Abstract：
:The application of molecular dynamics simulations to study the folding and dynamics of peptides has attracted a lot of interest in the last couple of decades. Following the successful prediction of the folding of several proteins using molecular simulation, foldable peptides emerged as a favourable system mainly due to their application in improving protein structure prediction methods and in drug design studies. However, their performance is inherently linked to the accuracy of the empirical force fields used in the simulations, whose optimisation and validation is of paramount importance. Here we review the most important findings in the field of molecular peptide simulations and highlight the significant advancements made over the last twenty years. Special reference is made on the simulation of disordered peptides and the remaining challenge to find a force field able to describe accurately their conformational landscape.
journal_name
Arch Biochem Biophysjournal_title
Archives of biochemistry and biophysicsauthors
Georgoulia PS,Glykos NMdoi
10.1016/j.abb.2019.01.033subject
Has Abstractpub_date
2019-03-30 00:00:00pages
76-88eissn
0003-9861issn
1096-0384pii
S0003-9861(18)30734-3journal_volume
664pub_type
杂志文章,评审abstract：:This work reports the first functional characterization of leishmanial PEPCK. The recombinant Leishmania major enzyme (Lmj_PEPCK) exhibits equivalent kcat values for the phosphoenolpyruvate (PEP) and oxaloacetate (OAA) forming reactions. The apparent Km towards OAA is 10-fold lower than that for PEP, while the Km valu...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/j.abb.2015.07.015
更新日期：2015-10-01 00:00:00
abstract：:Arginase activity is elevated in livers of diabetic animals compared to controls and there is evidence that this is due in part to increased specific activity (activity/mg arginase protein). To investigate the molecular basis of this increased activity, the physicochemical and kinetic properties of hepatic arginase fr...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(89)90455-4
更新日期：1989-11-01 00:00:00
abstract：:A neutral proteolytic activity that converts human Big endothelin-1 (Big Et-1) to endothelin-1 has been identified from a human endothelial hybrid cell line, EAHY 926. This enzyme is an integral membrane protein and cofractionates with other enzymes typically found in the plasma membrane. The activity has been solubil...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1006/abbi.1994.1034
更新日期：1994-01-01 00:00:00
abstract：:The tandem repeat 23-residue sequence [TRS23 (145-167): T-T-A-A-P-P-T-P-S-A-T-T-P-A-P-P-S-S-S-A-P-P-E] of human salivary mucin glycoprotein MG2 was examined for its in vitro bactericidal activity against four oral microorganisms, Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Streptococcus gordonii, a...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1006/abbi.1998.0779
更新日期：1998-08-15 00:00:00
abstract：:A novel action of the gonadotropic hormones of the adenohypophysis on the regulation of kidney heme metabolism and cytochrome P-450 concentrations is described. The treatment of rats with cis-platinum for 7 days caused a greater than twofold increase in the microsomal cytochrome P-450 and heme concentrations in the ki...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(85)90007-4
更新日期：1985-07-01 00:00:00
abstract：:Tryparedoxin peroxidase (TXNPx) of Trypanosomatidae is the terminal peroxidase of a complex redox cascade that detoxifies hydroperoxides by NADPH (Nogoceke et al., Biol. Chem. 378, 827-836, 1997). A gene putatively coding for a peroxiredoxin-type TXNPx was identified in L. donovani and expressed in Escherichia coli to...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1006/abbi.2001.2688
更新日期：2002-01-15 00:00:00
abstract：:The site of superoxide production in spinach thylakoids was found to be the aprotic interior of the thylakoid membranes near the P700 chlorophyll a protein at the reaction center of photosystem I complexes. This conclusion was drawn from the following findings. (i) Cytochrome c reduction by illuminated thylakoids, whi...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(88)90080-x
更新日期：1988-12-01 00:00:00
abstract：:Angiotensin II (Ang II) plays an important role in inflammatory process. Acute lung injury (ALI), an inflammatory disorder of the lung, is commonly associated with endotoxemia; however, the mechanism that endotoxin (lipopolysaccharide, LPS) induces the inflammatory response in ALI is not well defined. Here, we showed,...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/j.abb.2008.09.019
更新日期：2009-01-01 00:00:00
abstract：:We have observed abnormally high membrane cholesterol levels and a subsequent deficiency of oxidative energy production in mitochondria from cultured Morris hepatoma cells (MH7777). Using cholesterol affinity chromatography and MALDI-TOF Mass Spectrometry, we have identified the voltage dependent anion channel (VDAC) ...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/j.abb.2007.06.012
更新日期：2007-10-15 00:00:00
abstract：:Lipoxygenase-induced lipid oxidation contributes to plasma lipoprotein oxidation and may be an underlying pathogenic mechanism of atherogenesis. Since inactivation of the vasorelaxant actions of nitric oxide (.NO) plays a critical role in the impaired function of atherosclerotic vessels and because .NO reacts rapidly ...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1006/abbi.1995.9935
更新日期：1995-12-01 00:00:00
abstract：:The objective of this study was to investigate the antiproliferative activity and apoptosis-inducing mechanism of Concanavalin A (ConA) on human melanoma A375 cells. We firstly simulated the three-dimensional structure of ConA. Subsequently, we found that ConA possessed remarkable antiproliferative effect on A375 cell...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/j.abb.2008.12.003
更新日期：2009-02-01 00:00:00
abstract：:The serine carboxylesterase from horse serum was characterized by amino acid composition, peptide mapping, molecular and subunit weights, and sequencing of the amino acids around the essential serine residue at the active site. A protocol was developed for using reversed-phase high-performance liquid chromatography as...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(88)90032-x
更新日期：1988-11-15 00:00:00
abstract：:The binding site for ATP to tubulin was established by use of the photoaffinity label [gamma-32P]N3ATP. Photolysis of the analog in the presence of tubulin resulted in covalent modification of the protein as revealed by autoradiography of electropherograms. Scanning the autoradiograms showed that the ATP analog was bo...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(83)90056-5
更新日期：1983-09-01 00:00:00
abstract：:Macrophages play a pivotal role in the defense response against harmful pathogens and stimuli by releasing various pro-inflammatory mediators. However, overproduction of pro-inflammatory mediators will do harm to the organism and cause inflammation-associated diseases. Omentin-1, which is a newly discovered adipokine,...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/j.abb.2019.108187
更新日期：2020-01-15 00:00:00
abstract：:Phorbol esters induce rapid downregulation of PAF receptors on human neutrophils. The molecular mechanism responsible for this observation has not been elucidated. In the present study, treatment of neutrophils with PMA (10(-7) M) for 10 min caused a complete loss of PAF receptors from the cell surface as determined b...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1006/abbi.1994.1375
更新日期：1994-08-15 00:00:00
abstract：:Diphtheria toxin (DT) induces the leakage of dipalmitoylphosphatidic acid (DPPA) membranes but not neutral dipalmitoylphosphatidylcholine (DPPC) membranes. Cholesterol incorporated into liposomes enhances the membrane leakage induced by DT in acidic DPPA membranes but not in neutral DPPC membranes. Membrane leakage wa...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(84)90317-5
更新日期：1984-10-01 00:00:00
abstract：:Hippocampal-dependent cognitive functions rely on production of new neurons and maintenance of dendritic structures to provide the synaptic plasticity needed for learning and formation of new memories. Hippocampal formation is exquisitely sensitive to patho-physiological changes, and reduced antioxidant capacity and e...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章,评审
doi：10.1016/j.abb.2015.03.014
更新日期：2015-06-15 00:00:00
abstract：:Previously, we reported that several charged amino acids located in the alpha1-beta4 loop of the iron-sulfur protein are required to maintain the stability of the protein and its assembly into the cytochrome bc1 complex. The current study extends this analysis to several amino acids localized in the single alpha-helix...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1006/abbi.1998.0894
更新日期：1998-11-01 00:00:00
abstract：:In the presence of glucose and ample oxygen, insect form African trypanosomes release pyruvate more than 100-fold more slowly than do bloodstream forms. This rate decrease could not be accounted for simply by an increased mitochondrial pyruvate oxidation rate as inhibiting mitochondrial respiration increases pyruvate ...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1006/abbi.1994.1361
更新日期：1994-08-15 00:00:00
abstract：:There is evidence to suggest that extracellular matrix molecules, such as proteoglycans, are involved in the regulation of mineral deposition in calcifying tissues. One mineralizing system which is characterized by extremely rapid mineralization is the hen eggshell. This eggshell consists of a pair of nonmineralized e...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(92)90126-h
更新日期：1992-10-01 00:00:00
abstract：:Here, we investigated the structure-activity relationship of major green tea catechins and their corresponding epimers on cell-surface binding and inhibitory effect on histamine release. Galloylated catechins; (-)-epigallocatechin-3-O-gallate (EGCG), (-)-gallocatechin-3-O-gallate (GCG), (-)-epicatechin-3-O-gallate (EC...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/j.abb.2008.03.002
更新日期：2008-08-15 00:00:00
abstract：:The nonenzymatic reaction of the cytotoxic compounds menadione (2-methyl-1,4-naphthoquinone) and 1,4-naphthoquinone (a reactive metabolite of 1-naphthol) with reducing agents such as NADPH and glutathione led to the formation of semiquinone-free radicals, which were detected with electron spin resonance spectroscopy. ...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(87)90006-3
更新日期：1987-01-01 00:00:00
abstract：:Glucocorticoids will enhance the growth of cultured human skin fibroblasts in serum-containing medium. In serum-free cultures hydrocortisone (5 X 10(-6) M) will enhance insulin stimulation of sugar transport and DNA synthesis (as measured by thymidine incorporation into trichloroacetic acid-precipitable material). The...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(83)90319-3
更新日期：1983-10-15 00:00:00
abstract：:Glycosylasparaginase (EC 3.5.1.26) is a lysosomal amidase which hydrolyzes the bond between asparagine and the sugar moiety in N-linked glycoproteins. Deficiency of the enzyme results in aspartylglycosaminuria (AGU), the most common disorder of glycoprotein degradation. Mature enzyme is formed by two proteolytic cleav...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1006/abbi.1996.0144
更新日期：1996-04-01 00:00:00
abstract：:The enzyme ketol acid reductoisomerase catalyzes the second common reaction in the biosynthesis of the branched chain amino acids. The reaction is complex as an alkyl migration and a ketone reduction apparently occur as separate steps during the conversion of acetolactate to 2,3-dihydroxy-3-methylbutyrate. This paper ...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(92)90710-e
更新日期：1992-05-01 00:00:00
abstract：:gG.2 glycoprotein was purified by H966 monoclonal antibodies linked to Sepharose from herpes simplex virus type 2-infected HEp-2 cells labeled with [3H] glucosamine. The glycoprotein was subjected to Pronase digestion and the glycopeptides were fractionated by Con A-Sepharose in a major fraction (88.5% of total radioa...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(85)90097-9
更新日期：1985-08-01 00:00:00
abstract：:Tyr-503 of beta-galactosidase was specifically replaced with Phe, His, Cys, and Lys using site-directed mutagenesis. The normal enzyme and the substituted enzymes were purified. The activities of each of the substituted enzymes with o-nitrophenyl-beta-D-galactopyranoside (ONPG) and p-nitrophenyl-beta-D-galactopyronosi...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(90)90652-f
更新日期：1990-12-01 00:00:00
abstract：:Prothymosin alpha, a polypeptide of 109 to 111 amino acid residues, contains the entire thymosin alpha 1 sequence (residues 1-28) at its amino terminal. Human peripheral blood monocytes incubated with prothymosin alpha release thymosin alpha 1 in the culture supernatants. In addition total RNA is found to increase. Th...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(92)90570-m
更新日期：1992-07-01 00:00:00
abstract：:The objective of this study was to develop straightforward processes that could be applied to the large-scale production of β-cryptoxanthin in an attempt to facilitate investigation of its biological activity. An oleoresin obtained from crude extracts of marigold flowers (Tagetes erecta) with approximately 24% total l...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/j.abb.2018.06.012
更新日期：2018-09-01 00:00:00
abstract：:1-O-Alkyl-2-acetyl-sn-glycero-3-phosphocholine (AGEPC) induced phosphorylation of two proteins having molecular masses of approximately 20- and 40-kDa in washed rabbit platelets in a concentration- and time-dependent manner. Sequential stimulation with AGEPC did not induce additional protein phosphorylation, supportin...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(86)90342-5
更新日期：1986-05-01 00:00:00
