From alpha-helix to beta-sheet--a reversible metal ion induced peptide secondary structure switch

Here we introduce a peptide model based on an alpha-helical coiled coil peptide, providing a simple system which can be used for a systematic study of the impact of different metal ions in different oxidation states on peptide secondary structure on a molecular level; histidine residues were incorporated into the heptad repeat to generate possible complexation sites for Cu2+ and Zn2+ ions.     

Micelle structure: a surfactant-block model

A structure of spheroidal micelles is developed by model building. It is a hybrid of two classical micelle models, the compact droplet and the bilayer fragment : droplet-like in overall shape and bilaver-like in local configuration. The micelle appears as a tiny isometric liquid crystal with particular architecture and dynamics.     

蛋白质和变性蛋白质二级结构的FTIR分析进展

蛋白质结构的研究一直是人们研究的一个热点,蛋白质在发生变性后,二级结构会改变,从而导致生物活性丧失,这些与医药学及食品科学等领域密切相关。傅里叶变换红外光谱(FTIR)作为一种无损、快速的分析方法在蛋白质二级结构的研究中发挥重要的作用,本文就FTIR对于蛋白质二级结构的研究作一初步概述,主要介绍FTIR研究蛋白质结构的主要方法、红外光谱的谱学特点。     

Prediction of protein secondary structure content by artificial neural network

The neural network method was applied to the prediction of the content of protein secondary structure elements, including alpha-helix, beta-strand, beta-bridge, 3(10)-helix, pi-helix, H-bonded turn, bend, and random coil. The "pair-coupled amino acid composition" originally proposed by K. C. Chou [J Protein Chem 1999, 18, 473] was adopted as the input. Self-consistency and independent-dataset tests were used to appraise the performance of the neural network. Results of both tests indicated high performance of the method.     

Rational design of a reversible pH-responsive switch for peptide self-assembly

Peptide TZ1H, based on the heptad sequence of a coiled-coil trimer, undergoes fully reversible, pH-dependent self-assembly into long-aspect-ratio helical fibers. Substitution of isoleucine residues with histidine at the core d-positions of alternate heptads introduces a mechanism by which self-assembly is coupled to the protonation state of the imidazole side chain. Circular dichroism spectroscopy, transmission electron microscopy, and microrheology techniques revealed that the self-assembly of TZ1H coincides with a distinct coil-helix conformational transition that occurs within a narrow pH range near the pKa of the imidazole side chains of the core histidine residues.     

The LOV2 domain of phototropin: a reversible photochromic switch

Light, oxygen, or voltage (LOV) domains constitute a new class of photoreceptor proteins that are sensitive to blue light through a noncovalently bound flavin chromophore. Blue-light absorption by the LOV2 domain initiates a photochemical reaction that results in formation of a long-lived covalent adduct between a cysteine and the flavin cofactor. We have applied ultrafast spectroscopy on the photoaccumulated covalent adduct state of LOV2 and find that, upon absorption of a near-UV photon by the adduct state, the covalent bond between the flavin and the cysteine is broken and the blue-light-sensitive ground state is regained on an ultrafast time scale of 100 ps. We thus demonstrate that the LOV2 domain is a reversible photochromic switch, which can be activated by blue light and deactivated by near-UV light.     

Theoretical study of the photochemistry of a reversible three-state bis-thiaxanthylidene molecular switch

The ground- and the lowest singlet excited-state potential energy surfaces of the bis-thiaxanthylidene (3) molecular switch are investigated using a density functional method specifically designed to treat molecular systems typified by strong non-dynamic electron correlation. The results of the theoretical calculations suggest that the unique ability of substituted bis-thiaxanthylidenes to switch between three states of luminescence-non-fluorescent state, blue fluorescent state, and red fluorescent state-can be explained by specific features on the excited state potential energy surface: the potential barrier around the Franck-Condon point of the anti-folded conformer and the existence of conical intersection in the vicinity of the syn-folded conformer. It is suggested that the twisted conformer, if made more stable via chemical modification, should fluoresce in the near-infrared region (λ≈740-760 nm), thus offering a possibility for a four-state switching of luminescence in a single-component molecular system.     

Elucidating protein secondary structure with circular dichroism and a neural network

Circular dichroism spectroscopy is a quick method for determining the average secondary structures of proteins, probing their interactions with their environment, and aiding drug discovery. This article describes the development of a self‐organising map structure‐fitting methodology named secondary structure neural network (SSNN) to aid this process and reduce the level of expertise required. SSNN uses a database of spectra from proteins with known X‐ray structures; prediction of structures for new proteins is then possible. It has been designed as 3 units: SSNN1 takes spectra for known proteins, clusters them into a map, and SSNN2 creates a matching structure map. SSNN3 places unknown spectra on the map and gives them structure vectors. SSNN3 output illustrates the process and results obtained. We detail the strengths and weaknesses of SSNN and compare it with widely accepted structure fitting programs. Current input format is Δ? per amino acid residue from 240 to 190 nm in 1 nm steps for the known and unknown proteins and a vector summarizing the secondary structure elements of the known proteins. The format is readily modified to include input data with, for example, extended wavelength ranges or different assignment of secondary structures. SSNN can be used either pretrained with a reference set from the CDPro web site (direct application of SSNN3, with the provided output from SSNN1 and SSNN2) or all three modules can be used as required. SSNN3 is available trained (with the reference set of the 48‐spectra set used in this work complemented by five additional spectra) at http://www2.warwick.ac.uk/fac/sci/chemistry/research/arodger/arodgergroup/research_intro/instrumentation/ssnn/ . © 2013 Wiley Periodicals, Inc.     

Protection of protein secondary structure by saccharides of different molecular weights during freeze-drying

The protective effects of saccharides with various molecular weights (glucose, maltose, maltotriose, maltotetraose, maltopentaose, maltoheptaose, dextran 1060, dextran 4900, and dextran 10200) against lyophilization-induced structural perturbation of model proteins (BSA, ovalbumin) were studied. Fourier transform infrared (FT-IR) analysis of the proteins in initial solutions and freeze-dried solids indicated that maltose conferred the greatest protection against secondary structure change. The structure-stabilizing effect of maltooligosaccharides decreased in increasing the number of saccharide units. Larger molecules of dextran also showed a smaller structure-stabilizing effect. Increasing the effective saccharide molecular size by a borate-saccharide complexation reduced the protein structure-stabilizing effect of all of the saccharides except glucose. The results indicate that the larger saccharide molecules, and/or the complex formation with borate ion, reduce the free and accessible hydroxyl groups to interact with and stabilize the protein structure by a water-substitution mechanism.     

Water penetration into protein secondary structure revealed by hydrogen-deuterium exchange two-dimensional infrared spectroscopy

Two-dimensional infrared spectroscopy in conjunction with hydrogen-deuterium exchange experiments provides detailed information about solvent penetration into protein structure. Correlating the secondary-structure sensitivity of the amide I vibration and the solvent-exposure sensitivity of amide II provides a direct probe of solvent-inaccessible residues of proteins embedded in the hydrophobic core or those involved in strong hydrogen bonds in secondary structures. Distinct spectral signatures of the cross-peak region arising from the coupling of the amide I and II modes imply a significant degree of structural stability of hydrogen-bonded contacts in alpha-helices and beta-sheets in a series of proteins. Ubiquitin, an alpha/beta-protein, exhibits strong alpha-helical signatures and lacks those of the beta-sheet in the cross-peak region, demonstrating that ubiquitin's beta-sheet exchanges protons with the surrounding solvent and is conformationally unstable.     

Theoretical study on photoisomerization effect with a reversible nonlinear optical switch for dithiazolylarylene

DFT and TDDFT methods have been performed to investigate the photoisomerization effect for dithiazolylarylene on solution. The weak S···N interaction and CH···N hydrogen bond restrain the rotation of the side-chain thiazolyl ring in open-isomer 1a, the higher stability of which prefers to show a high quantum yield of photoisomerization. The calculated UV-Vis spectrum at around 320 nm for open-isomer 1a is bathochromically shifted to 647 nm for closed-isomer 1b, in excellent agreement with the experimental photochromic phenomenon. The electron transition in ECD (electron circular dichroism) spectra for closed-isomer 1b with two chiral carbon atoms is dominated by ICT (intramolecular charge transition) and LE (local excitation) corresponding to one positive (440 nm) and one negative Cotton effect (650 nm), respectively, where the two chiral carbon atoms play a slight role in these transitions. The PES in the S(1) and S(0) states, respectively, indicates that the cyclization reaction from open-isomer 1a to closed-isomer 1b is allowed in the photoexcited state with high-conversion quantum efficiency, while it is forbidden in the thermodynamic process. In addition, the second-order nonlinear optical response for closed-isomer 1b is nearly six times larger than that for open-isomer 1a. It is also confirmed that the photoirradiation evokes the photoisomerization character to show dramatic difference in the second-order NLO response, which can be applied to designing photochromic materials and reversible NLO switches.     

Design of a universal reversible bidirectional current switch based on the fullerene-phthalocyanine supramolecular system

A novel bidirectional current ON-OFF switch controlled by electron injection and deprivation was proposed on the basis of the density functional theory (DFT) calculation over a fullerene-phthalocyanine supramolecular system PcCoC(60) for the first time. The electron density for PcCoC(60) was revealed to move from fullerene to phthlocyanine only in the oxidized form and from phthlocyanine to fullerene only in the reduced form, reaching the control of electron movement direction by changing the oxidation state of this supramolecular system.     

Integrating protein secondary structure prediction and multiple sequence alignment

Modern protein secondary structure prediction methods are based on exploiting evolutionary information contained in multiple sequence alignments. Critical steps in the secondary structure prediction process are (i) the selection of a set of sequences that are homologous to a given query sequence, (ii) the choice of the multiple sequence alignment method, and (iii) the choice of the secondary structure prediction method. Because of the close relationship between these three steps and their critical influence on the prediction results, secondary structure prediction has received increased attention from the bioinformatics community over the last few years. In this treatise, we discuss recent developments in computational methods for protein secondary structure prediction and multiple sequence alignment, focus on the integration of these methods, and provide some recommendations for state-of-the-art secondary structure prediction in practice.     

A distance-controlled oligopeptide linker as a novel photo-induced energy transfer switch by secondary structural transition

By using an oligopeptide chain as a functional linker and introducing coumarin 2 and coumarin 343 at the chain ends, an effective photo-induced energy transfer system was constructed and energy transfer from coumarin 2 to coumarin 343 was switched on and off by a solvent-induced helix-coil secondary transition of the oligopeptide chain.     

Prediction of protein secondary structure content using support vector machine

In this paper, the support vector machine was trained to grasp the relationship between the pair-coupled amino acid composition and the content of protein secondary structural elements, including -helix, 3₁₀-helix, π-helix, β-strand, β-bridge, turn, bend and the rest random coil. Self-consistency and cross validation tests were made to assess the performance of our method. Results superior to or competitive with the popular theoretical and experimental methods have been obtained.     

Prediction of protein secondary structure based on continuous wavelet transform

In this paper, continuous wavelet transform (CWT) is used to extract the number and the relevant positions of the α-helices and short peptides connecting α-helices and β-strands (connecting peptides) from the amino acid sequences of proteins. The amino acid sequence is first mapped into hydrophobicity sequence, and then transformed into CWT value of sequence domain in appropriate scale via CWT. The number and the relevant positions of the α-helices and connecting peptides can be extracted easily and accurately according to the minima of wavelet coefficient in corresponding CWT plot of hydrophobic value sequences with appropriate scale. The analytical results demonstrate that α-helices and connecting peptides can be predicted conveniently and rapidly when this method is used in the processing of 100 non-homologous sequences. However, this method is not suitable for predicting the length of α-helices and connecting peptides.     

Atomic resolution density maps reveal secondary structure dependent differences in electronic distribution

The X-ray crystal structure of the flavoenzyme cholesterol oxidase, SCOA (Streptomyces sp.SA-COO) has been determined to 0.95 A resolution. The large size (55kDa) and the high-resolution diffraction of this protein provides a unique opportunity to observe detailed electronic effects within a protein environment and to obtain a larger sampling for which to analyze these electronic and structural differences. It is well-known through spectroscopic methods that peptide carbonyl groups are polarized in alpha-helices. This electronic characteristic is evident in the sub-Angstrom electron density of SCOA. Our analysis indicates an increased tendency for the electron density of the main chain carbonyl groups within alpha-helices to be polarized toward the oxygen atoms. In contrast, the carbonyl groups in beta-sheet structures tend to exhibit a greater charge density between the carbon and oxygen atoms. Interestingly, the electronic differences observed at the carbonyl groups do not appear to be correlated to the bond distance of the peptide bond or the peptide planarity. This study gives important insight into the electronic effects of alpha-helix dipoles in enzymes and provides experimentally based observations that have not been previously characterized in protein structure.