The syn-oriented 2-OH provides a favorable proton transfer geometry in 1,2-diol monoester aminolysis: implications for the ribosome mechanism

A computational study of 1-formyl 1,2-ethanediol aminolysis predicts a stepwise mechanism involving syn-2-OH-assisted proton transfer. The syn-oriented 2-OH takes over the catalytic role of the external water or amine molecule previously observed in 2-deoxy ester aminolysis. It provides more favorable, that is, more linear, proton transfer geometry for the rate-limiting transition state resulting in an almost billion-fold rate acceleration of the overall reaction. These findings provide structural basis for explanation of the efficiency of the proton shuttling mechanism and imply double proton transfer catalysis by peptidyl tRNA A76 2'-OH as a possible catalytic strategy used by ribosome.     

Role of chirality of the sugar ring in the ribosomal peptide synthesis

We present a theoretical analysis of the role of the natural chirality of the sugar ring ( D-enantiomeric form) in the peptide synthesis reaction in ribosome. The study is based on a model from the crystal structure of the ribosomal subunit of Haloarcula marismortui using hybrid quantum mechanical-molecular mechanical method. The result indicates that the natural heterochiral sugar-amino acid combination ( D: L) is most favorable for the formation of the peptide bond within the structure of peptidyl transferase center (PTC). Other possible combinations of unnatural chiral form of the sugar-amino acid pair are unfavorable to perform the reaction within the PTC. The presence of the sugar ring has favorable influence on the rotatory path. The chirality of the 2' carbon of the sugar ring is vital for the peptide synthesis. Alteration of the stereochemistry or removal of chirality at the 2' center makes the rate as several orders slower in magnitude. This is in agreement with the recent experimental result that the replacement of the 2' OH by H or F reduces the rate by several orders of magnitude. Two different mechanisms for the catalytic effect of the stereochemistry of 2' OH are investigated. In one mechanism, the 2' OH is involved in proton shuttle, and in the second mechanism, the OH group acts as an anchoring group. The transition state barriers of both mechanisms are found to be comparable. The natural chirality of the 2' center helps lowering the transition state barrier height of the reaction substantially compared with the cases where the 2' center is made achiral or with altered chirality. Thus, the stereochemistry of the 2' center has a major role in synthesis. Few surrounding residues like U2620, A2486, G2618, and C2487 have favorable influence on rotatory path, while the residues like U2541, C2104, C2105, A2485, C2542, C2608, U2619, and A2637 have little influence. The present study shows that the natural chirality of the sugar ring and amino acid makes a perfect heteropair within the PTC to carry out peptide synthesis with high efficiency.     

Efficient ribosomal peptidyl transfer critically relies on the presence of the ribose 2'-OH at A2451 of 23S rRNA

The ribosomal peptidyl transferase center is a ribozyme catalyzing peptide bond synthesis in all organisms. We applied a novel modified nucleoside interference approach to identify functional groups at 9 universally conserved active site residues. Owing to their immediate proximity to the chemical center, the 23S rRNA nucleosides A2451, U2506 and U2585 were of particular interest. Our study ruled out U2506 and U2585 as contributors of vital chemical groups for transpeptidation. In contrast the ribose 2'-OH of A2451 was identified as the prime ribosomal group with potential functional importance. This 2'-OH renders almost full catalytic power to the ribosome even when embedded into an active site of six neighboring 2'-deoxyribose nucleosides. These data highlight the unique functional role of the A2451 2'-OH for peptide bond synthesis among all other functional groups at the ribosomal peptidyl transferase active site.     

Is tRNA binding or tRNA mimicry mandatory for translation factors?

tRNA is the adaptor in the translation process. The ribosome has three sites for tRNA, the A-, P-, and E-sites. The tRNAs bridge between the ribosomal subunits with the decoding site and the mRNA on the small or 30S subunit and the peptidyl transfer site on the large or 50S subunit. The possibility that translation release factors could mimic tRNA has been discussed for a long time, since their function is very similar to that of tRNA. They identify stop codons of the mRNA presented in the decoding site and hydrolyse the nascent peptide from the peptidyl tRNA in the peptidyl transfer site. The structures of eubacterial release factors are not yet known, and the first example of tRNA mimicry was discovered when elongation factor G (EF-G) was found to have a closely similar shape to a complex of elongation factor Tu (EF-Tu) with aminoacyl-tRNA. An even closer imitation of the tRNA shape is seen in ribosome recycling factor (RRF). The number of proteins mimicking tRNA is rapidly increasing. This primarily concerns translation factors. It is now evident that in some sense they are either tRNA mimics, GTPases or possibly both.     

Identification of novel macrocyclic peptidase substrates via on-bead enzymatic cyclization

Peptidase-catalyzed formation of macrocyclic lactams on solid phase identifies ring systems that are favorably bound in the enzyme active site. We evaluated several cyclic peptide motifs linked by ester bonds between the P2 and P1' or the P1 and P2' side chains. The depsipeptide represented by structure 5 was readily generated by a variety of peptidases from precursor omega-amino acids or omega-amino esters. This strategy for identifying ring systems for potential macrocyclic transition state analogues was demonstrated with the serine peptidases trypsin and chymotrypsin, with the aspartic peptidase pepsin, and with the zinc peptidase thermolysin.     

Peptidyl transferase: ancient and exiguous

The finding that the universal ribosomal peptidyl transferase is an RNA enzyme casts new light on its ancient origins, on the use of transition state analogues for ribozymes, and on the role of selection-amplification in studies of molecular evolution.     

Selective removal of the 2'- and 3'-O-acyl groups from 2',3',5'-tri-O-acylribonucleoside derivatives with lithium trifluoroethoxide

Selective cleavage of O2' and O3' ester groups from ribonucleoside derivatives has been accomplished with Dowex 1 x 2 (CF3CH2O-) in 2,2,2-trifluoroethanol (TFE) or lithium trifluoroethoxide/TFE. Deacylations with Li+ -OCH2CF3/TFE proceed at ambient temperature (or with mild heating) to give the 5'-O-acyl derivatives in superior yields and higher purity than prior approaches for selective O2' and O3' ester deprotection.     

Translation of genetic information on the ribosome

The information for protein structure that is contained in the base sequence of the nucleic acids is translated on the ribosome into the amino acid sequence. This translation can be divided into chain initiation, chain growth, and chain termination. Several specific protein factors and nucleic acids are involved in each section.—For chain initiation, start complexes are formed from the initiating amino acyl-tRNA, mRNA carrying the start signal, and the small and large subunits of a ribosome. GTP and the initiating factors are also involved in this process.—In chain elongation, one amino acid at a time is transferred, in a reaction cycle, from the linkage with tRNA into a linkage with the polypeptide chain. The amino acid to be incorporated is initially bound to the ribosome as amino acyl-tRNA, a process for which GTP and protein factors are necessary. The subsequent formation of a peptide linkage is catalyzed by the peptidyl transferase of the large ribosomal subunit. The peptidyl-tRNA with its newly added amino acid residue is then transferred from the amino acyl-tRNA acceptor site A to the peptidyl donor site P of the ribosome. This requires another protein factor and cleavage of GTP into GDP and phosphate.–Ghain termination begins as soon as one of the three terminator triplets UAA, UAG, or UGA in the mRNA reaches the ribosome. The mRNA is moving in relation to the ribosome from the 5′ end to the 3′ end. Release of the completed polypeptide chain from the ribosome is dependent on release factors. Before initiation of a new polypeptide chain, the ribosomes dissociate into their subunits.     

Biomimetic protecting-group-free 2', 3'-selective aminoacylation of nucleosides and nucleotides

Aminoacyl phosphate monoesters can be prepared free of an amino-protecting group and used directly in lanthanum-promoted selective monoacylation of either the 2' or 3'-hydroxyl of nucleosides and nucleotides. For example, phenylalanyl ethyl phosphate rapidly forms esters with either of the 2' or 3'-hydroxyls of ribonucleosides and nucleotides in the presence of lanthanum ions in aqueous buffer. Oligomerization of the aminoacyl phosphate is much slower than ester formation and is not a competitive process. Competing hydrolysis of the reagent is slow. By extension, this route should provide a simplified general route to synthetically aminoacylated derivatives of tRNA.     

The origin of diastereofacial control in allylboration reactions using tartrate ester derived allylboronates: attractive interactions between the Lewis acid coordinated aldehyde carbonyl group and an ester carbonyl oxygen

Transition-state structures for the allylboration reaction between the tartrate ester and tartramide modified allylboronates and acetaldehyde are located at the B3LYP/6-31G* level of theory. An attractive interaction between the boron-activated aldehyde and the ester or amide carbonyl oxygen lone pair is found to play a major role in the favored transition states 11a and 13. This attractive interaction appears to be electrostatic in origin. However, an n --> pi* charge-transfer type of interaction has not been ruled out. The distance (2.77 A) between the aldehydic hydrogen and the carbonyl oxygen in transition state 13 is beyond the sum of van der Waals radii. The formyl C-H...O bond angle (109 degrees) in this transition structure deviates far from linearity. Therefore, hydrogen-bonding interactions between the formyl C-H and the amide carbonyl oxygen are considered negligible. The distance (3.81 A) between the aldehydic oxygen and the amide carbonyl oxygen in the diastereomeric, disfavored transition state 14 is also beyond the van der Waals radii, which suggests that n/n electronic repulsion plays a lesser role in stereodifferentiation in the allylboration reaction than originally proposed.     

Synthesis and characterization of a dinuclear iron(II) spin crossover complex with wide hysteresis

The magnetic properties and results from X-ray structure analysis for a new pair of iron(II) spin-crossover complexes [FeL1(meim) 2](meim) ( 1(meim)) and [Fe 2L2(meim) 4](meim) 4 ( 2(meim) 4), with L1 being a tetradentate N 2O 2 (2-) coordinating Schiff-base-like ligand [([3,3']-[1,2-phenylenebis(iminomethylidyne)]bis(2,4-pentane-dionato)(2-)N,N',O (2),O (2)'], L2 being an octadentate, dinucleating N 2O 2 (2-) coordinating Schiff-base-like ligand [3,3',3',3']-[1,2,4,5-phenylenetetra(iminomethylidyne)]tetra(2,4-pentanedionato)(2-) N, N', N', N', O (2), O (2) ', O (2) ', O (2) '], and meim being N-methylimidazole, are discussed in this work. Crystalline samples of both complexes show a cooperative spin transition with an approximately 2-K-wide thermal hysteresis loop in the case of 1(meim) ( T 1/2 increase = 179 K and T 1/2 decrease = 177 K) and an approximately 21-K-wide thermal hysteresis loop in the case of dinuclear complex 2(meim) 4 ( T 1/2 increase= 199 K and T 1/2 decrease= 178 K). For a separately prepared powder sample of 2, a gradual spin transition with T 1/2 = 229 K is observed that was additionally followed by Mossbauer spectroscopy. The results from X-ray structure analysis give a deeper insight into the molecule packing in the crystal and, by this, help to explain the increase of cooperative interactions during the spin transition when going from the mononuclear to the dinuclear complex. Both compounds crystallize in the triclinic space group P1, and the X-ray structure was analyzed before and after the spin transition. The change of the spin state at the iron center is accompanied by a change of the O-Fe-O angle, the so-called bite of the equatorial ligand, from about 109 degrees in the high-spin state to 89 degrees in the low-spin state. The cooperative interactions responsible for the thermal hysteresis loop are due to elastic interactions between the complex molecules in both cases. However, due to the higher symmetry of the dinucleating ligand in 2(meim) 4, a 3D network of short contacts is formed, while for mononuclear complex 1(meim), a 2D layer of linked molecules is observed. The spin transition was additionally followed in solution using (1)H NMR spectroscopy for both complexes. In both cases, a gradual spin transition is observed, and the increase of cooperative interactions when going from the mononuclear to the dinuclear system is solely attributed to the extended network of intermolecular contacts.     

Efficient Access to Peptidyl‐RNA Conjugates for Picomolar Inhibition of Non‐ribosomal FemXWv Aminoacyl Transferase

Peptidyl–RNA conjugates have various applications in studying the ribosome and enzymes participating in tRNA‐dependent pathways such as Fem transferases in peptidoglycan synthesis. Herein a convergent synthesis of peptidyl–RNAs based on Huisgen–Sharpless cycloaddition for the final ligation step is developed. Azides and alkynes are introduced into tRNA and UDP‐MurNAc‐pentapeptide, respectively. Synthesis of 2′‐azido RNA helix starts from 2′‐azido‐2′‐deoxyadenosine that is coupled to deoxycytidine by phosphoramidite chemistry. The resulting dinucleotide is deprotected and ligated to a 22‐nt RNA helix mimicking the acceptor arm of Ala‐tRNA^Ala by T4 RNA ligase. For alkyne UDP‐MurNAc‐pentapeptide, meso‐cystine is enzymatically incorporated into the peptidoglycan precursor and reduced, and L ‐Cys is converted to dehydroalanine with O‐(mesitylenesulfonyl)hydroxylamine. Reaction of but‐3‐yne‐1‐thiol with dehydroalanine affords the alkyne‐containing UDP‐MurNAc‐pentapeptide. The Cu^I‐catalyzed azide alkyne cycloaddition reaction in the presence of tris[(1‐hydroxypropyl‐1H‐1,2,3‐triazol‐4‐yl)methyl]amine provided the peptidyl‐RNA conjugate, which was tested as an inhibitor of non‐ribosomal FemX_Wv aminoacyl transferase. The bi‐substrate analogue was found to inhibit FemX_Wv with an IC₅₀ of (89±9) pM , as both moieties of the peptidyl–RNA conjugate contribute to high‐affinity binding.     

Density functional theory study of trans-dioxo complexes of iron, ruthenium, and osmium with saturated amine ligands, trans-[M(O)2(NH3)2(NMeH2)2]2+ (M=Fe, Ru, Os), and detection of [Fe(qpy)(O)2]n+ (n=1, 2) by high-resolution ESI mass spectrometry

Density functional theory (DFT) calculations on trans-dioxo metal complexes containing saturated amine ligands, trans-[M(O)2(NH3)2(NMeH2)2]2+ (M=Fe, Ru, Os), were performed with different types of density functionals (DFs): 1) pure generalized gradient approximations (pure GGAs): PW91, BP86, and OLYP; 2) meta-GGAs: VSXC and HCTH407; and 3) hybrid DFs: B3LYP and PBE1PBE. With pure GGAs and meta-GGAs, a singlet d2 ground state for trans-[Fe(O)2(NH3)2(NMeH2)2]2+ was obtained, but a quintet ground state was predicted by the hybrid DFs B3LYP and PBE1PBE. The lowest transition energies in water were calculated to be at lambda approximately 509 and 515 nm in the respective ground-state geometries from PW91 and B3LYP calculations. The nature of this transition is dependent on the DFs used: a ligand-to-metal charge-transfer (LMCT) transition with PW91, but a pi(Fe-O)-->pi*(Fe-O) transition with B3LYP, in which pi and pi* are the bonding and antibonding combinations between the dpi(Fe) and ppi(O(2-)) orbitals. The FeVI/V reduction potential of trans-[Fe(O)2(NH3)2NMeH2)2]2+ was estimated to be +1.30 V versus NHE based on PW91 results. The [Fe(qpy)(O)2](n+) (qpy=2,2':6',2':6',2':6',2'-quinquepyridine; n=1 and 2) ions, tentatively assigned to dioxo iron(V) and dioxo iron(VI), respectively, were detected in the gas phase by high-resolution ESI-MS spectroscopy.     

Photodissociation studies of the electronic and vibrational spectroscopy of Ni(+)(H2O)

The electronic spectrum of Ni?(H?O) has been measured from 16200 to 18000 cm?1 using photofragment spectroscopy. Transitions to two excited electronic states are observed; they are sufficiently long-lived that the spectrum is vibrationally and partially rotationally resolved. An extended progression in the metal-ligand stretch is observed, and the absolute vibrational quantum numbering is assigned by comparing isotopic shifts between ??Ni?(H?O) and ??Ni?(H?O). Time-dependent density functional calculations aid in assigning the spectrum. Two electronic transitions are observed, from the 2A? ground state (which correlates to the 2D, 3d? ground state of Ni?) to the 32A? and 22A? excited states. These states are nearly degenerate and correlate to the 2F, 3d?4s excited state of Ni?. Both transitions are quite weak, but surprisingly, the transition to the 2A? state is stronger, although it is symmetry-forbidden. The 3d?4s states of Ni? interact less strongly with water than does the ground state; therefore, the excited states observed are less tightly bound and have a longer metal-ligand bond than the ground state. Calculations at the CCSD(T)/aug-cc-pVTZ level predict that binding to Ni? increases the H-O-H angle in water from 104.2 to 107.5° as the metal removes electron density from the oxygen lone pairs. The photodissociation spectrum shows well-resolved rotational structure due to rotation about the Ni-O axis. This permits determination of the spin rotation constants ε(αα)' = -12 cm?1 and ε(αα)' = -3 cm?1 and the excited state rotational constant A' = 14.5 cm?1. This implies a H-O-H angle of 104 ± 1° in the 22A? excited state. The O-H stretching frequencies of the ground state of Ni?(H?O) were measured by combining IR excitation with visible photodissociation in a double resonance experiment. The O-H symmetric stretch is ν?' = 3616.5 cm?1; the antisymmetric stretch is ν?' = 3688 cm?1. These values are 40 and 68 cm?1 lower, respectively, than those in bare H?O.     

Studies related to the relative thermodynamic stability of C-terminal peptidyl esters of O-hydroxy thiophenol: emergence of a doable strategy for non-cysteine ligation applicable to the chemical synthesis of glycopeptides

A pathway has been devised, wherein a phenolic ester of a C-terminal peptide is ligated with an N-terminal peptide through two consecutive acyl migrations. In the first transacylation, the C-terminus is transferred from a phenol to a newly liberated ortho-thiol function. Subsequently, the acyl group is transported to a proximal benzylamine through a six-membered transition state.     

Transition state structure of E. coli tRNA-specific adenosine deaminase

Bacterial tRNA-specific adenosine deaminase (TadA) catalyzes the essential deamination of adenosine to inosine at the wobble position of tRNAs and is necessary to permit a single tRNA species to recognize multiple codons. The transition state structure of Escherichia coli TadA was characterized by kinetic isotope effects (KIEs) and quantum chemical calculations. A stem loop of E. coli tRNA(Arg2) was used as a minimized TadA substrate, and its adenylate editing site was isotopically labeled as [1'-(3)H], [5'-(3)H2], [1'-(14)C], [6-(13)C], [6-(15)N], [6-(13)C, 6-(15)N] and [1-(15)N]. The intrinsic KIEs of 1.014, 1.022, 0.994, 1.014 and 0.963 were obtained for [6-(13)C]-, [6-(15)N]-, [1-(15)N]-, [1'-(3)H]-, [5'-(3)H2]-labeled substrates, respectively. The suite of KIEs are consistent with a late SNAr transition state with a complete, pro-S-face hydroxyl attack and nearly complete N1 protonation. A significant N6-C6 dissociation at the transition state of TadA is indicated by the large [6-(15)N] KIE of 1.022 and corresponds to an N6-C6 distance of 2.0 A in the transition state structure. Another remarkable feature of the E. coli TadA transition state structure is the Glu70-mediated, partial proton transfer from the hydroxyl nucleophile to the N6 leaving group. KIEs correspond to H-O and H-N distances of 2.02 and 1.60 A, respectively. The large inverse [5'-(3)H] KIE of -3.7% and modest normal [1'-(3)H] KIE of 1.4% indicate that significant ribosyl 5'-reconfiguration and purine rotation occur on the path to the transition state. The late SNAr transition-state established here for E. coli TadA is similar to the late transition state reported for cytidine deaminase. It differs from the early SNAr transition states described recently for the adenosine deaminases from human, bovine, and Plasmodium falciparum sources. The ecTadA transition state structure reveals the detailed architecture for enzymatic catalysis. This approach should be readily transferable for transition state characterization of other RNA editing enzymes.     

Soluble peptidyl phosphoranes for metal-free, stereoselective ligations in organic and aqueous solution

Protocols for solid-phase syntheses of soluble peptidyl phosphoranes are presented. Various supported phosphoranylidene acetates were prepared on Rink amide or via alkylation of trialkyl- and triarylphosphines with bromoacetyl Wang ester. C-Acylation was conducted racemization-free with activated Fmoc-amino acids, followed by SPPS (solid-phase peptide synthesis). Acidic conditions released decarboxylated peptidyl phosphoranes into solution. The protocol allowed for the electronic variation of peptidyl phosphoranes which were investigated in ligation reactions with azides in organic and aqueous solvents.     

Ketene-ketenimine rearrangements in the gas phase and in polar media. 1,3-Migration intermediates and sequential transition states

[reaction: see text] Calculations of the activation barrier for the 1,3-shifts of substituents X in alpha-imidoylketenes 1 (HN=C(X)-CH=C=O), which interconverts them with alpha-oxoketenimines 3 (HN=C=CH-C(X)=O) via a four-membered cyclic transition state TS2 have been performed at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G* level. Substituents with accessible lone pairs have the lowest activation barriers for the 1,3-shift (halogens, OR, NR2). The corresponding activation barriers for the alpha-oxoketene-alpha-oxoketene rearrangement of 4 via TS5 are generally lower by 1-30 kJ/mol. A polar medium (acetonitrile, epsilon = 36.64) was simulated using the polarizable continuum (PCM) solvation model. The effect of the solvent field is a reduction of the activation barrier by an average of 12 kJ/mol. In the cases of 1,3-shifts of amino and dimethylamino groups, the stabilization of the transition state TS2 in a solvent field is so large that it becomes an intermediate, Int2, flanked by transition states (TS2' and TS2') that are due primarily to internal rotation of the amine functions, and secondarily to the 1,3-bonding interaction. In the case of the alpha-oxoketene-alpha-oxoketene rearrangement of 4, there is a corresponding intermediate Int5 for the 1,3-amine shift already in the gas phase.     

Syntheses,structures, and fluxionality of blue luminescent zinc(II) complexes: Zn(2,2',2"-tpa)Cl2, Zn(2,2',2"-tpa)2(O2CCF3)2, and Zn(2,2',3"-tpa)4(O2CCF3)2 (tpa = tripyridylamine)

Three novel Zn(II) complexes containing either 2,2',2"-tripyridylamine (2,2',2"-tpa) or 2,2',3"-tripyridylamine (2,2',3"-tpa) have been synthesized and structurally characterized. Compound 1, Zn(2,2',2"-tpa)Cl2, has a tetrahedral geometry while compounds 2, Zn(2,2',2"-tpa)2(O2CCF3)2, and 3, Zn(2,2',3"-tpa)4(O2CCF3)2, have an octahedral geometry. The 2,2',2"-tpa ligand in 1 and 2 functions as a bidentate ligand, chelating to the zinc center, while the 2,2",3"-tpa ligand in 3 functions as a terminal ligand, binding to the zinc center through the 3-pyridyl nitrogen atom. All three compounds emit a blue color in solution and in the solid state. The emission maxima for the three compounds in solution are at lambda = 422, 426, and 432 nm, respectively. The blue luminescence of the complexes is due to a pi *-->pi transition of the tpa ligand as established by an ab initio calculation on the free ligand 2,2',2"-tpa and complex 1. Compounds 1 and 2 are fluxional in solution owing to an exchange process between the coordinate and noncoordinate 2-pyridyl rings of the 2,2',2"-tpa ligand. Compound 2 is also fluxional owing to a cis-trans isomerization process, as determined by variable-temperature 1H NMR spectroscopic analysis.