Etude par spectroscopie infrarouge de la transformation hélice–chaîne statistique des polypeptides. II. Etude de l'interaction de quelques polypeptides à chaînes latérales polaires avec l'acide trifluoracétique

The various polymer–acid solvation possibilities occuring in the helix–coil transition process of polypeptides with polar side chains were systematically analyzed by infrared spectroscopy. The following samples have been considered: poly-γ-benzyl-L -glutamate (PBLG), alternating poly-γ-benzyl-D ,L -glutamate (PBD-LG), and poly-β-benzyl-L -as-partate (PBLA). The behavior of the amide A, I, II, and νC?O ester absorptions of each polymer dissolved in trifluoroacetic acid–chloroform mixtures was studied in depth. The classical assumptions concerning the interaction between a polypeptide and a proton donor solvent are discussed. This interaction was previously proposed in a theoretical model of helix–coil transition. For PBLG, the spectral characteristics of the cooperative transition are evidenced by the amide bands. These bands also show main chain–acid hydrogen bonding (I) Quantitative analysis of phenomenon (I) was performed in order to localize the “binding sites” of the polymer. In agreement with the theory, only the complexation of peptide units belonging to random coil and terminal helical regions were observed. However, in contrast to the theory in which the association constants KCO and KNH of these residues are generally kept equal, the present results have shown that the main binding site is the carbonyl group (KNH ? 0 or « KCO ). The behavior of the polar side chains of these polypeptides were analyzed during the transition. Similarly to the peptide backbone, they bind the acid by hydrogen bonding (II) Furthermore, this association is more important when the side chains are localized in the coiled regions than in the helical ones. This result suggests, by analogy with the main chain behavior, that the helix–coil transition theory should take into account two more association constants for polar side chains, namely k₁ for the helical regions and k₂ > k₁ for the coiled ones.     

Stereochemical constraints in peptide design: Analysis of the influence of a disulfide bridge and an α-aminoisobutyryl residue on the conformation of a hexapeptide

The competing effects of a disulfide bridge and an α-aminoisobutyryl residue (Aib) in determining the conformation of a hexapeptide have been investigated, by comparing the cyclic disulfide (1) and the acylic peptide Boc-Cys(SBzl)-Val-Aib-Ala-Leu-Cys(SBzl)-NHMe ( 2 ). Previously published nmr and crystallographic studies [R. Kishore, S. Raghothama, and P. Balaram (1987) Biopolymers, Vol. 26, pp. 873–891; I. L. Karle, R. Kishore, S. Raghothama, & P. Balaram, (1988) Journal of the American Chemical Society Vol. 110, pp. 1958–1963] have established an antiparallel β-hairpin structure for 1 with a central Aib-Ala β-turn. A comparison of nmr data for 1 and 2 in chloroform and dimethylsulfoxide reveals that the acyclic peptide is conformationally labile. Evidence for a 3₁₀-helical conformation in CDCl₃ is obtained from sensitivity of NH chemical shifts to temperature and solvent perturbation and low J_HNCαH values. Studies in solvent mixtures establish a conformational transition on going from CDCl₃ to (CD₃)₂SO. The changes in NH nmr parameters, together with the observation of several interresidue C H-N_{i + 1}H nuclear Overhauser effects support a conformation having a central β-turn with extended arms in (CD₃)₂SO. A single Aib residue appears to stabilize a helix in apolar solvents, for the acyclic hexapeptide, while the disulfide bridge serves to lock the β-hairpin conformation. © 1993 John Wiley & Sons, Inc.     

Das Gesetz der absoluten Geschwindigkeiten biologischer Prozesse

The dependency of the velocity of biological processes from the temperature is described by the “Law of absolute velocity of biological processes”, which has only the individual parameters energy of activation ΔE, and the universal constant C. The law holds for all biological processes and is expressed by the equation: where C is: .     

Inside Front Cover: Uniform light delivery in volumetric optoacoustic tomography (J. Biophotonics 6/2019)

Optimized light delivery allows for single shot whole organ optoacoustic imaging. The authors present an optimized illumination concept for volumetric tomography that utilizes 3D printing in combination with custom‐made optical fiber illumination. The new approach showed a clear advantage over conventional, single‐sided illumination strategies by eliminating the need to correct for illumination variances and resulting in enhancement of the effective field of view, greater penetration depth and significant improvements in the overall image quality. Further details can be found in the article by Benedict Mc Larney, Johannes Rebling, Zhenyue Chen, et al. ( e201800387 )

     

Inside Cover: In situ diode laser fenestration: An ex‐vivo evaluation of irradiation effects on human aortic tissue (J. Biophotonics 9/2019)

The laser technology can be successfully used for the intraoperative modification of an endograft during the endovascular aneurysm repair procedure. This paper presents the first diode laser irradiation study to assess whether the laser operative conditions, which ensure the fabric alteration, are harmless for the biological tissue surrounding the endoprosthesis. The work provides a microscopic and histological evaluation of its effects on ex‐vivo human aortic tissue. Further details can be found in the article by Roberta Piazza, Filippo Micheletti, Sara Condino, et al. ( e201900032 ).

     

Transfer function matrix of the continuous cultivation system of Morchella crassipes in ammonia base waste sulfite liquor

A continuous stirred tank fermentor (CSTF) used for cultivation of the fungus Morchella crassipes in ammonia base waste sulfite liquor (NH₃-WSL) was considered as a multivariable linear system around its operating point. Pulse testing on the inputs (inlet jacket temperature, inlet pH, inlet substrate concentration) and their responses at the outputs (biomass, outlet temperature, outlet jacket temperature, outlet pH, outlet substrate concentration) were used for numerical determination of the transfer function matrix:      

Issue Information

Cover Image Evening sun bathing flowers of Cymbidium dayanum. Photographed by Naoto Sugiura, Minami-Osumi, Kagoshima, Japan.

     

Interactions of molecules with nucleic acids. VI. Computer design of chromophoric intercalating agents

The mode of action of many antitumor agents entails the inhibition of nucleic acid synthesis. Because many of the drugs can intercalate, it is assumed that intercalation is an important step in the mechanism of biological activity. As intercalants contain a planar chromophore as an ingredient essential for intercalation, chromophores that should fit into DNA are desired. This is the main theme of this investigation. Binding to DNA of fundamental moieties, protonated pyridine, aniline, phenol, quinone, and 4H-thiopyran-4-one, is studied to determine their optimum placement in DNA. The optimum orientations for each moiety are superimposed to form polyaromatic systems that can intercalate in a manner in which functional groups on these chromophores are oriented as in the moieties themselves. Ideal intercalants proposed contain three and four fused ring system, have protonated ring nitrogen atoms located to maximize the electrostatic interactions with DNA, hydroxy and amino groups that can hydrogen bond to the O_II and O_5′ phosphate backbone atoms, and carbonyl and sulfur groups in the central position of the ring system to provide variations in the chromophore and to interact with the relatively positive region in the intercalation site. The optimum orientation occurs when the chromophore and the base pairs overlap to the maximum extent. The ideal intercalants are fundamentally of the type:      

Inside Cover: Three‐dimensional intravital imaging in bone research (J. Biophotonics 12/2019)

This review is aimed at interpreting development and advantages of intravital imaging as an emerging invaluable methodology and summarizing related representative discoveries in bone physiologies and pathologies. It also indicates current limitations, further refinement, and extended application of intravital imaging in bone research. Further details can be found in the article by Yuhao Liu, Quan Yuan, and Shiwen Zhanget ( e201960075 ).

     

Potentiometric neutralization of oligomers represented by the general formula shown was studied. II (author's transl)

Potentiometric neutralization of oligomers represented by the general formula shown was studied. The intrinsic pK of carboxyl function was found to be 4.40 at 25°C; the variation of the apparent pK_a, ΔK(α), was studied as a function of the degree of neutralization: the influence of the degree of neutralization on the accumulation of ionic sites along the chain is clearly shown. The experimental curves of polyglutamic acid allowed us to deduce the sequence of ionic selectivity and the energy of conformational transition. The theoretical interpretation of the results was proposed in terms of the rod like model from Katchalsky's theory. The intrinsic pK_o for the polymer was set equal to the value experimentally obtained on oligomers. By activity measurements on Na⁺ and Ca²⁺ counterions in salt-free solutions, the free fraction of counterions was deduced on the different samples. The results were interpreted with the electrostatic model previously proposed; in this view, the oligomers are assimilated to imaginary polyelectrolytes. This allowed us to determine the values of ΔpK and the fraction of free ions at the same time.     

Issue Information

Cover Image A large population (left) and various life history stages (right), e.g. seedling, one-leaf, three-leaved and flowering, of Trillium camschatcense. (cf. Ohara & Kawano, 2005, Plant Species Biology 20:75–82, DOI: 10.1111/j.1442-1984.2005.00126.x ) Photographed by Masashi Ohara, Tokachi, Hokkaido, Japan.

     

Inside Cover: Investigation of the source‐detector separation in near infrared spectroscopy for healthy and clinical applications (J. Biophotonics 11/2019)

Near infrared spectroscopy (NIRS) neuroimaging sensors use light source and detector pairs placed over scalp to measure underlying neurophysiology. Source detector separation (SDS) is a critical design parameter and should aim a balanced trade‐off for detected light intensity and sensitivity to brain tissue. In this study, we used multi‐layer digital head models to systematically evaluate the role of SDS on NIRS spatial sensitivity profiles within both healthy and clinical conditions. Further details can be found in the article by Lei Wang, Hasan Ayaz, and Meltem Izzetoglu ( e201900175 ).

     

Issue Information

Cover Photograph: A SEM micrograph of developing PGCs in the genital ridge of Columba livia (see Olea et al. pp 56-65).

     

Confidence Estimation of an Unknown Component of the Vector of Regressor Variables in Multivariate Linear Regression

The model used in this paper is Y = Xβ, where with unknown x₀. Estimators of x₀ are derived by putting β_mx₀ =β_m+1 regarding β_m+1 as a new unknown parameter. Formally we use the model Y = X₁β₊ + e where β′₊ = (β₀, …β_m+1 and Then β_m+1/ β_m is a point estimator of x₀. Assuming normality for e and taking the random variable z=β_mx₀?β_m+1 we get a t-distributed variable and finally a confidence estimator of x₀. The formulas are applied in dose response relations in antibiotic assays refering to a standard. Now we can take into account not only the dependence on the dose/concentration but also on the position on the test agar plate where the test solution is filled in. As a consequence the confidence interval of the unknown dose/concentration x₀ becomes shorter and by it the statements more precise.     

Inside Cover: Measuring expansion from macro‐ to nanoscale using NPC as intrinsic reporter (J. Biophotonics 8/2019)

Nuclear pore complex imaged at three different resolutions by confocal, expansion, and Ex‐STED microscopy, respectively. NUP become a ruler to measure the expansion process. Further details can be found in the article by Luca Pesce, Marco Cozzolino, Luca Lanzanò, Alberto Diaspro, and Paolo Bianchini ( e201900018 ).

     

Identification of D-galactose-(1 → 7)-3-deoxy-d-manno-2-octulo-pyranosonate as component of the inner core region of escherichia coli EH 100 lipopolysaccharide

The dissaccharide D-galactosyl-3-deoxy-D-manno-2-octulosonic acid (Gal-KDO) from lipopolysaccharides (LPS) of the inner core region of the rough mutant EH100 of E. coli 0100 was isolated after mild acid hydrolysis of LPS by means of dialysis, ion-exchange chromatography, gelfiltration and high-voltage paper electrophresis. By chemical analysis galactose and KDO were identified in a molar ratio of approximately 1 : 1. ¹³C-NMR and ¹H-NMR studies, methylation analysis and GLC of the acetylated R.( – )-2-butyl-galactoside identified the structure .     

News & ISN April 2019

We are very sad that the ISN lost its President Kazuhiro Ikenaka, Professor and Chairman at National Institute for Physiological Sciences (NIPS), Director of Okazaki Institute of Integrative Biology. JNeurochem published an Obituary to value his outstanding achievements: Akio Wanaka et al. (2019) OBITUARY Kazuhiro Ikenaka (1952‐2018). https://doi.org/10.1111/jnc.14679

     

Inside Front Cover: Slide‐free imaging of hematoxylin‐eosin stained whole‐mount tissues using combined third‐harmonic generation and three‐photon fluorescence microscopy (J. Biophotonics 5/2019)

Intraoperative margin assessment is clinically important, especially for tissue conserving surgery like Mohs micrographic surgery in which minimization of the surgical area is crucial. Instead of the complex frozen pathology protocol, slide‐free histopathological imaging of hematoxylin‐eosin stained whole‐mount skin tissues is demonstrated by using nonlinear microscopy, thus facilitating rapid intraoperative assessment of surgical tissues for future applications. Further details can be found in the article by Chi‐Kuang Sun, Chien‐Ting Kao, Ming‐Liang Wei, et al. ( e201800341 ).