Abstract:
:Antimicrobial peptides (AMPs) are short, cationic, membrane-interacting proteins that exhibit broad-spectrum antimicrobial activity, and are hence of significant biomedical interest. They exert their activity by selectively binding to and lysing target cell membranes, but the precise molecular details of their mechanism are not known. This is further complicated by the fact that their structural characteristics are dependent upon the local lipid environment. As a result, molecular dynamics (MD) simulations have been applied to understand the conformation and mechanism of AMPs, as well as related viral and cell-penetrating peptides. In particular, atomically detailed MD simulation studies on the timescale of tens to hundreds of nanoseconds have successfully helped to: (i) model or refine the conformation of AMPs and their aggregates in the presence of membrane-mimicking solvent mixtures, detergent micelles, and lipid bilayers; (ii) follow the process of adsorption of individual AMPs to membrane surfaces; and (iii) observe the spontaneous assembly of multiple peptides and subsequent cooperative membrane lysis. More recently, coarse-grained (CG) models have been developed to extend the time and length scales accessible to simulations of membrane/peptide systems. CG simulations on the order of microseconds have provided insight into AMP lytic mechanisms, and how they depend upon such factors as peptide concentration, lipid composition, and bilayer curvature. These studies have been supplemented by combined atomistic/CG and integrated multiscale models. Together, simulations have deepened our understanding of the interactions between AMPs and biological membranes, and will help to design new synthetic peptides with enhanced biomedical potential.
journal_name
Protein Pept Lettjournal_title
Protein and peptide lettersauthors
Bond PJ,Khalid Sdoi
10.2174/0929866511009011313subject
Has Abstractpub_date
2010-11-01 00:00:00pages
1313-27issue
11eissn
0929-8665issn
1875-5305pii
BSP/ PPL/ E pub/0196journal_volume
17pub_type
杂志文章,评审abstract::C-terminal peptide alpha-thioesters are valuable intermediates in the synthesis/semisynthesis of proteins by native chemical ligation. They are prepared either by solid-phase peptide synthesis (SPPS) or biosynthetically by protein splicing techniques. The present paper reviews the different methods available for the c...
journal_title:Protein and peptide letters
pub_type: 杂志文章,评审
doi:10.2174/0929866054864166
更新日期:2005-11-01 00:00:00
abstract::Influenza viruses cause a significant level of morbidity and mortality in the population every year. Their resistance to current anti-influenza drugs increases the difficulty of flu treatment. Thus, development of new anti-influenza drugs is necessary in regards of prevent the tragedy of influenza pandemic. The Polyme...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986611796378675
更新日期:2011-10-01 00:00:00
abstract::Interaction between S100P and its target protein is an essential step in several cellular functions. The amphipathic mellitin peptide binds tightly to S100P protein in the presence of calcium cation. Since little is known about the recognition sequence, mellitin interaction form a model for S100P. Interaction between ...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986606775338380
更新日期:2006-01-01 00:00:00
abstract::This work describes the investigations of electrochemical interactions of naphthalene acetic acid (NAA) with stabilized lipid films supported on a methacrylate polymer on a glass fiber filter with incorporated auxin-binding protein 1 receptor for the development of a biosensor for the rapid detection of this compound ...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986608785203692
更新日期:2008-01-01 00:00:00
abstract::Red blood cell (RBC) encapsulated L-asparaginase is a novel therapeutic for the treatment of asparagine auxotrophic malignancies. The enzyme-loaded red blood cells function as bioreactors to deplete bloodstream substrate. This delivery system provides improved pharmacodynamics with protection from circulating proteoly...
journal_title:Protein and peptide letters
pub_type: 杂志文章,评审
doi:
更新日期:2013-04-01 00:00:00
abstract::Human butyrylcholinesterase (BuChE) is a serine enzyme present in most organs and plasma. No clear physiological function has yet been assigned to BuChE, but it is a pharmacologically and toxicologically important enzyme that plays a role in degradation of numerous ester-containing drugs and poisonous esters. Thus, Bu...
journal_title:Protein and peptide letters
pub_type: 杂志文章,评审
doi:10.2174/092986609789071207
更新日期:2009-01-01 00:00:00
abstract::A 6.5 kDa serine protease inhibitor was purified by anion-exchange chromatography from the crude extract of the Inga umbratica seeds, containing inhibitor isoforms ranging from 6.3 to 6.7 kDa and protease inhibitors of approximately 19 kDa. The purified protein was characterized as a potent inhibitor against trypsin a...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/0929866054395888
更新日期:2005-08-01 00:00:00
abstract::Bacterial ADP-ribosyltransferases (BADPRTs) are extensively contributed to determine the strain-specific virulence state and pathogenesis in human hosts. Understanding molecular evolution and functional diversity of the BADPRTs is an important standpoint to describe the fundamental behind in the vaccine designing for ...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/0929866511320090012
更新日期:2013-09-01 00:00:00
abstract::Numerous small molecules including cytokines primarily associated with immune response have been shown to play a role in normal mesenchymal stem cells (MSC) and tumour cells' communication. One characteristic that distinguishes MSC from fibroblast and other cells of mesenchymal origin is their pro-tumour migratory beh...
journal_title:Protein and peptide letters
pub_type: 杂志文章,评审
doi:10.2174/0929866522666150131123808
更新日期:2015-01-01 00:00:00
abstract::Aspergillus sp. phytase contains five disulfide bonds. In order to elucidate their role, the reactivation and refolding of phytase in the absence and presence of dithiothreitol (DTT) was investigated. The results indicated that the disulfide bonds play an important role in the catalytic activity and conformational sta...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/0929866054395752
更新日期:2005-08-01 00:00:00
abstract::Prediction of protein structure from its amino acid sequence is still a challenging problem. The complete physicochemical understanding of protein folding is essential for the accurate structure prediction. Knowledge of residue solvent accessibility gives useful insights into protein structure prediction and function ...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986612798472875
更新日期:2012-01-01 00:00:00
abstract::Catalase is an enzyme that occurs in almost all aerobic organisms. Its main metabolic function is to prevent oxidative damage to tissues induced by hydrogen peroxide which is a strong oxidizing agent. Catalase is very effective in performing this task, since it has the highest turnover rate among all the enzymes. The ...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986611796011392
更新日期:2011-09-01 00:00:00
abstract::We present two efficient network propagation algorithms that operate on a binary tree, i.e., a sparse-edged substitute of an entire similarity network. TreeProp-N is based on passing increments between nodes while TreeProp-E employs propagation to the edges of the tree. Both algorithms improve protein classification e...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986608784567492
更新日期:2008-01-01 00:00:00
abstract::In this paper, a 3D map of protein fold space was produced using Dali structure alignment and nonmetric multidimensional scaling. The fold space comprises four radial clusters, which correspond to the four classes of SCOP. The overall structure of the protein fold space is largely determined by three factors: secondar...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/0929866054395257
更新日期:2005-07-01 00:00:00
abstract:BACKGROUND:Paraoxonase (PON; arilesterase, [EC 3.1.8.1]) is an enzyme from the group arilesterases (ARE). This enzyme is capable of hydrolyzing paraoxone which is the active metabolite of parathion, an organic phosphorus insecticide. PON activity was found to be low in individuals prone to development of atherosclerosi...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/0929866526666190124144622
更新日期:2019-01-01 00:00:00
abstract::E. coli small heat shock proteins IbpA and IbpB (inclusion body binding proteins A and B) are known to act as holding chaperones on denaturing, aggregate-prone proteins. But, there is no clear understanding about which of the IbpA and IbpB has more holdase activity and how the holdase activity of one was influenced by...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/0929866521666131224094408
更新日期:2014-06-01 00:00:00
abstract::A 26-kDa trypsin inhibitor with an N-terminal sequence resembling storage proteins was purified from moth beans (Phaseolus acutifolius). It dose-dependently inhibited trypsin with an IC(50) value of about 0.38 microM. It inhibited [methyl-(3)H] thymidine incorporation by lymphoma MBL2 cells with an IC(50) value of 20 ...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986610791190408
更新日期:2010-06-01 00:00:00
abstract::The development of a stable L-BDH chimera was attempted by exchanging whole domains between two native structural analogs, L-BDH and meso-BDH, because the S-configuration specificity of L-BDH is valuable from the standpoint of its application but its activity is unstable, whereas meso-BDH is stable. The domain chimera...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986611795713970
更新日期:2011-08-01 00:00:00
abstract::The polypeptide leptin exerts a multitude of regulatory functions. It has been implicated in the pathophysiology of inflammatory, metabolic and psychiatric disorders and has been found to be differentially expressed in men and women. Although a clear increase of leptin levels with age has been repeatedly observed in m...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/0929866511009011436
更新日期:2010-11-01 00:00:00
abstract::The study of rat proteins is an indispensable task in experimental medicine and drug development. The function of a rat protein is closely related to its subcellular location. Based on the above concept, we construct the benchmark rat proteins dataset and develop a combined approach for predicting the subcellular loca...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986611795222768
更新日期:2011-06-01 00:00:00
abstract::We report the physical-chemical characterization of the major alcohol-soluble proteins present in seeds of pearl millet (Pennisetum glaucum) by SDS-PAGE, bidimensional gel electrophoresis, MALDI-TOF/MS and RP-HPLC. We demonstrate the presence of three major prolamins, called A-, B- and C-pennisetin with mass values ar...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/0929866023408724
更新日期:2002-06-01 00:00:00
abstract::G-protein betagamma dimers are prime regulators transmitting extracellular signals to wide-ranging cellular effectors including phosphoinositide 3-kinase (PI3K) isoforms beta and gamma. Recombinant Gbetagamma purified from Sf9 cells via metal-affinity and anion exchange chromatography exhibited a wortmannin-insensitiv...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986609789055340
更新日期:2009-01-01 00:00:00
abstract::Calcineurin (CN) is a heterodimer of a catalytic subunit, calcineurin A (CNA), and a regulatory subunit (CNB). Here, we find that the mechanism by which CNB regulates CNA depends on the substrate involved. The regulation mechanism involving tau and its truncation segments is distinct from that involving RII peptide, a...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986609787316243
更新日期:2009-01-01 00:00:00
abstract::The physiological stability curve--a plot of the free energy of unfolding versus temperature--is calculated for hen egg white lysozyme from a combination of extrapolated unfolding thermodynamic data from reversible conditions and isothermal titrations with guanidine hydrochloride. The shape of the curve suggests the e...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986606777841163
更新日期:2006-01-01 00:00:00
abstract::Annual ryegrass (Lolium multiflorum) is widely used as a cool-season forage grass for its luxuriant growth, palatable and high digestible. To investigate the salt tolerance mechanism in annual ryegrass under salt stress, salt-tolerant genotype 'R102-3' and salt-sensitive genotype 'Tetragold' were subject to 300mmol/L ...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/0929866523666160314153618
更新日期:2016-01-01 00:00:00
abstract::A significant association between increased level of blood homocysteine (hyperhomocysteinimia) and various eye pathological disorders including cataract has been reported. This metabolic byproduct is converted into a highly reactive cyclic thioester compound, homocysteine thiolactone (HCTL), which can potentially reac...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/0929866523666151106123944
更新日期:2016-01-01 00:00:00
abstract::A novel cellulase was isolated from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius ATCC27009 grown in medium containing carboxymethylcellulose. The enzyme is a glycosylated monomer of 56.2 kDa, relatively thermostable, with optimal pH and temperature of 4.0 and 65 degrees C, respectively. Enzymatic as...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986608785849209
更新日期:2008-01-01 00:00:00
abstract::To achieve the food-grade expression of bile salt hydrolase (BSH, EC 3.5.1.24) from Lactobacillus plantarum BBE7, the nisin controlled gene expression system (NICE), food-grade selection maker and signal peptide of Lactococcus lactis were used in this study. The open reading frame of BSH was optimized based on the cod...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/0929866522666150610094829
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:The biocatalytic oxidation of UDP-glucose in the presence of NAD+ is catalyzed by UDP-glucose dehydrogenases. OBJECTIVES:The main objective of this study was the characterization of a UDP-glucose dehydrogenase (AmUGD) from Akkermansia muciniphila, a bacterium originally isolated from human faeces in an anae...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/0929866524666170724111147
更新日期:2017-01-01 00:00:00
abstract::From the extensive analysis, we identified three highly conserved sequence segments in HCV NS5A proteins and one binding motif in human proteins. The binding motif of human proteins often forms a full helix or an extended strand-loop structure, and is in good agreement with the experimental findings of previous studie...
journal_title:Protein and peptide letters
pub_type: 杂志文章
doi:10.2174/092986608784567500
更新日期:2008-01-01 00:00:00