Abstract:
:Protein 3D structures support their biological functions. As the number of protein structures is negligible in regards to the number of available protein sequences, prediction methodologies relying only on protein sequences are essential tools. In this field, protein secondary structure prediction (PSSPs) is a mature area, and is considered to have reached a plateau. Nonetheless, proteins are highly dynamical macromolecules, a property that could impact the PSSP methods. Indeed, in a previous study, the stability of local protein conformations was evaluated demonstrating that some regions easily changed to another type of secondary structure. The protein sequences of this dataset were used by PSSPs and their results compared to molecular dynamics to investigate their potential impact on the quality of the secondary structure prediction. Interestingly, a direct link is observed between the quality of the prediction and the stability of the assignment to the secondary structure state. The more stable a local protein conformation is, the better the prediction will be. The secondary structure assignment not taken from the crystallized structures but from the conformations observed during the dynamics slightly increase the quality of the secondary structure prediction. These results show that evaluation of PSSPs can be done differently, but also that the notion of dynamics can be included in development of PSSPs and other approaches such as de novo approaches.
journal_name
Biochimiejournal_title
Biochimieauthors
de Brevern AGdoi
10.1016/j.biochi.2020.09.006subject
Has Abstractpub_date
2020-12-01 00:00:00pages
14-22eissn
0300-9084issn
1638-6183pii
S0300-9084(20)30213-3journal_volume
179pub_type
杂志文章相关文献
BIOCHIMIE文献大全abstract::Over the last couple of decades, the PPAR family of transcription factors has received much attention from the pharmaceutical industry due to their profound ability to improve glucose and lipid metabolism upon agonist activation. However, more recently the interest in these nuclear receptors has faded because several ...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/j.biochi.2016.10.017
更新日期:2017-05-01 00:00:00
abstract::Three mutanase (alpha-1,3-glucanase)-producing microorganisms isolated from soil samples were identified as a relatives of Paenibacillus. A mutanase was purified to homogeneity from cultures of each, and the molecular masses of the purified enzymes were approximately 132, 141, and 141kDa, respectively. The correspondi...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/j.biochi.2007.09.018
更新日期:2008-03-01 00:00:00
abstract::High plasma choline has been associated with the metabolic syndrome and risk of chronic diseases, including cardiovascular disease. However, dietary choline is not correlated with choline plasma concentrations, and there are few studies and contradictory evidence regarding dietary choline and cardiovascular events. In...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/j.biochi.2019.11.001
更新日期:2020-06-01 00:00:00
abstract::Honeybee-plant relationships are based on a conditioning process in which olfactory (plant aroma) and gustatory cues (mainly nectars) are closely linked, leading to a selective foraging behaviour. Among crops dependent upon entomophilous cross-pollination, the sunflower has recently undergone extensive expansion due t...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/0300-9084(87)90186-6
更新日期:1987-06-01 00:00:00
abstract::The development of in vitro repair assays with human cell-free extracts led to new insights on the mechanism of excision of DNA damage which consists of incision/excision and repair synthesis/ligation. We have adapted the repair synthesis reaction with cells extracts incubated with damaged plasmid DNA performed in liq...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/s0300-9084(99)80038-8
更新日期:1999-01-01 00:00:00
abstract::Since the initial identification of leptin as the product of the ob gene in 1994, the signaling pathways by which this hormone alters cell physiology have been the subject of extensive investigations. The fact that leptin can induce nitric oxide (NO) production was first demonstrated in studies of the pituitary gland ...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/j.biochi.2012.06.017
更新日期:2012-10-01 00:00:00
abstract::Bacterial type II fatty acid synthesis (FASII) is a target for novel antibiotic development. All bacteria encode for mechanisms to incorporate exogenous fatty acids, and some bacteria can use exogenous fatty acids to bypass FASII inhibition. Bacteria encode three different mechanisms for activating exogenous fatty aci...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/j.biochi.2017.06.015
更新日期:2017-10-01 00:00:00
abstract::Calcium-independent receptor of alpha-latrotoxin (CIRL-1) is an adhesion G protein-coupled receptor implicated in the regulation of exocytosis. CIRL-1 biosynthesis involves constitutive proteolytic processing that takes place in the endoplasmic reticulum, requires the receptor's GPS domain, and yields heterologous two...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/j.biochi.2010.01.015
更新日期:2010-04-01 00:00:00
abstract::The effects on intra- and extracellular pH of two polyenic derivatives of amphotericin B, N-fructosyl amphotericin B and N-fructosyl amphotericin B methyl-ester, were tested on HL-60 promyelocytic leukemia cells. Both derivatives raised the internal pH and reduced the external pH in weakly buffered medium. These resul...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/0300-9084(89)90133-8
更新日期:1989-01-01 00:00:00
abstract::We describe PGtrans, a new and freely available protein sequence databank (2625 sequences, 554198 amino-acids). This data bank is routinely produced by automatic computer translation of the nucleotide sequence library GenBank. The information needed for the translation process (transcriptional orientation, location of...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/s0300-9084(85)80261-3
更新日期:1985-05-01 00:00:00
abstract::Adipose tissue is an endocrine organ that plays an essential role in regulating several metabolic functions through the secretion of biological mediators called "adipokines". Dysregulation of adipokines plays a crucial role in obesity-related diseases. Adiponectin (APN) is the most abundant adipokine accounting for th...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/j.biochi.2012.06.030
更新日期:2012-10-01 00:00:00
abstract::Ligation of CD47 by its natural ligand thrombospondin (TSP), or cross-linking by CD47 antibodies, triggers caspase-independent cell death in normal and leukemic cells. This kind of cell death is characterised by the cytoplasmic events of apoptosis including externalisation of phosphatidylserines and mitochondria swell...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/s0300-9084(03)00129-9
更新日期:2003-08-01 00:00:00
abstract::The 11 kb las locus, present on the 50 kb plasmid pCIM1, specifies the production of the lantibiotic lactocin S in Lactobacillus sakei L45. The gene cluster is organized into two oppositely orientated operons, lasAMNTUVPJW (lasA-W) and lasXY, the former of which contains the biosynthetic, immunity and transport genes....
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/s0300-9084(02)01420-7
更新日期:2002-05-01 00:00:00
abstract::In recent years an increasing number of inherited decreases in man has been identified in which there is an impairment of one or more peroxisomal functions. Sofar 15 different peroxisomal disorders have been identified which can be subdivided into three distinct groups depending upon whether there is a generalized (gr...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/0300-9084(93)90087-9
更新日期:1993-01-01 00:00:00
abstract::Intracellular cytoplasmic peptidoglycan (PG) intermediate levels were determined in Staphylococcus aureus during log-phase growth in enriched media. Levels of UDP-linked intermediates were quantitatively determined using ion pairing LC-MS/MS in negative mode, and amine intermediates were quantitatively determined ster...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/j.biochi.2015.11.017
更新日期:2016-02-01 00:00:00
abstract::We have analysed the complete sequence of the Escherichia coli K12 isolate MG1655 genome for chromatin-associated protein binding sites, and compared the predicted location of predicted sites with experimental expression data from 'DNA chip' experiments. Of the dozen proteins associated with chromatin in E. coli, only...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/s0300-9084(00)01225-6
更新日期:2001-02-01 00:00:00
abstract::The functions of residues 57-RY-58, G60, L77, 80-GSGR-83, I101, T104, 134-GY-135, N155, V157 and 160-LV-161 in human arsenic (III) methyltransferase (hAS3MT) 5 Å around S-adenosylmethionine (SAM) have not been studied. Herein, sixteen mutants were designed by substituting these residues with Ala. Mutants G60A, G80A, I...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/j.biochi.2014.10.014
更新日期:2014-12-01 00:00:00
abstract::TP53 is mutated in most types of human cancers and is one of the most popular genes in cancer research. The p53 protein is a sensor of multiple forms of genotoxic, oncogenic and non-genotoxic stress. It suppresses growth and controls survival of stressed cells, and as such, is the focal point of selection pressures in...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/s0300-9084(01)01356-6
更新日期:2002-01-01 00:00:00
abstract::In around 10% of SARS-CoV-2 infected patients, coronavirus disease-2019 (Covid-19) symptoms are complicated with a severe lung damage called Acute Respiratory Distress Syndrome (ARDS), which is often lethal. ARDS is mainly associated with an uncontrolled overproduction of immune cells and cytokines, called "cytokine s...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/j.biochi.2020.09.003
更新日期:2020-12-01 00:00:00
abstract::Alteration of the epigenome is associated with a wide range of human diseases. Therefore, deciphering the pathways that regulate the epigenetic modulation of gene expression is a major milestone for the understanding of diverse biological mechanisms and subsequently human pathologies. Although often evoked, little is ...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/j.biochi.2007.07.022
更新日期:2008-01-01 00:00:00
abstract::The vasoactive hormone bradykinin, its N-and C-terminal fragments and some structural analogues were studied by Circular Dichroism. Conformational features of the peptide can be detected by comparative analysis of the various CD spectra recorded as a function of aqueous pH, solvent and temperature. It is shown that th...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/s0300-9084(79)80316-8
更新日期:1979-01-01 00:00:00
abstract::mRNAs extracted from human pheochromocytoma were translated in vitro in a lysate of a rabbit reticulocytes. Two enzymes of the biosynthetic pathway of the catecholamines, tyrosine-hydroxylase (TH) and dopamine-beta-hydroxylase (DBH), were characterized as translation products after immunoprecipitation by specific anti...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/s0300-9084(85)80198-x
更新日期:1985-06-01 00:00:00
abstract::The mitochondria have arisen as a consequence of endosymbiosis of an ancestral α-proteobacterium with a methane-producing archae. The main function of the canonical aerobic mitochondria include ATP generation via oxidative phosphorylation, heme and phospholipid synthesis, calcium homeostasis, programmed cell death, an...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/j.biochi.2013.11.018
更新日期:2014-05-01 00:00:00
abstract::A variety of species of GPDH undergo acylation at two of the four active cystein sites per mole of tetrameric enzyme. This reaction requires tightly bound NAD+, a situation restricted to two of the four NAD sites per tetramer. S leads to N acyl transfer from cysteins to lysine in the diacyl enzyme yields an inactive e...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/s0300-9084(81)80177-0
更新日期:1981-02-01 00:00:00
abstract::The bovine oxytocin precursor was expressed in Escherichia coli as a fusion protein by cloning the hormone encoding cDNA in frame behind the replicase gene of the RNA phage MS2. By step-wise extraction with different urea concentrations, the fusion protein was enriched in the 7 M urea fraction and further purified by ...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/0300-9084(88)90165-4
更新日期:1988-01-01 00:00:00
abstract::Since discovery of high-temperature superconductive (HTS) ceramics by Bednorz and Muller in 1986, there has been an accelerated development of cold technologies in industry, including the domain of NMR detection. The purpose of this paper is to fix ideas about the stage that cryogenic radio frequency (RF) probe techni...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/j.biochi.2003.09.016
更新日期:2003-09-01 00:00:00
abstract::Nitrogen fixation in A. vinelandii and R. leguminosarum bacteroides shows identical characteristics with respect to the dependence on membrane energization, the sensitivity to uncouplers, the ATP/ADP-ratio, and the dependences on flavodoxinhydroquinone as electrondonor. Although we have been successful in preparing in...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/s0300-9084(78)80820-7
更新日期:1978-01-01 00:00:00
abstract::After 30 years of effort, the mammalian adenylate cyclase catalytic subunit has now been purified. It is a glycoprotein of 155 kDa, representing less than 0.01% of synaptosomal membrane protein. As measured in the presence of forskolin, its specific activity is 10-20 mumol of cAMP X mg-1 X min-1. The enzyme obtained i...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/0300-9084(87)90016-2
更新日期:1987-04-01 00:00:00
abstract::An alkaline aminopeptidase was isolated from the culture medium of Penicillium roqueforti. The enzyme was purified by ammonium sulfate precipitation, filtration on Bio-Gel P-100, chromatography on D.E.A.E.-cellulose and hydroxylapatite, filtration on Bio-Gel P-150 and electrofusing. The purified preparation was homoge...
journal_title:Biochimie
pub_type: 杂志文章
doi:10.1016/s0300-9084(77)80246-0
更新日期:1977-01-01 00:00:00
abstract::IL-28 and IL-29 were recently described as members of a new cytokine family that shares with type I interferon (IFN) the same Jak/Stat signalling pathway driving expression of a common set of genes. Accordingly, they have been named IFN lambda. IFNs lambda exhibit several common features with type I IFNs: antiviral ac...
journal_title:Biochimie
pub_type: 杂志文章,评审
doi:10.1016/j.biochi.2007.01.008
更新日期:2007-06-01 00:00:00