A small tripeptide AFA undergoes two state cooperative conformational transitions: implications for conformational biases in unfolded states.

Abstract:

:It is important to understand the conformational biases that are present in unfolded states to understand protein folding. In this context, it is surprising that even a short tripeptide like AFA samples folded/ordered conformation as demonstrated recently by NMR experiments of the peptide in aqueous solution at 280 K. In this paper, we present molecular dynamics simulation of the peptide in explicit water using OPLS-AA/L all-atom force field. The results are in overall agreement with NMR results and provide some further insights. The peptide samples turn and extended conformational forms corresponding to minima in free energy landscape. Frequent transitions between the minima are observed due to modest free energy barriers. The turn conformation seems to be stabilized by hydrophobic interactions and possibly by bridging water molecules between backbone donors and acceptors. Thus the peptide does not sample conformations randomly, but samples well defined conformations. The peptide served as a model for folding-unfolding equilibrium in the context of peptide folding. Further, implications for drug design are also discussed.

journal_name

Protein Pept Lett

authors

Patel S,Taimni R,Sasidhar YU

doi

10.2174/092986607780989886

subject

Has Abstract

pub_date

2007-01-01 00:00:00

pages

581-9

issue

6

eissn

0929-8665

issn

1875-5305

journal_volume

14

pub_type

杂志文章
  • Leptin plasma levels in the general population: influence of age, gender, body weight and medical history.

    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

    authors: Fulda S,Linseisen J,Wolfram G,Himmerich S,Gedrich K,Pollmächer T,Himmerich H

    更新日期:2010-11-01 00:00:00

  • Prediction of nicotinamide adenine dinucleotide interacting sites based on ensemble support vector machine.

    abstract::Nicotinamide adenine dinucleotide (NAD) plays an important role in cellular metabolism and acts as hydrideaccepting and hydride-donating coenzymes in energy production. Identification of NAD protein interacting sites can significantly aid in understanding the NAD dependent metabolism and pathways, and it could further...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/092986612800191017

    authors: Wang X,Wang CC,Zhang YQ,Mi G,Zhang J,Li ML

    更新日期:2012-05-01 00:00:00

  • Kinetics for Zinc Ion Induced Sepia Pharaonis Arginine Kinase Inactivation and Aggregation.

    abstract::Arginine kinase is an essential enzyme which is closely related to energy metabolism in marine invertebrates. Arginine kinase provides a significant role in quick response to environmental change and stress. In this study, we simulated a tertiary structure of Sepia pharaonis arginine kinase (SPAK) based on the gene se...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/0929866523666160331144049

    authors: Si YX,Lee J,Cheng JG,Yin SJ,Park YD,Qian GY,Jiang XM

    更新日期:2016-01-01 00:00:00

  • Peptoid analogues of anoplin show antibacterial activity.

    abstract::We have synthesised nine analogues of the antibacterial peptide anoplin with a peptoid residue at position 5 (H-GLLKXIKTLL-NH(2)). The most active compounds showed MIC-values of 12.5 and 25 microM against E.coli and S.aureus. These MIC-values are comparable with anoplin which showed 23 microM and 11 microM against E. ...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/092986609789055421

    authors: Meinike K,Hansen PR

    更新日期:2009-01-01 00:00:00

  • Quantifying Serum Derived Differential Expressed and Low Molecular Weight Protein in Breast Cancer Patients.

    abstract:BACKGROUND:Searching the biomarker from complex heterogeneous material for early detection of disease is a challenging task in the field of biomedical sciences. OBJECTIVE:The study has been arranged to explore the proteomics serum derived profiling of the differential expressed and low molecular weight protein in brea...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/0929866527666200110155609

    authors: Zafar A,Jabbar M,Manzoor Y,Gulzar H,Hassan SG,Nazir MA,Ain-Ul-Haq,Mustafa G,Sahar R,Masood A,Iqbal A,Hussain M,Hasan M

    更新日期:2020-01-01 00:00:00

  • Improved performance in protein secondary structure prediction by combining multiple predictions.

    abstract::In this paper(1) we present a novel framework for protein secondary structure prediction. In this prediction framework, firstly we propose a novel parameterized semi-probability profile, which combines single sequence with evolutionary information effectively. Secondly, different semi-probability profiles are respecti...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/092986606778777551

    authors: Huang DS,Huang X

    更新日期:2006-01-01 00:00:00

  • An RGD-Modified Endostatin Peptide Expressed at E. coli Shows Anti-Tumor Activity In vivo.

    abstract::Tumor vasculatures express high levels of α(V)β(3)/α(V)β(5) and α(5)β(1) integrins. Peptide containing the RGD (Arg-Gly-Asp) sequence, which is present in ligands of integrins, is effective in targeting therapeutic reagents to tumor vascular endothelium. In this study, we investigated whether the biological activity o...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:

    authors: Zhang HT,Li HC,Li ZW,Guo CH,Chen YJ

    更新日期:2011-06-15 00:00:00

  • Alternative nucleophilic residues in intein catalysis of protein splicing.

    abstract::Protein-splicing inteins are widespread in nature and have found many applications in protein research and engineering. The mechanism of protein splicing typically requires a nucleophilic amino acid residue at both position 1 (first residue of intein) and position +1 (first residue after intein), however it was not cl...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/092986611797642760

    authors: Qi X,Wang J,Meng Q,Liu XQ

    更新日期:2011-12-01 00:00:00

  • The C-terminal domain of eukaryotic acidic ribosomal P2 proteins is intrinsically disordered with conserved structural propensities.

    abstract::The P2 protein (equivalent of L7/L12 in prokaryotes), a member of the ribosomal stalk in eukaryotes, is highly conserved, particularly its C-terminal domain. In order to understand the sequence-structure-function relationships in eukaryotic C-terminal stretches, about which nothing is known at the moment, we have inve...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/0929866521666141121160523

    authors: Mishra P,Rajagopal S,Sharma S,Hosur RV

    更新日期:2014-01-01 00:00:00

  • Comparison of expression of monomeric and multimeric adenoregulin genes in Escherichia coli and Pichia pastorias.

    abstract::Adenoregulin is a 33 amino acid antibiotic peptide who belongs to dermaseptin family which is the first vertebrate family to show lethal effects against filamentous fungi, as well as a broad spectrum of pathogenic microorganisms. Synthetic adenoregulin gene was cloned in 2, 4 and 6 tandem repeats and subcloned in pET3...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/0929866053765671

    authors: Zhou Y,Cao W,Wang J,Ma Y,Wei D

    更新日期:2005-05-01 00:00:00

  • Interaction between two residues in the inter-domain interface of Escherichia coli peptidase N modulates catalytic activity.

    abstract::The role of interaction between Asn259 (catalytic domain) with Gln821 (C-terminal domain) in PeptidaseN was investigated. The k(cat) of PeptidaseN containing Asn259Asp or Gln821Glu is enhanced whereas it is suppressed in Asn259AspGln821Glu. Structural analysis shows this interaction to change the relative disposition ...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/092986609787848081

    authors: Kumar A,Reddy S,Srinivasan N,Nandi D

    更新日期:2009-01-01 00:00:00

  • Role of Seminal Plasma Proteins in Effective Zygote Formation- A Success Road to Pregnancy.

    abstract::Seminal plasma proteins contributed by secretions of accessory glands plays a copious role in fertilization. Their role is overlooked for decades and even now, as Artificial Reproduction Techniques (ART) excludes the plasma components in the procedures. Recent evidences suggest the importance of these proteins startin...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章,评审

    doi:10.2174/0929866526666190208112152

    authors: Kumar A,Sridharn TB,Rao KA

    更新日期:2019-01-01 00:00:00

  • A novel thermoacidophilic cellulase from Alicyclobacillus acidocaldarius.

    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

    authors: Morana A,Esposito A,Maurelli L,Ruggiero G,Ionata E,Rossi M,La Cara F

    更新日期:2008-01-01 00:00:00

  • A protein block based fold recognition method for the annotation of twilight zone sequences.

    abstract::The description of protein backbone was recently improved with a group of structural fragments called Structural Alphabets instead of the regular three states (Helix, Sheet and Coil) secondary structure description. Protein Blocks is one of the Structural Alphabets used to describe each and every region of protein bac...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/0929866511320030003

    authors: Suresh V,Ganesan K,Parthasarathy S

    更新日期:2013-03-01 00:00:00

  • Sialic acid recognition of the pandemic influenza 2009 H1N1 virus: binding mechanism between human receptor and influenza hemagglutinin.

    abstract::Quantum mechanical fragment molecular orbital calculations have been performed for receptor binding of the hemagglutinin protein of the recently pandemic influenza 2009 H1N1, A/swine/Iowa/1930, and A/Puerto Rico/8/1934 viruses to α2-6 linked sialyloligosaccharides, as analogs of human receptors. The strongest receptor...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/092986611794927893

    authors: Fukuzawa K,Omagari K,Nakajima K,Nobusawa E,Tanaka S

    更新日期:2011-05-01 00:00:00

  • The "Tilted Peptide Theory" links membrane insertion properties and fusogenicity of viral fusion peptides.

    abstract::Class I fusion glycoproteins of viruses are involved in the fusion between viral envelope and cell membrane. A region located in the N-terminal domain of these glycoproteins, called the fusion peptide, is essential for fusion. Fusion peptides are able to induce by themselves in vitro membrane fusion. In this paper, we...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章,评审

    doi:10.2174/092986609788681724

    authors: Charloteaux B,Lorin A,Brasseur R,Lins L

    更新日期:2009-01-01 00:00:00

  • Peptides, proteins and peptide/protein-polymer conjugates as drug delivery system.

    abstract::In the last few decades, novel drug delivery strategies have been a big priority to the formulation scientists. Peptides and proteins have drawn a special attention for their wide scope in the area. Serum albumin, transferrin, recom- binant proteins, virus capsids etc. are used as carrier for drug and biomolecules. Co...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章,评审

    doi:10.2174/0929866521666140804160907

    authors: Mukherjee B,Karmakar SD,Hossain CM,Bhattacharya S

    更新日期:2014-01-01 00:00:00

  • Phylogenetic approach for inferring the origin and functional evolution of bacterial ADP-ribosylation superfamily.

    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

    authors: Chellapandi P,Sakthishree S,Bharathi M

    更新日期:2013-09-01 00:00:00

  • A new binding site involving the C-terminal domain to design specific inhibitors of PepX.

    abstract::PepX is a X-prolyl dipeptidyl aminopeptidase of S15 family that cleaves dipeptides from the N-terminus of polypeptides having a proline or alanine residue at the second position. Involved in bacterial nutrition and in peptide maturation, this serine exopeptidase, counterpart of the mammalian DDP-4, has been proposed t...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:

    authors: André J,Bach M,Xie J,Rigolet P

    更新日期:2013-01-01 00:00:00

  • Effect of Temperature and pH on the Secondary Structure and Denaturation Process of Jumbo Squid Hepatopancreas Cathepsin D.

    abstract:BACKGROUND:Cathepsin D is a lysosomal enzyme that is found in all organisms acting in protein turnover, in humans it is present in some types of carcinomas, and it has a high activity in Parkinson's disease and a low activity in Alzheimer disease. In marine organisms, most of the research has been limited to corroborat...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/0929866526666190405124353

    authors: Francisco CC,Luis CJ,Marina EJ,Javier CF,Alexis LA,Del Carmen SH,Alfredo RI

    更新日期:2019-01-01 00:00:00

  • Evidences of monomer, dimer and trimer of recombinant human cyclophilin A.

    abstract::Cyclophilin A (CyPA) is a cytosolic receptor of immunosuppressive drug cyclosporin A (CsA) which possesses peptidyl-prodyl cis/trans isomerase (PPIase) activity. The recombinant human CyPA (rhCyPA) gene has been expressed in E. coli M15. Purification was performed using salting-out, as well as Sephacryl S-100 and DEAE...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/092986611797642670

    authors: Zhang XC,Wang WD,Wang JS,Pan JC,Zou GL

    更新日期:2011-12-01 00:00:00

  • Spectroscopy and Molecular Modeling Study on Binding of Nickel Phthalocyanine to Human Serum Albumin.

    abstract::The interaction of nickel tetra sulfunated phthalocyanine( NiTSPc) with human serum albumin (HSA), in 20 mM phosphate buffer pH 7.4 was investigated using advanced techniques including fluorescence, synchronous fluorescence, Fourier transform infrared (FT-IR), circular dichroism (CD) spectroscopy and molecular docking...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/0929866523666160719101707

    authors: Dezhampanah H,Firouzi R,Hasani L

    更新日期:2016-01-01 00:00:00

  • Drugs against Mycobacterium tuberculosis 3-isopropylmalate dehydrogenase can be developed using homologous enzymes as surrogate targets.

    abstract::3-Isopropylmalate dehydrogenase (IPMDH) from Mycobacterium tuberculosis (Mtb) may be a target for specific drugs against this pathogenic bacterium. We have expressed and purified Mtb IPMDH and determined its physicalchemical and enzymological properties. Size-exclusion chromatography and dynamic light scattering measu...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:

    authors: Graczer E,Bacso A,Konya D,Kazi A,Soos T,Molnar L,Szimler T,Beinrohr L,Szilagyi A,Zavodszky P,Vas M

    更新日期:2014-01-01 00:00:00

  • Contribution of halophilic nucleoside diphosphate kinase sequence to the heat stability of chimeric molecule.

    abstract::A halophilic nucleoside diphosphate kinase from a moderate halophile, Halomonas sp. 593 (593NDK), was found to be resistant to heat treatment, as indicated by the high level of activity recovery after heating at high temperatures. This is due to reversibility of thermal unfolding, not the high melting temperature, of ...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/092986606776819628

    authors: Tokunaga H,Oda Y,Yonezawa Y,Arakawa T,Tokunaga M

    更新日期:2006-01-01 00:00:00

  • Red blood cell-encapsulated L-asparaginase: potential therapy of patients with asparagine synthetase deficient acute myeloid leukemia.

    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:

    authors: Agrawal V,Woo JH,Borthakur G,Kantarjian H,Frankel AE

    更新日期:2013-04-01 00:00:00

  • Crystallization and preliminary x-ray diffraction analysis of three mastoparans.

    abstract::Mastoparans are tetradecapeptides found to be the major component of wasp venoms. These peptides possess a variety of biological activities. Three related mastoparans, mastoparan from Polistes jadwagae (MP-PJ), mastoparanX (MP-X) and its carboxyl-free C-terminal form (MP-X-COO-), were crystallized. X-ray diffraction d...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/092986606777145896

    authors: Wang F,Liu X,Li H,Lang X,Peng H,Liu S,Jiang T

    更新日期:2006-01-01 00:00:00

  • Solubility improvement of an anthrax toxin peptide inhibitor by rational amino acid randomization.

    abstract::We previously described a potent anthrax toxin inhibitor, based on a phage-library-selected peptide sequence, synthesized as a tetra-branched molecule on a lysine core and further modified for improvement of activity [Pini et al., Biochem. J., 2006, 395, 157]. This branched peptide had very low solubility because of s...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/092986608784966958

    authors: Pini A,Brunetti J,Falciani C,Fabbrini M,Bracci L

    更新日期:2008-01-01 00:00:00

  • The role of tyrosine residues in the RNA N-glycosidase activity of cinnamomin A-chain.

    abstract::Cinnamomin is a type II ribosome-inactivating protein (RIP) and its A-chain (CTA) is a RNA N-glycosidase. It is observed that modification of tyrosine residues by N-acetylimidazole (N-AI) causes almost complete loss of CTA activity. Adenine partially protects tyrosine residues from modification by N-AI. It is proposed...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/0929866033478771

    authors: Xu H,Liu WY

    更新日期:2003-10-01 00:00:00

  • Pyridoxamine, an inhibitor of advanced glycation end product (AGE) formation ameliorates insulin resistance in obese, type 2 diabetic mice.

    abstract::There is a growing body of evidence that the formation and accumulation of advanced glycation end products (AGE) have been known to progress under diabetic conditions, thereby being involved in diabetic vascular complications. Further, we, along with others, have recently found AGE could disturb insulin actions in cul...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/092986610791760423

    authors: Unoki-Kubota H,Yamagishi S,Takeuchi M,Bujo H,Saito Y

    更新日期:2010-09-01 00:00:00

  • Brown recluse spider venom: proteomic analysis and proposal of a putative mechanism of action.

    abstract::Loxosceles intermedia spider venom was subjected to proteomic analysis through a MudPIT shot-gun approach to identify the protein composition. Were identified 39 proteins which seem to responsible by the lesion of different types of tissues, to some physiopathological actions and by the prevention of structural damage...

    journal_title:Protein and peptide letters

    pub_type: 杂志文章

    doi:10.2174/092986609788923383

    authors: dos Santos LD,Dias NB,Roberto J,Pinto AS,Palma MS

    更新日期:2009-01-01 00:00:00