Correlation between the backbone and side chain conformations in 5′-nucleotides. The concept of a ‘rigid’ nucleotide conformation

Conformational energies of the 5′-adenosine monophosphate have been computed as a function of χ and ψ, of the torsion angles about the side-chain glycosyl C(1′)–N(9) and of the main-chain exocyclic C(4′)–C(5′) bonds by considering nonbonded, torsion, and electrostatic interactions. The two primary modes of sugar puckering, namely, C(2′)-endo and C(3′)-endo have been considered. The results indicate that there is a striking correlation between the conformations about the side-chain glyocsyl bond and the backbone C(4′)–C(5′) bond of the nucleotide unit. It is found that the anti and the Gauche–Gauche (gg), conformations about the glycosyl and the C(4′)–C(5′) bonds, respectively, are energetically the most favored conformations for 5′-adenine nucleotide irrespective of whether the puckering of the ribose is C(2′)-endo or C(3′)-endo. Calculations have also shown that the other common 5′-pyrimidine nucleotides will show similar preferences for the glycosyl and C(4′)–C(5′) bond conformations. These results are in remarkable agreement with the concept of the “rigid” nucleotide unit that has been developed from available data on mononucleotides and dinucleoside monophosphates. It is found that the conformational ‘rigidity’ in 5′-nucleotides compared with that of nucleosides is a consequence of, predominantly, the coulombic interactions between the negatively charged phosphate group and the base. The above result permits one to consider polynucleotide conformations in terms of a “rigid” C(2′)-endo or C(3′)-endo nucleotide unit with the major conformational changes being brought about by rotations about the P–O bonds linking the internucleotide phosphorus atom. IT is predicted that the anti and the gg conformations about the glycosyl and the C(4′)–C(5′) bonds would be strongly preferred in the mononucleotide components of different purine and pyrimidine coenzymes and also in the nucleotide phosphates like adenodine di- and triphosphates.     

CD and Fourier transform ir spectroscopic studies of peptides. II. Detection of β-turns in linear peptides

Comparative CD and Fourier transform ir (FTIR) spectroscopic data on N-Boc protected linear peptides with or without the (Pro-Gly) β-turn motif (e.g., Boc-Tyr-Pro-Gly-Phe-Leu-OH and Boc-Tyr-Gly-Pro-Phe-Leu-OH) are reported herein. The CD spectra, reflecting both backbone and aromatic contributions, were not found to be characteristic of the presence of β-turns. In the amide I region of the FTIR spectra, analyzed by self-deconvolution and curve-fitting methods, the β-turn band shewed up between 1639 and 1633 cm^?1 in trifluoroethanol (TFE) but only for models containing the (Pro-Gly) core. This band war-also present in the spectra in chloroform but absent in dimethylsulfoxide. These findings, in agreement with recent ir data on cyclic models and 3₁₀-helical polypeptides and protein in D₂O [see S. J. Prestrelski, D. M. Byler, and M. P. Thompson (1991), International Journal of Peptide and Protein Research, Vol. 37, pp. 508–512; H. H. Mantsch, A. Perczel. M. Hollósi, and G. D. Fasman (1992), FASEB Journal, Vol. 6, p. A341; H. H. Mantsch. A. Perczel, M. Hollósi, and G. Fasman (1992), Biopolymers. Vol. 33, pp. 201–207; S. M. Miick, G. V. Martinez, W. R. Fiori, A. P. Tedd, and G. L. Millhauser (1992). Nature, Vol. 359, pp. 653–655], suggest that the amide I band, with a major contribution from the acceptor C ? O of the 1 ← 4 intramolecular H bond of β-turns, appears near or below 1640 cm^?1, rather than above 1660 cm^?1. In TFE, bands between 1670 and 1660 cm^?1 are mainly due to “free” carbonyls, that is, C ? O's of amides that are solvated but not involved in the characteristic H bonds of periodic secondary structures or β-turns. © 1994 John Wiley & Sons, Inc.     

Conformational interconversions in peptide β-turns: Discrimination between enantiomeric conformations by chiral perturbation

The crystal structure of the model tripeptide Boc-Aib-Gly-Leu-OMe ( 1 ) reveals two independent molecules in the asymmetric unit that adopt “enantiomeric” type I and type I′ β-turn conformations with the Aib and Gly residues occupying the corner (i + 1 and i + 2) positions. ¹³C cross polarization and magic angle sample spinning spectra in the solid state also support the coexistence of two conformational species. ¹³C-nmr in CDCl₃ establishes the presence of a single species or rapid exchange between conformations. 400 MHz ¹H-nmr provides evidence for conformational exchange involving a major and minor species, with β-turn conformations supported by the low solvent exposure of Leu(3) NH and the observation of N_iH ↔ N_i+1H nuclear Overhauser effects. CD bands in the region 190–230 nm are positive, supporting a major population of type I′ β-turns. The isomeric peptide, Boc-Gly-Leu-Aib-OMe ( 2 ), adopts an “open” type II′ β-turn conformation in crystals. Solid state and solution nmr support population of a single conformational species. Chiral perturbation introduced outside the folded region of peptides may provide a means of modulating screw sense in achiral sequences. © 1998 John Wiley & Sons, Inc. Biopoly 45: 191–202, 1998     

Letter: Equilibrium and kinetic studies of hemoglobin I: a functionally silent amino acid substitution at an invariant residue;

Hemoglobin I is an uncommon hemoglobin variant in which the lysine residue at position 16 of the a chain has been replaced by glutamic acid. Lysine is the invariant residue in all myoglobin and hemoglobin subunits that have been sequenced, with the exception of the hemoglobin of the lamprey. Replacement of invariant residues is generally reflected in altered functional properties of the hemoglobin molecule and such invariance may be indicative of a unique functional role. However, a study of the oxygen equilibrium and kinetic properties of hemoglobin I showed the functional properties of this hemoglobin to be indistinguishable from those of normal adult hemoglobin.     

Protein-primed DNA replication: a transition between two modes of priming by a unique DNA polymerase.

Phage phi29 from Bacillus subtilis is a paradigm of the protein-primed replication mechanism, in which a single-subunit DNA polymerase is involved in both the specific protein-primed initiation step and normal DNA elongation. To start phi29 DNA replication, the viral DNA polymerase must interact with a free molecule of the viral terminal protein (TP), to prime DNA synthesis once at each phi29 DNA end. The results shown in this paper demonstrate that the DNA polymerase-primer TP heterodimer is not dissociated immediately after initiation. On the contrary, there is a transition stage in which the DNA polymerase synthesizes a five nucleotide-long DNA molecule while complexed with the primer TP, undergoes some structural change during replication of nucleotides 6-9, and finally dissociates from the primer protein when nucleotide 10 is inserted onto the nascent DNA chain. This behaviour probably reflects the polymerase requirement for a DNA primer of a minimum length to efficiently catalyze DNA elongation. The significance of such a limiting transition stage is supported by the finding of abortive replication products consisting of the primer TP linked up to eight nucleotides, detected during in vitro replication of phi29 TP-DNA particularly under conditions that decrease the strand-displacement capacity of phi29 DNA polymerase.     

Conformational studies of N-acetyl-N′-methylamide derivatives of α-aminobutyric acid,norvaline, and valine. I. Preferred conformations in solution as studied by 1H-nmr spectroscopy

The ¹H-nmr studies were extensively carried out to elucidate preferred conformations of dipeptides CH₃C*O—X—NHCH₃, with X = Abu, nVal, and Val in various solvents. The vicinal ¹H—¹H coupling constants for the NH—C^αH moiety and those around the C^α—C^β bond in the articulated side chain provided the information regarding the average conformation of these molecules. The results indicate that transformation of skeletal conformations takes place in solution among conformers having similar dihedral angles, θ, in the Karplus expression.     

Mimicking hemoproteins: a new synthetic metalloenzyme based on a Fe(III)‐mesoporphyrin functionalized by two helical decapeptides

A new metalloenzyme formed by a Fe(III)‐mesoporphyrin IX functionalized by two helical decapeptides was synthesized to mimic function and structural features of a hemoprotein active site. Each decapeptide comprises six 2‐aminoisobutyric acid residues, which constrain the peptide to attain a helical conformation, and three glutamic residues for improving the solubility of the catalyst in aqueous solutions. The new compound shows a marked amphiphilic character, featuring a polar outer surface and a hydrophobic inner cavity that hosts the reactants in a restrained environment where catalysis may occur. The catalytic activity of this synthetic mini‐protein was tested with respect to the oxidation of l ‐ and d ‐Dopa by hydrogen peroxide, showing moderate stereoselectivity. Structural information on the new catalyst and its adduct with the l ‐ or d ‐Dopa substrate were obtained by the combined use of spectroscopic techniques and molecular mechanics calculations. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Light-induced linear dichroism in photoreversibly photochromic sensor pigments. – VI. Relation between the two pigments of the mycochrome system in Alternaria cichorii

Conidiation in Alternaria cichorii Nattras is reversibly stimulated by near ultraviolet radiation (NUV, ca 313 nm) and inhibited by blue light (ca 450 nm) and seems to be a mycochrome-mediated process. After induction with plane-polarized NUV, blue light polarized perpendicularly to the NUV was more effective in counteracting the induction than was blue light polarized parallel to the NUV. From this the conclusions are drawn that (a) both the blue-absorbing component (presumably a flavo-protein) and the P_NUV of the mycochrome system are membrane-bound and that (b) the transition moment associated with blue light absorption in the presumed flavoprotein forms an angle of at least 53° with the transition moment associated with NUV absorption in P_NUV.     

Kinetics of poly-enzyme system reactions. II. Nonsteady-state kinetics. Presteady-state and relation modes in a bi-enzyme system and linear sequences

Kinetic aspects of reactions in homogeneous multienzyme systems under nonsteady state conditions were investigated. An analysis of formal-kinetic relationships, describing the time course of system was conducted with a bienzyme system. Presteady state kinetics of processes in lineal multienzyme systems was investigated. Relax-kinetics methods were applied for the analysis of processes in lineal sequences. Methods of determination of number of stages initial substrate transformations and of number of enzymes were developed as well as methods for the analysis of sequences of intermediates in reaction pathway. Methods of determination of Vmax and Kmax for each individual enzyme are considered.     

The epidemiologic transition in a frontier town — Manti,Utah: 1849–1977

Census reports and information in burial records of Manti, Utah from 1849 to July 1977 are examined in order to (1)document mortality trends and differentials by age, sex, cause-of-death, and seasonality as Manti passed from a frontier settlement to a rural agricultural community; and (2) ascertain whether the shifts in the cause-of-death structure follow those patterns outlined by Omran (1971, 1974, 1977) in his theory of the epidemiologic transition. Findings parallel patterns suggested by Omran. Major factors accounting for mortality reductions are (1) elimination of the population's dependence upon a contaminated water supply, and (2) adoption of medical advances as they became available.     

Helix–coil transition in copolypeptides. II. Poly(γ-benzyl L-glutamate-co-ε-carbobenzoxy-L-lysine)

The thermal helix–coil transition of poly(γ-benzyl L -glutamate-co-ε-carbobenzoxy-L -lysine) copolypeptides was studied in solvent mixtures of different compositions. The cooperativity parameter v changes linearly with polymer (and solvent) composition, whereas the heat of the transition shows a very pronounced minimum as a function of polymer composition. This minimum cannot be due only or mainly to the solvent changes and must be attributed to the effect on the transition of the side chains of the polypeptides.     

Cooperative cross-linking between two sets of membrane receptors: a model for B and T lymphocyte collaboration in immune response.

A molecular mechanism for B and T lymphocyte collaboration is proposed. Two sets of polivalent receptors, each one on a cell type, would interact with different epitopes of the antigen, resulting in a cross-linking of the receptors as the initial step in B lymphocyte activation. The mechanism can explain many known featrues of humoral immune response and accords with experimental findings on the blast transformation of B lymphocytes.     

Domains for G-protein coupling in angiotensin II receptor type I: studies by site-directed mutagenesis.

To delineate domains essential for G-protein coupling in angiotensin II type 1 receptor (AT1), we mutated the receptor cDNA in the putative cytosolic regions and determined consequent changes in the effect of GTP analogs on angiotensin II (Ang II) binding and in inositol trisphosphate production in response to Ang II. Polar residues in targeted areas were replaced by small neutral residues. Mutations in the second cytosolic loop, carboxy terminal region of the third cytosolic loop or deletional mutation in the carboxyl terminal tail simultaneously abolished both the GTP-induced shift to the low affinity form and Ang II-induced stimulation of inositol trisphosphate production. These results suggest that polar residues in the second cytosolic loop, the carboxy terminal region of the third cytosolic loop, and the carboxy terminal cytosolic tail are important for G-protein coupling of AT1 receptor.     

Outcome in colorectal adenocarcinoma: two seven-year studies of a population.

OBJECTIVE--To record every patient with proved colorectal adenocarcinoma presenting from a defined population over two years in 1968-9 and during 1980-2, and to compare treatment and outcome over seven years. DESIGN--Retrospective in 1968-9 and prospective in 1980-2. SETTING--Aberdeen general hospitals. SUBJECTS--Every patient presenting to the four general surgical units with histological proof of colorectal adenocarcinoma. MAIN FINDINGS--On average, one new patient presented each week per 100,000 population. The proportion of patients aged 65 and over rose from 67% to 71%. An operation was performed on 385 patients in 1968-9 and on 399 during 1980-2. At laparotomy the proportion of patients who seemed to be curable and had a radical operation rose slightly, from 56% to 61%, and operative mortality fell from 9% to 5%. In all there were 421 survivors of curative surgery, and seven years later three quarters were either alive (51%) or had died without recurrence (25%). In both studies some 40% of patients were considered incurable when they presented, but the number who had a palliative resection rose from 59% to 85%. CONCLUSIONS--The contribution of radical surgery to the treatment of colorectal adenocarcinoma is substantial, with three quarters of patients so treated showing no evidence of recurrence after seven years. Operative mortality in an elderly population is now low, and improvement in late outcome is more likely to come from developments in adjuvant therapy than in operative technique. A continuing problem is that 40% of patients are not curable when they present, although palliative resection can now be offered to over 80%.