Protein secondary structure

A secondary structure prediction technique is proposed which includes nucleation site determination through multiplication of conformational preference parameters as well as weighting factors to represent structurally stabilizing short range interactions. The prediction accuracy of the method is calculated using data bases categorized according to the four protein structural classes and with differing assignments of secondary structural regions. The results indicate that nearest neighbor prediction techniques (a) are insensitive to various assignment criteria for the secondary structural spans, (b) have nearly achieved their upper limit of prediction accuracy, and (c) can be somewhat improved through the use of stereochemical weighting factors and conformational parameters derived from the four structural groups.     

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.     

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.     

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.     

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.     

Residue contacts in protein structures and implications for protein folding

The preferential association of amino acid side groups with specific side chain atoms are examined in 44 known protein structures. The resulting association potentials among residue side groups are used to detect structural homology in proteins displaying little or no homology in their primary sequences. Suggestions are also made regarding the nature of the protein folding process. They are based on statistical observations that delineate the extent of short and long range interactions and that display side group bias in association with other side chain atoms on their N-terminal side.     

Prediction of protein secondary structures from their hydrophobic characteristics

Deciphering the native conformation of proteins from their amino acid sequences is one of the greatest challenges in the field of molecular biology. The successful prediction of structural class may help to improve the accuracy levels of structure (secondary and tertiary) predictive schemes in globular proteins. In our earlier works we developed a new surrounding hydrophobicity scale for the 20 amino acid residues applicable for both globular and membrane proteins and used it successfully to predict the transmembrane helical and strand segments in membrane proteins. In this article we propose (i) rules to predict the structural class of proteins and (ii) a new predictive scheme for forecasting secondary structures of globular proteins, with the use of the new hydrophobicity scale. This scheme predicts the structural class and secondary structures of globular proteins to 92 and 82% levels of accuracy, respectively, far better than the levels from other existing methods.     

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.     

细胞色素P450 CYP2E1酶构型特征及其表达调控机制的研究进展

细胞色素P450CYP2E1酶参与代谢活化及失活多种前毒物、前致癌物和少数药物。在细胞色素P450超家族中,CYP2E1具有易介导自由基生成引发氧化应激反应的特征。CYP2E1表达水平可能是机体对环境和工业毒物或致癌物敏感程度的重要因素。研究表明,CYP2E1可被多种内、外源性物质所调控,并且CYP2E1的药理和毒理学功能与其以蛋白构型为基础的代谢行为密切相关。本文综述了CYP2E1基因多态性、酶构型特征与其代谢活性间的关系,并分析了其区别于其他细胞色素P450亚型的表达调控机制。     

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.     

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     

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).     

Structure of secretory protein IV from rat seminal

The complete amino acid sequence of rat SVS-IV protein, consisting of 90 residues, has been determined. The sequence of rat SVS-IV protein is the first seminal vesicle secretory protein determined and it does not show any homology with other known protein sequences. The secondary structure of SVS-IV protein as analyzed by methods of Fasman and Chou indicates that this protein contains 53%α-helix, 36%ß-turn and 11% random coil.     

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.     

SLC26蛋白家族成员功能及意义的研究进展

目前研究发现人类许多疾病与离子通道蛋白相关,故对于离子通道蛋白如何参与人类疾病的发展已成为各大学者的研究热点。 SLC26阴离子通道蛋白家族作为目前一类研究较多的离子通道蛋白,具有成员多、结构功能复杂多样等特点,可作为SO42-转运蛋白、阴离子交换器、阴离子通道蛋白等在组织上的特异性表达来发挥其功能,SLC26阴离子通道蛋白家族的表达及功能受多种机制调节,其家庭成员结构及功能变化与人类先天性营养不良、先天性氯化物腹泻、先天性耳聋及消化道疾病等多种人类疾病相关。本文就SLC26蛋白家族其结构功能、各家族成员及其主要功能、相关调节因素及其与相关疾病的关系等进行综述。     

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%.