Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose

The major cell wall polysaccharide of mycobacteria is a branched-chain arabinogalactan in which arabinan chains are attached to the 5 carbon of some of the 6-linked galactofuranose residues; these arabinan chains are composed exclusively of D-arabinofuranose (Araf) residues. The immediate precursor of the polymerized Araf is decaprenylphosphoryl-D-Araf, which is derived from 5-phosphoribose 1-diphosphate (pRpp) in an undefined manner. On the basis of time course, feedback, and chemical reduction experiment results we propose that decaprenylphosphoryl-Araf is synthesized by the following sequence of events. (i) pRpp is transferred to a decaprenyl-phosphate molecule to form decaprenylphosphoryl-beta-D-5-phosphoribose. (ii) Decaprenylphosphoryl-beta-D-5-phosphoribose is dephosphorylated to form decaprenylphosphoryl-beta-D-ribose. (iii) The hydroxyl group at the 2 position of the ribose is oxidized and is likely to form decaprenylphosphoryl-2-keto-beta-D-erythro-pentofuranose. (iv) Decaprenylphosphoryl-2-keto-beta-D-erythro-pentofuranose is reduced to form decaprenylphosphoryl-beta-D-Araf. Thus, the epimerization of the ribosyl to an arabinosyl residue occurs at the lipid-linked level; this is the first report of an epimerase that utilizes a lipid-linked sugar as a substrate. On the basis of similarity to proteins implicated in the arabinosylation of the Azorhizobium caulidans nodulation factor, two genes were cloned from the Mycobacterium tuberculosis genome and expressed in a heterologous host, and the protein was purified. Together, these proteins (Rv3790 and Rv3791) are able to catalyze the epimerization, although neither protein individually is sufficient to support the activity.     

Tertiary structure of myelopeptides. II. Conformational analysis of Phe-Arg-Pro-Arg-Ile-Met-Thr-Pro, Val-Val-Tyr-Pro-Asp, and Val-Asp-Pro-Pro

Theoretical conformational analysis was used to study the spatial structure and conformational properties of myelopeptides, bone marrow peptide mediators. The low-energy conformations of myelopeptides MP-4 (Phe-Arg-Pro-Arg-Ile-Met-Thr-Pro), MP-5 (Val-Val-Tyr-Pro-Asp), and MP-6 (Val-Asp-Pro-Pro) were found; the values of dihedral angles of backbone and side chains of the amino acid residues were determined; and the energies of intra- and interresidual interactions were estimated.     

Conformational analysis of aminoacyladenylates II. EHT study of glycyladenylate

The lowest energy conformations for the glycyladenylate molecule are predicted for the first time by a quantum mechanical method of conformational analysis (Extended Hückel Theory). This paper is the continuation of our previous work on the common skeleton of all the aminoacyladenylates; it treats the simultaneous study of the two rotations around the phosphate group. These studies have shown that glycyladenylate presents a flexibility correlated with both the 5′ AMP and the glycine conformations. The number of energy minima, equal to seven when 5′ AMP is in ANTI gt conformation, is restricted when the conformation becomes ANTI gg; this fact is due, for this last 5′ AMP conformation, to a steric obstacle between the adenine base and the sugarphosphate-glycine chain. The knowledge of the possible configurations can constitute a first step towards the understanding of the recognition process between the glycyladenylate molecule and the glycyladenylate t-RNA synthetase.     

Conformational analysis of cyclic angiotensin II analogues

Summary Conformationally restricted cyclic analogues of angiotensin II (ANG II), Asp¹-Arg²-Val³-Tyr⁴-Val⁵-His⁶-Pro⁷-Phe⁸, with a link between positions 3 and 5 have considerable biological activity. It is proposed that the spatial arrangement of the pharmacophore groups of Tyr⁴, His⁶ and Phe⁸ side chains and the C-terminal carboxyl group in ANG II and active analogues is similar. Conformational analysis of ANG II and two cyclic analogues c[Sar¹, Lys³,Glu⁵]ANG II and c[Sar¹,Hcy³,Mpt⁵]ANG II was performed, and a geometrical comparison of the low-energy conformations of these compounds allowed one to propose a model of receptor-bound conformation in terms of the spatial arrangement of the pharmacophore groups. This model is characterised by the close spatial location of the His⁶-Phe⁸ side chains and the Tyr⁴ C-terminal carboxyl group and is stabilised by the electrostatic interaction of Arg² and the C-terminal carboxyl group.Abbreviations ANG II angiotensin II - Hcy homocysteine - Mpt trans-4-mercaptoproline     

Spatial structure of myelopeptides: II. Conformational analysis of MP-4, MP-5, and MP-6

Theoretical conformational analysis was used to study the spatial structure and conformational properties of myelopeptides, bone-marrow peptide mediators. The low-energy conformations of myelopeptides MP-4 (Phe-Arg-Pro-Arg-Ile-Met-Thr-Pro), MP-5 (Val-Val-Tyr-Pro-Asp), and MP-6 (Val-Asp-Pro-Pro) were found; the values of dihedral angles of backbone and side chains of the amino acid residues were determined; and the energies of intra- and interresidual interactions were estimated.__________Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 2, 2005, pp. 140–146.Original Russian Text Copyright © 2005 by Ismailova, Akhmedov, Abbasli, Godjaev.     

Cyclic retro-inverso dipeptides with two aromatic side chains. II. Conformational analysis.

The conformations of cis and trans cyclic retro-inverso dipeptides--2-[(4-hydroxy)benzyl]-5-benzyl-4,6(1H,2H,3H,5H)-pyrimidinedi one (c[mTyr-gPhe]), and 2-benzyl-5-amino-5-[(4-hydroxy)benzyl]-4,6(1H,2H,3H,5H)-pyrimidinedione (c[mTyr-gPhe]), and 2-benzyl-5-amino-5-[(4-hydroxy)benzyl]-4,6(1H,2H,3H,5H)-pyrimidinedione (c[(alpha-amino)mTyr-gPhe])--and the parent cyclic dipeptides--c[tyrosyl-phenylalanine] (cis-c[L-Tyr-L-Phe]) and c[tyrosyl-D-phenylalanine] (trans-c[L-Tyr-D-Phe])--were studied by using 1H-nmr spectroscopy and semiempirical energy calculations. In the cis compounds of all the cyclic retro-inverso and parent dipeptides, the most stable conformer has both aromatic side chains sharing the space over the backbone ring in a "face-to-face" fashion. All the trans compounds predominantly assume a "sandwich" conformation in which the two aromatic rings are folded back over the backbone ring on opposite sides. However, different conformational preferences were observed for the backbones between the retro-inverso and parent cyclic dipeptides. The parent cyclic dipeptide trans-c[L-Tyr-D-Phe] adopts two types of boat structures with different side-chain orientations in almost equal amounts: one with the Tyr side chain in a pseudoaxial position and the Phe side chain in a pseudoequatorial position, the other with the Tyr side chain in a pseudoequatorial position and the Phe side chain in a pseudoaxial position. On the other hand, the cyclic retro-inverso dipeptides trans-c[mPhe-gTyr] and trans c[mTyr-gPhe] assume only one type of boat structure in which the malonyl side chain is in a pseudoequatorial and the gem-diamino side chain is in a pseudoaxial position. In addition to the preferred conformations, the conformational energies of the C alpha--C beta bonds in the malonyl and gem-diamino residues were estimated from the temperature variation of vicinal 1H--1H coupling constants for the H--C alpha--C beta--H groupings observed for the trans isomers of cyclic retro-inverso dipeptides. The energies were evaluated to be 1.1 and 1.8 kcal mol-1 for the malonyl and gem-diamino residues, respectively. Applying these energies to the parent cyclic dipeptide trans-c[L-Tyr-D-Phe], the observed fractions of three side-chain conformations are reasonably reproduced. The conformational energies as well as conformational properties of the molecules estimated in this investigation may be useful to refine force constants for both parent and retro-inverso peptides with aromatic side chains.     

Conformational analysis of cyclic dipeptides: I. , , , and

Conformational analysis of two pairs of synthetic cyclodipeptides formed by interaction of both side chain functional groups ( , and ) and of the main and side chains ( , and ) was achieved by the method of molecular mechanics. The energetically optimal conformational states of the molecules under study were determined. It was shown that the conformational motility of cyclic system of the compounds under study depends on the relative arrangement of the amide groups and the number of atoms in the cycle.     

Conformational energy calculations on alginic acid. II. Conformational statistics of the copolymers

Conformational energy maps have been calculated for α-D -mannuronic acid (1–4) α-L -guluronic acid and for α-L -guluronic acid (1–4) β-D -mannuronic acid. These have been used, together with maps previously calculated for the homomonomeric dimers, to estimate the characteristic ratios and Kuhn lengths of the alternating copolymer and of a stochastic copolymer similar in composition to that extracted from L. digitata.The results show that the alternating copolymer is less extended than either homopolymer. Kuhn lengths calculated for the stochastic copolymer agree well with experimental results on high ionic strength solutions of alginate isolated from L digitata.     

Synthetic fragments and analogues of elastin. II. Conformational studies

Conformational studies on synthetic repetitive sequences and analogues of elastin are described. CD and nmr measurements gave evidence of flexible beta-turns as the dominant structural feature whose stability was found to decrease by increasing the number of repetitive units. The sequences comprised the structural unit Gly-X-Gly (X = Val, Leu, Ala), with X-Gly or Gly-Gly located at the corners of the bend. Based on that, it is proposed that these regions of elastin, unlike the proline-containing sequences, contribute to the elasticity of the protein through a classical mechanism in terms of the rotational isomeric state theory.     

Conformational analysis of glycosaminoglycans. I. Charge distributions, torsional potentials, and steric maps

An initial study of the charge distributions and torsional potentials for (1→4)-linked disaccharides, and a steric energy-map for (1→4)-linked disaccharides is reported for six acidic glycosaminoglycans. The charge distributions have been computed by the CNDO quantum-mechanical procedure, together with a molecular-decomposition technique. The intrinsic torsional potential has been computed by using CNDO energies and empirical potential-energies. The intrinsic torsional potential is two-dimensional. The general steric-map for a (1→4)-linked disaccharide will be useful for simplifying future conformational analyses of glycosaminoglycans. Wherever possible, comparisons between theory and experiment are presented or cited.     

Poly(L-lysyl-L-alanyl-alpha-L-glutamic acid). II. Conformational studies.

The solution characterization of poly(Lys-Ala-Glu) is described. This polytripeptide is zwitterionic at neutral pH and is shown to take on a conformation which is dictated by the state of ionization, molecular weight, temperature, and solvent. The polypeptide is almost entirely α-helical at low pH and temperature for polymers of greater than 25,000 molecular weight. Melting profiles for these conditions show t_m ～ 20°C. Analysis of circular dichroism curves shows the α-helical content to vary in a linear manner with molecular weight in the range 3000–30,000. At neutral pH the charged polypeptide is essentially random, but substantial α-helix could be induced by addition of methanol or trifluoroethanol. At temperatures where the sequential polypeptide is a random coil, addition of trifluoroethanol produces a polymer which is mostly α-helical but also contains an appreciable ammount of β-structure. The infrared spectrum of a low-molecular-weight fraction assumed to be cyclo(Lys-Ala-Glu)₂ was tentatively assigned a β-pleated sheet structure. A comparison of this polytripeptide in various ionization states with other polytripeptides containing L -alanine and L -glutamate or L -lysine shows the α-helix directing properties for the (uncharged) residues to lie in the order Ala > Glu > Lys.     

Conformational study of angiotensin II

Conformational free energy calculations using an empirical potential ECEPP/3 (Empirical Conformational Energy Program for Peptides, Version 3) were carried out on angiotensin II (AII) of sequence Asp-Arg-Val-Tyr-Ile-His-Pro-Phe to find the stable conformations of the free state in the unhydrated and the hydrated states. A conformational analysis of the unhydrated state was carried out using the buildup procedure. The free energy calculation using the hydration shell model was also carried out to obtain the stable conformation of the hydrated state. The calculated stable conformations of AII in both states have a partially right-handed α-helical structure stabilized by short- and medium-range interactions. The similarity between the lowest free energy conformations of the unhydrated and hydrated states suggests that the hydration might not be important to stabilize the overall conformation of AII in a free state. The absence of any intramolecular interaction of the Tyr side chain suggests the possible interaction of this residue with the receptor. In this study, we found that the low free energy conformations contain both the parallel-plate and the perpendicular-plate geometries of the His and Phe rings, suggesting the coexistence of both conformations. © 1996 John Wiley & Sons, Inc.     

Conformational studies of sphingolipids by NMR spectroscopy. II. Sphingomyelin

Sphingomyelin (SM) is the most prevalent sphingolipid in the majority of mammalian membranes. Proton and 31P nuclear magnetic resonance spectral data were acquired to establish the nature of intra- and intermolecular H-bonds in the monomeric and aggregated forms of SM and to assess possible differences between this lipid and dihydrosphingomyelin (DHSM), which lacks the double bond between carbons 4 and 5 of the sphingoid base. The spectral trends suggest the formation of an intramolecular H-bond between the OH group of the sphingosine moiety and the phosphate ester oxygen of the head group. The narrower linewidth and the downfield shift of the resonance corresponding to OH proton in SM suggest that this H-bond is stronger in SM than in DHSM. The NH group appears to be involved predominantly in intramolecular H-bonding in the monomer. As the concentration of SM increases and the molecules come in closer proximity, these intramolecular bonds are partially disrupted and the NH group becomes involved in lipid-water interactions. The difference between the SM and DHSM appears to be not in the nature of these interactions but rather in the degree to which these intermolecular interactions prevail. As SM molecules cannot come as close together as DHSM molecules can, both the NH and OH moieties remain, on average, more intramolecularly bonded as compared to DHSM.     

Conformational stability of ribonuclease T1. II. Salt-induced renaturation.

In the presence of high concentrations of the monovalent salts, sodium chloride and potassium fluoride, disulfide-reduced RNase T1 having four cysteinyl residues intact regenerates the spectral properties characteristic of native RNase T1, e.e., the fluorescence spectrum of the aromatic side chains and the ultraviolet circular dichroism spectrum. The folding of the polypeptide chain proceeded without formation of disulfide bonds to yield an enzymatically active species having an activity toward RNA equivalent to 25% of that of the native enzyme at the same salt concentration of 2 m. Unfolding of RNase T1 by a denaturant, urea, was suppressed in the presence of salts, and the salt-induced chain folding was observed spectroscopically even in 6.9 m urea solution. The salts also induced the chain folding of disulfide reduced and modified (carboxymethylated or carboxamidomethylated) RNase T1 into the native conformation, as indicated by its spectroscopic properties, but did not restore the enzymatic activity.