Computerised version of the Chou and Fasman protein secondary structure predictive method

A DEC-SYSTEM 10 FORTRAN computer program to carry out secondary structure prediction of proteins, according to the algorithm of Chou & Fasman (1, 2), is described. Program results are compared with predictions made by Chou & Fasman.     

Generating plausible protein folds by secondary structure similarity

We extend a standard method of comparing protein sequences to develop a method for quantitatively comparing the secondary structures of two proteins and finding the best alignment between them. We introduce a new approach to generating a set of plausible folds for a protein given only an assigned secondary structure (a query) and use this secondary structure comparison method to search the set of proteins with known tertiary structures for an array of secondary structure elements similar to the query. A large fraction of the similar arrays found in known proteins have folds that can be taken as candidate folds for the query. The approach is analogous to “protein extension” based on primary structure. We show, for example, how the method can produce plausible folds for the secondary structure of flavodoxin, including the correct one.     

Secondary structure prediction of 11 mammalian growth hormones

The secondary structure of 11 mammalian growth hormones has been predicted by combining five different methods. Three long helical regions located around residues 20, 120, and 170 constitute the most prominent common feature in the species studied. The strong amphiphilic character of these helices suggests that they can play an important role in protein folding or stability.     

Are secondary structures secondary?

Crystallographically observed secondary structures in globular proteins are divided into two categories based on calculated potential values for these structures. Type I secondary structures are those which have maximum potential in observed structural state. These type I structures consist of those amino acids which intrinsically prefer that structural state. On the other hand type II secondary structures have a calculated potential value which is not maximum for the observed state. Type II structures are composed of those amino acid residues which do not intrinsically prefer the observed state and thus seem to have been formed due to tertiary interactions. All the observed secondary structures have been identified as type I or type II in 31 different globular proteins considered. It is suggested that type II structures are formed at a latter stage of protein folding mainly due to favourable tertiary interactions.     

Secondary structure prediction and determination of proteins — a review

The rapid increase in sequence data in combination with a greater understanding of the forces regulating protein structure has been the impetus for an upsurge in the development of theoretical prediction methods. These methods have afforded protein chemists the ability to identify and quantify the various secondary structures along the protein chain. Concurrently, various physico-chemical techniques have been developed such as nuclear Overhauser enhancement n.m.r. and laser Raman spectroscopy. In addition, traditional methods such as infrared and circular dichroism spectroscopy have been refined. Although both predictive and physico-chemical techniques are limited in the types of secondary structure they are capable of determining, they have provided valuable information with regards to protein folding and topology in the absence of X-ray data, and have formed the basis for the development of improved methods for secondary structure determination. This paper reviews some of the predictive and physico-chemical methods presently used to determine protein secondary structure.     

Interaction with model membrane systems induces secondary structure in amino-terminal fragments of parathyroid hormone related protein

The secondary structure of amino terminal fragments of human parathyroid hormone related protein (PTHrP) in aqueous solution, in trifluoroethanol solution and in the presence of model membrane systems has been studied by circular dichroism (CD) spectroscopy. Far-UV CD spectra of PTHrP 1–40, 1–34 amide, 7–34 amide and 1–16 are consistent with a predominantly unordered structure. Addition of trifluoroethanol stabilized α-helical structure in the 1–34 amide and 7–34 amide peptides. The effect reached a plateau at a trifluoroethanol concentration of approximately 40%, and a helix content of some 23 residues was determined. PTHrP 1–34 amide interacted with palmitoyloleoylphosphatidyl serine vesicles and exhibited an increased α-helix content of approximately 12 helical residues. Similar results were observed for monomyristoyllecithin micelles and sodium dodecyl sulfate micelles. No interaction with dimyristoylphosphatidylcholine vesicles was detected by CD. The ability to bind to palmitoyloleoylphosphotidyl serine vesicles was also a feature of the 1–40 and 7–34 fragments, while the 1–16 fragment was apparently unaffected by interaction with this model membrane system. These results indicate that the conformational properties of the functionally significant amino terminal 1–34 region of PTHrP parallel those reported for the corresponding, but largely nonhomologous, region of parathyroid hormone. Conformational similarities may account for the ability of PTHrP to mimic the functional properties of parathyroid hormone.     

Myoglobin structure and regulation of solvent accessibility of heme pocket

The effects of heme removal on the molecular structure of tuna and sperm whale myoglobin have been investigated by comparing the solvent accessibility to the heme pocket of the two proteins with that of the corresponding apoproteins. Although the heme microenvironment of tuna myoglobin is more polar than that of sperm whale myoglobin, the accessibility of solvent to heme is identical in the two proteins as revealed by thermal perturbation of Soret absorption. The removal of heme produces loss of helical folding and increase of solvent accessibility but the effects are rather different for the two proteins. More precisely, the loss of helical structure upon heme removal is 50% for tuna myoglobin and 15% for sperm whale myoglobin; moreover, the solvent accessibility of the heme pocket of tuna apomyoglobin is 2–3-fold greater than that of sperm whale apomyoglobin. These results have been explained in terms of the lack of helical folding in segment D, the structural organization of which may have a relevant effect in regulating the accessibility of ligands to the heme. The effects produced by charged quenchers reveal that the ligand path from the surface of the molecule to the ion atom of the heme involves a positively charged residue which may reasonably be identified as Arg-45 (sperm whale myoglobin) or Lys-41 (tuna myoglobin) on the basis of recent X-ray crystallographic information.     

基于结构分类的BP神经网络预测蛋白质二级结构

提出一种基于结构分类的BP神经网络系统，用于蛋白质二级结构的预测。与其他方法相比较，该法可以显著提高预测率，平均预测率为71．12％，最高预测率可达78．27％。     

Disulfide pairing and secondary structure of ASP1, an olfactory‐binding protein from honeybee (Apis mellifera L)

Abstract: In insects, the transport of airborne, hydrophobic odorants and pheromones through the sensillum lymph is accomplished by olfactory‐binding proteins (OBPs). We report the structural characterization of a honeybee OBP called ASP1 found in workers and drones, previously observed to bind queen pheromone components. A novel method based on ion‐spray mass spectrometry analysis of cyanylation‐induced cleavage products of partially reduced protein with Tris(2‐carboxyethyl)phosphine was needed to determine the recombinant ASP1 disulfide bond pairing. It was observed to be Cys(I)‐Cys(III), Cys(II)‐Cys(V), Cys(IV)‐Cys(VI), similar to those already described for other OBPs from honeybee and Bombyx mori suggesting that this pattern occurs commonly throughout the diverse family of insect OBPs. Circular dichroism revealed that ASP1 is an all‐alpha protein in accordance with NMR preliminary data, but unlike lipocalin‐like vertebrate OBPs.     

曲克芦丁对牛血清白蛋白溶液二级结构影响的研究

目的:采用红外光谱研究曲克芦丁对牛血清白蛋白溶液二级结构的影响。方法:利用红外差谱([蛋白质+药物溶液]-[药物溶液])来研究反应前后蛋白质酰胺带的变化。结果:蛋白质与药物作用后蛋白质分子发生了由螺旋结构向折叠结构的转变。结合蛋白质酰胺Ⅰ带的拟合结果对酰胺Ⅲ带各二级结构的谱峰进行了初步指认:1330~1290 cm-1为α-螺旋;1290~1270 cm-1为β-转角;1270~1250 cm-1为无规则卷曲;1250~1220 cm-1为β-折叠。结论:运用红外光谱的方法研究曲克芦丁和蛋白质的相互作用,为研究其他蛋白质与中药有效成分的相互作用提供一种新的实验方法。     

Predicted secondary structure of bovine prothrombin fragment 1 and related proteins in different environments by circular dichroism spectroscopy

Circular dichroism spectroscopy was used to investigate the structure of bovine prothrombin fragment 1 (BF1) and related proteins in several environments. The conformational change induced in BF1 by the addition of Mg[II] ions was found to be different from that induced by Ca[II] or Sr[II]. The Ca[II] and Sr[II] conformations appear to differ only slightly from the apo-metal conformation. The conformation of the 1–45 fragment of prothrombin, however, is markedly different than the conformation of the same fragment in the presence of either Ca[II] of Mg[II]; both of the latter structures differ substantially from one another. The presence of phospholipids has almost no effect on the structure of either BF1 or the 1–45 fragment; in the presence of both phospholipids and Ca[II] a structural change is seen for the 1–45 fragment but not BF1 (relative to the protein alone). The addition of phospholipids to the Mg[II]/BFl structure did not induce a CD-detectable conformational change, while the addition of phospholipids to the Ca[II]/BFl or Sr[II]/BFl structures induced a change to a conformation similar in secondary structure composition to the relative apometal structures.     

Influence of secondary structure of polyglycine on some conformational properties

Values of four conformational properties, namely unperturbed dimension < r²>₀, dipole moment < μ² >, mean squared optical anisotropy < γ² >, and molar Kerr constant < _mK >, have been calculated for polyglycine chains allowing several combinations of the secondary structure with the aim of studying the dependence of these magnitudes on the secondary structure of the chain. Two different approaches to the secondary structure have been used. In the first, chains with all their units in a given conformation (random coil, α-helix or β-sheet) are interrupted at several positions by one unit in a different conformation. In the second, chains with varying composition of two conformations α-helix/β-sheet and β-sheet/random coil were allowed and the results obtained compared with previous work for α-helix/random coil chains.     

Long-Term and High-Temperature Storage of Supercritically-Processed Microparticulate Protein Powders

Purpose. The long-term and high-temperature storage of dry, micron-sized particles of lysozyme, trypsin, and insulin was investigated. Subsequent to using supercritical carbon dioxide as an antisolvent to induce their precipitation from a dimethylsulfoxide solution, protein microparticles were stored in sealed containers at -25, -15, 0, 3, 20, 22, and 60°C. The purpose of this study was to investigate the suitability of supercritical antisolvent precipitation as a finishing step in protein processing. Methods. Karl Fisher titrations were used to determine the residual moisture content of commercial and supercritically-processed protein powders. The secondary structure of the dry protein particles was determined periodically during storage using Raman spectroscopy. The proteins were also redissolved periodically in aqueous buffers and assayed spectrophotometrically for biological activity and by circular dichroism for structural conformation in solution. Results. Amide I band Raman spectra indicate that the secondary structure of the protein particles, while perturbed from that of the solution state, remained constant in time, regardless of the storage temperature. The recoverable biological activity upon reconstitution for the supercritically-processed lysozyme and trypsin microparticles was also preserved and found to be independent of storage temperature. Far UV circular dichroism spectra support the bioactivity assays and further suggest that adverse structural changes, with potential to hinder renaturation upon redissolution, do not take place during storage. Conclusions. The present study suggests that protein precipitation using supercritical fluids may yield particles suitable for long-term storage at ambient conditions.     

Sequence-dependence of secondary structure formation II*

The conformational influence of the insertion of two guest amino acids into a homooligopeptide consisting of L-Val residues was investigated by circular dichroism and infrared spectroscopy. L-Ala, L-Ile and L-Leu were chosen as guest amino acids and their β-structure disrupting properties studied with respect to size and symmetry of their side-chains. These studies were complemented by investigations concerning the aggregation behaviour of the various peptides by means of gel permeation chromatography. It is shown that the tendency of the various peptides to form β-structures and to aggregate increases with increasing similarity in the spatial size of the side-chains between guest and host amino acids. The impact of those results on the prediction of peptide secondary structure as well as their importance for peptide synthesis is briefly discussed.     

Secondary structure prediction of seed storage proteins

The comparison of partial primary structure of seed storage proteins leads to show homologies inside of each considered family (Legume seed legumins and cereal prolamins). Predicted secondary structures deduced from the presently known sequences also exhibit considerable homologies, which implies a severe conservatism of these proteins. Short repetitive segments of sequence of 5–20 residues are frequently occurring and give rise to the prediction either of β-structure (or α-helix) bonded by β-turns or of successive β-turns. The latter conformation, which would be able to form a helicoidal arrangement, could contribute to a maximal packing of the protein molecules inside of the subcellular organelles (protein bodies) within which they are confined. As the only known function of seed storage proteins is to provide amino acids to the embryo, it is suggested that their ability to occupy a minimal volume is actually a reasonable explanation of their extreme conservatism in the course of evolution.     

反义药物作用中的“靶二级结构域”

目的　在计算机模拟mRNA二级结构与定量构效关系分析的基础上优化反义药物设计。方法　使用软件RNAstructure模拟mRNA二级结构,针对二级结构单元进行反义药物设计,用肺腺癌细胞株A5 49评价反义药物的体外抗肿瘤生物活性,用软件SPSS进行多元回归分析。结果　有效药物作用靶点相对集中地分布于由若干二级结构单元组成的局部二级结构区域。我们称之为“靶二级结构域(靶域)”。“靶域”结构相对稳定,但其中包含不稳定二级结构单元(ΔG°>0 )。针对不同“靶域”设计的反义药物显示不同的生物活性(P<0.01) ,但靶向同一“靶域”的反义药物生物活性无统计差别。结论　“靶域”现象有助于反义药物靶点的选择,并对探针、引物设计及mRNA局部功能的研究具有重要意义     

膜蛋白数据库介绍

在整个蛋白质家族中膜蛋白的结构和功能的特殊性,使得跨膜蛋白拓扑结构预测已成为生物信息学的研究热点之一.而在用生物信息学方法对膜蛋白结构功能进行研究的过程中,一种优秀的跨膜区计算方法直接影响到数据库的准确性和完整性,因此,文章对比了几个现有的膜蛋白数据库,并选择其中较为优秀的数据库PDB_TM,对它和相关算法及其应用前景进行了比较详细的阐述,这不仅为我们自己构建跨膜区预测方法提供了很好的启迪,而且对我们构建生物信息资源数据库提供很好的指导思想.     

Identification of secondary structures in globular proteins - a new algorithm*

A new algorithm has been developed for identifying helices, extended structures, and bends from the positions of the α-carbon atoms using the virtual bond approach. The parameters used are two virtual bond angles (Δ₁ and Δ₂), the virtual dihedral angle (θ), and the distance (D) between the terminal α-carbon atoms of the tripeptide. The criteria for classification have been worked out by model building as well as from proteins whose complete secondary structures are known. These criteria are as follows: (i) |θ| ≤ 60° and (Δ₁+Δ₂) ≤ 230° for a bend, (ii) for a helix, successive θ's should not differ by more than 30°, and (iii) for an extended structure, the cumulative deviation of the above parameters should not vary by more than 20% from the ideal extended chain. The method developed has been applied successfully to three proteins wherein the coordinates of α-carbon atoms alone are known and a complete mapping of the secondary structures has now been obtained. One interesting observation is that the percentage of residues not taking part in helices, extended structures, and bends is very small - of the order of 4%.     

基于人工智能的蛋白质属性预测的潜能与应用

蛋白质作为生命系统的核心构成要素,其结构和功能的精准理解对揭示生物学过程及药物开发至关重要。随着人工智能技术的飞速发展,其在蛋白质工程领域的应用,特别是在蛋白质属性预测方面,已成为研究的热点。综述简介了生物医学工程领域的最新动态,突出了人工智能技术在蛋白质工程中的重要作用,并着重讨论了人工智能在蛋白质属性预测方面取得的创新性成果,及其在此领域的应用潜力与面临挑战。     

Effect of freeze-drying,cryoprotectants and storage conditions on the stability of secondary structure of insulin-loaded solid lipid nanoparticles

This study aims to monitor the secondary structure behaviour of insulin when it is encapsulated into solid lipid nanoparticles (SLN), under the influence of several critical processing parameters. Insulin was used as a therapeutic protein model. Physicochemical properties of insulin-loaded SLN (Ins-SLN) were assessed, with special focus on the insulin secondary structure after its encapsulation into SLN and after freeze-drying using different cryoprotectants (glucose, fructose and sorbitol). Additionally, a 6-month stability study was performed to evaluate the maintenance of insulin secondary structure over time at different storage conditions (4 °C/60% RH, 25 °C/60% RH, 40 °C/75% RH).