共查询到20条相似文献,搜索用时 250 毫秒
1.
Background
β-turn is a secondary protein structure type that plays significant role in protein folding, stability, and molecular recognition. To date, several methods for prediction of β-turns from protein sequences were developed, but they are characterized by relatively poor prediction quality. The novelty of the proposed sequence-based β-turn predictor stems from the usage of a window based information extracted from four predicted three-state secondary structures, which together with a selected set of position specific scoring matrix (PSSM) values serve as an input to the support vector machine (SVM) predictor. 相似文献2.
Protein β-turn classification remains an area of ongoing development in structural biology research. While the commonly used nomenclature defining type I, type II and type IV β-turns was introduced in the 1970s and 1980s, refinements of β-turn type definitions have been introduced as recently as 2019 by Dunbrack, Jr and co-workers who expanded the number of β-turn types to 18 (Shapovalov et al, PLOS Computat. Biol., 15, e1006844, 2019). Based on their analysis of 13 030 turns from 1074 ultrahigh resolution (≤1.2 Å) protein structures, they used a new clustering algorithm to expand the definitions used to classify protein β-turns and introduced a new nomenclature system. We recently encountered a specific problem when classifying β-turns in crystal structures of pentapeptide repeat proteins (PRPs) determined in our lab that are largely composed of β-turns that often lie close to, but just outside of, canonical β-turn regions. To address this problem, we devised a new scheme that merges the Klyne-Prelog stereochemistry nomenclature and definitions with the Ramachandran plot. The resulting Klyne-Prelog-modified Ramachandran plot scheme defines 1296 distinct potential β-turn classifications that cover all possible protein β-turn space with a nomenclature that indicates the stereochemistry of i + 1 and i + 2 backbone dihedral angles. The utility of the new classification scheme was illustrated by re-classification of the β-turns in all known protein structures in the PRP superfamily and further assessed using a database of 16 657 high-resolution protein structures (≤1.5 Å) from which 522 776 β-turns were identified and classified. 相似文献
3.
Philip B Wedegaertner 《BMC cell biology》2002,3(1):12-11
Background
Alternative mRNA splicing of αi2, a heterotrimeric G protein α subunit, has been shown to produce an additional protein, termed sαi2. In the sαi2 splice variant, 35 novel amino acids replace the normal C-terminal 24 amino acids of αi2. Whereas αi2 is found predominantly at cellular plasma membranes, sαi2 has been localized to intracellular Golgi membranes, and the unique 35 amino acids of sαi2 have been suggested to constitute a specific targeting signal. 相似文献4.
José Luis Baeza M. Ángeles Bonache M. Teresa García-López Rosario González-Muñiz Mercedes Martín-Martínez 《Amino acids》2010,39(5):1299-1307
Conveniently substituted 2-alkyl-2-carboxyazetidine amino acids have been incorporated into NGF and NT3 tetrapeptide sequences
to investigate their utility as reverse turn inducers (γ- vs. β-turns). Despite the presence of an Asp residue at i position, highly preferred in β-turns, molecular modeling and NMR studies indicated that the azetidine-containing peptides
mainly stabilized γ-turn conformations. 相似文献
5.
Background
Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are αβ-motifs, asx-motifs, asx-turns, β-bulges, β-bulge loops, β-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns. 相似文献6.
Anette Schreiber Peter Schramm Hans-Jörg Hofmann 《Journal of molecular modeling》2011,17(6):1393-1400
The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employing the methods of ab initio MO theory in vacuum (HF/6-31G*, B3LYP/6-311?+?G*) and in solution (CPCM/HF/6-31G*). Only few α-turn structures with glycine and alanine backbones fulfill the geometry criteria for the i←(i?+?4) hydrogen bond satisfactorily. The most stable representatives agree with structures found in the Protein Data Bank. There is a general tendency to form additional hydrogen bonds for smaller pseudocycles corresponding to β- and γ-turns with better hydrogen bond geometries. Sometimes, this competition weakens or even destroys the i←(i?+?4) hydrogen bond leading to very stable double β-turn structures. This is also the reason why an “ideal” α-turn with three central amino acids having the perfect backbone angle values of an α-helix could not be localized. There are numerous hints for stable α-turns with a distance between the \( {{\hbox{C}}_\alpha } \)-atoms of the first and fifth amino acid smaller than 6-7 Å, but without an i←(i?+?4) hydrogen bond. 相似文献
7.
Zehui Tang Tonghua Li Rida Liu Wenwei Xiong Jiangming Sun Yaojuan Zhu Guanyan Chen 《BMC bioinformatics》2011,12(1):283
8.
Leitgeb B Kerényi A Bogár F Paragi G Penke B Rákhely G 《Journal of molecular modeling》2007,13(11):1141-1150
Poly-(Ala) and poly-(Gln) peptides have important biological effects, and can cause various human illnesses and neurodegenerative
diseases. Conformational analysis of these homo-oligopeptides (HOPs) was carried out by simulated annealing in order to identify
their structural properties regarding secondary structures and intramolecular H-bonding patterns. Poly-(Ala) and poly-(Gln)
peptides composed of 7, 10, 14 or 20 amino acids were modelled in both charged and terminally blocked forms. In the case of
conformers derived from simulated annealing calculations, the presence of various secondary structural elements (different
types of β-turns, α-helix, 310-helix, poly-proline II helix, parallel and antiparallel β-strands) was investigated. Moreover, the intramolecular H-bonding
patterns formed either between the backbone atoms for both HOPs or between the backbone and side-chain atoms for the poly-(Gln)
peptides were examined. Our results showed that different secondary structural elements (type I and type III β-turns, α-helix,
310-helix, antiparallel β-strand) could be observed in both poly-(Ala) and poly-(Gln) peptides and, according to their presence,
characteristic H-bonding patterns formed mainly by i←i+3 and i←i+4 H-bonds could be found. 相似文献
9.
Circular dichroism spectra of proteins are extremely sensitive to secondary structure. Nevertheless, circular dichroism spectra
should not be analyzed for protein secondary structure unless they are measured to at least 184 nm. Even if all the various
types ofβ-turns are lumped together, there are at least 5 different types of secondary structure in a protein (α-helix, antiparallelβ-sheet, parallelβ-sheet,β-turn, and other structures not included in the first 4 categories). It is not possible to solve for these 5 parameters unless
there are 5 equations. Singular value decomposition can be used to show that circular dichroism spectra of proteins measured
to 200 nm contain only 2 pieces of information, while spectra measured to 190 nm contain about 4. Adding the constraint that
the sum of secondary structures must equal 1 provides another piece of information, but even with this constraint, spectra
measured to 190 nm simply do not analyze well for the 5 unknowns in secondary structure. Spectra measured to 184 nm do contain
5 pieces of information and we have used such spectra successfully to analyze a variety of proteins for their component secondary
structures. 相似文献
10.
Background
The basal metabolic rate (BMR) of a mammal of mass M is commonly described by the power function αM β where α and β are constants determined by linear regression of the logarithm of BMR on the logarithm of M (i. e., β is the slope and α is the intercept in regression analysis). Since Kleiber's demonstration that, for 13 measurements of BMR, the logarithm of BMR is closely approximated by a straight line with slope 0.75, it has often been assumed that the value of β is exactly 3/4 (Kleiber's law). 相似文献11.
Nobue Shishioh-Ikejima Tokiko Ogawa Kouzi Yamaguti Yasuyoshi Watanabe Hirohiko Kuratsune Hiroshi Kiyama 《BMC neurology》2010,10(1):73
Background
Despite extensive research, no reliable biological marker for chronic fatigue syndrome (CFS) has yet been identified. However, hyperactivation of melanotrophs in the pituitary gland and increased levels of plasma alpha-melanocyte-stimulating hormone (α-MSH) have recently been detected in an animal model of chronic stress. Because CFS is considered to be caused partly by chronic stress events, increased α-MSH plasma levels may also occur in CFS patients. We therefore examined α-MSH levels in CFS patients. 相似文献12.
Background
β-turns are secondary structure elements usually classified as coil. Their prediction is important, because of their role in protein folding and their frequent occurrence in protein chains. 相似文献13.
Ai-Hua Jin Hemma Brandstaetter Simon T Nevin Chia Chia Tan Richard J Clark David J Adams Paul F Alewood David J Craik Norelle L Daly 《BMC structural biology》2007,7(1):28
Background
α-Conotoxins have exciting therapeutic potential based on their high selectivity and affinity for nicotinic acetylcholine receptors. The spacing between the cysteine residues in α-conotoxins is variable, leading to the classification of sub-families. BuIA is the only α-conotoxin containing a 4/4 cysteine spacing and thus it is of significant interest to examine the structure of this conotoxin. 相似文献14.
Numerous methods for predicting γ-turns in proteins have been developed. However, the results they generally provided are
not very good, with a Matthews correlation coefficient (MCC) ≤0.18. Here, an attempt has been made to develop a method to
improve the accuracy of γ-turn prediction. First, we employ the geometric mean metric as optimal criterion to evaluate the
performance of support vector machine for the highly imbalanced γ-turn dataset. This metric tries to maximize both the sensitivity
and the specificity while keeping them balanced. Second, a predictor to generate protein shape string by structure alignment
against the protein structure database has been designed and the predicted shape string is introduced as new variable for
γ-turn prediction. Based on this perception, we have developed a new method for γ-turn prediction. After training and testing
the benchmark dataset of 320 non-homologous protein chains using a fivefold cross-validation technique, the present method
achieves excellent performance. The overall prediction accuracy Q
total can achieve 92.2% and the MCC is 0.38, which outperform the existing γ-turn prediction methods. Our results indicate that
the protein shape string is useful for predicting protein tight turns and it is reasonable to use the dihedral angle information
as a variable for machine learning to predict protein folding. The dataset used in this work and the software to generate
predicted shape string from structure database can be obtained from anonymous ftp site freely. 相似文献
15.
Jasmin Kirchner Emese Vissi Sascha Gross Balazs Szoor Andrey Rudenko Luke Alphey Helen White-Cooper 《BMC molecular biology》2008,9(1):36
Background
Protein phosphatase 1 (PP1) is involved in diverse cellular processes, and is targeted to substrates via interaction with many different protein binding partners. PP1 catalytic subunits (PP1c) fall into PP1α and PP1β subfamilies based on sequence analysis, however very few PP1c binding proteins have been demonstrated to discriminate between PP1α and PP1β. 相似文献16.
Background
Despite the importance of β -strands as main building blocks in proteins, the propensity of amino acid in β -strands is not well-understood as it has been more difficult to determine experimentally compared to α -helices. Recent studies have shown that most of the amino acids have significantly high or low propensity towards both ends of β -strands. However, a comprehensive analysis of the sequence dependent amino acid propensities at positions between the ends of the β -strand has not been investigated. 相似文献17.
Fiona C Gray J Richard G Pohler Emma Warbrick Stuart A MacNeill 《BMC molecular biology》2004,5(1):21-16
Background
DNA polymerases α and δ play essential roles in the replication of chromosomal DNA in eukaryotic cells. DNA polymerase α (Pol α)-primase is required to prime synthesis of the leading strand and each Okazaki fragment on the lagging strand, whereas DNA polymerase δ (Pol δ) is required for the elongation stages of replication, a function it appears capable of performing on both leading and lagging strands, at least in the absence of DNA polymerase ε (Pol ε). 相似文献18.
B David Silverman 《BMC structural biology》2007,7(1):77
Background
Comparison of different protein x-ray structures has previously been made in a number of different ways; for example, by visual examination, by differences in the locations of secondary structures, by explicit superposition of structural elements, e.g. α-carbon atom locations, or by procedures that utilize a common symmetry element or geometrical feature of the structures to be compared. 相似文献19.
Joshua B Kelley Ashley M Talley Adam Spencer Daniel Gioeli Bryce M Paschal 《BMC cell biology》2010,11(1):63
Background
Classical nuclear localization signal (NLS) dependent nuclear import is carried out by a heterodimer of importin α and importin β. NLS cargo is recognized by importin α, which is bound by importin β. Importin β mediates translocation of the complex through the central channel of the nuclear pore, and upon reaching the nucleus, RanGTP binding to importin β triggers disassembly of the complex. To date, six importin α family members, encoded by separate genes, have been described in humans. 相似文献20.
Takakazu Oka Yoko Tamagawa Sota Hayashida Yuko Kaneda Naoki Kodama Sadatoshi Tsuji 《BioPsychoSocial medicine》2007,1(1):1-6