Determination of the amino acid residues required for the activity of the anti-rhizobial peptide antibiotic trifolitoxin

AIMS: The first aim was to determine those amino acid residues required for the biological activity of the potent peptide antibiotic, trifolitoxin (TFX). The second aim was to determine the concentrations of TFX1 and TFX2 that cause 50% inhibition of bacterial growth (Ki), the two predominant isomeric forms of TFX made by Rhizobium. METHODS AND RESULTS: Site-directed mutagenesis of tfxA was used to produce strains that made mutant TFX peptides. The mutant tfxA genes were placed on a vector and inserted in Rhizobium leguminosarum b. trifolii Tn54A112, a tfxA mutant of strain T24 that lacks trifolitoxin activity. Our standard bioassay was used to assess the activity of these mutants. TFX1 and TFX2 were purified by reverse phase chromatography. Several concentrations of each peptide were assayed for biological activity to determine Ki. The unmodified TFX peptide (DIGGSRQGCVA) was synthesized and was found to lack any biological activity. Four of the 11 amino acid residues in ribosomally synthesized, post-translationally modified peptide were required for TFX activity. These required amino acids include arginine (R37), glutamine (Q38), glycine (G39) and cysteine (C40). S36T and S36Y mutants showed reduced TFX activity. The numbering system is based on the 42-amino acid TfxA peptide that is post-translationally modified to form the active TFX peptide. The Ki of TFX2 was determined to be 10-fold lower than TFX1. CONCLUSIONS: The post-translational modifications of the TfxA peptide are required for biological activity. TFX2 is far more active than TFX1. SIGNIFICANCE AND IMPACT OF THE STUDY: The sequence of the TfxA peptide appears to have been optimized for maximum activity through the course of evolution. Even conservative changes to any of the amino acid residues required for activity results in a complete loss of activity. The understanding of the action of this peptide is critical for its proposed action as a control agent for crown gall disease.     

Synthesis and spectroscopic properties of 4-ethoxymethylene-2-(1)-naphthyl-5(4H)-oxazolone-labeled fluorescent peptides

Strategies for the preparation of new fluorescent oligopeptide conjugates labeled with 4-ethoxymethylene-2-[1]-naphthyl-5(4H)-oxazolone (naOx-OEt) at the N-terminal on solid support or in solution have been devised. These procedures are simple and easy to carry out by reacting naOx-OEt or N(alpha)-naOx-amino acid with side chain protected peptide chains attached to resins. The integrity of the N-alkyl bond was maintained even after the trifluoracetic acid or HF based cleavages procedures. Our data show that the naOx fluorophore is compatible with both Fmoc/tBu and Boc/Bzl methods and also suggest that naOx-amino acid could be utilized as building blocks for solid phase peptide synthesis. Comparative analysis of fluorescence properties of naOx-conjugates indicated that the spectral properties of the fluorophore do not change after incorporating into peptides. The compact size, the definite chemical reaction for its introduction in combination with the appropriate spectral features (e.g., intense emission, pH independent fluorescent characteristics, and beneficial photobleaching dose constant and rates) and with chemical and spectral stability, naOx-based labeling could be attractive for novel cellular fluorescent techniques (e.g., in laser scanning confocal FRET) to study peptide-protein and protein-protein interactions even in biological matrices.     

鼎湖山南亚热带常绿阔叶林叶功能性状沿群落垂直层次的种内变异

探究功能性状沿着环境梯度如何变化一直以来是基于性状的群落生态学的核心问题之一。尽管功能性状存在种内和种间变异, 但种内变异沿环境梯度如何变化仍有待探究。本文以鼎湖山南亚热带常绿阔叶林1.44 ha塔吊样地内16个树种的2,820个个体为研究对象, 探究4种叶功能性状(比叶面积、叶干物质含量、叶厚度和叶面积)沿群落垂直层次的种内变异。首先, 利用随机效应线性模型量化塔吊样地内的种内变异和种间变异; 其次, 利用Kmeans函数将森林的垂直层次划分为灌木层、亚冠层和林冠层, 并通过构建回归模型探究叶功能性状在群落垂直层次中的种内变异格局。最后, 应用混合线性模型和单因素方差分析的方法探究叶功能性状沿垂直层次的种内变异是否具有物种依赖性。结果表明: 在局域群落中, 并非所有叶功能性状的种内变异都低于种间变异; 叶功能性状在不同垂直层次的种内变异格局存在显著差异, 且种内变异与垂直范围呈正相关; 叶功能性状的种内变异具有较强的物种依赖性, 因此树种差异相对于小环境解释了更多的性状变异; 此外, 不同叶功能性状的种内变异沿垂直层次的变化趋势并不一致。本研究发现种内变异对于物种共存具有重要作用。     

To twist or not to twist: From chromophore structure to dynamics inside engineered photoconvertible and photoswitchable fluorescent proteins

Green-to-red photoconvertible fluorescent proteins (FPs) are vital biomimetic tools for powerful techniques such as super-resolution imaging. A unique Kaede-type FP named the least evolved ancestor (LEA) enables delineation of the evolutionary step to acquire photoconversion capability from the ancestral green fluorescent protein (GFP). A key residue, Ala69, was identified through several steady-state and time-resolved spectroscopic techniques that allows LEA to effectively photoswitch and enhance the green-to-red photoconversion. However, the inner workings of this functional protein have remained elusive due to practical challenges of capturing the photoexcited chromophore motions in real time. Here, we implemented femtosecond stimulated Raman spectroscopy and transient absorption on LEA-A69T, aided by relevant crystal structures and control FPs, revealing that Thr69 promotes a stronger π–π stacking interaction between the chromophore phenolate (P-)ring and His193 in FP mutants that cannot photoconvert or photoswitch. Characteristic time constants of ~60–67 ps are attributed to P-ring twist as the onset for photoswitching in LEA (major) and LEA-A69T (minor) with photoconversion capability, different from ~16/29 ps in correlation with the Gln62/His62 side-chain twist in ALL-GFP/ALL-Q62H, indicative of the light-induced conformational relaxation preferences in various local environments. A minor subpopulation of LEA-A69T capable of positive photoswitching was revealed by time-resolved electronic spectroscopies with targeted light irradiation wavelengths. The unveiled chromophore structure and dynamics inside engineered FPs in an aqueous buffer solution can be generalized to improve other green-to-red photoconvertible FPs from the bottom up for deeper biophysics with molecular biology insights and powerful bioimaging advances.     

Photoelectrochemical Cycle of Bacteriorhodopsin

The scheme of the bacteriorhodopsin photocycle associated with a transmembrane proton transfer and electrogenesis is considered. The role of conformational changes in the polypeptide chain during the proton transport is discussed.     

Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel

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Solid-State H NMR spectroscopy of retinal proteins in aligned membranes

Solid-state ²H NMR spectroscopy gives a powerful avenue to investigating the structures of ligands and cofactors bound to integral membrane proteins. For bacteriorhodopsin (bR) and rhodopsin, retinal was site-specifically labeled by deuteration of the methyl groups followed by regeneration of the apoprotein. ²H NMR studies of aligned membrane samples were conducted under conditions where rotational and translational diffusion of the protein were absent on the NMR time scale. The theoretical lineshape treatment involved a static axial distribution of rotating C-C²H₃ groups about the local membrane frame, together with the static axial distribution of the local normal relative to the average normal. Simulation of solid-state ²H NMR lineshapes gave both the methyl group orientations and the alignment disorder (mosaic spread) of the membrane stack. The methyl bond orientations provided the angular restraints for structural analysis. In the case of bR the retinal chromophore is nearly planar in the dark- and all-trans light-adapted states, as well upon isomerization to 13-cis in the M state. The C13-methyl group at the “business end” of the chromophore changes its orientation to the membrane upon photon absorption, moving towards W182 and thus driving the proton pump in energy conservation. Moreover, rhodopsin was studied as a prototype for G protein-coupled receptors (GPCRs) implicated in many biological responses in humans. In contrast to bR, the retinal chromophore of rhodopsin has an 11-cis conformation and is highly twisted in the dark state. Three sites of interaction affect the torsional deformation of retinal, viz. the protonated Schiff base with its carboxylate counterion; the C9-methyl group of the polyene; and the β-ionone ring within its hydrophobic pocket. For rhodopsin, the strain energy and dynamics of retinal as established by ²H NMR are implicated in substituent control of activation. Retinal is locked in a conformation that is twisted in the direction of the photoisomerization, which explains the dark stability of rhodopsin and allows for ultra-fast isomerization upon absorption of a photon. Torsional strain is relaxed in the meta I state that precedes subsequent receptor activation. Comparison of the two retinal proteins using solid-state ²H NMR is thus illuminating in terms of their different biological functions.     

Application and prospects of high-throughput screening for in vitro neurogenesis

Over the past few decades, high-throughput screening (HTS) has made great contributions to new drug discovery. HTS technology is equipped with higher throughput, minimized platforms, more automated and computerized operating systems, more efficient and sensitive detection devices, and rapid data processing systems. At the same time, in vitro neurogenesis is gradually becoming important in establishing models to investigate the mechanisms of neural disease or developmental processes. However, challenges remain in generating more mature and functional neurons with specific subtypes and in establishing robust and standardized three-dimensional (3D) in vitro models with neural cells cultured in 3D matrices or organoids representing specific brain regions. Here, we review the applications of HTS technologies on in vitro neurogenesis, especially aiming at identifying the essential genes, chemical small molecules and adaptive microenvironments that hold great prospects for generating functional neurons or more reproductive and homogeneous 3D organoids. We also discuss the developmental tendency of HTS technology, e.g., so-called next-generation screening, which utilizes 3D organoid-based screening combined with microfluidic devices to narrow the gap between in vitro models and in vivo situations both physiologically and pathologically.     

Mechanism of Nonlinear Photoinduced Anisotropy in Bacteriorhodopsin and its Derivatives

Polymer films made with photosensitive chromophore protein bacteriorhodopsin (BR) from the extreme halophile Halobacterium salinarium as well as films made with BR derivatives exhibit a nonlinear photoinduced anisotropy. Two different methods can be used to induce anisotropy in polymer BR films. The first method is based on the anisotropic properties of the initial form of the photocycle, BR570 (B-type anisotropy). Another method is based on the anisotropic properties of the longest-lived photocycle intermediate M412 (M-type anisotropy). CW gas lasers were employed to induce a reversible anisotropy in polymer BR films. Nonlinear photoinduced anisotropy is discussed in the context of a model for the anisotropic photoselection of BR molecules under linearly polarized light. A comparison of the experimental dependencies of nonlinear photoinduced anisotropy on laser intensity with similar calculated dependencies enables one to determine the molecular dichroism of BR and its derivatives not only for the initial form of the photocycle, B but also for the longest-lived intermediate M. Here we present the data showing the correlation between the laser induced nonlinear anisotropic properties and chromophore/protein interactions in BR. The effect of polymer binder on the nonlinear photoanisotropic properties of polymer BR films is also described.     

A new approach in exciton-coupled circular dichroism (ECCD)—insertion of an auxiliary stereogenic center

There are cases in which exciton coupling between two chromophores does not occur because the two electric transition moments which should interact are coplanar. This is seen with cyclohexane-1,4-diols (both ee or ea) and a wide variety of 3-hydroxy carotenoids, 3-hydroxyretinoids, etc. A general approach to deal with such cases is to acylate one of the hydroxyl groups with a chiral allenic acid substituted with a suitable chromophore, e.g., CHROM? CH?C?CH-COOH. The allenic bond introduces a 90° twist at the italicized central carbon so that the allenic CHROM now couples with the second chromophore. This concept of introducing an auxiliary allenic center should be of general applicability in other similar cases. © 1995 Wiley-Liss, Inc.