminescence at 600 nm. Emission, UV, and CD titrations along with X-ray absorption studies indicate that the luminescent cofactor is likely a Cu4S4 cluster in which each Cu atom is bridged by the side chains of two cysteine residues and has terminal N/O ligation.     

Iminopyridine complexes of manganese, rhenium, and molybdenum derived from amino ester methylserine and peptides Gly-Gly, Gly-Val, and Gly-Gly-Gly: self-assembly of the peptide chains

Complexes containing pyridine-2-carboxaldehyde (pyca) ligand acting as κ(2)-(N,O) chelates in [MX(CO)(3)(pyca)] (M = Mn, Re; X = Cl, Br), or [MoX(methallyl)(CO)(2)(pyca)] (X = Cl, Br), are good precursors for iminopyridine complexes derived from amino esters and peptides of formula [MX(CO)(3)(py-2-C(H)═NCHX-COOY)] or [MoX(methallyl)(CO)(2)(py-2-C(H)═NCHX-COOY)], via Schiff condensation of the aldehyde function of pyca with the terminal NH(2) group of the amino ester or peptide. X-ray determinations confirm the structures and show that in solid phase the peptide chains assemble through H-bonds adopting different patterns which depend on the geometry of the metal-ligand fragments. The H-bonding patterns have been analyzed in detail and described by using graph set methods. In most cases, Mo complexes show intramolecular arrangement involving the halogen (Cl or Br) and an NH group of the side chain. For the Mn and Re complexes, the peptide side arms form infinite chains, helices, and rings. In many cases, the terminal carboxylic O-H function is engaged in a "terminal" H-bond with a polar molecule of solvent (THF or acetone), instead of forming the usual head-to-head arrangement found in simple carboxylic acids. For the longer tripeptide Gly-Gly-Gly, a discrete, dimeric association is observed, in which the peptide chains show antiparallel arrangement with a complementary disposition of the internal N-H and C═O functions. DOSY experiments in solution show significant changes in the diffusion rates upon addition of OPBu(3), which indicate H-bonding interaction of OPBu(3) with the peptide hydrogens.     

Hydrogel-Stiffening and Non-Cell Adhesive Properties of Amphiphilic Peptides with Central Alkylene Chains

Amphiphilic peptides bearing terminal alkyl tails form supramolecular nanofibers that are increasingly used as biomaterials with multiple functionalities. Insertion of alkylene chains in peptides can be designed as another type of amphiphilic peptide, yet the influence of the internal alkylene chains on self-assembly and biological properties remains poorly defined. Unlike the terminal alkyl tails, the internal alkylene chains can affect not only the hydrophobicity but also the flexibility and packing of the peptides. Herein, we demonstrate the supramolecular and biological effects of the central alkylene chain length inserted in a peptide. Insertion of the alkylene chain at the center of the peptide allowed for strengthened β-sheet hydrogen bonds and modulation of the packing order, and consequently the amphiphilic peptide bearing C2 alkylene chain formed a hydrogel with the highest stiffness. Interestingly, the amphiphilic peptides bearing internal alkylene chains longer than C2 showed a diminished cell-adhesive property. This study offers a novel molecular design to tune mechanical and biological properties of peptide materials.     

Self‐Assembly of Imidazolium‐Based Rodlike Ionic Liquid Crystals: Transition from Lamellar to Micellar Organization

By using aryl‐amination chemistry, a series of rodlike 1‐phenyl‐1H‐imidazole‐based liquid crystals (LCs) and related imidazolium‐based ionic liquid crystals (ILCs) has been prepared. The number and length of the C‐terminal chains (at the noncharged end of the rodlike core) and the length of the N‐terminal chain (on the imidazolium unit in the ILCs) were modified and the influence of these structural parameters on the mode of self‐assembly in LC phases was investigated by polarizing microscopy, differential scanning calorimetry, and X‐ray diffraction. For the single‐chain imidazole derivatives nematic phases (N) and bilayer SmA₂ phases were found, but upon increasing the number of alkyl chains the LC phases were lost. For the related imidazolium salts LC phases were preserved upon increasing the number and length of the C‐terminal chains and in this series it leads to the phase sequence SmA–columnar (Col)–micellar cubic (Cub_I/Pm3n). Elongation of the N‐terminal chain gives the reversed sequence. Short N‐terminal chains prefer an end‐to‐end packing of the mesogens in which these chains are separated from the C‐terminal chains. Elongation of the N‐terminal chain leads to a mixing of N‐ and C‐terminal chains, which is accompanied by complete intercalation of the aromatic cores. In the smectic phases this gives rise to a transition from bilayer (SmA₂) to monolayer smectic (SmA) phases. For the columnar and cubic phases the segregated end‐to‐end packing leads to core–shell aggregates. In this case, elongation of the N‐terminal chains distorts core–shell formation and removes Cub_I and Col phases in favor of single‐layer SmA phases. Hence, by tailoring the length of the N‐terminal chain, a crossover from taper‐shaped to polycatenar LC tectons was achieved, which provides a powerful tool for control of self‐assembly in ILCs.     

Fragmentation–Rearrangement of Peptide Backbones Mediated by the Air Pollutant NO2.

The fragmentation–rearrangement of peptide backbones mediated by nitrogen dioxide, NO₂^., was explored using di‐, tri‐, and tetrapeptides 8 – 18 as model systems. The reaction, which is initiated through nonradical N‐nitrosation of the peptide bond, shortens the peptide chain by the expulsion of one amino acid moiety with simultaneous fusion of the remaining molecular termini through formation of a new peptide bond. The relative rate of the fragmentation–rearrangement depends on the nature of the amino acids and decreases with increasing steric bulk at the α carbon in the order Gly>Ala>Val. Peptides that possessed consecutive aromatic side chains only gave products that resulted from nitrosation of the sterically less congested N‐terminal amide. Such backbone fragmentation–rearrangement occurs under physiologically relevant conditions and could be an important reaction pathway for peptides, in which sections without readily oxidizable side chains are exposed to the air pollutant NO₂^.. In addition to NO₂^.‐induced radical oxidation processes, this outcome shows that ionic reaction pathways, in particular nitrosation, should be factored in when assessing NO₂^. reactivity in biological systems.     

Theoretical Analysis of the Detailed Mechanism of Native Chemical Ligation Reactions

The method of native chemical ligation between an unprotected peptide α‐thioester and an N‐terminal cysteine–peptide to give a native peptide in aqueous solution is one of the most effective peptide ligation methods. In this work, a systematic theoretical study was carried out to fully understand the detailed mechanism of ligation. It was found that for the conventional native chemical ligation reaction between a peptide thioalkyl ester and a cysteine in combination with an added aryl thiol as catalyst, both the thiol‐thioester exchange step and the transthioesterification step proceed by an anionic concerted S_N2 displacement mechanism, whereas the intramolecular rearrangement proceeds by an addition–elimination mechanism, and the rate‐limiting step is the thiol‐thioester exchange step. The theoretical method was then extended to study the detailed mechanism of the auxiliary‐mediated peptide ligation between a peptide thiophenyl ester and an N‐2‐mercaptobenzyl peptide in which both the thiol‐thioester exchange step and intramolecular acyl‐transfer step proceed by a concerted S_N2‐type displacement mechanism. The energy barrier of the thiol‐thioester exchange step depends on the side‐chain steric hindrance of the C‐terminal amino acid, whereas that of the acyl‐transfer step depends on the side‐chain steric hindrance of the N‐terminal amino acid.     

Synthesis of Bifunctional Azobenzene Glycoconjugates for Cysteine‐Based Photosensitive Cross‐Linking with Bioactive Peptides

Azobenzene linker molecules can be utilized to control peptide/protein function when they are ligated to appropriately spaced amino acid side chains of the peptide. This is because the photochemical E/Z isomerization of the azobenzene N?N double bond allows to switch peptide conformation between folded and unfolded. In this context, we have introduced carbohydrate‐functionalized azobenzene derivatives in order to advance the biocompatible properties of azobenzene peptide linkers. Chloroacetamide‐functionalized and O‐allylated carbohydrate derivatives were synthesized and conjugated with azobenzene to achieve new bifunctional cross‐linkers, in order to allow ligation to cysteine side chains by nucleophilic substitution or thiol‐ene reaction, respectively. The photochromic properties of the new linker glycoconjugates were determined and first ligation reactions performed.     

Photoprotected Peptide α‐Ketoacids and Hydroxylamines for Iterative and One‐Pot KAHA Ligations: Synthesis of NEDD8

The convergent synthesis of proteins by multiple ligations requires segments protected at the N‐ and/or C‐terminus with masking groups that are orthogonal to the acid‐ and base‐labile protecting groups used in Fmoc‐SPPS. They must be stable to solid‐phase peptide synthesis, HPLC purification, and ligation conditions and easily removed in the presence of unprotected side chains. In this report, we document photolabile protecting groups for both α‐ketoacids and hydroxylamines, the key functional groups employed in the α‐ketoacid–hydroxylamine (KAHA) ligation. The novel photoprotected α‐ketoacid is easily installed onto numerous different C‐terminal peptide α‐ketoacids and removed by UV light under aqueous conditions. These advances were applied to the one‐pot synthesis of NEDD8, an important modifier protein, by three different convergent routes. These new protecting groups provide greater flexibility on the order of fragment assembly and reduce the number of reaction and purification steps needed for protein synthesis with the KAHA ligation.     

Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations

We implemented molecular dynamics simulations of the 13-residue antimicrobial peptide indolicidin (ILPWKWPWWPWRR-NH2) in dodecylphosphocholine (DPC) and sodium dodecyl sulfate (SDS) micelles. In DPC, a persistent cation-pi interaction between TRP11 and ARG13 defined the structure of the peptide near the interface. A transient cation-pi interaction was also observed between TRP4 and the choline group on DPC lipids. We also implemented simulation of a mutant of indolicidin in the DPC micelle where TRP11 was replaced by ALA11. As a result of the mutation, the boat-shaped conformation is lost and the structure becomes significantly less defined. On the basis of this evidence, we argue that cation-pi interactions determine the experimentally measured, well-defined boat-shaped structure of indolicidin. In SDS, the lack of such interactions and the electrostatic binding of the terminal arginine residues to the sulfate groups leads to an extended peptide structure. To the best of our knowledge, this is the first time that a cation-pi interaction between peptide side chains has been shown to stabilize the structure of a small antimicrobial peptide. The simulations are in excellent agreement with available experimental measurements: the backbone of the peptide is more ordered in DPC than in SDS; the tryptophan side chains pack against the backbone in DPC and point away from the backbone in SDS; the rms fluctuation of the peptide backbone and peptide side chains is greater in SDS than in DPC; and the peptide backbone order parameters are higher in DPC than in SDS.     

Quantitative analysis of the structure-hydrophobicity relationship for di- and tripeptides based on voltammetric measurements with an oil/water interface

The transfer of 18 di- and 27 tripeptides with un-ionizable amino acid side chains at a nitrobenzene/water (NB/W) interface was studied by cyclic voltammetry. The reversible half-wave potential (E(r)(1/2)), i.e., the midpoint potential could be accurately determined at pH 2 for both the facilitated and non-facilitated transfers, respectively, in the presence and absence of dibenzo-18-crown-6 (DB18C6) in NB. A multiple linear regression analysis was then performed for the E(r)(1/2) using the 'corrected' Dubois steric parameter for amino acid side chain substitutents. The result shows that the hydrophobicity of the peptides is governed not only by the intrinsic hydrophobicity of the peptide backbone and side chains, but also by the steric effects of side chain substituents. For the non-facilitated transfer of peptides, the steric effect of a bulky side chain is more significant at the N-terminus than at the C-terminus (and central for tripeptides). The more bulky the side chain at the N-terminus, the less hydrophobic the peptide becomes due to inhibition of the solvation of a terminal -NH(3)(+) group by organic solvents. For the facilitated transfer by DB18C6, however, the steric effect of a bulky side chain is the most significant at the central position of a tripeptide. A MOPAC calculation of optimized structures of DB18C6-peptide complexes has also shown that there is a notable steric hindrance between the central side chain and the benzene rings of DB18C6, which would reduce the 'apparent' hydrophobicity or transferability of the tripeptide.     

Cysteine/Penicillamine Ligation Independent of Terminal Steric Demands for Chemical Protein Synthesis

The chemical ligation of two unprotected peptides to generate a natural peptidic linkage specifically at the C‐ and N‐termini is a desirable goal in chemical protein synthesis but is challenging because it demands high reactivity and selectivity (chemo‐, regio‐, and stereoselectivity). We report an operationally simple and highly effective chemical peptide ligation involving the ligation of peptides with C‐terminal salicylaldehyde esters to peptides with N‐terminal cysteine/penicillamine. The notable features of this method include its tolerance of steric hinderance from the side groups on either ligating terminus, thereby allowing flexible disconnection at sites that are otherwise difficult to functionalize. In addition, this method can be expanded to selective desulfurization and one‐pot ligation‐desulfurization reactions. The effectiveness of this method was demonstrated by the synthesis of VISTA (216‐311), PD‐1 (192‐288) and Eglin C.     

Solid-state NMR yields structural constraints on the V3 loop from HIV-1 Gp120 bound to the 447-52D antibody Fv fragment

Solid-state NMR measurements were performed on the complex of an 18-residue peptide derived from the V3 loop sequence of the gp120 envelope glycoprotein of the HIV-1 MN strain with Fv fragments of the human anti-gp120 monoclonal antibody 447-52D in a frozen glycerol/water solution. The peptide was uniformly (15)N- and (13)C-labeled in a 7-residue segment containing the conserved GPGR motif in the epitope. (15)N and (13)C NMR chemical shift assignments for the labeled segment were obtained from two-dimensional (13)C-(13)C and (15)N-(13)C magic-angle spinning NMR spectra. Reductions in (13)C NMR line widths and changes in chemical shifts upon complex formation indicate the adoption of a well-defined, antibody-dependent structure. Intramolecular (13)C-(13)C distances in the complex, which constrain the peptide backbone and side chain conformations in the GPGR motif, were determined from an analysis of rotational resonance (RR) data. Structural constraints from chemical shifts and RR measurements are in good agreement with recent solution NMR and crystallographic studies of this system, although differences regarding structural ordering of certain peptide side chains are noted. These experiments explore and help delineate the utility of solid state NMR techniques as structural probes of peptide/protein complexes in general, potentially including membrane-associated hormone/receptor complexes.     

Signature of mobile hydrogen bonding of lysine side chains from long-range 15N-13C scalar J-couplings and computation

Amino acid side chains involved in hydrogen bonds and electrostatic interactions are crucial for protein function. However, detailed investigations of such side chains in solution are rare. Here, through the combination of long-range (15)N-(13)C scalar J-coupling measurements and an atomic-detail molecular dynamics (MD) simulation, direct insight into the structural dynamic behavior of lysine side chains in human ubiquitin has been gained. On the basis of (1)H/(13)C/(15)N heteronuclear correlation experiments selective for lysine NH(3)(+) groups, we analyzed two different types of long-range (15)N-(13)C J-coupling constants: one between intraresidue (15)Nζ and (13)Cγ nuclei ((3)J(NζCγ)) and the other between (15)Nζ and carbonyl (13)C' nuclei across a hydrogen bond ((h3)J(NζC')). The experimental (3)J(NζCγ) data confirm the highly mobile nature of the χ(4) torsion angles of lysine side chains seen in the MD simulation. The NH(3)(+) groups of Lys29 and Lys33 exhibit measurable (h3)J(NζC') couplings arising from hydrogen bonds with backbone carbonyl groups of Glu16 and Thr14, respectively. When interpreted together with the (3)J(NζCγ)-coupling constants and NMR-relaxation-derived S(2) order parameters of the NH(3)(+) groups, they strongly suggest that hydrogen bonds involving NH(3)(+) groups are of a transient and highly dynamic nature, in remarkably good agreement with the MD simulation results.     

Proton Switch in the Secondary Coordination Sphere to Control Catalytic Events at the Metal Center: Biomimetic Oxo Transfer Chemistry of Nickel Amidate Complex

High-valent metal-oxo species are key intermediates for the oxygen atom transfer step in the catalytic cycles of many metalloenzymes. While the redox-active metal centers of such enzymes are typically supported by anionic amino acid side chains or porphyrin rings, peptide backbones might function as strong electron-donating ligands to stabilize high oxidation states. To test the feasibility of this idea in synthetic settings, we have prepared a nickel(II) complex of new amido multidentate ligand. The mononuclear nickel complex of this N5 ligand catalyzes epoxidation reactions of a wide range of olefins by using mCPBA as a terminal oxidant. Notably, a remarkably high catalytic efficiency and selectivity were observed for terminal olefin substrates. We found that protonation of the secondary coordination sphere serves as the entry point to the catalytic cycle, in which high-valent nickel species is subsequently formed to carry out oxo-transfer reactions. A conceptually parallel process might allow metalloenzymes to control the catalytic cycle in the primary coordination sphere by using proton switch in the secondary coordination sphere.     

Double affinity amplification of galectin-ligand interactions through arginine-arene interactions: synthetic, thermodynamic, and computational studies with aromatic diamido thiodigalactosides

A series of aromatic mono- or diamido-thiodigalactoside derivatives were synthesized and studied as ligands for galectin-1, -3, -7, -8N terminal domain, and -9N terminal domain. The affinity determination in vitro with competitive fluorescence-polarization experiments and thermodynamic analysis by isothermal microcalorimetry provided a coherent picture of structural requirements for arginine-arene interactions in galectin-ligand binding. Computational studies were employed to explain binding preferences for the different galectins. Galectin-3 formed two almost ideal arene-arginine stacking interactions according to computer modeling and also had the highest affinity for the diamido-thiodigalactosides (K(d) below 50 nM). Site-directed mutagenesis of galectin-3 arginines involved in binding corroborated the importance of their interaction with the aromatic diamido-thiodigalactosides. Furthermore, the arginine mutants revealed distinct differences between free, flexible, and solvent-exposed arginine side chains and tightly ion-paired arginine side chains in interactions with aromatic systems.     

Membrane insertion of a lipidated ras peptide studied by FTIR,solid-state NMR,and neutron diffraction spectroscopy

Membrane binding of a doubly lipid modified heptapeptide from the C-terminus of the human N-ras protein was studied by Fourier transform infrared, solid-state NMR, and neutron diffraction spectroscopy. The 16:0 peptide chains insert well into the 1,2-dimyristoyl-sn-glycero-3-phosphocholine phospholipid matrix. This is indicated by a common main phase transition temperature of 21.5 degrees C for both the lipid and peptide chains as revealed by FTIR measurements. Further, (2)H NMR reveals that peptide and lipid chains have approximately the same chain length in the liquid crystalline state. This is achieved by a much lower order parameter of the 16:0 peptide chains compared to the 14:0 phospholipid chains. Finally, proton/deuterium contrast variation of neutron diffraction experiments indicates that peptide chains are localized in the membrane interior analogous to the phospholipid chains. In agreement with this model of peptide chain insertion, the peptide part is localized at the lipid-water interface of the membrane. This is revealed by (1)H nuclear Overhauser enhancement spectra recorded under magic angle spinning conditions. Quantitative cross-peak analysis allows the examination of the average location of the peptide backbone and side chains with respect to the membrane. While the backbone shows the strongest cross-relaxation rates with the phospholipid glycerol, the hydrophobic side chains of the peptide insert deeper into the membrane interior. This is supported by neutron diffraction experiments that reveal a peptide distribution in the lipid-water interface of the membrane. Concurring with these experimental findings, the amide protons of the peptide show strong water exchange as seen in NMR and FTIR measurements. No indications for a hydrogen-bonded secondary structure of the peptide backbone are found. Therefore, membrane binding of the C-terminus of the N-ras protein is mainly due to lipid chain insertion but also supported by interactions between hydrophobic side chains and the lipid membrane. The peptide assumes a mobile and disordered conformation in the membrane. Since the C-terminus of the soluble part of the ras protein is also disordered, we hypothesize that our model for membrane binding of the ras peptide realistically describes the membrane binding of the lipidated C-terminus of the active ras protein.     

Peptide tic-tac-toe: heterotrimeric coiled-coil specificity from steric matching of multiple hydrophobic side chains

Specific coiled-coil heterotrimers result from steric matching of hydrophobic core side chains. A 2:1 heterotrimer is formed by peptides containing alanine or cyclohexylalanine, respectively, at a central core residue. Detailed thermodynamic analysis reveals that the designed complex is considerably more stable than the corresponding alanine homotrimer (deltaT(m) = 25 degrees C, deltadeltaG(unf) = 4.5 kcal/mol), while control complexes with naphthylalanine or cyclopropylalanine peptides are much less stable. However, the cyclohexylalanine homotrimer is of comparable stability to the 2:1 complex, prompting an investigation of multiply substituted peptides. A specific 1:1:1 heterotrimer is formed from three independent peptide strands, each bearing one large (cyclohexylalanine) and two small (alanine) side chains at the same three core positions but in different order. The combined impact of three substitutions improves specificity to the point where each pure peptide and all pairwise equimolar mixtures form significantly less stable complexes (deltaTm = 22-24 degrees C). The capacity for specific complex formation governed by multiple unnatural core side chains should facilitate design of numerous new peptide assemblies.     

N8H8链状异构体结构与稳定性的理论研究

采用密度泛函理论(DFT), 在B3LYP/6-311＋＋G(d,p)基组上计算得到了21种N₈H₈链状异构体, 并研究了这些异构体间可能的互变异构情况. 为了得到更为精确的能量信息, 计算了QCISD(T)/6-311G(d,p)基组水平上各物质的能量. 所得的21种异构体分为4类(4种类型链状化合物): A为直链, B有一个支链, C有2个支链, D有3个支链; D类只有一种, A类稳定构型2种, B类稳定构型12种, C类稳定构型6种; 相对稳定的分别为: B2-1构型, B2-3构型和C23-2构型. 我们研究发现N₈H₈链状异构体中含有明显N＝N双键特征有利于化合物稳定性的提高.     

Ionic peptide aggregation: exploration of conformational dynamics in aqueous solution by computational techniques

The effects of end groups on KEK peptide conformational characteristics and self-assembling properties in water solution are investigated by using long lasting all-atom molecular dynamics simulations. The analysis of the structural macroscopic and microscopic properties and the examination of intra- and intermolecular interactions suggest, in agreement with experimental observations, the role played by side chains and terminal regions in determining the characteristic features of the assemblages. Competition between intra- and interchain interactions greatly affects the diffusivity of peptide molecules and the conformational space that they can sample, ultimately controlling the shape, size, and distribution of the aggregate configurations. Different peptide end groups influence peptide flexibility and seem to play a crucial role in determining the aggregates' supramolecular architectures.     

Unnatural multidentate metal ligating α-amino acids

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.