Fluorinated amino acids: compatibility with native protein structures and effects on protein-protein interactions

Fluorinated analogues of the canonical α-L-amino acids have gained widespread attention as building blocks that may endow peptides and proteins with advantageous biophysical, chemical and biological properties. This critical review covers the literature dealing with investigations of peptides and proteins containing fluorinated analogues of the canonical amino acids published over the course of the past decade including the late nineties. It focuses on side-chain fluorinated amino acids, the carbon backbone of which is identical to their natural analogues. Each class of amino acids--aliphatic, aromatic, charged and polar as well as proline--is presented in a separate section. General effects of fluorine on essential properties such as hydrophobicity, acidity/basicity and conformation of the specific side chains and the impact of these altered properties on stability, folding kinetics and activity of peptides and proteins are discussed (245 references).     

Characterization of an NH-pi interaction in Co(III) ternary complexes with aromatic amino acids

The NH-pi interaction has been detected in the crystal structures of Co(III) ternary complexes with N,N-bis(carboxymethyl)-(S)-phenylalanine (BCMPA) and aromatic amino acids including (S)-phenylalanine ((S)-Phe), (R)-phenylalanine ((R)-Phe), and (S)-tryptophan ((S)-Trp)). Additionally, this interaction has been studied in solution for Co(III) ternary complexes with BCMPA or NTA (NTA = nitrilotriacetic acid) and several amino acids (AA) by means of electronic absorption, circular dichroism (CD), and (1)H NMR spectroscopies. The CD intensities of the Co(III) complexes with aromatic amino acids measured in the d-d region ( approximately 20.5 x 10(3) cm(-)(1)) are significantly decreased in ethanol solutions relative to water. Analogous complexes with aliphatic amino acids do not exhibit this solvent effect. The (1)H NMR spectra of the Co(III) complexes with aromatic amino acids measured in DMSO-d(6) exhibit upfield shifts of the NH peaks compared with those with aliphatic amino acids, which suggest a shielding effect due to the aromaticity. The upshift values coincide with those experimentally evaluated from the crystal structures. The magnitude of the upfield shifts agrees well with Hammett's rule, indicating that the increase of pi-electron densities on the aromatic rings leads attractive NH-pi interaction that exerts a larger shielding effect for the NH protons. In ligand-substitution reactions of the carbonatocobalt(III) complexes with amino acids, the yields of those with aromatic amino acids are higher than the yields obtained for complexes with aliphatic amino acids. This observation is discussed in connection with the important contribution of the NH-pi interaction as one of the promotion factors in the reaction.     

Design of luminescent iridium(III) and rhenium(I) polypyridine complexes as in vitro and in vivo ion,molecular and biological probes

Many luminescent transition metal polypyridine complexes display intense and long-lived triplet charge-transfer and intraligand transition emission with a large Stokes’ shift. These properties render them promising candidates as luminescent probes for ions, DNA, peptides, proteins and other biological entities. In this review article, we have summarised recent reports on ion, molecular and biological probes derived from luminescent rhenium(I) and iridium(III) polypyridine complexes. These complexes have been appended with different recognition moieties that interact with ions and biological molecules. The recognition is reflected by a change of spectroscopic and/or photophysical properties of the probes. The use of these complexes as cellular probes and imaging reagents has also been discussed.     

Complexation reaction of metal ions with peptide systems. Part IV. A potentiometric study of rare earth complexes of glycyl-L-proline

Amino acids and dipeptides are of biological importance and therefore their metal complexes are of special interest. Many workers have studied the complexes of various peptides with different transition metals in solution^{1 – 5}. Although the stability of complexes of lanthanum with amino acids has been studied^{6 – 11}, no work appears to have been done with dipeptide systems. In continuation to our previous work^{12, 13} on the complexation reactions of lanthanides with dipeptide systems, the present communication reports the stability constants and thermodynamic functions of Y(III), La(III), Ce(III), Pr(III) and Nd(III) with glycyl-L-proline in aqueous medium at 25, 35 and 45°C at 0.15 M (KNO₃) ionic strength. The Calvin—Bjerrum titration technique^{14, 15} as modified by Irving and Rossotti¹⁶ was used.     

Homochirality and life

Before the emergence of life, left-handed amino acids (L-enantiomers) were selected and right-handed amino acids (D-enantiomers) were eliminated on the primal earth. Nevertheless, with the progress of analytical methods, D-amino acids have recently been found in higher order living organisms in the form of free amino acids, peptides, and proteins. Free D-amino acids have numerous physiological functions. D-amino acids containing animal peptides are well known as opioid peptides. D-amino acids in protein are related to aging. In this review, we describe the D-amino acids that are present and function as D-amino acid biosystems in our bodies.     

Direct asymmetric intermolecular aldol reactions catalyzed by amino acids and small peptides

In nature there are at least nineteen different acyclic amino acids that act as the building blocks of polypeptides and proteins with different functions. Here we report that alpha-amino acids, beta-amino acids, and chiral amines containing primary amine functions catalyze direct asymmetric intermolecular aldol reactions with high enantioselectivities. Moreover, the amino acids can be combined into highly modular natural and unusual small peptides that also catalyze direct asymmetric intermolecular aldol reactions with high stereoselectivities, to furnish the corresponding aldol products with up to >99 % ee. Simple amino acids and small peptides can thus catalyze asymmetric aldol reactions with stereoselectivities matching those of natural enzymes that have evolved over billions of years. A small amount of water accelerates the asymmetric aldol reactions catalyzed by amino acids and small peptides, and also increases their stereoselectivities. Notably, small peptides and amino acid tetrazoles were able to catalyze direct asymmetric aldol reactions with high enantioselectivities in water, while the parent amino acids, in stark contrast, furnished nearly racemic products. These results suggest that the prebiotic oligomerization of amino acids to peptides may plausibly have been a link in the evolution of the homochirality of sugars. The mechanism and stereochemistry of the reactions are also discussed.     

螯合金属离子亲和色谱法分离α-氨基酸和肽

 以ＳｅｐｈａｄｅｘＧ１０为基质螯合二价铜离子的亲和色谱法分离α－氨基酸和肽，使之得以完全分离。对分离过程的原理进行了讨论。     

Peptide/protein-polymer conjugates: synthetic strategies and design concepts

This feature article provides a compilation of tools available for preparing well-defined peptide/protein-polymer conjugates, which are defined as hybrid constructs combining (i) a defined number of peptide/protein segments with uniform chain lengths and defined monomer sequences (primary structure) with (ii) a defined number of synthetic polymer chains. The first section describes methods for post-translational, or direct, introduction of chemoselective handles onto natural or synthetic peptides/proteins. Addressed topics include the residue- and/or site-specific modification of peptides/proteins at Arg, Asp, Cys, Gln, Glu, Gly, His, Lys, Met, Phe, Ser, Thr, Trp, Tyr and Val residues and methods for producing peptides/proteins containing non-canonical amino acids by peptide synthesis and protein engineering. In the second section, methods for introducing chemoselective groups onto the side-chain or chain-end of synthetic polymers produced by radical, anionic, cationic, metathesis and ring-opening polymerization are described. The final section discusses convergent and divergent strategies for covalently assembling polymers and peptides/proteins. An overview of the use of chemoselective reactions such as Heck, Sonogashira and Suzuki coupling, Diels-Alder cycloaddition, Click chemistry, Staudinger ligation, Michael's addition, reductive alkylation and oxime/hydrazone chemistry for the convergent synthesis of peptide/protein-polymer conjugates is given. Divergent approaches for preparing peptide/protein-polymer conjugates which are discussed include peptide synthesis from synthetic polymer supports, polymerization from peptide/protein macroinitiators or chain transfer agents and the polymerization of peptide side-chain monomers.     

Flash photolysis studies of charge-transfer photochemistry of nickel(II) and cobalt(III) complexes

The photochemical behavior of cobalt(III) and nickel(II) complexes on excitation in the charge-transfer bands is reviewed in this article with particular reference to the study of intermediates. Investigations on the photoredox reactions of cobalt(III) and nickel(II) complexes using flash kinetic spectroscopic methods reveal details on the characteristics of the intermediates produced from the charge-transfer excited states of these metal complexes. The reactive species produced on photolysis of cobalt(III)-amine complexes activate molecular oxygen, producing mononuclear and dinuclear dioxygen species coordinated as superoxo and peroxo forms. Cobalt(III)-amino-acid complexes on photolysis lead to the formation of cobalt(III)-alkyl complexes which are identified as transients. The spectra and the decay kinetics are described with the view to elucidate mechanistic details. Nickel(II) macrocyclic complexes on excitation in the charge-transfer bands lead to oxidation of the metal centre. Scavenging experiments using dioxygen, alcohols and acids were carried out to understand the mechanistic details.     

Matrix-assisted laser desorption/ionization mass spectrometry for the characterization of ionic liquids and the analysis of amino acids, peptides and proteins in ionic liquids

Ionic liquids are interesting solvents for a number of applications in chemistry and biotechnology. We characterized five different ionic liquids by laser desorption/ionization (LDI) and by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) and studied the analysis of amino acids, peptides and proteins dissolved in these solvents. Signals of both anions and cations of the ionic liquids could be observed both in LDI- and in MALDI-MS. In the latter case, adduct formation between anions and cations of the analytes was observed. Amino acids, peptides and proteins could be analyzed in ionic liquids after addition of matrix substances. Sodium and potassium adducts were not observed in any analysis involving ionic liquids. Low molecular mass compounds and peptides could be analyzed best in the presence of water-immiscible ionic liquids, whereas proteins gave the best results in water-miscible ionic liquids. Optimal analysis conditions such as molar matrix-to-analyte and ionic liquid-to-matrix ratios were determined. Homogeneity of samples in the presence of ionic liquids was reduced compared with classical MALDI preparations. Relative quantitation of amino acids was possible using isotope-labeled internal standards. MALDI-MS thus can be used for the analysis of chemical reactions and the screening of enzyme-catalyzed reactions in ionic liquids and for the analysis of the biocatalysts dissolved in these solvents. Theoretical aspects of ion formation in the presence of ionic liquids both in LDI and MALDI analysis are discussed.     

Probing the stability and structure of metalloporphyrin complexes with basic peptides by mass spectrometry

The stability and structure of non-covalent complexes of various peptides contatining basic amino acid residues (Arg, Lys) with metalloporphyrins were studied in a quadrupole ion trap mass spectrometer. The complexes of heme and three other metalloporphyrins with a variety of basic peptides and model systems were formed via electrospray ionization (ESI) and their stability was probed by energy-variable collision-induced dissociation (CID). A linear dependence for basic peptides and model compounds/metalloporphyrin complexes was observed in the plots of stability versus degrees of freedom and was used to evaluate relative bond strength. These results were then compared with previous data obtained for complexes of metalloporphyrins with His-containing peptides and peptides containing no basic amino acids. The binding strengths of Lys-containing peptide complexes in the gas phase was found to be almost as strong as that of Arg-containing complexes. Both systems showed stronger binding than His- containing peptides studied previously. To probe the structure of Arg and Lys non-covalent complexes (charge solvation versus salt bridges), two techniques, CID and ionmolecule reactions, were used. CID experiments indicate that the gas-phase complexes are most likely formed by charge solvation of the central metal ion in the metalloporphyrin by basic side chains of Arg or Lys. Results from the ionmolecule reaction studies are consistent with the charge solvation structure as well.     

Ternary complexes involving copper(II) and amino acids,peptides and DNA constituents. The kinetics of hydrolysis of α-amino acid esters

Binary and ternary complexes of copper(II) involving picolylamine (Pic) and amino acids, peptides (HL) or DNA constituents have been investigated. Ternary complexes of amino acids or peptides are formed by simultaneous reactions. Amino acids form the Cu(Pic)L complex, whereas peptides form Cu(Pic)L and Cu(Pic)(LH_–1). The ternary complexes of copper(II) with picolylamine and DNA are formed in a stepwise process, whereby binding of copper(II) to picolylamine is followed by ligation of the DNA components. The stability of the ternary complexes is compared with the stabilities of the corresponding binary complexes. The hydrolysis of glycine methyl ester (MeGly) is catalysed by the Cu(pic)²⁺ complex. The kinetic data is fitted assuming that the hydrolysis proceeds in two steps. The first step, involving coordination of the amino acid ester by the amino and carbonyl groups, is followed by rate-determining attack by the OH^– ion. The second step involves equilibrium formation of the hydroxo-complex, Cu(pic)(MeGly)(OH), followed by intramolecular attack.     

Thermodynamics of axial substitution and kinetics of reactions with amino acids for the paddlewheel complex tetrakis(acetato)chloridodiruthenium(II,III)

The known paddlewheel, tetrakis(acetato)chloridodiruthenium(II,III), offers a versatile synthetic route to a novel class of antitumor diruthenium(II,III) metallo drugs, where the equatorial ligands are nonsteroidal anti-inflammatory carboxylates. This complex was studied here as a soluble starting prototype model for antitumor analogues to elucidate the reactivity of the [Ru(2)(CH(3)COO)(4)](+) framework. Thermodynamic studies on equilibration reactions for axial substitution of water by chloride and kinetic studies on reactions of the diaqua complexes with the amino acids glycine, cysteine, histidine, and tryptophan were performed. The standard thermodynamic reaction parameters ΔH°, ΔS°, and ΔV° were determined and showed that both of the sequential axial substitution reactions are enthalpy driven. Kinetic rate laws and rate constants were determined for the axial substitution reactions of coordinated water by the amino acids that gave the corresponding aqua(amino acid)-Ru(2) substituted species. The results revealed that the [Ru(2)(CH(3)COO)(4)](+) paddlewheel framework remained stable during the axial ligand substitution reactions and was also mostly preserved in the presence of the amino acids.     

Oxidative protein labeling in mass-spectrometry-based proteomics

Oxidation of proteins and peptides is a common phenomenon, and can be employed as a labeling technique for mass-spectrometry-based proteomics. Nonspecific oxidative labeling methods can modify almost any amino acid residue in a protein or only surface-exposed regions. Specific agents may label reactive functional groups in amino acids, primarily cysteine, methionine, tyrosine, and tryptophan. Nonspecific radical intermediates (reactive oxygen, nitrogen, or halogen species) can be produced by chemical, photochemical, electrochemical, or enzymatic methods. More targeted oxidation can be achieved by chemical reagents but also by direct electrochemical oxidation, which opens the way to instrumental labeling methods. Oxidative labeling of amino acids in the context of liquid chromatography(LC)–mass spectrometry (MS) based proteomics allows for differential LC separation, improved MS ionization, and label-specific fragmentation and detection. Oxidation of proteins can create new reactive groups which are useful for secondary, more conventional derivatization reactions with, e.g., fluorescent labels. This review summarizes reactions of oxidizing agents with peptides and proteins, the corresponding methodologies and instrumentation, and the major, innovative applications of oxidative protein labeling described in selected literature from the last decade.     

A thermodynamic study of reactions of amino acids with crown ethers in nonaqueous media as examples of guest—host molecular complex formation

Our findings and the literature data on the effect of binary aqueous organic solvents on the enthalpy and entropy of molecular complexation reactions of 18-crown-6 with glycine, D, L-alanine, and L-phenylalanine and on the stability of the resulting complexes were reviewed. The relationships between the thermodynamic parameters of the complexation reactions and the reactant solvation were analyzed to reveal the key factors that are crucial for the stability of the complexes and the increasing exothermicity of the processes under study in water—ethanol, water—DMSO, and water—acetone. The changes in the stability of 18-crown-6 complexes with amino acids were assumed to be predicted from the Gibbs energy changes in the transsolvation of the amino acids. This criterion was proposed as a basic thermodynamic parameter for estimating the changes in the stability of 18-crown-6 complexes with peptides and ammoniumtype cations (structurally related to amino acids) when the composition of the binary aqueous organic solvent is varied.     

Contemporary Approaches to α,β-Dehydroamino Acid Chemical Modifications

As one of the most common unnatural amino acids(uAAs), α, β-dehydroamino acids(α,β-dhAAs) can be found in various ribosomally synthesized and post-translationally modified peptides(RiPPs) and other naturally occurring peptides. In recent years, novel reactions for α,β-dhAA modification continue to emerge. Due to their unique electrophilicity different from 20 natural amino acids, α,β-dhAAs, especially dehydroalanine(Dha), have become powerful tools for site-selective protein modification. In this review, we mainly focus on the latest research progress of C-C and C-heteroatom(C-X, X=S, N, Se, Si, P, B) bond formation methods based on α,β-dhAAs in the past five years. Particularly, we pay much attention to the α,β-dhAA derivatization methodologies used in the late-stage modification for natural peptides and proteins. In addition, we also focus on the downstream functionalization and therapeutic biologic applications of these modifications.     

Binary and Ternary Complexes of Copper(II) Involving N,N,N′,N′-Tetramethylethylenediamine (Me4en) and Various Biologically Relevant Ligands

Binary and ternary complexes of copper(II) involving N,N,N′,N′-tetramethylethylene-diamine (Me₄en) and various biologically relevant ligands containing different functional groups are investigated. The ligands (L) used are dicarboxylic acids, amino acids, peptides and DNA unit constituents. The ternary complexes of amino acids, dicarboxylic acids or peptides are formed by simultaneous reactions. The results showed the formation of Cu(Me₄en)(L) complexes with amino acids and dicarboxylic acids. The effect of chelate ring size of the dicarboxylic acid complexes on their stability constants was examined. Peptides form both Cu(Me₄en)(L) complexes and the corresponding deprotonated amide species Cu(Me₄en)(LH₋₁). The ternary complexes of copper(II) with (Me₄en) and DNA are formed in a stepwise process, whereby binding of copper(II) to (Me₄en) is followed by ligation of the DNA components. DNA constituents form both 1:1 and 1:2 complexes with Cu(Me₄en)²⁺. The concentration distribution of the complexes in solution was evaluated. [Cu(Me₄en)(CBDCA)] and [Cu(Me₄en)(malonate)] are isolated and characterized by elemental analysis and infrared measurements.     

Solution Coordination Chemistry of Organotin(IV) Cations with Bio-relevant Ligands

A comprehensive review of organotin(IV) ⁿ⁺ hydrolysis and complex formation equilibria with amino acids, peptides and DNA constituents is presented with special reference to solution and coordination chemistry studies. The review focuses on results obtained in the author??s laboratory and related work of other groups. Also, published studies on these complexes were reviewed with emphasis on their biological aspects.     

Electron transfer reactions of nickel(III) and nickel(IV) complexes

This review narrates the electron transfer reactions of various nickel(III) and nickel(IV) complexes reported during the period 1981 until today. The reactions have been categorized mainly with respect to the type of nickel complexes. The reactivity of nickel(III) complexes of macrocycles, 2,2′-bipyridyl and 1,10-phenanthroline, peptides and oxime–imine, and of nickel(IV) complexes derived from oxime–imine, oxime and miscellaneous ligands with various organic and inorganic electron donors have been included. Kinetic and mechanistic features associated with such interactions have been duly analyzed. The relevance of Marcus cross-relation equations in the delineation of the electron transfer paths has also been critically discussed.     

Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors

To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.