scholarly journals Acceleration of Disulfide-Coupled Protein Folding by Positively Charged Glutathione Derivatives

2012 ◽  
Vol 102 (3) ◽  
pp. 57a
Author(s):  
Yuji Hidaka ◽  
Masaki Okumura ◽  
Masatoshi Saiki ◽  
Hiroshi Yamaguchi
Keyword(s):  
Protein Folding ◽  
Positively Charged ◽  
Glutathione Derivatives

scholarly journals Acceleration of disulfide-coupled protein folding using glutathione derivatives

FEBS Journal ◽  
2011 ◽  
Vol 278 (7) ◽  
pp. 1137-1144 ◽  
Author(s):  
Masaki Okumura ◽  
Masatoshi Saiki ◽  
Hiroshi Yamaguchi ◽  
Yuji Hidaka
Keyword(s):  
Protein Folding ◽  
Glutathione Derivatives

scholarly journals Effects of positively charged redox molecules on disulfide-coupled protein folding

FEBS Letters ◽  
2012 ◽  
Vol 586 (21) ◽  
pp. 3926-3930 ◽  
Author(s):  
Masaki Okumura ◽  
Shigeru Shimamoto ◽  
Takeyoshi Nakanishi ◽  
Yu-ichiro Yoshida ◽  
Tadafumi Konogami ◽  
...  
Keyword(s):  
Protein Folding ◽  
Redox Molecules ◽  
Positively Charged

The VES KM: a pathway for protein folding in vivo

2020 ◽  
Vol 92 (1) ◽  
pp. 179-191
Author(s):  
Leonor Cruzeiro
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Protein Structures ◽  
Kinetic Mechanism ◽  
Thermal Bath ◽  
Charged Amino Acids ◽  
Nascent Chain ◽  
Dynamics Simulations ◽  
Positively Charged

AbstractWhile according to the thermodynamic hypothesis, protein folding reproducibility is ensured by the assumption that the native state corresponds to the minimum of the free energy in normal cellular conditions, here, the VES kinetic mechanism for folding in vivo is described according to which the nascent chain of all proteins is helical and the first and structure defining step in the folding pathway is the bending of that initial helix around a particular amino acid site. Molecular dynamics simulations are presented which indicate both the viability of this mechanism for folding and its limitations in the presence of a Markovian thermal bath. An analysis of a set of protein structures formed only of helices and loops suggests that bending sites are correlated with regions bounded, on the N-side, by positively charged amino acids like Lysine and Histidine and on the C-side by negatively charged amino acids like Aspartic acid.

scholarly journals Positively Charged Redox Agents Accelerate Disulfide Coupled Protein Folding

2014 ◽  
Vol 106 (2) ◽  
pp. 472a
Author(s):  
Takeyoshi Nakanishi ◽  
Masaki Okumura ◽  
Shigeru Shimamoto ◽  
Yuji Hidaka
Keyword(s):  
Protein Folding ◽  
Redox Agents ◽  
Positively Charged

Protamine-DNA interaction

1978 ◽  
Vol 36 (2) ◽  
pp. 200-201
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Small Volume ◽  
Double Helix ◽  
Dna Interaction ◽  
Dark Field ◽  
Sperm Head ◽  
Nuclear Proteins ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Dna Double Helix ◽  
Positively Charged

Dark field electron microscopy has been used for the study of the structure of individual macromolecules with a resolution to at least the 5Å level. The use of this technique has been extended to the investigation of structure of interacting molecules, particularly the interaction between DNA and fish protamine, a class of basic nuclear proteins of molecular weight 4,000 daltons.Protamine, which is synthesized during spermatogenesis, binds to chromatin, displaces the somatic histones and wraps up the DNA to fit into the small volume of the sperm head. It has been proposed that protamine, existing as an extended polypeptide, winds around the minor groove of the DNA double helix, with protamine's positively-charged arginines lining up with the negatively-charged phosphates of DNA. However, viewing protamine as an extended protein is inconsistent with the results obtained in our laboratory.

Structure and Interaction of Protamine by Dark Field Electron Microscopy

1976 ◽  
Vol 34 ◽  
pp. 160-161
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Electron Microscopy ◽  
Dark Field ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
3 Dimensional ◽  
Field Electron ◽  
Proposed Model ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Positively Charged

It has been shown for some time that it is possible to obtain images of small unstained proteins, with a resolution of approximately 5Å using dark field electron microscopy (1,2). Applying this technique, we have observed a uniformity in size and shape of the 2-dimensional images of pure specimens of fish protamines (salmon, herring (clupeine, Y-l) and rainbow trout (Salmo irideus)). On the basis of these images, a model for the 3-dimensional structure of the fish protamines has been proposed (2).The known amino acid sequences of fish protamines show stretches of positively charged arginines, separated by regions of neutral amino acids (3). The proposed model for protamine structure (2) consists of an irregular, right-handed helix with the segments of adjacent arginines forming the loops of the coil.

Enhanced type I photoreaction of indocyanine green via electrostatic-force-driven aggregation

Nanoscale ◽  
2020 ◽  
Vol 12 (17) ◽  
pp. 9517-9523 ◽  
Author(s):  
Huizhen Fan ◽  
Yu Fan ◽  
Wenna Du ◽  
Rui Cai ◽  
Xinshuang Gao ◽  
...  
Keyword(s):  
Mesoporous Silica ◽  
Indocyanine Green ◽  
Electrostatic Force ◽  
Type I ◽  
Positively Charged

ICG forms aggregates in positively charged mesoporous silica, which show an enhanced type I photoreaction pathway.

Influence of nascent polypeptide positive charges on translation dynamics

2020 ◽  
Vol 477 (15) ◽  
pp. 2921-2934
Author(s):  
Rodrigo D. Requião ◽  
Géssica C. Barros ◽  
Tatiana Domitrovic ◽  
Fernando L. Palhano
Keyword(s):  
Mrna Decay ◽  
Translation Termination ◽  
Published Data ◽  
Translation Efficiency ◽  
Amino Acid Residues ◽  
High Concentration ◽  
Strong Argument ◽  
Translation Arrest ◽  
Exit Tunnel ◽  
Positively Charged

Protein segments with a high concentration of positively charged amino acid residues are often used in reporter constructs designed to activate ribosomal mRNA/protein decay pathways, such as those involving nonstop mRNA decay (NSD), no-go mRNA decay (NGD) and the ribosome quality control (RQC) complex. It has been proposed that the electrostatic interaction of the positively charged nascent peptide with the negatively charged ribosomal exit tunnel leads to translation arrest. When stalled long enough, the translation process is terminated with the degradation of the transcript and an incomplete protein. Although early experiments made a strong argument for this mechanism, other features associated with positively charged reporters, such as codon bias and mRNA and protein structure, have emerged as potent inducers of ribosome stalling. We carefully reviewed the published data on the protein and mRNA expression of artificial constructs with diverse compositions as assessed in different organisms. We concluded that, although polybasic sequences generally lead to lower translation efficiency, it appears that an aggravating factor, such as a nonoptimal codon composition, is necessary to cause translation termination events.

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