Amino acid selective unlabeling for sequence specific resonance assignments in proteins

Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative approach is the method of amino acid selective `unlabeling' or reverse labeling, which involves selective unlabeling of specific amino acid types against a uniformly C-13/N-15 labeled background. Based on this method, we present a novel approach for sequential assignments in proteins. The method involves a new NMR experiment named, {(CO)-C-12 (i) -N-15 (i+1)}-filtered HSQC, which aids in linking the H-1(N)/N-15 resonances of the selectively unlabeled residue, i, and its C-terminal neighbor, i + 1, in HN-detected double and triple resonance spectra. This leads to the assignment of a tri-peptide segment from the knowledge of the amino acid types of residues: i - 1, i and i + 1, thereby speeding up the sequential assignment process. The method has the advantage of being relatively inexpensive, applicable to H-2 labeled protein and can be coupled with cell-free synthesis and/or automated assignment approaches. A detailed survey involving unlabeling of different amino acid types individually or in pairs reveals that the proposed approach is also robust to misincorporation of N-14 at undesired sites. Taken together, this study represents the first application of selective unlabeling for sequence specific resonance assignments and opens up new avenues to using this methodology in protein structural studies.

Analysis of the effects of amino-acid-sequence on the structure of proteins

The conformation of amino acid side chains as observed in well-determined structures of globular proteins has earlier been extensively investigated. In contrast, the structural features of the polypeptide backbone that result from the occurrence of specific amino acids along the polypeptide have not been analysed. In this article, we present the statistically significant features in the backbone geometry that appear to be a consequence of the occurrence of rotamers of different amino acid side chains by analysing 102 well-refined structures that form a random collection of proteins. It is found that the persistence of helical segments around each residue is influenced by the residue type. Several residues exert asymmetrical influence between the carboxyl and amino terminal polypeptide segments. The degree to which secondary structures depart from an average geometry also appears to depend on residue type. These departures are correlated to the corresponding Chou and Fasman parameters of amino acid residues. The frequency distribution of the side chain rotamers is influenced by polypeptide secondary structure. In turn, the rotamer conformation of side chain affects the extension of the secondary structure of the backbone. The strongest correlation is found between the occurrence of g+ conformation and helix propagation on the carboxyl side of many residues.

A salt of a protonated (amino)spirocyclic cyclotriphosphazene

The title compound 4,4,6,6-tetrakis(dimethylamino)-2 lambda(5),4 lambda(5),6 lambda(5)-cyclotriphosphaza- 1,3,5-trien-1-ium-2-spiro-2'-(2'-phospha-1',3'-diazacyclohexane) tetrachloroplatinate, [HN3P3(NMe(2))(4)(NHCH2CH2CH2NH)](2)-[PtCl4], contains a cyclophosphazenium cation in which the hetero-substituted (amino)spirocyclic cyclotriphosphazene is protonated. The protonation has occurred on one of the P3N3 ring N atoms adjacent to the spiro P atom. The protonation results in lengthening of the ring P-N bonds and puckering of the phosphazene ring. In the crystal lattice, 2n cyclophosphazenium cations are connected by n [PtCl4](2-) anions mediated by N-H...Cl hydrogen bonds to form a linear polymeric structure.

Calcium ionophore, A23187 and its amino acid complexes: spectroscopic and molecular modeling studies.

The circular dichroism, fluorescence, Nuclear Magnetic Resonance and BLM conductance studies indicate that A23187 forms a stable complex with amino acids at low ionophore concentrations (<10(-4)M). However, A23187 prefers to be in a dimeric structure with no significant binding to amino acids, at concentrations higher than 10(-4)M. It was also observed that at lower concentrations, at which the amino acids bind to the ionophore, the affinity for calcium ions was several orders of magnitude lower than that at higher ionophore concentrations. We have also conducted molecular modeling studies to examine the structure of the A23187 dimer and its amino acid complexes. The results of these modeling studies strongly support our experimental results and validate the formation of a hydrogen bonded and energetically stable A23187 dimer and its amino acid complexes.

High Yield Room Temperature Synthesis And Spectral Studies Of Tri(Amino)Silanes: (R2n)3SIH

Tri(amino)silanes were prepared by the condensation of trichlorosilane with secondary amines in 1:6 molar ratio. Reactions of trichlorosilane with pyrrolidine, piperidine, hexamethyleneimine, morpholine, N-methylpiperazine and diethylamine afford the tri(amino)silanes in nearly quantitative yields. Their physical and spectroscopic properties are discussed. All these compounds are highly sensitive to moisture and hydrolyse to silica and the respective amine with the evolution of hydrogen. The compounds have been characterised by IR, 1H NMR, [1H]29Si NMR spectroscopic methods and CHN elemental analysis.

Group-VI metal-carbonyl-complexes of (amino)spirocyclic cyclotriphosphosphazenes

The reactions of (amino)spirocyclotriphosphazenes, N3P3(NMe2)4(NHCH2CH2NH) (1) and N3P3(NMe2)4(NHCH2CH2CH2NH) (2) with molybdenum- and tungsten-hexacarbonyls give complexes of the type [M(CO)4(L)] (L = 1 or 2) in which the phosphazenes act as bidentate chelating ligands via one of the phosphazene ring nitrogen atoms and one of the nitrogen atoms of the diaminoalkane moiety.

Thiol-ene Clickable Hyperscaffolds Bearing Peripheral Allyl Groups

Radical catalyzed thiol-ene reaction has become a useful alternative to the Huisgen-type click reaction as it helps to expand the variability in reaction conditions as well as the range of clickable entities. Thus, direct generation of hyper-branched polymers bearing peripheral allyl groups that could be clicked using a variety of functional thiols would be of immense value. A specifically designed AB(2) type monomer, that carries two allyl benzyl ethers groups and one alcohol functionality, was shown to undergo self-condensation under acid-catalyzed melt-transetherification to yield a hyperbranched polyether that carries numerous allyl end-groups. Importantly, it was shown that the kinetics of polymerization is not dramatically affected by the change of the ether unit from previously studied methyl benzyl ether to an allyl benzyl ether. The peripheral allyl groups were readily clicked quantitatively, using a variety of thiols, to generate an hydrocarbon-soluble octadecyl-derivative, amphiphilic systems using 2-mercaptoethanol and chiral amino acid (N-benzoyl cystine) derivatized hyperbranched structures; thus demonstrating the versatility of this novel class of clickable hyperscaffolds. (C) 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 49:1735-1744, 2011

Reactions of palladium chloride with amino spirocyclic cyclotriphosphazenes: Isolation and Crystal Structures of Novel Mono- and Bimetallic Complexes Formed by the Hydrolysis of a .lambda.5-Diazaphospholane Ring

The reaction of the amino spirocyclic cyclotriphosphazene N3P3(NMe2)4(NHCH2CH2CH2NH) (2) with palladium chloride gives the stable chelate complex [PdCl2.2] (4). An X-ray crystallographic study reveals that one of the nitrogen atoms of the diaminoalkane moiety and an adjacent phosphazene ring nitrogen atom are bonded to the metal. An analogous reaction with the phosphazene N3P3(NMe2)4(NHCH2CH2NH) (1) gives initially a similar complex which undergoes facile hydrolysis to give the novel monometallic and bimetallic complexes [PdCl2.HN3P3(O)(NMe2)4(NHCH2CH2NH2)] (5) and [PdCl{N3P3(NMe2)4(NCH2CH2NH2)}]2(O) (6), which have been structurally characterized; in the former, an (oxophosphazadienyl)ethylenediamine is chelated to the metal whereas, in the latter, an oxobridged bis(cyclotriphosphazene) acts as a hexadentate nitrogen donor ligand in its dianionic form. Crystal data for 4 : a = 14.137(1) angstrom, b = 8.3332(5) angstrom, c = 19.205(2) angstrom, beta = 96.108(7)degrees, P2(1)/c, Z = 4, R = 0.027 with 3090 reflections (F > 5sigma(F)). Crystal data for 5 : a = 8.368(2) angstrom, b = 16.841(4) A, c = 16.092(5) angstrom, beta = 98.31(2)degrees, P2(1)/n, Z = 4, R = 0.049 with 3519 reflections (F > 5sigma(F)). Crystal data for 6 : a = 22.455(6) angstrom, b = 14.882(3) angstrom, c = 13.026(5) angstrom, 6 = 98.55(2)degrees, C2/c, Z = 4, R = 0.038 with 3023 reflections (F > 5sigma(F)).

Important role of the amino acid attached to tRNA in formylation and in initiation of protein synthesis in Escherichia coli

In attempts to convert an elongator tRNA to an initiator tRNA, we previously generated a mutant elongator methionine tRNA carrying an anticodon sequence change from CAU to CUA along with the two features important for activity of Escherichia coli initiator tRNA in initiation. This mutant tRNA (Mi:2 tRNA) was active in initiation in vivo but only when aminoacylated with methionine by overproduction of methionyl-tRNA synthetase. Here we show that the Mi:2 tRNA is normally aminoacylated in vivo with lysine and that the tRNA aminoacylated with lysine is a very poor substrate for formylation compared with the same tRNA aminoacylated with methionine. By introducing further changes at base pairs 4:69 and 5:68 in the acceptor stem of the Mi:2 tRNA to those found in the E. coli initiator tRNA, we show that change of the U4:A69 base pair to G4:C69 and overproduction of lysyl-tRNA synthetase and methionyl-tRNA transformylase results in partial formylation of the mutant tRNA and activity of the formyllysyl-tRNAs in initiation of protein synthesis. Thus, the G4:C69 base pair contributes toward formylation of the tRNA and protein synthesis in E. coli can be initiated with formyllysine. We also discuss the implications of these and other results on recognition of tRNAs by E. coli lysyl-tRNA synthetase and on competition in cells among aminoacyl-tRNA synthetases.

Comparative Nucleotide and Amino Acid Sequence Analysis of the Sequence-Specific RNA-Binding Rotavirus Nonstructural Protein NSP3

NSP3, an acidic nonstructural protein, encoded by gene 7 has been implicated as the key player in the assembly of the 11 viral plus-strand RNAs into the early replication intermediates during rotavirus morphogenesis. To date, the sequence or NSP3 from only three animal rotaviruses (SA11, SA114F, and bovine UK) has been determined and that from a human strain has not been reported. To determine the genetic diversity among gene 7 alleles from group A rotaviruses, the nucleotide sequence of the NSP3 gene from 13 strains belonging to nine different G serotypes, from both humans and animals, has been determined. Based on the amino acid sequence identity as well as phylogenetic analysis, NSP3 from group A rotaviruses falls into three evolutionarily related groups, i.e., the SA11 group, the Wa group, and the S2 group. The SA 11/SA114F gene appears to have a distant ancestral origin from that of the others and codes for a polypeptide of 315 amino acids (aa) in length. NSP3 from all other group A rotaviruses is only 313 aa in length because of a 2-amino-acid deletion near the carboxy-terminus, While the SA114F gene has the longest 3' untranslated region (UTR) of 132 nucleotides, that from other strains suffered deletions of varying lengths at two positions downstream of the translational termination codon. In spite of the divergence of the nucleotide (nt) sequence in the protein coding region, a stretch of about 80 nt in the 3' UTR is highly conserved in the NSP3 gene from all the strains. This conserved sequence in the 3' UTR might play an important role in the regulation of expression of the NSP3 gene. (C) 1995 Academic Press, Inc.

Synthesis of amino thiols and isocysteines via regioselective ring opening of sulfamidates with tetrathiomolybdate

Herein we present a simple and highly efficient method for the synthesis of beta and gamma-amino thiols via regioselective ring opening of sulfamidates with tetrathiomolybdate 1. The generality of this methodology has been shown by synthesizing carbohydrate derived beta-amino thiol. The scope and versatility of this methodology has been demonstrated by synthesizing biologically important unnatural amino acids like isocysteines in optically pure form. (C) 2011 Elsevier Ltd. All rights reserved.

Microwave Assisted Synthesis and Antimicrobial Study of Schiff Base Vanadium(IV) Complexes of Phenyl Esters of Amino Acids

Schiff base vanadium(IV) complexes of phenyl esters of the two acidic amino acids, i.e., aspartic and glutamic acid, were synthesized. The phenyl esters of these amino acids were synthesized by conventional method whereas the Schiff base vanadium(IV) complexes were synthesized using microwave irradiation. The complexes were characterized by spectroscopic tools such as IR, 1H NMR, mass (ES), ESR, and UV visible spectroscopy. All the complexes were studied for antibacterial and antifungal activity and found to be moderately active.

Synthesis and reactivity of chiral tellurium azomethines: Pseudopolymorphism of [o-((((1S,2R)-2-hydroxy-2-phenyl-1-methylethyl)amino)methinyl)phenyl] tellurium(IV) bromide

A range of novel chiral tellurium compounds having an azomethine functional group in the position ortho to tellurium has been synthesized by the reaction of the tellurium-containing aldehydes bis(o-formylphenyl) telluride (1) and o-(butyltelluro)benzaldehyde (4) with chiral amines (R)-(+)-(1-pheylethylamine) and (1R,2S)-(-)-norephedrine, respectively. The precursor aldehydes were prepared by using a reported procedure with slight but advantageous modifications. During the preparation of o-(butyltelluro)benzaldehyde, interesting side products, namely bis(o-formylphenyl) ditelluride ethylene acetal 5, bis(o-formylphenyl) tritelluride (6), and bis(o-formylphenyl) ditelluride (7) were isolated in moderate yields. The ditelluride 7 has been characterized by single-crystal X-ray diffraction studies. The liquid Schiff bases 10 and 11 were further characterized by derivatizing with liquid bromine. The title compound was obtained in excellent yield by reacting the Schiff base 11 with elemental bromine. Detailed NMR studies indicated the presence of a rigid environment for the hydroxyl group. Single-crystal X-ray determinations of the crystals obtained from the different batches indicated. the presence of the two pseudopolymorphic forms 13a and 13b, respectively. In the case of 13a there is one molecule of CH3CN as solvent of crystallization, whereas in 13b half a molecule of CH3CN per molecule of the title compound lies along the 2-fold axis. In 13a the hydroxyl hydrogen is hydrogen-bonded to the nitrogen of the solvent molecule, whereas in 13b it is hydrogen-bonded to the bromine of the neighboring molecule.

Synthesis based on cyclohexadienes .22. Formal syntheses of patchouli alcohol and norpatchoulenol

The preparation of 6-endo-formyl-1,3,3-trimethylbicyclo[2.2.2]octan-2-one 7 and 6-endo-acetyl-1,3,3-trimethylbicyclo[2.2.2]octan-2-one 8, the two key intermediates for the synthesis of patchouli alcohol 1 and norpatchoulenol 2, is reported by a simple and short method from 2-methylbenzoic acid.